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Pierre Dehoux, Jean Christophe Marvaud, Amr Abouelleil, Ashlee M Earl, Thierry Lambert, Catherine Dauga
BACKGROUND: Clostridium bolteae and Clostridium clostridioforme, previously included in the complex C. clostridioforme in the group Clostridium XIVa, remain difficult to distinguish by phenotypic methods. These bacteria, prevailing in the human intestinal microbiota, are opportunistic pathogens with various drug susceptibility patterns. In order to better characterize the two species and to obtain information on their antibiotic resistance genes, we analyzed the genomes of six strains of C...
October 21, 2016: BMC Genomics
Sofian Berrouiguet, Maria Luisa Barrigón, Sara A Brandt, Santiago Ovejero-García, Raquel Álvarez-García, Juan Jose Carballo, Philippe Lenca, Philippe Courtet, Enrique Baca-García
PURPOSE: The emergence of electronic prescribing devices with clinical decision support systems (CDSS) is able to significantly improve management pharmacological treatments. We developed a web application available on smartphones in order to help clinicians monitor prescription and further propose CDSS. METHOD: A web application ( was developed to assess patients and collect data regarding gender, age, diagnosis and treatment. We analyzed antipsychotic prescriptions in 4345 patients attended in five Psychiatric Community Mental Health Centers from June 2014 to October 2014...
2016: PloS One
Cheng-Yu Hou, Wen-Chi Lee, Hsiao-Chun Chou, Ai-Ping Chen, Shu-Jen Chou, Ho-Ming Chen
High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5'-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and soybean (Glycine max)...
October 14, 2016: Plant Cell
G I Nazarenko, E B Kleimenova, S A Payushchik, V A Otdelenov, D A Sychev
AIM: To reduce the number of preventable hospital-acquired venous thromboembolic events (HA-VTE) and to improve the quality of VTE prophylaxis at multiprofile hospital. MATERIAL AND METHODS: A comprehensive approach to preventing HA-VTE was developed, which involved the global trigger tool method to assess adverse events, as well as the computerized clinical decision support system (CDSS) to prevent HA-VTE on the basis of relevant clinical practice guidelines, and HA-VTE registry...
2016: Terapevticheskiĭ Arkhiv
Han Young Chung, Kyu-Ho Lee, Sangryeol Ryu, Hyunjin Yoon, Ju-Hoon Lee, Hyeun Bum Kim, Heebal Kim, Hee Gon Jeong, Sang Ho Choi, Bong-Soo Kim
Bacillus cereus causes food-borne illness through contaminated foods; therefore, its pathogenicity and genome sequences have been analyzed in several studies. We sequenced and analyzed the B. cereus strain FORC_021 isolated from a sashimi restaurant. The genome sequence consists of 5,373,294 bp with 35.36% GC contents, 5,350 predicted CDSs, 42 rRNA genes, and 107 tRNA genes. Based on in silico DNA-DNA hybridization values, B. cereus ATCC 14579(T) was closest to FORC_021 among the complete genome-sequenced strains...
October 12, 2016: Journal of Microbiology and Biotechnology
Sang-Mo Kang, Sajjad Asaf, Sang-Jun Kim, Byung-Wook Yun, In-Jung Lee
Leifsonia xyli SE134 is a potential plant growth-promoting bacterium isolated from a soil in Daegu, Republic of Korea, which produces large amounts of gibberellin (GA) and indole acetic acid (IAA). In this study, we sequenced the complete genome of L. xyli SE134 by the Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. The genome of L. xyli SE134 contains a single chromosome that is 3,596,761bp in length, with 70.2% G+C content. The genome contains 3466 protein-coding genes (CDSs) and 51 rRNA- and 46 tRNA-coding genes...
October 7, 2016: Journal of Biotechnology
Rubina Paradiso, Serena Lombardi, Maria Grazia Iodice, Marita Georgia Riccardi, Massimiliano Orsini, Sergio Bolletti Censi, Giorgio Galiero, Giorgia Borriello
The bacteriophage 100268_sal2 was isolated from water buffalo feces in southern Italy, exhibiting lytic activity against several subspecies of Salmonella enterica This bacteriophage belongs to the Siphoviridae family and has a 125,114-bp double-stranded DNA (ds-DNA) genome containing 188 coding sequences (CDSs).
