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 24682
  • Item
    A neurotechnological aid for semi-autonomous suction in robotic-assisted surgery
    (Springer, 2022-03-16) Barragan, Juan Antonio; Yang, Jing; Yu, Denny; Wachs, Juan P.; Surgery, School of Medicine
    Adoption of robotic-assisted surgery has steadily increased as it improves the surgeon’s dexterity and visualization. Despite these advantages, the success of a robotic procedure is highly dependent on the availability of a proficient surgical assistant that can collaborate with the surgeon. With the introduction of novel medical devices, the surgeon has taken over some of the surgical assistant’s tasks to increase their independence. This, however, has also resulted in surgeons experiencing higher levels of cognitive demands that can lead to reduced performance. In this work, we proposed a neurotechnology-based semi-autonomous assistant to release the main surgeon of the additional cognitive demands of a critical support task: blood suction. To create a more synergistic collaboration between the surgeon and the robotic assistant, a real-time cognitive workload assessment system based on EEG signals and eye-tracking was introduced. A computational experiment demonstrates that cognitive workload can be effectively detected with an 80% accuracy. Then, we show how the surgical performance can be improved by using the neurotechnological autonomous assistant as a close feedback loop to prevent states of high cognitive demands. Our findings highlight the potential of utilizing real-time cognitive workload assessments to improve the collaboration between an autonomous algorithm and the surgeon.
  • Item
    Race, Ethnicity, and Other Cultural Background Factors in Trials of Internet-Based Cognitive Behavioral Therapy for Depression: Systematic Review
    (JMIR, 2024-02-01) De Jesús-Romero, Robinson; Holder-Dixon, Amani R.; Buss, John F.; Lorenzo-Luaces, Lorenzo; Psychiatry, School of Medicine
    Background: There is a growing interest in developing scalable interventions, including internet-based cognitive behavioral therapy (iCBT), to meet the increasing demand for mental health services. Given the growth in diversity worldwide, it is essential that the clinical trials of iCBT for depression include diverse samples or, at least, report information on the race, ethnicity, or other background indicators of their samples. Unfortunately, the field lacks data on how well diversity is currently reported and represented in the iCBT literature. Objective: Thus, the main objective of this systematic review was to examine the overall reporting of racial and ethnic identities in published clinical trials of iCBT for depression. We also aimed to review the representation of specific racial and ethnic minoritized groups and the inclusion of alternative background indicators such as migration status or country of residence. Methods: Studies were included if they were randomized controlled trials in which iCBT was compared to a waiting list, care-as-usual, active control, or another iCBT. The included papers also had to have a focus on acute treatment (eg, 4 weeks to 6 months) of depression, be delivered via the internet on a website or a smartphone app and use guided or unguided self-help. Studies were initially identified from the METAPSY database (n=59) and then extended to include papers up to 2022, with papers retrieved from Embase, PubMed, PsycINFO, and Cochrane (n=3). Risk of bias assessment suggested that reported studies had at least some risk of bias due to use of self-report outcome measures. Results: A total of 62 iCBT randomized controlled trials representing 17,210 participants are summarized in this study. Out of those 62 papers, only 17 (27%) of the trials reported race, and only 12 (19%) reported ethnicity. Reporting outside of the United States was very poor, with the United States accounting for 15 (88%) out of 17 of studies that reported race and 9 (75%) out of 12 for ethnicity. Out of 3,623 participants whose race was reported in the systematic review, the racial category reported the most was White (n=2716, 74.9%), followed by Asian (n=209, 5.8%) and Black (n=274, 7.6%). Furthermore, only 25 (54%) out of the 46 papers conducted outside of the United States reported other background demographics. Conclusions: It is important to note that the underreporting observed in this study does not necessarily indicate an underrepresentation in the actual study population. However, these findings highlight the poor reporting of race and ethnicity in iCBT trials for depression found in the literature. This lack of diversity reporting may have significant implications for the scalability of these interventions.
