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https://www.readbyqxmd.com/read/27920955/patma-parser-of-archival-tissue-microarray
#1
Lukasz Roszkowiak, Carlos Lopez
Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide...
2016: PeerJ
https://www.readbyqxmd.com/read/27905489/the-mammalian-linc-complex-regulates-genome-transcriptional-responses-to-substrate-rigidity
#2
Samer G Alam, Qiao Zhang, Nripesh Prasad, Yuan Li, Srikar Chamala, Ram Kuchibhotla, Birendra Kc, Varun Aggarwal, Shristi Shrestha, Angela L Jones, Shawn E Levy, Kyle J Roux, Jeffrey A Nickerson, Tanmay P Lele
Mechanical integration of the nucleus with the extracellular matrix (ECM) is established by linkage between the cytoskeleton and the nucleus. This integration is hypothesized to mediate sensing of ECM rigidity, but parsing the function of nucleus-cytoskeleton linkage from other mechanisms has remained a central challenge. Here we took advantage of the fact that the LINC (linker of nucleoskeleton and cytoskeleton) complex is a known molecular linker of the nucleus to the cytoskeleton, and asked how it regulates the sensitivity of genome-wide transcription to substratum rigidity...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899678/virus-variation-resource-improved-response-to-emergent-viral-outbreaks
#3
Eneida L Hatcher, Sergey A Zhdanov, Yiming Bao, Olga Blinkova, Eric P Nawrocki, Yuri Ostapchuck, Alejandro A Schäffer, J Rodney Brister
The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898342/voice-sensitive-brain-networks-encode-talker-specific-phonetic-detail
#4
Emily B Myers, Rachel M Theodore
The speech stream simultaneously carries information about talker identity and linguistic content, and the same acoustic property (e.g., voice-onset-time, or VOT) may be used for both purposes. Separable neural networks for processing talker identity and phonetic content have been identified, but it is unclear how a singular acoustic property is parsed by the neural system for talker identification versus phonetic processing. In the current study, listeners were exposed to two talkers with characteristically different VOTs...
November 26, 2016: Brain and Language
https://www.readbyqxmd.com/read/27896736/structural-and-functional-annotation-of-long-noncoding-rnas
#5
Martin A Smith, John S Mattick
Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, unannotated transcripts, especially long noncoding RNAs (lncRNAs) that are derived from genomic regions that are antisense, intronic, intergenic, and overlapping protein-coding loci...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895883/alexithymia-but-not-autism-spectrum-disorder-may-be-related-to-the-production-of-emotional-facial-expressions
#6
Dominic A Trevisan, Marleis Bowering, Elina Birmingham
BACKGROUND: A prominent diagnostic criterion of autism spectrum disorder (ASD) relates to the abnormal or diminished use of facial expressions. Yet little is known about the mechanisms that contribute to this feature of ASD. METHODS: We showed children with and without ASD emotionally charged video clips in order to parse out individual differences in spontaneous production of facial expressions using automated facial expression analysis software. RESULTS: Using hierarchical multiple regression, we sought to determine whether alexithymia (characterized by difficulties interpreting one's own feeling states) contributes to diminished facial expression production...
