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Brown Hamish E - - 2013
Background and AimsA model to predict anthesis time of a wheat plant from environmental and genetic information requires integration of current concepts in physiological and molecular biology. This paper describes the structure of an integrated model and quantifies its response mechanisms.MethodsLiterature was reviewed to formulate the components of the model. ...
Nims Robert J - - 2013
Large-sized cartilage constructs suffer from inhomogeneous extracellular matrix deposition due to insufficient nutrient availability. Computational models of nutrient consumption and tissue growth can be utilized as an efficient alternative to experimental trials to optimize the culture of large constructs; models require system-specific growth and consumption parameters. To inform models of ...
Ledbetter Michael P - - 2013
Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. In vitro directed evolution (IVDE) frequently serves as a model system for the study of Darwinian evolution but produces ...
Ozcan Ozer - - 2013
To understand the effect of the long intracellular loop 3 (ICL3) on the intrinsic dynamics of human beta2-adrenergic receptor, molecular dynamics (MD) simulations were performed on two different models, both of which were based on the inactive crystal structure in complex with carazolol (after removal of carazolol and T4-lysozyme). In ...
Sharifi Mohsen - - 2013
Biliary excretion is one of the main elimination pathways for drugs and/or their metabolites. Therefore, an insight into the structural profile of cholephilic compounds through accurate modelling of the biliary excretion is important for the estimation of clinical pharmacokinetics in early stages of drug discovery. The aim of this study ...
Abrams Peter A - - 2013
How will evolution or other forms of adaptive change alter the response of a consumer species' population density to environmentally driven changes in population growth parameters? This question is addressed by analyzing some simple consumer-resource models to separate the ecological and evolutionary components of the population's response. Ecological responses are ...
Hanamoto Seiya - - 2013
Existing stochastic models for predicting concentrations of down-the-drain chemicals in aquatic environments do not account for the diurnal variation of direct photolysis by sunlight, despite its being an important factor in natural attenuation. To overcome this limitation, we developed a stochastic model incorporating temporal variations in direct photolysis. To verify ...
Lang Nadine R - - 2013
The pore size of biopolymer networks governs their mechanical properties and strongly impacts the behavior of embedded cells. Confocal reflection microscopy and second harmonic generation microscopy are widely used to image biopolymer networks; however, both techniques fail to resolve vertically oriented fibers. Here, we describe how such directionally biased data ...
Chen Yu - - 2013
In this paper, a new linear dimension reduction method called supervised orthogonal discriminant subspace projection (SODSP) is proposed, which addresses high-dimensionality of data and the small sample size problem. More specifically, given a set of data points in the ambient space, a novel weight matrix that describes the relationship between ...
Barker David H - - 2013
To introduce and illustrate recent advances in statistical approaches to simultaneous modeling of multiple change processes. Provide a general overview of how to use structural equations to simultaneously model multiple change processes and illustrate the use of a theoretical model of change to guide selection of an appropriate specification from ...
Blanco Celia - - 2013
Simulations of a chemical kinetics model, based on the free-energy relationships of classical primary nucleation theory, show that the deracemization phenomenon in systems of achiral or fast racemizing compounds yielding enantiopure crystals as the more stable solid phase is a true spontaneous mirror symmetry breaking process (SMSB). That is, the ...
Di-Ling Chen - - 2013
ABSTRACT. Alzheimer's disease irreversibly and progressively damages the brain, but the treatments in clinical trials are too slow. So, we hypothesized that the presence of erythrocyte variants with AD could be used as a noninvasive means to predict or trigger for administration of the preventive therapeutics, and the aim of ...
Cuervo Pablo F - - 2013
Dirofilariosis, caused by Dirofilaria immitis and D. repens, is spreading in several geographic regions. The development of infective larvae in the mosquito vector (extrinsic incubation) needs an accumulated total of 130 degree-days above the 14 °C threshold, normally expressed as heartworm development units (HDUs). Based on this information, temperature- based ...
