Shared Data Sets Research Articles

A Fresh Look at the Health-Wealth Correlation: A Case Study of European Countries

This paper contributes to the development-health literature by studying the correlation between development measures (see below) and health measures - one subjective ('self-assessed-health-status'), and the other one objective (the individual's 'number of chronic diseases'). Correlations are examined for 29 European countries, using the SHARE data set, and country-level development measures. Specifically, we examine whether country fixed-effects in regressions of health measures, controlling for individual socio-demographic variables, are significantly correlated with country development variables, which include: logarithm of per-capita GDP; the Human Development Index; the Social Progress Index; life expectancy; percentage of GDP spent on health; and the novel measure expressed by the Environmental Health Index. The novelty of our study is the introduction of a channel for the significant health-wealth correlation, speculating that the driving forces are psychological.

Impact of Nonmalignant Portal Vein Thrombosis in Transplant Recipients With Nonalcoholic Steatohepatitis.

Nonalcoholic fatty liver disease is an increasingly prevalent condition, and its more severe progressive state, nonalcoholic steatohepatitis (NASH), is currently the second most common indication for wait-listed adults in the United States. The association of portal vein thrombosis (PVT) prior to or at transplant and poor graft and patient outcomes is not well established, particularly among NASH patients who inherently have an increased hypercoagulable profile. Using the United Network for Organ Sharing data set, we analyzed graft and patient outcomes of patients transplanted for the indication of NASH with and without PVT. Of 3689 NASH transplant recipients, the prevalence of PVT was 12% (450 with PVT and 3239 without PVT). NASH transplant recipients with PVT had inferior graft and patient survival compared with NASH transplant recipients without PVT, even after adjusting for recipient and donor demographic characteristics, body mass index, synthetic dysfunction, and presence of diabetes. In a multivariate Cox regression model, NASH transplant recipients with PVT had a 37% increased risk of graft failure (hazard ratio [HR], 1.37; 95% confidence interval [CI], 1.15-1.63; P < 0.001) and 31% increased risk of overall death (HR, 1.31; 95% CI, 1.09-1.58; P < 0.001) compared with NASH transplant recipients without PVT at transplant. This difference in graft and patient survival was most pronounced in the early posttransplant period. These results demonstrate that NASH patients with PVT have decreased graft and patient survival independent of recipient and donor factors.

Hepatic Dysfunction in Deceased Donors in the Age of the Opioid Epidemic.

Because of the opioid epidemic, deaths from drug overdoses have nearly tripled over the last 10 years.1 Although it has been reported that deceased donors who died of a drug overdose are now the fastest-growing donor demographic, the impact this mechanism of death has on hepatic function has not been well described.2 Opioids do not have a direct hepatotoxic effect, but opioid overdose may cause ischemic injury through respiratory depression, subsequent cardiovascular collapse and shock. We hypothesize that organs from these donors are more likely to have hepatic dysfunction through ischemic injury than from donors with alternate mechanisms of death demonstrated by massively elevated liver enzymes. Whereas acute kidney injury (AKI) in the setting of organ donation has been extensively studied, there are few published data on ischemic hepatitis and organ transplantation.3 We analyzed United Network for Organ Sharing data of all deceased donors between May 1, 2007, and September 30, 2016. The United Network for Organ Sharing data set included all laboratory data available in UNet, rather than simply the terminal laboratory values. Ischemic hepatitis was defined as ≥1 record of serum alanine aminotransferase of 1000 IU/L or greater.4 We also evaluated donors for the presence of severe AKI, defined as a donor serum creatinine greater than 2 mg/dL, as co-occurrence of ischemic hepatitis and AKI further supports prolonged ischemia as the mechanism of end-organ injury. Study deemed IRB exempt. Of the 78 692 deceased donors in the study period, 2929 (3.7%) had ischemic hepatitis. Over this time, ischemic hepatitis increased from 3.5% (2007) to 6.6% (2016) of donors. Of donors whose mechanism of death was categorized as a “drug intoxication,” 16.1% had ischemic hepatitis (71.3% had concomitant AKI) while an additional 13.0% had alanine aminotransferase elevations between 500 and 999 IU/L (40.2 % had AKI). In contrast, the prevalence of ischemic hepatitis among donors dying from stroke or cardiovascular death were less than 1% (41.7 % had AKI) and 6.7% (59.6 % had AKI), respectively. In multivariable models adjusting for donor clinical and demographic characteristics, death due to drug intoxication was associated with the highest odds of developing ischemic hepatitis, odds ratio: 12.5 (95% confidence interval, 17.7-23.5; intracranial hemorrhage/stroke as the reference). In contrast, the adjusted odds ratio for ischemic hepatitis in donors dying from cardiovascular causes was 6.2 (95% confidence interval, 5.4-7.1). One limitation is the inability to differentiate between opioid and nonopioid related deaths; however, approximately two thirds of drug overdoses in 2014 were related to opioids.5 This brief report leverages longitudinal deceased donor data to describe ischemic hepatitis in deceased organ donation. This unexplored clinical condition in deceased donors is occurring at higher rates given the marked increase in deaths from drug intoxication. This injury has become more common as the opioid epidemic continues, yet it has remained understudied in direct contrast to AKI. Recognition of this association is important because it is potentially more reversible than other hepatic injuries with improved viability for solid donor organs. More research is needed into the impact of this injury on donor organ utilization and graft survival.

