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https://www.readbyqxmd.com/read/29149264/sim3c-simulation-of-hi-c-and-meta3c-proximity-ligation-sequencing-technologies
#1
Matthew Z DeMaere, Aaron E Darling
Background: Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. Findings: We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences...
November 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29145486/geography-of-current-and-future-global-mammal-extinction-risk
#2
Ana D Davidson, Kevin T Shoemaker, Ben Weinstein, Gabriel C Costa, Thomas M Brooks, Gerardo Ceballos, Volker C Radeloff, Carlo Rondinini, Catherine H Graham
Identifying which species are at greatest risk, what makes them vulnerable, and where they are distributed are central goals for conservation science. While knowledge of which factors influence extinction risk is increasingly available for some taxonomic groups, a deeper understanding of extinction correlates and the geography of risk remains lacking. Here, we develop a predictive random forest model using both geospatial and mammalian species' trait data to uncover the statistical and geographic distributions of extinction correlates...
2017: PloS One
https://www.readbyqxmd.com/read/29143980/white-matter-maturation-during-12-months-in-individuals-at-ultra-high-risk-for-psychosis
#3
K Krakauer, M Nordentoft, B Y Glenthøj, J M Raghava, D Nordholm, L Randers, L B Glenthøj, B H Ebdrup, E Rostrup
OBJECTIVE: The neurodevelopmental hypothesis of psychosis suggests that disrupted white matter (WM) maturation underlies disease onset. In this longitudinal study, we investigated WM connectivity and compared WM changes between individuals at ultra-high-risk for psychosis (UHR) and healthy controls (HCs). METHOD: Thirty UHR individuals and 23 HCs underwent MR diffusion tensor imaging before and after 12 months of non-manualized standard care. Positive and negative symptoms and level of functioning were assessed...
November 16, 2017: Acta Psychiatrica Scandinavica
https://www.readbyqxmd.com/read/29141385/-clinical-observation-of-visual-quality-after-the-individual-implantation-of-intraocular-lens-guided-by-corneal-q-value
#4
F F Cai, G Y Zheng, H J Wang, L Li, Y Liu
Objective: To describe the feasibility of individual IOL implantation guided by corneal Q value and observe patients postoperative visual quality under different residual spherical aberration. Methods: Prospective study. One hundred and twenty cases (171 eyes)cataract patients in our hospital were selected for the individual implantation of intraocular lens guided by corneal Q value which obtained by Oberscan before operation. Based on spherical aberration calculated by corneal Q value, choose appropriate IOL personalitily to make postoperative whole eye surface aberration +0...
November 11, 2017: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
https://www.readbyqxmd.com/read/29141338/-spatial-and-temporal-clustering-characteristics-of-typhoid-and-paratyphoid-fever-and-its-change-pattern-in-3-provinces-in-southwestern-china-2001-2012
#5
L X Wang, B Yang, M Y Yan, Y Q Tang, Z C Liu, R Q Wang, S Li, L Ma, B Kan
Objective: To analyze the spatial and temporal clustering characteristics of typhoid and paratyphoid fever and its change pattern in Yunnan, Guizhou and Guangxi provinces in southwestern China in recent years. Methods: The incidence data of typhoid and paratyphoid fever cases at county level in 3 provinces during 2001-2012 were collected from China Information System for Diseases Control and Prevention and analyzed by the methods of descriptive epidemiology and geographic informatics. And the map showing the spatial and temporal clustering characters of typhoid and paratyphoid fever cases in three provinces was drawn...
November 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/29140113/prediction-of-pancreatic-neuroendocrine-tumor-grade-based-on-ct-features-and-texture-analysis
#6
Rodrigo Canellas, Kristine S Burk, Anushri Parakh, Dushyant V Sahani
OBJECTIVE: The purposes of this study were to assess whether CT texture analysis and CT features are predictive of pancreatic neuroendocrine tumor (PNET) grade based on the World Health Organization (WHO) classification and to identify features related to disease progression after surgery. MATERIALS AND METHODS: Preoperative contrast-enhanced CT images of 101 patients with PNETs were assessed. The images were evaluated for tumor location, tumor size, tumor pattern, predominantly solid or cystic composition, presence of calcification, presence of heterogeneous enhancement on contrast-enhanced images, presence of pancreatic duct dilatation, presence of pancreatic atrophy, presence of vascular involvement by the tumor, and presence of lymphadenopathy...
