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Gavin M Bidelman
Event-related brain potentials (ERPs) reveal musical experience refines neural encoding and confers stronger categorical perception (CP) and neural organization for speech sounds. In addition to evoked brain activity, the human EEG can be decomposed into induced (non-phase-locked) response whose various frequency bands reflect different mechanisms of perceptual-cognitive processing. Here, we aimed to clarify which spectral properties of these neural oscillations are most prone to music-related neuroplasticity and which are linked to behavioral benefits in the categorization of speech...
February 15, 2017: Neuroscience
Jeramie D Watrous, Mir Henglin, Brian Claggett, Kim A Lehmann, Martin G Larson, Susan Cheng, Mohit Jain
Untargeted liquid-chromatography-mass spectrometry (LC-MS)-based metabolomics analysis of human biospecimens has become among the most promising strategies for probing the underpinnings of human health and disease. Analysis of spectral data across population scale cohorts, however, is precluded by day-to-day nonlinear signal drifts in LC retention time or batch effects that complicate comparison of thousands of untargeted peaks. To date, there exists no efficient means of visualization and quantitative assessment of signal drift, correction of drift when present, and automated filtering of unstable spectral features, particularly across thousands of data files in population scale experiments...
February 7, 2017: Analytical Chemistry
Lauren A Fromont, Salvador Soto-Faraco, Emmanuel Biau
During natural speech perception, listeners rely on a wide range of cues to support comprehension, from semantic context to prosodic information. There is a general consensus that prosody plays a role in syntactic parsing, but most studies focusing on ambiguous relative clauses (RC) show that prosodic cues, alone, are insufficient to reverse the preferred interpretation of sentence. These findings suggest that universally preferred structures (e.g., Late Closure principle) matter far more than prosodic cues in such cases...
2017: Frontiers in Psychology
Leah Bakst, Jerome Fleuriet, Michael J Mustari
Neurons in the smooth eye movement subregion of the Frontal Eye Field (FEFsem) are known to play an important role in voluntary smooth pursuit eye movements. Underlying this function are projections to parietal and prefrontal visual association areas and subcortical structures, all known to play vital, but differing roles in the execution of smooth pursuit. Additionally, the FEFsem has been shown to carry a diverse array of signals (e.g. eye velocity, acceleration, gain control). We hypothesized that distinct subpopulations of FEFsem neurons subserve these diverse functions and projections, and that the relative weights of retinal and extraretinal signals could form the basis for categorization of units...
February 15, 2017: Journal of Neurophysiology
Teng Teng, Afsaneh Gaillard, Aude Muzerelle, Patricia Gaspar
Serotonin (5-HT) neurotransmission in the brain relies on a widespread axon terminal network originating from the hindbrain raphe nuclei. These projections are topographically organized such that the dorsal (DR), and median raphe (MnR) nuclei have different brain targets. However, the guidance molecules involved in this selective targeting in development are unknown. Here, we show the implication of ephrinA5 signaling in this process. We find that the EphA5 gene is selectively expressed in a subset of 5-HT neurons during embryonic and postnatal development...
January 2017: ENeuro
Jamie Lorimer
The scientific proposal that the Earth has entered a new epoch as a result of human activities - the Anthropocene - has catalysed a flurry of intellectual activity. I introduce and review the rich, inchoate and multi-disciplinary diversity of this Anthropo-scene. I identify five ways in which the concept of the Anthropocene has been mobilized: scientific question, intellectual zeitgeist, ideological provocation, new ontologies and science fiction. This typology offers an analytical framework for parsing this diversity, for understanding the interactions between different ways of thinking in the Anthropo-scene, and thus for comprehending elements of its particular and peculiar sociabilities...
February 2017: Social Studies of Science
Justin D Smith, Ulrich Schlecht, Weihong Xu, Sundari Suresh, Joe Horecka, Michael J Proctor, Raeka S Aiyar, Richard A O Bennett, Angela Chu, Yong Fuga Li, Kevin Roy, Ronald W Davis, Lars M Steinmetz, Richard W Hyman, Sasha F Levy, Robert P St Onge
The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI), which involves integration of a complex library into yeast, site-specific recombination to index library DNA, and next-generation sequencing to identify desired clones...
February 13, 2017: Molecular Systems Biology
Tyler Borrman, Jennifer Cimons, Michael Cosiano, Michael Purcaro, Brian G Pierce, Brian M Baker, Zhiping Weng
The ATLAS (Altered TCR Ligand Affinities and Structures) database ( is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest...
February 3, 2017: Proteins
Alexandra M V Wennberg, Rodolfo Savica, Michelle M Mielke
BACKGROUND: Approximately 30% of older adults have disrupted gait. It is associated with increased risk of cognitive decline, disability, dementia, and death. Additionally, most older adults present with 1 or more neuropathologies at autopsy. Recently, there has been an effort to investigate the association between subclinical neuropathology and gait. SUMMARY: We reviewed studies that investigated the association between gait and neuropathologies. Although all pathologies reviewed were associated with gait, grey matter atrophy was most consistently linked with poorer gait performance...
