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https://www.readbyqxmd.com/read/27903896/img-abc-new-features-for-bacterial-secondary-metabolism-analysis-and-targeted-biosynthetic-gene-cluster-discovery-in-thousands-of-microbial-genomes
#1
Michalis Hadjithomas, I-Min A Chen, Ken Chu, Jinghua Huang, Anna Ratner, Krishna Palaniappan, Evan Andersen, Victor Markowitz, Nikos C Kyrpides, Natalia N Ivanova
Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903252/shifting-tides-in-the-emigration-patterns-of-canadian-physicians-to-the-united-states-a-cross-sectional-secondary-data-analysis
#2
Thomas R Freeman, Stephen Petterson, Sean Finnegan, Andrew Bazemore
BACKGROUND: The relative ease of movement of physicians across the Canada/US border has led to what is sometimes referred to as a 'brain drain' and previous analysis estimated that the equivalent of two graduating classes from Canadian medical schools were leaving to practice in the US each year. Both countries fill gaps in physician supply with international medical graduates (IMGs) so the movement of Canadian trained physicians to the US has international ramifications. Medical school enrolments have been increased on both sides of the border, yet there continues to be concerns about adequacy of physician human resources...
December 1, 2016: BMC Health Services Research
https://www.readbyqxmd.com/read/27888178/perceived-causes-of-differential-attainment-in-uk-postgraduate-medical-training-a-national-qualitative-study
#3
Katherine Woolf, Antonia Rich, Rowena Viney, Sarah Needleman, Ann Griffin
OBJECTIVES: Explore trainee doctors' experiences of postgraduate training and perceptions of fairness in relation to ethnicity and country of primary medical qualification. DESIGN: Qualitative semistructured focus group and interview study. SETTING: Postgraduate training in England (London, Yorkshire and Humber, Kent Surrey and Sussex) and Wales. PARTICIPANTS: 137 participants (96 trainees, 41 trainers) were purposively sampled from a framework comprising: doctors from all stages of training in general practice, medicine, obstetrics and gynaecology, psychiatry, radiology, surgery or foundation, in 4 geographical areas, from white and black and minority ethnic (BME) backgrounds, who qualified in the UK and abroad...
November 25, 2016: BMJ Open
https://www.readbyqxmd.com/read/27876102/structural-functional-brain-changes-in-depressed-patients-during-and-after-electroconvulsive-therapy
#4
Antoine Yrondi, Patrice Péran, Anne Sauvaget, Laurent Schmitt, Christophe Arbus
OBJECTIVES: Electroconvulsive therapy (ECT) is a non-pharmacological treatment that is effective in treating severe and treatment-resistant depression. Although the efficacy of ECT has been demonstrated to treat major depressive disorder (MDD), the brain mechanisms underlying this process remain unclear. Structural-functional changes occur with the use of ECT as a treatment for depression based on magnetic resonance imaging (MRI). For this reason, we have tried to identify the changes that were identified by MRI to try to clarify some operating mechanisms of ECT...
November 23, 2016: Acta Neuropsychiatrica
https://www.readbyqxmd.com/read/27852927/evolution-of-trnaphe-img2-methyltransferases-involved-in-the-biosynthesis-of-wyosine-derivatives-in-archaea
#5
Jaunius Urbonavičius, Rasa Rutkienė, Anželika Lopato, Daiva Tauraitė, Jonita Stankevičiūtė, Agota Aučynaitė, Laura Kaliniene, Herman van Tilbeurgh, Rolandas Meškys
Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNA(Phe) In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N(1)-methylation of guanosine to yield m(1)G; and C(7)-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity...
December 2016: RNA
https://www.readbyqxmd.com/read/27821527/left-right-analysis-of-mammary-gland-development-in-retinoid-x-receptor-%C3%AE-mice
#6
Jacqulyne P Robichaux, John W Fuseler, Shrusti S Patel, Steven W Kubalak, Adam Hartstone-Rose, Ann F Ramsdell
Left-right (L-R) differences in mammographic parenchymal patterns are an early predictor of breast cancer risk; however, the basis for this asymmetry is unknown. Here, we use retinoid X receptor alpha heterozygous null (RXRα(+/-)) mice to propose a developmental origin: perturbation of coordinated anterior-posterior (A-P) and L-R axial body patterning. We hypothesized that by analogy to somitogenesis-in which retinoic acid (RA) attenuation causes anterior somite pairs to develop L-R asynchronously-that RA pathway perturbation would likewise result in asymmetric mammary development...
