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Joel A Boyd, Ben J Woodcroft, Gene W Tyson
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees...
March 19, 2018: Nucleic Acids Research
Jade-Emmanuelle Deshaies, Lulzim Shkreta, Alexander J Moszczynski, Hadjara Sidibé, Sabrina Semmler, Aurélien Fouillen, Estelle R Bennett, Uriya Bekenstein, Laurie Destroismaisons, Johanne Toutant, Quentin Delmotte, Kathryn Volkening, Stéphanie Stabile, Anaïs Aulas, Yousra Khalfallah, Hermona Soreq, Antonio Nanci, Michael J Strong, Benoit Chabot, Christine Vande Velde
The RNA binding proteins TDP-43 (encoded by TARDBP) and hnRNP A1 (HNRNPA1) are each mutated in certain amyotrophic lateral sclerosis cases and are often mislocalized in cytoplasmic aggregates within motor neurons of affected patients. Cytoplasmic inclusions of TDP-43, which are accompanied by a depletion of nuclear TDP-43, are observed in most amyotrophic lateral sclerosis cases and nearly half of frontotemporal dementia cases. Here, we report that TDP-43 binds HNRNPA1 pre-mRNA and modulates its splicing, and that depletion of nuclear TDP-43 results in increased inclusion of a cassette exon in the HNRNPA1 transcript, and consequently elevated protein levels of an isoform containing an elongated prion-like domain, referred to as hnRNP A1B...
March 19, 2018: Brain: a Journal of Neurology
Paul D Blischak, Julia Chifman, Andrea D Wolfe, Laura S Kubatko
The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees...
March 19, 2018: Systematic Biology
Sherry Masoud, Stephen P McAdoo, Rachna Bedi, Thomas D Cairns, Liz Lightstone
Objective: B cell depletion, most commonly with rituximab, is an evolving therapeutic approach in SLE. Infusion reactions after rituximab are common, and may prevent re-treatment in patients who previously demonstrated beneficial response. We have used ofatumumab, a fully humanized anti-CD20 mAb, as an alternative B cell-depleting agent in patients with SLE who are rituximab-intolerant due to severe infusion reactions. Methods: A single-centre retrospective case series of 16 patients were treated with ofatumumab for SLE between 2012 and 2015...
March 19, 2018: Rheumatology
Paulo Gentil, Vítor A Marques, Josaphat P P Neto, Anna C G Santos, James Steele, James P Fisher, Antonio Paoli, Martim Bottaro
The purpose of the present study was to evaluate the changes in movement velocity during resistance training with different loads while the trainees are attempting to move the load at a pre-determined repetition duration. Twenty-one resistance-trained men (age: 25.7 ± 5 years; height: 177.0 ± 7.2 cm; mass: 85.4 ± 13.56 kg) volunteered to participate in the study. Participants performed two tests sessions. The first to determine 1 repetition maximum (1RM) load, and the second to evaluate velocity loss during a set to failure performed at 75% and 50% of 1RM using a 2 second concentric and 2 second eccentric repetition duration, controlled by a mobile app metronome...
March 21, 2018: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
Nadavala Siva Kumar, Mohammad Asif, Mansour I Al-Hazzaa, Ahmed A Ibrahim
Most industrial waste discharges are often contaminated with phenolic compounds, which constitute a major source of water pollution owing to their toxicity and low biodegradability. Development of cost-effective treatment of such industrial wastewater is therefore of paramount importance. Towards this end, we explore the efficacy of Pine bark powder (PBP), which is an agricultural solid waste material, as a low-cost biosorbent without any pre-treatment, for the adsorptive removal of 2,4,6-trichlorophenol (2,4,6-TCP) from aqueous media...
March 2018: Acta Chimica Slovenica
Burcu Şerbetçioğlu Sert, Benan İnan, Didem Özçimen
In recent years, algal bioethanol production comes into prominence as a trend towards sustainable development. Due to being sustainable energy source and environmental friendly, bioethanol production from algae is becoming increasingly popular all over the world. However, yield of bioethanol production from algae is lower than first generation feedstock's currently, and needs to be improved. In order to increase bioethanol yield, pre-treatments should be performed as cell disruption process on algal biomass...
March 2018: Acta Chimica Slovenica
Willamis José Araújo, Evelyn Maria Braga Quirino, Clarissa Mourão Pinho, Maria Sandra Andrade
OBJECTIVE: Learn about the perception of health professionals who perform rapid tests in Health Centers (HCs). METHOD: This is a descriptive and qualitative study conducted in nine HCs in Recife. Data were collected through individual interviews and evaluated using Bardin's content analysis, in its thematic category. RESULTS: Challenges were observed in rapid tests related to the supply of products, physical structure, training for pre- and post-test counseling, and the need for improvements in permanent education actions...
