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Trial sequence analysis

Bingjie Shi, Juan Li, Xuanling Shi, Wenxu Jia, Yi Wen, Xiongbing Hu, Fengfeng Zhuang, Jianzhong Xi, Linqi Zhang
Transcription activator-like effector nuclease (TALEN) represents a valuable tool for genomic engineering due to its single-nucleotide precision, high nuclease activity and low cytotoxicity. We report here systematic design and characterization of twenty eight novel TALENs targeting multiple regions of CCR5 gene (CCR5-TALEN) which encodes the co-receptor critical for entry of human immunodeficiency virus type I (HIV-1). By systemic characterization of these CCR5-TALENs, we have identified one (CCR5-TALEN-515) with higher nuclease activity, specificity and lower cytotoxicity compared to zinc-finger nuclease (CCR5-ZFN) currently undergoing clinical trials...
October 3, 2016: Journal of Acquired Immune Deficiency Syndromes: JAIDS
Veerasamy Yengopal, Soraya Yasin Harnekar, Naren Patel, Nandi Siegfried
BACKGROUND: Childhood caries (tooth decay) consists of a form of tooth decay that affects the milk teeth (also known as baby or primary teeth) of children. This may range from tooth decay in a single tooth to rampant caries affecting all the teeth in the mouth. Primary teeth in young children are vital to their development and every effort should be made to retain these teeth for as long as is possible. Dental fillings or restorations have been used as an intervention to repair these damaged teeth...
October 17, 2016: Cochrane Database of Systematic Reviews
Joanne E Sordillo, Yanjiao Zhou, Michael J McGeachie, John Ziniti, Nancy Lange, Nancy Laranjo, Jessica R Savage, Vincent Carey, George O'Connor, Megan Sandel, Robert Strunk, Leonard Bacharier, Robert Zeiger, Scott T Weiss, George Weinstock, Diane R Gold, Augusto A Litonjua
BACKGROUND: The gut microbiome in infancy influences immune system maturation, and may have an important impact allergic disease risk. OBJECTIVE: To determine how prenatal and early life factors impact the gut microbiome in a relatively large, ethnically diverse study population of infants at 3-6 months of age, who were enrolled in VDAART, a clinical trial of vitamin D supplementation in pregnancy to prevent asthma and allergies in offspring. METHODS: We performed 16S rRNA gene sequencing on 333 infants' stool samples...
October 13, 2016: Journal of Allergy and Clinical Immunology
John C Victor, Kristen D C Lewis, Aldiouma Diallo, Mbayame N Niang, Bou Diarra, Ndongo Dia, Justin R Ortiz, Marc-Alain Widdowson, Jodi Feser, Rebecca Hoagland, Shannon L Emery, Kathryn E Lafond, Kathleen M Neuzil
BACKGROUND: Live attenuated influenza vaccines have been shown to significantly reduce influenza in diverse populations of children, but no efficacy studies have been done in resource-poor tropical settings. In Senegal, we assessed the efficacy and safety of a live attenuated influenza vaccine based on Russian-derived master donor viruses and licensed as a single dose. METHODS: In this double-blind, placebo-controlled, parallel group, single-centre trial done near Niakhar, Senegal, generally healthy children aged 2-5 years were randomly allocated (2:1) to receive a single intranasal dose of masked trivalent live attenuated influenza vaccine or placebo...
October 13, 2016: Lancet Global Health
Mandira Paul, Sharad D Iyengar, Birgitta Essén, Kristina Gemzell-Danielsson, Kirti Iyengar, Johan Bring, Marie Klingberg-Allvin
BACKGROUND: Post-abortion contraceptive use in India is low and the use of modern methods of contraception is rare, especially in rural areas. This study primarily compares contraceptive use among women whose abortion outcome was assessed in-clinic with women who assessed their abortion outcome at home, in a low-resource, primary health care setting. Moreover, it investigates how background characteristics and abortion service provision influences contraceptive use post-abortion. METHODS: A randomized controlled, non-inferiority, trial (RCT) compared clinic follow-up with home-assessment of abortion outcome at 2 weeks post-abortion...
October 17, 2016: BMC Public Health
Rajesh Patel, Michael J Sweeting, Janet T Powell, Roger M Greenhalgh
BACKGROUND: Short-term survival benefits of endovascular aneurysm repair (EVAR) versus open repair of intact abdominal aortic aneurysms have been shown in randomised trials, but this early survival benefit is lost after a few years. We investigated whether EVAR had a long-term survival benefit compared with open repair. METHODS: We used data from the EVAR randomised controlled trial (EVAR trial 1), which enrolled 1252 patients from 37 centres in the UK between Sept 1, 1999, and Aug 31, 2004...
October 12, 2016: Lancet
Andreas Bender, Christine Adrion, Luzia Fischer, Martin Huber, Kerstin Jawny, Andreas Straube, Ulrich Mansmann
BACKGROUND: Patients with acquired brain injury who have been discharged from inpatient neurological rehabilitation often continue to suffer from limited independence, participation, and quality of life. Participation-focused outpatient treatment (in German: teilhabeorientierte ambulan. METHODS: In a randomized, controlled trial, 53 patients who had sustained an acquired brain injury approximately four years earlier were allotted to two different sequences of treatment (26 TEAM/control, 27 control/TEAM)...
