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https://read.qxmd.com/read/30786165/integrating-bacterial-chip-seq-and-rna-seq-data-with-snakechunks
#1
Claire Rioualen, Lucie Charbonnier-Khamvongsa, Julio Collado-Vides, Jacques van Helden
Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on big datasets. Although user-friendly interfaces now exist, there remains a strong need for accessible solutions that allow experimental biologists to analyze and explore their results in an autonomous and flexible way. The protocols here describe a modular system that enable a user to compose and fine-tune workflows based on SnakeChunks, a library of rules for the Snakemake workflow engine (Köster and Rahmann, 2012)...
February 20, 2019: Current Protocols in Bioinformatics
https://read.qxmd.com/read/30784635/effect-of-a-novel-vital-sign-device-on-maternal-mortality-and-morbidity-in-low-resource-settings-a-pragmatic-stepped-wedge-cluster-randomised-controlled-trial
#2
Nicola Vousden, Elodie Lawley, Hannah L Nathan, Paul T Seed, Muchabayiwa Francis Gidiri, Shivaprasad Goudar, Jane Sandall, Lucy C Chappell, Andrew H Shennan
BACKGROUND: In 2015, an estimated 303 000 women died in pregnancy and childbirth. Obstetric haemorrhage, sepsis, and hypertensive disorders of pregnancy account for more than 50% of maternal deaths worldwide. There are effective treatments for these pregnancy complications, but they require early detection by measurement of vital signs and timely administration to save lives. The primary aim of this trial was to determine whether implementation of the CRADLE Vital Sign Alert and an education package into community and facility maternity care in low-resource settings could reduce a composite of all-cause maternal mortality or major morbidity (eclampsia and hysterectomy)...
March 2019: Lancet Global Health
https://read.qxmd.com/read/30784059/from-identification-to-functional-characterization-of-cyriotoxin-1a-an-antinociceptive-toxin-from-cyriopagopus-schioedtei-spider
#3
Tânia C Gonçalves, Evelyne Benoit, Michael Kurz, Laetitia Lucarain, Sophie Fouconnier, Stéphanie Combemale, Lucie Jaquillard, Brigitte Schombert, Jean-Marie Chambard, Rachid Boukaiba, Gerhard Hessler, Andrees Bohme, Laurent Bialy, Stéphane Hourcade, Rémy Béroud, Michel De Waard, Denis Servent, Michel Partiseti
BACKGROUND AND PURPOSE: NaV 1.7 channel subtype is highly expressed in dorsal root ganglia of the sensory nervous system and plays a central role in the pain signaling process. We investigated a library prepared from original venoms of 117 different animals to identify new selective inhibitors of this target. EXPERIMENTAL APPROACH: We used high-throughput screening of a large venom collection using automated patch-clamp experiments on human voltage-gated sodium channel subtypes, and then in vitro and in vivo electrophysiological experiments to characterize the active peptides that have been purified, sequenced and chemically synthesized...
February 19, 2019: British Journal of Pharmacology
https://read.qxmd.com/read/30783988/aav-mediated-gene-delivery-to-the-enteric-nervous-system-by-intracolonic-injection
#4
Reshma Gore, Maureen S Riedl, Kelley F Kitto, Carolyn A Fairbanks, Lucy Vulchanova
The enteric nervous system of the lower gastrointestinal tract comprises intrinsic neural circuits as well as extrinsic afferent and efferent innervation. The development of strategies for neuronal gene transfer has created new opportunities for functional analysis, circuit mapping, and neuromodulation in the enteric nervous system. Studies of AAV-mediated gene transfer to enteric neurons and dorsal root ganglion neurons (DRG) have provided proofs-of-concept for the utility of AAV vectors for genetic manipulations of the intrinsic and extrinsic components of the enteric nervous system...
2019: Methods in Molecular Biology
https://read.qxmd.com/read/30783975/aav-mediated-gene-delivery-to-the-spinal-cord-by-intrathecal-injection
#5
Cristina D Peterson, Alexander G J Skorput, Kelley F Kitto, George L Wilcox, Lucy Vulchanova, Carolyn A Fairbanks
Gene therapy targeting the spinal cord is an important tool for analyzing mechanisms of nervous system diseases and the development of gene therapies. Analogous to a lumbar puncture in humans, the rodent spinal cord can be accessed through an efficient, noninvasive injection. Here we describe a method for AAV-mediated gene transfer to cells of the spinal cord by intrathecal injection of small quantities of AAV vector.
