ScholarWorks shares over 30,000 articles, working papers, chapters, presentations, posters, theses, historical documents and other items submitted by members of the IU Indianapolis campus community.
Get started! Login with your IU credentials to share freely with 2 million readers per year.
Communities in ScholarWorks
Select a community to browse its collections.
Recent Submissions
Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
(American Chemical Society, 2024-06-04) Jiang, Yuming; Rex, Devasahayam Arokia Balaya; Schuster, Dina; Neely, Benjamin A.; Rosano, Germán L.; Volkmar, Norbert; Momenzadeh, Amanda; Peters-Clarke, Trenton M.; Egbert, Susan B.; Kreimer, Simion; Doud, Emma H.; Crook, Oliver M.; Yadav, Amit Kumar; Vanuopadath, Muralidharan; Hegeman, Adrian D.; Mayta, Martín L.; Duboff, Anna G.; Riley, Nicholas M.; Moritz, Robert L.; Meyer, Jesse G.; Biochemistry and Molecular Biology, School of Medicine
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
Accuracy of nine-item Patient Health Questionnaire against psychiatric diagnosis for depression among people with HIV
(Wolters Kluwer, 2024) Yotebieng, Marcel; Zotova, Natalia; Bernard, Charlotte; Goodrich, Suzanne; Rogers Awoh, Ajeh; Watnick, Dana; Nsonde, Dominique Mahambu; Tchiengang Moungang, Elodie Flore; Nguemo Noumedem, Julie Laure; Nko'o Mbongo'o, Guy Calvin; Minga, Albert; Seydi, Moussa; Gandou, Paul; Kwobah, Edith Kamaru; Atwoli, Lukoye; Jaquet, Antoine; Wools-Kaloustian, Kara; Anastos, Kathryn; IeDEA Consortium; Medicine, School of Medicine
Objective: The aim of this study was to assess the performance of the nine-item Patient Health Questionnaire (PHQ-9) against psychiatrist diagnosis in people with HIV (PWH).
Design: Cross-sectional analysis of data collected between January 2018 and July 2022 across five sites in Cameroon, Cote d'Ivoire, Kenya, Senegal, and the Republic of Congo. Participants were ≥18 years and receiving HIV care at the participating site. PHQ-9 was administered by study staff followed by a psychiatrist's evaluation within 3 days.
Results: Overall, 778 participants with complete data were included: 297 (38.2%) in Cameroon, 132 (17.0%) in Congo, 148 (19.0%) in Cote d'Ivoire, 98 (12.6%) in Kenya, and 103 (13.2%) in Senegal. The area under the curve for PHQ-9 score was generally high ranging from 0.935 [95% confidence interval (CI): 0.893, 0.977] in Cote d'Ivoire to 0.768 (95% CI: 0.589, 0.947) in Congo. However, for the common cut-off score ≥10, sensitivity was low: 50% or lower in Cameroon, Congo and Senegal, 66.7% in Kenya and 70.6% in Cote d'Ivoire. But negative predictive values (NPV) were high: 98.9% (95% CI: 96.9%, 99.8%) in Cameroon, 96.1 (95% CI: 91.1, 98.7) in Cote d'Ivoire, 96.3% (95% CI: 89.7%, 99.2%) in Kenya, 95.7% (95% CI: 90.2%, 98.6%) in Congo, and 89.0% (95% CI: 81.2%, 94.4%) in Senegal.
Interpretation: Across all countries, PHQ-9 score ≥10 performed very poorly (low sensitivity) as a tool to identify psychiatrist diagnosed depression. However, the observed high NPV suggests it can be used to rule out depression.
Evaluation of Emergency Department Treat-and-Release Encounters After Major Gastrointestinal Surgery
(Wiley, 2023) Brajcich, Brian C.; Johnson, Julie K.; Holl, Jane L.; Bilimoria, Karl Y.; Shallcross, Meagan L.; Chung, Jeanette; Joung, Rachel Hae Soo; Iroz, Cassandra B.; Odell, David D.; Bentrem, David J.; Yang, Anthony D.; Franklin, Patricia D.; Slota, Jennifer M.; Silver, Casey M.; Skolarus, Ted; Merkow, Ryan P.; Surgery, School of Medicine
Background and objectives: Emergency department (ED) utilization after gastrointestinal cancer operations is poorly characterized. Our study objectives were to determine the incidence of, reasons for, and predictors of ED treat-and-release encounters after gastrointestinal cancer operations.
Methods: Patients who underwent elective esophageal, hepatobiliary, gastric, pancreatic, small intestinal, or colorectal operations for cancer were identified in the 2015-2017 Healthcare Cost and Utilization Project State Inpatient and State Emergency Department Databases for New York, Maryland, and Florida. The primary outcomes were the incidence of ED treat-and-release encounters and readmissions within 30 days of discharge.
Results: Among 51 527 patients at 406 hospitals, 4047 (7.9%) had an ED treat-and-release encounter, and 5573 (10.8%) had an ED encounter with readmission. In total, 40.7% of ED encounters were treat-and-release encounters. ED treat-and-release encounters were most frequently for pain (12.0%), device/ostomy complaints (11.7%), or wound complaints (11.4%). ED treat-and-release encounters predictors included non-Hispanic Black race/ethnicity (odds ratio [OR] 1.24, 95% confidence interval [CI] 1.12-1.37) and Medicare (OR 1.27, 95% CI 1.16-1.40) or Medicaid (OR 1.82, 95% CI 1.62-2.40) coverage.
