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https://www.readbyqxmd.com/read/28651252/combined-diffusion-tensor-and-magnetic-resonance-spectroscopic-imaging-methodology-for-automated-regional-brain-analysis-application-in-a-normal-pediatric-population
#1
Nirmalya Ghosh, Barbara Holshouser, Udo Oyoyo, Stanley Barnes, Karen Tong, Stephen Ashwal
During human brain development, anatomic regions mature at different rates. Quantitative anatomy-specific analysis of longitudinal diffusion tensor imaging (DTI) and magnetic resonance spectroscopic imaging (MRSI) data may improve our ability to quantify and categorize these maturational changes. Computational tools designed to quickly fuse and analyze imaging information from multiple, technically different datasets would facilitate research on changes during normal brain maturation and for comparison to disease states...
June 27, 2017: Developmental Neuroscience
https://www.readbyqxmd.com/read/28635323/preserving-employee-privacy-in-wellness
#2
Paul E Terry
The proposed "Preserving Employee Wellness Programs Act" states that the collection of information about the manifested disease or disorder of a family member shall not be considered an unlawful acquisition of genetic information. The bill recognizes employee privacy protections that are already in place and includes specific language relating to nondiscrimination based on illness. Why did legislation expressly intending to "preserve wellness programs" generate such antipathy about wellness among journalists? This article argues that those who are committed to preserving employee wellness must be equally committed to preserving employee privacy...
July 2017: American Journal of Health Promotion: AJHP
https://www.readbyqxmd.com/read/28630944/clinvar-data-parsing
#3
Xiaolei Zhang, Eric V Minikel, Anne H O'Donnell-Luria, Daniel G MacArthur, James S Ware, Ben Weisburd
This software repository provides a pipeline for converting raw ClinVar data files into analysis-friendly tab-delimited tables, and also provides these tables for the most recent ClinVar release. Separate tables are generated for genome builds GRCh37 and GRCh38 as well as for mono-allelic variants and complex multi-allelic variants. Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants. Overall, this work provides ClinVar data in a format that is easier to work with and can be directly loaded into a variety of popular analysis tools such as R, python pandas, and SQL databases...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28626013/sleep-disrupts-high-level-speech-parsing-despite-significant-basic-auditory-processing
#4
Shiri Makov, Omer Sharon, Nai Ding, Michal Ben-Shachar, Yuval Nir, Elana Zion Golumbic
The extent to which the sleeping brain processes sensory information remains unclear. This is particularly true for continuous and complex stimuli, such as speech, in which information is organized into hierarchically embedded structures. Recently, novel metrics for assessing the neural representation of continuous speech have been developed, using non-invasive brain recordings. Those were so far tested during wakefulness. Here we investigated, for the first time, the sleeping brain's capacity to process continuous speech at different hierarchical levels, using a newly developed Concurrent Hierarchical Tracking (CHT) approach that can online monitor the neural representation and processing-depth of continuous speech...
June 16, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28626011/effects-of-ventral-striatum-lesions-on-stimulus-versus-action-based-reinforcement-learning
#5
Kathryn M Rothenhoefer, Vincent D Costa, Ramón Bartolo, Raquel Vicario-Feliciano, Elisabeth A Murray, Bruno B Averbeck
Learning the values of actions versus stimuli may depend on separable neural circuits. In the current study, we evaluated ventral striatum (VS) lesioned macaques' performance on a two-arm bandit task that had randomly interleaved blocks of stimulus based and action based reinforcement learning (RL). Compared to controls, monkeys with VS lesions had deficits in learning to select rewarding images but not rewarding actions. We used a RL model to quantify learning and choice consistency and found that, in stimulus based RL, the VS lesion monkeys were more influenced by negative feedback and had lower choice consistency than controls...
June 16, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28624971/excelautomat-a-tool-for-systematic-processing-of-files-as-applied-to-quantum-chemical-calculations
#6
Jalal Z A Laloo, Nassirah Laloo, Lydia Rhyman, Ponnadurai Ramasami
The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language...
