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https://www.readbyqxmd.com/read/29142289/comprehensive-genomic-analysis-of-a-plant-growth-promoting-rhizobacterium-pantoea-agglomerans-strain-p5
#1
Vahid Shariati J, Mohammad Ali Malboobi, Zeinab Tabrizi, Elahe Tavakol, Parviz Owilia, Maryam Safari
In this study, we provide a comparative genomic analysis of Pantoea agglomerans strain P5 and 10 closely related strains based on phylogenetic analyses. A next-generation shotgun strategy was implemented using the Illumina HiSeq 2500 technology followed by core- and pan-genome analysis. The genome of P. agglomerans strain P5 contains an assembly size of 5082485 bp with 55.4% G + C content. P. agglomerans consists of 2981 core and 3159 accessory genes for Coding DNA Sequences (CDSs) based on the pan-genome analysis...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141959/an-integrative-strategy-to-identify-the-entire-protein-coding-potential-of-prokaryotic-genomes-by-proteogenomics
#2
Ulrich Omasits, Adithi R Varadarajan, Michael Schmid, Sandra Goetze, Damianos Melidis, Marc Bourqui, Olga Nikolayeva, Maxime Québatte, Andrea Patrignani, Christoph Dehio, Juerg E Frey, Mark D Robinson, Bernd Wollscheid, Christian H Ahrens
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29126196/interface-information-interaction-a-narrative-review-of-design-and-functional-requirements-for-clinical-decision-support
#3
Kristen Miller, Danielle Mosby, Muge Capan, Rebecca Kowalski, Raj Ratwani, Yaman Noaiseh, Rachel Kraft, Sanford Schwartz, William S Weintraub, Ryan Arnold
Objective: Provider acceptance and associated patient outcomes are widely discussed in the evaluation of clinical decision support systems (CDSSs), but critical design criteria for tools have generally been overlooked. The objective of this work is to inform electronic health record alert optimization and clinical practice workflow by identifying, compiling, and reporting design recommendations for CDSS to support the efficient, effective, and timely delivery of high-quality care. Material and Methods: A narrative review was conducted from 2000 to 2016 in PubMed and The Journal of Human Factors and Ergonomics Society to identify papers that discussed/recommended design features of CDSSs that are associated with the success of these systems...
November 6, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29125228/routine-follow-up-of-preterm-infants-in-new-zealand
#4
Nicole Gledhill, Gabrielle Scott, Nathalie Ks de Vries
AIM: To describe the routine follow-up of preterm infants by different District Health Boards (DHBs) in New Zealand (NZ), and to compare current practice with international guidelines. METHODS: A descriptive survey of the existing routine follow-up management of preterm infants in NZ. From November 2015 until January 2016, a questionnaire was sent out across NZ to one paediatrician (n = 24) and one Child Development Service (CDS) (n = 20) from each DHB. All paediatricians responded and 85% of the CDSs responded...
November 10, 2017: Journal of Paediatrics and Child Health
https://www.readbyqxmd.com/read/29119468/clinical-decision-support-and-optional-point-of-care-testing-of-renal-function-for-safe-use-of-antibiotics-in-elderly-patients-a-retrospective-study-in-community-pharmacy-practice
#5
Mette Heringa, Annemieke Floor-Schreudering, Peter A G M De Smet, Marcel L Bouvy
OBJECTIVE: The aim was to investigate the management of drug therapy alerts on safe use of antibiotics in elderly patients with (potential) renal impairment and the contribution of optional creatinine point of care testing (PoCT) in community pharmacy practice. METHODS: Community pharmacists used a clinical decision support system (CDSS) for seven antibiotics. Alerts were generated during prescription processing in the case of previously registered renal impairment and when no information on renal function was available for patients aged 70 and over...
