Deep generative models of genetic variation capture the effects of mutations Deep generative models of genetic variation capture the effects of mutations, Published online: 24 September 2018; doi:10.1038/s41592-018-0138-4 DeepSequence is an unsupervised deep latent-variable model that predicts the effects of mutations on the basis of evolutionary sequence information.
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We found that machine learning using RSCU can predict presence of viral contigs in metagenomic sequencing data. Firstly, we investigated the possibility to use RSCU values to predict viral origin of sequences originating from complete protein coding genes at NCBI Genbank (the data was obtained from http://www.kazusa.or.jp/codon/). Using 10-fold cross-validation on this dataset, random forest
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Computational protein design is the task of finding an energy-optimal amino acid sequence for a backbone structure. Simplifying assumptions, such as fixed backbone atoms and discrete side chain conformations [1, 2], have been necessary because of the prohibitive size of the computational sequence search space. But, as computational resources improve, simplifying assumptions are falling away
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Reducing effects of particle adsorption to the air–water interface in cryo-EM Reducing effects of particle adsorption to the air–water interface in cryo-EM, Published online: 24 September 2018; doi:10.1038/s41592-018-0139-3 Reducing the length of time that protein particles spend on a sample grid prior to freezing mitigates deleterious effects caused by particle adsorption to the air–water interface
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Elon Musk has provided several new, rare, and telling glimpses into how his rocket company, SpaceX, is building a spacecraft to reach Mars. On September 17, Musk announced that SpaceX would fly Japanese billionaire Yusaku Maezawa around the moon on the company’s Big Falcon Rocket or BFR. During that event, Musk showed off new renderings of the launch system,
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According to the Big Bang cosmological model, our Universe began 13.8 billion years ago when all the matter and energy in the cosmos began expanding. This period of “cosmic inflation” is believed to be what accounts for the large-scale structure of the Universe and why space and the Cosmic Microwave Background (CMB) appear to be largely uniform in all
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Book covers for ANXIETY AND THE EQUATION and TOTALLY RANDOM.Cover images combined by Chad Orzel As someone whose primary claim to fame is writing physics books starring a talking dog, I am obviously often on the lookout for pop-physics books that take a different slant on the subject. I ran across a couple of these
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It’s invisible, and yet the motions of galaxies suggest it must be there. But a recent discovery has just deepened the mystery of the universe we cannot see NASA/CXO/Fabian et al.; Radio: Gendron-Marsolais et al.; NRAO/AUI/NSF Optical: NASA, SDS By Stuart Clark Mystery: Does dark matter really exist? FOR two factions of cosmologists, the universe
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Trial Design Details about the design of the Cardiovascular Outcomes Assessment of the MitraClip Percutaneous Therapy for Heart Failure Patients with Functional Mitral Regurgitation (COAPT) trial have been published previously.10 In brief, the COAPT trial was a multicenter, randomized, controlled, parallel-group, open-label trial of transcatheter mitral-valve repair with the MitraClip device in symptomatic patients with
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Contrary to what many advertised drug tests might promise, not all substances leave their telltale chemical signature in the body for the same amount of time. The moment we take a drug – whether we snort, smoke, or swallow it – our bodies begin to break it down. In the process, metabolites, or byproducts, of
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Getty royalty free “Eat more fiber” is dietary advice that’s earned the right of repetition. High-fiber diets are linked to lower rates of heart disease and certain types of cancer, along with the daily bonus of keeping our digestive system running efficiently. New research suggests another potentially big benefit: high-fiber diets may set off a chemical
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Inexpensive clean energy sounds like a pipe dream. Scientists have long thought that nuclear fusion, the type of reaction that powers stars like the Sun, could be one way to make it happen, but the reaction has been too difficult to maintain.  Now, we’re closer than ever before to making it happen — physicists from the University of
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The very first episode of Mr. Rogers was taped on September 21, 1967.Google Doodle Mr. Rogers taught three generations of kids about a lot of things: kindness, imagination, how to handle really tough feelings, how to face their fears, and how to button a cardigan. But he also taught them about science, art, and technology,
