Algorithmic cancer diagnosis: Raman spectra reveal pre-cancer

Improving cervical cancer detection

From Chemometrics and Informatics

A genetic algorithm can be applied to Raman spectra for the rapid, in vivo identification of pre-cancerous tissues in the cervix, according to work recently published in The Analyst. 

Shiyamala Duraipandian, Wei Zheng and Zhiwei Huang of the Optical Bioimaging Laboratory, in the Department of Bioengineering, at the National University of Singapore and Joseph Ng, Jeffrey Low, and A. Ilancheran in the Division of Gynecologic Oncology, at the National University Hospital explain how cancer of the cervix is the second most common malignancy and the fifth leading cause of cancer deaths among women worldwide. Early, accurate diagnosis is essential for good outcomes but the Papanicolaou (Pap) smear test and colposcopy although routine procedures in cervical cancer screening have inherent false positives and negatives. An approach that can be carried out in vivo that precludes false positives and negatives and can spot pre-cancerous cells readily could shift the statistics on this disease towards lower morbidity. 

Writing in The Analyst, the team explains how they have evaluated the clinical utility of near-infrared (NIR) Raman spectroscopy in detecting pre-cancerous cells. The team used a genetic algorithm-partial least squares-discriminant analysis (GA-PLS-DA) technique to allow them to interpret the Raman NIR spectra. Such a cheminformatics analysis would allow them to quickly detect biomolecular changes in cervical tissues associated with the earliest stages of cancer, so-called neoplastic transformations. 

The team tested their approach on 105 NIR Raman spectra obtained from 29 recruited patients from 57 different sites on the cervix, 35 normal and 22 known pre-cancerous sites. The genetic algorithm incorporated into PLS allowed them to investigate the significant biochemical Raman bands for differentiation between normal and pre-cancerous cervical tissues. As such, they identified seven diagnostically significant Raman bands related to proteins, nucleic acids and lipids in tissue. "This yielded a diagnostic accuracy of 82.9% (sensitivity of 72.5% (29/40) and specificity of 89.2% (58/65)) for pre-cancer detection," the team says.

Ailing smear campaign

By comparison, the Pap smear has a diagnostic sensitivity and specificity in the range 30 to 87% and 86 to 100%, respectively. However, it cannot offer high detection sensitivity and specificity simultaneously. Likewise, colposcopy is highly sensitive at about 96% but has specificity as low as 48% for cervical pre-cancer/cancer examination. "Distinguishing low-grade pre-cancer from normal/benign cervical tissue is also difficult even in the hands of expert colposcopists because the benign changes in the cervix tissues may also express similar features of low-grade pre-cancer," the team explains. All of which means that many women end up having unnecessary biopsies and treatments to allow their oncologist to make a diagnosis and to achieve a positive outcome for their patient. 

The team suggests that their NIR Raman approach with its robust statistical analysis could radically change how cervical cancer and pre-cancer are diagnosed. The researchers believe that, "The results of this exploratory study suggest that Raman spectroscopy in conjunction with GA-PLS-DA and dCV methods has the potential to provide clinically significant discrimination between normal and pre-cancer cervical tissues at the molecular level." 

The researchers are currently carrying out additional in vivo Raman measurements with a group of an additional fifty patients. This, they say, will provide them with a larger Raman spectroscopic data set on which to build and even more stable analytical model. They are also working to log factors that might confounding the genetic algorithm during analysis, such as biomolecular differences due to age, menopausal status, race, human papilloma virus (HPV) infection and whether the patients are smoker or non-smokers. These factors will ultimately be incorporated into the model to improve accuracy still further. "We anticipate that in vivo Raman spectroscopy associated with robust GA-PLS-DA and dCV modelling can become a clinically useful tool for rapid, non-invasive detection of cervical pre-cancer at the molecular level during clinical colposcopic examination," the team concludes.

