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Chemical imaging brings cancer tissue analysis into the digital age

Chemical imaging brings cancer tissue analysis into the digital age | Future biomed | Scoop.it

Imperial College London researchers have developed a new method for analyzing biological samples based on their chemical makeup that could transform the way medical scientists examine diseased tissue.

 

When tests are carried out on a patient’s tissue today, such as looking for cancer, the test has to be interpreted by a histology specialist, which can take weeks to get a full result.

 

Scientists have proposed using mass spectrometry imaging (MSI), which uses technologies that reveal how hundreds or thousands of chemical components are distributed in a tissue sample. But currently proposed MSI workflows are subject to several limitations, including nonoptimized raw data preprocessing, imprecise image coregistration, and limited pattern recognition capabilities.

 

In PNAS, the Imperial College London researchers have now outlined a comprehensive new strategy for effectively processing MSI data and building a database of tissue types. In MSI, a beam moves across the surface of a sample, producing a pixelated image. Each pixel contains data on thousands of chemicals present in that part of the sample. By analyzing many samples and comparing them to the results of traditional histological analysis, a computer can learn to identify different types of tissue.


A single test taking a few hours can provide much more detailed information than standard histological tests, for example showing not just if a tissue is cancerous, what the type and sub-type of cancer, which can be important for choosing the best treatment. The technology can also be applied in research to offer new insights into cancer biology.

 

According to Kirill Veselkov, M.D., corresponding author of the study from the Department of Surgery and Cancer at Imperial College London, “MSI is an extremely promising technology, but the analysis required to provide information that doctors or scientists can interpret easily is very complex. This work overcomes some of the obstacles to translating MSI’s potential into the clinic. It’s the first step towards creating the next generation of fully automated histological analysis.”

 

The technology will also be useful in drug development. To study where a new drug is absorbed in the body, pharmaceutical scientists attach a radioactive label to the drug molecule, then look at where the radiation can be detected in a laboratory animal. If the label is detached when the drug is processed in the body, it is impossible to determine how and where the drug has been metabolized. MSI would allow researchers to look for the drug and any metabolic products in the body, without using radioactive labels.


Via Dr. Stefan Gruenwald
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MS Imaging differentiation of tissues

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Tiny edible batteries could be the future of biomedical gadgets - Ecopreneurist

Tiny edible batteries could be the future of biomedical gadgets - Ecopreneurist | Future biomed | Scoop.it
Tiny edible batteries could be the future of biomedical gadgets
Ecopreneurist
A low-cost non-toxic sodium ion battery could be swallowed like a pill and used to power biomedical sensors or other biodegradable medical gadgets.
Dmitry Alexeev's insight:

edible batteries))

 

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Illumina Speaks About Plans for Clinical Sequencing

Illumina Speaks About Plans for Clinical Sequencing | Future biomed | Scoop.it
Clinical Informatics News | Illumina will use 2014 to continue development of new diagnostic applications for the MiSeqDx, including in the oncology space, and to submit the HiSeq 2500 for FDA approval.
Dmitry Alexeev's insight:

8 MisSeqDX are sold

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Functional annotation of noncoding sequence variants : Nature Methods : Nature Publishing Group

Functional annotation of noncoding sequence variants : Nature Methods : Nature Publishing Group | Future biomed | Scoop.it
The genome-wide annotation of variants (GWAVA) software predicts whether noncoding variants are likely to be functional using a classifier trained on a range of genomic and epigenomic annotations.
Dmitry Alexeev's insight:

significance of non-coding SNPs estimated

 

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Variations in predicted risks in personal genome testing for common complex diseases : Genetics in Medicine : Nature Publishing Group

Variations in predicted risks in personal genome testing for common complex diseases : Genetics in Medicine : Nature Publishing Group | Future biomed | Scoop.it

Via Yurii Aulchenko
Dmitry Alexeev's insight:

well what to expect other then the result - however i'm not sure if snp simulation was completely correct - as no info for epistatis is surely used