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Papahanaumokuakea Marine National Monument, the nation’s largest protected area, stretches over half-a-million square miles of sea and land in Hawaii. It also includes wonderfully odd and stretchy critters, as a research team aboard the exploration vessel Nautilus observed Thursday. The Nautilus, operated by the nonprofit Ocean Exploration Trust, has been streaming excursions online since 2012. (The Nautilus team
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Citation: Lyu Y, Xue L, Zhang F, Koch H, Saba L, Kechris K, et al. (2018) Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network. PLoS Comput Biol 14(9): e1006436. https://doi.org/10.1371/journal.pcbi.1006436 Editor: Ziv Bar-Joseph, Carnegie Mellon University, UNITED STATES Received: March 20, 2018; Accepted: August 15, 2018; Published: September 21,
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We know that plastic pollution is a major problem for the world’s oceans, but scientists just discovered a new way that discarded microplastics are making their way out of the water and into other food chains – through mosquitoes. What’s happening is mosquito larvae are ingesting microplastics as water-dwelling larvae, and those plastic particles are
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Oil painting by Hugh Chevins, 1955, showing Huygens and Coster with their first pendulum clock. Christiaan Huygens (1629-1693), a Dutch physicist, designed the first clock controlled by the motion of a pendulum. Huygens based his clock on the observations made by the scientist Galileo (1564-1642), but improved the design and brought the pendulum clock to
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A deadly virus that plagues parrots, destroying their feathers and immune systems, has recently been detected in eight countries where it was previously unknown, raising concerns for the long-term conservation of this threatened group of birds A wild male rose-ringed parakeet, Psittacula krameri, Lakhota Lake, Gujarat, India.(Credit: Dr. Raju Kasambe / CC-BY-SA 4.0)Dr. Raju Kasambe
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Within a few years quantum computers could catch up to or even outperform classical computers thanks to significant work on hardware and the algorithms to run on it. Quantum computers exploit quantum mechanics to perform calculations. Their basic unit of computation, the qubit, is analogous to the standard bit (zero or one), but it is
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Writing in Scientific American in 2007, Harry A. Atwater of the California Institute of Technology predicted that a technology he called “plasmonics” could eventually lead to an array of applications, from highly sensitive biological detectors to invisibility cloaks. A decade later various plasmonic technologies are already a commercial reality, and others are transitioning from the
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Share to facebook Share to twitter Share to linkedin An artist’s rendering of the AI. SpaceFactory MARSHA habitat.AI. SpaceFactory This is part three of a three-part series on Martian infrastructure. You can read Part One on Martian communications infrastructure here and Part Two on resource development on Mars here. You’re an astronaut living and working
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Scientists in Japan made progress recently in the quest to combat infertility, creating the precursor to a human egg cell in a dish from nothing but a woman’s blood cells. The research is an important step toward what scientists call a “game-changing” technology that has the potential to transform reproduction. The primitive reproductive cell the
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Posted by: RNA-Seq Blog in Publications, Workflow 10 hours ago 191 Views High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how these individual events
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BERGEN, Norway (Reuters) – From the safety of their research vessel, scientists are exploring one of Earth’s last frontiers – the sea floor – to discover more about valuable minerals vital in the manufacture of smartphones. FILE PHOTO: A bastnaesite mineral containing rare earth is pictured at a laboratory of Yasuhiro Kato, an associate professor
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Molokai, Hawaii, United States of America A group of recent University of Oregon graduates has a plan to tackle the global plastic problem, and their solution is even edible, too. AlgoTek was formed by CEO David Crinnion and his college friends to develop a new, algae-based plastic that’s 100 percent sustainable and biodegradable. The main ingredients are
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The discovery of an aggressive feedback loop between the build-up of protein and nerve damage could be the key to explaining why so many trials of promising new treatments for Alzheimer’s disease end in failure. Researchers have managed to pin down the signalling pathway responsible for this vicious circle of damage in rodents, providing a new
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