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https://www.readbyqxmd.com/read/27924257/a-unified-statistical-model-of-protein-multiple-sequence-alignment-integrating-direct-coupling-and-insertions
#1
Akira R Kinjo
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27923290/computerised-analysis-of-antepartum-foetal-heart-parameters-new-reference-ranges
#2
Natascia Giuliano, Maria Laura Annunziata, Francesca Giovanna Esposito, Salvatore Tagliaferri, Andrea Di Lieto, Giovanni Magenes, Maria Gabriella Signorini, Marta Campanile, Domenico Arduini
We selected 4012 cCTG records (one trace for each patient) performed in healthy pregnancies from 30th to 42nd gestational week using foetal heart rate (FHR), short-term variability (STV), long-term irregularity (LTI), Delta, approximate entropy (ApEn), spectral components as low frequency (LF), median frequency (MF), high frequency (HF) and LF/(HF + MF) ratio were analysed. Reference nomograms were created and sensitivity and specificity for the prediction of foetal compromise were calculated which were 90% and 89%, respectively...
December 6, 2016: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/27908130/exploring-connections-between-statistical-mechanics-and-green-s-functions-for-realistic-systems-temperature-dependent-electronic-entropy-and-internal-energy-from-a-self-consistent-second-order-green-s-function
#3
Alicia Rae Welden, Alexander A Rusakov, Dominika Zgid
Including finite-temperature effects from the electronic degrees of freedom in electronic structure calculations of semiconductors and metals is desired; however, in practice it remains exceedingly difficult when using zero-temperature methods, since these methods require an explicit evaluation of multiple excited states in order to account for any finite-temperature effects. Using a Matsubara Green's function formalism remains a viable alternative, since in this formalism it is easier to include thermal effects and to connect the dynamic quantities such as the self-energy with static thermodynamic quantities such as the Helmholtz energy, entropy, and internal energy...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908116/energetic-and-entropic-components-of-the-tolman-length-for-mw-and-tip4p-2005-water-nanodroplets
#4
Mark N Joswiak, Ryan Do, Michael F Doherty, Baron Peters
The surface free energy of a droplet is approximately γ(R)=γ(∞)(1-2δ/R), with R being the droplet radius and δ being the Tolman length. Here we use the mitosis method to compute δ=-0.56±0.1Å at 300 K for mW water, indicating that γ(R) increases as the droplet size decreases. The computed Tolman length agrees quite well with a previous study of TIP4P/2005 water. We also decompose the size-dependent surface free energy into energetic and entropic contributions for the mW and TIP4P/2005 force fields...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27895588/influence-of-heart-rate-in-non-linear-hrv-indices-as-a-sampling-rate-effect-evaluated-on-supine-and-standing
#5
Juan Bolea, Esther Pueyo, Michele Orini, Raquel Bailón
The purpose of this study is to characterize and attenuate the influence of mean heart rate (HR) on nonlinear heart rate variability (HRV) indices (correlation dimension, sample, and approximate entropy) as a consequence of being the HR the intrinsic sampling rate of HRV signal. This influence can notably alter nonlinear HRV indices and lead to biased information regarding autonomic nervous system (ANS) modulation. First, a simulation study was carried out to characterize the dependence of nonlinear HRV indices on HR assuming similar ANS modulation...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27891669/a-molecular-dynamics-study-of-the-binary-complexes-of-app-jip1-and-the-cargo-binding-domain-of-klc
#6
Cooper A Taylor, Bill R Miller, Soleil S Shah, Carol A Parish
Mutations in the amyloid precursor protein (APP) are responsible for the formation of amyloid-β peptides. These peptides play a role in Alzheimer's and other dementia-related diseases. The cargo binding domain of the kinesin-1 light chain motor protein (KLC1) may be responsible for transporting APP either directly or via interaction with C-jun N-terminal kinase-interacting protein 1 (JIP1). However, to date there has been no direct experimental or computational assessment of such binding at the atomistic level...
November 7, 2016: Proteins
https://www.readbyqxmd.com/read/27881971/familial-longevity-is-not-associated-with-major-differences-in-the-hypothalamic-pituitary-gonadal-axis-in-healthy-middle-aged-men
#7
Evie van der Spoel, Ferdinand Roelfsema, Steffy W Jansen, Abimbola A Akintola, Bart E Ballieux, Christa M Cobbaert, Gerard J Blauw, P Eline Slagboom, Rudi G J Westendorp, Hanno Pijl, Diana van Heemst
CONTEXT: A trade-off between fertility and longevity possibly exists. The association of the male hypothalamic-pituitary-gonadal (HPG) axis with familial longevity has not yet been investigated. OBJECTIVE: To study 24-h hormone concentration profiles of the HPG axis in men enriched for familial longevity and controls. DESIGN: We frequently sampled blood over 24 h in 10 healthy middle-aged male offspring of nonagenarian participants from the Leiden Longevity Study together with 10 male age-matched controls...
