Faculty Open Access Articles

Permanent link for this collectionhttps://hdl.handle.net/2022/30149

This collection contains articles made publicly available under the IU Bloomington Faculty Open Access Policy. The IU Libraries Scholarly Communication Department facilitates the deposit of articles into this collection.

Browse

Now showing 1 - 20 of 2952

Association of cognitive deficits with sociodemographic characteristics among adults with post-COVID conditions: Findings from the United States household pulse survey
(Oxford University Press, 2025-01-24) Liu, Nianjun
People infected with coronavirus disease-19 (COVID-19) may continue to experience symptoms for several weeks or even months after acute infection, a condition known as long COVID. Cognitive problems such as memory loss are among the most commonly reported symptoms of long COVID. However, a comprehensive evaluation of the risks of cognitive decline following COVID-19 infection among different sociodemographic groups has not been undertaken at the national level in the USA. We conducted a secondary analysis on the datasets from the U.S. Census Bureau Household Pulse Survey, encompassing data collected from 1 June 2022 to 19 December 2022. Based on a cohort of 385 370 individuals aged 18 years or older, we employed logistic regression analysis to examine the association between self-reported cognitive deficits and different sociodemographic factors among individuals with long COVID conditions. We have demonstrated that individuals with long COVID had a significantly higher risk of cognitive deficits compared to those with no history of COVID infection. Cognitive deficits vary across sociodemographic groups. In individuals without long COVID, men, older adults, and those with higher education reported fewer cognitive deficits, while Hispanics and residents of the South reported more. Long COVID had similar impacts across genders and regions but appeared to have the smallest impact on Hispanics compared to other racial groups. Conversely, the effects of long COVID were most significant in older adults and individuals with higher education. The state-level analysis further suggests potential variation in long COVID’s effects across different states. The risks of cognitive deficits among adults with post-COVID conditions are substantial. Various sociodemographic groups can have different risks of developing cognitive deficits after experiencing long COVID. The findings of this large-scale study can help identify sociodemographic groups at higher risk of cognitive deficits, facilitate medical interventions, and guide resource allocation to target populations at risk and prioritize areas with a high rate of cognitive decline.
Metabolomic Studies in Drosophila
(2017-06-29) Cox, J. E.; Thummel, C. S.; Tennessen, Jason
Metabolomic analysis provides a powerful new tool for studies of Drosophila physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in Drosophila, often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in Drosophila and highlight new directions for future research.
Conformational heterogeneity and the affinity of substrate molecular recognition by cytochrome P450cam
(2017-06-14) Basom, Edward John; Manifold, Bryce A.; Thielges, Megan Corrine
The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
Sound gradual typing: only mostly dead
(2017-10-12) Bauman, Spenser; Bolz-Tereick, Carl Friedrich; Siek, Jeremy; Tobin-Hochstadt, Sam
While gradual typing has proven itself attractive to programmers, many systems have avoided sound gradual typing due to the run time overhead of enforcement. In the context of sound gradual typing, both anecdotal and systematic evidence has suggested that run time costs are quite high, and often unacceptable, casting doubt on the viability of soundness as an approach. We show that these overheads are not fundamental, and that with appropriate improvements, just-in-time compilers can greatly reduce the overhead of sound gradual typing. Our study takes benchmarks published in a recent paper on gradual typing performance in Typed Racket (Takikawa et al., POPL 2016) and evaluates them using a experimental tracing JIT compiler for Racket, called Pycket. On typical benchmarks, Pycket is able to eliminate more than 90% of the gradual typing overhead. While our current results are not the final word in optimizing gradual typing, we show that the situation is not dire, and where more work is needed. Pycket's performance comes from several sources, which we detail and measure individually. First, we apply a sophisticated tracing JIT compiler and optimizer, automatically generated in Pycket using the RPython framework originally created for PyPy. Second, we focus our optimization efforts on the challenges posed by run time checks, implemented in Racket by chaperones and impersonators. We introduce representation improvements, including a novel use of hidden classes to optimize these data structures.
