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https://www.readbyqxmd.com/read/27902881/the-chimeric-nature-of-the-genomes-of-marine-magnetotactic-coccoid-ovoid-bacteria-defines-a-novel-group-of-proteobacteria
#1
Boyang Ji, Sheng-Da Zhang, Wei-Jia Zhang, Zoe Rouy, François Alberto, Claire-Lise Santini, Sophie Mangenot, Séverine Gagnot, Nadège Philippe, Nathalie Pradel, Lichen Zhang, Sébastien Tempel, Ying Li, Claudine Médigue, Bernard Henrissat, Pedro M Coutinho, Valérie Barbe, Emmanuel Talla, Long-Fei Wu
Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared to other bacterial taxonomic groups remain to be illustrated. Here, we analyzed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1...
November 30, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27899620/mrprimerv-a-database-of-pcr-primers-for-rna-virus-detection
#2
Hyerin Kim, NaNa Kang, KyuHyeon An, Doyun Kim, JaeHyung Koo, Min-Soo Kim
Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27894822/a-parallel-group-randomised-open-blinded-evaluation-of-acceptance-and-commitment-therapy-for-depression-after-psychosis-pilot-trial-outcomes-adapt
#3
Andrew Gumley, Ross White, Andy Briggs, Ian Ford, Sarah Barry, Corinna Stewart, Sara Beedie, Jacqueline McTaggart, Caoimhe Clarke, Rachel MacLeod, Emma Lidstone, Bruno Salgado Riveros, Robin Young, Hamish McLeod
BACKGROUND: Depression is one of the major contributors to poorer quality of life amongst individuals with psychosis and schizophrenia. The study was designed as a Pilot Trial to determine the parameters of a larger, definitive pragmatic multi-centre randomised controlled trial of Acceptance and Commitment Therapy for depression after psychosis (ACTdp) for individuals with a diagnosis of schizophrenia who also meet diagnostic criteria for major depression. METHODS: Participants were required to meet criteria for schizophrenia and major depression...
November 25, 2016: Schizophrenia Research
https://www.readbyqxmd.com/read/27894220/the-role-of-the-pharmacist-in-the-design-development-and-implementation-of-medication-prescription-support-systems
#4
Nuria Sola Bonada, Ana María Álvarez Díaz, Carlos Codina Jané
Clinical Decision Support Systems (CDSS) are computerized tools designed to help healthcare professionals to make clinical and therapeutic decisions, with the objective of improving patient care. Prescription-targeted CDSS have the highest impact in improving patient safety. Although there are different designs and functionalities, all these systems will combine clinical knowledge and patient information in a smart manner, in order to improve the prescription process. With the emergence of new technologies and advances in smart decision systems, the implementation of said systems can achieve an important improvement in terms of the prescription process and patient safety...
November 1, 2016: Farmacia Hospitalaria
https://www.readbyqxmd.com/read/27884165/implementing-an-evidence-based-computerized-decision-support-system-linked-to-electronic-health-records-to-improve-care-for-cancer-patients-the-onco-codes-study-protocol-for-a-randomized-controlled-trial
#5
Lorenzo Moja, Alessandro Passardi, Matteo Capobussi, Rita Banzi, Francesca Ruggiero, Koren Kwag, Elisa Giulia Liberati, Massimo Mangia, Ilkka Kunnamo, Michela Cinquini, Roberto Vespignani, Americo Colamartini, Valentina Di Iorio, Ilaria Massa, Marien González-Lorenzo, Lorenzo Bertizzolo, Peter Nyberg, Jeremy Grimshaw, Stefanos Bonovas, Oriana Nanni
BACKGROUND: Computerized decision support systems (CDSSs) are computer programs that provide doctors with person-specific, actionable recommendations, or management options that are intelligently filtered or presented at appropriate times to enhance health care. CDSSs might be integrated with patient electronic health records (EHRs) and evidence-based knowledge. METHODS/DESIGN: The Computerized DEcision Support in ONCOlogy (ONCO-CODES) trial is a pragmatic, parallel group, randomized controlled study with 1:1 allocation ratio...
