Open Access Policy Articles

Permanent URI for this collection

The IUPUI Faculty Council adopted an open access policy on October 7th, 2014 (available from: This policy shows IUPUI's commitment to disseminating the fruits of research and scholarship as widely as possible. Open access policies increase authors’ rights, readership and citation rates for scholarly articles. The opt out provision ensures that all faculty authors have the freedom to publish in the journal of their choice.

Please choose one of the following methods to participate.


Recent Submissions

Now showing 1 - 10 of 24121
  • Item
    The COVID-19 pandemic and associated rise in pediatric firearm injuries: A multi-institutional study
    (Elsevier, 2022) Collings, Amelia T.; Farazi, Manzur; Van Arendonk, Kyle J.; Fallat, Mary E.; Minneci, Peter C.; Sato, Thomas T.; Speck, K. Elizabeth; Deans, Katherine J.; Falcone, Richard A., Jr.; Foley, David S.; Fraser, Jason D.; Gadepalli, Samir K.; Keller, Martin S.; Kotagal, Meera; Landman, Matthew P.; Leys, Charles M.; Markel, Troy A.; Rubalcava, Nathan; St. Peter, Shawn D.; Flynn-O’Brien, Katherine T.; Midwest Pediatric Surgery Consortium; Surgery, School of Medicine
    Background: Firearm sales in the United States (U.S.) markedly increased during the COVID-19 pandemic. Our objective was to determine if firearm injuries in children were associated with stay-at-home orders (SHO) during the COVID-19 pandemic. We hypothesized there would be an increase in pediatric firearm injuries during SHO. Methods: This was a multi institutional, retrospective study of institutional trauma registries. Patients <18 years with traumatic injuries meeting National Trauma Data Bank (NTDB) criteria were included. A "COVID" cohort, defined as time from initiation of state SHO through September 30, 2020 was compared to "Historical" controls from an averaged period of corresponding dates in 2016-2019. An interrupted time series analysis (ITSA) was utilized to evaluate the association of the U.S. declaration of a national state of emergency with pediatric firearm injuries. Results: Nine Level I pediatric trauma centers were included, contributing 48,111 pediatric trauma patients, of which 1,090 patients (2.3%) suffered firearm injuries. There was a significant increase in the proportion of firearm injuries in the COVID cohort (COVID 3.04% vs. Historical 1.83%; p < 0.001). There was an increased cumulative burden of firearm injuries in 2020 compared to a historical average. ITSA showed an 87% increase in the observed rate of firearm injuries above expected after the declaration of a nationwide emergency (p < 0.001). Conclusion: The proportion of firearm injuries affecting children increased during the COVID-19 pandemic. The pandemic was associated with an increase in pediatric firearm injuries above expected rates based on historical patterns.
  • Item
    Assessing Progress Toward the Vision of a Comprehensive, Shared Electronic Care Plan: Scoping Review
    (JMIR, 2022-06-10) Norton, Jenna M.; Ip, Alex; Ruggiano, Nicole; Abidogun, Tolulope; Camara, Djibril Souleymane; Fu, Helen; Hose, Bat-Zion; Miran, Saadia; Hsiao, Chun-Ju; Wang, Jing; Bierman, Arlene S.; Epidemiology, School of Public Health
    Background: Care plans are central to effective care delivery for people with multiple chronic conditions. But existing care plans-which typically are difficult to share across care settings and care team members-poorly serve people with multiple chronic conditions, who often receive care from numerous clinicians in multiple care settings. Comprehensive, shared electronic care (e-care) plans are dynamic electronic tools that facilitate care coordination and address the totality of health and social needs across care contexts. They have emerged as a potential way to improve care for individuals with multiple chronic conditions. Objective: To review the landscape of e-care plans and care plan-related initiatives that could allow the creation of a comprehensive, shared e-care plan and inform a joint initiative by the National Institutes of Health and the Agency for Healthcare Research and