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https://www.readbyqxmd.com/read/28314062/a-community-perspective-on-resilience-analytics-a-visual-analysis-of-community-mood
#1
Armando López-Cuevas, José Ramírez-Márquez, Gildardo Sanchez-Ante, Kash Barker
Social networks are ubiquitous in everyday life. Although commonly analyzed from a perspective of individual interactions, social networks can provide insights about the collective behavior of a community. It has been shown that changes in the mood of social networks can be correlated to economic trends, public demonstrations, and political reactions, among others. In this work, we study community resilience in terms of the mood variations of the community. We have developed a method to characterize the mood steady-state of online social networks and to analyze how this steady-state is affected under certain perturbations or events that affect a community...
March 17, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/28306519/variability-in-variability-out-best-practice-recommendations-to-standardize-pre-analytical-variables-in-the-detection-of-circulating-and-tissue-micrornas
#2
Jenna Khan, Joshua A Lieberman, Christina M Lockwood
MicroRNAs (miRNAs) hold promise as biomarkers for a variety of disease processes and for determining cell differentiation. These short RNA species are robust, survive harsh treatment and storage conditions and may be extracted from blood and tissue. Pre-analytical variables are critical confounders in the analysis of miRNAs: we elucidate these and identify best practices for minimizing sample variation in blood and tissue specimens. Pre-analytical variables addressed include patient-intrinsic variation, time and temperature from sample collection to storage or processing, processing methods, contamination by cells and blood components, RNA extraction method, normalization, and storage time/conditions...
March 17, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28297429/method-and-phantom-to-study-combined-effects-of-in-plane-x-y-and-z-axis-resolution-for-3d-ct-imaging
#3
David Goodenough, Josh Levy, Smari Kristinsson, Jesper Fredriksson, Hildur Olafsdottir, Austin Healy
Increasingly, the advent of multislice CT scanners, volume CT scanners, and total body spiral acquisition modes has led to the use of Multi Planar Reconstruction and 3D datasets. In considering 3D resolution properties of a CT system it is important to note that both the in-plane (x,y) and z-axis (slice thickness) influence the visualization and detection of objects within the scanned volume. This study investigates ways to consider both the in-plane resolution and the z-axis resolution in a single phantom wherein analytic or visualized analysis can yield information on these combined effects...
September 2016: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28294468/memory-impairment-and-the-mediating-role-of-task-difficulty-in-patients-with-schizophrenia
#4
REVIEW
Kyrsten M Grimes, Anosha Zanjani, Konstantine K Zakzanis, C Psych
Using meta-analytic methods, we sought to synthesize the research literature on memory impairment in schizophrenia. Additionally, we compared performances across memory measures to determine if task difficulty (e.g., effortful encoding and retrieval versus non effortful encoding and retrieval) could account for variance across studies. Our primary measures of interest included the California Verbal Learning Test, Wechsler Memory Scale, Rey Auditory Verbal Learning Test, Hopkins Verbal Learning Test, Rey Osterrieth Complex Figure Test, and the Benton Visual Retention Test...
March 14, 2017: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/28293433/eye-tracking-as-a-tool-to-evaluate-functional-ability-in-everyday-tasks-in-glaucoma
#5
REVIEW
Enkelejda Kasneci, Alex A Black, Joanne M Wood
To date, few studies have investigated the eye movement patterns of individuals with glaucoma while they undertake everyday tasks in real-world settings. While some of these studies have reported possible compensatory gaze patterns in those with glaucoma who demonstrated good task performance despite their visual field loss, little is known about the complex interaction between field loss and visual scanning strategies and the impact on task performance and, consequently, on quality of life. We review existing approaches that have quantified the effect of glaucomatous visual field defects on the ability to undertake everyday activities through the use of eye movement analysis...
2017: Journal of Ophthalmology
https://www.readbyqxmd.com/read/28289224/patterns-of-coordinated-cortical-remodeling-during-adolescence-and-their-associations-with-functional-specialization-and-evolutionary-expansion
#6
Aristeidis Sotiras, Jon B Toledo, Raquel E Gur, Ruben C Gur, Theodore D Satterthwaite, Christos Davatzikos
During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of brain development, but frequently have been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28282239/the-role-of-teamwork-in-the-analysis-of-big-data-a-study-of-visual-analytics-and-box-office-prediction
#7
Verica Buchanan, Yafeng Lu, Nathan McNeese, Michael Steptoe, Ross Maciejewski, Nancy Cooke
Historically, domains such as business intelligence would require a single analyst to engage with data, develop a model, answer operational questions, and predict future behaviors. However, as the problems and domains become more complex, organizations are employing teams of analysts to explore and model data to generate knowledge. Furthermore, given the rapid increase in data collection, organizations are struggling to develop practices for intelligence analysis in the era of big data. Currently, a variety of machine learning and data mining techniques are available to model data and to generate insights and predictions, and developments in the field of visual analytics have focused on how to effectively link data mining algorithms with interactive visuals to enable analysts to explore, understand, and interact with data and data models...
