Tag: nevin manimala

Genomics Proteomics Bioinformatics. 2024 Nov 22:qzae083. doi: 10.1093/gpbjnl/qzae083. Online ahead of print.

ABSTRACT

Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, with personalized medicine, systems biology, and biomedical applications. The application of MS-based proteomics advances our understanding of protein function, cellular signaling, and complex biological systems. MS data analysis is a critical process that includes identifying and quantifying proteins and peptides and then exploring their biological functions in downstream analysis. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets with DIA-NN preinstalled. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analyses. ProtPipe provides downstream analyses, including protein and peptide differential abundance identification, pathway enrichment analysis, protein-protein interaction analysis, and Major histocompatibility complex (MHC) -peptide binding affinity analysis. ProtPipe generates annotated tables and visualizations by performing statistical postprocessing and calculating fold changes between predefined pairwise conditions in an experimental design. It is an open-source, well-documented tool available online at https://github.com/NIH-CARD/ProtPipe, with a user-friendly web interface.

PMID:39576693 | DOI:10.1093/gpbjnl/qzae083

Interact J Med Res. 2024 Nov 22;13:e60942. doi: 10.2196/60942.

ABSTRACT

BACKGROUND: Chronically elevated inflammation is implicated in many conditions, including obesity, metabolic syndrome, and cardiovascular disease, and has been associated with increased mortality risk. Whole-body cryotherapy (W-BC) is a promising modality to treat inflammation with demonstrated benefits for clinical subpopulations including those with arthritis, obesity, and type 2 diabetes. However, it is unclear whether the benefit from W-BC extends to healthy individuals prior to chronic disease-related inflammation. In addition, the long-term durability of W-BC effect is unknown.

OBJECTIVE: This study investigates the inflammatory response to W-BC in healthy adults with a biomarker of inflammation, high-sensitivity C-reactive protein (hsCRP), and clinical biomarkers of metabolism including fasting glucose, hemoglobin A_1c (HbA_1c), low-density lipoprotein (LDL) and high-density lipoprotein (HDL), and triglycerides.

METHODS: Fifteen individuals (n=9 female) participated in frequent recreational W-BC (3 minutes of cold exposure at -110 ℃) over approximately 9 months and had blood draws at baseline plus follow-up visits. Biomarkers were modeled as linear functions of W-BC sessions received in the month prior to blood draw.

RESULTS: The mean amount of W-BC received was 6.78 (SD 4.26) times per month with the cumulative total ranging from 13 to 157 W-BC sessions over the course of the study. On average, participants completed 1-2 sessions per week throughout the intervention. The number of W-BC sessions were associated with decreased hsCRP (-0.14 mg/L in hsCRP per W-BC session; P<.01) and with durability of up to 9 months. Increased W-BC was also associated with a downward trend in fasting glucose. This trend failed to reach significance at 1 month (-0.73 mg/dL in fasting glucose per W-BC session; P<.10) but was significant for 2- and 3-month windows (P<.05). HbA_1c was increased significantly after 9 months (P<.01); however, the change occurred within normal ranges (difference=0.13% and <5.7%) and was not clinically significant. There was no association between W-BC and LDL cholesterol, HDL cholesterol, or triglycerides (P>.10), although LDL trended lower over the time period examined (P=.07).

CONCLUSIONS: These results suggest that W-BC beneficially impacts systemic inflammation by lowering hsCRP levels in healthy individuals and may also have some modulating effect on fasting glucose.

PMID:39576692 | DOI:10.2196/60942

JMIR Diabetes. 2024 Nov 22;9:e63434. doi: 10.2196/63434.

ABSTRACT

BACKGROUND: The management of type 2 diabetes mellitus (T2DM) includes mastery of complex care activities, self-management skills, and routine health care encounters to optimize glucose control and achieve good health. Given the lifelong course of T2DM, patients are faced with navigating complex medical and disease-specific information. This health-seeking behavior is a driver of health disparities and is associated with hospitalization and readmission. Given that health-seeking behavior is a potentially intervenable social determinant of health, a better understanding of how people navigate these complex systems is warranted.

OBJECTIVE: To address this need, we aimed to develop new patient-reported outcome (PRO) measures that evaluate health-seeking behavior in persons with T2DM. These new PROs were designed to be included in the Re-Engineered Discharge for Diabetes-Computer Adaptive Test (REDD-CAT) measurement system, which includes several other PROs that capture the importance of social determinants of health.

