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Spatial patterning

Sinem Acar, Ece Bulut, Bora Durul, Ilhan Uner, Mehmet Kur, M Dilek Avsaroglu, Hüseyin Avni Kirmaci, Yasar Osman Tel, Fadile Y Zeyrek, Yesim Soyer
192 Food samples (commonly consumed 8 food types), 355 animal samples (animal feces of bovine, ovine, goat and chicken) and 50 samples from clinical human cases in Sanliurfa city, Turkey in a year were collected to determine the Salmonella enterica subsp. enterica mosaic in Turkey. 161 Salmonella isolates represented 17 serotypes, 20 sequence types (STs) and 44 PFGE patterns (PTs). 3 serotypes, S. Enteritidis, S. Typhimurium and S. Kentucky, were recovered from three different hosts. The highest discriminatory power was obtained by PFGE (SID=0...
October 8, 2016: International Journal of Food Microbiology
Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
J M Glownia, A Natan, J P Cryan, R Hartsock, M Kozina, M P Minitti, S Nelson, J Robinson, T Sato, T van Driel, G Welch, C Weninger, D Zhu, P H Bucksbaum
Time-resolved femtosecond x-ray diffraction patterns from laser-excited molecular iodine are used to create a movie of intramolecular motion with a temporal and spatial resolution of 30 fs and 0.3 Å. This high fidelity is due to interference between the nonstationary excitation and the stationary initial charge distribution. The initial state is used as the local oscillator for heterodyne amplification of the excited charge distribution to retrieve real-space movies of atomic motion on ångstrom and femtosecond scales...
October 7, 2016: Physical Review Letters
Tommi L Gaines, Daniel Werb, Jaime Arredondo, Victor M Alaniz, Carlos Vilalta, Leo Beletsky
BACKGROUND: In 2009, Mexico enacted a drug policy reform (Narcomenudeo) designed to divert persons possessing small amounts of illicit drugs to treatment rather than incarceration. To assess reform impact, this study examines the spatial-temporal trends of drug-related policing in Tijuana, Mexico post-enactment. METHOD: Location of self-reported arrests (N = 1,160) among a prospective, community-recruited cohort of people who inject drugs (PWID) in Tijuana (N = 552) was mapped across city neighborhoods...
October 21, 2016: Substance Use & Misuse
Yiwen Li Hegner, Axel Lindner, Christoph Braun
The processes underlying perceptual decision making are diverse and typically engage a distributed network of brain areas. It is a particular challenge to establish a sensory-to-motor functional hierarchy in such networks. This is because single-cell recordings mainly study the nodes of decision networks in isolation but seldom simultaneously. Moreover, imaging methods, which allow simultaneously accessing information from overall networks, typically suffer from either the temporal or the spatial resolution necessary to establish a detailed functional hierarchy in terms of a sequential recruitment of areas during a decision process...
October 21, 2016: Human Brain Mapping
Shui'er Han, Claudia Lunghi, David Alais
Continuous flash suppression (CFS) is a psychophysical technique where a rapidly changing Mondrian pattern viewed by one eye suppresses the target in the other eye for several seconds. Despite the widespread use of CFS to study unconscious visual processes, the temporal tuning of CFS suppression is currently unknown. In the present study we used spatiotemporally filtered dynamic noise as masking stimuli to probe the temporal characteristics of CFS. Surprisingly, we find that suppression in CFS peaks very prominently at approximately 1 Hz, well below the rates typically used in CFS studies (10 Hz or more)...
October 21, 2016: Scientific Reports
R Kelman Wieder, Melanie A Vile, Kimberli D Scott, Cara M Albright, Kelly McMillen, Dale H Vitt, Mark Fenn
Oil extraction and development activities in the Athabasca Oil Sands Region of northern Alberta, Canada release NOx, SOx, and NHx to the atmosphere, ultimately resulting in increasing N and S inputs to surrounding ecosystems through atmospheric deposition. Peatlands are a major feature of the northern Alberta landscape, with bogs covering 6-10% of the land area, and fens covering 21-53%. Bulk deposition of NH4+-N, NO3--N, total inorganic N (TIN), and SO42--S, was quantified using ion exchange resin collectors deployed at 23 locations, over 1-6 years, reveal maximum N and S deposition of 9...
