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https://www.readbyqxmd.com/read/28812194/amorphous-silica-promoted-lysine-dimerization-a-thermodynamic-prediction
#1
Norio Kitadai, Kumiko Nishiuchi, Akari Nishii, Keisuke Fukushi
It has long been suggested that mineral surfaces played a crucial role in the abiotic polymerization of amino acids that preceded the origin of life. Nevertheless, it remains unclear where the prebiotic process took place on the primitive Earth, because the amino acid-mineral interaction and its dependence on environmental conditions have yet to be understood adequately. Here we examined experimentally the adsorption of L-lysine (Lys) and its dimer (LysLys) on amorphous silica over a wide range of pH, ionic strength, adsorbate concentration, and the solid/water ratio, and determined the reaction stoichiometries and the equilibrium constants based on the extended triple-layer model (ETLM)...
August 15, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28809685/human-motion-segmentation-via-robust-kernel-sparse-subspace-clustering
#2
Guiyu Xia, Huaijiang Sun, Lei Feng, Guoqing Zhang, Yazhou Liu
Studies on human motion have attracted a lot of attentions. Human motion capture data, which much more precisely records human motion than videos do, has been widely used in many areas. Motion segmentation is an indispensable step for many related applications, but current segmentation methods for motion capture data do not effectively model some important characteristics of motion capture data, such as Riemannian manifold structure and containing non-Gaussian noise. In this paper, we convert the segmentation of motion capture data into a temporal subspace clustering problem...
August 10, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28807870/an-open-multi-vendor-multi-field-strength-brain-mr-dataset-and-analysis-of-publicly-available-skull-stripping-methods-agreement
#3
REVIEW
Roberto Souza, Oeslle Lucena, Julia Garrafa, David Gobbi, Marina Saluzzi, Simone Appenzeller, Letícia Rittner, Richard Frayne, Roberto Lotufo
This paper presents an open, multi-vendor, multi-field strength magnetic resonance (MR) T1-weighted volumetric brain imaging dataset, named Calgary-Campinas-359 (CC-359). The dataset is composed of images of older healthy adults (29-80 years) acquired on scanners from three vendors (Siemens, Philips and General Electric) at both 1.5 T and 3 T. CC-359 is comprised of 359 datasets, approximately 60 subjects per vendor and magnetic field strength. The dataset is approximately age and gender balanced, subject to the constraints of the available images...
August 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/28806354/trends-in-adult-chlamydia-and-gonorrhea-prevalence-incidence-and-urethral-discharge-case-reporting-in-morocco-over-1995-2015-estimates-using-the-spectrum-sexually-transmitted-infection-model
#4
Amina El-Kettani, Guy Mahiané, Aziza Bennani, Laith Abu-Raddad, Alex Smolak, Jane Rowley, Nico Nagelkerke, Houssine El-Rhilani, Kamal Alami, Amina Hançali, Eline Korenromp
BACKGROUND: Evolving health priorities and resource constraints mean that countries require data on sexually transmitted infections (STI) trends to inform program planning and resource allocation. METHODS: The Spectrum modeling tool estimated prevalence and incidence of gonorrhea and chlamydia in Morocco's 15- to 49-year-old population, based on prevalence surveys. Incident cases, broken down between symptomatic and asymptomatic, and treated versus untreated, were compared with urethral discharge (UD) case reports, to estimate reporting completeness among treated UD cases...
September 2017: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/28805729/systems-biology-approach-to-bioremediation-of-nitroaromatics-constraint-based-analysis-of-2-4-6-trinitrotoluene-biotransformation-by-escherichia-coli
#5
Maryam Iman, Tabassom Sobati, Yunes Panahi, Meysam Mobasheri
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E...
August 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28802825/the-role-of-nuclear-mechanics-in-cell-deformation-under-creeping-flows
#6
Francisco Serrano-Alcalde, José Manuel García-Aznar, María José Gómez-Benito
Despite the relevant regulatory role that nuclear deformation plays in cell behaviour, a thorough understanding of how fluid flow modulates the deformation of the cell nucleus in non-confined environments is lacking. In this work, we investigated the dynamics of cell deformation under different creeping flows as a general simulation tool for predicting nuclear stresses and strains. Using this solid-fluid modelling interaction framework, we assessed the stress and strain levels that the cell nucleus experiences as a function of different microenvironmental conditions, such as physical constraints, fluid flows, cytosol properties, and nucleus properties and size...