Finding useful biomarkers for Parkinson's disease.

The recent advent of an "ecosystem" of shared biofluid sample biorepositories and data sets will focus biomarker efforts in Parkinson's disease, boosting the therapeutic development pipeline and enabling translation with real-world impact.

Detecting Alzheimer's Disease on Small Dataset: A Knowledge Transfer Perspective.

Computer-aided diagnosis (CAD) is an attractive topic in Alzheimer's disease (AD) research. Many algorithms are based on a relatively large training dataset. However, small hospitals are usually unable to collect sufficient training samples for robust classification. Although data sharing is expanding in scientific research, it is unclear whether a model based on one dataset is well suited for other data sources. Using a small dataset from a local hospital and a large shared dataset from the AD neuroimaging initiative, we conducted a heterogeneity analysis and found that different functional magnetic resonance imaging data sources show different sample distributions in feature space. In addition, we proposed an effective knowledge transfer method to diminish the disparity among different datasets and improve the classification accuracy on datasets with insufficient training samples. The accuracy increased by approximately 20% compared with that of a model based only on the original small dataset. The results demonstrated that the proposed approach is a novel and effective method for CAD in hospitals with only small training datasets. It solved the challenge of limited sample size in detection of AD, which is a common issue but lack of adequate attention. Furthermore, this paper sheds new light on effective use of multi-source data forneurological disease diagnosis.

DTRS: A catalyst for research in design thinking

• Reflections on the particular features of the DTRS series, including use of shared data sets. • Questions and suggestions on the future development of the series.

Importance of Donor Hypoxemia in Lung Transplantation: A Comprehensive Analysis of Serial Blood Gases

Previous studies have shown that donor PaO2/FiO2 ratio (P/F ratio) in lung transplantation (LTx) has little impact on recipients’ survival. However, these investigations looked at a single P/F ratio per donor, but a unique United Network for Organ Sharing (UNOS) dataset allows us to examine serial arterial blood gases (ABGs). We examined this UNOS database to assess a more accurate and “real world” effect of donor P/F ratio on donor utilization and post-LTx outcomes.