Sexual-perception processes in acquaintance-targeted sexual aggression
(2018-03-01) Treat, T. A.; Viken, Richard J
This study analyzes data from seven published studies to examine whether three performance‐based indices of men's misperception of women's sexual interest (MSI), derived from a self‐report questionnaire, are associated with sexual‐aggression history, rape‐supportive attitudes, sociosexuality, problem drinking, and self‐reported MSI. Almost 2000 undergraduate men judged the justifiability of a man's increasingly unwanted advances toward a woman on the Heterosocial Perception Survey‐Revised. Participants self‐reported any sexual‐aggression history, and some completed questionnaires assessing rape‐supportive attitudes, sociosexuality, problem drinking, and self‐reported MSI. A three‐parameter logistic function was fitted to participants’ justifiability ratings within a non‐linear mixed‐effects framework, which provided precise participant‐specific estimates of three sexual‐perception processes (baseline justifiability, bias, and sensitivity). Sexual‐aggression history and rape‐supportive attitudes predicted: (a) reduced sensitivity to women's affect; (b) more liberal biases, such that the woman's affect had to be more negative before justifiability ratings dropped substantially; and (c) greater baseline justifiability of continued advances after a positive response. Sexual‐aggression history and attitudes correlated more strongly with sensitivity than baseline justifiability; remaining variables showed the opposite pattern. This work underscores the role of sexual‐perception processes in sexual aggression and illustrates the derivation of performance‐based estimates of sexual‐perception processes from questionnaire responses.
Metabolomic Analysis Reveals That the Drosophila Gene lysine Influences Diverse Aspects of Metabolism
(2017-10-05) St. Clair, S. L.; Li, H.; Ashraf, U.; Karty, Jonathan Allen; Tennessen, Jason
The fruit fly Drosophila melanogaster has emerged as a powerful model for investigating the molecular mechanisms that regulate animal metabolism. However, a major limitation of these studies is that many metabolic assays are tedious, dedicated to analyzing a single molecule, and rely on indirect measurements. As a result, Drosophila geneticists commonly use candidate gene approaches, which, while important, bias studies toward known metabolic regulators. In an effort to expand the scope of Drosophila metabolic studies, we used the classic mutant lysine (lys) to demonstrate how a modern metabolomics approach can be used to conduct forward genetic studies. Using an inexpensive and well-established gas chromatography-mass spectrometry-based method, we genetically mapped and molecularly characterized lys by using free lysine levels as a phenotypic readout. Our efforts revealed that lys encodes the Drosophila homolog of Lysine Ketoglutarate Reductase/Saccharopine Dehydrogenase, which is required for the enzymatic degradation of lysine. Furthermore, this approach also allowed us to simultaneously survey a large swathe of intermediate metabolism, thus demonstrating that Drosophila lysine catabolism is complex and capable of influencing seemingly unrelated metabolic pathways. Overall, our study highlights how a combination of Drosophila forward genetics and metabolomics can be used for unbiased studies of animal metabolism, and demonstrates that a single enzymatic step is intricately connected to diverse aspects of metabolism.
Methods for studying the metabolic basis of Drosophila development
(2017-05-26) Li, H.; Tennessen, Jason
The field of metabolic research has experienced an unexpected renaissance. While this renewed interest in metabolism largely originated in response to the global increase in diabetes and obesity, studies of metabolic regulation now represent the frontier of many biomedical fields. This trend is especially apparent in developmental biology, where metabolism influences processes ranging from stem cell differentiation and tissue growth to sexual maturation and reproduction. In this regard, the fruit fly Drosophila melanogaster has emerged as a powerful tool for dissecting conserved mechanisms that underlie developmental metabolism, often with a level of detail that is simply not possible in other animals. Here we describe why the fly is an ideal system for exploring the relationship between metabolism and development, and outline a basic experimental strategy for conducting these studies.