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Yurii Aulchenko's curator insight, January 30, 6:41 AM

Example of methodology to be used while evaluating consumer genomic tests. While based on simulations and hence not perfect, it is scientifically sound, and possible to implement without investing millions in new samples

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Genome Medicine | Full text | Pervasive sequence patents cover the entire human genome

The scope and eligibility of patents for genetic sequences have been debated for decades, but a critical case regarding gene patents (Association of Molecular Pathologists v. Myriad Genetics) is now reaching the US Supreme Court. Recent court rulings have supported the assertion that such patents can provide intellectual property rights on sequences as small as 15 nucleotides (15mers), but an analysis of all current US patent claims and the human genome presented here shows that 15mer sequences from all human genes match at least one other gene. The average gene matches 364 other genes as 15mers; the breast-cancer-associated gene BRCA1 has 15mers matching at least 689 other genes. Longer sequences (1,000 bp) still showed extensive cross-gene matches. Furthermore, 15mer-length claims from bovine and other animal patents could also claim as much as 84% of the genes in the human genome. In addition, when we expanded our analysis to full-length patent claims on DNA from all US patents to date, we found that 41% of the genes in the human genome have been claimed. Thus, current patents for both short and long nucleotide sequences are extraordinarily non-specific and create an uncertain, problematic liability for genomic medicine, especially in regard to targeted re-sequencing and other sequence diagnostic assays.
Dmitry Alexeev's insight:

Gene patenting issue)

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Bioinformatics skills help Stanford beat Illumina to $40M stell cell genomics grant

Bioinformatics skills help Stanford beat Illumina to $40M stell cell genomics grant | Future biomed | Scoop.it
Over the past year, Illumina's share price has soared 180% as it has established a dominant position in what is potentially a $20 billion market.
Dmitry Alexeev's insight:

data management and visualization tools beat Illumina experience

 

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Scientists Discover the Very First Hipster | Symbiartic, Scientific American Blog Network

Scientists Discover the Very First Hipster | Symbiartic, Scientific American Blog Network | Future biomed | Scoop.it
You've seen the cartoon before: a fish hoisting itself up on land with its front fins, being greeted with some snarky sign like,
Dmitry Alexeev's insight:

tiktaalik

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Curoverse Raises $1.5 Million to Build Open Source Platform for Genomic and ... - PR Web (press release)

Curoverse Raises $1.5 Million to Build Open Source Platform for Genomic and ... - PR Web (press release) | Future biomed | Scoop.it
Curoverse Raises $1.5 Million to Build Open Source Platform for Genomic and ...
Dmitry Alexeev's insight:

intresting is how to cope with privicy on open platform

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Blood Vessel Bio-Printing to Enter Clinical Trials - ENGINEERING.com

Blood Vessel Bio-Printing to Enter Clinical Trials - ENGINEERING.com | Future biomed | Scoop.it
Blood Vessel Bio-Printing to Enter Clinical Trials ENGINEERING.com A joint effort between researchers at Saga University in Japan and startup Cyfuse Biomedical has yielded a breakthrough in bio-printing that could make it to market in the near...
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Innovation Game Changer: Lee Hood

Innovation Game Changer: Lee Hood | Future biomed | Scoop.it
Dr. Lee Hood appeared in a video series produced by World Free From Cancer and Value of Innovation about five "game changers" who will help make this a cancer-free world.
 

Via Pedro Fernandes
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PLOS Computational Biology: Perturbation Biology: Inferring Signaling Networks in Cellular Systems

PLOS Computational Biology: Perturbation Biology: Inferring Signaling Networks in Cellular Systems | Future biomed | Scoop.it
PLOS Computational Biology is an open-access
Dmitry Alexeev's insight:

i like pictures - don't like formulas)

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PLOS Computational Biology: The Roots of Bioinformatics in Theoretical Biology

PLOS Computational Biology: The Roots of Bioinformatics in Theoretical Biology | Future biomed | Scoop.it

From the late 1980s onward, the term “bioinformatics” mostly has been used to refer to computational methods for comparative analysis of genome data. However, the term was originally more widely defined as the study of informatic processes in biotic systems. In this essay, I will trace this early history (from a personal point of view) and I will argue that the original meaning of the term is re-emerging.

