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https://www.readbyqxmd.com/read/28430780/the-importance-of-standardization-for-biodiversity-comparisons-a-case-study-using-autonomous-reef-monitoring-structures-arms-and-metabarcoding-to-measure-cryptic-diversity-on-mo-orea-coral-reefs-french-polynesia
#1
Emma Ransome, Jonathan B Geller, Molly Timmers, Matthieu Leray, Angka Mahardini, Andrianus Sembiring, Allen G Collins, Christopher P Meyer
The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data...
2017: PloS One
https://www.readbyqxmd.com/read/28429739/a-large-scale-benchmark-of-gene-prioritization-methods
#2
Dimitri Guala, Erik L L Sonnhammer
In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429644/a-systematic-review-of-discomfort-due-to-toe-or-ear-clipping-in-laboratory-rodents
#3
Kimberley E Wever, Florentine J Geessink, Michelle A E Brouwer, Alice Tillema, Merel Ritskes-Hoitinga
Toe clipping and ear clipping (also ear notching or ear punching) are frequently used methods for individual identification of laboratory rodents. These procedures potentially cause severe discomfort, which can reduce animal welfare and distort experimental results. However, no systematic summary of the evidence on this topic currently exists. We conducted a systematic review of the evidence for discomfort due to toe or ear clipping in rodents. The review methodology was pre-specified in a registered review protocol...
January 1, 2017: Laboratory Animals
https://www.readbyqxmd.com/read/28428162/the-use-of-intervention-mapping-to-develop-a-tailored-web-based-intervention-condom-him
#4
Joyal Miranda, José Côté
BACKGROUND: Many HIV (human immunodeficiency virus) prevention interventions are currently being implemented and evaluated, with little information published on their development. A framework highlighting the method of development of an intervention can be used by others wanting to replicate interventions or develop similar interventions to suit other contexts and settings. It provides researchers with a comprehensive development process of the intervention. OBJECTIVE: The objective of this paper was to describe how a systematic approach, intervention mapping, was used to develop a tailored Web-based intervention to increase condom use among HIV-positive men who have sex with men...
April 19, 2017: JMIR Public Health and Surveillance
https://www.readbyqxmd.com/read/28426943/how-strong-is-the-evidence-for-using-blood-biomarkers-alone-to-screen-for-alcohol-consumption-during-pregnancy-a-systematic-review
#5
Helen Howlett, Sarah Abernethy, Nigel W Brown, Judith Rankin, William K Gray
Accurate and early identification of women at risk from alcohol consumption during pregnancy allows education and support programmes to be targeted at those most in need. We aimed to conduct a systematic review to compare the efficacy of blood analysis and maternal self-report in detecting at risk women during pregnancy. This review investigated diagnostic accuracy. We searched four databases (Medline, Embase, Psychinfo and CINAHL) for relevant articles and conducted hand searches of recent issues of key journals in the field...
April 5, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28424553/the-world-of-targeted-therapies-in-kidney-cancers-pitfalls-tips-and-tricks
#6
Alexis Vallard, Jane-Chloé Trone, Julien Langrand-Escure, Sophie Espenel, Jean-Baptiste Guy, Chloé Rancoule, Yaoxiong Xia, Anis El Meddeb Hamrouni, Majed Ben Mrad, Nicolas Magné
In the past few years, metastatic renal cell carcinoma prognosis was improved by the development of molecular targeted therapies (TTs). At the metastatic stage, the tolerance to treatment is a major concern, not only because of the challenge of the efficacy/toxicity ratio improvement but also because of the importance of an optimal adherence to oral treatments. The present case series relates the issues of dealing with uncommon and sometimes never described side effects of sunitinib and sorafenib. The first case report deals with grade 3 vomiting during hemodialysis with concurrent administration of sunitinib...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28424546/perspectives-of-older-people-living-in-long-term-care-facilities-and-of-their-family-members-toward-advance-care-planning-discussions-a-systematic-review-and-thematic-synthesis
#7
REVIEW
Veronica Mignani, Francesca Ingravallo, Elena Mariani, Rabih Chattat
OBJECTIVE: We aimed to search and synthesize qualitative studies exploring the perspectives of older people living in long-term care facilities and of their family members about advance care planning (ACP) discussions. METHODS: The enhancing transparency in reporting the synthesis of qualitative research (ENTREQ) framework was used to guide the review and report its results. PubMed, CINAHL, and PsycINFO were searched for studies published between January 2000 and November 2015...
2017: Clinical Interventions in Aging
https://www.readbyqxmd.com/read/28424054/an-unusual-delusion-of-duplication-in-a-patient-affected-by-dementia-with-lewy-bodies
#8
Paolo Solla, Gioia Mura, Antonino Cannas, Gianluca Floris, Davide Fonti, Gianni Orofino, Mauro Giovanni Carta, Francesco Marrosu
BACKGROUND: Dementia with Lewy bodies (DLB) is the second most frequent diagnosis of progressive degenerative dementia in older people. Delusions are common features in DLB and, among them, Capgras syndrome represents the most frequent disturbance, characterized by the recurrent and transient belief that a familiar person, often a close family member or caregiver, has been replaced by an identical-looking imposter. However, other delusional conditions near to misidentification syndromes can occur in DLB patients and may represent a major psychiatric disorder, although rarely studied systematically...
