LabLink Blog

This is a post written with the new LiveWriter Beta from Microsoft.

Looks pretty good!

s3DAV: "s3DAV is a webDAV server which allows you to access a virtual file system using your Amazon s3 account.
Once s3DAV is installed on your computer, you can drag and drop files to your s3 account from your file explorer."

Amazon.com Amazon Web Services Store: Amazon S3 / Amazon Web Services: "Amazon S3 - Simple Storage Service

Amazon S3 is storage for the Internet. It is designed to make web-scale computing easier for developers.

Amazon S3 provides a simple web services interface that can be used to store and retrieve any amount of data, at any time, from anywhere on the web. It gives any developer access to the same highly scalable, reliable, fast, inexpensive data storage infrastructure that Amazon uses to run its own global network of web sites. The service aims to maximize benefits of scale and to pass those benefits on to developers.

Amazon S3 Functionality

Amazon S3 is intentionally built with a minimal feature set.

* Write, read, and delete objects containing from 1 byte to 5 gigabytes of data each. The number of objects you can store is unlimited.
* Each object is stored and retrieved via a unique, developer-assigned key.
* Authentication mechanisms are provided to ensure that data is kept secure from unauthorized access. Objects can be made private or public, and rights can be granted to specific users.
* Uses standards-based REST and SOAP interfaces designed to work with any Internet-development toolkit.
* Built to be flexible so that protocol or functional layers can easily be added. Default download protocol is HTTP. A BitTorrent™ protocol interface is provided to lower costs for high-scale distribution. Additional interfaces will be added in the future.

Pricing

* Pay only for what you use. There is no minimum fee, and no start-up cost.
* $0.15 per GB-Month of storage used.
* $0.20 per GB of data transferred.

(Amazon S3 is sold by Amazon Digital Services, Inc.)"

Homeland Security report tracks down rogue open source code:

"By Gavin Clarke
Published Friday 3rd March 2006 13:29 GMT
Get breaking Reg news straight to your desktop - click here to find out how

The authors of a US government-sponsored report claim to have delivered the first reliable guide into judging the safety and reliability of open source software.

The report, backed by the US Department of Homeland Security (DHS), has evaluated 31 popular open source packages searching for defects that will cause 'hard crashes' - problems that leave users open to hackers or cause downtime.
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And fortunately for many a young Silicon Valley start-up and entrepreneur, the report, conducted by fault tracking specialist Coverity, has effectively given the Linux, Apache, MySQL and Perl/PHP/Python (LAMP) stack a healthy rating.

LAMP 'showed significantly better software quality' above the report's baseline with an average of .32 defects per 1,000 lines of code, according to Coverity. The average for open source projects analyzed is .42 per 1,000 lines.

Coverity co-founder Dave Park called the report a first because it provides a single standard to evaluate software from different open source projects. Increasingly, developers use open source form multiple projects to build applications, making it important to provide an overall measurement for things like bugs.

Park told The Register: 'This is one clear metric to decide how reliable or secure open source is. No real or proper yardstick existed before.'

Coverity's report, Stacking up the LAMP stack: a study of open source quality, was produced as part of a $1.24m, three-year DHS Science and Technology Directorate effort to evaluate and improve the security of open source.

Coverity evaluated 15m lines of open source code with Stamford University's Computer Science Department. The report has identified bugs that can corrupt a machine's memory space, memory leaks, buffer overruns and crashes. Coverity said it would now engage with open source developers to improve code, and identify potential reasons for why some projects have more bugs than others."

Geeking with Greg: Scalable hierarchical models of the neocortex: "Scalable hierarchical models of the neocortex

Googler Corinna Cortes just posted a bunch of links on the Google Research Blog, including a link to talks various researchers have done at Google.

Following that, I discovered a talk that Brown University Professor Tom Dean did at Google in Jan 2006 called 'Scalable Learning and Inference in Hierarchical Models of the Neocortex'.

Eyes glazing over? Okay, right, that might be an intimidating title.

But, really, if you have any interest this kind of thing, check out the talk. It is a fascinating discussion of how parts of the brain work and techniques for pattern recognition inspired by neurological processes. Tom does a great job with the talk, so I think it should be reasonably accessible even if you have no background in this stuff.

Even if this kind of thing is old hat for you, you still should check out the talk starting at around 44:00. That's when Tom Dean starts talking about how to parallelize a hierarchical Bayesian network across a cluster of computers.

Of particular interest to me was that he presented MapReduce code for the computation and seemed to be arguing he could do very large scale Bayesian networks in parallel on the Google cluster. I was surprised by this -- I would have thought that the communication overhead would be a serious issue -- but Tom was claiming that the computation supported coarse-grained parallelism due to the hierarchical structure of the models.

If this really is true, it would be a fascinating application of the massive computational power of the Google cluster. Maybe it is my inner geek talking, but I'm drooling just thinking about it.

If you want to dig in more, Tom Dean also has three recent papers on this work. I haven't gotten to his new papers yet, but I will soon.

posted by Greg Linden at 3:30 PM"

Transistor-Cantilever Combo Detects Biomolecules With High Sensitivity

Reseachers coupled a microcantilever with a metal-oxide semiconductor field-effect transistor to yield a device that generates a direct electrical signal whenever the cantilever bends in response to biomolecule binding.

It is capable of detecting bending of as little as five nanometers, sufficient to reliably detect binding of DNA, antibodies, and prostate specific antigen (PSA) to the microcantilevers.

It can also be mass-produced using standard computer chip design and manufacturing techniques.

Microcantilevers, tiny devices that resemble a diving board, show great promise for detecting rare disease-related molecules that might be present in biological samples. Indeed, researchers have developed several prototype devices that measure the nanoscale bending that occurs when such a molecule binds to an antibody or complementary nucleic acid sequence attached to the cantilevers. In most cases, these devices have successfully used lasers and other optical systems to measure cantilever bending, but such optical methods are likely to be difficult to manufacture and have limited use with turbid or opaque biological samples.

To get around these potential limitations, a team led by Vinayak Dravid, Ph.D., and Gajendra Shekhawat, Ph.D., colleagues at Northwestern University, coupled a microcantilever with a metal-oxide semiconductor field-effect transistor, or MOSFET, to yield a device that generates a direct electrical signal whenever the cantilever bends in response to biomolecule binding. This new device, note the researchers, can be mass-produced using standard computer chip design and manufacturing techniques. The results of this effort will appear in the journal Science.

In order to create a device with the greatest sensitivity, the investigators embedded the MOSFET in part of a gold-coated silicon nitride microcantilever that undergoes the greatest stress during bending. In this way, any bending produces a sharp change in electrical current flowing through the transistor. Indeed, this device was capable of detecting bending of as little as five nanometers, which was more than sufficient to reliably detect binding of DNA, antibodies, and prostate specific antigen (PSA) to the microcantilevers.

“We believe our work ushers a new era in biochemical sensing, wherein emerging bio-nano-structures can now be integrated on established engineering platforms such as CMOS and MOSFET,” wrote Vinayak in a note to Cancer Nanotech News. “We are excited by the prospects that MOSFET-embedded microcantilever approach may open up new vistas in biochemical sensing via high sensitivity, on-chip electronic detection that is amenable to massively parallel, multiplexed and remotely addressable networked systems.”

Stealth sharks to patrol the high seas

• 01 March 2006
• From New Scientist Print Edition
• Susan Brown

IMAGINE getting inside the mind of a shark: swimming silently through the ocean, sensing faint electrical fields, homing in on the trace of a scent, and navigating through the featureless depths for hour after hour.

We may soon be able to do just that via electrical probes in the shark's brain. Engineers funded by the US military have created a neural implant designed to enable a shark's brain signals to be manipulated remotely, controlling the animal's movements, and perhaps even decoding what it is feeling.

That team is among a number of groups around the world that have gained ethical approval to develop implants that can monitor and influence the behaviour of animals, from sharks and tuna to rats and monkeys. These researchers hope such implants will improve our understanding of how the animals interact with their environment, as well as boosting research into tackling human paralysis.

