IU Indianapolis ScholarWorks :: Browsing by Subject "Validation"

Browsing by Subject "Validation"

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A Reference Database for the DNA-Based Identification of North American Calliphorinae
(North American Forensic Entomological Association (NAFEA), 2023) Picard, Christine J.; Balaji, Adhitya; Benson, Diamond
DNA-based species identifications are a robust tool for the forensic entomologist to identify immature or damaged specimens to species or genus taxonomic levels for further forensic analyses. However, much of that identification is dependent on the use of a reliable database that encompasses all species possible for a given geographic area. Here, we queried databases for DNA records of COI sequence data of 18 species of Calliphorinae present in North America to determine the applicability and reliability of DNA-based identifications, and to provide a resource for the community. Our results indicate that approximately 650bp of the standard DNA barcode is sufficient to classify most Calliphorinae species, however, some species the ~650bp COI barcode is insufficient to resolve to species for the North American Calliphorinae subfamily. We tested this reference dataset by selecting records that were deemed reliable (using the same criteria as establishing the reference dataset) to test the accuracy of the identifications based on DNA COI sequences and found that all test specimens were accurately identified except for the two paraphyletic species present in the dataset. We furthermore state what species can and cannot be reliably classified and provide guidance on using this database in future applications.
A target discovery pipeline identified ILT3 as a target for immunotherapy of multiple myeloma
(Elsevier, 2023) Di Meo, Francesco; Iyer, Anjushree; Akama, Keith; Cheng, Rujin; Yu, Christina; Cesarano, Annamaria; Kurihara, Noriyoshi; Tenshin, Hirofumi; Aljoufi, Arafat; Marino, Silvia; Soni, Rajesh K.; Roda, Julie; Sissons, James; Vu, Ly P.; Guzman, Monica; Huang, Kun; Laskowski, Tamara; Broxmeyer, Hal E.; Roodman, David G.; Perna, Fabiana; Medicine, School of Medicine
Multiple myeloma (MM) is an incurable malignancy of plasma cells. To identify targets for MM immunotherapy, we develop an integrated pipeline based on mass spectrometry analysis of seven MM cell lines and RNA sequencing (RNA-seq) from 900+ patients. Starting from 4,000+ candidates, we identify the most highly expressed cell surface proteins. We annotate candidate protein expression in many healthy tissues and validate the expression of promising targets in 30+ patient samples with relapsed/refractory MM, as well as in primary healthy hematopoietic stem cells and T cells by flow cytometry. Six candidates (ILT3, SEMA4A, CCR1, LRRC8D, FCRL3, IL12RB1) and B cell maturation antigen (BCMA) present the most favorable profile in malignant and healthy cells. We develop a bispecific T cell engager targeting ILT3 that shows potent killing effects in vitro and decreased tumor burden and prolonged mice survival in vivo, suggesting therapeutic relevance. Our study uncovers MM-associated antigens that hold great promise for immune-based therapies of MM.
Assessing Validity of Self-Reported Dietary Intake within a Mediterranean Diet Cluster Randomized Controlled Trial among US Firefighters
(MDPI, 2019-09-19) Sotos-Prieto, Mercedes; Christophi, Costas; Black, Alicen; Furtado, Jeremy D.; Song, Yiqing; Magiatis, Prokopios; Papakonstantinou, Aikaterini; Melliou, Eleni; Moffatt, Steven; Kales, Stefanos N.; Epidemiology, School of Public Health
Collecting dietary intake data is associated with challenges due to the subjective nature of self-administered instruments. Biomarkers may objectively estimate the consumption of specific dietary items or help assess compliance in dietary intervention studies. Our aim was to use a panel of plasma and urine biomarkers to assess the validity of self-reported dietary intake using a modified Mediterranean Diet Scale (mMDS) among firefighters participating in Feeding America's Bravest (FAB), an MD cluster-randomized controlled trial. In our nested biomarker pilot study, participants were randomly selected from both the MD intervention group (n = 24) and the control group (n = 24) after 12-months of dietary intervention. At baseline data collection for the pilot study (t = 12-months of FAB), participants in the control group crossed-over to receive the MD intervention (active intervention) for 6-months. Participants in the intervention group continued in a self-sustained continuation phase (SSP) of the intervention. Food frequency questionnaires (FFQ), 13-item-mMDS questionnaires, 40 plasma fatty acids, inflammatory biomarkers and urinary hydroxytyrosol and tyrosol were analyzed at both time points. Spearman's correlation, t-tests and linear regression coefficients were calculated using SAS software. Overall, the mMDS derived from the FFQ was highly correlated with the specific 13-domain-mMDS (r = 0.74). The concordance between the two questionnaires for low and high adherence to