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https://www.readbyqxmd.com/read/29050227/identification-of-two-novel-biomarkers-of-rectal-carcinoma-progression-and-prognosis-via-co-expression-network-analysis
#1
Min Sun, Taojiao Sun, Zhongshi He, Bin Xiong
mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied weighted gene co-expression network analysis to parse DEGs and eight clinical traits in 66 eligible RC samples...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049390/do-two-and-three-year-old-children-use-an-incremental-first-np-as-agent-bias-to-process-active-transitive-and-passive-sentences-a-permutation-analysis
#2
Kirsten Abbot-Smith, Franklin Chang, Caroline Rowland, Heather Ferguson, Julian Pine
We used eye-tracking to investigate if and when children show an incremental bias to assume that the first noun phrase in a sentence is the agent (first-NP-as-agent bias) while processing the meaning of English active and passive transitive sentences. We also investigated whether children can override this bias to successfully distinguish active from passive sentences, after processing the remainder of the sentence frame. For this second question we used eye-tracking (Study 1) and forced-choice pointing (Study 2)...
2017: PloS One
https://www.readbyqxmd.com/read/29048466/pybel-a-computational-framework-for-biological-expression-language
#3
Charles Tapley Hoyt, Andrej Konotopez, Christian Ebeling
Summary: Biological Expression Language (BEL) assembles knowledge networks from biological relations across multiple modes and scales. Here, we present PyBEL; a software package for parsing, validating, converting, storing, querying, and visualizing networks encoded in BEL. Availability: PyBEL is implemented in platform-independent, universal Python code. Its source is distributed under the Apache 2.0 License at https://github.com/pybel. Contact: charles...
October 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29044763/theta-band-oscillations-reflect-more-than-entrainment-behavioral-and-neural-evidence-demonstrate-an-active-chunking-process
#4
Xiangbin Teng, Xing Tian, Keith Doelling, David Poeppel
Parsing continuous acoustic streams into perceptual units is fundamental to auditory perception. Previous studies have uncovered a cortical entrainment mechanism in the delta and theta bands (~1-8 Hz) that correlates with formation of perceptual units in speech, music, and other quasi-rhythmic stimuli. Whether cortical oscillations in the delta-theta bands are passively entrained by regular acoustic patterns or play an active role in parsing the acoustic stream is debated. Here we investigate cortical oscillations using novel stimuli with 1/f modulation spectra...
October 17, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29042512/in-vitro-reconstitution-of-t-cell-receptor-mediated-segregation-of-the-cd45-phosphatase
#5
Catherine B Carbone, Nadja Kern, Ricardo A Fernandes, Enfu Hui, Xiaolei Su, K Christopher Garcia, Ronald D Vale
T cell signaling initiates upon the binding of peptide-loaded MHC (pMHC) on an antigen-presenting cell to the T cell receptor (TCR) on a T cell. TCR phosphorylation in response to pMHC binding is accompanied by segregation of the transmembrane phosphatase CD45 away from TCR-pMHC complexes. The kinetic segregation hypothesis proposes that CD45 exclusion shifts the local kinase-phosphatase balance to favor TCR phosphorylation. Spatial partitioning may arise from the size difference between the large CD45 extracellular domain and the smaller TCR-pMHC complex, although parsing potential contributions of extracellular protein size, actin activity, and lipid domains is difficult in living cells...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29035691/how-we-hear-the-perception-and-neural-coding-of-sound
#6
Andrew J Oxenham
Auditory perception is our main gateway to communication with others via speech and music, and it also plays an important role in alerting and orienting us to new events. This review provides an overview of selected topics pertaining to the perception and neural coding of sound, starting with the first stage of filtering in the cochlea and its profound impact on perception. The next topic, pitch, has been debated for millennia, but recent technical and theoretical developments continue to provide us with new insights...
October 16, 2017: Annual Review of Psychology
https://www.readbyqxmd.com/read/29031919/parsing-anatomical-dysconnectivity-in-psychosis
#7
Edward T Bullmore
No abstract text is available yet for this article.