More controversially, the Pentagon hopes to exploit sharks' natural ability to glide quietly through the water, sense delicate electrical gradients and follow chemical trails. By remotely guiding the sharks' movements, they hope to transform the animals into stealth spies, perhaps capable of following vessels without being spotted. The project, funded by the Defense Advanced Research Projects Agency (DARPA), based in Arlington, Virginia, was presented at the Ocean Sciences Meeting in Honolulu, Hawaii, last week.

Neural implants consist of a series of electrodes that are embedded into the animal's brain, which can then be used to stimulate various functional areas. Biologist Jelle Atema of Boston University and his students are using them to "steer" spiny dogfish in a tank via a phantom odour. As the dogfish swims about, the researchers beam a radio signal from a laptop to an antenna attached to the fish at one end and sticking up out of the water at the other. The electrodes then stimulate either the right or left of the olfactory centre, the area of the brain dedicated to smell. The fish flicks round to the corresponding side in response to the signal, as if it has caught a whiff of an interesting smell: the stronger the signal, the more sharply it turns.

The team is not the first to attempt to control animals in this way. John Chapin of the State University of New York Health Science Center in Brooklyn has used a similar tactic to guide rats through rubble piles (New Scientist, 25 September 2004, p 21). Chapin's implant stimulates a part of the brain that is wired to their whiskers, so the rats instinctively turn toward the tickled side to see what has brushed by. Chapin rewards that response by stimulating a pleasure centre in the rats' brains. Using this reward process, he has trained the rodents to pause for 10 seconds when they smell a target chemical such as RDX, a component of plastic explosives.

The New York Police Department is considering recruiting Chapin's rats to its disaster response team, where they could be used to detect bombs or even trapped people, and Chapin met them to discuss the possibility last month.

However, Chapin's "mind patch" only works in one direction: he can stimulate movement or reward an action, but he cannot directly measure what the rat smells, which is why he has to train them to reveal what they are sensing. DARPA's shark researchers, in contrast, want to use their implant to detect and decipher the different patterns of neural activity that indicate the animal has detected an ocean current, a scent or an electrical field. The implant sports a small pincushion of wires that sink into the brain to record activity from many neurons at once. The team plans to program a microprocessor to recognise which patterns of brain activity correlate with which scents.

Atema plans to use the implants to study how sharks track chemical trails. We know that sharks have an extremely acute sense of smell, but exactly how the animals deploy that sense in the wild has so far been a matter of conjecture. Neural implants could change all that. "You get much better information from a swimming shark than from an anaesthetised animal that is strapped down," says Atema. "It could open up a whole new window into how these animals interact with their world."

At the Hawaii Institute of Marine Biology, Tim Tricas is using the implant to investigate what information scalloped hammerhead sharks glean from their electric field sensors. Gel-filled pores, scattered across a shark's head connect to nerve endings that make them sensitive to voltage gradients. Sharks can use these electroreceptors to spot the weak bioelectric fields around hidden prey, such as a flounder buried in sand.

For decades, marine biologists have suspected that sharks might also use these electroreceptors for navigation. Tiger and blue sharks can swim mile after mile in a straight line with no view of the ocean floor and only scattered, changing light coming from above. Some researchers suspect they maintain their heading by using the Earth's magnetic field.

When a conductor - in this case the shark - passes through a magnetic field, the interaction sets up a voltage across the conductor. The strength and orientation of that voltage depends on the conductor's angle to the magnetic field. If a shark could detect those changes, it could use its electrical receptors like a compass. The only way to test this, Tricas says, is to monitor electroreception in a freely swimming shark.

Other animal behaviour researchers are setting their subjects loose too. Jaideep Mavoori at the University of Washington in Seattle has developed a neural implant for monkeys that can monitor brain activity while the primates play. "We believe we are the first to record neural activity from a monkey doing a somersault," Mavoori says.

Mavoori's implant can also stimulate one part of the brain in response to activity in another, and has a microchip that can interpret the neural signals and send a message to another part of the brain or a muscle accordingly. He and his colleagues believe such an implant might ultimately help humans compensate for lost nerve function caused by injury or disease.

They have found that when a monkey is free to move around, sets of neurons controlling opposing muscle groups - those that extend and flex a joint - are both active throughout many movements. However, when a monkey is restrained in a chair and taught to extend its hand for a food reward, say, only the neurons that control the extensor muscles tend to be active.

Understanding this difference may be vital in creating a muscle-stimulating prosthesis to restore movement to a limb paralysed by nerve damage. For some loose movements, such as gently extending your arm in and out, sending signals to opposing muscles in turn works quite well. However, for movements that require some rigidity in the joint, such as inserting a book into a bookcase, you need to engage opposing muscles simultaneously. A successful neural prosthesis will need to mimic both patterns.

Meanwhile DARPA too plans to take its shark implants out of the laboratory. Project engineer Walter Gomes of the Naval Undersea Warfare Center in Newport, Rhode Island, says the team's next step will be to implant the device into blue sharks and release them into the ocean off the coast of Florida.

However, the radio signals used to direct the dogfish in the tank will not penetrate water, so the engineers plan to communicate with the sharks using sonar. According to Gomes, the navy already has acoustic signalling towers in the area that are suitable for relaying messages from a ship to a shark up to 300 kilometres away. The team has designed a sonar receiver shaped like a remora fish to minimise drag when attached to the animal.

The scientists will be particularly interested in the sharks' health during the tests. As wild predators, it is very easy to exhaust them, and this will place strict limits on how long the researchers can control their movements in any one session without harming them. Despite this limitation, though, remote controlled sharks do have advantages that robotic underwater surveillance vehicles just cannot match: they are silent, and they power themselves.

Bruce Schneier: Your vanishing privacy: "

Bruce Schneier

O ver the past 20 years, there's been a sea change in the battle for personal privacy.

The pervasiveness of computers has resulted in the almost constant surveillance of everyone, with profound implications for our society and our freedoms. Corporations and the police are both using this new trove of surveillance data. We as a society need to understand the technological trends and discuss their implications. If we ignore the problem and leave it to the "market," we'll all find that we have almost no privacy left.

Most people think of surveillance in terms of police procedure: Follow that car, watch that person, listen in on his phone conversations. This kind of surveillance still occurs. But today's surveillance is more like the NSA's model, recently turned against Americans: Eavesdrop on every phone call, listening for certain keywords. It's still surveillance, but it's wholesale surveillance.

Wholesale surveillance is a whole new world. It's not "follow that car," it's "follow every car." The National Security Agency can eavesdrop on every phone call, looking for patterns of communication or keywords that might indicate a conversation between terrorists. Many airports collect the license plates of every car in their parking lots, and can use that database to locate suspicious or abandoned cars. Several cities have stationary or car-mounted license-plate scanners that keep records of every car that passes, and save that data for later analysis.

More and more, we leave a trail of electronic footprints as we go through our daily lives. We used to walk into a bookstore, browse, and buy a book with cash. Now we visit Amazon, and all of our browsing and purchases are recorded. We used to throw a quarter in a toll booth; now EZ Pass records the date and time our car passed through the booth. Data about us are collected when we make a phone call, send an e-mail message, make a purchase with our credit card, or visit a website.

Much has been written about RFID chips and how they can be used to track people. People can also be tracked by their cell phones, their Bluetooth devices, and their WiFi-enabled computers. In some cities, video cameras capture our image hundreds of times a day.

The common thread here is computers. Computers are involved more and more in our transactions, and data are byproducts of these transactions. As computer memory becomes cheaper, more and more of these electronic footprints are being saved. And as processing becomes cheaper, more and more of it is being cross-indexed and correlated, and then used for secondary purposes.

