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Palm Margriet M MM Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The - - 2015
Computational, cell-based models, such as the cellular Potts model (CPM), have become a widely used tool to study tissue formation. Most cell-based models mimic the physical properties of cells and their dynamic behavior, and generate images of the tissue that the cells form due to their collective behavior. Due to ...
Sykes John M JM 4th Zoological Health Program, Wildlife Conservation Society, Bronx Zoo, 2300 Southern Boulevard, Bronx, NY 10460, USA. Electronic address: - - 2015
The basic principles of hematology used in mammalian medicine can be applied to reptiles. The appearances of the blood cells are significantly different from those seen in most mammals, and vary with taxa and staining method used. Many causes for abnormalities of the reptilian hemogram are similar to those for ...
Spidlen Josef J Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, - - 2014
Identifying homogenous sets of cell populations in flow cytometry is an important process for sorting and selecting populations of interests for further data acquisition and analysis. Many computational methods are now available to automate this process, with several algorithms partitioning cells based on high-dimensional separation versus the traditional pairwise two-dimensional ...
Bruce Karen L KL School of Chemical and Physical Sciences, Flinders University, Sturt Road, Bedford Park, Adelaide, SA, 5042, - - 2014
Blooms of microscopic algae in our waterways are becoming an increasingly important environmental concern. Many are sources of harmful biotoxins that can lead to death in humans, marine life and birds. Additionally, their biomass can cause damage to ecosystems such as oxygen depletion, displacement of species and habitat alteration. Globally, ...
Wang Ling - - 2014
To discover new agents active against methicillin-resistant Staphylococcus aureus (MRSA), in silico models derived from 5,451 cell-based anti-MRSA assay data were developed using four machine learning methods, including naïve Bayesian, support vector machine (SVM), recursive partitioning (RP), and k-nearest neighbors (k-NN). A total of 876 models have been constructed based ...
Howard Jonathon J Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 - - 2014
Quantitative biology is a hot area, as evidenced by the recent establishment of institutes, graduate programs, and conferences with that name. But what is quantitative biology? What should it be? And how can it contribute to solving the big questions in biology? The past decade has seen very rapid development ...
Phair Robert D RD Integrative Bioinformatics, Inc., Mountain View, CA 94041 - - 2014
Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) ...
Gölgeli Matur Meltem M 1 Institute of Computational Biology, Helmholtz Zentrum München , Neuherberg, Germany - - 2014
Abstract Quorum sensing, a special kind of cell-cell communication, has originally been described for well-mixed homogeneous bacterial cultures. However, recent perception supports its ecological relevance for spatially heterogeneous distributed cells, like colonies and biofilms. New experimental techniques allow for single cell analysis under these conditions, which is crucial to understanding ...
Abbas Syed Saiden - - 2014
Millions of cells are present in thousands of images created in high-throughput screening (HTS). Biologists could classify each of these cells into a phenotype by visual inspection. But in the presence of millions of cells this visual classification task becomes infeasible. Biologists train classification models on a few thousand visually ...
Nair Richard R School of Geosciences, University of Edinburgh, Crew Building, West Mains Road, Edinburgh EH9 3JN, Midlothian, Scotland - - 2014
Stem injection techniques can be used to introduce (15)N into trees to overcome a low variation in natural abundance and label biomass with a distinct (15)N signature, but have tended to target small and young trees, of a variety of species, with little replication. We injected 98 atom% (15)N ammonium ...
Hickling Timothy P TP Pharmacokinetics, Dynamics and Metabolism - New Biological Entities, Pfizer, Andover, MA, - - 2014
A key role of B cells in the mammalian immune response is the generation of antibodies that serve to protect the organism against antigenic challenges. The same process may also be detrimental in the context of autoimmunity. Several modeling approaches have been applied to this aspect of the immune response, ...
Higa Masaru M Mechanical Engineering, University of Hyogo, Shosha 21267, Himeji, Hyogo, 671-2280, Japan, - - 2014
This study proposes novel optimized stem geometry with low stress values in the cement using a finite element (FE) analysis combined with an optimization procedure and experimental measurements of cement stress in vitro. We first optimized an existing stem geometry using a three-dimensional FE analysis combined with a shape optimization ...
Ramm Steven A SA Evolutionary Biology, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany - - 2014
Spermatogenesis is a long and complex process that, despite the shared overall goal of producing the male gamete, displays striking amounts of interspecific diversity. In this review, we argue that sperm competition has been an important selection pressure acting on multiple aspects of spermatogenesis, causing variation in the number and ...
