Daily Archives: February 25, 2017

Discovery of genetic mutation may boost cancer therapies – Medical Xpress

Posted: February 25, 2017 at 2:49 pm

February 24, 2017 by Geri Clark Killer T cells surround a cancer cell. Credit: NIH

A newly discovered type of genetic mutation that occurs frequently in cancer cells may provide clues about the disease's origins and offer new therapeutic targets, according to research from Weill Cornell Medicine and the New York Genome Center.

Using next-generation sequencing technology, scientists have previously traced cancer's roots to mutations that disrupt the sequence of proteins. As a result, the cell either creates hyperactive or dysfunctional versions of proteins, or fails to produce them at all, leading to cancer. Now, a study published Jan. 12 in Cell illuminates a possible new type of driver of the disease: small (one- to 50-letter) insertions or deletions of DNA sequence, also called "indels," in regions of the genome that do not code for protein.

"Those noncoding regions are still important because they contain sequences that affect how genes are regulated, which is critical for normal cell development," said lead author Dr. Marcin Imielinski, an assistant professor of pathology and laboratory medicine at Weill Cornell Medicine and a core member at the New York Genome Center. "We already know they are biologically important. The question is whether they can impact cancer development."

In the study, Imielinski and his colleagues analyzed sequencing data from several publicly available databases of tumor samples, focusing on the 98 percent of the genome that does not code for protein. They initially looked at lung adenocarcinoma, the most common type of lung cancer, and found that the most frequent indel-mutated regions in their genomes landed in genes encoding surfactant proteins.

Though these genes are essential for healthy lung function, they had not previously been associated with lung cancer. However, they are highly and specifically expressed by the cell type that gives rise to lung adenocarcinoma.

The researchers then looked at the genomes of 12 other cancer types and found similar patterns in liver, stomach and thyroid tumors.

"In each cancer, noncoding indels clustered in genes that are critical to organ function, but had not been associated with the cancer," said Imielinski, who is also an assistant professor of computational genomics in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine and a member of the Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine.

Most strikingly, these noncoding indels are very common, occurring in 20 to 50 percent of the associated cancers.

"They occur as frequently as the most famous cancer-causing mutations," said Imielinski, a paid consultant for the company 10X Genomics, which sells devices and technology to analyze genetic information. "Any gene or any sequence that mutated at this frequency has been shown to play a causal role in cancer. That would be an exciting outcome, if we can prove it."

Even if these mutations are not shown to cause cancer, they can be used in the future to improve cancer diagnosis and treatment.

"These mutations can be biomarkers that help us to diagnose a cancer early, or they could be used to pinpoint a primary cancer when there are metastases and we can't find the original cancer," Imielinski said. "There are a lot of potential clinical implications from these findings."

Explore further: Researchers pinpoint key regulatory role of noncoding genes in prostate cancer development

More information: Marcin Imielinski et al. Insertions and Deletions Target Lineage-Defining Genes in Human Cancers, Cell (2017). DOI: 10.1016/j.cell.2016.12.025

Journal reference: Cell

Provided by: Cornell University

Prostate cancer researchers studying genetic variations have pinpointed 45 genes associated with disease development and progression.

The steroid dexamethasone could potentially deter the growth of a prostate cancer subtype that was previously thought to be difficult to treat with medications, Weill Cornell Medicine researchers report. Their findings were ...

New research shows that current approaches to genome analysis systematically miss detecting a certain type of complex mutation in cancer patients' tumors. Further, a significant percentage of these complex mutations are found ...

Researchers from several major U.S. universities and ITMO University in Russia have identified a number of new driver mutations in lung cancer cells that may be responsive to genomically targeted therapies and to immunotherapy.

A Yale-led study describes how a known cancer gene, EGFR, silences genes that typically suppress tumors. The finding, published in Cell Reports, may lead to the development of more effective, individualized treatment for ...

Short, unstable stretches of DNA, called microsatellites, may play a far greater role in the development and progression of cancer than previously thought, UW Medicine researchers report in a study appearing Oct. 3 in the ...

Massachusetts General Hospital (MGH) researchers have identified a mechanism that controls the expression of genes regulating the growth of the most aggressive form of medulloblastoma, the most common pediatric brain tumor. ...

A new discovery by researchers at the Fred Hutchinson Cancer Research Center in Seattle makes an important step in identifying which specific T cells within the diverse army of a person's immune system are best suited to ...

