Open Access Publishing Fund
Permanent URI for this collection
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: http://ulib.iupui.edu/digitalscholarship/openaccess/oafund
Annual reports on the progress of the fund are available from: https://scholarworks.iupui.edu/handle/1805/11935
Annual reports on the progress of the fund are available from: https://scholarworks.iupui.edu/handle/1805/11935
Browse
Recent Submissions
Item National Institutes of Health Stroke Scale (NIHSS) scoring inconsistencies between neurologists and emergency room nurses(Frontiers, 2022) Comer, Amber R.; Templeton, Evan; Glidden, Michelle; Bartlett, Stephanie; D'Cruz, Lynn; Nemati, Donya; Zabel, Samantha; Slaven, James E.BACKGROUND: Little is known about the consistency of initial NIHSS scores between neurologists and RNs in clinical practice. METHODS: A cohort study of patients with a code stroke was conducted at an urban academic Primary Stroke Center in the Midwest between January 1, 2018, and December 31, 2019 to determine consistency in National Institutes of Health Stroke Scale Scores (NIHSS) between neurologists and registered nurses (RNs). RESULTS: Among the 438 patients included in this study 65.3% (n = 286) of neurologist-RN NIHSS scoring pairs had congruent scores. One-in-three, (34.7%, n = 152) of neurologist-RN NIHSS scoring pairs had a clinically meaningful scoring difference of two points or greater. Higher NIHSS (p ≤ 0.01) and aphasia (p ≤ 0.01) were each associated with incongruent scoring between neurologist and emergency room RN pairs. CONCLUSIONS: One-in-three initial NIHSS assessed by both a neurologist and RN had a clinically meaningful score difference between providers. More severe stroke, as indicated by a higher NIHSS was associated with scoring inconsistency between neurologist-RN pairs. Subjective scoring measures, especially those involving a patient having aphasia, was associated with greater score incongruency. Score differences may be attributed to differences in NIHSS training requirements between neurologists and RNs.Item Transcriptome Profiling of the Hippocampal Seizure Network Implicates a Role for Wnt Signaling during Epileptogenesis in a Mouse Model of Temporal Lobe Epilepsy(MDPI, 2022-10) Mardones, Muriel D.; Gupta, Kunal; Neurological Surgery, School of MedicineMesial temporal lobe epilepsy (mTLE) is a life-threatening condition characterized by recurrent hippocampal seizures. mTLE can develop after exposure to risk factors such as febrile seizure, trauma, and infection. Within the latent period between exposure and onset of epilepsy, pathological remodeling events occur that contribute to epileptogenesis. The molecular mechanisms responsible are currently unclear. We used the mouse intrahippocampal kainite model of mTLE to investigate transcriptional dysregulation in the ipsilateral and contralateral dentate gyrus (DG), representing the epileptogenic zone (EZ) and peri-ictal zone (PIZ). DG were analyzed after 3, 7, and 14 days by RNA sequencing. In both the EZ and PIZ, transcriptional dysregulation was dynamic over the epileptogenic period with early expression of genes representing cell signaling, migration, and proliferation. Canonical Wnt signaling was upregulated in the EZ and PIZ at 3 days. Expression of inflammatory genes differed between the EZ and PIZ, with early expression after 3 days in the PIZ and delayed expression after 7–14 days in the EZ. This suggests that critical gene changes occur early in the hippocampal seizure network and that Wnt signaling may play a role within the latent epileptogenic period. These findings may help to identify novel therapeutic targets that could prevent epileptogenesis.Item The Ex Vivo Human Translaminar Autonomous System to Study Spaceflight Associated Neuro-ocular Syndrome Pathogenesis(Nature, 2022-10) Peng, Michael; Curry, Stacy M.; Liu, Yang; Lohawala, Husain; Sharma, Gaurav; Sharma, Tasneem P.; Ophthalmology, School of MedicineSpaceflight-Associated Neuro-ocular Syndrome (SANS) is a significant unexplained adverse reaction to long-duration spaceflight. We employ an ex vivo translaminar autonomous system (TAS) to recreate a human ocular ground-based spaceflight analogue model to study SANS pathogenesis. To recapitulate the human SANS conditions, human ocular posterior