Measuring pathway database coverage of the phosphoproteome.
Ontology highlight
ABSTRACT:
SUBMITTER: Huckstep H
PROVIDER: S-EPMC8162239 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In low-income settings, vaccination campaigns supplement routine immunization but often fail to achieve coverage goals due to uncertainty about target population size and distribution. Accurate, updated estimates of target populations are rare but critical; short-term fluctuations can greatly impact population size and susceptibility. We use satellite imagery to quantify population fluctuations and the coverage achieved by a measles outbreak response vaccination campaign in urban Niger and compare campaign estimates to measurements from a post-campaign survey. Vaccine coverage was overestimated because the campaign underestimated resident numbers and seasonal migration further increased the target population. We combine satellite-derived measurements of fluctuations in population distribution with high-resolution measles case reports to develop a dynamic model that illustrates the potential improvement in vaccination campaign coverage if planners account for predictable population fluctuations. Satellite imagery can improve retrospective estimates of vaccination campaign impact and future campaign planning by synchronizing interventions with predictable population fluxes.
| S-EPMC5050518 | biostudies-literature
Project description:Human Protein Reference Database (HPRD) is a rich resource of experimentally proven features of human proteins. Protein information in HPRD includes protein-protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein-protein interaction data from HPRD has been widely used by the scientific community, its phosphoproteome data has not been exploited to its full potential. HPRD is one of the largest documentations of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95,016 phosphosites mapped on to 13,041 proteins. Additionally, enzyme-substrate reactions responsible for 5930 phosphorylation events were also documented. Significant improvements in technologies and high-throughput platforms in biomedical investigations led to an exponential increase of biological data and phosphoproteomic data in recent years. Human Proteinpedia, a community annotation portal developed by us, has also contributed to the significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia.
| S-EPMC3804167 | biostudies-other
Project description:Ongoing optimization of proteomic methodologies seeks to improve both the coverage and confidence of protein identifications. The optimization of sample preparation, inclusion of technical replicates (repeated instrumental analysis of the same sample), and biological replicates (multiple individual samples) are crucial in proteomic studies to avoid the pitfalls associated with single point analysis and under-sampling. Phosphopeptides were isolated from HeLa cells and analyzed by nano-reversed phase liquid chromatography electrospray ionization tandem mass spectrometry (nano-RP-LC-MS/MS). We observed that a detergent-based protein extraction approach, followed with additional steps for nucleic acid removal, provided a simple alternative to the broadly used Trizol extraction. The evaluation of four technical replicates demonstrated measurement reproducibility with low percent variance in peptide responses at approximately 3%, where additional peptide identifications were made with each added technical replicate. The inclusion of six technical replicates for moderately complex protein extracts (approximately 4000 uniquely identified peptides per data set) affords the optimal collection of peptide information.
| S-EPMC2517255 | biostudies-literature
Project description:Global monitoring of intervention coverage is a cornerstone of international efforts to improve reproductive, maternal, newborn, and child health. In this review, we examine the process and implications of selecting a core set of coverage indicators for global monitoring, using as examples the processes used by the Countdown to 2015 for Maternal, Newborn and Child Survival and the Commission on Accountability for Women's and Children's Health. We describe how the generation of data for global monitoring involves five iterative steps: development of standard indicator definitions and measurement approaches to ensure comparability across countries; collection of high-quality data at the country level; compilation of country data at the global level; organization of global databases; and rounds of data quality checking. Regular and rigorous technical review processes that involve high-level decision makers and experts familiar with indicator measurement are needed to maximize uptake and to ensure that indicators used for global monitoring are selected on the basis of available evidence of intervention effectiveness, feasibility of measurement, and data availability as well as programmatic relevance. Experience from recent initiatives illustrates the challenges of striking this balance as well as strategies for reducing the tensions inherent in the indicator selection process. We conclude that more attention and continued investment need to be directed to global monitoring, to support both the process of global database development and the selection of sets of coverage indicators to promote accountability. The stakes are high, because these indicators can drive policy and program development at the country and global level, and ultimately impact the health of women and children and the communities where they live.
