On Inferences from Completed Data

Matrix completion has become an extremely important technique as data scientists are routinely faced with large, incomplete datasets on which they wish to perform statistical inferences. We investigate how error introduced via matrix completion affects statistical inference. Furthermore, we prove recovery error bounds which depend upon the matrix recovery error for several common statistical inferences. We consider matrix recovery via nuclear norm minimization and a variant, $\ell_1$-regularized nuclear norm minimization for data with a structured sampling pattern. Finally, we run a series of numerical experiments on synthetic data and real patient surveys from MyLymeData, which illustrate the relationship between inference recovery error and matrix recovery error. These results indicate that exact matrix recovery is often not necessary to achieve small inference recovery error

Rural Health in Virginia: Disparities, Dilemmas, and Overview of a JMU School of Nursing Solution

Background: There is no unified definition of rurality; this makes studying rurality, rural health, and associated health disparities and health outcomes difficult. Rural Americans constitute approximately 15% of the U.S. population, and they experience multiple barriers to healthcare and numerous health disparities as a result, particularly related to chronic disease, mental health, and increased lifestyle-linked health risks. Rural Americans should be viewed as a unique and vulnerable population, one with specific health promotion and disease prevention needs. Local problem: Although Virginia as a whole is a wealthy state, much inequity exists between the “Golden Crescent” and the “Rural Horseshoe” regions of Virginia, which includes the western portion of the State. Rural Virginians face higher unemployment, a higher poverty rate, and decreased access to care. One such area is Page County, Virginia, a local underserved health professional shortage area. Methods: In 2018, JMU obtained a HRSA grant focusing on Nursing Education, Practice, Quality, and Retention called, “The Undergraduate Primary Care and Rural Education (UPCARE) Project: a Community-based Nursing Education Collaboration. Intervention: The UPCARE Project allows JMU School of Nursing to respond to the needs for 1) BSN student education focusing on community health and primary care in a rural area, and 2) the creation two RN preceptor positions which incorporate a enhanced primary care RN role within 4 Rural Health Clinics (RHCs), all of whom are facilitated by a faculty-led grant team, including a Nurse Liaison. This two-pronged approach enables nurses to work to meet the health needs of the residents of Page County, Virginia. It is an innovative approach in keeping with Virginia’s State Rural Health Plan. Results: The JMU UPCARE Project is a collaborative, community-focused solution to the rural health disparities facing Page County. To date, nine students have started their clinical experiences in Page County, and two RN preceptors are starting their enhanced primary care RN role in the Rural Health Clinics. Conclusions/ Implications: This presentation will focus on rural health nursing in general, rural health disparities in Virginia, the creation of the UPCARE Project as part of the solution to meet the health care needs of rural Virginians. In keeping with the theme of the conference, the presentation will focus on the development of an enhanced primary care RN role, which is designed for RNs to work at the top of their practice scope

Cardiff sciSCREEN: A model for using film screenings to engage publics in University research

Cardiff sciSCREEN is a public engagement programme that brings together local experts and publics to discuss issues raised by contemporary cinema. Since 2010, Cardiff sciSCREEN (short for science on screen) has exhibited more than 50 films alongside short talks and discussions that draw on a range of disciplinary perspectives to explore the broad repertoire of themes found within different film genres. The aim of Cardiff sciSCREEN is to increase the local community's access to university research, while enabling university staff and students to engage a variety of publics with their work. In this paper, we first describe our method of public engagement, and then draw on data from a research survey we administered to sciSCREENers to discuss the relationship between the theory and practice of public engagement. Using research from public understanding of science (PUS), public engagement with science and technology (PEST), science and technology studies (STS) and film literacy, we discuss the ways in which our flexible characterization of science has made the programme inclusive, attracting a wide and varied audience. We consider the benefits of cross-disciplinary perspectives when communicating and engaging contemporary developments in science, where the term 'science' is taken to stand for the breadth of academic research and not merely the natural sciences, as well as discussing the importance of space in public engagement events

Global, regional, and national causes of under-5 mortality in 2000-15: an updated systematic analysis with implications for the Sustainable Development Goals.