Xu Xijun - - 2013
Simultaneous removal of sulfide (S(2-)), nitrate (NO3(-)) and acetate (Ac(-)) under denitrifying sulfide removal process (DSR) is a novel biological wastewater treatment process. This work developed a mathematical model to describe the kinetic behavior of sulfur-nitrogen-carbon and interactions between autotrophic denitrifiers and heterotrophic denitrifiers. The kinetic parameters of the model ...
Hosseini S M - - 2013
Proteoglycan loss and surface roughening, early signs of osteoarthritis, are likely preceded by softening of the ground substance and the collagen network. Insight in their relative importance to progression of osteoarthritis may assist the development of treatment strategies for early osteoarthritis. To support interpretation of experimental data, a numerical model ...
Moore A C - - 2013
For nearly a century, articular cartilage has been known for its exceptional tribological properties. For nearly as long, there have been research efforts to elucidate the responsible mechanisms for application toward biomimetic bearing applications. It is now widely accepted that interstitial fluid pressurization is the primary mechanism responsible for the ...
Marsolier-Kergoat Marie-Claude - - 2013
Whereas GC-biased gene conversion (gBGC) following meiotic recombination seems the most probable mechanism accounting for large-scale variations in GC content for many eukaryotes, it cannot explain such variations for organisms belonging to ancient asexual lineages, like the pathogenic fungi Candida albicans and Candida dubliniensis. Analysis of the substitution patterns for ...
González González Nieves Luisa - - 2013
Abstract Objetives: To construct a model of customized birthweight curves for use in a Spanish population. Material and Method: Data of 20,331 newborns were used to construct a customized birthweight model. Multiple regression analysis was performed with newborn weight as the dependent variable and gestational age (GA), sex and maternal ...
Bultmann Christoph André - - 2013
Gene expression analysis by quantitative PCR is a standard laboratory technique for RNA quantification with high accuracy. In particular real-time PCR techniques using SYBR Green and melting curve analysis allowing verification of specific product amplification have become a well accepted laboratory technique for rapid and high throughput gene expression quantification. ...
Heredia-Ortiz Roberto - - 2013
3-Hydroxybenzo(a)pyrene (3-OHBaP) in urine has been proposed as a biomarker of occupational exposure to polycyclic aromatic hydrocarbons. However, to reconstruct exposure doses in workers from biomarker measurements, a thorough knowledge of the kinetics of the benzo(a)pyrene (BaP) and 3-OHBaP given different routes of exposure is needed. A rat physiologically-based pharmacokinetic ...
Skacel Pavel - - 2013
Several constitutive models have been proposed for the description of mechanical behaviour of soft tissues containing collagen fibres. Some of the commonly used approaches accounting for the dispersion of fibre orientations are based on the summation of (mechanical) contributions of differently oriented fibre families. This leads to the need of ...
Hope Bruce K BK CH2M HILL, Portland, Oregon, - - 2013
Mercury (Hg) has been entering the environment from both natural and anthropogenic sources for millennia, and humans have been influencing its environmental transport and fate from well before the Industrial Revolution. Exposure to Hg (as neurotoxic monomethylmercury [MeHg]) occurs primarily through consumption of finfish, shellfish, and marine mammals, and regulatory ...
Varadi Mihaly M VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, Germany, CEA, CNRS, UJF-Grenoble 1, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble 38027, France, Indiana University School of Medicine; Indianapolis, IN, USA, Department of Chemistry, Center of Magnetic Resonance (CERM), University of Florence, Sesto Fiorentino, Italy, Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA, Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, Department of Chemistry, University of Cambridge, Cambridge, UK, Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, - - 2014
The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, ...
Landberg Tobias - - 2014
Egg size is a key life history trait affecting fitness, and it varies abundantly. The value of egg size to a mother and her offspring is often determined by a trade-off between investing more yolk in a few large eggs or less yolk into many more, smaller eggs. Smaller eggs ...
Wang Zhuo - - 2013
Biomechanical study of double-level pedicle screw constructs with or without crosslinks in an unstable model. The purpose of this study is to investigate the optimal position and orientation of the crosslink. Several reports have described biomechanical research on such crosslink, but no definite consensus has been reached regarding the effects. ...