Quality to develop e-care planning tools for people with multiple chronic conditions. Methods: We conducted a scoping review, searching literature from 2015 to June 2020 using Scopus, Clinical Key, and PubMed; we also searched the gray literature. To identify initiatives potentially missing from this search, we interviewed expert informants. Relevant data were then identified and extracted in a structured format for data synthesis and analysis using an expanded typology of care plans adapted to our study context. The extracted data included (1) the perspective of the initiatives; (2) their scope, (3) network, and (4) context; (5) their use of open syntax standards; and (6) their use of open semantic standards. Results: We identified 7 projects for e-care plans and 3 projects for health care data standards. Each project provided critical infrastructure that could be leveraged to promote the vision of a comprehensive, shared e-care plan. All the e-care plan projects supported both broad goals and specific behaviors; 1 project supported a network of professionals across clinical, community, and home-based networks; 4 projects included social determinants of health. Most projects specified an open syntax standard, but only 3 specified open semantic standards. Conclusions: A comprehensive, shared, interoperable e-care plan has the potential to greatly improve the coordination of care for individuals with multiple chronic conditions across multiple care settings. The need for such a plan is heightened in the wake of the ongoing COVID-19 pandemic. While none of the existing care plan projects meet all the criteria for an optimal e-care plan, they all provide critical infrastructure that can be leveraged as we advance toward the vision of a comprehensive, shared e-care plan. However, critical gaps must be addressed in order to achieve this vision.
  • Item
    The Reproducibility Movement in Psychology: Does Researcher Gender Affect How People Perceive Scientists With a Failed Replication?
    (Frontiers Media, 2022-06-13) Ashburn-Nardo, Leslie; Moss-Racusin, Corinne A.; Smith, Jessi L.; Sanzari, Christina M.; Vescio, Theresa K.; Glick, Peter; Psychology, School of Science
    The reproducibility movement in psychology has resulted in numerous highly publicized instances of replication failures. The goal of the present work was to investigate people’s reactions to a psychology replication failure vs. success, and to test whether a failure elicits harsher reactions when the researcher is a woman vs. a man. We examined these questions in a pre-registered experiment with a working adult sample, a conceptual replication of that experiment with a student sample, and an analysis of data compiled and posted by a psychology researcher on their public weblog with the stated goal to improve research replicability by rank-ordering psychology researchers by their “estimated false discovery risk.” Participants in the experiments were randomly assigned to read a news article describing a successful vs. failed replication attempt of original work from a male vs. female psychological scientist, and then completed measures of researcher competence, likability, integrity, perceptions of the research, and behavioral intentions for future interactions with the researcher. In both working adult and student samples, analyses consistently yielded large main effects of replication outcome, but no interaction with researcher gender. Likewise, the coding of weblog data posted in July 2021 indicated that 66.3% of the researchers scrutinized were men and 33.8% were women, and their rank-ordering was not correlated with researcher gender. The lack of support for our pre-registered gender-replication hypothesis is, at first glance, encouraging for women researchers’ careers; however, the substantial effect sizes we observed for replication outcome underscore the tremendous negative impact the reproducibility movement can have on psychologists’ careers. We discuss the implications of such negative perceptions and the possible downstream consequences for women in the field that are essential for future study.