Information about us has value. It has value to the police, but it also has value to corporations. The Justice Department wants details of Google searches, so they can look for patterns that might help find child pornographers. Google uses that same data so it can deliver context-sensitive advertising messages. The city of Baltimore uses aerial photography to surveil every house, looking for building permit violations. A national lawn-care company uses the same data to better market its services. The phone company keeps detailed call records for billing purposes; the police use them to catch bad guys.

In the dot-com bust, the customer database was often the only salable asset a company had. Companies like Experian and Acxiom are in the business of buying and reselling this sort of data, and their customers are both corporate and government.

Computers are getting smaller and cheaper every year, and these trends will continue. Here's just one example of the digital footprints we leave:

It would take about 100 megabytes of storage to record everything the fastest typist input to his computer in a year. That's a single flash memory chip today, and one could imagine computer manufacturers offering this as a reliability feature. Recording everything the average user does on the Internet requires more memory: 4 to 8 gigabytes a year. That's a lot, but "record everything" is GMail's model, and it's probably only a few years before ISPs offer this service.

The typical person uses 500 cell phone minutes a month; that translates to 5 gigabytes a year to save it all. My iPod can store 12 times that data. A "life recorder" you can wear on your lapel that constantly records is still a few generations off: 200 gigabytes/year for audio and 700 gigabytes/year for video. It'll be sold as a security device, so that no one can attack you without being recorded. When that happens, will not wearing a life recorder be used as evidence that someone is up to no good, just as prosecutors today use the fact that someone left his cell phone at home as evidence that he didn't want to be tracked?

In a sense, we're living in a unique time in history. Identification checks are common, but they still require us to whip out our ID. Soon it'll happen automatically, either through an RFID chip in our wallet or face-recognition from cameras. And those cameras, now visible, will shrink to the point where we won't even see them.

We're never going to stop the march of technology, but we can enact legislation to protect our privacy: comprehensive laws regulating what can be done with personal information about us, and more privacy protection from the police. Today, personal information about you is not yours; it's owned by the collector. There are laws protecting specific pieces of personal data -- videotape rental records, health care information -- but nothing like the broad privacy protection laws you find in European countries. That's really the only solution; leaving the market to sort this out will result in even more invasive wholesale surveillance.

Most of us are happy to give out personal information in exchange for specific services. What we object to is the surreptitious collection of personal information, and the secondary use of information once it's collected: the buying and selling of our information behind our back.

In some ways, this tidal wave of data is the pollution problem of the information age. All information processes produce it. If we ignore the problem, it will stay around forever. And the only way to successfully deal with it is to pass laws regulating its generation, use and eventual disposal.

Bruce Schneier is the CTO of Counterpane Internet Security and the author of "Beyond Fear: Thinking Sensibly About Security in an Uncertain World.""

UCR News: UCR Researchers Unlock New Information About How Cells Determine Their Functions: "

Photo Caption: At left is a schematic showing how the Ash1 epigenetic activator interacts with the DNA of the fruit fly drosophila. At right is Ultrabithorax expression in the fruit fly wing."

Biochemistry Professor Frank Sauer and colleagues uncover new information about how embryonic fruit fly cells differentiate, a process that may advance cancer and stem-cell research.
(February 24, 2006)

RIVERSIDE, Calif. – www.ucr.edu – Researchers at the University of California, Riverside have discovered a molecular mechanism that directs the fate and function of cells during animal development. The findings could hold promise for the advancement of cancer and stem-cell research.

The research is published in the Feb. 24 edition of the journal Science. UCR Biochemistry Professor Frank Sauer, with German colleague Elisabeth Kremmer of the Institut für Molekulare Immunologie in Munich, and fellow UCR researchers Tilman Sanchez-Elsner and Dawei Gou authored the paper titled, Noncoding RNAs of Trithorax Response Elements Recruit Dosphila Ash1 to Ultrabithorax.
The paper explains how proteins, known as epigenetic activators (such as Ash1 from the fruit fly Drosophila), bind to their target DNA and activate genes that determine what function a cell will have in the body.

“The fact that these epigenetic activators, such as Ash1, turn on the expression of specific target genes has been known for some time. However, the mechanisms by which epigenetic activators recognize and bind these target genes was not yet known” Sauer pointed out.

“What we were able to show is that the epigenetic activator Ash1is recruited to a target gene through cell-type specific non-coding RNA” he said.

The paper examined how the activator Ash1 binds to target DNA elements, known as Trithorax-reponse elements (TREs), located in the gene Ultrabithorax (Ubx). Non-coding RNA is produced by and retained at the TREs of Ubx, and helps activate the expression of the Ubx gene by attracting Ash1 to the TREs. The transgenic transcription of non-coding TRE RNA can change the type and function of cells.

“As a result, we can now use non-coding RNAs as tools to actively determine cell fate,” Sauer said.

“Over the last few years, researchers have focused on how noncoding RNAs silence genes,” said Anthony Carter, of the National Institute of General Medical Sciences, which partially funded the research. “Dr. Sauer’s work has revealed that noncoding RNAs have a broader range of functions than was previously known, and suggests a model for how they can help activate, rather than silence, a key regulator of animal development.”

The research was funded in part through the National Institute of General Medical Sciences at the National Institutes of Health in Bethesda, Md, the Volkswagen Stiftung of Hannover, Germany, Deutsche Forschungsgenmeinschaft (DFG) Transregio 5 and a Postdoctoral fellowship from the (DFG).

At left is a schematic showing how the Ash1 epigenetic activator interacts with the DNA of the fruit fly drosophila. At right is Ultrabithorax expression in the fruit fly wing.

Technology News: Cutting Edge : Robodude, Where's My Car?: "Robodude, Where's My Car?

By Thomas C. Palmer Jr.
The Boston Globe
02/12/06 5:00 AM PT

The pallet carries the car into the garage, moves the vehicle through the building on steel wheels and tracks, and deposits it into an available slot in a steel rack. Before parking the car, a mechanical device swivels it around 180 degrees, to speed up retrieval."

Harvard Medical School Researchers Discover How Gold and Other Medicinal Metals in its Class Function Against Rheumatoid Arthritis and other Autoimmune Diseases
Finding Makes Possible A New, More Effective Generation of Gold-based Drugs With Fewer Side Effects

BOSTON-February 26, 2006-Gold compounds have been used for the treatment of rheumatoid arthritis and other autoimmune diseases for more than 75 years, but until now, how the metals work has been a mystery. Harvard Medical School researchers report in the Feb. 27 issue of Nature Chemical Biology that special forms of gold, platinum, and other classes of medicinal metals work by stripping bacteria and virus particles from the grasp of a key immune system protein.

"We were searching for a new drug to treat autoimmune diseases," says Brian DeDecker, PhD, HMS post-doctoral student in the Department of Cell Biology and a study co-author. At the time of this work, DeDecker was in the Harvard Medical School Institute of Chemistry and Cell Biology, which uses powerful chemical tools to illuminate complex biological processes and provide new leads for drug development. "But instead we discovered a biochemical mechanism that may help explain how an old drug works."

DeDecker and co-author Stephen De Wall, PhD, undertook a large-scale search for new drugs that would suppress the function of an important component of the immune system, MHC class II proteins, which are associated with autoimmune diseases. MHC class II proteins normally hold pieces of invading bacteria and virus on the surface of specialized antigen presentation cells. Presentation of these pieces alerts other specialized recognition cells of the immune system called lymphocytes, which starts the normal immune response. Usually this response is limited to harmful bacteria and viruses, but sometimes this process goes awry and the immune system turns towards the body itself causing autoimmune diseases such as Juvenile diabetes, Lupus, and rheumatoid arthritis.

During their search through thousands of compounds they found that the known cancer drug, Cisplatin, a drug containing the metal platinum, directly stripped foreign molecules from the MHC class II protein. From there, they found that platinum was just one member of a class of metals, including a special form of gold, that all render MHC class II proteins inactive.

