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Showing posts from 2011

Increased arterial tortuosity in hypertensives

My co-authors and I published a peer reviewed journal paper developing a method to measure  arterial tortuosity and validated the method by measuring an increase in tortuosity in a hypertensive population. The idea is that vascular disease may twist the arteries and we developed a method to measure this twisting. Other significant findings included the use of interpolating lower resolution images to higher resolution in order to compare images taking at different resolution. This is important because it allows comparison of existing images. Researchers won't have to reimage patients all at the same resolution reducing the cost of conducting research and clinically patients can be tracked over time even if different medical imaging equipment and resolutions are used. The full article is here: http://www.biomedcentral.com/1471-2105/12/S10/S15

Liberal Sciences

The recession set off discussions on the value of a humanities or liberal arts education[ 1 ]. The argument against a liberal arts education is that students accumulate debt to get the degree and then can't get a job to pay it off. The argument for a liberal arts education is that it creates global citizens that can use their broad skills to do anything. I don't think a liberal arts education is so broad compared to more technical or scientific degrees. Our world is very technological. How can an education be broad and enable students to go do anything if it doesn't include technical and mathematical skills? Computers and the Internet are such a big part of our lives now. I think a liberal arts education should include learning the basics of computer programming because anyone in any career will use computer tools that have computer control interface that is a lot like computer programming. I have seen professors of music using computer software to compose music. Englis

Alternatives to academic research for PhD

There are so many news articles lately on the value of college degrees. Of particular importance to me is the value of a science PhD. The basic problem is that there are too many science PhDs for traditional tenure track academic research positions. The number of PhDs generated at universities is based on available funding and the need for (cheap) labor for research projects, not on the job market for tenure track academic research positions. If PhD programs prepare students for other kinds of careers I don't think this is a problem. It really isn't a problem if PhD researchers are trained to transfer new technologies into new business ventures. That way some new PhDs will create new businesses to employ PhD scientists outside of academia. I have seen some suggestions that universities should grant more masters and less PhDs. Then the masters can pursue research careers. The problem I see with this is the PhDs are more likely to gain the top leadership positions. This  would

Biologics are the future of drug development

Drug development expenses have been going up while FDA approvals of new drug treatments have been going down. We know more about biology now than in the past so this increased understanding should make us more efficient and effective at finding new and improved treatments. This could be a low hanging fruit problem where we found the easier treatments and new treatment are getting harder to find. One of the main problems stopping new drug treatment approvals is side effects. To develop new drugs we identify a gene->protein target in a disease pathway, develop an assay that measures the activity of the gene->protein and test chemicals that down regulate or up regulate the gene target that affect other genes->proteins as little as possible. Finding a chemical compound that only affects the target and nothing else is quite difficult. A non-repetitive sequence of 20-25 nucleic acid base pairs is unique in the human genome. This means a biologic drug like an siRNA, anti-sense RN

Medical informatics aligned with health costs

I have been asked if medical informatics, computers and software in medicine, the field I am getting a PhD in, can reduce medical costs. I think medical informatics CAN reduce medical costs with emphasis on CAN if and only if there is motivation to use computers and software to reduce medical costs. Computer systems can track, remind, enable reuse of medical data like images, increase efficiency, reduce errors, determine the most cost effective treatments - reducing costs. All these good things ONLY end up reducing costs if our medical system is structured to motivate the stakeholders involved to reduce costs. I have heard one use of electronic medical records to increase the bill. It turns out when you go to the hospital and a dizzying assortment of physicians, nurses and medical specialists visit you and you receive a separate bill from almost every single person that saw you, they often forget to bill you for something. Electronic medical record systems can be used to make sure no

Prefer building software libraries to platforms

Build software as libraries. Prefer libraries to platforms. A library is made up of reusable functions, classes and objects that software developers include in their projects. And multiple libraries can be reused in the software developer's projects. A platform is often designed as software that gives software developers lots of features to reuse but makes  software developers add their project to the platform; the reverse of the library. Adding libraries to software developers' projects has many advantages to adding the project to the platform. Many libraries with different functionality can be combined together in the project. Adding a project to a platform means only the functionality of the platform can be reused. Platforms have another limitation. Functionality from a platform for building one kind of application, like command line applications is difficult to reuse in another kind of application, like a Graphical User Interface (GUI) or a web app or a cell phone app. Li

Academy and industry growing the science pie

Like anyone who has worked in the commercial biotechnology science industry I have also spent time in academic science research in graduate school. There is definitely some rift between the two worlds of science. I find industry often doesn't know what is going on in nearby academic science centers, and academic science centers often don't want them to know because they think industry will steal their ideas just when they start working (There could be some truth to this.). The two science worlds should work closer together to grow the science pie. The government invests in academic research to improve health, improve the environment, improve lives and stimulate the economy and stimulating the economy is getting top billing now. Government investment is a fixed amount allocated each year. Academic scientists write grants to compete for their share of the pie. When one scientist wins another loses. Industry starts with basic science and applies it to problems (like diseases) to

Medical imaging genomic disease subtypes

Image
The genomics revolution is happening introducing personalized medicine but slower than most of us involved had hoped. One issue is that a disease have multiple genetic causes making traditional methods difficult. Medical imaging has the potential to separate subtypes of a disease based on what is seen in the medical image. Hopefully there are fewer genes involved in the medical image subtype making the genetic causes easier to identify. This explains why I have moved from genomic research to medical image processing. And I love creating these images.

Contribute back; even for your own sanity

Open source software allows you to modify the code for your own uses. I use so many different open source tools that I haven't become a regular contributor to any one project. The regular contributors are amazing, I don't know where they find the time. When you fix, modify or improve an open source software project, even if you don't become a regular contributor, send your changes to the project manager. People have been very good at including changes I have sent in. This will help you in the long run. If you change your code and don't send it back the project will release a new version that doesn't have your changes. If you upgrade to the new version you won't have your changes and will have to make the change over again. Eventually  you will end up with a forked older version and cannot benefit from the improvements in the new versions. For an organization this can turn into a really large problem when they hire new computer programmers that are used to th

Glass Research Towers instead of Research Parks

Research should be done in Towers not Parks to increase collaborations. Let's call them Glass Research Towers instead of Ivory Towers which have such an uncollaborative reputation. Buildings for research and technology venture companies should foster collaboration, Glass Towers can do this, Research Parks cannot. The typical Research Park is a large piece of land outside of town and one relatively low building is made for each institute or company. Companies or Institutes sign long term leases for the Park to make them a building. If an organization wants to expand it involves another long term lease and a long time to make a new low lying building. A small organization just getting started doesn't have the resources to sign a long term lease for an entire building. Small companies end up somewhere else in some kind of incubator. The Park employees drive their cars into their Institute, work, eat in the company or drive out of park (through a few limited access road s

Internet leads to in person collaborations

Collaborations have led to my best research results. Since my research involves developing software to analyze data I am always in need of useful data. I have received very interesting data from multiple sources. My collaborators and I will have publications out soon. The Internet, web-sites and e-mails are useful for finding and conducting collaborations. Interestingly the best collaborations always get going after we meet in person. The e-connections actually help us meet in  person other researchers we normally never would have met. Being able to transfer and share data through the Internet makes continuing work possible but it also means meeting more researchers in person.