November 25, 2016: Implementation Science: IS
https://www.readbyqxmd.com/read/27878205/iterative-development-and-evaluation-of-a-pharmacogenomic-guided-clinical-decision-support-system-for-warfarin-dosing
#6
Brittany L Melton, Alan J Zillich, Jason Saleem, Alissa L Russ, James E Tisdale, Brian R Overholser
OBJECTIVE: Pharmacogenomic-guided dosing has the potential to improve patient outcomes but its implementation has been met with clinical challenges. Our objective was to develop and evaluate a clinical decision support system (CDSS) for pharmacogenomic-guided warfarin dosing designed for physicians and pharmacists. METHODS: Twelve physicians and pharmacists completed 6 prescribing tasks using simulated patient scenarios in two iterations (development and validation phases) of a newly developed pharmacogenomic-driven CDSS prototype...
November 23, 2016: Applied Clinical Informatics
https://www.readbyqxmd.com/read/27872587/the-association-between-anomalous-self-experiences-self-esteem-and-depressive-symptoms-in-first-episode-schizophrenia
#7
Elisabeth Haug, Merete G Øie, Ole A Andreassen, Unni Bratlien, Kristin L Romm, Paul Møller, Ingrid Melle
Background: Anomalous self-experiences (ASEs) aggregate in schizophrenia spectrum disorders, but the relationship between ASEs, and depression has been studied to a limited extent. Lower self-esteem has been shown to be associated with depression in early psychosis. Our hypothesis is that ASEs in early phases of schizophrenia are linked to lower levels of self-esteem, which in turn is associated with depression. Aim: The aim is to examine the relationship between ASEs, self-esteem and depression in first-episode schizophrenia spectrum disorders...
2016: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/27869877/-computerized-decision-support-systems-ebm-at-the-bedside
#8
Matteo Capobussi, Rita Banzi, Lorenzo Moja, Stefanos Bonovas, Marien González-Lorenzo, Elisa Giulia Liberati, Hernan Polo Friz, Oriana Nanni, Massimo Mangia, Francesca Ruggiero
INTRODUCTION: One of the aims of Evidence-Based Medicine is to improve quality and appropriateness of care by the expedition of the knowledge transfer process. Computerized Decision Support Systems (CDSSs) are computer programs that provide alerts to the prescribing doctor directly at the moment of medical examination. In fact, alerts are integrated within the single patient electronic health record. CDSS based on the best available and updated evidence and guidelines may be an efficient tool to facilitate the transfer of the latest results from clinical research directly at the bedside, thus supporting decision-making...
November 2016: Recenti Progressi in Medicina
https://www.readbyqxmd.com/read/27867120/transforaminal-resection-of-cervical-dumbbell-schwannomas-in-patients-with-additional-tumors
#9
Ji Zhang, Xiang-Heng Zhang, Zi-Feng Wang, You-Ping Li, Zheng-Quan Zhu, Ji-Cheng Sun, Zheng-He Chen, Shao-Yong Wu, Ke Sai, Jian Wang, Yong-Gao Mou, Zhong-Ping Chen
BACKGROUND: It is rare for two primary tumors to occur simultaneously in a patient. Management of cervical dumbbell schwannomas (CDSs) with concurrent tumors (CTs) requires a specific neurosurgical strategy. The primary objective of this study is to investigate surgical strategies for CDSs with CTs while preserving as much of the mechanically relevant bone structures as possible. MATERIAL AND METHODS: Twelve patients with concurrent CTs and CDSs were identified from three medical centers...
November 17, 2016: World Neurosurgery
https://www.readbyqxmd.com/read/27856572/complete-genome-sequences-of-three-siphoviridae-bacteriophages-infecting-salmonella-enterica-serovar-enteritidis
#10
Rubina Paradiso, Serena Lombardi, Maria Grazia Iodice, Marita Georgia Riccardi, Massimiliano Orsini, Sergio Bolletti Censi, Giorgio Galiero, Giorgia Borriello
Three bacteriophages, 118970_sal1, 118970_sal2, and 64795_sal3, were isolated from water buffalo feces in southern Italy, exhibiting lytic activity against Salmonella enterica serovar Enteritidis. These bacteriophages belong to the Siphoviridae family and have a 60,113-bp, 123,930-bp, and 48,094-bp double-stranded DNA (dsDNA) genome containing 72, 173, and 80 coding sequences (CDSs), respectively.
