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Diagrams and Visualization

Shibao Wang, Yinghui Huang, Xupeng Mu, Tianyang Qi, Sha Qiao, Zhenxia Lu, Hongjun Li
The present study aimed to explore whether culture method had an influence on DNA methylation in colorectal cancer (CRC). In the present study, CRC cells were cultured in two-dimensional (2D), three-dimensional (3D) and mouse orthotopic transplantation (Tis) cultures. Principal component analysis (PCA) was used for global visualization of the three samples. A Venn diagram was applied for intersection and union analysis for different comparisons. The methylation condition of 5'-C-phosphate-G-3' (CpG) location was determined using unsupervised clustering analysis...
April 2018: Experimental and Therapeutic Medicine
Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
Xuewen Ni, Kai Wang, Kao Wu, Harold Corke, Katsuyoshi Nishinari, Fatang Jiang
This study aims to investigate the stability, microstructure and rheological properties of konjac glucomannan (KGM)/zein mixed systems in different mixing ratios. A phase diagram was established by centrifugation and visual observation. KGM/zein could form a stable homogeneous dispersion with appropriate mixing formula, and the particle size in mixed systems increased with increasing zein content. During storage, zein particles increased in size but were homogeneously distributed in the continuous phase of KGM without flocculation as observed by confocal light scanning microscopy...
May 15, 2018: Carbohydrate Polymers
Pietro Mancosu, Giorgia Nicolini, Giulia Goretti, Fiorenza De Rose, Davide Franceschini, Chiara Ferrari, Giacomo Reggiori, Stefano Tomatis, Marta Scorsetti
BACKGROUND & PURPOSE: Lean Six Sigma Methodology (LSSM) was introduced in industry to provide near-perfect services to large processes, by reducing improbable occurrence. LSSM has been applied to redesign the 2D-2D breast repositioning process (Lean) by the retrospective analysis of the database (Six Sigma). MATERIALS & METHODS: Breast patients with daily 2D-2D matching before RT were considered. The five DMAIC (define, measure, analyze, improve, and control) LSSM steps were applied...
March 6, 2018: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
Sarah Jane Hobbs, Mark A Robinson, Hilary M Clayton
Background: Ground reaction forces (GRF) measured during equine gait analysis are typically evaluated by analyzing discrete values obtained from continuous force-time data for the vertical, longitudinal and transverse GRF components. This paper describes a simple, temporo-spatial method of displaying and analyzing sagittal plane GRF vectors. In addition, the application of statistical parametric mapping (SPM) is introduced to analyse differences between contra-lateral fore and hindlimb force-time curves throughout the stance phase...
2018: PeerJ
E Kerzner, A Lex, C L Sigulinsky, T Umess, B W Jones, R E Marc, M Meyer
Multivariate graphs are prolific across many fields, including transportation and neuroscience. A key task in graph analysis is the exploration of connectivity, to, for example, analyze how signals flow through neurons, or to explore how well different cities are connected by flights. While standard node-link diagrams are helpful in judging connectivity, they do not scale to large networks. Adjacency matrices also do not scale to large networks and are only suitable to judge connectivity of adjacent nodes. A key approach to realize scalable graph visualization are queries: instead of displaying the whole network, only a relevant subset is shown...
June 2017: Computer Graphics Forum: Journal of the European Association for Computer Graphics
Emine Aslan Telci, Feride Yarar, Uğur Cavlak, Orcin Telli Atalay
OBJECTIVE: The aim of this study was to compare the musculoskeletal pain distribution, quality of life, and the hopelessness level in mothers with disabled children in different ambulation levels. METHODS: This study included a total of 177 mothers (mean age: 36.1 ± 6.5 years) of children with disabilities. The mothers were divided into 3 different groups according to the ambulation level of their disabled children: Ambulatory children (Group 1), partially ambulatory children (Group 2) and non-ambulatory children (Group 3)...
February 2, 2018: Journal of Back and Musculoskeletal Rehabilitation
Frazier N Baker, Aleksey Porollo
Similarity and distance matrices are general data structures that describe reciprocal relationships between the objects within a given dataset. Commonly used methods for representation of these matrices include heatmaps, hierarchical trees, dimensionality reduction, and various types of networks. However, despite a well-developed foundation for the visualization of such representations, the challenge of creating an interactive view that would allow for quick data navigation and interpretation remains largely unaddressed...