In subsequent experiments in cell culture, gold compounds were shown to render the immune system antigen presenting cells inactive, further strengthening this connection. These findings now give researches a mechanism of gold drug action that can be tested and explored directly in diseased tissues.

In 1890, a German doctor named Robert Koch found that gold effectively killed the bacteria that caused tuberculosis. In the 1930s, based on a widely held but probably erroneous connection at the time between tuberculosis and rheumatoid arthritis, a French doctor, Jacques Forestier, developed the use of gold drugs for the treatment of rheumatoid arthritis. Gold drugs have been used since then as an effective treatment for this and other autoimmune diseases such as Lupus, but treatment can take months for action and sometimes presents severe side effects which have diminished their use in recent years.

With this new understanding of how these metals function, it may now be possible to develop a new generation of gold-based drugs for treating rheumatoid arthritis and other autoimmune diseases that are more effective with fewer side effects.

Biosingularity » Fluorescent Nanosensor Detects Cell Death: "Fluorescent Nanosensor Detects Cell Death

A team of investigators at Massachusetts General Hospital has developed a nanoparticle that signals when cells are undergoing apoptosis, the kind of cell death triggered by cancer therapies. The new nanoparticles could finally provide oncologists with a rapid assay that could tell them that a given therapy is working. This groundbreaking work was published in the journal Nano Letters.
Nanoparticles.jpg

Too often, oncologists have to wait weeks, or more often months, to learn if the treatment prescribed for a particular patient is working, a predicament that can have dire results. For the patient, receiving a therapy that is not working means unnecessary suffering, both from the tumor continuing to grow and any side effects that accompany the ineffective treatment. Receiving ineffective therapy for longer than needed also delays the start of second-line therapies that might work. Worse still, the failed treatment can trigger genetic defense mechanisms in tumor cells that can render ineffective these second-line therapies using other drugs. This phenomenon is known as cross-resistance.

To develop their apoptosis detector, Ching-Hsuan Tung, Ph.D., Ralph Weissleder, M.D., and Luisa Quinti, Ph.D., honed in on the molecule phosphatidylserine. Phosphatidylserine, or PS, is found normally on the inside of the cell membrane, but this molecule moves to the outside layer of the cell membrane when a cell begins apoptosis. To detect this early indicator of apoptosis, the researchers constructed an artificial small, fluorescent protein that would bind to four different molecules of PS. Test tube experiments showed this construct did indeed bind to PS but not to other membrane components; however, when the investigators tried to use it to detect apoptotic cells, the experiments were a failure. Evidently, their test construct did not bind strongly enough and for a long enough time to apoptotic cells to be detectable.

Next, the researchers turned to a magnetic iron oxide nanoparticle that Weissleder, who is co-director of the MIT-Harvard Center of Cancer Nanotechnology Excellence, has been developing for imaging tumor metastasis. They reasoned that they could attach an average of 41 of the PS-binding molecules to each nanoparticle, which should increase dramatically the ability of the resulting construct to not only bind to PS, but remain stuck to the apoptotic cell through a process called cooperative binding. Cooperative binding is what gives such enormous sticking power to the hundreds of tiny loops and hooks on matching pieces of Velcro®.

In fact, the nanoparticle worked like a charm. When the investigators added the nanoparticle-based PS-binder to cells triggered to undergo apoptosis, they were able to easily identify the apoptotic cells using a fluorescent microscope or a standard cell sorting apparatus. The researchers note that because the nanoparticle they used has already been optimized for use in humans, their new apoptosis detector holds significant promise for use in cancer imaging applications.

Source: National Cancer institute

Abstract at: http://pubs.acs.org/cgi-bin/abstract.cgi/nalefd/asap/abs/nl0524694.html"

IronPython: "Overview
IronPython is the codename for a beta release of the Python programming language for the .NET platform.
It supports an interactive interpreter with fully dynamic compilation. It is well integrated with the rest of the framework and makes all .NET libraries easily available to Python programmers.
IronPython 1.0 Beta 3 is now available. Download it here."

code.enthought.com - Python-Enthought Edition: "Enhanced Python Distribution - Python 2.3.5 for Windows (Enthought Edition)

Carrying on Python's batteries included tradition of providing lots of great functionality right out of the box, Enthought, Inc. is pleased to make available Python 2.3.5 for Windows (Enthought Edition), a Python distribution that comes with even more useful capabilities already installed and ready for use. Download now.

In addition to all of the features provided with the standard Python 2.3.5 distribution, Python 2.3.5 for Windows (Enthought Edition) also includes the following packages:

* wxPython 2.6.1.0: wxWindows for Python
* PIL 1.1.4: Python Imaging Library
* VTK 4.4.2: 3D Visualization Toolkit
* MayaVi 1.5: 3D Data Visualization Tool
* Numeric 24.2: Numerical Python
* SciPy 0.3.3_303.4602: Scientific Library for Python
* ScientificPython 2.4.5: A collection of Python modules for scientific computing
* F2PY 2.45.241_1926: A Fortran to Python interface generator
* ZODB3 3.1: ZODB and ZEO Object DataBase
* Gadfly 1.0.0: An SQL Relational Database in Python
* PySQLite 0.5.0: A Python Extension for the SQLite embedded relational database
* ctypes 0.6.3: A package to create and manipulate C data types in Python
* pyxml: XML Tools
* IPython 0.6.15: A Python Shell done right.
* Enthought Tool Suite 1.0.2: A tool suite for building extensible python applications. This includes chaco, traits, kiva, envisage, etc.
* elementtree 1.2.6-20050316:
* celementtree 1.0.5-20051216:

Simply run the .exe file to begin installation. The file is a standard Windows installer program that will guide you step-by-step through the installation process. When installation is complete, you can click the Window's Start button to view the programs and available documentation."

http://lorentz.sourceforge.net/: "peak-o-mat - a curve fitting program written in python C.Kristukat (ckkart@users.sf.net) prak-o-mat is a curve fitting program mainly aimed for the fitting of spectroscopic data. You can select various pre-defined peak shapes and backgrounds and place them on the plot. Furthermore you can supply an arbitrary function as fitting model, the parser will identify all independent parameters for which you have to guess an initial value. The fitting procedure uses the LM least-squares algorithm from MULTIPACK provided by SciPy.

Optional:
- xmgrace for nicer output
- matplotlib for theoretically even nicer EPS output (matplotlib.sf.net)
- mencoder for creation of spectra animations"

Epsilon-Delta: Storing a Tree in a Database: "
Posted by Ted Dziuba under Mathematics , Computer Programming

A friend of mine brought a good question to me the other day: Given a labeled tree, what’s the best way totree.jpg store it in a database and retrieve it later? If you’ve worked with SQL enough, you could probably hash out some kind of solution storing edges and nodes of the tree and joining tables on unique identifiers. However, given the acyclical structure of a tree, it seems like you should be able to retrieve a tree from a database with a single SELECT statement and then reconstitute it in a reasonable amount of time. Where there is a will, there is a way.

The Theorem of Cayley and Prüfer

British mathematician Arthur Cayley has given us significant results in a variety of fields of mathematics. Cayley discovered a very important property of labeled trees, which is, given n vertices, there are 2^n-2 possible labeled trees on those vertices. (For the interested, Wikipedia has a proof.) This theorem was subsequently re-proven by German mathematician Heinz Prüfer, who offered a constructive version, which established a one-to-one correspondence between labeled trees on n vertices and (n-2) tuples. Such a tuple is known as a Prüfer Code. Applying this concept to our problem, if we use the unique identifer of each vertex in the graph as its label, we can encode a tree as an (n-2) tuple of such identifiers, and re-constitute this code to a tree with a single SELECT statement, given the tuple. There are many different algorithms to do this, but a basic algorithm can be found here. In “Combinatorial Algorithms” by Nijenhuis and Wilf, there are methods given to encode and decode a graph in O(n) time.