September 23, 2016: Deutsches Ärzteblatt International
Michelangelo Fiorentino, Elisa Gruppioni, Francesco Massari, Francesca Giunchi, Annalisa Altimari, Chiara Ciccarese, Davide Bimbatti, Aldo Scarpa, Roberto Iacovelli, Camillo Porta, Sarhadi Virinder, Giampaolo Tortora, Walter Artibani, Riccardo Schiavina, Andrea Ardizzoni, Matteo Brunelli, Sakari Knuutila, Guido Martignoni
Renal cell cancer (RCC) is characterized by histological and molecular heterogeneity that may account for variable response to targeted therapies. We evaluated retrospectively with a next generation sequencing (NGS) approach using a pre-designed cancer panel the mutation burden of 32 lesions from 22 metastatic RCC patients treated with at least one tyrosine kinase or mTOR inhibitor. We identified mutations in the VHL, PTEN, JAK3, MET, ERBB4, APC, CDKN2A, FGFR3, EGFR, RB1, TP53 genes. Somatic alterations were correlated with response to therapy...
October 10, 2016: Oncotarget
Yuko M Komesu, Holly E Richter, Darrell L Dinwiddie, Nazema Y Siddiqui, Vivian W Sung, Emily S Lukacz, Beri Ridgeway, Lily A Arya, Halina M Zyczynski, Rebecca G Rogers, Marie Gantz
INTRODUCTION AND HYPOTHESIS: We describe the rationale and methods of a study designed to compare vaginal and urinary microbiomes in women with mixed urinary incontinence (MUI) and similarly aged, asymptomatic controls. METHODS: This paper delineates the methodology of a supplementary microbiome study nested in an ongoing randomized controlled trial comparing a standardized perioperative behavioral/pelvic floor exercise intervention plus midurethral sling versus midurethral sling alone for MUI...
October 13, 2016: International Urogynecology Journal
Aaron M Fleming, Yun Ding, Anton Alenko, Cynthia J Burrows
Zika virus has emerged as a global concern because neither a vaccine nor antiviral compounds targeting it exist. A structure for the positive-sense RNA genome has not been established, leading us to look for potential G-quadruplex sequences (PQS) in the genome. The analysis identified >60 PQSs in the Zika genome. To minimize the PQS population, conserved sequences in the Flaviviridae family were found by sequence alignment, identifying seven PQSs in the prM, E, NS1, NS3, and NS5 genes. Next, alignment of 78 Zika strain genomes identified a unique PQS near the end of the 3'-UTR...
October 14, 2016: ACS Infectious Diseases
Pedro Shiozawa, July Silveira Gomes, Daniella Valverde Ducos, Henrique Teruo Akiba, Álvaro Machado Dias, Alisson Paulino Trevizol, Ricardo R Uchida, Natasza Orlov, Quirino Cordeiro
Introduction: We report a transcranial direct current stimulation (tDCS) protocol over the dorsolateral prefrontal cortex (DLPFC) combined with cognitive training in schizophrenia. Method: We assessed psychotic symptoms in nine patients using the Positive and Negative Syndrome Scale (PANSS). All evaluations were scored at baseline, at the end of the intervention protocol, and during a 4-week follow-up. The tDCS protocol consisted of 10 consecutive sessions over 5-day periods...
July 2016: Trends in Psychiatry and Psychotherapy
David J Keene, Dipesh Mistry, Julian Nam, Elizabeth Tutton, Robert Handley, Lesley Morgan, Emma Roberts, Bridget Gray, Andrew Briggs, Ranjit Lall, Tim Js Chesser, Ian Pallister, Sarah E Lamb, Keith Willett
BACKGROUND: Close contact casting (CCC) may offer an alternative to open reduction and internal fixation (ORIF) surgery for unstable ankle fractures in older adults. OBJECTIVES: We aimed to (1) determine if CCC for unstable ankle fractures in adults aged over 60 years resulted in equivalent clinical outcome compared with ORIF, (2) estimate cost-effectiveness to the NHS and society and (3) explore participant experiences. DESIGN: A pragmatic, multicentre, equivalence randomised controlled trial incorporating health economic evaluation and qualitative study...
October 2016: Health Technology Assessment: HTA
Bryan P Schneider, Dongbing Lai, Fei Shen, Guanglong Jiang, Milan Radovich, Lang Li, Laura Gardner, Kathy D Miller, Anne O'Neill, Joseph A Sparano, Gloria Xue, Tatiana Foroud, George W Sledge
PURPOSE: Taxane-induced peripheral neuropathy (TIPN) is one of the most important survivorship issues for cancer patients. African Americans (AA) have previously been shown to have an increased risk for this toxicity. Germline predictive biomarkers were evaluated to help identify a priori which patients might be at extraordinarily high risk for this toxicity. EXPERIMENTAL DESIGN: Whole exome sequencing was performed using germline DNA from 213 AA patients who received a standard dose and schedule of paclitaxel in the adjuvant, randomized phase III breast cancer trial, E5103...
