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Spatial dependence analysis

K M Meiburger, S Y Nam, E Chung, L J Suggs, S Y Emelianov, F Molinari
Blood vessels are the only system to provide nutrients and oxygen to every part of the body. Many diseases can have significant effects on blood vessel formation, so that the vascular network can be a cue to assess malicious tumor and ischemic tissues. Various imaging techniques can visualize blood vessel structure, but their applications are often constrained by either expensive costs, contrast agents, ionizing radiations, or a combination of the above. Photoacoustic imaging combines the high-contrast and spectroscopic-based specificity of optical imaging with the high spatial resolution of ultrasound imaging, and image contrast depends on optical absorption...
November 21, 2016: Physics in Medicine and Biology
Krzysztof Fujarewicz, Krzysztof Lakomiec
We investigate a spatial model of growth of a tumor and its sensitivity to radiotherapy. It is assumed that the radiation dose may vary in time and space, like in intensity modulated radiotherapy (IMRT). The change of the final state of the tumor depends on local differences in the radiation dose and varies with the time and the place of these local changes. This leads to the concept of a tumor's spatiotemporal sensitivity to radiation, which is a function of time and space. We show how adjoint sensitivity analysis may be applied to calculate the spatiotemporal sensitivity of the finite difference scheme resulting from the partial differential equation describing the tumor growth...
December 1, 2016: Mathematical Biosciences and Engineering: MBE
Allison C Nugent, Bruce Luber, Frederick W Carver, Stephen E Robinson, Richard Coppola, Carlos A Zarate
Recently, independent components analysis (ICA) of resting state magnetoencephalography (MEG) recordings has revealed resting state networks (RSNs) that exhibit fluctuations of band-limited power envelopes. Most of the work in this area has concentrated on networks derived from the power envelope of beta bandpass-filtered data. Although research has demonstrated that most networks show maximal correlation in the beta band, little is known about how spatial patterns of correlations may differ across frequencies...
October 22, 2016: Human Brain Mapping
Yanling Zhang, Aizhi Liu, Changyin Sun
For large quantities of spatial models, the multi-strategy selection under weak selection is the sum of two competition terms: the pairwise competition and the competition of multiple strategies with equal frequency. Two parameters σ1 and σ2 quantify the dependence of the multi-strategy selection on these two terms, respectively. Unlike previous studies, we here do not require large populations for calculating σ1 and σ2, and perform the first quantitative analysis of the effect of migration on them in group-structured populations of any finite sizes...
October 21, 2016: Scientific Reports
Mutlu Mete, Unal Sakoglu, Jeffrey S Spence, Michael D Devous, Thomas S Harris, Bryon Adinoff
BACKGROUND: Neuroimaging studies have yielded significant advances in the understanding of neural processes relevant to the development and persistence of addiction. However, these advances have not explored extensively for diagnostic accuracy in human subjects. The aim of this study was to develop a statistical approach, using a machine learning framework, to correctly classify brain images of cocaine-dependent participants and healthy controls. In this study, a framework suitable for educing potential brain regions that differed between the two groups was developed and implemented...
October 6, 2016: BMC Bioinformatics
Matthieu Barbier, James R Watson
Predators of all kinds, be they lions hunting in the Serengeti or fishermen searching for their catch, display various collective strategies. A common strategy is to share information about the location of prey. However, depending on the spatial characteristics and mobility of predators and prey, information sharing can either improve or hinder individual success. Here, our goal is to investigate the interacting effects of space and information sharing on predation efficiency, represented by the expected rate at which prey are found and consumed...
October 2016: PLoS Computational Biology
Udo A Ernst, Alina Schiffer, Malte Persike, Günter Meinhardt
Processing natural scenes requires the visual system to integrate local features into global object descriptions. To achieve coherent representations, the human brain uses statistical dependencies to guide weighting of local feature conjunctions. Pairwise interactions among feature detectors in early visual areas may form the early substrate of these local feature bindings. To investigate local interaction structures in visual cortex, we combined psychophysical experiments with computational modeling and natural scene analysis...