Prüfer Encoding in Practice

So let’s say we want to use the Prüfer Code to store a tree in a database. Assuming each vertex in the graph contains data of its own, you would create a table for the vertices, where each vertex had an identifer for the tree it was in (assuming you were working with more than one tree), an identifer for its label within that tree, and a field for its data. Now, if you were given the Prüfer Code for a tree, you could simply SELECT all the vertices contained within that tree and decode the Prüfer Code, which would yield the tree. Adding vertices to the tree would be the logical reverse of this process, an INSERT for each vertex, followed by a re-encoding of the tree.

So now, after a bit of mathematical analysis, we’ve found a very simple method for storing a tree structure in an object relational database. It is very straightforward, and isn’t database intensive in the least. Assuming that an O(n) operation isn’t prohibitive (it shouldn’t be, after all, iterating over a SQL return result takes the same amount of time), you can encode and decode a tree in your application code, which keeps logic out of the database. I’m not passing judgment on the legitimacy of logic in the database, but this does make your data more atomic. All in all, this goes to show that a little bit of math can take your code a long way."

Scientific study finds meetings at work decrease employee well-being, but not for everyone: "Scientific study finds meetings at work decrease employee well-being, but not for everyone
How are things going at work? While there has plenty written on a wide variety of factors affecting employee well-being – on everything from management style and organizational structure to the effects of ergonomic furniture and natural lighting – the 'elephant in the room' in our workplaces is something that almost everyone complains about but no one has studied: how much time we spend in meetings.

In the average workplace, there are lots of meetings. Reports indicate that the average number of meetings at work more than doubled in the second half of the 20th Century and time spent in meetings keeps growing. While the importance of this change has been largely unnoticed, a new study on the effects of meetings on worker well-being reveals some surprising dynamics behind modern meeting mania, with broad implications for the effects on morale and productivity.

The report, written by a team of researchers led by industrial and organizational psychologist Steven G. Rogelberg from the University of North Carolina at Charlotte, appears in the March issue of the Journal of Applied Psychology. It describes the first international scientific study ever performed on the effects of meeting time on employee well-being, based on the responses of 980 employees to two work surveys.

One of the report's findings was that more people actually view meetings as a positive part of the workday than they will admit publicly.

'When speaking publicly, people generally claim that they hate meetings,' said Rogelberg, 'but in the surveys you see a different story – some people's private sentiments are much more positive.

'It's an interesting finding because it really helps to explain why we have all these meetings. And, though they are typically publicly negative, overwhelmingly people say that they want the day to have at least one meeting. They have to feel like they are accomplishing something positive in their meetings to produce this response,' he said.

The two surveys tested the impact of meetings on employees in two different contexts – at the end of a specific day and in general, by examining the number of meetings employees had in a typical week.

The study finds that for some individuals meetings function as interruptions and for others they are welcome events. The effects of meetings on worker well-being is 'moderated' by three different factors – by whether jobs specifically require group work, by whether the meetings were efficiently run, and, perhaps critically, by where the worker falls on the personality scale of her/his 'accomplishment striving.'

'People differ on this accomplishment striving personality scale,' Rogelberg explained. 'In general, you can think of people who are high in accomplishment striving are those individuals who are very task-focused, who are very goal-focused, who have goals and objectives for the day that they want to get accomplished. People who have low accomplishment striving are not slackers, though -- they are just individuals with a much more flexible orientation to work and like to allow the agenda for the day to emerge much more naturally.'

The study finds that people who are high in accomplishment striving are predictably and negatively impacted by meetings, particularly when they are frequent. Numerous short meetings have a greater impact on their well-being than a few long meetings taking the same amount of time.

However, survey participants who scored low in accomplishment striving were positively impacted by meetings. They appeared to be welcome events rather than interruptions. More time in meetings was associated with a greater sense of well-being.

'People who are high in accomplishment striving look at meetings more from the perspective of seeing them as barriers to getting real work done,' Rogelberg said. 'But the others may view meetings as a way to structure their day or a way to network and socialize. As a result, these people see meetings as a good thing.'

Rogelberg notes that there are some curious social paradigms operating that disguise the dynamic.

'It is socially unacceptable to talk about liking meetings, unless someone else starts talking about it,' he said, explaining why the low accomplishment striving folks do not go public with their preference for meeting. 'And it is also interesting that the people who are high on accomplishment striving are not complaining more the others. The toll that meetings take seems to be much more subtle. If you ask these individuals if they are more dissatisfied with the meetings, they don't report anything different from those who enjoy meetings,' he said.

Steven Rogelberg is Associate Professor of Psychology at UNC Charlotte, where he is director of the Industrial and Organizational Psychology and Organizational Science graduate programs as well as the Organizational Science Consulting and Research Unit. He also affiliated with UNC Charlotte's Department of Management ."

How to make PCB's with a laser printer: "How to make PCB's with a laser printer"

Painless JavaScript Using Prototype [JavaScript & DHTML Tutorials]: "Prototype is an object oriented JavaScript library (written by Sam Stephenson and friends) that makes JavaScript fun. So it says on the site, anyway. Those of you who are familiar with the open source community's latest and greatest application framework, Rails, may recognise Prototype as it actually forms the backbone of Rails' JavaScript helper. However, Prototype can be used independently of Rails to aid the coding of many JavaScript doodads and Web 2.0 thingy wangles."

Undersea microbes active but living on the slow side

University Park, Pa. – Deeply buried ocean sediments may house populations of tiny organisms that have extremely low maintenance energy needs and population turnover rates of anywhere from 200 to 2,000 years, according to an international team of researchers.

"The microbial ecosystem in deeply buried marine sediments may comprise a tenth of Earth's living biomass, but little is known about the organisms, their physiologies, and their influence on surface environments," says Jennifer F. Biddle, graduate student in biochemistry, microbiology and molecular biology and member of the NASA- sponsored Penn State Astrobiology Research Center.

The populations of interest are two groups of Archaea – tiny bacteria-like organisms that are often found in extreme environments such as deep-sea hot vents, inside cows or termites or in deep sediments. The samples were gathered during the National Science Foundation-sponsored Ocean Drilling Program Leg 201 off the coast of Peru.

"The samples showed strikingly elevated concentrations of cells in deeply buried sulfate-methane transition zones," says Christopher H. House, assistant professor of geosciences, Penn State. "Sulfate methane transition zones are areas where both methane and sulfate diffuse and both compounds are used by local denizens."

The researchers looked for 16S rRNA in the sediment samples and found the transition zones dominated by two groups – Marine Benthic Group B and Miscellaneous Crenarchaeotal Group. rRNA is found in a cell's ribosome and is part of the protein manufacturing mechanism of a cell. The presence of a specific sequence of 16S rRNA distinguishes the types of Archaea and the analysis also identifies Archaea that are active, excluding inactive cells and fossils.

"Other researchers have found DNA analysis of sediments from some sites to indicate that the majority of organisms were Bacteria and not Archaea," says House. "We used methods that identify only active cells and found Archaea."

Another method of identifying the active populations – both in size and type – looked at intact polar lipids, an indication of live rather than fossil cells.

"These tests and others indicate that there is a sizeable and active archaeal community," says House.

Besides simply knowing that populations of Archaea exist in the deep sediment layers at the sulfate-methane transition zones, the researchers looked at the energy sources for these microbes. Many organisms living in environments with methane use the methane for energy and use the methane's carbon to grow, repair and reproduce. Looking at the carbon isotopes the researchers found that few, if any, of these Archaea used methane as a carbon source. They also found that conversion of carbon dioxide to methane was not fueling these Archaea.

"Because the carbon isotopes from the Archaea match the total organic carbon found in the sediment in general, it suggests that the bulk archaeal community uses organic compounds derived from fossil organic matter," says House.

The researchers suggest in this week’s issue of the Proceedings of the National Academy of Sciences online, that degradation of organic matter in the sediment, especially the formation of small molecules like acetate and formate, are the likely sources of carbon.