November 17, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27834851/negative-glucocorticoid-response-like-element-from-the-first-intron-of-the-chicken-growth-hormone-gene-represses-gene-expression-in-the-rat-pituitary-tumor-cell-line
#11
Jing-E Ma, Qian-Qian Lang, Feng-Fang Qiu, Li Zhang, Xiang-Guang Li, Wen Luo, Juan Wang, Xing Wang, Xi-Ran Lin, Wen-Sheng Liu, Qing-Hua Nie, Xi-Quan Zhang
The effects of introns, especially the first intron, on the regulation of gene expression remains unclear. Therefore, the objective of the present study was to investigate the transcriptional regulatory function of intron 1 on the chicken growth hormone (cGH) gene in the rat pituitary tumor cell line (GH4-C1). Transient transfection using first-intron-inserted cGH complete coding sequences (CDSs) and non-intron-inserted cGH CDS plasmids, quantitative RT-PCR (qRT-PCR) and western blot assays were used to detect the expression of cGH...
November 9, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27833663/genome-sequencing-assembly-annotation-and-analysis-of%C3%A2-staphylococcus-xylosus%C3%A2-strain-dmb3-bh1-reveals-genes-responsible-for-pathogenicity
#12
Gurwinder Kaur, Amit Arora, Sathyaseelan Sathyabama, Nida Mubin, Sheenam Verma, Shanmugam Mayilraj, Javed N Agrewala
BACKGROUND: Staphylococcus xylosus is coagulase-negative staphylococci (CNS), found occasionally on the skin of humans but recurrently on other mammals. Recent reports suggest that this commensal bacterium may cause diseases in humans and other animals. In this study, we present the first report of whole genome sequencing of S. xylosus strain DMB3-Bh1, which was isolated from the stool of a mouse. RESULTS: The draft genome of S. xylosus strain DMB3-Bh1 consisted of 2,81,0255 bp with G+C content of 32...
2016: Gut Pathogens
https://www.readbyqxmd.com/read/27830247/computerized-clinical-decision-support-contributions-from-2015
#13
V Koutkias, J Bouaud
OBJECTIVE: To summarize recent research and select the best papers published in 2015 in the field of computerized clinical decision support for the Decision Support section of the IMIA yearbook. METHOD: A literature review was performed by searching two bibliographic databases for papers related to clinical decision support systems (CDSSs) and computerized provider order entry (CPOE) systems. The aim was to identify a list of candidate best papers from the retrieved papers that were then peer-reviewed by external reviewers...
November 10, 2016: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/27822542/rna-sequencing-based-genome-reannotation-of-the-dermatophyte-arthroderma-benhamiae-and-characterization-of-its-secretome-and-whole-gene-expression-profile-during-infection
#14
Van Du T Tran, Niccolò De Coi, Marc Feuermann, Emanuel Schmid-Siegert, Elena-Tatiana Băguţ, Bernard Mignon, Patrice Waridel, Corinne Peter, Sylvain Pradervand, Marco Pagni, Michel Monod
Dermatophytes are the most common agents of superficial mycoses in humans and animals. The aim of the present investigation was to systematically identify the extracellular, possibly secreted, proteins that are putative virulence factors and antigenic molecules of dermatophytes. A complete gene expression profile of Arthroderma benhamiae was obtained during infection of its natural host (guinea pig) using RNA sequencing (RNA-seq) technology. This profile was completed with those of the fungus cultivated in vitro in two media containing either keratin or soy meal protein as the sole source of nitrogen and in Sabouraud medium...
July 2016: MSystems
https://www.readbyqxmd.com/read/27821408/a-novel-translational-control-mechanism-involving-rna-structures-within-coding-sequences
#15
Jennifer Jungfleisch, Danny D Nedialkova, Ivan Dotu, Katherine E Sloan, Neus Martinez-Bosch, Lukas Brüning, Emanuele Raineri, Pilar Navarro, Markus T Bohnsack, Sebastian A Leidel, Juana Diez
The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features...