October 21, 2016: Environmental Science & Technology
Chuanjun Zhuo, Jiajia Zhu, Chunli Wang, Hongru Qu, Xiaolei Ma, Wen Qin
Alterations in grey matter structure and functional connectivity (FC) are pathological features of major depressive disorder (MDD). However, the relationship between brain structural and functional impairments in MDD remains uncertain. Thus, the aim of this study was to investigate the relationship between alterations in grey matter volume (GMV) and resting-state global functional connectivity density (rs-gFCD) in MDD. Forty-five patients with MDD and 48 healthy controls underwent structural and resting-state functional magnetic resonance imaging (fMRI)...
October 20, 2016: Brain Imaging and Behavior
Johanna M Kraus, Polly P Gibson, David M Walters, Marc A Mills
Riparian spiders are being used increasingly to track spatial patterns of contaminants in and fluxing from aquatic ecosystems. However, our understanding of the circumstances under which spiders are effective sentinels of aquatic pollution is limited. Here we test the hypothesis that riparian spiders may be effectively used to track spatial patterns of sediment pollution by polychlorinated biphenyls (PCBs) in aquatic ecosystems with high habitat heterogeneity. We found that spatial pattern of ΣPCB concentrations in two common families of riparian spiders sampled in 2011-2013 generally tracked spatial variation in sediment ΣPCBs across all sites within the Manistique River Great Lakes Area of Concern (AOC), a rivermouth ecosystem located on the south shore of the Upper Peninsula, Manistique, MI, that includes harbor, river, backwater, and lake habitats...
October 20, 2016: Environmental Toxicology and Chemistry
Sheel Shah, Eric Lubeck, Wen Zhou, Long Cai
Identifying the spatial organization of tissues at cellular resolution from single-cell gene expression profiles is essential to understanding biological systems. Using an in situ 3D multiplexed imaging method, seqFISH, we identify unique transcriptional states by quantifying and clustering up to 249 genes in 16,958 cells to examine whether the hippocampus is organized into transcriptionally distinct subregions. We identified distinct layers in the dentate gyrus corresponding to the granule cell layer and the subgranular zone and, contrary to previous reports, discovered that distinct subregions within the CA1 and CA3 are composed of unique combinations of cells in different transcriptional states...
October 19, 2016: Neuron
Sebastian Sippel, Holger Lange, Miguel D Mahecha, Michael Hauhs, Paul Bodesheim, Thomas Kaminski, Fabian Gans, Osvaldo A Rosso
Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena...
2016: PloS One
Yinjun Zhao, Aizhong Ding
River classification is a very useful tool for river management yet still a difficult task. This paper proposed a new decision classifier (DCF) to classify rivers for Chinese river management based on existing classification systems. Aimed at river function management, the DCF with the five-layers frame was developed on reach level in a spatially nested pattern that from top to bottom are natural province, basin, valley, reach, habitat and microhabitat. Five indexes (artificial degree, closeness, sinuosity, bed material texture, geomorphic units (GUs)) were selected and organized into the DCF according to the importance of the influence on river structure from macro to micro, large to small and top to bottom, because they represent main aspects of river structures and are easy to obtain...
October 2016: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Yi Shi, Xian-Bin Su, Kun-Yan He, Bing-Hao Wu, Bo-Yu Zhang, Ze-Guang Han
Somatic mutations of many cancer genes tend to co-occur (termed co-mutations) in certain patterns during tumor initiation and progression. However, the genetic and epigenetic mechanisms that contribute to the co-mutations of these cancer genes have yet to be explored. Here, we systematically investigated the association between the somatic co-mutations of cancer genes and high-order chromatin conformation. Significantly, somatic point co-mutations in protein-coding genes were closely associated with high-order spatial chromatin folding...
