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Category Archives: Transhuman News

How the GOAST in the machine takes the fear out of genomics computing – The Register

Posted: October 5, 2021 at 4:31 am

Sponsored Theres nothing like a crisis to spur innovation, so its no surprise that the last couple of years has brought the issue of how HPC can power genomics research from the rarified to the mainstream.

And while much of the recent focus has been on issues that affect society on a mass scale, there has been steady progress in Precision Medicine, which aims to provide individualised prevention, diagnosis and treatment based on an individuals specific genomic and environmental backgrounds.

But this all depends on massive efforts to sequence large populations, often at a national level, to capture the genetic variation needed to enable precision treatments.

And while this is a formidable human challenge, it is also a massive technical challenge given that current technology can take over 150 hours to process a single entire genome, even when pushing GPU accelerators to the limit.

Lenovos response to this challenge is its Genomics Optimization and Stability Tool, a hardware and software combination that is up to 167 times faster than traditional environments, but which doesnt rely on specialised accelerators, and therefore comes in at up to 50 per cent lower cost.

Or to put it another way, it enables GPU level speeds, and CPU level costs. And if this makes you prick up your ears, youll want to tune into this webinar on The Role of Genomics Analytics in Precision Medicine, courtesy of Intel and Lenovo on October 13 at 1pm BST.

Youll hear about the latest trends in genomics enabled precision medicine and hear how researchers are now able to analyse an entire genome in minutes, rather than days. All without speciality hardware.

Youll also hear about lessons learned in deploying large-scale omics analytics from seasoned learners and expert panellists who have done just that.

Whether youre a data scientist, bioinformatician, researcher or IT administrator, youll come away better informed as to how GOAST has the potential to transform not just precision medicine, but also virology and agriculture.

So, if you want join Lenovo, Intel, and some of the incredible folks working at the cutting edge of genomics, head here and register now.

Sponsored by Lenovo.

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How the GOAST in the machine takes the fear out of genomics computing - The Register

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In vivo structure and dynamics of the SARS-CoV-2 RNA genome – DocWire News

Posted: at 4:31 am

This article was originally published here

Nat Commun. 2021 Sep 28;12(1):5695. doi: 10.1038/s41467-021-25999-1.

ABSTRACT

The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5-UTR and 3-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.

PMID:34584097 | DOI:10.1038/s41467-021-25999-1

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In vivo structure and dynamics of the SARS-CoV-2 RNA genome - DocWire News

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Comprehensive Genomic Features, Therapeutic Biomarkers Identified in Clear Cell Renal Cell Carcinoma – AJMC.com Managed Markets Network

Posted: at 4:31 am

Investigators reported comprehensive genomic features of patients with clear cell renal cell carcinoma, potentially giving providers a better understanding of the molecular features associated with the disease.

In a recent study, investigators reported the comprehensive genomic features of patients with clear cell renal cell carcinoma (ccRCC), which detailed the relationship between immunotherapy biomarkers and gene alterations. The analysis was published in Frontiers in Oncology.

This is the first large-scale comprehensive genomic analysis for Chinese ccRCC patients, and these results might provide a better understanding of molecular features in Chinese ccRCC patients, which can lead to an improvement in the personalized treatment for these patients, wrote the investigators.

ccRCC is the most common subtype of RCC, accounting for 70% to 85% of RCC cases, and is almost uniformly lethal and is considered critical. ccRCC often lacks sensitivity to radiation and chemotherapy and many efforts are being made to establish a biomarker-oriented therapy.

Some targeted therapies targeting vascular endothelial growth factor (VEGF) have greatly improved the prognosis of patients with ccRCC and the use of an immune checkpoint inhibitor, either alone or in combination with other medications, may also be a potential therapeutic target for patients with ccRCC.

Although some studies have reported on the genomic landscape of ccRCC, most of the data had been collected from patients from Western countries or focused on how gene alterations can help determine disease prognosis. Because of this, the genomic landscape in Chinese patients with ccRCC is in need of further investigation.