Abstract P127: Gene-Lifestyle Interactions Detect Novel Blood Pressure Loci

Introduction: Gene-lifestyle interaction effects (GxE more generally) on blood pressure (BP), a promising approach for novel loci discovery, is being actively pursued in the CHARGE Gene-Lifestyle Interactions Working Group using individual lifestyle domains, such as smoking status. Objectives: To explore the potential utility of a “lifestyle index” (aggregating multiple lifestyle domains) for identifying novel BP loci in a GxE context, we performed genome-wide interaction analysis with two lifestyle index variables. Methods: For each of 6,257 subjects (19 – 80 years, 46.9% male) in the Framingham Heart Study SHARe dataset, lifestyle index was defined as the sum of risk scores for four lifestyle factors: smoking status (0 = Never, 1 = Former, 2 = Current), alcohol intake (0 = Moderate, 1 = Never, 2 = Heavy), physical activity (0 = Active, 1= Inactive), and educational level (0=College degree, 1 = Some college, and 2 = No college). We examined GxE for systolic BP using the quantitative index (ranging from 0 to 7) and a binary form of the index (≥ vs &lt; the median), while adjusting for sex, age, and kinship. Promising loci were identified using a 2 df joint test of main and interaction effects at α = 5 x 10 -6 . Results: Sixteen promising single nucleotide polymorphisms (SNPs) representing 8 loci were found when using the quantitative lifestyle index, and 43 SNPs representing 4 loci when using the binary lifestyle index (Table 1), with only one locus common to both indices. Of the 11 unique loci detected, 3 are within 500 kb of known BP loci and 6 are in or near a gene with a known function. Conclusions: We demonstrate that a composite of multiple lifestyle factors can enhance novel discovery.

How We Fall Apart: Similarities of Human Aging in 10 European Countries.

We analyze human aging-understood as health deficit accumulation-for a panel of European individuals, using four waves of the Survey of Health, Aging and Retirement in Europe (SHARE data set) and constructing a health deficit index. Results from log-linear regressions suggest that, on average, elderly European men and women develop approximately 2.5% more health deficits from one birthday to the next. In nonlinear regressions (akin to the Gompertz-Makeham model), however, we find much greater rates of aging and large differences between men and women as well as between countries. Interestingly, these differences follow a particular regularity (akin to the compensation effect of mortality) and suggest an age at which average health deficits converge for men and women and across countries. This age, which may be associated with human life span, is estimated as 102 ± 2.6 years.

A Multi-Dimensional Context-Aware Recommendation Approach Based on Improved Random Forest Algorithm

Context-aware recommender systems focus on improving recommendation accuracy by adding contextual information and have been widely used in the real-world applications. However, conventional context-aware recommendation approaches have the drawbacks of giving the same weight to all context features, ignoring that users may have different preferences to different contexts, and the effects of context features on the process of recommendations may be different. In this paper, we propose a multi-dimensional context-aware recommendation approach based on improved random forest (MCRIRF) algorithm. The MCRIRF first improves the random forest algorithm by randomly selecting features from multiple feature subspaces that are classified by the importance of features. In addition, the MCRIRF uses the improved random forest algorithm to decompose and reduce the dimensions of context features of users, items, and contexts. Then, the MCRIRF calculates the weights of the 3-D user-item-context recommendation model. In the end, the MCRIRF recommends top- ${n}$ items with high forecasting ratings to users with similar contexts. LDOS-CoMoDa data set and Cycle Share data set are used for simulation, and six other recommendation approaches are considered in comparison. The experimental results indicate that the MCRIRF can reduce the mean absolute error and root mean squared error of the two data sets by about 2%–16% and 2%–13%, respectively. Thus, the evaluation presents encouraging results, indicating that the MCRIRF would be useful in the context-aware recommendation.

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.

High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community’s founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).