2016: Frontiers in Systems Neuroscience
Raphael Gasper, Isabelle Effenberger, Piotr Kolesinski, Barbara Terlecka, Eckhard Hofmann, Andreas Schaller
Dirigent proteins impart stereoselectivity to phenoxy radical coupling reactions in plants and thus play an essential role in the biosynthesis of biologically active natural products. This includes the regio- and enantioselective coupling and subsequent cyclization of two coniferyl alcohol radicals to pinoresinol as the committed step of lignan biosynthesis. The reaction is controlled by dirigent proteins which, depending on the species and protein, direct the reaction to either (+)- or (-)-pinoresinol. We present the crystal structure of the (-)-pinoresinol forming Dirigent Protein 6 from Arabidopsis thaliana (AtDIR6) with data to 1...
October 17, 2016: Plant Physiology
Benoit Gendreau-Berthiaume, S Ellen Macdonald, J John Stadt
Understanding processes driving mortality in forests is important for comprehension of natural stand dynamics and for informing natural disturbance-based ecosystem management. There has been considerable study of mortality in forests during the self-thinning phase but we know much less about processes driving mortality in stands at later successional stages. We addressed this through study of five 1-ha spatially explicit permanent plots in mature (111-186 yr old in 2012) Pinus contorta stands in the Canadian Rocky Mountains using data from repeated measurements over a 45-yr period, dendrochronological information, and point pattern analysis...
July 2016: Ecological Applications: a Publication of the Ecological Society of America
Laura Mosimann, Abdallah Traoré, Stephanie Mauti, Monique Léchenne, Brigit Obrist, René Véron, Jan Hattendorf, Jakob Zinsstag
In the framework of the research network on integrated control of zoonoses in Africa (ICONZ) a dog rabies mass vaccination campaign was carried out in two communes of Bamako (Mali) in September 2014. A mixed method approach, combining quantitative and qualitative tools, was developed to evaluate the effectiveness of the intervention towards optimization for future scale-up. Actions to control rabies occur on one level in households when individuals take the decision to vaccinate their dogs. However, control also depends on provision of vaccination services and community participation at the intermediate level of social resilience...
October 14, 2016: Acta Tropica
Carmine Di Rienzo, Paolo Annibale
The determination of the mode and rapidity of motion of individual molecules within a biological sample is becoming a more and more common analysis in biophysical investigations. Single molecule tracking (SMT) techniques allow reconstructing the trajectories of individual molecules within a movie, provided that the position from one frame to the other can be correctly linked. The outcomes, however, appear to depend on the specific method used, and most techniques display a limitation to capture fast modes of motion in a crowded environment...
October 1, 2016: Optics Letters
Erica Roitero, Federico Lasserre, Marc Anglada, Frank Mücklich, Emilio Jiménez-Piqué
OBJECTIVE: The aim of this work is to generate micrometric linear patterns with different topography on dental grade zirconia by means of UV laser interference and to assess the quality of the produced surface, both in term of the geometry produced and of the surface damage induced in the material. METHODS: The third harmonic of a Q-switched Nd:YAG laser (355nm, pulse duration of 10ns and repetition rate of 1Hz) was employed to pattern the surface of 3Y-TZP with micrometric-spaced lines...
October 10, 2016: Dental Materials: Official Publication of the Academy of Dental Materials
Christopher N Morrison, Beidi Dong, Charles C Branas, Therese S Richmond, Douglas J Wiebe
AIMS: This study estimated, with high spatial and temporal specificity, individuals' risk of being assaulted relative to their momentary proximity to alcohol outlets during daily activities. DESIGN: Case-control study. SETTING: Philadelphia, Pennsylvania, USA. PARTICIPANTS: Cases were 194 non-gun assault victims and 135 gun assault victims aged between 10 and 24 years. Age-matched controls (n = 274) were selected using random-digit dialing...
October 14, 2016: Addiction
D Giridharan, P Sabareesan, M Daniel
We investigate nonlinear localized magnetic excitations in a one-dimensional bicomponent magnonic crystal under a periodic magnetic field of spatially varying strength. The governing Landau-Lifshitz equation is transformed into a variable coefficient nonlinear Schrödinger (VCNLS) equation using stereographic projection. In general, the VCNLS equation is nonintegrable and by using Painlevé analysis, we obtain necessary conditions for the VCNLS equation to pass the Weiss-Tabor-Carnevale Painlevé test. A sufficient integrability condition is obtained by further exploring a transformation, which can map the VCNLS equation into the well-known standard nonlinear Schrödinger equation...
