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https://www.readbyqxmd.com/read/28934976/desman-a-new-tool-for-de-novo-extraction-of-strains-from-metagenomes
#1
Christopher Quince, Tom O Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E Darling, Gavin Collins, A Murat Eren
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28932695/disequilibrium-calorimetry-for-determination-of-ultrasonic-power-in-sonochemistry
#2
Mario Plattes, Christian Köhler, Tom Gallé
The two most characteristic properties of an ultrasonic wave are the frequency and the power. It is therefore important to determine the power in a given reactor. This can be done by calorimetry, i.e. by measuring the temperature rise in the vessel during sonication starting at thermal equilibrium with the surroundings (classic calorimetry) [1-3]. However, the classic ultrasonic calorimetry has drawbacks. In particular it is difficult to evaluate the temperature rise at thermal equilibrium, because the relevant initial time and temperature intervals are small and measurement errors in the temperature readings are large...
2017: MethodsX
https://www.readbyqxmd.com/read/28920952/mk2-phosphorylation-of-ripk1-regulates-tnf-mediated-cell-death
#3
Yves Dondelinger, Tom Delanghe, Diego Rojas-Rivera, Dario Priem, Tinneke Delvaeye, Inge Bruggeman, Franky Van Herreweghe, Peter Vandenabeele, Mathieu J M Bertrand
TNF is a master proinflammatory cytokine whose pathogenic role in inflammatory disorders can, in certain conditions, be attributed to RIPK1 kinase-dependent cell death. Survival, however, is the default response of most cells to TNF stimulation, indicating that cell demise is normally actively repressed and that specific checkpoints must be turned off for cell death to proceed. We identified RIPK1 as a direct substrate of MK2 in the TNFR1 signalling pathway. Phosphorylation of RIPK1 by MK2 limits cytosolic activation of RIPK1 and the subsequent assembly of the death complex that drives RIPK1 kinase-dependent apoptosis and necroptosis...
September 18, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28915904/tiga-cub-manualised-psychoanalytic-child-psychotherapy-versus-treatment-as-usual-for-children-aged-5-11-years-with-treatment-resistant-conduct-disorders-and-their-primary-carers-study-protocol-for-a-randomised-controlled-feasibility-trial
#4
Elizabeth Edginton, Rebecca Walwyn, Kayleigh Burton, Robert Cicero, Liz Graham, Sadie Reed, Sandy Tubeuf, Maureen Twiddy, Alex Wright-Hughes, Lynda Ellis, Dot Evans, Tom Hughes, Nick Midgley, Paul Wallis, David Cottrell
BACKGROUND: The National Institute for Health and Care Excellence (NICE) recommends evidence-based parenting programmes as a first-line intervention for conduct disorders (CD) in children aged 5-11 years. As these are not effective in 25-33% of cases, NICE has requested research into second-line interventions. Child and Adolescent Psychotherapists (CAPTs) address highly complex problems where first-line treatments have failed and there have been small-scale studies of Psychoanalytic Child Psychotherapy (PCP) for CD...
September 15, 2017: Trials
https://www.readbyqxmd.com/read/28915897/development-of-a-complex-intervention-to-promote-appropriate-prescribing-and-medication-intensification-in-poorly-controlled-type-2-diabetes-mellitus-in-irish-general-practice
#5
Mark E Murphy, Molly Byrne, Atieh Zarabzadeh, Derek Corrigan, Tom Fahey, Susan M Smith
BACKGROUND: Poorly controlled type 2 diabetes mellitus (T2DM) can be seen as failure to meet recommended targets for management of key risk factors including glycaemic control, blood pressure and lipids. Poor control of risk factors is associated with significant morbidity, mortality and healthcare costs. Failure to intensify medications for patients with poor control of T2DM when indicated is called clinical inertia and is one contributory factor to poor control of T2DM. We aimed to develop a theory and evidence-based complex intervention to improve appropriate prescribing and medication intensification in poorly controlled T2DM in Irish general practice...