segments are cultured in the TAS model for 14 days. Translaminar pressure differentials are generated by simulating various flow rates within intracranial pressure (ICP) and intraocular (IOP) chambers to maintain hydrostatic pressures of ICP: IOP (12:16, 15:16, 12:21, 21:16 mmHg). In addition, optic nerves are mechanically kinked by 6- and 10-degree tilt inserts for the ICP: IOP;15:16 mmHg pressure paradigm. The TAS model successfully maintains various pressure differentials for all experimental groups over 14 days. Post culture, we determine inflammatory and extracellular component expression changes within posterior segments. To further characterize the SANS pathogenesis, axonal transport capacity, optic nerve degeneration and retinal functional are measured. Identifiable pathogenic alterations are observed in posterior segments by morphologic, apoptotic, and inflammatory changes including transport and functional deficits under various simulated SANS conditions. Here we report our TAS model provides a unique preclinical application system to mimic SANS pathology and a viable therapeutic testing device for countermeasures.Item The current state of lesbian, gay, bisexual and transgender (LGBT) cultural competency among U.S. dermatology residents(Wolters Kluwer, 2022-10) Nowaskie, Dustin Z.; Garcia-Dehbozorgi, Sara; Cortez, Jose L.; Medicine, School of MedicineBackground: Lesbian, gay, bisexual, and transgender (LGBT) people interface with dermatology providers for many reasons. Implementing culturally competent LGBT dermatologic care necessitates evaluating provider competency to identify where gaps remain. Objectives: To assess the LGBT cultural competency among U.S. dermatology residents. Methods: A self-reporting, cross-sectional survey was emailed to U.S. dermatology program coordinators (N = 143). LGBT patient exposure, LGBT educational hours, and LGBT cultural competency via the LGBT-Development of Clinical Skills Scale (with the subscales Clinical Preparedness, Attitudinal Awareness, and Basic Knowledge) were measured. Results: Dermatology residents (N = 119) across the United States completed the survey. They reported caring for less than 20 LGBT patients per year and receiving less than 75 minutes of LGBT education per year. They reported significantly higher Attitudinal Awareness than both Clinical Preparedness and Basic Knowledge; they reported significantly higher Basic Knowledge than Clinical Preparedness. They reported significantly less adequate clinical training and supervision, experience, and competence to assess transgender patients compared to lesbian, gay, and bisexual patients. In general, dermatology residents who reported more LGBT patients and LGBT education also reported higher LGBT cultural competency. Limitations: A larger national sample of U.S. dermatology residents is necessary for generalizability. Conclusions: Currently, there is a lack of LGBT education in U.S. dermatology residency curricula, which may delay addressing the health disparities that exist in this patient population. Due to such dearth of standardized LGBT education, dermatology residents likely do not feel adequately knowledgeable or prepared to address LGBT needs. Both LGBT education and LGBT patient experiences may help alleviate these shortcomings and help LGBT patients feel affirmed in their dermatologic care.Item The reflexive relationship between available university services and mental health ideations: A complexity informed perspective(Frontiers, 2022-09) Watson, Jacob; Lee, Taylor; Handayani, Sri; Communication Studies, School of Liberal ArtsUsing Communication Complex as our theoretical framework, we explored socially constructed notions about mental health from a complexity informed perspective. Through qualitative interviews we investigated the availability of mental health services provided at three universities—one in Wrocław, Poland; one in Semarang, Indonesia; and the third in Indianapolis, Indiana, United States. From our interviews we interpreted several salient themes across all three cultures. Discussions about mental health services are meaningless without first defining mental health in pursuit of ascertaining what counts as caring for one's mental health—a process which raises a host of epistemological and ontological