  • Item
    Corrigendum: Iatrogenic air embolism: pathoanatomy, thromboinflammation, endotheliopathy, and therapies
    (Frontiers Media, 2024-02-06) Marsh, Phillip L.; Moore, Ernest E.; Moore, Hunter B.; Bunch, Connor M.; Aboukhaled, Michael; Condon, Shaun M., II; Al-Fadhl, Mahmoud D.; Thomas, Samuel J.; Larson, John R.; Bower, Charles W.; Miller, Craig B.; Pearson, Michelle L.; Twilling, Christopher L.; Reser, David W.; Kim, George S.; Troyer, Brittany M.; Yeager, Doyle; Thomas, Scott G.; Srikureja, Daniel P.; Patel, Shivani S.; Añón, Sofía L.; Thomas, Anthony V.; Miller, Joseph B.; Van Ryn, David E.; Pamulapati, Saagar V.; Zimmerman, Devin; Wells, Byars; Martin, Peter L.; Seder, Christopher W.; Aversa, John G.; Greene, Ryan B.; March, Robert J.; Kwaan, Hau C.; Fulkerson, Daniel H.; Vande Lune, Stefani A.; Mollnes, Tom E.; Nielsen, Erik W.; Storm, Benjamin S.; Walsh, Mark M.; Medicine, School of Medicine
    [This corrects the article DOI: 10.3389/fimmu.2023.1230049.].
  • Item
    Clinical, immunological features, treatments, and outcomes of autoimmune hemolytic anemia in patients with RAG deficiency
    (American Society of Hematology, 2024) Wang, Chen; Sun, Bijun; Wu, Kevin; Farmer, Jocelyn R.; Ujhazi, Boglarka; Geier, Christoph B.; Gordon, Sumai; Westermann-Clark, Emma; Savic, Sinisa; Secord, Elizabeth; Sargur, Ravishankar; Chen, Karin; Jin, Jay J.; Dutmer, Cullen M.; Kanariou, Maria G.; Adeli, Mehdi; Palma, Paolo; Bonfim, Carmem; Lycopoulou, Evangelia; Wolska-Kusnierz, Beata; Dbaibo, Ghassan; Bleesing, Jack; Moshous, Despina; Neven, Benedicte; Schuetz, Catharina; Geha, Raif S.; Notarangelo, Luigi D.; Miano, Maurizio; Buchbinder, David K.; Csomos, Krisztian; Wang, Wenjie; Wang, Ji-Yang; Wang, Xiaochuan; Walter, Jolan E.; Pediatrics, School of Medicine
  • Item
    Neurocognition after motor vehicle collision and adverse post-traumatic neuropsychiatric sequelae within 8 weeks: Initial findings from the AURORA study
    (Elsevier, 2022) Germine, Laura T.; Joormann, Jutta; Passell, Eliza; Rutter, Lauren A.; Scheuer, Luke; Martini, Paolo; Hwang, Irving; Lee, Sue; Sampson, Nancy; Barch, Deanna M.; House, Stacey L.; Beaudoin, Francesca L.; An, Xinming; Stevens, Jennifer S.; Zeng, Donglin; Linnstaedt, Sarah D.; Jovanovic, Tanja; Clifford, Gari D.; Neylan, Thomas C.; Rauch, Scott L.; Lewandowski, Christopher; Hendry, Phyllis L.; Sheikh, Sophia; Storrow, Alan B.; Musey, Paul I.; Jones, Christopher W.; Punches, Brittney E.; McGrath, Meghan E.; Pascual, Jose L.; Mohiuddin, Kamran; Pearson, Claire; Peak, David A.; Domeier, Robert M.; Bruce, Steven E.; Rathlev, Niels K.; Sanchez, Leon D.; Pietrzak, Robert H.; Pizzagalli, Diego A.; Harte, Steven E.; Elliott, James M.; Koenen, Karesten C.; Ressler, Kerry J.; McLean, Samuel A.; Kessler, Ronald C.; Emergency Medicine, School of Medicine
    Background: Previous work has indicated that differences in neurocognitive functioning may predict the development of adverse post-traumatic neuropsychiatric sequelae (APNS). Such differences may be vulnerability factors or simply correlates of APNS-related symptoms. Longitudinal studies that measure neurocognitive functioning at the time of trauma are needed to determine whether such differences precede the development of APNS. Methods: Here, we present findings from a subsample of 666 ambulatory patients from the AURORA (Advancing Understanding of RecOvery afteR trumA) study. All patients presented to EDs after a motor vehicle collision (MVC). We examined associations of neurocognitive test performance shortly after MVC with peritraumatic symptoms in the ED and APNS (depression, post-traumatic stress, post-concussive symptoms, and pain) 2 weeks and 8 weeks later. Neurocognitive tests assessed processing speed, attention, verbal reasoning, memory, and social perception. Results: Distress in the ED was associated with poorer processing speed and short-term memory. Poorer short-term memory was also associated with depression at 2 weeks post-MVC, even after controlling for peritraumatic distress. Finally, higher vocabulary scores were associated with pain 2 weeks post-MVC. Limitations: Self-selection biases among those who present to the ED and enroll in the study limit generalizability. Also, it is not clear whether observed neurocognitive differences predate MVC exposure or arise in the immediate aftermath of MVC exposure. Conclusions: Our results suggest that processing speed and short-term memory may be useful predictors of trauma-related characteristics and the development of some APNS, making such measures clinically-relevant for identifying at-risk individuals.
