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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
#1
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
https://www.readbyqxmd.com/read/28439835/the-uea-small-rna-workbench-a-suite-of-computational-tools-for-small-rna-analysis
#2
Irina Mohorianu, Matthew Benedict Stocks, Christopher Steven Applegate, Leighton Folkes, Vincent Moulton
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28438115/an-auditory-display-tool-for-dna-sequence-analysis
#3
Mark D Temple
BACKGROUND: DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorithms are logically designed from the simple through to the more complex. Three of these parse individual nucleotides, nucleotide pairs or codons into musical notes to give rise to 4, 16 or 64 notes, respectively. Codons may also be parsed degenerately into 20 notes with respect to the genetic code...
April 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28433079/utilization-of-whole-exome-next-generation-sequencing-variant-read-frequency-for-detection-of-lesion-specific-somatic-loss-of-heterozygosity-in-a-neurofibromatosis-type-1-cohort-with-tibial-pseudarthrosis
#4
Rebecca L Margraf, Chad VanSant-Webb, David Sant, John Carey, Heather Hanson, Jacques D'Astous, Dave Viskochil, David A Stevenson, Rong Mao
A subset of neurofibromatosis type 1 patients develop tibial dysplasia, which can lead to pseudarthrosis. The tissue from the tibial pseudarthrosis region commonly has a somatic second hit in NF1: single-nucleotide variants, small deletions, or loss of heterozygosity (LOH). We used exome next-generation sequencing (NGS) variant frequency data (allelic imbalance analysis) to detect somatic LOH in pseudarthrosis tissue from three individuals with clinically and diagnostically confirmed neurofibromatosis type 1, and verified the results with microarray...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28431131/dnaprodb-an-interactive-tool-for-structural-analysis-of-dna-protein-complexes
#5
Jared M Sagendorf, Helen M Berman, Remo Rohs
Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA-protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA-protein complexes...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28426976/alternative-electron-transport-pathways-in-photosynthesis-a-confluence-of-regulation
#6
REVIEW
Jean Alric, Xenie Johnson
Photosynthetic reactions proceed along a linear electron transfer chain linking water oxidation at photosystem II (PSII) to CO2 reduction in the Calvin-Benson-Bassham cycle. Alternative pathways poise the electron carriers along the chain in response to changing light, temperature and CO2 inputs, under prolonged hydration stress and during development. We describe recent literature that reports the physiological functions of new molecular players. Such highlights include the flavodiiron proteins and their important role in the green lineage...
April 17, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28422973/camera-trap-arrays-improve-detection-probability-of-wildlife-investigating-study-design-considerations-using-an-empirical-dataset
#7
Kelly M O'Connor, Lucas R Nathan, Marjorie R Liberati, Morgan W Tingley, Jason C Vokoun, Tracy A G Rittenhouse
Camera trapping is a standard tool in ecological research and wildlife conservation. Study designs, particularly for small-bodied or cryptic wildlife species often attempt to boost low detection probabilities by using non-random camera placement or baited cameras, which may bias data, or incorrectly estimate detection and occupancy. We investigated the ability of non-baited, multi-camera arrays to increase detection probabilities of wildlife. Study design components were evaluated for their influence on wildlife detectability by iteratively parsing an empirical dataset (1) by different sizes of camera arrays deployed (1-10 cameras), and (2) by total season length (1-365 days)...
2017: PloS One
https://www.readbyqxmd.com/read/28421225/using-telephony-data-to-facilitate-discovery-of-clinical-workflows
#8
Donald W Rucker
BACKGROUND:  Discovery of clinical workflows to target for redesign using methods such as Lean and Six Sigma is difficult. VoIP telephone call pattern analysis may complement direct observation and EMR-based tools in understanding clinical workflows at the enterprise level by allowing visualization of institutional telecommunications activity. OBJECTIVE:  To build an analytic framework mapping repetitive and high-volume telephone call patterns in a large medical center to their associated clinical units using an enterprise unified communications server log file and to support visualization of specific call patterns using graphical networks...
