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https://www.readbyqxmd.com/read/27920748/multidimensional-recurrence-quantification-analysis-mdrqa-for-the-analysis-of-multidimensional-time-series-a-software-implementation-in-matlab-and-its-application-to-group-level-data-in-joint-action
#1
Sebastian Wallot, Andreas Roepstorff, Dan Mønster
We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels-from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27919382/a-clinical-decision-support-system-for-prediction-of-pregnancy-outcome-in-pregnant-women-with-systemic-lupus-erythematosus
#2
Khadijeh Paydar, Sharareh R Niakan Kalhori, Mahmoud Akbarian, Abbas Sheikhtaheri
OBJECTIVE: Pregnancy among systemic lupus erythematosus (SLE)-affected women is highly associated with poor obstetric outcomes. Predicting the risk of foetal outcome is essential for maximizing the success of pregnancy. This study aimed to develop a clinical decision support system (CDSS) to predict pregnancy outcomes among SLE-affected pregnant women. METHODS: We performed a retrospective analysis of 149 pregnant women with SLE, who were followed at Shariati Hospital (104 pregnancies) and a specialized clinic (45 pregnancies) from 1982 to 2014...
January 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/27918893/spectrum-image-analysis-tool-a-flexible-matlab-solution-to-analyze-eel-and-cl-spectrum-images
#3
Franz-Philipp Schmidt, Ferdinand Hofer, Joachim R Krenn
Spectrum imaging techniques, gaining simultaneously structural (image) and spectroscopic data, require appropriate and careful processing to extract information of the dataset. In this article we introduce a MATLAB based software that uses three dimensional data (EEL/CL spectrum image in dm3 format (Gatan Inc.'s DigitalMicrograph(®))) as input. A graphical user interface enables a fast and easy mapping of spectral dependent images and position dependent spectra. First, data processing such as background subtraction, deconvolution and denoising, second, multiple display options including an EEL/CL moviemaker and, third, the applicability on a large amount of data sets with a small work load makes this program an interesting tool to visualize otherwise hidden details...
November 21, 2016: Micron: the International Research and Review Journal for Microscopy
https://www.readbyqxmd.com/read/27917358/rigorous-solution-for-1-d-consolidation-of-a-clay-layer-under-haversine-cyclic-loading-with-rest-period
#4
Nina Müthing, Sabah S Razouki, Maria Datcheva, Tom Schanz
Presented in this paper is a rigorous solution of the conventional Terzaghi one-dimensional consolidation under haversine cyclic loading with any rest period. The clay deposit is either permeable at both top and bottom or permeable at the top and impermeable at the bottom. This exact analytical solution was achieved using Fourier harmonic analysis for the periodic function representing the rate of imposition of excess pore water pressure. The double Fourier series in the rigorous solution was found to be rapidly convergent...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27916666/rhythmic-entrainment-source-separation-optimizing-analyses-of-neural-responses-to-rhythmic-sensory-stimulation
#5
Michael X Cohen, Rasa Gulbinaite
Steady-state evoked potentials (SSEPs) are rhythmic brain responses to rhythmic sensory stimulation, and are often used to study perceptual and attentional processes. We present a data analysis method for maximizing the signal-to-noise ratio of the narrow-band steady-state response in the frequency and time-frequency domains. The method, termed rhythmic entrainment source separation (RESS), is based on denoising source separation approaches that take advantage of the simultaneous but differential projection of neural activity to multiple electrodes or sensors...
December 1, 2016: NeuroImage
https://www.readbyqxmd.com/read/27914344/evaluation-of-thymus-vulgaris-plant-extract-as-an-eco-friendly-corrosion-inhibitor-for-stainless-steel-304-in-acidic-solution-by-means-of-electrochemical-impedance-spectroscopy-electrochemical-noise-analysis-and-density-functional-theory
#6
A Ehsani, M G Mahjani, M Hosseini, R Safari, R Moshrefi, H Mohammad Shiri
Inhibition performance of Thymus vulgaris plant leaves extract (thyme) as environmentally friendly (green) inhibitor for the corrosion protection of stainless steel (SS) type 304 in 1.0molL(-1) HCl solution was studied by potentiodynamic polarization, electrochemical impedance (EIS) and electrochemical noise measurements (EN) techniques. The EN data were analyzed with FFT technique to make the spectral power density plots. The calculations were performed by MATLAB 2014a software. Geometry optimization and calculation of the structural and electronic properties of the molecular system of inhibitor have been carried out using UB3LYP/6-311++G(∗∗) level...