2019: Methods in Molecular Biology
https://read.qxmd.com/read/30783821/quantitative-magnetic-resonance-evaluation-of-the-trigeminal-nerve-in-familial-dysautonomia
#6
Eugene Won, Jose-Alberto Palma, Horacio Kaufmann, Sarah S Milla, Benjamin Cohen, Lucy Norcliffe-Kaufmann, James S Babb, Yvonne W Lui
PURPOSE: Familial dysautonomia (FD) is a rare autosomal recessive disease that affects the development of sensory and autonomic neurons, including those in the cranial nerves. We aimed to determine whether conventional brain magnetic resonance imaging (MRI) could detect morphologic changes in the trigeminal nerves of these patients. METHODS: Cross-sectional analysis of brain MRI of patients with genetically confirmed FD and age- and sex-matched controls. High-resolution 3D gradient-echo T1-weighted sequences were used to obtain measurements of the cisternal segment of the trigeminal nerves...
February 19, 2019: Clinical Autonomic Research: Official Journal of the Clinical Autonomic Research Society
https://read.qxmd.com/read/30782680/corticosteroids-injections-versus-corticosteroids-with-hyaluronic-acid-injections-in-rhizarthrosis-the-randomised-multicentre-rhiz-art-trial-study-protocol
#7
Grégoire Cormier, Benoit Le Goff, Amélie Denis, Stéphane Varin, Lucie Auzanneau, Jérôme Dimet, Aurélie Le Thuaut
INTRODUCTION: Osteoarthritis of the trapeziometacarpal joint affects approximately 10%-25% of women, especially those who are postmenopausal. It may result in thumb dysfunction. Among the treatments, intra-articular injections of corticosteroid (CS) and hyaluronic acid (HA) are both effective and recommended. However, clinical trials have shown that HA improves functional capacity, whereas CS only produces a decrease in pain. The synergy of these two drugs has not been evaluated. The primary goal of this study was to determine whether the association between HA and CS produce an additional decrease of more pain during thumb movement at three months postinjection, compared to the level of pain relief from CS alone...
January 9, 2019: BMJ Open
https://read.qxmd.com/read/30782668/early-life-microbiota-exposure-restricts-myeloid-derived-suppressor-cell-driven-colonic-tumorigenesis
#8
Akihito Harusato, Emilie Viennois, Lucie Etienne-Mesmin, Shingo Matsuyama, Hirohito Abo, Satoru Osuka, Nicholas W Lukacs, Yuji Naito, Yoshito Itoh, Jian-Dong Li, Didier Merlin, Andrew T Gewirtz, Timothy L Denning
Gut microbiota and their metabolites are instrumental in regulating homeostasis at intestinal and extra-intestinal sites. However, the complex effects of prenatal and early postnatal microbial exposure on adult health and disease outcomes remain incompletely understood. Here, we showed that mice raised under germ-free conditions until weaning and then transferred to specific-pathogen free conditions, harbored altered microbiota composition, augmented inflammatory cytokine and chemokine expression, and were hyper-susceptible to colitis-associated tumorigenesis later in adulthood...
February 19, 2019: Cancer Immunology Research
https://read.qxmd.com/read/30782142/physical-activity-related-health-and-economic-benefits-of-building-walkable-neighbourhoods-a-modelled-comparison-between-brownfield-and-greenfield-developments
#9
Belén Zapata-Diomedi, Claire Boulangé, Billie Giles-Corti, Kath Phelan, Simon Washington, J Lennert Veerman, Lucy Dubrelle Gunn
BACKGROUND: A consensus is emerging in the literature that urban form can impact health by either facilitating or deterring physical activity (PA). However, there is a lack of evidence measuring population health and the economic benefits relating to alternative urban forms. We examined the issue of housing people within two distinct types of urban development forms: a medium-density brownfield development in an established area with existing amenities (e.g. daily living destinations, transit), and a low-density suburban greenfield development...
February 20, 2019: International Journal of Behavioral Nutrition and Physical Activity
https://read.qxmd.com/read/30779744/functional-lability-of-rna-dependent-rna-polymerases-in-animals
#10
Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Hector Escrivá, Hervé Seitz
RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency...
February 19, 2019: PLoS Genetics
https://read.qxmd.com/read/30778868/the-experience-of-intolerance-of-uncertainty-for-young-people-with-a-restrictive-eating-disorder-a-pilot-study
#11
Anna Konstantellou, Lucy Hale, Lot Sternheim, Mima Simic, Ivan Eisler
PURPOSE: Research is consistently reporting elevated levels of intolerance of uncertainty (IU) in individuals with an eating disorder (ED). Less is known about the phenomenology of uncertainty for this clinical group. The present study aims to advance our understanding of the relationship between IU and restrictive EDs by providing insight into young people's subjective experiences of uncertainty. METHODS: Thirteen young people with a restrictive ED were recruited from multi-family therapy groups run within the Maudsley Centre for Child and Adolescent Eating Disorders at the South London and Maudsley NHS Foundation Trust...