November 15, 2017: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/29138468/increasing-frequency-and-spatial-extent-of-concurrent-meteorological-droughts-and-heatwaves-in-india
#7
Shailza Sharma, Pradeep Mujumdar
The impacts of concurrent droughts and heatwaves could be more serious compared to their individual occurrence. Meteorological drought condition is generally characterized by low rainfall, but impact of such an event is amplified with simultaneous occurrence of heatwaves. Positive feedback between these two extremes can worsen the rainfall deficit situation to serious soil moisture depletion due to enhanced evapotranspiration. In this study, the concurrence of meteorological droughts and heatwaves is investigated in India using Indian Meteorological Department (IMD) high resolution gridded data over a period of 60 years...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136658/community-ecology-in-3d-tensor-decomposition-reveals-spatio-temporal-dynamics-of-large-ecological-communities
#8
Romain Frelat, Martin Lindegren, Tim Spaanheden Denker, Jens Floeter, Heino O Fock, Camilla Sguotti, Moritz Stäbler, Saskia A Otto, Christian Möllmann
Understanding spatio-temporal dynamics of biotic communities containing large numbers of species is crucial to guide ecosystem management and conservation efforts. However, traditional approaches usually focus on studying community dynamics either in space or in time, often failing to fully account for interlinked spatio-temporal changes. In this study, we demonstrate and promote the use of tensor decomposition for disentangling spatio-temporal community dynamics in long-term monitoring data. Tensor decomposition builds on traditional multivariate statistics (e...
2017: PloS One
https://www.readbyqxmd.com/read/29136606/heavy-metals-in-soils-of-hechuan-county-in-the-upper-yangtze-sw-china-comparative-pollution-assessment-using-multiple-indices-with-high-spatial-resolution-sampling
#9
Maofei Ni, Rong Mao, Zhongmin Jia, Ruozhu Dong, Siyue Li
In order to assess heavy metals (HMs) in soils of the upper Yangtze Basin, a very high-spatial-resolution sampling (582 soil samples) was conducted from Hechuan County, an important agricultural practice area in the Southwest China. Multiple indices including geoaccumulation index (Igeo), enrichment factor (EF), sediment pollution index (SPI) and risk index (RI), as well as multivariate statistics were employed for pollution assessment and source identification of HMs in soils. Our results demonstrated that the averages of eight HMs decreased in the following order: Zn (82...
November 11, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29135876/effectiveness-of-directional-microphones-in-bilateral-bimodal-cochlear-implant-users-impact-of-spatial-and-temporal-noise-characteristics
#10
Tobias Weissgerber, Tobias Rader, Uwe Baumann
OBJECTIVE: To measure speech reception thresholds (SRTs) in co-located (S0N0) and diffuse noise conditions (multi-source noise field, MSNF) and to assess the impact of beamforming algorithms in MSNF in cochlear implant (CI) users. STUDY DESIGN: Non-randomized, open, prospective study. SETTING: Tertiary referral cochlear implantation center. PATIENTS: Participants included 14 CI users (7 bimodal, 7 bilateral) and 14 normal hearing young adults...
December 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/29134327/effects-of-land-use-types-on-dissolved-trace-metal-concentrations-in-the-le-an-river-basin-china
#11
Yinghui Jiang, Zhenglei Xie, Hua Zhang, Huanqing Xie, Yun Cao
Using land use types in multiple spatial scales (entire basin, buffer zones, and slopes) as well as statistical and spatial analysis, relationships between land use types and concentrations of dissolved trace metals were determined in the Le'an River Basin, China. The result showed that farmland and urban land were determined as the source of the pollutants, while forestland and grassland were identified as the sink of the pollutants. The temporal differences of relationships between land use types and concentrations of dissolved trace metals mainly due to the discrepancy of rainfall characteristics...
November 13, 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/29133425/matter-wave-speckle-observed-in-an-out-of-equilibrium-quantum-fluid
#12
Pedro E S Tavares, Amilson R Fritsch, Gustavo D Telles, Mahir S Hussein, François Impens, Robin Kaiser, Vanderlei S Bagnato
We report the results of the direct comparison of a freely expanding turbulent Bose-Einstein condensate and a propagating optical speckle pattern. We found remarkably similar statistical properties underlying the spatial propagation of both phenomena. The calculated second-order correlation together with the typical correlation length of each system is used to compare and substantiate our observations. We believe that the close analogy existing between an expanding turbulent quantum gas and a traveling optical speckle might burgeon into an exciting research field investigating disordered quantum matter...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29133418/normalized-value-coding-explains-dynamic-adaptation-in-the-human-valuation-process
#13
Mel W Khaw, Paul W Glimcher, Kenway Louie
The notion of subjective value is central to choice theories in ecology, economics, and psychology, serving as an integrated decision variable by which options are compared. Subjective value is often assumed to be an absolute quantity, determined in a static manner by the properties of an individual option. Recent neurobiological studies, however, have shown that neural value coding dynamically adapts to the statistics of the recent reward environment, introducing an intrinsic temporal context dependence into the neural representation of value...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29133266/mapping-suicide-mortality-in-ohio-a-spatial-epidemiological-analysis-of-suicide-clusters-and-area-level-correlates
#14
Cynthia A Fontanella, Daniel M Saman, John V Campo, Danielle L Hiance-Steelesmith, Jeffrey Bridge, Helen Anne Sweeney, Elisabeth D Root
Previous studies have investigated spatial patterning and associations of area characteristics with suicide rates in Western and Asian countries, but few have been conducted in the United States. This ecological study aims to identify high-risk clusters of suicide in Ohio and assess area level correlates of these clusters. We estimated spatially smoothed standardized mortality ratios (SMR) using Bayesian conditional autoregressive models (CAR) for the period 2004 to 2013. Spatial and spatio-temporal scan statistics were used to detect high-risk clusters of suicide at the census tract level (N=2952)...
