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https://www.readbyqxmd.com/read/28637232/phyloligo-a-package-to-identify-contaminant-or-untargeted-organism-sequences-in-genome-assemblies
#1
Ludovic Mallet, Tristan Bitard-Feildel, Franck Cerutti, Hélène Chiapello
Motivation: Genome sequencing projects sometimes uncover more organisms than expected, especially for complex and/or non-model organisms. It is therefore useful to develop software to identify mix of organisms from genome sequence assemblies. Here we present PhylOligo, a new package including tools to explore, identify and extract organism-specific sequences in a genome assembly using the analysis of their DNA compositional characteristics. Availability: The tools are written in Python3 and R under the GPLv3 Licence and can be found at https://github...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637206/improving-combination-osteoporosis-therapy-in-a-preclinical-model-of-heightened-osteoanabolism
#2
Yu Shao, Selene Hernandez-Buquer, Paul Childress, Keith R Stayrook, Marta B Alvarez, Hannah Davis, Lilian Plotkin, Yongzheng He, Keith W Condon, David B Burr, Stuart J Warden, Alexander G Robling, Feng-Chun Yang, Ronald C Wek, Matthew R Allen, Joseph P Bidwell
Combining anti-catabolic agents with parathyroid hormone (PTH) to enhance bone mass has yielded mixed results in osteoporosis patients. Towards the goal of enhancing the efficacy of these regimens, we tested their utility in combination with loss of the transcription factor Nmp4 since disabling this gene amplifies PTH-induced increases in trabecular bone in mice by boosting osteoblast secretory activity. We addressed whether combining a sustained anabolic response with an anti-catabolic results in superior bone acquisition compared to PTH mono-therapy...
June 20, 2017: Endocrinology
https://www.readbyqxmd.com/read/28636825/a-new-mixed-all-atom-coarse-grained-model-application-to-melittin-aggregation-in-aqueous-solution
#3
Mee Y Shelley, Myvizhi Esai Selvan, Jun Zhao, Volodymyr Babin, Chenyi Liao, Jianing Li, John Clarence Shelley
We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG) for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636816/impacts-of-the-mitochondrial-genome-on-the-relationship-of-long-term-ambient-fine-particle-exposure-with-blood-dna-methylation-age
#4
Jamaji Nwanaji-Enwerem, Elena Colicino, Lingzhen Dai, Akin Cayir, Marco Sanchez-Guerra, Hannah E Laue, Vy T Nguyen, Qian Di, Allan Just, Lifang Hou, Pantel Vokonas, Brent A Coull, Marc Weisskopf, Andrea Baccarelli, Joel Schwartz
The mitochondrial genome has long been implicated in age-related disease, but no studies have examined its role in the relationship of long-term fine particle (PM2.5) exposure and DNA methylation age (DNAm-age) - a novel measure of biological age. In this analysis based on 940 observations between 2000 and 2011 from 552 Normative Aging Study participants, we determined the roles of mitochondrial DNA haplogroup variation and mitochondrial genome abundance in the relationship of PM2.5 with DNAm-age. We used the GEOS-chem transport model to estimate address-specific, one-year PM2...
June 21, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28636787/a-co-drug-conjugate-of-naringenin-and-lipoic-acid-mediates-neuroprotection-in-a-rat-model-of-oxidative-stress
#5
Tarek M Saleh, Monique C Saleh, Barry J Connell, Yang-Heon Song
Using our in vitro and in vivo models of oxidative stress, the current study was designed to determine the neuroprotective potential of naringenin, alone or in combination with lipoic acid. In our mixed neuronal culture exposed to hypoxia and subsequent reoxygenation, naringenin was shown to provide significant neuroprotection against cell death at a concentration of 2.5 μM. Lipoic acid (LA) did not produce neuroprotection at any concentration tested (0.25 to 100 μM). In contrast, when naringenin was covalently combined with LA, producing a novel compound named "VANL-100", significant neuroprotection was observed at a concentration as low as 2 x 10(-2) μM (100-fold more potent)...