November 16, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27908705/a-novel-method-for-in-silico-identification-of-regulatory-snps-in-human-genome
#7
Rong Li, Dexing Zhong, Ruiling Liu, Hongqiang Lv, Xinman Zhang, Jun Liu, Jiuqiang Han
Regulatory single nucleotide polymorphisms (rSNPs), kind of functional noncoding genetic variants, can affect gene expression in a regulatory way, and they are thought to be associated with increased susceptibilities to complex diseases. Here a novel computational approach to identify potential rSNPs is presented. Different from most other rSNPs finding methods which based on hypothesis that SNPs causing large allele-specific changes in transcription factor binding affinities are more likely to play regulatory functions, we use a set of documented experimentally verified rSNPs and nonfunctional background SNPs to train classifiers, so the discriminating features are found...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27908188/polymer-gel-dosimetry-for-measuring-the-dose-near-thin-high-z-materials-irradiated-with-high-energy-photon-beams
#8
Leighton L Warmington, N Gopishankar, John H Broadhurst, Yoichi Watanabe
PURPOSE: To investigate the feasibility of three-dimensional (3D) dose measurements near thin high-Z materials placed in a water-like medium by using a polymer gel dosimeter (PGD) when the medium was irradiated with high energy photon beams. METHODS: PGD is potentially a useful tool for this application because it can record the dose around a small object made of a high-Z material in a continuous 3D medium. In this study, the authors manufactured a methacrylic acid-based normoxic PGD, nMAG...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908006/generation-and-dynamics-analysis-of-n-scrolls-existence-in-new-translation-type-chaotic-systems
#9
Yue Liu, Shuxu Guo
In this paper, we propose two kinds of translation type chaotic systems for creating 2 N + 1-and 2(N + 1)-scrolls chaotic attractors from a simple three-dimensional system, which are named the translation-2 chaotic system (a12a21 < 0) and the translation-3 chaotic system (a12a21 > 0). We also propose the successful design criterion for constructing 2 N + 1-and 2(N + 1)-scrolls, respectively. Then, the dynamics property of the translation-2 chaotic system is studied in detail...
November 2016: Chaos
https://www.readbyqxmd.com/read/27896789/mhd-natural-convection-flow-of-casson-nanofluid-over-nonlinearly-stretching-sheet-through-porous-medium-with-chemical-reaction-and-thermal-radiation
#10
Imran Ullah, Ilyas Khan, Sharidan Shafie
In the present work, the effects of chemical reaction on hydromagnetic natural convection flow of Casson nanofluid induced due to nonlinearly stretching sheet immersed in a porous medium under the influence of thermal radiation and convective boundary condition are performed numerically. Moreover, the effects of velocity slip at stretching sheet wall are also examined in this study. The highly nonlinear-coupled governing equations are converted to nonlinear ordinary differential equations via similarity transformations...
December 2016: Nanoscale Research Letters
https://www.readbyqxmd.com/read/27893991/saclab-a-toolbox-for-saccade-analysis-to-increase-usability-of-eye-tracking-systems-in-clinical-ophthalmology-practice
#11
Laura Cercenelli, Guido Tiberi, Ivan Corazza, Giuseppe Giannaccare, Michela Fresina, Emanuela Marcelli
PURPOSE: Many open source software packages have been recently developed to expand the usability of eye tracking systems to study oculomotor behavior, but none of these is specifically designed to encompass all the main functions required for creating eye tracking tests and for providing the automatic analysis of saccadic eye movements. The aim of this study is to introduce SacLab, an intuitive, freely-available MATLAB toolbox based on Graphical User Interfaces (GUIs) that we have developed to increase the usability of the ViewPoint EyeTracker (Arrington Research, Scottsdale, AZ, USA) in clinical ophthalmology practice...
November 22, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/27893379/blasst-band-limited-atomic-sampling-with-spectral-tuning-with-applications-to-utility-line-noise-filtering
#12
Kenneth R Ball, W David Hairston, Piotr J Franaszczuk, Kay A Robbins
OBJECTIVE: In this paper we present and test a new method for the identification and removal of non-stationary utility line noise from biomedical signals. METHODS: The method, Band Limited Atomic Sampling with Spectral Tuning (BLASST), is an iterative approach that is designed to (1) fit non-stationarities in line noise by searching for best-fit Gabor atoms at predetermined time points, (2) self-modulate its fit by leveraging information from frequencies surrounding the target frequency, and (3) terminate based on a convergence criterion obtained from the same surrounding frequencies...