November 7, 2016: Genome Research
https://www.readbyqxmd.com/read/27818093/genome-sequence-of-bradyrhizobium-embrapense-strain-cnpso-2833-t-isolated-from-a-root-nodule-of-desmodium-heterocarpon
#16
Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Douglas Fabiano Gomes, Renata Carolini Souza, Ligia Maria Oliveira Chueire, Mariangela Hungria
Bradyrhizobium embrapense CNPSo 2833(T) is a nitrogen-fixing symbiont of the legume pasture Desmodium. Its draft genome contains 8,267,832bp and 7876 CDSs. The symbiotic island includes nodulation and nitrogen fixation genes resembling the operon organization of B. japonicum. Several CDSs related to secretion proteins and stress tolerance were also identified.
November 3, 2016: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/27816636/characterization-of-a-new-chlorovirus-type-with-permissive-and-non-permissive-features-on-phylogenetically-related-algal-strains
#17
Cristian F Quispe, Ahmed Esmael, Olivia Sonderman, Michelle McQuinn, Irina Agarkova, Mohammed Battah, Garry A Duncan, David D Dunigan, Timothy P L Smith, Cristina De Castro, Immacolata Speciale, Fangrui Ma, James L Van Etten
A previous report indicated that prototype chlorovirus PBCV-1 replicated in two Chlorella variabilis algal strains, NC64A and Syngen 2-3, that are ex-endosymbionts isolated from the protozoan Paramecium bursaria. Surprisingly, plaque-forming viruses on Syngen 2-3 lawns were often higher than on NC64A lawns from indigenous water samples. These differences led to the discovery of viruses that exclusively replicate in Syngen 2-3 cells, named Only Syngen (OSy) viruses. OSy-NE5, the prototype virus for the proposed new species, had a linear dsDNA genome of 327kb with 44-nucleotide-long, incompletely base-paired, covalently closed hairpin ends...
January 2017: Virology
https://www.readbyqxmd.com/read/27811087/genome-sequence-of-paraburkholderia-nodosa-strain-cnpso-1341-a-n2-fixing-symbiont-of-the-promiscuous-legume-phaseolus-vulgaris
#18
Rebeca Fuzinatto Dall'Agnol, Maira Rejane Costa, Renan Augusto Ribeiro, Jakeline Renata Marçon Delamuta, Ligia Maria Oliveira Chueire, Mariangela Hungria
Paraburkholderia nodosa CNPSo 1341 is a N2-fixing symbiont of Phaseolus vulgaris isolated from an undisturbed soil of the Brazilian Cerrado. Its draft genome contains 8,614,032 bp and 8,068 coding sequences (CDSs). Nodulation and N2-fixation genes were clustered in the genome that also contains several genes of secretion systems and quorum sensing.
November 3, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27793675/detection-of-the-cryptic-prophage-like-molecule-pbtic235-in-bacillus-thuringiensis-subsp-israelensis
#19
Annika Gillis, Suxia Guo, Alexandre Bolotin, Lionel Makart, Alexei Sorokin, Jacques Mahillon
Bacillus thuringiensis has long been recognized to carry numerous extrachromosomal molecules. Of particular interest are the strains belonging to the B. thuringiensis subsp. israelensis lineage, as they can harbor at least seven extrachromosomal molecules. One of these elements seems to be a cryptic molecule that may have been disregarded in strains considered plasmid-less. Therefore, this work focused on this cryptic molecule, named pBtic235. Using different approaches that included transposition-tagging, large plasmid gel electrophoresis and Southern blotting, conjugation and phage-induction experiments, in combination with bioinformatics analyses, it was found that pBtic235 is a hybrid molecule of 235,425 bp whose genome displays potential plasmid- and phage-like modules...
October 25, 2016: Research in Microbiology
https://www.readbyqxmd.com/read/27788226/identification-of-immunoglobulin-gene-sequences-from-a-small-read-number-of-mrna-seq-using-hybridomas
#20
Yuki Kuniyoshi, Kazumitsu Maehara, Takeshi Iwasaki, Masayasu Hayashi, Yuichiro Semba, Masatoshi Fujita, Yuko Sato, Hiroshi Kimura, Akihito Harada, Yasuyuki Ohkawa
Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs) but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately...
2016: PloS One
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