March 2017: Big Data
https://www.readbyqxmd.com/read/28281270/liposome-enhanced-lateral-flow-assays-for-clinical-analyses
#8
Katie A Edwards, Ricki Korff, Antje J Baeumner
Clinical and environmental analyses frequently necessitate rapid, simple, and inexpensive point-of-care or field tests. These semiquantitative tests may be later followed up by confirmatory laboratory-based assays, but provide an initial scenario assessment important for resource mobilization and threat confinement. Lateral-flow assays (LFAs) and dip-stick assays, which are typically antibody-based and yield a visually detectable signal, provide an assay format suiting these applications extremely well. Signal generation is commonly obtained through the use of colloidal gold or latex beads, which yield a colored band either directly proportional or inversely proportional to the concentration of the analyte of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28281239/an-agent-based-clustering-approach-for-gene-selection-in-gene-expression-microarray
#9
Juan Ramos, José A Castellanos-Garzón, Alfonso González-Briones, Juan F de Paz, Juan M Corchado
Gene selection is a major research area in microarray analysis, which seeks to discover differentially expressed genes for a particular target annotation. Such genes also often called informative genes are able to differentiate tissue samples belonging to different classes of the studied disease. Despite the fact that there is a wide number of proposals, the complexity imposed by this problem remains a challenge today. This research proposes a gene selection approach by means of a clustering-based multi-agent system...
March 9, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28268852/distance-metric-learning-using-random-forest-for-cytometry-data
#10
M Baran Pouyan, J Birjandtalab, M Nourani
Visualization and clustering of single-cell mass cytometry (CyTOF) data are analytic techniques to identify different cell types. Most of such techniques, such as Euclidean norm, lose their effectiveness when the data dimension increases due to the curse of dimensionality. In this paper, we propose a new cell distance (called CytoRFD) that works based on Random Forest (RF) concept. The experimental results show that the proposed distance can achieve a much higher quality and effectiveness in large data analysis than traditional metrics specially for CyTOF data...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28264159/streamlined-synthesis-and-assembly-of-a-hybrid-sensing-architecture-with-solid-binding-proteins-and-click-chemistry
#11
Brian J F Swift, Jared A Shadish, Cole A DeForest, François Baneyx
Combining bioorthogonal chemistry with the use of proteins engineered with adhesive and morphogenetic solid-binding peptides is a promising route for synthesizing hybrid materials with the economy and efficiency of living systems. Using optical sensing of chloramphenicol as a proof of concept, we show here that a GFP variant engineered with zinc sulfide and silica-binding peptides on opposite sides of its β-barrel supports the fabrication of protein-capped ZnS:Mn nanocrystals that exhibit the combined emission signatures of organic and inorganic fluorophores...
March 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28263960/visualization-and-analysis-of-single-cell-rna-seq-data-by-kernel-based-similarity-learning
#12
Bo Wang, Junjie Zhu, Emma Pierson, Daniele Ramazzotti, Serafim Batzoglou
We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art methods. We show that SIMLR is scalable and greatly enhances clustering performance while improving the visualization and interpretability of single-cell sequencing data.
March 6, 2017: Nature Methods
https://www.readbyqxmd.com/read/28263004/improving-the-analyte-ion-signal-in-matrix-assisted-laser-desorption-ionization-imaging-mass-spectrometry-via-electrospray-deposition-by-enhancing-incorporation-of-the-analyte-in-the-matrix
#13
Brian J Malys, Kevin G Owens
RATIONAL: Matrix assisted laser desorption ionization (MALDI) is widely used as the ionization method in high resolution chemical imaging studies that seek to visualize the distribution of analytes within sectioned biological tissues. This work extends the use of electrospray deposition (ESD) to apply matrix with an additional solvent spray to incorporate and homogenize analyte within the matrix overlayer. METHODS: Analytes and matrix are sequentially and independently applied by ESD to create a sample from which spectra are collected, mimicking a MALDI imaging mass spectrometry (IMS) experiment...
March 6, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28257176/a-two-input-fluorescent-logic-gate-for-glutamate-and-zinc
#14
Caixia Yin, Fangjun Huo, Nicholas P Cooley, David Spencer, Kyle Bartholomew, Charles L Barnes, Timothy E Glass
The direct visualization of neurotransmitters is a continuing problem in neuroscience; however, functional fluorescent sensors for organic analytes are still rare. Herein, we describe a fluorescent sensor for glutamate and zinc ions. The sensor acts as a fluorescent logic gate, giving a turn-off response to glutamate or zinc ion alone. The combination of analytes produces a large increase in fluorescence. This type of sensor will aid in the study of neurotransmission, in this case, for neurons that copackage high concentrations of zinc and glutamate...