Revealing comprehensive genomic features is of great importance for understanding ccRCC and developing new therapeutic lines for patients with ccRCC, the investigators said.

The investigators analyzed genomic profiling of DNA of Chinese patients with ccRCC, who had undergone next-generation sequencing (NGS) between January 2017 and March 2020. In total, 880 patients with ccRCC and NGS data were included in the analysis. Immunohistochemistry staining for programmed death-ligand 1 (PD-L1) expression was also conducted for 460 patients of those patients.

PD-L1 expression is associated with improved overall response rates and longer progression-free survival in patients with metastatic RCC who are being administered immunotherapy.

Among the patients, 95.8% harbored at least 1 pathogenic mutation, with somatic alterations for VHL being the most commonly detected mutation among the samples (59.7%). Mutations in PBRM1 were detected in 18.0% of samples and SETD2 alteration were identified in 12.2% of samples. BAP1 alterations were found in 10.2% of samples and TP53 mutations were found in 9.4%.

When comparing the results to the Center Genome Atlas database, the investigators found a higher mutation frequency of VHL (50.0% vs 59.7%; P < .001) and TP53 (3.5% vs 9.4%; P < .001) among the Chinese cohort. Additionally, the Chinese cohort had a lower mutation frequency of PBRM1 than the database (18.0% vs 31.0%; P < .001).

VHL is a tumor suppressor gene that plays a prominent role in cellular oxygen sensing of ccRCC as well as the tumorigenesis that is associated with the disease. Inactivation of VHL is not associated with anti-VEGF receptor inhibitors, but it may help providers predict the effectiveness of hypoxia-inducible factor-2 inhibitors in ccRCC.

Of the patients who were evaluated for expression of PD-L1, 139 (30.2%) were positive for PD-L1 expression. Five (0.7%) patients were classified as microsatellite instability-high. Moreover, 5.9% (n = 52) of the patients were identified to carry pathogenic or likely pathogenic germline mutations for 22 cancer predisposition genes.

The retrospective nature of the analysis was listed as a study limitation as it prevented the investigators from eliminating a potential selection bias. Another limitation involved the lack of information on the cancer subtypes, treatment histories, and survival outcomes of the patients.

Thus, the effect of the biomarkers on treatment decisions and its correlation with survival outcomes need to be further confirmed in further studies, the investigators suggested.

Reference

Huang J, Cai W, Cai B, et al. Comprehensive genomic landscape in Chinese clear cell renal cell carcinoma patients. Front Oncol. Published online September 9, 2021. doi: 10.3389/fonc.2021.697219

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Comprehensive Genomic Features, Therapeutic Biomarkers Identified in Clear Cell Renal Cell Carcinoma - AJMC.com Managed Markets Network

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A first step towards unlocking the power of gene editing – The John Innes Centre

Posted: at 4:31 am

The Environment Secretary George Eustice has announced changes to the regulation of gene edited crop trials for research purposes.

The John Innes Centre welcomes the proposed changes which will allow field trials of genome edited crops, where the genetic changes could have occurred naturally or as a result of traditional breeding methods, to progress without requiring the same level of regulation that applies to genetically modified organisms.

The Government state this change could be implemented as early as the end of the year.

Professor Dale Sanders, Director of the John Innes Centre said, Im pleased that the Government is acting to change the regulation of gene edited plants and I welcome todays announcement. But while DEFRAs announcement is a step forward for crop trials, it is disappointing that the decision applies only to research and development.

The benefits of these technologies will only be realised if crops developed this way are able to reach supermarkets and customers. It is frustrating when scientific breakthroughs cannot lead to genuine improvements to the foods that we eat.

The Governments response provides a first step towards the adoption of genome editing, which has great potential to address the challenge of providing sufficient food in the most sustainable way possible.

Genome editing can be used to develop new crop varieties, allowing a precise, targeted mutation in the DNA of an organism. This technology could be used to significantly speed up the crop breeding process and help us to make advances in addressing some of the worlds most pressing challenges climate change, food security and sustainable food production.