questions in both the academic setting and the larger social milieu. These conversations also reified the importance of considering one's whole health, how stigma plays a role in defining mental health “issues”, and what stories are being told about the nature of mental health across several cultures. We argue that there is a deeper, reflexive relationship between the ways people talk about mental health and what services are offered that goes beyond traditional notions of what mental health “is” and what counts as a mental health service.Item Differential Splicing of Skipped Exons Predicts Drug Response in Cancer Cell Lines(Elsevier, 2021-12) Simpson, Edward; Chen, Steven; Reiter, Jill L.; Liu, Yunlong; BioHealth Informatics, School of Informatics and ComputingAlternative splicing of pre-mRNA transcripts is an important regulatory mechanism that increases the diversity of gene products in eukaryotes. Various studies have linked specific transcript isoforms to altered drug response in cancer; however, few algorithms have incorporated splicing information into drug response prediction. In this study, we evaluated whether basal-level splicing information could be used to predict drug sensitivity by constructing doxorubicin-sensitivity classification models with splicing and expression data. We detailed splicing differences between sensitive and resistant cell lines by implementing quasi-binomial generalized linear modeling (QBGLM) and found altered inclusion of 277 skipped exons. We additionally conducted RNA-binding protein (RBP) binding motif enrichment and differential expression analysis to characterize cis- and trans-acting elements that potentially influence doxorubicin response-mediating splicing alterations. Our results showed that a classification model built with skipped exon data exhibited strong predictive power. We discovered an association between differentially spliced events and epithelial-mesenchymal transition (EMT) and observed motif enrichment, as well as differential expression of RBFOX and ELAVL RBP family members. Our work demonstrates the potential of incorporating splicing data into drug response algorithms and the utility of a QBGLM approach for fast, scalable identification of relevant splicing differences between large groups of samples.Item Serologic Presentation of Lamotrigine-Induced Lupus(Hindawi, 2022) Dempsey, Hannah; Aitcheson, Gabriella; Goble, Gretchen; Snook, Riley; Medicine, School of MedicineThis paper discusses the presentation of a rare drug side effect, a case of drug-induced lupus presenting with weight loss, weakness, hepatitis, and pancreatitis. A 24-year-old male with a history of major depressive disorder and childhood seizures presented to the ER with symptoms of abdominal pain, significant weight loss, and weakness. Initial workup revealed acute pancreatitis, elevated liver function enzymes (LFTs), and abnormal anti-double-stranded DNA antibody (anti-dsDNA) 1 : 640. He showed no classical clinical signs of lupus including rash, arthritis, or photosensitivity. He had multiple hospitalizations in the previous 6 months for excessive weight loss, malnutrition, weakness, and altered mental status. He had been taking lamotrigine for seizure prevention and mood stabilization while on a selective serotonin reuptake inhibitor (SSRI) and had a decline in health since the lamotrigine dose was increased. Antihistone antibodies were positive suggesting a drug-induced lupus syndrome. We hope to bring awareness to the possible rare complication of lamotrigine-induced lupus.Item The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline(eLife Sciences, 2021-01-15) Janosevic, Danielle; Myslinski, Jered; McCarthy, Thomas W.; Zollman, Amy; Syed, Farooq; Xuei, Xiaoling; Gao, Hongyu; Liu, Yun-Long; Collins, Kimberly S.; Cheng, Ying-Hua; Winfree, Seth; El-Achkar, Tarek M.; Maier, Bernhard; Ferreira, Ricardo Melo; Eadon, Michael T.; Hato, Takashi; Dagher, Pierre C.; Medicine, School of MedicineSepsis is a dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires a thorough knowledge of the evolution of cellular and molecular events at the tissue level. Here, we investigated the kidney, an organ central to the pathophysiology of sepsis. Single-cell RNA-sequencing in a murine endotoxemia model revealed