September 2016: Physical Review. E
Yohannes Shiferaw
Spontaneous calcium (Ca) waves in cardiac myocytes are known to underlie a wide range of cardiac arrhythmias. However, it is not understood which physiological parameters determine the onset of waves. In this study, we explore the relationship between Ca signaling between ion channels and the nucleation of Ca waves. In particular, we apply a master equation approach to analyze the stochastic interaction between neighboring clusters of ryanodine receptor (RyR) channels. Using this analysis, we show that signaling between clusters can be described as a barrier hopping process with exponential sensitivity to system parameters...
September 2016: Physical Review. E
Jo-Hanna Ivers, Jacqueline Fitzgerald, Christopher Whelan, Brion Sweeney, Eamon Keenan, Andrew Fagan, Jason McMarrow, Jim Meany, Joe Barry, Thomas Frodl
White matter impairment is associated with opioid dependence. However, the specific neuropathology related to opioid dependence is still not fully understood. The main aims of this study were to: (1) assess the association between white matter impairment and duration of dependence; (2) examine whether this impairment correlates with treatment outcome measures in opioid-dependent patients post-detoxification. Fifty-eight opioid-dependent patients participated, 20 females and 38 males, across three groups: less than 10 years use (n = 18), 10-15 years use (n = 26) and 16-25+ years use (n = 14)...
October 13, 2016: Addiction Biology
Andrzej Świerniak, Michał Krześlak
BACKGROUND: Evolutionary game theory (EGT) has been widely used to simulate tumour processes. In almost all studies on EGT models analysis is limited to two or three phenotypes. Our model contains four main phenotypes. Moreover, in a standard approach only heterogeneity of populations is studied, while cancer cells remain homogeneous. A multilayer approach proposed in this paper enables to study heterogeneity of single cells. METHOD: In the extended model presented in this paper we consider four strategies (phenotypes) that can arise by mutations...
October 13, 2016: Biology Direct
Alessia Deglincerti, Fred Etoc, M Cecilia Guerra, Iain Martyn, Jakob Metzger, Albert Ruzo, Mijo Simunovic, Anna Yoney, Ali H Brivanlou, Eric Siggia, Aryeh Warmflash
Fate allocation in the gastrulating embryo is spatially organized as cells differentiate into specialized cell types depending on their positions with respect to the body axes. There is a need for in vitro protocols that allow the study of spatial organization associated with this developmental transition. Although embryoid bodies and organoids can exhibit some spatial organization of differentiated cells, methods that generate embryoid bodies or organoids do not yield consistent and fully reproducible results...
November 2016: Nature Protocols
Haley L Kenyon, Miguel Alcaide, David P L Toews, Darren E Irwin
Elucidating the relationship between genetic and cultural evolution is important in understanding speciation, as learned premating barriers might be involved in maintaining species differences. Here we test this relationship by examining a widely recognized premating barrier, bird song, in a hybrid zone between black-throated green (Setophaga virens) and Townsend's warblers (S. townsendi). We use song analysis, genomic techniques and playback experiments to characterize the cultural and genetic backgrounds of individuals in this region, expecting that if song is an important reproductive barrier between these species, there should be a strong relationship between song and genotype...
October 12, 2016: Journal of Evolutionary Biology
Sara Mohebbi, Florian Erfurth, Philipp Hennersdorf, Axel A Brakhage, Hans Peter Saluz
Hyperspectral imaging (HSI) is a technique based on the combination of classical spectroscopy and conventional digital image processing. It is also well suited for the biological assays and quantitative real-time analysis since it provides spectral and spatial data of samples. The method grants detailed information about a sample by recording the entire spectrum in each pixel of the whole image. We applied HSI to quantify the constituent pH variation in a single infected apoptotic monocyte as a model system...
2016: PloS One
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