Professor Wendy Harwood, Head of the Crop Transformation Group at the John Innes Centre said, Genome editing is the most exciting technology that I have seen in my many years working in crop science. The technology makes it possible to introduce small changes in DNA that lead to the characteristics we need to combat climate change, develop food with better nutritional quality or that are more resistant to diseases.

To fully realise the positive impact of gene editing, it is essential that we can assess genome edited plants in the field. So, I welcome todays announcement, which offers changes that make this process less of a burden for researchers, while still having the necessary oversight.

The traditional methods that plant breeders use to introduce traits into crop plants can take between 8 and 15 years. Gene editing offers the opportunity to speed up the breeding process to just a few years, bringing about essential scientific development much sooner at a much lower cost.

As an example, gene editing can be used to make changes to the genetic code of oil seed rape to make their valuable seed pods less prone to pod shatter. Pod shatter causes large losses to the yield, meaning that many seeds are lost to the ground before harvest.

The announcement also indicates a review of Englands approach to GMO regulation more broadly.

Professor Sanders continues, We need fundamental change to the way we regulate crops produced by genetic technologies if were going to make the most of the opportunities that recent advances in genetics have given us.

We call on the Government to progress the plans to bring these products to market as a matter of urgency. We now have an opportunity to streamline the process and looking ahead we should be regulating crops based on the characteristics they possess rather than how they are produced.

Gene, or genome editing is one of the many ways we can use mutations to develop better plants for our food.

Find out more about how we use genetic technologies in plant and microbial science.

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A first step towards unlocking the power of gene editing - The John Innes Centre

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Blue Origin Employees Say They Don’t Think Its Rocket Is Safe, Wouldn’t Ride In It – Futurism

Posted: at 4:21 am

"Blue Origin has been lucky that nothing has happened so far."Hard Pass

A small cohort of current and former employees of Blue Origin, Jeff Bezoss spaceflight company, recently penned an article questioning the companys commitment to safety.

We wrote yesterday about the employees claims that Blue Origin harbors a shockingly sexist work culture.Another alarming takeaway from the letter, though, comes from a completely different direction, claiming that the company also has a poor safety culture around its rockets. The problems are so bad that the authors say they wouldnt feel safe riding in a Blue Origin rocket, given the chance.

Many of us have spent our careers dreaming of helping to launch a crewed rocket into space and seeing it safely touch back down on Earth, the employees wrote. But when Jeff Bezos flew to space this July, we did not share his elation. Instead, many of us watched with an overwhelming sense of unease. Some of us couldnt bear to watch at all.

Notably, the authors dont list any single safety issue with Blue Origins New Shepard rocket. Instead, they describe a work culture in which overstretched teams had more and more work piled onto them without reasonable increases in personnel or budget.

That culture, coupled with a lack of overarching safety regulations for the nascent commercial spaceflight industry, they argue, forced the staff to prioritize speed over safety, increasing the chances that safety issues flew under the radar.

Blue Origin has been lucky that nothing has happened so far, one anonymous engineer contributed to the article. Many of this essays authors say they would not fly on a Blue Origin vehicle. And no wonder we have all seen how often teams are stretched beyond reasonable limits.

READ MORE: Bezos Wants to Create a Better Future in Space. His Company Blue Origin Is Stuck in a Toxic Past. [Lioness]

More on Blue Origin: More Than 20 Blue Origin Employees Say Its a Horrible Place to Work

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Company Claims Pill Cuts Risk of Dying of COVID-19 in Half – Futurism

Posted: at 4:21 am

Pharmaceutical company Merck claims its new COVID-19 pill, called molnupiravir, can reduce the risk of hospitalization and even death from the coronavirus by half, according to newly announced Phase III clinical trial results.

The company is now applying for Emergency Use Authorization from the US Food and Drug Administration.

Its a promising development for new treatments against severe cases of COVID-19 but the news should also serve as a reminder that getting vaccinated is by far the best preventative step, regardless of the availability of effective treatments.

COVID remains a highly dangerous disease. A staggering 1 in 500 Americans have now died from it.