Dropbox

By Edward Mendelson

Dropbox is the simplest, most elegant file-synchronization tool I've ever used. Dropbox Basic provides 2GB of storage free, and Dropbox Pro gives you 50GB for $9.95 per month or $99.95 per year. The service stores files with strong encryption on multiple servers in Amazon's S3 service and works equally smoothly on Windows, Mac, and Linux PCs. If you prefer to synchronize folders you already have on your system, or if you want to keep several folders fully synchronized between multiple machines, Dropbox may not be for you. It synchronizes only files stored in a single dedicated folder. But its smooth and hassle-free operation make it our Editors' Choice. 

You start by signing up on Dropbox's Web site, then downloading and installing the client program. This creates a new folder called "My Dropbox" in your Documents folder (you can move it later) and a system tray icon that lets you open it with just a double click. From this same icon, you can also reach other preference settings, such as the folder's location and throttles on upload and download speeds. Another nice option on the pop-up menu is the "Forums" item, which opens a browser window on Dropbox's user support forum; you'll find the dialogue between users and developers livelier than on most competing services' sites.

Like its rival services, Dropbox stores synchronized files in the cloud so they're available at any machine on which you've installed Dropbox. You can also reach your files through a Web interface from any Internet-connected system. Dropbox's storage preserves copies of earlier versions of the files in My Dropbox, so you always have the most current copy on your computers. I liked that you can still access older versions (or files you deleted or moved) with just an Internet connection. One attractive feature (also available in SugarSync) is Dropbox's bandwidth-saving ability to upload and download only the parts of files that change during revisions. This isn't always possible, but I've made frequent changes in a 125MB file I synchronize and sometimes found that Dropbox needed to transfer only 2 to 3MB of data to update the file. That's a decent bandwidth savings. 

When the installer creates the My Dropbox folder, it also creates a subfolder called Public. Files placed there aren't immediately visible to anyone, but by right-clicking on one and choosing the Copy Public Link, you create a Web address of a permanent, public link to the file that you can publish on the Web or send to friends or colleagues—even if they don't use Dropbox. (You should use this feature only for files you don't need to restrict to specific users, because there's no password protection.) I even built a small Web site in my Public folder by filling it with an HTML file and images and sending the link to friends so they could open it in their browsers. A similar feature with another subfolder called Photos lets you send a link to a Public Gallery that anyone can use to view any photos you've copied into it.

A slightly different feature uses invitation-only shared access to folders you create anywhere in My Dropbox. Right-click the icon of the folder you want to share, then choose an option to share the folder. The Dropbox Web interface opens, and you can send invitations to friends and colleagues that let them add, edit, or delete the files in the folder. They'll need a free Dropbox account, but they won't need to install the client if they're satisfied with accessing the folder over the Web. If they do install the Dropbox client, the shared folder will automatically download to their My Dropbox folder.

One major plus for Dropbox is its clean, intelligent design. When you right-click on a file in My Dropbox, you can choose the "Revisions…" option to start the Web interface and see a list of changes for that file. This is far more convenient than anything offered by SugarSync or Syncplicity, which force you to hunt down files you want in either a Web interface or a separate program and then choose to see revisions made to them.

The Web interface is clean and efficient—it looks a bit like Facebook without the clutter. At the top is a collapsible list of Recent Events listing files you've recently edited, added, or removed from Dropbox. You can even create an RSS feed of these recent changes, so you can be alerted to changes friends or colleagues make to shared files. Beneath the Recent Events is a list of your files, complete with icons for downloading earlier revisions of current files or deleted files, or removing files entirely.

I said earlier that Dropbox can sync only files in its Dropbox folder, but expert users can overcome that limitation fairly easily. On Vista (but not XP), Mac, or Linux, you can create a symbolic link inside My Dropbox to any file or folder anywhere on the system, and those files or folders will be synchronized as if they're actually in My Dropbox. Dropbox promises to add a "Watch Any Folder" feature in the future that will make it work in the same way its rival products do.