"Real maintenance energies in subsurface environments must be much lower than what has been experimentally determined in laboratory cultures," says Biddle. "If conventional maintenance energies are used, only about 2 percent maximum of the population could survive. However, cellular maintenance energies are expected to be significantly lower when cells divide at extremely low rates."

In fact, the researchers estimate that these Archaea may completely turn over population as frequently as every 70 years, or as infrequently as 2,150 years. They also suggest that the sulfate-methane transition zone is a much better environment than other areas in the sediment and that turnover rates are even lower away from the transition zone.

This is because the Archaea in the transition zone, while not using the carbon from methane oxidation, are still getting some energy from breaking down the methane molecules, energy that is not available in other portions of the sediment.

"These Archaea subsist on the sedimentary organic carbon available and the energy from breaking down methane until they accumulate enough resources to divide," says House. "Surprisingly they require much less energy to maintain and take much longer than expected until they can divide."

This international research team was lead by House, Kai-Uwe Hinrichs from the University of Bremen and Woods Hole Oceanographic Institution, and Andreas Teske from the University of North Carolina. The team included graduate students Biddle, Julius S. Lipp, Mark Lever and Karen Lloyd.

The National Science Foundation, NASA Astrobiology Institute, Deutcsche Forschungsgemeinschaft and the U.S. Department of Energy supported this work.

Intelligently Designed Molecular Evolution

BERKELEY, CA — Evolutionary paths to new therapeutic drugs, as well as a wide assortment of other enzyme products, have been created through, of all things, intelligent design. A team of researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California at Berkeley have developed a technique in which the evolution of an important class of proteins is steered towards a desired outcome. The Grand fir, largest of all the fir trees, produces the ultimate in "promiscuous enzymes," a sesquiterpene synthase capable of producing as many as 52 different enzyme products. “We’ve taken enzymes that are promiscuous, meaning they have the capacity to evolve along many different functional lines, and trained them to become specialists,” said chemical engineer Jay Keasling, who led this study. “This technology could be used by pharmaceutical manufacturers in the future to create specific enzyme products.” Keasling is director of Berkeley Lab’s Physical Biosciences Division, and a professor of chemical engineering with UC Berkeley’s Chemical Engineering Department. Collaborating with him on this project were his graduate student, Yasuo Yoshikuni, and Thomas Ferrin, a professor of pharmaceutical chemistry and biopharmaceutical sciences at UC San Francisco. The results of this study were reported in the February 22, 2006, on-line edition of the journal Nature. According to the theory of divergent molecular evolution, primordial enzymes and other proteins started out as “promiscuous” so that primitive organisms would be better able to adapt to their environment. Driven by selective pressures, these promiscuous enzymes and other proteins evolved along divergent lines to acquire the specialized functions needed by a host organism to survive. “This process is highly dependent on the fact that the functions of promiscuous proteins can be altered with just a small number of amino acid substitutions, a property known as plasticity,” said Keasling. “It was our contention that the application of the theory of divergent molecular evolution to promiscuous enzymes would enable us to design enzymes with greater specificity and higher activity.” Jay Keasling, a chemical engineer and leading authority on synthetic biology, led a study in which the promiscuous enzyme of the Grand fir was trained, through designed molecular evolution, to produce specific protein products. To test this idea, Keasling and his students worked with a type of naturally occurring hydrocarbon compounds, called sesquiterpenes, that is widely used in a variety of products. For their model enzyme, they selected a sesquiterpene synthase produced by the Grand fir tree, which has the capacity to develop into any of 52 different sesquiterpenes from a sole substrate. “This Grand fir sesquiterpene synthase represents the ultimate in promiscuous enzymes,” said Yoshikuni. “We were able to take it and construct seven specific and active enzymes synthases. These seven enzymes use different reaction pathways to produce specific products that are as diverse as they can be from one another.” In nature, the divergent evolution of promiscuous enzymes is achieved through trial and error, similar to the way in which the human immune system works. Multiple combinations of many different amino acid substitutions are tested in promiscuous enzymes until an evolutionary path that achieves a desired result is found. The amino acid substitutions that significantly drive molecular evolution are called “plasticity residues.” The Berkeley researchers identified the plasticity residues for the Grand fir sesquiterpene synthase, then systematically recombined mutations of these residues through site-directed mutagenesis, based on a mathematical model developed by Yoshikuni. Construction of the seven sesquiterpene synthases was accomplished with the screening of fewer than 2,500 mutants. An alterative approach, called directed evolution or molecular breeding, that is currently being tested at other laboratories, requires the screening of tens of thousands to a million or more mutants. Yasuo Yoshikuni, a grad student in Jay Keasling’s research group, developed a mathematical model that was used to “intelligently design” the molecular evolution of a Grand fir sesquiterpene synthase. “The enzyme synthase was there ready to be evolved, and with our methodology, we were able to rapidly and efficiently evolve it down a pathway of our choice,” Keasling said. “We are recapitulating evolution into intelligent design. In the case of this particular Grand fir enzyme synthase, it naturally makes a soup of small amounts of 52 different products. We were able to focus it instead on making large amounts of one of seven of those products.” While the researchers have not yet reached the point where they can design a promiscuous enzyme to make any kind of product they want, even one that does not occur in nature, this demonstration represents a significant step in that direction. The idea would be to one day be able to design an enzyme synthase that would evolve along a specific functional pathway to yield a desired molecular product, then introduce it into microbes for mass production. In addition to synthesizing therapeutic drugs, other possible applications would include flavors, fragrances and nutraceuticals. “Our ultimate goal is to be able to put as much chemistry as we can into microbes,” said Keasling, a pioneer and leading authority in the burgeoning scientific field of synthetic biology. “We can use microbes to do a lot of complicated chemistry, and the way in which this will be done is through the use of enzymes. One can imagine where you could take a series of promiscuous enzymes that would make different parts of a molecular compound, and combine them to obtain a final product that could do whatever you needed it to do.” Since plasticity residues also play other important biological roles, in addition to the evolution of promiscuous proteins, Keasling and Yoshikuni said their technology, with some modifications, could prove useful for designing novel functions into other types of enzymes and proteins, as well as protein ligands and receptors, transcription factors and antibodies. This research was largely funded through grants by the Bill and Melinda Gates Foundation, the National Science Foundation, and the U.S. Department of Agriculture. Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California. Visit our Website at www.lbl.gov.

Rochester scientists develop fast-working biosensor

University of Rochester Medical Center scientists have demonstrated a new technology that accurately and rapidly detects the meat-spoiling and sometimes dangerous E. coli bacteria.

The unique technology uses a protein from the suspect bacteria as part of the sensing system that also includes a silicon chip and a digital camera.

The journal Biosensors and Bioelectronics published an article on the technology in its February issue. Benjamin Miller, Ph.D., an associate professor of dermatology at the Medical Center, is the lead author of the article.

"We've developed a very inexpensive technology that can detect an infectious agent," said Miller, who is part of the university's Center for Future Health "It's clearly faster and cheaper than any competing technology. This is another step on the way to point-of-care diagnostics."

The technology potentially could detect any biological entity, Miller said. A physician someday, for example, could use the technology in his office to confirm a streptococcal infection in a patient with a sore throat.

The Rochester research team calls the technology "arrayed imaging reflectometry." The system utilizes a silicon chip that is made so that laser light reflected off the chip is invisible unless the target bacteria are present.

The target described in the Biosensors and Bioelectronics article is the bacteria Escherichia coli.

A protein from the bacteria, Translocated Intimin Receptor or Tir, is placed on the chip. The Tir can be seen as a "molecular harpoon," Miller said. The E. coli sends out the harpoon into a cell. Once it is in the cell, the Tir then binds with an E. coli protein called Intimin. A similar process occurs between the Tir placed on the chip and any E. coli in the sample being tested. The binding of the probe and the bacteria alters the surface of the chip. A digital camera image of the chip captures the changes for analysis and confirmation of detection.

Traditional methods of detection of bacteria can take days. "This takes as much time as it takes for a snapshot," Miller said.