November 8, 2017: Drugs & Aging
https://www.readbyqxmd.com/read/29108803/factor-analysis-of-symptom-dimensions-psychotic-affective-and-obsessive-compulsive-symptoms-in-schizophrenia
#6
Sandeep Grover, Devakshi Dua, Subho Chakrabarti, Ajit Avasthi
AIM: To carryout factor analysis of symptom profile of patients with schizophrenia assessed by using positive and negative syndrome scale (PANSS), Calgary depression rating scale (CDSS), Young mania rating scale (YMRS) and YBOCS checklist. METHODOLOGY: 181 patients of schizophrenia were assessed on PANSS, CDSS, YMRS and YBOCS checklist. RESULTS: Factor analysis of PANSS yielded 3 factor structure (positive, negative, anxiety). When the items of CDSS were added to the PANSS items, total number of factors increased to 4 with depression emerging as a separate factor...
October 23, 2017: Asian Journal of Psychiatry
https://www.readbyqxmd.com/read/29102816/leukocyte-telomere-length-variation-in-different-stages-of-schizophrenia
#7
Pawan Kumar Maurya, Lucas Bortolotto Rizzo, Gabriela Xavier, Priscila Farias Tempaku, Vanessa Kiyomi Ota, Marcos L Santoro, Letícia M Spíndola, Patrícia S Moretti, Diego R Mazzotti, Ary Gadelha, Eduardo S Gouvea, Cristiano Noto, Michael Maes, Quirino Cordeiro, Rodrigo A Bressan, Elisa Brietzke, Sintia Iole Belangero
Recent research has demonstrated that telomere maintenance might be a key integrating point for the cumulative effect of genetic and environmental factors in patients with first-episode psychosis (FEP) and schizophrenia (SCZ). Eighty-one participants with antipsychotic-naïve FEP, 173 with SCZ and 438 HC were enrolled in this study. Psychiatric diagnosis was assessed using the Semi-Structured Clinical Interview for DSM-IV Axis-I (SCID-I). The Positive and Negative Syndrome Scale (PANSS), Young Mania Rating Scale (YMRS) and Calgary Depression Scale for Schizophrenia (CDSS) were used to measure symptoms severity...
October 21, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/29097621/clinical-decision-support-for-in-hospital-aki
#8
Mohammed Al-Jaghbeer, Dilhari Dealmeida, Andrew Bilderback, Richard Ambrosino, John A Kellum
AKI carries a significant mortality and morbidity risk. Use of a clinical decision support system (CDSS) might improve outcomes. We conducted a multicenter, sequential period analysis of 528,108 patients without ESRD before admission, from October of 2012 to September of 2015, to determine whether use of a CDSS reduces hospital length of stay and in-hospital mortality for patients with AKI. We compared patients treated 12 months before (181,696) and 24 months after (346,412) implementation of the CDSS. Coprimary outcomes were hospital mortality and length of stay adjusted by demographics and comorbidities...
November 2, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29083303/deep-transcriptome-annotation%C3%A2-enables-the-discovery-and-functional-characterization-of-cryptic-small-proteins
#9
Sondos Samandi, Annie V Roy, Vivian Delcourt, Jean-François Lucier, Jules Gagnon, Maxime C Beaudoin, Benoît Vanderperre, Marc-André Breton, Julie Motard, Jean-François Jacques, Mylène Brunelle, Isabelle Gagnon-Arsenault, Isabelle Fournier, Aïda Ouangraoua, Darel J Hunting, Alan A Cohen, Christian R Landry, Michelle S Scott, Xavier Roucou
Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs...
October 30, 2017: ELife
https://www.readbyqxmd.com/read/29076113/a-knowledge-modeling-approach-to-integrate-multiple-clinical-practice-guidelines-to-provide-evidence-based-clinical-decision-support-for-managing-comorbid-conditions
#10
Samina Abidi
Clinical management of comorbidities is a challenge, especially in a clinical decision support setting, as it requires the safe and efficient reconciliation of multiple disease-specific clinical procedures to formulate a comorbid therapeutic plan that is both effective and safe for the patient. In this paper we pursue the integration of multiple disease-specific Clinical Practice Guidelines (CPG) in order to manage co-morbidities within a computerized Clinical Decision Support System (CDSS). We present a CPG integration framework-termed as COMET (Comorbidity Ontological Modeling & ExecuTion) that manifests a knowledge management approach to model, computerize and integrate multiple CPG to yield a comorbid CPG knowledge model that upon execution can provide evidence-based recommendations for handling comorbid patients...