Malek Mehrnoush M Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, - - 2014
Summary: flowDensity facilitates reproducible, high-throughput analysis of flow cytometry data by automating a predefined manual gating approach. The algorithm is based on a sequential bivariate gating approach that generates a set of predefined cell populations. It chooses the best cut-off for individual markers using characteristics of the density distribution. The ...
Legg David A DA Oxford University Museum of Natural History, Parks Road, Oxford, OX1 3PW, UK, - - 2014
The morphology of the arthropod Sanctacaris uncata, from the Middle Cambrian Burgess Shale of Canada, is reinterpreted based on a restudy of previously described material. Although originally considered a chelicerate-like arthropod, these affinities were dismissed based primarily on interpretations of the anterior appendages and hypotheses which considered the megacheirans ('great-appendage' ...
Doutres O O GAUS, Department of Mechanical Engineering, Universite de Sherbrooke, Quebec J1K 2R1, - - 2014
This paper deals with the prediction of the macroscopic sound absorption behavior of highly porous polyurethane foams using two unit-cell microstructure-based models recently developed by Doutres, Atalla, and Dong [J. Appl. Phys. 110, 064901 (2011); J. Appl. Phys. 113, 054901 (2013)]. In these models, the porous material is idealized as ...
Font Vivanco David - - 2014
This article presents a stepwise, refined and practical analytical framework to model the microeconomic environmental rebound effect (ERE) stemming from cost differences of electric cars in terms of changes in multiple life cycle environmental indicators. The analytical framework is based on marginal consumption analysis and hybrid life cycle assessment (LCA). ...
Barrett Paul M PM Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK - - 2014
Current characterizations of early dinosaur evolution are incomplete: existing palaeobiological and phylogenetic scenarios are based on a fossil record dominated by saurischians and the implications of the early ornithischian record are often overlooked. Moreover, the timings of deep phylogenetic divergences within Dinosauria are poorly constrained owing to the absence of ...
Li Mingji M The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, 2970, Hørsholm, - - 2014
Synthetic biology and metabolic engineering enable generation of novel cell factories that efficiently convert renewable feedstocks into biofuels, bulk and fine chemicals, thus creating the basis for biosustainable economy independent on fossil resources. While over a hundred proof-of-concept chemicals have been made in yeast, only a very small fraction of ...
Hacke Uwe G UG Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, - - 2014
The standard centrifuge method has been frequently used to measure vulnerability to xylem cavitation. This method has recently been questioned. It was hypothesized that open vessels lead to exponential vulnerability curves, which were thought to be indicative of measurement artifact. We tested this hypothesis in stems of olive (Olea europea) ...
Putzu Lorenzo L Department of Mathematics and Computer Science, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy. Electronic address: - - 2014
The counting and classification of blood cells allow for the evaluation and diagnosis of a vast number of diseases. The analysis of white blood cells (WBCs) allows for the detection of acute lymphoblastic leukaemia (ALL), a blood cancer that can be fatal if left untreated. Currently, the morphological analysis of ...
Yang Peng - - 2014
In this paper, a novel multiple sub-models maintenance technique, named maintaining and processing sub-models (MAPS), is proposed. MAPS aims to enhance the ability of estimation of distribution algorithms (EDAs) on multimodal problems. The advantages of MAPS over the existing multiple sub-models based EDAs stem from the explicit detection of the ...
Wang Ruifei R Chalmers University of Technology, Department of Chemical and Biological Engineering, Division of Life Sciences - Industrial Biotechnology, SE-412 96 Göteborg, - - 2014
Fed-batch simultaneous saccharification and fermentation (SSF) is a feasible option for bioethanol production from lignocellulosic raw materials at high substrate concentrations. In this work, a segregated kinetic model was developed for simulation of fed-batch simultaneous saccharification and co-fermentation (SSCF) of steam-pretreated birch, using substrate, enzymes and cell feeds. The model ...
van Bodegom Peter M PM Department of Ecological Science, Section of Systems Ecology, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands - - 2014
Dynamic Global Vegetation Models (DGVMs) are indispensable for our understanding of climate change impacts. The application of traits in DGVMs is increasingly refined. However, a comprehensive analysis of the direct impacts of trait variation on global vegetation distribution does not yet exist. Here, we present such analysis as proof of ...
Paczesny Sophie S Indiana University School of Medicine, Indianapolis, IN, United States of - - 2014
Biomarkers have the potential to improve diagnosis and prognosis, facilitate targeted treatment, and reduce health care costs. Thus, there is great hope that biomarkers will be integrated in all clinical decisions in the near future. A decade ago, the biomarker field was launched with great enthusiasm because mass spectrometry revealed ...