MD was high for all the participants in the parent trial (κ = 0.76). After 6 months of intervention in the pilot study, plasma saturated fatty acid decreased in both groups (active intervention: -1.3 ± 1.7; p = 0.002; SSP: -1.12 ± 1.90; p = 0.014) and oleic acid improved in the SSP (p = 0.013). Intake of olive oil was positively associated with plasma omega-3 (p = 0.004) and negatively with TNF-α (p < 0.001) at baseline. Choosing olive oil as a type of fat was also associated with higher levels of plasma omega-3 (p = 0.019) at baseline and lower TNF-α (p = 0.023) at follow up. Intake of red and processed meats were associated with lower serum omega-3 (p = 0.04) and fish consumption was associated with lower IL-6 at baseline (p = 0.022). The overall mMDS was associated with an increase in plasma omega-3 (p = 0.021). Good correlation was found between nutrient intake from the FFQ and the corresponding plasma biomarkers (omega-3, EPA and DHA). In this MD randomized controlled trial, some key plasma biomarkers were significantly associated with key MD diet components and the overall mMDS supporting the validity of the mMDS questionnaire as well as compliance with the intervention.
Clinical Proteomics for Post-Hematopoeitic Stem Cell Transplantation Outcomes
(Wiley, 2019-03) Paczesny, Sophie; Metzger, Jochen; Pediatrics, School of Medicine
Allogeneic hematopoietic stem cell transplantation (HSCT) is the most effective form of tumor immunotherapy available to date. However, while HSCT can induce beneficial graft-versus-leukemia (GVL) effect, the adverse effect of graft-versus-host disease (GVHD), which is closely linked to GVL, is the major source of morbidity and mortality following HSCT. Until recently, available diagnostic and staging tools frequently fail to identify those at higher risk of disease progression or death. Furthermore, there are shortcomings in the prediction of the need for therapeutic interventions or the response rates to different forms of therapy. The past decade has been characterized by an explosive evolution of proteomics technologies, largely due to important advances in high-throughput MS instruments and bioinformatics. Building on these opportunities, blood biomarkers have been identified and validated both as promising diagnostic tools, prognostic tools that risk-stratify patients before future occurrence of GVHD and as predictive tools for responsiveness to GVHD therapy and non-relapse mortality. These biomarkers might facilitate timely and selective therapeutic intervention. This review summarizes current information on clinical proteomics for GVHD as well as other complications following HSCT. Finally, it proposes future directions for the translation of clinical proteomics to discovery of new potential therapeutic targets to the development of drugs.
The Cognitive Change Index as a Measure of Self and Informant Perception of Cognitive Decline: Relation to Neuropsychological Tests
(IOS Press, 2016-02-25) Rattanabannakit, Chatchawan; Risacher, Shannon L.; Gao, Sujuan; Lane, Kathleen A.; Brown, Steven A.; McDonald, Brenna C.; Unverzagt, Frederick W.; Apostolova, Liana G.; Saykin, Andrew J.; Farlow, Martin R.; Department of Neurology, IU School of Medicine
BACKGROUND: The perception of cognitive decline by individuals and those who know them well ("informants") has been inconsistently associated with objective cognitive performance, but strongly associated with depressive symptoms. OBJECTIVE: We investigated associations of self-report, informant-report, and discrepancy between self- and informant-report of cognitive decline obtained from the Cognitive Change Index (CCI) with cognitive test performance and self-reported depressive symptoms. METHODS: 267 participants with normal cognition, mild cognitive impairment (MCI), or mild dementia were included from a cohort study and memory clinic. Association of test performance and self-rated depression (Geriatric Depression Scale, GDS) with CCI scores obtained from subjects (CCI-S), their informants (CCI-I), and discrepancy scores between subjects and informants (CCI-D; CCI-S minus CCI-I) were analyzed using correlation and analysis of covariance (ANCOVA) models. RESULTS: CCI-S and CCI-I scores showed high internal consistency (Cronbach alpha 0.96 and 0.98, respectively). Higher scores on CCI-S and CCI-I, and lower scores on the CCI-D, were associated with lower performance on various cognitive tests in both univariate and in ANCOVA models adjusted for age, gender, and education. Adjustment for GDS slightly weakened the relationships between CCI and test performance but most remained significant. CONCLUSION: Self- and informant-report of cognitive decline, as measured by the CCI, show moderately strong relationships with objective test performance independent of age, gender, education, and depressive symptoms. The CCI appears to be a valid cross-sectional measure of self and informant perception of cognitive decline across the continuum of functioning. Studies are needed to address the relationship of CCI scores to longitudinal outcome.
