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https://www.readbyqxmd.com/read/28541377/asap-a-web-based-platform-for-the-analysis-and-interactive-visualization-of-single-cell-rna-seq-data
#1
Vincent Gardeux, Fabrice P A David, Adrian Shajkofci, Petra C Schwalie, Bart Deplancke
Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet these groups often lack the expertise to handle complex scRNA-seq data sets. Results: We developed a fully integrated, web-based platform aimed at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28515864/the-planispheric-optic-array
#2
Jan Koenderink, Andrea van Doorn
The "planispheric optic array" is a full-horizon Mercator projection of the optic array. Such pictures of the environment are coming in common use with the availability of cheap full-view cameras of reasonable quality. This introduces the question of whether the public will actually profit from such pictorial information in terms of an understanding of the spatial layout of the depicted scene. Test images include four persons located at the corners of a square centered at the camera. The persons point at each other in various combinations...
May 2017: I-Perception
https://www.readbyqxmd.com/read/28510521/a-seer-of-trump-s-coming-parses-repeal-and-replace
#3
Richard Mark Kirkner
Diana Furchtgott-Roth, a senior fellow at the Manhattan Institute, a freemarket think tank, confidently predicted back in October what few people saw coming-Donald Trump's electoral victory. Now she gives her take on the dismantling of the ACA and what might come after.
March 2017: Managed Care
https://www.readbyqxmd.com/read/28500598/characterization-and-functional-phenotyping-of-renal-immune-cells-via-flow-cytometry
#4
Nathan P Rudemiller, Steven D Crowley
A variety of immune cell subsets contribute to the pathogenesis of hypertension and associated kidney damage following inappropriate activation of the renin-angiotensin system (RAS). These immune cell subsets often express common surface markers, which complicates their separation and characterization in vivo. Accordingly, flow cytometry has become an invaluable tool for parsing immune cell populations because this technique permits the simultaneous detection of up to 18 markers on a single cell. Below we describe a process by which one can determine the immune cell subsets in the kidney via flow cytometry...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28500014/three-dimensional-visual-patient-based-on-electronic-medical-diagnostic-records
#5
Liehang Shi, Jianyong Sun, Yuanyuan Yang, Tonghui Ling, Mingqing Wang, Yiping Gu, Zhiming Yang, Yanqing Hua, Jianguo Zhang
OBJECTIVE: An innovative concept and method is introduced to use a three Dimensional (3D) anatomical graphic pattern called Visual Patient (VP) visually to index, represent and render the medical diagnostic records (MDRs) of a patient, so that a doctor can quickly learn the current and historical medical status of the patient by manipulating VP. The MDRs can be imaging diagnostic reports and DICOM images, laboratory reports and clinical summaries which can have clinical information relating to medical status of human organs or body parts...
May 8, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28497802/data-driven-subgroups-in-depression-derived-from-directed-functional-connectivity-paths-at-rest
#6
Rebecca B Price, Kathleen Gates, Thomas E Kraynak, Michael E Thase, Greg J Siegle
Depressed patients show abnormalities in brain connectivity at rest, including hyperconnectivity within the Default Mode Network (DMN). However, there is well-known heterogeneity in the clinical presentation of depression that is overlooked when averaging connectivity data. We used data-driven parsing of neural connectivity to reveal subgroups among 80 depressed patients completing resting state fMRI. Directed functional connectivity paths (eg, region A influences region B) within a depression-relevant network were characterized using Group Iterative Multiple Model Estimation, a method shown to accurately recover the direction and presence of connectivity paths in individual participants...
May 12, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28489947/determination-of-ion-atmosphere-effects-on-the-nucleic-acid-electrostatic-potential-and-ligand-association-using-ah-%C3%A2-c-wobble-formation-in-double-stranded-dna
#7
Benjamin Allred, Magdalena Gebala, Daniel Herschlag
The high charge density of nucleic acids and resulting ion atmosphere profoundly influence the conformational landscape of RNA and DNA and their association with small molecules and proteins. Electrostatic theories have been applied to quantitatively model the electrostatic potential surrounding nucleic acids and the effects of the surrounding ion atmosphere, but experimental measures of the potential and tests of these models have often been complicated by conformational changes and multi-site binding equilibria, among other factors...