Häkkinen Antti A Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Tampere, - - 2014
MS2-GFP-tagging of RNA is currently the only method to measure intervals between consecutive transcription events in live cells. For this, new transcripts must be accurately detected from intensity time traces. We present a novel method for automatically estimating RNA numbers and production intervals from temporal data of cell fluorescence intensities ...
Croft Wayne W School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, - - 2014
We present a novel parameter identification algorithm for the estimation of parameters in models of cell motility using imaging data of migrating cells. Two alternative formulations of the objective functional that measures the difference between the computed and observed data are proposed and the parameter identification problem is formulated as ...
Panchal Mitesh B MB Vibration and Noise Control Laboratory, Mechanical and Industrial Engineering Department, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India. - - 2014
In this study, the feasibility of single walled boron nitride nanotube (SWBNNT)-based biosensors has been ensured considering the continuum modelling-based simulation approach, for mass-based detection of various bacterium/viruses. Various types of bacterium or viruses have been taken into consideration at the free-end of the cantilevered configuration of the SWBNNT, as ...
Panchal Mitesh B MB Vibration and Noise Control Laboratory, Mechanical and Industrial Engineering Department, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India. - - 2014
The unprecedented dynamic characteristics of nanoelectromechanical systems make them suitable for nanoscale mass sensing applications. Owing to superior biocompatibility, boron nitride nanotubes (BNNTs) are being increasingly used for such applications. In this study, the feasibility of single walled BNNT (SWBNNT)-based bio-sensor has been explored. Molecular structural mechanics-based finite element (FE) ...
Xavier Joana C JC Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Braga, Portugal Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, - - 2014
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we ...
Reji G - - 2014
Rice stem borer is an important insect pest causing severe damage to rice crop in India. The relationship between weather parameters such as maximum (T(max)) and minimum temperature (T(min)), morning (RH1) and afternoon relative humidity (RH2) and the severity of stem borer damage (SB) were studied. Multiple linear regression analysis ...
Johnston Stuart T ST School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, - - 2014
Quantifying the impact of biochemical compounds on collective cell spreading is an essential element of drug design, with various applications including developing treatments for chronic wounds and cancer. Scratch assays are a technically simple and inexpensive method used to study collective cell spreading; however, most previous interpretations of scratch assays ...
Holmes Tyson H TH Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 401 Quarry Road, Stanford, CA, 94305-5718, USA. Electronic address: - - 2014
Bayesian estimation techniques offer a systematic and quantitative approach for synthesizing data drawn from the literature to model immunological systems. As detailed here, the practitioner begins with a theoretical model and then sequentially draws information from source data sets and/or published findings to inform estimation of model parameters. Options are ...
Feher Kristen K Deutsches Rheuma-Forschungszentrum, Berlin D-10117, Germany. - - 2014
The tried and true approach of flow cytometry data analysis is to manually gate on each biomarker separately, which is feasible for a small number of biomarkers, e.g. < 5. However, this rapidly becomes confusing as the number of biomarker increases. Furthermore, multivariate structure is not taken into account. Recently, ...
Engel Konrad K Institut für Mathematik, Universität Rostock, 18057, Rostock, Germany, - - 2014
The multichannel recordings of signals of many cells cultivated on a multielectrode array (MEA) impose some challenging problems. A meanwhile classic problem is the separation of the recordings of a single electrode into classes of recordings where each class is caused by a single cell. This is the well-known spike ...
Higham Tom T Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology &the History of Art, University of Oxford, Oxford OX1 3QY, - - 2014
The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the ...
Buffa R R Department of Environmental and Life Sciences, University of Cagliari, Cittadella Universitaria, Monserrato, - - 2014
This review is directed to define the efficacy of bioelectrical impedance vector analysis (BIVA) for assessing two-compartment body composition. A systematic literature review using MEDLINE database up to 12 February 2014 was performed. The list of papers citing the first description of BIVA, obtained from SCOPUS, and the reference lists ...
Zhang Ying - - 2014
A lack of X-ray or NMR structures of proteins inhibits their further study and characterization, motivating the development of new ways of analyzing structural information without crystal structures. The combination of hydrogen deuterium exchange mass spectrometry (HDX-MS) data in conjunction with homology modeling (HM) can provide improved structure and mechanistic ...
Lee Mong-Chuan MC Institute of Biotechnology, Central Taiwan University of Science and Technology, 666, Bu-zih Road, Bei-tun District, Taichung, 40601, - - 2014
A mathematical model system was derived to describe the kinetics of ammonium nitrification in a fixed biofilm reactor using dewatered sludge-fly ash composite ceramic particle as a supporting medium. The model incorporates diffusive mass transport and Monod kinetics. The model was solved using a combination of the orthogonal collocation method ...