  • Item
    Insight Into Rho Kinase Isoforms in Obesity and Energy Homeostasis
    (Frontiers Media, 2022-06-13) Wei, Lei; Shi, Jianjian; Pediatrics, School of Medicine
    Obesity and associated complications increasingly jeopardize global health and contribute to the rapidly rising prevalence of type 2 diabetes mellitus and obesity-related diseases. Developing novel methods for the prevention and treatment of excess body adipose tissue expansion can make a significant contribution to public health. Rho kinase is a Rho-associated coiled-coil-containing protein kinase (Rho kinase or ROCK). The ROCK family including ROCK1 and ROCK2 has recently emerged as a potential therapeutic target for the treatment of metabolic disorders. Up-regulated ROCK activity has been involved in the pathogenesis of all aspects of metabolic syndrome including obesity, insulin resistance, dyslipidemia and hypertension. The RhoA/ROCK-mediated actin cytoskeleton dynamics have been implicated in both white and beige adipogenesis. Studies using ROCK pan-inhibitors in animal models of obesity, diabetes, and associated complications have demonstrated beneficial outcomes. Studies via genetically modified animal models further established isoform-specific roles of ROCK in the pathogenesis of metabolic disorders including obesity. However, most reported studies have been focused on ROCK1 activity during the past decade. Due to the progress in developing ROCK2-selective inhibitors in recent years, a growing body of evidence indicates more attention should be devoted towards understanding ROCK2 isoform function in metabolism. Hence, studying individual ROCK isoforms to reveal their specific roles and principal mechanisms in white and beige adipogenesis, insulin sensitivity, energy balancing regulation, and obesity development will facilitate significant breakthroughs for systemic treatment with isoform-selective inhibitors. In this review, we give an overview of ROCK functions in the pathogenesis of obesity and insulin resistance with a particular focus on the current understanding of ROCK isoform signaling in white and beige adipogenesis, obesity and thermogenesis in adipose tissue and other major metabolic organs involved in energy homeostasis regulation.
  • Item
    The IeDEA harmonist data toolkit: A data quality and data sharing solution for a global HIV research consortium
    (Elsevier, 2022) Lewis, Judith T.; Stephens, Jeremy; Musick, Beverly; Brown, Steven; Malateste, Karen; Ostinelli, Cam Ha Dao; Maxwell, Nicola; Jayathilake, Karu; Shi, Qiuhu; Brazier, Ellen; Kariminia, Azar; Hogan, Brenna; Duda, Stephany N.; Biostatistics and Health Data Science, School of Medicine
    We describe the design, implementation, and impact of a data harmonization, data quality checking, and dynamic report generation application in an international observational HIV research network. The IeDEA Harmonist Data Toolkit is a web-based application written in the open source programming language R, employs the R/Shiny and RMarkdown packages, and leverages the REDCap data collection platform for data model definition and user authentication. The Toolkit performs data quality checks on uploaded datasets, checks for conformance with the network's common data model, displays the results both interactively and in downloadable reports, and stores approved datasets in secure cloud storage for retrieval by the requesting investigator. Including stakeholders and users in the design process was key to the successful adoption of the application. A survey of regional data managers as well as initial usage metrics indicate that the Toolkit saves time and results in improved data quality, with a 61% mean reduction in the number of error records in a dataset. The generalized application design allows the Toolkit to be easily adapted to other research networks.
  • Item
    Developmental origins of disease highlight the immediate need for expanded access to comprehensive prenatal care
    (Frontiers, 2022-11-23) McDonald, Chloe R.; Weckman , Andrea M.; Wright , Julie K.; Conroy, Andrea L.; Kain, Kevin C.; Pediatrics, School of Medicine
    The prenatal environment plays a critical role in shaping fetal development and ultimately the long-term health of the child. Here, we present data linking prenatal health, via maternal nutrition, comorbidities in pregnancy (e.g., diabetes, hypertension), and infectious and inflammatory exposures, to lifelong health through the developmental origins of disease framework. It is well-established that poor maternal health puts a child at risk for adverse outcomes in the first 1,000 days of life, yet the full health impact of the in utero environment is not confined to this narrow window. The developmental origins of disease framework identifies cognitive, neuropsychiatric, metabolic and cardiovascular disorders, and chronic diseases in childhood and adulthood that have their genesis in prenatal life. This perspective highlights the enormous public health implications for millions of pregnancies where maternal care, and therefore maternal health and fetal health, is lacking. Despite near universal agreement that access to antenatal care is a priority to protect the health of women and children in the first 1,000 days of life, insufficient progress has been achieved. Instead, in some regions there has been a political shift toward deprioritizing maternal health, which will further negatively impact the health and safety of pregnant people and their children across the lifespan. In this article we argue that the lifelong health impact attributed to the perinatal environment justifies policies aimed at improving access to comprehensive antenatal care globally.
