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https://www.readbyqxmd.com/read/29156285/modelling-spatial-and-temporal-variations-of-annual-suspended-sediment-yields-from-small-agricultural-catchments
#1
A Rymszewicz, M Bruen, J J O'Sullivan, J N Turner, D M Lawler, J R Harrington, E Conroy, M Kelly-Quinn
Estimates of sediment yield are important for ecological and geomorphological assessment of fluvial systems and for assessment of soil erosion within a catchment. Many regulatory frameworks, such as the Convention for the Protection of the Marine Environment of the North-East Atlantic, derived from the Oslo and Paris Commissions (OSPAR) require reporting of annual sediment fluxes. While they may be measured in large rivers, sediment flux is rarely measured in smaller rivers. Measurements of sediment transport at a national scale can be also challenging and therefore, sediment yield models are often utilised by water resource managers for the predictions of sediment yields in the ungauged catchments...
November 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29155998/limited-impact-of-adolescent-meningococcal-acwy-vaccination-on-group-w-carriage-in-university-students
#2
Neil J Oldfield, Luke R Green, Julian Parkhill, Christopher D Bayliss, David P J Turner
Background: In the UK rising disease levels due to Neisseria meningitidis serogroup W clonal complex ST-11 (MenW:cc11) strains led to introduction of conjugate MenACWY vaccination for teenagers. We investigated the impact of immunization on carriage of targeted meningococci by whole genome sequencing of isolates recovered from a cohort of vaccinated university students. Methods: Strain designation data were extracted from whole genome sequence data. Genomes from carried and invasive MenW:cc11 were compared using a gene-by-gene approach...
November 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29155928/modeling-positional-effects-of-regulatory-sequences-with-spline-transformations-increases-prediction-accuracy-of-deep-neural-networks
#3
Žiga Avsec, Mohammadamin Barekatain, Jun Cheng, Julien Gagneur
Motivation: Regulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries, or polyadenylation site. Deep learning has become the approach of choice for modeling regulatory sequences because of its strength to learn complex sequence features. However, modeling relative distances to genomic landmarks in deep neural networks has not been addressed. Results: Here we developed spline transformation, a neural network module based on splines to flexibly and robustly model distances...
November 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29155820/mass-spectrometry-based-quantification-of-the-cellular-response-to-ultraviolet-radiation-in-hela-cells
#4
Hong Xu, Xuanyi Chen, Nanjiao Ying, Meixia Wang, Xiaoli Xu, Rongyi Shi, Yuejin Hua
Ultraviolet (UV) irradiation is a common form of DNA damage that can cause pyrimidine dimers between DNA, which can cause gene mutations, even double-strand breaks and threaten genome stability. If DNA repair systems default their roles at this stage, the organism can be damaged and result in disease, especially cancer. To better understand the cellular response to this form of damage, we applied highly sensitive mass spectrometry to perform comparative proteomics of phosphorylation in HeLa cells. A total of 4367 phosphorylation sites in 2100 proteins were identified, many of which had not been reported previously...
2017: PloS One
https://www.readbyqxmd.com/read/29155816/liposomal-amphotericin-b-in-travelers-with-cutaneous-and-muco-cutaneous-leishmaniasis-not-a-panacea
#5
Romain Guery, Benoit Henry, Guillaume Martin-Blondel, Claire Rouzaud, Florence Cordoliani, Gundel Harms, Jean-Pierre Gangneux, Françoise Foulet, Emmanuelle Bourrat, Michel Baccard, Gloria Morizot, Paul-Henri Consigny, Antoine Berry, Johannes Blum, Olivier Lortholary, Pierre Buffet
BACKGROUND: Complex cutaneous and muco-cutaneous leishmaniasis (CL and MCL) often requires systemic therapy. Liposomal amphotericin B (L-AmB) has a strong potential for a solid clinical benefit in this indication. METHODS: We conducted a retrospective analysis of data from a French centralized referral treatment program and from the "LeishMan" European consortium database. All patients with parasitologically proven CL or MCL who received at least one dose of L-AmB were included...
