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Sacchi Lucia L Dipartimento di Ingegneria Industriale e dell'Informazione, Università degli Studi di Pavia, Via Ferrata 1, Pavia, 27100, Italy, - - 2015
In recent years, data coming from hospital information systems (HIS) and local healthcare organizations have started to be intensively used for research purposes. This rising amount of available data allows reconstructing the compete histories of the patients, which have a strong temporal component. This chapter introduces the major challenges faced ...
Mak Rachel R Department of Physics & Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. - - 2014
X-Ray absorption spectromicroscopy provides rich information on the chemical organization of materials down to the nanoscale. However, interpretation of this information in studies of "natural" materials such as biological or environmental science specimens can be complicated by the complex mixtures of spectroscopically complicated materials present. We describe here the shortcomings ...
Nandi Anjan K AK Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India - - 2014
Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical ...
Wilson Laura A B LA School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, - - 2014
Keeping pace with the forward progression of evolutionary developmental studies and their trajectory toward ever-more integrative and broad-scale study presents a challenge for researchers from diverse disciplines. Increasing the capacity for discourse and opening opportunity to further interdisciplinary work is highly desirable, and one way that activities can be hindered ...
Farley Kevin J KJ Department of Civil and Environmental Engineering, Manhattan College, Riverdale, New York, - - 2014
As part of the Metal Mixture Modeling Evaluation (MMME) project, models were developed by the National Institute of Advanced Industrial Science and Technology (Japan), the U.S. Geological Survey (USA), HDR׀HydroQual, Inc. (USA), and the Centre for Ecology and Hydrology (UK) to address the effects of metal mixtures on biological responses ...
Veltman Karin - - 2014
ToxicoKinetic ToxicoDynamic (TKTD) models are considered essential tools to further advance acute toxicity prediction of metals for a range of species and exposure conditions, but they are currently underutilized. We present a mechanistic TKTD model for acute toxicity prediction of silver (Ag) in freshwater organisms. In this new approach, we ...
Jones Graham G Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, - - 2014
The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches of the species tree. None of the available approaches so far have simultaneously co-estimated all the relevant parameters in the model, without restricting the parameter space ...
Marcatili S S UMR 1037 INSERM-Centre de Recherche en Cancérologie de Toulouse, Toulouse, - - 2014
The accuracy of radiopharmaceutical absorbed dose distributions computed through Monte Carlo (MC) simulations is mostly limited by the low spatial resolution of 3D imaging techniques used to define the simulation geometry. This issue also persists with the implementation of realistic hybrid models built using polygonal mesh and/or NURBS as they ...
Madden Judith C JC School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom St., Liverpool L3 3AF, UK - - 2014
There is a long history of using both in silico and in vitro methods to predict adverse effects in humans and environmental species where toxicity data are lacking. Currently, there is a great deal of interest in applying these methods to the development of so-called 'adverse outcome pathway' (AOP) constructs. ...
Kyoda Koji K Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, - - 2014
Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools ...
Koskella Britt B BioSciences, University of Exeter, Penryn Campus, Tremough, Cornwall, TR10 9EZ, UK. - - 2014
Explaining the generation and maintenance of biodiversity is a central aim of evolutionary biology. This requires the integration of studies focused on explaining within-population diversity through to the organization of biodiversity at the ecosystem level. The combination of such comparative studies in nature with those employing experimental evolution in the ...
Donoso-Bravo Andres A a Escuela de Ingeniería Bioquímica, Facultad de Ingeniería , Pontificia Universidad Católica de Valparaíso . General Cruz 34, Valparaíso , - - 2014
Abstract Two-phase anaerobic systems are being increasingly implemented for the treatment of both sewage sludge and organic fraction of municipal solid waste. Despite the good amount of mathematical models in anaerobic digestion, few have been applied in two phase systems. In this study, a three-reaction mechanistic model has been developed, ...
Neumaier P F-X PF German Aerospace Center, Institute of Optical Sensor Systems, Rutherfordstr. 2, 12489 Berlin, Germany. Philipp.Neumaier@dlr.de - - 2014
We describe a spectrometer consisting of a vector network analyzer, a gas absorption cell, and a quasi-optical bench that acquires terahertz spectra of gaseous substances and mixtures. We tested volatile organic compounds that are medical biomarkers or chemicals which can be found on the US Environment Protection Agency list of ...