Temporal associations between psychological and physical intimate partner violence: A cross-lag analysis
(2020-01-01) Cadely, Hans Saint-Eloi; Pittman, Joe F.; Pettit, Gregory S.; Lansford, Jennifer E.; Bates, John E.; Dodge, Kenneth A.; Holtzworth-Munroe, Amy
The present study examined the relationship between psychological and physical forms of intimate partner violence (IPV) across four waves of data during the developmental period of young adulthood. The links from early psychological aggression to later physical aggression and from early physical aggression to later psychological aggression across waves were tested while controlling for their cross-time stabilities and concurrent associations. IPV data were collected annually from 434 young adult respondents involved in a romantic relationship at least once during the respective years from the ages of 22-25. On average, participants provided IPV data for three out of the four years covered by the study (M = 2.82; SD = 1.14). Results of a crosslagged SEM model indicated significant cross-time stabilities as well as significant, positive concurrent associations for both forms of aggression. Most important to this study were the findings that, controlling for these stabilities and concurrent associations, early psychological aggression was a consistent positive predictor of later physical aggression across waves whereas the opposite direction from early physical aggression to later psychological aggression was either non-significant or significant and negative.
The case for studying criminal nonfatal shootings: Evidence from four Midwest cities
(2019-11-13) Hipple, Natalie Kroovand; Huebner, Beth M; Lentz, Theodore S; McGarrell, Edmund F; O'Brien, Mallory
Using law enforcement data from four Midwestern communities, we document the similarities and differences between criminal nonfatal and fatal shooting incidents, including the spatial dimensions of the events. We present a definition for a nonfatal shooting incident that guides our victim and incident characteristic comparisons. Our work suggests that law enforcement agencies should build capacity for standardized data collection surrounding gun violence to include nonfatal shootings especially for use in evaluations of gun violence prevention strategies.
Persuasive brand messages in social media: A mental imagery processing perspective
(2019-05-01) Ha, Sejin; Huang, Ran; Park, Jee-Sun
This research examines how mental imagery affects the persuasive effectiveness of a brand’s SNS (Social Networking Service) and whether transportability moderates such processing in SNS. Study 1 investigates the model with fashion retail brands’ SNS communications, and Study 2 replicates the design of Study 1 in the context of luxury hotel brands’ SNS for verification purpose. A web-based survey method in which participants evaluated their interaction with a brand’s SNS communication was used. Results show that two dimensions of mental imagery, quality and elaboration, facilitate favorable attitude toward a brand’s SNS advertising directly and indirectly via positive affect. Furthermore, the effect of transportability as a moderator was shown to be inconsistent between the studies. This research highlights key elements to assist in the design of SNS messages/content and the importance of taking users’ characteristics into account for effective brand communication in SNS.
Air Quality in Association With Rural Coal Mining and Combustion in New South Wales Australia
(2019-02-11) Hendryx, Michael Shawn; Higginbotham, Nicholas; Ewald, Benjamin; Connor, Linda H.
Purpose. Rural areas may face under-recognized threats to air quality. We tested two hypotheses that 1) rural areas in New South Wales, Australia would have better air quality than metropolitan Sydney, and that 2) the rural Upper Hunter region characterized by coal mining and coal combustion would have worse air quality than other rural areas of the state. Methods. We analyzed 2017 daily mean values for New South Wales, Australia for particulate matter (PM2.5 and PM10), sulfur dioxide (SO$_2$), nitric oxide (NO), nitrogen dioxide (NO$_2$) and NO$_x$ (sum of NO and NO$_2$). Forty-six air monitoring stations were grouped into six rural and urban regional areas. Linear regression models examined pollution levels in association with rural and urban regions and meteorological covariates. Results. Findings show that daily mean pollutant levels in the rural Upper Hunter were the highest of all regions, and were significantly higher than metropolitan Sydney, with and without control for weather conditions, for every pollutant. For example, daily mean PM2.5 was 8.64 $μ$g/m$^3$ in the rural Upper Hunter, compared to 7.23 μg/m$^3$ in metropolitan Sydney. Conclusions. Results highlight the need to consider both urban and rural sources of pollution in air quality studies, and appropriate policy steps to address likely rural air pollution from coal mining.