June 21, 2017: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/28636773/comparison-of-different-insulin-pump-makes-under-routine-care-conditions-in-adults-with-type-1-diabetes
#6
L Leelarathna, S A Roberts, A Hindle, K Markakis, T Alam, A Chapman, J Morris, A Urwin, P Jinadev, M K Rutter
AIMS: To compare long-term HbA1c changes associated with different insulin pumps during routine care in a large cohort of adults with Type 1 diabetes representative of other clinic populations. METHODS: Observational, retrospective study of 508 individuals starting pump therapy between 1999 and 2014 (mean age, 40 years; 55% women; diabetes duration, 20 years; 94% Type 1 diabetes; median follow-up, 3.7 years). Mixed linear models compared covariate-adjusted HbA1c changes associated with different pump makes...
June 21, 2017: Diabetic Medicine: a Journal of the British Diabetic Association
https://www.readbyqxmd.com/read/28636758/fetal-overnutrition-and-offspring-insulin-resistance-and-%C3%AE-cell-function-the-exploring-perinatal-outcomes-among-children-epoch-study
#7
K A Sauder, C W Hockett, B M Ringham, D H Glueck, D Dabelea
AIMS: To examine the associations of intrauterine exposure to maternal diabetes and obesity with offspring insulin resistance, β-cell function and oral disposition index in a longitudinal observational study of ethnically diverse offspring. METHODS: A total of 445 offspring who were exposed (n=81) or not exposed (n=364) to maternal diabetes in utero completed two fasting blood measurements at mean (sd) ages of 10.5 (1.5) and 16.5 (1.2) years, respectively, and an oral glucose tolerance test at the second visit...
June 21, 2017: Diabetic Medicine: a Journal of the British Diabetic Association
https://www.readbyqxmd.com/read/28636697/role-of-positive-parenting-in-the-association-between-neighborhood-social-disadvantage-and-brain-development-across-adolescence
#8
Sarah Whittle, Nandita Vijayakumar, Julian G Simmons, Meg Dennison, Orli Schwartz, Christos Pantelis, Lisa Sheeber, Michelle L Byrne, Nicholas B Allen
Importance: The negative effects of socioeconomic disadvantage on lifelong functioning are pronounced, with some evidence suggesting that these effects are mediated by changes in brain development. To our knowledge, no research has investigated whether parenting might buffer these negative effects. Objective: To establish whether positive parenting behaviors moderate the effects of socioeconomic disadvantage on brain development and adaptive functioning in adolescents...
June 21, 2017: JAMA Psychiatry
https://www.readbyqxmd.com/read/28636656/selective-propagation-of-mouse-passaged-scrapie-prions-with-long-incubation-period-from-a-mixed-prion-population-using-gt1-7-cells
#9
Kohtaro Miyazawa, Kentaro Masujin, Hiroyuki Okada, Yuko Ushiki-Kaku, Yuichi Matsuura, Takashi Yokoyama
In our previous study, we demonstrated the propagation of mouse-passaged scrapie isolates with long incubation periods (L-type) derived from natural Japanese sheep scrapie cases in murine hypothalamic GT1-7 cells, along with disease-associated prion protein (PrPSc) accumulation. We here analyzed the susceptibility of GT1-7 cells to scrapie prions by exposure to infected mouse brains at different passages, following interspecies transmission. Wild-type mice challenged with a natural sheep scrapie case (Kanagawa) exhibited heterogeneity of transmitted scrapie prions in early passages, and this mixed population converged upon one with a short incubation period (S-type) following subsequent passages...
2017: PloS One
https://www.readbyqxmd.com/read/28636642/in-vivo-evaluation-of-inter-operator-reproducibility-of-digital-dental-and-conventional-impression-techniques
#10
Emi Kamimura, Shinpei Tanaka, Masayuki Takaba, Keita Tachi, Kazuyoshi Baba
PURPOSE: The aim of this study was to evaluate and compare the inter-operator reproducibility of three-dimensional (3D) images of teeth captured by a digital impression technique to a conventional impression technique in vivo. MATERIALS AND METHODS: Twelve participants with complete natural dentition were included in this study. A digital impression of the mandibular molars of these participants was made by two operators with different levels of clinical experience, 3 or 16 years, using an intra-oral scanner (Lava COS, 3M ESPE)...
