Use of grid tools to support CMS distributed analysis

In order to prepare the Physics Technical Design Report, due by end of 2005, the CMS experiment needs to simulate, reconstruct and analyse about 100 million events, corresponding to more than 200 TB of data. The data will be distributed to several Computing Centres. In order to provide access to the whole data sample to all the world-wide dispersed physicists, CMS is developing a layer of software that uses the Grid tools provided by the LCG project to gain access to data and resources and that aims to provide a user friendly interface to the physicists submitting the analysis jobs. To achieve these aims CMS will use Grid tools from both the LCG-2 release and those being developed in the framework of the ARDA project. This work describes the current status and the future developments of the CMS analysis system

Attenuation-Corrected vs. Nonattenuation-Corrected 2-Deoxy-2-[F-18]fluoro-d-glucose-Positron Emission Tomography in Oncology, A Systematic Review

Purpose: To perform a systematic review and meta-analysis to determine the diagnostic accuracy of attenuation-corrected (AC) vs. nonattenuation-corrected (NAC) 2-deoxy-2-[F-18] fluoro-D-glucose-positron emission tomography (FDG-PET) in oncological patients. Procedures: Following a comprehensive search of the literature, two reviewers independently assessed the methodological quality of eligible studies. The diagnostic value of AC was studied through its sensitivity/specificity compared to histology, and by comparing the relative lesion detection rate reported with NAC-PET vs. AC, for full-ring and dual-head coincidence PET (FRand DH-PET, respectively). Results: Twelve studies were included. For FR-PET, the pooled sensitivity/specificity on a patient basis was 64/97 % for AC and 62/99 % for NAC, respectively. Pooled lesion detection with NAC vs. AC was 98 % [95 % confidence interval (95 % CI): 96Y99%, n=1,012 lesions] for FR-PET, and 88 % (95 % CI:81Y94%, n=288 lesions) for DH-PET. Conclusions: Findings suggest similar sensitivity/specificity and lesion detection for NAC vs. AC FR-PET and significantly higher lesion detection for NAC vs. AC DH-PET

Perioperative PET/CT lymphoscintigraphy and fluorescent real-time imaging for sentinel lymph node mapping in early staged colon cancer

Contains fulltext : 207332.pdf (publisher's version ) (Open Access

Feasibility and reliability of PRISMA-Medical for specialty-based incident analysis

Aims and objectives: In this study, the feasibility and reliability of the Prevention Recovery Information System for Monitoring and Analysis (PRISMA)-Medical method for systematic, specialty-based analysis and classification of incidents in the neonatal intensive care unit (NICU) were determined. Methods: After the introduction of a Neonatology System for Analysis and Feedback on Medical Events (NEOSAFE) in eight tertiary care NICUs and one paediatric surgical ICU, PRISMA-Medical was started to be used to identify root causes of voluntary reported incidents by multidisciplinary unit patient safety committees. Committee members were PRISMA-trained and familiar with the department and its processes. In this study, the results of PRISMA-analysis of incidents reported during the first year are described. At t¿=¿3 months and t¿=¿12 months after introduction, test cases were performed to measure agreement at three levels of root cause classification using PRISMA-Medical. Inter-rater reliability was determined by calculating generalised ¿ values for each level of classification. Results: During the study period, 981 out of 1786 eligible incidents (55%) were analysed for underlying root causes. In total, 2313 root causes were identified and classified, giving an average of 2.4 root causes for every incident. Although substantial agreement (¿ 0.70–0.81) was reached at the main level of root cause classification of the test cases (discrimination between technical, organisational and human failure) and agreement among the committees at the second level (discrimination between skill-based, rule-based and knowledge-based errors) was acceptable (¿ 0.53–0.59), discrimination between rule-based errors (the third level of classification) was more difficult to assess (¿ 0.40–0.47). Conclusion: With some restraints, PRISMA-Medical proves to be both feasible and acceptably reliable to identify and classify multiple causes of medical events in the NICU

Distributed Computing Grid Experiences in CMS

The CMS experiment is currently developing a computing system capable of serving, processing and archiving the large number of events that will be generated when the CMS detector starts taking data. During 2004 CMS undertook a large scale data challenge to demonstrate the ability of the CMS computing system to cope with a sustained data-taking rate equivalent to 25% of startup rate. Its goals were: to run CMS event reconstruction at CERN for a sustained period at 25 Hz input rate; to distribute the data to several regional centers; and enable data access at those centers for analysis. Grid middleware was utilized to help complete all aspects of the challenge. To continue to provide scalable access from anywhere in the world to the data, CMS is developing a layer of software that uses Grid tools to gain access to data and resources, and that aims to provide physicists with a user friendly interface for submitting their analysis jobs. This paper describes the data challenge experience with Grid infrastructure and the current development of the CMS analysis system