In the trials, Merck tested the drug on participants who recently tested positive for COVID and who also had at least one additional risk factor including obesity, diabetes, heart disease or being above the age of 60.

After 29 days, 53 out of 377 participants who received the placebo were hospitalized after contracting the coronavirus. Eight of the placebo group died.

Only 28 out of 385 participants who received the drug, in contrast, were hospitalized. None of them died.

Promisingly, Merck also noted that its drug worked just as well against dangerous new strains of the virus, including the widespread delta variant.

If granted authorization, the pill would be the third antiviral drug approved by the FDA to treat COVID. Remdesivir, an injection, has also proven to be effective at staving off serious cases of COVID-19. Monoclonal antibody therapy has also shown promise.

All those treatments, though, are very expensive. According to The New York Times, a five day course of molnupiravir currently costs about $700 per patient. Two doses of the Pfizer vaccine,in contrast, cost just $39 and are available for free at locations across the United States and in many other countries worldwide.

While theres meaningful progress toward developing effective treatments for COVID, one simple fact remains: those who are unvaccinated are far more likely eleven times to be hospitalized.

Granted, breakthrough infections do happen, albeit quite infrequently. But at the end of the day, the vaccine is a great way to stay safe.

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Company Claims Pill Cuts Risk of Dying of COVID-19 in Half - Futurism

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Doctors Alarmed by Man Who Quit Drinking and Started Swallowing Metal Nails and Screws – Futurism

Posted: at 4:21 am

Doctors in Lithuania recently cut open a patients stomach so that they could safely remove the roughly two-and-a-half pounds of miscellaneous metal objects that he had swallowed over the course of a month.

As the story goes, the man had quit drinking, but for one reason or another replaced it with an even more destructive vice, Agence France-Presse reports. Its a bizarre case, but the doctors say that the man recovered and was resting in stable condition following the procedure.

If youre not feeling too squeamish, feel free to check out the Lithuanian-language publication LRT, which published an image of the surgical tray full of all the nails, screws, nuts, and other metal bits that the man had swallowed.

Weve never seen anything like it, head surgeon Algirdas Slepavicius told AFP.

The doctors told LRT that the surgery itself was fairly straightforward and that patients coming in after swallowing various objects all the time. But this particular surgery took a long time about three hours because of the sheer number of objects the man consumed. The doctors were also slowed down by the fact that they needed to frequently take and retake x-rays to ensure they found all of the small metal bits, which LRT reports ranged in size from two millimeters to an alarming 10 centimeters.

They also had to make sure that the sharp metal hadnt pierced through the wall of his stomach, but that didnt seem to be the case. Apparently the man hasnt said much, according to LRT, but hes currently under psychological care to try and figure out where his metal-eating habit came from and why.

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Creators of Amazon’s New Robot Secretly Admitted It’s "Terrible" – Futurism

Posted: at 4:21 am

According to developer documents and video meeting recordings obtained by Vice, the engineers behind Amazons new $999 robot arent thrilled with the finished product.

The e-retailer recently announced the Astro, a stalkerish two-wheeled robot designed to keep track of everything you do, and even spy on anybody unlucky enough to enter your home.

Even if you sign on to that troubling premise, the bots developers apparently werent happy with the final product.

Astro is terrible and will almost certainly throw itself down a flight of stairs if presented the opportunity, an unnamed developer said, as quoted by Vice. The person detection is unreliable at best, making the in-home security proposition laughable.

The device feels fragile for something with an absurd cost, the developer added.

Vices source also criticized the devices marketing as an accessibility device, telling the outlet that its at best, absurdist nonsense and marketing and, at worst, potentially dangerous for anyone whod actually rely on it for accessibility purposes.

A second source who also worked on the project called it a disaster thats not ready for release, noting that they break themselves and will almost certainly fall down stairs in real world users homes.

Senior PR manager Kristy Schmidt called the allegations simply inaccurate, telling Vice that the robot went through rigorous testing on both quality and safety, including tens of thousands of hours of testing with beta participants.

Its almost poetic: a highly invasive robot hellbent on throwing itself down a flight of stairs.