Dropbox is an example of software that gets virtually everything right—including automatic updating of itself when a new version appears. When the "Watch Any Folder" feature arrives, Dropbox will be all the more useful. Even without that ability, however, I was impressed enough to buy a year's subscription after testing it for this review. Dropbox is our Editors' Choice for file-synchronization services.

   

Video - What is Dropbox?

ජීමේල් වෙතින් නොමිලේ ජංගම දුරකථන සඳහා SMS චැට් පහසුකම

gossip9.com වලින්

දැන් ගූගල් සමාගමේ ජීමේල් සේවාව මගින් එස්.එම්.එස් මගින් චැට් කිරීමේ පහසුකම හදුන්වා දී තිබෙනවා.ශ්‍රී ලංකාව තුල මෙයට ක්‍රියාත්මක කල හැක්කේ ඩයලොග් හා මොබිටෙල් දුරකථන තුල පමණි.

ජීමේල් තුලින් එස්.එම්.එස් චැට් සිදුකරනා ආකාරය පහතින්.

ජීමේල් ගිණුමේ වම්පස ඇති මෙනුවේ Send SMS යන කොටුව තුලට පණිවුඩය යැවිය යුතු ජංගම දුරකථන අංකය යොදන්න.

ඉන්පසු එම දුරකථන අංකයට නමක් යොදා සේව් කරගන්න.

 දැන් ඔබට සුපුරුදු පරිදි ඔබ යෙදු ජංගම දුරකථන අංකයද සහිතව චැට් බොක්ස් එකක් ලැබෙන අතර එහි ටයිප් කරන දෑ අදාළ දුරකථන අංකයට එස්.එම්.එස් පණිවිඩයක් ආකාරයෙන් ලැබේ.

යවනු ලබන පණිවිඩයට ජංගම දුරකථනය මගින්ම රිප්ලයි කල හැකි අතර එය ජීමේල් චැට් බොක්ස් එක තුල පණිවුඩය යවන්නාට දර්ශනය වේ.

• ඔබට නොමිලේ ලැබෙන එස්.එම්.එස් සලාකය එස්.එම්.එස් 50 ක් වේ. 
• ඔබ පණිවිඩය යවන ජංගම දුරකථන ඔබට පිළිතුරු සැපයුවහොත් එම එක් පිළිතුරක් පාසා තවත් එස්.එම්.එස් 5 ක් නොමිලේ යැවීමට ඔබට හැකියාව ලැබෙනවා.(උපරිමය 50 දක්වා) 
• ඔබට නොමිලේ ලැබෙන පණිවුඩ ප්‍රමාණය 0 වුවහොත් පැය 24 ක් තුල නැවත නොමිලේ එස්.එම්.එස් ප්‍රමාණයක් ලැබෙනු ඇත.

එස්.එම්.එස් කොටුව ඔබේ දර්ශන වන්නේ නැත්නම් පහත පියවර අනුගමනය කරන්න.

Evernote

From Wikipedia, the free encyclopedia

Evernote is a suite of software and services designed for notetaking and archiving. A "note" can be a piece of formatted text, a full webpage or webpage excerpt, a photograph, a voice memo, or a handwritten "ink" note. Notes can also have file attachments. Notes can be sorted into folders, then tagged, annotated, edited, given comments, searched and exported as part of a notebook. Evernote supports a number of operating system platforms (including Microsoft Windows, Mac OS X, Android, iOS and WebOS), and also offers online synchronization and backup services.

The Evernote web service launched into open beta on June 24, 2008^[1] and has reached 11 million users.^[2] In October 2010, the company raised a $20 million USD funding round led by Sequoia Capital with participation from Morgenthaler Ventures and DoCoMo Capital.^[3] Since then, the company also has raised an additional USD $50 million in funding led by Sequoia Capital and Morganthaler Ventures.^[4]

Evernote is available in a paid version or a more restricted, advertising-supported, "free" version. Use of the online server is free up to a certain monthly usage limit, with additional monthly use reserved for paying subscribers.

Fore more details please visit Evernote  and Video Tutorial.

