tag:blogger.com,1999:blog-31927559432157450752024-03-05T14:07:57.553-05:00SISTEMA bio~SIGNA Computing for Medicine
by Exploring and Developing Tools for Improving HealthDoc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.comBlogger33125tag:blogger.com,1999:blog-3192755943215745075.post-27425266245744596292013-07-05T04:10:00.002-04:002013-07-05T04:48:44.263-04:00Scientific Programming:Of Processors and Software<div class="separator" style="clear: both; text-align: center;">
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<span style="font-family: Verdana, sans-serif;">Hello everyone. I was hoping to post this some weeks ago,
but, pardonnez-moi, I had a lot on my hands: Visual problems, plus moving
residence (for the nth time), to say the least. Sorting, packing: I think you
know that last one. At any rate, here in my new abode, I had to do some
unpacking and getting stuff in order. Whew! In addition, I had to undergo laser treatment
for my right eye. My vision is quite a lot better. I still have to manage my
scientific bearings though. Not to mention my app development project, which I
hope to monetize. So here we go with our topic for this week or so: Scientific
Programming.<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">Processor Challenges<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">The evolution of microprocessor technology is upon us.
Financial straits, partly due to the decrease in sales of PCs, and power constraints
are driving companies to maximize IC space related to better energy efficiency.
Maybe the consumer production ICs for PCs are following a downward trend. However, big
machines plus big data are enabling big-time computer setups and startups. The mobile
environment is changing the computing landscape. But I still have to see a
tablet that can process petabytes of data using 16-core computing power, in
addition to linking all the servers that big search giants can enable. The
mobile device, to me, is at this point, a window to the sky. Big machines are
here to stay. Meanwhile, we still have to build bigger and better programs in
the name of discovery of better treatments and the improvement of health care.
Even now, not all Medical Centers or clinics can afford electronic health
records, let alone the qualification for big brother’s reimbursements. We’ll
leave politics to the experts. Our concern is with programs and the development
systems for discovery, diagnoses, and streamlined systems. So let’s move on in
that direction.<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">Corpus</span></div>
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<span style="font-family: Verdana, sans-serif;">A scientific understanding of the physical world has allowed
us to interact with a multitude of aspects of life, whether our own, or of our
environment. In so doing, we have been able to improve the lives of countless
individuals, by adding unique properties, or by correcting deficiencies. This
has not come about in one big chunk but rather in incremental steps in the
informatics evolution. We are getting better at understanding homeostasis and
the elements that disturb it. While we have not yet modelled “feeling good” in
the computer laboratory, it has become clear that the various organ systems are
involved in a tightly knit web of actions and interactions. As a matter of
fact, we can now “imitate” nature in the process known as cloning. At least we
had an idea of cloning via the Star Wars saga.<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">For now though, we will just concern ourselves with the
representation of biologic processes and interventions through scientific coding
or programming. Curiously, one can ask if there is a difference between
computing for science and computing for banking, or even computing for internet
media (music anyone?). Well, it is at
this juncture that we can see the differences between the structures and
functions in each cell-tissue-organ-body system and an online bookstore giant.
There is a striking similarity though (analogous, if you will) between an air traffic
controller’s job and that of our brain’s. There is also a similarity between the
cardiovascular system and a city, with all its inhabitants, buildings and
thoroughfares.<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">Let’s remember that regardless of the computational
platform, the essence is to enhance the Scientific Process:<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">1)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Observe</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">2)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Question</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">3)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Hypothesize</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">4)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Experiment</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">5)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Conclude</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">6)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Communicate</span><br />
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<span style="font-family: Verdana, sans-serif;">Programming software<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">How well one represents different systems in the body
depends on both the skill of the programmer and the programming language used. The
evolution of computer languages started with a mathematically stringent code,
and as in mathematics, depends a lot on the terse symbolisms used. Anyone
familiar with FORTRAN (derived from “<b><u>For</u></b>mula <b><u>Tran</u></b>slator”)
will know, parenthetical operations are as important as the keywords and
syntax. In the 90s, FORTRAN was the predominant programming language for
numeric and most scientific applications, the version then being Fortran-77 and
supercomputers were primarily used to run large-scale numeric and scientific
applications. While FORTRAN is still used for “heavy duty” programming, there
is now more competition in the C family of languages, as well as Python (more
on that later in this series). BASIC was derived from FORTRAN, but tried to
make it easier to code, and, as a result, many people start learning
programming via the former. As a matter of fact, many have settled on and even
still monetize their BASIC programs, such as in the multitude of add-ons for
the Microsoft Office Suite, definitely no small feat in the commerce of
computing. Then came Pascal, FORTH, the C family, Java, Python (examples of
high-level languages): the list goes on. Of course, there is Assembly Language,
a low-level language, which “speaks directly” to the CPU. Many linguistic
features are shared by the different languages, however, one may have more
benefits than the other for a particular purpose. The latter may depend a lot on the computing job to be
built. There are at least 50 programming languages available, and their
individual popularities can be surveyed at the Tiobe website here. <a href="http://www.tiobe.com/index.php/content/paperinfo/tpci/index.html">http://www.tiobe.com/index.php/content/paperinfo/tpci/index.html</a><span class="MsoHyperlink"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;">Choosing which one to use depends on each one’s familiarity
with the language’s structure, syntax, and level of learning and maintenance difficulty.
There are proponents for every language, and their takes on each one’s utility
varies of course. If one were to work with signal analysis, a language’s
ability to interface patient subject and equipment is tantamount in importance.
In this respect, there are software packages that take full advantage of the
complex waveforms and then perform tasks available in the software modules. These
modules are also sometimes called toolboxes.</span></div>
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<span style="font-family: Verdana, sans-serif;">Among the applications these
software packages are capable of performing and/or facilitating are:</span></div>
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<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">1)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Signal processing;</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">2)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Numerical data analysis;</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">3)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Modelling;</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">4)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Simulation;</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">5)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Computer graphic
visualization;</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">6)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Robotics; and</span><br />
<span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">7)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Computer/Machine vision.</span><br />
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<span style="font-family: Verdana, sans-serif;">One such software package is MATLAB </span><span style="font-family: Trebuchet MS, sans-serif;">(<b><u>mat</u></b>rix <b><u>lab</u></b>oratory)</span><span style="font-family: Verdana, sans-serif;"> /Simulink, where a
programmer can also write program routines for a specialized purpose. LabVIEW is another such platform. Maple and Mathematica can also handle operations in
scientific computing. If one individual, or group, needs its own home-grown
procedures, then a good knowledge of programming language/s is essential.</span></div>
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<span style="font-family: Verdana, sans-serif;">Another factor that is important in scientific programming, is
the mode of data transfer from user to software (as well as computing machine)
and back. Will it be an online app, or an offline one? Will it be embedded in the measuring unit
itself (such as an ICU monitor), or is it an interface between machine and
patient/subject. The bottom line, as it turns out, is shortening the path
between source of data and the user: The quicker, the better. With the
continuous evolution of microprocessors, the need for speed of number crunching
and analysis is always at our doorstep. The accumulation of data and the “Big
Data” environment will put strain on man and machine. It’s not just a cold
machine doing the work when it’s turned on, but also the efficiency of the
program, and the professional performing the crunching and analysis<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">There are four (4) basic characteristics to be understood
regarding the better programming language/software environment:<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">1)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><b style="font-family: Verdana, sans-serif; text-indent: -0.25in;"><u>L</u></b><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">earnability -
Is the learning curve acceptable? ;</span><span style="font-family: Verdana, sans-serif;"><br /></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">2)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><b style="font-family: Verdana, sans-serif; text-indent: -0.25in;"><u>U</u></b><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">sability - Is
the language/software environment best for the purpose? ;</span><span style="font-family: Verdana, sans-serif;"><br /></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">3)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><b style="font-family: Verdana, sans-serif; text-indent: -0.25in;"><u>M</u></b><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">aintainability
- Is the language/software project easy to maintain? ;</span><span style="font-family: Verdana, sans-serif;"><br /></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">4)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><b style="font-family: Verdana, sans-serif; text-indent: -0.25in;"><u>P</u></b><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">ortability –
Is the language/software multiplatform (can it be adapted for an Operating
System other than the native)?</span><span style="font-family: Verdana, sans-serif;"><br /></span><br />
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<span style="font-family: Verdana, sans-serif;">The aforementioned factors will be of prime importance to at
least four parties:</span><br />
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</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Developer (individual, or
team);</span></li>
<li><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">B)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;"> </span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Testing/Quality Assurance
team;</span></li>
<li><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">C)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;"> </span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Distribution team;</span></li>
<li><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">D)</span><span style="font-family: Verdana, sans-serif; font-size: 7pt; text-indent: -0.25in;">
</span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;">Marketing team (if a
commercial project is considered.</span></li>
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<span style="font-family: Verdana, sans-serif;">Optimization of available technology to digest all the
information is therefore the first goal of scientific computing. There is also needed
necessary ability to identify and quantify technical defects in the whole
man-machine interface. Who will judge a technology’s quality? The most common
deficiencies in the technology we easily detect. If a heart rate monitor says
you have a pulse of 3000, we know there’s something wrong. That is why software
programmers have to put their programs to meticulous testing stages. And if
the error escapes our detection we have to be continuously on the test, verify,
correct and improve the system race track. In a
way, program error detection starts with the identification by tracing our
steps back to the beginning of the problem. Nowadays, there is a rise in
malicious code which can seriously impede an application’s functions. Web
applications are a burgeoning way of delivery of functionality for a wide
variety of programs. However, it is turning out to be also a major point of
vulnerability in organizations today. <o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">Definitely, the line between embedded software and systems
for offline analyses is blurring. The ubiquity of mobile devices is also
widening the user base. From a telemedicine thermometer patch on your forehead,
to the analyses of data to determine the incidence of isolated systolic hypertension
in each town of the European Union, one will have no choice but to improve the
abilities of our wits. And likewise improve health outcomes. No question about
that.<o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">Great links to visit on this subject:</span><o:p></o:p></div>
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<span style="font-family: Verdana, sans-serif;">Programming4scientists.com: <a href="http://www.programming4scientists.com/">http://www.programming4scientists.com/</a><o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">Scientific Sentence.net: <a href="http://scientificsentence.net/">http://scientificsentence.net/</a></span></div>
<h1>
<span style="font-family: Verdana, sans-serif; font-size: small; font-weight: normal;">What is Scientific Programming?<a href="http://www.blogger.com/goog_660776824">:</a></span><span style="font-family: Verdana, sans-serif; font-size: small;"><span style="font-weight: normal;"><a href="http://www.linuxforu.com/2011/05/what-is-scientific-programming/">http://www.linuxforu.com/2011/05/what-is-scientific-programming/</a></span></span></h1>
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<span style="font-family: Verdana, sans-serif;">Have a great day- and listen to the music...</span><br />
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<span style="font-family: Verdana, sans-serif;">Fernando Yaakov Lalana, M.D.</span>Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-16295081545218690682013-04-19T06:06:00.003-04:002013-04-19T07:55:50.163-04:00<div class="separator" style="clear: both; text-align: center;">
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif; font-size: large;">Scientific
Computing: Algorithm and Analysis - Part One</span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Over the
last decade and some, the life sciences have seen an exponential growth due to,
in a large part, to the methods employed in modelling, analysis, and
simulation. What was once the domain of the engineering sciences is now
likewise the province of bioinformatics and biophysics. And the software used
by aeronautics engineers is now applied by bioengineers to study molecular
dynamics simulations and their role in exploring the synthesis of large
molecules. Physical and chemical processes are understood more clearly today
owing to the application of algorithms and computer languages open to practically
every biological systems analyst. We would not have an implantable cardiac
defibrillator were it not for the biomedical engineers, clinicians and
researchers working together as a team. In the past, research was reserved for
the university and large institutions which could afford the resources, and were
either often gifted with large grants e.g. by the government, a drug company,
or by a foundation. </span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">In addition,
during the last decade or so, Health IT is making the electronic medical record
system available to clinicians and hospitals. This has improved patient
management in many cases. The OR (operating room) has seen PCs and mobile
devices used by physicians to view x-rays, and even robotics guided surgical
equipment is being used, for example, by the OB-GYN to extirpate a uterine
mass. We are also witnessing the increasing use of nanotechnology to treat
cancer and other difficult cases. </span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">All of the
preceding scenarios involve the use of algorithms and applications. Some use
low-level languages, while some use high-level ones. All require writing a
program whether for an embedded system, such as in robotics, or a program for
use in chemometrics which is an interdisciplinary field that combines statistics
and chemistry. </span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="font-size: 14.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">ALGORITHMS.</span><o:p></o:p></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Several
books have been written on the description, nature, design, analysis, language
specifics, and optimization of algorithms. What is an algorithm? An algorithm
is a sequence of well-defined instructions that takes a value or set of values
entered as input into a computer (or other programmable device) to obtain a
specific result or group of results, as output.<sup>[1] </sup>An algorithm then is a “computable” solution
to a problem.</span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;">An example algorithm is Euclid’s
algorithm which calculates the greatest common divisor (GCD) of two natural numbers</span> <i style="font-family: Verdana, sans-serif;">a</i><span style="font-family: Verdana, sans-serif;"> and </span><i style="font-family: Verdana, sans-serif;">b</i><span style="font-family: Verdana, sans-serif;">.
The greatest common divisor </span><i style="font-family: Verdana, sans-serif;">g</i><span style="font-family: Verdana, sans-serif;"> is the largest natural number that divides
both </span><i style="font-family: Verdana, sans-serif;">a</i><span style="font-family: Verdana, sans-serif;"> and </span><i style="font-family: Verdana, sans-serif;">b</i><span style="font-family: Verdana, sans-serif;"> without leaving a remainder. The identity bases on gcd(a, b) = gcd(a-b, b).
Synonyms for the GCD include the </span><i style="font-family: Verdana, sans-serif;">greatest common factor</i><span style="font-family: Verdana, sans-serif;"> (GCF), the </span><i style="font-family: Verdana, sans-serif;">highest
common factor</i><span style="font-family: Verdana, sans-serif;"> (HCF), and the </span><i style="font-family: Verdana, sans-serif;">greatest common measure</i><span style="font-family: Verdana, sans-serif;"> (GCM). Euclid’s
algorithm, which computes the GCD of two integers, suffices to calculate the
GCD of arbitrarily many integers. To find the GCD of two numbers by this
algorithm, repeatedly replace the larger by subtracting the smaller from it
until the two numbers are equal. E.g. 132, 168 -> 132, 36 -> 96, 36 ->
60, 36 -> 24, 36 -> 24, 12 -> 12, 12 so the GCD of 132 and 168 is 12. The following block of code is design to express Euclid's algorithm.</span><span style="font-family: Verdana, sans-serif; font-size: 14pt;"><o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">For the following C++
code, you could use Code:Blocks available at this site: </span><a href="http://www.codeblocks.org/"><span style="font-family: Verdana, sans-serif;">http://www.codeblocks.org/</span></a><span style="font-size: 14pt;"><o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;">C++ code for Euclid’s algorithm would be as follows:</span><span style="font-size: 14pt;"><o:p></o:p></span></div>
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<span style="font-size: 14.0pt;"><span style="font-family: Verdana, sans-serif;"><u>START of
CODE</u></span></span><br />
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#include
<iostream.h> <br />
// Fundamental idea of Euclid's algorithm (one of the oldest known
algorithms) <br />
// gcd(a,0) = a <br />
// gcd(a,b) = gcd(b,a%b) <br />
int gcd (int a, int b) <br />
{ <br />
int temp; <br />
while (b != 0) <br />
{ <br />
temp = a % b; <br />
a = b; <br />
b = temp; <br />
} <br />
return(a); <br />
} <br />
int main () <br />
{ <br />
int x, y; <br />
cout << "Enter two natural numbers: ";
<br />
cin >> x >> y; <br />
cout << "gcd(" << x <<
", " << y << ") = " << gcd(x,y) <<
endl; <br />
return(0); <br />
} <span style="font-size: 14pt;"><o:p></o:p></span></div>
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<span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; line-height: 115%; mso-ansi-language: EN-PH; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><span style="font-family: Verdana, sans-serif;"><u>END of
CODE</u></span></span></div>
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<span style="font-family: Verdana, sans-serif;">The binary GCD algorithm,
also known as Stein's algorithm, is an algorithm that computes the <span style="color: windowtext; text-decoration: none;">greatest common divisor</span> of two non-negative integers. By replacing divisions
and multiplications with shifts, it gains more efficiency by using the binary
nature of computers, especially in embedded platforms that have no direct
processor support for division. For
large integers, a fast <span style="color: windowtext; text-decoration: none;">GCD</span> <span style="color: windowtext; text-decoration: none;">algorithm</span>
is Lehmer’s, an improvement on the simpler but slower <span style="color: windowtext; text-decoration: none;">Euclidean algorithm</span>.</span><span style="font-size: 14pt;"><o:p></o:p></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Example
Applications.</span><o:p></o:p></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">The problem
may be to compute for the interest on a time-deposit. Or, the problem may be to
sort all the city’s residents’ names (e.g. in alphabetical order, last name
first), addresses, phone numbers, and zip codes, for the purpose of publishing
a directory, for print or online access. Either way, the algorithm input values
may be numerical, or alphabetical, or both (alphanumeric). All this information
may then be stored in databases, for later retrieval.<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Another
example of this process is the Human Genome Project (HGP) which has been able
to determine the sequence of chemical base pairs which make up DNA as well as identifying
and mapping the approximately 20,000 of the human genome. The genome was broken
into smaller pieces, approximately 150,000 base pairs in length. From the start
to completion of this project, it took approximately two decades to study.
Scientists have made strides in identifying particular genes that underlie a
large number of diseases, both genetic and acquired. This project was
officially completed in 2003, but the data continues to provide leads into the
origin and nature of certain illnesses. Now, it is evolving into public and
private ventures to provide individuals, with tissue samples, with a profile of
their DNA and their propensities to a certain a disease or diseases. This then
gives clinicians an insight into the possible means of either prevention or
treatment of the patient’s condition. <o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">The same algorithm may be coded differently,
depending on the programming language chosen. And conversely, specific
languages may be “better” suited for a specific algorithm or purpose.<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Languages of
Choice.</span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">We’ll just take up a few
of these, since already known ones are now applied to biology, and new ones are
steadily being developed. The choice of language depends on at least 4 items: </span></span></div>
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<ol>
<li><span style="font-family: Verdana, sans-serif;"><span style="text-indent: -0.25in;"><span style="line-height: normal;"> </span></span><span dir="LTR" style="text-indent: -0.25in;"></span><span style="line-height: 115%; text-indent: -0.25in;">Familiarity.
Previous exposure or work with a particular programming language, and its
derivatives. Consider FORTRAN and its child, BASIC. Then we would have Visual
Basic, Visual Basic for Applications (VBA), True Basic, etc.</span></span></li>
<li><span style="font-family: Verdana, sans-serif; text-indent: -0.25in;"> </span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; line-height: 115%; text-indent: -0.25in;">Ease of learning
and use. Since Theory and Experiment are melding, the ability to express one’s
ideas (or hypothesis) depends on how rapidly the scientists can develop a
program or module to test it. At this point there has to be a computer
programmer, or a team member who is adept at this craft. This is where the
algorithms are tested, possibly with computer generated “normal” test data
first to make sure the algorithms make sense. Once you have actual subject data
(animal model or human patient), you can run the actual findings in the same
computer program in place of the test data.</span></li>
<li><span style="font-family: Verdana, sans-serif;"><span style="text-indent: -0.25in;"><span style="line-height: 21px;"> </span><span style="line-height: normal;"> </span></span><span dir="LTR" style="text-indent: -0.25in;"></span><span style="line-height: 115%; text-indent: -0.25in;">Time
factor. From protocol design to analysis
of results, the ability of the research team to come up with the study publication
depends, in no small way, on the effort to learn and apply technology in less
time than previously known. The pressure is on to produce a significant
outcome. By this I mean, whether the results are positive or negative, it must
sensibly add and improve on previously held concepts.</span></span></li>
<li><span style="font-family: Verdana, sans-serif; line-height: 115%; text-indent: -0.25in;"> </span><span style="font-family: Verdana, sans-serif; line-height: 115%; text-indent: -0.25in;"><span style="line-height: normal;"> </span></span><span dir="LTR" style="font-family: Verdana, sans-serif; text-indent: -0.25in;"></span><span style="font-family: Verdana, sans-serif; line-height: 115%; text-indent: -0.25in;">Cost. The team
head and his colleagues must have a firm grasp on the financial needs of the
experiment itself. If it’s tight on a budget, then it has to consider using free
open source software, or usually, build a program. If there is a free software
package that meets its requirements, then you’re good to go. Otherwise, you’ll
have to shop around for cost-effective software.</span></li>
</ol>
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This will be
all for now. On the next post, we’ll be looking into different languages which make
good candidates for scientific programming.</span></span><br />
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<span style="font-family: Calibri, sans-serif; line-height: 115%;"><span style="font-size: x-small;">1.) Adapted from: Introduction to Algorithms, 3<sup>rd</sup>
Edition; T.H.Cormen, C.E. Leiserson, R.L.Rivest, C. Stein. ©2009 Massachussets
Institute of Technology</span></span></div>
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<span style="line-height: 115%; text-indent: -0.25in;"><span style="font-family: Verdana, sans-serif;">Happy coding.</span></span><br />
<span style="line-height: 115%; text-indent: -0.25in;"><span style="font-family: Verdana, sans-serif;">Fernando Yaakov Lalana, M.D.</span></span><br />
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<i><span style="font-size: 16.0pt; line-height: 115%;">Sites you
may want to visit:<o:p></o:p></span></i><br />
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<span style="font-family: Verdana, sans-serif; font-size: 16pt; line-height: 115%;"><b><i>Applications Websites</i></b></span><br />
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">QResearch: <o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"><a href="http://www.qresearch.org/SitePages/Home.aspx">http://www.qresearch.org/SitePages/Home.aspx</a></span><span style="line-height: 115%;"><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Scientific
Computing:<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><a href="http://www.scientificcomputing.com/">http://www.scientificcomputing.com/</a></span></span><span style="font-size: 12.0pt; line-height: 115%;"><o:p></o:p></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Empower 3 Chromatography:<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"><a href="http://www.waters.com/waters/en_US/Empower-3-Chromatography-Data-Software/nav.htm?cid=513188&xcid=x6202&locale=en_US">http://www.waters.com/waters/en_US/Empower-3-Chromatography-Data-Software/nav.htm?cid=513188&xcid=x6202&locale=en_US</a></span><span style="line-height: 115%;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><b><i>Databases</i></b></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
</div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Science
Direct:<o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><a href="http://www.sciencedirect.com/">http://www.sciencedirect.com/</a><o:p></o:p></span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
</div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Bioinformatics
Factsheet:<o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><a href="http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html">http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html</a></span><span style="font-size: 14pt;"><o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
</div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Entrez, The
Life Sciences Search Engine:<o:p></o:p></span></span></div>
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><a href="http://www.ncbi.nlm.nih.gov/sites/gquery">http://www.ncbi.nlm.nih.gov/sites/gquery</a></span></span><br />
<div class="MsoNormal">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
</div>
<div class="MsoNormal">
<i><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><b>Application
to try out… </b></span><b style="font-size: 14pt;"><o:p></o:p></b></span></i></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Find the
Greatest Common Divisor [Web App]:<o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><a href="http://www.math.sc.edu/~sumner/numbertheory/euclidean/euclidean.html"><span style="line-height: 115%;">http://www.math.sc.edu/~sumner/numbertheory/euclidean/euclidean.html</span></a><span style="line-height: 115%;"><o:p></o:p></span></span></div>
<br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
</div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">VSEncryptor
64-bit [Encryption Software, Windows Free,]:<o:p></o:p></span></span></div>
<span style="line-height: 115%;"><a href="http://download.cnet.com/VSEncryptor-64-Bit/3000-2092_4-75629878.html?tag=mncol;2"><span style="font-family: Verdana, sans-serif;">http://download.cnet.com/VSEncryptor-64-Bit/3000-2092_4-75629878.html?tag=mncol;2</span></a></span></div>
<br />
<br />
<br />
<br /></div>
Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-13567911841866312142013-03-08T08:57:00.002-05:002013-04-19T08:20:58.415-04:00<div class="separator" style="clear: both; text-align: center;">
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<span style="font-size: large;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">Problem
Solving as Programming Principle: Begin with the end in mind.</span></span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">Problems can
be solved by different algorithms:</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">First, a
solution is reached by the obvious way. Then, secondly, it is getting to the solution
by the methodological or structural way. Then, you have the “smart” way,
meaning, using clever insight into the different aspects of the algorithm,
thereby devising the best approach to the problem. I would say that this is the
best problem solving algorithm. Lastly, but not the least, is the serendipitous
way. But this last method relies almost on a hunch. Hunches are not bad at all. But the problem
with that is the inability to write the solution so as to get the right results
given different values.</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<br /></div>
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</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">Once, a young
lady came up with a question which had to do with an item that she bought at a
discounted price. She knew how much she finally paid, but did not know the
actual discount percentage. Then her older sister said that the percentage was
such and such. She just "knew" the answer but could not explain how
she got it. I, in the meantime, wrote out the equation on paper and did the
calculations by testing the algorithms I came up with. Well, I did get the same
answer as the older sister. We were both right, the difference being that I
could repeat the calculations with different variables. She, on the other hand, could not verify
her answer.</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">This is what
we are after, devising the best algorithm so as to be able to come up with
the ideal solution regardless of the variables, meaning, reproducible results.
We cannot rely on hunches or even educated guesses. As in evidence-based
medicine, we rely on logical, verifiable methods, taking into consideration all
the possible variations as well as mitigating circumstances. Even if one had a
eureka moment, we still have to verify the methods involved. That is the
hallmark of science- reproducible results. It is a discipline.</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<br /></div>
<div class="MsoNormal">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b><span style="line-height: 115%;">To code
or not to code…</span></b></span></span></div>
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<br /></div>
<div class="MsoNormal">
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">Given the
conditions above, there is then the question: do I need to develop programs?
The path to this activity has six points to follow along the way. We will go
over those six points briefly.</span></span></span></div>
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<br /></div>
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<br /></div>
<br />
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<span style="font-size: 14.0pt; line-height: 115%; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="mso-list: Ignore;"><span style="font-family: Verdana,sans-serif;"> <span style="font-size: small;">1.)<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></span></span><span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span dir="LTR"></span><span style="line-height: 115%;">Do I need a
program for myself, for my own needs? Or for others’ needs? Question: What are
my goals? If you were to write a program for yourself, or for the department
you were working in, then you have a stronger motivation, whether or not you
were compensated materially for it.</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<br /></div>
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpMiddle" style="text-indent: -0.25in;">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"> 2.)<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span><span dir="LTR"></span><span style="line-height: 115%;">What do I hope
to achieve, or to make progress in? Think more, and think better. Considering
the path that lies along the programming road, you will do well to concentrate
on the different activities that are necessary for this task. (e.g. seminars,
classes, online training). Become a project manager at heart.</span></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="text-indent: -0.25in;">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpMiddle" style="text-indent: -0.25in;">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"> 3.)<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span><span dir="LTR"></span><span style="line-height: 115%;">Can I do it on
my own? Or, do I invite others to collaborate in the project? Feel competent!
If you must work alone, do so, remembering that your battles will be yours
alone. There are circumstances when working alone is of utmost importance.
Like, for example writing a program as part of school tests. Otherwise, there
is strength in numbers, and it would be best for the project to form some team
for collaboration. Which brings us to the next point…</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpFirst" style="text-indent: -0.25in;">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"> 4.)<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span><span dir="LTR"></span><span style="line-height: 115%;">Equip yourself,
equip others. Study well what you’ll need. Prepare, prepare, prepare. As
mentioned before, get a good look at what you need to do to continue working strong.
And if you’re part of a team, your good insights will strengthen everybody as
well. No man is an island in this scenario.</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpMiddle" style="text-indent: -0.25in;">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"> </span></span></span></div>
<div class="MsoListParagraphCxSpMiddle" style="text-indent: -0.25in;">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"> 5.)<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span><span dir="LTR"></span><span style="line-height: 115%;">Follow set
guidelines, follow through with development milestones. Be disciplined, not
stressed out. Stick to the roadmap, and in so doing you will be avoiding
latency. In the aspect of agile development, cooperation throughout the course
will give a more holistic view, as well as strength.</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpMiddle">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoListParagraphCxSpMiddle" style="text-indent: -0.25in;">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"> 6.)<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span><span dir="LTR"></span><span style="line-height: 115%;">Give credit to
whom it is due, to others and yourself as well. This may be the most important
factor for the success of the project and the group itself. Let everybody own
the project. That way the outcome is far better than a lackadaisical product.</span></span></span></div>
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</span></i></b></span></span></div>
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;"><span style="line-height: 115%;">Now that we
have laid out the rules, let’s take a look at some code which will be useful,
not just for today’s purpose, but will serve as a template if you will.</span></span></span></span></span></div>
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;"><span style="line-height: 115%;">The code is
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previous post, and which are repeated f<span style="font-size: small;">or you </span>below.</span></span></span></span></span></div>
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</span><span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; line-height: 115%; mso-ansi-language: EN-PH; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"></span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>#include <iostream.h> </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>#include <conio.h> </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>void main() </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>{ </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>clrscr();
</span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>int
choice; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>float ctemp,ftemp; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cout
<< "1.Celsius to Fahrenheit" << endl; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cout
<< "2.Fahrenheit to Celsius" << endl; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cout
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<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cin>>choice; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>if
(choice==1) </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>{ </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cout << "Enter the temperature in
Celsius : " << endl; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cin>>ctemp; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>ftemp=(1.8*ctemp)+32;
</span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cout
<< "Temperature in Fahrenheit = " << ftemp << endl;
</span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>} </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>else </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>{ </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cout << "Enter the temperature in
Fahrenheit : " << endl; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cin>>ftemp; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>ctemp=(ftemp-32)/1.8; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span>cout << "Temperature in Celsius =
" << ctemp << endl; </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>} </span></div>
<div class="MsoNormal" style="text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>getch(); </span></div>
<div style="border-bottom: solid windowtext 1.0pt; border: none; mso-border-bottom-alt: solid windowtext .75pt; mso-element: para-border-div; padding: 0in 0in 1.0pt 0in;">
<div class="MsoNormal" style="border: medium none; padding: 0in; text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><span style="mso-spacerun: yes;"> </span>}</span></div>
<div class="MsoNormal" style="border: medium none; padding: 0in; text-align: left;">
<br /></div>
<div class="MsoNormal" style="border: medium none; padding: 0in; text-align: left;">
<span style="font-size: 14.0pt; line-height: 115%;"><br /></span></div>
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<div style="text-align: center;">
<u><span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; line-height: 115%; mso-ansi-language: EN-PH; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"></span></u>---------------------------------------------------------------------------------------</div>
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<span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; line-height: 115%; mso-ansi-language: EN-PH; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><br /></span></div>
<div align="center" class="MsoNormal" style="margin-left: 0.25in; text-align: center;">
<span style="font-family: "Calibri","sans-serif"; font-size: 14.0pt; line-height: 115%; mso-ansi-language: EN-PH; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><br /></span></div>
<div class="MsoNormal" style="margin-left: 0.25in; text-align: left;">
<br />
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<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
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<m:smallFrac m:val="off"/>
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</div>
<div class="MsoNormal">
<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><b><span style="line-height: 115%;">Tools for
C, C++</span></b></span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">C++ Standards
Foundation website </span><a href="http://isocpp.org/"><span style="line-height: 115%;">http://isocpp.org/</span></a><span style="line-height: 115%;">, </span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">C++ FAQ from
its founder’s website </span><a href="http://www.stroustrup.com/"><span style="line-height: 115%;">http://www.stroustrup.com/</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span lang="ES" style="line-height: 115%;">C++ Tutorials </span><a href="http://www.cplusplus.com/doc/tutorial/"><span lang="ES" style="line-height: 115%;">http://www.cplusplus.com/doc/tutorial/</span></a><span lang="ES" style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">C and C++
Programming tutorials </span><a href="http://www.cprogramming.com/tutorial.html"><span style="line-height: 115%;">http://www.cprogramming.com/tutorial.html</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">MinGW-Minimalist
GNU for Windows </span><a href="http://www.mingw.org/"><span style="line-height: 115%;">http://www.mingw.org/</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">MinGW –W64 for
32 and 64 bit Windows </span><a href="http://mingw-w64.sourceforge.net/"><span style="line-height: 115%;">http://mingw-w64.sourceforge.net/</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">Dev-C++
(Windows, Linux) </span><a href="http://sourceforge.net/projects/dev-cpp/?source=directory"><span style="line-height: 115%;">http://sourceforge.net/projects/dev-cpp/?source=directory</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">ARM Linux
GCC – OS X Mountain Lion (Mac, of course) </span><a href="http://www.benmont.com/tech/crosscompiler.html"><span style="line-height: 115%;">http://www.benmont.com/tech/crosscompiler.html</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b><span style="line-height: 115%;">For
Commercial Options:</span></b></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">Microsoft
Visual Studio (2012) </span><a href="http://www.microsoft.com/visualstudio/eng/team-foundation-service"><span style="line-height: 115%;">http://www.microsoft.com/visualstudio/eng/team-foundation-service</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">Embarcadero
C++ Builder XE3 for Windows 8 and Mac </span><a href="http://www.embarcadero.com/products/cbuilder"><span style="line-height: 115%;">http://www.embarcadero.com/products/cbuilder</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br />
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<div style="text-align: center;">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">-----------------------------------------------------------</span></span></span></div>
</div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNoSpacing">
<br /></div>
<div class="MsoNoSpacing">
<i><span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b>Other application tools you can use:</b></span></span></i></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNoSpacing">
<br /></div>
<div class="MsoNoSpacing">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNoSpacing">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNoSpacing">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b>For structural biology, check out:</b></span></span><br />
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b> COMPLEAT</b> – Protein Complex
Enrichment Analysis Tool</span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNoSpacing">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><a href="http://www.flyrnai.org/compleat/">http://www.flyrnai.org/compleat/</a></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b><span style="line-height: 115%;">For
statistical operations,</span></b></span></span><br />
<b style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">the R language<u> </u>is a really good tool.</span></b></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">The Comprehensive
<b>R</b> Archive Network</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><a href="http://cran.r-project.org/"><span style="line-height: 115%;">http://cran.r-project.org/</span></a><span style="line-height: 115%;"></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b><span style="line-height: 115%;">R</span></b><span style="line-height: 115%;"> bioinformatics Packages (for
genetics)-Bioconductor</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><a href="http://www.bioconductor.org/help/workflows/"><span style="line-height: 115%;">http://www.bioconductor.org/help/workflows/</span></a><span style="line-height: 115%;"></span></span></span></div>
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b><span style="line-height: 115%;">R</span></b><span style="line-height: 115%;"> Graph Gallery</span></span></span></div>
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</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">A collection
of graphics entirely generated with R.</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><a href="http://gallery.r-enthusiasts.com/"><span style="line-height: 115%;">http://gallery.r-enthusiasts.com/</span></a><span style="line-height: 115%;"></span></span></span></div>
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b><span style="line-height: 115%;">R</span></b><span style="line-height: 115%;"> Projects of interest</span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><a href="http://www.r-project.org/other-projects.html"><span style="line-height: 115%;">http://www.r-project.org/other-projects.html</span></a><span style="line-height: 115%;"></span></span></span></div>
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</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><b><i><span style="line-height: 115%;">Good Read:</span></i></b></span></span></div>
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"><i>Science
Magazine</i> online<b> </b></span><a href="http://www.sciencemag.org/"><span style="line-height: 115%;">http://www.sciencemag.org/</span></a><span class="MsoHyperlink"><span style="line-height: 115%;"></span></span></span></span></div>
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="background-color: black; font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">
</span></span><br />
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<span style="font-family: Verdana, sans-serif;">Stay Curious. Stay Busy.</span><br />
<br />
<span style="font-family: Verdana, sans-serif;">Fernando Yaakov Lalana, M.D.</span></div>
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<br /></div>
Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-36026527857265547862013-02-19T00:18:00.000-05:002013-02-24T10:54:08.289-05:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyqujKxheNnf6tKYdqjWMWBKsT2tp_582VyoVkchiJKlxH-RdEeXsf-luOsKiJN3RTJCwp0PhLxxX9w1n4yON-80_y4oLAGczAv1EdAib-mFxZjGBneSNgxhyphenhyphenV-S0DOimjAJfclMC1ZKxn/s1600/MP900444155-lady_looking_at_computer.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="214" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyqujKxheNnf6tKYdqjWMWBKsT2tp_582VyoVkchiJKlxH-RdEeXsf-luOsKiJN3RTJCwp0PhLxxX9w1n4yON-80_y4oLAGczAv1EdAib-mFxZjGBneSNgxhyphenhyphenV-S0DOimjAJfclMC1ZKxn/s320/MP900444155-lady_looking_at_computer.jpg" width="320" /></a></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><span style="font-size: large;">Math
Programming,</span></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><span style="font-size: large;">et al<o:p></o:p></span></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">In the
previous post we talked about math programming, calculations, and coding.