Dmitry Alexeev's insight:

beautiful story from the author of the term bioinformatics

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Lab on a Chip  Home-Miniaturisation for chemistry, physics, biology, materials science and bioengineering

Lab on a Chip  Home-Miniaturisation for chemistry, physics, biology, materials science and bioengineering | Future biomed | Scoop.it
Miniaturisation for chemistry, physics, biology, materials science and bioengineering
Dmitry Alexeev's insight:

wow nver really saw the journal before

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Ever Heard of a Patent Map? They Can Help Predict the Future. - Reuters

Ever Heard of a Patent Map? They Can Help Predict the Future.
Dmitry Alexeev's insight:

patents and publications 

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GenoSpace builds portal for multiple myeloma foundation - Boston Business Journal

GenoSpace builds portal for multiple myeloma foundation - Boston Business Journal | Future biomed | Scoop.it
Less than six months after GenoSpace LLC emerged from stealth mode, and the company has landed a partnership with the Multiple Myeloma Research Founda...
Dmitry Alexeev's insight:

genospace - now that news - but i need this information)

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Rescooped by Dmitry Alexeev from Complexity - Complex Systems Theory
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Puppies! Now that I’ve got your attention, complexity theory

Animal behavior isn't complicated, but it is complex. Nicolas Perony studies how individual animals -- be they Scottish Terriers, bats or meerkats -- follow simple rules that, collectively, create larger patterns of behavior. And how this complexity born of simplicity can help them adapt to new circumstances, as they arise.

Via Bernard Ryefield
Dmitry Alexeev's insight:

gotta save for alter

 

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Chemical imaging brings cancer tissue analysis into the digital age

Chemical imaging brings cancer tissue analysis into the digital age | Future biomed | Scoop.it

Imperial College London researchers have developed a new method for analyzing biological samples based on their chemical makeup that could transform the way medical scientists examine diseased tissue.

 

When tests are carried out on a patient’s tissue today, such as looking for cancer, the test has to be interpreted by a histology specialist, which can take weeks to get a full result.

 

Scientists have proposed using mass spectrometry imaging (MSI), which uses technologies that reveal how hundreds or thousands of chemical components are distributed in a tissue sample. But currently proposed MSI workflows are subject to several limitations, including nonoptimized raw data preprocessing, imprecise image coregistration, and limited pattern recognition capabilities.

 

In PNAS, the Imperial College London researchers have now outlined a comprehensive new strategy for effectively processing MSI data and building a database of tissue types. In MSI, a beam moves across the surface of a sample, producing a pixelated image. Each pixel contains data on thousands of chemicals present in that part of the sample. By analyzing many samples and comparing them to the results of traditional histological analysis, a computer can learn to identify different types of tissue.


A single test taking a few hours can provide much more detailed information than standard histological tests, for example showing not just if a tissue is cancerous, what the type and sub-type of cancer, which can be important for choosing the best treatment. The technology can also be applied in research to offer new insights into cancer biology.

 

According to Kirill Veselkov, M.D., corresponding author of the study from the Department of Surgery and Cancer at Imperial College London, “MSI is an extremely promising technology, but the analysis required to provide information that doctors or scientists can interpret easily is very complex. This work overcomes some of the obstacles to translating MSI’s potential into the clinic. It’s the first step towards creating the next generation of fully automated histological analysis.”

 

The technology will also be useful in drug development. To study where a new drug is absorbed in the body, pharmaceutical scientists attach a radioactive label to the drug molecule, then look at where the radiation can be detected in a laboratory animal. If the label is detached when the drug is processed in the body, it is impossible to determine how and where the drug has been metabolized. MSI would allow researchers to look for the drug and any metabolic products in the body, without using radioactive labels.