November 15, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/29028176/a-biclique-approach-to-reference-anchored-gene-blocks-and-its-applications-to-genomic-islands
#8
Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson
We formalize a new problem variant in gene-block discovery, denoted Reference-Anchored Gene Blocks (RAGB), given a query sequence Q of length n, representing the gene array of a DNA element, a window size bound d on the length of a substring of interest in Q, and a set of target gene sequences [Formula: see text]. Our objective is to identify gene blocks in [Formula: see text] that are centered in a subset q of co-localized genes from Q, and contain genomes from [Formula: see text] in which the corresponding orthologs of the genes from q are also co-localized...
October 13, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29017874/temporal-relationships-between-food-acquisition-and-voluntary-exercise-in-mice
#9
Neil E Rowland, Melissa R Cervantez, Kimberly L Robertson
Patterns of operant food acquisition in a closed economy and bouts of either voluntary wheel running (WR) or spontaneous locomotor activity in a standard condition (SC) with no wheel were examined in young adult male and female C57BL/6 mice across a range of nose poke prices (FUP) per food pellet. Both sexes showed vigorous WR or locomotor activity. At each FUP, WR groups had higher food intake than SC groups. Despite substantially higher mean body weight of males compared with females, intakes and activity did not differ by sex in the SC groups and males lost weight more rapidly as FUP increased...
October 7, 2017: Behavioural Processes
https://www.readbyqxmd.com/read/28994813/a-primary-human-trophoblast-model-to-study-the-effect-of-inflammation-associated-with-maternal-obesity-on-regulation-of-autophagy-in-the-placenta
#10
Bailey Simon, Matthew Bucher, Alina Maloyan
Maternal obesity is associated with an increased risk of adverse perinatal outcomes that are likely mediated by compromised placental function that can be attributed to, in part, the dysregulation of autophagy. Aberrant changes in the expression of autophagy regulators in the placentas from obese pregnancies may be regulated by inflammatory processes associated with both obesity and pregnancy. Described here is a protocol for sampling of villous tissue and isolation of villous cytotrophoblasts from the term human placenta for primary cell culture...
September 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28994010/parsing-the-neural-correlates-of-anxious-apprehension-and-anxious-arousal-in-the-grey-matter-of-healthy-youth
#11
Peter J Castagna, Scott Roye, Matthew Calamia, Joshua Owens-French, Thompson E Davis, Steven G Greening
Neuroscientific and psychological research posits that there are two transdiagnostic facets of anxiety: anxious arousal and anxious apprehension. Though these two facets of anxiety are distinct, they are often subsumed into one domain (e.g., trait anxiety). The primary goal of the current study was to delineate the relationship between anxious arousal and cortical thickness versus the relationship between anxious apprehension and cortical thickness in a sample of typically functioning youth. The secondary aim was to determine where in the brain cortical thickness significantly correlated with both components of anxiety...
October 9, 2017: Brain Imaging and Behavior
https://www.readbyqxmd.com/read/28993614/mammal-diversity-influences-the-carbon-cycle-through-trophic-interactions-in-the-amazon
#12
Mar Sobral, Kirsten M Silvius, Han Overman, Luiz F B Oliveira, Ted K Rabb, José M V Fragoso
Biodiversity affects many ecosystem functions and services, including carbon cycling and retention. While it is known that the efficiency of carbon capture and biomass production by ecological communities increases with species diversity, the role of vertebrate animals in the carbon cycle remains undocumented. Here, we use an extensive dataset collected in a high-diversity Amazonian system to parse out the relationship between animal and plant species richness, feeding interactions, tree biomass and carbon concentrations in soil...
October 9, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28993427/fate-and-the-clinic-a-multidisciplinary-consideration-of-fatalism-in-health-behaviour
#13
Angela Ross Perfetti
The role of fatalism in health behaviour has stirred significant controversy in literature across several disciplines. Some researchers have demonstrated a negative correlation between fatalistic beliefs and healthy behaviours such as cancer screening, arguing that fatalism is a barrier to health-seeking behaviours. Other studies have painted a more complicated picture of fatalistic beliefs and health behaviours that ultimately questions fatalism's causality as a distinct factor. Unpacking this debate raises thought-provoking questions about how epistemological and methodological frameworks present particular pictures about the connections between belief, race, class and behaviour...