Before I proceed, I’d like to apologize for my long hiatus from this series. In
actuality, I had laser surgery in my left eye and am still awaiting the same
surgery, this time in my right eye. (My health insurance will not allow
treatment in both eyes on the same day, but rather, at least 90 days in
between.) So, of course, I had some post treatment irritations in the left eye
for which I had to drop some meds in the affected one. Nevertheless, as is said, "Keep on coding."<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">On a lighter
note, I recently updated my armamentarium gadget-wise. The gadgets namely are a
Nexus 7 tablet with 32GB internal memory along with wifi and 3G capabilities. Along with that, I gota separate Android smartphone: an LG Optimus L E615 Dual Sim.
This gives my eyes some exercise to perform. The reason for the acquisitions
was not an electronic whim, but rather work purposes. I’m developing
medical apps for the Android platform, mathematical apps in particular for
calculating biophysics values. </span></span><br />
<br />
<br />
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">But do let me proceed from where I last covered
a few days ago, and that was, commercial software for math purposes eg MATLAB,
Maple, and Mathematica.<o:p></o:p> To be fair
to the <i>open-source</i> arena, we have MATLAB-based progs such as <b>Freemat</b>, <b>SciLab</b>,
and <b>GNU-Octave</b>. For more data analysis and visualization needs you can try out
<b>SciDAVIS </b>(requires Python 2.6) along with the aforementioned programs all available on the
<i><a href="http://sourceforge.net/">sourceforge.net</a></i> website. There are quite a number of math and information
analysis programs and one should be willing to search for the apps for one’s specific
needs. </span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Incidentally, several of these programs need pre-installed JVM (Java
Virtual Machine), C++ compiler, or Python in any of its specific versions. It
is worthwhile noting that these programming languages are cross-platform. So
whether PC or Mac, or even Linux, there is a recipe just cut out for you, more
or less. <o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><i>You, and the User</i></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Your needs, as
well as user’s needs, will narrow down your choices for programming language or
environment. Programs aren’t built in a day. So experience and patience are keys
to your development timeline. Did we mention budget too? Let’s not forget that
one.<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">What is the
best language for your needs? The answer is open to discussion. If you are
developing for the Windows platform, then C++ (Visual, or Intel) compilers will
be quite useful. Like I mentioned earlier, these languages are mostly cross-platform
and the compiler you use will depend on your own machine and for your intended
audience. </span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Python is quite handy for mathematics applications. You will need to
install the Python environment on your computer. Python is a high-level
language and is used a lot as a <i>scripting </i>language, available from the
2.4 version to the latest 3.3 version and above.</span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">Java, both a programming language and a
software platform, is almost always needed as a necessary environment on
basically every computing machine, from desktops to car auto-navigation, and
operating environments. In this regard, you may be using these a lot for </span><i style="line-height: 115%;">embedded</i><span style="line-height: 115%;">
systems or Android </span><i style="line-height: 115%;">app development</i><span style="line-height: 115%;">.</span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;">Let me not forget Sage, a great
piece of scientific and mathematics software system. And it’s free too! It does
work on a Virtual Machine app like Virtual Box in Windows.</span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><i>Time and Patience</i></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><i><br /></i></span></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">It will take
a bit of time learning how to encode your algorithms in any of the intended
platform languages. You will have to learn basic computer programming
principles. There are a plethora of books, Wikis, and videos to learn from. I
will include a list of sources below, and hope you can make use of them. In the
meantime understand your needs and what platform you are writing programs for.
If you are hoping to deliver this program to the community, or even monetize
the program, then it will be wise to learn certain distribution principles
(even Marketing principles) so you get to see where your activity is intended
for. From Medical Imaging to Electronic Health Record (EHR) needs, it’s all
coding.<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">I can’t
possibly cover all there is to know about programming in a blog post as this
for now. If you send comments, or email me about your interest in specific
programming issues then I will send you a bit of programming nuggets. Keep in touch:
no worthwhile programming is done in total isolation from the community. And do link back to this blog. Or, Like this
on your Facebook page, or Twitter. Many
thanks as always!<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Links:<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">For Open
Source:<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Sage <a href="http://sagemath.org/">http://sagemath.org/</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><b>Python></b></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Python
official website <a href="http://www.python.org/">http://www.python.org/</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span lang="ES" style="line-height: 115%;">Python 2.7 Tutorial </span><span style="line-height: 115%;"><span lang="ES"><a href="http://docs.python.org/2/tutorial/">http://docs.python.org/2/tutorial/</a></span></span><span lang="ES" style="line-height: 115%;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Python 3.3 Documentation
<a href="http://docs.python.org/2/tutorial/">http://docs.python.org/2/tutorial/</a><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;">matplotlib (a mathematics plotting environment for Python) </span><a href="http://matplotlib.org/" style="font-family: Verdana, sans-serif;">http://matplotlib.org/</a><br />
<br />
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><b>C++></b></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">C++ Standards
Foundation website <a href="http://isocpp.org/">http://isocpp.org/</a>, <o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">C++ FAQ from
its founder’s website <a href="http://www.stroustrup.com/">http://www.stroustrup.com/</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span lang="ES" style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">C++ Tutorials <a href="http://www.cplusplus.com/doc/tutorial/">http://www.cplusplus.com/doc/tutorial/</a><o:p></o:p></span></span></div>
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<span lang="ES" style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">C and C++
Programming tutorials <a href="http://www.cprogramming.com/tutorial.html">http://www.cprogramming.com/tutorial.html</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">MinGW-Minimalist
GNU for Windows <a href="http://www.mingw.org/">http://www.mingw.org/</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">MinGW –W64 for
32 and 64 bit Windows <a href="http://mingw-w64.sourceforge.net/">http://mingw-w64.sourceforge.net/</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Dev-C++
(Windows, Linux) <a href="http://sourceforge.net/projects/dev-cpp/?source=directory">http://sourceforge.net/projects/dev-cpp/?source=directory</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">ARM Linux
GCC – OS X Mountain Lion (Mac, of course) <a href="http://www.benmont.com/tech/crosscompiler.html">http://www.benmont.com/tech/crosscompiler.html</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"><br /></span></span>
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"><b>JAVA></b></span></span><br />
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"><b><br /></b></span></span>
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">JAVA for end-users </span><span lang="ES" style="line-height: 115%;"><a href="http://www.java.com/en/"><span lang="EN-PH">http://www.java.com/en/</span></a></span><span style="line-height: 115%;"><o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span>
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">JAVA for
developers (Oracle website) <a href="http://www.oracle.com/technetwork/java/index.html">http://www.oracle.com/technetwork/java/index.html</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">BioJAVA for processing biologic data </span><span style="line-height: 25px;"><a href="http://biojava.org/wiki/Main_Page">http://biojava.org/wiki/Main_Page</a></span></span><br />
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 25px;"><br /></span></span>
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span>
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">For
Commercial Options:<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Microsoft
Visual Studio (2012) <a href="http://www.microsoft.com/visualstudio/eng/team-foundation-service">http://www.microsoft.com/visualstudio/eng/team-foundation-service</a><o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Embarcadero
C++ Builder XE3 for Windows 8 and Mac <a href="http://www.embarcadero.com/products/cbuilder">http://www.embarcadero.com/products/cbuilder</a><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">Intel Developer Zone for Different Platforms</span><br />
<span style="font-family: Verdana, sans-serif;"><a href="http://software.intel.com/">http://software.intel.com/</a>,</span><br />
<span style="font-family: Verdana, sans-serif;"><a href="http://software.intel.com/en-us/intel-parallel-studio-xe">http://software.intel.com/en-us/intel-parallel-studio-xe</a></span><br />
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Other
Commercial options are mentioned on the Official Websites for the specific
languages as cited above.<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Extra: 3
Tips for a Good Presentation:<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">1: Be Real;<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">2: Be Interactive;<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">3: Be
Simple.<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Productivity
App for the week:<o:p></o:p></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><a href="http://sourceforge.net/projects/chuletas/files/Chuletas/Cribr-setup.exe/download" target="_blank">Cribr</a> (for Windows) for making Cheat Sheets.</span></span><br />
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Happy
Coding! Develop for the Future and not the Past.<o:p></o:p></span></span></div>
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<span lang="ES" style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Fernando Yaakov Lalana, M.D. <o:p></o:p></span></span><br />
<span lang="ES" style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span>
<span lang="ES" style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">PS: Remember- A 64-bit operating system can run 32-bit software, but a 32-bit operating system can not run 64-bit software.</span></span><br />
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Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-79590290561158694442013-01-09T07:55:00.002-05:002013-01-09T08:35:14.961-05:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBRIJI5_oBU174p-qeffKzqhUC1QhkQSJOfNp7zRDMDhsItgeAMUHhrS7pBytDayEkZq1azZVefdkhJep6RFCAmQ5N3RyFQBUtGEav_Sjz0QEm_conR960J7J2F-GmkuCfBduToa74Khwp/s1600/MP900439531-math_equations.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="212" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBRIJI5_oBU174p-qeffKzqhUC1QhkQSJOfNp7zRDMDhsItgeAMUHhrS7pBytDayEkZq1azZVefdkhJep6RFCAmQ5N3RyFQBUtGEav_Sjz0QEm_conR960J7J2F-GmkuCfBduToa74Khwp/s320/MP900439531-math_equations.jpg" width="320" /></a></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif; font-size: large;">Math:
Getting it Right</span><span style="font-size: 16pt;"><o:p></o:p></span></span></div>
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<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Whether you’re
baking Grandma’s favourite chocolate cake, or working on file encryption
routines, one principle stands out- get the math right. While some jobs are
satisfactory with an estimate, more often than not, it is a rigorous working
out of an algorithm that is vital to the success of the work. Intuitive
calculations do play a role in program design. But to get an accurate outcome
one must be able to code the algorithm with precision. We’ve all heard of GIGO.
And this holds true in program design and testing. Even if one has the latest
digital programmable calculator, or a robust 64-bit computer, the flow of program
instructions leaves no room for guesswork. For our purpose today we will talk
about the importance of accuracy in application development.<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><b><span style="font-size: 12pt; line-height: 115%;">Application</span></b><span style="font-size: 12pt; line-height: 115%;"> <b>development</b>, or, software development
holds at its core “<i>solutions programming</i>.” This means the process of
design and writing of programs that intends to solve a particular problem or
group of problems with a common purpose. This process oftentimes begins with
back-of-the-envelope notes and/or diagrams. Such notes may delineate the
program flow. Crucial to the flow of the program is the algorithm, input values,
and output characteristics. But before actual code is written, the developer or
team of developers must engage in program <b>design</b>. A classic tool for
this is flowcharting. Whether one uses flowcharting programs, or plastic layout
stencils (of previous years), the process is inherently similar. But let’s make
one thing clear: at the heart of an algorithm is a mathematical formula. It may
be a solution for an ordinary differential equation, or a character sorting
algorithm. Therefore, the <b>requirements</b> for a program, based on research and/or
market demand, must be well delineated before any design begins. In a competitive
world we must also be able to create </span><span style="font-size: 12pt; line-height: 115%;">a better
product than the competition. Of course, in a market based economy there’s room
for everybody. Nevertheless we must improve continuously or lay waste by the
wayside.</span></span></div>
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<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">The choice
of <b>computer language</b> for the application will depend on several factors.
If the application is an extension of a preexisting system, the application
will be written in the language of that system. The application in this
scenario is usually called a module, or “add-in.” Some languages are better fit
for scientific programs. In this case, the language has a large library of
functions, and “calls” to the specific functions are easier to implement than
writing a function from scratch. Some mathematical software packages are used
by industrial, scientific, and engineering sectors. These packages are
available in commercial offerings and cost a major investment to an
organization. Examples of these offerings are Matlab, Maple, and Mathematica.
Sometimes these programs become the lingua franca of the industry. These
packages offer advantages easily adapted for a particular engineering problem.</span></span><br />
<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span>
<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span>
<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Open-source programs have been developed for a wide array of applications as
well. Like the commercial mainstream applications, these open-source
applications are also extensible. These extensions may be available “off-the-shelf”
or written by the particular industry team whose programmers are familiar with
the engineering process. Whether the
application is a “stand alone” program, or a module, the same principles of
design are applicable.<o:p></o:p></span></span></div>
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<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Writing the
program once it is designed is a laborious process that can be undertaken by an
individual, or a <b>coding</b> team. If one
solitary author writes the code, he may be better able to tie the pieces of
code together. This may take a very long time though, since he has to check
everything him- or herself. This may be fine
for small- to medium- size projects. But large-scale programs are better
written by a team of developers, each responsible for a certain portion of the
program. The task of syncing the program sections or components is distributed among the program
writers. The project leader, or leaders, then checks and rechecks the code. The use of an IDE (Integrated Development Environment) facilitates both coding and checking your program. IDEs have been developed with the programmer in mind, and are available for specific languages and frameworks.The IDE is in itself a program for writing programs.<o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: 12pt; line-height: 115%;">The integrity of the code is verified only
by <b>rigorous testing</b>. It is not just a question of whether the program runs, but
also if the code is optimized or tuned. Software testing is carried out by both, members of the programming team and the potential users. The question is then-does the program do its job and do it well? And this oftentimes differentiates
between a lackluster program and a beautifully coded and optimized application.
It is not a matter of adding unnecessary bells-and-whistles to a program, that in turn create </span><i style="font-size: 12pt; line-height: 115%;">bloatware</i><span style="font-size: 12pt; line-height: 115%;">. Not
only that- it can differentiate between your program and that of the
competition.</span></span></div>
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<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Both
software testing and <b>application lifecycle management</b> (ALM) are essential activities
of the software maker. In spite of the initial development of a good product, software
updates and upgrades are necessary and keep the program evolving. Needs change
and new needs arise. Software development
teams listen to market trends in order to deliver a relevant product. One frequently overlooked activity in software development is good documentation. This activity aims to assist the developer as well as the user. For the developer, good documentation keeps the project in focus. Also, it helps the software developer assist the user with regards to overall structure of the program as well as its functions.</span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: 12pt; line-height: 115%;">Launching of
the product comes only after several <b>cycles of testing</b> in all operating conditions.
Whether one is a freelance programmer or a member of a software development
team, the rules of software maintenance are the same. Some teams or companies
release small frequent updates, or, upgrades with major improvements and features</span></span><span style="font-family: Verdana, sans-serif; font-size: 16px; line-height: 18px;">, with release dates </span><span style="font-family: Verdana, sans-serif; font-size: 12pt; line-height: 115%;">somewhat far between.</span><span style="font-family: Verdana, sans-serif; font-size: 12pt; line-height: 115%;"> </span><span style="font-family: Verdana, sans-serif; font-size: 12pt; line-height: 115%;">From designing to prototyping to actual
coding, the software author commits himself to a tough discipline.</span><span style="font-family: Verdana, sans-serif; font-size: 12pt; line-height: 115%;"> </span><span style="font-family: Verdana, sans-serif; font-size: 12pt; line-height: 115%;">Whether one belongs to a Fortune 500 company,
a university biomedical statistics team, or a game-programming outfit, or even
an enthusiast web- or mobile- app designer, the stages of software development
are essentially the same. It is a creative process, with ups and downs.</span><span style="font-family: Verdana, sans-serif; font-size: 12pt; line-height: 115%;"> </span><span style="font-family: Verdana, sans-serif; font-size: 12pt; line-height: 115%;">With writer’s block, and with free-flowing
moments; it is a craft, and an art.</span></div>
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<span style="font-size: 12pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;">In any case: get the math right.</span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="line-height: 18px;">Work smart.</span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="line-height: 18px;">Fernando Yaakov Lalana, M.D.</span></span></div>
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<span style="font-size: 12.0pt; line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><o:p></o:p></span></span></div>
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<br />Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-31638782906294876162012-12-24T07:54:00.000-05:002012-12-24T07:54:32.578-05:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAIvDjYV6IUIBFmCer041tDwjoNXO_Tt3HVNiQVoRutCflOv1cA-EDh_N3p-aVmvo66SBysXILtSeJkyostOQlnVD4_QcXHKwffjcIrPdFraGepY5aBN2OVXsGp1a_OTVM2R8PrZ3PKUoz/s1600/MP900284905-man_with_phone.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAIvDjYV6IUIBFmCer041tDwjoNXO_Tt3HVNiQVoRutCflOv1cA-EDh_N3p-aVmvo66SBysXILtSeJkyostOQlnVD4_QcXHKwffjcIrPdFraGepY5aBN2OVXsGp1a_OTVM2R8PrZ3PKUoz/s1600/MP900284905-man_with_phone.jpg" /></a></div>
<br />
<span style="font-family: Verdana, sans-serif; font-size: x-large;">Lest I forget...</span><br />
<span style="font-family: Verdana, sans-serif; font-size: x-large;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: x-large;">May Everybody have a </span><br />
<span style="font-family: Verdana, sans-serif; font-size: x-large;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: x-large;">Great Holiday Season!</span><br />
<span style="font-family: Verdana, sans-serif; font-size: x-large;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: x-large;">May all your days be</span><span style="font-family: Verdana, sans-serif; font-size: x-large;"> Healthy and Bright!!</span><br />
<span style="font-family: Verdana, sans-serif; font-size: x-large;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: x-large;">from:</span><br />
<span style="font-family: Verdana, sans-serif; font-size: x-large;">Fernando Yaakov Lalana, M.D.</span><br />
<span style="font-size: large;"><b style="font-family: Verdana, sans-serif;">SISTEMA</b> <span style="color: red; font-family: Trebuchet MS, sans-serif;"><i><b>Bio~</b></i></span><b style="font-family: Verdana, sans-serif;">SIGNA</b></span>Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-40760639806620399942012-12-13T09:37:00.000-05:002012-12-13T09:57:24.656-05:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1hwmV4GMqFJnlmUZDJunUIWSTq3WntARifmD0IW2yvcUzmnxlQqImsX7TVoRk7WnKvcLUGmdaTa1b7aasMhlxslLkewC_7lRSilpTf0hgNUjJ8XUj8ZFw2FF6PFbFVZW50kxZZnUHkxqN/s1600/thCAFZT9ZI-teacher.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1hwmV4GMqFJnlmUZDJunUIWSTq3WntARifmD0IW2yvcUzmnxlQqImsX7TVoRk7WnKvcLUGmdaTa1b7aasMhlxslLkewC_7lRSilpTf0hgNUjJ8XUj8ZFw2FF6PFbFVZW50kxZZnUHkxqN/s320/thCAFZT9ZI-teacher.jpg" width="300" /></a></div>
<b>Maths? Are you talking to me?</b>
<br />
<blockquote>
If we were to make a survey of math attitudes in the public, the results would vary depending from what sector we would be making it. I might propose roughly 3 different responses: 1) My everyday work depends on it, 2) I use it only when my activity might warrant it, 3) I don’t like math.
</blockquote>
<blockquote>
Attitudes and responses to math depend on conditioning and experience, like most any attitudes. If one is born with a talent, math might not be as problematic as with the rest of the group. But math requires also a skill honed over time. If, for example, the child is taught at home before he even starts formal schooling, he/she may be at a fairly good advantage. The school instructors also play a crucial and long lasting impression on the student. A memory, whether encouraging or discouraging, is imprinted on the individual learner, and at that, for a considerable length of time. That will spell the difference between initiative or simple lack of interest. If the student was rewarded for a right answer to the problem, the school instructor will be playing an important positive learning experience that will last for a long time beyond the school arena.</blockquote>
<blockquote>
The instructor should fertilize an environment of openness and adaptability in the classroom and in the student. And there must be an application of the subject learned, an application without which the material may be forgotten. The student must be, thence, a good and practical problem solver. After all, we are to be life-long problem solvers.
</blockquote>
<blockquote>
This will be it for now. For your info, this post was written on a new Samsung i5 (Third Generation Micro processor) based laptop with 4GB RAM, and 2GB graphics memory. This I purchased just yesterday because the laptop I had been using went bonkers and I would have to replace the hard disk, cooling fan, heat sink, and a new battery as well. This new laptop is on a 1-week test drive. I hope it doesn’t give me any problems. If it does, I’m replacing it.</blockquote>
<br />
<blockquote>
Stay safe. Be a problem solver.</blockquote>
<br />
<blockquote>
Fernando Yaakov Lalana, M.D.</blockquote>
Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-2579025259553086612012-11-30T04:53:00.000-05:002012-11-30T04:56:41.260-05:00
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Hello guys. These are indeed difficult times. But not without some relief. A long good look at the budget deficit, or, the weather, and you will agree that the grey clouds will be around a bit more. But we must be hopeful, whichever way.
Well, to be honest, the past week has been a tad difficult for myself and my family. We've had a death in the family, namely, my 92-year-old foster mom. She was the last of that batch of great folks that weathered wars here and there. I need not say more.
Oh yes, my PC has been in and out of the technician's shop. I had to fix the Windows aspect, while the repair people still have to install a new cooling fan and heat sink. So either tomorrow or on Monday, this laptop will be in for surgery. Quite simply, a overheating problem caused the unit to shut down by itself quite a number of times. This caused a corruption of Windows that eventually was unrecoverable.
Hopefully, things will work out. An ultrabook in the horizon? Who knows. In the meantime, I'm preparing for the up and coming posts, which I hope will tickle your frontal lobe.
Stay tuned. Stay safe.
Fernando Yaakov Lalana, M.D.
Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-28491609017592927912012-11-15T00:20:00.001-05:002012-11-15T00:20:36.671-05:00NOTICE:
Please be patient.
Experiencing difficulties
due to Windows and hardware issues.
Will be back soon.
Thank you.
-Fernando Yaakov Lalana,M.D.Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-12309501149471773722012-11-01T23:09:00.000-04:002012-11-01T23:09:35.896-04:00<span style="font-family: Verdana, sans-serif;"><span style="font-size: large;">Lives Lost-Lives Changed</span></span><br />
<br />
<span style="font-family: Verdana, sans-serif;">In lieu of the new scheduled post, I choose to send a message to the people of the US eastern seaboard. My heart goes out to all those who lost their loved ones in the worst disaster to hit the East Coast in a century. Likewise, to all those who lost property as well as life's memories my heartiest embrace and sympathy. These are indeed trying times, to say the least. But it is in times like these that the courage and love for their fellow neighbors shine through. Government officials, Firefighters, Medical Personnel and Ordinary Citizens have shown extraordinary love and resilience, hurdles notwithstanding, in reaching out and caring for the weak and the afflicted. All of these things demonstrate the devotion they have for the good of their fellow man. May all this serve as an example to the rest of the nation and the world.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">Stay Safe.</span><br />
<br />
<span style="font-family: Verdana, sans-serif;">Fernando Yaakov Lalana, M.D.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><br /></span>
<br />
<br />Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-14697505350941029522012-10-17T08:02:00.001-04:002012-10-17T09:58:40.162-04:00<div class="separator" style="clear: both; text-align: center;">
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<![endif]--><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span></span></b><span style="font-size: small;"><span style="line-height: 115%;"><span style="line-height: 115%;">- Before we go into the
topic for today, we must take a quick l</span></span><span style="line-height: 115%;"><span style="line-height: 115%;">ook at the just recently held Nobel
Prize awards (Science). Every year since 1901, the Nobel Prize has been awarded
for accomplishments in physics, chemistry, physiology or medicine, literature
and for peace. Alfred Bernhard Nobel, a Swedish chemist, engineer, innovator,
and armaments manufacturer, held 350 different patents, dynamite being the most
famous. He used his fortune to posthumously institute the Nobel Prizes. Three
of the Nobel prizes are relevant to bioinformatics: Chemistry, Physics, and
Physiology and Medicine</span></span></span></span></span><br />
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: large;"><b><span style="font-size: small;"><b><i><span style="line-height: 115%;">Nobel
Prize - Chemistry 2012</span></i></b></span></b></span></span></div>
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<span style="font-size: large;"><b>
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<span style="font-size: large;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;"><span style="font-size: small;"><span style="line-height: 115%;">The Nobel Prize
in Chemistry 2012 was awarded jointly to Robert J. Lefkowitz and Brian K.
Kobilka" for studies of G-protein-coupled receptors" "The Nobel
Prize in Chemistry". Nobelprize.org. 12 Oct 2012 </span><a href="http://www.nobelprize.org/nobel_prizes/chemistry/"><span style="line-height: 115%;">http://www.nobelprize.org/nobel_prizes/chemistry/</span></a></span></span></span></span></div>
<span style="font-size: large;"><span style="font-family: Verdana,sans-serif;"><span style="line-height: 115%;">
</span></span><b><span style="line-height: 115%;"></span></b></span>
<br />
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<span style="font-size: large;"><b><span style="line-height: 115%;"><br /></span></b></span></div>
<span style="font-size: large;"><b><span style="line-height: 115%;">
</span></b></span>
<br />
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><b><i><span style="line-height: 115%;">Nobel
Prize - Physics 2012</span></i></b></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">The Nobel
Prize in Physics 2012 was awarded jointly to Serge Haroche and David J.
Wineland "for ground-breaking experimental methods that enable measuring
and manipulation of individual quantum systems" "The Nobel Prize in
Physics". Nobelprize.org. 12 Oct 2012 </span><a href="http://www.nobelprize.org/nobel_prizes/physics/"><span style="line-height: 115%;">http://www.nobelprize.org/nobel_prizes/physics/</span></a></span></span></div>
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</xml><![endif]--><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;"> </span><b><i><span style="line-height: 115%;">Nobel
Prize - Physiology or Medicine 2012</span></i></b></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">The Nobel
Prize in Physiology or Medicine 2012 was awarded jointly to Sir John B. Gurdon
and Shinya Yamanaka "for the discovery that mature cells can be
reprogrammed to become pluripotent" "The Nobel Prize in Physiology or
Medicine 2012". Nobelprize.org. 12 Oct 2012 </span><a href="http://www.nobelprize.org/nobel_prizes/medicine/laureates/2012/"><span style="line-height: 115%;">http://www.nobelprize.org/nobel_prizes/medicine/laureates/2012/</span></a></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">For more Nobel Prize info,visit </span></span></span><br />
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><b><i><span style="line-height: 115%;">Nobel
Prize Main Web Page <a href="http://www.nobelprize.org/nobel_prizes/" target="_blank">here</a> </span></i></b></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;">Regarding the prize for Chemistry involving G-Protein
Coupled Receptors, there is a noteworthy webpage dealing with this study and
development area. It is </span></span><a href="http://gpcr.scripps.edu/outreach.htm" target="_blank"><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;">here</span></span></a><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> <a href="http://gpcr.scripps.edu/outreach.htm"></a></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;">There are quite a few applications using the G-CPR
mechanism. One salient one has been in the chemistry of opioid substances in
the area of Structural Neurobiology. For more on this feature, kindly visit <a href="http://stevens.scripps.edu/" target="_blank">The StevensLaboratory</a> </span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;">Having mentioned the above, we now move on to what may
be, in my opinion, the next arena for prize-winning developments. </span></span></div>
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<b><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><i>Theranostics - Buzzword?, or, the next Big Thing?</i></span></span></b></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - As mentioned earlier, Theranostics is an area of Medical
development that combines the principles of therapeutics and the processes of
diagnostics. It is touted as the very important facet of personalized Medicine,
pharmacogenomics, and molecular imaging. In this arena, a treatment option,
whether a patient can be either helped, or harmed by a treatment modality, can
be identified by imaging with nanopores, Quantum Dots, “tagged” immunoglobulins,
and others. What’s more is that theranostics aims to improve treatment outcomes
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and more specialized training. So it must demonstrate cost-effectiveness across
the board. <span style="mso-spacerun: yes;"></span>However, if developed
judiciously, theranostics may well be the eventual cost-effective business
model for this decade and the next and beyond.</span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><b><i>Four Facets of Theranostics:</i></b></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><b>1. Diagnostic agent. 2. Carrier agent. </b></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - We will start with the
diagnostic elements. There are many developments involving MRI and the use of
magnetic particles as the contrast agent. In atherosclerosis, for example, in
one study, atherosclerotic lesions (in rabbits) containing
accumulations of ultrasmall superparamagnetic iron oxides (USPIO) were
detected. The study protocol entailed performing
MRI and histologic studies to compare the uptake of dextran- and
mannan-dextran-coated USPIO (D-USPIO and DM-USPIO, respectively) by the
atherosclerotic walls of rabbits.<sup>[1] </sup>Dextran, a polysaccharide consisting of
many glucose units,<sup> </sup>has been used extensively clinically and in the
laboratory owing to its ability to exert osmotic pressure<sup>[2].</sup> Mannans
are polysaccharides consisting of mannose
units and have diverse effects depending on the fraction used and the state of
purification. Mannans’ different mechanisms function at different levels
depending upon the specific phenomenon being influenced. Whereas dextran is a polymer of glucose,
yeast mannan is a polymer consisting entirely of mannose. In
this study, the investigators analyzed the signal to-noise ratio (SNR) of the
aortic wall in the same region of interest (ROI) and this was calculated in
both in vivo and in vitro studies. Next, histologic assessment was carried out
and showed that iron-positive regions were
significantly larger in rabbits injected with DM- rather than D-USPIO (P <
0.05) for all doses. The investigators suggest that DM-USPIO
is superior to D-USPIO for the study of atherosclerotic lesions in rabbits. </span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - This is an example of a diagnostic
agent, supermagnetic iron-oxide particles, delivered by the Mannan-Dextran as
the carrier agent, and the diagnostic modality was imaging via nuclear magnetic
resonance. It is almost like the proverbial golden shoe that fit the damsel’s
foot. </span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><br /></span></span>
<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><br /></span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><b>3. Targeting agent. 4. Therapeutic agent.</b></span></span></div>
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<span style="font-size: small;"> <span style="font-family: Verdana,sans-serif;">- Tests, regardless of modality, would be of no import if
there was no therapeutic system that would improve treatment outcome.