September 16, 2017: Implementation Science: IS
https://www.readbyqxmd.com/read/28912165/holistic-care-of-complicated-tuberculosis-in-healthcare-settings-with-limited-resources
#6
Trevor Duke, Sharon Kasa Tom, Harry Poka, Henry Welch
In recent years, most of the focus on improving the quality of paediatric care in low-income countries has been on improving primary care using the Integrated Management of Childhood Illness, and improving triage and emergency treatment in hospitals aimed at reducing deaths in the first 24 hours. There has been little attention paid to improving the quality of care for children with chronic or complex diseases. Children with complicated forms of tuberculosis (TB), including central nervous system and chronic pulmonary TB, provide examples of acute and chronic multisystem paediatric illnesses that commonly present to district-level and second-level referral hospitals in low-income countries...
September 14, 2017: Archives of Disease in Childhood
https://www.readbyqxmd.com/read/28911095/understanding-mutational-effects-in-digenic-diseases
#7
Andrea Gazzo, Daniele Raimondi, Dorien Daneels, Yves Moreau, Guillaume Smits, Sonia Van Dooren, Tom Lenaerts
To further our understanding of the complexity and genetic heterogeneity of rare diseases, it has become essential to shed light on how combinations of variants in different genes are responsible for a disease phenotype. With the appearance of a resource on digenic diseases, it has become possible to evaluate how digenic combinations differ in terms of the phenotypes they produce. All instances in this resource were assigned to two classes of digenic effects, annotated as true digenic and composite classes...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28910288/genomics-enabled-analysis-of-the-emergent-disease-cotton-bacterial-blight
#8
Anne Z Phillips, Jeffrey C Berry, Mark C Wilson, Anupama Vijayaraghavan, Jillian Burke, J Imani Bunn, Tom W Allen, Terry Wheeler, Rebecca S Bart
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv...
September 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28901669/automating-tasks-in-protein-structure-determination-with-the-clipper-python-module
#9
Stuart McNicholas, Tristan Croll, Tom Burnley, Colin M Palmer, Soon Wen Hoh, Huw T Jenkins, Eleanor Dodson, Kevin Cowtan, Jon Agirre
Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalised for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language...
September 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28898696/a-dual-role-of-caspase-8-in-triggering-and-sensing-proliferation-associated-dna-damage-a-key-determinant-of-liver-cancer-development
#10
Yannick Boege, Mohsen Malehmir, Marc E Healy, Kira Bettermann, Anna Lorentzen, Mihael Vucur, Akshay K Ahuja, Friederike Böhm, Joachim C Mertens, Yutaka Shimizu, Lukas Frick, Caroline Remouchamps, Karun Mutreja, Thilo Kähne, Devakumar Sundaravinayagam, Monika J Wolf, Hubert Rehrauer, Christiane Koppe, Tobias Speicher, Susagna Padrissa-Altés, Renaud Maire, Jörn M Schattenberg, Ju-Seong Jeong, Lei Liu, Stefan Zwirner, Regina Boger, Norbert Hüser, Roger J Davis, Beat Müllhaupt, Holger Moch, Henning Schulze-Bergkamen, Pierre-Alain Clavien, Sabine Werner, Lubor Borsig, Sanjiv A Luther, Philipp J Jost, Ricardo Weinlich, Kristian Unger, Axel Behrens, Laura Hillert, Christopher Dillon, Michela Di Virgilio, David Wallach, Emmanuel Dejardin, Lars Zender, Michael Naumann, Henning Walczak, Douglas R Green, Massimo Lopes, Inna Lavrik, Tom Luedde, Mathias Heikenwalder, Achim Weber
Concomitant hepatocyte apoptosis and regeneration is a hallmark of chronic liver diseases (CLDs) predisposing to hepatocellular carcinoma (HCC). Here, we mechanistically link caspase-8-dependent apoptosis to HCC development via proliferation- and replication-associated DNA damage. Proliferation-associated replication stress, DNA damage, and genetic instability are detectable in CLDs before any neoplastic changes occur. Accumulated levels of hepatocyte apoptosis determine and predict subsequent hepatocarcinogenesis...