The scientists currently are defining the sensitivity levels of the technology, previously called reflective interferometry, and extending the system to other biological targets.

In addition to Miller, the authors of the journal article include Lewis J. Rothberg, professor of chemistry and member of the Center for Future Health, Scott R. Horner, who earned a doctorate in biophysics at the University of Rochester, and Charles R. Mace, a University of Rochester doctoral student in biophysics.

Pathologics, a Rochester area start-up company, was launched to further develop and commercialize the technology. Miller, Rothberg and Horner have a financial interest in the company. Horner is chief technical officer at Pathologics.

Research for the work was supported by grants from the U.S. Department of Energy and the National Institutes of Health.

LEARNING TO LOVE BACTERIA: STANFORD SCIENTIST HIGHLIGHTS BUGS’ BENEFITS

STANFORD, Calif. — Bacteria are bad. Mothers and doctors, not to mention the cleaning product industry, repeatedly warn of their dangers. But a Stanford University School of Medicine microbiologist is raising the intriguing idea that persistent bacterial and viral infections have benefits.

Stanley Falkow, PhD, the Robert W. and Vivian K. Cahill Professor in Cancer Research, is publishing his thoughts on this topic in an essay in the Feb. 24 issue of the journal Cell, in which he asks, “Is persistent bacterial infection good for your health?” The essay is based on a talk he was invited to give at Cambridge University in November.

Falkow points out that the medical community and those who fund medical research focus on curing disease. He wonders if this single-mindedness might distract researchers from appreciating the beneficial contributions of micro-organisms to the body.

“Organisms that cause disease are usually considered in the context of harm and epidemics and so on,” said Falkow. “But the fact is that a great number of organisms that infect humans come in and set up housekeeping as it were. There are no clinical symptoms of anything wrong and people take the organisms with them to their graves.”

It’s not that the organisms in question — such as the bacteria that cause pneumonia or meningitis — are innocuous, he said. It’s just that most of the individuals do not get disease from being infected.

The best recent example of this, said Falkow, is H. pylori. First identified only 25 years ago, the organism earned researchers last year’s Nobel Prize in Medicine or Physiology for being implicated as a cause of ulcers and stomach cancer.

As is typical in the world of microbiology, though, it’s not a simple equation: being infected = ulcers or cancer. At least 80 percent of the world’s population is infected with H. pylori yet has no overt symptoms.

What makes the study of H. pylori even more perplexing is that as such advances as clean water and pasteurization are adopted, the prevalence of H. pylori infection has declined. On the one hand, this has been accompanied by a drop in the incidence of gastric cancer and ulcers. On the other, there has been an increase in esophageal cancer. H. pylori appear to protect against cancer of the esophagus. “So that says that there might be something about persistent infection that might be protective,” said Falkow.

This raises the conundrum: By messing with the microbes, are we just replacing one disease with another?

Falkow’s lab has been studying the phenomenon of persistent infection for decades, in particular with H. pylori and Salmonella. He and his colleagues have shown that when infected with these organisms, mice initially show an inflammatory response that then settles down and stays with them for the rest of their lives.

Although very few of these organisms remain in the mice, it is enough to cause the immune system to have an ongoing response. “It’s not so much that the immune system has failed,” Falkow explained, “but that the organisms have manipulated the immune system in such a way that they can’t be cleared.” If the infections are cleared by antibiotic intervention, the mice are highly susceptible to re-infection, and the re-infection is more likely to progress to disease than the initial infection.

Furthermore, as many infectious diseases have decreased, autoimmune diseases such as ulcerative colitis, Crohn’s disease and diabetes have increased.

“All these observations have been made without necessarily trying to pull it all together,” said Falkow. “So what I tried to do in this article is to point out that the continued presence of these organisms in human society may actually be beneficial to the host and that is why they are tolerated by the immune system.”

It’s an intriguing idea that requires more research in animal models. “We don’t know what to look for per se,” he said. “But we can guess that since a persistently infected host is constantly having its immune system stimulated and refined, that may provide it with resistance to other things.”

He wondered whether, as seen with H. pylori, humans are also unknowingly causing the disappearance of other things that have been with us for all of our evolution, and that might play some role in our health. “Could it be this that is responsible for some of the things we see such as the failure of the immune system to act appropriately?” he asked.

The only answer to date is: “It’s complicated.” Instead of a persistent infection, some people get very ill from organisms such as Salmonella, H. pylori, tuberculosis and meningitis. How the immune system responds differently in individuals demands further research.

Falkow credits his colleagues for providing the fodder for his essay.

Quantum computer solves problem, without running: "Quantum computer solves problem, without running
By combining quantum computation and quantum interrogation, scientists at the University of Illinois at Urbana-Champaign have found an exotic way of determining an answer to an algorithm – without ever running the algorithm.

Using an optical-based quantum computer, a research team led by physicist Paul Kwiat has presented the first demonstration of 'counterfactual computation,' inferring information about an answer, even though the computer did not run. The researchers report their work in the Feb. 23 issue of Nature.

Quantum computers have the potential for solving certain types of problems much faster than classical computers. Speed and efficiency are gained because quantum bits can be placed in superpositions of one and zero, as opposed to classical bits, which are either one or zero. Moreover, the logic behind the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to some surprising effects.

'It seems absolutely bizarre that counterfactual computation – using information that is counter to what must have actually happened – could find an answer without running the entire quantum computer,' said Kwiat, a John Bardeen Professor of Electrical and Computer Engineering and Physics at Illinois. 'But the nature of quantum interrogation makes this amazing feat possible.'

Sometimes called interaction-free measurement, quantum interrogation is a technique that makes use of wave-particle duality (in this case, of photons) to search a region of space without actually entering that region of space.

Utilizing two coupled optical interferometers, nested within a third, Kwiat's team succeeded in counterfactually searching a four-element database using Grover's quantum search algorithm. 'By placing our photon in a quantum superposition of running and not running the search algorithm, we obtained information about the answer even when the photon did not run the search algorithm,' said graduate student Onur Hosten, lead author of the Nature paper. 'We also showed theoretically how to obtain the answer without ever running the algorithm, by using a 'chained Zeno' effect.'

Through clever use of beam splitters and both constructive and destructive interference, the researchers can put each photon in a superposition of taking two paths. Although a photon can occupy multiple places simultaneously, it can only make an actual appearance at one location. Its presence defines its path, and that can, in a very strange way, negate the need for the search algorithm to run.

'In a sense, it is the possibility that the algorithm could run which prevents the algorithm from running,' Kwiat said. 'That is at the heart of quantum interrogation schemes, and to my mind, quantum mechanics doesn't get any more mysterious than this.'

While the researchers' optical quantum computer cannot be scaled up, using these kinds of interrogation techniques may make it possible to reduce errors in quantum computing, Kwiat said. 'Anything you can do to reduce the errors will make it more likely that eventually you'll get a large-scale quantum computer.'"

VisIt: "VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range. See the table below for more details about the tool’s features.
History

VisIt was developed by the Department of Energy (DOE) Advanced Simulation and Computing Initiative (ASCI) to visualize and analyze the results of terascale simulations. It was developed as a framework for adding custom capabilities and rapidly deploying new visualization technologies. After an initial prototype effort, work on VisIt began in the summer of 2000, and the initial version of VisIt was released in the fall of 2002. Although the primary driving force behind the development of VisIt was for visualizing terascale data, it is also well suited for visualizing data from typical simulations on desktop systems. Because of its applicability beyond visualizing terascale data, we are making VisIt freely available as open source software."

Liquid Level Sensor: "Operating Principle
Our sensor incorporates proprietary transducer technology employing piezoelectric material. When piezoelectric material is excited, it creates an acoustic signal as a function of the natural resonance of the material. ExOsense™ sensors generate this acoustic signal, direct it through the bottle wall and sense the reflected pulse. The amount of energy that is reflected is determined by the “acoustic impedance* mismatch” of the materials in use. For example, if sound passes through two materials with similar acoustic impedances (figure 1), very little energy will be reflected. If sound passes through two materials with dissimilar impedance values (figure 2), the majority of the acoustic energy will be reflected. This acoustic impedance mismatch provides the basis for the detection of liquid level.