September 29, 2016: Genome Announcements
Rubina Paradiso, Massimiliano Orsini, Sergio Bolletti Censi, Giorgia Borriello, Giorgio Galiero
The bacteriophage 118970_sal3 was isolated from water buffalo feces in southern Italy, exhibiting lytic activity against Salmonella enterica serovar Typhimurium. This bacteriophage belongs to the Myoviridae family and has a 39,464-bp double-stranded DNA (ds-DNA) genome containing 53 coding sequences (CDSs).
September 29, 2016: Genome Announcements
Hugo Oliveira, Graça Pinto, Ana Oliveira, Carla Oliveira, Maria Alberta Faustino, Yves Briers, Lucília Domingues, Joana Azeredo
Citrobacter spp., although frequently ignored, is emerging as an important nosocomial bacterium able to cause various superficial and systemic life-threatening infections. Considered to be hard-to-treat bacterium due to its pattern of high antibiotic resistance, it is important to develop effective measures for early and efficient therapy. In this study, the first myovirus (vB_CfrM_CfP1) lytic for Citrobacter freundii was microbiologically and genomically characterized. Its morphology, activity spectrum, burst size, and biophysical stability spectrum were determined...
September 28, 2016: Applied Microbiology and Biotechnology
Dustin W Ballard, Ridhima Vemula, Uli K Chettipally, Mamata V Kene, Dustin G Mark, Andrew K Elms, James S Lin, Mary E Reed, Jie Huang, Adina S Rauchwerger, David R Vinson
OBJECTIVE: Adoption of clinical decision support (CDS) tools by clinicians is often limited by workflow barriers. We sought to assess characteristics associated with clinician use of an electronic health record-embedded clinical decision support system (CDSS). METHODS: In a prospective study on emergency department (ED) activation of a CDSS tool across 14 hospitals between 9/1/14 to 4/30/15, the CDSS was deployed at 10 active sites with an on-site champion, education sessions, iterative feedback, and up to 3 gift cards/clinician as an incentive...
2016: Applied Clinical Informatics
Wen-Hua Qi, Chao-Chao Yan, Wu-Jiao Li, Xue-Mei Jiang, Guang-Zhou Li, Xiu-Yue Zhang, Ting-Zhang Hu, Jing Li, Bi-Song Yue
As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5'UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3'UTRs, TEs, and intergenic regions...
September 16, 2016: Aging
Rose-Marie Johansson-Pajala, Lena-Karin Gustafsson, Kerstin Jorsäter Blomgren, Johan Fastbom, Lene Martin
AIM: To describe variations in nurses' perceptions of using a computerised decision support system (CDSS) in drug monitoring. BACKGROUND: There is an increasing focus on incorporating informatics into registered nurses' (RNs) clinical practice. Insight into RNs' perceptions of using a CDSS in drug monitoring can provide a basis for further development of safer practices in drug management. METHOD: A qualitative interview study of 16 RNs. Data were analysed using a phenomenographic approach...
September 13, 2016: Journal of Nursing Management
Sintia Almeida, Dan Loureiro, Ricardo W Portela, Diego C B Mariano, Thiago J Sousa, Felipe L Pereira, Fernanda A Dorella, Alex F Carvalho, Lilia F Moura-Costa, Carlos A G Leal, Henrique C Figueiredo, Roberto Meyer, Vasco Azevedo
We present here the genome sequence of the attenuated Corynebacterium pseudotuberculosis strain T1. The sequencing was performed with an Ion Torrent Personal Genome Machine platform. The genome is a circular chromosome of 2,337,201 bp, with a G+C content of 52.85% and a total of 2,125 coding sequences (CDSs), 12 rRNAs, 49 tRNAs, and 24 pseudogenes.
2016: Genome Announcements
Lucas M Marques, Izadora S Rezende, Maysa S Barbosa, Ana M S Guimarães, Hellen B Martins, Guilherme B Campos, Naíla C do Nascimento, Andrea P Dos Santos, Aline T Amorim, Verena M Santos, Sávio T Farias, Fernanda  C Barrence, Lauro M de Souza, Melissa Buzinhani, Victor E Arana-Chavez, Maria E Zenteno, Gustavo P Amarante-Mendes, Joanne B Messick, Jorge Timenetsky
Whole genome sequencing and analyses of Ureaplasma diversum ATCC 49782 was undertaken as a step towards understanding U. diversum biology and pathogenicity. The complete genome showed 973,501 bp in a single circular chromosome, with 28.2% of G+C content. A total of 782 coding DNA sequences (CDSs), and 6 rRNA and 32 tRNA genes were predicted and annotated. The metabolic pathways are identical to other human ureaplasmas, including the production of ATP via hydrolysis of the urea. Genes related to pathogenicity, such as urease, phospholipase, hemolysin, and a Mycoplasma Ig binding protein (MIB)-Mycoplasma Ig protease (MIP) system were identified...