Design optimisation by evolution

From Cambridge Research Blog

By adopting the principles of natural selection, engineers are using survival of the fittest to breed better design solutions.

An important legacy of Charles Darwin’s theories, unimaginable 150 years ago, has been the development of a thriving field of computational science based around the ideas of evolution by natural selection. Evolutionary computation, as it is known, encompasses a variety of methods, the most well known being evolution strategies, genetic algorithms and genetic programming. All seek to solve challenging optimisation problems (the problem of finding the best solution from all feasible solutions) in a vast range of application areas.

Although the methods differ in the detail of their implementation, they all follow the same basic blueprint: ‘parents’ are selected from a current population of available solutions, with better (fitter) solutions being selected more often; ‘offspring’ are bred by combining portions of the parents’ ‘chromosomes’ (the set of parameters that define the solution); and finally, small random ‘mutations’ are made to the offspring’s chromosomes, analogous to the copying errors that occur in real-world biological reproduction. The end result – the algorithm – can often succeed in solving problems where other methods fail.

 

Engineering design

The Computational Design Group, led by Dr Geoff Parks within the Cambridge Engineering Design Centre, aims to improve the design process and designed products by developing methods that effectively exploit the potential of computational optimisation to enhance the creativity and decision-making of engineering designers.

The optimisation of an engineering design is usually a multi-objective task: the designer wants to improve several objectives, or attributes, of the design simultaneously. Inevitably these objectives are often in conflict as it’s frequently not possible to improve one objective for an optimised design without making another worse. Evolutionary computation methods can readily be adapted to tackle multi-objective problems. In so doing, they identify the trade-off surface – the set of solutions for which it is impossible to improve one objective without another deteriorating – allowing the designer to make a fully informed choice of final design.

There is widespread interest in applying these types of optimisation technique to real-world engineering design problems. Researchers in the Computational Design Group are using evolutionary computation to tackle a diverse range of design optimisation problems: from improving hybrid electric vehicle drive systems; to trading off reduction in pollutants and noise in aeroengines; to designing cheaper, more compact space satellites.

 

Selective breeding

Developing evolutionary algorithms that perform well on particular applications can pose challenges. It is not always straightforward to find a suitable way to encode designs ‘genetically’ such that when two good solutions are combined there is a reasonable chance that the characteristics that made them good are preserved in their offspring. Interesting research questions under investigation by the group also surround the issues of how parents are selected. In a virtual world, one can try schemes that would be physically or ethically impossible in the real one. The rules of the game can change too: for instance, the group has found that, in multi-objective optimisation problems, genetic diversity is often naturally maintained in the population as it spreads out across the trade-off surface and therefore highly selective breeding schemes in which only the best solutions are allowed to reproduce can be very effective.

By adapting the principles of Darwinian evolution, we can develop methods that enable engineers to design better submarine propulsion systems or nuclear reactor reload cores or… in fact, the potential applications are about as diverse as the natural world itself.

For more information, please contact the author Dr Geoff Parks (gtp10 AT cam.ac.uk) in the Engineering Design Centre at the Department of Engineering. Much of the group’s research is supported by the Engineering and Physical Sciences Research Council (EPSRC)

Vacancies at Motorola Solutions

DNA's Role In Computer Evolution

By Paul Elias  (CBS  News)

(AP)  It almost sounds too fantastic to be true, but a growing amount of research supports the idea that DNA, the basic building block of life, could also be the basis of a staggeringly powerful new generation of computers.

If it happens, the revolution someday might be traced to the night a decade ago when University of Southern California computer scientist Leonard Adleman lay in bed reading James Watson's textbook "Molecular Biology of the Gene."

"This is amazing stuff," he said to his wife, and then a foggy notion robbed him of his sleep: Human cells and computers process and store information in much the same way.

Computers store data in strings made up of the numbers 0 and 1. Living things store information with molecules represented by the letters A,T,C and G.