2016: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/27875872/obtaining-the-solid-liquid-interfacial-free-energy-via-multi-scheme-thermodynamic-integration-ag-ethylene-glycol-interfaces
#8
Xin Qi, Ya Zhou, Kristen A Fichthorn
The solid-liquid interfacial free energy γsl is an important quantity in wetting, nucleation, and crystal growth. Although various methods have been developed to calculate γsl with atomic-scale simulations, such calculations still remain challenging for multi-component interfaces between molecular fluids and solids. We present a multi-scheme thermodynamic integration method that is inspired by the "cleaving-wall" method and aimed at obtaining γsl for such systems using open-source simulation packages. This method advances two aspects of its predecessor methods...
November 21, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27836039/an-elaborated-sir-model-for-haemonchosis-in-sheep-in-south-africa-under-a-targeted-selective-anthelmintic-treatment-regime
#9
Nlingisisi D Babayani, Jan A van Wyk, Eric R Morgan
Infection with the abomasal nematode Haemonchus contortus is responsible for considerable production loss in small ruminants globally, and especially in warm, summer-rainfall regions. Previous attempts to predict infection levels have followed the traditional framework for macroparasite models, i.e. tracking parasite population sizes as a function of host and climatic factors. Targeted treatment strategies, in which patho-physiological indices are used to identify the individuals most affected by parasites, could provide a foundation for alternative, incidence-based epidemiological models...
November 1, 2016: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/27831888/fuzzy-rough-entropy-measure-and-histogram-based-patient-selection-for-mirna-ranking-in-cancer
#10
Jayanta Kumar Pal, Shubhra Sankar Ray, Sung-Bae Cho, Sankar K Pal
MicroRNAs (miRNAs) are known as an important indicator of cancers. Presence of cancer can be detected by identifying the responsible miRNAs. A fuzzy-rough entropy measure (FREM) is developed which can rank the miRNAs and thereby identifying the relevant ones. FREM is used to determine the relevance of a miRNA in terms of separability between normal and cancer classes. While computing the FREM for a miRNA, fuzziness takes care of the overlapping between normal and cancer expressions, whereas rough lower approximation determines their class sizes...
November 1, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27806007/effects-of-pitch-area-restrictions-on-tactical-behavior-physical-and-physiological-performances-in-soccer-large-sided-games
#11
Bruno Gonçalves, Pedro Esteves, Hugo Folgado, Angel Ric, Carlota Torrents, Jaime Sampaio
The aim of this study was to identify how pitch area-restrictions affects the tactical behavior, physical and physiological performances of players during soccer large-sided games. A 10 vs. 9 large-sided game was performed under three experimental conditions: (i) restricted-spacing, the pitch was divided into specific areas where players were assigned and they should not leave it; (ii) contiguous-spacing, the pitch was divided into specific areas where the players were only allowed to move to a neighboring one; (iii) free-spacing, the players had no restrictions in space occupation...
October 27, 2016: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/27802697/seamless-measurement-technology-of-transient-signals-based-on-approximate-entropy
#12
Jun Jiang, Shulin Tian, Lianping Guo, Wuhuang Huang
The acquisition of waveforms and the analysis of transient characteristics of signals are the fundamental tasks for time-domain measurement, while the reduction of the measuring gap till seamless measurement is extremely important to the acquisition, measurement, and analysis of transient signals. This paper, aimed at the seamless time-domain measurement of non-stationary transient signals, proposes an approximate entropy-based characteristic signal extraction algorithm on the basis of information entropy theories...
October 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27802274/topology-cross-frequency-and-same-frequency-band-interactions-shape-the-generation-of-phase-amplitude-coupling-in-a-neural-mass-model-of-a-cortical-column
#13
Roberto C Sotero
Phase-amplitude coupling (PAC), a type of cross-frequency coupling (CFC) where the phase of a low-frequency rhythm modulates the amplitude of a higher frequency, is becoming an important indicator of information transmission in the brain. However, the neurobiological mechanisms underlying its generation remain undetermined. A realistic, yet tractable computational model of the phenomenon is thus needed. Here we analyze a neural mass model of a cortical column, comprising fourteen neuronal populations distributed across four layers (L2/3, L4, L5 and L6)...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27785502/a-theoretical-study-of-the-atmospherically-important-radical-radical-reaction-bro-ho2-the-product-channel-o2-a-1-%C3%AE-g-hobr-is-formed-with-the-highest-rate
#14
Ronald Chow, Daniel K W Mok, Edmond P F Lee, John M Dyke
A theoretical study has been made of the BrO + HO2 reaction, a radical-radical reaction which contributes to ozone depletion in the atmosphere via production of HOBr. Reaction enthalpies, activation energies and mechanisms have been determined for five reaction channels. Also rate coefficients have been calculated, in the atmospherically important temperature range 200-400 K, for the two channels with the lowest activation energies, both of which produce HOBr: (R1a) HOBr(X(1)A') + O2(X(3)Σ) and (R1b) HOBr(X(1)A') + O2(a(1)Δg)...