June 17, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28621146/dissociation-of-executive-and-attentional-elements-of-the-digit-span-task-in-a-population-of-older-adults-a-latent-class-analysis
#7
Denise R LaBelle, Bern G Lee, Justin B Miller
The prevailing model for working memory proposes the existence of a "central executive" responsible for coordinating and prioritizing incoming information from sensory and association cortices. The Digit Span task is commonly used by clinicians to parse attentional and executive components of working memory; however, the interrelatedness of these constructs in the context of advanced age and neurodegenerative disease remains an area of active investigation. The current study details a procedure and rationale for the use of latent class analysis, a data-driven, person-centered method, in the investigation of older adults and dementia...
June 1, 2017: Assessment
https://www.readbyqxmd.com/read/28606167/rdml-a-mathematica-package-for-parsing-and-importing-real-time-qpcr-data
#8
Ramiro Magno, Isabel Duarte, Raquel P Andrade, Isabel Palmeirim
OBJECTIVE: The purpose and objective of the research presented is to provide a package for easy importing of Real-Time PCR data markup language (RDML) data to Mathematica. RESULTS: Real-Time qPCR is the most widely used experimental method for the accurate quantification of gene expression. To enable the straightforward archiving and sharing of qPCR data and its associated experimental information, an XML-based data standard was developed-the Real-Time PCR data markup language (RDML)-devised by the RDML consortium...
June 12, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28605506/multi-locus-and-long-amplicon-sequencing-approach-to-study-microbial-diversity-at-species-level-using-the-miniontm-portable-nanopore-sequencer
#9
Alfonso Benítez-Páez, Yolanda Sanz
Background: The miniaturised and portable DNA sequencer MinION TM has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION TM platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. Results: After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67,000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION TM device using R9 and R9...
June 12, 2017: GigaScience
https://www.readbyqxmd.com/read/28605449/fqc-dashboard-integrates-fastqc-results-into-a-web-based-interactive-and-extensible-fastq-quality-control-tool
#10
Joseph Brown, Meg Pirrung, Lee Ann McCue
Summary: FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data. Availability and Implementation: FQC is implemented in Python 3 and Javascript, and is maintained under an MIT license...
June 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28602941/hormonal-correlates-of-energetic-condition-in-mantled-howler-monkeys
#11
Pedro Américo D Dias, Alejandro Coyohua-Fuentes, Domingo Canales-Espinosa, Roberto Chavira-Ramírez, Ariadna Rangel-Negrín
Hormones have a key role in energy allocation, so their study allows understanding individual metabolic strategies. Because different hormones convey different information on the responses of individuals to energetic demands, a simultaneous analysis of variation in multiple hormones may offer a more reliable picture of metabolic strategies than single hormone assessments. In this study we focused on determining which factors were related to variation in fecal glucocorticoid and thyroid hormone metabolites in wild mantled howler monkeys (Alouatta palliata)...
June 21, 2017: Hormones and Behavior
https://www.readbyqxmd.com/read/28600239/scene-segmentation-with-dag-recurrent-neural-networks
#12
Bing Shuai, Zhen Zup, Bing Wang, Gang Wang
In this paper, we address the challenging task of scene segmentation. In order to capture the rich contextual dependencies over image regions, we propose Directed Acyclic Graph - Recurrent Neural Networks (DAG-RNN) to perform context aggregation over locally connected feature maps. More specifically, DAG-RNN is placed on top of pre-trained CNN (feature extractor) to embed context into local features so that their representative capability can be enhanced. In comparison with plain CNN (as in Fully Convolutional Networks - FCN), DAG-RNN is empirically found to be significantly more effective at aggregating context...
June 6, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28595849/on-the-relation-between-dependency-distance-crossing-dependencies-and-parsing-comment-on-dependency-distance-a-new-perspective-on-syntactic-patterns-in-natural-languages-by-haitao-liu-et-al
#13
https://www.readbyqxmd.com/read/28594939/ambiguity-in-the-processing-of-mandarin-chinese-relative-clauses-one-factor-cannot-explain-it-all
#14
Michael P Mansbridge, Katsuo Tamaoka, Kexin Xiong, Rinus G Verdonschot
This study addresses the question of whether native Mandarin Chinese speakers process and comprehend subject-extracted relative clauses (SRC) more readily than object-extracted relative clauses (ORC) in Mandarin Chinese. Presently, this has been a hotly debated issue, with various studies producing contrasting results. Using two eye-tracking experiments with ambiguous and unambiguous RCs, this study shows that both ORCs and SRCs have different processing requirements depending on the locus and time course during reading...