An interaction between two proteins enables cancer cells to use the physical forces of healthy cells to start spreading to other parts of the body.

Scientists at The Wistar Institute and Inovio Pharmaceuticals, Inc. have devised a novel DNA vaccine approach through molecular design to improve the immune responses elicited against one of the most important cancer antigen ...

A newly discovered type of genetic mutation that occurs frequently in cancer cells may provide clues about the disease's origins and offer new therapeutic targets, according to research from Weill Cornell Medicine and the ...

(Medical Xpress)One major challenge in pathology is to determine if a group of cells are cancerous. By 'cancerous' one generally means that they have the potential to grow and spread, or that they have already spread from ...

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New app to bring awareness to internet censorship – Western Herald

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Here in the United States, if the internet isnt working, or is working slowly, the solution is often as simple as calling tech support. In most cases, theyll have the user run a speedtest, and there are millions of sites and applications that provide this service. However, there arent so many sites that allow users to see who has access to their information, and for people in countries where the internet is censored or restricted, even the fastest internet connection wont grant them open access to information.

This is one issue the team working on the Open Observatory of Network Interference project hope to address with their new Ooniprobe app, which, as of Feb. 9, is available in a beta version for free on Google Play and in the App store. The app has three main features, a speed test, a web connectivity test and a test that detects the presence of components that could be responsible for censorship or surveillance.

Without a tool like Ooniprobe, governments have plausible deniability in terms of censorship events, and actually, people claiming that they can't access a website is not in itself proof of intentional, government-commissioned censorship, Arturo Filast the creator of the app said. Now, anyone around the world can run Ooniprobe and can inspect how their network is working and whether censorship is being implemented. The type of data collected by Ooniprobe cannot really be denied by governments since it provides a clear picture into what is happening in a user's network.

Filast believes access information is a fundamental human right, but in the current state of affairs, many countries either censor or severely restrict the internet; with countries such as China, Russia, Saudi Arabia and India showing thousands of blocked sites - including many messaging sites like WhatsApp and Telegram, according to OONI World Map Explorer.

While countries like the United States have considerably fewer reports of censorship and blocked sites, the country isnt entirely free of censorship. Even here at Western Michigan University types of censorship are in place, but according to Chief Technology Officer Tom Wolf, there is a fine line between censorship and internet security.

In my opinion preventing malicious cyber activities that are illegal in nature and/or intended to disrupt normal internet traffic would not be considered a form of censorship. I would view this as cyber security, Wolf said.

This begs the question of exactly where one should draw the line between security and censorship. Most firewalls, such as Merits Palo Alto - the firewall currently in place here at WMU - scan for evidence of malicious activities and dont otherwise censor content.

Filast addressed the very fine line between security and censorship, distinguishing that security measures should restrict themselves solely to universally bad content.

Internet censorship, in any form and of any type of content, is a slippery slope. We see this in countless occasions where it's implementation is passed as an excuse to restrict access to content that is universally bad, but then the same system gets used to implement censorship for content whose value is much debatable, Filast said.

However, Nathan Tabor, a visiting professor and historian focusing on South Asia, expressed concerns over this slippery slope mentality, pointing out that when someone knows their internet activity is being censored, theyre more likely to change their patterns of consumption in a form of implicit censorship.

A lot of my work is in Persian, so I often access sites from Iran, another place that has very restricted internet access. The things that I access have to do with history and literature, pretty innocuous subjects, but perhaps my internet history comes up on the radar of some overzealous homeland security official because Im accessing sites from Iran. With the data mining that happens with my search history, Id look like a terrorist, Tabor said. The sites that you read will fall into some kind of aggravated pattern decided by a security apparatus, regardless whether or not youre doing anything wrong.

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White House media ban is ‘unconstitutional censorship’, America’s National Press Club warns – The Independent

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The National Press Club has condemned Donald Trumps exclusion of select media outlets from a White House press conference, calling the unprecedented action deeply disturbing and likening it to censorship.

Senior figures from the world's leading professional organisation for journalistsjoined a host of other industry leadersin protesting the decision announced by White House Press Secretary Sean Spicer to block news outlets including CNN, TheNew York Times, BBC, TheGuardian and BuzzFeed from the off-camera gaggle.

I find it deeply disturbing and completely unacceptable that the White House is actively running a campaign against a constitutionally enshrined free and independent press, the club's president, Jeffrey Ballou, saidin a statement.

