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https://www.readbyqxmd.com/read/28334306/peptidemapper-efficient-and-versatile-amino-acid-sequence-and-tag-mapping
#1
Dominik Kopczynski, Harald Barsnes, Pål R Njølstad, Albert Sickmann, Marc Vaudel, Robert Ahrends
Summary: The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334291/smartr-an-open-source-platform-for-interactive-visual-analytics-for-translational-research-data
#2
Sascha Herzinger, Wei Gu, Venkata Satagopam, Serge Eifes, Kavita Rege, Adriano Barbosa Da Silva, Reinhard Schneider
In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical, or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334231/protvista-visualization-of-protein-sequence-annotations
#3
Xavier Watkins, Leyla J Garcia, Sangya Pundir, Maria J Martin, The UniProt Consortium
Summary: ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations...
March 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333181/candida-auris-candidaemia-in-indian-icus-analysis-of-risk-factors
#4
Shivaprakash M Rudramurthy, Arunaloke Chakrabarti, Raees A Paul, Prashant Sood, Harsimran Kaur, Malini R Capoor, Anupma J Kindo, Rungmei S K Marak, Anita Arora, Raman Sardana, Shukla Das, Deepinder Chhina, Atul Patel, Immaculata Xess, Bansidhar Tarai, Pankaj Singh, Anup Ghosh
Objectives: To identify the risk factors associated with Candida auris candidaemia, as this fungus now poses a global threat. Methods: We performed a subgroup analysis of a previously reported study of 27 Indian ICUs. The clinical data of candidaemia cases due to C. auris and other Candida species were compared to determine significant risk factors associated with C. auris infection. Results: Of the 1400 candidaemia cases reported earlier, 74 (5...
February 20, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28332853/correlations-between-lp-pla2-gene-polymorphisms-and-susceptibility-and-severity-of-acute-pancreatitis-in-a-chinese-population
#5
Min Ma, Chun-Xia Zhai, Cai-Xia Sun
OBJECTIVE: This case-control study explored correlations between LP-PLA2 gene polymorphisms (A379V, V279F, and R92H) and susceptibility and severity of acute pancreatitis (AP) in a Chinese population. MATERIALS AND METHODS: From October 2013 to October 2015, 94 AP patients were chosen as the case group. According to the Acute Physiology and Chronic Health Evaluation (APACHE) II score standard, AP patients were divided into a mild AP (MAP) group (n = 46) and severe AP (SAP) group (n = 48)...
March 23, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28329734/elevated-mif-2-levels-predict-mortality-in-critically-ill-patients
#6
Julia Pohl, Ulrike B Hendgen-Cotta, Pia Stock, Peter Luedike, Tienush Rassaf
PURPOSE: D-dopachrome tautomerase (MIF-2 or DDT) is a member of the macrophage migration inhibitory factor (MIF) superfamily and a close structural homolog to MIF. Circulating MIF-2 has been described to be elevated in patients suffering from sepsis, severe burn injury and after surgery. We sought to evaluate the prognostic value of MIF-2 in critically ill patients. METHODS: A total of 72 patients were studied upon admission to the medical intensive care unit (ICU)...
March 16, 2017: Journal of Critical Care
https://www.readbyqxmd.com/read/28327177/intestinal-t-lymphocyte-homing-is-associated-with-gastric-emptying-and-epithelial-barrier-function-in-critically-ill-a-prospective-observational-study
#7
Christian Greis, Zohal Rasuly, Rolf A Janosi, Lambros Kordelas, Dietrich W Beelen, Tobias Liebregts
BACKGROUND: Impaired gastric emptying is common in critically ill patients. Intestinal dysmotility, a major cause of feed intolerance, may foster infectious complications due to mucosal barrier disruption. However, little is known about gut-directed immune activation, intestinal barrier function and its association with impaired gastric emptying in critically ill patients at ICU admission. METHODS: We conducted a prospective observational study at two tertiary care medical ICUs...
March 22, 2017: Critical Care: the Official Journal of the Critical Care Forum
https://www.readbyqxmd.com/read/28323290/incidence-and-risk-factors-for-delirium-development-in-icu-patients-a-prospective-observational-study
#8
Marcela Kanova, Peter Sklienka, Roman Kula, Michal Burda, Jana Janoutova
BACKGROUND AND AIMS: Delirium is an acute brain dysfunction and a frequent complication in critically ill patients. When present it significantly worsens the prognosis of patients. The aim of this study was to evaluate the incidence of delirium and risk factors for delirium in a mixed group of trauma, medical and surgical ICU patients. METHODS: A prospective observational study was conducted in one of the six-bed Intensive Care Units of the University Hospital Ostrava in the Czech Republic during a 12-month period...