October 20, 2016: Scientific Reports
Rebecca E Young, Andrew D C Maccoll
Patterns in parasite community structure are often observed in natural systems and an important question in parasite ecology is whether such patterns are repeatable across time and space. Field studies commonly look at spatial or temporal repeatability of patterns, but they are rarely investigated in conjunction. We use a large dataset on the macroparasites of the three-spined stickleback, Gasterosteus aculeatus L., collected from 14 locations on North Uist, Scotland over an 8-year period to investigate: (1) repeatability of patterns in parasite communities among populations and whether variation is consistent across years, (2) whether variation between years can be explained by climatic variation and progression of the season and (3) whether variation in habitat characteristics explain population differences...
October 20, 2016: Parasitology
Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Hélène Badouin, Christopher E Ellison, Nhu H Nguyen, Rytas Vilgalys, Kabir G Peay, John W Taylor, Thomas D Bruns
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation...
October 20, 2016: Molecular Ecology
Mingkai Qu, Weidong Li, Chuanrong Zhang, Biao Huang, Yongcun Zhao
To effectively understand the availability of soil nitrogen and assist in soil nitrogen control at the regional scale, it is essential to understand the accurate spatial distribution patterns of the three soil nitrogen parameters [i.e., total nitrogen (TN), available nitrogen (AN) and nitrogen availability ratio (NAR)] and explore the spatially varying influences of major impact factors on soil AN. Land use affects the spatial distributions of soil TN, AN and NAR (i.e., AN/TN). To explore the effects of different land use types and improve mapping accuracy, residual kriging with land use information and ordinary kriging (without land use information) were compared based on the sample data of soil TN and AN in Hanchuan county, China...
October 20, 2016: Environmental Science. Processes & Impacts
Klaus Kopitzki, Andreas Oldag, Catherine M Sweeney-Reed, Judith Machts, Maria Veit, Jörn Kaufmann, Hermann Hinrichs, Hans-Jochen Heinze, Katja Kollewe, Susanne Petri, Bahram Mohammadi, Reinhard Dengler, Andreas R Kupsch, Stefan Vielhaber
PURPOSE: Aim of the present study was to investigate potential impairment of non-motor areas in amyotrophic lateral sclerosis (ALS) using near-infrared spectroscopy (NIRS) and diffusion tensor imaging (DTI). In particular, we evaluated whether homotopic resting-state functional connectivity (rs-FC) of non-motor associated cortical areas correlates with clinical parameters and disease-specific degeneration of the corpus callosum (CC) in ALS. MATERIAL AND METHODS: Interhemispheric homotopic rs-FC was assessed in 31 patients and 30 healthy controls (HCs) for 8 cortical sites, from prefrontal to occipital cortex, using NIRS...
2016: NeuroImage: Clinical
Juan Pablo Amaya, Juan I Areta, Veronica S Valentinuzzi, Emmanuel Zufiaurre
The underground environment poses particular communication challenges for subterranean rodents. Some loud and low-pitched acoustic signals that can travel long distances are appropriate for long-range underground communication and have been suggested to be territorial signals. Long-range vocalizations (LRVs) are important in long-distance communication in Ctenomys tuco-tucos. We characterized the LRV of the Anillaco Tuco-Tuco (Ctenomys sp.) using recordings from free-living individuals and described the behavioral context in which this vocalization was produced during laboratory staged encounters between individuals of both sexes...
2016: PeerJ
Scott Ferrenberg, Alexander S Martinez, Akasha M Faist
BACKGROUND: Understanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces...
2016: PeerJ
Hesham Dahshan, Ayman Mohamed Megahed, Amr Mohamed Mohamed Abd-Elall, Mahdy Abdel-Goad Abd-El-Kader, Ehab Nabawy, Mariam Hassan Elbana
BACKGROUND: Persistent organic pollutants represent about 95 % of the industrial sector effluents in Egypt. Contamination of the River Nile water with various pesticides poses a hazardous risk to both human and environmental compartments. Therefore, a large scale monitoring study was carried on pesticides pollution in three geographical main regions along the River Nil water stream, Egypt. METHODS: Organochlorine and organophosphorus pesticides were extracted by liquid-liquid extraction and analyzed by GC-ECD...
2016: Journal of Environmental Health Science & Engineering
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