October 26, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/29060445/reconciliation-of-snomed-ct-and-domain-clinical-model-for-interoperable-medical-knowledge-creation
#11
Taqdir Ali, Sungyoung Lee
Use of heterogeneous data models in hospital information systems (HIS), obstructs the integration of clinical decision support system (CDSS) with clinical workflows. The diverse concepts diminish the interoperability level among the CDSS knowledge bases and data models of HIS. Standard terminology utilization in knowledge acquisition and its reconciliation with HIS data models are the candidate solution to overcome the interoperability barrier. We propose a reconciliation model to map concepts of diverse domain clinical models (DCM) with the standard terminology...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29059819/smartool-a-tool-for-clinical-decision-support-for-the-management-of-patients-with-coronary-artery-disease-based-on-modeling-of-atherosclerotic-plaque-process
#12
Antonis I Sakellarios, George Rigas, Vassiliki Kigka, Panagiotis Siogkas, Panagiota Tsompou, Georgia Karanasiou, Themis Exarchos, Ioannis Andrikos, Nikolaos Tachos, Gualtriero Pelosi, Oberdan Parodi, Dimitrios I Fotiaids
SMARTool aims to the development of a clinical decision support system (CDSS) for the management and stratification of patients with coronary artery disease (CAD). This will be achieved by performing computational modeling of the main processes of atherosclerotic plaque growth. More specifically, computed tomography coronary angiography (CTCA) is acquired and 3-dimensional (3D) reconstruction is performed for the arterial trees. Then, blood flow and plaque growth modeling is employed simulating the major processes of atherosclerosis, such as the estimation of endothelial shear stress (ESS), the lipids transportation, low density lipoprotein (LDL) oxidation, macrophages migration and plaque development...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29051020/draft-genome-sequences-of-three-multidrug-resistant-cutibacterium-formerly-propionibacterium-acnes-strains-isolated-from-acne-patients-china
#13
Nanxue Zhang, Zhong Lu, Ying Ma
OBJECTIVES: Cutibacterium acnes (formerly Propionibacterium acnes), an anaerobic Gram-positive bacterium, is a skin commensal and is considered to be associated with acne. Here we report the draft genome sequences of three multidrug-resistant (MDR) C. acnes strains (CA17, CA39 and CA51) isolated from skin lesions of acne patients in China. METHODS: The whole genomes of the three MDR C. acnes strains were sequenced using an Illumina HiSeq 2500 platform. De novo assembly and annotation were performed with SPAdes 3...
October 16, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29036587/latent-profile-analysis-and-conversion-to-psychosis-characterizing-subgroups-to-enhance-risk-prediction
#14
Kristin M Healey, David L Penn, Diana Perkins, Scott W Woods, Richard S E Keefe, Jean Addington
BACKGROUND: Groups at clinical high risk (CHR) of developing psychosis are heterogeneous, composed of individuals with different clusters of symptoms. It is likely that there exist subgroups, each associated with different symptom constellations and probabilities of conversion. METHOD: Present study used latent profile analysis (LPA) to ascertain subgroups in a combined sample of CHR (n = 171) and help-seeking controls (HSCs; n = 100; PREDICT study). Indicators in the LPA model included baseline Scale of Prodromal Symptoms (SOPS), Calgary Depression Scale for Schizophrenia (CDSS), and neurocognitive performance as measured by multiple instruments, including category instances (CAT)...
July 14, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29036406/effects-of-computerized-decision-support-system-implementations-on-patient-outcomes-in-inpatient-care-a-systematic-review
#15
Julian Varghese, Maren Kleine, Sophia Isabella Gessner, Sarah Sandmann, Martin Dugas
Objectives: To systematically classify the clinical impact of computerized clinical decision support systems (CDSSs) in inpatient care. Materials and Methods: Medline, Cochrane Trials, and Cochrane Reviews were searched for CDSS studies that assessed patient outcomes in inpatient settings. For each study, 2 physicians independently mapped patient outcome effects to a predefined medical effect score to assess the clinical impact of reported outcome effects. Disagreements were measured by using weighted kappa and solved by consensus...