November 10, 2017: Preventive Medicine
https://www.readbyqxmd.com/read/29132779/reliability-assessment-of-bioreactor-landfills-using-monte-carlo-simulation-and-coupled-hydro-bio-mechanical-model
#15
Krishna R Reddy, Girish Kumar, Rajiv K Giri, B Munwar Basha
The performance of a bioreactor landfill is highly influenced by the simultaneous interactions of several coupled processes that occur within the landfill. In addition, the high uncertainty and spatial variability in the geotechnical properties of municipal solid waste (MSW) poses significant challenge in accurately predicting the performance of bioreactor landfills. In this study, a 2D coupled hydro-bio-mechanical (CHBM) model was employed to predict the behavior of MSW in bioreactor landfills. The numerical model integrated a two-phase flow hydraulic model, a plane-strain formulation of Mohr-Coulomb constitutive model, and a first order decay biodegradation model...
November 10, 2017: Waste Management
https://www.readbyqxmd.com/read/29132048/brain-white-matter-structure-and-language-ability-in-preschool-aged-children
#16
Matthew Walton, Deborah Dewey, Catherine Lebel
Brain alterations are associated with reading and language difficulties in older children, but little research has investigated relationships between early language skills and brain white matter structure during the preschool period. We studied 68 children aged 3.0-5.6 years who underwent diffusion tensor imaging and participated in assessments of Phonological Processing and Speeded Naming. Tract-based spatial statistics and tractography revealed relationships between Phonological Processing and diffusion parameters in bilateral ventral white matter pathways and the corpus callosum...
November 10, 2017: Brain and Language
https://www.readbyqxmd.com/read/29132042/long-range-interactions-keep-bacterial-cells-from-liquid-solid-interfaces-evidence-of-a-bacteria-exclusion-zone-near-nafion-surfaces-and-possible-implications-for-bacterial-attachment
#17
Yifan Cheng, Carmen I Moraru
Hydrophilic surfaces of both abiotic and biological origin have been shown to bear particle-exclusion zones as large as hundreds of micrometers at liquid-solid interfaces. Here we present the first systematic investigation and evidence for bacteria-free exclusion zones for several bacterial strains, including pathogens associated with hospital infections and/or foodborne outbreaks: Staphylococcus aureus, Escherichia coli O157:H7, and Listeria monocytogenes. Tests were carried out both in a phosphate buffer, as well as triptic soy broth (TSB) of high ionic strength...
November 10, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29132008/characterization-of-antibiotics-in-a-large-scale-river-system-of-china-occurrence-pattern-spatiotemporal-distribution-and-environmental-risks
#18
Haiyang Chen, Lijun Jing, Yanguo Teng, Jinsheng Wang
Antibiotics and antibiotic resistance genes in the river system have received growing attention in recent years due to their potential threat to aquatic ecosystems and public health. Recognizing the occurrence and distribution of antibiotics in river environment and assessing their ecological risks are of important precondition for proposing effective strategies to protect basin safety. In this study, a comprehensive investigation was conducted to identify the contamination and risk characteristics of antibiotics in the aquatic environment of Hai River system (HRS) which is the largest water system in northern China...
November 10, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29132005/discriminant-analysis-as-a-decision-making-tool-for-geochemically-fingerprinting-sources-of-groundwater-salinity
#19
Nathaniel P Chien, Laura K Lautz
Concern over contamination of groundwater resources in areas impacted by anthropogenic activities has led to an increasing number of baseline groundwater quality surveys intended to provide context for interpreting water quality data. Flexible screening tools that can parse through these large, regional datasets to identify spatial or temporal changes in water quality are becoming more important to groundwater scientists. One such tool, developed from previous work by the authors, makes use of linear discriminant analysis (LDA) to identify the most probable source of chloride salinity in groundwater samples based on their geochemical fingerprints...
November 10, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29131869/assessing-current-temporal-and-space-time-anomalies-of-disease-incidence
#20
Chih-Chieh Wu, Chien-Hsiun Chen, Sanjay Shete
Approaches used to early and accurately characterize epidemiologic patterns of disease incidence in a temporal and spatial series are becoming increasingly important. Cluster tests are generally designed for retrospective detection of epidemiologic anomalies in a temporal or space-time series. Timely identification of anomalies of disease or poisoning incidence during ongoing surveillance or an outbreak requires the use of sensitive statistical methods that recognize an incidence pattern at the time of occurrence...
2017: PloS One
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