October 27, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27782531/nature-of-the-cubic-to-tetragonal-phase-transition-in-methylammonium-lead-iodide-perovskite
#15
Wissam A Saidi, Joshua J Choi
Hybrid organic-inorganic perovskites, as well as the perovskites in general, are known for their phase complexity evidenced by the stabilization of different polymorphs, and thus an understanding of their regions of stability and transitions can be important for their photovoltaic and optoelectronic technologies. Here we use a multiscale approach based on first-principles calculations with van der Waals corrections and classical force-field molecular dynamics to determine the finite-temperature properties of the tetragonal and cubic phases of CH3NH3PbI3...
October 14, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27781215/strong-shear-driven-large-scale-formation-of-hybrid-shish-kebab-in-carbon-nanofiber-reinforced-polyethylene-composites-during-the-melt-second-flow
#16
Xiao-Chao Xia, Wei Yang, Zheng-Ying Liu, Rui-Yan Zhang, Dan-Dan Xie, Ming-Bo Yang
The formation of a hybrid shish-kebab (HSK) structure with different degrees of lamellar orientations was first observed in the solution crystallization of polyethylene (PE) in the presence of carbon nanofibers (CNFs). In this study, PE crystal lamellae were periodically decorated on the surface of CNFs and were aligned approximately perpendicular to the long axes of the CNFs, forming aligned hybrid shish-kebab nanostructures. More importantly, the fascinating structure was directly formed in all regions of the injection molded bars of HDPE/CNF composites, via a gas-assisted injection molding (GAIM), instead of the shell-core structure...
October 26, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27780261/inverting-monotonic-nonlinearities-by-entropy-maximization
#17
Jordi Solé-Casals, Karmele López-de-Ipiña Pena, Cesar F Caiafa
This paper proposes a new method for blind inversion of a monotonic nonlinear map applied to a sum of random variables. Such kinds of mixtures of random variables are found in source separation and Wiener system inversion problems, for example. The importance of our proposed method is based on the fact that it permits to decouple the estimation of the nonlinear part (nonlinear compensation) from the estimation of the linear one (source separation matrix or deconvolution filter), which can be solved by applying any convenient linear algorithm...
2016: PloS One
https://www.readbyqxmd.com/read/27774083/comparison-of-classical-kinematics-entropy-and-fractal-properties-as-measures-of-complexity-of-the-motor-system-in-swimming
#18
Tiago M Barbosa, Wan X Goh, Jorge E Morais, Mário J Costa, David Pendergast
The aim of this study was to compare the non-linear properties of the four competitive swim strokes. Sixty-eight swimmers performed a set of maximal 4 × 25 m using the four competitive swim strokes. The hip's speed-data as a function of time was collected with a speedo-meter. The speed fluctuation (dv), approximate entropy (ApEn) and the fractal dimension by Higuchi's method (D) were computed. Swimming data exhibited non-linear properties that were different among the four strokes (14.048 ≤ dv ≤ 39.722; 0...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27770676/the-complexity-of-electrodermal-activity-is-altered-in-mental-cognitive-stressors
#19
Zuzana Visnovcova, Michal Mestanik, Michal Gala, Andrea Mestanikova, Ingrid Tonhajzerova
The aim of this study was to evaluate potential changes in the electrodermal activity (EDA) to enable the detection of variations in the sympathetic nervous system during mental load and recovery period. Several EDA parameters were used: SCA (skin conductance amplitude), frequency of NS-EDR (nonspecific electrodermal responses), SIE (symbolic information entropy), and ApEn (approximate entropy). The cohort consisted of 50 healthy students (average age: 23.33±0.24yr., 25 women). The stress profile consisted of five phases: baseline (P1), Stroop test (P2), recovery (P3), mental arithmetic test (P4), and recovery (P5)...
October 14, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/27754668/predicting-molecular-crystal-properties-from-first-principles-finite-temperature-thermochemistry-to-nmr-crystallography
#20
Gregory J O Beran, Joshua D Hartman, Yonaton N Heit
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties...
October 18, 2016: Accounts of Chemical Research
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