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https://www.readbyqxmd.com/read/29245136/small-maf-functions-in-the-maintenance-of-germline-stem-cells-in-the-drosophila-testis
#1
Sharon Wui Sing Tan, George W Yip, Toshio Suda, Gyeong Hun Baeg
Reactive oxygen species (ROS) are byproducts generated during normal cellular metabolism, and redox states have been shown to influence stem cell self-renewal and lineage commitment across phyla. However, the downstream effectors of ROS signaling that control stem cell behavior remain largely unexplored. Here, we used the Drosophila testis as an in vivo model to identify ROS-induced effectors that are involved in the differentiation process of germline stem cells (GSCs). In the Affymetrix microarray analysis, 152 genes were either upregulated or downregulated during GSC differentiation induced by elevated levels of ROS, and a follow-up validation of the gene expression by qRT-PCR showed a Spearman's rho of 0...
December 8, 2017: Redox Biology
https://www.readbyqxmd.com/read/29244758/protein-subcellular-localization-with-gaussian-kernel-discriminant-analysis-and-its-kernel-parameter-selection
#2
Shunfang Wang, Bing Nie, Kun Yue, Yu Fei, Wenjia Li, Dongshu Xu
Kernel discriminant analysis (KDA) is a dimension reduction and classification algorithm based on nonlinear kernel trick, which can be novelly used to treat high-dimensional and complex biological data before undergoing classification processes such as protein subcellular localization. Kernel parameters make a great impact on the performance of the KDA model. Specifically, for KDA with the popular Gaussian kernel, to select the scale parameter is still a challenging problem. Thus, this paper introduces the KDA method and proposes a new method for Gaussian kernel parameter selection depending on the fact that the differences between reconstruction errors of edge normal samples and those of interior normal samples should be maximized for certain suitable kernel parameters...
December 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29244640/cross-frequency-phase-amplitude-coupling-as-a-mechanism-for-temporal-orienting-of-attention-in-childhood
#3
Giovanni Mento, Duncan E Astle, Gaia Scerif
Temporal orienting of attention operates by biasing the allocation of cognitive and motor resources in specific moments in time, resulting in the improved processing of information from expected compared with unexpected targets. Recent findings have shown that temporal orienting operates relatively early across development, suggesting that this attentional mechanism plays a core role for human cognition. However, the exact neurophysiological mechanisms allowing children to attune their attention over time are not well understood...
December 15, 2017: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/29244567/temporal-variation-in-predation-risk-may-explain-daily-rhythms-of-foraging-behavior-in-an-orb-weaving-spider
#4
J Colton Watts, Thomas C Jones, Ashley Herrig, Madeleine Miller, Brigitte Tenhumberg
Daily rhythms occur in numerous physiological and behavioral processes across an immense diversity of taxa, but there remain few cases in which mechanistic links between rhythms of trait expression and organismal fitness have been established. We construct a dynamic optimization model to determine whether risk allocation provides an adaptive explanation for the daily foraging rhythm observed in many species using the orb-weaving spider Cyclosa turbinata as a case study. Our model predicts that female C. turbinata should generally start foraging at lower levels of energy reserves (i...
January 2018: American Naturalist
https://www.readbyqxmd.com/read/29244508/diffusion-of-supercritical-fluids-through-single-layer-nanoporous-solids-theory-and-molecular-simulations
#5
Fouad Oulebsir, Romain Vermorel, Guillaume Galliero
With the advent of graphene material, membranes based on single-layer nanoporous solids appear as promising devices for fluid separation, be it liquid or gaseous mixtures. The design of such architectured porous materials would greatly benefit from accurate models that can predict their transport and separation properties. More specifically, there is no universal understanding of how parameters such as temperature, fluid loading conditions or the ratio of the pore size to the fluid molecular diameter influence the permeation process...
December 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29244501/origins-of-enzyme-catalysis-experimental-findings-for-c-h-activation-new-models-and-their-relevance-to-prevailing-theoretical-constructs
#6
Judith P Klinman, Adam R Offenbacher, Shenshen Hu
The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases...
December 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29244193/comparative-peptidomic-profile-between-human-hypertrophic-scar-tissue-and-matched-normal-skin-for-identification-of-endogenous-peptides-involved-in-scar-pathology
#7
Jingyun Li, Ling Chen, Qian Li, Jing Cao, Yanli Gao, Jun Li
Endogenous peptides recently attract increasing attention for their participation in various biological processes. Their roles in the pathogenesis of human hypertrophic scar remains poorly understood. In this study, we used liquid chromatography-tandem mass spectrometry to construct a comparative peptidomic profiling between human hypertrophic scar tissue and matched normal skin. A total of 179 peptides were significantly differentially expressed in human hypertrophic scar tissue, with 95 upregulated and 84 downregulated peptides between hypertrophic scar tissue and matched normal skin...