2016: PloS One
Raquel Guerrero-Alba, Eduardo E Valdez Morales, J Nestor Jimenez-Vargas, Cintya Lopez Lopez, Josue Jaramillo Polanco, Takanobu Okamoto, Yasmin Nasser, Nigel W Bunnett, Alan E Lomax, Stephen J Vanner
AIMS AND BACKGROUND: Psychological stress accompanies chronic inflammatory diseases such as IBD, and stress hormones can exacerbate pain signalling. In contrast, the endogenous opioid system has an important analgesic action during chronic inflammation. This study examined the interaction of these pathways. METHODS: Mouse nociceptive dorsal root ganglia (DRG) neurons were incubated with supernatants from segments of inflamed colon collected from patients with chronic UC and mice with dextran sodium sulfate (cDSS)-induced chronic colitis...
September 2, 2016: Gut
Chen Wang, Lukasz Jakub Kubiak, Lian-Ming Du, Wu-Jiao Li, Zuo-Yi Jian, Ce Tang, Zhen-Xin Fan, Xiu-Yue Zhang, Bi-Song Yue
In this study, we characterized the distribution of microsatellites in the genomes and genes of Centruroides exilicauda and Mesobuthus martensii, carried out Gene Ontology (GO) analysis and GO enrichment analysis of coding sequences (CDSs) with microsatellite (SSR). In addition, over-represented GO functions related to environmental interactions, development process and methylation were identified to develop functional markers and facilitate further analysis of microsatellite function in the genes of scorpions...
December 5, 2016: Gene
Yahya Hani, Suhaila Ghuloum, Ziyad Mahfoud, Mark Opler, Anzalee Khan, Arij Yehya, Abdulmoneim Abdulhakam, Samer Hammoudeh, Azza Al-Mujalli, Reem Elsherbiny, Hassen Al-Amin
BACKGROUND: Patients with schizophrenia commonly show both depressive and negative symptoms that can differentially affect the prognosis and course of treatment. The Calgary Depression Scale for Schizophrenia (CDSS) was designed to distinguish between depression and negative symptoms in patients with schizophrenia. The purpose of this study is to validate an Arabic version of the CDSS among patients with schizophrenia. METHODS: The diagnosis of schizophrenia was confirmed using the Arabic Mini International Neuropsychiatric Interview 6 (MINI 6)...
2016: PloS One
Olga Laszczyńska, Milton Severo, Ana Azevedo
Patients with acute kidney injury (AKI) are at risk for increased morbidity and mortality. Lack of specific treatment has meant that efforts have focused on early diagnosis and timely treatment. Advanced algorithms for clinical assistance including AKI prediction models have potential to provide accurate risk estimates. In this project, we aim to provide a clinical decision supporting system (CDSS) based on a self-learning predictive model for AKI in patients of an acute care hospital. Data of all in-patient episodes in adults admitted will be analysed using "data mining" techniques to build a prediction model...
2016: Studies in Health Technology and Informatics
Xiaoxu Zhou, Hongdi Wang, Jun Cui, Xuemei Qiu, Yaqing Chang, Xiuli Wang
Tube foot as one of the ambulacral appendages types in Aspidochirote holothurioids, is known for their functions in locomotion, feeding, chemoreception, light sensitivity and respiration. In this study, we explored the characteristic of transcriptome in the tube foot of sea cucumber (Apostichopus japonicus). Our results showed that among 390 unigenes which specifically expressed in the tube foot, 190 of them were annotated. Based on the assembly transcriptome, we found 219,860 SNPs from 34,749 unigenes, 97,683, 53,624, 27,767 and 40,786 were located in CDSs, 5'-UTRs, 3'-UTRs and non-CDS separately...
August 4, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
S Avellan, I Uhr, D McKelvey, Soren Sondergaard
The central venous pressure, CVP, is an important variable in the management of selected perioperative and intensive care cases and in clinical decision support systems, CDSS. In current routine, when measuring CVP the health care provider may use anatomical landmarks and a spirit level, SL, to adjust the pressure transducer to the level of the tricuspid valve, i.e. the phlebostatic axis. The aim of the study was to assess the agreement in the postoperative setting between the SL method and electromagnetic 3D positioning (EM)...
August 10, 2016: Journal of Clinical Monitoring and Computing
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