How Well Do Automated Linking Methods Perform? Lessons from U.S. Historical Data.
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ABSTRACT:
SUBMITTER: Bailey M
PROVIDER: S-EPMC8294155 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:MotivationCross-linking mass spectrometry has made remarkable advancements in the high-throughput characterization of protein structures and interactions. The resulting pairs of cross-linked peptides typically require geometric assessment and validation, given the availability of their corresponding structures.ResultsCLAUDIO (Cross-linking Analysis Using Distances and Overlaps) is an open-source software tool designed for the automated analysis and validation of different varieties of large-scale cross-linking experiments. Many of the otherwise manual processes for structural validation (i.e. structure retrieval and mapping) are performed fully automatically to simplify and accelerate the data interpretation process. In addition, CLAUDIO has the ability to remap intra-protein links as inter-protein links and discover evidence for homo-multimers.Availability and implementationCLAUDIO is available as open-source software under the MIT license at https://github.com/KohlbacherLab/CLAUDIO.
| S-EPMC10994719 | biostudies-literature
Project description:BACKGROUND:The movement of animals is strongly influenced by external factors in their surrounding environment such as weather, habitat types, and human land use. With advances in positioning and sensor technologies, it is now possible to capture animal locations at high spatial and temporal granularities. Likewise, scientists have an increasing access to large volumes of environmental data. Environmental data are heterogeneous in source and format, and are usually obtained at different spatiotemporal scales than movement data. Indeed, there remain scientific and technical challenges in developing linkages between the growing collections of animal movement data and the large repositories of heterogeneous remote sensing observations, as well as in the developments of new statistical and computational methods for the analysis of movement in its environmental context. These challenges include retrieval, indexing, efficient storage, data integration, and analytical techniques. RESULTS:This paper contributes to movement ecology research by presenting a new publicly available system, Environmental-Data Automated Track Annotation (Env-DATA), that automates annotation of movement trajectories with ambient atmospheric observations and underlying landscape information. Env-DATA provides a free and easy-to-use platform that eliminates technical difficulties of the annotation processes and relieves end users of a ton of tedious and time-consuming tasks associated with annotation, including data acquisition, data transformation and integration, resampling, and interpolation. The system is illustrated with a case study of Galapagos Albatross (Phoebastria irrorata) tracks and their relationship to wind, ocean productivity and chlorophyll concentration. Our case study illustrates why adult albatrosses make long-range trips to preferred, productive areas and how wind assistance facilitates their return flights while their outbound flights are hampered by head winds. CONCLUSIONS:The new Env-DATA system enhances Movebank, an open portal of animal tracking data, by automating access to environmental variables from global remote sensing, weather, and ecosystem products from open web resources. The system provides several interpolation methods from the native grid resolution and structure to a global regular grid linked with the movement tracks in space and time. The aim is to facilitate new understanding and predictive capabilities of spatiotemporal patterns of animal movement in response to dynamic and changing environments from local to global scales.
| S-EPMC4337772 | biostudies-literature
Project description:In order to improve patient care in the United States there, the government made a mandate called HIE (Health Information Exchange). This order was created from the belief that sharing digital health information between, across, and within health communities will improve one's healthcare experience across their lifespan. Patient health information, i.e. the personal health record, should be shareable between healthcare providers; such as private practice physicians, home health agencies, hospitals and nursing care facilities. Most of the U.S. hospitals now have electronic health records, however, with a lack of standards for structuring health information and unified communication protocols to share health information across providers, only a small percentage of U.S. hospitals engage in computerized HIE. In order to understand barriers and facilitators in the U.S. of HIE adoption, we reviewed the published research literature between 2010 and 2015. Our search yielded 664 articles from Medline, PsychInfo, Global health, InSpec, Scopus and Business Source Complete databases. Thirty-nine articles met our inclusion criteria. This article presents the compiled organizational and end user barriers and facilitators along with suggested methods to achieve continuity of care through HIE.
| S-EPMC6626162 | biostudies-literature
Project description:An association between income and life satisfaction has been well documented, however, little is known of how income trajectories affect different facets of subjective well-being (SWB). The aim of this study was to examine how several aspects of income dynamics are related to life satisfaction and affect balance. Longitudinal information on income from administrative records covering 13 years (1999-2011) is linked to cross-sectional data on SWB collected in 2011/12 from the nationally representative Study on Mental Health at Work (S-MGA; n = 3364). Parameters from subject-specific regression analyses of income over time were used as indicators of income development in regressions over all participants, conducted separately for men and women. Associations between income and life satisfaction were stronger and more consistent than associations between income and affect balance. Major findings were that longer-term income change was more strongly related to SWB than current deviation from expected income. Higher stability in income development was associated with higher SWB. A higher share of income from benefits predicted lower life satisfaction and a more negative affect balance. Our results show the importance of examining income trajectories and taking into account source of income to gain a more differentiated view on the income-SWB association.