2017: PloS One
https://www.readbyqxmd.com/read/28636615/family-living-sets-the-stage-for-cooperative-breeding-and-ecological-resilience-in-birds
#11
Michael Griesser, Szymon M Drobniak, Shinichi Nakagawa, Carlos A Botero
Cooperative breeding is an extreme form of cooperation that evolved in a range of lineages, including arthropods, fish, birds, and mammals. Although cooperative breeding in birds is widespread and well-studied, the conditions that favored its evolution are still unclear. Based on phylogenetic comparative analyses on 3,005 bird species, we demonstrate here that family living acted as an essential stepping stone in the evolution of cooperative breeding in the vast majority of species. First, families formed by prolonging parent-offspring associations beyond nutritional independency, and second, retained offspring began helping at the nest...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28636536/intake-of-red-and-processed-meat-and-risk-of-renal-cell-carcinoma-a-meta-analysis-of-observational-studies
#12
Shaojing Zhang, Qingwei Wang, Juanjuan He
BACKGROUND: Findings on the association between intake of red and processed meat with renal cell carcinoma (RCC) risk are mixed. We conducted a meta-analysis to investigate this association. MATERIALS AND METHODS: Eligible studies up to August 31, 2016, were identified and retrieved by searching the MEDLINE and Embase databases along with manual review of the reference lists from the retrieved studies. The quality of the included studies was evaluated using the Newcastle-Ottawa Quality Assessment Scale...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636469/ten-new-species-of-macalpinomyces-on-eriachne-in-northern-australia
#13
Ying-Ming Li, Roger G Shivas, Alistair R McTaggart, Peng Zhao, Lei Cai
Macalpinomyces was established in 1977, with the type species M. eriachnes described from a specimen collected in northern Australia on the grass Eriachne sp. in 1855. Subsequently, M. eriachnes has been reported on more than 21 species of Eriachne in northern Australia. In this study, a polyphasic approach was employed to determine whether M. eriachnes masked cryptic diversity. On the basis of morphology, multilocus phylogeny, and coalescent methods of generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) models, 26 specimens of Macalpinomyces on 13 species of Eriachne held in Australian herbaria were studied...
May 12, 2017: Mycologia
https://www.readbyqxmd.com/read/28636201/an-exploration-of-the-relationship-between-use-of-safety-seeking-behaviours-and-psychosis-a-systematic-review-and-meta-analysis
#14
Sarah Tully, Adrian Wells, Anthony P Morrison
Safety-seeking behaviours are responses employed to protect against perceived threat. In relation to anxiety disorders, safety-seeking behaviours have been implicated in both the formation and maintenance of distress. Several studies have highlighted similar findings in relation to psychosis; however, this literature has not yet been synthesized. This review is, therefore, being conducted in order to synthesize the literature on safety seeking in people with psychosis to increase the understanding of this relationship...
June 21, 2017: Clinical Psychology & Psychotherapy
https://www.readbyqxmd.com/read/28635546/physical-activity-and-asthma-a-longitudinal-and-multi-country-study
#15
Melissa A Russell, Christer Janson, Francisco Gómez Real, Ane Johannessen, Marie Waatevik, Bryndis Benediktsdóttir, Mathias Holm, Eva Lindberg, Vivi Schlünssen, Wasif Raza, Shyamali C Dharmage, Cecilie Svanes
OBJECTIVE: To investigate the impact of physical activity on asthma in middle-aged adults, in one longitudinal analysis, and one multi-centre cross-sectional analysis. METHODS: The Respiratory Health in Northern Europe (RHINE) is a population-based postal questionnaire cohort study. Physical activity, height and weight were self-reported in Bergen, Norway, at RHINE II (1999-2001) and all centres at RHINE III (2010-2012). A longitudinal analysis of Bergen data investigated the association of baseline physical activity with follow-up asthma, incident asthma and symptoms, using logistic and zero-inflated Poisson regression (n = 1782)...
February 16, 2017: Journal of Asthma: Official Journal of the Association for the Care of Asthma
https://www.readbyqxmd.com/read/28635526/a-randomized-lifestyle-intervention-preventing-gestational-diabetes-effects-on-self-rated-health-from-pregnancy-to-postpartum
#16
Elina Engberg, Beata Stach-Lempinen, Kristiina Rönö, Hannu Kautiainen, Johan G Eriksson, Saila B Koivusalo
INTRODUCTION: The purpose was to examine the effects of a randomized lifestyle intervention on self-rated health from pregnancy to postpartum in participants at high risk for gestational diabetes mellitus. METHODS: We included 266 women with a history of gestational diabetes and/or prepregnancy BMI ≥30 kg/m(2). The intervention group (n = 144) received individualized counseling on diet, physical activity, and weight management from trained nurses at six timepoints between the first trimester of pregnancy and 12 months postpartum, and met three times with a dietitian...