September 11, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28888283/in-home-firearm-access-among-us-adolescents-and-the-role-of-religious-subculture-results-from-a-nationally-representative-study
#11
Samuel Stroope, Joshua C Tom
Religious participation is linked to numerous positive safety outcomes for adolescents. Scant attention, however, has been paid to associations between religious participation and safety risks among adolescents. Using data from Add Health (N = 18,449), a nationally representative school-based sample of US adolescents, this study examines the relationship between adolescents' religious affiliation and easy access to firearms at home. Regression analyses adjust for complex sampling design and compare easy firearm access at home among conservative Protestant adolescents to adolescent firearm access in other religious traditions...
September 2017: Social Science Research
https://www.readbyqxmd.com/read/28887948/psoriasis-pathogenesis-and-the-development-of-novel-targeted-immune-therapies
#12
REVIEW
Jason E Hawkes, Tom C Chan, James G Krueger
Psoriasis is caused by a complex interplay between the immune system, psoriasis-associated susceptibility loci, autoantigens, and multiple environmental factors. Over the last 2 decades, research has unequivocally shown that psoriasis represents a bona fide T cell-mediated disease primarily driven by pathogenic T cells that produce high levels of IL-17 in response to IL-23. The discovery of the central role for the IL-23/type 17 T-cell axis in the development of psoriasis has led to a major paradigm shift in the pathogenic model for this condition...
September 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28887226/reconciling-the-different-faces-of-hippocampal-theta-the-role-of-theta-oscillations-in-cognitive-emotional-and-innate-behaviors
#13
REVIEW
Tatiana Korotkova, Alexey Ponomarenko, Caitlin K Monaghan, Steven L Poulter, Francesca Cacucci, Tom Wills, Michael E Hasselmo, Colin Lever
The theta oscillation (5-10Hz) is a prominent behavior-specific brain rhythm. This review summarizes studies showing the multifaceted role of theta rhythm in cognitive functions, including spatial coding, time coding and memory, exploratory locomotion and anxiety-related behaviors. We describe how activity of hippocampal theta rhythm generators - medial septum, nucleus incertus and entorhinal cortex, links theta with specific behaviors. We review evidence for functions of the theta-rhythmic signaling to subcortical targets, including lateral septum...
September 5, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28884668/borrelia-lanei-sp-nov-extends-the-diversity-of-borrelia-species-in-california
#14
Gabriele Margos, Natalia Fedorova, Joyce E Kleinjan, Christine Hartberger, Tom G Schwan, Andreas Sing, Volker Fingerle
The diversity of Borrelia species discovered in California appears to be particularly high. A divergent group of Borrelia strains collected from Ixodes ticks in California was described by Postic and co-workers and designated 'genomospecies 2' (Postic D, Garnier M, Baranton G. Int J Med Microbiol 2007;297:263-271; Postic D, Ras NM, Lane RS, Hendson M, Baranton G. J Clin Microbiol 1998;36:3497-3504). We performed multilocus sequence analysis (MLSA) using eight housekeeping loci (clpA, clpX, nifS, pepX, pyrG, recG, rplB and uvrA) on 12 strains of this Borreliagenospecies to confirm that these strains form a distinct group within the Borreliaburgdorferi s...