December 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27799466/img-vr-a-database-of-cultured-and-uncultured-dna-viruses-and-retroviruses
#7
David Paez-Espino, I-Min A Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Ernest Szeto, Manoj Pillay, Jinghua Huang, Victor M Markowitz, Torben Nielsen, Marcel Huntemann, T B K Reddy, Georgios A Pavlopoulos, Matthew B Sullivan, Barbara J Campbell, Feng Chen, Katherine McMahon, Steve J Hallam, Vincent Denef, Ricardo Cavicchioli, Sean M Caffrey, Wolfgang R Streit, John Webster, Kim M Handley, Ghasem H Salekdeh, Nicolas Tsesmetzis, Joao C Setubal, Phillip B Pope, Wen-Tso Liu, Adam R Rivers, Natalia N Ivanova, Nikos C Kyrpides
Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples...
October 30, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27796642/genomic-analysis-of-the-multi-drug-resistant-clinical-isolate-myroides-odoratimimus-pr63039
#8
Shaohua Hu, Tao Jiang, Yajun Zhou, Desong Ming, Hongzhi Gao, Mingxi Wang
Myroides odoratimimus (M. odoratimimus) has been gradually implicated as an important nosocomial pathogen that poses a serious health threat to immunocompromised patients owing to its multi-drug resistance. However, the resistance mechanism is currently unclear. To clarify the antibiotic resistance and infectivity mechanisms of M. odoratimimus, whole genome sequencing was performed on the multi-drug-resistant M. odoratimimus strain PR63039. The genome sequence was completed with single molecule real-time (SMRT) technologies...
October 28, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27794040/genomes-online-database-gold-v-6-data-updates-and-feature-enhancements
#9
Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Olena Verezemska, Michelle Isbandi, Alex D Thomas, Rida Ali, Kaushal Sharma, Nikos C Kyrpides, T B K Reddy
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects...
October 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27777690/how-residents-say-they-learn-a-national-multi-specialty-survey-of-first-and-second-year-residents
#10
DeWitt C Baldwin, Steven R Daugherty
Relatively little is known about how, from whom, and under what conditions residents say they most effectively learn. We examined the relationships between residents' self-reported ratings of 11 different sources of learning and a number of empirical variables, using a national, random sample of postgraduate year (PGY) 1 and PGY-2 residents in the 1998-1999 training year. Residents were surveyed by mail. Completed surveys were received from 64.2% of 5616 residents contacted. The most often reported sources of learning were other residents and attending physicians...
October 2016: Journal of Graduate Medical Education
https://www.readbyqxmd.com/read/27744073/does-decorin-protect-neuronal-tissue-via-its-antioxidant-and-antiinflammatory-activity-from-traumatic-brain-injury-an-experimental-study
#11
Rafet Özay, Erhan Türkoğlu, Bora Gürer, Habibullah Dolgun, Oya Evirgen, Berrin İmge Ergüder, Nazlı Hayırlı, Levent Gürses, Zeki Şekerci, Erdal Reşit Yılmaz
BACKGROUND: The development of secondary brain injury via oxidative stress after traumatic brain injury (TBI) is well known. Decorin inactivates Transforming growth factor-β1 (TGF-β1), complement system (CS) and Tumor necrosis factor-α (TNF-α) which are related the oxidative stress and apoptosis. Consequently, the aim of the present study was to evaluate the role of Decorin (DC) on TBI. METHODS: A total of 24 male rats were used and divided into four groups as follows; control, trauma, DC, and methylprednisolone (MP)...
October 12, 2016: World Neurosurgery
https://www.readbyqxmd.com/read/27738135/img-m-integrated-genome-and-metagenome-comparative-data-analysis-system
#12
I-Min A Chen, Victor M Markowitz, Ken Chu, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Evan Andersen, Marcel Huntemann, Neha Varghese, Michalis Hadjithomas, Kristin Tennessen, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides
The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives...
October 13, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27688874/medical-education-in-israel-2016-five-medical-schools-in-in-a-period-of-transition
#13
Shmuel Reis, Jacob Urkin, Rachel Nave, Rosalie Ber, Amitai Ziv, Orit Karnieli-Miller, Dafna Meitar, Peter Gilbey, Dror Mevorach
ABSTRACT: We reviewed the existing programs for basic medical education (BME) in Israel as well as their output, since they are in a phase of reassessment and transition. The transition has been informed, in part, by evaluation in 2014 by an International Review Committee (IRC). The review is followed by an analysis of its implications as well as the emergent roadmap for the future. The review documents a trend of modernizing, humanizing, and professionalizing Israeli medical education in general, and BME in particular, independently in each of the medical schools...
