Open Access Publishing Fund

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The IUPUI Open Access Fund underwrites reasonable publication charges for articles published in fee-based, peer-reviewed journals that are openly accessible. This fund addresses changes in scholarly communications while increasing the impact of and access to scholarship created by IUPUI faculty. Learn more at: https://library.indianapolis.iu.edu/digitalscholarship/oa/fund-oa

Annual reports on the progress of the fund are available from: https://scholarworks.indianapolis.iu.edu/handle/1805/11935

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Now showing 1 - 10 of 294

Finding your lane: experiences and beyond for adults learning to swim
(Springer Nature, 2023) Wilson, Shawn; Miller, Alison Moira; Casson, Destiny; Ramos, William D.; Pediatrics, School of Medicine
The purpose of this study was to examine experiences and impacts from participating in an adult swim instruction program. We conducted 20 semi-structured interviews with adults aged 18 + who had participated in an adult learn to swim program. Participants were interviewed through a virtual platform using a semi-structured protocol. Data were coded individually by each member of the research team for emerging thematic outcomes with final consensus among all those involved in the analysis. Participants expressed adult learn to swim programs had an effect in three areas: (a) life affordance, (b) emotional affect, and (c) interpersonal relationships. Public health experts and aquatics leaders should consider targeting programs aimed at teaching adults to learn how to swim, especially to marginalized individuals and those who did not grow up in the United States. The authors highlight how these programs can create life affordances well beyond lap swimming and even water safety.
The AIMS approach: Regulating receptivity in patient-provider vaccine conversations
(Frontiers, 2023-06-01) Parrish-Sprowl, John; Thomson, Angus; Johnson, Rodger D.; Parrish-Sprowl, Susan; Communication Studies, School of Liberal Arts
The World Health Organization named vaccine hesitancy a leading global health threat of modern time. Addressing this public health issue requires a multi-front strategy, one such strategic effort is training health care professionals to respond to reluctant patients/caregivers or those who refuse vaccines. AIMS (Announce, Inquire, Mirror, and Secure) is designed to help HCPs engaged in more productive conversations with patients/caregivers to secure trust, a key behavior leading to higher vaccination rates.
Transcriptomic analyses of ovarian clear-cell carcinoma with concurrent endometriosis
(Frontiers, 2023-08-08) Collins, Kaitlyn E.; Wang, Xiyin; Klymenko, Yuliya; Davis, Noah B.; Martinez, Maria C.; Zhang, Chi; So, Kaman; Buechlein, Aaron; Rusch, Douglas B.; Creighton, Chad J.; Hawkins, Shannon M.; Obstetrics and Gynecology, School of Medicine
Introduction: Endometriosis, a benign inflammatory disease whereby endometrial-like tissue grows outside the uterus, is a risk factor for endometriosis-associated ovarian cancers. In particular, ovarian endometriomas, cystic lesions of deeply invasive endometriosis, are considered the precursor lesion for ovarian clear-cell carcinoma (OCCC). Methods: To explore this transcriptomic landscape, OCCC from women with pathology-proven concurrent endometriosis (n = 4) were compared to benign endometriomas (n = 4) by bulk RNA and small-RNA sequencing. Results: Analysis of protein-coding genes identified 2449 upregulated and 3131 downregulated protein-coding genes (DESeq2, P< 0.05, log2 fold-change > |1|) in OCCC with concurrent endometriosis compared to endometriomas. Gene set enrichment analysis showed upregulation of pathways involved in cell cycle regulation and DNA replication and downregulation of pathways involved in cytokine receptor signaling and matrisome. Comparison of pathway activation scores between the clinical samples and publicly-available datasets for OCCC cell lines revealed significant molecular similarities between OCCC with concurrent endometriosis and OVTOKO, OVISE, RMG1, OVMANA, TOV21G, IGROV1, and JHOC5 cell lines. Analysis of miRNAs revealed 64 upregulated and 61 downregulated mature miRNA molecules (DESeq2, P< 0.05, log2 fold-change > |1|). MiR-10a-5p represented over 21% of the miRNA molecules in OCCC with endometriosis and was significantly upregulated (NGS: log2fold change = 4.37, P = 2.43e-18; QPCR: 8.1-fold change, P< 0.05). Correlation between miR-10a expression level in OCCC cell lines and IC50 (50% inhibitory concentration) of carboplatin in vitro revealed a positive correlation (R2 = 0.93). MiR-10a overexpression in vitro resulted in a significant decrease in proliferation (n = 6; P< 0.05) compared to transfection with a non-targeting control miRNA. Similarly, the cell-cycle analysis revealed a significant shift in cells from S and G2 to G1 (n = 6; P< 0.0001). Bioinformatic analysis predicted that miR-10a-5p target genes that were downregulated in OCCC with endometriosis were involved in receptor signaling pathways, proliferation, and cell cycle progression. MiR-10a overexpression in vitro was correlated with decreased expression of predicted miR-10a target genes critical for proliferation, cell-cycle regulation, and cell survival including [SERPINE1 (3-fold downregulated; P< 0.05), CDK6 (2.4-fold downregulated; P< 0.05), and RAP2A (2-3-fold downregulated; P< 0.05)]. Discussion: These studies in OCCC suggest that miR-10a-5p is an impactful, potentially oncogenic molecule, which warrants further studies.