April 19, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28423600/systematic-screening-of-isogenic-cancer-cells-identifies-dusp6-as-context-specific-synthetic-lethal-target-in-melanoma
#9
Stephanie Wittig-Blaich, Rainer Wittig, Steffen Schmidt, Stefan Lyer, Melanie Bewerunge-Hudler, Sabine Gronert-Sum, Olga Strobel-Freidekind, Carolin Müller, Markus List, Aleksandra Jaskot, Helle Christiansen, Mathias Hafner, Dirk Schadendorf, Ines Block, Jan Mollenhauer
Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few technologies are available for the systematic downstream evaluation of these results to identify novel starting points of future cancer therapies.We improved and extended a site-specific recombination-based system for systematic analysis of the individual functions of a large number of candidate genes...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419600/reformulations-of-well-known-active-ingredients-in-the-topical-treatment-of-psoriasis-vulgaris-can-improve-clinical-outcomes-for-patients
#10
REVIEW
L Iversen, E Dauden, S Segaert, K Freeman, S Magina, D Rigopoulos, D Thaci
BACKGROUND: Although the majority of patients with psoriasis vulgaris are treated exclusively with topical therapies, research to develop more effective topical therapies that are associated with higher patient satisfaction has lagged behind the development of systemic agents. OBJECTIVE: The aim of this literature review was to determine whether there is documented evidence that applying an innovative approach to improving the formulation of active ingredients commonly used in the topical treatment of psoriasis can have a positive effect on clinical outcomes and patient-reported outcomes (PROs)...
April 17, 2017: Journal of the European Academy of Dermatology and Venereology: JEADV
https://www.readbyqxmd.com/read/28419194/dminda-2-0-integrated-and-systematic-views-of-regulatory-dna-motif-identification-and-analyses
#11
Jinyu Yang, Xin Chen, Adam McDermaid, Qin Ma
Motivation: Motif identification and analyses are important and have been long-standing computational problems in bioinformatics. Substantial efforts have been made in this field during the past several decades. However, the lack of intuitive and integrative web servers impedes the progress of making effective use of emerging algorithms and tools. Results: Here we present an integrated web server, DMINDA 2.0, which contains: (i) five motif prediction and analyses algorithms, including a phylogenetic footprinting framework; (ii) 2,125 species with complete genomes to support the above five functions, covering animals, plants, and bacteria; and (iii) bacterial regulon prediction and visualization...
April 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28418257/investigating-acquisition-performance-on-the-orbitrap-fusion-when-using-tandem-ms-ms-ms-scanning-with-isobaric-tags
#12
Christopher S Hughes, Victor Spicer, Oleg V Krokhin, Gregg B Morin
Methods for isobaric-tagged peptide analysis (e.g., TMT, iTRAQ), such as the synchronous precursor selection (SPS) tandem MS/MS/MS (MS(3)) approach, enable maintenance of reporter ion accuracy and precision by reducing the ratio compression caused by coisolated precursor ions. However, the decreased throughput of the MS(3) approach necessitates careful optimization of acquisition strategies and methods to ensure maximal proteome coverage. We present a systematic analysis of acquisition parameters used to analyze isobaric-tagged peptide samples on current generation Orbitrap mass spectrometer (MS) hardware...
April 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28416131/discovery-of-benzophosphadiazine-drug-candidate-idx375-a-novel-hepatitis-c-allosteric-ns5b-rdrp-inhibitor
#13
Jean-Laurent Paparin, Agnès Amador, Eric Badaroux, Stéphanie Bot, Catherine Caillet, Thierry Convard, Daniel Da Costa, David Dukhan, Ludovic Griffe, Jean-François Griffon, Massimiliano LaColla, Frédéric Leroy, Michel Liuzzi, Anna Giulia Loi, Joe McCarville, Valeria Mascia, Julien Milhau, Loredana Onidi, Claire Pierra, Rachid Rahali, Elodie Rosinosky, Efisio Sais, Maria Seifer, Dominique Surleraux, David Standring, Cyril B Dousson
Hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells, and as a consequence is an attractive target for selective inhibition. This paper describes the discovery of a novel family of HCV NS5B non-nucleoside inhibitors inspired by the bioisosterism between sulfonamide and phosphonamide. Systematic structural optimization in this new series led to the identification of IDX375, a potent non-nucleoside inhibitor that is selective for genotypes 1a and 1b...
January 13, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28414904/in-silico-prediction-of-chemicals-binding-to-aromatase-with-machine-learning-methods
#14
Hanwen Du, Yingchun Cai, Hongbin Yang, Hongxiao Zhang, Yuhan Xue, Guixia Liu, Yun Tang, Weihua Li
Environmental chemicals may affect endocrine systems through multiple mechanisms, one of which is via effects on aromatase (also known as CYP19A1), an enzyme critical for maintaining the normal balance of estrogens and androgens in the body. Therefore, rapid and efficient identification of aromatase-related endocrine disrupting chemicals (EDCs) is important for toxicology and environment risk assessment. In this study, on the basis of the Tox21 10K compound library, in silico classification models for predicting aromatase binders/non-binders were constructed by machine learning methods...