The action harkens back to the darkest chapters of US history and reeks of undemocratic, un-American and unconstitutional censorship. The National Press Club supports our colleagues in the White House Correspondents Association in its protest and calls on the White House to reverse course.Mr Spicer did not give any justification as to why the news outlets had been excluded, however far-right organisations Breitbart News, One America News Network and The Washington Times were all granted access.

Othermajor outlets approved included ABC, CBS, NBC, Fox News, Reuters and Bloomberg, with Associated Press and Time both boycotting the gaggle after the exclusions emerged.

It came just two months after the press secretary promisedthe Trump administration would never ban press access regardless of the political leaning of the publication.

We have a respect for the press when it comes to the government, that that is something you cant ban an entity from, he said. You know conservative, liberal, otherwise I think that is what makes a democracy a democracy versus a dictatorship.

Donald Trump: We are fighting the phoney, fake news

National Press Club Journalism Institute President, Barbara Cochran, also accused Mr Trump of hypocrisy for claiming he loves the First Amendment, which defends the freedom of the press.

The president said, No one loves the First Amendment more than me. We call on the president and his staff to prove that and stop interfering with the ability of all news organisations to do their job of covering the White House, she wrote.

TheNew York Times and Buzzfeed both issued written statements protesting their exclusion from the briefing.

Fox News anchor Bret Baier discouraged conservative news outlets who celebrated the gaggle, citing organisations who defended his network when former President Obama tried to freeze out Fox News in 2009.

Some at CNN and New York Times stood with Fox News when the Obama admin attacked us and tried to exclude us, he wrote on Twitter, a White House gaggle should be open to all credentialed orgs.

It came as the US President renewed his attack on the mainstream media at the Conservative Political Action Conference.

I want you all to know that we are fighting the fake news. Its phony, fake, he said.I called the fake news the enemy of the people. They are the enemy of the people, because they have no sources. They just make them up when there are none.

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Metallica’s James Hetfield on Chinese Censorship: Hopefully One Day They’ll Realize We’re Not a Political Threat – Loudwire

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Raymond Ahner, Loudwire

When bands perform in China, it is no secret that they must submit their song lyrics to the government, who then return to the band with a list of songs they can and cant play as well as allowing certain songs as long as the lyrics are altered to something permissible. Metallicas recent trek to the country was no different, though James Hetfield seemed nonplussed by being forbidden from playing classics like Master of Puppets.

In an interview with South Morning China Post, the frontman was more than understanding about the censorship, stating,Why shouldnt you respect their culture when youre there as a guest and youve been invited to play? We want to be respectful and just because we do things differently, it doesnt mean it should be forced upon [others].

Hetfield is optimistic about returning to China and having the ability to play not just Master of Puppets, but other exclusions like One (in Shanghai) and Hardwired. But hopefully well keep coming back and theyll realize were not a threat politically and we have no agenda except to cross boundaries with music and let people enjoy the songs, he continued. Were not trying to bring a secret message to anybody.

During Iron Maidens performances in China last year, Bruce Dickinson toed the line with the censors, mouthing curse words and instructing the crowd to take a picture despite cameras not being allowed at the concert.

Metallica will embark on a North American stadium tour this summer, bringing along Avenged Sevenfold, Volbeat and Gojira on select dates. For more info and a list of all stops, check our 2017 Guide to Rock + Metal Tours.

Where Do Metallica Ranks Among the Top 50 Hard Rock + Metal Live Acts of All Time?

10 Bands That Were Banned From Countries

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10 Unforgettable James Hetfield Moments

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Behold the censorship machine! – Personal Liberty Digest

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Personal Liberty Poll

Exercise your right to vote.

In an effort to make websites more advertiser friendly some media outlets have taken to eliminating comment sections where, without considerable effort from moderators, they are unable to control the direction of reader conversations. But a Google-funded algorithm could change that via censorship.

The technology, called Perspective, uses machine-learning to ferret out toxic comments. Its designers reportedly based the technologys moderation standards on those used by the team of human moderators tasked with keeping discourse civil on The New York Times website. The Times is also reportedly now using Perspective to expand the number of articles it allows comments to appear on without overtaxing its moderation team.