October 9, 2017: Medical Humanities
https://www.readbyqxmd.com/read/28988727/the-mycobiome-role-in-health-and-disease-and-as-a-potential-probiotic-target-in-gastrointestinal-disease
#14
REVIEW
Christopher L Hager, Mahmoud A Ghannoum
The human gastrointestinal (GI) tract is home to trillions of microorganisms, some beneficial and others potentially harmful. Recent advances in science have allowed us to identify the multitude of organisms inhabiting the GI tract and parse out those that play a role in inflammatory bowel disease (IBD). Unfortunately, most research has focused on studying only the bacteria while ,overlooking a key player, fungus. In order to address this issue, we have focused our efforts on studying the fungal community in the GI tract known as the mycobiome...
November 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28982288/mptm-a-tool-for-mining-protein-post-translational-modifications-from-literature
#15
Dongdong Sun, Minghui Wang, Ao Li
Due to the importance of post-translational modifications (PTMs) in human health and diseases, PTMs are regularly reported in the biomedical literature. However, the continuing and rapid pace of expansion of this literature brings a huge challenge for researchers and database curators. Therefore, there is a pressing need to aid them in identifying relevant PTM information more efficiently by using a text mining system. So far, only a few web servers are available for mining information of a very limited number of PTMs, which are based on simple pattern matching or pre-defined rules...
October 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28973073/parsing-heterogeneity
#16
Stephen M Lawrie
No abstract text is available yet for this article.
September 27, 2017: JAMA Psychiatry
https://www.readbyqxmd.com/read/28969354/paradigms-for-assessing-hedonic-processing-and-motivation-in-humans-relevance-to-understanding-negative-symptoms-in-psychopathology
#17
Deanna M Barch, James M Gold, Ann M Kring
Clinicians and researchers have long known that one of the debilitating aspects of psychotic disorders is the presence of "negative symptoms," which involve impairments in hedonic and motivational function, and/or alterations in expressive affect. We have a number of excellent clinical tools available for assessing the presence and severity of negative symptoms. However, to better understand the mechanisms that may give rise to negative symptoms, we need tools and methods that can help distinguish among different potential contributing causes, as a means to develop more targeted intervention pathways...
July 1, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/28967166/variantvalidator-accurate-validation-mapping-and-formatting-of-sequence-variation-descriptions
#18
Peter J Freeman, Reece K Hart, Liam J Gretton, Anthony J Brookes, Raymond Dalgleish
The Human Genome Variation Society (HGVS) variant nomenclature is widely used to describe sequence variants in scientific publications, clinical reports and databases. However, the HGVS recommendations are complex and this often results in inaccurate variant descriptions being reported. The open-source hgvs Python package (https://github.com/biocommons/hgvs) provides a programmatic interface for parsing, manipulating, formatting and validating of variants according to the HGVS recommendations, but does not provide a user-friendly web interface...
October 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28966147/understanding-psychiatric-disease-by-capturing-ecologically-relevant-features-of-learning-and-decision-making
#19
REVIEW
Jacqueline Scholl, Miriam Klein-Flügge
Recent research in cognitive neuroscience has begun to uncover the processes underlying increasingly complex voluntary behaviours, including learning and decision-making. Partly this success has been possible by progressing from simple experimental tasks to paradigms that incorporate more ecological features. More specifically, the premise is that to understand cognitions and brain functions relevant for real life, we need to introduce some of the ecological challenges that we have evolved to solve. This often entails an increase in task complexity, which can be managed by using computational models to help parse complex behaviours into specific component mechanisms...
September 28, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/28961181/alienness-rapid-detection-of-candidate-horizontal-gene-transfers-across-the-tree-of-life
#20
Corinne Rancurel, Ludovic Legrand, Etienne G J Danchin
Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library...
September 29, 2017: Genes
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