March 6, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28254746/what-strategies-can-be-used-to-effectively-reduce-the-risk-of-concussion-in-sport
#15
REVIEW
Carolyn A Emery, Amanda M Black, Ash Kolstad, German Martinez, Alberto Nettel-Aguirre, Lars Engebretsen, Karen Johnston, James Kissick, David Maddocks, Charles Tator, Mark Aubry, Jiří Dvorák, Shinji Nagahiro, Kathryn Schneider
AIM OR OBJECTIVE: To examine the effectiveness of concussion prevention strategies in reducing concussion risk in sport. DESIGN: Systematic review according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. DATA SOURCES: Eleven electronic databases searched and hand-search of references from selected studies. ELIGIBILITY CRITERIA FOR SELECTING STUDIES: The following were the study inclusion criteria: (1) contained original human research data; (2) investigated an outcome of concussion or head impact; (3) evaluated a concussion prevention intervention; (4) included sport participants; (5) analytical study designand (6) peer-reviewed...
March 2, 2017: British Journal of Sports Medicine
https://www.readbyqxmd.com/read/28254068/phxnlme-an-r-package-that-facilitates-pharmacometric-workflow-of-phoenix-nlme-analyses
#16
Chay Ngee Lim, Shuang Liang, Kevin Feng, Jason Chittenden, Ana Henry, Samer Mouksassi, Angela K Birnbaum
BACKGROUND AND OBJECTIVE: Pharmacometric analyses are integral components of the drug development process, and Phoenix NLME is one of the popular software used to conduct such analyses. To address current limitations with model diagnostic graphics and efficiency of the workflow for this software, we developed an R package, Phxnlme, to facilitate its workflow and provide improved graphical diagnostics. METHODS: Phxnlme was designed to provide functionality for the major tasks that are usually performed in pharmacometric analyses (i...
March 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28253701/time-domain-nearfield-acoustical-holography-without-wrap-around-error-and-spectral-leakage-for-forward-propagation
#17
Jean-Michel Attendu, Annie Ross
Nearfield acoustical holography can be used to visualize time domain evolution of non-stationary sound fields. It requires sampling of the pressure field with a microphone array to calculate the sound field on other parallel surfaces, either toward the source or farther away from it. This paper focuses on forward propagation of fields sampled with a planar array. Several formulations exist to perform such calculation; however, despite being mathematically well-posed, they generate significant errors, especially for larger propagation distances...
February 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28252576/apoa5-gene-polymorphisms-and-cardiovascular-diseases-metaprediction-in-global-populations
#18
Yen-Chun Lin, Veronica Nunez, Robin Johns, S Pamela K Shiao
BACKGROUND: Apolipoprotein A5 (APOA5) 1131 is one of the most investigated gene polymorphisms in association with cardiovascular diseases (CVD) for its roles in epigenetics pathways. OBJECTIVES: The major objective of this metaprediction study was to comprehensively examine the association of polymorphism risk subtypes of APOA5 1131 gene and potential contributing factors of CVD risks in global populations. METHODS: This study is a meta-analysis to determine APOA5 gene polymorphisms as risk factors for CVDs...
March 2017: Nursing Research
https://www.readbyqxmd.com/read/28251868/unboxing-cluster-heatmaps
#19
Sophie Engle, Sean Whalen, Alark Joshi, Katherine S Pollard
BACKGROUND: Cluster heatmaps are commonly used in biology and related fields to reveal hierarchical clusters in data matrices. This visualization technique has high data density and reveal clusters better than unordered heatmaps alone. However, cluster heatmaps have known issues making them both time consuming to use and prone to error. We hypothesize that visualization techniques without the rigid grid constraint of cluster heatmaps will perform better at clustering-related tasks. RESULTS: We developed an approach to "unbox" the heatmap values and embed them directly in the hierarchical clustering results, allowing us to use standard hierarchical visualization techniques as alternatives to cluster heatmaps...
February 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28248511/optimization-of-the-small-glycan-presentation-for-binding-a-tumor-associated-antibody-application-to-the-construction-of-an-ultrasensitive-glycan-biosensor
#20
Filip Kveton, Anna Blšáková, Andras Hushegyi, Pavel Damborsky, Ola Blixt, Bo Jansson, Jan Tkac
The main aim of the study was to optimize the interfacial presentation of a small antigen-a Tn antigen (N-acetylgalactosamine)-for binding to its analyte anti-Tn antibody. Three different methods for the interfacial display of a small glycan are compared here, including two methods based on the immobilization of the Tn antigen on a mixed self-assembled monolayer (SAM) (2D biosensor) and the third one utilizing a layer of a human serum albumin (HSA) for the immobilization of a glycan forming a 3D interface. Results showed that the 3D interface with the immobilized Tn antigen is the most effective bioreceptive surface for binding its analyte...
March 8, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
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