  • Item
    Bariatric Surgery and Risk of Death in Persons with Chronic Kidney Disease
    (Wolters Kluwer, 2022-12-01) Coleman, Karen J.; Shu , Yu-Hsiang; Fischer , Heidi; Johnson , Eric; Yoon , Tae K.; Taylor , Brianna; Imam, Talha; DeRose , Stephen; Haneuse , Sebastien; Herrinton , Lisa J.; Fisher, David; Li , Robert A.; Theis, Mary Kay; Liu , Liyan; Courcoulas, Anita P.; Smith, David H.; Arterburn, David E.; Friedman, Allon N.; Medicine, School of Medicine
    Objective: A retrospective cohort study investigated the association between having surgery and risk of mortality for up to five years and if this association was modified by incident End Stage Renal Disease (ESRD) during the follow-up period. Summary Background Data: Mortality risk in individuals with pre-dialysis chronic kidney disease (CKD) is high and few effective treatment options are available. Whether bariatric surgery can improve survival in people with CKD is unclear. Methods: Patients with class II and III obesity and pre-dialysis CKD stages 3 – 5 who underwent bariatric surgery between 1/1/2006 and 9/30/2015 (n = 802) were matched to patients who did not have surgery (n = 4,933). Mortality was obtained from state death records and ESRD was identified through state-based or healthcare system-based registries. Cox regression models were used to investigate the association between bariatric surgery and risk of mortality and if this was moderated by incident ESRD during the follow-up period. Results: Patients were primarily women (79%), non-Hispanic White (72%), under 65 years old (64%), who had a BMI ≥ 40 kg/m2 (59%), diabetes (67%) and hypertension (89%). After adjusting for incident ESRD, bariatric surgery was associated with a 79% lower 5-year risk of mortality compared to matched controls (HR = 0.21; 95% CI: 0.14-0.32; p < .001). Incident ESRD did not moderate the observed association between surgery and mortality (HR = 1.59; 95% CI 0.31-8.23; p = .58). Conclusions: Bariatric surgery is associated with a reduction in mortality in pre-dialysis patients regardless of developing ESRD. These findings are significant because patients with CKD are at relatively high risk for death with few efficacious interventions available to improve survival.
  • Item
    A Pilot Randomized Controlled Trial Investigating MBSR for Parkinson’s Disease Patients and Their Caregiving Partners: Effects on Distress, Social support, Cortisol, and Inflammation
    (Springer, 2022) Siwik, Chelsea J.; Phillips, Kala; Litvan, Irene; Salmon, Paul; Rodgers, Allison; Jablonski, Megan; Sephton, Sandra E.; Psychology, School of Science
    Objectives: To examine the preliminary effects of the mindfulness-based stress reduction (MBSR) program in the management of biopsychosocial stress–related changes associated with Parkinson’s disease (PD) among patient/caregiving-partner dyads. Methods: PD patient/caregiving-partner dyads (N = 18) early in the disease trajectory were recruited from a university-affiliated movement disorders clinic and were randomized (1:1) to either the MBSR intervention or the control condition (treatment as usual [TAU]). Mixed methods ANOVAs were conducted to examine primary outcomes (disease-specific distress, perceived social support, circadian rhythmicity [cortisol], and markers of inflammation [IL-6, TNF-alpha, IL-1beta]) between groups (MBSR vs. TAU) among patients and caregiving partners separately. Results: No participants were lost to follow-up. Given the pilot nature of the current investigation, findings should be interpreted as exploratory opposed to confirmatory. Following MBSR, PD patients reported an increase in disease-specific distress and intrusive thoughts and demonstrated a decrease in mean bedtime cortisol and IL-1beta from baseline to follow-up compared to TAU. Caregiving partners who received MBSR reported an increase in perceived social support and demonstrated improved rhythmicity of diurnal cortisol slopes from baseline to follow-up compared to TAU. Conclusions: Both patients and caregiving partners who received MBSR demonstrated improvements in biomarkers of circadian function, and patients evidenced a decrease in a biomarker of systemic inflammation, pointing to an important area of further investigation. Given that patients reported an increase in disease-specific distress and intrusive thoughts, the salutary effects of MBSR may be experienced physiologically prior to, or in lieu of, psychological effects, although this should be explored further, especially given the improvement in perceived social support reported by caregiving partners.
