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Velazquez Miguel A MA a Centre for Biological Sciences , University of Southampton, Southampton General Hospital , Southampton , United - - 2014
Ovarian transvaginal ultrasonography (OTU) has been used world-wide for commercial ovum pick-up programs for in vitro embryo production in elite herds, providing an excellent model for the elucidation of factors controlling bovine oocyte developmental competence. Noninvasive sampling and treatment of ovarian structures is easily accomplished with bovine OTU techniques providing ...
Hall Benjamin A BA Microsoft Research, 21 Station Road, Cambridge CB1 2FB, UK - - 2014
Caenorhabditis elegans vulval development is a paradigm system for understanding cell differentiation in the process of organogenesis. Through temporal and spatial controls, the fate pattern of six cells is determined by the competition of the LET-23 and the Notch signalling pathways. Modelling cell fate determination in vulval development using state-based ...
Mashanov Gregory I GI Division of Physical Biochemistry, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK - - 2014
The analysis of single molecule imaging experiments is complicated by the stochastic nature of single molecule events, by instrument noise and by the limited information which can be gathered about any individual molecule observed. Consequently, it is important to cross check experimental results using a model simulating single molecule dynamics ...
Colin R R http://orcid.org/0000-0001-9051-8003 The Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge, MA 02142, USA - - 2014
Swimming bacteria explore their environment by performing a random walk, which is biased in response to, for example, chemical stimuli, resulting in a collective drift of bacterial populations towards 'a better life'. This phenomenon, called chemotaxis, is one of the best known forms of collective behaviour in bacteria, crucial for ...
Goswami A A Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, UK - - 2014
Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. ...
Tamariz Monica M School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh EH8 9LL, - - 2014
Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed ...
Johnston Stuart T ST Mathematical Sciences, Queensland University of Technology, Brisbane, Australia Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, - - 2014
Moving cell fronts are an essential feature of wound healing, development and disease. The rate at which a cell front moves is driven, in part, by the cell motility, quantified in terms of the cell diffusivity D, and the cell proliferation rate λ. Scratch assays are a commonly reported procedure ...
Rosser Gabriel G Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK Department of Civil, Environmental and Geomatic Engineering, Faculty of Engineering Science, University College London, Chadwick Building, Gower Street, London WC1E 6BT, - - 2014
Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly understood reorientation mechanism in the monoflagellate species Rhodobacter sphaeroides. The flagellum ...
Tucker R P RP Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, UK - - 2014
In vitro mechanotransduction studies, uncovering the basic science of the response of cells to mechanical forces, are essential for progress in tissue engineering and its clinical application. Many varying investigations have described a multitude of cell responses; however, as the precise nature and magnitude of the stresses applied are infrequently ...
Fan Zizhu - - 2014
We modify the conventional principal component analysis (PCA) and propose a novel subspace learning framework, modified PCA (MPCA), using multiple similarity measurements. MPCA computes three similarity matrices exploiting the similarity measurements: 1) mutual information; 2) angle information; and 3) Gaussian kernel similarity. We employ the eigenvectors of similarity matrices to ...
Eiben Jesse J College of Agriculture, Forestry and Natural Resource Management, University of Hawaii at Hilo, 200 W. Kawili Street, Hilo, HI 96720, U.S.A.. - - 2014
Insects that should be considered for conservation attention are often overlooked because of a lack of data. The detailed information necessary to assess population growth, decline, and maximum range is particularly difficult to acquire for rare and cryptic species. Many of these difficulties can be overcome with the use of ...
Di Costanzo E E Dipartimento di Scienze di Base e Applicate per l'Ingegneria-Sezione di Matematica, Sapienza University of Rome, Via A. Scarpa 16, 00161 , Rome, Italy, - - 2014
In this paper we propose a discrete in continuous mathematical model for the morphogenesis of the posterior lateral line system in zebrafish. Our model follows closely the results obtained in recent biological experiments. We rely on a hybrid description: discrete for the cellular level and continuous for the molecular level. ...
Lueders Cora C Deutsches Herzzentrum Berlin, Laboratory for Tissue Engineering, Berlin, - - 2014
Three-dimensional (3D) printing technologies have reached a level of quality that justifies considering rapid manufacturing for medical applications. Herein, we introduce a new approach using 3D printing to simplify and improve the fabrication of human heart valve scaffolds by tissue engineering (TE). Custom-made human heart valve scaffolds are to be ...
van Hateren J H JH Johann Bernouilli Institute for Mathematics and Computer Science, University of Groningen, Groningen, The Netherlands, - - 2014
Purpose and meaning are necessary concepts for understanding mind and culture, but appear to be absent from the physical world and are not part of the explanatory framework of the natural sciences. Understanding how meaning (in the broad sense of the term) could arise from a physical world has proven ...