August 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28801647/reconstruction-of-a-genome-scale-metabolic-network-of-komagataeibacter-nataicola-rzs01-for-cellulose-production
#7
Heng Zhang, Chao Ye, Nan Xu, Chuntao Chen, Xiao Chen, Fanshu Yuan, Yunhua Xu, Jiazhi Yang, Dongping Sun
Bacterial cellulose (BC) is widely used in industries owing to its high purity and strength. Although Komagataeibacter nataicola is a representative species for BC production, its intracellular metabolism leading to BC secretion is unclear. In the present study, a genome-scale metabolic network of cellulose-producing K. nataicola strain RZS01 was reconstructed to understand its metabolic behavior. This model iHZ771 comprised 771 genes, 2035 metabolites, and 2014 reactions. Constraint-based analysis was used to characterize and evaluate the critical intracellular pathways...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801577/effects-of-disulfide-bridges-and-backbone-connectivity-on-water-sorption-by-protein-matrices
#8
Sang Beom Kim, Rakesh S Singh, Prem K C Paul, Pablo G Debenedetti
Understanding the water sorption behavior of protein powders is important in applications such as the preservation of protein-based pharmaceuticals. Most globular proteins exhibit a characteristic sigmoidal water adsorption isotherm at ambient conditions. However, it is not well understood how water sorption behavior is influenced by intrinsic factors that are related to structural properties of proteins. We investigate computationally how structural constraints on proteins influence the water sorption isotherms of amorphous protein powders...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797224/the-adaptive-landscape-of-wildtype-and-glycosylation-deficient-populations-of-the-industrial-yeast-pichia-pastoris
#9
Josef W Moser, Iain B H Wilson, Martin Dragosits
BACKGROUND: The effects of long-term environmental adaptation and the implications of major cellular malfunctions are still poorly understood for non-model but biotechnologically relevant species. In this study we performed a large-scale laboratory evolution experiment with 48 populations of the yeast Pichia pastoris in order to establish a general adaptive landscape upon long-term selection in several glucose-based growth environments. As a model for a cellular malfunction the implications of OCH1 mannosyltransferase knockout-mediated glycosylation-deficiency were analyzed...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28792577/-implementation-evaluation-of-the-pare-chocs-program-in-high-school
#10
Martine Poirier, Diane Marcotte, Jacques Joly, Laurier Fortin
Despite the important increase in the prevalence of depression during adolescence, a low proportion of adolescent presenting elevated depressive symptoms receive school-based mental health services. Moreover, programs implemented in school settings often suffer of a less rigorous implementation, thus limiting their potential effectiveness. The identification of factors influencing implementation fidelity is essential to improve the quality of services. Guided by a theory-driven evaluation model, we assessed the quality of implementation of the Pare-Chocs program and the factors that affected this quality with the elements of action model of Chen (2005)...
2017: Santé Mentale Au Québec
https://www.readbyqxmd.com/read/28792544/triple-dissociation-of-duration-perception-regulating-mechanisms-top-down-attention-is-inherent
#11
Yong-Jun Lin, Shinsuke Shimojo
The brain constantly adjusts perceived duration based on the recent event history. One such lab phenomenon is subjective time expansion induced in an oddball paradigm ("oddball chronostasis"), where the duration of a distinct item (oddball) appears subjectively longer when embedded in a series of other repeated items (standards). Three hypotheses have been separately proposed but it remains unresolved which or all of them are true: 1) attention prolongs oddball duration, 2) repetition suppression reduces standards duration, and 3) accumulative temporal preparation (anticipation) expedites the perceived item onset so as to lengthen its duration...
2017: PloS One
https://www.readbyqxmd.com/read/28790954/object-categorization-in-finer-levels-relies-more-on-higher-spatial-frequencies-and-takes-longer
#12
Matin N Ashtiani, Saeed R Kheradpisheh, Timothée Masquelier, Mohammad Ganjtabesh
The human visual system contains a hierarchical sequence of modules that take part in visual perception at different levels of abstraction, i.e., superordinate, basic, and subordinate levels. One important question is to identify the "entry" level at which the visual representation is commenced in the process of object recognition. For a long time, it was believed that the basic level had a temporal advantage over two others. This claim has been challenged recently. Here we used a series of psychophysics experiments, based on a rapid presentation paradigm, as well as two computational models, with bandpass filtered images of five object classes to study the processing order of the categorization levels...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28783625/non-rigid-contour-based-registration-of-cell-nuclei-in-2d-live-cell-microscopy-images-using-a-dynamic-elasticity-model
#13
Dmitry V Sorokin, Igor Peterlik, Marco Tektonidis, Karl Rohr, Pavel Matula
The analysis of the pure motion of subnuclear structures without influence of the cell nucleus motion and deformation is essential in live cell imaging. In this work, we propose a 2D contour-based image registration approach for compensation of nucleus motion and deformation in fluorescence microscopy time-lapse sequences. The proposed approach extends our previous approach which uses a static elasticity model to register cell images. Compared to that scheme, the new approach employs a dynamic elasticity model for forward simulation of nucleus motion and deformation based on the motion of its contours...
July 31, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28780106/economic-effect-of-reducing-nitrogen-and-phosphorus-mass-balance-on-wisconsin-and-qu%C3%A3-bec-dairy-farms
#14
D Pellerin, E Charbonneau, L Fadul-Pacheco, O Soucy, M A Wattiaux
Our objective was to explore the trade-offs between economic performance (farm net income, FNI) and environmental outcomes (whole-farm P and N balances) of dairy farms in Wisconsin (WI; United States) and Québec (QC; Canada). An Excel-based linear program model (N-CyCLES; nutrient cycling: crops, livestock, environment, and soil) was developed to optimize feeding, cropping, and manure management as a single unit of management. In addition to FNI, P and N balances model outputs included (1) the mix of up to 9 home-grown and 17 purchased feeds for up to 5 animal groups, (2) the mix of up to 5 crop rotations in up to 5 land units and c) the mix of up to 7 fertilizers (solid and liquid manure and 5 commercial fertilizers) to allocate in each land unit...