Currently, the standards for diagnostic examination are still in the hands of
the classic clinical laboratory, radiology, and physiologic signal analysis
(e.g. EEG, EKG, EMG). Nevertheless, clinical bedside diagnostics still play a
vital part of patient care. This is when the clinician and patient set the tone
for a better outlook, and where confidence between patient and clinician is
irreplaceable. Why? Because the ethical, psychological, and cognitive aspects
in Medical Practice dictate that the patient is above any test and of foremost
importance in decision making.</span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - Drug, chemical, or other treatment choices may be either
broad spectrum or highly selective. On many occasions clinicians are faced with
a patient with aggressive, late stage malignancy. When the most “suitable” (for reducing the
tumor) drug(s) are toxic to the patient, the physician has to maximize new
technology that may be of help. And this is an area where theranostics will be
of utmost help to the patient. After histologic and surgical classification (of
the tumor), the next appropriate step would be to utilize a diagnostic
procedure as mentioned in the study above, or other specialized imaging
modality. </span></span></div>
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<span style="font-family: Verdana,sans-serif;"> - Quercetin, a plant-derived flavonoid, is derived from
quercetum (oak forest), and is a hydrophobic antioxidant-- which purportedly scavenges
damaging particles in the body known as free radicals, which damage cell
membranes, tamper with DNA, and even cause cell death. Found in fruits,
vegetables, leaves and grains, it has been used since the late 1800s for a wide
variety of purposes. It is sold as a herbal dietary supplement, and touted to
have anti-infllammatory, anti-viral, and anti-cancer agent, to name a few
properties. While neither the US FDA nor the American Cancer Society have approved
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - In one study, quercitin was loaded into monomethoxy
poly(ethylene glycol)-poly(ε-caprolactone). These loaded micelles (QU/MPEG-PCL)
given via intravenous route significantly suppressed the growth of
established xenograft A2780S ovarian tumors through causing cancer cell
apoptosis and inhibiting angiogenesis in vivo. Furthermore, the anticancer
activity of quercetin on ovarian cancer cells was studied in vitro. <sup>[3]</sup>
This is an example of nano-formulation of treatment agent (quercitin) and drug
delivery agent (MPEG-PCL).</span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - We have talked about a few examples where new
technologies improve health outcome, or at least identified available tools in
theranostics, which make it more possible to select the treatment of choice in
difficult clinical circumstances. A thorough understanding of the potentials of
theranostics, as well as its current
limitations will make us more competent in our own sphere of work. While this
management modality is still in its infancy, a good systematic review and analysis of
clinical and laboratory data will allow us to wield new weapons in our fight
against disease.</span></span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;">References:</span></span></div>
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<li><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Tsuchiya%20K%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Tsuchiya K</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Nitta%20N%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Nitta N</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Sonoda%20A%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Sonoda A</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Nitta-Seko%20A%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Nitta-Seko A</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Ohta%20S%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Ohta S</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Takahashi%20M%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Takahashi M</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Murata%20K%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Murata K</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Mukaisho%20K%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Mukaisho K</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Shiomi%20M%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Shiomi M</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Tabata%20Y%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Tabata Y</span></a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed?term=Nohara%20S%5BAuthor%5D&cauthor=true&cauthor_uid=22619561"><span style="color: windowtext; text-decoration: none;">Nohara S</span></a>.;Evaluation of atherosclerotic lesions using dextran-
and mannan-dextran-coated USPIO: MRI analysis and pathological findings.
Int J Nanomedicine. 2012;80. Epub 2012 May<span style="font-size: small;"> </span></span></span></li>
<li><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span lang="ES">Dextran /PHARMACOSMOS;</span><span lang="ES" style="line-height: 115%;"> </span><a href="http://www.dextran.net/dextran-chemistry.html"><span lang="ES" style="line-height: 115%;">http://www.dextran.net/dextran-chemistry.html</span></a></span></span></li>
<li><span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"></span>Xiang Gao , BiLan Wang,
XiaWei Wei , Ke Men , Fengjin Zheng , <span style="font-size: small;"></span>Yingfeng Zhou , Yu Zheng , MaLing Gou ,
Meijuan Huang, Gang Guo, Ning Huang,
ZhiYong Qian and Yuquan Wei Anticancer effect and mechanism of
polymer micelle-encapsulated quercetin on ovarian cancer Nanoscale, 2012,
Advance Article </span></span></li>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - </span>Stay focused. Work smart. 'Til the next...</span></div>
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<span style="font-family: Verdana,sans-serif;"><span style="font-size: small;"> - Fernando Yaakov Lalana, M.D.</span></span></div>
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Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-82356688088319597772012-10-05T09:42:00.003-04:002012-10-05T10:03:17.027-04:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwVZxjt04xVGqZ_hDCB89WlHXyGNHwvErag7dLyFmYePzDOxdJkdUQyncIYA3JKw-AMNcwwwgACT7kV79Ob1hFuY0tN88_tXXaR56GmVw15Fhx3zwwK0SQEp93NUD7YPfsvLF1IaFcMg7Q/s1600/MB900390113-DNA_purple.JPG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwVZxjt04xVGqZ_hDCB89WlHXyGNHwvErag7dLyFmYePzDOxdJkdUQyncIYA3JKw-AMNcwwwgACT7kV79Ob1hFuY0tN88_tXXaR56GmVw15Fhx3zwwK0SQEp93NUD7YPfsvLF1IaFcMg7Q/s200/MB900390113-DNA_purple.JPG" width="200" /></a></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif; font-size: large;">It’s in the
Genes!</span><span style="font-size: medium;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"> - A person’s genome contains information showing possible
advance of a disease, or a propensity for the individual to develop a
particular disorder. However, you need a fast, reliable and economical way of
sequencing each patient's genes to take full advantage of them. This is not a
one-time deal and there is the need to continually sequence an individual's DNA
over his or her lifetime, because the genetic code can be modified by many
factors.</span></div>
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<i><span style="font-family: Verdana, sans-serif;"><b>DNA Primer</b></span><b><o:p></o:p></b></i></div>
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<i><span style="font-family: Verdana, sans-serif;"><b><br /></b></span></i></div>
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<span style="font-family: Verdana, sans-serif;"> - Deoxyribonucleic acid is a <span style="color: windowtext; text-decoration: none; text-underline: none;">nucleic acid</span>,
in a ladder-like, double helix structure (discovered in 1953 by James Watson
and Francis Crick), containing the <span style="color: windowtext; text-decoration: none; text-underline: none;">genetic</span>
instructions used in the development and functioning of all known living <span style="color: windowtext; text-decoration: none; text-underline: none;">organisms</span>
(with the exception of <span style="color: windowtext; text-decoration: none; text-underline: none;">RNA viruses</span>). The rungs of the ladder-like
helix DNA consists of the consistent pairing of A==T and G==C base pairs. This
complementary relationship is critical in gene function. Within cells, DNA is
organized into long structures called <span style="color: windowtext; text-decoration: none; text-underline: none;">chromosomes</span>
The DNA segments carrying this genetic <span style="color: windowtext; text-decoration: none; text-underline: none;">information</span>
are called <span style="color: windowtext; text-decoration: none; text-underline: none;">genes</span>.
During <span style="color: windowtext; text-decoration: none; text-underline: none;">cell division</span> these chromosomes are duplicated
in the process of <span style="color: windowtext; text-decoration: none; text-underline: none;">DNA replication</span>, providing each cell its own
complete set of chromosomes. Along with <span style="color: windowtext; text-decoration: none; text-underline: none;">RNA</span> and <span style="color: windowtext; text-decoration: none; text-underline: none;">proteins</span>,
DNA is one of the three major <span style="color: windowtext; text-decoration: none; text-underline: none;">macromolecules</span>
that are essential for all known forms of <span style="color: windowtext; text-decoration: none; text-underline: none;">life</span>.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - DNA consists of two long <span style="color: windowtext; text-decoration: none; text-underline: none;">polymers</span>
of simple units called <span style="color: windowtext; text-decoration: none; text-underline: none;">nucleotides</span>, with <span style="color: windowtext; text-decoration: none; text-underline: none;">backbones</span>
made of <span style="color: windowtext; text-decoration: none; text-underline: none;">sugars</span> and <span style="color: windowtext; text-decoration: none; text-underline: none;">phosphate</span>
groups joined by <span style="color: windowtext; text-decoration: none; text-underline: none;">ester</span>
bonds. Genomic DNA is tightly and orderly packed in the process called <span style="color: windowtext; text-decoration: none; text-underline: none;">DNA
condensation</span> to fit the small available volumes of the cell. In
eukaryotes (<span style="color: windowtext; text-decoration: none; text-underline: none;">animals</span>,
<span style="color: windowtext; text-decoration: none; text-underline: none;">plants</span>,
<span style="color: windowtext; text-decoration: none; text-underline: none;">fungi</span>,
and <span style="color: windowtext; text-decoration: none; text-underline: none;">protists</span>),
DNA is located in the <span style="color: windowtext; text-decoration: none; text-underline: none;">cell nucleus</span>, as well as small amounts in <span style="color: windowtext; text-decoration: none; text-underline: none;">mitochondria</span>
and <span style="color: windowtext; text-decoration: none; text-underline: none;">chloroplasts</span>.
<span style="color: windowtext; text-decoration: none; text-underline: none;">Eukaryotic
organisms</span> store most of their DNA inside the <span style="color: windowtext; text-decoration: none; text-underline: none;">cell nucleus</span>
and some of their DNA in <span style="color: windowtext; text-decoration: none; text-underline: none;">organelles</span>, such as <span style="color: windowtext; text-decoration: none; text-underline: none;">mitochondria</span>
or <span style="color: windowtext; text-decoration: none; text-underline: none;">chloroplasts</span>.<sup>[1] </sup> Eukaryotic cells, in general, are bigger and
more elaborate than bacteria and archaea. In many <span style="color: windowtext; text-decoration: none; text-underline: none;">species</span>,
only a small fraction of the total sequence of the <span style="color: windowtext; text-decoration: none; text-underline: none;">genome</span>
encodes protein. Only about 1.5% of the human genome consists of protein-coding
<span style="color: windowtext; text-decoration: none; text-underline: none;">exons</span>, with
over 50% of human DNA consisting of non-coding <span style="color: windowtext; text-decoration: none; text-underline: none;">repetitive sequences</span>.</span><sup><span style="font-family: Verdana, sans-serif;">[2]</span><o:p></o:p></sup></div>
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<span style="font-family: Verdana, sans-serif;"><span style="color: windowtext; text-decoration: none; text-underline: none;"> - Bioinformatics</span> (one of the thrusts of this
website) involves the manipulation, searching, and <span style="color: windowtext; text-decoration: none; text-underline: none;">data mining</span>
of biological data, and this includes DNA sequence data. Computer science,
utilizing string searching string algorithms, machine learning, and database
theory have led to big advances in genomics. Many of these processes deal with
pattern recognition. The technology involved in DNA sequencing is quite
expensive, running into the thousands. There is therefore a demand for a more
cost-effective method for this job. </span></div>
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<i><b><span style="font-family: Verdana, sans-serif;">New Approach to Old Data…</span><o:p></o:p></b></i></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> - Researchers from the
National Institute of Standards and Technology (NIST) and Columbia University's
School of Engineering and Applied Science are collaborating<sup>[3] </sup>to
devise a new rapid and less-expensive procedure that can be commercialized
effectively. If this pushes through that means that doctors and other health
personnel will be able to order these tests from their clinic or offices with
greater ease. </span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> - The new method, which is
some kind of molecular ticker-tape, can perform DNA sequences by attaching
distinct molecular "tags" to each of the four chemical building
blocks, or "bases," that comprise the genetic information in a strand
of DNA —abbreviated as G, A, C and T. That’s G=Guanine, A=Adenine, C=Cytosine,
and T=Thymine. Each of these polymer tags can then be cut from the strand and
passed, one by one, through a nanometer-size hole in a membrane. A steady
stream of fluid and ions flows through this "nanopore,"<sup>[4] </sup>which is large enough to contain only
one tag at a time. As the polymer tags are different sizes, the change in
electrical current caused by altered fluid flow shows which of the four bases
sits at each point on the DNA strand. Columbia University has applied for
patents for the commercialization of the technology. </span></span></div>
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<b><i><span style="font-family: Verdana, sans-serif;">DNA Works</span><o:p></o:p></i></b></div>
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<span style="font-family: Verdana, sans-serif;"> - Transcription factors are the DNA binding proteins that
carry out the organic process whereby the DNA sequence in a gene is copied into
mRNA.<sup>[5]</sup> Gene expression, then, is the process by which a gene’s
coded information is converted into the structures present and operating in the
cell. Expressed genes include those that are transcribed into mRNA and then
translated into protein, and, those that are transcribed into RNA but not
translated into protein (e.g., transfer and ribosomal RNAs). </span></div>
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<span style="font-family: Verdana, sans-serif;"> - DNA can be damaged, wherein there is a DNA
alteration that has an abnormal structure, which cannot itself be replicated
when the DNA is replicated, but which may be repaired. Mutation can occur too,
wherein there is a change in the sequence of DNA base pairs, but which may be
replicated and thus inherited. DNA is subject to a wide variety of chemical
reactions that might be expected of any such molecule in a warm aqueous medium.
In any cell, however, some DNA damage may remain unrepaired despite repair
processes.</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOH7RvGmi-KaUBzgPdBZMmm_dZdQWPY0i5_kTTN5qYTmg2Z_7U0vgNHbvlPz_OtIsnVUUX7KvF68XE1vMTlMxUsETzCThgoYuu3__ccmM3HZYFd89ZROBUOpWkM33Ihyphenhyphen3JRqPNVAurw0-I/s1600/ADN_animation.gif" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOH7RvGmi-KaUBzgPdBZMmm_dZdQWPY0i5_kTTN5qYTmg2Z_7U0vgNHbvlPz_OtIsnVUUX7KvF68XE1vMTlMxUsETzCThgoYuu3__ccmM3HZYFd89ZROBUOpWkM33Ihyphenhyphen3JRqPNVAurw0-I/s1600/ADN_animation.gif" /></a></div>
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<b><i><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></i></b></div>
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<span style="font-family: Verdana, sans-serif; line-height: 18px;">Animation of a rotating DNA structure. </span></div>
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<b><i><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> </span></span></i></b></div>
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<span style="font-size: x-small;"><span style="font-family: 'Times New Roman', serif; line-height: 115%;">Created
in the free program </span><span style="font-family: Calibri, sans-serif; line-height: 115%;"><span style="color: blue; font-family: 'Times New Roman', serif; line-height: 115%;"><a href="http://www.bernstein-plus-sons.com/software/rasmol/">RasMol 2.7.2.1.1</a></span></span></span></div>
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<span style="font-size: x-small;"><span style="font-family: 'Times New Roman', serif; line-height: 115%;"> using the </span><span style="font-family: Calibri, sans-serif; line-height: 115%;"><a href="http://www.wellesley.edu/Chemistry/Flick/molecules/bdna.pdb"><span style="color: blue; font-family: 'Times New Roman', serif; line-height: 115%;">bdna.pdb</span></a></span><span style="font-family: 'Times New Roman', serif; line-height: 115%;"> dataset and the following commands:</span></span></div>
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<span style="font-size: x-small;"><span style="font-family: 'Times New Roman', serif; line-height: 115%;"><br /></span></span></div>
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</div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;">GUI options were: Options->Specular,
Display->Sticks</span></div>
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</div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;">Then, in the command line</span></div>
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</div>
<div class="MsoNoSpacing">
<span style="font-family: Verdana, sans-serif; font-size: x-small;">where script.txt was a separate text file </span></div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;">in the same
directory, consisting of the</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;">same two repeating lines: </span></div>
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</div>
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<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">rotate
x 3<o:p></o:p></span></div>
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<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">write
frame-07.gif<o:p></o:p></span></div>
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<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">rotate
x 03<o:p></o:p></span></div>
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<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">write
frame-05.gif<o:p></o:p></span></div>
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<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">rotate
x 3<o:p></o:p></span></div>
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<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">write
frame-03.gif<o:p></o:p></span></div>
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<span style="font-family: "Courier New"; font-size: 10.0pt; mso-fareast-font-family: "Times New Roman";">...</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;"><br /></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: Verdana, sans-serif; font-size: x-small;">from 001 up to 119
(for a total of 120 images when </span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<span style="font-family: Verdana, sans-serif; font-size: x-small;">combined with frame-000.gif).This was then loaded</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;">in Adobe ImageReady, and saved as an
animated GIF.</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;"><span class="int-own-work">Own work:</span> Author <a href="https://en.wikipedia.org/wiki/User:Brian0918" title="en:User:Brian0918">brian0918</a><a href="https://en.wikipedia.org/wiki/User_talk:Brian0918" title="en:User talk:Brian0918">™</a></span> </div>
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<b><i><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></i></b></div>
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<b><i><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></i></b></div>
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<b><i><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;">Father of Genetics</span></span></i></b></div>
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<b><i><span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></i></b></div>
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</div>
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<span style="font-family: Verdana, sans-serif;">- In 1866, Gregor Mendel, an Augustinian monk, put forth
the postulates of inheritance based on a decade long work in pea plants. Today,
we can have a DNA test in an hour or so. Mendel did his work before the
structure and role of chromosomes were known. About 20 years after his work,
advances in microscopy allowed researches to identify chromosomes and to
establish that in eukaryotic organisms (meaning those with a nucleus and cell
membranes), each species has a identifiable characteristic number of
chromosomes called the diploid number. You and I have a diploid number of 46.
Chromosomes in diploid cells exist in pairs called homologous chromosomes, and
members of a pair are identical in size and location of the centromere where
the spindle fibers attach to during division.</span></div>
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<sup><span style="font-family: Verdana, sans-serif;"><br /></span></sup></div>
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<b><i><span style="font-family: Verdana, sans-serif;">From Genotype to Phenotype</span><o:p></o:p></i></b></div>
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<b><i><span style="font-family: Verdana, sans-serif;"><br /></span></i></b></div>
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<span style="font-family: Verdana, sans-serif;"> - In living organisms DNA does not usually exist as a
single molecule, but instead as a pair of molecules that are held tightly
together. These two long strands entwine like vines, in the shape of the now
known <span style="color: windowtext; text-decoration: none; text-underline: none;">double helix</span>.
DNA is a long <span style="color: windowtext; text-decoration: none; text-underline: none;">polymer</span>
made from repeating units called <span style="color: windowtext; text-decoration: none; text-underline: none;">nucleotides</span>.
Polymers comprising multiple linked nucleotides are called a <span style="color: windowtext; text-decoration: none; text-underline: none;">polynucleotide</span>.
The backbone of the DNA strand is made from alternating <span style="color: windowtext; text-decoration: none; text-underline: none;">phosphate</span>
and <span style="color: windowtext; text-decoration: none; text-underline: none;">sugar</span>
residues. The D in DNA stands for 2-deoxyribose, which is a <span style="color: windowtext; text-decoration: none; text-underline: none;">pentose</span>
(five-<span style="color: windowtext; text-decoration: none; text-underline: none;">carbon</span>)
sugar. In turn, the sugars are joined together by phosphate groups that form <span style="color: windowtext; text-decoration: none; text-underline: none;">phosphodiester bonds</span> between the third and
fifth carbon <a href="https://en.wikipedia.org/wiki/Atom" title="Atom"><span style="color: windowtext; text-decoration: none; text-underline: none;">atoms</span></a>
of adjacent sugar rings.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - Proteins are the end products of gene expression. Once a
protein is made, its action or location plays a role in producing a phenotype.
When mutation alters a gene, it may abolish or alter that protein’s function
and cause an altered phenotype. Genomics grew out of recombinant DNA technology
which began in the early 1970s, when researchers discovered that bacteria could
protect themselves by making enzymes that restrict or block infection by
cutting viral DNA at specific sites. When cut, the viral DNA could not
orchestrate the synthesis of more phage particles which when released kill the
infected bacterial cell.</span></div>
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<b><i><span style="font-family: Verdana, sans-serif;">Genome Libraries</span><o:p></o:p></i></b></div>
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<br /></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> - A cell’s genome, that
is, the entire library of genetic information in its DNA, provides a genetic
program that instructs the cell how to function, and, for plant and animal
cells, how to grow into an organism with hundreds of different cell types. The
DNA contains the information that not only determines form, but also the
function of the cell and organism. Once genomic “libraries” became available,
researchers started working on ways and means to sequence all the clones in a
genomic library in an organized way, so as to obtain the neucleotide sequence
of an organism’s genome.</span></span></div>
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<span style="font-family: Verdana, sans-serif; line-height: 115%;"> - In 2001, the Human Genome Project reported the first
template of the human genome. Then in 2003, the remaining portion of the genome
sequence was published. Work is focused now on the non-coding portions of the
genome. Genomics arose as a new field of Medicine as more complete genomes were
discovered and published. Now, we have gene sequences of a variety of
organisms, ranging from bacteria and fungi, to insects, all the way to large mammals.
Hemophilus influenza, which causes respiratory illness and meningitis, was the
first free-living organism to have its genome sequenced. The third generation
of model organisms include the roundworm (C. elegans), the plant Arabidopsis,
and , the Zebrafish. We also have gene sequences of plants, which is a boon to
the agricultural industry. It is estimated that more than 60% of the processed
food in the United States contains ingredients made from genetically modified
crop plants.</span><sup style="font-family: Verdana, sans-serif; line-height: 115%;">[6] </sup><span style="font-family: Verdana, sans-serif; line-height: 115%;">These
modifications are done to provide crops with different enhancements, ranging
from herbicide resistance, drought- or flood-resistance, all the way to delayed
ripening.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - The screening of an individual’s genome to determine a
person’s risk for developing a disease uses DNA microarrays or DNA chips. Each
chip contains thousands of fields, each carrying a different gene. Chips
containing the human genome are widely available, making it feasible to scan
one’s entire genome to check for a propensity for a disease. Pharmagenomics
checks out which chemical compound best treats a certain illness. In addition,
we have gene therapy, which involves transferring normal genes into an abnormal
cell or tissue. The molecular basis for hundreds of genetic disorders is now known. We must remember that genetic studies rely on
known model organisms. Gene sequencing involves the comparison of gene
sequences of one organism to a reference sequence.</span></div>
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<b><i><span style="font-family: Verdana, sans-serif;">We are all connected</span><o:p></o:p></i></b></div>
<br />
<br />
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> - So now, one can visit
the BLAST portal online, for access to gene sequences from many organisms with
known sequences. Model organisms used to
study human disease include, for example, yeast, for: cell cycle, cancer, and
Werner Syndrome; Drosophila (fruit fly) for: cell signaling, cancer, and human
neurodegenerative disease<sup>[7]</sup>; Zebrafish, for developmental pathways,
and cardiovascular disease. These model organisms have a rich history in
genetic studies. One should remember that whatever controls a certain process
in yeast will also be the same for the human. The development and use of model
organisms is only one of the ways genetics and biotechnology are rapidly
changing every aspect of our lives. I hope that the reader will look into the
wealth of material on genetics, epigenetics, as well as the other omics (e.g.
proteomes, exomes).</span></span></div>
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<b><i><span style="font-family: Verdana, sans-serif;"><br /></span></i></b></div>
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</div>
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<b><i><span style="font-family: Verdana, sans-serif;">Some Tools of the Trade</span><o:p></o:p></i></b></div>
<br />
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<b><i><span style="font-family: Verdana, sans-serif;"><br /></span></i></b></div>
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<span style="font-family: Verdana, sans-serif;"> - There are an ever-growing number of bioinformatics resources that are available to the interested
worker. Depending on what area of specialty you’re in, you will find work
opportunities as well. To get one started, do read further on in all the published
documents available now on the Web. Check out the BLAST portal here. Equipment
can range from a light microscope all the way to the transmission- and scanning
electron microscope. On the software side, there are several sequencing programs
available. Some are free and open-sourced, while others come at a big price. A
brief listing of software is on this site. As new developments are pursued, the
armamentarium of the bioinformatics worker will grow exponentially. All it
takes is a good helping of resourcefulness and you’re on your way to making the
next big discovery.</span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="color: #0c343d; font-family: Verdana, sans-serif; font-size: large;"><i><b>Think Big. Think Forward</b></i></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNoSpacing">
<span style="font-family: Verdana, sans-serif;"> - Fernando Yaakov Lalana, M.D.</span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;">References:</span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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</div>
<div class="MsoNoSpacing" style="margin-left: .25in; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;">1)<span style="font-size: 7pt;"> </span><span class="citation">Russell, Peter (2001). <i>iGenetics</i>.
New York: Benjamin Cummings. </span><a href="https://en.wikipedia.org/wiki/International_Standard_Book_Number" title="International Standard Book Number">ISBN</a><span class="citation"> </span><a href="https://en.wikipedia.org/wiki/Special:BookSources/0-8053-4553-1" title="Special:BookSources/0-8053-4553-1">0-8053-4553-1</a><span class="citation">.</span></span></div>
<div class="MsoNoSpacing" style="margin-left: .25in; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span class="citation"><span style="font-family: Verdana, sans-serif;"><br /></span></span></div>
<div class="MsoNoSpacing" style="margin-left: .25in; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span class="citation">2)<span style="font-size: 7pt;">
</span></span><!--[endif]--><span class="citation">Wolfsberg T, McEntyre J, Schuler G (2001). "Guide to the
draft human genome". <i>Nature</i> <b>409</b> (6822): 824–6. </span><a href="https://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier">doi</a><span class="citation">:</span><a href="http://dx.doi.org/10.1038%2F35057000">10.1038/35057000</a><span class="citation">. </span><a href="https://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier">PMID</a><span class="citation"> </span><a href="https://www.ncbi.nlm.nih.gov/pubmed/11236998">11236998</a><span class="citation">.<o:p></o:p></span></span></div>
<h3 style="margin-left: .25in; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="font-size: 11pt; font-weight: normal;">3)<span style="font-size: 7pt;"> </span></span><span style="font-size: 11pt; font-weight: normal;"><span style="font-size: small;">Engineers collaborate on inexpensive DNA sequencing method. R & D
Magazine</span> </span><a href="http://www.rdmag.com/News/2012/10/Life-Science-Genetics-Analytical-Instrumentation-Engineers-collaborate-on-inexpensive-DNA-sequencing-method/?et_cid=2880813&et_rid=424458894&linkid=http%3a%2f%2fwww.rdmag.com%2fNews%2f2012%2f10%2fLife-Science-Genetics-Analytical-Instrumentation-Engineers-collaborate-on-inexpensive-DNA-sequencing-method%2f"><span style="font-size: 11pt; font-weight: normal;">http://www.rdmag.com/News/2012/10/Life-Science-Genetics-Analytical-Instrumentation-Engineers-collaborate-on-inexpensive-DNA-sequencing-method/?et_cid=2880813&et_rid=424458894&linkid=http%3a%2f%2fwww.rdmag.com%2fNews%2f2012%2f10%2fLife-Science-Genetics-Analytical-Instrumentation-Engineers-collaborate-on-inexpensive-DNA-sequencing-method%2f</span></a><span class="citation"><span style="font-size: 11pt; font-weight: normal;"> </span></span><span style="font-size: 11pt; font-weight: normal;"><o:p></o:p></span></span></h3>
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<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;"><span style="font-size: 9.5pt;">4)<span style="font-size: 7pt;"> </span></span><span style="font-size: small;">PEG-Labeled
Nucleotides and Nanopore Detection for Single Molecule DNASequencing by</span><span style="font-size: small;">
Synthesis,</span><span style="font-size: small;"> Shiv Kumar, Chuanjuan, Tao, Minchen, Chien, Hellner, Brittney,
Balijepalli, Arvind </span></span><span style="font-family: Verdana, sans-serif;">Robertson,
Joseph W. F. , Li, Zengmin, Russo, James J., Reiner, Joseph E., Kasianowicz, John
J.,<span style="font-size: small;">& Ju,, Jingyue.; Nature.com,
Scientific Reports.</span><o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;"> <a href="http://www.nature.com/srep/2012/120921/srep00684/pdf/srep00684.pdf">http://www.nature.com/srep/2012/120921/srep00684/pdf/srep00684.pdf</a><span class="citation"><o:p></o:p></span></span></div>
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<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;">5)<span style="font-size: 7pt;"> </span>Leff ,Todd and Granneman, James G., in Encyclopedia of Molecular
Cell Biology and Molecular </span></div>
<div class="MsoNoSpacing" style="margin-left: .25in; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span style="font-family: Verdana, sans-serif;"> Medicine, 2nd Edition. Edited by Robert A. Meyers., Copyright
2004 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. ISBN: 3-527-30543-2</span></div>
<div class="MsoNoSpacing" style="margin-left: .25in; mso-list: l0 level1 lfo1; text-indent: -.25in;">
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<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;">6) <span style="font-size: 7pt;"> </span>Klug, William S., Cummings, Michael R., Spencer Charlotte A.,
Concepts Of Genetics 8th Ed.,©2006,2003,2000,1997 by William S. Klug and
Michael R. Cummings. Published by Pearson Education, Inc. Pearson Prentice Hall.
ISBN: 0131918338</span></div>
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<!--[if !supportLists]--><span style="font-family: Verdana, sans-serif;">7)<span style="font-size: 7pt;"> </span>Fortini, M. and
Bonini,N.M.;2000 Modeling human neurodegenerative disease in Drosophila. Trends
Genet.16:161-167</span><o:p></o:p></div>
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<br />Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-30960027300759432712012-09-28T07:00:00.000-04:002012-09-28T10:30:20.610-04:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirXpph8C3NeZhVCuOXuf7i2sfFfvamSYymA1BfYW-aQXqif_yxbydjRmtyRB07Cfixa33RB8IOMfw8vuitMKYkNv5oQMCGgLFHWuh0dWp-G03er7gqqWwPC3vE612ogD0OeH-Ivc1s1jPP/s1600/MB900440293-red+hearts+among+white.JPG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><span style="font-family: Verdana, sans-serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirXpph8C3NeZhVCuOXuf7i2sfFfvamSYymA1BfYW-aQXqif_yxbydjRmtyRB07Cfixa33RB8IOMfw8vuitMKYkNv5oQMCGgLFHWuh0dWp-G03er7gqqWwPC3vE612ogD0OeH-Ivc1s1jPP/s1600/MB900440293-red+hearts+among+white.JPG" /></span></a></div>
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<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><span style="font-size: large;"> </span></span></span><br />
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><span style="font-size: large;">The Heart of
the Matter</span></span></span><br />
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<h1>
<span style="font-family: Verdana, sans-serif; font-size: small; font-weight: normal;"><span style="line-height: 115%;"> - In the
year 2000, the World Heart Federation proclaimed Sept. 29 World Heart Day. A
couple of years before that, I did a post-doc dissertation on how advances in
technology had influenced the prognosis in coronary artery disease over the
last decade. At that time, 2D Echocardiography was making waves </span><span style="line-height: 115%;">and </span><span style="line-height: 115%;">so was Positron Emission Tomography Scanning.</span></span></h1>
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<span style="font-family: Verdana, sans-serif;"><i><b>Pass the Stent Please </b></i></span><br />
<br />
<span style="font-family: Verdana, sans-serif;"> - 2012 marks the 35th anniversary of the first percutaneous
transluminal coronary angioplasty (PTCA) which was performed in 1977 by Dr.