April 19, 2017: Applied Clinical Informatics
https://www.readbyqxmd.com/read/28412593/bootstrapping-language-acquisition
#9
Omri Abend, Tom Kwiatkowski, Nathaniel J Smith, Sharon Goldwater, Mark Steedman
The semantic bootstrapping hypothesis proposes that children acquire their native language through exposure to sentences of the language paired with structured representations of their meaning, whose component substructures can be associated with words and syntactic structures used to express these concepts. The child's task is then to learn a language-specific grammar and lexicon based on (probably contextually ambiguous, possibly somewhat noisy) pairs of sentences and their meaning representations (logical forms)...
April 13, 2017: Cognition
https://www.readbyqxmd.com/read/28404537/building-a-comprehensive-syntactic-and-semantic-corpus-of-chinese-clinical-texts
#10
Bin He, Bin Dong, Yi Guan, Jinfeng Yang, Zhipeng Jiang, Qiubin Yu, Jianyi Cheng, Chunyan Qu
OBJECTIVE: To build a comprehensive corpus covering syntactic and semantic annotations of Chinese clinical texts with corresponding annotation guidelines and methods as well as to develop tools trained on the annotated corpus, which supplies baselines for research on Chinese texts in the clinical domain. MATERIALS AND METHODS: An iterative annotation method was proposed to train annotators and to develop annotation guidelines. Then, by using annotation quality assurance measures, a comprehensive corpus was built, containing annotations of part-of-speech (POS) tags, syntactic tags, entities, assertions, and relations...
April 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28402395/mzml2isa-nmrml2isa-generating-enriched-isa-tab-metadata-files-from-metabolomics-xml-data
#11
Martin Larralde, Thomas N Lawson, Ralf J M Weber, Pablo Moreno, Kenneth Haug, Philippe Rocca-Serra, Mark R Viant, Christoph Steinbeck, Reza M Salek
Summary: Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28402069/anorexia-nervosa-theory-and-treatment-where-are-we-35%C3%A2-years-on-from-hilde-bruch-s-foundation-lecture
#12
REVIEW
Janet Treasure, Valentina Cardi
Hilde Bruch's foundation lecture in 1982 is a milestone from which to survey current theory and treatment for anorexia nervosa. Bruch described problems in body perception, emotion processing and interpersonal relationships as core theoretical aspects of the illness and built her theory of psychopathology on these aspects, as well as on animal studies on attachment. She also noted that many psychological problems result as consequence of starvation. In the first part of this paper, we parse Bruch's clinical descriptions into elements of psychopathology (disturbances in body perception, attachment, emotion expression, perception and regulation, social comparison, interpersonal, and family and therapeutic relationships), in order to assemble and update the theoretical evidence for a model of the illness...
May 2017: European Eating Disorders Review: the Journal of the Eating Disorders Association
https://www.readbyqxmd.com/read/28398502/pygold-a-python-based-api-for-docking-based-virtual-screening-workflow-generation
#13
Hitesh Patel, Tobias Brinkjost, Oliver Koch
Motivation: Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28395645/domains-of-social-support-that-predict-bereavement-distress-following-homicide-loss
#14
Jamison S Bottomley, Laurie A Burke, Robert A Neimeyer
Psychological adaptation following homicide loss can prove more challenging for grievers than other types of losses. Although social support can be beneficial in bereavement, research is mixed in terms of identifying whether it serves as a buffer to distress following traumatic loss. In particular, studies have not parsed out specific domains of social support that best predict positive bereavement outcomes. Recruiting a sample of 47 African Americans bereaved by homicide, we examined six types of social support along with the griever's perceived need for or satisfaction with each and analyzed them in relation to depression, anxiety, complicated grief, and posttraumatic stress disorder outcomes...
May 2017: Omega
https://www.readbyqxmd.com/read/28390697/smoking-prevalence-and-attributable-disease-burden-in-195-countries-and-territories-1990-2015-a-systematic-analysis-from-the-global-burden-of-disease-study-2015
#15
(no author information available yet)
BACKGROUND: The scale-up of tobacco control, especially after the adoption of the Framework Convention for Tobacco Control, is a major public health success story. Nonetheless, smoking remains a leading risk for early death and disability worldwide, and therefore continues to require sustained political commitment. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) offers a robust platform through which global, regional, and national progress toward achieving smoking-related targets can be assessed...