September 8, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28878643/homologous-basal-ganglia-network-models-in-physiological-and-parkinsonian-conditions
#15
Jyotika Bahuguna, Tom Tetzlaff, Arvind Kumar, Jeanette Hellgren Kotaleski, Abigail Morrison
The classical model of basal ganglia has been refined in recent years with discoveries of subpopulations within a nucleus and previously unknown projections. One such discovery is the presence of subpopulations of arkypallidal and prototypical neurons in external globus pallidus, which was previously considered to be a primarily homogeneous nucleus. Developing a computational model of these multiple interconnected nuclei is challenging, because the strengths of the connections are largely unknown. We therefore use a genetic algorithm to search for the unknown connectivity parameters in a firing rate model...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/28873422/evaluating-multiple-causes-of-persistent-low-microwave-backscatter-from-amazon-forests-after-the-2005-drought
#16
Steve Frolking, Stephen Hagen, Bobby Braswell, Tom Milliman, Christina Herrick, Seth Peterson, Dar Roberts, Michael Keller, Michael Palace
Amazonia has experienced large-scale regional droughts that affect forest productivity and biomass stocks. Space-borne remote sensing provides basin-wide data on impacts of meteorological anomalies, an important complement to relatively limited ground observations across the Amazon's vast and remote humid tropical forests. Morning overpass QuikScat Ku-band microwave backscatter from the forest canopy was anomalously low during the 2005 drought, relative to the full instrument record of 1999-2009, and low morning backscatter persisted for 2006-2009, after which the instrument failed...
2017: PloS One
https://www.readbyqxmd.com/read/28866643/influence-of-muscle-mass-in-the-assessment-of-lower-limb-strength-in-copd-validation-of-the-prediction-equation
#17
Ruth Trethewey, Dale Esliger, Emily Petherick, Rachael Evans, Neil Greening, Benjamin James, Andrew Kingsnorth, Mike Morgan, Mark Orme, Lauren Sherar, Sally Singh, Nicole Toms, Michael Steiner
Absence of established reference values limits application of quadriceps maximal voluntary contraction (QMVC) measurement. The impact of muscle mass inclusion in predictions is unclear. Prediction equations encompassing gender, age and size with (FFM+) and without (FFM-), derived in healthy adults (n=175), are presented and compared in two COPD cohorts recruited from primary care (COPD-PC, n=112) and a complex care COPD clinic (COPD-CC, n=189). Explained variance was comparable between the prediction models (R2: FFM+: 0...
September 2, 2017: Thorax
https://www.readbyqxmd.com/read/28863340/assessing-the-long-term-effects-of-land-use-changes-on-runoff-patterns-and-food-production-in-a-large-lake-watershed-with-policy-implications
#18
Zhandong Sun, Tom Lotz, Ni-Bin Chang
Effects of land use development on runoff patterns are salient at a hydrological response unit scale. However, quantitative analysis at the watershed scale is still a challenge due to the complex spatial heterogeneity of the upstream and downstream hydrological relationships and the inherent structure of drainage systems. This study aims to use the well-calibrated Soil and Water Assessment Tool (SWAT) to assess the response of hydrological processes under different land use scenarios in a large lake watershed (Lake Dongting) in the middle Yangtze River basin in China...
August 29, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28855312/cyclodextrin-reduces-cholesterol-crystal-induced-inflammation-by-modulating-complement-activation
#19
Siril S Bakke, Marie H Aune, Nathalie Niyonzima, Katrine Pilely, Liv Ryan, Mona Skjelland, Peter Garred, Pål Aukrust, Bente Halvorsen, Eicke Latz, Jan K Damås, Tom E Mollnes, Terje Espevik
Cholesterol crystals (CC) are abundant in atherosclerotic plaques and promote inflammatory responses via the complement system and inflammasome activation. Cyclic oligosaccharide 2-hydroxypropyl-β-cyclodextrin (BCD) is a compound that solubilizes lipophilic substances. Recently we have shown that BCD has an anti-inflammatory effect on CC via suppression of the inflammasome and liver X receptor activation. The putative effects of BCD on CC-induced complement activation remain unknown. In this study, we found that BCD bound to CC and reduced deposition of Igs, pattern recognition molecules, and complement factors on CC in human plasma...
August 30, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28851439/on-the-global-crispr-array-behavior-in-class-i-systems
#20
Alice Toms, Rodolphe Barrangou
BACKGROUND: Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes...
August 29, 2017: Biology Direct
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