Developers explain how the tool works thusly:

Perspective is an API that makes it easier to host better conversations. The API uses machine learning models to score the perceived impact a comment might have on a conversation. Developers and publishers can use this score to give realtime feedback to commenters or help moderators do their job, or allow readers to more easily find relevant information, as illustrated in two experiments below. Well be releasing more machine learning models later in the year, but our first model identifies whether a comment could be perceived as toxic to a discussion.

The level of potential toxicity appears largely based on the use of vulgarity or insulting language in comments.

Here are a few examples of comments the technology would deem highly toxic in comments:

And here are a few that are considered the least toxic:

Personal insults and name calling cheapen any pointand theres certainly no shortage of uncomfortable language on the internet. But is the top-down sanitation of comment sections really the answer?

How long before the machine decides whole topics are too uncomfortable for discussion and are likely to cause readers to leave?

And if the problem is online harassment, are we really going to pretend that simply silencing the true assholes among us will make them disappear? Theyll still be out there Ever been in a big city traffic jam?

Civility is important. But pretending that life isnt uncomfortable, and partially so because of the personalities of people we have to deal with, isnt the answer.

Besides, sometimes you just have to call a spade a spade or a f*cking moron.

. Bookmark the

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Jerome Tuccille, Libertarian Author and Trump Biographer, Dies at 79 – New York Times

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New York Times
Jerome Tuccille, Libertarian Author and Trump Biographer, Dies at 79
New York Times
Jerome Tuccille, who wrote one of the first manifestoes of the American libertarian movement and the first biography of Donald J. Trump, died on Feb. 16 at his home in Severna Park, Md. He was 79. The cause was complications of multiple myeloma, his ...

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Viral Facebook post alleging human trafficking tactic was just a poorly attempted prank – The Daily Dot

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Last week a grim Facebook post by 19-year-old Ashley Hardacre went viral with a warning to other women: Beware of items left on your car's windshieldthey could cost you your safety.

According to Women in the World, Hardacre detailed a strange anecdote regarding her own car's windshield. She had just left the mall where she works in Flint, Michigan, and when she arrived at her car, she found a flannel shirt on her windshield.

Next to her, however, were two other carsone of them runningand Hardacre said she immediately felt uneasy and didn't want to get out of her car. She thought it might have just been a mistake, the shirt left by accident, so she tried to remove the shirt with her wipers. It didn't workthe shirt had been completely wrapped around one of the blades.

"Luckily I knew better than to remove the shirt with cars around me so I drove over to a place where I was safe and quickly rolled down my window and got the shirt off," Hardacre wrote.

She had recalled hearing about this tactic before, however, being used by human traffickers to abduct young women. Traffickers would make targets get out of their cars to remove the item from their windshields, and then take women when they were distracted.

Hardacre reported her story to Flint police, who said they had never seen anything like her situation before. Though her Facebook post has since been taken down, it was shared more than100,000 times.

"There have been no other incidences like this. Its kind of unknown as to what or why or who [did this]," Brad Wangler, a Flint Township police detective sergeant, told CBS News earlier this week.

But as it turns out, Hardacre wasn't being targeted by traffickers. No, she wasn't in danger that nightat least not because of the flannel shirt itself. According to MLive, the mysterious shirt was courtesy of dumb, not funny pranksters.

According to Flint police they were able to identify the description of a car as well as two men with the help of the mall where Hardacre works.

"As a result of these interviews, they admitted to putting the shirt on the vehicle as a random prank," a statement from police read. "Also, interior video surveillance at the Genesee Valley Center corroborated their presence at the mall."

The police said the men had no idea that putting the flannel on the car could have been interpreted as a human trafficking tactic, and that they left the parking lot more than an hour before Hardacre left work. They've also apologized to her, because "their actions caused her to feel scared that night."

So, don't worry folks, there is no spiking trend of shirts on cars being used to lure human trafficking victimsjust jerks trying to think up of idiotic ways to scare people.

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New Brain-Reading Computers Let the Paralyzed Communicate Using Their Thoughts – Futurism

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Typing With Thought

Researchers from Stanford University have built a new brain-computer interface (BCI) that allows paralyzed people to type with their brains at a rate faster than was previously possible.

For their study, they worked with threeparticipants with severe limb weakness, two due to Lou Gehrigs disease and one with limited movement due to a spinal cord injury. All three participants had electrode arrays embedded in their brains to record signals from the motor cortex, which controls muscle movement. A cable then transmitted the brain signals to a computer, and they were then translated by algorithms into point-and-click commands that prompted a cursor to move over letters. Basically, participants were able to move the cursor by imagining their own hand movements.