Weaving many strands

The healthcare home model drives major change in the way general practice is delivered, strengthens the basics of primary care, (access, coordination, comprehensive, continuity) and adds into the mix the opportunities that arise from technological advances and reorienting the system so it is patient and whanau focussed. That’s the theory but what does it look like practically? Northland DHB in collaboration with the two Northland PHOs, and supported by the broader national NZ Healthcare Home Care Collaborative have embarked on a major change process to establish Neighbourhood Healthcare Homes (NHH). We are working with six general practices in the first year, (small and large, rural and urban, traditional private business, corporate and iwi owned to make the NHH changes. New joint (NDHB and PHOs) change facilitation and financial analyst positons have been established to support practices with the NHH model changes. Northland DHB has funded release time for the establishment phase and contributed $16 per ESU capitation funding for the re designed practices. The PHOs have redirected Care Plus and SIA funding. The NHH model of care includes the standard healthcare home building blocks which are designed to release capacity within the general practice so that high needs /risk patients can be managed more proactively. These standard building blocks include practice teams driving portal uptake, using Doctor triage for patients requesting urgent appointments, expanding nurse roles and establishing new roles, reorganising appointment systems, including LEAN methodology into planning. In addition to these standard healthcare home offerings Northland is actively developing equity management tools and processes and social and health integration responses. The preparation for the NHH development included two key pieces of work to establish baseline, but also to support practices to make change using their individualised evidence. Firstly the DHB and the PHO collaborated on the piece of work with the former Health Partners Consulting Group to develop a shared dataset to inform General Practices about their current delivery of care. This information is packaged up and delivered by a public health physician who helps the practices to interpret results. There is a particular focus on equity markers. Secondly a multi-facetted piece of research looked at appointment availability, using the TNAA methodology and complemented by a manual acute appointment query. In communicating the outcomes, the team delivered the results to the practices with opportunities for discussion and with additional academic papers and a MOPs point’s audit tool to support further development. Concurrently work revising the way community and primary nurses link with general practices has been in development, with a new primary secondary navigator role to be implemented within the emerging NHHs, in Whangarei.

Web‐based visual data exploration for improved radiological source detection

SummaryRadiation detection can provide a reliable means of detecting radiological material. Such capabilities can help to prevent nuclear and/or radiological attacks, but reliable detection in uncontrolled surroundings requires algorithms that account for environmental background radiation. The Berkeley Data Cloud (BDC) facilitates the development of such methods by providing a framework to capture, store, analyze, and share data sets. In the era of big data, both the size and variety of data make it difficult to explore and find data sets of interest and manage the data. Thus, in the context of big data, visualization is critical for checking data consistency and validity, identifying gaps in data coverage, searching for data relevant to an analyst's use cases, and choosing input parameters for analysis. Downloading the data and exploring it on an analyst's desktop using traditional tools are no longer feasible due to the size of the data. This paper describes the design and implementation of a visualization system that addresses the problems associated with data exploration within the context of the BDC. The visualization system is based on a JavaScript front end communicating via REST with a back end web server.

A single-copy Sleeping Beauty transposon mutagenesis screen identifies new PTEN-cooperating tumor suppressor genes.

The overwhelming amount of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. We developed a novel whole-body insertional mutagenesis screen in mice, designed for the discovery of Pten-cooperating tumor suppressors, in which mobilization of a single-copy inactivating Sleeping Beauty transposon is coupled to Pten disruption within the same genome. The analysis of 278 transposition-induced prostate, breast and skin tumors detected tissue-specific and shared datasets of known and candidate cancer genes. We validated ZBTB20, CELF2, PARD3, AKAP13 and WAC, identified by our screens in multiple cancer types, as new tumor suppressors in prostate cancer: we demonstrated their synergy with PTEN for preventing invasion in vitro and confirmed their clinical relevance. Further characterization of Wac in vivo revealed obligate haploinsufficiency for this autophagy-regulating gene in a Pten-deficient context. Our study identifies complex PTEN-cooperating tumor suppressor networks in different cancer types with potential clinical implications.

Implications and outcomes of cardiac grafts refused by pediatric centers but transplanted by adult centers