Granato Daniel D RIKILT - Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700, AE, Wageningen, The Netherlands; Food Quality and Design Group, Wageningen University and Research Centre, P. O. Box 17, 6700, AA, Wageningen, The Netherlands; Departament of Food Engineering, State University of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, - - 2014
Organic, biodynamic, and conventional purple grape juices (PGJ; n = 79) produced in Brazil and Europe were characterized by volatile organic compounds (m/z 20-160) measured by proton transfer reaction mass spectrometry (PTR-MS) and classification models were built using supervised statistical techniques. K-nearest neighbours (KNN) and soft independent modelling of class analogy (SIMCA) ...
Tadmor Eitan E Center for Scientific Computation and Mathematical Modeling, University of Maryland, College Park, MD 20742, USA Department of Mathematics, University of Maryland, College Park, MD 20742, USA Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA - - 2014
We study the large-time behaviour of Eulerian systems augmented with non-local alignment. Such systems arise as hydrodynamic descriptions of agent-based models for self-organized dynamics, e.g. Cucker & Smale (2007 IEEE Trans. Autom. Control 52, 852-862. (doi:10.1109/TAC.2007.895842)) and Motsch & Tadmor (2011 J. Stat. Phys. 144, 923-947. (doi:10.1007/s10955-011-0285-9)) models. We prove ...
Juhász Z Z Department of Complex Systems, Research Centre for Natural Sciences of the HAS, Budapest, - - 2014
The goal of this study is to show two new clustering and visualising techniques developed to find the most typical clusters of 18-dimensional Y chromosomal haplogroup frequency distributions of 90 Western Eurasian populations. The first technique called "self-organizing cloud (SOC)" is a vector-based self-learning method derived from the Self Organising ...
Duan Yuping - - 2014
An interactive surgical simulation system needs to meet three main requirements, speed, accuracy and stability. In this paper, we present a stable and accurate method for animating mass-spring systems in real-time. An integration scheme derived from explicit integration is used to obtain interactive realistic animation for a multi-object environment. We ...
Speck-Planche Alejandro - - 2014
Nanomaterials have revolutionized modern science and technology due to their multiple applications in engineering, physics, chemistry, and biomedicine. Nevertheless, the use and manipulation of nanoparticles (NPs) can bring serious damages to living organisms and their ecosystems. For this reason, ecotoxicity and cytotoxicity assays are of special interest, in order to ...
Kimura Hiroshi H Institute of Industrial Science, the University of Tokyo, Tokyo, Japan Department of Mechanical Engineering, Tokai University, Kanagawa, Japan Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, - - 2014
Testing of drug effects and cytotoxicity by using cultured cells has been widely performed as an alternative to animal testing. However, the estimation of pharmacokinetics by conventional cell-based assay methods is difficult because of the inability to evaluate multiorgan effects. An important challenge in the field is to mimic the ...
Sutton N J NJ Ecology and Evolutionary Biology Department, The University of Tennessee, Knoxville, 569 Dabney Hall, 1416 Circle Drive, Knoxville, TN, 37996, - - 2014
Facing tight resource constraints, conservation organizations must allocate funds available for habitat protection as effectively as possible. Often, they combine spatially referenced economic and biodiversity data to prioritize land for protection. We tested how sensitive these prioritizations could be to differences in the spatial grain of these data by demonstrating ...
Szolnoki Attila A http://orcid.org/0000-0002-0907-0406 Institute of Technical Physics and Materials Science, Research Centre for Natural Sciences, Hungarian Academy of Sciences, PO Box 49, 1525 Budapest, Hungary - - 2014
Rock is wrapped by paper, paper is cut by scissors and scissors are crushed by rock. This simple game is popular among children and adults to decide on trivial disputes that have no obvious winner, but cyclic dominance is also at the heart of predator-prey interactions, the mating strategy of ...
Fronhofer Emanuel A EA Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, - - 2014
1.Movement and dispersal are critical processes for almost all organisms in natural populations. Understanding their causes and consequences is therefore of high interest. While both theoretical and empirical work suggests that dispersal, more exactly emigration, is plastic and may be a function of local population density, the functional relationship between ...
Wodke Judith A H JA EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain Theoretical Biophysics, Humboldt-Universitt zu Berlin, Invalidenstr 42, 10115 Berlin, Germany guglielmo.roma@crg.eu - - 2014
MyMpn (http://mympn.crg.eu) is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. Due to its small size, its ability to grow in vitro, and the amount of data produced over the past decades, M. pneumoniae is an interesting model organisms ...
McLeod Anne M AM Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset, Windsor, ON, N9B 3P4, - - 2014
Trophic magnification factors (TMFs) provide a method of assessing chemical biomagnification in food webs and are increasingly being used by policy makers to screen emergent chemicals. Recent reviews have encouraged the use of bioaccumulation models as screening tools for assessing TMFs for emergent chemicals of concern. The present study used ...
