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https://www.readbyqxmd.com/read/27920366/a-graphical-perspective-of-marginal-structural-models-an-application-for-the-estimation-of-the-effect-of-physical-activity-on-blood-pressure
#1
Denis Talbot, Amanda M Rossi, Simon L Bacon, Juli Atherton, Geneviève Lefebvre
Estimating causal effects requires important prior subject-matter knowledge and, sometimes, sophisticated statistical tools. The latter is especially true when targeting the causal effect of a time-varying exposure in a longitudinal study. Marginal structural models are a relatively new class of causal models that effectively deal with the estimation of the effects of time-varying exposures. Marginal structural models have traditionally been embedded in the counterfactual framework to causal inference. In this paper, we use the causal graph framework to enhance the implementation of marginal structural models...
December 5, 2016: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/27918986/hybrid-chitosan-polyaniline-polypyrrole-biomaterial-for-enhanced-adsorption-and-antimicrobial-activity
#2
Rajeev Kumar, Mohammad Oves, Talla Ameelbi, Naief H Al-Makishah, M A Barakat
In this work, chitosan (CS) functionalized polyaniline-polypyrrole (Pani-Ppy) copolymer (CS/Pani-Ppy) was synthesized applying a facile one pot method for the enhanced adsorption of Zn(II) and antimicrobial activity for E. coli and E. agglomerans. The synthesized materials were characterized using scanning electron microscopy, energy dispersive X-ray spectroscopy, Fourier transform inferred spectroscopy and X-ray photoelectron spectroscopy. The adsorption of the Zn(II) on the synthesized materials was highly dependent on the pH of the solution, the initial metal ion concentration, and temperature...
November 24, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27918530/a-probabilistic-approach-to-demixing-odors
#3
Agnieszka Grabska-Barwińska, Simon Barthelmé, Jeff Beck, Zachary F Mainen, Alexandre Pouget, Peter E Latham
The olfactory system faces a hard problem: on the basis of noisy information from olfactory receptor neurons (the neurons that transduce chemicals to neural activity), it must figure out which odors are present in the world. Odors almost never occur in isolation, and different odors excite overlapping populations of olfactory receptor neurons, so the central challenge of the olfactory system is to demix its input. Because of noise and the large number of possible odors, demixing is fundamentally a probabilistic inference task...
December 5, 2016: Nature Neuroscience
https://www.readbyqxmd.com/read/27918482/fuzzy-computing-model-of-activity-recognition-on-wsn-movement-data-for-ubiquitous-healthcare-measurement
#4
Shu-Yin Chiang, Yao-Chiang Kan, Yun-Shan Chen, Ying-Ching Tu, Hsueh-Chun Lin
Ubiquitous health care (UHC) is beneficial for patients to ensure they complete therapeutic exercises by self-management at home. We designed a fuzzy computing model that enables recognizing assigned movements in UHC with privacy. The movements are measured by the self-developed body motion sensor, which combines both accelerometer and gyroscope chips to make an inertial sensing node compliant with a wireless sensor network (WSN). The fuzzy logic process was studied to calculate the sensor signals that would entail necessary features of static postures and dynamic motions...
December 3, 2016: Sensors
https://www.readbyqxmd.com/read/27917701/design-synthesis-mtt-assay-dna-interaction-studies-of-platinum-ii-complexes
#5
Miral V Lunagariya, Khyati P Thakor, Bhargav N Waghela, Foram U Vaidya, Chadramani Pathak, Mohan N Patel
The square planar Pt(II) complexes of the type [Pt(L(n))(Cl2)] (where L(n) = L(1-3) = thiophene-2-carboxamide derivatives and L(4-6) = thiophene-2-carbothioamide derivatives) have been synthesized and characterized by physicochemical and various spectroscopic studies. MIC method was employed to inference the antibacterial potency of complexes in reference to free ligands and metal salt. Characteristic binding constant (Kb) and binding mode of complexes with calf thymus DNA (CT-DNA) were determined using absorption titration (0...