* Acoustic Impedance: a material property defined as the product of sound velocity and material density. The relative transmission and reflection at an interface are governed in part by the acoustic impedances of the materials on each side of the interface. The letter Z is used for acoustic impedance and is expressed in [kg/s m2] = 1 Rayl: Water Z = 1.5 MRayls; Air Z = 0 MRayls"

Wiky: A Bidirectional Markup Converter: "Wiky: A Bidirectional Markup Converter

Wiky is a clientside Wiki markup to HTML converter written in javascript. As it is bidirectional, it can convert Wiki markup to HTML and later convert that generated HTML text back to Wiki markup. Optionally Wiky will create math formulas from a simple notation similar to LaTeX.

Wiky is neither an editor nor a widget, though it might be used by these. It is just a converter.

The primary object of Wiky's developement was its use in a lightweight eLearning environment. It had to meet the requirements:

* Clientside only.
* Creating validating XHTML markup, which is …
* … cross browser with no need of plugins or addons.
* Minimal CSS dependency.
* Suitable for inplace editing with Ajax components and weblogs.
* Easily extensible and modifyable Syntax.

You can play with it in the WikyBox and download the most current version. I have tested Wiky for several month now with a couple of students using

* Firefox 1.5
* Internet Explorer 6
* Opera 8.5

You may use it freely under the Creative Commons GNU LGPL License."

Learning and memory stimulated by gut hormone: "Learning and memory stimulated by gut hormone
Researchers at Yale School of Medicine have found evidence that a hormone produced in the stomach directly stimulates the higher brain functions of spatial learning and memory development, and further suggests that we may learn best on an empty stomach.

Published in the February 19 online issue of Nature Neuroscience by investigators at Yale and other institutes, the study showed that the hormone ghrelin, produced in the stomach and previously associated with growth hormone release and appetite, has a direct, rapid and powerful influence on the hippocampus, a higher brain region critical for learning and memory.

The team, led by Tamas L. Horvath, chair and associate professor of the Section of Comparative Medicine at Yale School of Medicine, and associate professor in the Department of Obstetrics, Gynecology & Reproductive Sciences, and Neurobiology, first observed that peripheral ghrelin can enter the hippocampus and bind to local neurons promoting alterations in connections between nerve cells in mice and rats. Further study of behavior in the animals showed that these changes in brain circuitry are linked to enhanced learning and memory performance.

Because ghrelin is highest in the circulation during the day and when the stomach is empty, these results also indicate that learning may be most effective before meal-time.

'Based on our observations in animal models, a practical recommendation could be that children may benefit from not overeating at breakfast in order to make the most out of their morning hours at school,' said Horvath. 'The current obesity epidemic among American school children, which to some degree has been attributed to bad eating habits in the school environment, has been paralleled by a decline of learning performance. It is however too early to speculate if hormonal links between eating and learning are involved in that phenomenon.'

Horvath said that high ghrelin levels or administration of ghrelin-like drugs could also protect against certain forms of dementia, because aging and obesity are associated with a decline in ghrelin levels and an increased incidence of conditions of memory loss like Alzheimer's disease."

"Welcome to the BASIS web site

* BASIS is a new project developing web-based services for quantitative study of the biology of ageing.

* BASIS is a collaborative project, coordinated from the multidisciplinary Institute for Ageing and Health at the University of Newcastle Upon Tyne.

* BASIS is currently funded by the UK Biotechnology and Biological Sciences Research Council, the Medical Research Council, and Department for Trade and Industry.

* For a fuller description of the BASIS project see Nature Reviews Molecular Cell Biology (2003) 4, 243-249 (abstract)

Goals of the BASIS project

Ageing is highly complex involving multiple biochemical and cellular mechanisms affecting multiple tissues within the organism.
This inherent complexity means that although work on the biology of ageing is now advancing fast, information remains highly fragmented.
Our goal is to deliver a web-based system that will serve the biology-of-ageing research community by helping to integrate data and hypotheses from diverse biological sources.
We aim to create a community-based web of activity that will sustain the functions of BASIS beyond the initial 4-year period of funding. Please join us in making this happen."

MZmine - LC/MS Toolbox: "Key features

The MZmine toolbox as described in the BMC Bioinformatics paper (v. 0.42) contains:

* GUI for import, visualization, processing, and export of spectra.
* Smoothing and filtering of spectra.
* Peak detection for continuous and centroid spectral data.
* Spectral alignment.
* Normalization methods.

The latest (v. 0.52) also includes (see also change log):

* Compatibility with NetCDF and mzXML data formats.
* Possibility to distribute data processing on multi-processor computers and computing clusters.
* Batch processing.
* Improved visualization and processing of centroided data.
* New filtering methods.

For the future versions, we are working on

* Isotope pattern detection.
* Handling multiple data files from the same sample (e.g. MS/MS, ESI+/-, ...).
* Database connectivity.
* New normalization algorithms.
* Compatibility with mzData format."

TrimSpreadsheet - TrimPath - Trac: "TrimSpreadsheet

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Detection of DNA on nanotubes offers new sensing, sequencing technologies: "Detection of DNA on nanotubes offers new sensing, sequencing technologies

James E. Kloeppel, Physical Sciences Editor
217-244-1073; kloeppel@uiuc.edu
2/17/06

Michael Strano, professor of chemical and biomolecular engineering, and his students have found that DNA-wrapped nanotubes can be used to target specific DNA sequences.

CHAMPAIGN, Ill. — Researchers at the University of Illinois at Urbana-Champaign who recently reported that DNA-wrapped carbon nanotubes could serve as sensors in living cells now say the tiny tubes can be used to target specific DNA sequences. Potential applications for the new sensors range from rapid detection of hazardous biological agents to simpler and more efficient forensic identification.

In the Jan. 27 issue of the journal Science, chemical and biomolecular engineering professor Michael Strano and his students reported that single-walled carbon nanotubes coated with DNA could be placed in living cells and detect trace amounts of harmful contaminants. In a paper accepted for publication in the journal Nano Letters, and posted on its Web site, the researchers report they have taken the technique a significant step further.

“We have successfully demonstrated the optical detection of selective DNA hybridization on the surface of a nanotube,” said Strano, who is also a researcher at the Beckman Institute for Advanced Science and Technology and at the university’s Micro and Nanotechnology Laboratory. “This work opens possibilities for new types of nanotube-based sensing and sequencing technologies.”

In its natural state, DNA is in the double stranded form, consisting of two complementary strands, each resembling the side of a ladder and having a specific sequence of nucleotide bases as rungs. Hybridization refers to the spontaneous binding of two complementary strands through base pair matching.

By wrapping one strand of DNA around the surface of a carbon nanotube, the researchers can create a sensor that is targeted for a particular piece of complementary DNA. When the complementary DNA then binds to the DNA probe, the nanotube’s natural near-infrared fluorescence is shifted slightly, and can readily be detected.

“The optical detection of specific DNA sequences through hybridization with a complementary DNA probe has many potential applications in medicine, microbiology and environmental science,” said Esther Jeng, a graduate student at Illinois and the paper’s lead author. “For example, this system could be used in genomic screening to detect sequences that encode for genetic disorders, and that are precursors to diseases such as breast cancer.”

“Optical detection allows for passive sensing of hybridization, meaning there is no need to pass voltage or current through the system,” Jeng said. “Furthermore, optics yield high-resolution signals and require a relatively simple setup. And, because our detection setup is in solution, we can sense in a natural biological environment.”

Co-authors of the paper with Strano and Jeng are undergraduate students Joseph Gastala, Anthonie Moll and Amanda Roy. The work was funded by the National Science Foundation."