  • Item
    Recent Advances on Capacitive Proximity Sensors: From Design and Materials to Creative Applications
    (MDPI, 2022) Moheimani, Reza; Hosseini, Paniz; Mohammadi, Saeed; Dalir, Hamid; Mechanical and Energy Engineering, School of Engineering and Technology
    Capacitive proximity sensors (CPSs) have recently been a focus of increased attention because of their widespread applications, simplicity of design, low cost, and low power consumption. This mini review article provides a comprehensive overview of various applications of CPSs, as well as current advancements in CPS construction approaches. We begin by outlining the major technologies utilized in proximity sensing, highlighting their characteristics and applications, and discussing their advantages and disadvantages, with a heavy emphasis on capacitive sensors. Evaluating various nanocomposites for proximity sensing and corresponding detecting approaches ranging from physical to chemical detection are emphasized. The matrix and active ingredients used in such sensors, as well as the measured ranges, will also be discussed. A good understanding of CPSs is not only essential for resolving issues, but is also one of the primary forces propelling CPS technology ahead. We aim to examine the impediments and possible solutions to the development of CPSs. Furthermore, we illustrate how nanocomposite fusion may be used to improve the detection range and accuracy of a CPS while also broadening the application scenarios. Finally, the impact of conductance on sensor performance and other variables that impact the sensitivity distribution of CPSs are presented.
  • Item
    Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya
    (Springer, 2022-01-27) Tawe, Leabaneng; Choga, Wonderful T.; Paganotti, Giacomo M.; Bareng, Ontlametse T.; Ntereke, Tlhalefo D.; Ramatlho, Pleasure; Ditshwanelo, Doreen; Gaseitsiwe, Simani; Kasvosve, Ishmael; Ramogola-Masire, Doreen; Orang’o, Omenge E.; Robertson, Erle; Zetola, Nicola; Moyo, Sikhulile; Grover, Surbhi; Ermel , Aaron C.; Medicine, School of Medicine
    Background The variation of human papillomavirus (HPV) genotypes shapes the risks of cervical cancer and these variations are not well defined in Africa. Nucleotide changes within the L1 gene, nucleotide variability, and phylogeny were explored in relation to HIV in samples from Botswana and Kenya. Methods A total of 98 HPV-positive cervical samples were sequenced to identify different HPV variants. Phylogenetic inferences were used to determine HPV genotypes and investigate the clustering of sequences between women living with HIV (WLWHIV) and -women not living with HIV (WNLWHIV). Results Out of 98 generated sequences, 83.7% (82/98) participants had high-risk (HR) HPV genotypes while 16.3% (16/98) had low-risk (LR) HPV genotypes. Among participants with HR-HPV genotypes, 47.6% (39/82) were coinfected with HIV. The prevalence of HR-HPV genotypes was statistically higher in the Botswana population compared to Kenya (p-value < 0.001). Multiple amino acid mutations were identified in both countries. Genetic diversity differed considerably among WLWHIV and WNLWHIV. The mean pairwise distances between HPV-16 between HIV and HIV/HPV as well as for HPV-18 were statistically significant. Six (6) new deleterious mutations were identified in the HPV genotypes based on the sequencing of the L1 region, HPV-16 (L441P, S343P), HPV-18 (S424P), HPV-45 (Q366H, Y365F), and HPV-84 (F458L). The majority of the patients with these mutations were co-infected with HIV. Conclusions Genomic diversity and different genomic variants of HPV sequences were demonstrated. Candidate novel mutations within the L1 gene were identified in both countries which can be further investigated using functional assays.