2016: Molecular Autism
https://www.readbyqxmd.com/read/27895552/computational-models-of-auditory-scene-analysis-a-review
#7
REVIEW
Beáta T Szabó, Susan L Denham, István Winkler
Auditory scene analysis (ASA) refers to the process (es) of parsing the complex acoustic input into auditory perceptual objects representing either physical sources or temporal sound patterns, such as melodies, which contributed to the sound waves reaching the ears. A number of new computational models accounting for some of the perceptual phenomena of ASA have been published recently. Here we provide a theoretically motivated review of these computational models, aiming to relate their guiding principles to the central issues of the theoretical framework of ASA...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27872489/experience-driven-differences-in-childhood-cortisol-predict-affect-relevant-brain-function-and-coping-in-adolescent-monozygotic-twins
#8
Cory A Burghy, Michelle E Fox, M Daniela Cornejo, Diane E Stodola, Sasha L Sommerfeldt, Cecilia A Westbrook, Carol Van Hulle, Nicole L Schmidt, H Hill Goldsmith, Richard J Davidson, Rasmus M Birn
Stress and emotion involve diverse developmental and individual differences. Partially attributed to the development of the prefrontal cortex (PFC), the amygdala, and hypothalamic-pituitary-adrenal axis, the precise genetic and experiential contributions remain unknown. In previous work, childhood basal cortisol function predicted adolescent resting-state functional connectivity (rs-FC) and psychopathology. To parse experience-driven (non-genetic) contributions, we investigated these relations with a monozygotic (MZ) twin design...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27866311/unforced-revision-in-processing-relative-clause-association-ambiguity-in-japanese-evidence-against-revision-as-last-resort
#9
Toshiyuki Yamada, Manabu Arai, Yuki Hirose
The current study tackles a long standing question of whether comprehenders perform structural revision when it is not forced by grammar or not. Using an eye-tracking reading paradigm, we addressed this issue by making use of global structural ambiguity in Japanese. Our results show that comprehenders initially associate a relative clause with the first potential head noun and that they revise this analysis when the second noun is lexico-semantically possible as the relative clause head, but do not when it is impossible...
November 19, 2016: Journal of Psycholinguistic Research
https://www.readbyqxmd.com/read/27856854/scientists-start-to-parse-a-trump-presidency
#10
Jeffrey Mervis
No abstract text is available yet for this article.
November 18, 2016: Science
https://www.readbyqxmd.com/read/27855268/hitting-a-moving-target-a-strategic-tool-for-analyzing-terrorist-threats
#11
Ken Coleman, Noriko Ishisoko, Milana Trounce, Kenneth Bernard
The subject of terrorism risk can be confusing for both the general public and for those responsible for protecting us from attack. Relatively minor terrorist threats are often conflated with much more serious ones, in part because it is hard to quantify either intent or technical ability to carry out an attack. Plotting threats on a "potential mass casualties" versus "ease of obtainment or production" matrix creates some order out of a seemingly endless array of worldwide threats, and it highlights those threats that are in need of more urgent attention...
November 17, 2016: Health Security
https://www.readbyqxmd.com/read/27852785/dorsolateral-prefrontal-cortex-gaba-concentration-in-humans-predicts-working-memory-load-processing-capacity
#12
Jong H Yoon, Anthony Grandelis, Richard J Maddock
: The discovery of neural mechanisms of working memory (WM) would significantly enhance our understanding of complex human behaviors and guide treatment development for WM-related impairments found in neuropsychiatric conditions and aging. Although the dorsolateral prefrontal cortex (DLPFC) has long been considered critical for WM, we still know little about the neural elements and pathways within the DLPFC that support WM in humans. In this study, we tested whether an individual's DLPFC gamma-aminobutryic acid (GABA) content predicts individual differences in WM task performance using a novel behavioral approach...
November 16, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27849004/performance-error-related-activity-in-monkey-striatum-during-social-interactions
#13
Raymundo Báez-Mendoza, Wolfram Schultz
Monitoring our performance is fundamental to motor control while monitoring other's performance is fundamental to social coordination. The striatum is hypothesized to play a role in action selection, action initiation, and action parsing, but we know little of its role in performance monitoring. Furthermore, the striatum contains neurons that respond to own and other's actions. Therefore, we asked if striatal neurons signal own and conspecific's performance errors. Two macaque monkeys sitting across a touch-sensitive table in plain view of each other took turns performing a simple motor task to obtain juice rewards while we recorded single striatal neurons from one monkey at a time...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27844502/therapist-empathy-homework-compliance-and-outcome-in-cognitive-behavioral-therapy-for-generalized-anxiety-disorder-partitioning-within-and-between-therapist-effects
#14
Kimberley M Hara, Adi Aviram, Michael J Constantino, Henny A Westra, Martin M Antony
Although client-perceived therapist empathy relates to positive therapy outcomes, including in cognitive behavioral therapy (CBT), little is known about how empathy exerts its ameliorative effect. One possible way is by promoting clients' subsequent homework compliance, a variable that also predicts positive outcomes in CBT. The present study sought to investigate simultaneously, in the context of 43 therapist-client dyads receiving 15 sessions of CBT for generalized anxiety disorder, (1) the association of early client-perceived therapist empathy (averaged over sessions 1, 3, 5) with mid-treatment client homework compliance (averaged over sessions 6, 8, 10); (2) the association of mid-treatment homework compliance on client posttreatment worry severity; and (3) the indirect effect of early perceived therapist empathy on posttreatment worry through mid-treatment homework compliance...