Developing and Validating a PubMed Infant Hedge: An MLA Pediatrics Librarians Caucus Initiative
(2022-05) Brennan, Emily; Willis, Christine; Kysh, Lynn; Bogucka, Roxanne; Hinrichs, Rachel J.
Development of a computerized adaptive substance use disorder scale for screening, measurement and diagnosis - The CAT-SUD-E
(Elsevier, 2022-03-23) Hulvershorn, Leslie A.; Adams, Zachary W.; Smoker, Michael P.; Aalsma, Matthew C.; Gibbons, Robert D.; Psychiatry, School of Medicine
Introduction: The Computerized Adaptive Test for Substance Use Disorder (CAT-SUD), an adaptive test based on multidimensional item response theory, has been expanded to include 7 specific Diagnostic and Statistical Manual, 5th edition (DSM-5) defined SUDs. Initial testing of the new measure, the CAT-SUD expanded (CAT-SUD-E) is reported here. Methods: 275 Community-dwelling adults (ages 18-68) responded to public and social-media advertisements. Participants virtually completed both the CAT-SUD-E and the Structured Clinical Interview for DSM-5, Research Version (SCID) to assess the validity of the CAT-SUD-E in determining whether participants met criteria for specific DSM-5 SUDs. Diagnostic classifications were based on 7 SUDs, each with 5 items, for current and lifetime SUDs. Results: For SCID-based presence of any lifetime SUD, predictions based on the overall CAT-SUD-E diagnosis and severity score were AUC=0.92, 95% CI = 0.88, 0.95 for current and AUC=0.94, 95% CI = 0.91, 0.97 for lifetime. For individual diagnoses, classification accuracy for current SUDs ranged from an AUC=0.76 for alcohol to AUC=0.92 for nicotine/tobacco. Classification accuracy for lifetime SUDs ranged from an AUC=0.81 for hallucinogens to AUC=0.96 for stimulants. Median CAT-SUD-E completion time was under 4 min. Conclusions: The CAT-SUD-E quickly produces similar results as lengthy structured clinical interviews for overall SUD and substance-specific SUDs, with high precision and accuracy, through a combination of fixed-item responses for diagnostic classification and adaptive SUD severity measurement. The CAT-SUD-E harmonizes information from mental health, trauma, social support and traditional SUD items to provide a more complete characterization of SUD and provides both diagnostic classification and severity measurement.
Examination of the SUPPS-P Impulsive Behavior Scale among Male and Female Youth: Psychometrics and Invariance
(MDPI, 2021-04-07) Pechorro, Pedro; Revilla, Rebecca; Palma, Victor H.; Nunes, Cristina; Martins, Cátia; Cyders, Melissa A.; Psychology, School of Science
The UPPS-P Impulsive Behavior Scale is one of the most used and easily administered self-report measures of impulsive traits. The main objective of this study was to examine the psychometric properties of the shorter SUPPS-P scale among a school sample of 470 youth (Mage = 15.89 years, SD = 1.00) from Portugal, subdivided into males (n = 257, Mage = 15.97 years, SD = 0.98) and females (n = 213, Mage = 15.79 years, SD = 1.03). Confirmatory factor analysis results revealed that the latent five-factor structure (i.e., Negative urgency, Lack of perseverance, Lack of premeditation, Sensation seeking, and Positive urgency) obtained adequate fit and strong measurement invariance demonstrated across sex. The SUPPS-P scale also demonstrated satisfactory psychometric properties in terms of internal consistency, discriminant and convergent (e.g., with measures of youth delinquency, aggression) validities, and criterion-related validity (e.g., with crime seriousness). Findings support the use of the SUPPS-P scale in youth. Given the importance of adolescence as a critical period characterized by increases in impulsive behaviors, having a short, valid, reliable, and easily administered assessment of impulsive tendencies is important and clinically impactful.