Cisek Paul P Groupe de Recherche sur le Système Nerveux Central (GRSNC), Département de Neuroscience, Université de Montréal, C.P. 6128 Succursale Centre-ville, Montréal, Québec, Canada H3C 3J7 - - 2014
Neurophysiological studies of decision-making have focused primarily on elucidating the mechanisms of classic economic decisions, for which the relevant variables are the values of expected outcomes and action is simply the means of reporting the selected choice. By contrast, here we focus on the particular challenges of embodied decision-making faced ...
Yu Yun Y Departments of Computer Science and nakhleh@cs.rice.edu - - 2014
Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method ...
Peng Ying Y Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA peng.ying@mayo.edu - - 2014
Recent advances in the targeted modification of complex eukaryotic genomes have unlocked a new era of genome engineering. From the pioneering work using zinc-finger nucleases (ZFNs), to the advent of the versatile and specific TALEN systems, and most recently the highly accessible CRISPR/Cas9 systems, we now possess an unprecedented ability ...
Pinho Ricardo R Department of Biology, Stanford University, Stanford, California, United States of America; PhD Program in Computational Biology, Instituto Gulbenkian de Ciência, Oeiras, - - 2014
Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. Moreover, how specific ...
Rummel John D JD 1 Department of Biology, East Carolina University , Greenville, North Carolina, USA - - 2014
Abstract A committee of the Mars Exploration Program Analysis Group (MEPAG) has reviewed and updated the description of Special Regions on Mars as places where terrestrial organisms might replicate (per the COSPAR Planetary Protection Policy). This review and update was conducted by an international team (SR-SAG2) drawn from both the ...
Simon Steven L SL a  Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, - - 2014
In this article, we describe recent methodological enhancements and findings from the dose reconstruction component of a study of health risks among U.S. radiologic technologists. An earlier version of the dosimetry published in 2006 used physical and statistical models, literature-reported exposure measurements for the years before 1960, and archival personnel ...
Beisken Stephan S European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Welcome Trust, Genome Campus, Hinxton, CB10 1SD, Cambridgeshire, - - 2014
Small molecules within biological systems provide powerful insights into the biological roles, processes and states of organisms. Metabolomics is the study of the concentrations, structures and interactions of these thousands of small molecules, collectively known as the metabolome. Metabolomics is at the interface between chemistry, biology, statistics and computer science, ...
Beese Allison M AM Department of Mechanical Engineering, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3111, United - - 2014
Studies of carbon nanotube (CNT) based composites have been unable to translate the extraordinary load-bearing capabilities of individual CNTs to macroscale composites such as yarns. A key challenge lies in the lack of understanding of how properties of filaments and interfaces across yarn hierarchical levels govern the properties of macroscale ...
Couteron P P http://orcid.org/0000-0002-4627-1696 IRD, UMR AMAP, c/o Cirad, 34000 Montpellier, France - - 2014
We propose here to interpret and model peculiar plant morphologies (cushions and tussocks) observed in the Andean Altiplano as localized structures. Such structures resulting in a patchy, aperiodic aspect of the vegetation cover are hypothesized to self-organize thanks to the interplay between facilitation and competition processes occurring at the scale ...
Cunningham Fiona F http://orcid.org/0000-0002-7445-2419 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, - - 2014
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using ...
Lekschas Fritz F Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany - - 2014
Advancing technologies generate large amounts of molecular and phenotypic data on cells, tissues and organisms, leading to an ever-growing detail and complexity while information retrieval and analysis becomes increasingly time-consuming. The Semantic Body Browser is a web application for intuitively exploring the body of an organism from the organ to ...
Wong Yong Chiat YC 1Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 2Saw Swee Hock School of Public Health, National University of - - 2014
Traumatic injury remains a major cause of morbidity and mortality worldwide and patients who survived the initial insult are susceptible to an overwhelming inflammatory dysfunction that will lead to acute coagulopathy of trauma (ACOT) and subsequently multiple organ dysfunction syndrome (MODS). MODS related scoring systems, while they measure organ dysfunction, ...
Qian Jinjie J Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, China. - - 2014
With the help of the ligand-oriented method, we have successfully embedded independent copper-based units into the indium-organic framework system for the first time, in which the Cu4I4 clusters and In3O(CO2)6 clusters coexist. This heterometallic cluster-based framework has a large porosity with extra-open channels along the c-axis, and its sorption capacity ...