2018: Revista Brasileira de Enfermagem
Aisha Aguiar Morais, Urjel Aguiar Bouissou Morais, Maria Marta Sarquis Soares, Márcia Christina Caetano Romano, Joel Alves Lamounier
OBJECTIVE: To critically analyze articles on the relation between neck circumference (NC) in adolescents and: body mass index, fat distribution, metabolic syndrome and its individual components, and cardiovascular risk. METHOD: Systematic review undertaken by two independent researchers using the Pubmed/Medline, Lilacs/Medline, Scielo and Cochrane databases in English, Spanish and Portuguese in the period comprising the past 5 years. RESULTS: Eighteen (18) articles were selected...
January 2018: Revista da Associação Médica Brasileira
Patrini Silveira Vesz, Rafael Viegas Cremonese, Regis Goulart Rosa, Juçara Gasparetto Maccari, Cassiano Teixeira
OBJECTIVE: To evaluate the impact of the need for mechanical ventilation (MV) and its duration throughout ICU stay on the quality of life (QoL) and physical functional status (PFS) after the immediate ICU discharge. METHOD: This was a cross-sectional study including all subjects consecutively discharged from the ICU during 1-year period. During the first week after ICU discharge, QoL was assessed through WHOQoL-Bref questionnaire and PFS through the Karnofsky Performance Status and modified-Barthel index, and retrospectively compared with the pre-admission status (variation [Δ] of indexes)...
January 2018: Revista da Associação Médica Brasileira
W C Chen, Y T Chang, S F Chen, W C Lin, Y Y Su, S D Luo
BACKGROUND: Dysregulation of the autonomic system can affect sinonasal physiological function and may exacerbate the symptom burden associated with rhinosinusitis. However, the association between autonomic dysfunction and chronic rhinosinusitis (CRS) has seldom been studied. Here, we investigated the relationship between autonomic dysfunction and CRS. METHODS: Patients with CRS who failed medical treatment were prospectively enrolled. All patients underwent pre-operative examinations and completed questionnaires, including the reflux symptom index (RSI) and the Sino-nasal Outcome Test-22 (SNOT-22)...
March 21, 2018: Rhinology
Ivan Wen Wen Lau, Dongting Liu, Lei Xu, Zhanming Fan, Zhonghua Sun
OBJECTIVE: Current diagnostic assessment tools remain suboptimal in demonstrating complex morphology of congenital heart disease (CHD). This limitation has posed several challenges in preoperative planning, communication in medical practice, and medical education. This study aims to investigate the dimensional accuracy and the clinical value of 3D printed model of CHD in the above three areas. METHODS: Using cardiac computed tomography angiography (CCTA) data, a patient-specific 3D model of a 20-month-old boy with double outlet right ventricle was printed in Tango Plus material...
2018: PloS One
Paula Finatto, Edson Soares Da Silva, Alexandre B Okamura, Bruna P Almada, Henrique B Oliveira, Leonardo A Peyré-Tartaruga
PURPOSE: Strength training improves distance running economy and performance. This finding is based predominantly on maximal and explosive strength programmes applied to locomotor muscles, particularly on the lower limbs. It is not certain whether a minimization of metabolic cost (Cmet) and an improvement in running performance is feasible with strength training of the postural and trunk muscles. METHODS: Using kinematic, neuromuscular and metabolic measurements of running at two different speeds before and after a 12-week Pilates training programme, we tested the hypothesis that core training might improve the running Cmet and performance of trained runners...
2018: PloS One
Rupert W Major, Mark R I Cheng, Robert A Grant, Saran Shantikumar, Gang Xu, Issaam Oozeerally, Nigel J Brunskill, Laura J Gray
BACKGROUND AND OBJECTIVES: Chronic kidney disease (CKD) is a global health burden and is independently associated with increased cardiovascular disease risk. Assessment of cardiovascular risk in the general population using prognostic models based on routinely collected risk factors is embedded in clinical practice. In CKD, prognostic models may misrepresent risk due to the interplay of traditional atherosclerotic and non-traditional risk factors. This systematic review's aim was to identify routinely collected risk factors for inclusion in a CKD-specific cardiovascular prognostic model...