  • Item
    Individual bioenergetic capacity as a potential source of resilience to Alzheimer's disease
    (medRxiv, 2024-01-24) Arnold, Matthias; Buyukozkan, Mustafa; Doraiswamy, P. Murali; Nho, Kwangsik; Wu, Tong; Gudnason, Vilmundur; Launer, Lenore J.; Wang-Sattler, Rui; Adamski, Jerzy; The Alzheimer’s Disease Neuroimaging Initiative; Alzheimer’s Disease Metabolomics Consortium; De Jager, Philip L.; Ertekin-Taner, Nilüfer; Bennett, David A.; Saykin, Andrew J.; Peters, Annette; Suhre, Karsten; Kaddurah-Daouk, Rima; Kastenmüller, Gabi; Krumsiek, Jan; Radiology and Imaging Sciences, School of Medicine
    Impaired glucose uptake in the brain is one of the earliest presymptomatic manifestations of Alzheimer's disease (AD). The absence of symptoms for extended periods of time suggests that compensatory metabolic mechanisms can provide resilience. Here, we introduce the concept of a systemic 'bioenergetic capacity' as the innate ability to maintain energy homeostasis under pathological conditions, potentially serving as such a compensatory mechanism. We argue that fasting blood acylcarnitine profiles provide an approximate peripheral measure for this capacity that mirrors bioenergetic dysregulation in the brain. Using unsupervised subgroup identification, we show that fasting serum acylcarnitine profiles of participants from the AD Neuroimaging Initiative yields bioenergetically distinct subgroups with significant differences in AD biomarker profiles and cognitive function. To assess the potential clinical relevance of this finding, we examined factors that may offer diagnostic and therapeutic opportunities. First, we identified a genotype affecting the bioenergetic capacity which was linked to succinylcarnitine metabolism and significantly modulated the rate of future cognitive decline. Second, a potentially modifiable influence of beta-oxidation efficiency seemed to decelerate bioenergetic aging and disease progression. Our findings, which are supported by data from more than 9,000 individuals, suggest that interventions tailored to enhance energetic health and to slow bioenergetic aging could mitigate the risk of symptomatic AD, especially in individuals with specific mitochondrial genotypes.
  • Item
    Obstacles and Opportunities in Managing Coexisting Obesity and CKD: Report of a Scientific Workshop Cosponsored by the National Kidney Foundation and The Obesity Society
    (Wiley, 2022-12) Friedman, Allon N.; Schauer, Philip R.; Beddhu, Srinivasan; Kramer, Holly; le Roux, Carel W.; Purnell, Jonathan Q.; Sunwold, Duane; Tuttle, Katherine R.; Jastreboff, Ania M.; Kaplan, Lee M.; Medicine, School of Medicine
    The National Kidney Foundation (NKF) and The Obesity Society (TOS) cosponsored a multispecialty international workshop in April 2021 to advance the understanding and management of obesity in adults with chronic kidney disease (CKD). The underlying rationale for the workshop was the accumulating evidence that obesity is a major contributor to CKD and adverse outcomes in individuals with CKD, and that effective treatment of obesity, including lifestyle intervention, weight loss medications, and metabolic surgery, can have beneficial effects. The attendees included a range of experts in the areas of kidney disease, obesity medicine, endocrinology, diabetes, bariatric/metabolic surgery, endoscopy, transplant surgery, and nutrition, as well as patients with obesity and CKD. The group identified strategies to increase patient and provider engagement in obesity management, outlined a collaborative action plan to engage nephrologists and obesity medicine experts in obesity management, and identified research opportunities to address gaps in knowledge about the interaction between obesity and kidney disease. The workshop's conclusions help lay the groundwork for development of an effective, scientifically based, and multidisciplinary approach to the management of obesity in people with CKD.