| S-EPMC3646210 | biostudies-literature
Project description:BackgroundThis paper aims to develop a Chinese version of Universal Health Coverage (UHC) indices and to measure China's progress towards UHC.MethodsNineteen indicators were selected based on expert consultations to construct indices of accessibility and affordability to measure UHC. Data were drawn from health statistics yearbooks, nationally representative surveys, and health system reform surveillance. The index of accessibility includes absolute accessibility (to essential health services), relative accessibility (to hospital care) and people's subjective perceptions. The index of affordability includes absolute affordability (the incidence of catastrophic health expenditure, CHE), relative affordability (the composition of health expenditure), and people's subjective perceptions.ResultsThe indices of accessibility and affordability both showed steady increases over the 17 years considered. Absolute accessibility had the most significant improvement (from 23.6 in 2002 to 73.8 in 2018), while the index of relative accessibility decreased from 81.4 in 2002 to 67.3 in 2018. The index of absolute affordability decreased significantly from 46.6 in 2002 to 30.5 in 2010 and then exhibited an increasing trend afterwards, reaching 52.1 in 2018. The index of relative affordability continuously increased during the observation period, from 35.3 to 75.4.ConclusionsChina has made great progress in increasing the accessibility and affordability of health services since the health system reforms in 2009. However, integrating primary health care and hospital care and containing escalating medical expenditure to further reduce patients' financial burdens are key challenges for strengthening the Chinese health system.
| S-EPMC8088770 | biostudies-literature
Project description:This article describes the first release version of a new lexicostatistical database of Northern Eurasia, which includes Europe as the most well-researched linguistic area. Unlike in other areas of the world, where databases are restricted to covering a small number of concepts as far as possible based on often sparse documentation, good lexical resources providing wide coverage of the lexicon are available even for many smaller languages in our target area. This makes it possible to attain near-completeness for a substantial number of concepts. The resulting database provides a basis for rich benchmarks that can be used to test automated methods which aim to derive new knowledge about language history in underresearched areas.
| S-EPMC7067722 | biostudies-literature
Project description:Protein phosphorylation is critically important for many cellular processes, including progression through the cell cycle, cellular metabolism, and differentiation. Isobaric labeling, for example, tandem mass tags (TMT), in phosphoproteomics workflows enables both relative and absolute quantitation of these phosphorylation events. Traditional TMT workflows identify peptides using fragment ions at the MS2 level and quantify reporter ions at the MS3 level. However, in addition to the TMT reporter ions, MS3 spectra also include fragment ions that can be used to identify peptides. Here we describe using MS3 spectra for both phosphopeptide identification and quantification, a process that we term MS3-IDQ. To maximize quantified phosphopeptides, we optimize several instrument parameters, including the modality of mass analyzer (i.e., ion trap or Orbitrap), MS2 automatic gain control (AGC), and MS3 normalized collision energy (NCE), to achieve the best balance of identified and quantified peptides. Our optimized MS3-IDQ method included the following parameters for the MS3 scan: NCE = 37.5 and AGC target = 1.5 × 105, and scan range = 100-2000. Data from the MS3 scan were complementary to those of the MS2 scan, and the combination of these scans can increase phosphoproteome coverage by >50%, thereby yielding a greater number of quantified and accurately localized phosphopeptides.
| S-EPMC5984591 | biostudies-literature
Project description:PURPOSE:To evaluate the coverage and accuracy of whole-exome sequencing (WES) across vendors. METHODS:Blood samples from three trios underwent WES at three vendors. Relative performance of the three WES services was measured for breadth and depth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern within each trio. RESULTS:Mean depth of coverage for all genes was 189.0, 124.9, and 38.3 for the three vendor services. Fifty-five of the American College of Medical Genetics and Genomics 56 genes, but only 56 of 63 pharmacogenes, were 100% covered at 10 × in at least one of the nine individuals for all vendors; however, there was substantial interindividual variability. For the two vendors with mean depth of coverage >120 ×, analytic positive predictive values (aPPVs) exceeded 99.1% for single-nucleotide variants and homozygous indels, and sensitivities were 98.9-99.9%; however, heterozygous indels showed lower accuracy and sensitivity. Among the trios, FNRs in the offspring were 0.07-0.62% at well-covered variants concordantly called in both parents. CONCLUSION:The current standard of 120 × coverage for clinical WES may be insufficient for consistent breadth of coverage across the exome. Ordering clinicians and researchers would benefit from vendors' reports that estimate sensitivity and aPPV, including depth of coverage across the exome.