Simpson Julie A JA Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia, - - 2014
Mechanistic within-host models integrating blood anti-malarial drug concentrations with the parasite-time profile provide a valuable decision tool for determining dosing regimens for anti-malarial treatments, as well as a formative component of population-level drug resistance models. We reviewed published anti-malarial pharmacokinetic-pharmacodynamic models to identify the challenges for these complex models where ...
Ganguli Deep D Howard Hughes Medical Institute, Center for Neural Science and Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, U.S.A. - - 2014
The efficient coding hypothesis posits that sensory systems maximize information transmitted to the brain about the environment. We develop a precise and testable form of this hypothesis in the context of encoding a sensory variable with a population of noisy neurons, each characterized by a tuning curve. We parameterize the ...
Tian Ye - - 2014
BackgroundModeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be ...
Maschke Rüdiger W RW Institute of Food Technology and Bioprocess Engineering, Technische Universität Dresden, Dresden, - - 2014
Plant cell and tissue cultivations are of growing interest for the production of structurally complex and expensive plant-derived products, especially in pharmaceutical production. Problems with up-scaling, low yields and high-priced process conditions result in an increased demand for models to provide comprehension, simulation, and optimization of production processes. In the ...
Percival Christopher J - - 2014
Morphometric quantification of subtle craniofacial variation in studies of experimentally modified embryonic mice has proved valuable in determining the effects of developmental perturbations on craniofacial morphogenesis. The direct comparison of landmark coordinate data from embryos of many different mouse strains and mouse models can advance our understanding of the bases ...
Morrissey Kathryn L KL Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, - - 2014
Microalgae-derived biofuels have potential advantages over other renewable, crop-based resources, however, large-scale production is not currently economical due, in part, to challenges in the harvesting step. In this article we present a novel approach for the dewatering and harvesting of microalgae using flocculants that can be recovered and recycled. Polyampholytes ...
Shavit Yoli Y Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK. - - 2014
The Fluorescence in situ Hybridization (FISH) method has been providing valuable information on physical distances between loci (via image analysis) for several decades. Recently, high-throughput data on nearby chemical contacts between and within chromosomes became available with the Hi-C method. Here, we present FisHiCal, an R package for an iterative ...
Ibarz Albert A Department of Food Technology (DTA), School of Agricultural and Forestry Engineering (ETSEA), University of Lleida (UdL), Lleida, Spain, - - 2014
The mathematical modelling of the behaviour of microbial growth is widely desired in order to control, predict and design food and bioproduct processing, stability and safety. This work develops and proposes a new semi-empirical mathematical model, based on an autocatalytic kinetic, to describe the microbial growth through its biomass concentration. ...
Ong Cynthia C Department of Anatomy, Yong Loo Lin School of Medicine , National University of Singapore , Singapore - - 2014
Abstract Drosophila melanogaster has been used as an in vivo model organism for the study of genetics and development since 100 years ago. Recently, the fruit fly Drosophila was also developed as an in vivo model organism for toxicology studies, in particular, the field of nanotoxicity. The incorporation of nanomaterials ...
Mahto Sanjeev Kumar SK Department of Biomedical Engineering, Technion-Israel Institute of Technology , Haifa , Israel - - 2014
Abstract In the past few years, promising efforts to utilize microfabrication-based technologies have laid the foundation for developing advanced, and importantly more physiologically-realistic, microfluidic methods for risk assessment of engineered nanomaterials (ENMs). In the present review, we discuss the wave of recent developments using microfluidic-based in vitro models and platforms ...
Hedegaard Martin A B MA Departments of Materials and Bioengineering, The Institute of Biomedical Engineering, Imperial College London, SW7 2AZ, UK. - - 2014
In vitro Raman spectroscopy used for non-invasive, non-destructive characterization of single cells and tissues has proven to be a powerful tool for understanding the complex biochemical processes within these biological systems. Additionally it enables the comparison of a wide range of in vitro model systems by discriminating them based on ...
Fu Andrew S AS Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, - - 2014
Systems composed of high density cells incorporated with growth factor-releasing polymer microspheres have recently been shown to promote chondrogenic differentiation and cartilage formation. Within these systems, the effects of spatial and temporal patterning of growth factor release on hyaline cartilage-specific extracellular matrix production have been examined. However, at present, it ...