December 15, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29244191/the-role-of-oat2-slc22a7-in-the-cyclic-nucleotide-biokinetics-of-human-erythrocytes
#8
Georg Sager, Natalia Smaglyukova, Ole-Martin Fuskevaag
The present study was conducted to characterise the transporter(s) responsible for the uptake of cyclic nucleotides to human erythrocytes. Western blotting showed that hRBC expressed OAT2 (SLC22A7), but detection of OAT1 (SLC22A6) or OAT3 (SLC22A8) was not possible. Intact hRBC were employed to clarify the simultaneous cyclic nucleotide egression and uptake. Both these opposing processes were studied. The Km -values for high affinity efflux was 3.5 ± 0.1 and 39.4 ± 5.7 µM for cGMP and cAMP, respectively...
December 15, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29244062/longitudinal-course-and-predictors-of-apathetic-symptoms-after-severe-traumatic-brain-injury
#9
Annabelle Arnould, Lucien Rochat, Philippe Azouvi, Martial Van der Linden
Objectives: Apathy is one of the most common behavioral symptoms encountered after traumatic brain injury (TBI). However, very little is known about the longitudinal course and predictors of apathetic manifestations. The aims of the present study were to examine how apathy changes and the predictive value of cognitive factors (memory, attention/executive mechanisms, and multitasking) and personal identity factors (self-esteem and self-efficacy beliefs) for apathy over a period of 10 months...
December 13, 2017: Archives of Clinical Neuropsychology: the Official Journal of the National Academy of Neuropsychologists
https://www.readbyqxmd.com/read/29244012/utilizing-knowledge-base-of-amino-acids-structural-neighborhoods-to-predict-protein-protein-interaction-sites
#10
Jan Jelínek, Petr Škoda, David Hoksza
BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. RESULTS: We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29244011/a-deep-learning-method-for-lincrna-detection-using-auto-encoder-algorithm
#11
Ning Yu, Zeng Yu, Yi Pan
BACKGROUND: RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29244010/rocsampler-regularizing-overlapping-protein-complexes-in-protein-protein-interaction-networks
#12
Osamu Maruyama, Yuki Kuwahara
BACKGROUND: In recent years, protein-protein interaction (PPI) networks have been well recognized as important resources to elucidate various biological processes and cellular mechanisms. In this paper, we address the problem of predicting protein complexes from a PPI network. This problem has two difficulties. One is related to small complexes, which contains two or three components. It is relatively difficult to identify them due to their simpler internal structure, but unfortunately complexes of such sizes are dominant in major protein complex databases, such as CYC2008...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29243993/modeling-the-bioconversion-of-starch-to-p-hb-co-hv-optimized-by-experimental-design-using-bacillus-megaterium-bbst4-strain
#13
Mauricio A Porras, Fernando D Ramos, María S Diaz, María A Cubitto, Marcelo A Villar
Poly(hydroxybutyrate-co-hydroxyvalerate) (P(HB-co-HV)) is a prominent biopolymer as a potential candidate for use in the biomedical area. Several Bacillus spp. strains show promising characteristics in the use of several carbon sources and are an interesting alternative for the production of P(HB-co-HV). Sewage from the agricultural and food processing industries can be used to obtain abundantly starch as a carbon source for PHA production. The aim of the present study was to optimize the production of PHA using a Bacillus megaterium strain using starch as sole carbon source and develop dynamic mathematical model as a predictive tool of the process...
December 15, 2017: Environmental Technology
https://www.readbyqxmd.com/read/29243847/utility-of-complete-blood-count-parameters-to-detect-premature-ovarian-insufficiency-in-cases-with-oligomenorrhea-amenorrhea
#14
Ilhan Sanverdi, Cetin Kilicci, Ebru Cogendez, Cigdem Abide Yayla, Enis Ozkaya
BACKGROUND: There are very few biomarkers available to diagnose cases with premature ovarian failure. Some complete blood count parameters have been introduced to be diagnostic biomarkers for several disorders associated with inflammatory process. Due to the evidence that indicated chronic inflammatory process to be underlying pathophysiology in premature ovarian insufficiency (POI), we aimed to assess the predictive value of complete blood count parameters for POI diagnosis. METHOD: A total of 96 women diagnosed to have premature ovarian failure were compared with 110 otherwise healthy women in terms of some basal hormone levels and complete blood count parameters...