March 14, 2017: Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia
https://www.readbyqxmd.com/read/28322314/the-prognostic-value-of-n-terminal-prob-type-natriuretic-peptide-in-patients-with-acute-respiratory-distress-syndrome
#9
Chih-Cheng Lai, Mei-I Sung, Chung-Han Ho, Hsiao-Hua Liu, Chin-Ming Chen, Shyh-Ren Chiang, Chien-Ming Chao, Wei-Lun Liu, Shu-Chen Hsing, Kuo-Chen Cheng
We investigated whether N-terminal proB-type natriuretic peptide (NT-proBNP) predicts the prognosis of patients with acute respiratory distress syndrome (ARDS). Between December 1, 2012, and May 31, 2015, this observational study recruited patients admitted to our tertiary medical center who met the Berlin criteria for ARDS and who had their NT-proBNP measured. The main outcome was 28-day mortality. We enrolled 61 patients who met the Berlin criteria for ARDS: 7 were classified as mild, 29 as moderate, and 25 as severe...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320561/the-effects-of-oral-rinse-with-0-2-and-2-chlorhexidine-on-oropharyngeal-colonization-and-ventilator-associated-pneumonia-in-adults-intensive-care-units
#10
Farid Zand, Leili Zahed, Parisa Mansouri, Freshte Dehghanrad, Maryam Bahrani, Mohammad Ghorbani
BACKGROUND: Ventilator Associated Pneumonia (VAP) is the most common nosocomial infection in Intensive Care Units (ICUs) which increases the length of ICU stay, duration of mechanical ventilation, and mortality. The present study used an oral care protocol and compared the effects of two different concentrations of chlorhexidine on reduction of oropharyngeal colonization and VAP. MATERIALS AND METHODS: This study was performed on 114 patients from trauma, surgery, neurosurgery, and general ICUs randomly allocated to two groups under oral care with 0...
March 1, 2017: Journal of Critical Care
https://www.readbyqxmd.com/read/28317049/programming-and-runtime-support-to-blaze-fpga-accelerator-deployment-at-datacenter-scale
#11
Muhuan Huang, Di Wu, Cody Hao Yu, Zhenman Fang, Matteo Interlandi, Tyson Condie, Jason Cong
With the end of CPU core scaling due to dark silicon limitations, customized accelerators on FPGAs have gained increased attention in modern datacenters due to their lower power, high performance and energy efficiency. Evidenced by Microsoft's FPGA deployment in its Bing search engine and Intel's 16.7 billion acquisition of Altera, integrating FPGAs into datacenters is considered one of the most promising approaches to sustain future datacenter growth. However, it is quite challenging for existing big data computing systems-like Apache Spark and Hadoop-to access the performance and energy benefits of FPGA accelerators...
October 2016: Proc ACM Symp Cloud Comput
https://www.readbyqxmd.com/read/28316653/large-scale-virtual-screening-on-public-cloud-resources-with-apache-spark
#12
Marco Capuccini, Laeeq Ahmed, Wesley Schaal, Erwin Laure, Ola Spjuth
BACKGROUND: Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure rate hardware and fast network connection. Google's MapReduce revolutionized large-scale analysis, enabling the processing of massive datasets on commodity hardware and cloud resources, providing transparent scalability and fault tolerance at the software level...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28297816/-population-pharmacokinetics-of-vancomycin-from-severe-in-patients-with-lower-respiratory-tract-infection
#13
W Yang, B He, C H Deng
Objective: To develop a population pharmacokinetic (PPK) model of vancomycin in Chinese inpatients with severe lower respiratory tract infection. Methods: We gathered serum concentrations of vancomycin from inpatients who received vancomycin during Nov 2011 to Nov 2012.Vancomycin serum concentrations was measured by high performance liquid chromatography. Vancomycin PPK analysis was performed using nonlinear mixed effects model (NONMEM) program. Results: We gathered the data of 70 inpatients with lower respiratory tract infection at respiratory ward or respiratory intensive care unit(RICU) between Nov 2011 to Nov 2012 [58 males, 12 females; 78(23-91) years old; the mean of APACHⅡ score was 16...