December 4, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27917349/effect-of-acute-salinity-stress-on-ion-homeostasis-na-k-atpase-and-histological-structure-in-sea-cucumber-apostichopus-japonicus
#6
Chenfan Geng, Yi Tian, Yanpeng Shang, Liqiang Wang, Yanan Jiang, Yaqing Chang
BACKGROUND: Sea cucumbers (Apostichopus japonicus) are an imperiled fauna exposed to a variety of environmental condition such as salinity and studies are urgently needed to assess their effects to guide aquaculture efforts. The effects of acute salinity stress on coelomic fluid osmotic pressure, ion concentrations, the activity of Na(+)/K(+)-ATPase in respiratory trees and the histological variations were measured to evaluate the salinity tolerance of sea cucumbers. RESULTS: Significant correlations in osmotic pressure were observed between coelomic fluid and ambient environmental salinity...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27917230/local-equilibrium-in-bird-flocks
#7
Thierry Mora, Aleksandra M Walczak, Lorenzo Del Castello, Francesco Ginelli, Stefania Melillo, Leonardo Parisi, Massimiliano Viale, Andrea Cavagna, Irene Giardina
The correlated motion of flocks is an instance of global order emerging from local interactions. An essential difference with analogous ferromagnetic systems is that flocks are active: animals move relative to each other, dynamically rearranging their interaction network. The effect of this off-equilibrium element is well studied theoretically, but its impact on actual biological groups deserves more experimental attention. Here, we introduce a novel dynamical inference technique, based on the principle of maximum entropy, which accodomates network rearrangements and overcomes the problem of slow experimental sampling rates...
December 2016: Nature Physics
https://www.readbyqxmd.com/read/27915291/the-landscape-of-microbial-phenotypic-traits-and-associated-genes
#8
Maria Brbić, Matija Piškorec, Vedrana Vidulin, Anita Kriško, Tomislav Šmuc, Fran Supek
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27914690/c1q-as-an-autocrine-and-paracrine-regulator-of-cellular-functions
#9
REVIEW
Berhane Ghebrehiwet, Kinga H Hosszu, Ellinor I B Peerschke
Most of the complement proteins in circulation are, by and large, synthesized in the liver. However data accumulated over the past several decades provide incontrovertible evidence that some if not most of the individual complement proteins are also synthesized extrahepatically by activated as well as non-activated cells. The question that is finally being addressed by various investigators is: are the locally synthesized proteins solely responsible for the myriad of biological functions in situ without the contribution of systemic complement? The answer is probably "yes"...
November 30, 2016: Molecular Immunology
https://www.readbyqxmd.com/read/27914546/analysis-of-transferred-fragrance-and-its-forensic-implications
#10
Simona Gherghel, Ruth M Morgan, Christopher S Blackman, Kersti Karu, Ivan P Parkin
Perfumes are widely used by many people in developed countries, and a large number of both men and women wear perfumes on a daily basis. Analysis of perfume trace materials from clothing is not commonly employed within forensic casework, yet as a form of trace evidence it has the potential to provide valuable intelligence. In order to appreciate the value of trace evidence there is a fundamental need for an evidence base that can both offer insight into how a trace material behaves under different scenarios and activities, and from which inferences can be made...
December 2016: Science & Justice: Journal of the Forensic Science Society
https://www.readbyqxmd.com/read/27914092/synthesis-characterization-and-study-of-in-vitro-cytotoxicity-of-zno-fe3o4-magnetic-composite-nanoparticles-in-human-breast-cancer-cell-line-mda-mb-231-and-mouse-fibroblast-nih-3t3
#11
Gunjan Bisht, Sagar Rayamajhi, Biplab Kc, Siddhi Nath Paudel, Deepak Karna, Bhupal G Shrestha
Novel magnetic composite nanoparticles (MCPs) were successfully synthesized by ex situ conjugation of synthesized ZnO nanoparticles (ZnO NPs) and Fe3O4 NPs using trisodium citrate as linker with an aim to retain key properties of both NPs viz. inherent selectivity towards cancerous cell and superparamagnetic nature, respectively, on a single system. Successful characterization of synthesized nanoparticles was done by XRD, TEM, FTIR, and VSM analyses. VSM analysis showed similar magnetic profile of thus obtained MCPs as that of naked Fe3O4 NPs with reduction in saturation magnetization to 16...
December 2016: Nanoscale Research Letters
https://www.readbyqxmd.com/read/27913150/juvenile-hormone-titers-ovarian-status-and-epicuticular-hydrocarbons-in-gynes-and-workers-of-the-paper-wasp-belonogaster-longitarsus
#12
Hans C Kelstrup, Klaus Hartfelder, Nanike Esterhuizen, Theresa C Wossler
The prevailing paradigm for social wasp endocrinology is that of juvenile hormone (JH) functioning pleiotropically in potential and actual queens, where it fuels dominance behaviors, stimulates ovarian growth and/or affects the production of status-linked cuticular compounds. In colonies with annual cycles (e.g., temperate-zone species), female adults produced at the end of the summer (called gynes) are physiologically primed to hibernate. Despite the absence of egg-laying in the pre-overwintering phase, gynes engage in dominance interactions that may affect reproductive potential following hibernation...