November 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29155792/assessment-of-dictyostelium-discoideum-response-to-acute-mechanical-stimulation
#6
Yulia Artemenko, Peter N Devreotes
Chemotaxis, or migration up a gradient of a chemoattractant, is the best understood mode of directed migration. Studies using social amoeba Dictyostelium discoideum revealed that a complex signal transduction network of parallel pathways amplifies the response to chemoattractants, and leads to biased actin polymerization and protrusion of a pseudopod in the direction of a gradient. In contrast, molecular mechanisms driving other types of directed migration, for example, due to exposure to shear flow or electric fields, are not known...
November 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155710/dna-nanotubes-as-a-versatile-tool-to-study-semiflexible-polymers
#7
Jörg Schnauß, Martin Glaser, Jessica S Lorenz, Carsten Schuldt, Christin Möser, Martin Sajfutdinow, Tina Händler, Josef A Käs, David M Smith
Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of flexible polymers nor of rigid rods. Underlying filaments remain outstretched due to their non-vanishing backbone stiffness, which is quantified via the persistence length (lp), but they are also subject to strong thermal fluctuations. Their finite bending stiffness leads to unique, non-trivial collective mechanics of bulk networks, enabling the formation of stable scaffolds at low volume fractions while providing large mesh sizes...
October 25, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155589/the-reaction-mechanism-of-isopentenyl-phosphate-kinase-a-qm-mm-study
#8
James McClory, David J Timson, Warispreet Singh, Jian Zhang, Meilan Huang
Isopentenyl phosphate kinase (IPK) catalyzes the Mg2+-ATP dependent phosphorylation reactions to produce isopentenyl diphosphate, an important precursor in the synthesis of isopentenols. However, the position of the divalent metal ion in the crystal structures of IPK in complex with ATP and its native substrate IP has not been definitively resolved, and as a result ambiguity surrounds the catalytic mechanism of IP, limiting its exploitation as a biofuel and in drug design. Here we report the conformational change caused by substrate binding and the catalytically competent structure in complex with the metal ion Mg2+ using molecular dynamic simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B97d/AMBER99)...
November 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29155562/quantification-of-nanomaterial-nanomedicine-trafficking-in-vivo
#9
Liming Wang, Liang Yan, Jing Liu, Chunying Chen, Yuliang Zhao
Absorption, distribution, metabolism and excretion (ADME) of nanomaterials (NMs) or nanomedicines (NMs), are fundamental biological processes that dominate their nanomedical functions or nanotoxicities. Mostly, NMs exist in biological systems as a form of nanoparticles (NPs). However, to determine the composition, spatial distribution, and states of existence of NMs/NPs in vivo, upon entry into the body, as well as to monitor the dynamic changes of these information over time remain a challenge for the current analytical methodology due to their limited efficiently in characterizing interactions between these complex(nano)-complex(bio) systems...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29155296/optogenetic-manipulation-of-ens-the-brain-in-the-gut
#10
REVIEW
Wei Wang
Optogenetics has emerged as an important tool in neuroscience, especially in central nervous system research. It allows for the study of the brain's highly complex network with high temporal and spatial resolution. The enteric nervous system (ENS), the brain in the gut, plays critical roles for life. Although advanced progress has been made, the neural circuits of the ENS remain only partly understood because the appropriate research tools are lacking. In this review, I highlight the potential application of optogenetics in ENS research...
November 16, 2017: Life Sciences
https://www.readbyqxmd.com/read/29154818/microrna-21-promotes-wound-healing-via-the-smad7-smad2-3-elastin-pathway
#11
Xiaoyan Li, Lijia Guo, Yitong Liu, Yingying Su, Yongmei Xie, Juan Du, Songling Wang, Hao Wang, Yi Liu
Wound healing is regulated by a complex network of cells, molecules, and cytokines, as well as microRNAs (miRNAs). miRNAs were confirmed to influence the wound healing process, and miR-21, an important member of the miRNA family, was also shown to regulate wound healing. The aim of the present study was to investigate the role of miR-21 in the wound healing process and the possible underlying cell signaling pathways. We isolated GMSCs from WT and miR-21-KO mouse gingiva. Flow cytometric analysis and immunocytofluorescense staining were used to identify the GMSCs acquired from WT and miR-21-KO mice...