Andreas R. Gruentzig in Zurich, Switzerland. This angioplasty procedure
utilized an expandable balloon, fashioned on a kitchen table in Gruentzig’s
apartment by Gruentzig’s assistant, Maria Schlumpf.</span><o:p></o:p></div>
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<span style="font-family: Verdana, sans-serif;"> - It was an idea
first conceived by a U.S. radiologist, Dr. Charles Dotter, in the early 60′s. At the time, Dotter’s concept was deemed crazy
by the surgical community and it took quite a bit of time for the concept to
take hold. His idea had to travel to Europe where eventually Dr. Gruentzig
heard about it. With Dr. Myler ( of San Francisco), the procedure was done
first intra-operatively. Then eventually, after a few surgical cases, the
procedure was done using the principle of the angiogram. What started out as a
mad idea has turned into a procedure carried out by dozens of M.D.s at dozens
of clinics and hospitals globally, to become a branch of Medicine on its own.</span></div>
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<span style="font-family: Verdana, sans-serif;"><i><b>For Ladies Too</b></i></span><br />
<span style="font-family: Verdana, sans-serif;"><i><b><br /></b></i></span></div>
<span style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"> - While heart disease has always been considered a
feature of middle-aged men, the statistics show, however, that up to a fourth
of all deaths in women in the U.S. are seen in females with heart disease. Two thirds of
women who die suddenly of CHD (Coronary Heart Disease) have had no symptoms. This
statistic alone is sufficient reason to focus our resources on increased
awareness into women’s CHD. Microvascular coronary artery disease (MVD) and
broken heart syndrome, also pose a risk for women. Many of the tests for CHD
have focused on men. So, in effect, we still have to understand the possible
different pathologic processes seen in women </span></span><span style="font-family: Verdana, sans-serif;">and determine if we can apply the same tests and the
normal variants in exam results.</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWN_hrKSamJnPBpRrm2qEpaBqrdUKSwhimwWBcFY4FGywI2jMNZS1a-eeIN_PtfUmOjQ59llg5MXipYjnUY6wpUinM0Z6UwudYdSGm7qNFD74KbDeJGSfF_BEaMQU0__8UAkZ6w7DsBNde/s1600/320px-Anatomy_Heart_English_Tiesworks.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: Verdana, sans-serif;"><img border="0" height="208" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWN_hrKSamJnPBpRrm2qEpaBqrdUKSwhimwWBcFY4FGywI2jMNZS1a-eeIN_PtfUmOjQ59llg5MXipYjnUY6wpUinM0Z6UwudYdSGm7qNFD74KbDeJGSfF_BEaMQU0__8UAkZ6w7DsBNde/s320/320px-Anatomy_Heart_English_Tiesworks.jpg" width="320" /></span></a></div>
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<span class="description"><span lang="EN" style="font-family: Verdana, sans-serif;">Anatomy of the human heart, </span></span><br />
<span class="description" style="font-size: x-small;"><span lang="EN" style="font-family: Verdana, sans-serif;">in English, by Ties van Brusse </span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;"><span class="description"><span lang="EN"><a href="http://www.tiesworks.nl/">http://www.tiesworks.nl</a></span></span><span lang="EN"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: x-small;">Date 30 September 2010 </span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: x-small;">Source </span><span class="int-own-work" style="font-size: x-small;">Own
work</span><span style="font-size: x-small;"> Author <a href="https://commons.wikimedia.org/w/index.php?title=User:Tvanbr&action=edit&redlink=1" title="User:Tvanbr (page does not exist)">Tvanbr</a></span> <o:p></o:p></span></div>
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<span style="font-family: Verdana, sans-serif;"> - In developed
countries, various indicators of low socio-economic position (SEP) have clearly been shown to be associated with a higher risk of
cardiovascular disease and
diabetes (Davey Smith,1997). The
effect of SEP on risk of CVD or diabetes in developing countries is poorly
understood, given the paucity of cause-specific mortality and morbidity data.
However little may be the statistics, it appears that there is a preponderance of
CHD among the higher income groups in the developing countries. The particular<o:p></o:p> nature of the
social inequalities in CVD depends upon
how lower socioeconomic position within
a particular country affects the social distribution of risk factors for CVD, such as smoking, unhealthy diet and physical
inactivity. </span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<b><i><span style="font-family: Verdana, sans-serif;">Not Child's Play</span></i></b><br />
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"> - The dangers of heart disease in children can occur early
on, particularly in the context of congenital heart disease. The cause of
congenital heart disease may be either genetic or environmental, but is usually
a combination of both. In addition, an unhealthy diet and sedentary behaviors
early in life can lead to heart disease in adulthood, even in children with no
family history of heart disease. In developed countries, the problem of excess caloric
intake has led to the preponderance of obesity in the young in the same way
that it is seen in the adult population. The current trend in weight gain may
spell more ominous health deterioration by the time today’s children reach
adulthood. A high salt intake in the young can lead to a higher blood pressure
in adolescence. With an earlier “head start” in the process of hypertensive and
coronary artery disease development, the health infrastructure will have to
deal with the increased burden of cost.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - With improved and increasing technology, what was once a
sure fatal disease is now better treated in many ways. Advances in imaging
procedures have enabled us to better visualize the diseased heart (in addition
to other organ systems). Biomarkers, such as genomic data, are now helping us
see who is at greater risk for the disease. Pharmagenomics is helping us better
determine what is the best treatment for
a given patient. At the center of these technological tools lie better algorithms
for the detection, identification and diagnostics, and finally- treatment.
However, the application of these tools lie ultimately on clinical wisdom.</span><br />
<br /></div>
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<span style="font-family: Verdana, sans-serif;"> - Embrace wisdom.</span></div>
<br />
<span style="font-family: Verdana, sans-serif;">- Fernando Yaakov Lalana, M.D.</span><br />
<br />
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American writer (1902 - 1984) </span></div>
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<span style="font-family: Verdana, sans-serif;"><a href="http://www.nhlbi.nih.gov/health/health-topics/topics/cad/" target="_blank">Coronary artery disease</a><o:p></o:p></span><br />
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<br />Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-72617282877032187062012-09-19T05:16:00.001-04:002012-09-19T06:01:22.280-04:00<div style="font-family: Verdana,sans-serif;">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIa14rXMbtuOOqM475rSetmu7rSucNG3Kom1tSSHaT2P0WQoBOdMtO9eIEIsbEI5IXFzOIaJa_xoEiEZ75C45M6GVQrpvyMgy1767hSICqzJ9EhLOUPl3wnIQY6EExCFpaUnzc5z_aA2EO/s1600/MB900365662-boy_stat.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><span style="font-family: Verdana, sans-serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIa14rXMbtuOOqM475rSetmu7rSucNG3Kom1tSSHaT2P0WQoBOdMtO9eIEIsbEI5IXFzOIaJa_xoEiEZ75C45M6GVQrpvyMgy1767hSICqzJ9EhLOUPl3wnIQY6EExCFpaUnzc5z_aA2EO/s1600/MB900365662-boy_stat.jpg" /></span></a></div>
<span style="font-family: Verdana, sans-serif;"><span style="font-size: large;"><br /></span>
<span style="font-size: large;">Outliers and Outbreaks</span></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: small;"><b><i>Outliers: the Stats</i></b></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"> - An outlier<sup>[1]</sup>,
in statistical terminology, is an observation that is numerically distant from
the rest of the <span style="color: windowtext; text-decoration: none;">data</span>.
In effect, an observation that is towards either extreme end of the spectrum is
an outlier. Extreme values show large or small data values that are relative to
other data values. Outliers can occur by chance in any distribution, but they
are often indicative either of <span style="color: windowtext; text-decoration: none;">measurement
error</span> or that the population has a <span style="color: windowtext; text-decoration: none;">heavy-tailed distribution</span>. A physical
apparatus for taking measurements may have suffered a transient malfunction.
There may have been an error in data transmission or transcription. Outliers
arise due to changes in system behaviour, fraudulent behaviour, human error,
instrument error or simply through natural deviations in populations. In
addition, the pathological appearance of outliers of a certain form appears in
a variety of datasets, indicating that the causative mechanism for the data
might differ at the extreme end.</span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - When you look at
frequency polygons or histograms[<sup>2]</sup>, the question asked is whether
the curve is bell-shaped at the middle, peaked at either end, or is the curve
flat. Are the data values spread out, or do they cluster at one segment? The
extreme values where there are few entries could be outliers. A better method
of data visualization is the <i>bagplot</i> which is an approach to detecting outliers
in <i>bivariate data</i>. This type of plot visualizes location, spread, correlation,
skewness and the tails of the data without making assumptions about the data
being symmetrically distributed.<sup>[3] </sup>The Galbraith plot is a graphical method
for identifying outliers in a meta-analysis. The standardized effect size is
plotted against precision (the reciprocal of the standard error).<sup>[5] </sup>The
arithmetic mean may be affected by outliers thereby giving an inaccurate value.
The alpha-trimmed mean, which is less affected by outliers than the arithmetic
mean, involves dropping a proportion (alpha) of the observations from both ends
of the sample before calculating the mean of the remainder.<sup>[4] </sup></span><span style="font-size: small;"> </span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - Outliers, being the most
extreme observations, may include the <span style="color: windowtext; text-decoration: none;">sample
maximum</span> or <span style="color: windowtext; text-decoration: none;">sample minimum</span>, or both, depending on whether
they are extremely high or low. However, the sample maximum and minimum are not
always outliers because they may not be unusually far from other observations.
Simplistic interpretation of statistics derived from data sets that include
outliers may be misleading. The median is a robust statistic, while the
arithmetic mean is not, as we read earlier.</span><span style="font-size: small;">
Existing methods that are seen for finding outliers in large data-sets
can only deal with two dimensions or attributes. </span><span style="font-size: small;">Knowledge discovery in databases,
commonly referred to as data mining, is generating enormous interest in both
the research
and software arenas. </span><span style="font-size: small;">With the development of better analytic algorithms
for statistical exploration (and studying outliers), high-powered computing (HPC), and the progress of
graphic ability, we are now better equipped to not only calculate significant
values, but also to visualize data that will facilitate our decision making
processes. </span></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - Nevertheless, one should remember that “the whole is greater than
the sum of its parts.” It is highly important to realize, that unless it can be
ascertained that the deviation is not significant, it is ill-advised to ignore
the presence of outliers. Outliers that cannot be readily explained demand
special attention. In this area, we deal with probability and how we can
conclude, with a reasonable assurance, hat we are dealing with either a
numerical anomaly, or a more serious situation. This brings us then to the
other question on hand: what constitutes an epidemic? </span><span style="font-size: small;"> Since we are dealing with life, the right
analysis and decision will spell the difference between a case-to-case
response, </span><span style="font-size: small;"> or a nationwide pathogen
alert.</span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
<div class="MsoNoSpacing">
<span style="font-family: Verdana, sans-serif; font-size: small;"><b><i>Outbreaks</i></b></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
<div class="MsoNoSpacing">
<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - Outbreak is a term used in <span style="color: windowtext; text-decoration: none;">epidemiology</span>
to describe an occurrence of <span style="color: windowtext; text-decoration: none;">disease</span> greater than would otherwise be expected at a
particular time and place. It may affect a small group of the population in a
specific location, or it may impact hundreds of the population, either in one
specific location or across states. According to the CDC, an </span><span style="font-size: small;"> <b><i>outbreak</i></b> </span><span style="font-size: small;"> </span><span style="font-size: small;"> is the
occurrence of more cases of disease, injury, or other health condition than
expected in a given area or among a specific group of persons during a specific
period. Usually, the cases are presumed to have a common cause or to be related
to one another in some way. It is a phenomenon that is more localized, and less
likely to invoke panic in the population than an epidemic. (Not to be confused
with the word <b>endemic</b>, which is the term given to an ailment that is
found commonly in a certain location)</span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - According to the CDC, an <b>epidemic</b>
is the occurrence of more cases of disease, injury, or other health condition
than expected in a given area or among a specific group of persons during a
particular period. Usually, the cases are presumed to have a common cause or to
be related to one another in some way. At this point, there appears to be no
difference between an outbreak and an epidemic. In <span style="color: windowtext; text-decoration: none;">epidemiology</span>,
an epidemic occurs when new cases of a certain <span style="color: windowtext; text-decoration: none;">disease</span>,
in a given human population, and during a given period, substantially exceed
what is expected based on recent experience. For this reason, it is very
important to stratify the conditions we set for differentiating an outbreak
from an epidemic. One authority <sup>[6] </sup>describes an epidemic as an
increased unusual widespread infection in the community causing</span><span style="font-size: small;"> waves of infection. These spread
through communities and affect all people who have no active immunity to that
infection. </span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
<div class="MsoNoSpacing">
<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - While epidemics due to exogenous pathogens have
diminished in developed countries with a good health system, they may still be
found in third-world areas where nutrition and other aspects of healthcare are
substandard. There have been exceptions however. An example of an epidemic in
the last two decades was in</span><span style="font-size: small;"> the
1990s</span><span style="font-size: small;"> where there</span><span style="font-size: small;"> was</span><span style="font-size: small;">
a</span><span style="font-size: small;"> large diphtheria</span><span style="font-size: small;"> epidemic</span><span style="font-size: small;">
in</span><span style="font-size: small;"> Russia</span><span style="font-size: small;"> as</span><span style="font-size: small;">
the</span><span style="font-size: small;"> result of the collapse of the
public health infrastructure, demonstrating that pathogenic</span><span style="font-size: small;"> microbes</span><span style="font-size: small;">
are</span><span style="font-size: small;"> still</span><span style="font-size: small;"> in</span><span style="font-size: small;">
the</span><span style="font-size: small;"> environment</span><span style="font-size: small;"> and</span><span style="font-size: small;">
can</span><span style="font-size: small;"> become epidemic even in
technologically advanced countries if we relax our efforts to contain them.</span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - A mechanism that may give rise to epidemics, for example, is the antigenic
shift which refers to the emergence of a novel influenza virus in humans, due
to direct introduction of an avian strain or to a new strainproduced by recombination and reassortment of two
different influenza viruses. Recent influenza A pandemics occurred in 1957 (the
H2N2‘Asian Flu’) and 1968 (the H3N2‘Hong Kong Flu’). An</span><span style="font-size: small;"> outbreak</span><span style="font-size: small;">
of</span><span style="font-size: small;"> avian</span><span style="font-size: small;"> influenza</span><span style="font-size: small;">
from</span><span style="font-size: small;"> exposure</span><span style="font-size: small;"> to</span><span style="font-size: small;">
infected</span><span style="font-size: small;"> poultry</span><span style="font-size: small;"> in Hong</span><span style="font-size: small;">
Kong</span><span style="font-size: small;"> in</span><span style="font-size: small;"> 1997 </span><span style="font-size: small;"> caused</span><span style="font-size: small;">
18</span><span style="font-size: small;"> human</span><span style="font-size: small;"> deaths.</span><span style="font-size: small;">
A genetically</span><span style="font-size: small;"> different strain of
A/H5N1 circulated in domestic birds throughout Asia, causing 387 cases and 245
deaths between 2003 and 2008, raising concerns that a new pandemic might arise.<sup>[7]
</sup></span><span style="font-size: small;"> Another infection that is being
tracked is TB. Since 1998, the percent-age of US-born patients with MDR-TB has
remained at less than 0.7%. However, the frequency of resistant infections in
foreign-born persons increased from 25% (103 of 407) in 1993 to 80% (73 of 91)
in 2006.</span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"> </span><br />
<b><i><u><span style="font-family: Verdana, sans-serif;">Current Hantavirus Outbreak</span></u></i></b><br />
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyUdjL0cpAAUUGy-Hna2Lk9QC7KUNiBdYDs50UgyGxC6RHX0hPYrq2X9Fn4pMYdsUdj9ZN96Pkur25FhXt1JvEhvO2ZgmQ1biliPRmn34LDcwK7lYzCoeRdY9jRcmOrngggrARyv6URIGP/s1600/MB900240793-lab_rat.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><span style="font-family: Verdana, sans-serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyUdjL0cpAAUUGy-Hna2Lk9QC7KUNiBdYDs50UgyGxC6RHX0hPYrq2X9Fn4pMYdsUdj9ZN96Pkur25FhXt1JvEhvO2ZgmQ1biliPRmn34LDcwK7lYzCoeRdY9jRcmOrngggrARyv6URIGP/s1600/MB900240793-lab_rat.jpg" /></span></a><span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - As of September 13, the National Park Service (NPS) has
announced a total of 9 confirmed cases of hantavirus infection in people who
recently visited Yosemite National Park. Officials believe that 8 out of the 9
patients acquired the virus while staying at the Signature Tent Cabins in Curry
Village in Yosemite National Park. The 9<sup>th</sup> person may have acquired
it at a location in the park 15 miles from Curry Village. </span><span style="font-size: small;">The
visitors to Yosemite are residents of: California (7), Pennsylvania (1), and
West Virginia (1). Three of the confirmed cases were fatal. The National Park
Service issued a notification to all Park visitors. You can view this at the
NPS page <a href="http://www.nps.gov/yose/planyourvisit/hantaletter.htm" target="_blank">here.</a></span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;">Decision Making and Response</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"> - The park is contacting visitors who stayed in the
Signature Tent Cabins from mid-June through the end of August, advising them to
seek immediate medical attention if they exhibit symptoms of Hantavirus Pulmonary
Syndrome (HPS), a rare but serious illness caused by hantavirus. The park is
also providing information about HPS risks and symptoms to visitors who stayed
at the High Sierra Camps this summer. In addition to closing down the Signature
Tent Cabins, the CDC is supporting the NPS response with testing of patient
samples for evidence of hantavirus infection, providing guidance on clinical
management of HPS and epidemiologic support for the response, and maintaining a
Hantavirus Hotline for public inquiries. The park is providing educational
materials about hantavirus and HPS to all visitors to the park.</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - While the number of hantavirus cases is very small, the
fatality rate is </span><span class="text-underline" style="font-size: small;"><</span><span style="font-size: small;">40%. So it makes it
imperative to track the illness, carry out decontamination where possible, test
persons who were exposed, and ensure rapid hospitalization of cases even it was
just a suspicion. </span></span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: small;"> - The question to be asked at this point is: are the victims of this current outbreak actually outliers in the immunocompetent population? Are they any more susceptible to the viral illness than all the rest of the visitors to the Yosemite Park? While we dig deeper into this scenario it is likely that we shall discover a novel mechanism for the outbreak. In the meantime we have to respond and take care of those who have fallen sick.</span></div>
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<span style="font-family: Verdana, sans-serif;">Yosemite National Park Hantavirus Infection Epi Curves:</span><br /><a href="http://www.cdc.gov/hantavirus/outbreaks/yosemite/epi.html" style="font-family: Verdana, sans-serif;">http://www.cdc.gov/hantavirus/outbreaks/yosemite/epi.html</a></div>
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<br />
<dt style="text-align: justify;"><span style="font-family: Trebuchet MS, sans-serif;"><i>"Statistics: The only science that enables different experts using the same figures to draw different conclusions."</i></span></dt>
<dd class="author"><div style="text-align: justify;">
<b style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: small;">Evan Esar</b><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: x-small;">, </span><i style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: small;">Esar's Comic Dictionary </i></div>
<div style="text-align: justify;">
<i style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: small;">American Humorist (1899 - 1995)</i><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; font-size: x-small;"> </span></div>
</dd><br />
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<span style="font-family: Verdana, sans-serif;"><span style="font-size: small;"> - Time to wrap this up for now. </span><span style="font-size: small;"> </span><span lang="ES" style="font-size: small;">Stay
safe…</span></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span lang="ES" style="font-family: Verdana, sans-serif; font-size: small;"> - Fernando
Yaakov Lalana, M.D </span></div>
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<span lang="ES" style="font-family: Verdana, sans-serif; font-size: small;">Bibliography:</span></div>
<div style="text-align: left;">
<span class="reference-text" style="font-family: Verdana,sans-serif; font-size: small;">1.<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><span class="reference-text" style="font-family: Verdana,sans-serif; font-size: small;">Barnett, V. and Lewis, T.: 1994, Outliers in Statistical
Data. John Wiley & Sons., 3rd edition.</span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;">2.<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><span style="font-family: Verdana,sans-serif; font-size: small;">Bluman, Allan G.:Elementary
Statistics-A Step by Step Approach, 8<sup>th</sup> Ed., Copyright © 2012 by The
McGraw-Hill Companies, Inc.</span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;">3.<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><span style="font-family: Verdana,sans-serif; font-size: small;">Everitt, B.S. and Skrondal,
A.:The Cambridge Dictionary of Statistics, 4<sup>th</sup> Ed., Cambridge
University Press, © B. S. Everitt and A. Skrondal 2010,; First, Second and
Third Editions © Cambridge University Press 1998, 2002, 2006</span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;">4.<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><span style="font-family: Verdana,sans-serif; font-size: small;">Fisher, L. D. and Van
Belle, G., 1993, Biostatistics, J. Wiley & Sons, New York.</span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;">5.<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><span style="font-family: Verdana,sans-serif; font-size: small;">Everitt, B.S.; Medical
Statistics from A to Z, 2<sup>nd</sup> Ed.; Cambridge University Press, © B.
Everitt 2006</span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;">6.<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><span style="font-family: Verdana,sans-serif; font-size: small;">Kumar, P. and Clark, M.,
Kumar and Clark’s Clinical Medicine, © 2009, Elsevier Limited. All rights
reserved</span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;">7.<span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><span style="font-family: Verdana,sans-serif; font-size: small;">Cohen, J., Opal,S.M., Powderly,W.G.,Editors,;
Infectious Diseases, 3<sup>rd</sup> Ed., © 2010, Elsevier Limited. All rights
reserved.</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;">Helpful Links:</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;">Calculation & Visualization of Outlier</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><a href="http://mathworld.wolfram.com/Outlier.html">http://mathworld.wolfram.com/Outlier.html</a></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: small;">CDC Glossary of Terms</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><a href="http://www.cdc.gov/excite/library/glossary.htm#outbreakcommonsource">http://www.cdc.gov/excite/library/glossary.htm#outbreakcommonsource</a></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: small;">CDC TB Report </span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><a href="http://www.cdc.gov/tb/statistics/reports/2007/default.htm">http://www.cdc.gov/tb/statistics/reports/2007/default.htm</a></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><br /></span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;">Journal of Statistical Software </span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><a href="http://www.jstatsoft.org/">http://www.jstatsoft.org/</a></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: small;">Yosemite National Park Hantavirus Infection Epi Curves:</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><a href="http://www.cdc.gov/hantavirus/outbreaks/yosemite/epi.html">http://www.cdc.gov/hantavirus/outbreaks/yosemite/epi.html</a></span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif; font-size: small; line-height: 115%;">Electron Cryo-Tomography of Tula Hantavirus</span></div>
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<span style="font-family: Verdana, sans-serif; font-size: small;"><a href="http://jvi.asm.org/content/early/2010/03/10/JVI.00057-10.full.pdf">http://jvi.asm.org/content/early/2010/03/10/JVI.00057-10.full.pdf</a></span></div>
Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-37557245450140708682012-09-10T11:32:00.000-04:002012-09-11T02:54:49.759-04:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgpEu6FSp8y_npsa67v5-Hclpye5HprtW5vj8uypT0hVVeWKmRxMBwb5-joVoWlL26_dKzeR41F9RbJNy4WWkdR9jVvB1TfM1ZFqSd0UJAQZlhqqqSCSdMddQ95oG1uEyXn2nYYjTyydV99/s1600/MB900262274-rodent.JPG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><span style="font-family: Verdana, sans-serif;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgpEu6FSp8y_npsa67v5-Hclpye5HprtW5vj8uypT0hVVeWKmRxMBwb5-joVoWlL26_dKzeR41F9RbJNy4WWkdR9jVvB1TfM1ZFqSd0UJAQZlhqqqSCSdMddQ95oG1uEyXn2nYYjTyydV99/s320/MB900262274-rodent.JPG" width="320" /></span></a></div>
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<span style="font-family: Verdana, sans-serif; font-size: large;">Hanta in the Park</span><br />
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<span style="font-family: Verdana, sans-serif;"> - The Yosemite National Park has become famous now, not
because of the grandeur of the place, but because it is now in alarm mode owing
to the Hanta Virus outbreak there. The RNA virus is acquired from contamination
with rodent urine, saliva or contact with rodent waste products. Hantavirus are
genetically stable in their natural rodent host. Hantavirus (genus Bunyavirus)
co-evolution with its rodent host, suggests a 20 million year association.
There are now many examples of species-specific RNA virus/host co-evolution,
indicating very slow rates of virus evolution. The infamous rodent family in
this current outbreak is the Deer Mouse. Phlebovirus (causing Rift Valley fever),
and Nairovirus (causing Crimean-Congo HF) are </span><span style="font-family: Verdana, sans-serif;">two </span><span style="font-family: Verdana, sans-serif;">other known members of the
Bunyavirus genus.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - Hantaviruses cause millions of cases of haemorrhagic
fever each year in many parts of the world. This rodent-borne Negative-sense
single-strand RNA virus can cause serious and fatal disease in humans, the major
problem of which would be hantavirus pulmonary syndrome (HPS). Another
condition caused by this virus would be hemorrhagic fever with renal syndrome
(HFRS). From the time of infection to clinical manifestations of this disease,
the period could be </span><span style="font-family: Verdana, sans-serif;">even </span><span style="font-family: Verdana, sans-serif;">as long as 6 weeks, at which time of clinical discovery the condition
could be potentially fatal. While rodent material to human transmission is the
classic link, recent human-to-human transmission has been reported with the </span><span style="color: windowtext; font-family: Verdana, sans-serif;">Andes virus</span><span style="font-family: Verdana, sans-serif;">
in South America. The first identification of this virus was in the late 1970s
in the South Korean River named Hantaan. In</span><span style="font-family: Verdana, sans-serif;">
</span><span style="font-family: Verdana, sans-serif;">the beginning, the name given to this febrile hemorrhagic condition was
Korean </span><span style="color: windowtext; font-family: Verdana, sans-serif;">hemorrhagic fever</span><span style="font-family: Verdana, sans-serif;">. This condition was actually
responsible for the thousands of soldiers getting infected during the Korean
War.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - The Southwestern United States witnessed an outbreak in
the early 90s.The viral cause of the disease was found only weeks later. Its
rodent host, the Deer mouse (<i><a href="http://en.wikipedia.org/wiki/Peromyscus_maniculatus" title="Peromyscus maniculatus">Peromyscus maniculatus</a></i>) was first
identified by a professor at the <span style="color: windowtext; text-decoration: none; text-underline: none;">University of New Mexico</span>.<sup> </sup>Initially,
in the outbreak, the virus was called Sin Nombre (meaning, Without Name) Virus.
It is
now known that at
least three different
hantaviruses cause HFRS
and four different viruses cause HPS. By 1995, HPS had been recognized
in 102 patients in 21 states of the United States, in seven patients in Canada,
and in three in Brazil,</span></div>
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<span style="font-family: Verdana, sans-serif;">with an
overall mortality rate
of approximately 40%.</span></div>
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<span style="font-family: Verdana, sans-serif;"><b><i>Genetic Characteristics</i></b></span></div>
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<span style="font-family: Verdana, sans-serif;"> - More than 16 different genotypes or serotypes have been
identified (e.g., Puumala, Hantaan, Dobrava-Belgrade, Seoul, Sin Nombre). The
family Bunyaviridae includes <b><i>four medically significant genera</i></b>. The
genomes of negative-strand viruses are frequently segmented. Like other members
of the Bunyavirus family, hantaviruses are lipid enveloped viruses with a
genome that consists of three single-stranded, negative sense RNA segments where
the genome is
comprised of three
molecules: L (8.5 kb), M (5.7 kb), and
S (0.9 kb). The S RNA encodes the <span style="color: windowtext; text-decoration: none; text-underline: none;">nucleocapsid</span>
(N) protein. The M RNA encodes a <span style="color: windowtext; text-decoration: none; text-underline: none;">polyprotein</span>
that is cotranslationally cleaved to yield the envelope <span style="color: windowtext; text-decoration: none; text-underline: none;">glycoproteins</span>
Gn (formerly G1) and Gc (formerly G2). All three RNA species are linear, but in
the virion they appear circular because the ends are held together by
base-pairing. The three segments are not present in virus preparations in
equimolar amounts.</span></div>
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<span style="font-family: Verdana, sans-serif;"><b><i>Tools for Studying the Virus Genetic Make-up</i></b></span></div>
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<span style="font-family: Verdana, sans-serif;"> - Although viral genomes were the first to be sequenced,
the initial focus was simply to identify similarity between viral genes, not to
evaluate distant evolutionary relationships. The most
popular tool for
finding similarity is BLAST
(Basic Local Alignment Search Tool) from the National Centers for Biotechnology
Information (NCBI),which calculates similarity between query sequences and
infers a probability based on a matrix database. The BLAST resource is located
<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" target="_blank">here</a> Basic BLAST and Specialized BLAST are
available at the site. This site now features DELTA-BLAST “a more sensitive
protein-protein” search. There are at least a dozen (plant, and animal) genome
references that can be used to compare sequences. It is through comparison that
one is able to get insight into the characteristics of the organism studied.
BLAST finds regions of similarity between biological sequences. Another tool
for genetic studies is the BioJava <a href="http://biojava.org/wiki/BioJava:Download" target="_blank">Project</a></span><span style="font-family: Verdana, sans-serif;"><a href="http://biojava.org/wiki/BioJava:Download" target="_blank"> </a>suite of biologic
analysis modules which can be downloaded here (now at version 3.0.4</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjf-isyWORGGzIappRDRjVNW0P8LHnxuJ9ZUm2qXRbBQNMVllXP34GntjdEv08MiRLbdZNkz65Id6EP8YpB0x3pKKZxx9DU6FcP_cx-x-xI-4MpGk3OBUTLJpXGjlGDn2rVpH2FcbHRgusH/s1600/Sin_Nombre_hanta_virus_TEM_PHIL_1136_lores.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="212" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjf-isyWORGGzIappRDRjVNW0P8LHnxuJ9ZUm2qXRbBQNMVllXP34GntjdEv08MiRLbdZNkz65Id6EP8YpB0x3pKKZxx9DU6FcP_cx-x-xI-4MpGk3OBUTLJpXGjlGDn2rVpH2FcbHRgusH/s320/Sin_Nombre_hanta_virus_TEM_PHIL_1136_lores.jpg" width="320" /></a></div>
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<span class="description"><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Transmission electron
micrograph of the Sin Nombre Hantavirus.</span></span><br />
<span class="description"><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Date:1993 </span></span><span style="font-size: x-small;">Content Providers(s):
CDC/Cynthia Goldsmith</span><br />
<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Permission:</span><span style="font-family: Calibri, sans-serif; font-size: 11pt; line-height: 115%;">PD-USGov-HHS-CDC</span><br />
<span style="font-family: Calibri, sans-serif; font-size: 11pt; line-height: 115%;"><br /></span>
<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span></div>
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<span style="font-family: Verdana, sans-serif;">Clinical Manifestations of Hantavirus Infections</span></div>
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<span style="font-family: Verdana, sans-serif;"> - In all these situations, infection begins on an
epithelial or mucosal surface and spreads along the mucosa and into deeper
tissues. Disease manifestations usually arise as a consequence of viral
replication, infected cell injury or death, and local inflammatory and innate
immune responses. An immediate assessment of the patient's general appearance
can yield valuable information. Presenting
symptoms are frequently nonspecific. A review of systems should focus on any
neurologic signs or sensorium alterations, rashes or skin lesions, and focal
pain or tenderness and should also include a general review of respiratory,
gastrointestinal, or genitourinary symptoms. The most common symptoms of
nephropathia epidemica are fever, nausea, vomiting, headache, stomach ache,
back pain, tenderness in the kidney area, diarrhea or constipation. Therefore it is most important to know the
recent history of the patient, and his whereabouts in the days immediately
preceding the report of the patient to a physician or nurse at the health
facility. In the case of Hantavirus, there will probably be a form of cardiopulmonary
distress, or a renal syndrome that’s not explained by intoxication, prior
kidney disease, or metabolic disorder. After a quick clinical assessment,
specimens must be collected from all accessible material (i.e. blood, urine,
sputum, feces) rapidly, and antibiotic and supportive treatment begun. Empirical
antibiotic therapy is critical and should be administered without undue delay.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - The viruses in the Bunyaviridae genus that have to be
distinguished now are the Hantavirus, California Encephalitis virus and the
Sandfly Fever Virus. European hantaviruses, such as the Dobrova-Belgrade virus
(from Slovenia), and the Puumala (identified in Scandinavian locations) which
causes nephropathia epidemica. These are emerging viruses that can cause
hemorrhagic fever with renal syndrome (HFRS) of differing severities. Both the
Dobrova and Puumala varieties are likewise by rodents in those geographic
locations. This important to note because of the possible introduction of “foreign”
virus strains into a immune-naïve setting. The optimal use of antiviral
compounds requires a specific and timely diagnosis. </span></div>
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<span style="font-family: Verdana, sans-serif;"><b><i>Clinical Management</i></b></span></div>
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<span style="font-family: Verdana, sans-serif;"> - Firstly, acute management of the airways is crucial. If
difficult airways are encountered, camera guided intubation is carried out. A
CT scan is used for visualizing the pulmonary status after intubation.
Occasionaly, emphysema may be present
especially in older individuals, and in heavy smokers. A previous history of
lung infection (e.g. pulmonary tuberculosis, aspergilliosis) and pulmonary
fibrosis may make pulmonary stabilization more challenging. But even before any
anti-viral drugs are decided upon, proper antibiotic coverage must be provided.