Via Dr. Stefan Gruenwald
Dmitry Alexeev's insight:

MS Imaging differentiation of tissues

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Cambridge: From the lab to the limelight - Cambridge Network

Cambridge: From the lab to the limelight - Cambridge Network | Future biomed | Scoop.it
Dmitry Alexeev's insight:

old report on cambridge startups - however makes sense to read and understand the scale and inetrconnection

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This is real innovation: Illumina's new machine could slash cost of ...

This is real innovation: Illumina's new machine could slash cost of ... | Future biomed | Scoop.it
50 startup lessons for 2014: AngelList, KISSmetrics founders help kick off Launch This Year · 21 hrs ago ....
Dmitry Alexeev's insight:

According to Illumina chief executive Jay Flatley, the HiSeq X Ten can sequence human genomes accurately enough to reliably identify DNA variants 10 times faster than its predecessor.  - WOW What a brearkthrough - you put 10 machines together and it is working 10 times faster - scalability.  
It is cheaper -  however you need to sequence 2500 genomes to save the money (every genome saves 4000) and it will take you 156 days of only running time and additional 2.5 M $ - so it makes sense to start only with 15 - 20 M projects

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New Pills Deliver Bacteria, Not Drugs, To Cure Us

New Pills Deliver Bacteria, Not Drugs, To Cure Us | Future biomed | Scoop.it

It seems that nearly every day, scientists connect another medical condition to atypical gut bacteria populations. Researchers have claimed that gut bacteria play a role not just in digestive health but even in basic brain function and mental health.
Certain bacteria are so clearly good for us that several companies are looking to market pills filled not with chemical drugs, but with bacteria.
A few pharmaceutical startups have already begun testing bacterial medicines in hopes of finding the right strain or stains of bacteria to cure widespread and still mysterious illnesses.


Via Szabolcs Kósa
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Ji-Wei's curator insight, January 17, 1:02 AM

New pills are being developed that cure us by using something different. These new pills are not using drugs but are using help bacteria. Scientists are testing these new drugs to find cures for widespread and mysterious diseases. I am wondering when these pills will become more widespread?

 

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3-D printed livers offer glimpse into the future of biomedical research - NBCNews.com

3-D printed livers offer glimpse into the future of biomedical research - NBCNews.com | Future biomed | Scoop.it
3-D printed livers offer glimpse into the future of biomedical research
NBCNews.com
Scientists have already used 3-D printing technology to help produce human body parts like an ear, but what about a full-blown organ like a liver, kidney or heart?
Dmitry Alexeev's insight:

prometeus project)

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What is it like to work with Elon Musk?

What is it like to work with Elon Musk? | Future biomed | Scoop.it
Answer (1 of 8): After working for Elon for over 5 years at SpaceX as the Head of Talent Acquisition, there are many potential answers to this question.
Dmitry Alexeev's insight:

leader he is

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$1,000 Pill For Hepatitis C Spurs Debate Over Drug Prices

$1,000 Pill For Hepatitis C Spurs Debate Over Drug Prices | Future biomed | Scoop.it
A drug to cure hepatitis C has FDA approval. But at $84,000 per person, who will have access to it?

Via Yurii Aulchenko
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Getting Genetics Done: Curoverse raises $1.5M to develop & support an open-source bioinformatics data analysis platform

Getting Genetics Done: Curoverse raises $1.5M to develop & support an open-source bioinformatics data analysis platform | Future biomed | Scoop.it
Dmitry Alexeev's insight:

getting done for sure

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A 1024-sample serum analyzer chip for cancer diagnostics - Lab on a Chip (RSC Publishing)

A 1024-sample serum analyzer chip for cancer diagnostics - Lab on a Chip (RSC Publishing) | Future biomed | Scoop.it
We present a platform that combines microarrays and microfluidic techniques to measure four protein biomarkers in 1024 serum samples for a total of 4096 assays per device.
Dmitry Alexeev's insight:

formal clinical screens will be done it this manner

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