Camina Martín M A MA Area of Nutrition and Food Science, Faculty of Medicine, Universidad de Valladolid, Valladolid, - - 2014
In clinical practice, geriatric nutritional assessment usually includes nutritional screening, a simple anthropometric assessment, measurement of various biochemical parameters, such as serum albumin, and sometimes (not always) body composition analysis (BCA). However, there is a high prevalence of undiagnosed malnutrition in patients with dementia. Several factors contribute to this situation; ...
Sack Lawren L Department of Ecology and Evolution, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, California 90095, USA - - 2014
It has been recently proposed that leaf vein length per area ( VLA : ) is the major determinant of leaf mass per area ( LMA : ), and would thereby determine other traits of the leaf economic spectrum (LES), such as photosynthetic rate per mass (A mass), nitrogen concentration ...
Pernet C R CR Centre for Clinical Brain Sciences, Neuroimaging Sciences, University of Edinburgh, Edinburgh, UK. Electronic address: - - 2014
In recent years, analyses of event related potentials/fields have moved from the selection of a few components and peaks to a mass-univariate approach in which the whole data space is analysed. Such extensive testing increases the number of false positives and correction for multiple comparisons is needed. Here we review ...
Traill Lochran W LW Division of Biology, Imperial College London, Silwood Park, Berkshire SL5 7PY, United Kingdom;School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Wits 2050, South Africa; and lochran.traill@gmail.com - - 2014
Selective harvest, such as trophy hunting, can shift the distribution of a quantitative character such as body size. If the targeted character is heritable, then there will be an evolutionary response to selection, and where the trait is not, then any response will be plastic or demographic. Identifying the relative ...
Tarabini Marco M a Department of Mechanical Engineering , Politecnico di Milano , Lecco , - - 2014
The human response to vibration is typically studied using linear estimators of the frequency response function, although different literature works evidenced the presence of non-linear effects in whole-body vibration response. This paper analyses the apparent mass of standing subjects using the conditioned response techniques in order to understand the causes ...
Giannini Norberto Pedro NP Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Tucumán, Argentina; Universidad Nacional de Tucumán, Facultad de Ciencias Naturales e Instituto Miguel Lillo, San Miguel de Tucumán, Tucumán, Argentina; Department of Mammalogy, American Museum of Natural History, New York, New - - 2014
Following the embryonic period of organogenesis, most development is allometric growth, which is thought to produce most of the evolutionary morphological divergence between related species. Bivariate or multivariate coefficients of allometry are used to describe quantitative developmental data and are comparable across taxa; as such, these coefficients are amenable to ...
Lalonde Trent L TL Department of Applied Statistics, University of Northern Colorado, Greeley, CO 80639, - - 2014
When analyzing longitudinal data, it is essential to account both for the correlation inherent from the repeated measures of the responses as well as the correlation realized on account of the feedback created between the responses at a particular time and the predictors at other times. As such one can ...
Melià P P Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, via Ponzio 34/5, 20133 Milano, - - 2014
A simple approach is proposed to fit a body growth model for the European eel Anguilla anguilla to data-poor case studies. The model is a modified von Bertalanffy curve allowing for delayed sex determination and sexual dimorphism. The proposed procedure provides preliminary estimates of model parameters on the basis of ...
Yanosky Jeff D - - 2014
Exposure to atmospheric particulate matter (PM) remains an important public health concern, although it remains difficult to quantify accurately across large geographic areas with sufficiently high spatial resolution. Recent epidemiologic analyses have demonstrated the importance of spatially- and temporally-resolved exposure estimates, which show larger PM-mediated health effects as compared to ...
Christensen Krista K National Center for Environmental Assessment, Office of Research and Development, United States Environmental Protection Agency, Washington, DC, - - 2014
The use of human biomonitoring data to characterize exposure to environmental contaminants in epidemiology studies has expanded greatly in recent years. Substantial variability in effect measures may arise when using different exposure metrics for a given contaminant, and it is often not clear which metric is the best surrogate for ...
Legg Benjamin Adam - - 2014
Aggregation impacts the reactivity, colloidal stability, and transport behavior of nanomaterials, yet methods to characterize basic structural features of aggregates are limited. Here, cryo-transmission electron microscope (Cryo-TEM) based tomography is utilized as a method for directly imaging fragile aggregates of nanoparticles in aqueous suspension and an approach for extracting quantitative ...
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