While it took some training, the subjects were able to achieve BCI results that outperformed any available platform today. One patient was able to type 39 correct characters per minute, which is around eight words per minute, proving that BCIs have the potential to enhance communication among people with impaired movement. It should be noted that these typing-rates were achieved without the use of automatic word-completion.

The performance is really exciting. Were achieving communication rates that many people with arm and hand paralysis would find useful. Thats a critical step for making devices that could be suitable for real-world use, says Chethan Pandarinath, one of the authors of the paper, told Stanford.

The Stanford teams contribution toward advancing peoples ability to control machines with just their thoughts reflects the progressbeing made in this field. In addition to this breakthrough, a team from the Wyss Center for Bio and Neuroengineering in Geneva, Switzerland, built a BCI that can decipher thoughts of people with complete locked-in syndrome, giving them the ability to answer yes or no questions. Meanwhile, researchers at Harvard are using BCI tech to restore sight in the blind.

In the U.S. alone, millions of people suffer from paralysis, some from degenerative conditions like ALS and others from unfortunate accidents that cause severe spinal cord injury.This point-and-click approach developed at Stanford could be the key to making a more efficient BCI geared toward improving the quality of life for those people. It could restore their ability to communicate while teams like that at the Center for Sensorimotor Neural Engineering (CSNE)work on ways to use BCIs to help the paralyzed walk again.

With some modifications, the team believes its system could be applied to other devices, including smartphones or tablets. Were approaching half of what, for example, I could probably type on a cell phone, neurosurgeon and co-senior authorJaimie Henderson of Stanford University told Scientific American. This study reports the highest speed and accuracy, by a factor of three, over whats been shown before. In the future, the team hopes to refine the technology so that it becomes wireless, fully implanted, and self-calibrating, thus being able to provide around-the-clock support.

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Our Computers Are Learning How to Code Themselves – Futurism

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On the Hunt for Code

Those of you who followed the first season of HBOs Westworld know that one of the things that made an artificially intelligent (AI) host in the show truly intelligent, so to speak, was the ability to write its own code. Its a form of reasoning with itself something that current AI technology is still far from capable of doing. One company is trying to close that gap viadeep learning algorithms that use probabilistic programming,and now, researchers from Microsoft and the University of Cambridge are bringing us closer to self-coding AI with a system they call DeepCoder.

DeepCoder is a machine learning system that can write its own code. It does this using a technique called program synthesis. Essentially, it creates new programs by combining existing lines of code taken from other software, which is what human coders do. With a particular output in mind, DeepCoder was able to determinewhich lines or pieces of code would be particularly useful.

The approach is to train a neural network to predict properties of the program that generated the outputs from the inputs. We use the neural networks predictions to augment search techniques from the programming languages community, including enumerative search and an SMT-based solver, writes the research team, which is led by Alexander Gaunt from Microsoft Research and Matej Balog from Cambridge. Their study is currently being reviewed for the 5th International Conference on Learning Representations (ICLR 2017) this coming April.

DeepCoder successfully plowed through the basic, input-output style challenges usually set by programming competitions. It was able to search through lines of code more thoroughly and widely than a human coder could, piecing together code in a manner humans might not think of and more quickly. And because DeepCoder is essentially a deep learning algorithm, every time its given a new problem, it gets better at combining lines from source codes.

Ultimately, this algorithm can make programming accessible to non-coders, allowing anyone to easilybuild simple programs. Researcher Marc Brockschmidt, one of DeepCoders creators from Microsoft Research in Cambridge, UK, believes that their approach would make it possible for non-coders to just describe a program and leave the system to build it. All of a sudden, people could be so much more productive, Massachusetts Institute of Technology (MIT) associate professor Armando Solar-Lezama, who wasnt part of the research,told New Scientist. They could build systems that it [would be] impossible to build before.

DeepCoders current version only allows it to handle programming challenges with around five lines of code. Brockschmidt said that future versions of DeepCode could facilitate building routine programs that do information scraping from websites without the need for human coders.The potential for automation that this kind of technology offers could really signify an enormous [reduction] in the amount of effort it takes to develop code, Solar-Lezama said. No need for programmers to start updating their resumes, though, as this tech wouldnt replace humans. Instead, DeepCoder could handle the more tedious parts of programming, while human coders could focus on more sophisticated work.

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