February 16, 2019: Eating and Weight Disorders: EWD
https://read.qxmd.com/read/30778715/oncology-nurse-phone-calls-halve-the-risk-of-reduced-dose-intensity-of-immunochemotherapy-results-of-the-randomized-fortis-study-in-chronic-lymphocytic-leukemia
#12
Loic Ysebaert, Marie Larcher, Gisele Compaci, Lucie Oberic, Laurence Sahnes, Anne Banos, Carla Araujo, Agnes Sommet, Guy Laurent, Fabien Despas
Delivering of > 80% planned relative dose intensity (RDI) of fludarabine-cyclophosphamide-rituximab (FCR) is key to benefit from longer progression free survival (PFS) and survivals in CLL. In this randomized trial, we sought to investigate whether a telephone intervention strategy (called AMA) delivered by an oncology nurse could reduce the risk of RDI < 80% by alleviating adverse events and supporting patients' adherence. Sixty FCR patients were randomized 1:1 for AMA (stratified on Binet stage C)...
February 18, 2019: Annals of Hematology
https://read.qxmd.com/read/30778122/metabolic-adaptation-of-adherent-invasive-escherichia-coli-to-exposure-to-bile-salts
#13
Julien Delmas, Lucie Gibold, Tiphanie Faïs, Sylvine Batista, Martin Leremboure, Clara Sinel, Emilie Vazeille, Vincent Cattoir, Anthony Buisson, Nicolas Barnich, Guillaume Dalmasso, Richard Bonnet
The adherent-invasive Escherichia coli (AIEC), which colonize the ileal mucosa of Crohn's disease patients, adhere to intestinal epithelial cells, invade them and exacerbate intestinal inflammation. The high nutrient competition between the commensal microbiota and AIEC pathobiont requires the latter to occupy their own metabolic niches to survive and proliferate within the gut. In this study, a global RNA sequencing of AIEC strain LF82 has been used to observe the impact of bile salts on the expression of metabolic genes...
February 18, 2019: Scientific Reports
https://read.qxmd.com/read/30777900/clinical-effectiveness-of-single-dose-of-intravenous-dexamethasone-on-the-duration-of-ropivacaine-axillary-brachial-plexus-block-the-randomized-placebo-controlled-adexa-trial
#14
Jean-Christophe Clement, Guillaume Besch, Marc Puyraveau, Tommy Grelet, David Ferreira, Lucie Vettoretti, Sébastien Pili-Floury, Emmanuel Samain, Francis Berthier
BACKGROUND AND OBJECTIVES: The effect of intravenous dexamethasone on the duration of axillary plexus block performed using ropivacaine is not described. The aim of this study is to assess the effect of intravenous dexamethasone on the duration of axillary plexus block analgesia after distal upper arm surgery. METHODS: In this prospective, randomized, placebo-controlled, double-blinded trial, consenting patients scheduled for hand or forearm surgery under ultrasound-guided axillary plexus block performed using 0...
March 2019: Regional Anesthesia and Pain Medicine
https://read.qxmd.com/read/30777678/distal-skin-vasodilation-in-sleep-preparedness-and-its-impact-on-thermal-status-in-preterm-neonates
#15
Véronique Bach, Stéphane Delanaud, Lucie Barcat, Emilie Bodin, Pierre Tourneux, Jean-Pierre Libert
OBJECTIVE: Prior to sleep onset in human adults, distal body temperatures change progressively from wakefulness levels (low skin temperatures and a high core temperature) to sleep levels (high skin temperatures and a low core temperature) due to distal skin vasodilation and greater body cooling. It is not known whether this sleep preparedness exists in preterm neonates, even though sleep has a key role in neonatal health and neurodevelopment. The present study's objectives were to determine whether sleep preparedness (as observed in adults) can be evidenced in preterm neonates, and to assess repercussions on thermal stress...
February 1, 2019: Sleep Medicine
https://read.qxmd.com/read/30776675/generation-of-human-ipscs-from-fetal-prostate-fibroblasts-hprf
#16
Zuzana Kahounová, Eva Slabáková, Lucia Binó, Ján Remšík, Radek Fedr, Jan Bouchal, Radek Vrtěl, Lucie Jurečková, Volodymyr Porokh, Darja Páralová, Aleš Hampl, Karel Souček
Human induced pluripotent stem cell line was generated from commercially available primary human prostate fibroblasts HPrF derived from a fetus, aged 18-24 weeks of gestation. The fibroblast cell line was reprogrammed with Yamanaka factors (OCT4, SOX2, c-MYC, KLF4) using CytoTune™-iPS 2.0 Sendai Reprogramming Kit. Pluripotency of the derived transgene-free iPS cell line was confirmed both in vitro by detecting the expression of factors of pluripotency on a single-cell level, and in vivo using teratoma formation assay...