Air pollution exposures from multiple point sources and risk of incident chronic obstructive pulmonary disease (COPD) and asthma
(2019-12-01) Hendryx, Michael Shawn; Luo, Juhua; Chojenta, Catherine; Byles, Julie E.
Background. Exposure to environmental air pollutants exacerbates respiratory illness, but prospective studies of disease incidence are uncommon. Further, attempts to estimate effects from multiple point sources have rarely been undertaken. The current study examined risk of incident chronic obstructive pulmonary disease (COPD) and asthma in association with emissions of multiple air pollutants from point pollution sources in Australia. Methods. We analyzed prospective cohort data from the Australian Longitudinal Study on Women’s Health. Women from three age-cohorts (N=35,755) were followed for up to 21 years for incident COPD and asthma. Exposures were measured from the National Pollutant Inventory and included carbon monoxide, nitrogen oxides, sulfur dioxide, and particulate matter (PM2.5 and PM10). We identified inverse-distance weighted emissions in kilograms that women experienced over time from point sources within 10 kilometers of their residences. Cox proportional hazards regression models examined risk of self-reported doctor-diagnosed COPD and asthma in association with pollutant exposures and covariates. Results. New COPD cases numbered 3,616 (11.5%) and new asthma cases numbered 2,725 (9.4%). Participants were exposed to an average of 47 to 59 sites with air pollution emissions within 10 km of their residences. Fossil fuel electricity generation and mining made the largest contributions to air pollution but hundreds of other types of emissions also occurred. Controlling for covariates, all five air pollutants modeled individually were significantly associated with risk of COPD. Modeled jointly, only sulfur dioxide (SO2) remained significantly associated with COPD (HR=1.038, 95% CI=1.010-1.067), although the five pollutants were highly correlated (r=.89). None of the pollutants were significantly associated with adult onset asthma. Cohort-specific analyses indicated that COPD risk was significantly associated with SO2 exposure for younger (HR=1.021, CI=1.001-1.047), middle-age (HR=1.019, CI=1.004-1.034) and older cohorts (HR=1.025, CI=1.004-1.047). Conclusions. Multiple exposure sources and pollutants contributed to COPD risk, including electricity generation and mining but extending to many industrial processes. The results highlight the importance of policy efforts and technological improvements to reduce harmful air pollution emissions across the industrial landscape.
Mountaintop removal mining and multiple illness symptoms: A latent class analysis
(2019-03-20) Hendryx, Michael Shawn; Yonts, Sarah D.; Li, Yueyao; Luo, Juhua
Background: Mountaintop removal mining has been associated with multiple types of disease outcomes for populations living nearby. The current study tested whether latent classes identifying people with symptoms from multiple organ systems were associated with residence in mountaintop mining communities. Methods: We used data from three cross-sectional household community surveys conducted in three Appalachian states (N = 2756). The surveys contained information on 29 recent illness symptoms grouped into eight organ systems (respiratory, cardiovascular, gastrointestinal, musculoskeletal, skin, eye-ear-nose-throat, neurological, and other.) We identified latent classes, and then tested whether classes with higher probabilities of multiple symptoms would be associated with residence in mountaintop removal areas after control for covariates. Results: Three latent classes were identified, including a low-symptom referent class, an intermediate class, and a class with high symptom probability across organ systems. Controlling for covariates, latent classes characterized by intermediate and high multi-symptom probabilities were significantly associated with residence near mountaintop removal mining, with the highest odds ratio for the MTR versus control condition for the high multi-symptom group (OR = 2.17, 95% CI = 1.80–2.61). Conclusions: Symptoms across multiple organ systems were related to residential proximity to mountaintop removal mining. Prior research has established multiple environmental contaminants related to mining that may contribute to poor population health through more than one exposure route or chemical of concern.