2018: PloS One
Fleur P Paling, Karina Olsen, Kristin Ohneberg, Martin Wolkewitz, Vance G Fowler, Mark J DiNubile, Hasan S Jafri, Frangiscos Sifakis, Marc J M Bonten, Stephan J Harbarth, Jan A J W Kluytmans
BACKGROUND: Identifying patients undergoing cardiothoracic surgery at high risk of Staphylococcus aureus surgical site infection (SSI) is a prerequisite for implementing effective preventive interventions. The objective of this study was to develop a risk prediction model for S. aureus SSI or bacteremia after cardiothoracic surgery based on pre-operative variables. MATERIALS/METHODS: Data from the Merck Phase IIb/III S. aureus vaccine (V710-P003) clinical trial were analyzed...
2018: PloS One
Wing Lee Chan, Magdalena Steiner, Tomasz Witkos, Johannes Egerer, Björn Busse, Shuji Mizumoto, Jan M Pestka, Haikuo Zhang, Ingrid Hausser, Layal Abo Khayal, Claus-Eric Ott, Mateusz Kolanczyk, Bettina Willie, Thorsten Schinke, Chiara Paganini, Antonio Rossi, Kazuyuki Sugahara, Michael Amling, Petra Knaus, Danny Chan, Martin Lowe, Stefan Mundlos, Uwe Kornak
Gerodermia osteodysplastica (GO) is characterized by skin laxity and early-onset osteoporosis. GORAB, the responsible disease gene, encodes a small Golgi protein of poorly characterized function. To circumvent neonatal lethality of the GorabNull full knockout, Gorab was conditionally inactivated in mesenchymal progenitor cells (Prx1-cre), pre-osteoblasts (Runx2-cre), and late osteoblasts/osteocytes (Dmp1-cre), respectively. While in all three lines a reduction in trabecular bone density was evident, only GorabPrx1 and GorabRunx2 mutants showed dramatically thinned, porous cortical bone and spontaneous fractures...
March 21, 2018: PLoS Genetics
Youkyung Bae, Gwenlyn Pfeil
OBJECTIVE: To evaluate the feasibility/effectiveness of using magnetic resonance imaging (MRI) to document velopharyngeal (VP) structural changes induced by continuous positive airway pressure (CPAP) therapy. OUTCOME MEASURES: Changes in velar length and thickness, levator veli palatini (LVP) length and thickness, velar volume, and intravelar muscular proportion along the course of CPAP therapy participation (Pre-CPAP, Post-CPAP, and withdrawal). RESULTS: Velar and LVP lengths remained nearly the same, with the median changes (Δ) less than 0...
January 1, 2018: Cleft Palate-craniofacial Journal
Jie Han, Leslie A Goldstein, Wen Hou, Suman Chatterjee, Timothy F Burns, Hannah Rabinowich
Macroautophagy/autophagy has emerged as a resistance mechanism to anticancer drug treatments that induce metabolic stress. Certain tumors, including a subset of KRAS-mutant NSCLCs have been shown to be addicted to autophagy, and potentially vulnerable to autophagy inhibition. Currently, autophagy inhibition is being tested in the clinic as a therapeutic component for tumors that utilize this degradation process as a drug resistance mechanism. The current study provides evidence that HSP90 (heat shock protein 90) inhibition diminishes the expression of ATG7, thereby impeding the cellular capability of mounting an effective autophagic response in NSCLC cells...
March 21, 2018: Autophagy
Eui Seon Baek, Soonshin Hwang, Yoon Jeong Choi, Mi Ryung Roh, Tung Nguyen, Kyung-Ho Kim, Chooryung J Chung
OBJECTIVES: The objectives of this study were to evaluate the quantitative and perceived visual changes of the nasolabial fold (NLF) after maximum retraction in adults and to determine its contributing factors. MATERIALS AND METHODS: A total of 39 adult women's cone-beam computed tomography images were collected retrospectively and divided into the retraction group (age 26.9 ± 8.80) that underwent maximum retraction following 4 premolar extraction and the control group (age 24...
March 21, 2018: Angle Orthodontist
Shereef Shahen, Gennaro Carrino, Rossella Carrino, Reham Abdelsalam, Carlos Flores-Mir, Letizia Perillo
OBJECTIVES: The objective of this study was to develop a reproducible method to measure the change of palatal volume and area through superimposition using maxillary expansion digital cast models. MATERIALS AND METHODS: A total of 10 pre- and 10 postexpansion dental cast models were scanned by the same cone-beam computed tomography machine. Superimposition was performed using a fully automated surface-best fit of the palatal surfaces on the digital cast models. A gingival plane, identified only once on superimposed casts, and a distal plane with the lateral closing border and the palatal surface were used to localize this selection of air...
March 21, 2018: Angle Orthodontist
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