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Visualization and Diagrams

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https://www.readbyqxmd.com/read/28649585/data-on-the-genome-wide-identification-of-cnl-r-genes-in-setaria-italica-l-p-beauv
#1
Ethan J Andersen, Madhav P Nepal
We report data associated with the identification of 242 disease resistance genes (R-genes) in the genome of Setaria italica as presented in "Genetic diversity of disease resistance genes in foxtail millet (Setaria italica L.)" (Andersen and Nepal, 2017) [1]. Our data describe the structure and evolution of the Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) R-genes in foxtail millet. The CNL genes were identified through rigorous extraction and analysis of recently available plant genome sequences using cutting-edge analytical software...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28645171/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties
#2
Jake R Conway, Alexander Lex, Nils Gehlenborg
Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability: UpSetR is available at https://github...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28638896/a-scalable-cyberinfrastructure-for-interactive-visualization-of-terascale-microscopy-data
#3
A Venkat, C Christensen, A Gyulassy, B Summa, F Federer, A Angelucci, V Pascucci
The goal of the recently emerged field of connectomics is to generate a wiring diagram of the brain at different scales. To identify brain circuitry, neuroscientists use specialized microscopes to perform multichannel imaging of labeled neurons at a very high resolution. CLARITY tissue clearing allows imaging labeled circuits through entire tissue blocks, without the need for tissue sectioning and section-to-section alignment. Imaging the large and complex non-human primate brain with sufficient resolution to identify and disambiguate between axons, in particular, produces massive data, creating great computational challenges to the study of neural circuits...
August 2016: N Y Sci Data Summit NYSDS
https://www.readbyqxmd.com/read/28635122/sketching-the-invisible-to-predict-the-visible-from-drawing-to-modeling-in-chemistry
#4
Melanie M Cooper, Mike Stieff, Dane DeSutter
Sketching as a scientific practice goes beyond the simple act of inscribing diagrams onto paper. Scientists produce a wide range of representations through sketching, as it is tightly coupled to model-based reasoning. Chemists in particular make extensive use of sketches to reason about chemical phenomena and to communicate their ideas. However, the chemical sciences have a unique problem in that chemists deal with the unseen world of the atomic-molecular level. Using sketches, chemists strive to develop causal mechanisms that emerge from the structure and behavior of molecular-level entities, to explain observations of the macroscopic visible world...
June 21, 2017: Topics in Cognitive Science
https://www.readbyqxmd.com/read/28630034/fall-prevention-self-assessments-via-mobile-3d-visualization-technologies-community-dwelling-older-adults-perceptions-of-opportunities-and-challenges
#5
Julian Hamm, Arthur Money, Anita Atwal
BACKGROUND: In the field of occupational therapy, the assistive equipment provision process (AEPP) is a prominent preventive strategy used to promote independent living and to identify and alleviate fall risk factors via the provision of assistive equipment within the home environment. Current practice involves the use of paper-based forms that include 2D measurement guidance diagrams that aim to communicate the precise points and dimensions that must be measured in order to make AEPP assessments...
June 19, 2017: JMIR Human Factors
https://www.readbyqxmd.com/read/28622657/patterns-of-multimorbidity-in-people-with-severe-or-profound-intellectual-and-motor-disabilities
#6
E A van Timmeren, A Waninge, H M J van Schrojenstein Lantman-de, A A J van der Putten, C P van der Schans
BACKGROUND: People with severe or profound intellectual and motor disabilities (SPIMD) experience multimorbidity and have complex health needs. Multimorbidity increases mortality, decreases functioning, and negatively influences quality of life. Information regarding patterns of multimorbidity in people with SPIMD may lead to proactive prevention, specifically detection and treatment of physical health problems at an early stage and prevention of secondary complications. AIM: The aim of this study was to explore patterns of multimorbidity in individuals with SPIMD...
June 13, 2017: Research in Developmental Disabilities
https://www.readbyqxmd.com/read/28600227/mirtarvis-web-based-interactive-visual-analytics-tool-for-microrna-target-predictions
#7
Sehi L'Yi, Daekyoung Jung, Minsik Oh, Bohyoung Kim, Robert J Freishtat, Mamta Giri, Eric Hoffman, Jinwook Seo
In this paper, we present miRTarVis+, a Web-based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Various microRNA (miRNA) target prediction algorithms have been developed to improve sequence-based miRNA target prediction by exploiting miRNA-mRNA expression profile data. There are also a few analytics tools to help researchers predict targets of miRNAs. However, there still is a need for improving the performance for miRNA prediction algorithms and more importantly for interactive visualization tools for an integrative analysis of multiple prediction results...