| S-EPMC6926602 | biostudies-literature
Project description:BackgroundMortality records identify cancer as the leading cause of death among living kidney donors, but information on the burden of cancer outside death records is limited in this population.MethodsWe examined a database wherein U.S. Organ Procurement and Transplantation Network identifiers for 4,650 living kidney donors in 1987 to 2007 were linked to administrative data of a U.S. private health insurer (2000-2007 claims) to identify postdonation cancer diagnoses. Skin cancer and non-skin cancer diagnoses were ascertained from International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis codes on billing claims. Donors were also matched one-to-one with general insurance beneficiaries by sex and age when benefits began. Diagnosis rates within observation windows were compared as rate ratios.ResultsThe median time from donation to the end of plan insurance enrollment was 7.7 years, with a median observation period of 2.1 years. Skin cancer rates were similar among prior living donors in the observation period and nondonor controls (rate ratio, 0.91; 95% confidence interval [CI], 0.59-1.40). In contrast, the rate of total non-skin cancers was significantly less common among donors than among controls (rate ratio, 0.74; 95% CI, 0.55-0.99), although reduced relative risk was limited to donors captured earlier in relation to donation. Several cases of cancer diagnosis (uterine, melanoma, "other") were identified within the first year after donation. Prostate cancer diagnosis was significantly more common among living donors compared with controls (rate ratio, 3.80; 95% CI, 1.42-10.2).ConclusionsContinued study of cancer after kidney donation is warranted to ensure that evaluation, selection, and long-term follow-up support overall good health of the donor.
| S-EPMC4447490 | biostudies-literature
Project description:BackgroundLimited data exist on correlates of psychological outcomes after kidney donation.MethodsWe used a database integrating Organ Procurement and Transplantation Network registrations for 4650 living kidney donors from 1987 to 2007 with administrative data of a U.S. private health insurer (2000-2007 claims) to identify depression diagnoses among prior living donors. The burden and demographic correlates of depression after enrollment in the insurance plan were estimated by Cox regression. Graft failure and death of the donor's recipient were examined as time-varying exposures.ResultsAfter start of insurance benefits, the cumulative frequency of depression diagnosis was 4.2% at 1 year and 11.5% at 5 years, and depression among donors was less common than among age- and gender-matched general insurance beneficiaries (rate ratio, 0.70; 95% confidence intervals [CI], 0.60-0.81). Demographic and clinical correlates of increased likelihood of depression diagnoses among the prior donors included female gender, white race, and some perioperative complications. After adjustment for donor demographic factors, recipient death (adjusted hazard ratio (aHR), 2.23; 95% CI, 1.11-4.48) and death-censored graft failure (aHR, 3.30; 95% CI, 1.49-7.34) were associated with two to three times the relative risk of subsequent depression diagnosis among nonspousal unrelated donors. There were trends toward increased depression diagnoses after recipient death and graft failure among spousal donors but no evidence of associations of these recipient events with the likelihood of depression diagnosis among related donors.ConclusionsRecipient death and graft loss predict increased depression risk among unrelated living donors in this privately insured sample. Informed consent and postdonation care should consider the potential impact of recipient outcomes on the psychological health of the donor.
| S-EPMC4447542 | biostudies-literature
Project description:Highly mobile species, such as migratory birds, respond to seasonal and interannual variability in resource availability by moving to better habitats. Despite the recognized importance of resource thresholds, species-distribution models typically rely on long-term average habitat conditions, mostly because large-extent, temporally resolved, environmental data are difficult to obtain. Recent advances in remote sensing make it possible to incorporate more frequent measurements of changing landscapes; however, there is often a cost in terms of model building and processing and the added value of such efforts is unknown. Our study tests whether incorporating real-time environmental data increases the predictive ability of distribution models, relative to using long-term average data. We developed and compared distribution models for shorebirds in California's Central Valley based on high temporal resolution (every 16 days), and 17-year long-term average surface water data. Using abundance-weighted boosted regression trees, we modeled monthly shorebird occurrence as a function of surface water availability, crop type, wetland type, road density, temperature, and bird data source. Although modeling with both real-time and long-term average data provided good fit to withheld validation data (the area under the receiver operating characteristic curve, or AUC, averaged between 0.79 and 0.89 for all taxa), there were small differences in model performance. The best models incorporated long-term average conditions and spatial pattern information for real-time flooding (e.g., perimeter-area ratio of real-time water bodies). There was not a substantial difference in the performance of real-time and long-term average data models within time periods when real-time surface water differed substantially from the long-term average (specifically during drought years 2013-2016) and in intermittently flooded months or locations. Spatial predictions resulting from the models differed most in the southern region of the study area where there is lower water availability, fewer birds, and lower sampling density. Prediction uncertainty in the southern region of the study area highlights the need for increased sampling in this area. Because both sets of data performed similarly, the choice of which data to use may depend on the management context. Real-time data may ultimately be best for guiding dynamic, adaptive conservation actions, whereas models based on long-term averages may be more helpful for guiding permanent wetland protection and restoration.