In the case of a cardiopulmonary picture, the stage at which the patient is
seen will impact the treatment chosen. Nevertheless, one has to treat not just
the viral infection, but also the opportunistic organisms that may be present
at that point. If the patient has been previously admitted to a health facility
one has to consider a community-acquired pneumonia as well as a nosocomial
infection. Focal abscesses necessitate immediate CT or MRI as part of an
evaluation for surgical intervention. If there is a necrosing organ or tissue,
or if there is fulminating sepsis, more aggressive antibiotic treatment is
required. </span></div>
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<span style="font-family: Verdana, sans-serif;"> - Two anti-viral drugs that are of help in Influenza A are
Zanamivir and Oseltamivir, which are inhibitors of the influenza viral
neuraminidase enzyme, which is essential for release of the virus from infected
cells and for its subsequent spread throughout the respiratory tract of the
infected host. This information is important because a patient presenting with
pulmonary manifestations may either be super-infected, or, not given the proper
anti-infectious therapy coverage. Orally inhaled zanamivir is generally well
tolerated is administered orally via a hand-held inhaler, and where about 15%
of the dose is deposited in the lower respiratory tract, and low plasma levels
of the drug are detected. The drug is excreted unmetabolized by the kidneys. </span></div>
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<span style="font-family: Verdana, sans-serif;"> - IV Ribavirin in the picture of hanta virus
cardiopulmonary syndrome has not shown clearcut benefits in the U.S..
Nevertheless, it is the opinion of this author that this treatment must be
tried, particularly when no “ideal” pharmacotherapeutic agent available. In the
acute setting, empirical antibiotic therapy is critical and should be
administered without undue delay </span></div>
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<span style="font-family: Verdana, sans-serif;"><b><i>Prevention</i></b></span></div>
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<span style="font-family: Verdana, sans-serif;"> - Hantavirus ranks among the dozen or so viruses that have
no vaccine available. In this light, avoidance of contact with the Deer Mouse (and
other rodent vectors) and its waste products, and in its extended habitat (meaning
“out-of-the-woods and into-the-homes”) such as summer camps, tents and homes
close to the exterior of normal human habitat. Since there is no available
vaccine, and quite uncertain benefit of immunoglobulin therapy, prevention of
exposure is the best approach. Travelers or vacationers would do well to avoid
staying in less than optimal lodgings. And even then, it would be beast to stay
away from any locations which would be in the periphery of the vector’s habitat.
For those whose residences are in the nearby areas, judicious use of pest
control measures should be exercised. </span></div>
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<span style="font-family: Verdana, sans-serif;">The Deer Mouse (<em><b>Peromyscus maniculatus</b></em>),
Cotton Rat (<em><b>Sigmodon hispidus</b></em>), Rice Rat (<em><b>Oryzomys palustris</b></em>), and White-footed mouse (<em><b>Peromyscus leucopus</b></em>) have been identified as
vectors of HantaVirus. For the geographic distributions of these rodents,
kindly consult the CDC page <a href="http://www.cdc.gov/hantavirus/rodents/index.html" target="_blank">here</a> :</span></div>
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<span style="font-family: Verdana, sans-serif;"><b><i><u>Current Situation of Hantavirus Outbreak</u></i></b></span></div>
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<span style="font-family: Verdana, sans-serif;">According to the CDC, “As of September 6, 2012, The
National Park Service (NPS) announced that there were 8 confirmed cases of
Hantavirus Pulmonary Syndrome (HPS) in visitors who stayed at Curry Village in
Yosemite National Park since June of this year. Public health officials believe
that these visitors may have been exposed to Hantavirus while staying at the
Signature Tent Cabins in Curry Village.”</span></div>
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<span style="font-family: Verdana, sans-serif;">For more Clinical and Technical Information, kindly visit
this <a href="http://www.cdc.gov/hantavirus/technical/hanta/index.html" target="_blank">page</a>: </span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">-Til next time, keep posted.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;">_ Fernando Yaakov Lalana, M.D.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
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Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-82687653417822124422012-09-05T14:13:00.000-04:002012-09-05T14:13:57.047-04:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp2OQPPkgnTZ55IWN2YTX74xO9a0OCJ7D46jQO9hDmlQqrsJCaVIAkcC4cGN86Db3isvYxF3_177-z65RlaLiNqGFlPX8Q9cpFzr_80uAh-Ts-kwtBG-FZtmF0NwYj3ukwtuAcEfqDMtaW/s1600/MB900182805-flask_Research.JPG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp2OQPPkgnTZ55IWN2YTX74xO9a0OCJ7D46jQO9hDmlQqrsJCaVIAkcC4cGN86Db3isvYxF3_177-z65RlaLiNqGFlPX8Q9cpFzr_80uAh-Ts-kwtBG-FZtmF0NwYj3ukwtuAcEfqDMtaW/s200/MB900182805-flask_Research.JPG" width="200" /></a></div>
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<span style="font-family: Verdana, sans-serif; font-size: large;">Laboratory Precision</span></div>
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<span style="font-family: Verdana, sans-serif;"> - At one time or another, we hear or say, “with laboratory
precision.” Depending on the image we see on hearing the phrase, we conjure up
ideas on what a lab does, and does not do. Whoever reads this blog post would
have had prior experience in a certain environment that required utmost
diligence, accuracy and mental concentration. And let’s not forget the long
white coats. At that point, we still have to describe the actual environment
inside the lab: whether particle physics with an accelerator, or even a kitchen
responsible for preparing specially packed savory meals to be “shipped” to the
International Space Station.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - Since we are dealing with a medical environment, we’ll
devote the next words to the biochemistry lab, or a physiology lab. Of course,
now with the ubiquity of computing resources, the lab has already adopted the
laptop, desktop, and now, the mobile device. Amidst the seeming clutter of
equipment and lab paraphernalia, we can notice that there is actually order in
procedure and function. With order comes accuracy. Of course, to be able to
perform an experiment in several iterations, one will exercise exceptional
concentration and diligence. That’s not to say that the setting is cold
and calculated. There is actually an aura of camaraderie (more or less) and
mutual respect, and the occasional jest. </span></div>
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<span style="font-family: Verdana, sans-serif;"><b><i>Procedure and Structure</i></b></span></div>
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<span style="font-family: Verdana, sans-serif;"><b><i><br /></i></b></span></div>
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<span style="font-family: Verdana, sans-serif;"><b> - Planning:</b> Laboratory work encompasses a spectrum of
activity and detail. To have things clearly in mind, the laboratory scientist
must start off with the clear vision of the prime purpose of the job on hand, like
any competent project manager will have. In the course of the experiment,
several issues may come up, some expectedly, while others not. The worker must likewise
be flexible enough to allow for dynamic alterations in the project course. But,
at the same time he should not waver from the goal. There are interesting
programs that involve brainstorming, or mind-mapping. The chief study scientist
can make use of this software, of which there are paid versions, and free ones.
The brainstorming can start off with the study head, then eventually include
members of staff. This way, there is a sense of cooperation and one-mindedness </span></div>
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<span style="font-family: Verdana, sans-serif;"><b> - Safety:</b> Safety
is a top priority in chemical and biological laboratories. The lab can, and
oftentimes will carry hazardous materials that can cause quite a problem if not
properly handled. Thus, we need to comply with safety standards of the highest
order. The <b>OSHA </b>(Occupational Safety and Health Administration) in the
United States, and in European Countries <span style="line-height: 115%;">(check out the European lasboratory safety standards documentation
<a href="http://osha.europa.eu/legislation/directives/A/1/1" target="_blank">here</a>)</span></span></div>
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<span style="font-family: Verdana, sans-serif;">is responsible for formulating and enforcing safety
standards, so as to safeguard the worker and his workplace. Each lab has its
pockets of danger and due precautions must be maintained rigorously. </span></div>
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<span style="font-family: Verdana, sans-serif;"> - It is necessary
to understand the requirements of the lab and the safety protocols. The
standards of chemical laboratory protocol (of <b>OSHA</b>) require that a lab
produce a Chemical Hygiene Plan (<b>CHP</b>) which addresses the specific
hazards found in its environment, and its approach to them. Then they could
work on the Chemical Hygiene Plan and stick to that plan, not just to satisfy
the OSHA, but to make reasonably sure and feasible that the lab is a safe place
to spend most of the working day in. In addition to safety standards, the lab
also has to keep its books straight in terms of recording expenditures and
inventory of each material used in the lab. This is business management,
laboratory style. It has to be managed with care because the materials are not
only expensive, but it is part of the stakeholders’ investment. Since haste makes
waste, a modicum of entrepreneurial zeal and accounting savvy will set the lab
in its precision in all areas of its activity. And necessarily so because the
lab is the heart of research and development, that which makes the way for a
cure, or even the Higg’s Boson.</span></div>
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<span style="font-family: Verdana, sans-serif;"><b> - Documentation
and the Electronic Notebook:</b> Habits don’t go away easily. There is a point where the pocket
notebook has to give way to the <b>ELN </b>(Electronic Laboratory Notebook). While
it may be pure habit of scribbling notes on a small lab pocket notebook, the
lab scientist now deals with the computer technology that has fostered the new
paradigm of recording on a virtual device, which is part of the new Laboratory
Information System. We have to budge out of our comfort zones so as to grow
along the lines of forward thinking. Does one port his or her own mental recording
system to the ELN? There is a place for both ELN and paper notebook. The
problem is that going back and forth consumes time which could be spent doing
the experiment. But if the lab and its crew work on optimal procedures, they
will be even more productive. It’s a matter of organizational management, whether
human or material resources.<span class="A3"> Many scientists are reluctant to rely on commercial software because
it can require them to adapt their processes to conform to out-of-the-box
functionality. For example, with an ELN, the reviewer simply opens the record
for that solution and reviews the usage log. This then shows every instance where the specific
solution was used, either as a reagent in an experiment or as a component in
another solution. This would be impossible with a paper notebook system. Some
will definitely calculate the cost of the e-notebook system and shy away from
its true value. There are commercial electronic lab recording software packages
with robust features that may outshine free open source software (FOSS). This “disadvantage”
of free software may not hold for long because there are already software
systems that can cater to the science group.</span><span style="color: #211d1e;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><b> - Workflow:</b> A current
study or experiment must adhere to a type of hierarchy of workflow. One would do well to use a model or template
for the record. There is a record for materials and one for lab process per se,
and so on. Once we have formulated the workflow, one must record the names and
numbers of the materials (like the chemical name and stock number). So,
inventory must start in point zero, log the materials, proceed with care. <span class="A3">Because
bioanalytical labs operate in a collaborative fashion, the project or study
chief will have had a lab organization, each devoted to specific work. It would
be most practical to have a template of recording and sub-planning. A “dry run”
is carried out to evaluate the efficiency of the template and the workflow
embedded therein. Such a sample analysis, and the calculations that are vital,
can be served up for all to give their feedback on. Computations done on a
computer must be tested for accuracy, thereby reducing the cumulative errors in
calculations. The scientist has the option to make a change, but if they proceed,
the exception will be logged in the audit trail along with a mandatory
annotation from the scientist. </span><span style="color: #211d1e;"><o:p></o:p></span></span></div>
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<span style="font-family: Verdana, sans-serif;"><span class="A3"><span style="line-height: 115%;"> - Since documentation is vital to the quality
of the study, teams of analysts and editors may devote their time on auditing
the study’s records’ to spot any errors as they come. While redundancy of
recording can provide a better degree of accuracy, one must make sure there is
no haphazard and inadvertent duplication in different database records pointing
to the same variable. </span></span><span class="A3"><span style="line-height: 115%;">The Q</span></span><span class="A3"><span style="line-height: 115%;">uality </span></span><span class="A3"><span style="line-height: 115%;">A</span></span><span class="A3"><span style="line-height: 115%;">ssurance</span></span><span class="A3"><span style="line-height: 115%;"> reviewers </span></span><span class="A3"><span style="line-height: 115%;">can </span></span><span class="A3"><span style="line-height: 115%;">scan lab notebooks, instrument log books and
archived instrument data files.</span></span><span class="A3"><span style="line-height: 115%;"> This adds a
certain degree of confidence that, because there is cross-referencing in
different record devices, one can double check all the data for errors to a
certain degree of accuracy. If the data is not</span></span> subjected to this
scrutiny, errors will multiply and in the end, the work is found inaccurate and
of little value.</span></div>
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<span style="font-family: Verdana, sans-serif;"> - Thus far, we have scanned the operations of a laboratory,
regardless of type of science. There may be differences in scope of work but
they entail the same working principle. As technology grows, the devices and
techniques will change, and the laboratory has to match it. </span></div>
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<span style="font-family: Verdana, sans-serif;"> - Begin with the end in mind; work with others in mind;
Finish with everybody in mind.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> - 'Til another iteration...</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"> - Fernando Yaakov Lalana, M.D.</span><br />
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><br /></span>
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-725628274970227882012-08-30T02:37:00.001-04:002012-08-30T09:58:24.497-04:00<!--[if gte mso 9]><xml>
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<span style="font-size: large; text-indent: -0.25in;"> Experimentation in Medicine</span></div>
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- - More often than not, when people think of science (and scientists), they imagine a person peering into his or her microscope, handling test tubes, or even performing vivisection. While the first two are modern methods, the last one (vivisection) <span style="font-family: Verdana,sans-serif; font-size: small;">was</span> a procedure carried out even by the Patriarchs of present day Medicine. Hippocrates (c.460-370 B.C.E.), Galen (c.129-200 B.C.E.), Avicenna (c.980-1037 B.C.E.), Maimonides (1136-1204 B.C.E.) had one thing in common: they didn’t have the scientific resources we have today. These grand men had to rely on unaided observation of the natural world. And yet, they have passed down a legacy for all researchers and students to build on.</div>
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- Then, and now, workers in the medical community rely on heuristic methods of learning. Examination and discovery still are the crucial characteristics of the schools of scientific thought and deliberation. Not only that, these pioneers taught their principles to countless students, who in turn shared this wisdom to whoever was interested enough and who would put in long hours of study and debate. Observing, copying and then teaching scientific methods still echo in the halls of academia, laboratories and hospitals. Through vivisection and analysis, men and women of science have developed principles, pharmacopeia, and procedures for healing the everyday man.</div>
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Error Detection and Correction</div>
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- As true as there was, and there is, discipline in education, there is also the necessary element of error detection and correction. We have heard of the acronym CLAYGO (Clean as You Go) used in workplaces where there is the tendency to spillage and disorder. In clinical trials there are sets of tests encompassing procedures that foster, not only <span style="color: windowtext;">drug development</span>, but also that which generate safety and <span style="color: windowtext;">efficacy</span> data.</div>
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- Information about <span style="color: windowtext;">adverse drug reactions</span> and other undesirable effects of drugs, and other therapeutic agents, are logged down and recorded in laboratory notebooks or computers for further analysis. Clinical and laboratory sciences still use heuristic methods, methods based on experience, problem solving, learning and discovery. Examples of this method include using a <span style="color: windowtext;">rule of thumb</span>, an <span style="color: windowtext;">educated guess</span>, an intuitive judgment, or <span style="color: windowtext;">common sense</span>. In more precise terms, heuristics are strategies using readily accessible, though loosely applicable, information to control <span style="color: windowtext;">problem solving</span> in human beings and machines.</div>
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Empirical Science</div>
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- The word empirical denotes information acquired by means of <span style="color: windowtext;">observation</span> or <span style="color: windowtext;">experimentation</span>; and empirical data are <span style="color: windowtext;">data</span> produced by an observation or experiment. All scientific method must be based on empirical evidence, which means that all that all learning must be dependent on evidence or <span style="color: windowtext;">consequences</span> that are observable by the <span style="color: windowtext;">senses</span>. It is usually differentiated from the philosophic usage of <span style="color: windowtext;">empiricism</span> by the use of the adjective empirical or the adverb empirically. The term refers to the use of working <span style="color: windowtext;">hypotheses</span> that are <span style="color: windowtext;">testable</span> using observation or experiment. In this sense of the word, scientific statements are subject to, and derived from, our experiences or observations.</div>
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Theory and Hypothesis</div>
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- A theory denotes an act of rational thought or idea based on guided knowledge; some might call this a guess or other intuitive process. As such, a theory is an intelligent process and not just conjecture or whim. Once a theory is held in the mind, it goes through the phase which is called hypothesis, which requires the method of substantiation or proof. While the terms theory and hypothesis are used interchangeably, they are not the same. Once a hypothesis is formulated, it takes the character of working hypothesis: a framework for subsequent investigation. Null hypothesis in <span style="color: windowtext;">science</span> involves formulating and testing <span style="color: windowtext;">hypotheses</span>, assertions that are <span style="color: windowtext;">capable of being proven false</span> using a test of observed data. This typically corresponds to a general or default position. For example, the null hypothesis means that there is no relationship between two factors or phenomena. One thing comes to mind though, that, causation and correlation are not the same, and both are matters to be differentiated in a further study. All the data that is collected is put through a battery of statistical analysis, thereby giving importance, or negating the influence of a certain element on a given phenomenon.</div>
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- Whether it be digital or medical information, error detection and correction (or, debugging) play a vital role in the integrity of the whole system. Workers have to communicate their observations and analyses in a clear manner. Communication channels are of paramount importance from the beginning of a project or study and throughout the whole process. Everybody has a role to play, and since the weakest link is many times unnoticed, diligence in procedural details is necessary. From the study protocol, and all the way to the statistical analyses, communication and coordination are keys to the study’s success. And of course, everyone on the team must have done their prior review of eminent literature, whether books, journals, or medical notes.<br />
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- The next time you take an aspirin, think of the man who first learned that the willow tree bark made his friends pains and fever go away...<br />
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- Fernando Yaakov Lalana, M.D.</div>
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<span style="font-family: "Verdana","sans-serif";"> <i>"To study the phenomenon of disease without books is to sail an uncharted sea, while to study books without patients is not to go to sea at all.”</i></span></div>
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<span style="font-size: small;">Sir William Osler (1849-1919)</span><br />
<span style="font-size: small;"> British (Canadian-born) Physician</span><br />
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Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-19253809899087199432012-08-22T12:03:00.000-04:002012-08-24T12:39:13.220-04:00<div class="separator" style="clear: both; font-family: Verdana,sans-serif; text-align: center;">
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<span style="font-size: large;">Microbes:</span><span style="font-size: large;"> </span><span style="font-size: large;">Enemy and
Friend</span></div>
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- Nowhere is <b>biologic diversity</b> demonstrated more
dramatically than by microorganisms. Clearly by now, we have observed how viruses,
bacteria and other microorganisms can upset the balance of our ecosystem. <span style="mso-spacerun: yes;"> </span>Our initial image of breakouts is that these
minute organisms are nothing but trouble, and, not only that, they do it big
time. We see that they can easily evolve and adapt to our own defense
mechanisms, then strike in an insidious manner. Right when we think it’s over,
they mutate and defeat us in a couple of ways. But first, let’s review the
basic differences between a bacterium and a virus. </div>
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- To be fair, there are
species of microorganisms that serve a useful purpose. One example is Bti (<b><i>Bacillus thuringiensis</i></b><i> serovar</i> <b>israelensis)</b>, a gram-positive soil bacterium that produces crystalline inclusions with a
highly specific insecticidal activity. It produces toxins which are effective
in killing various species of mosquitoes, fungus gnats, and blackflies, while
having almost no effect on other organisms. Bti strains possess the pBtoxis plasmid which
encodes numerous Cry and Cyt toxins, including Cry4, Cry10, Cry11, Cyt1 and
Cyt2. They have been used as a larvicide for many years and is
now becoming widely available for you to buy and use yourself at home. - Formulations
include small, donut-shaped <span style="mso-spacerun: yes;"> </span>form "Mosquito
Dunks"/"Mosquito Bits". It is also available in bulk liquid or
granular formulations for commercial and public agency use. A home gardener’s
spray,“GET OFF ME! Natural Bug Spray”, is also available. These Bti solutions can
be produced in small batches making them practical for local area mosquito
control. Another natural solution is made from efficacious isolates of <i>Bacillus
sphaericus</i> Neide. <i>B. sphaericus</i> has been shown to persist longer
than <i>Bti</i> in polluted habitats and under certain circumstances. A
disadvantage of <i>B. sphaericus</i> has been the development of resistance in
certain populations of <i>Culex quinquefasciatus</i> Say and <i>Culex pipiens</i>
Linnaeus. </div>
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- The factors for their larvicidal
action depend on the nature of the breeding potential of the environment, type
of mosquito, their respective feeding strategies, rate of ingestion, age and
density of larvae, habitat factors (temperature, solar radiation, depth of
water, turbidity, tannin and organic content, presence of vegetation, etc.),
and the different aspects<span style="mso-spacerun: yes;"> </span>of the formulations. <span style="mso-spacerun: yes;"> </span>Let us remember though, that the
best way to control mosquitoes is still to get rid of standing water on your
property.<i> Prevention and control begin with understanding disease transmission
and insect vector life cycle. </i>This is probably the most neglected aspect in
the control of disease. The seasonal pattern of WNV parallels the proliferation
(life cycle) of the insect. This makes this quite relevant to our current West
Nile Virus-mosquito epidemic connection. </div>
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<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif;">
<span style="font-size: small;">Back to Bacterial Basics</span></div>
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<i> - Eukaryotes</i> are organisms containing a membrane-bound nucleus.
Among the groups of eukaryotic microorganisms are the <b>algae,</b> the <b>protozoa,</b>
the <b>fungi,</b> and the <b>slime molds.</b> On the other hand, <i>prokaryotes</i>
are organisms in which DNA is not physically separated from the cytoplasm. Eukaryotes
and <i>prokaryotes </i>are organisms because they contain all of the enzymes required
for their replication. Furthermore, they possess the biologic equipment
necessary for the production of metabolic energy. <span style="mso-spacerun: yes;"> </span>Bacteria are a large domain of prokaryotic
microorganisms.
Typically a few micrometres in length, and have a wide range of shapes,
ranging from spheres
to rods and spirals. They thrive in soil, plants, water, as well as in the gut
flora and integument. </div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEid110s7csG-YQKgZrHXBw99VyoiIlsmBtoFG4534eU99pa1Yl2-dYElnWZIXzVma3CZlATmSpL1ab3H85Bmec0xVwj2D_QaBNQqnLlXbubBK9FZvavs_2RFKZgC7gUuxP6GSPKFIjTYw9T/s1600/200px-Average_prokaryote_cell-_en.svg.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="260" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEid110s7csG-YQKgZrHXBw99VyoiIlsmBtoFG4534eU99pa1Yl2-dYElnWZIXzVma3CZlATmSpL1ab3H85Bmec0xVwj2D_QaBNQqnLlXbubBK9FZvavs_2RFKZgC7gUuxP6GSPKFIjTYw9T/s320/200px-Average_prokaryote_cell-_en.svg.png" width="320" /></a></div>
<br />
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: center;">
<span style="font-size: small;">Gram Positive Bacterium</span></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: center;">
<span style="font-size: small;"><span class="language"></span><span class="description">A diagram of a typical <span style="color: windowtext; text-decoration: none;">prokaryotic</span>
<span style="color: windowtext; text-decoration: none;">cell</span>.</span></span></div>
<div class="MsoNoSpacing" style="text-align: center;">
<span style="font-family: Verdana,sans-serif; font-size: x-small;">March 2008; Author Mariana Ruiz
Villarreal </span><span class="description"></span></div>
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<br /></div>
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- There are approximately ten times as many bacterial cells
in the human
flora as there are human cells in the body.<span style="mso-spacerun: yes;">
</span>Bacteria display a wide diversity of shapes and sizes. <span style="mso-spacerun: yes;"> </span>Most bacterial species are either spherical (cocci), or
elongated (bacilli). They are broadly classified as Gram positive (no outer membrane), and Gram negative (outer membrane present). Gram stain primarily detects peptidoglycan, which is present in a thick layer in Gram positive bacteria. They exist simply as single cells, others associate in
characteristic patterns. <i>Neisseria,</i> (e.g. gonococcus), form diploids
(pairs).<span style="mso-spacerun: yes;"> </span>They have a cell wall and
self-preserving intracellular structures, responsible for the respiration and
metabolism of the organism. The bacteria’s outer lipid membrane, or cell
membrane, encloses the contents of the cell and acts as a barrier to hold
nutrients, proteins
and other essential components of the cytoplasm
within the cell. Biochemical reactions, such as energy generation, occur by concentration
gradients across membranes. Internally, there is a lack of membranes<span style="mso-spacerun: yes;"> </span>which means reactions such as electron transport occur across the cell
membrane between the cytoplasm and the periplasmic
space (region bordered by two selective permeable barriers, i.e. biological membranes, which are the inner membrane (i.e. cytoplasmic membrane) and the outer membrane in Gram-negative bacteria). They may need oxygen (aerobic
bacteria), or not (anaerobic bacteria). They thrive on extracellular ions and
the like, and do not need a host to give it the ability to multiply. </div>
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<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<span style="font-size: small;">Going Viral</span></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<span style="font-size: small;">- </span>In 1892, Dimitri Ivanovsky described a
non-bacterial pathogen infecting tobacco plants. Then in 1898 Martinus
Beijerinck eventually identified the tobacco mosaic virus. a positive-sense single stranded RNA virus that infects plants, especially tobacco and other members of the family Solanaceae, known as the nightshade or potato family. Since that time, at
least 5000 viruses have been described, quite a few of which still have to be
properly studied in detail. The unique properties of viruses set them apart
from living creatures. </div>
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<br /></div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbhgyZl_eRr7h7YbNVZuPCwdRpZWSJ7sniz272OOvGJexT9OAEKvKUSn7eDfzbP7m-bMvQyhN6wYN47PPvstcqlPqUMXPcEMojJjxU0VIVhdirmBXZDqRnFD_LCfkyGo8Brqo81ndPGxV1/s1600/Em_wnvirus_j7908i.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbhgyZl_eRr7h7YbNVZuPCwdRpZWSJ7sniz272OOvGJexT9OAEKvKUSn7eDfzbP7m-bMvQyhN6wYN47PPvstcqlPqUMXPcEMojJjxU0VIVhdirmBXZDqRnFD_LCfkyGo8Brqo81ndPGxV1/s320/Em_wnvirus_j7908i.jpg" width="320" /></a></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: center;">
<span class="description">Electron microscopy of West Nile virus, taken from lab, </span></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: center;">
<span class="description">rights retained to displayed author.</span> </div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: center;">
<span style="font-size: x-small;">20 November 2007 (first version); 10 June 2010 (last version) </span></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: center;">
<span style="font-size: x-small;">Original uploader was PhD Dre</span></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: center;">
<br />
<span style="font-size: x-small;">[Magnification in a Scanning Electron Microscope </span><span style="font-size: x-small;">] </span><span style="font-size: x-small;"> </span></div>
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<br />
<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: left;">
- There are seven classes of viruses. (The term virus is
from the Latin<i>, virulentus</i>, meaning poisonous.) Viruses are not cells,
but rather particles consisting of 2 to 3 things, i.e. genetic material made
from DNA or RNA, the protein coat that protects these genetic materials, and in
a few cases a lipid envelope that that surrounds the protein coat when the
virus is not inside a host cell. The virus is of an extremely smaller size, at 1/100 the size of the usual bacterium. Viruses can
be shaped as a helix, or can be icosahedral (20 identical equilateral triangular faces, 30 edges and 12 vertices), and in some still more complex
geometries. Of course, because of its minute size, they cannot be seen using
the optical microscope commonly found in labs.
They can be visualized usually through special imaging techniques such an electron microscope such as a
SEM (scanning electron microscope) which can render a magnification <span style="text-align: center;">over a range </span><span style="text-align: center;">of up to 6</span><span style="text-align: center;"> </span><span style="text-align: center;">orders of magnitude</span><span style="text-align: center;"> </span><span style="text-align: center;">from about 10 to 500,000 times. Polymerase Chain Reaction (PCR) is another method for studying </span><span style="text-align: center;">bacteria. </span><span style="text-align: center;">This technique enhances (amplifies) the DNA sequence wherein a short region </span><span style="text-align: center;">of the </span>DNA (fragments <span style="text-align: center;">containing a few copies) is amplified</span> up to ~10 kilo base pairs (kb). The underlying mechanism for PCR is called thermal cycling.</div>
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<br /></div>
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-<span style="font-family: Verdana,sans-serif; font-size: small;"> The range of host cells that a virus can infect is called
its "host range". This is how viruses can be transmitted from
plant to plant, plant to arthropod, arthropod to animal, or man, and this is carried
out by a vector like an insect feeding on the infected plant’s nutrients. Virus
transmission is also often times effected through droplets such as sneezing, and
that is exemplified by respiratory viral illnesses. Still others are
transmitted through blood products. Viruses lack many of the attributes of
cells, including the ability to replicate.</span></div>
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<br /></div>
<div class="MsoNormal">
<span style="font-family: Verdana,sans-serif; font-size: small;"> - Viruses are obligatory parasites,
meaning they need a host cell to invade and where they then hijack the host
cell’s genetic material. There the virus redirects the host's enzymatic
machinery to functions associated with replication of the virus. As they
infiltrate the host’s immune cells, they have the ability to knock out the
immune system resulting in severe and long-term disease. Viral infections
however, are also capable of inducing immunity of the host. This way, the host’s
immune system protects against future infection. A number of transmissible
plant diseases are caused by viroids, which are small, single-stranded,
covalently closed circular RNA molecules existing as highly base-paired
rod-like structures; they do not possess capsids. The extracellular form of the viroid is naked
RNA—there is no capsid of any kind. The RNA molecule contains no
protein-encoding genes, and the viroid is therefore totally dependent on host
functions for its replication. </span></div>
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<![endif]--><span style="font-size: small;"><span style="line-height: 115%;">Antibiotics have no
effect on viruses, unlike bacteria that are usually eliminated by this drug
class by different mechanisms. It is asked, where and when did viruses begin to appear? Are they
primitive genetic molecules that have evolved into infectious agents? One might
ask, “Were they remnants of decaying plant or animal tissue, remnant particles that became a rogue
part of the environment, very much like plants and animals?” One thing seems
sure, and that is, viruses need the host to exist, multiply, and thrive. Recent developments involve using viruses as vectors for delivery of therapeutic substances.</span></span></div>
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<span style="font-size: small;">The Virus-Mosquito-Bacteria Circle</span></div>
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<br /></div>
<span style="font-family: Verdana,sans-serif; font-size: small;"><span style="line-height: 115%;">- In the current West Nile Virus outbreak, we can see
how knitted together are the different infectious elements and their targets. First, the mosquito
bites an infected animal, a vertebrate such as birds, humans, horses,
alligators and others, which then serves as a host. The mosquito can also
acquire the virus from an infected animal. The
mosquito then lays its eggs in standing water. Some lay eggs near the water's
edge; others attach their eggs to aquatic plants, where it goes through its
different stages: egg, larva, pupa,
and adult or imago .
Thus, as the juvenile forms mature, they become vectors - multiplied
exponentially. Enter now the bacteria, Bti (<b><i>Bacillus thuringiensis</i></b><i> serovar <b>israelensis</b></i>)
which kill off the mosquito larvae. This in turn markedly reduces the numbers of
the vector. As we apply the Bti, we are using the mosquito larva’s natural
enemy to control our own natural enemy, the mosquito with West Nile Virus. In
other words: bacteria controls virus, indirectly. While Bti may help in the
control of mosquito populations, its persistence in the environment may raise a
few questions. Anything in inordinate numbers can spell imbalance in an already
threatened ecosystem. Controlling the buildup of stagnant water is still the
best way of controlling the multiplication of mosquitoes. </span></span><br />
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<span style="font-size: small;"> - On a lighter note, horticulturists as well as ornamental
plant growers can both use Bti to control mosquitoes that may thrive in irrigation
water barrels and pails. In a big plot of land, good drainage should be
encouraged thereby limiting the mosquitoes and the use of any control agent.
Those who own dipping or swimming pools should keep them clean with the
appropriate disinfectants (e.g. sodium hypochlorite and copper sulfate).</span></div>
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<span style="font-size: small;"><span style="line-height: 115%;"> </span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5tw1rXAIuMpGH0idebzOB9-0vAHnXe4l4nkLs_YFkiUmeUB6i2cZ9SOASpF0rOCWJuE5eaWcBbnZmPrGlZ14F-YRfkb_LYw3uf1snnsgiCUdcCVQ49qfbYsV_cEv26u3rdb55fPLfWWfQ/s1600/320px-Anopheles_larve.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5tw1rXAIuMpGH0idebzOB9-0vAHnXe4l4nkLs_YFkiUmeUB6i2cZ9SOASpF0rOCWJuE5eaWcBbnZmPrGlZ14F-YRfkb_LYw3uf1snnsgiCUdcCVQ49qfbYsV_cEv26u3rdb55fPLfWWfQ/s1600/320px-Anopheles_larve.jpg" /></a></div>
<span style="font-family: Verdana,sans-serif; font-size: small;"><span class="description">Larvae of an Anopheles
sp., about 8 mm long. Found in a pond in Munich, Germany, in June 2007.