BACKGROUND: Despite remarkable progress in the improvement of child survival between 1990 and 2015, the Millennium Development Goal (MDG) 4 target of a two-thirds reduction of under-5 mortality rate (U5MR) was not achieved globally. In this paper, we updated our annual estimates of child mortality by cause to 2000-15 to reflect on progress toward the MDG 4 and consider implications for the Sustainable Development Goals (SDG) target for child survival. METHODS: We increased the estimation input data for causes of deaths by 43% among neonates and 23% among 1-59-month-olds, respectively. We used adequate vital registration (VR) data where available, and modelled cause-specific mortality fractions applying multinomial logistic regressions using adequate VR for low U5MR countries and verbal autopsy data for high U5MR countries. We updated the estimation to use Plasmodium falciparum parasite rate in place of malaria index in the modelling of malaria deaths; to use adjusted empirical estimates instead of modelled estimates for China; and to consider the effects of pneumococcal conjugate vaccine and rotavirus vaccine in the estimation. FINDINGS: In 2015, among the 5·9 million under-5 deaths, 2·7 million occurred in the neonatal period. The leading under-5 causes were preterm birth complications (1·055 million [95% uncertainty range (UR) 0·935-1·179]), pneumonia (0·921 million [0·812 -1·117]), and intrapartum-related events (0·691 million [0·598 -0·778]). In the two MDG regions with the most under-5 deaths, the leading cause was pneumonia in sub-Saharan Africa and preterm birth complications in southern Asia. Reductions in mortality rates for pneumonia, diarrhoea, neonatal intrapartum-related events, malaria, and measles were responsible for 61% of the total reduction of 35 per 1000 livebirths in U5MR in 2000-15. Stratified by U5MR, pneumonia was the leading cause in countries with very high U5MR. Preterm birth complications and pneumonia were both important in high, medium high, and medium child mortality countries; whereas congenital abnormalities was the most important cause in countries with low and very low U5MR. INTERPRETATION: In the SDG era, countries are advised to prioritise child survival policy and programmes based on their child cause-of-death composition. Continued and enhanced efforts to scale up proven life-saving interventions are needed to achieve the SDG child survival target. FUNDING: Bill & Melinda Gates Foundation, WHO

Rural and Urban Differences in the Adoption of New Health Information and Medical Technologies

Background This statewide survey sought to understand the adoption level of new health information and medical technologies, and whether these patterns differed between urban and rural populations. Methods A random sample of 7,979 people aged 18‐75 years, stratified by rural status and race, who lived in 1 of 34 Indiana counties with high cancer mortality rates and were seen at least once in the past year in a statewide health system were surveyed. Results Completed surveys were returned by 970 participants. Rural patients were less likely than urban to use electronic health record messaging systems (28.3% vs 34.5%, P = .045) or any communication technology (43.0% vs 50.8%, P = .017). Rural patients were less likely to look for personal health information for someone else's medical record (11.0% vs 16.3%, P = .022), look‐up test results (29.5% vs 38.3%, P = .005), or use any form of electronic medical record (EMR) access (57.5% vs 67.1%, P = .003). Rural differences in any use of communication technology or EMRs were no longer significant in adjusted models, while education and income were significantly associated. There was a trend in the higher use of low‐dose computed tomography (CT) scan among rural patients (19.1% vs 14.4%, P = .057). No significant difference was present between rural and urban patients in the use of the human papilloma virus test (27.1% vs 26.6%, P = .880). Conclusions Differences in health information technology use between rural and urban populations may be moderated by social determinants. Lower adoption of new health information technologies (HITs) than medical technologies among rural, compared to urban, individuals may be due to lower levels of evidence supporting HITs

Racial and Socioeconomic Disparities in Cancer-Related Knowledge, Beliefs, and Behaviors in Indiana

Background: This statewide survey examined differences in cancer-related knowledge, beliefs, and behaviors between racial and socioeconomic groups in select counties in Indiana. Methods: A stratified random sample of 7,979 people aged 18–75 who lived in one of 34 Indiana counties with higher cancer mortality rates than the state average, and were seen at least once in the past year in a statewide health system were mailed surveys. Results: Completed surveys were returned by 970 participants, yielding a 12% response rate. Black respondents were less likely to perceive they were at risk for cancer and less worried about getting cancer. Individuals most likely to perceive that they were unlikely to get cancer were more often black, with low incomes (less than $20,000) or high incomes ($50,000 or more), or less than a high school degree. Black women were greater than six times more likely to be adherent to cervical cancer screening. Higher income was associated with receiving a sigmoidoscopy in the last 5 years and a lung scan in the past year. Those with the highest incomes were more likely to engage in physical activity. Both income and education were inversely related to smoking. Conclusions: Socioeconomic and racial disparities were observed in health behaviors and receipt of cancer screening. Black individuals had less worry about cancer. Impact: Understanding populations for whom cancer disparities exist and geographic areas where the cancer burden is disproportionately high is essential to decision-making about research priorities and the use of public health resources

Adverse Events of Interest Following Influenza Vaccination in the First Season of Adjuvanted Trivalent Immunization:Retrospective Cohort Study

BACKGROUND: Vaccination is the most effective form of prevention of seasonal influenza; the United Kingdom has a national influenza vaccination program to cover targeted population groups. Influenza vaccines are known to be associated with some common minor adverse events of interest (AEIs), but it is not known if the adjuvanted trivalent influenza vaccine (aTIV), first offered in the 2018/2019 season, would be associated with more AEIs than other types of vaccines. OBJECTIVE: We aim to compare the incidence of AEIs associated with different types of seasonal influenza vaccines offered in the 2018/2019 season. METHODS: We carried out a retrospective cohort study using computerized medical record data from the Royal College of General Practitioners Research and Surveillance Centre sentinel network database. We extracted data on vaccine exposure and consultations for European Medicines Agency–specified AEIs for the 2018/2019 influenza season. We used a self-controlled case series design; computed relative incidence (RI) of AEIs following vaccination; and compared the incidence of AEIs associated with aTIV, the quadrivalent influenza vaccine, and the live attenuated influenza vaccine. We also compared the incidence of AEIs for vaccinations that took place in a practice with those that took place elsewhere. RESULTS: A total of 1,024,160 individuals received a seasonal influenza vaccine, of which 165,723 individuals reported a total of 283,355 compatible symptoms in the 2018/2019 season. Most AEIs occurred within 7 days following vaccination, with a seasonal effect observed. Using aTIV as the reference group, the quadrivalent influenza vaccine was associated with a higher incidence of AEIs (RI 1.46, 95% CI 1.41-1.52), whereas the live attenuated influenza vaccine was associated with a lower incidence of AEIs (RI 0.79, 95% CI 0.73-0.83). No effect of vaccination setting on the incidence of AEIs was observed. CONCLUSIONS: Routine sentinel network data offer an opportunity to make comparisons between safety profiles of different vaccines. Evidence that supports the safety of newer types of vaccines may be reassuring for patients and could help improve uptake in the future