April 17, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28414017/the-prevalence-of-antenatal-and-postnatal-co-morbid-anxiety-and-depression-a-meta-analysis
#15
K Falah-Hassani, R Shiri, C-L Dennis
To date, the precise prevalence of co-morbidity of anxiety and depression in the perinatal period is not well known. We aimed to estimate the prevalence of co-morbid anxiety and depression in the antenatal and postnatal periods. Systematic searches of multiple electronic databases were conducted for studies published between January 1950 and January 2016. We included 66 (24 published and 42 unpublished) studies incorporating 162 120 women from 30 countries. Prevalence of self-reported antenatal anxiety symptoms and mild to severe depressive symptoms was 9...
April 17, 2017: Psychological Medicine
https://www.readbyqxmd.com/read/28413938/psychiatric-service-users-experiences-of-emergency-departments-a-cerqual-review-of-qualitative-studies
#16
Kathrine Carstensen, Stina Lou, Lotte Groth Jensen, Nina Konstantin Nissen, Lisbeth Ortenblad, Margarete Pfau, Pia Vedel Ankersen
BACKGROUND: There is increased clinical and political attention towards integrating general and psychiatric emergency departments (ED). However, research into psychiatric service users' experiences regarding general EDs is limited. AIM: To identify and summarize current, qualitative evidence regarding service users' experiences attending EDs. A secondary aim is to apply and test the newly developed CERQual approach to summarizing qualitative review findings. METHODS: A systematic literature review of five databases based on PRISMA guidelines yielded 3334 unique entries...
May 2017: Nordic Journal of Psychiatry
https://www.readbyqxmd.com/read/28413135/a-systematic-review-of-the-diagnosis-and-treatment-of-patients-with-neurogenic-hyperactivity-of-the-detrusor-muscle
#17
A Borau, J M Adot, M Allué, S Arlandis, D Castro, M Esteban, J Salinas
BACKGROUND: Neurogenic detrusor hyperactivity (NDH) is a urodynamic observation characterised by involuntary detrusor contractions during the filling phase that are caused by an underlying neurological disease. The common and severe complications that can result from NDH warrant the preparation of healthcare protocols for the proper management of patients with NDH. OBJECTIVE: The aim of this study is to standardise the criteria for the decision-making process in the management of patients with diagnosed or suspected NDH, providing personalised medical care...
April 13, 2017: Actas Urologicas Españolas
https://www.readbyqxmd.com/read/28410573/risk-factors-for-necrotizing-enterocolitis-in-neonates-a-systematic-review-of-prognostic-studies
#18
Noor Samuels, Rob A van de Graaf, Rogier C J de Jonge, Irwin K M Reiss, Marijn J Vermeulen
BACKGROUND: Necrotizing enterocolitis (NEC) is a severe multifactorial disease in preterm neonates associated with high morbidity and mortality. Better insight into prognostic values of the many reported factors associated with NEC is needed to enable identification of neonates at risk for NEC. The aim was to systematically review the literature to identify independent risk factors for NEC from the literature. METHODS: Medline, Cochrane, Embase, Pubmed and Google Scholar were searched systematically for cohort studies reporting prognostic factors for NEC in neonates using multivariable analysis...
April 14, 2017: BMC Pediatrics
https://www.readbyqxmd.com/read/28407781/early-identification-of-patients-requiring-massive-transfusion-embolization-or-hemostatic-surgery-for-traumatic-hemorrhage-a-systematic-review-protocol
#19
Alexandre Tran, Maher Matar, Ewout W Steyerberg, Jacinthe Lampron, Monica Taljaard, Christian Vaillancourt
BACKGROUND: Hemorrhage is a major cause of early mortality following a traumatic injury. The progression and consequences of significant blood loss occur quickly as death from hemorrhagic shock or exsanguination often occurs within the first few hours. The mainstay of treatment therefore involves early identification of patients at risk for hemorrhagic shock in order to provide blood products and control of the bleeding source if necessary. The intended scope of this review is to identify and assess combinations of predictors informing therapeutic decision-making for clinicians during the initial trauma assessment...
April 13, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28407054/procalcitonin-as-a-marker-of-etiology-in-adults-hospitalized-with-community-acquired-pneumonia
#20
Wesley H Self, Robert A Balk, Carlos G Grijalva, Derek J Williams, Yuwei Zhu, Evan J Anderson, Grant W Waterer, D Mark Courtney, Anna M Bramley, Christopher Trabue, Sherene Fakhran, Anne J Blaschke, Seema Jain, Kathryn M Edwards, Richard G Wunderink
Background: Recent trials suggest procalcitonin-based guidelines can reduce antibiotic use for respiratory infections. However, the accuracy of procalcitonin to discriminate between viral and bacterial pneumonia requires further dissection. Methods: We evaluated the association between serum procalcitonin concentration at hospital admission with pathogens detected in a multicenter prospective surveillance study of adults hospitalized with community-acquired pneumonia...
April 12, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
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