There were many more intriguing similarities, Adleman realized as he hopped out of bed. He began sketching the basics of DNA computing.

Those late-night scribbles have long since given way to hard science, backed by research grants from NASA, the Pentagon and other federal agencies. Now a handful of researchers around the world are creating tiny biology-based computers, hoping to harness the powers of life itself.

They call their creations "machines" and "devices." Really, they are nothing more than test tubes of DNA-laden water, and yet this liquid has been coaxed to crunch algorithms and spit out data.

The problems solved by DNA computers to date are rudimentary. Children could come up with the answers more quickly with a pencil and paper.

But the researchers hope to someday inject tiny computers into humans to zap viruses, fix good cells gone bad and otherwise keep us healthy.

They're also pursuing the idea that genetic material can self-replicate and grow into processors so powerful that they can handle problems too complex for silicon-based computers to solve.

Eventually, the scientists aim to create self-sustaining computers that can be used, for instance, on deep-space voyages, to monitor and maintain the health of humans on board.

What struck Adleman most that night he jumped out of bed was how a living enzyme "reads" DNA much the same way computer pioneer Alan Turing first contemplated in 1936 how a machine could read data.

"If you look inside the cell you find a bunch of amazing little tools," said Adleman, who made the first DNA-based computation in 1994. "The cell is a treasure chest."

Adleman used his computer to solve the classic "traveling salesman" mathematical problem — how a salesman can visit a given number of cities without passing through any city twice — by exploiting the predictability of how DNA interacts.

Adleman assigned each of seven cities a different strip of DNA, 20 molecules long, then dropped them into a stew of millions of more strips of DNA that naturally bonded with the "cities." That generated thousands of random paths, in much the same way that a computer can sift through random numbers to break a code.

From this hodgepodge of connected DNA, Adleman eventually extracted a satisfactory solution — a strand that led directly from the first city to the last, without retracing any steps. DNA computing was born.

What these researchers are essentially trying to do is control, predict and understand life itself. So there's little wonder that their machines are decades away from being anything more than a neat laboratory trick.

Biologists are only now grasping the basics of how and why DNA unzips, recombines and sends and receives information. DNA is notoriously fragile and prone to transcription errors — as the world's cancer rates prove.

These realizations and others have tempered initial expectations that DNA would ultimately replace silicon chips. Still, researchers in this field believe they remain on the vanguard of a computational revolution.

After all, a single gram of dried DNA, about the size of a half-inch sugar cube, can hold as much information as a trillion compact discs. Adelman senses that can be exploited somehow, some way.

"I'm just not sure how," he said.

One problem is that setting up DNA computers and extracting results from them can take days, sometimes weeks. Perhaps a bigger obstacle is controlling biological developments to generate accurate calculations. DNA doesn't always behave like it's expected to.

Columbia University researcher Milan Strojanovic, using NASA money, is developing a biology-based machine that doesn't need hands-on human help to compute.

"We want to use that technology for astronauts for health maintenance," said NASA scientist Paul Fung, who helps administer Strojanovic's grant as part of a $15 million program to develop biomechanical sensors for use in space travel.

Ehud Shapiro of Israel's Weizmann Institute of Science envisions programming tiny molecules with medical information and injecting them into people. He received a U.S. patent in 2001 for a "computer" within a single droplet of water that uses DNA molecules and enzymes as input, output, software and hardware.

This year, researchers in his lab added a power source to the device, capitalizing on the energy created when DNA molecules naturally break apart. In February, Guinness World Records Ltd. called the team's invention "the smallest biological computing device."

Shapiro also doubts genetics will supplant silicon, but remains optimistic.

"I think they will live together happily," he said, "and be used for different applications."

On Sunday, Strojanovic and a colleague published a paper in the journal Nature Biotechnology describing how they built a biological-based computer that can't lose a game of tic-tac-toe to man, and doesn't need any prompting from outside sources to compete.

"This is the kind of clever use of DNA computation," Adleman said, "that may eventually lead to practical applications."