Thrombocytopenic, thromboembolic and haemorrhagic events following second dose with BNT162b2 and ChAdOx1: self-controlled case series analysis of the English national sentinel cohort

Thrombosis associated with thrombocytopenia was a matter of concern post first and second doses of BNT162b2 and ChAdOx1 COVID-19 vaccines. Therefore, it is important to investigate the risk of thrombocytopenic, thromboembolic and haemorrhagic events following a second dose of BNT162b2 and ChAdOx1 COVID-19 vaccines. We conducted a large-scale self-controlled case series analysis, using routine primary care data linked to hospital data, among 12.3 million individuals (16 years old and above) in England. We used the nationally representative Oxford-Royal College of General Practitioners (RCGP) sentinel network database with baseline and risk periods between 8th December 2020 and 11th June 2022. We included individuals who received two vaccine (primary) doses of the BNT162b2 mRNA (Pfizer-BioNTech) and two vaccine doses of ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines in our analyses. We carried out a self-controlled case series (SCCS) analysis for each outcome using a conditional Poisson regression model with an offset for the length of risk period. We reported the incidence rate ratios (IRRs) and 95% confidence intervals (CI) of thrombocytopenic, thromboembolic (including arterial and venous events) and haemorrhagic events, in the period of 0-27 days after receiving a second dose of BNT162b2 or ChAdOx1 vaccines compared to the baseline period (14 or more days prior to first dose, 28 or more days after the second dose and the time between 28 or more days after the first and 14 or more days prior to the second dose). We adjusted for a range of potential confounders, including age, sex, comorbidities and deprivation. Between December 8, 2020 and February 11, 2022, 6,306,306 individuals were vaccinated with two doses of BNT162b2 and 6,046,785 individuals were vaccinated with two doses of ChAdOx1. Compared to the baseline, our analysis show no increased risk of venous thromboembolic events (VTE) for both BNT162b2 (IRR 0.71, 95% CI: 0.65-0.770) and ChAdOx1 (IRR 0.91, 95% CI: 0.84-0.98); and similarly there was no increased risk for cerebral venous sinus thrombosis (CVST) for both BNT162b2 (IRR 0.87, 95% CI: 0.41-1.85) and ChAdOx1 (IRR 1.73, 95% CI: 0.82-3.68). We additionally report no difference in IRR for pulmonary embolus, and deep vein thrombosis, thrombocytopenia, including idiopathic thrombocytopenic purpura (ITP), and haemorrhagic events post second dose for both BNT162b2. Reassuringly, we found no associations between increased risk of thrombocytopenic, thromboembolic and haemorrhagic events post vaccination with second dose for either of these vaccines. Data and Connectivity: COVID-19 Vaccines Pharmacovigilance study

Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation

The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of ∼1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large germline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (Fst = 0.3–0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested

Applying learning health systems thinking in codeveloping integrated tuberculosis interventions in the contexts of COVID-19

The COVID-19 pandemic reversed much of global progress made in combatting tuberculosis, with South Africa experiencing one of the largest impacts on tuberculosis detection. The aim of this paper is to share our experiences in applying learning health systems (LHS) thinking to the codevelopment of an intervention improving an integrated response to COVID-19 and tuberculosis in a South African district. A sequential partially mixed-methods study was undertaken between 2018 and 2021 in the district of Amajuba in KwaZulu-Natal. Here, we report on the formulation of a Theory of Change, codesigning and refining proposed interventions, and piloting and evaluating codesigned interventions in primary healthcare facilities, through an LHS lens. Following the establishment and formalisation of a district Learning Community, diagnostic work and a codevelopment of a theory of change, intervention packages tailored according to pandemic lockdowns were developed, piloted and scaled up. This process illustrates how a community of learning can generate more responsive, localised interventions, and suggests that the establishment of a shared space of research governance can provide a degree of resilience to facilitate adaption to external shocks. Four main lessons have been gleaned from our experience in adopting an LHS approach in a South African district, which are (1) the importance of building and sustaining relationships, (2) the utility of colearning, coproduction and adaptive capacity, (3) the centrality of theory-driven systems strengthening and (4) reflections on LHS as a framework