the involvement of various cell populations to be temporally organized and highly orchestrated. Endothelial and stromal cells were the first responders. At later time points, epithelial cells upregulated immune-related pathways while concomitantly downregulating physiological functions such as solute homeostasis. Sixteen hours after endotoxin, there was global cell-cell communication failure and organ shutdown. Despite this apparent organ paralysis, upstream regulatory analysis showed significant activity in pathways involved in healing and recovery. This rigorous spatial and temporal definition of murine endotoxemia will uncover precise biomarkers and targets that can help stage and treat human sepsis.Item PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature(Springer, 2022) Binkheder, Samar; Wu, Heng-Yi; Quinney, Sara K.; Zhang, Shijun; Zitu, Md. Muntasir; Chiang, Chien-Wei; Wang, Lei; Jones, Josette; Li, Lang; BioHealth Informatics, School of Informatics and ComputingBackground Adverse events induced by drug-drug interactions are a major concern in the United States. Current research is moving toward using electronic health record (EHR) data, including for adverse drug events discovery. One of the first steps in EHR-based studies is to define a phenotype for establishing a cohort of patients. However, phenotype definitions are not readily available for all phenotypes. One of the first steps of developing automated text mining tools is building a corpus. Therefore, this study aimed to develop annotation guidelines and a gold standard corpus to facilitate building future automated approaches for mining phenotype definitions contained in the literature. Furthermore, our aim is to improve the understanding of how these published phenotype definitions are presented in the literature and how we annotate them for future text mining tasks. Results Two annotators manually annotated the corpus on a sentence-level for the presence of evidence for phenotype definitions. Three major categories (inclusion, intermediate, and exclusion) with a total of ten dimensions were proposed characterizing major contextual patterns and cues for presenting phenotype definitions in published literature. The developed annotation guidelines were used to annotate the corpus that contained 3971 sentences: 1923 out of 3971 (48.4%) for the inclusion category, 1851 out of 3971 (46.6%) for the intermediate category, and 2273 out of 3971 (57.2%) for exclusion category. The highest number of annotated sentences was 1449 out of 3971 (36.5%) for the “Biomedical & Procedure” dimension. The lowest number of annotated sentences was 49 out of 3971 (1.2%) for “The use of NLP”. The overall percent inter-annotator agreement was 97.8%. Percent and Kappa statistics also showed high inter-annotator agreement across all dimensions. Conclusions The corpus and annotation guidelines can serve as a foundational informatics approach for annotating and mining phenotype definitions in literature, and can be used later for text mining applications.Item Rates of Tobacco Use Disorder, Pharmacologic Treatment, and Associated Mental Health Disorders in a Medicaid Claim Review Among Youth in Indiana, USA(Sage, 2022) McBrayer, Kimberly; Ouyang, Fangqian; Adams, Zachary; Hulvershorn, Leslie; Aalsma, Matthew C.; Pediatrics, School of MedicinePurpose This study delineates a number of Medicaid youth with tobacco use disorder (TUD), prescribing habits for treatment, and associated externalizing disorders. Methods Youth Medicaid claims from 2007-2017 processed in a large Midwestern city were analyzed for a diagnosis of TUD, related pharmacotherapy, and externalizing mental health and substance use disorders. Results Claims connected 6541 patients with 42 890 visits. Mean age was 16.4 with 40% female. 1232 of the 6541 charts contained a TUD diagnosis equating to 1848 visits. A comorbid diagnosis of ADHD, cannabis use, and conduct disorder were more common in males (3.9% vs 1.3% in females; 3.4% vs .8%; and 2.8% vs .8%; P < .05). 808 scripts were provided to 152 of the 1232 youths, with 4.7% of those scripts a nicotine replacement product. Conclusions Pharmacotherapy is underutilized in this Medicaid claims data set. Certain externalizing factors were associated with males with TUD more than females.