Exposure to heavy metals from point pollution sources and risk of incident type 2 diabetes among women: a prospective cohort analysis
(2019-09-19) Hendryx, Michael Shawn; Luo, Juhua; Chojenta, Catherine; Byles, Julie E.
Heavy metal exposures may contribute to diabetes risk but prospective studies are uncommon. We analyzed the Australian Longitudinal Study on Women’s Health (three cohorts aged 18-23, 45-50, or 70-75 at baseline in 1996, N=34,191) merged with emissions data for 10 heavy metals (As, Be, Co, Cr, Cu, Hg, Mn, Ni, Pb, Zn) from the National Pollutant Inventory. Over 20-year follow-up, 2,584 women (7.6%) reported incident diabetes. Cox proportional hazards regression models showed that women aged 45-50 at baseline had higher diabetes risk in association with exposure to total air emissions, total water emissions, all individual metals air emissions, and six individual water emissions. After correction for false discovery rate, nine of 11 air emissions and five water emissions remained significant. Associations were not observed for land-based emissions, or for younger or older cohorts. Emissions were dominated by mining, electricity generation and other metals-related industrial processes.
Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks
(2017-02-20) Raisaro, Jean Louis; Tramer, Florian; Ji, Zhanglong; Bu, Diyue; Zhao, Yongan; Carey, Knox; Lloyd, David; Sofia, Heidi; Baker, Dixie; Flicek, Paul; Shringarpure, Suyash; Bustamante, Carlos; Wang, Shuang; Jiang, Xiaoqian; Ohno-Machado, Lucila; Tang, Haixu; Wang, XiaoFeng; Hubaux, Jean-Pierre
The Global Alliance for Genomics and Health (GA4GH) created the Beacon Project as a means of testing the willingness of data holders to share genetic data in the simplest technical context—a query for the presence of a specified nucleotide at a given position within a chromosome. Each participating site (or “beacon”) is responsible for assuring that genomic data are exposed through the Beacon service only with the permission of the individual to whom the data pertains and in accordance with the GA4GH policy and standards. While recognizing the inference risks associated with large-scale data aggregation, and the fact that some beacons contain sensitive phenotypic associations that increase privacy risk, the GA4GH adjudged the risk of re-identification based on the binary yes/no allele-presence query responses as acceptable. However, recent work demonstrated that, given a beacon with specific characteristics (including relatively small sample size and an adversary who possesses an individual’s whole genome sequence), the individual’s membership in a beacon can be inferred through repeated queries for variants present in the individual’s genome. In this paper, we propose three practical strategies for reducing re-identification risks in beacons. The first two strategies manipulate the beacon such that the presence of rare alleles is obscured; the third strategy budgets the number of accesses per user for each individual genome. Using a beacon containing data from the 1000 Genomes Project, we demonstrate that the proposed strategies can effectively reduce re-identification risk in beacon-like datasets.
Biased recommendations from biased and unbiased experts
(2018-11-28) Chung, Wonsuk; Harbaugh, Rick
When can an expert be trusted to provide useful advice? We experimentally test a simplified recommendation game where an expert recommends one of two actions to a decision maker who may take either action or instead pursue an outside option. Consistent with predictions from the cheap talk literature, we find that decision makers partially discount recommendations for the action a biased expert favors, but that recommendations can still be persuasive in that they reduce the chance of the outside option. If the decision maker is uncertain whether the expert is biased toward an action, biased experts lie even more, while unbiased experts follow a political correctness strategy of recommending the opposite action so as to be more persuasive by appearing unbiased. Even if experts are known to be unbiased, experts pander by recommending the action that the decision maker already favors, and decision makers discount the recommendation. The results highlight that transparency of expert incentives can improve communication, but need not ensure unbiased advice.