August 2, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28777325/rgca-a-reliable-gpu-cluster-architecture-for-large-scale-internet-of-things-computing-based-on-effective-performance-energy-optimization
#15
Yuling Fang, Qingkui Chen, Neal N Xiong, Deyu Zhao, Jingjuan Wang
This paper aims to develop a low-cost, high-performance and high-reliability computing system to process large-scale data using common data mining algorithms in the Internet of Things (IoT) computing environment. Considering the characteristics of IoT data processing, similar to mainstream high performance computing, we use a GPU (Graphics Processing Unit) cluster to achieve better IoT services. Firstly, we present an energy consumption calculation method (ECCM) based on WSNs. Then, using the CUDA (Compute Unified Device Architecture) Programming model, we propose a Two-level Parallel Optimization Model (TLPOM) which exploits reasonable resource planning and common compiler optimization techniques to obtain the best blocks and threads configuration considering the resource constraints of each node...
August 4, 2017: Sensors
https://www.readbyqxmd.com/read/28776694/linear-programming-an-alternative-approach-for-developing-formulations-for-emergency-food-products
#16
Ershad Sheibani, Arasb Dabbagh Moghaddam, Anoosheh Sharifan, Zahra Afshari
BACKGROUND: To minimize the mortality rates of individuals affected by disasters, providing high-quality food relief during the initial stages of an emergency is crucial. The goal of this study was to develop a formulation for a high-energy, nutrient-dense prototype using linear programming (LP) model as a novel method for developing formulations for food products. RESULTS: The model consisted of the objective function and the decision variables which were the formulation costs and the weights of the selected commodities, respectively...
August 4, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28774468/knee-joint-kinematics-and-kinetics-during-the-hop-and-cut-after-soft-tissue-artifact-suppression-time-to-reconsider-acl-injury-mechanisms
#17
Kenneth B Smale, Brigitte M Potvin, Mohammad S Shourijeh, Daniel L Benoit
The recent development of a soft tissue artifact (STA) suppression method allows us to re-evaluate the tibiofemoral kinematics currently linked to non-contact knee injuries. The purpose of this study was therefore to evaluate knee joint kinematics and kinetics in six degrees of freedom (DoF) during the loading phases of a jump lunge and side cut using this in silico method. Thirty-five healthy adults completed these movements and their surface marker trajectories were then scaled and processed with OpenSim's inverse kinematics (IK) and inverse dynamics tools...
July 8, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/28774099/modelling-of-granular-fracture-in-polycrystalline-materials-using-ordinary-state-based-peridynamics
#18
Ning Zhu, Dennj De Meo, Erkan Oterkus
An ordinary state-based peridynamic formulation is developed to analyse cubic polycrystalline materials for the first time in the literature. This new approach has the advantage that no constraint condition is imposed on material constants as opposed to bond-based peridynamic theory. The formulation is validated by first considering static analyses and comparing the displacement fields obtained from the finite element method and ordinary state-based peridynamics. Then, dynamic analysis is performed to investigate the effect of grain boundary strength, crystal size, and discretization size on fracture behaviour and fracture morphology...
December 2, 2016: Materials
https://www.readbyqxmd.com/read/28772794/strain-localization-of-elastic-damaging-frictional-cohesive-materials-analytical-results-and-numerical-verification
#19
Jian-Ying Wu, Miguel Cervera
Damage-induced strain softening is of vital importance for the modeling of localized failure in frictional-cohesive materials. This paper addresses strain localization of damaging solids and the resulting consistent frictional-cohesive crack models. As a supplement to the framework recently established for stress-based continuum material models in rate form (Wu and Cervera 2015, 2016), several classical strain-based damage models, expressed usually in total and secant format, are considered. Upon strain localization of such damaging solids, Maxwell's kinematics of a strong (or regularized) discontinuity has to be reproduced by the inelastic damage strains, which are defined by a bounded characteristic tensor and an unbounded scalar related to the damage variable...
April 20, 2017: Materials
https://www.readbyqxmd.com/read/28771536/flow-assignment-model-for-quantitative-analysis-of-diverting-bulk-freight-from-road-to-railway
#20
Chang Liu, Boliang Lin, Jiaxi Wang, Jie Xiao, Siqi Liu, Jianping Wu, Jian Li
Since railway transport possesses the advantage of high volume and low carbon emissions, diverting some freight from road to railway will help reduce the negative environmental impacts associated with transport. This paper develops a flow assignment model for quantitative analysis of diverting truck freight to railway. First, a general network which considers road transportation, railway transportation, handling and transferring is established according to all the steps in the whole transportation process. Then general functions which embody the factors which the shippers will pay attention to when choosing mode and path are formulated...
2017: PloS One
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