June 6, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28596611/design-and-deposition-of-a-metal-like-and-admittance-matching-metamaterial-as-an-ultra-thin-perfect-absorber
#8
Yi-Jun Jen, Wei-Chih Liu, Tso-Kuei Chen, Shan-Wen Lin, Yi-Ciang Jhang
A stratiform metamaterial, comprising metal and dielectric thin films, exhibits both near-perfect antireflection and strong light extinction to function as a perfect and ultra-thin light absorber. The equivalent admittance and extinction coefficient of the metamaterial are tailored using a visual method that is based on an admittance diagram. A five-layered metamaterial was designed and deposited with a total thickness of 260 nm on a mirror to exhibit strong and wide angle absorption over wavelengths from 400 nm to 2000 nm...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28594549/playmolecule-proteinprepare-a-web-application-for-protein-preparation-for-molecular-dynamics-simulations
#9
Gerard Martinez-Rosell, Toni Giorgino, Gianni De Fabritiis
Protein preparation is a critical step in molecular simulations consisting in refining a protein PDB structure by assigning titration states and optimizing the hydrogen bonding network. In this application note, we describe ProteinPrepare, a web application designed to interactively support the preparation of protein structures. Users can upload a PDB file, choose the solvent pH value, and inspect the resulting protonated residues and H-bonding network within a 3D web interface. Protonation states are suggested automatically, but can be manually changed using the visual aid of the hydrogen bond network...
June 8, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28578244/performance-of-raphidocelis-subcapitata-exposed-to-heavy-metal-mixtures
#10
Nora Expósito, Vikas Kumar, Jordi Sierra, Marta Schuhmacher, Gemma Giménez Papiol
Microalgae growth inhibition assays are candidates for referent ecotoxicological assays, and are a fundamental part in the strategy to reduce the use of fish and other animal models in aquatic toxicology. In the present work, the performance of Raphidocelis subcapitata exposed to heavy metals following standardized growth inhibition assays has been assessed in three different scenarios: 1) dilutions of single heavy metals, 2) artificial mixture of heavy metals at similar levels than those found in natural rivers and, 3) natural samples containing known mixtures of contaminants (heavy metals)...
June 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28573030/graphic-kinematics-visual-virtual-work-and-elastographics
#11
Allan McRobie, Marina Konstantatou, Georgios Athanasopoulos, Laura Hannigan
In this paper, recent progress in graphic statics is combined with Williot displacement diagrams to create a graphical description of both statics and kinematics for two- and three-dimensional pin-jointed trusses. We begin with reciprocal form and force diagrams. The force diagram is dissected into its component cells which are then translated relative to each other. This defines a displacement diagram which is topologically equivalent to the form diagram (the structure). The various contributions to the overall Virtual Work appear as parallelograms (for two-dimensional trusses) or parallelopipeds (for three-dimensional trusses) that separate the force and the displacement pieces...
May 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28569135/intervene-a-tool-for-intersection-and-visualization-of-multiple-gene-or-genomic-region-sets
#12
Aziz Khan, Anthony Mathelier
BACKGROUND: A common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments. While several tools exist to intersect and visualize sets of genes, similar tools dedicated to the visualization of genomic region sets are currently limited. RESULTS: To address this gap, we have developed the Intervene tool, which provides an easy and automated interface for the effective intersection and visualization of genomic region or list sets, thus facilitating their analysis and interpretation...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28535555/paresthesia-independence-an-assessment-of-technical-factors-related-to-10-khz-paresthesia-free-spinal-cord-stimulation
#13
Giuliano De Carolis, Mery Paroli, Lara Tollapi, Matthew W Doust, Abram H Burgher, Cong Yu, Thomas Yang, Donna M Morgan, Kasra Amirdelfan, Leonardo Kapural, B Todd Sitzman, Richard Bundschu, Ricardo Vallejo, Ramsin M Benyamin, Thomas L Yearwood, Bradford E Gliner, Ashley A Powell, Kerry Bradley
BACKGROUND: Spinal cord stimulation (SCS) has been successfully used to treat chronic intractable pain for over 40 years. Successful clinical application of SCS is presumed to be generally dependent on maximizing paresthesia-pain overlap; critical to achieving this is positioning of the stimulation field at the physiologic midline. Recently, the necessity of paresthesia for achieving effective relief in SCS has been challenged by the introduction of 10 kHz paresthesia-free stimulation...
