Initially, we perform two simulation studies for assessing how accurately our proposed model identifies true genotype states when hypersegmentation occurs. For these two studies, we generate 500 datasets with true genotype sequences of size N=10,000 based on a Markov chain with a given transition probability, using the R- package markovchain. We consider four genotypes as
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RNA sequencing (RNA-Seq), despite being the choice technique for transcriptome-wide identification of differentially expressed genes, is still rapidly evolving. A number of tools are available for each major processing step in data analysis: read alignment, expression modeling, and differential gene identification [1], but their performance in concert is only beginning to be understood [2–6]. Additionally,
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Abstract The efficient coding hypothesis predicts that sensory neurons adjust their coding resources to optimally represent the stimulus statistics of their environment. To test this prediction in the moth olfactory system, we have developed a stimulation protocol that mimics the natural temporal structure within a turbulent pheromone plume. We report that responses of antennal olfactory
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Introduction Most cellular processes are carried out by interacting proteins. Functional protein-protein interactions allow multi-protein complexes to assemble, and ensure proper signal transduction in various pathways. Hence, mapping functional protein-protein interactions is an important fundamental question. High-throughput experiments have recently elucidated a substantial fraction of protein-protein interactions in a few model organisms [1], but such
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Measurement noise. For models (such as our core models) where the relationship between reliability (i.e., contrast or ellipse eccentricity) and noise was parametric, we assumed a power law relationship between reliability c and measurement noise variance σ2: σ2(c) = γ + αc−β. We have previously [30] used this power law relationship because it encompasses a
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Abstract Population genetic modeling can enhance Bayesian phylogenetic inference by providing a realistic prior on the distribution of branch lengths and times of common ancestry. The parameters of a population genetic model may also have intrinsic importance, and simultaneous estimation of a phylogeny and model parameters has enabled phylodynamic inference of population growth rates, reproduction
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How much radiation are the astronauts exposed to on the ISS? originally appeared on Quora: the place to gain and share knowledge, empowering people to learn from others and better understand the world. Answer by Robert Frost, works at NASA, on Quora: For ISS astronauts, measurements from the crew’s personal dosimeters indicate a range from
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California is burning again. These latest wildfires are already the deadliest yet. And they continue to blaze. Wildfires make headlines every few months. They’ve been called “the new normal.” But California Governor Jerry Brown isn’t having that. He says it’s “the new abnormal.” To be clear, humans are part of this. The effects of climate
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Across the planet, shorebirds are in serious trouble. In the past 50 years their well-documented North American populations are estimated to have plummeted by at least 70 percent on average, and shorebirds elsewhere are hardly doing better, if not worse. Reasons are many—the shorelines and mudflats where the birds feed are polluted or disappearing, and
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Posted by: RNA-Seq Blog in Publications 1 hour ago 60 Views The usual analysis of RNA-Seq reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly.
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Over 100 captured whales are being held in small, crowded enclosures in a so-called ‘whale jail’ off the coast of Russia, where they await suspected sale to Chinese theme parks, according to local media reports. The discovery of the marine containment facility near the city of Nakhodka in Russia’s south-east is being investigated by Russian
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The evolutionary arms race between predator and prey has given rise to many impressive defence mechanisms; as it turns out, the lowly moth is no exception. These unassuming creatures may not have the charming appearance of their butterfly cousins, but their furry facade conceals some tricks that would impress the most advanced military division. Over
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The percentage of US adults with Alzheimer disease and related dementias is projected to grow from 1.6% in 2014 to 3.3% in 2060, according to a study by the CDC in the journal Alzheimer & Dementia. Centers for Disease Control and Prevention The study authors estimated the future prevalence of Alzheimer and related conditions using
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Most medical centers today acquire supplies, medications, and devices through group purchasing organizations (GPOs) rather than directly from a manufacturer. GPOs are intermediaries that catalog medical supplies so medical centers can purchase them from manufacturers. According to the American Hospital Association, 68% of hospitals used a GPO for their main purchasing needs in 2000, and
