A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum

Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large‐scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta‐analysis. We identified a total of 201 996 and 39 953 peptide‐spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein‐level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA‐Seq‐derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA‐Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes

Capturing diagnosis-timing in ICD-coded hospital data: recommendations from the WHO ICD-11 topic advisory group on quality and safety

Purpose To develop a consensus opinion regarding capturing diagnosis-timing in coded hospital data. Methods As part of the World Health Organization International Classification of Diseases-11th Revision initiative, the Quality and Safety Topic Advisory Group is charged with enhancing the capture of quality and patient safety information in morbidity data sets. One such feature is a diagnosis-timing flag. The Group has undertaken a narrative literature review, scanned national experiences focusing on countries currently using timing flags, and held a series of meetings to derive formal recommendations regarding diagnosis-timing reporting. Results The completeness of diagnosis-timing reporting continues to improve with experience and use; studies indicate that it enhances risk-adjustment and may have a substantial impact on hospital performance estimates, especially for conditions/procedures that involve acutely ill patients. However, studies suggest that its reliability varies, is better for surgical than medical patients (kappa in hip fracture patients of 0.7-1.0 versus kappa in pneumonia of 0.2-0.6) and is dependent on coder training and setting. It may allow simpler and more precise specification of quality indicators. Conclusions As the evidence indicates that a diagnosis-timing flag improves the ability of routinely collected, coded hospital data to support outcomes research and the development of quality and safety indicators, the Group recommends that a classification of ‘arising after admission' (yes/no), with permitted designations of ‘unknown or clinically undetermined', will facilitate coding while providing flexibility when there is uncertainty. Clear coding standards and guidelines with ongoing coder education will be necessary to ensure reliability of the diagnosis-timing fla

How many diagnosis fields are needed to capture safety events in administrative data? Findings and recommendations from the WHO ICD-11 Topic Advisory Group on Quality and Safety

Objective As part of the WHO ICD-11 development initiative, the Topic Advisory Group on Quality and Safety explores meta-features of morbidity data sets, such as the optimal number of secondary diagnosis fields. Design The Health Care Quality Indicators Project of the Organization for Economic Co-Operation and Development collected Patient Safety Indicator (PSI) information from administrative hospital data of 19-20 countries in 2009 and 2011. We investigated whether three countries that expanded their data systems to include more secondary diagnosis fields showed increased PSI rates compared with six countries that did not. Furthermore, administrative hospital data from six of these countries and two American states, California (2011) and Florida (2010), were analysed for distributions of coded patient safety events across diagnosis fields. Results Among the participating countries, increasing the number of diagnosis fields was not associated with any overall increase in PSI rates. However, high proportions of PSI-related diagnoses appeared beyond the sixth secondary diagnosis field. The distribution of three PSI-related ICD codes was similar in California and Florida: 89-90% of central venous catheter infections and 97-99% of retained foreign bodies and accidental punctures or lacerations were captured within 15 secondary diagnosis fields. Conclusions Six to nine secondary diagnosis fields are inadequate for comparing complication rates using hospital administrative data; at least 15 (and perhaps more with ICD-11) are recommended to fully characterize clinical outcomes. Increasing the number of fields should improve the international and intra-national comparability of data for epidemiologic and health services research, utilization analyses and quality of care assessmen

Diagenetic Evolution and Porosity Destruction of Turbiditic Hybrid Arenites and Siliciclastic Sandstones of Foreland Basins: Evidence from the Eocene Hecho Group, Pyrenees, Spain