Kiani Narsis A - - 2014
Network inference deals with the reconstruction of molecular networks from experimental data. Given N molecular species, the challenge is to find the underlying network. Due to data limitations, this typically is an ill-posed problem, and requires the integration of prior biological knowledge or strong regularization. We here focus on the ...
Kirby Simon S University of Edinburgh, Edinburgh, Scotland, United Kingdom. Electronic address: - - 2014
Iterated learning describes the process whereby an individual learns their behaviour by exposure to another individual's behaviour, who themselves learnt it in the same way. It can be seen as a key mechanism of cultural evolution. We review various methods for understanding how behaviour is shaped by the iterated learning ...
Ryll A A Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, D-39106 Magdeburg, Germany. Electronic address: - - 2014
Systems Biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g., metabolism, signalling, and gene ...
Russell Deborah J F DJ Sea Mammal Research Unit, University of St Andrews, St Andrews, Fife, KY16 8LB, UK; Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Fife, KY16 9LZ, UK. Electronic address: - - 2014
On land, species from all trophic levels have adapted to fill vacant niches in environments heavily modified by humans (e.g. [1]). In the marine environment, ocean infrastructure has led to artificial reefs, resulting in localized increases in fish and crustacean density [2]. Whether marine apex predators exhibit behavioural adaptations to ...
Sakata Yoshitaka Y Faculty of Science, Division of Earth and Planetary Dynamics, Hokkaido University, North-10, West-8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan; Division of Environmental Engineering, Geotechnical Department, Docon Co., Ltd, 1-5 Atsubetsu-chuo, Atsubetsu-ku, Sapporo, Hokkaido 004-8585, Japan. - - 2014
Depth dependence of permeability can appear in any geologic setting; however, vertical trends in alluvial gravel deposits are poorly understood because of the high variability of hydraulic conductivity K in monotonic sequences. This paper examines the sensitivity of depth-decaying permeability through heat transport simulation around a river's losing reach in ...
Branco J R JR CMUC & Polytechnic Institute of Coimbra, ISEC, DFM, Coimbra, Portugal. Electronic address: - - 2014
In this paper we propose a mathematical model to describe the evolution of glioma cells taking into account the viscoelastic properties of brain tissue. The mathematical model is established considering that the glioma cells are of two phenotypes: migratory and proliferative. The evolution of the migratory cells is described by ...
Begley Dale A DA The Jackson Laboratory, Bar Harbor, ME, - - 2014
In recent years the scientific community has generated an ever-increasing amount of data from a growing number of animal models of human cancers. Much of these data come from genetically engineered mouse models. Identifying appropriate models for skin cancer and related relevant genetic data sets from an expanding pool of ...
Schiffner Susanne S University of Regensburg, Institute of Pathology, Molecular Pathology, Franz-Joseph-Strauss-Allee 11, 93053 Regensburg, - - 2014
Although rare, uveal melanoma (UM) is the most common primary intraocular tumor in adults. About half of UM patients develop metastatic disease typically in the liver and die within a short period, due to ineffective systemic therapies. UM has unique and distinct genetic features predictive of metastasis. Animal models are ...
Scheid Patrick P Central Institute of the Bundeswehr Medical Service, Laboratory of Medical Parasitology, Andernacherstr. 100, Koblenz, 56070, Germany, - - 2014
In this article, the results of a long effort to derive valuable phylogenetic data about an extraordinary spore-like infectious particle (endocytobiont) within host amoebae (Acanthamoeba sp.) recently isolated from the contact lens and the inflamed eye of a patient with keratitis are presented. The development of these endocytobionts has already ...
White Diana D University of Alberta, Edmonton, AB, Canada, - - 2014
In this paper, we construct a novel nonlocal transport model that describes the evolution of microtubules (MTs) as they interact with stationary distributions of motor proteins. An advection term accounts for directed MT transport (sliding due to motor protein action), and an integral term accounts for reorientation of MTs due ...
Anazawa Masahiro M Department of Environment and Energy, Tohoku Institute of Technology, Sendai , 982-8577, Japan, - - 2014
In order to clarify the theoretical relationship between individual behavior and population-level competition between two species with spatial correlation, this paper describes how discrete-time competition equations for the two species can be derived from local resource competition among individuals. Competition type of each species is either scramble, contest, or modified ...
Mei Suyu - - 2014
Human T-cell leukemia viruses (HTLV) tend to induce some fatal human diseases like Adult T-cell Leukemia (ATL) by targeting human T lymphocytes. To indentify the protein-protein interactions (PPI) between HTLV viruses and Homo sapiens is one of the significant approaches to reveal the underlying mechanism of HTLV infection and host ...