Risk Factors for Necrotizing Enterocolitis:A Prospective Multicenter Case-Control Study

BACKGROUND: The identification of independent clinical risk factors for necrotizing enterocolitis (NEC) may contribute to early selection of infants at risk, allowing for the development of targeted strategies aimed at the prevention of NEC. OBJECTIVE: The objective of this study was to identify independent risk factors contributing to the development of NEC in a large multicenter cohort. METHODS: This prospective cohort study was performed in 9 neonatal intensive care units. Infants born at a gestational age </=30 weeks were included. Demographic and clinical data were collected daily until day 28 postnatally. Factors predictive of the development of NEC were identified using univariate and multivariable analyses in a 1: 5 matched case-control cohort. RESULTS: In total, 843 infants (56 NEC cases) were included in this study. In the case-control cohort, univariate analysis identified sepsis prior to the onset of NEC and formula feeding to be associated with an increased risk of developing NEC, whereas the administration of antibiotics directly postpartum was inversely associated with NEC. In a multivariable logistic regression model, enteral feeding type and the number of days parenterally fed remained statistically significantly associated with NEC, whereas the administration of antibiotics directly after birth was associated with a lower risk of developing NEC. CONCLUSIONS: Formula feeding and prolonged (duration of) parenteral feeding were associated with an increased risk of NEC. Contrary to expectations, the initiation of treatment with antibiotics within 24 h after birth was inversely associated with NEC

Profound Pathogen-Specific Alterations in Intestinal Microbiota Composition Precede Late-Onset Sepsis in Preterm Infants:A Longitudinal, Multicenter, Case-Control Study

BACKGROUND: The role of intestinal microbiota in the pathogenesis of late-onset sepsis (LOS) in preterm infants is largely unexplored but could provide opportunities for microbiota-targeted preventive and therapeutic strategies. We hypothesized that microbiota composition changes before the onset of sepsis, with causative bacteria that are isolated later in blood culture. METHODS: This multicenter case-control study included preterm infants born under 30 weeks of gestation. Fecal samples collected from the 5 days preceding LOS diagnosis were analyzed using a molecular microbiota detection technique. LOS cases were subdivided into 3 groups: gram-negative, gram-positive, and coagulase-negative Staphylococci (CoNS). RESULTS: Forty LOS cases and 40 matched controls were included. In gram-negative LOS, the causative pathogen could be identified in at least 1 of the fecal samples collected 3 days prior to LOS onset in all cases, whereas in all matched controls, this pathogen was absent (P = .015). The abundance of these pathogens increased from 3 days before clinical onset. In gram-negative and gram-positive LOS (except CoNS) combined, the causative pathogen could be identified in at least 1 fecal sample collected 3 days prior to LOS onset in 92% of the fecal samples, whereas these pathogens were present in 33% of the control samples (P = .004). Overall, LOS (expect CoNS) could be predicted 1 day prior to clinical onset with an area under the curve of 0.78. CONCLUSIONS: Profound preclinical microbial alterations underline that gut microbiota is involved in the pathogenesis of LOS and has the potential as an early noninvasive biomarker

Specialty-based, voluntary incident reporting in neonatal intensive care: description of 4846 incident reports

OBJECTIVES: To examine the characteristics of incidents reported after introduction of a voluntary, non-punitive incident reporting system for neonatal intensive care units (NICUs) in the Netherlands; and to investigate which types of reported incident pose the highest risk to patients in the NICU. DESIGN: Prospective multicentre survey. METHODS: Voluntary, non-punitive incident reporting was introduced in eight level III NICUs and one paediatric surgical ICU. An incident was defined as any unintended event which (could have) reduced the safety margin for the patient. Multidisciplinary, unit-based patient safety committees systematically collected and analysed incident reports, and assigned risk scores to each reported incident. Data were centrally collected for specialty-based analysis. This paper describes the characteristics of incidents reported during the first year. Bivariate logistic regression analysis was conducted to identify high-risk incident categories. RESULTS: There were 5225 incident reports on 3859 admissions, of which 4846 were eligible for analysis. Incidents with medication were most frequently reported (27%), followed by laboratory (10%) and enteral nutrition (8%). Severe harm was described in seven incident reports, and moderate harm in 63 incident reports. Incidents involving mechanical ventilation and blood products were most likely to be assigned high-risk scores, followed by those involving parenteral nutrition, intravascular lines and medication dosing errors. CONCLUSIONS: Incidents occur much more frequently in Dutch NICUs than has been previously observed, and their impact on patient morbidity is considerable. Reported incidents concerning mechanical ventilation, blood products, intravascular lines, parenteral nutrition and medication dosing errors pose the highest risk to patients in the NIC