International audienceThis study aims to unravel the impact of diagenetic alterations on porosity loss of foreland-basin turbiditic hybrid arenites and associated siliciclastic sandstones of the Eocene Hecho Group (south-central Pyrenees, Spain). In this succession, hybrid arenites and calclithites are extensively cemented by mesogenetic calcite cement (delta18O VPDB = –10.0 per thousand to –5.8per thousand ; Th, mode = 80° C; salinity mode = 18.8 wt% eq. NaCl), Fe-dolomite (delta18O VPDB = –8.5 per thousand to –6.3 per thousand ) and trace amounts of siderite. The extent of carbonate cementation is interpreted to be related to the amounts of extrabasinal and intrabasinal carbonate grains, which provided nuclei and sources for the precipitation and growth of carbonate cements. Other diagenetic alterations, such as pyrite and albitization, had no impact on reservoir quality. Scarce early diagenetic cements, coupled with abundant ductile carbonate and siliciclastic framework grains, have led to rapid porosity loss owing to compaction. Conversely, abundant quartz in the sandstones prevented rapid loss of porosity by mechanical compaction. Reservoir quality was affected by mesogenetic cementation by quartz overgrowths, calcite and dolomite intergranular pressure dissolution of quartz grains, and formation of fracture-filling calcite cement (delta 18O V-PDB values from –10.4 per thousand to –7.8 per thousand ; Th temperatures of circa 150° C), which are attributed to deep circulation of hot meteoric waters during extensional stages of tectonism. The results of this study illustrate that diagenetic evolution pathways of the arenites and sandstones are closely linked to the variation in detrital composition, particularly the proportion and types of extrabasinal noncarbonates, extrabasinal carbonates, and intrabasinal carbonate grains. These insights suggest that marine turbiditic hybrid arenites and calclithites of foreland basins are subjected to more rapid and extensive porosity loss owing to compaction and cementation than associated siliciclastic sandstones. Degradation of reservoir quality makes these hybrid arenites, calclithites, and sandstones suitable as tight gas reservoirs, but only if fracture porosity and permeability develop during tectonic deformation

Process evaluation for complex interventions in primary care: understanding trials using the normalization process model

Background: the Normalization Process Model is a conceptual tool intended to assist in understanding the factors that affect implementation processes in clinical trials and other evaluations of complex interventions. It focuses on the ways that the implementation of complex interventions is shaped by problems of workability and integration.Method: in this paper the model is applied to two different complex trials: (i) the delivery of problem solving therapies for psychosocial distress, and (ii) the delivery of nurse-led clinics for heart failure treatment in primary care.Results: application of the model shows how process evaluations need to focus on more than the immediate contexts in which trial outcomes are generated. Problems relating to intervention workability and integration also need to be understood. The model may be used effectively to explain the implementation process in trials of complex interventions.Conclusion: the model invites evaluators to attend equally to considering how a complex intervention interacts with existing patterns of service organization, professional practice, and professional-patient interaction. The justification for this may be found in the abundance of reports of clinical effectiveness for interventions that have little hope of being implemented in real healthcare setting

International variation in the definition of ‘main condition' in ICD-coded health data

Hospital-based medical records are abstracted to create International Classification of Disease (ICD) coded discharge health data in many countries. The ‘main condition' is not defined in a consistent manner internationally. Some countries employ a ‘reason for admission' rule as the basis for the main condition, while other countries employ a ‘resource use' rule. A few countries have recently transitioned from one of these approaches to the other. The definition of ‘main condition' in such ICD data matters when it is used to define a disease cohort to assign diagnosis-related groups and to perform risk adjustment. We propose a method of harmonizing the international definition to enable researchers and international organizations using ICD-coded health data to aggregate or compare hospital care and outcomes across countries in a consistent manner. Inter-observer reliability of alternative harmonization approaches should be evaluated before finalizing the definition and adopting it worldwid

Application of patient safety indicators internationally: a pilot study among seven countries

