Month: July 2018

Abstract Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and theoretical modeling to study the factors that control the size and morphology of a protein shell assembling around hundreds to thousands of molecules. We perform
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The mantle beneath Tibet has been torn into four massive pieces, according to a new computer model that gives an unprecedented glimpse at what’s going on under the surface our planet. Determining exactly what’s happening so far underground isn’t always easy, but can help in everything from predicting earthquakes to understanding how terrain evolves over
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The Russian attacks on the 2016 US presidential election and the country’s continuing election-related hacking have happened across all three dimensions of cyberspace – physical, informational and cognitive. The first two are well-known: For years, hackers have exploited hardware and software flaws to gain unauthorized access to computers and networks – and stolen information they’ve
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Cyber criminals shut down parts of the Web in October 2016 by attacking the computers that serve as the internet’s switchboard. Their weapon of choice? Poorly secured Web cameras and other internet-connected gadgets that have collectively come to be known as the Internet of Things (IoT). The attack created a minor panic among people trying
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Posted by: RNA-Seq Blog in Library Preparation, Sequencing Protocols, Workflow 4 hours ago 113 Views Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. Stanford University researchers have developed and applied a technology for 3D intact-tissue RNA
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Before being elected to Congress in 2008, Representative Bill Foster of Illinois, a Democrat, worked for more than 20 years as a physicist at the Fermi National Accelerator Laboratory in Batavia, Ill. Now, as the only member of Congress with a Ph.D. in science, he says there is an urgent need for more scientists in
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A panel of 19 microRNAs identified using next-generation sequencing could categorize indeterminate thyroid nodule samples into malignant and benign, according to results published in Cancer Epidemiology, Biomarkers & Prevention, a journal of the American Association for Cancer Research. “Thyroid nodules are extremely common and occasionally harbor cancer,” explained first author Haggi Mazeh, MD, FACS, chief
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Theoretical research by an international team of physicists has discovered that the Great Pyramid of Giza can concentrate electromagnetic energy in its internal chambers and under its base. And although the ancient Egyptian’s probably weren’t aware of this weird design quirk, the study could be important for nanoparticle research in the future. “Applications of modern
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The world’s largest king penguin colony has dramatically collapsed, and as yet scientists just don’t know why. From 2 million members in the 1980s, including 500,000 breeding pairs, the population on the sub-Antarctic Île aux Cochons has shrunk to just 60,000 breeding pairs. Using recent high-resolution satellite data from 2005 onwards, and helicopter and satellite
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“The probability that ‘In My Life’ was written by McCartney is .018.” “Which basically means it’s pretty convincingly a Lennon song.” And with that, Harvard researcher and passionate Beatles fan Mark Glickman made his telling contribution to one of the eternal pop music pub arguments – who wrote the Beatles’ best tracks? The difference this
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Finally: development of humanized lymph nodes Finally: development of humanized lymph nodes, Published online: 31 July 2018; doi:10.1038/s41592-018-0080-5 Overexpression of mouse thymic-stromal-cell-derived lymphopoietin in immune-compromised mice that harbor a reconstituted human immune system rescues lymph node formation and enhances adaptive immune responses.
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Quanti.us: a tool for rapid, flexible, crowd-based annotation of images Quanti.us: a tool for rapid, flexible, crowd-based annotation of images, Published online: 31 July 2018; doi:10.1038/s41592-018-0069-0 Annotated image data are required for image analysis, to test analytical methods, and to train learning algorithms. This paper describes and characterizes a tool that allows researchers to crowdsource
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High throughput genotyping data have been used extensively in many contexts to explain phenotypic variation of complex traits in a wide range of Genome Wide Association Studies (GWAS). GWAS can however, only partially explain observed phenotypic variation [1], and phenotypic variation has been shown to eclipse genotypic variation in the same population [2]. For example,
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Water content, not stiffness, dominates Brillouin spectroscopy measurements in hydrated materials Water content, not stiffness, dominates Brillouin spectroscopy measurements in hydrated materials, Published online: 31 July 2018; doi:10.1038/s41592-018-0076-1 Water content, not stiffness, dominates Brillouin spectroscopy measurements in hydrated materials
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We presented TOPAZ, a protein homology search method based on asymmetric suffix array neighbourhood search, scored seeds and optimal substitution ordering. All BLAST alternatives trade-off sensitivity in exchange for speed. In doing so, database search can be used in high-throughput and time-sensitive applications that would have otherwise taken a prohibitively long time. This trade-off was
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Hi-C data representation and properties HiCcompare focuses on the joint analysis of multiple Hi-C datasets represented by chromatin interaction matrices, where rows and columns represent genomic regions (bins), and cells contain interaction counts (frequencies). A chromosome-specific Hi-C matrix is a square matrix of size N × N, where N is the number of genomic regions (bins) of
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Regulation of proteasome assembly and activity in health and disease Regulation of proteasome assembly and activity in health and disease, Published online: 31 July 2018; doi:10.1038/s41580-018-0040-z Protein degradation by the proteasome is crucial for the control of many cellular processes, and defects in proteasomal degradation may lead to cancer and neurodegeneration. TOR complex 1 has
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Abstract The accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good ground truth data typically involves trained professionals; however, this can be costly in time, effort, and money. Here we explore the use of crowdsourcing to generate a large number of training data of good
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Introduction In everyday life, we are continuously engaged in selecting visual information to achieve our action goals, as the amount of information we receive at any time exceeds the available processing capacity. The mechanisms mediating attentional selection enable us to act efficiently by prioritizing task-relevant, and deprioritizing irrelevant, information. Of importance for the question at
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The headlines in recent months read like an international eco-thriller. At Mauna Loa Observatory, perched high on a Hawaiian volcano, researchers measure unusual levels of CFC-11 in the atmosphere. The measurements baffle the scientific community: CFC-11, a potent ozone-depleting gas, has been carefully monitored since it was banned under the 1987 Montreal Protocol. But the
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