May 10, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28487263/a-pragmatic-method-for-transforming-clinical-research-data-from-the-research-electronic-data-capture-redcap-to-clinical-data-interchange-standards-consortium-cdisc-study-data-tabulation-model-sdtm-development-and-evaluation-of-redcap2sdtm
#8
Keiichi Yamamoto, Keiko Ota, Ippei Akiya, Ayumi Shintani
The Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM) can be used for new drug application studies as well as secondarily for creating a clinical research data warehouse to leverage clinical research study data across studies conducted within the same disease area. However, currently not all clinical research uses Clinical Data Acquisition Standards Harmonization (CDASH) beginning in the set-up phase of the study. Once already initiated, clinical studies that have not utilized CDASH are difficult to map in the SDTM format...
May 6, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28486116/active-vision-dynamic-reformatting-of-visual-information-by-the-saccade-drift-cycle
#9
Igor Kagan, David C Burr
Visual processing depends on rapid parsing of global features followed by analysis of fine detail. A new study suggests that this transformation is enabled by a cycle of saccades and fixational drifts, which reformat visual input to match the spatiotemporal sensitivity of fast and slow neuronal pathways.
May 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28484022/biological-origins-of-color-categorization
#10
Alice E Skelton, Gemma Catchpole, Joshua T Abbott, Jenny M Bosten, Anna Franklin
The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants' categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mapped infants' categorical recognition memory for hue onto a stimulus array used previously to document the color lexicons of 110 nonindustrialized languages...
May 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28479982/logic-passion-and-the-problem-of-convergence
#11
Daniel W McShea
Our estimate of the likelihood of convergence on human-style intelligence depends on how we understand our various mental capacities. Here I revive David Hume's theory of motivation and action to argue that the most common understanding of the two conventionally recognized components of intelligence-reason and emotion-is confused. We say things like, 'Reason can overcome emotion', but to make this statement meaningful, we are forced to treat reason as a compound notion, as a forced and unhappy mixture of concepts that are incommensurate...
June 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28477208/bcc-ner-bidirectional-contextual-clues-named-entity-tagger-for-gene-protein-mention-recognition
#12
Gurusamy Murugesan, Sabenabanu Abdulkadhar, Balu Bhasuran, Jeyakumar Natarajan
Tagging biomedical entities such as gene, protein, cell, and cell-line is the first step and an important pre-requisite in biomedical literature mining. In this paper, we describe our hybrid named entity tagging approach namely BCC-NER (bidirectional, contextual clues named entity tagger for gene/protein mention recognition). BCC-NER is deployed with three modules. The first module is for text processing which includes basic NLP pre-processing, feature extraction, and feature selection. The second module is for training and model building with bidirectional conditional random fields (CRF) to parse the text in both directions (forward and backward) and integrate the backward and forward trained models using margin-infused relaxed algorithm (MIRA)...
December 2017: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28460376/encoding-of-rapid-time-varying-information-is-impaired-in-poor-readers
#13
Richard Johnston, Nicola J Pitchford, Neil W Roach, Timothy Ledgeway
A characteristic set of eye movements and fixations are made during reading, so the position of words on the retinae is constantly being updated. Effective decoding of print requires this temporal stream of visual information to be segmented or parsed into its constituent units (e.g., letters or words). Poor readers' difficulties with word recognition could arise at the point of segmenting time-varying visual information, but the mechanisms underlying this process are little understood. Here, we used random-dot displays to explore the effects of reading ability on temporal segmentation...
May 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/28459961/crowdsourcing-seizure-detection-algorithm-development-and-validation-on-human-implanted-device-recordings
#14
Steven N Baldassano, Benjamin H Brinkmann, Hoameng Ung, Tyler Blevins, Erin C Conrad, Kent Leyde, Mark J Cook, Ankit N Khambhati, Joost B Wagenaar, Gregory A Worrell, Brian Litt
There exist significant clinical and basic research needs for accurate, automated seizure detection algorithms. These algorithms have translational potential in responsive neurostimulation devices and in automatic parsing of continuous intracranial electroencephalography data. An important barrier to developing accurate, validated algorithms for seizure detection is limited access to high-quality, expertly annotated seizure data from prolonged recordings. To overcome this, we hosted a kaggle.com competition to crowdsource the development of seizure detection algorithms using intracranial electroencephalography from canines and humans with epilepsy...