November 14, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/29154475/identification-and-analysis-of-a-key-long-non-coding-rnas-lncrnas-associated-module-reveal-functional-lncrnas-in-cardiac-hypertrophy
#12
Jian Zhang, Chenchen Feng, Chao Song, Bo Ai, Xuefeng Bai, Yuejuan Liu, Xuecang Li, Jianmei Zhao, Shengshu Shi, Xin Chen, Xiaojie Su, Chunquan Li
Cardiac hypertrophy (CH) is a common disease that originates from long-term heart pressure overload and finally leads to heart failure. Recently, long non-coding RNAs (lncRNAs) have attracted attention because they have broad and crucial functions in regulating complex biological processes. Some studies had found that lncRNAs play vital roles in complex cardiovascular diseases. However, the function and mechanism of lncRNAs in CH have not been elucidated. In our study, to investigate the potential roles of lncRNAs in CH, the Cardiac Hypertrophy-associated LncRNAs-Protein coding genes Network (CHLPN) was constructed by integrating gene microarray re-annotation and subpathway enrichment analyses...
November 20, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29153892/penalized-estimation-of-sparse-concentration-matrices-based-on-prior-knowledge-with-applications-to-placenta-elemental-data
#13
Jai Woo Lee, Tracy Punshon, Erika L Moen, Margaret R Karagas, Jiang Gui
Identifying patterns of association or dependency among high-dimensional biological datasets with sparse precision matrices remains a challenge. In this paper, we introduce a weighted sparse Gaussian graphical model that can incorporate prior knowledge to infer the structure of the network of trace element concentrations, including essential elements as well as toxic metals and metaloids measured in the human placentas. We present the weighted L1 penalized regularization procedure for estimating the sparse precision matrix in the setting of Gaussian graphical models...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29152994/decreased-connectivity-and-increased-bold-complexity-in-the-default-mode-network-in-individuals-with-chronic-fatigue-syndrome
#14
Zack Y Shan, Kevin Finegan, Sandeep Bhuta, Timothy Ireland, Donald R Staines, Sonya M Marshall-Gradisnik, Leighton R Barnden
The chronic fatigue syndrome / myalgic encephalomyelitis (CFS) is a debilitating disease with unknown pathophysiology and no diagnostic test. This study investigated the default mode network (DMN) in order to understand the pathophysiology of CFS and to identify potential biomarkers. Using functional MRI (fMRI) collected from 72 subjects (45 CFS and 27 controls) with a temporal resolution of 0.798s, we evaluated the default mode network using static functional connectivity (FC), dynamic functional connectivity (DFC) and DFC complexity, blood oxygenation level dependent (BOLD) activation maps and complexity of activity...
November 20, 2017: Brain Connectivity
https://www.readbyqxmd.com/read/29152905/the-gait-translational-control-system
#15
REVIEW
Abul Arif, Peng Yao, Fulvia Terenzi, Jie Jia, Partho Sarothi Ray, Paul L Fox
The interferon (IFN)-γ-activated inhibitor of translation (GAIT) system directs transcript-selective translational control of functionally related genes. In myeloid cells, IFN-γ induces formation of a multiprotein GAIT complex that binds structural GAIT elements in the 3'-untranslated regions (UTRs) of multiple inflammation-related mRNAs, including ceruloplasmin and VEGF-A, and represses their translation. The human GAIT complex is a heterotetramer containing glutamyl-prolyl tRNA synthetase (EPRS), NS1-associated protein 1 (NSAP1), ribosomal protein L13a (L13a), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH)...
November 20, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29152819/the-application-of-systems-thinking-concepts-methods-and-tools-to-global-health-practices-an-analysis-of-case-studies
#16
Jessica Wilkinson, Morgan Goff, Evan Rusoja, Carl Hanson, Robert Chad Swanson
OBJECTIVES: This review of systems thinking (ST) case studies seeks to compile and analyse cases from ST literature and provide practitioners with a reference for ST in health practice. Particular attention was given to (1) reviewing the frequency and use of key ST terms, methods, and tools in the context of health, and (2) extracting and analysing longitudinal themes across cases. METHODS: A systematic search of databases was conducted, and a total of 36 case studies were identified...