Objective To explore the potential for international comparison of patient safety as part of the Health Care Quality Indicators project of the Organization for Economic Co-operation and Development (OECD) by evaluating patient safety indicators originally published by the US Agency for Healthcare Research and Quality (AHRQ). Design A retrospective cross-sectional study. Setting Acute care hospitals in the USA, UK, Sweden, Spain, Germany, Canada and Australia in 2004 and 2005/2006. Data sources Routine hospitalization-related administrative data from seven countries were analyzed. Using algorithms adapted to the diagnosis and procedure coding systems in place in each country, authorities in each of the participating countries reported summaries of the distribution of hospital-level and overall (national) rates for each AHRQ Patient Safety Indicator to the OECD project secretariat. Results Each country's vector of national indicator rates and the vector of American patient safety indicators rates published by AHRQ (and re-estimated as part of this study) were highly correlated (0.821-0.966). However, there was substantial systematic variation in rates across countries. Conclusions This pilot study reveals that AHRQ Patient Safety Indicators can be applied to international hospital data. However, the analyses suggest that certain indicators (e.g. ‘birth trauma', ‘complications of anesthesia') may be too unreliable for international comparisons. Data quality varies across countries; undercoding may be a systematic problem in some countries. Efforts at international harmonization of hospital discharge data sets as well as improved accuracy of documentation should facilitate future comparative analyses of routine database

Experimental and Theoretical Analysis of the Fast Charging Polymer Lithium-Ion Battery Based on Cuckoo Optimization Algorithm (COA)

Fast charging of the electric-vehicles is one of the paramount challenges in solar smart cities. This paper investigates intelligent optimization methodology to improvise the existing approaches in order to speed up the charging process whilst reducing the energy consumption without degradation in the light of the outrageous demand for lithium-ion battery in the electric vehicles (EVs). Two fitness functions are combined as the targeted objective function: energy losses (EL) and charging interval time (CIT). An intelligent optimization methodology based on Cuckoo Optimization Algorithm (COA) is implemented to the objective function for improving the charging performance of the lithium-ion battery. COA is applied through two main techniques: The Hierarchical technique (HT) and the Conditional random technique (CRT). The experimental results show that the proposed techniques permit a full charging capacity of the polymer lithium-ion battery (0 to 100% SOC) within 91 mins. Compared with the constant current-constant voltage (CCCV) technique, an improvement in the efficiency of 8% and 14.1% was obtained by the Hierarchical technique (HT) and the Conditional random technique (CRT) respectively, in addition to a reduction in energy losses of 7.783% and 10.408% respectively and a reduction in charging interval time of 18.1% and 22.45% respectively. Experimental and theoretical analyses are performed and are in good agreement on the polymer lithium-ion battery fast charging method

Osteogenesis evaluation of duck’s feet derived collagen/hydroxyapatite sponges immersed in dexamethasone

Background: The aim of this study was to investigate the osteogenesis effects of DC and DC/HAp sponge immersed in without and with dexamethasone. Methods: The experimental groups in this study were DC and DC/HAp sponge immersed in without dexamethasone (Dex(â )DC and Dex(â )-DC/HAp group) and with dexamethasone (Dex(+)-DC and Dex(+)-DC/HAp group). We characterized DC and DC/HAp sponge using compressive strength, scanning electron microscopy (SEM). Also, osteogenic differentiation of BMSCs on sponge (Dex(â )DC, Dex(â )-DC/HAp, Dex(+)-DC and Dex(+)-DC/HAp group) was assessed by SEM, 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazoliumbromide (MTT) assay, alkaline phosphatase (ALP) activity assay and reverse transcription-PCR (RT-PCR). Results: In this study, we assessed osteogenic differentiation of BMSCs on Duckâ s feet-derived collagen (DC)/ HAp sponge immersed with dexamethasone Dex(+)-DC/HAp. These results showed that Dex(+)-DC/HAp group increased cell proliferation and osteogenic differentiation of BMSCs during 28 days. Conclusion: From these results, Dex(+)-DC/HAp can be envisioned as a potential biomaterial for bone regeneration applications.This work was supported by Technology Commercialization Support Program [grant number 814005-03-3-HD020], Ministry for Food, Agriculture, Forestry and Fisheries (MIFAFF).info:eu-repo/semantics/publishedVersio