| S-EPMC9286402 | biostudies-literature
Project description:BackgroundThe first aim of the study was to investigate the accuracy and intra-laboratory variation of serum creatinine measurements in clinical laboratories in Flanders. The second purpose was to check the effect of this variation in serum creatinine concentration results on the calculated estimated glomerular filtration rate (eGFR) and the impact on classification of patients into a chronic kidney disease (CKD) stage.Methods26 routine instruments were included, representing 13 different types of analyzers from 6 manufacturers and covering all current methodologies (Jaffe, compensated Jaffe, enzymatic liquid and dry chemistry methods). Target values of five serum pools (creatinine concentrations ranging from 35 to 934 μmol/L) were assigned by the gold standard method (ID-GC/MS).ResultsIntra-run CV (%) (n = 5) and bias (%) from the target values were higher for low creatinine concentrations. Especially Jaffe and enzymatic dry chemistry methods showed a higher error. The calculated eGFR values corresponding with the reported creatinine concentration ranges resulted in a different CKD classification in 47% of cases.ConclusionsAlthough most creatinine assays claim to be traceable to the gold standard (ID-GC/MS), large inter-assay differences still exist. The inaccuracy in the lower concentration range is of particular concern and may lead to clinical misinterpretation when the creatinine-based eGFR of the patient is used for CKD staging. Further research to improve harmonization between methods is required.
| S-EPMC4358903 | biostudies-literature
Project description:Purpose Among homicides in the United States, intimate partners kill almost 50% of female and 10% of male victims. Intimate partner violence (IPV) also contributes to an estimated 6% of suicides. These trends suggest that opportunities for IPV interventions prior to the fatalities may have been missed. Thus, researchers must investigate the context and circumstances of IPV-related fatalities to inform effective prevention strategy development. There are two primary national fatality databases that can be used to examine such factors: the National Violent Death Reporting System (NVDRS, homicide and suicides); and the Uniform Crime Reporting-Supplementary Homicide Reports (UCR-SHR, homicides). These datasets include data on many IPV-related violent deaths but are limited by variations in data quality. Method This critical review summarizes opportunities and challenges when examining IPV-related fatalities using these national datasets. To document how the current literature is conceptualizing IPV, a rapid review on IPV-related homicide and suicide articles was performed (2019–2022). Missingness analyses were conducted to describe limitations in key dataset variables. Results These datasets enable tracking IPV-related fatalities nationally over time. However, issues with the operationalization of variables that record IPV circumstances, particularly in the UCR-SHR, and high levels of missingness represent significant barriers to research. Novel methodologies can optimize the use of these datasets. Conclusion National-level datasets enable researchers to examine IPV-related fatalities, evaluate policy differences between states, and monitor trends and disparities. This research can inform key recommendations for interventions to prevent IPV-related fatalities. Supplementary Information The online version contains supplementary material available at 10.1007/s10896-022-00487-2.
| S-EPMC9838333 | biostudies-literature
Project description:In only a few months after initial discovery in Wuhan, China, SARS-CoV-2 and the associated coronavirus disease 2019 (COVID-19) have become a global pandemic causing significant mortality and morbidity and implementation of strict isolation measures. In the absence of vaccines and effective therapeutics, reliable serological testing must be a key element of public health policy to control further spread of the disease and gradually remove quarantine measures. Serological diagnostic tests are being increasingly used to provide a broader understanding of COVID-19 incidence and to assess immunity status in the population. However, there are discrepancies between claimed and actual performance data for serological diagnostic tests on the market. In this study, we conducted a review of independent studies evaluating the performance of SARS-CoV-2 serological tests. We found significant variability in the accuracy of marketed tests and highlight several lab-based and point-of-care rapid serological tests with high levels of performance. The findings of this review highlight the need for ongoing independent evaluations of commercialized COVID-19 diagnostic tests.
| S-EPMC7400479 | biostudies-literature