Astro represents the kind of future weve been warning about for all these years: a largely autonomous robot actively spying on strangers, developed by a company that has built its success on collecting every bit of information it can glean from its customers.

Fortunately, it isnt likely to fly off the shelves given its hefty price tag.

READ MORE: Leaked Documents Show How Amazons Astro Robot Tracks Everything You Do [Vice]

More on Amazon: Companies Are Ditching Drug Tests Because Theyre Blocking Good Candidates

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New AR Glasses Are for Streaming Video and Ignoring the Real World – Futurism

Posted: at 4:21 am

The Nreal glasses don't have any outward-facing cameras.Picture-in-Picture

The augmented reality developer Nreal just announced a new, cheaper model of its AR glasses, which its calling the Nreal Air.

But unlike previous Nreal models, and just about every other mixed reality headset out there, the new system will focus solely on streaming video or displaying other media. As The Verge notes, the Nreal Air will be missing the components, like outward-facing cameras or hand-tracking tech, that would help a wearer actually interact with the world around them while using AR. Its an interesting move using AR to turn inward and binge shows or go down YouTube rabbit holes that contrasts against other developers moves to build metaverses that blur the line between virtual and tangible realities.

Because hand controls wont work, users will need to control the Nreal Air which a spokesperson told The Verge will cost a fraction of the Nreal Lights $600 pricetag through a smartphone app. Using a phone instead of actually being able to reach out and touch parts of the AR display with your hands may break some of the immersion, but that fits in with the companys goal of building a more compact, stripped-down, and especially more affordable version of AR made for watching videos.

Consumers today are seeking lighter, but longer lasting AR glasses exclusively for streaming media and working from home, Nreal founder Chi Xu said in a statement provided to The Verge.

Plus, theres the added bonus of not creeping out every single person you walk past. Without external cameras on your glasses something Facebook recently unveiled with its creepy new covert surveillance Ray-Bans AR users can go about their days without getting weird looks from strangers wondering if theyre being filmed.

READ MORE: Nreals new AR sunglasses are made for binge watching TV [The Verge]

More on AR: Facebook Is Working on an Amazingly Hideous Augmented Reality Fedora

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Every Mars Rover Is About To Go Into Safe Mode – Futurism

Posted: at 4:21 am

That pesky Sun is getting in the way of NASA's research.Laying Low

NASA and the China National Space Administration (CNSA), the only two space agencies with robotic rovers currently exploring and studying Mars, are both being forced to put their research on hold for a little while.

The problem? The Sun is literally getting in the way. A period called Mars solar conjunction, in which the Sun passes in between the two planets, is expected to begin next week on October 2, according to a NASA announcement. While its there, the space agencies decided that it would be safest to take a break and not beam any new commands to their various Mars rovers.

NASA engineers are concerned that the Suns ionizing rays could interfere with any instructions that engineers send to their respective Mars rovers, potentially corrupting the signals and prompting unexpected, possibly dangerous behavior from the off-world robots. Therefore, NASA wont send any new instructions to their rovers between October 2 and 16, according to the agencys announcement.

Similarly, the CNSA told the Chinese state-run news outlet Global Times that its Tianwen-1 space probe and Zhurong rover will pause their work and enter safe mode during the transit.

But just because the rovers arent getting any new instructions doesnt mean theyre stopping altogether.

Though our Mars missions wont be as active these next few weeks, theyll still let us know their state of health, the NASA Jet Propulsion Laboratorys Mars Relay Network manager, Roy Gladden, said in the NASA announcement. Each mission has been given some homework to do until they hear from us again.

For instance, the Perseverance and Curiosity rovers will continue to record the weather on Mars, though several of their instruments will be shut off. Meanwhile, the InSight lander will continue to detect marsquakes, and NASAs Mars orbiters will continue to act as relay stations between Earth and the rovers whenever possible.

READ MORE: NASAs Mars Fleet Lies Low As Sun Moves Between Earth and Red Planet [NASA]

More on Mars rovers: It Worked! NASAs Mars Rover Definitely Scooped up Rock Samples This Time

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