December 15, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29243483/relative-binding-free-energy-calculations-in-drug-discovery-recent-advances-and-practical-considerations
#15
Zoe Cournia, Bryce Allen, Woody Sherman
Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects...
December 15, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29243271/dynamic-modelling-of-limitations-on-improving-leaf-co2-assimilation-under-fluctuating-irradiance
#16
Alejandro Morales, Elias Kaiser, Xinyou Yin, Jeremy Harbinson, Jaap Molenaar, Steven M Driever, Paul C Struik
A dynamic model of leaf CO2 assimilation was developed as an extension of the canonical steady-state model, by adding the effects of energy-dependent non-photochemical quenching (qE), chloroplast movement, photoinhibition, regulation of enzyme activity in the Calvin cycle, metabolite concentrations, and dynamic CO2 diffusion. The model was calibrated and tested successfully using published measurements of gas exchange and chlorophyll fluorescence on Arabidopsis thaliana ecotype Col-0 and several photosynthetic mutants and transformants affecting the regulation of Rubisco activity (rca-2 and rwt43), NPQ (npq4-1 and npq1-2) and sucrose synthesis (spsa1)...
December 15, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29243252/predicting-calvarial-growth-in-normal-and-craniosynostotic-mice-using-a-computational-approach
#17
Arsalan Marghoub, Joseph Libby, Christian Babbs, Erwin Pauws, Michael J Fagan, Mehran Moazen
During postnatal calvarial growth the brain grows gradually and the overlying bones and sutures accommodate that growth until the later juvenile stages. The whole process is coordinated through a complex series of biological, chemical and perhaps mechanical signals between various elements of the craniofacial system. The aim of this study was to investigate to what extent a computational model can accurately predict the calvarial growth in wild-type (WT) and mutant type (MT) Fgfr2C342Y/+ mice displaying bicoronal suture fusion...
December 15, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29243200/the-cascading-effects-of-multiple-dimensions-of%C3%A2-implementation-on-program-outcomes-a-test-of-a-theoretical-model
#18
Cady Berkel, Anne M Mauricio, Irwin N Sandler, Sharlene A Wolchik, Carlos G Gallo, C Hendricks Brown
This study tests a theoretical cascade model in which multiple dimensions of facilitator delivery predict indicators of participant responsiveness, which in turn lead to improvements in targeted program outcomes. An effectiveness trial of the 10-session New Beginnings Program for divorcing families was implemented in partnership with four county-level family courts. This study included 366 families assigned to the intervention condition who attended at least one session. Independent observers provided ratings of program delivery (i...
December 14, 2017: Prevention Science: the Official Journal of the Society for Prevention Research
https://www.readbyqxmd.com/read/29242638/re-calibration-of-coronary-risk-prediction-an-example-of-the-seven-countries-study
#19
Paolo Emilio Puddu, Paolo Piras, Daan Kromhout, Hanna Tolonen, Anthony Kafatos, Alessandro Menotti
We aimed at performing a calibration and re-calibration process using six standard risk factors from Northern (NE, N = 2360) or Southern European (SE, N = 2789) middle-aged men of the Seven Countries Study, whose parameters and data were fully known, to establish whether re-calibration gave the right answer. Greenwood-Nam-D'Agostino technique as modified by Demler (GNDD) in 2015 produced chi-squared statistics using 10 deciles of observed/expected CHD mortality risk, corresponding to Hosmer-Lemeshaw chi-squared employed for multiple logistic equations whereby binary data are used...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29242597/rheological-droplet-interface-bilayers-rheo-dibs-probing-the-unstirred-water-layer-effect-on-membrane-permeability-via-spinning-disk-induced-shear-stress
#20
Nathan E Barlow, Guido Bolognesi, Stuart Haylock, Anthony J Flemming, Nicholas J Brooks, Laura M C Barter, Oscar Ces
A new rheological droplet interface bilayer (rheo-DIB) device is presented as a tool to apply shear stress on biological lipid membranes. Despite their exciting potential for affecting high-throughput membrane translocation studies, permeability assays conducted using DIBs have neglected the effect of the unstirred water layer (UWL). However as demonstrated in this study, neglecting this phenomenon can cause significant underestimates in membrane permeability measurements which in turn limits their ability to predict key processes such as drug translocation rates across lipid membranes...
December 14, 2017: Scientific Reports
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