April 27, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28459277/verbal-and-visual-spatial-working-memory-what-develops-over-a-life-span
#15
H Lee Swanson
This study investigates whether age-related changes in the structure of 5 complex working memory (WM) tasks (a) reflect a general or domain specific system, (b) follows a similar trajectory across different age spans, and (c) contribute domain general or domain specific resources to achievement measures. The study parsed the sample (N = 2,471) into 11 age groups (mean ages of 6, 7, 8, 9, 11, 13, 15, 18, 26, 41, and 66 years), and compared their performances on verbal and visuospatial WM measures. Three important findings emerged: (a) a confirmatory factor analysis and Schmid-Leiman transformation to a high-order model solution supported a domain general factor model for the total sample as well as separately for children and adults, (b) performance on visual-spatial WM tasks as a function of age decreased at a faster rate than verbal WM tasks, and (c) both verbal and visual-spatial WM measures in concert with each other uniquely predicted reading and math measures, suggesting that a domain general WM system contributed to performance on achievement measures...
May 2017: Developmental Psychology
https://www.readbyqxmd.com/read/28458050/comparing-different-kinds-of-words-and-word-word-relations-to-test-an-habituation-model-of-priming
#16
Cory A Rieth, David E Huber
Huber and O'Reilly (2003) proposed that neural habituation exists to solve a temporal parsing problem, minimizing blending between one word and the next when words are visually presented in rapid succession. They developed a neural dynamics habituation model, explaining the finding that short duration primes produce positive priming whereas long duration primes produce negative repetition priming. The model contains three layers of processing, including a visual input layer, an orthographic layer, and a lexical-semantic layer...
June 2017: Cognitive Psychology
https://www.readbyqxmd.com/read/28453679/biopaxviz-a-cytoscape-application-for-the-visual-exploration-of-metabolic-pathway-evolution
#17
Fotis E Psomopoulos, Dimitrios M Vitsios, Shakuntala Baichoo, Christos A Ouzounis
Summary: 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...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28450537/being-first-matters-topographical-representational-similarity-analysis-of-erp-signals-reveals-separate-networks-for-audiovisual-temporal-binding-depending-on-the-leading-sense
#18
Roberto Cecere, Joachim Gross, Ashleigh Willis, Gregor Thut
In multisensory integration, processing in one sensory modality is enhanced by complementary information from other modalities. Inter-sensory timing is crucial in this process as only inputs reaching the brain within a restricted temporal window are perceptually bound. Previous research in the audiovisual field has investigated various features of the temporal binding window (TBW), revealing asymmetries in its size and plasticity depending on the leading input (auditory-visual, AV; visual-auditory, VA). We here tested whether separate neuronal mechanisms underlie this AV-VA dichotomy in humans...
April 27, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28443119/parsing-the-regulatory-network-between-small-rnas-and-target-genes-in-ethylene-pathway-in-tomato
#19
Yunxiang Wang, Qing Wang, Lipu Gao, Benzhong Zhu, Zheng Ju, Yunbo Luo, Jinhua Zuo
Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28441748/convergent-validity-of-a-wearable-sensor-system-for-measuring-sub-task-performance-during-the-timed-up-and-go-test
#20
James Beyea, Chris A McGibbon, Andrew Sexton, Jeremy Noble, Colleen O'Connell
BACKGROUND: The timed-up-and-go test (TUG) is one of the most commonly used tests of physical function in clinical practice and for research outcomes. Inertial sensors have been used to parse the TUG test into its composite phases (rising, walking, turning, etc.), but have not validated this approach against an optoelectronic gold-standard, and to our knowledge no studies have published the minimal detectable change of these measurements. METHODS: Eleven adults performed the TUG three times each under normal and slow walking conditions, and 3 m and 5 m walking distances, in a 12-camera motion analysis laboratory...
April 23, 2017: Sensors
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