Sahneh Faryad Darabi FD Institute of Computational Comparative Medicine, Kansas State University, Manhattan, KS 66506, - - 2014
Aim: To assess the impact of biocorona kinetics on expected tissue distribution of nanoparticles (NPs) across species. Materials & methods: The potential fate of NPs in vivo is described through a simple and descriptive pharmacokinetic model using rate processes dependent upon basal metabolic rate coupled to dynamics of protein corona. ...
Pham H P HP Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Pathology and Cell Biology, Columbia University Medical Center and the New York-Presbyterian Hospital, New York, NY, - - 2014
Patients with abnormal placentation are hospitalized approximately 21 days prior to scheduled delivery due to risk of peri-partum bleeding. It is required to have at least one red blood cell (RBC) unit ready throughout hospitalization. This can be accomplished by performing a type and cross (T&C) every 72 h (traditional method) or ...
Ko Ming-Tse MT Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Kaohsiung, - - 2014
Allergic rhinitis (AR) is a common worldwide disease. Animal studies on AR were adopted in various investigations. However, animal studies simply aimed at establishing an animal model for AR have been seldom seen. The purpose of this study was to introduce an easy-to-establish experimental mouse model of AR. To develop ...
Thattai Mukund M National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, - - 2014
This is an exciting time to be an evolutionary biologist. Indeed, it is difficult to keep up with all the studies that fall under the broad category of "Evolution" since they span species, traits, and scales of organization. This special issue gives a flavor of exciting new approaches in evolutionary ...
de Almeida Valber Elias VE Centro de Ciência e Tecnologia, Laboratório de Química Analítica e Quimiometria (LQAQ), Universidade Estadual da Paraíba, CEP 58.429-500, Campina Grande, Paraíba, - - 2014
In this work, a new approach is proposed to verify the differentiating characteristics of five bacteria (Escherichia coli, Enterococcus faecalis, Streptococcus salivarius, Streptococcus oralis, and Staphylococcus aureus) by using digital images obtained with a simple webcam and variable selection by the Successive Projections Algorithm associated with Linear Discriminant Analysis (SPA-LDA). ...
Martínez Verónica S VS Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, - - 2014
Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as ...
Petzoldt Tibor T Technische Universität Chemnitz, Chemnitz, Germany. Electronic address: - - 2014
The identification of safe gaps between passing cars when crossing a street is a task most of us accomplish successfully on a daily basis. Objectively, how safe a specific gap is, is mainly dependent on how long it would take the approaching vehicle to arrive (time to arrival; TTA). Common ...
Greco Viviana V Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, - - 2014
Measurement of biochemical markers represents an important aid to clinicians in the early diagnosis and prognosis of neurological diseases. Many factors can contribute to increase the chances that a biomarkers study becomes successful. In a cerebrospinal fluid analysis (CSF), more than 84% of laboratory errors can be attributed to several ...
García Sánchez Carlos Eduardo CE Grupo de Investigación en Fluidos y Energía, Corporación Centro de Desarrollo Tecnológico del Gas, Parque Tecnológico UIS Guatiguará Km 2 vía Refugio, Piedecuesta, Santander, - - 2014
Flux Balance Analysis (FBA) is currently one of the most important and used techniques for estimation of metabolic reaction rates (fluxes). This mathematical approach utilizes an optimization criterion in order to select a distribution of fluxes from the feasible space delimited by the metabolic reactions and some restrictions imposed over ...
Greenberg Michael R MR EJ Bloustein School, Rutgers University, New Brunswick, NJ, - - 2014
This tutorial focuses on how to produce reliable and generalizable data from random-digit-dialing (RDD) landline and cell phone surveys. The article notes that RDD response rates have declined and explores the impact of this pronounced decline. The tutorial addresses order, response mode, and many other biases, sample size, cooperation and ...
Fernández Rosa R Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: - - 2014
Spiders constitute one of the most successful clades of terrestrial predators [1]. Their extraordinary diversity, paralleled only by some insects and mites [2], is often attributed to the use of silk, and, in one of the largest lineages, to stereotyped behaviors for building foraging webs of remarkable biomechanical properties [1]. ...
Wéra A-C AC Ion Beam Centre, University of Surrey, Guildford, Surrey GU2 7XH, - - 2014
It is well known that broad beam irradiation with heavy ions leads to variation in the number of hit(s) received by each cell as the distribution of particles follows the Poisson statistics. Although the nucleus area will determine the number of hit(s) received for a given dose, variation amongst its ...
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