  • Item
    Impact of the COVID-19 pandemic on social media utilization, influences related to parental vaccine decision making, and opinions on trustworthy social media vaccination campaigns: A qualitative analysis
    (Taylor & Francis, 2024) Fontenot, Holly B.; Quist, Kevin M.; Glauberman, Gary; Michel, Alexandra; Zimet, Gregory; Pediatrics, School of Medicine
    There is a continued need for research to better understand the influence social media has on parental vaccination attitudes and behaviors, especially research capturing the effects of the COVID-19 pandemic. The goal of this study was to explore parents' perspectives related to the impact the pandemic had on 1) social media engagement, 2) vaccine messaging on social media, and 3) factors to guide future intervention development. Between February and March 2022, 6 online, synchronous, text-based focus groups were conducted with parents of adolescents aged 11 to 17 years. Participants who all utilized social media were recruited from across the United States. Qualitative data were analyzed using content analysis. A total of 64 parents participated. Average age was 47 years, and participants were predominantly White (71.9%), female (84.3%), and engaged with social media multiple times per day (51.6%). Participants (95.3%) viewed obtaining all recommended vaccines as important or very important; however, overall vaccination rates for their adolescents were varied (50% ≥1 dose HPV; 59.4% MenACWY; 78.1% Tdap; 65.6% Flu; 81.3% COVID-19). Three themes emerged highlighting the pandemic's impact on parent's (1) general patterns of social media use, (2) engagement about vaccines on social media and off-line behaviors related to vaccination, and (3) perspectives for developing a credible and trustworthy social media intervention about vaccination. Participants reported fatigue from contentious vaccine-related content on social media and desired future messaging to be from recognizable health institutions/associations with links to reputable resources. Plus, providers should continue to provide strong vaccine recommendations in clinic.
  • Item
    Collagenase-based wound debridement agent induces extracellular matrix supporting phenotype in macrophages
    (Springer Nature, 2024-02-08) Banerjee, Pradipta; Das, Amitava; Singh, Kanhaiya; Khanna, Savita; Sen, Chandan K.; Roy, Sashwati; Surgery, School of Medicine
    Macrophages assume diverse phenotypes and functions in response to cues from the microenvironment. Earlier we reported an anti-inflammatory effect of Collagenase Santyl® Ointment (CSO) and the active constituent of CSO (CS-API) on wound macrophages in resolving wound inflammation indicating roles beyond debridement in wound healing. Building upon our prior finding, this study aimed to understand the phenotypes and subsets of macrophages following treatment with CS-API. scRNA-sequencing was performed on human blood monocyte-derived macrophages (MDM) following treatment with CS-API for 24 h. Unbiased data analysis resulted in the identification of discrete macrophage subsets based on their gene expression profiles. Following CS-API treatment, clusters 3 and 4 displayed enrichment of macrophages with high expression of genes supporting extracellular matrix (ECM) function. IPA analysis identified the TGFβ-1 pathway as a key hub for the CS-API-mediated ECM-supportive phenotype of macrophages. Earlier we reported the physiological conversion of wound-site macrophages to fibroblasts in granulation tissue and impairment of such response in diabetic wounds, leading to compromised ECM and tensile strength. The findings that CSO can augment the physiological conversion of macrophages to fibroblast-like cells carry significant clinical implications. This existing clinical intervention, already employed for wound care, can be readily repurposed to improve the ECM response in chronic wounds.
  • Item
    Mechanical loading is required for initiation of extracellular matrix deposition at the developing murine myotendinous junction
    (Elsevier, 2023) Lipp, Sarah N.; Jacobson, Kathryn R.; Colling, Haley A.; Tuttle, Tyler G.; Miles, Dalton T.; McCreery, Kaitlin P.; Calve, Sarah; Medicine, School of Medicine
    The myotendinous junction (MTJ) contributes to the generation of motion by connecting muscle to tendon. At the adult MTJ, a specialized extracellular matrix (ECM) is thought to contribute to the mechanical integrity of the muscle-tendon interface, but the factors that influence MTJ formation during mammalian development are unclear. Here, we combined 3D imaging and proteomics with murine models in which muscle contractility and patterning are disrupted to resolve morphological and compositional changes in the ECM during MTJ development. We found that MTJ-specific ECM deposition can be initiated via static loading due to growth; however, it required cyclic loading to develop a mature morphology. Furthermore, the MTJ can mature without the tendon terminating into cartilage. Based on these results, we describe a model wherein MTJ development depends on mechanical loading but not insertion into an enthesis.