March 12, 2017: Chinese Journal of Tuberculosis and Respiratory Diseases
https://www.readbyqxmd.com/read/28296656/severity-and-outcome-of-acute-on-chronic-liver-failure-is-dependent-on-the-etiology-of-acute-hepatic-insults-analysis-of-368-patients
#14
Shalimar, Saurabh Kedia, Soumya J Mahapatra, Baibaswata Nayak, Deepak Gunjan, Bhaskar Thakur, Subrat K Acharya
BACKGROUND: Acute-on-chronic liver failure (ACLF) may be precipitated by various hepatic insults. The present study evaluated the outcomes of ACLF with different acute insults. PATIENTS AND METHODS: A total of 368 ACLF patients were included. Data collected included etiologies of acute hepatic insult and underlying chronic liver disease, and organ failure. Model for end-stage liver disease (MELD), chronic liver failure consortium (CLIF)-C ACLF, and acute physiology and chronic health evaluation (APACHE) II scores were calculated...
March 14, 2017: Journal of Clinical Gastroenterology
https://www.readbyqxmd.com/read/28293298/rapid-development-of-entity-based-data-models-for-bioinformatics-with-persistence-object-oriented-design-and-structured-interfaces
#15
Elishai Ezra Tsur
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed...
2017: BioData Mining
https://www.readbyqxmd.com/read/28293095/different-phenotypes-of-monocytes-in-patients-with-new-onset-mild-acute-pancreatitis
#16
Man-Li Zhang, Yan-Fang Jiang, Xin-Rui Wang, Li-Li Ding, Hong-Juan Wang, Qing-Qing Meng, Pu-Jun Gao
AIM: To evaluate the numbers of different subsets of monocytes and their associations with the values of clinical measures in mild acute pancreatitis (MAP) patients. METHODS: The study included one group of 13 healthy controls and another group of 24 patients with new-onset MAP. The numbers of different subsets of monocytes were examined in these two groups of subjects by flow cytometry. The concentrations of plasma interleukin (IL)-10 and IL-12 were determined by cytometric bead array...
February 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28292533/assessment-of-hydration-status-using-bioelectrical-impedance-vector-analysis-in-critical-patients-with-acute-kidney-injury
#17
Ana Cláudia da Rosa Hise, Maria Cristina Gonzalez
BACKGROUND & AIMS: The state of hyperhydration in critically ill patients with acute kidney injury (AKI) is associated with increased mortality. Bioelectrical impedance vector analysis (BIVA) appears to be a viable method to access the fluid status of critical patients but has never been evaluated in critical patients with AKI. The objective of this study is to evaluate the hydration status measured using BIVA in critical patients under intensive care at the time of AKI diagnosis and to correlate this measurement with mortality...
February 21, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/28292397/mortality-prediction-in-patients-admitted-in-surgical-intensive-care-unit-by-using-apache-iv
#18
Hassan Shoukat, Yar Muhammad, Khalid Masood Gondal, Imran Aslam
OBJECTIVE: To predict the mortality by the mean Acute Physiology and Chronic Health Evaluation (APACHE) IV score of all the patients admitted in a Surgical Intensive Care Unit (ICU) and comparing the score of the survivors and non-survivors. STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Surgical Intensive Care Unit, Mayo Hospital, Lahore, from June 2013 to November 2014. METHODOLOGY: All adult patients admitted in the Surgical ICU were included in this study...
November 2016: Journal of the College of Physicians and Surgeons—Pakistan: JCPSP
https://www.readbyqxmd.com/read/28291480/human-contrast-acuity-variability
#19
Morris R Lattimore
BACKGROUND: Army vision standards have varied little from Aviation's nominal birth. On the basis of classic Snellen acuity, we simply cannot predict threshold skill levels of any one individual(s). A growing number of Army Flight Surgeons, clinicians, and vision scientists have argued for the inclusion of contrast acuity metrics within flight physical standards. METHODS: Previous monitoring of operational contact lens utility in 223 Apache pilots, visual acuity data were gathered under two conditions: high illuminance; low illuminance combined with low contrast...
March 2017: Military Medicine
https://www.readbyqxmd.com/read/28286820/deep-vein-thrombosis-among-intensive-care-unit-patients-an-epidemiologic-study
#20
MirMohammad Miri, Reza Goharani, Mohammad Sistanizad
INTRODUCTION: Deep vein thrombosis (DVT) is a major cause of morbidity and mortality in intensive care unit (ICU) patients despite use of prophylactic anticoagulant therapy. The aim of the present study was to determine the incidence of DVT among medical and surgical ICU patients. METHODS: In this cross sectional study, patients older than 18 years who were hospitalized in the ICU of Imam Hossein educational Hospital, Tehran, Iran, for ≥ 2 days, during August 2008 to July 2011 were evaluated regarding DVT incidence...
2017: Emergency (Tehran, Iran)
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