February 7, 2019: Stem Cell Research
https://read.qxmd.com/read/30776510/genome-mining-and-prospects-for-antibiotic-discovery
#17
REVIEW
Lucy Foulston
Natural products are a rich source of bioactive compounds that have been used successfully in the areas of human health from infectious disease to cancer; however, traditional fermentation-based screening has provided diminishing returns over the last 20-30 years. Solutions to the unmet need of resistant bacterial infection are critically required. Technological advances in high-throughput genomic sequencing, coupled with ever-decreasing cost, are now presenting a unique opportunity for the reinvigoration of natural product discovery...
February 15, 2019: Current Opinion in Microbiology
https://read.qxmd.com/read/30776136/real-world-insights-into-risk-of-developing-cardiovascular-disease-following-gnrh-agonists-versus-antagonists-for-prostate-cancer-a-methodological-protocol-to-a-study-using-five-european-databases
#18
Gincy George, Lucie-Marie Scailteux, Hans Garmo, Frédéric Balusson, Christopher Cardwell, Greet De Coster, Harlinde De Schutter, Josephina G Kuiper, Úna McMenamin, Julie Verbeeck, Mieke Van Hemelrijck
One of the more recently investigated adverse long-term side effects of gonadotropin-releasing hormone (GnRH) agonists for prostate cancer (PCa) is cardiovascular disease (CVD). Studies suggest lower risk of CVD following GnRH antagonists (degarelix) than GnRH agonists. This protocol describes precise codes used to extract variables from five European databases for a study that compares risk of CVD following GnRH agonists and antagonists for PCa. PCa men on primary GnRH agonists or antagonists were identified from the UK THIN (The Health Improvement Network) database, National Health Service (NHS) Scotland, Belgian Cancer Registry (BCR), Dutch PHARMO Database Network and French National Database (SNIIRAM)...
February 18, 2019: Fundamental & Clinical Pharmacology
https://read.qxmd.com/read/30775267/a-web-based-intervention-for-carers-of-individuals-with-anorexia-nervosa-we-can-trial-protocol-of-a-randomised-controlled-trial-investigating-the-effectiveness-of-different-levels-of-support
#19
Lucy Spencer, Juliane Schmidt-Hantke, Karina Allen, Gemma Gordon, Rachel Potterton, Peter Musiat, Franziska Hagner, Ina Beintner, Bianka Vollert, Barbara Nacke, Dennis Görlich, Jennifer Beecham, Eva-Maria Bonin, Corinna Jacobi, Ulrike Schmidt
Background: Anorexia nervosa (AN) is a life-threatening mental disorder that is associated with substantial caregiver burden. Carers of individuals with AN report high levels of distress and self-blame, and insufficient knowledge to help their loved ones. However, carers can have a very important role to play in aiding recovery from AN, and are often highly motivated to assist in the treatment process. This manuscript presents the protocol for a randomised controlled trial (RCT) of We Can, a web-based intervention for carers for people with AN...
April 2019: Internet Interventions: the Application of Information Technology in Mental and Behavioural Health
https://read.qxmd.com/read/30775263/web-based-indicated-prevention-of-common-mental-disorders-in-university-students-in-four-european-countries-study-protocol-for-a-randomised-controlled-trial
#20
Peter Musiat, Rachel Potterton, Gemma Gordon, Lucy Spencer, Michael Zeiler, Karin Waldherr, Stefanie Kuso, Martina Nitsch, Tanja Adamcik, Gudrun Wagner, Andreas Karwautz, David Daniel Ebert, Alyson Dodd, Barbara Dooley, Amy Harrison, Emma Whitt, Mark Haselgrove, Helen Sharpe, Jo Smith, Rosie Tressler, Nicholas Troop, Chantal Vinyard, Dennis Görlich, Jenny Beecham, Eva Bonin, Corinna Jacobi, Ulrike Schmidt
Background: Mental disorders and their symptoms are highly prevalent in the university student population, and the transition from secondary to tertiary education is associated with a rise in mental health problems. Existing web-based interventions for the prevention of common mental disorders in student populations often focus on just one disorder and have not been designed specifically for students. There is thus a need for transdiagnostic, student-specific preventative interventions that can be widely disseminated...
April 2019: Internet Interventions: the Application of Information Technology in Mental and Behavioural Health
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