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The US Preventive Services Task Force (USPSTF) has recently published recommendations on screening and counseling to reduce unhealthy alcohol use in adults and adolescents. What Is Unhealthy Alcohol Use? Unhealthy alcohol use means drinking more than the recommended amount of alcohol. This includes exceeding daily or weekly recommended limits as well as alcohol use disorder
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Despite decades-long improvement, recent evidence suggests that rates of myocardial infarction, stroke, and other cardiovascular disease (CVD) events have plateaued and are increasing among certain groups, including adults aged 35 to 64 years.1,2 These events are common, costly, and largely preventable. Million Hearts, a national initiative co-led by the Centers for Disease Control and Prevention
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Gadolinium-based contrast agents (GBCAs) revolutionized magnetic resonance imaging (MRI) examinations by depiction of pathology otherwise undetectable on unenhanced MRI or other imaging modalities. Since initial regulatory approval in 1988, it is estimated that more than 450 million GBCA doses have been administered worldwide. In the United States, it is estimated that approximately 8.8 million MRI
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Patients with heart failure may develop secondary mitral regurgitation, in which a dysfunctional heart valve allows blood to leak back into the organ’s left atrium and the lungs, further worsening the condition. Some patients remain symptomatic despite receiving maximal heart failure therapies. Abbott An investigational transcatheter mitral-valve repair device from Abbott called the MitraClip may
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mTOR signalling and cellular metabolism are mutual determinants in cancer mTOR signalling and cellular metabolism are mutual determinants in cancer, Published online: 13 November 2018; doi:10.1038/s41568-018-0074-8 This Review discusses the interdependencies of mTOR signalling and metabolism pathways in cancer and how metabolic reprogramming in response to changes in mTOR signalling and vice versa can sustain
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In Reply In discussing the topic of injection drug use–associated infective endocarditis in our review,1 our intent was to highlight the lack of certainty with respect to the use of surgery and outcomes in these patients. Cardiac surgery in patients with injection drug use–associated infective endocarditis has been associated with higher mortality and reoperation in
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Functions and mechanisms of epigenetic inheritance in animals Functions and mechanisms of epigenetic inheritance in animals, Published online: 13 November 2018; doi:10.1038/s41580-018-0074-2 Epigenetic profiling of germline and zygotic genomes has revealed that a fraction of mammalian genomes do not undergo epigenetic reprogramming during early development, highlighting the importance of epigenetic inheritance in animals. Inheritance of
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Abstract Neural oscillations have been recorded and implicated in many different basic brain and cognitive processes. For example, oscillatory neural activity has been suggested to play a role in binding and in the maintenance of information in working memory. With respect to the latter, the majority of work has focused primarily on oscillations in terms
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Abstract Neurons collect their inputs from other neurons by sending out arborized dendritic structures. However, the relationship between the shape of dendrites and the precise organization of synaptic inputs in the neural tissue remains unclear. Inputs could be distributed in tight clusters, entirely randomly or else in a regular grid-like manner. Here, we analyze dendritic
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Citation: Giaimo S, Arranz J, Traulsen A (2018) Invasion and effective size of graph-structured populations. PLoS Comput Biol 14(11): e1006559. https://doi.org/10.1371/journal.pcbi.1006559 Editor: Sebastian Schreiber, UC Davis, UNITED STATES Received: February 7, 2018; Accepted: October 9, 2018; Published: November 12, 2018 Copyright: © 2018 Giaimo et al. This is an open access article distributed under the
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Citation: Henderson JA, Gong P (2018) Functional mechanisms underlie the emergence of a diverse range of plasticity phenomena. PLoS Comput Biol 14(11): e1006590. https://doi.org/10.1371/journal.pcbi.1006590 Editor: Abigail Morrison, Research Center Jülich, GERMANY Received: January 8, 2018; Accepted: October 23, 2018; Published: November 12, 2018 Copyright: © 2018 Henderson, Gong. This is an open access article distributed
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Ethics statement All experiments, animal treatment and surgical protocols were carried out with authorization from the Institutional Animal care and Use Committee of the Allen Institute in accordance with the Public Health Service (PHS) Policy on Humane Care and Use of Laboratory Animals. Model building and simulation details All simulations were performed with the parallelized
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