Fife Gwendoline R GR Stichting Restauratie Atelier Limburg, Avenue Ceramique 224, 6221 KX, Maastricht, the - - 2014
Typical experiments conducted with single-sided NMR are incapable of unique chemical identification and, thus, often rely on comparative measurements in scientific study. However, cultural heritage objects have unique natures and histories, making a genuine 'control' sample a rarity and complicating many scientific investigations. In this paper, we present some comparative ...
Carter Laura J - - 2014
Current guidelines for determining bioconcentration factors (BCF) and uptake and depuration rate constants require labour intensive studies with large numbers of organisms. A minimised approach has recently been proposed for fish BCF studies but its applicability to other taxonomic groups is unknown. In this study, we therefore evaluate the use ...
Jones Timothy Deryck - - 2014
The first dynamic model of dissolved organic carbon (DOC) export in streams derived directly from high frequency (sub-hourly) observations sampled at a regular interval through contiguous storms is presented. The optimal model, identified using the recently developed RIVC algorithm, captured the rapid dynamics of DOC load from 15-minute monitored rainfall ...
Pearcy Nicole N School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK. - - 2014
At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models. Metabolic networks, in particular, are fundamental to the proper functioning of many important biological processes, and thus, have been widely studied over ...
Wang Chen - - 2014
The presence of inorganic salts significantly influences the partitioning behavior of organic compounds between environmentally relevant aqueous phases, such as sea water or aqueous aerosol, and other, non-aqueous phases (gas phase, organic phase, etc.). In this study, salting-out coefficients (or Setschenow constants) (KS [M-1]) for 38 diverse neutral compounds in ...
Liu Li - - 2014
Pesticides and their degradation products occur ubiquitously in natural aquatic environments at trace concentrations (μg L-1 and lower). Microbial biodegradation processes have long been known to contribute to the attenuation of pesticides in contaminated environments. However, challenges remain in developing engineered remediation strategies for pesticide-contaminated environments because the fundamental processes ...
Hamann Andreas A Department of Renewable Resources, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, 751 General Services Building, Edmonton, AB, T6G 2H1, - - 2014
The velocity of climate change is an elegant analytical concept that can be used to evaluate the exposure of organisms to climate change. In essence, one divides the rate of climate change by the rate of spatial climate variability to obtain a speed at which species must migrate over the ...
Liotta Flavia F a Department of Civil and Mechanical Engineering , University of Cassino and the Southern Lazio , via Di Biasio 43, 03043 Cassino (FR) , Italy - - 2014
Abstract The role of Total Solids (TS) content in anaerobic digestion of selected complex organic matter, e.g. rice straw and food waste, was investigated. A range of TS from wet (4.5%) to dry (23%) was evaluated. A modified version of the Anaerobic Digestion Model No.1 for complex organic substrate is ...
Witten Tarynn M TM Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Va., - - 2015
This chapter will briefly address the history of systems biology and complexity theory and its use in understanding the dynamics of aging at the 'omic' level of biological organization. Using the idea of treating a biological organism like a network, we will examine how network mathematics, particularly graph theory, can ...
Mulvaney Shawn P SP Chemistry Division, U.S. Naval Research Laboratory , Washington, DC 20375, United - - 2014
The world is filled with widely varying chemical, physical, and biological stimuli. Over millennia, organisms have refined their senses to cope with these diverse stimuli, becoming virtuosos in differentiating closely related antigens, handling extremes in concentration, resetting the spent sensing mechanisms, and processing the multiple data streams being generated. Nature ...
Karpinka J Brad JB University of Calgary-Computer Science, Calgary, Alberta, - - 2014
Xenbase (http://www.xenbase.org), the Xenopus frog model organism database, integrates a wide variety of data from this biomedical model genus. Two closely related species are represented: the allotetraploid Xenopus laevis that is widely used for microinjection and tissue explant-based protocols, and the diploid Xenopus tropicalis which is used for genetics and ...
Andersen Nina Blom NB Roskilde University, Denmark - - 2014
This article discusses how residents in a local area contributed to the construction of knowledge in regard to scientific assessments in relation to a fire in a storage dump of burnable waste. Building on analytical concepts primarily from Social Worlds theory as well as some concepts from Actor-Network Theory, the ...
Bray Dennis D Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, - - 2014
Are we close to a complete inventory of living processes so that we might expect in the near future to reproduce every essential aspect necessary for life? Or are there mechanisms and processes in cells and organisms that are presently inaccessible to us? Here I argue that a close examination ...
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