2016: Israel Journal of Health Policy Research
https://www.readbyqxmd.com/read/27663453/respiratory-self-gated-3d-ute-for-lung-imaging-in-small-animal-mri
#14
Marta Tibiletti, Andrea Bianchi, Åsmund Kjørstad, Stefan Wundrak, Detlef Stiller, Volker Rasche
PURPOSE: To investigate retrospective respiratory gating of three-dimensional ultrashort echo time (3D UTE) lung acquisition in free-breathing rats using k-space center self gating signal (DC-SG) and 3D image-based SG (3D-Img-SG). METHODS: Seven rats were investigated with a quasi-random 3D UTE protocol. Low-resolution time-resolved sliding-window images were reconstructed with a 3D golden-angle radial sparse parallel (GRASP) reconstruction to extract a 3D-Img-SG signal, whereas DC-SG was extracted from the center of k-space...
September 23, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/27628719/supporting-international-medical-graduates-transition-to-their-host-country-realist-synthesis
#15
REVIEW
Amelia Kehoe, John McLachlan, Jane Metcalf, Simon Forrest, Madeline Carter, Jan Illing
CONTEXT: Many health services and systems rely on the contribution of international medical graduates (IMGs) to the workforce. However, concern has grown around their regulation and professional practice. There is a need, in the absence of strong evidence and a robust theoretical base, for a deeper understanding of the efficacy of interventions used to support IMGs' transition to their host countries. This study seeks to explore and synthesise evidence relating to interventions developed for IMGs...
October 2016: Medical Education
https://www.readbyqxmd.com/read/27603039/the-characteristics-of-international-medical-graduates-who-have-been-disciplined-by-professional-regulatory-colleges-in-canada-a-retrospective-cohort-study
#16
Asim Alam, John J Matelski, Hanna R Goldberg, Jessica J Liu, Jason Klemensberg, Chaim M Bell
PURPOSE: This study evaluated the proportion and characteristics of international medical graduates (IMGs) who have been disciplined by professional regulatory colleges in Canada in comparison with disciplined North American medical graduates (NAMGs). METHOD: The authors compiled a database of the nature of professional misconduct and penalties incurred by disciplined physicians from January 2000 to May 2015 using public records. They compared discipline data for IMGs versus those for NAMGs, and calculated risk ratios (RRs) and 95% confidence intervals (CIs) for select outcomes...
September 6, 2016: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/27591628/lab-on-a-chip-based-biosensor-for-the-real-time-detection-of-aflatoxin
#17
Yıldız Uludag, Elif Esen, Guzin Kokturk, Hayrettin Ozer, Turghun Muhammad, Zehra Olcer, H Imge Oktay Basegmez, Senay Simsek, Serkan Barut, M Yagmur Gok, Mete Akgun, Zeynep Altintas
Polymers were synthesized and utilized for aflatoxin detection coupled with a novel lab-on-a-chip biosensor: MiSens and high performance liquid chromatography (HPLC). Non-imprinted polymers (NIPs) were preferred to be designed and used due to the toxic nature of aflatoxin template and also to avoid difficult clean-up protocols. Towards an innovative miniaturized automated system, a novel biochip has been designed that consists of 6 working electrodes (1mm diameter) with shared reference and counter electrodes...
November 1, 2016: Talanta
https://www.readbyqxmd.com/read/27583782/experience-of-clinical-supervisors-of-international-medical-graduates-in-an-australian-district-hospital
#18
David Henderson, Pam D McGrath, Mary Anne Patton
Objective Herein we record the experience of clinical supervisors of international medical graduates (IMGs) working as junior staff in a district hospital by examining supervisor perspectives on IMG performance, the factors affecting their performance and the requirements of supervision under these circumstances.Methods The present study had an open-ended exploratory qualitative design. Thirteen 13 open-ended, in-depth interviews were undertaken with supervisors of IMGs employed in a public district hospital in Queensland, Australia...
September 2, 2016: Australian Health Review: a Publication of the Australian Hospital Association
https://www.readbyqxmd.com/read/27581267/composite-reliability-of-workplace-based-assessment-for-international-medical-graduates
#19
Balakrishnan Kichu R Nair, Joyce Mw Moonen-van Loon, Mulavana S Parvathy, Cees Pm van der Vleuten
OBJECTIVE: The fitness to practise of international medical graduates (IMGs) is usually evaluated with standardised assessment tests. Practising doctors should, however, be assessed on their performance rather than their competency, for which reason workplace-based assessment (WBA) has gained increasing attention. Our aim was to assess the composite reliability of WBA instruments for assessing the performance of IMGs. DESIGN AND SETTING: Between June 2010 and April 2015, 142 IMGs were assessed by 99 calibrated assessors; each cohort was assessed at their workplace over 6 months...
September 5, 2016: Medical Journal of Australia
https://www.readbyqxmd.com/read/27570522/species-divergence-vs-functional-convergence-characterizes-crude-oil-microbial-community-assembly
#20
Yong Nie, Jie-Yu Zhao, Yue-Qin Tang, Peng Guo, Yunfeng Yang, Xiao-Lei Wu, Fangqing Zhao
Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited in IMG database (until October 2013)...
2016: Frontiers in Microbiology
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