Determinants of undernutrition and overnutrition among reproductive-age women in Bangladesh: Trend analysis using spatial modeling
(PLOS, 2023-07-18) Vatsa, Richa; Ghimire, Umesh; Yasmin, Khaleda; Hasan, Farhana Jesmine; Health Policy and Management, School of Public Health
Background Bangladesh is facing a dual burden of malnutrition, with high rates of undernutrition and increasing rates of overnutrition. The complex scenario of malnutrition in Bangladesh varies across different regions, making it a challenging public health concern to address. Objectives This study analyzes the spatial and temporal dependence of underweight and overweight Bangladeshi women of reproductive age. Methods Nationally representative cross-sectional data from the Bangladesh Demographic and Health Surveys in 2014 and 2017–18 were utilized to study the changes in weight status in 15–49-year-old women who were either underweight or overweight. A Bayesian geo-additive regression model was used to account for non-linear and linear effects of continuous and categorical covariates and to incorporate spatial effects of geographical divisions. Results The prevalence of overweight or obese women in rural, city corporations, and other urban areas increased significantly over the four years from 2014 to 2017–18. Women in the categories ‘richer’ and ‘richest’ were more likely to be overweight or obese. Women from Sylhet were more likely to be underweight in both survey years; however, the spatial effects were significant for underweight women in Mymensingh for the year 2017–18. Women in Rajshahi and Khulna were more likely to be overweight or obese in 2014, and women from Barishal and Chittagong were more likely to be overweight in the year 2017–18. Conclusions Underweight and overweight statuses in women vary unevenly across Bangladesh, with a substantially higher prevalence of overweight or obese women in more urbanized areas. The growing burden of overweight and obesity among Bangladeshi women should be addressed with interventions aimed at those in the reproductive age group.
Relationship between klotho and physical function in healthy aging
(Springer, 2023-11-30) Arroyo, Eliott; Leber, Cecilia A.; Burney, Heather N.; Narayanan, Gayatri; Moorthi, Ranjani; Avin, Keith G.; Warden , Stuart J.; Moe, Sharon M.; Lim, Kenneth; Medicine, School of Medicine
Epidemiological studies have reported a strong association between circulating Klotho and physical function; however, the cohorts were comprised of older adults with multiple comorbidities. Herein, we examined the relationship between Klotho and physical function in a community-based cohort of healthy adults. In this cross-sectional study, serum Klotho was measured in 80 adults who visited the Musculoskeletal Function, Imaging, and Tissue Resource Core of the Indiana Center for Musculoskeletal Health. Participants (n = 20, 10 [50%] men per group) were chosen into four age groups: 20–34, 35–49, 50–64, and ≥ 65 years, and were further grouped based on performance (low vs. high) on grip strength and chair stand tests. Klotho levels were lower in the ≥ 65 years group (703.0 [189.3] pg/mL; p = 0.022) and the 50–64 years group (722.6 [190.5] pg/mL; p = 0.045) compared to 20–34 years (916.1 [284.8] pg/mL). No differences were observed in Klotho between the low and high performers. The ≥ 65 years group walked a shorter distance during the 6-min walk test (6MWT) compared to 20–34 years (p = 0.005). Klotho was correlated with age (p < 0.001), body fat (p = 0.037), and 6MWT distance (p = 0.022). Klotho levels decline as early as the fifth decade of life, potentially before the onset of age-related impairment in exercise capacity.
Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria
(Springer, 2023-10-13) Mandal, Rabindra K.; Mandal, Anita; Denny, Joshua E.; Namazii, Ruth; John, Chandy C.; Schmidt, Nathan W.; Pediatrics, School of Medicine
Malaria is caused by Plasmodium species and remains a significant cause of morbidity and mortality globally. Gut bacteria can influence the severity of malaria, but the contribution of specific bacteria to the risk of severe malaria is unknown. Here, multiomics approaches demonstrate that specific species of Bacteroides are causally linked to the risk of severe malaria. Plasmodium yoelii hyperparasitemia-resistant mice gavaged with murine-isolated Bacteroides fragilis develop P. yoelii hyperparasitemia. Moreover, Bacteroides are significantly more abundant in Ugandan children with severe malarial anemia than with asymptomatic P. falciparum infection. Human isolates of Bacteroides caccae, Bacteroides uniformis, and Bacteroides ovatus were able to cause susceptibility to severe malaria in mice. While monocolonization of germ-free mice with Bacteroides alone is insufficient to cause susceptibility to hyperparasitemia, meta-analysis across multiple studies support a main role for Bacteroides in susceptibility to severe malaria. Approaches that target gut Bacteroides present an opportunity to prevent severe malaria and associated deaths.
Atlas of Plasmodium falciparum intraerythrocytic development using expansion microscopy
(eLife Sciences, 2023-12-18) Liffner, Benjamin; Cepeda Diaz, Ana Karla; Blauwkamp, James; Anaguano, David; Frolich, Sonja; Muralidharan, Vasant; Wilson, Danny W.; Dvorin, Jeffrey D.; Absalon, Sabrina; Pharmacology and Toxicology, School of Medicine
Apicomplexan parasites exhibit tremendous diversity in much of their fundamental cell biology, but study of these organisms using light microscopy is often hindered by their small size. Ultrastructural expansion microscopy (U-ExM) is a microscopy preparation method that physically expands the sample by ~4.5×. Here, we apply U-ExM to the human malaria parasite Plasmodium falciparum during the asexual blood stage of its lifecycle to understand how this parasite is organized in three dimensions. Using a combination of dye-conjugated reagents and immunostaining, we have cataloged 13 different P. falciparum structures or organelles across the intraerythrocytic development of this parasite and made multiple observations about fundamental parasite cell biology. We describe that the outer centriolar plaque and its associated proteins anchor the nucleus to the parasite plasma membrane during mitosis. Furthermore, the rhoptries, Golgi, basal complex, and inner membrane complex, which form around this anchoring site while nuclei are still dividing, are concurrently segregated and maintain an association to the outer centriolar plaque until the start of segmentation. We also show that the mitochondrion and apicoplast undergo sequential fission events while maintaining an association with the outer centriolar plaque during cytokinesis. Collectively, this study represents the most detailed ultrastructural analysis of P. falciparum during its intraerythrocytic development to date and sheds light on multiple poorly understood aspects of its organelle biogenesis and fundamental cell biology.
Using transfer learning-based causality extraction to mine latent factors for Sjögren’s syndrome from biomedical literature
(Cell Press, 2023-09) VanSchaik, Jack T.; Jain, Palak; Rajapuri, Anushri; Cheriyan, Biju; Thyvalikakath, Thankam P.; Chakraborty, Sunandan; Human-Centered Computing, School of Informatics and Computing
Understanding causality is a longstanding goal across many different domains. Different articles, such as those published in medical journals, disseminate newly discovered knowledge that is often causal. In this paper, we use this intuition to build a model that leverages causal relations to unearth factors related to Sjögren's syndrome from biomedical literature. Sjögren's syndrome is an autoimmune disease affecting up to 3.1 million Americans. Due to the uncommon nature of the illness, symptoms across different specialties coupled with common symptoms of other autoimmune conditions such as rheumatoid arthritis, it is difficult for clinicians to diagnose the disease timely. Due to the lack of a dedicated dataset for causal relationships built from biomedical literature, we propose a transfer learning-based approach, where the relationship extraction model is trained on a wide variety of datasets. We conduct an empirical analysis of numerous neural network architectures and data transfer strategies for causal relation extraction. By conducting experiments with various contextual embedding layers and architectural components, we show that an ELECTRA-based sentence-level relation extraction model generalizes better than other architectures across varying web-based sources and annotation strategies. We use this empirical observation to create a pipeline for identifying causal sentences from literature text, extracting the causal relationships from causal sentences, and building a causal network consisting of latent factors related to Sjögren's syndrome. We show that our approach can retrieve such factors with high precision and recall values. Comparative experiments show that this approach leads to 25% improvement in retrieval F1-score compared to several state-of-the-art biomedical models, including BioBERT and Gram-CNN. We apply this model to a corpus of research articles related to Sjögren's syndrome collected from PubMed to create a causal network for Sjögren's syndrome. The proposed causal network for Sjögren's syndrome will potentially help clinicians with a holistic knowledge base for faster diagnosis.