Revisiting diagenesis on the Ontong Java Plateau: Evidence for authigenic crust precipitation in Globorotalia tumida

The calcite tests of foraminifera lie in marine sediments for thousands to millions of years, before being analysed to generate trace element and isotope palaeoproxy records. These sediments constitute a distinct physio-chemical environment from the conditions in which the tests formed. Storage in sediments can modify the trace element and isotopic content of foraminiferal calcite through diagenetic alteration, which has the potential to confound their palaeoceanographic interpretation. A previous study of G. tumida from the Ontong Java Plateau, western equatorial Pacific, found that preferential dissolution of higher-Mg chamber calcite, and the preservation of a low-Mg crust on the tests significantly reduced whole-test Mg/Ca and Sr/Ca [Brown and Elderfield, 1996]. Here, we revisit these specimens with a combination of synchrotron X-ray computed tomography (sXCT) and electron probe micro-analyses (EPMA) to re-evaluate the nature of their diagenetic alteration. The dissolution of higher-Mg calcite with depth was directly observed in the sXCT data, confirming the inference of the previous study. The sXCT data further reveal a thickening of the chemically and structurally distinct calcite crust with depth. We propose that these crusts have a diagenetic origin, driven by the simultaneous dissolution of high-Mg chamber calcite and precipitation of low-Mg crust from the resulting modified pore-water solution. While the breadth of the study is limited by the nature of the techniques, the observation of both dissolution and re-precipitation of foraminiferal calcite serves to demonstrate the action of two simultaneous diagenetic alteration processes, with significant impacts on the resulting palaeoproxy signals.The authors would like to acknowledge Aleksey Sadekov, Gerald Langer, India Weidle, Alberto de Fanis, Andrew Bodey, Joan Vila-Comamala and Ulrich Wagner for their help with the project. The work was funded by the Diamond Light Source and by the ERC (2010-NEWLOG ADG-267931 grant to HE).This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/2014PA00275

Short- and long-term follow-up after fecal microbiota transplantation as treatment for recurrent Clostridioides difficile infection in patients with inflammatory bowel disease

Background: Patients with inflammatory bowel disease (IBD) are at an increased risk of developing Clostridioides difficile infection (CDI). Treatment of CDI in patients with IBD is challenging due to higher failure rates and concomitant IBD activity. Objectives: We performed a multicentre cohort study in patients with IBD who received fecal microbiota transplantation (FMT) for recurrent CDI (rCDI), to further investigate factors that influence the clinical outcome and course of both rCDI and IBD. Design: This is a multicentre cohort study conducted in five European FMT centres. Methods: Adult IBD patients treated with FMT for rCDI were studied. Cure was defined as clinical resolution of diarrhoea or diarrhoea with a negative C. difficile test. The definition of an IBD flare was record based. Long-term follow-up data were collected including new episodes of CDI, IBD flares, infections, hospital admissions, and death. Results  In total, 113 IBD patients underwent FMT because of rCDI. Mean age of the patients was 48 years; 64% had ulcerative colitis. Concomitant rCDI was associated with an IBD flare in 54%, of whom 63% had received IBD remission-induction therapy prior to FMT. All FMT procedures were preceded by vancomycin treatment, 40% of patients received FMT via colonoscopy. CDI cure rate was 71%. Long-term follow-up data were available in 90 patients with a median follow-up of 784 days (402-1251). IBD activity decreased in 39% of patients who had active IBD at baseline, whereas an IBD flare occurred in only 5%. During follow-up of up to 2 years, 27% of the patients had infections, 39% were hospitalized, 5% underwent colectomy, and 10% died (median age of these latter patients: 72 years). Conclusion: FMT for rCDI in IBD patients is safe and effective, and IBD exacerbation after FMT is infrequent. Further studies should investigate the effects on IBD course following FMT.Cellular mechanisms in basic and clinical gastroenterology and hepatolog