October 9, 2016: Oncotarget
Asger Paludan-Müller, David Ruben Teindl Laursen, Asbjørn Hróbjartsson
BACKGROUND: Selective allocation of patients into the compared groups of a randomised trial may cause allocation bias, but the mechanisms behind the bias and its directionality are incompletely understood. We therefore analysed the mechanisms and directionality of allocation bias in randomised clinical trials. METHODS: Two systematic reviews and a theoretical analysis. We conducted one systematic review of empirical studies of motives/methods for deciphering patient allocation sequences; and another review of methods publications commenting on allocation bias...
October 7, 2016: BMC Medical Research Methodology
Christopher S Hughes, Melissa K McConechy, Dawn R Cochrane, Tayyebeh Nazeran, Anthony N Karnezis, David G Huntsman, Gregg B Morin
Although re-sequencing of gene panels and mRNA expression profiling are now firmly established in clinical laboratories, in-depth proteome analysis has remained a niche technology, better suited for studying model systems rather than challenging materials such as clinical trial samples. To address this limitation, we have developed a novel and optimized platform called SP3-Clinical Tissue Proteomics (SP3-CTP) for in-depth proteome profiling of practical quantities of tumour tissues, including formalin fixed and paraffin embedded (FFPE)...
October 7, 2016: Scientific Reports
Monika R Asnani, Kim R Quimby, Nadia R Bennett, Damian K Francis
BACKGROUND: Sickle cell disease is a group of genetic diseases which is especially prevalent in tropical and subtropical regions; however, forced migration and ongoing population movement have spread it throughout the world, with estimated birth rates reaching 0.49 per 1000 in the Americas, 0.07 per 1000 in Europe, 0.68 per 1000 in South and Southeast Asia, and 10.68 per 1000 in Africa. Life for individuals with sickle cell disease can be affected by repeated acute complications and compounded by progressive organ damage...
October 6, 2016: Cochrane Database of Systematic Reviews
D A Souza, M Balestre, A K A Pamplona, M E Leite, J A Dias, J B Santos
We aimed to identify simple sequence repeat (SSR) markers linked to quantitative trait loci (QTLs) associated with white mold resistance in a segregating population derived from a cross between common bean cultivars Jalo and Small White, in the Southern State of Minas Gerais. Parents were crossed to obtain the F2 generation of 190 plants. From these, F2:3 and F2:4 progenies were obtained for phenotypic evaluation. DNA was extracted from F2 plants and parents for genotyping with SSR primers. For phenotypic assessment by the straw test, we used 190 F2:3 progenies and six lines in a triple-lattice design of 14 x 14 m...
August 26, 2016: Genetics and Molecular Research: GMR
Saran Vardhanabhuti, David Katzenstein, John Bartlett, Nagalingeswaran Kumarasamy, Carole L Wallis
Background.  The mechanism of virologic failure (VF) of lopinavir/ritonavir (LPV/r) monotherapy is not well understood. We assessed sequence changes in human immunodeficiency virus-1 reverse-transcriptase (RT) and protease (PR) regions. Methods.  Human immunodeficiency virus-1 pol sequences from 34 participants who failed second-line LPV/r monotherapy were obtained at study entry (SE) and VF. Sequence changes were evaluated using phylogenetic analysis and hamming distance. Results.  Human immunodeficiency virus-1 sequence change was higher over drug resistance mutation (DRM) sites (median genetic distance, 2...
September 2016: Open Forum Infectious Diseases
He Huang, Shangmian Yie, Yuliang Liu, Chengdong Wang, Zhigang Cai, Wenping Zhang, Jingchao Lan, Xiangming Huang, Li Luo, Kailai Cai, Rong Hou, Zhihe Zhang
The functional adaptive changes in cyanide detoxification in giant panda appear to be response to dietary transition from typical carnivore to herbivorous bear. We tested the absorption of cyanide contained in bamboo/bamboo shoots with a feeding trial in 20 adult giant pandas. We determined total cyanide content in bamboo shoots and giant panda's feces, levels of urinary thiocyanate and tissue rhodanese activity using color reactions with a spectrophotometer. Rhodanese expression in liver and kidney at transcription and translation levels were measured using real-time RT-PCR and immunohistochemistry, respectively...
October 5, 2016: Scientific Reports
Niko C Bock, Laura Seibold, Christian Heumann, Erhard Gnandt, Miriam Röder, Sabine Ruf
BACKGROUND: White spot lesions (WSL) frequently occur as side-effect of multibracket appliance treatment. The clinical effects of local fluoridation on post-orthodontic WSL and oral health development are however inconclusive. OBJECTIVE: In vivo monitoring of clinical WSL and oral health changes in response to weekly 1.25 per cent fluoride gel application after multibracket appliance treatment. TRIAL DESIGN: Randomized, single-centre, double-blind, parallel-group, placebo-controlled study...
October 4, 2016: European Journal of Orthodontics
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