2017: PloS One
https://www.readbyqxmd.com/read/28594819/wide-open-accelerating-public-data-release-by-automating-detection-of-overdue-datasets
#15
Maxim Grechkin, Hoifung Poon, Bill Howe
Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28593606/gazepath-an-eye-tracking-analysis-tool-that-accounts-for-individual-differences-and-data-quality
#16
Daan R van Renswoude, Maartje E J Raijmakers, Arnout Koornneef, Scott P Johnson, Sabine Hunnius, Ingmar Visser
Eye-trackers are a popular tool for studying cognitive, emotional, and attentional processes in different populations (e.g., clinical and typically developing) and participants of all ages, ranging from infants to the elderly. This broad range of processes and populations implies that there are many inter- and intra-individual differences that need to be taken into account when analyzing eye-tracking data. Standard parsing algorithms supplied by the eye-tracker manufacturers are typically optimized for adults and do not account for these individual differences...
June 7, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28589265/effects-of-ketamine-on-the-unconditioned-and-conditioned-locomotor-activity-of-preadolescent-and-adolescent-rats-impact-of-age-sex-and-drug-dose
#17
Sanders A McDougall, Andrea E Moran, Timothy J Baum, Matthew G Apodaca, Vanessa Real
RATIONALE: Ketamine is used by preadolescent and adolescent humans for licit and illicit purposes. OBJECTIVE: The goal of the present study was to determine the effects of acute and repeated ketamine treatment on the unconditioned behaviors and conditioned locomotor activity of preadolescent and adolescent rats. METHODS: To assess unconditioned behaviors, female and male rats were injected with ketamine (5-40 mg/kg), and distance traveled was measured on postnatal day (PD) 21-25 or PD 41-45...
June 7, 2017: Psychopharmacology
https://www.readbyqxmd.com/read/28584543/comparing-the-concept-of-caring-in-islamic-perspective-with-watson-and-parse-s-nursing-theories
#18
Akram-Sadat Sadat-Hoseini, Abdoul-Hosein Khosropanah
BACKGROUND: In the nursing profession, it is apparent that the definition of caring differs between various perspectives. This article compares the difference of caring in Islamic with the Parse and Watson theories. MATERIALS AND METHODS: In this study, we use concept analyses of Walker-Avants and compare research methods. Material used is all Islamic documents. RESULTS: According to Islamic documents, there are four major types of caring, namely, (1) God taking care of humans, (2) Humans taking care of themselves, (3) Other humans taking care of humans, and (4) The universe taking care of humans and vice versa...
March 2017: Iranian Journal of Nursing and Midwifery Research
https://www.readbyqxmd.com/read/28578876/noise-and-pitch-interact-during-the-cortical-segregation-of-concurrent-speech
#19
Gavin M Bidelman, Anusha Yellamsetty
Behavioral studies reveal listeners exploit intrinsic differences in voice fundamental frequency (F0) to segregate concurrent speech sounds-the so-called "F0-benefit." More favorable signal-to-noise ratio (SNR) in the environment, an extrinsic acoustic factor, similarly benefits the parsing of simultaneous speech. Here, we examined the neurobiological substrates of these two cues in the perceptual segregation of concurrent speech mixtures. We recorded event-related brain potentials (ERPs) while listeners performed a speeded double-vowel identification task...
May 25, 2017: Hearing Research
https://www.readbyqxmd.com/read/28574982/mmtf-an-efficient-file-format-for-the-transmission-visualization-and-analysis-of-macromolecular-structures
#20
Anthony R Bradley, Alexander S Rose, Antonín Pavelka, Yana Valasatava, Jose M Duarte, Andreas Prlić, Peter W Rose
Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues...
June 2017: PLoS Computational Biology
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