February 9, 2017: Journal of Psychosomatic Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28635181/buprenorphine-requires-concomitant-activation-of-nop-and-mop-receptors-to-reduce-cocaine-consumption
#17
Marsida Kallupi, Qianwei Shen, Giordano de Guglielmo, Dennis Yasuda, V Blair Journigan, Nurulain T Zaveri, Roberto Ciccocioppo
Buprenorphine's clinical use is approved for the treatment of heroin addiction; however, evidence supporting its efficacy in cocaine abuse also exists. While for heroin it has been demonstrated that the effect of buprenorphine is mediated by its ability to activate μ-opioid peptide receptor (MOP) receptors, the mechanism through which it attenuates cocaine intake remains elusive. We explored this mechanism using operant models where rodents were trained to chronically self-administer cocaine for 2 hours daily...
June 21, 2017: Addiction Biology
https://www.readbyqxmd.com/read/28635163/early-pregnancy-body-mass-index-modifies-the-association-of-pre-pregnancy-dietary-patterns-with-serum-polyunsaturated-fatty-acid-concentrations-throughout-pregnancy-in-brazilian-women
#18
Camila Benaim, Ana Amélia Freitas-Vilela, Thatiana de Jesus Pereira Pinto, Jaqueline Lepsch, Dayana Rodrigues Farias, Juliana Dos Santos Vaz, Tatiana El-Bacha, Gilberto Kac
Dietary patterns (DPs) have been described as an important factor that may influence polyunsaturated fatty acid (PUFA) concentrations and body mass index (BMI) during pregnancy. We aim to evaluate the association between pre-pregnancy DPs and serum PUFA percentages throughout pregnancy considering early pregnancy BMI as a possible effect modifier. A prospective cohort of 154 pregnant women was followed (5th-13th, 20th-26th, and 30th-36th gestational weeks). Serum PUFA concentrations (total n-3 and total n-6, eicosapentaenoic + docosahexaenoic acids) were measured in each trimester and expressed as percentages...
June 21, 2017: Maternal & Child Nutrition
https://www.readbyqxmd.com/read/28634839/outcomes-of-kidney-donors-over-60%C3%A2-years-old-a-single-center-cohort-study
#19
Daniel Gero, Fadia Dib, Maurice Matter, Manuel Pascual, Jean-Pierre Venetz, Nicolas Demartines, Emmanuel Melloul
AIM: To evaluate outcomes and post-donation kidney function of older living kidney donors (LKD). METHODS: Retrospective analysis of prospective database including all consecutive LKD undergoing laparoscopic nephrectomy in a single center (09/1998-12/2013). LKD aged ≥60 years were compared to younger LKD. Renal function assessed by creatinine levels and estimated glomerular filtration rates (eGFR). Surgical complications classified according to the Clavien-Dindo classification...
June 20, 2017: World Journal of Surgery
https://www.readbyqxmd.com/read/28634748/exposure-response-relationship-of-ramucirumab-in-east-asian-patients-from-rainbow-a-randomized-clinical-trial-in-second-line-treatment-of-gastric-cancer
#20
Tae You Kim, Chia-Jui Yen, Salah-Eddin Al-Batran, David Ferry, Ling Gao, Yanzhi Hsu, Rebecca Cheng, Mauro Orlando, Atsushi Ohtsu
BACKGROUND: Ramucirumab is a recombinant human IgG1 neutralizing monoclonal antibody specific for vascular endothelial growth factor receptor-2. Second-line ramucirumab, in conjunction with paclitaxel (ramucirumab 8 mg/kg or placebo in combination with 80 mg/m(2) paclitaxel), has been shown to be effective and safe in patients with advanced gastric or gastroesophageal junction (GEJ) adenocarcinoma in RAINBOW, a global phase III randomized clinical trial. We conducted an exploratory exposure-response analysis of efficacy and safety of ramucirumab in East Asian patients from the RAINBOW trial...
June 20, 2017: Gastric Cancer
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