April 5, 2017: Lancet
https://www.readbyqxmd.com/read/28387585/parsing-the-roles-of-the-frontal-lobes-and-bg-in-task-control-using-multivoxel-pattern-analysis
#16
Angie A Kehagia, Rong Ye, Dan W Joyce, Orla M Doyle, James B Rowe, Trevor W Robbins
Cognitive control has traditionally been associated with pFC based on observations of deficits in patients with frontal lesions. However, evidence from patients with Parkinson's disease indicates that subcortical regions also contribute to control under certain conditions. We scanned 17 healthy volunteers while they performed a task-switching paradigm that previously dissociated performance deficits arising from frontal lesions in comparison with Parkinson's disease, as a function of the abstraction of the rules that are switched...
April 7, 2017: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/28383955/event-segmentation-improves-event-memory-up-to-one-month-later
#17
Shaney Flores, Heather R Bailey, Michelle L Eisenberg, Jeffrey M Zacks
When people observe everyday activity, they spontaneously parse it into discrete meaningful events. Individuals who segment activity in a more normative fashion show better subsequent memory for the events. If segmenting events effectively leads to better memory, does asking people to attend to segmentation improve subsequent memory? To answer this question, participants viewed movies of naturalistic activity with instructions to remember the activity for a later test, and in some conditions additionally pressed a button to segment the movies into meaningful events or performed a control condition that required button-pressing but not attending to segmentation...
April 6, 2017: Journal of Experimental Psychology. Learning, Memory, and Cognition
https://www.readbyqxmd.com/read/28379724/parsing-the-phenotype-of-obsessive-compulsive-tic-disorder-octd-a-multidisciplinary-consensus
#18
Bernardo Dell'Osso, Donatella Marazziti, Umberto Albert, Stefano Pallanti, Orsola Gambini, Antonio Tundo, Carlotta Zanaboni, Domenico Servello, Renata Rizzo, Luciana Scalone, Beatrice Benatti, A Carlo Altamura, Mauro Porta
Obsessive-Compulsive Disorder (OCD) and Tic Disorder (TD) are highly disabling and often comorbid conditions. Of note, the DSM-5 acknowledged a new 'tic-related' specifier for OCD, which might be referred to as Obsessive-Compulsive Tic Disorder (OCTD), raising new interest toward a better clinical characterisation of affected patients. Available literature indicates that early onset, male gender, sensory phenomena and obsessions of symmetry, aggressiveness, hoarding, exactness and sounds as well as comorbidity with Attention Deficit Hyperactivity Disorder (ADHD) may be of more frequent observation in patients with OCTD...
February 24, 2017: International Journal of Psychiatry in Clinical Practice
https://www.readbyqxmd.com/read/28379377/eliie-an-open-source-information-extraction-system-for-clinical-trial-eligibility-criteria
#19
Tian Kang, Shaodian Zhang, Youlan Tang, Gregory W Hruby, Alexander Rusanov, Noémie Elhadad, Chunhua Weng
Objective: To develop an open-source information extraction system called Eli gibility Criteria I nformation E xtraction (EliIE) for parsing and formalizing free-text clinical research eligibility criteria (EC) following Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) version 5.0. Materials and Methods: EliIE parses EC in 4 steps: (1) clinical entity and attribute recognition, (2) negation detection, (3) relation extraction, and (4) concept normalization and output structuring...
April 1, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28371736/on-demand-dissolution-of-modular-synthetic-extracellular-matrix-reveals-local-epithelial-stromal-communication-networks
#20
Jorge Valdez, Christi D Cook, Caroline Chopko Ahrens, Alex J Wang, Alexander Brown, Manu Kumar, Linda Stockdale, Daniel Rothenberg, Kasper Renggli, Elizabeth Gordon, Douglas Lauffenburger, Forest White, Linda Griffith
Methods to parse paracrine epithelial-stromal communication networks are a vital need in drug development, as disruption of these networks underlies diseases ranging from cancer to endometriosis. Here, we describe a modular, synthetic, and dissolvable extracellular matrix (MSD-ECM) hydrogel that fosters functional 3D epithelial-stromal co-culture, and that can be dissolved on-demand to recover cells and paracrine signaling proteins intact for subsequent analysis. Specifically, synthetic polymer hydrogels, modified with cell-interacting adhesion motifs and crosslinked with peptides that include a substrate for cell-mediated proteolytic remodeling, can be rapidly dissolved by an engineered version of the microbial transpeptidase Sortase A (SrtA) if the crosslinking peptide includes a SrtA substrate motif and a soluble second substrate...
June 2017: Biomaterials
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