BackgroundAccording to Organ Procurement Transplant Network policy, hearts from donors age <18 years are offered to pediatric recipients before being offered to adults of the same health status. We aimed to analyze differences in the use of adolescent donor hearts between adult and pediatric candidates and also to analyze the outcomes of pediatric candidates in which an adolescent donor heart was refused and later used in an adult recipient. MethodsAll adolescent donors (age 12-17 years) for 2000 to 2015 were identified using the standard United Network of Organ Sharing dataset and matched against the Potential Transplant Recipient dataset. ResultsOf the 2457 adults who received an adolescent heart, 855 (35%) received it after at least 1 refusal by a pediatric candidate (n = 844). Of the 844 pediatric candidates, 643 (76%) subsequently underwent transplantation (designated PCTs) and 201 (24%) never underwent transplantation (designated PCNTs). Among the latter group, 87 patients (43%) died or became too ill for transplantation. These 87 PCNTs refused 256 hearts that were later accepted by adult recipients. Donor quality was the most common reason for refusal. Overall, adult recipients had similar post-transplantation survival compared with PCTs, all pediatric transplants, and all adult transplants (P > .10). A breakdown of adolescent heart donors by year shows a trend toward increased use in pediatric candidates. ConclusionsA significant number of adolescent donor hearts that are refused by pediatric centers result in excellent post-transplantation outcomes in adult recipients. One in 10 pediatric candidates died on the waitlist after refusal of these hearts used by adult recipients. This warrants careful evaluation of the refusal criteria used by pediatric centers. Encouragingly, there now appears to be a trend toward an increased use of adolescent donor hearts by pediatric centers.

How We Fall Apart: Similarities of Human Aging in 10 European Countries

We analyze human aging, understood as health deficit accumulation, for a panel of European individuals. For that purpose, we use four waves of the Survey of Health, Aging and Retirement in Europe (SHARE dataset) and construct a health deficit index. Results from log-linear regressions suggest that, on average, elderly European men and women develop about 2.5 percent more health deficits from one birthday to the next. In non-linear regression (akin to the Gompertz-Makeham model), however, we find much greater rates of aging and large differences between men and women as well as between countries. Interestingly, these differences follow a particular regularity (akin to the compensation effect of mortality). They suggest an age at which average health deficits converge for men and women and across countries.

Decreased graft survival in liver transplant recipients of donors with positive blood cultures: a review of the United Network for Organ Sharing dataset.

Liver transplantation using blood culture positive donors (BCPD) has allowed a significant expansion of the donor pool. We aimed to characterize BCPD and assess the outcomes of BCPD liver transplant recipients. We retrieved data from the United Network for Organ Sharing (UNOS) registry on all adults who underwent primary, single-organ deceased-donor liver transplantation in the USA between 2008 and 2013. Patients were classified into two cohorts: the BCPD cohort and the non-BCPD cohort. One-year graft and patient survival were compared between cohorts using Kaplan-Meier estimates and Cox models. A total of 28 961 patients were included. There were 2316 (8.0%) recipients of BCPD. BCPD were more likely to be older, female, black, diabetic, hypertensive, and obese compared to non-BCPD. Graft survival was significantly lower in BCPD recipients compared to non-BCPD recipients (Kaplan-Meier, 0.85 vs. 0.87; P = 0.009). Results remained significant in propensity-matched analysis (P = 0.038). BCPD was independently associated with decreased graft survival (adjusted HR; 1.10, 95% CI 1.01-1.20; P = 0.04). There were no significant differences in patient survival between study groups. BCPD was associated with decreased graft survival in liver transplant recipients. Studies are needed to identify subgroups of BCPD with the highest risk of graft failure and characterize the underlying pathogenic mechanisms.

In-Hospital Vital Status and Heart Transplants After Intervention for Congenital Heart Disease in the Pediatric Cardiac Care Consortium: Completeness of Ascertainment Using the National Death Index and United Network for Organ Sharing Datasets.

BackgroundThe long‐term outcomes of patients undergoing interventions for congenital heart disease (CHD) remain largely unknown. We linked the Pediatric Cardiac Care Consortium (PCCC) with the National Death Index (NDI) and the United Network for Organ Sharing Dataset (UNOS) registries to study mortality and transplant occurring up to 32 years postintervention. The objective of the current analysis was to determine the sensitivity of this linkage in identifying patients who are known to have died or undergone heart transplant.Methods and ResultsWe used direct identifiers from 59 324 subjects registered in the PCCC between 1982 and 2003 to test for completeness of case ascertainment of subjects with known vital and heart transplant status by linkage with the NDI and UNOS registries. Of the 4612 in‐hospital deaths, 3873 were identified by the NDI as “true” matches for a sensitivity of 84.0% (95% CI, 82.9–85.0). There was no difference in sensitivity across 25 congenital cardiovascular conditions after adjustment for age, sex, race, presence of first name, death year, and residence at death. Of 455 known heart transplants in the PCCC, there were 408 matches in the UNOS registry, for a sensitivity of 89.7% (95% CI, 86.9–92.3). An additional 4851 deaths and 363 transplants that occurred outside the PCCC were identified through 2014.ConclusionsThe linkage of the PCCC with the NDI and UNOS national registries is feasible with a satisfactory sensitivity. This linkage provides a conservative estimate of the long‐term death and heart transplant events in this cohort.