November 29, 2016: Journal of Insect Physiology
https://www.readbyqxmd.com/read/27913018/potential-impact-of-flowback-water-from-hydraulic-fracturing-on-agricultural-soil-quality-metal-metalloid-bioaccessibility-microtox-bioassay-and-enzyme-activities
#13
Season S Chen, Yuqing Sun, Daniel C W Tsang, Nigel J D Graham, Yong Sik Ok, Yujie Feng, Xiang-Dong Li
Hydraulic fracturing has advanced the development of shale gas extraction, while inadvertent spills of flowback water may pose a risk to the surrounding environment due to its high salt content, metals/metalloids (As, Se, Fe and Sr), and organic additives. This study investigated the potential impact of flowback water on four representative soils from shale gas regions in Northeast China using synthetic flowback solutions. The compositions of the solutions were representative of flowback water arising at different stages after fracturing well establishment...
November 29, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27908788/time-to-wake-up-studying-neurovascular-coupling-and-brain-wide-circuit-function-in-the-un-anesthetized-animal
#14
REVIEW
Yu-Rong Gao, Yuncong Ma, Qingguang Zhang, Aaron T Winder, Zhifeng Liang, Lilith Antinori, Patrick J Drew, Nanyin Zhang
Functional magnetic resonance imaging (fMRI) has allowed the noninvasive study of task-based and resting-state brain dynamics in humans by inferring neural activity from blood-oxygenation-level dependent (BOLD) signal changes. An accurate interpretation of the hemodynamic changes that underlie fMRI signals depends on the understanding of the quantitative relationship between changes in neural activity and changes in cerebral blood flow, oxygenation and volume. While there has been extensive study of neurovascular coupling in anesthetized animal models, anesthesia causes large disruptions of brain metabolism, neural responsiveness and cardiovascular function...
November 28, 2016: NeuroImage
https://www.readbyqxmd.com/read/27907891/analysis-of-translation-using-polysome-profiling
#15
Héloïse Chassé, Sandrine Boulben, Vlad Costache, Patrick Cormier, Julia Morales
During the past decade, there has been growing interest in the role of translational regulation of gene expression in many organisms. Polysome profiling has been developed to infer the translational status of a specific mRNA species or to analyze the translatome, i.e. the subset of mRNAs actively translated in a cell. Polysome profiling is especially suitable for emergent model organisms for which genomic data are limited. In this paper, we describe an optimized protocol for the purification of sea urchin polysomes and highlight the critical steps involved in polysome purification...
October 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27905633/-failure-to-radical-cure-in-plasmodium-vivax-malaria
#16
Julián García, Agustín Seijo, Andrés Benchetrit, Esteban Couto, Sofía Echazarreta, Susana Lloveras, Tomás Orduna
Relapsing Plasmodium vivax malaria is due to activation of dormant intrahepatic parasitic forms known as hypnozoits. Primaquine is the only available drug effective against hypnozoits and, alongside a schizonticidal drug, constitutes the radical treatment of malaria. Failure of radical treatment is frequently attributed to inadequate dosing, poor adherence, or reinfection. However, several cases of radical treatment failure without these factors have been reported, inferring that metabolic properties of the host or tolerance mechanisms of the parasite may be implied...
August 2016: Revista Chilena de Infectología: órgano Oficial de la Sociedad Chilena de Infectología
https://www.readbyqxmd.com/read/27903631/genomics-of-compensatory-adaptation-in-experimental-populations-of-aspergillus-nidulans
#17
Jeremy R Dettman, Nicolas Rodrigue, Sijmen E Schoustra, Rees Kassen
Knowledge of the number and nature of genetic changes responsible for adaptation is essential for understanding and predicting evolutionary trajectories. Here, we study the genomic basis of compensatory adaptation to the fitness cost of fungicide resistance in experimentally evolved strains of the filamentous fungus Aspergillus nidulans The original selection experiment tracked the fitness recovery of lines founded by an ancestral strain that was resistant to fludioxonil, but paid a fitness cost in the absence of the fungicide...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27900688/degradation-network-reconstruction-guided-by-metagenomic-data
#18
Rafael Bargiela, Manuel Ferrer
Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#19
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896997/improved-performance-of-gene-set-analysis-on-genome-wide-transcriptomics-data-when-using-gene-activity-state-estimates
#20
Thomas Kamp, Micah Adams, Craig Disselkoen, Nathan Tintle
Gene set analysis methods continue to be a popular and powerful method of evaluating genome-wide transcriptomics data. These approach require a priori grouping of genes into biologically meaningful sets, and then conducting downstream analyses at the set (instead of gene) level of analysis. Gene set analysis methods have been shown to yield more powerful statistical conclusions than single-gene analyses due to both reduced multiple testing penalties and potentially larger observed effects due to the aggregation of effects across multiple genes in the set...
2016: Pacific Symposium on Biocomputing
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