February 3, 2017: Dementia and Geriatric Cognitive Disorders
Florence Allain, David C S Roberts, Daniel Lévesque, Anne-Noël Samaha
The choice between smoking, injecting or swallowing a drug influences the risk of addiction, as this determines both how much drug gets into the brain and how fast. Most animal studies on addiction focus on how much drug it takes to produce pathological drug use. How fast drugs get to the brain is generally ignored. A few studies have examined the influence of the speed of drug onset, but speed varied along with cumulative intake. Here we held average cumulative intake constant and determined whether variation in the speed of cocaine onset alone predicts outcome...
January 27, 2017: Neuropharmacology
A Koneti Rao, Natthapol Songdej
No abstract text is available yet for this article.
January 26, 2017: Blood
M J Sanderson, Marius Nicolae, M M McMahon
Obstacles to inferring species trees from whole genome data sets range from algorithmic and data management challenges to the wholesale discordance in evolutionary history found in different parts of a genome. Recent work that builds trees directly from genomes by parsing them into sets of small k-mer strings holds promise to streamline and simplify these efforts, but existing approaches do not account well for gene tree discordance. We describe a "seed and extend" protocol that finds nearly exact matching sets of orthologous k-mers and extends them to construct data sets that can properly account for genomic heterogeneity...
January 25, 2017: Systematic Biology
Fotis E Psomopoulos, Dimitrios M Vitsios, Shakuntala Baichoo, Christos A Ouzounis
: BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway...
January 25, 2017: Bioinformatics
Cassandra E Nelson, Artur Rogowski, Carl Morland, Joshua A Wilhide, Harry J Gilbert, And Jeffrey G Gardner
Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell...
January 24, 2017: Molecular Microbiology
Alexander Bauer, Shinichi Nakajima, Klaus-Robert Muller
Structural support vector machine (SVM) is an elegant approach for building complex and accurate models with structured outputs. However, its applicability relies on the availability of efficient inference algorithms--the state-of-the-art training algorithms repeatedly perform inference to compute a subgradient or to find the most violating configuration. In this paper, we propose an exact inference algorithm for maximizing nondecomposable objectives due to special type of a high-order potential having a decomposable internal structure...
August 19, 2016: IEEE Transactions on Neural Networks and Learning Systems
Florin C Ghesu, Edward Krubasik, Bogdan Georgescu, Vivek Singh, Yefeng Zheng, Joachim Hornegger, Dorin Comaniciu
Robust and fast solutions for anatomical object detection and segmentation support the entire clinical workflow from diagnosis, patient stratification, therapy planning, intervention and follow-up. Current state-of-the-art techniques for parsing volumetric medical image data are typically based on machine learning methods that exploit large annotated image databases. There are two main challenges that need to be addressed, these are the efficiency in processing large volumetric input images and the need for strong, representative image features...
March 7, 2016: IEEE Transactions on Medical Imaging
Sarah Campbell
In the epic endeavor to sequence the human genome, it was as though the size of the equipment and amount of effort required were inversely proportional to the microscopic materials being parsed (Figure 1). "Imagine thousands of people, many laboratories … hundreds, hundreds, hundreds of these machines just to generate that first human genome sequence over a six to eight year period," says Dr. Eric Green, director of the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH) (Figure 2)...
September 2016: IEEE Pulse
Sian Lewis
No abstract text is available yet for this article.
January 20, 2017: Nature Reviews. Neuroscience
Mauricio Dias Martins, Bruno Gingras, Estela Puig-Waldmueller, W Tecumseh Fitch
The human ability to process hierarchical structures has been a longstanding research topic. However, the nature of the cognitive machinery underlying this faculty remains controversial. Recursion, the ability to embed structures within structures of the same kind, has been proposed as a key component of our ability to parse and generate complex hierarchies. Here, we investigated the cognitive representation of both recursive and iterative processes in the auditory domain. The experiment used a two-alternative forced-choice paradigm: participants were exposed to three-step processes in which pure-tone sequences were built either through recursive or iterative processes, and had to choose the correct completion...
January 16, 2017: Cognition
Patrick K Kimes, Yufeng Liu, David Neil Hayes, James Stephen Marron
Cluster analysis has proved to be an invaluable tool for the exploratory and unsupervised analysis of high-dimensional datasets. Among methods for clustering, hierarchical approaches have enjoyed substantial popularity in genomics and other fields for their ability to simultaneously uncover multiple layers of clustering structure. A critical and challenging question in cluster analysis is whether the identified clusters represent important underlying structure or are artifacts of natural sampling variation...
January 18, 2017: Biometrics
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