METHODS: Overall, 225 participants with T2DM completed 56 self-report items that examined health-seeking behaviors. Classical Test Theory and Item Response Theory were used for measurement development. Exploratory factor analysis (EFA; criterion ratio of eigenvalue 1 to eigenvalue 2 being >4; variance for eigenvalue 1 ≥40%) and confirmatory factor analysis (CFA; criterion 1-factor CFA loading <.50; 1-factor CFA residual correlation >.20; comparative fit index ≥0.90; Tucker-Lewis index ≥0.90; root mean square error of approximation <0.15) were used to determine unidimensional sets of items. Items with sparse responses, low-adjusted total score correlations, nonmonotonicity, low factor loading, and high residual correlations of high error modification indices were candidates for exclusion. A constrained graded response model was used to examine item misfit, and differential item functioning was examined to identify item bias. Cronbach α was used to examine internal consistency reliability for the new PROs (criterion ≥0.70), and floor and ceiling effects were examined (criterion ≤20%).

RESULTS: Four unidimensional sets of items were supported by EFA (all EFA eigenvalue ratios >4; variance for eigenvalue 1=41.4%-67.3%) and CFA (fit statistics all exceeded criterion values). This included (1) “Health-Seeking Behavior: PCP-Specific” (6 items); (2) “Health-Seeking Behavior: General Beliefs” (13 items); (3) “Health-Seeking Behavior: Family or Friends-Specific” (5 items); and (4) “Health-Seeking Behavior: Internet-Specific” (4 items). All items were devoid of differential item functioning for age, sex, education, or socioeconomic status factors. “Health-Seeking Behavior: General Beliefs” was developed to include both a computer adaptive test and a 6-item short form version; all other PROs were developed as static short forms. The psychometric reliability of these new PROs was supported; internal consistency ranged from acceptable to excellent (Cronbach α=.78-.91), and measures were free of significant floor or ceiling effects (floor effects range: 0%-8.9%; ceiling effects range: 0%-8.4%).

CONCLUSIONS: The new REDD-CAT Health-Seeking Behavior PROs provide reliable assessments of health-seeking behaviors among those with T2DM.

PMID:39576685 | DOI:10.2196/63434

Ophthalmic Plast Reconstr Surg. 2024 Nov 22. doi: 10.1097/IOP.0000000000002722. Online ahead of print.

ABSTRACT

PURPOSE: To employ a validated survey for evaluation of quality of life (QoL) outcomes and associated factors in a US cohort of adult patients with acquired anophthalmia wearing a prosthesis.

METHODS: A retrospective cohort study was performed at a single, US academic institution of patients cared for between 2012 and 2021. The electronic medical record database was queried for adult patients with a history of evisceration or enucleation surgery and placement of an orbital implant. Identified patients were asked to anonymously complete a validated QoL questionnaire from which the Global Ocular Prosthesis Score was assessed. Summary statistics were reported, and analysis of variance was used to determine surgical and demographic factors associated with QoL survey scores.

RESULTS: A total of 81 patients completed the questionnaire. Mean age was 45.8 years (range: 18-96 years), and 54.3% of patients identified as women. Enucleation was performed in 81.4% of eyes (n = 66), while the remaining 17.3% underwent evisceration (n = 14). The mean and median Global Ocular Prosthesis Score (out of 100) were 67.51 and 68.00, respectively. Multivariate analysis demonstrated the etiologies of glaucoma (95% confidence interval: 0.84-25.40, p = 0.04) and endophthalmitis (95% confidence interval: 0.41-23.72, p = 0.04) to be significantly associated with higher total Global Ocular Prosthesis Score. Several other factors including employment status, etiology of anophthalmia, gender, and level of education were also significantly associated with subdomain scores (p < 0.05).

CONCLUSIONS: Among patients with anophthalmia wearing an ocular prosthesis, the etiology of anophthalmia was significantly associated with the Global Ocular Prosthesis Score. Employment status, etiology of anophthalmia, gender, and level of education were also observed to have statistically significant associations with subdomain scores. Knowledge of these factors moving forward may help the surgeon manage expectations, mitigate challenges, and promote higher QoL outcomes for patients with acquired anophthalmia.

PMID:39576673 | DOI:10.1097/IOP.0000000000002722

Int J Methods Psychiatr Res. 2024 Dec;33(4):e70000. doi: 10.1002/mpr.70000.

NO ABSTRACT

PMID:39576663 | DOI:10.1002/mpr.70000

JAMA Netw Open. 2024 Nov 4;7(11):e2429630. doi: 10.1001/jamanetworkopen.2024.29630.