Typical are the greenish color and a resting position parallel to the
water surface.</span></span><br />
<div style="font-family: Verdana,sans-serif;">
<span style="font-size: x-small;">17 June 2007</span></div>
<div style="font-family: Verdana,sans-serif;">
<span style="font-size: x-small;">by Steffen Dietzel</span></div>
<br />
<br />
<br />
-<span style="font-size: small;"><span style="font-family: Verdana, sans-serif;"> As far as the Preventive Medicine principles are concerned, the measures used to control the West Nile Virus carriers are also measures for other mosqui</span><span style="font-family: Verdana,sans-serif;">to</span></span><span style="font-family: Verdana,sans-serif;">-borne diseases.</span><br />
<br />
<span style="font-family: Verdana,sans-serif; font-size: small;">For </span><span style="font-family: Verdana,sans-serif; font-size: small;">U.S. </span><span style="font-family: Verdana,sans-serif; font-size: small;">West Nile Virus outbreak demographics</span><span style="font-family: Verdana,sans-serif;">,</span><span style="font-family: Verdana,sans-serif; font-size: small;"><span style="font-family: Verdana,sans-serif;"> visit this</span><a href="http://www.cdc.gov/ncidod/dvbid/westnile/index.htm" style="font-family: Verdana,sans-serif;" target="_blank"> page </a><span style="font-family: Verdana,sans-serif;">for updates</span></span><br />
<br />
<span style="font-family: Verdana,sans-serif; font-size: small;"><span style="font-family: Verdana,sans-serif;">- As far as August 14, there appears to be no new case of WNV. This is good. At least the proper surveillance and control methods are paying off, albeit a tad slow at first.Total number of cases as of</span></span><span style="font-family: Verdana,sans-serif; font-size: small;"> Aug. 14, 2012 is 693. Since 1999, more than 30,000 people in the United States have been reported as getting sick with West Nile virus. </span><br />
<br />
<span style="font-family: Verdana,sans-serif; font-size: small;"> - In the meantime, awareness and surveillance continues so as not to miss the patient with atypical clinical presentation. Travelers need to be cautious especially in going to areas with swamps, stagnant rivers, and other areas where their is an outbreak. So it would be wise to consult the map as noted in aforementioned </span><span style="font-family: Verdana,sans-serif; font-size: small;"><a href="http://www.cdc.gov/ncidod/dvbid/westnile/index.htm" style="font-family: Verdana,sans-serif;" target="_blank">page</a></span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;"><br /></span>
<span style="font-family: Verdana,sans-serif; font-size: small;"> - As newer technology and better preventive methodology develops, it is hoped that the big brothers in healthcare, eg., WHO and CDC, will be able to prepare us in any eventuality. In this outbreak alone, we have seen the melding of clinical acumen, public health/preventive medicine and various areas of bioinformatics. Sometimes, in all the hustle of the situation, we tend to overlook the role of the computer scientist and physician in their untiring efforts to keep us healthy.</span><br />
<br />
<span style="font-family: Verdana,sans-serif; font-size: small;"> - Keep smart, keep safe. Til another day...</span><br />
<br />
<span style="font-family: Verdana,sans-serif; font-size: small;"> - Fernando Yaakov Lalana, M.D. </span><br />
<span style="font-family: Verdana,sans-serif; font-size: small;"><br /></span>
<span style="font-family: Verdana,sans-serif; font-size: small;"> - P.S. If you would like to see some interesting Scanning Electron Microscope images do visit this <a href="http://www.mos.org/sln/sem/sem.html" target="_blank">page</a>.</span>Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-10578160581063129672012-08-19T06:37:00.000-04:002012-08-19T13:29:10.606-04:00<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_Mu1Xh-p2nd8JBqcFzAFvUxil0HZyWO0GuhcQw3Siu4Bw_drCQ_lD45U3_zcJ6nDAsZV33SSlSfBmZxXypSPVuxOUIbUd_R1APWIqexZsvDHJERJbiNkSYvJNEghvh8CHBl2d5LGcvhif/s1600/MC900438036-mosquito.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_Mu1Xh-p2nd8JBqcFzAFvUxil0HZyWO0GuhcQw3Siu4Bw_drCQ_lD45U3_zcJ6nDAsZV33SSlSfBmZxXypSPVuxOUIbUd_R1APWIqexZsvDHJERJbiNkSYvJNEghvh8CHBl2d5LGcvhif/s200/MC900438036-mosquito.png" width="200" /></a></div>
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<span style="font-size: large;">West Nile Virus Claims 26 Lives!</span></div>
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<span style="font-size: small;"> - 693 Cases reported in 43 U.S. States! As of August 14, 2012,
the West Nile Virus has been reported in people, birds, and mosquitoes. Of
these, 406 (59%) cases were classified as neuroinvasive disease (such as
meningitis or encephalitis) and 287 (41%) were classified as non-neuroinvasive
disease. This is the report from the CDC who has said that this is the biggest
infection rate ever.</span></div>
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<span style="font-size: small;"> - Furthermore, over 80 percent of the cases have been
reported from just six states (Texas, Mississippi, Louisiana, Oklahoma, South
Dakota, and California) and almost half of all cases have been reported from
Texas. For a state-by-state ArboNet case count please check their infographic
<a href="http://www.cdc.gov/ncidod/dvbid/westnile/surv&controlCaseCount12_detailed.htm" target="_blank">here</a> </span></div>
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<span style="font-size: small;"> - Why this epidemic has gotten this widespread is probably
multi-factorial. Because of changes in weather, the environment has facilitated
the infestation of mosquitoes. Alternating dry and damp weather, stagnant water pools and other
similar breeding grounds abound. </span> In most species, adult females lay their eggs in standing water; some
lay eggs near the water's edge; others attach their eggs to aquatic
plants. Each species selects the situation of the water into which it
lays its eggs and does so according to its own ecological adaptations. <span style="font-size: small;"> </span></div>
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<span style="font-size: small;"> - Although this is known to be a summer problem,
it does continue into the fall. The heat as well has contributed, as dust and
other minute particles are whipped up into the atmosphere thereby spreading
more infectious material. Those familiar with the desert areas know about dust
devils which also begin at boundaries between semi-dry soil and powdery sand. A
warm temperature in the area creates conditions favorable for these whirlwind
phenomena. <i>Culex</i> mosquitoes, still considered the main vectors, spend
the winter hibernating in protected structures such as root cellars, bank
barns, caves, abandoned tunnels and other subterranean locations. </span></div>
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<span style="font-size: small;"> - West Nile virus (WNV) belongs to <a href="http://www.blogger.com/goog_1102354004"> </a><a href="http://www.blogger.com/goog_1102354004" style="color: red;"><span class="group">Group IV </span></a><span class="group" style="color: blue;"><a href="http://www.blogger.com/goog_1102354004" style="color: red;">(</a><a href="http://www.blogger.com/goog_1102354004" style="color: red;" title="Positive-sense ssRNA virus"><span style="text-decoration: none;">(+)ssRNA</span></a><a href="http://en.wikipedia.org/wiki/RNA_virus" style="color: red;" target="_blank">)</a>,</span><span style="color: blue;"> </span>Family: <span class="family"><a href="http://en.wikipedia.org/wiki/Flaviviridae" title="Flaviviridae"><span style="color: windowtext; text-decoration: none;">Flaviviridae</span></a></span>,
Genus: <span class="genus"><a href="http://en.wikipedia.org/wiki/Flavivirus" title="Flavivirus"><span style="color: windowtext; text-decoration: none;">Flavivirus</span></a></span>is, and
is one of the <a href="http://en.wikipedia.org/wiki/Japanese_encephalitis" title="Japanese encephalitis"><span style="color: windowtext; text-decoration: none;">Japanese encephalitis</span></a> (JE) antigenic <a href="http://en.wikipedia.org/wiki/Serotype" title="Serotype"><span style="color: windowtext; text-decoration: none;">serocomplex</span></a>
of <a href="http://en.wikipedia.org/wiki/Virus" title="Virus"><span style="color: windowtext; text-decoration: none;">viruses</span></a>.
The flaviviruses comprise more than 70 members including important human
pathogens such as yellow fever virus, dengue virus, and West Nile virus. The
structures of two flaviviruses, dengue and West Nile virus, have been solved by
cryo-EM and image reconstruction techniques and have been shown to be similar.</span></div>
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<span style="font-size: small;"> - In WNV, image
reconstructions and <span style="color: windowtext; text-decoration: none;"><a href="http://en.wikibooks.org/wiki/Structural_Biochemistry/Proteins/Cryo-Electron_Microscopy%20" target="_blank">cryo-electron</a> microscopy</span>
reveal a 45–50 nm <a href="http://en.wikipedia.org/wiki/Virion" title="Virion">virion</a> covered with
a relatively smooth <span style="color: windowtext; text-decoration: none;">protein</span> surface. The flavivirus virion is made up of three
structural proteins: capsid (C), pre-membrane (prM), and envelope (E) that are
translated from the 5’ one-third of the RNA genome. The genetic material of WNV
is a <a href="http://en.wikipedia.org/wiki/Sense_%28molecular_biology%29" title="Sense (molecular biology)"><span style="color: windowtext; text-decoration: none;">positive-sense</span></a>, single strand of <a href="http://en.wikipedia.org/wiki/RNA" title="RNA"><span style="color: windowtext; text-decoration: none;">RNA</span></a>, which is between
11,000 and 12,000 <a href="http://en.wikipedia.org/wiki/Nucleotide" title="Nucleotide"><span style="color: windowtext; text-decoration: none;">nucleotides</span></a> long. These <span style="color: windowtext; text-decoration: none;">genes</span> encode seven
nonstructural proteins and three structural proteins. The RNA strand is held
within a nucleocapsid formed from 12-<a href="http://en.wikipedia.org/wiki/KDa" title="KDa"><span style="color: windowtext; text-decoration: none;">kDa</span></a> protein blocks; the capsid is contained within a
host-derived <span style="color: windowtext; text-decoration: none;">membrane</span> altered by two viral <a href="http://en.wikipedia.org/wiki/Glycoprotein" title="Glycoprotein"><span style="color: windowtext; text-decoration: none;">glycoproteins</span></a>.
</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW5JE0EGnaokotVv7zE4Rlt_CF6UmpM6PXlPBIC-KVauO9iKKYLd85M_P-7xDh3jyh0fH-TVINEJneWgBu_r9DnOd0v6YEwNJcv3SHieT4WbKffbBx_zuNz4PqjdM3rSNe-wMOoCy_7cjE/s1600/Em_wnvirus_j7908i.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW5JE0EGnaokotVv7zE4Rlt_CF6UmpM6PXlPBIC-KVauO9iKKYLd85M_P-7xDh3jyh0fH-TVINEJneWgBu_r9DnOd0v6YEwNJcv3SHieT4WbKffbBx_zuNz4PqjdM3rSNe-wMOoCy_7cjE/s320/Em_wnvirus_j7908i.jpg" width="320" /></a></div>
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<span class="description">Electron microscopy of West Nile virus, taken from lab, </span></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: center;">
<span class="description">rights retained to displayed author.</span></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: center;">
<span style="font-size: x-small;">Original uploader was <a class="extiw" href="http://en.wikipedia.org/wiki/User:PhD_Dre" title="en:User:PhD Dre">PhD Dre</a> at <a class="external text" href="http://en.wikipedia.org/">en.wikipedia</a><span class="description"> </span></span></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: center;">
<span style="font-size: x-small;">Permission: CC-BY-SA-3.0,2.5,2.0,1.0;</span></div>
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<span style="font-size: x-small;"> Released under the <a class="mw-redirect" href="http://commons.wikimedia.org/wiki/GNU_Free_Documentation_License" title="GNU Free Documentation License">GNU Free Documentation License</a>.<span class="description"> </span></span></div>
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<span style="font-size: small;"> - Some characteristics of viruses differ
on close examination by <span style="font-family: Verdana,sans-serif;">imaging. </span></span></div>
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<span style="font-size: small;">Non-enveloped
viruses provide model systems for high-resolution structural study of whole
virus capsids (and their components) and the principles of large-scale nucleo-protein
tertiary and quaternary interactions. In many cases, they are relatively small,
stable, and highly symmetric particles that can be purified as homogeneous
samples inlarge quantities. These properties make them suitable for the
techniques of X-ray crystallography, X-ray fiber diffraction, and cryoelectron
microscopy (cryo-EM) combined with image reconstruction. Enveloped virus
particles generally have greater flexibility and asymmetry, two features that
inhibit application of high-resolution techniques.</span></div>
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<span style="font-size: small;"> - Flaviviruses
enter cells via
receptor-mediated endocytosis. It is known to infect <span style="color: windowtext; text-decoration: none;">humans</span>, <span style="color: windowtext; text-decoration: none;">horses</span>, <span style="color: windowtext; text-decoration: none;">dogs</span>, <span style="color: windowtext; text-decoration: none;">cats</span>, <span style="color: windowtext; text-decoration: none;">bats</span>, <span style="color: windowtext; text-decoration: none;">chipmunks</span>,
<span style="color: windowtext; text-decoration: none;">skunks</span>,
<span style="color: windowtext; text-decoration: none;">squirrels</span>,
domestic <span style="color: windowtext; text-decoration: none;">rabbits</span>,
<span style="color: windowtext; text-decoration: none;">crocodiles</span>
and <span style="color: windowtext; text-decoration: none;">alligators</span>.
To survey the area of coverage of the infection, the approach would be to use the
blood sera of wild birds and sentinel chickens. Samples must be tested for the
presence of WNV <a href="http://en.wikipedia.org/wiki/Antibodies" title="Antibodies"><span style="color: windowtext; text-decoration: none;">antibodies</span></a> by use of <a href="http://www.piercenet.com/browse.cfm?fldID=F95B91A9-3DC1-4B56..." target="_blank"><span style="color: windowtext; text-decoration: none;">immunohistochemistry</span></a> (IHC : see Image of the Week below)
or Enzyme-Linked Immunosorbent Assay (ELISA). Dead birds, after <span style="color: windowtext; text-decoration: none;">necropsy</span>,
have their various tissues tested for virus by either <a href="http://en.wikipedia.org/wiki/RT-PCR" title="RT-PCR"><span style="color: windowtext; text-decoration: none;">RT-PCR</span></a> (<a href="http://www.ncbi.nlm.nih.gov/pubmed/11013345" target="_blank">Reversetranscription polymerase chain reaction</a>) or IHC , where virus shows up as
brown-stained tissue because of a substrate-<span style="color: windowtext; text-decoration: none;">enzyme</span> reaction. Pioneer experiments with RNA bacteriophages showed high levels of genetic variability, suggesting error-prone replication and, later on, RNA viruses were confirmed to show high per-base mutation rates and short genomes. RNA viruses critically rely on fast replication for survival. Their rapid infection cycles allow them to reach high titers before the onset of host defense mechanisms.</span></div>
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<span style="font-size: small;"> - About one in 150 people infected with WNV will develop
severe illness. The disease presents with symptoms that consist of high fever,
headache, neck stiffness, stupor, disorientation, coma, tremors, convulsions,
muscle weakness, vision loss, numbness and paralysis. The neurologic picture may be
permanent in these affected individuals. Apparently, the ratio of severe disease is low.
But who gets it may be explained by the location of the individual, surrounding environment,
and possibly a lowered immune response. In some people the illness is mild fever,
headache, and body aches, nausea, vomiting, and sometimes swollen lymph glands
or a skin rash on the chest, stomach and back. Duration of illness is shorter
but even apparently health people may suffer. In 80% of the cases it is
basically an asymptomatic illness.</span></div>
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<span style="font-size: small;"> - As mentioned
above, WNV is spread by the bite of an infected mosquito. The infected mosquito
species vary according to geographical area. In the US, <a href="http://en.wikipedia.org/wiki/Culex_pipiens" title="Culex pipiens"><span style="color: windowtext; text-decoration: none;">Culex pipiens</span></a>
(Eastern US) the common house mosquito, <a href="http://en.wikipedia.org/wiki/Culex_tarsalis" title="Culex tarsalis"><span style="color: windowtext; text-decoration: none;">Culex tarsalis</span></a> (Midwest and West), and <a href="http://en.wikipedia.org/wiki/Culex_quinquefasciatus" title="Culex quinquefasciatus"><span style="color: windowtext; text-decoration: none;">Culex quinquefasciatus</span></a> (Southeast) are the
main sources. <a href="http://www.issg.org/database/species/ecology.asp?si=109" target="_blank">A. albopictus</a> mosquito
(Asian tiger mosquito) - an <a href="http://en.wikipedia.org/wiki/Invasive_species" title="Invasive species"><span style="color: windowtext; text-decoration: none;">invasive
species</span></a> in <span style="color: windowtext; text-decoration: none;">North America</span> - is a <span style="color: windowtext; text-decoration: none;">vector</span> of various diseases including the
West Nile virus. West Nile virus can be sampled from the environment by the
pooling of trapped mosquitoes, testing avian blood samples drawn from wild
birds, dogs and sentinel monkeys, as well as testing brains of dead birds found
by various animal control agencies and the public. Mosquitoes become infected when they feed on infected
birds. Infected mosquitoes can then spread WNV to humans and other animals when
they bite. Tissue transfer like blood transfusions and organ transplant may
also be channels of spread. Mother-to-fetus transfer may also occur. It is not
spread by touch. </span></div>
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<span style="font-size: small;"> - There is no <span style="color: windowtext; text-decoration: none;">vaccine</span> for humans. A vaccine for horses (<a href="http://en.wikipedia.org/wiki/ATCvet" title="ATCvet"><span style="color: windowtext; text-decoration: none;">ATCvet</span></a> code: <a href="http://en.wikipedia.org/wiki/ATCvet_code_QI05" title="ATCvet code QI05"><span style="color: windowtext; text-decoration: none;">QI05</span></a><span class="reflink"><a href="http://www.whocc.no/atcvet/atcvet_index/?code=QI05AA10"><span style="color: windowtext; text-decoration: none;">AA10</span></a></span>)
based on killed viruses exists; some <a href="http://en.wikipedia.org/wiki/Zoo" title="Zoo"><span style="color: windowtext; text-decoration: none;">zoos</span></a> have given this vaccine to their birds, although its
effectiveness is unknown. Dogs and cats show few if any signs of infection.
There have been no known cases of direct canine-human or feline-human
transmission; although these pets can become infected, it is unlikely they are,
in turn, capable of infecting native mosquitoes and thus continuing the disease
cycle. Unlike malaria where one might take tablets for prophylaxis before
entering a high-risk area, there exists no oral drug equivalent for WNV.</span></div>
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<span style="font-size: small;"> - So, there are a few important guidelines to halt or
minimize the spread of infection. These consist of using EPA approved mosquito
repellant such as N,N-Diethyl-meta-toluamide
(DEET) intended to be applied to the <a href="http://en.wikipedia.org/wiki/Skin" title="Skin"><span style="color: windowtext; text-decoration: none;">skin</span></a> or to <span style="color: windowtext; text-decoration: none;">clothing</span>,
draining or disposing of stagnant water silos or puddles, as well as avoiding
slow running streams or swamps. Spraying of insecticides in hotspots could also
be carried out. Of course, this may pollute the environment. If the EPA can
make available an organic chemical that is harmless to animals then that would
be a more environment-friendly solution. Aside from staying indoors, wear long-covering clothing, apply bug repellant that contains <a href="http://en.wikipedia.org/wiki/DEET" title="DEET"><span style="color: windowtext; text-decoration: none;">DEET</span></a>, and ensure
mosquitoes cannot enter buildings. Those who plan to travel to risky
environments ought to arm themselves with the pesticide, in addition to long
protective clothing. Community members and volunteers of said areas who are
responsible for cleaning up their locales must be prepared just the same.</span></div>
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<span style="font-size: small;"> - A person may start manifesting the illness between 3 to
14 days. There is no specific treatment except for supportive therapy. People
who suspect they may have WNV infection should report to the hospital where
they will be evaluated by health professionals. If you are over 50 years of age
and linger outdoors then you are at a higher risk for the infection. So as soon
as there’s a fever and unusually severe headaches the recourse is to go to
hospital where you can get the best needed support. For further info and CDC resources kindly visit
this <a href="http://www.cdc.gov/ncidod/dvbid/westnile/wnv_factSheet.htm" target="_blank">page</a>. So one must remember, if in a risky environment, stay indoors, and
close all windows. If windows have screens make sure they are in order.
Before going outdoors, apply an EPA and FDA approved mosquito repellant. A suggestion would be to use citronella oil. </span>Citronella oil is also a renowned plant-based <a href="http://en.wikipedia.org/wiki/Insect_repellent" title="Insect repellent">insect repellent</a>, and has been registered for this use in the United States since 1948.<a href="http://en.wikipedia.org/wiki/Citronella_oil#cite_note-U.S._EPA_Citronella_Factsheet-1"></a><span style="font-size: small;"> At any rate, if
anyone develops a febrile malaise, it is best not delaying to report to hospital as soon as possible.</span></div>
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<span style="font-size: small;"> - Note that interesting cases of hoaxes for outbreaks have
occurred. In 1999, an article appeared suggesting that the CIA was
investigating whether Iraq was responsible for causing the outbreak of West
Nile fever in the New York City area. The story relied heavily on a previous story
written by an Iraqi defector, claiming that Saddam Hussein planned to use<a href="http://www.uniprot.org/uniprot/P06935" target="_blank"> WestNile virus strain SV 1417</a> to mount an attack. The investigation indicated that
there was no known evidence of bioterrorism involved in the spread of West Nile
virus. But one of the largest bioterrorism hoaxes occurred in 2000. According
to e-mail messages widely circulated on the Internet, an organization known
as the Klingerman Foundation was mailing blue envelopes containing sponges
contaminated with a fictional pathogen called the ‘Klingerman virus’. According
to the e-mail alert, 23 people had been infected with the virus, including 7
who died.</span><br />
<br />
<span style="font-size: small;"> >>> Watch You Tube video <a href="http://www.youtube.com/watch?v=JAsvSfDXIKg" target="_blank">here!</a></span><br />
<br />
<span style="font-size: small;">>>> For more videos on West Nile Virus, scroll down to the <b>Video Bar </b>below<b>!</b></span><br />
<br />
<span style="font-size: small;"> - For a catalog of viruses, you can visit the pages at <a href="http://wiki.medpedia.com/Virus" target="_blank">Medpedia</a> or <a href="http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&term=Arboviruses&field=entry" target="_blank">MeSH</a>. </span></div>
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<span style="font-size: small;">- Take care. This is it for now. Any new info will follow. </span></div>
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<span style="font-size: small;">- Fernando Yaakov Lalana, M.D.</span></div>
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Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-75311839633639105562012-08-17T07:53:00.003-04:002012-08-17T11:35:44.776-04:00<div class="separator" style="clear: both; font-family: Verdana,sans-serif; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNb4bTCS1X7BEukuND__J6sbxSlGGwsxiYk2VEav7_TjtliyQlHYtYeUmEtbCBuQtreOaKFcMjEEKB83Uohyphenhyphen2UGAFhwid_vY-ai5i6_QklYWtyf3qv5CLemZGlBJBn-4zDt3nAOWOpHUQ8/s1600/MP900439485-pencil_math.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="212" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNb4bTCS1X7BEukuND__J6sbxSlGGwsxiYk2VEav7_TjtliyQlHYtYeUmEtbCBuQtreOaKFcMjEEKB83Uohyphenhyphen2UGAFhwid_vY-ai5i6_QklYWtyf3qv5CLemZGlBJBn-4zDt3nAOWOpHUQ8/s320/MP900439485-pencil_math.jpg" width="320" /></a></div>
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<span style="font-size: large;"><span style="line-height: 115%;">Biomedical
Computing on a Budget</span></span></div>
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The Numbers and Your Wallet</div>
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- Let’s face it. How many Health Professionals are MBAs? Not
even all IT Pros are MBAs! And in the current economic world, ROI (return on
investment) is key.<span style="mso-spacerun: yes;"> </span>So what is one to
do? Do we pennypinch in all areas of our life? Some say no. But the majority of
you reading this blog are probably feeling the “ouch” of the recession. Even
big IT firms are restructuring, retrenching and recalculating all their moves
in their day-to-day operations. </div>
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- Even a number of hospitals have suspended normal
operations.<span style="mso-spacerun: yes;"> </span>And when I say "normal" I mean
feeling free and easy and generous. As a matter of fact, even malpractice
insurance premiums are becoming competitive. Just a few weeks ago I learned
that the small clinic practice setting has become a viable option for MDs. I
have been working in a medium sized diagnostic facility for easily 10 years and
I don’t regret it. We still had budget diagnostic packages being offered
without sacrificing Quality of Service (QoS). ROI in the health profession is
not just about big bucks, but rather, a commitment to care for those who need
us. I’m not going to get into a discussion about the budget deficit and my
suggestions. It’s getting downright complicated. Or so it seems. The bottom
line is: where do we want to spend our hard earned cash. If we all started
having to drive a Ferrari to work, then of course our overhead would shoot up.
And who takes the heat? The guy next door whose wife is about to give birth and
he’s out of work. </div>
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- It’s not just a financial crisis we have to deal with. It’s
also a crisis of moral and ethical behavior. We must remember, we are <i><b>called to
serve</b></i>. We start with that, stay with that, and live with that. No easy matter
at all. The temptation to “me first” is compelling. Why? Because we’re all in the
same financial boat- <span style="mso-spacerun: yes;"> </span>more or less. <span style="mso-spacerun: yes;"> </span>Admittedly, some have quite a fancier boat. No
problem with that at all. Just don’t pass the cost to the patient. No I’m not
an ordained minister. And neither am I a Navy Seal! Just your friendly neighborhood
mad scientist -internist-cardiologist with a laptop. Let’s keep a good sense of
humor. It’s a survival skill. So, just a word: keep focused on what really
matters. And if you have happened to get lost in the professional-financial
forest, try hacking your way through with some kind words and acts, and give thanks
to your Creator. Not tomorrow. Today.</div>
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- The Numbers Frenzy</div>
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To those of you who are currently working in the area of
Health Statistics, well, there are some free tools available from the National
Center for Health Statistics. You can visit the resources page <a href="http://www.cdc.gov/nchs/data_access.htm%20" target="_blank">here</a><span style="mso-spacerun: yes;"> </span>There is also a good epidemiologic tool know
as OpenEpi <span style="mso-spacerun: yes;"> </span>now in version 2.3.1 Check it
out <a href="http://www.openepi.com/OE2.3/Menu/OpenEpiMenu.htm" target="_blank">here.</a>
available in English, French, Spanish and Italian. So even if you’re in the
European Union, this tool may work for your needs. More <span style="mso-spacerun: yes;"></span>free statistics
software can be viewed<a href="http://freestatistics.altervista.org/en/stat.php%20%20" target="_blank"> here</a> <span style="mso-spacerun: yes;"></span>Since we’re dealing with budget issues, make
sure to read the fine print. If you’d like an interesting free online data
visualization tool check out Tableau Public available <a href="http://www.tableausoftware.com/public/" target="_blank">here.</a></div>
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- Like I said, we’re ever confounded by the gamble of Health
Technology and money. Different people have all sorts of suggestions. With the
explosion of mobile computing people have asked who will pay for the
development and adaption of mobile devices in the Medical arena. Businesses
have done reasonably well and they’re thinking, when will it be the same in the
hospital, clinic or research institute. Somebody’s going to have to pay for
this. But who? Will this mean an additional increase in health expenditures? We
have enough problems already. But then again, if we were going to go for the “people
care” paradigm, then that means it is essential to break the boundaries and
reprioritize costs for patients, health professionals as well as clinics and hospitals. And since the research has to go onward we better think of solutions
ASAP! Cures have to be found and patients need our utmost attention and QoS.
Healthcare can’t take a back seat behind Defense spending. Quite frankly, someone
I know once told me that it paid more to blast people out of existence than to cure
them. Is this what we’re coming to? I am optimistic though, that things will
get better. We just have to keep focus and ride the storm while it’s still
roaring. Maybe, once policy makers get their acts straight, we will progress.
Will the business model work for healthcare? At any rate, each of us has a
voice and we better tell government leaders to be straightforward with their service
priorities instead of the self-embellishment that serves no purpose other than to
anger their constituents. Those of us in the healthcare galleon should row our individual
oars and steer forward and do what we do best: serve and show the world we
care. Like I always say, mediocrity is a capital offense. Go and make the world
a better place, regardless of your place in the grand drama of things.<span style="mso-spacerun: yes;"> </span>And if eHealthcare is your calling, then do
it with a passion. Enjoy your work and work at what you enjoy. We in the
healthcare business are at a crossroads. The world is watching. Let’s keep
people healthy!<span style="mso-spacerun: yes;"> </span>Meanwhile, the medical
community is pioneering new modes of healthcare delivery based on the
continuous management of disease rather than expensive episodic care. Costs
decline as quality and access of care improve.</div>
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- Patient Numbers</div>
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- As personalized Medicine grows, data capture will have to
evolve too. And big numbers will be our challenge. And as we manage all those
numbers well <span style="mso-spacerun: yes;"></span>we will then see that our
efforts will have paid off. Patients will be as smart as can be, and we will
have to deliver top quality improvements in data analysis and consolidation.
There will have to be a central body or umbrella organization that will enforce
common grounds for handling information, akin to the UN/WHO ICD system. All
health professionals should participate in training and supervision, and of
course, as we deal with our own clients we shall be able to render care to the
best of our abilities. Everybody will know the basics of coding, operating and
managing the information warehouse. With the explosion of cloud technology, we
will have to be tech savvy. But it’s not the tech that’s the goal: it’s the
patient we care for. We need to see the big picture. I read once and I remember
it well. As a painter steps back from his work to see the big picture, we will
likewise need to step back once in a while and see that we are involved in a
huge ecosystem where everybody is a player. And we need to play right. Self-directed
education is blossoming and we need to get interested in things that we
typically shrug off as “not my thing.” Take responsibility for your own
education. Let’s all be mature. Like I told a resident once, “we’re not in
kindergarten anymore.“ Enough <span style="mso-spacerun: yes;"> </span>with the excuses.
We have reached an inflection point between the insular ‘sick care’ non-system
of the past and the collaborative, proactive, true ‘health and wellness’ system
of the future. As we have come to better understand the phenotypic, genotypic,
environmental, and lifestyle factors that determine our health, it has become
clear that disease and wellness are inherently personal. It should be. The
patient also has to learn to take responsibility for his or her education and
growth. There is such a thing as patient autonomy. But rather than burden the
patient with forms, and more forms, we must guide them safely along the way. Do
not underestimate the patient’s capacity for self-care. Of course, at times
they need a helping hand. Individualizing treatment for a given patient is a
truly daunting, data-driven task. Finding a treatment based on a patient’s
genes, proteins, and environment is essentially a signal-detection exercise.</div>
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- In
my previous post, I mentioned the need to not only capture the signal, but also
get the sense out of it. This will ultimately require data volumes and
manipulation techniques unprecedented in information science and technology.<span style="mso-spacerun: yes;"> </span>Businesses, banks, insurance firms and even
the governments are doing it. eHealthcare must tread the same path of growth. From
trial and protocol design all the way to the task of prescribing, all of this
may have to be coordinated in a group run. The last mile has always been the
hardest: obviously multifactorial, involving structural problems with our care
delivery systems, reimbursement policies, etc.<span style="mso-spacerun: yes;">
</span>Eventually, patients want a secure network of ‘friends’ around their
illness and they want their doctors to ‘like’ them. Regardless of the approach,
‘liking’ our patients—and our patients liking us in return—will be a really
large Big Data problem. I dare say that there are some of us healthcare
professionals who are in their comfort zones and find it hard to accept the
tech issues. Actually, I think that it’s basically a fear of the unknown which
can be daunting indeed. Then goes the thinking,<span style="mso-spacerun: yes;"> </span>“I did fine without it. Why bother with all
that now?” My answer is ”Because it behooves us as professionals.” It’s not a
threat, but rather, a challenge which we embarked on when we decided to become
a doctor, a nurse, and whatever branch of medical service.</div>
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- This is the reason why I include facts, figures, data, and
number crunching methods in my discourse- this blog. Just a short while back,
somebody told me that she couldn’t get her laptop to work. So I told her, “You
need to do such-and-such.” She responded, “I’m not a techie.” So I responded, “You
don’t need to be a techie. Just know your machine and start off with the
essentials.” Know your machine and what you are doing with it, and, to it.
After we overcome that inertia, everything else will come easier. We live in
exciting times. Technology is a three-course dinner at the best restaurant. Let’s
not get stuck at the soup phase. Let’s savor everything. Artificial
intelligence, neuro-linguistic programming, and statistical, decision based
systems will then come easy as pie.<br />
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<span style="font-size: small;"><span style="line-height: 115%;"> - <b>Back to the
Math Exercise</b></span></span></div>
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<b> - Jean Louis Marie Poiseuille</b> <span style="mso-spacerun: yes;">(</span>22 April 1797 – 26 December 1869) </div>
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was a <a href="http://www.blogger.com/goog_445323783" style="color: black;" title="France">French</a> physician and physiologist.