September 23, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29036296/unintended-adverse-consequences-of-a-clinical-decision-support-system-two-cases
#16
Erin G Stone
Many institutions have implemented clinical decision support systems (CDSSs). While CDSS research papers have focused on benefits of these systems, there is a smaller body of literature showing that CDSSs may also produce unintended adverse consequences (UACs). Detailed here are 2 cases of UACs resulting from a CDSS. Both of these cases were related to external systems that fed data into the CDSS. In the first case, lack of knowledge of data categorization in an external pharmacy system produced a UAC; in the second case, the change of a clinical laboratory instrument produced the UAC...
September 23, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29029694/prescriber-response-to-computerized-drug-alerts-for-electronic-prescriptions-among-hospitalized-patients
#17
Yael Zenziper Straichman, Daniel Kurnik, Ilan Matok, Hillel Halkin, Noa Markovits, Amitai Ziv, Ari Shamiss, Ronen Loebstein
BACKGROUND: Clinical decision support systems (CDSS) reduce prescription errors, but their effectiveness is reduced by high alert rates, "alert fatigue", and indiscriminate rejection. OBJECTIVES: To compare acceptance rates of alerts generated by the SafeRx(®) prescription CDSS among different alert types and departments in a tertiary care hospital, identify factors associated with alert acceptance, and determine whether alert overrides were justified. METHODS: In a retrospective study, we compared acceptance rates of all prescription alerts generated in 2013 in 18 departments of Israel's largest tertiary care center...
November 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29026458/safe-opioid-prescription-a-smart-on-fhir-approach-to-clinical-decision-support
#18
Shyamashree Sinha, Mark Jensen, Sarah Mullin, Peter L Elkin
Background Prescription opioid pain medication overuse, misuse and abuse have been a significant contributing factor in the opioid epidemic. The rising death rates from opioid overdose have caused healthcare practitioners and researchers to work on optimizing pain therapy and limiting the prescriptions for pain medications. The state of New York has implemented a prescription drug monitoring program(PDMP), amended public health law to limit the prescription of opioids for acute pain and utilized the resources of the state and county health departments to help in curbing this epidemic...
2017: Online Journal of Public Health Informatics
https://www.readbyqxmd.com/read/29026454/opportunities-and-obstacles-using-a-clinical-decision-support-system-for-maternal-care-in-burkina-faso
#19
S Alphonse Zakane, Lars L Gustafsson, Ali Sie, Göran Tomson, Svetla Loukanova, Pia Bastholm-Rahmner
OBJECTIVE: Maternal and neonatal mortality is high in sub-Saharan Africa. To support Healthcare Workers (HCWs), a computerized decision support system (CDSS) was piloted at six rural maternal care units in Burkina Faso. During the two years of the study period, it was apparent from reports that the CDSS was not used regularly in clinical practice. This study aimed to explore the reasons why HCWs failed to use the CDSS. METHODS: A workshop, organized as group discussions and a plenary session, was performed with 13 participants to understand their experience with the CDSS and suggest improvements if pertinent...
2017: Online Journal of Public Health Informatics
https://www.readbyqxmd.com/read/29025114/comprehensive-process-model-of-clinical-information-interaction-in-primary-care-results-of-a-best-fit-framework-synthesis
#20
Tiffany C Veinot, Charles R Senteio, David Hanauer, Julie C Lowery
Objective: To describe a new, comprehensive process model of clinical information interaction in primary care (Clinical Information Interaction Model, or CIIM) based on a systematic synthesis of published research. Materials and Methods: We used the "best fit" framework synthesis approach. Searches were performed in PubMed, Embase, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), PsycINFO, Library and Information Science Abstracts, Library, Information Science and Technology Abstracts, and Engineering Village...
September 2, 2017: Journal of the American Medical Informatics Association: JAMIA
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