November 20, 2017: Journal of Evaluation in Clinical Practice
https://www.readbyqxmd.com/read/29152666/neuroanatomical-background-and-functional-considerations-for-stereotactic-interventions-in-the-h-fields-of-forel
#17
REVIEW
Clemens Neudorfer, Mohammad Maarouf
The H fields of Forel constitute an intricate neuroanatomical structure that occupies a central position within the posterior subthalamus. Anatomically, it features a dense concentration of fiber bundles including corticofugal, pallidothalamic, cerebellothalamic and other projections that connect functionally relevant areas of the brain. Functionally, the fields of Forel are embedded within the cortico-striato-thalamo-cortical circuit and constitute the main link between the striatopallidal system and the thalamocortical network...
November 20, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/29152377/crystal-structure-of-bis-%C3%AE-2-4-bromo-2-2-2-5-bromo-2-oxidobenzylidene-amino-ethyl-sulfanyl-sulfonyl-ethyl-imino-methyl-phenolato-dicopper-ii-dimethylformamide-disolvate
#18
Julia A Rusanova, Dmytro Bederak
The title dinuclear copper(II) complex [Cu2(C18H16Br2N2O4S2)2] was prepared by direct synthesis of a dianionic Schiff base derived from 5-bromo-salicyl-aldehyde and cyste-amine. The discrete mol-ecules lie across inversion centers and crystallize with two di-methyl-formamide (DMF) mol-ecules of crystallization. The unique Cu(II) ion is four-coordinated by two tetra-dentate Schiff base ligands in a distorted square-planar N2O2 environment. In the crystal, short inter-molecular S⋯Br contacts, weak C-H⋯O hydrogen bonds and intra- and inter-molecular π-π stacking inter-actions between rings of the ligand link the components into a two-dimensional network parallel to (010)...
November 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/29152374/crystal-structure-of-bis-pyridine-4-carbo-thio-amide-%C3%AE%C2%BAn-1-bis-thio-cyanato-%C3%AE%C2%BAn-cobalt-ii-methanol-monosolvate
#19
Tristan Neumann, Inke Jess, Christian Näther
The asymmetric unit of the title compound, [Co(NCS)2(C6H6NS)4]·CH3OH, consists of one cobalt(II) cation, two thio-cyanate anions, four pyridine-4-carbo-thio-amide ligands and one methanol mol-ecule that are located in general positions. The Co(II) cations are coordinated by two terminal N-bonding thio-cyanate anions and four N-bonding pyridine-4-carbo-thio-amide ligands, resulting in discrete and slightly distorted octa-hedral complexes. These complexes are linked into a three-dimensional network via inter-molecular N-H⋯S hydrogen bonding between the amino H atoms and the thio-cyanate and pyridine-4-carbo-thio-amide S atoms...
November 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/29152368/synthesis-crystal-structure-and-hirshfeld-surface-analysis-of-a-polymeric-bis-muthate-iii-halide-complex-c6h6n3-2-bicl5-%C3%A2-2h2o
#20
Chaima Boukoum, Zouhaier Aloui, Valeria Ferretti, Sonia Abid
The synthesis and the crystal structure of a new halide-bridged polymer, namely catena-poly[bis-(1,2,3-benzotriazolium) [[tetra-chlorido-bis-muth(III)]-μ-chlorido] dihydrate], {(C6H6N3)2[BiCl5]·2H2O} n are reported. The structure comprises polyanionic zigzag chains of formula [(BiCl5)(2-)] n running along the c-axis direction. The 1,2,3-benzotriazolium cations are linked between these polymer chains, via the water mol-ecules, giving rise to left- and right-handed helical chains. Hirshfeld surface analysis and fingerprint plots were used to decode the inter-molecular inter-actions in the crystal network and determine the contribution of the component units for the construction of the three-dimensional architecture...
November 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
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