Kostylev Maxim - - 2013
Lignocellulosic biomass is digested in nature by the synergistic activities of enzymes with complementary properties and understanding synergistic interactions will improve the efficiency of industrial biomass use for sustainable fuels and chemicals. TfCel9A and TfCel48A from a model bacterium Thermobifida fusca are two cellulases with different properties and have previously ...
Moffitt Jeffrey R JR Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, - - 2014
Enzyme-catalyzed reactions are naturally stochastic, and precision measurements of these fluctuations, made possible by single-molecule methods, promise to provide fundamentally new constraints on the possible mechanisms underlying these reactions. We review some aspects of statistical kinetics: a new field with the goal of extracting mechanistic information from statistical measures of ...
Pandey Abhishek A Department of Mathematical Sciences, Clemson University, Clemson, South Carolina 29634, USA. Electronic address: - - 2013
Various simple mathematical models have been used to investigate dengue transmission. Some of these models explicitly model the mosquito population, while others model the mosquitoes implicitly in the transmission term. We study the impact of modeling assumptions on the dynamics of dengue in Thailand by fitting dengue hemorrhagic fever (DHF) ...
Li Xiao-Mei - - 2013
Circadian timing of anticancer medications has improved treatment tolerability and efficacy several-fold, yet with inter-subject variability. Using three C57BL/6-based mouse strains of both sexes, we identified three chronotoxicity classes, with distinct circadian toxicity patterns of irinotecan, a topoisomerase I inhibitor active against colorectal cancer. Liver and colon circadian 24-h expression ...
Shao Qing-Song - - 2013
Rhizoma Atractylodis Macrocephalae (RAM) is a commonly used food and traditional Chinese medicine (TCM), which traditionally strengthens the spleen, benefits vital energy, eliminates dampness, and promotes hidroschesis. Its primary effective constituents are polysaccharides and volatile oil, whose main components are atractylenolide I and III. Fourier transform near-infrared spectroscopy (FT-NIR) is ...
Li Yi-Nan - - 2013
Refined oil mixtures can be quantified using terahertz-absorption-coefficient spectra and dualistic linear regression fitting. However, when this method was used to quantify mixtures of 90# and 97# gasolines, the absolute error between the real and fitted value was large (25%), and this was due to the component similarity between 90# ...
Lebert André A INRA, Centre Clermont-Ferrand/Theix, UR 370: Qualité des Produits Animaux, 63 122, St Genes Champanelle, France; Université Blaise Pascal, Institut Pascal UMR CNRS/UBP/IFMA 6602, France. Electronic address: - - 2013
New beef products from low value cuts could be developed using marinating since this process has been shown to improve meat sensorial properties and shelf life. However, to optimise the process mathematical models are needed to predict evolution of the physicochemical properties that determine biochemical and structural changes. Two major ...
Prunescu Remus Mihail - - 2013
The enzymatic hydrolysis process is one of the key steps in second generation biofuel production. After being thermally pretreated, the lignocellulosic material is liquefied by enzymes prior to fermentation. The scope of this paper is to evaluate a dynamic model of the hydrolysis process on a demonstration scale reactor. The ...
Yang Daibin - - 2013
Tebuconazole is a triazole systemic fungicide that is commonly used to treat fungal pathogens of crops, but at high doses can reduce seed germination. Seeds with microcapsulated tebuconazole were investigated to determine effects of this method on maize seedlings and the bioefficacy against maize head smut (Sphacelotheca reiliana). The ethyl ...
de Sales Priscila F - - 2013
The effect of acid treatment on natural agalmatolite (AN) and natural kaolinite (KN) was investigated, together with the influence of those modifications on the removal of Coomassie Blue (CB) dye. The process was optimized using the Response Surface Methodology (RSM) developed by the application of the quadratic model associated with ...
Akagi Yuki - - 2013
We have investigated the fracture behaviors of tetra-arm polyethylene glycol (Tetra-PEG) gels with controlled network structures. Tetra-PEG gels were prepared by AB-type crosslink-coupling of mutually reactive tetra-arm prepolymers with different concentrations and molecular weights. This series of controlled network structures, for the first time, enabled us to quantitatively examine the ...
van der Hoeven-Hangoor E - - 2013
High litter moisture content, often referred to as wet litter, is a major problem in poultry production. Wet litter is often related to poor management, diseases, and digestive problems. In this experiment, the objective was to study the relationship between nutrient content and the moisture content of the excreta of ...