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<span style="font-size: x-small;"><b><span style="line-height: 115%;">Source: </span></b><a href="http://depa.fquim.unam.mx/filtracion/fundamentos.html">http://depa.fquim.unam.mx/filtracion/fundamentos.html</a></span></div>
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<b><span style="font-size: 12pt; line-height: 115%;"> </span></b><b><span style="font-size: 12pt; line-height: 115%;">Poiseuille’s
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<span style="font-size: 12pt; line-height: 115%;"><span style="font-size: small;">This law is important in cardiovascular physiology. However it is a feature in hydraulics, fluid dynamics, and electrical currents as well. So kindly take a good look at it and see the unifying characteristics of flow. It is very relevant to understanding cardiovascular pathology and eventually diagnosis and clinical investigation.</span></span><b><span style="font-size: 12pt; line-height: 115%;"><br /></span></b></div>
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This concerns the voluminal <a href="http://en.wikipedia.org/wiki/Laminar_flow" title="Laminar flow">laminar</a>
stationary flow of an <a href="http://en.wikipedia.org/wiki/Potential_flow" title="Potential flow">incompressible</a> uniform <a href="http://en.wikipedia.org/wiki/Viscosity" title="Viscosity">viscous</a>
liquid (so-called <a href="http://en.wikipedia.org/wiki/Newtonian_fluid" title="Newtonian fluid">Newtonian fluid</a>) through a cylindrical tube with
constant circular cross-section. In other words, it applies to non-turbulent
flow of liquids through pipes. It can be successfully applied to blood flow in <a href="http://en.wikipedia.org/wiki/Capillary" title="Capillary">capillaries</a>
and <a href="http://en.wikipedia.org/wiki/Vein" title="Vein">veins</a>, to air
flow in <a href="http://en.wikipedia.org/wiki/Lung" title="Lung">lung</a> <a href="http://en.wikipedia.org/wiki/Pulmonary_alveolus" title="Pulmonary alveolus">alveoli</a>, for the flow through a drinking straw
or through a <a href="http://en.wikipedia.org/wiki/Hypodermic_needle" title="Hypodermic needle">hypodermic needle</a>.</div>
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<b> - Gotthilf Heinrich Ludwig Hagen</b> (March 3, 1797 -
February 3, 1884) was a <a href="http://en.wikipedia.org/wiki/Germany" title="Germany"><span style="color: windowtext;">German</span></a> <a href="http://en.wikipedia.org/wiki/Physicist" title="Physicist"><span style="color: windowtext;">physicist</span></a> and <a href="http://www.blogger.com/goog_114883793" title="Hydraulic"><span style="color: windowtext;">hydraulic</span></a><a href="http://www.blogger.com/goog_114883793"> </a><a href="http://www.blogger.com/goog_114883793" title="Engineer"><span style="color: windowtext;">engineer</span></a><a href="http://www.blogger.com/goog_114883793"><span style="color: #1f497d; mso-themecolor: text2;">.</span></a></div>
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<span style="color: #1f497d;"><span style="color: black;">In the previous post, we talked about the </span></span></div>
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<span style="color: #1f497d;"><span style="color: black;">Hagen-</span></span><span style="font-size: 12.0pt; line-height: 115%;">Poiseuille’s</span><span style="color: #1f497d;"><span style="color: black;"></span> <span style="color: black;">Law. </span></span></div>
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<span style="color: #1f497d;"><span style="color: black;">For purposes of clarity, I'm including the formula again here.</span></span></div>
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<span style="font-size: small;"><span style="line-height: 115%;">A Formula
for Vascular Resistance: Standard Fluid Dynamics</span></span></div>
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<span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">The Hagen–Poiseuille equation, a </span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><a href="http://en.wikipedia.org/wiki/Physical_law" title="Physical law"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">physical law</span></a></span><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> that gives the </span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><a href="http://en.wikipedia.org/wiki/Pressure" title="Pressure"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">pressure</span></a></span><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> drop
in a fluid flowing through a long cylindrical pipe. The assumptions of the
equation are that the fluid is </span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><a href="http://en.wikipedia.org/wiki/Viscous" title="Viscous"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">viscous</span></a></span><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> and </span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><a href="http://en.wikipedia.org/wiki/Incompressible" title="Incompressible"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">incompressible</span></a></span><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">; the </span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><a href="http://en.wikipedia.org/wiki/Laminar_flow" title="Laminar flow"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">flow is laminar</span></a></span><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> through a pipe of constant circular cross-section that is substantially
longer than its diameter; and there is no </span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><a href="http://en.wikipedia.org/wiki/Acceleration" title="Acceleration"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">acceleration</span></a></span><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> of
fluid in the pipe. The equation is also known as the Hagen–Poiseuille law,
Poiseuille law and Poiseuille equation. </span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: Arial; mso-bidi-language: HE; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Actual
fluid flow is <a href="http://en.wikipedia.org/wiki/Turbulence" title="Turbulence">turbulent</a> (i.e., not laminar) for velocities and pipe
diameters above a threshold, leading to larger pressure drops than calculated
by the Hagen–Poiseuille equation</span><br />
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- Study the units used for the calculations, and consider the reasonable limits of the variables. Remember, math is the relationship between objects, whether numbers or words. Functions are intrinsic in calculus. When you start coding, you will come across OOP (Object-Oriented Programming). So get used to this principle. As you start working with different programming languages this knowledge will come in real handy. C, C++, Java, even Python (and all the hybrids) will deal with objects, classes, data structures and algorithms.</div>
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- Get some scratch paper and work it out. If you've got a whiteboard, you can draw out the process. If you've got the latest 10.1 tablet with pen, try doing it. It'll be fun and engaging. Can you imagine, up to 60% of a healthcare individual's time is spent on documentation. Work smart.</div>
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- I hope you do the exercise. Next time we'll talk about viscosity and the characteristics of the flow vessels. Also, we'll be taking a view of diagnostic procedures used in evaluating these elements. PhD not required...<br />
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<span style="font-size: large;"><b>"See One. Do One. Teach One."</b></span><br />
-anonymous <br />
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<span style="font-size: 12.0pt; line-height: 115%;"> - Take some
time to check out the following resources on Big Data</span></div>
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1) Infographic on <a href="http://www.autonomy.com/content/Technology/what-is-big-data/index.en.html?imm_mid=091c7d&cmp=em-strata-newsletters-aug15-elist" target="_blank">Big Data from Autonomy (an HP company):</a></div>
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<b><span style="color: windowtext; font-size: 12pt; font-weight: normal; line-height: 115%;">2) Roel Castelein (Global) - <a href="http://www.idgconnect.com/blog-abstract/599/roel-castelein-global-big-data-the-third-wave" target="_blank">Big Data: The Third Wave:</a></span></b></h2>
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- The weekend is just around the corner. Take time to step back and look at the big picture. You're part of it. </div>
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- Stay safe!</div>
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- Fernando Yaakov Lalana, M.D.</div>
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Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-57620434606324744542012-08-15T12:23:00.001-04:002012-08-15T14:13:05.403-04:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEir7ZEkZjKWrWhKXuV2hdjafqcwv7YnCTqSZzN8vv2p0W_ZVt6MBDS_OnElLjOxlyf_Uz5rzXq36GAH9SWx-4jqgNyhkDNE-15HLOl9lFqAgkcvFKFDQwT1Tb_ZTUwXCR5WmXnnn-hmJVAC/s1600/MC900388910-medal_med.gif" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEir7ZEkZjKWrWhKXuV2hdjafqcwv7YnCTqSZzN8vv2p0W_ZVt6MBDS_OnElLjOxlyf_Uz5rzXq36GAH9SWx-4jqgNyhkDNE-15HLOl9lFqAgkcvFKFDQwT1Tb_ZTUwXCR5WmXnnn-hmJVAC/s200/MC900388910-medal_med.gif" width="174" /></a></div>
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<span style="font-size: large;"><span style="line-height: 115%;">Markers,
Medals and Math:</span></span></div>
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<span style="font-size: large;"><span style="line-height: 115%;">Pushing the Envelope</span></span></div>
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<span style="font-size: small;"><span style="font-weight: normal;"> - “OK for me, but not OK for you.” Before we go to today’s agenda, I’ll
just talk a bit about the ractopamine issue mentioned in my previous post. The Member States of Codex
Alimentarius Commission adopted maximum residue limits for the amount of ractopamine, the animal growth
drug, allowed in the tissues of pigs and cattle. The Codex Commission reached a
decision through a vote, carried out in accordance with the Commission’s rules
and procedures. The limits were approved with 69 votes for, 67 against, and
seven abstentions. The decision was made after the assessment was carried out
by the Joint Expert Committee on Food Additives (an arm of the FAO/WHO) and
reached after a rigorous process of scientific assessment to ascertain that the
proposed levels of residues have no impact on human health.</span></span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;"> - Without going into statistical
elaborations and disrespecting committee members, or committee rules, we notice
that it was </span>not an overwhelming
vote<span style="font-weight: normal;">. Will a 2-vote difference (among 143 individuals) make the score and tell us that it’s
totally “safe” to ingest ractopamine-fed animal products? We’re dealing with
world health- our health. And yet we single-out and penalize an Olympic athlete
for using performance enhancing drugs. Why the disparity in decision making?
Honestly, this is a bit absurd. One might argue that the two situations are
different from one another. However, I believe that the WHO, and whoever is
deciding for our health outcomes, should adopt a policy that is consistent in
all settings. Not, “OK for me, but not OK for you.” I’ll leave you with that
food for thought. </span></span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;">For more information please contact: </span></span></h3>
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<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">Glenn Thomas<br />
WHO, Geneva <br />
Mobile: +41 79 509 0677<br />
E-mail: </span><a href="mailto:thomasg@who.int" style="font-family: Verdana,sans-serif;">thomasg@who.int</a></span><span style="font-size: 12pt;"></span></h3>
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<span style="font-size: 12pt; font-weight: normal;"> - Biomarkers of Human Health</span></h3>
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<span style="font-size: 12pt; font-weight: normal;"> </span></h3>
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<span style="font-size: 12pt; font-weight: normal;"> - A biomarker, or biological marker, is an </span><a href="http://en.wiktionary.org/wiki/indicator" title="wikt:indicator"><span style="font-size: 12pt; font-weight: normal;">indicator</span></a><span style="font-size: 12pt; font-weight: normal;"> of a
biological state. It is a characteristic that is objectively measured and
evaluated as an indicator of normal </span><span style="font-size: 12.0pt;"><a href="http://en.wikipedia.org/wiki/Biological_process" title="Biological process"><span style="font-weight: normal;">biological processes</span></a></span><span style="font-size: 12pt; font-weight: normal;">, </span><span style="font-size: 12.0pt;"><a href="http://en.wikipedia.org/wiki/Pathogenic" title="Pathogenic"><span style="font-weight: normal;">pathogenic</span></a></span><span style="font-size: 12pt; font-weight: normal;"> processes, or
</span><span style="font-size: 12.0pt;"><a href="http://en.wikipedia.org/wiki/Pharmacologic" title="Pharmacologic"><span style="font-weight: normal;">pharmacologic</span></a></span><span style="font-size: 12pt; font-weight: normal;"> responses to
a </span><span style="font-size: 12.0pt;"><a href="http://en.wikipedia.org/wiki/Therapeutic_intervention" title="Therapeutic intervention"><span style="font-weight: normal;">therapeutic intervention</span></a></span><span style="font-size: 12pt; font-weight: normal;">. It is used in many </span><span style="font-size: 12.0pt;"><a href="http://www.blogger.com/blogger.g?blogID=3192755943215745075" title="Scientific fields"><span style="font-weight: normal;">scientific fields</span></a></span><span style="font-size: 12pt; font-weight: normal;">. This marker
can be found in a specific tissue, organ, or throughout the body. It is an
index of either health or disease. It is meant to detect the smallest unit of a
certain molecule, or process (as in the electrocardiogram) in the body. </span></h3>
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<span style="font-size: 12pt; font-weight: normal;"> </span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;"> - While we know of blood
cholesterol levels and traces of zinc in the skin and nails, growth of the
knowledge and the technology to asses these elements is expanding remarkably. Now, with
the growth of genomics and </span><span style="font-weight: normal;">Medical Information Technology</span><span style="font-weight: normal;">, we are delving deeper,
not only with one person’s health, but also with the likelihood of disease in his
or her offspring. It is not sufficient to identify a molecule’s presence. We
are also measuring their specific levels. Laboratories are currently facing the
recession, and because of this we have to work smarter. For example, we could use mathemathical modeling and organ simulation in order to minimize animal or human experimentation whenever feasible. Chemical reagents and the sundry materials of the lab are getting way expensive. It would be possible to buy special computer programs for our particular area of study. If the program is not available, well, we can code one. A bit of study and a bit of practice go a long way. Oh yes, time is gold. If we can plan our experiments well beforehand (with the proper tools), we could save on energy and even possible mistakes.We should make use of the ELN (Electronic Laboratory Notebook) to log all our observations througout the experiment. It is a way of maximizing our observations and calculations thereby enabling us to see the minutiae as well as the bigger picture.</span></span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;"> - Math</span></span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;"> </span></span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;"> - Different computer
programs are now increasingly used to assess the significance of certain health
data. One such program is MATLAB, a mathematical analysis tool that is used in
cases ranging from aerodynamic data to abnormal physiological signals. The book
by Steven C. Chapra, “Applied Numerical Methods with MATLAB - for Engineers and
Scientists”, is a good resource dealing with computers: MATLAB features, computer uses and their
limitations in the scientific field. In this day and age, to eschew
information technology is a major offense. This also holds true in the health
professions. With the increasing portability of data access, we have to make
some notable changes in our diagnostic attitude. Physicians and nurses are
tapping into servers and cloud engines to support their skills and acumen. The
advent of telemedicine is further strengthening the role of health computing machines
in the workplace and wherever the patient may be. </span></span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;"> - It’s not enough, though,
to record signals or biologic phenomena. It is also imperative that we study and
make this data relevant to our roles as purveyors of health. How we carry out
our analysis will matter in the ways that data is relevant in an individual in a
given situation. In other words, it’s not just about collecting and storing
data, but rather understanding and making decisions that will impact your
health. Statistics, time-series analysis, signal processing, and biophysics
simulations are all important analytic processes. While it is true that there
may are special departments devoted to these applications, we must be cognizant
of their operations. The whole process eventually depends on the algorithms
used in the analysis of the data. Whether one is a clever clinical diagnostician
or a computer programmer, the formulas we utilize can spell the difference in
the diagnosis between a gastric reflux state, and a case of an impending
myocardial infarction. Obviously, we may not have time to review calculus and other maths in an
acute and potentially catastrophic 50/50 situation. That is why we should take as much time honing our tech
skills as we do our daily SOP (standard operating procedures). </span></span></h3>
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<span style="font-size: small;"><span style="font-weight: normal;"> - Actually, all this study
is a definite load on the time and energy of health practitioners. That is why
we should accept this responsibility and work more efficiently. If not, we will
all burn out eventually and that will put us out of reach with the patient
After many years dealing with critical cases in the ICU/CCU, it has become
second nature to me to make the most reasonable choices in a given
situation. But it is not boasting, but rather accepting that our competence
relies heavily on our clinical and technical aptitude. Now, we have
associations dealing with Medical Information Systems, and we have access to
the surmounting knowledge that is paving the way to a better health experience. </span></span></h3>
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<span style="font-size: 12.0pt; line-height: 115%;"> -In the
following days and weeks, I will be demonstrating to you certain ways of
computer-based math in the diagnostic arena. Our bodies are mysterious temples
with many hidden corridors and alleys. It is now our time to unravel bit by bit
what stuff we are made of. At the same time, we will be exercising our frontal lobes. It's not just calculating numbers, but rather picturing the process in our minds. Or, pen it at the back of an envelope if you have one. If you've got a mobile device with a stylus, that would be nice. It's good to remember that math is basically the relationships between objects. </span></div>
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<span style="font-size: 12pt; line-height: 115%;"> - Stuff for Exercise</span><br />
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<span style="font-size: 12.0pt; line-height: 115%;"> - A Formula
for Vascular Resistance: Standard Fluid Dynamics</span></div>
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<span style="font-size: 12.0pt; line-height: 115%;"> - We begin
with the Hagen–Poiseuille equation, a </span><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">physical law</span><span style="font-size: 12.0pt; line-height: 115%;"> that gives the </span><a href="http://en.wikipedia.org/wiki/Pressure" title="Pressure"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">pressure</span></a><span style="font-size: 12.0pt; line-height: 115%;"> drop in a fluid flowing through a long cylindrical pipe. The
assumptions of the equation are that the fluid is </span><a href="http://en.wikipedia.org/wiki/Viscous" title="Viscous"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">viscous</span></a><span style="font-size: 12.0pt; line-height: 115%;"> and </span><a href="http://en.wikipedia.org/wiki/Incompressible" title="Incompressible"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">incompressible</span></a><span style="font-size: 12.0pt; line-height: 115%;">; the </span><a href="http://en.wikipedia.org/wiki/Laminar_flow" title="Laminar flow"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">flow is laminar</span></a><span style="font-size: 12.0pt; line-height: 115%;"> through a pipe of constant circular cross-section that is
substantially longer than its diameter; and there is no </span><a href="http://en.wikipedia.org/wiki/Acceleration" title="Acceleration"><span style="color: windowtext; font-size: 12.0pt; line-height: 115%; text-decoration: none; text-underline: none;">acceleration</span></a><span style="font-size: 12.0pt; line-height: 115%;"> of fluid in the pipe. The equation is also known as the
Hagen–Poiseuille law, Poiseuille law and Poiseuille equation. </span>Actual
fluid flow is <a href="http://en.wikipedia.org/wiki/Turbulence" title="Turbulence">turbulent</a> (i.e., not laminar) for velocities and pipe
diameters above a threshold, leading to larger pressure drops than calculated
by the Hagen–Poiseuille equation. In the blood vessels, you have turbulence at bifurcations or stenosis. The change in flow can give rise to Eddy currents (also called <b>Foucault currents</b><sup class="reference" id="cite_ref-0"><a href="http://en.wikipedia.org/wiki/Eddy_currents#cite_note-0"></a></sup>). The term <i>eddy current</i> comes from currents seen in water when dragging an oar breadthwise. These localized areas of turbulence known as <i>eddies</i> give rise to persistent vortices. Any <a href="http://en.wikipedia.org/wiki/Spiral" title="Spiral">spiral</a> (or, spinning) motion with closed streamlines is vortex flow. In cardiology, eddy currents are important because these areas of spinning can facilitate the formation of thrombi. Blood flow in the opposite direction from normal is regurgitation. Alright, so now we begin our exercise.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzkPNlJTuL1UAU4tYBgCp6DuR4GGtZ9LTFAT1vZefuQrYSdmi4n4eSTn717YQIVGUWtlQu3kd_f-ITRo1kk1IlRwwG4bIIi-MRKkrr4hm_GGVHLaAOkaFRtFX9Of0xhZpOIobcgDeK3Lfi/s1600/Hagen-Poiseuille%2526s-Law.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzkPNlJTuL1UAU4tYBgCp6DuR4GGtZ9LTFAT1vZefuQrYSdmi4n4eSTn717YQIVGUWtlQu3kd_f-ITRo1kk1IlRwwG4bIIi-MRKkrr4hm_GGVHLaAOkaFRtFX9Of0xhZpOIobcgDeK3Lfi/s400/Hagen-Poiseuille%2526s-Law.jpg" width="345" /></a></div>
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1) To start: on the left is the first formula to take a good look at;</div>
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2) Try to determine the unit of measurement for the variables, such as <i style="font-family: "Courier New",Courier,monospace;">P</i>, <i style="font-family: "Courier New",Courier,monospace;">L</i>, and so on;</div>
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3) What would be the usual and reasonable limits for each of the variables;</div>
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4) Calculate.</div>
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Since we are dealing now with blood vessels, remember the characteristics of the vessel,</div>
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(e.g. artery or vein) and understand the different agents that may influence the characteristics, (e.g. hormones, blood gases, electrolytes).<br />
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- In the process you will be reviewing anatomy, physiology, biochemistry, and biophysics. Grab your favorite calculator and try it out. We will continue next time...<br />
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- Stay cool! See you. </div>
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- Fernando Yaakov Lalana, M.D.</div>
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<br />Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-88116419618152596862012-08-13T15:37:00.000-04:002012-08-13T16:15:46.488-04:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGwShCpxTu8xGJF0tG6jo4LCiJoDzn7D1Fr4IOYzaNBHg22t8bCzWWhErJQ5b4-2J6dPNK2jsZIngMrDMmwG7AeWmx3Ew5XE-5mlVWhEV1TI2DblLZxcjfedmE-L9eKaGPSZPxujxlXnhS/s1600/ractopamine-med_col.gif" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="115" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGwShCpxTu8xGJF0tG6jo4LCiJoDzn7D1Fr4IOYzaNBHg22t8bCzWWhErJQ5b4-2J6dPNK2jsZIngMrDMmwG7AeWmx3Ew5XE-5mlVWhEV1TI2DblLZxcjfedmE-L9eKaGPSZPxujxlXnhS/s320/ractopamine-med_col.gif" width="320" /></a></div>
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<span style="font-family: Verdana, sans-serif; font-size: large;">Ractopamine, Swine and Man</span></div>
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<span style="font-family: Verdana, sans-serif;">- The United Nations food standards body, the Codex
Alimentarius Commission, has decided to set residue limits of the animal growth
promoter, ractopamine, which also keeps pigs lean for the slaughter. Cattle are
also administered this beta-adrenoceptor agonist. The ractopamine limits set by
the Commission are 10 micrograms per kilogram of pig or cattle muscle, 40
micrograms per kilogram in liver and 90 micrograms per kilogram of the animals’
kidneys.</span></div>
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<span style="font-family: Verdana, sans-serif;">- Known as <i>Paylean</i> for swine and <i>Optaflexx</i> for cattle, <b>4-[3-[[2-Hydroxy-2-(4-hydroxyphenyl)ethyl]amino]butyl]pheno</b>l
is banned in the European Union, Republic of China (Taiwan) and Mainland
China. Curiously, in 27 countries,
including Japan, South Korea,
Mexico, Canada, the United
States and many others, have determined that meat from animals fed
ractopamine is safe for human consumption. As a leanness-enhancing agent, orally-given (in
animal feed) ractopamine is absorbed, distributed and eliminated rapidly in pigs,
cattle, laboratory animals and primates. It notably increases the rate of
weight gain, improves feed efficiency and increases carcass leanness in
finishing swine.</span></div>
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<span style="font-family: Verdana, sans-serif;">- In humans, this agent is likewise rapidly absorbed. In a study with volunteers given a single
oral dose of 40 mg, the mean half-life was around 4 hours, and it was not
detected in plasma 24 hours after said ingestion. The urinary metabolites were
monoglucuronide and monosulfate conjugates, with ractopamine monosulfate being
the major metabolite present.</span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;">- It is considered safe as a finishing feed for swine over 240
lbs. In studies in rats and mice, acute toxicity was observed and the oral <a href="http://en.wikipedia.org/wiki/Median_lethal_dose" title="Median lethal dose">LD<sub><span style="line-height: 115%;">50</span></sub></a> in mouse and rat are 3547-2545 mg/kg body weight
(male and female) and 474-365 (male and female), respectively. <sup> </sup>You can access a European Food Safety
Authority opinion <a href="http://www.efsa.europa.eu/en/scdocs/doc/1041.pdf" target="_blank">here</a>.<b> LD<sub>n </sub></b>represents “Lethal
Dose” and the subscript, n, represents the percentage of test organisms
killed by a specific dosage of a pathogen (a given substance or type of <a href="http://en.wikipedia.org/wiki/Radiation" title="Radiation">radiation</a>) and half will die at LD<sub>50</sub>. In effect,
it is the index indication of the <a href="http://en.wikipedia.org/wiki/Lethality" title="Lethality">lethality</a> of the
pathogen in a “normal individual.”</span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"> - This begs a question: if it is toxic to laboratory subjects
(here, rats and mice) then why is it considered safe for man’s
consumption? Why is also there a
disparity in the permissions and prohibitions among different countries? Under <a href="http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfCFR/CFRSearch.cfm?fr=556.570" target="_blank">21 CFR 556.570</a>, safe concentrations for
total residues of ractopamine hydrochloride are: 0.25 ppm in muscle, 0.75 ppm
in liver, and 1.5 ppm in kidney and fat. <i>(ppm=parts per million) </i>By the wa</span><span style="font-family: Verdana, sans-serif;">y, the l</span><span style="font-family: Verdana, sans-serif;">iver is the target tissue.</span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><i><br /></i></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><i>- </i><span style="line-height: 115%;">We’re getting into more
numbers here. In spite of the observations in the lab,
the Joint FAO/WHO Expert Committee on Food Additives has said that it is safe
for humans to consume these meats. So let’s see how technology is supposed to help
us now.</span><span style="line-height: 115%;"> </span><span style="line-height: 115%;">It is not mutagenic, genotoxic,
nor considered to be a direct carcinogenic agent. Anyone familiar with the
actions of beta-adrenergic agents will know that there will be some
irritability, restlessness, tremors, tachycardia, and an increase in cardiac
output. </span><a href="http://en.wikipedia.org/wiki/Clenbuterol" style="line-height: 115%;" title="Clenbuterol">Clenbuterol</a><span style="line-height: 115%;">
</span><span style="line-height: 115%;"> </span><span style="line-height: 115%;">(another beta-adrenergic agonist) is a
growth promoting compound. It is </span><span style="line-height: 115%;">known to have the effect
of enhancing weight gain and proportion of muscle to fat.</span></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;"><br /></span></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><span style="line-height: 115%;">- Lest we forget, this
beta-adrenergic agent is also banned by the international sports body and known
controversies concerning athletes with traces of clenbuterol have arisen. And
in a case of cycling recently, </span><span style="line-height: 115%;"> </span><span style="line-height: 115%;">I remember</span><span style="line-height: 115%;"> </span><span style="line-height: 115%;">that the athlete was basically
castigated for using performance-enhancing drugs. Compared to ractopamine, clenbuterol is known to have a much longer
half-life in blood than ractopamine and thus has a greater potential for </span><a href="http://en.wikipedia.org/wiki/Bioaccumulation" style="line-height: 115%;" title="Bioaccumulation">bioaccumulation</a></span></div>
<br />
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"> - So what are we going to use as a meter for the safety of
humans? Isn’t it possible that the continuous ingestion of meat of animals fed ractopamine
may be dangerous for man? I don’t think
we should wait a generation or two to come to some sense of “sobriety” or
realization that artificially enhanced food is not in our best interest. The
demand for more food worldwide is apparently governing the choices we make.
Even genetically modified grass is given to cattle to graze on. The reason for
this method of feeding was that there was more meat and more money to be made doing it this way. You may even have already consumed this artificially enhanced food earlier
today, or this week.</span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
</div>
<div class="MsoNormal">
- <span style="font-family: Verdana, sans-serif;">We are not talking about our individual decision to be herbivorous
or omnivorous. That will be a subject for another day. What we are arriving at here
is to consider, not just our safety (or self-interest), but the welfare of the
future generations. I, for one, will not want my own children or grandchildren to ask me later, “why did you allow all this to happen?” Maybe, some of you are quite
liberal in your choices, and that’s one’s lawful right. What we must decide is
to make the responsible decision today. </span></div>
<br />
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"> - If it’s not good for the athlete, it may not be good for
you. And mind you, I have had first-hand experience dealing with both national
and international sporting events. This reminds me now of the issue of
concussions in high-contact sports. I have witnessed athletes stagger even
after winning a match. I hope we will not stagger in our choices as well.</span></div>
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<span style="font-family: Verdana, sans-serif;"><br /></span></div>
<div class="MsoNormal">
<span style="font-family: Verdana, sans-serif;"> - Stay safe and have a nice day. <span lang="ES"><b>Bon </b></span></span><span lang="ES" style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><b>appétit!</b></span><span style="font-family: Tahoma, sans-serif; font-size: x-small;"><o:p></o:p></span></span></div>
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<span lang="ES" style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><b><br /></b></span></span></div>
<div class="MsoNormal">
<span lang="ES" style="line-height: 115%;"><span style="font-family: Verdana, sans-serif;"><b> </b>- Fernando Yaakov Lalana, M.D.</span></span></div>
Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-53828449343504390022012-08-10T08:28:00.001-04:002012-08-10T12:56:27.537-04:00<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfE-Kl_SFvRGDJuh4IugKvrpfN6fuxw97k4AHMb16Ex0FFVvRo_aoRG7vHeE_mcyyMUAorwilKiL0uEGvkWYa9FO3NZAMm0KqK4ySxft3NG7csAsBQNSqCNdUUTFoCCp8Ak7b4zaFOJGtc/s1600/MC900325596-pig-X-sml.gif" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="116" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfE-Kl_SFvRGDJuh4IugKvrpfN6fuxw97k4AHMb16Ex0FFVvRo_aoRG7vHeE_mcyyMUAorwilKiL0uEGvkWYa9FO3NZAMm0KqK4ySxft3NG7csAsBQNSqCNdUUTFoCCp8Ak7b4zaFOJGtc/s200/MC900325596-pig-X-sml.gif" width="200" /></a></div>
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<span style="font-size: large;"><span style="font-family: Verdana,sans-serif;">CDC and WHO are really busy! </span></span></div>
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<span style="font-size: large;"><span style="font-family: Verdana,sans-serif;">For a reason...</span></span></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
It’s not just the containment of the Ebola Virus in Uganda
the health authorities are dealing with, even though containment is being
carried out. Now they have to deal with Swine Influenza which has struck a few
U.S. states already.<span style="mso-spacerun: yes;"> </span>In one count, there
have a been a bit over 100 cases, where the young kids<span style="mso-spacerun: yes;"> </span>and young adults are of the majority of those
afflicted. These individuals have been in one way or another handling or having
contact with sick swine. A few cases have been documented in individuals
attending a fair or people working in the swine industry, such as farmers, and also veterinarians. There have been a limited
number of person-to-person transmissions. Health officials point out that this flu is <b>not a foodborne illness</b>.
Instead, it spreads like any other flu: someone sneezes or coughs,
spreading the virus to other mammals (humans included) and onto
surfaces.</div>
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<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif;">
- This is a new Variant strain of Swine Influenza possibly as
a result of an individual harboring concomitant strains. According to the CDC, human
infections with H1N1v, H3N2v and H1N2v viruses have been detected in the United
States.<span style="mso-spacerun: yes;"> </span>The “v” at the end of the strain
name stands for “variant.” So, what to do for now is for swine handlers and
others exposed to sick pigs is to practice strict precautions such as:</div>
<div class="MsoNoSpacing">
<br /></div>
<ol>
<li><span style="mso-spacerun: yes;"><span style="font-family: Verdana,sans-serif;"></span></span><span style="font-family: Verdana,sans-serif;">-Wash your hands with soap and water before and after touching pigs.</span></li>
<li style="font-family: Verdana,sans-serif;">-Don't drink or eat near pigs,
and don't take food into animal areas.</li>
<li style="font-family: Verdana,sans-serif;">-Avoiding contact with animals
such as pigs may be the best protection if you are among<span style="mso-spacerun: yes;"> </span>those likely to suffer severe symptoms if
you get the flu: people with lung disease or diabetes, for instance. </li>
</ol>
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<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- H3N2
flu viruses are common among pigs. H3N2 viruses are a subgroup of influenza A
viruses, and they are known to adapt in humans. This new version has picked up
a gene from the H1N1 virus that became a pandemic a couple of years ago. This variant
infection can occur if the person or animal has had a<span style="mso-spacerun: yes;"> </span>concomitant <span style="mso-spacerun: yes;"> </span>exposure to both viruses. The H1N1 serves as a
“matrix gene” from which the H3N2 picks up a novel gene. </div>
<div class="MsoNoSpacing" style="text-align: justify;">
<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- This variant of swine flu was
detected in 2010, according to an authority at the U.S. Department of
Agriculture. The human cases started to show up in mid-2011. The regular
seasonal flu vaccine contains a strain of the A-flu virus group, but it will
not prevent you from getting sick if you come into contact with the new flu
strain.</div>
<div class="MsoNoSpacing" style="text-align: justify;">
<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- The CDC posted this info on
Dec. 23, 2011, on their Morbidity and Mortality Weekly Report. (<a href="http://www.cdc.gov/mmwr">http://www.cdc.gov/mmwr</a>).</div>
<div class="MsoNoSpacing" style="text-align: justify;">
<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- From August 17 to December 23,
2011, CDC received reports of 12 human infections with influenza A (H3N2)v
viruses that have the matrix (M) gene from the influenza A (H1N1)pdm09 virus
(formerly called swine-origin influenza A [H3N2] and pandemic influenza A
[H1N1] 2009 viruses, respectively. The
12 cases occurred in five states (Indiana, Iowa, Maine, Pennsylvania, and West
Virginia), and 11 were in children. Six of the 12 patients had no identified recent exposure to swine. Three of the
12 patients were hospitalized, and all have recovered fully.</div>
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<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- A case in an adult male in
Indiana with occupational exposure to swine was among the 12, and two children
in West Virginia who regularly attended the same day care accounted for the
latest cases. This report describes those cases and swine influenza virus (SIV)
surveillance being conducted by the U.S. Department of Agriculture (USDA).