November 15, 2016: Cognitive Behaviour Therapy
https://www.readbyqxmd.com/read/27843717/rgfa-powerful-and-convenient-handling-of-assembly-graphs
#15
Giorgio Gonnella, Stefan Kurtz
The "Graphical Fragment Assembly" (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler...
2016: PeerJ
https://www.readbyqxmd.com/read/27826755/using-machine-learning-to-parse-breast-pathology-reports
#16
Adam Yala, Regina Barzilay, Laura Salama, Molly Griffin, Grace Sollender, Aditya Bardia, Constance Lehman, Julliette M Buckley, Suzanne B Coopey, Fernanda Polubriaginof, Judy E Garber, Barbara L Smith, Michele A Gadd, Michelle C Specht, Thomas M Gudewicz, Anthony J Guidi, Alphonse Taghian, Kevin S Hughes
PURPOSE: Extracting information from electronic medical record is a time-consuming and expensive process when done manually. Rule-based and machine learning techniques are two approaches to solving this problem. In this study, we trained a machine learning model on pathology reports to extract pertinent tumor characteristics, which enabled us to create a large database of attribute searchable pathology reports. This database can be used to identify cohorts of patients with characteristics of interest...
November 8, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/27826318/epigenetic-inheritance-across-the-landscape
#17
REVIEW
Amy V Whipple, Liza M Holeski
The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27824094/visual-perception-of-shape-altered-by-inferred-causal-history
#18
Patrick Spröte, Filipp Schmidt, Roland W Fleming
One of the main functions of vision is to represent object shape. Most theories of shape perception focus exclusively on geometrical computations (e.g., curvatures, symmetries, axis structure). Here, however, we find that shape representations are also profoundly influenced by an object's causal origins: the processes in its past that formed it. Observers placed dots on objects to report their perceived symmetry axes. When objects appeared 'complete'-created entirely by a single generative process-responses closely approximated the object's geometrical axes...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27819475/connecting-psychopathology-meta-structure-and-mechanisms
#19
Charles A Sanislow
A persistent challenge for the field of psychopathology has been how to best explain mental disorders and organize clinical symptoms into diagnoses. Meta-structural approaches have clarified fundamental problems and made substantial gains by using covariance structures to organize the nature of clinical symptom patterns. A remaining task is how to specify the connections between these patterns across behavioral, cognitive, and neural mechanisms. Together, meta-structural approaches and the National Institute of Mental Health (NIMH) Research Domain Criteria (RDoC) offer a means to parse out these connections...
November 2016: Journal of Abnormal Psychology
https://www.readbyqxmd.com/read/27819472/longitudinal-validation-of-general-and-specific-structural-features-of-personality-pathology
#20
Aidan G C Wright, Christopher J Hopwood, Andrew E Skodol, Leslie C Morey
Theorists have long argued that personality disorder (PD) is best understood in terms of general impairments shared across the disorders as well as more specific instantiations of pathology. A model based on this theoretical structure was proposed as part of the DSM-5 revision process. However, only recently has this structure been subjected to formal quantitative evaluation, with little in the way of validation efforts via external correlates or prospective longitudinal prediction. We used the Collaborative Longitudinal Study of Personality Disorders dataset to: (a) estimate structural models that parse general from specific variance in personality disorder features, (b) examine patterns of growth in general and specific features over the course of 10 years, and (c) establish concurrent and dynamic longitudinal associations in PD features and a host of external validators including basic personality traits and psychosocial functioning scales...
November 2016: Journal of Abnormal Psychology
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