Tarcsay Akos - - 2013
Formation of ligand-protein complexes requires simultaneous adaptation of the binding partners. In structure based virtual screening high throughput docking approaches typically consider the ligand flexibility but the conformational freedom of the protein is usually taken into account in limited way. The goal of this study is to elaborate a methodology ...
Staschen Carl-Michael - - 2013
Abstract Background: Allometric exponents in population pharmacokinetic analysis are regularly used but the issue of fixing or estimating an allometric exponent remains controversial. The objective of the current analysis is to evaluate the performance of a body-weight-dependent allometric exponent (BDE) model of remifentanil. Methods: The study was conducted in 34 ...
Chirwa Esnat D - - 2013
Abstract Background: Different structural and non-structural models have been used to describe human growth patterns. However, few studies have compared the fitness of these models in an African transitioning population. Aim: To find model(s) that best describe the growth pattern from birth to early childhood using mixed effect modelling. Subjects ...
Jenko J - - 2013
Survival analysis techniques for sire-maternal grandsire (MGS) and animal models were used to test the genetic evaluation of longevity in a Slovenian Brown cattle population characterized by small herds. Three genetic models were compared: a sire-MGS model for bulls and an approximate animal model based on estimated breeding values (EBV) ...
Ghaffari Noushin - - 2013
A key goal of systems biology and translational genomics is to utilize high-throughput measurements of cellular states to develop expression-based classifiers for discriminating among different phenotypes. Recent developments of Next Generation Sequencing (NGS) technologies can facilitate classifier design by providing expression measurements for tens of thousands of genes simultaneously via ...
Rohlfs Rori V - - 2013
Much of the phenotypic variation observed between even closely related species may be driven by differences in gene expression levels. The current availability of reliable techniques like RNA-Seq which can quantify expression levels across species has enabled comparative studies. Ornstein-Uhlenbeck (OU) processes have been proposed to model gene expression evolution ...
Deeb Omar - - 2013
Abstract Quantitative Structure-Activity Relationship (QSAR) models for binding affinity constants (log Ki) of 78 flavonoid ligands towards the benzodiazepine site of GABA (A) receptor complex were calculated using the machine learning methods: artificial neural network (ANN) and support vector machine (SVM) techniques. The models obtained were compared with those obtained ...
Underwood T L - - 2013
Differences in core level binding energies between atoms belonging to the same chemical species can be related to differences in their intra- and extra-atomic charge distributions, and differences in how their core holes are screened. With this in mind, we consider the charge-excess functional model (CEFM) for net atomic charges ...
Choi Minsung - - 2013
Arabic date is overproduced in Arabic countries such as Saudi Arabia and Iraq and is mostly composed of sugars (70-80 wt%). Here we developed a fed-batch fermentation process by using a kinetic model for the efficient production of lactic acid to a high concentration from Arabic date juice. First, a kinetic ...
Barkaoui Abdelwahed - - 2013
The complexity and heterogeneity of bone tissue require a multiscale modeling to understand its mechanical behavior and its remodeling mechanisms. In this paper, a novel multiscale hierarchical approach including microfibril scale based on hybrid neural network (NN) computation and homogenization equations was developed to link nanoscopic and macroscopic scales to ...
McCoy Airlie J - - 2013
A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed ...
Belanche A - - 2013
Currently, rapid methods are needed for feed analysis. This study examined the potential of Fourier-transform infrared (FTIR) spectroscopy to predict the nutritional value of a wide range of feeds for ruminants, as an alternative to the in situ technique. Moreover, we investigated whether universal equations could be developed that would ...
Kloosterman Fabian - - 2013
A fundamental task in neuroscience is to understand how neural ensembles represent information. Population decoding is a useful tool to extract information from neuronal populations based on the ensemble spiking activity. We propose a novel Bayesian decoding paradigm to decode unsorted spikes in the rat hippocampus. Our approach uses a ...
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