March 2018: Data
M W Jarosik, R Szczȩśniak, A P Durajski, J K Kalaga, W Leoński
We have determined the stability conditions of the hydrogen molecule under the influence of an external force of harmonic-type explicitly dependent on the amplitude (A) and frequency (Ω). The ground state of the molecule has been determined in the framework of the Born-Oppenheimer approximation, whereas the energy of the electronic subsystem has been calculated using the Hubbard model including all two-site electron interactions. The diagram of RT0 (A,Ω), where RT0 denotes the distance between protons after the fixed initial time T0, allowed us to visualize the area of the instability with the complicated structure...
January 2018: Chaos
Steven Jupe, Keith Ray, Corina Duenas Roca, Thawfeek Varusai, Veronica Shamovsky, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob
BACKGROUND: There is a wealth of biological pathway information available in the scientific literature but it is spread across many thousands of publications. Alongside publications that contain definitive experimental discoveries are many others that have been dismissed as spurious, or found to be irreproducible, or are contradicted by later results and consequently now considered controversial. Many descriptions and images of pathways are incomplete, stylized representations that assume the reader is an expert, familiar with the established details of the process, which are consequently not fully explained...
January 25, 2018: Journal of Allergy and Clinical Immunology
A Verma, J Maiti, V N Gaikwad
Large integrated steel plants employ an effective safety management system and gather a significant amount of safety-related data. This research intends to explore and visualize the rich database to find out the key factors responsible for the occurrences of incidents. The study was carried out on the data in the form of investigation reports collected from a steel plant in India. The data were processed and analysed using some of the quality management tools like Pareto chart, control chart, Ishikawa diagram, etc...
December 27, 2017: International Journal of Injury Control and Safety Promotion
Zhijun Wu, Xiuxiu Su, Haihui Sheng, Yanjia Chen, Xiang Gao, Le Bao, Wei Jin
BACKGROUND AND AIMS: Identifying gene-environment interaction in the context of multiple environmental factors has been a challenging task. We aimed to use conditional inference tree (CTREE) to strata myocardial infarction (MI) risk synthesizing information from both genetic and environmental factors. METHODS: We conducted a case-control study including 1440 Chinese men (730 MI patients and 710 controls). We first calculated a weighted genetic risk score (GRS) by combining 25 single nucleotide polymorphisms (SNPs) that had been identified to be associated with coronary artery diseases in previous genome wide association studies...
December 16, 2017: Archives of Medical Research
Staffan Schedin, Per Hallberg, Anders Behndig
A numerical 3D ray tracing model was used to evaluate the long-term visual effects of two regimens of corneal crosslinking (CXL) treatment of 48 patients with the corneal degeneration keratoconus. The 3D ray tracing analyses were based on corneal elevation data measured by Scheimpflug photography. Twenty-two patients were treated with standard CXL applied uniformly across the corneal surface, whereas 26 patients underwent a customized, refined treatment only at local zones on the cornea (photorefractive intrastromal CXL; PiXL)...
December 10, 2017: Applied Optics
Eliane Cristina Pereira, Cristina de Oliveira Rodrigues, Kelly Cristina Alves Silvério, Glaucya Madazio, Mara Behlau
PURPOSE: To compare vocal and acoustic parameters of HIV-infected children and non-HIV-infected children. METHODS: Vocal samples were submitted to auditory-perceptual and acoustic analysis. Samples of the sustained vowel /ε/ and continuous speech of 74 children between 6 and incomplete 12 years old were analyzed, divided into two groups: 37 HIV-infected children (GHIV) and 37 non-HIV-infected children, the control group (CG), age and gender-matched and without previous vocal evaluation; they were all prepubescent by the Tanner Stages (MS, 2014)...