Comparing gingivitis diagnoses by bleeding on probing (BOP) exclusively versus BOP combined with visual signs using large electronic dental records
(Springer, 2023-10-10) Patel, Jay S.; Shin, Daniel; Willis, Lisa; Zai, Ahad; Kumar, Krishna; Thyvalikakath, Thankam P.; Cariology, Operative Dentistry and Dental Public Health, School of Dentistry
The major significance of the 2018 gingivitis classification criteria is utilizing a simple, objective, and reliable clinical sign, bleeding on probing score (BOP%), to diagnose gingivitis. However, studies report variations in gingivitis diagnoses with the potential to under- or over-estimating disease occurrence. This study determined the agreement between gingivitis diagnoses generated using the 2018 criteria (BOP%) versus diagnoses using BOP% and other gingival visual assessments. We conducted a retrospective study of 28,908 patients' electronic dental records (EDR) from January-2009 to December-2014, at the Indiana University School of Dentistry. Computational and natural language processing (NLP) approaches were developed to diagnose gingivitis cases from BOP% and retrieve diagnoses from clinical notes. Subsequently, we determined the agreement between BOP%-generated diagnoses and clinician-recorded diagnoses. A thirty-four percent agreement was present between BOP%-generated diagnoses and clinician-recorded diagnoses for disease status (no gingivitis/gingivitis) and a 9% agreement for the disease extent (localized/generalized gingivitis). The computational program and NLP performed excellently with 99.5% and 98% f-1 measures, respectively. Sixty-six percent of patients diagnosed with gingivitis were reclassified as having healthy gingiva based on the 2018 diagnostic classification. The results indicate potential challenges with clinicians adopting the new diagnostic criterion as they transition to using the BOP% alone and not considering the visual signs of inflammation. Periodic training and calibration could facilitate clinicians' and researchers' adoption of the 2018 diagnostic system. The informatics approaches developed could be utilized to automate diagnostic findings from EDR charting and clinical notes.
Comparing exercise determinants between Black and White older adults with heart failure
(Springer, 2023-09-30) Kaushal, Navin; Nemati, Donya; Mann-Krzisnik, Dylan; de la Colina , Adrián Noriega; Health Sciences, School of Health and Human Sciences
Background Heart Failure is a leading cause of mortality among older adults. Engaging in regular exercise at moderate-to-vigorous intensity has been shown to improve survival rates. Theory-informed methodologies have been recommended to promote exercise, but limited application of theoretical framework has been conducted for understanding racial disparities among older adults with heart failure. This study aimed to use the Health Belief Model to compare exercise behavior determinants between Black and White older adults diagnosed with heart failure. Methods The HF-ACTION Trial is a multi-site study designed to promote exercise among individuals with heart failure that randomized participants to an experimental (three months of group exercise sessions followed by home-based training) or control arm. The present study used structural equation modeling to test the change in Health Belief Model constructs and exercise behavior across 12 months among older adults. Results Participants (n = 671) were older adults, 72.28 (SD = 5.41) years old, (Black: n = 230; White, n = 441) diagnosed with heart failure and reduced ejection fraction. The model found perceived benefits, self-efficacy, perceived threats, and perceived barriers to predict exercise behavior among Black and White older adults. However, among these constructs, only perceived benefits and self-efficacy were facilitated via intervention for both races. Additionally, the intervention was effective for addressing perceived barriers to exercise only among White participants. Finally, the intervention did not result in a change of perceived threats for both races. Conclusions Among health belief model constructs, perceived threats and barriers were not facilitated for both races in the experimental arm, and the intervention did not resolve barriers among Black older adults. Racial differences need to be considered when designing interventions for clinical populations as future studies are warranted to address barriers to exercise among Black older adults with heart failure.

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