The mode of sensitization and its influence on allograft outcomes in highly sensitized kidney transplant recipients.

We sought to determine whether the mode of sensitization in highly sensitized patients contributed to kidney allograft survival. An analysis of the United Network for Organ Sharing dataset involving all kidney transplants between 1997 and 2014 was undertaken. Highly sensitized adult kidney transplant recipients [panel reactive antibody (PRA) ≥98%] were compared with adult, primary non-sensitized and re-transplant recipients. Kaplan-Meier survival analyses were used to determine allograft survival rates. Cox proportional hazards regression analyses were conducted to determine the association of graft loss with key predictors. Fifty-three percent of highly sensitized patients transplanted were re-transplants. Pregnancy and transfusion were the only sensitizing event in 20 and 5%, respectively. The 10-year actuarial graft survival for highly sensitized recipients was 43.9% compared with 52.4% for non-sensitized patients, P < 0.001. The combination of being highly sensitized by either pregnancy or blood transfusion increased the risk of graft loss by 23% [hazard ratio (HR) 1.230, confidence interval (CI) 1.150-1.315, P < 0.001], and the combination of being highly sensitized from a prior transplant increased the risk of graft loss by 58.1% (HR 1.581, CI 1.473-1.698, P < 0.001). The mode of sensitization predicts graft survival in highly sensitized kidney transplant recipients (PRA ≥98%). Patients who are highly sensitized from re-transplants have inferior graft survival compared with patients who are highly sensitized from other modes of sensitization.

Catastrophic Health Care Expenditure among Older People with Chronic Diseases in 15 European Countries.

IntroductionIt is well-known that the prevalence of chronic diseases is high among older people, especially those who are poor. Moreover, chronic diseases can result in catastrophic health expenditure. The relationship between chronic diseases and their financial burden on households is thus double-sided, as financial difficulties can give rise to, and result from, chronic diseases. Our aim was to examine the levels of catastrophic health expenditure imposed by private out-of-pocket payments among older people diagnosed with diabetes mellitus, cardiovascular diseases and cancer in 15 European countries.MethodsThe SHARE dataset for individuals aged 50+ and their households, collected in 2010–2012 was used. The total number of participants included in this study was N = 51,661. The sample consisted of 43.8% male and 56.2% female participants. The average age was 67 years. We applied an instrumental variable approach for binary instrumented variables known as a treatment-effect model.ResultsWe found that being diagnosed with diabetes mellitus and cardiovascular diseases was associated with catastrophic health expenditure among older people even in comparatively wealthy countries with developed risk-pooling mechanisms. When compared to the Netherlands (the country with the lowest share of out-of-pocket payments as a percentage of total health expenditure in our study), older people diagnosed with diabetes mellitus in Portugal, Poland, Denmark, Italy, Switzerland, Belgium, the Czech Republic and Hungary were more likely to experience catastrophic health expenditure. Similar results were observed for diagnosed cardiovascular diseases. In contrast, cancer was not associated with catastrophic health expenditure.DiscussionOur study shows that older people with diagnosed chronic diseases face catastrophic health expenditure even in some of the wealthiest countries in Europe. The effect differs across chronic diseases and countries. This may be due to different socio-economic contexts, but also due to the specific characteristics of the different health systems. In view of the ageing of European populations, it will be crucial to strengthen the mechanisms for financial protection for older people with chronic diseases.