Differential dendritic remodeling in prelimbic cortex of male and female rats during recovery from chronic stress
(2017-06-09) Moench, Kelly M.; Wellman, Cara Lynn
Chronic stress produces differential dendritic remodeling of pyramidal neurons in medial prefrontal cortex of male and female rats. In males, this dendritic remodeling is reversible. However, the timeline of recovery, as well as the potential for reversibility in females, is unknown. Here, we examined dendritic recovery of pyramidal neurons in layer II–II of prelimbic cortex in male and female rats following chronic restraint stress (3 h/day for 10 days). Dendritic morphology and spine density were analyzed immediately following the cessation of stress, or following a 7 or 10 day recovery period. Chronic stress produced apical dendritic retraction in males, which was coupled with a decrease in the density of stubby spine on apical dendrites. Further, following a 10-day recovery period, the morphology of neurons from stressed rats resembled that of unstressed rats. Male rats given a 7 day recovery period had apical dendritic outgrowth compared to unstressed rats. Immediately after cessation of stress, females showed only minimal dendritic remodeling. The morphology of neurons in stressed females resembled those of unstressed rats following only 7 days of recovery, at which time there was also a significant increase in stubby spine density. Males and females also showed different changes in baseline corticosterone concentrations during recovery. These findings not only indicate that dendritic remodeling in prelimbic cortex following chronic stress is different between males and females, but also suggest chronic stress induces differential hypothalamic-pituitary-adrenal axis dysregulation in males and females. These differences may have important implications for responses to subsequent stressors.
Policy Regimes and Economic Accountability in Latin America
(2019-03-12) Carlin, Ryan E.; Hellwig, Timothy
The shifts from state-led development to neoliberalism in Latin America have prompted debates on the quality of democracy. While most discussions focus on responsiveness, we examine how economic policy regimes influence accountability. We argue that the policy regime matters for policy responsibility Citizens’ ability to hold executive to accounts strengthens where policy regimes are more statist and weakens where policy regimes are more market oriented. Time-series analyses of policy orientations, economic conditions, and presidential approval in 18 countries support this proposition, while complementary analyses at the individual-level support claims that a responsibility mechanism links policy regimes to accountability. Study findings imply that by embracing heterodox policy regimes, recent Latin American executives have improved accountability compared to the era in which the “Washington Consensus” held sway.
A Qualitative Study on the Digital Preservation of OER
(2019) Hare, Sarah Elaine; Sullivan, Madison
Libraries continue to spearhead initiatives to incentivize instructors to adopt, adapt, and create open educational resources (OER). However, these programs often do not explicitly require instructors to preserve the OER they create. Drawing on an analysis of semi-structured interviews with six experts, this article presents considerations for libraries interested in preserving OER and recommendations for OER librarians that are new to digital preservation. The study makes an argument for why and how libraries could begin to preserve OER. Future areas of investigation include better understanding how OER repositories preserve OER and consortia models to support this work.
New and Recurrent Concussions in High-School Athletes Before and After Traumatic Brain Injury Laws, 2005-2016
(2017-11-8) Yang, J.; Comstock, R. D.; Yi, H.; Harvey, H. H.; Xun, Pengcheng
Objectives. To examine the trends of new and recurrent sports-related concussions in high-school athletes before and after youth sports traumatic brain injury laws. Methods. We used an interrupted time-series design and analyzed the concussion data (2005–2016) from High School Reporting Injury Online. We examined the trends of new or recurrent concussion rates among US representative high-school athletes partici- pating in 9 sports across prelaw, immediate-postlaw, and postlaw periods by using general linear models. We defined 1 athlete exposure as attending 1 competition or practice. Results. We included a total of 8043 reported concussions (88.7% new, 11.3% re- current). The average annual concussion rate was 39.8 per 100 000 athlete exposures. We observed significantly increased trends of reported new and recurrent concussions from the prelaw, through immediate-postlaw, into the postlaw period. However, the recurrent concussion rate showed a significant decline 2.6 years after the laws went into effect. Football exhibited different trends compared with other boys’ sports and girls’ sports. Conclusions. Observed trends of increased concussion rates are likely attributable to increased identification and reporting. Additional research is needed to evaluate intended long-term impact of traumatic brain injury laws.

Browse

Recent Submissions