Cases of Swine Influenza are not that common. However these new cases bring into
question not only our understanding of this new virus, but also the new modes
of transmission we are still beginning to witness.</div>
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<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- According to the CDC
authorities, Guidance materials for persons who work with swine have been
published by OSHA.<span class="superscript"></span> In addition, the National
Pork Board, **CDC, and the National Association of State Public Health
Veterinarians have published guidance for persons exposed to swine in public
settings. Clinicians should consider variant influenza virus infection in the
differential diagnosis of patients with febrile respiratory illness who have
been near swine whether at work or at an agricultural event, such as a fair or
exhibit.</div>
<div class="MsoNoSpacing" style="text-align: justify;">
<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- To date, serologic studies in
children have not demonstrated a previous immunity to this virus which started
appearing in the 1990s. Young adults may not be prepared for this either. The
hemagglutinin genes of these viruses are related to human influenza A (H3N2). Certain
persons, including young children, pregnant women, persons with chronic health
conditions such as asthma, diabetes, or heart and lung disease, and persons
aged ≥65 years, are likely to be at greater risk for serious influenza-related
complications from variant influenza viruses such as influenza A (H3N2)v.</div>
<div class="MsoNoSpacing" style="text-align: justify;">
<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- The current Seasonal Influenza
vaccines are not likely to provide protection from this variant strain. Guidance
documents related to A(H3N2)v viruses are available online from CDC at <a href="http://www.cdc.gov/flu/swineflu/influenza-variant-viruses.htm">http://www.cdc.gov/flu/swineflu/influenza-variant-viruses.htm</a>.</div>
<div class="MsoNoSpacing" style="text-align: justify;">
<br /></div>
<div class="MsoNoSpacing" style="font-family: Verdana,sans-serif; text-align: justify;">
- To protect yourself, the CDC
has also put out a detailed <span style="mso-spacerun: yes;"> </span>fact sheet on
their site:<b> </b><span style="font-size: 12.0pt;">you can check it out at<b> <a href="http://www.cdc.gov/flu/swineflu/h3n2v-factsheet.htm"><span style="font-weight: normal;">http://www.cdc.gov/flu/swineflu/h3n2v-factsheet.htm</span></a></b></span></div>
<div class="MsoNoSpacing" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
- An updated official health advisory issued on Aug. 3, 20212
can be viewed here on the Health Alert Network: <span style="mso-spacerun: yes;"> </span><a href="http://www.bt.cdc.gov/HAN/han00325.asp">http://www.bt.cdc.gov/HAN/han00325.asp</a></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
A total of 145 cases of infection with influenza A (H3N2v)
variant virus have been confirmed by CDC since outbreaks began in July 2012,
the agency reported today (Aug.9, 2012) during a telebriefing. The total
includes 113 cases in Indiana, 30 cases in Ohio, and 1 case each in Hawaii and
Illinois.There have been no reported deaths from this outbreak. Nevertheless,
the CDC has posted the precautionary measures on their site. The usual
influenza vaccine offers no protection. At this point, no evidence exists for
sustained human-to-human spread of H3N2v in the community, and CDC does not
consider it to be a pandemic situation. Preliminary steps have been taken to develop a vaccine for the new H3N2 swine flu strain, a CDC official said</div>
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<br /></div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGHQSn6sbOCvuPThmwWBOEv4Omg_0x6QCN0K6XBjeKH2iU-LEIM3dn2y1vGWBkHVsHqadk1ZrvwZT-BAEDBM_jnzHHKNcOP1Sv2H9sPCMcWYm009FyZR-R03wKJARLkGBzYH7oDe-rayDG/s1600/CDC-11214-swine-flu-websml.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGHQSn6sbOCvuPThmwWBOEv4Omg_0x6QCN0K6XBjeKH2iU-LEIM3dn2y1vGWBkHVsHqadk1ZrvwZT-BAEDBM_jnzHHKNcOP1Sv2H9sPCMcWYm009FyZR-R03wKJARLkGBzYH7oDe-rayDG/s320/CDC-11214-swine-flu-websml.gif" width="272" /></a></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: left;">
<span class="description"> This colorized negative stained transmission
electron micrograph (TEM) depicted some of the ultrastructural
morphology of the A/CA/4/09 swine flu virus.</span></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: left;">
<span style="font-size: x-small;"><span class="description">Source: </span><a class="external free" href="http://www.cdc.gov/media/subtopic/library/diseases.htm" rel="nofollow">http://www.cdc.gov/media/subtopic/library/diseases.htm</a> (<a class="external text" href="http://phil.cdc.gov/PHIL_Images/11214/11214.tif" rel="nofollow">Original .tif</a>)</span></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif; text-align: left;">
<span style="font-size: x-small;">Author: Photo Credit: C. S. Goldsmith and A. Balish, CDC</span></div>
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<br /></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<span style="font-size: small;"><span style="line-height: 115%;">Swine Flu
in Asia</span></span></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<span style="color: black;"> - There have been reports of the
swine influenza in Vietnam in February of this year. Vietnam has released
sequences from swine trH3N2, and Hong Kong has recently released sequences from
swine cases which have Asian H3 and N2 on isolates with H1N1pdm09 internal
genes. The H3 sequences in Hong Kong and China (Guangxi) are similar to
those reported in Vietnam, and are easily distinguished from US cases. In the
US, all H3N2v cases were identified after the start of the 2009 pandemic.</span></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<span style="color: black;"> - Of course a match of the H3N2v in
Vietnam with the US cases would support widespread human transmission and
provide more evidence for an emerging pandemic. A match of Asian H3 would
signal more lineages / constellations of swine H3N2v cases which can jump to
humans.</span></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<span style="color: #330033;"> - Recombinomics' first paper,
"Swine Influenza A Evolution via Recombination - Genetic Drift
Reservoir" is available at Nature Procedings
(where it can be downloaded). Recombinomics will be submitting a number of
papers on recombination, which will conclusively demonstrate the role of
recombination in influenza evolution. These papers will <a href="http://www.recombinomics.com/News/04260701/H5N1_Tenet_Egypt.html">significantly
impact</a> the two basic tenets of influenza genetics, drift via "random
mutation", and shift via reassortment. Recombinomic’s website is at <a href="http://www.recombinomics.com/publications.html">http://www.recombinomics.com/publications.html</a></span></div>
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<br /></div>
<div class="MsoNormal" style="font-family: Verdana,sans-serif;">
<span style="color: #330033;"> - Also take a look at the FluBoard
site (Flu Tracker Forum): <a href="http://fluboard.rhizalabs.com/forum/viewtopic.php?f=5&t=7950">http://fluboard.rhizalabs.com/forum/viewtopic.php?f=5&t=7950</a></span></div>
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<br /></div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6Z7xgNDblucH4r_mQxhvD0eS1ot18qVvZ7WIU_IgkrkKh8goB1CheE6N7jlYpVBX6A9OH7Ga8-_Qe4CETQxHRgLQRNgwCzX9Lq3bANtBD-YoEhafEB8ayZDiIVWRQmGxbZZunXzq0Wif_/s1600/MP900443508-flu-masks.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="212" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6Z7xgNDblucH4r_mQxhvD0eS1ot18qVvZ7WIU_IgkrkKh8goB1CheE6N7jlYpVBX6A9OH7Ga8-_Qe4CETQxHRgLQRNgwCzX9Lq3bANtBD-YoEhafEB8ayZDiIVWRQmGxbZZunXzq0Wif_/s320/MP900443508-flu-masks.jpg" width="320" /></a></div>
<br />
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<span style="color: #330033;"> Preparedness is better than worriedness.</span></div>
<br />
<br />
<br />
<span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">A Bit of History and Development</span></span><br />
<br />
<div class="MsoNormal">
<span style="color: #330033;"> -<span style="font-family: Verdana,sans-serif;"> Viruses have been reported since the beginning of the 19th century. Then they were just known to be bacterial killers. The British bacteriologist Ernest H. Hankin reported in 1896 that the waters of the Jumna and Ganges rivers in India killed Vibrio cholerae bacteria. The responsible agent passed bacteriological filters and was destroyed by boiling. Then, in 1898, the Russian microbiologist Nikolai Gamaleya reported the lysis of Bacillus anthracis bacteria by a transmissible ‘ferment’. It is probable that these scientists would have discovered bacterial viruses, if suitable techniques<br />had been available.</span></span></div>
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<span style="color: #330033;"><span style="font-family: Verdana,sans-serif;">- The present period of phage research started in 1965 after D. E. Bradley published a seminal, still cited paper on phage morphology (republished in 1967). Novel phages were thereafter isolated at a rate of a 100 per year. Studies on their properties and manner of transmission have been rigorously investigated. It should be noted though, that these organisms exist in our environment in an ecosystem that makes them part of the normal life of animals, plants, and includes marine life. History shows that the study of virus infections of plants has led the overall subject of virology in the development of several major concepts including that of the entity of viruses<br />themselves. We learn for example that, in order for a plant virus to infect its host systemically, it must be capable of hijacking the host’s cellular machinery<br />to replicate and move from the initially infected cell. Once inside a cell, the virus initiates transcription (DNA viruses) and translation and replication (DNA and RNA viruses) activities. </span></span></div>
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<span style="color: #330033;"><span style="font-family: Verdana,sans-serif;"> - While there are many facets of virology studies, one particular aspect has been mentioned in this post. And that is, the molecular basis for variability and evolution in viruses, including the recognition that recombination is a widespread phenomenon among RNA viruses and that viruses can acquire host nucleotide sequences. </span></span><span style="font-family: Verdana,sans-serif;">Notable human diseases caused by RNA viruses include </span><a class="mw-redirect" href="http://en.wikipedia.org/wiki/SARS" style="font-family: Verdana,sans-serif;" title="SARS">SARS</a><span style="font-family: Verdana,sans-serif;">, </span><a href="http://en.wikipedia.org/wiki/Influenza" style="font-family: Verdana,sans-serif;" title="Influenza">influenza</a><span style="font-family: Verdana,sans-serif;">, </span><a href="http://en.wikipedia.org/wiki/Hepatitis_C" style="font-family: Verdana,sans-serif;" title="Hepatitis C">hepatitis C</a><span style="font-family: Verdana,sans-serif;">, </span><a class="mw-redirect" href="http://en.wikipedia.org/wiki/West_Nile_fever" style="font-family: Verdana,sans-serif;" title="West Nile fever">West Nile fever</a><span style="font-family: Verdana,sans-serif;"> and </span><a class="mw-redirect" href="http://en.wikipedia.org/wiki/Polio" style="font-family: Verdana,sans-serif;" title="Polio">polio</a><span style="font-family: Verdana,sans-serif;">. Viruses with RNA as their genetic material but which include DNA intermediates in their replication cycle are called retroviruses, which include </span><a href="http://en.wikipedia.org/wiki/HIV" style="font-family: Verdana,sans-serif;" title="HIV">HIV</a><span style="font-family: Verdana,sans-serif;">-1 and </span><a class="mw-redirect" href="http://en.wikipedia.org/wiki/HIV-2" style="font-family: Verdana,sans-serif;" title="HIV-2">HIV-2.</a></div>
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<span style="font-family: Verdana,sans-serif;">For an exhaustive listing of viruses, check out the</span><a href="http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi?mode=&term=RNA+Viruses&field=entry" style="font-family: Verdana,sans-serif;" target="_blank"> MeSH site.</a><span style="font-family: Verdana,sans-serif;"> </span>
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<span style="color: #330033;"><span style="font-family: Verdana,sans-serif;"> - There are now many examples of species-specific RNAvirus / host coevolution, indicating very slow rates of virus evolution. One example is Hantavirus (genus Bunyavirus) coevolution with its rodent host, that suggests a 20 million year association. Not all RNA virus populations show this dynamic of a continual change or even the diversity expected from quasispecies. Even in influenza virus A, avian isolates from natural host (waterfowl) can be genetically stable. </span></span></div>
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<span style="color: #330033;"><span style="font-family: Verdana,sans-serif;"> - Influenza vaccine has been the source of a number of issues related to safety over the years. Mass immunization against swine-like influenza was carried out in 1976–77 using the A/New Jersey swine-influenza vaccine. At first, it appeared that this vaccine generated an increased risk of acquiring vaccine-related Guillain–Barre syndrome (GBS).</span> In contrast, the 1978–79 influenza vaccine was not associated with a statistically significant excess risk of GBS. Although the original Centers for Disease Control study of the relation between A/New Jersey/8/76 (swine flu) vaccine and GBS demonstrated a statistical association and suggested a causal relation between the two events, controversy has persisted. There was no increase in the risk of vaccine-associated GBS from 1992–93 to 1993–94. A number of events in recent years has provoked concern that certain vaccines might be unsafe. Most of these concerns have proved to be unfounded, and some remain unproven or incompletely understood. Nevertheless, the U.S. FDA regularly advise regarding any injectable medication for any unwanted or deleterious ingredient. Sometimes, the medication in and of itself is beneficial, but the preservatives or packaging may be at fault and warrant that the product be withdrawn from the market.</span></div>
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<span style="color: #330033;"> - The design and manufacture of vaccines are of such high standards today that they have become extremely safe. But it will never be possible to say that everything is known about the subject and that vaccines are totally safe. Nor can the unpredictable human element in administration ever be totally excluded from the equation. </span></div>
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<span style="color: #330033;"> - The problem also lies however in media coverage that is hyperbolic and inaccurate, and instead of educating the public, they create panic. This is irresponsible on their part.</span></div>
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<span style="color: #330033;"> - New technologies will complement existing safety measures. However, communicating to vaccine recipients or their parents that the vaccine they are about to receive is neither totally effective nor totally safe makes health pro-<br />fessionals uncomfortable. They should explain to these worried parents and patients that the risk of potential harm with the vaccine is nothing compared to the actual disease. As time and experts continue to unravel the whole role of viruses in our lives, we can expect better protection, disease control, and treatment. </span>The incremental process involves finding a good vaccine candidate,
reassessing and testing the virus, developing seed vaccines and ensuring
their safety. The goal is to have a vaccine quickly available in case a
pandemic occurs, as with H1N1 in 2009.</div>
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<span style="color: #330033;"> - Stay safe. And have a nice day!</span></div>
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<span style="color: #330033;"> - Fernando Yaakov Lalana, M.D. </span></div>
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<br />Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-91674437951135388932012-08-08T14:15:00.001-04:002012-08-08T14:29:19.784-04:00<div class="separator" style="clear: both; text-align: center;">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-6wZ_YSFhUlcWA4y3uFyOBa9B96uCUTCR6QoYprAtgBbtgZHZOeN8g_Hz-U61KcQs5_Tt88ycu4-PuDTyPovozKLBD0FCTgIjIx6HHi2E-7hT-Le89G70wvbeCUiGxiSfoNSHzu0K3jM0/s1600/MP900185162-doc_syringe.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-6wZ_YSFhUlcWA4y3uFyOBa9B96uCUTCR6QoYprAtgBbtgZHZOeN8g_Hz-U61KcQs5_Tt88ycu4-PuDTyPovozKLBD0FCTgIjIx6HHi2E-7hT-Le89G70wvbeCUiGxiSfoNSHzu0K3jM0/s320/MP900185162-doc_syringe.jpg" width="218" /></a><span style="font-size: large;"><span style="line-height: 115%;"> Shot in the
arm: for the Patient?,</span></span></div>
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<span style="font-size: large;"><span style="line-height: 115%;"> for Pharma?, or for Both!?</span></span></div>
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- New vaccines and drugs are developed and made available
only after rigorous study, stringent methodologies, human effort, and enormous cost,
not to mention long nights in the lab. From a good idea or concept, to the
marketing phase of a new treatment, every step is laden with eureka moments as
well as downsides. Considering that we are in the age of new technology and
discovery, the number of new drugs approved has declined progressively in the
past decades. Billions of dollars are allocated for research and development,
and yet, the proportion of budget to production has not been compensatory. As a
matter of fact, all the “drug dollars” do not necessarily imply phenomenal pharmaceutical developments. Some things have lagged behind:definitely not ideas,
but rather the management of resources, methods, and the sub-optimal analyses of mountains of
data. But that is changing now, with the
advent of number crunching SaaS (Software-as-a-Service), PaaS
(Platform-as-a-Service) , and the systematic analysis of data that is either structured, loosely
structured, or unstructured. This is being done using new algorithms, improved programming languages, hardware,
and interfaces.</div>
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- In Medical School of past days, prospective M.D.s were
taught how to concoct cough syrup almost like an alchemist’s recipe. <b>(Do not try this at home!) </b>Of course, eventually the proud Medical Student would be beaming
with an explorer’s wonder. Well, as it goes, you could buy these compounds pre-packaged, over-the-counter at your favorite drugstore. But it was a great
achievement to be able to explore one’s own process of discovery. This element of
curiosity combined with guided instructions (and trial and error, or
experimentation) would be the hallmark of Pharma R&D. Nowadays,
pharmaceutical set-ups “hire” IT companies who specialize in the management of data
and costs that are an ever-present challenge. Budgets may be tighter now due to the
recession and this predicament actually compels drug developers to work smarter
and safer.</div>
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- Doctors and Pharma Professionals now team up with Medical
Informatics groups to make the most of the development process. This may mean
that a potential drug is either dropped totally at some point in the trial, thereby not
wasting any resources, or it continues towards the progressive trial phases.
The phases start with <a href="http://en.wikipedia.org/wiki/Drug_design" title="Drug design"><span style="color: windowtext; text-decoration: none; text-underline: none;">drug design</span></a> and <a href="http://en.wikipedia.org/wiki/Drug_discovery" title="Drug discovery"><span style="color: windowtext; text-decoration: none; text-underline: none;">drug
discovery</span></a>, go on to <a href="http://en.wikipedia.org/wiki/Animal_testing" title="Animal testing"><span style="color: windowtext; text-decoration: none; text-underline: none;">animal
testing</span></a>, then begin with testing in only a few selected <a href="http://en.wikipedia.org/wiki/Human_subject_research" title="Human subject research"><span style="color: windowtext; text-decoration: none; text-underline: none;">human subjects.</span></a> A good protocol design is necessary. If there has been no peril to the patient/s or "failure" of a drug candidate, or any undesirable effect, they then expand to test in many
study participants. If initial data look promising, the drug company can start working on submission of preliminary data to the Drug Safety and Regulatory Boards. All this effort leads
towards cure or amelioration of the pathologic condition, without sacrificing patient safety. Investigator/s' biases have to be set aside completely. (This may be debatable, considering nobody has absolute zero biases.) Financial disclosure must be revealed to authorities or to the public readership. Premature conclusions should not be announced to the news media carelessly. This has led to public confusion and even panic at times. </div>
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- With these goals
in mind, Doctors, and Pharmacologists (as well as Toxicologists) are now
embracing Medical Informatics well beyond the scope of the basic Electronic Health Record. The
enhanced abilities of drug development teams enable them to demonstrate to sponsors, giving them a
better understanding of the scope and significance of the drug in mind. In
effect, it is basically a kind of business proposal geared towards a humane
purpose and the rationalization of costs. Return on Investment (ROI) in terms of helping the community that needs the drug, and the financial reward are both imperative in the eyes of sponsors and stakeholders of the company. After all, we are all partners in this endeavor.</div>
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- The development of genomics and use of
biomarkers have consequently led to the process of pharmacogenomics. In this process, the
likelihood of cure is increased due to the pinpoint target concept. Genomics is
moving slowly but steadily year by year now. And let’s not forget stem cell
technology. Accumulating evidence is demonstrating that we need a paradigm
shift in mode of treatment. Possibly, within 5 years, we will see a jump in the
number of biological, proteomic, and nanovector (and virusvector) treatments,
all of these pointing to highly defined molecular targets. Nevertheless, whether
chemical, or molecular, Big Data from clinical trials and post-market vigilance is posing a tremendous challenge to analysts.
When it comes to data crunching, we have the offline spreadsheet type of tools,
or programs like <a href="http://www-01.ibm.com/software/analytics/spss/products/statistics/" target="_blank">SPSS</a> and <a href="http://www.sas.com/" target="_blank">SAS</a>, where we carry out our robust statistical calculations.
Now, online and cloud based services can equip us to handle mountains of data.
Some of these programs are geared towards clinical trials, while others such as <a href="http://www.openepi.com/OE2.3/Menu/OpenEpiMenu.htm" target="_blank">OpenEpi</a>, analyze
epidemiologic trends. You can find a number of free statistics programs <a href="http://freestatistics.altervista.org/en/stat.php" target="_blank">here</a>. Clinical trial protocols have become far more complex
during the past decade. Both clinical and epidemiologic study data are currently
subjected to more rigorous scrutiny by either new algorithms or graphic
mathematical procedures like meta-analyses. New programming languages are utilized and expanded
with the purpose of making all the data more relevant. Languages like <a href="http://www.r-project.org/" target="_blank">R</a>, <a href="http://www.ruby-lang.org/en/" target="_blank">Ruby</a>, <a href="http://www.python.org/" target="_blank">Python</a>,
<a href="http://www.java.com/en/" target="_blank">Java</a> (<a href="http://www.jython.org/" target="_blank">Jython</a> too), and even <a href="http://www.mathworks.com/products/matlab/" target="_blank">Matlab</a> are being used in ways that enhance our analytic
processes.</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhN82RcwY-qzTjXUVHUXXI93M3vrPvmPTM3dtisnCqNzpqcERFC243fnF31Lv12gIeLZC5AM8SWcECVKi5dYGB_aR-zuUxvafX6ubjPmzgFf1GapSl5ow1Tj1biw1a-smuy6VhUUIZkAYWz/s1600/MP900403584_tabs_pills-sml.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="251" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhN82RcwY-qzTjXUVHUXXI93M3vrPvmPTM3dtisnCqNzpqcERFC243fnF31Lv12gIeLZC5AM8SWcECVKi5dYGB_aR-zuUxvafX6ubjPmzgFf1GapSl5ow1Tj1biw1a-smuy6VhUUIZkAYWz/s320/MP900403584_tabs_pills-sml.jpg" width="320" /></a></div>
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<span style="font-family: Verdana,sans-serif;">- For example, one data
analysis group of consultants is <a href="http://www.mdsol.com/" target="_blank">Medidata Solutions</a></span><span style="font-family: Verdana,sans-serif;"> providing cost databases for clinical
trial analysis and “advanced reporting and analytics to drive clinical
development efficiencies.“ <a href="http://www.modgraph.co.uk/" target="_blank">ModgraphConsultants </a>Ltd. an international software company specializing in the
pharmaceutical industry, is offering software solutions in chemistry, cheminformatics
and molecular modeling</span><span style="font-family: Verdana,sans-serif;">.
Pharmaceutical departments are mostly
serving drug development projects. Systematic and secure document handling is of utmost
importance. These documents, recording all the processes and developments of the
drug in focus, have to be treated just
like any top-level dossier. This leads to an improvement in production and lesser
time-to-market. Drug companies as well
as the Regulatory Safety Boards in each country and continent also have to
consider post-market information, and adverse drug effects (ADE) recording and
collating. An example of such a service is the <a href="http://www.infotenha.com/" target="_blank">Infotenha Group</a></span><span style="font-family: Verdana,sans-serif;"> who, with their software
suite as their complete solution, “manage information dealing with </span><span style="font-family: Verdana,sans-serif; font-size: 12pt;">regulatory affairs, </span><span style="font-family: Verdana,sans-serif;">quality assurance / quality
control, Research & Development and Pharmacovigilance</span>.”</div>
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Drug companies have to increasingly adhere to auditing
activities and security protocols in their IT ecosystems. The U.S. F.D.A. has laid out <a href="http://www.blogger.com/%28http://www.fda.gov/ScienceResearch/SpecialTopics/RunningClinicalTrials/GuidancesInformationSheetsandNotices/ucm113709.htm%29" target="_blank">Guidelines for clinical trials</a> . You can check out this excellent <a href="https://docs.google.com/file/d/1wZmMkpRQNn03VfYN0mwywvIOZNZgoak3PlX4zNo4WFYmDr_OPb6544jFTYpy/edit" target="_blank">article on MRM</a>.This ensures that no stone is unturned and no leak unplugged. Drug discovery is
going through exciting times and new treatments and cures are becoming more promising, provided that the Medical and Pharma Communities meld with IT folks,
and cooperate in a new unified paradigm. At any rate, I think that this
approach will save us unnecessary losses, and push us further on towards great
heights.</div>
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<span style="font-size: 12.0pt;">- Hippocrates</span> (c. 460
BC – c. 370 BC)</div>
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<i><span style="font-size: 12pt;"> </span><span style="font-family: "Trebuchet MS",sans-serif; font-size: 12pt;"><span style="mso-spacerun: yes;"> </span>(Translated from the original Greek)</span></i></div>
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<i><span style="font-size: 12pt;">Vita brevis,</span><span style="font-size: 12pt;"></span></i></div>
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<i><span style="font-size: 12pt;">ars longa,</span><span style="font-size: 12pt;"></span></i></div>
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<i><span style="font-size: 12pt;">occasio praeceps,</span><span style="font-size: 12pt;"></span></i></div>
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<i><span style="font-size: 12pt;">experimentum periculosum,</span><span style="font-size: 12pt;"></span></i></div>
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<i><span style="font-size: 12pt;">iudicium difficile.</span></i></div>
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<i><span style="font-size: 12.0pt;"> Translated:</span></i></div>
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<i><span style="font-size: small;">Life is short,</span></i></div>
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<i><span style="font-size: small;">and Art long,</span></i></div>
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<i><span style="font-size: small;">opportunity fleeting,</span></i></div>
<div style="font-family: "Helvetica Neue",Arial,Helvetica,sans-serif; text-align: left;">
<i><span style="font-size: small;"><span style="line-height: 115%;"> experience perilous.</span></span></i></div>
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<i><span style="font-size: small;"><span style="line-height: 115%;"> - </span></span></i><span style="font-size: small;"><span style="line-height: 115%;">Keep moving forward and change the world. And remember, the patient is THE MOST IMPORTANT CLIENT! They deserve our very best.</span></span><i><span style="font-size: small;"><span style="line-height: 115%;"></span></span></i></div>
<div style="font-family: "Helvetica Neue",Arial,Helvetica,sans-serif; text-align: left;">
<i><span style="font-size: small;"><span style="line-height: 115%;"><br /></span></span></i></div>
<div style="font-family: "Helvetica Neue",Arial,Helvetica,sans-serif; text-align: left;">
<i><span style="font-size: small;"><span style="line-height: 115%;">- </span></span></i><span style="font-size: small;"><span style="line-height: 115%;">Fernando Yaakov Lalana, M.D.</span></span><i><span style="font-size: small;"><span style="line-height: 115%;"><br /></span></span></i></div>Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com0tag:blogger.com,1999:blog-3192755943215745075.post-57026498663387962642012-08-06T07:17:00.000-04:002012-08-06T07:48:31.711-04:00<br />
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<span style="font-size: 14pt; line-height: 115%;"> </span><span style="font-size: 14pt; line-height: 115%;">Ebola Outbreak:
<i>The Good, </i></span></div>
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<span style="font-size: 14pt; line-height: 115%;"><i> The Bad, and The Ugly</i> </span></div>
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<span style="font-size: small; line-height: 115%;">- What’s good
is that the Ebola episode is currently being controlled in the sense that all
persons who have had contact with patients have been isolated. This is
according to the WHO representative in Uganda, in effect halting the spread
of the deadly disease. The “contact list” is short under 200 individuals. The
CDC, WHO and the Doctors Without Borders have joined forces in helping Ugandan
officials to control the spread of Ebola. </span></div>
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<span style="font-size: small; line-height: 115%;">- Sadly, the first fatality was a three-month-old girl. As a matter of fact, over a
dozen participants in the funeral were infected.
The other bad and sad part is that at least 16 people have already succumbed to the
disease. Since then, authorities have taken bold steps in disposing or burying of the bodies.The ugly part is that the doctors were initially unaware of what they
were dealing with because the symptoms were atypical. They expected bloody
sputum which is a hallmark sign of Ebola. The outbreak was confirmed on July
28, </span><span style="font-size: small;">several days after villagers were dying in a remote corner of
western Uganda. The disease spread to more villages deep in the western
district of Kibaale because of the slow response in identifying the Ebola
culprit. </span><span style="font-size: small; line-height: 115%;">As of July 31, 2012,
there have been at least 38 cases and 16 deaths.</span></div>
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<span style="font-size: small; line-height: 115%;">- The highly
infectious and lethal Ebola virus was first identified in 1976 in Congo and was
named after a river in that area. This current outbreak appears to have started
in June of this year. Then on July 28, the Uganda
Virus Research Institute/CDC confirmed the outbreak. Because testing was
able to be done in-country at the new UVRI/CDC lab, instead of the out-of-town
rigmarole, the disease was identified and proper measures were taken. Better
late than never, we could say. Remember, this is a case of the Ebola Sudan
virus strain. The disease is native to African territories. It is spread by
direct contact with body fluids and blood of a person infected with Ebola
virus. It is also spread by contact with a contaminated object or
infected animal. Symptoms include fever, headache, joint and muscle aches, sore
throat, and weakness, followed by diarrhea, vomiting, and stomach pain. Skin
rash, red eyes, and internal and external bleeding may be seen in some
patients. </span><span style="font-size: small;">Endothelial cells, mononuclear phagocytes,
and hepatocytes
are the main targets of infection.</span><span style="font-size: small;"> After infection, in a
secreted glycoprotein, the Ebola virus glycoprotein is synthesized. Ebola
replication overwhelms protein synthesis of infected cells and host immune
defenses. Infected white blood cells also serve as carriers to transport the
virus throughout the entire body to places such as the lymph nodes, liver,
lungs, and spleen.</span></div>
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<span style="font-size: small; line-height: 115%;">- All epidemics of Ebola have occurred in
sub-optimal hospital conditions, </span><span style="font-size: small;">where practices of basic hygiene and
sanitation are often either luxuries or unknown to caretakers and where
disposable needles and sterilization equipment are unavailable or too expensive. In
modern hospitals with complete facilities, from nursing barriers to high-alert
procedures, there has not been any uncontrolled spread of this dreaded
affliction. </span><span style="font-size: small; line-height: 115%;">Researchers believe that the virus is
normally maintained in an animal host (zoonotic) that is native to the African
continent. The natural habitat, local conditions, and host animal is poorly
understood. Fruit bats have been suspected as carriers. In 2005, </span><span style="font-size: small;">researchers
had found evidence of Ebola infection in three species of fruit bats. But other
sources have been investigated, from plants, arthropods, to non-human primates.</span></div>
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<b><span lang="EN" style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-ansi-language: EN; mso-fareast-font-family: "Times New Roman";"> </span></b><span lang="EN" style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-ansi-language: EN; mso-fareast-font-family: "Times New Roman";"><span style="font-size: small;"><span style="font-family: Verdana,sans-serif;">Biosafety
level 4 hazmat suit: researcher is working with the Ebola virus.</span></span></span></div>
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<span style="font-size: small;"> <span style="font-size: x-small;"> Date: 21 September 2011 </span></span></div>
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<span style="font-size: x-small;"> Source: <a href="http://www.sciencenewsline.com/medicine/2010052012000036.html"><span style="color: blue;">http://www.sciencenewsline.com/medicine/2010052012000036.html</span></a> </span></div>
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<span style="font-size: x-small;"> Author: United States Army Medical Research Institute of Infectious Disease</span></div>
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<span style="font-size: 12pt;">- Confirmed cases of Ebola virus infections have
been reported in </span><span style="font-size: 12.0pt; mso-ascii-font-family: Calibri; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-hansi-font-family: Calibri;">the Democratic Republic of the Congo, Gabon,</span><span style="font-size: 12pt;"> </span><span style="font-size: 12.0pt; mso-ascii-font-family: Calibri; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-hansi-font-family: Calibri;">Sudan, the Ivory Coast,</span><span style="font-size: 12pt;"> and </span><span style="font-size: 12.0pt; mso-ascii-font-family: Calibri; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-hansi-font-family: Calibri;">Uganda. So, travellers take heed and
avoid contact. If you intend to help out in these areas, it would be best to consult the local health authorities first. Likewise, contact the WHO, CDC or Medicine Sans Frontiers, as well as the Uganda Virus Research Institute. If you have had contact with patients or infected material, report to the said authorities without delay.</span></div>
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<span style="font-size: 12pt;">- Fernando Yaakov Lalana, M.D.</span></div>Doc F. V. Lalanahttp://www.blogger.com/profile/16465485421459130802noreply@blogger.com2