December 11, 2017: CoDAS
Gerald Gartlehner, Marie-Therese Schultes, Viktoria Titscher, Laura C Morgan, Georgiy V Bobashev, Peyton Williams, Suzanne L West
BACKGROUND: Summary of findings tables in systematic reviews are highly informative but require epidemiological training to be interpreted correctly. The usage of fishbone diagrams as graphical displays could offer researchers an effective approach to simplify content for readers with limited epidemiological training. In this paper we demonstrate how fishbone diagrams can be applied to systematic reviews and present the results of an initial user testing. METHODS: Findings from two systematic reviews were graphically depicted in the form of the fishbone diagram...
December 12, 2017: BMC Medical Research Methodology
Alberto Garre, Juan Pablo Huertas, Gerardo A González-Tejedor, Pablo S Fernández, Jose A Egea, Alfredo Palop, Arturo Esnoz
This contribution presents a mathematical model to describe non-isothermal microbial inactivation processes taking into account the acclimation of the microbial cell to thermal stress. The model extends the log-linear inactivation model including a variable and model parameters quantifying the induced thermal resistance. The model has been tested on cells of Escherichia coli against two families of non-isothermal profiles with different constant heating rates. One of the families was composed of monophasic profiles, consisting of a non-isothermal heating stage from 35 to 70°C; the other family was composed of biphasic profiles, consisting of a non-isothermal heating stage followed by a holding period at constant temperature of 57...
February 2, 2018: International Journal of Food Microbiology
Askarbek Orakov, Nazgul Sakenova, Anatoly Sorokin, Igor Goryanin
Motivation: Functional and taxonomic analyses are critical steps in understanding interspecific interactions within microbial communities. Currently, such analyses are run separately, which complicates interpretation of results. Here we present the ASAR interactive tool for simultaneous analysis of metagenomic data in three dimensions: taxonomy, function, metagenome. Results: An interactive data analysis tool for selection, aggregation, and visualization of metagenomic data is presented...
December 1, 2017: Bioinformatics
Kyle I Diller, Alexander S Bayden, Joseph Audie, David J Diller
There is growing interest in peptide-based drug design and discovery. Due to their relatively large size, polymeric nature, and chemical complexity, the design of peptide-based drugs presents an interesting "big data" challenge. Here, we describe an interactive computational environment, PeptideNavigator, for naturally exploring the tremendous amount of information generated during a peptide drug design project. The purpose of PeptideNavigator is the presentation of large and complex experimental and computational data sets, particularly 3D data, so as to enable multidisciplinary scientists to make optimal decisions during a peptide drug discovery project...
January 1, 2018: Computers in Biology and Medicine
Theresa Diekmann, Laura M Schrems-Hoesl, Christian Y Mardin, Robert Laemmer, Folkert K Horn, Friedrich E Kruse, Wolfgang A Schrems
PURPOSE: The purpose of this study was to compare the ability of scanning laser polarimetry (SLP) and spectral-domain optical coherence tomography (SD-OCT) to predict future visual field conversion of subjects with ocular hypertension and early glaucoma. METHODS: All patients were recruited from the Erlangen glaucoma registry and examined using standard automated perimetry, 24-hour intraocular pressure profile, and optic disc photography. Peripapillary retinal nerve fiber layer thickness (RNFL) measurements were obtained by SLP (GDx-VCC) and SD-OCT (Spectralis OCT)...
February 2018: Journal of Glaucoma
Yoshiki Tanaka, Sho Yokoyama, Rie Horai, Takashi Kojima, Sato Hiroyuki, Yukihito Kato, Mari Takagi, Hideki Nakamura, Kiyoshi Tanaka, Kazuo Ichikawa, Shoko Tanabe
PURPOSE: To evaluate the color visual acuity (CVA) of young healthy subjects using colored Landolt rings and the effect of background luminance level on the CVA. MATERIALS AND METHODS: We measured the CVA of 20 young healthy subjects (age: 23.8 ± 3.8 years) with different colors using a computer and a liquid crystal display, with 15 Landolt ring colors (30 cd/m(2)) with a background luminance of 30 cd/m(2), and then 100 cd/m(2). We then used different background luminance levels (15-50 cd/m(2)) using four Landolt ring colors (red, green-yellow, green, and blue-green) to evaluate the effect of the background luminance level on CVA...
November 22, 2017: Current Eye Research
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