May 2017: Pain Physician
https://www.readbyqxmd.com/read/28533467/the-current-and-future-state-of-animal-coloration-research
#14
REVIEW
John A Endler, Johanna Mappes
Animal colour patterns are a model system for understanding evolution because they are unusually accessible for study and experimental manipulation. This is possible because their functions are readily identifiable. In this final paper of the symposium we provide a diagram of the processes affecting colour patterns and use this to summarize their functions and put the other papers in a broad context. This allows us to identify significant 'holes' in the field that only become obvious when we see the processes affecting colour patterns, and their interactions, as a whole...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28516277/analysis-of-cellular-autofluorescence-in-touch-samples-by-flow-cytometry-implications-for-front-end-separation-of-trace-mixture-evidence
#15
M Katherine Philpott, Cristina E Stanciu, Ye Jin Kwon, Eduardo E Bustamante, Susan A Greenspoon, Christopher J Ehrhardt
The goal of this study was to survey optical and biochemical variation in cell populations deposited onto a surface through touch or contact and identify specific features that may be used to distinguish and then sort cell populations from separate contributors in a trace biological mixture. Although we were not able to detect meaningful biochemical variation in touch samples deposited by different contributors through preliminary antibody surveys, we did observe distinct differences in red autofluorescence emissions (650-670 nm), with as much as a tenfold difference in mean fluorescence intensities observed between certain pairs of donors...
May 18, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28515983/a-conceptual-model-for-physical-therapists-treating-athletes-with-protracted-recovery-following-a-concussion
#16
Mark Lundblad
Sports-related concussions are receiving growing attention in healthcare. Most concussions resolve spontaneously with little or no treatment, but twenty percent of concussions take longer than three weeks to resolve. In some cases, symptoms can last for five years following a traumatic brain injury. Physical Therapists have unique skills that can assist patients experiencing protracted recovery. The purpose of this clinical commentary is to describe a new conceptual model that provides a framework for Physical Therapy management of patients with protracted recovery following a sports-related concussion...
April 2017: International Journal of Sports Physical Therapy
https://www.readbyqxmd.com/read/28506880/advanced-correlation-grid-analysis-and-visualisation-of-functional-connectivity-among-multiple-spike-trains
#17
Mohammad Shahed Masud, Roman Borisyuk, Liz Stuart
BACKGROUND: This study analyses multiple spike trains (MST) data, defines its functional connectivity and subsequently visualises an accurate diagram of connections. This is a challenging problem. For example, it is difficult to distinguish the common input and the direct functional connection of two spike trains. NEW METHOD: The new method presented in this paper is based on the traditional pairwise cross-correlation function (CCF) and a new combination of statistical techniques...
May 12, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28472372/proteinsplus-a-web-portal-for-structure-analysis-of-macromolecules
#18
Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey
With currently more than 126 000 publicly available structures and an increasing growth rate, the Protein Data Bank constitutes a rich data source for structure-driven research in fields like drug discovery, crop science and biotechnology in general. Typical workflows in these areas involve manifold computational tools for the analysis and prediction of molecular functions. Here, we present the ProteinsPlus web server that offers a unified easy-to-use interface to a broad range of tools for the early phase of structure-based molecular modeling...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28459666/stories-in-the-data
#19
Gary Singh
To some degree, comics have always been used to convert data into stories, from ancient Egyptian heiroglyphics to crude biology diagrams in grade-school textbooks. By their very nature, comics communicate through a variety of visualization techniques. Benjamin Bach, who along with his coauthors Nathalie Henry Riche, Sheelagh Carpendale, and Hanspeter Pfister created this issue's Art on Graphics special contribution about the emerging genre of data comics, here talks about their attempts to leverage the massive untapped potential for data-driven comics to explain multiple threads of simultaneous data...
2017: IEEE Computer Graphics and Applications
https://www.readbyqxmd.com/read/28412452/enhancement-of-dissolution-rate-through-eutectic-mixture-and-solid-solution-of-posaconazole-and-benznidazole
#20
Camila Bezerra Melo Figueirêdo, Daniela Nadvorny, Amanda Carla Quintas de Medeiros Vieira, José Lamartine Soares Sobrinho, Pedro José Rolim Neto, Ping I Lee, Monica Felts de La Roca Soares
Benznidazole (BNZ), the only commercialized antichagasic drug, and the antifungal compound posaconazole (PCZ) have shown synergistic action in the therapy of Chagas disease, however both active pharmaceutical ingredients (APIs) exhibit low aqueous solubility potentially limiting their bioavailability and therapeutic efficacy. In this paper, we report for the first time the formation of a eutectic mixture as well as an amorphous solid solution of PCZ and BNZ (at the same characteristic ratio of 80:20wt%), which provided enhanced solubility and dissolution rate for both APIs...
April 12, 2017: International Journal of Pharmaceutics
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