November 23, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27891096/systematic-characterization-of-dynamic-parameters-of-intracellular-calcium-signals
#13
Laurent Mackay, Nicholas Mikolajewicz, Svetlana V Komarova, Anmar Khadra
Dynamic processes, such as intracellular calcium signaling, are hallmark of cellular biology. As real-time imaging modalities become widespread, a need for analytical tools to reliably characterize time-series data without prior knowledge of the nature of the recordings becomes more pressing. The goal of this study is to develop a signal-processing algorithm for MATLAB that autonomously computes the parameters characterizing prominent single transient responses (TR) and/or multi-peaks responses (MPR). The algorithm corrects for signal contamination and decomposes experimental recordings into contributions from drift, TRs, and MPRs...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27891072/estimating-propensity-parameters-using-google-pagerank-and-genetic-algorithms
#14
David Murrugarra, Jacob Miller, Alex N Mueller
Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27889756/liquid-chromatography-mass-spectrometry-reveals-the-effect-of-lactobacillus-treatment-on-the-faecal-metabolite-profile-of-rats-with-chronic-renal-failure
#15
Bin Wu, Hongli Jiang, Quan He, Meng Wang, Jinhong Xue, Hua Liu, Kehui Shi, Meng Wei, Shanshan Liang, Liwen Zhang
BACKGROUND/AIM: Chronic kidney disease is accompanied by changes in the gut microbiome and by an increase in the number of gut pathogenic bacteria. The aim of this study was to investigate the difference of the faecal metabolic profiles in rats with uremia, and to determine whether the altered metabolites in the rats with uremia can be restored by Lactobacillus. METHODS: Thirty rats were randomly divided into 3 groups: sham, uremia and uremia + probiotic (UP) groups...
November 26, 2016: Nephron
https://www.readbyqxmd.com/read/27889662/pediatric-pineal-germinomas-epigenetic-and-genomic-approach
#16
Monserrat Pérez-Ramírez, Alejo Justino Hernández-Jiménez, Armando Guerrero-Guerrero, Alicia Georgina Siordia-Reyes, Marta Elena Hernández-Caballero, Antonio García-Méndez, Fernando Chico-Ponce de León, Fabio Abdel Salamanca-Gómez, Normand García-Hernández
OBJECTIVE: We identify and correlate chromosomal alterations, methylation patterns and gene expression in pediatric pineal germinomas. METHODS: CGH microarray, methylation and gene expression were performed through the Agilent platform. The results were analyzed with MatLab software, MapViewer, DAVID, GeneCards and Hippie. RESULTS: Amplifications were found in 1q24.2, 1q31.3, 2p11.2, 3p22.2, 7p13, 7p15.2, 8p22, 12p13.2, 14q24.3 y 22q12; and deletions were found in 1q21...
November 19, 2016: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/27888927/thermal-behavior-of-human-eye-in-relation-with-change-in-blood-perfusion-porosity-evaporation-and-ambient-temperature
#17
REVIEW
Aasma Rafiq, M A Khanday
Extreme environmental and physiological conditions present challenges for thermal processes in body tissues including multi-layered human eye. A mathematical model has been formulated in this direction to study the thermal behavior of the human eye in relation with the change in blood perfusion, porosity, evaporation and environmental temperatures. In this study, a comprehensive thermal analysis has been performed on the multi-layered eye using Pennes' bio-heat equation with appropriate boundary and interface conditions...
December 2016: Journal of Thermal Biology
https://www.readbyqxmd.com/read/27885259/trackntrace-a-simple-and-extendable-open-source-framework-for-developing-single-molecule-localization-and-tracking-algorithms
#18
Simon Christoph Stein, Jan Thiart
Super-resolution localization microscopy and single particle tracking are important tools for fluorescence microscopy. Both rely on detecting, and tracking, a large number of fluorescent markers using increasingly sophisticated computer algorithms. However, this rise in complexity makes it difficult to fine-tune parameters and detect inconsistencies, improve existing routines, or develop new approaches founded on established principles. We present an open-source MATLAB framework for single molecule localization, tracking and super-resolution applications...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27884718/micro-ct-analysis-of-naturally-arrested-brown-spot-enamel-lesions
#19
Mahdi Shahmoradi, Michael V Swain
OBJECTIVES: The aim of this study was to characterize the mineral density parameters through natural enamel brown spot lesions (BSLs) and to visualize and map their mineral distribution pattern in comparison to enamel whitespot lesions (WSLs). METHODS: Study specimens included seventeen proximal WSLs (ICDAS 1, 2), seventeen proximal BSLs and seventeen sound proximal specimens (ICDAS 0) collected from The Oral Surgery Department at Sydney Dental Hospital, Sydney, Australia...
November 21, 2016: Journal of Dentistry
https://www.readbyqxmd.com/read/27881521/is-famine-exposure-during-developmental-life-in-rural-bangladesh-associated-with-a-metabolic-and-epigenetic-signature-in-young-adulthood-a-historical-cohort-study
#20
S Finer, M S Iqbal, R Lowe, B W Ogunkolade, S Pervin, C Mathews, M Smart, D S Alam, G A Hitman
OBJECTIVES: Famine exposure in utero can 'programme' an individual towards type 2 diabetes and obesity in later life. We sought to identify, (1) whether Bangladeshis exposed to famine during developmental life are programmed towards diabetes and obesity, (2) whether this programming was specific to gestational or postnatal exposure windows and (3) whether epigenetic differences were associated with famine exposure. DESIGN: A historical cohort study was performed as part of a wider cross-sectional survey...
November 23, 2016: BMJ Open
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