| S-EPMC6185824 | biostudies-literature
Project description:Aside from breastfeeding, there are little data on use of essential newborn care practices, such as thermal protection and hygienic cord care, in high mortality countries. These practices have not typically been measured in national household surveys, often the main source for coverage data in these settings. The Every Newborn Action Plan proposed early breastfeeding as a tracer for essential newborn care due to data availability and evidence for the benefits of breastfeeding. In the past decade, a few national surveys have added questions on other practices, presenting an opportunity to assess the performance of early breastfeeding initiation as a tracer indicator.We identified twelve national surveys between 2005-2014 that included at least one indicator for immediate newborn care in addition to breastfeeding. Because question wording and reference populations varied, we standardized data to the extent possible to estimate coverage of newborn care practices, accounting for strata and multistage survey design. We assessed early breastfeeding as a tracer by: 1) examining associations with other indicators using Pearson correlations; and 2) stratifying by early breastfeeding to determine differences in coverage of other practices for initiators vs non-initiators in each survey, then pooling across surveys for a meta-analysis, using the inverse standard error as the weight for each observation.Associations between pairs of coverage indicators are generally weak, including those with breastfeeding. The exception is drying and wrapping, which have the strongest association of any two interventions in all five surveys where measured; estimated correlations for this range from 0.47 in Bangladesh's 2007 DHS to 0.83 in Nepal's 2006 DHS. The contrast in coverage for other practices by early breastfeeding is generally small; the greatest absolute difference was 6.7%, between coverage of immediate drying for newborns breastfed early compared to those who were not.Early initiation of breastfeeding is not a high performing tracer indicator for essential newborn care practices measured in previous national surveys. To have informative data on whether newborns are getting life-saving services, standardized questions about specific practices, in addition to breastfeeding initiation, need to be added to surveys.
| S-EPMC5804503 | biostudies-literature
Project description:BACKGROUND: To assess progress in the scale-up of rapid diagnostic tests and artemisinin-based combination therapies (ACTs) across Africa, malaria control programs have increasingly relied on standardized national household surveys to determine the proportion of children with a fever in the past 2 wk who received an effective antimalarial within 1-2 d of the onset of fever. Here, the validity of caregiver recall for measuring the primary coverage indicators for malaria diagnosis and treatment of children <5 y old is assessed. METHODS AND FINDINGS: A cross-sectional study was conducted in five public clinics in Kaoma District, Western Provence, Zambia, to estimate the sensitivity, specificity, and accuracy of caregivers' recall of malaria testing, diagnosis, and treatment, compared to a gold standard of direct observation at the health clinics. Compared to the gold standard of clinic observation, for recall for children with fever in the past 2 wk, the sensitivity for recalling that a finger/heel stick was done was 61.9%, with a specificity of 90.0%. The sensitivity and specificity of caregivers' recalling a positive malaria test result were 62.4% and 90.7%, respectively. The sensitivity and specificity of recalling that the child was given a malaria diagnosis, irrespective of whether a laboratory test was actually done, were 76.8% and 75.9%, respectively. The sensitivity and specificity for recalling that an ACT was given were 81.0% and 91.5%, respectively. CONCLUSIONS: Based on these findings, results from household surveys should continue to be used for ascertaining the coverage of children with a fever in the past 2 wk that received an ACT. However, as recall of a malaria diagnosis remains suboptimal, its use in defining malaria treatment coverage is not recommended.
| S-EPMC3646207 | biostudies-other