Open Access Publishing Fund

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https://hdl.handle.net/1805/6519

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.
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.
Impact of an Online Question Bank on Resident In-Training Exam Performance
(Sage, 2023-10-09) Scott, Nicole P.; Martin, Terrell W.; Schmidt, Alison M.; Shanks, Anthony L.; Obstetrics and Gynecology, School of Medicine
OBJECTIVE In-training exams (ITEs) are administered annually to Obstetrics and Gynecology (OBGYN) residents and have been demonstrated to correlate with success on licensing examinations. Our study objective was to determine the impact of a question bank and mock exam on the performance of Council on Resident Education in Obstetrics and Gynecology (CREOG) ITEs. Secondarily, we investigated the correlation between the extent of question bank usage and performance on the exam. METHODS Pre–post intervention study of resident performance on CREOG ITE before and after implementation of the question bank and mock ITE at Indiana University in 2018. Performance was measured as year-to-year improvement in percent correct on ITE exams. Scores were excluded if a resident did not have a prequestion bank score report or if they did not sit for all eligible ITE exams. RESULTS There were 51 OBGYN residents at Indiana University during the study period, with 38 available for analysis (75%). Before implementation, average year-to-year improvement for PGY1-2, PGY2-3 and PGY3-4 classes were 0.60%, 1.0% and −1.6%, respectively. After implementation, all resident classes had significant improvements in ITE scores of 6.6% (P < .01), 9.0% (P < .01), and 7.2% (P < .01), respectively. There was a moderate program-wide correlation between the number of questions completed and the percent improvement on the ITE of R = 0.36 (P = .046). CONCLUSIONS Our study demonstrated that access to a question bank and mock ITE significantly improved CREOG ITE performance of OBGYN residents at Indiana University.
A Perceptual Evaluation of Music Real-Time Communication Applications
(IEEE, 2023-04-28) Goot, Dana Kemack; Chaubey, Harshit; Hsu, Timothy Y.; Deal , William Scott; Music and Arts Technology, School of Engineering and Technology
Music Real-time Communication applications (M-RTC) enable music making (musiking) for musicians simultaneously across geographic distance. When used for musiking, M-RTC such as Zoom and JackTrip, require satisfactorily received acoustical perception of the transmitted music to the end user; however, degradation of audio can be a deterrent to using M-RTC for the musician. Specific to the audio quality of M-RTC, we evaluate the quality of the audio, or the Quality of Experience (QoE), of five network music conferencing applications through quantitative perceptual analysis to determine if the results are commensurate with data analysis. The ITU-R BS.1534-3 MUlti Stimulus test with Hidden Reference and Anchor (MUSHRA) analysis is used to evaluate the perceived audio quality of the transmitted audio files in our study and to detect differences between the transmitted audio files and the hidden reference file. A comparison of the signal-to-noise ratio (SNR) and total harmonic distortion (THD) analysis to the MUSHRA analysis shows that the objective metrics may indicate that SNR and THD are factors in perceptual evaluation and may play a role in perceived audio quality; however, the SNR and THD scores do not directly correspond to the MUSHRA analysis and do not adequately represent the preferences of the individual listener. Since the benefits of improved M-RTC continue to be face-to-face communication, face-to-face musiking, reduction in travel costs, and depletion of travel time, further testing with statistical analysis of a larger sample size can provide the additional statistical power necessary to make conclusions to that end.
Predictive Energy Management of Mild-Hybrid Truck Platoon Using Agent-Based Multi-Objective Optimization
(IEEE, 2023-07-11) Pramanik, Sourav; Anwar, Sohel; Mechanical and Energy Engineering, School of Engineering and Technology
The objective of this paper is to formulate and analyze the benefits of a predictive non-linear multi objective optimization method for a platoon of mild-hybrid line haul trucks. In this study a group of three trucks with hybrid electric powertrain are considered in a platoon formation where each truck has a predictive optimal control to save fuel with out any loss of trip time. While the controller on each truck uses the look ahead knowledge of the entire route in terms of road grade, the overall platoon controller used a multi agent method (Metropolis algorithm) to define coordination between the trucks. While the individual trucks, showed significant improvement in fuel economy when running on predictive mode, the true savings came from the entire platoon and showed promising results in terms of absolute fuel economy without trading off on total trip time. The proposed algorithm also proved to be significantly emission efficient. A platoon of 3 trucks achieved an average of 10% fuel savings while cutting back 13% on engine out NOx emissions for engine off coasting and 9.3% fuel saving with 8% emissions reduction for engine idle coast configuration when compared to non-predictive non-platoon configuration.

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