Conclusions: ED treat-and-release encounters are common after major gastrointestinal operations, making up nearly half of postdischarge ED encounters. The reasons for ED treat-and-release encounters differ from those for ED encounters with readmissions.
Anti-cytomegalovirus antibody levels stratify human immune profiles across the lifespan
(Springer, 2024) Watanabe, Makiko; Davidson, Lisa; Smith, Patricia; Castellucio, Peter F.; Jergovic, Mladen; Uhrlaub, Jennifer L.; Smithey, Megan J.; Fantry, Lori E.; Dechambre, Brett; Wilson, Rachel C.; Knox, Kenneth C.; Stowe, Raymond P.; Weinstock, George; Twigg, Homer, III; Nikolich, Janko Ž.; Biostatistics and Health Data Science, School of Medicine
Human cytomegalovirus (hCMV) is a ubiquitous latent persistent herpesvirus infecting 60-90% of the population worldwide. hCMV carriage in immunocompetent people is asymptomatic; thus, hCMV can be considered a component of normative aging. However, hCMV powerfully modulates many features of the immune, and likely other, systems and organs. Questions remain as to how hCMV carriage affects the human host. We used anti-CMV antibody titers as a stratifying criterion to examine the impact of "intensity" of hCMV infection as a potential biomarker of aging, inflammation, and immune homeostasis in a cohort of 247 participants stratified into younger (21-40 years) and older (> 65 years of age) groups. We showed that anti-CMV antibody titers increased with age and directly correlated to increased levels of soluble tumor necrosis factor (sTNFR) I in younger but not older participants. CD8 + cell numbers were reduced in the older group due to the loss in CD8 + T naïve (Tn) cells. In CMV carriers and, in particular, in anti-CMV Ab-high participants, this loss was mitigated or reversed by an increase in the numbers of CD8 + T effector memory (Tem) and T effector memory reexpressing CD45RA (Temra) cells. Analysis of CD38, HLA-DR, and CD57 expression revealed subset (CD4 or CD8)-specific changes that correlated with anti-CMV Ab levels. In addition, anti-CMV Ab levels predicted anti-CMV CD8 T cell responsiveness to different CMV open reading frames (ORFs) selectively in older participants, which correlated to the transcriptional order of expression of specific CMV ORFs. Implications of these results for the potential predictive value of anti-CMV Ab titers during aging are discussed.
Clinical Outcomes of Percutaneous Coronary Intervention in Amyloidosis, Sarcoidosis, and Hemochromatosis
(Elsevier, 2023-12-30) Hussain, Bilal; Malik, Hamza; Mamas, Mamas A.; Desai, Rupak; Aggarwal, Vikas; Kumar, Gautam; Alraies, M. Chadi; Kalra, Ankur; Paul, Timir K.; Medicine, School of Medicine
Background: Infiltrative diseases (IDs), including amyloidosis, sarcoidosis, and hemochromatosis, are characterized by abnormal cellular infiltration in multiple organs, including the heart. The prognosis of percutaneous coronary intervention (PCI) patients with underlying IDs has not been well-studied. We evaluated the prevalence of IDs in patients undergoing PCI and their association with post-PCI outcomes.
Methods: The National Inpatient Sample (NIS) 2016-2020 database was used to identify PCI patients with ICD-10 codes for a retrospective analysis. PCI patients were then divided into those with and without underlying IDs, which included amyloidosis, sarcoidosis, and hemochromatosis. Multivariable logistic regression was performed for composite post-PCI outcomes analyses.
Results: Among 2,360,860 patients admitted to undergo PCI, 7855 patients had underlying IDs. The highest prevalence was observed for sarcoidosis (0.2%) followed by hemochromatosis (0.07%) and amyloidosis (0.04%). Underlying amyloidosis was associated with worse composite post-PCI outcomes (odds ratio [OR], 1.6; 95% CI, 1.1-2.44; P = .02), including higher in-hospital mortality (OR, 1.9; 95% CI, 1.1-3.4; P = .04), higher risk of intra/post-PCI stroke (OR, 4.0; 95% CI, 1.1-16.0; P = .04), but not major bleeding (OR, 2.2; 95% CI, 0.97-5.03; P = .058). In contrast, underlying sarcoidosis (OR, 1.1; 95% CI, 0.87-1.41; P = .4), and hemochromatosis (OR, 1.18; 95% CI, 0.77-1.8; P = .44) were not associated with composite post-PCI outcomes. Amyloidosis patients undergoing PCI also had higher hospitalization charges ($212,123 vs $141,137; P = .03) and longer length of stay (8.2 vs 3.9 days; P < .001).
Conclusions: Underlying amyloidosis was associated with worse post-PCI outcomes including higher in-hospital mortality, intra/post-PCI stroke, and socioeconomic burden. A multidisciplinary approach and future studies are needed to investigate the screening and treatment strategies in these patients.