Patient-Centered Data Home: A Path Towards National Interoperability
(Frontiers Media, 2022-07-13) Williams, Karmen S.; Grannis, Shaun J.; Medicine, School of Medicine
Objective: National interoperability is an agenda that has gained momentum in health care. Although several attempts to reach national interoperability, an alerting system through interconnected network of Health Information Exchange (HIE) organizations, Patient-Centered Data Home (PCDH), has seen preliminary success. The aim was to characterize the PCDH initiative through the Indiana Health Information Exchange's participation in the Heartland Region Pilot, which includes HIEs in Indiana, Ohio, Michigan, Kentucky, and Tennessee. Materials and methods: Admission, Discharge, and Transfer (ADT) transactions were collected between December 2016 and December 2017 among the seven HIEs in the Heartland Region. ADTs were parsed and summarized. Overlap analyses and patient matching software were used to characterize the PCDH patients. R software and Microsoft Excel were used to populate descriptive statistics and visualization. Results: Approximately 1.5 million ADT transactions were captured. Majority of patients were female, ages 56-75 years, and were outpatient visits. Top noted reasons for visit were labs, screening, and abdominal pain. Based on the overlap analysis, Eastern Tennessee HIE was the only HIE with no duplicate service areas. An estimated 80 percent of the records were able to be matched with other records. Discussion: The high volume of exchange in the Heartland Region Pilot established that PCDH is practical and feasible to exchange data. PCDH has the posture to build better comprehensive medical histories and continuity of care in real time. Conclusion: The value of the data gained extends beyond clinical practitioners to public health workforce for improved interventions, increased surveillance, and greater awareness of gaps in health for needs assessments. This existing interconnection of HIEs has an opportunity to be a sustainable path toward national interoperability.
The Nimble Stage 1 Study Validates Diagnostic Circulating Biomarkers for Nonalcoholic Steatohepatitis
(Springer Nature, 2023) Sanyal, Arun J.; Shankar, Sudha S.; Yates, Katherine P.; Bolognese, James; Daly, Erica; Dehn, Clayton A.; Neuschwander-Tetri, Brent; Kowdley, Kris; Vuppalanchi, Raj; Behling, Cynthia A.; Tonascia, James; Samir, Anthony; Sirlin, Claude; Sherlock, Sarah P.; Fowler, Kathryn; Heymann, Helen; Kamphaus, Tania N.; Loomba, Rohit; Calle, Roberto A.; Medicine, School of Medicine
There are no approved diagnostic biomarkers for at-risk non-alcoholic steatohepatitis (NASH), defined by the presence of NASH, high histological activity and fibrosis stage ≥2, which is associated with higher incidence of liver-related events and mortality. FNIH-NIMBLE is a multi-stakeholder project to support regulatory approval of NASH-related biomarkers. The diagnostic performance of five blood-based panels was evaluated in an observational (NASH CRN DB2) cohort (n = 1,073) with full spectrum of non-alcoholic fatty liver disease (NAFLD). The panels were intended to diagnose at-risk NASH (NIS4), presence of NASH (OWLiver) or fibrosis stages >2, >3 or 4 (enhanced liver fibrosis (ELF) test, PROC3 and FibroMeter VCTE). The prespecified performance metric was an area under the receiver operating characteristic curve (AUROC) ≥0.7 and superiority over alanine aminotransferase for disease activity and the FIB-4 test for fibrosis severity. Multiple biomarkers met these metrics. NIS4 had an AUROC of 0.81 (95% confidence interval: 0.78–0.84) for at-risk NASH. The AUROCs of the ELF test, PROC3 and FibroMeterVCTE for clinically significant fibrosis (≥stage 2), advanced fibrosis (≥stage 3) or cirrhosis (stage 4), respectively, were all ≥0.8. ELF and FibroMeter VCTE outperformed FIB-4 for all fibrosis endpoints. These data represent a milestone toward qualification of several biomarker panels for at-risk NASH and also fibrosis severity in individuals with NAFLD.

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