ABSTRACT

IMPORTANCE: Test accuracy studies often use small datasets to simultaneously select an optimal cutoff score that maximizes test accuracy and generate accuracy estimates.

OBJECTIVE: To evaluate the degree to which using data-driven methods to simultaneously select an optimal Patient Health Questionnaire-9 (PHQ-9) cutoff score and estimate accuracy yields (1) optimal cutoff scores that differ from the population-level optimal cutoff score and (2) biased accuracy estimates.

DESIGN, SETTING, AND PARTICIPANTS: This study used cross-sectional data from an existing individual participant data meta-analysis (IPDMA) database on PHQ-9 screening accuracy to represent a hypothetical population. Studies in the IPDMA database compared participant PHQ-9 scores with a major depression classification. From the IPDMA population, 1000 studies of 100, 200, 500, and 1000 participants each were resampled.

MAIN OUTCOMES AND MEASURES: For the full IPDMA population and each simulated study, an optimal cutoff score was selected by maximizing the Youden index. Accuracy estimates for optimal cutoff scores in simulated studies were compared with accuracy in the full population.

RESULTS: The IPDMA database included 100 primary studies with 44 503 participants (4541 [10%] cases of major depression). The population-level optimal cutoff score was 8 or higher. Optimal cutoff scores in simulated studies ranged from 2 or higher to 21 or higher in samples of 100 participants and 5 or higher to 11 or higher in samples of 1000 participants. The percentage of simulated studies that identified the true optimal cutoff score of 8 or higher was 17% for samples of 100 participants and 33% for samples of 1000 participants. Compared with estimates for a cutoff score of 8 or higher in the population, sensitivity was overestimated by 6.4 (95% CI, 5.7-7.1) percentage points in samples of 100 participants, 4.9 (95% CI, 4.3-5.5) percentage points in samples of 200 participants, 2.2 (95% CI, 1.8-2.6) percentage points in samples of 500 participants, and 1.8 (95% CI, 1.5-2.1) percentage points in samples of 1000 participants. Specificity was within 1 percentage point across sample sizes.

CONCLUSIONS AND RELEVANCE: This study of cross-sectional data found that optimal cutoff scores and accuracy estimates differed substantially from population values when data-driven methods were used to simultaneously identify an optimal cutoff score and estimate accuracy. Users of diagnostic accuracy evidence should evaluate studies of accuracy with caution and ensure that cutoff score recommendations are based on adequately powered research or well-conducted meta-analyses.

PMID:39576645 | DOI:10.1001/jamanetworkopen.2024.29630

JAMA Netw Open. 2024 Nov 4;7(11):e2446901. doi: 10.1001/jamanetworkopen.2024.46901.

ABSTRACT

IMPORTANCE: The COVID-19 pandemic has placed a burden on the health of many people, including significant disparities in American Indian and Alaska Native communities.

OBJECTIVE: This study examines the associations between coping behaviors, social support, and emotional health among American Indian and Alaska Native peoples during the COVID-19 pandemic.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study included survey data collected from November 2021 to May 2022 from American Indian and Alaska Native adults aged 18 years or older without dementia or other serious cognitive impairments who were seen at 6 urban health organizations primarily in urban settings (in New Mexico, Alaska, Colorado, Minnesota, Utah, and Kansas) in the year prior to the survey.

EXPOSURES: Exposures of interest included avoidant and direct problem-solving coping behaviors and functional and emotional social support.

MAIN OUTCOME AND MEASURES: The study outcome was self-reported change in emotional health since COVID-19 pandemic onset. Poisson regression was used to model adjusted multivariate associations. Data were weighted to account for age, nonresponse, and disproportionate representation by clinic population.

RESULTS: A total of 1164 participants were included in the analysis, with a mean (SD) age of 42.5 (13.4) years; 830 (61%, weighted sample percentage) were female. Since COVID-19 pandemic onset, 465 patients (39% weighted) reported worsened emotional health. Problem-solving coping mean (SD) utilization score was 2.5 (0.5), avoidant coping mean (SD) utilization score was 2.3 (0.5), mean (SD) functional social support score was 11.4 (2.9), and 219 participants (18% weighted) reported that emotional support was always available. Using problem-solving coping skills was associated with better emotional health (adjusted prevalence ratio [APR], 0.66 [95% CI, 0.54-0.81] for highest vs lowest tertile), as was always (vs never or rarely) getting emotional support (APR, 0.40; 95% CI, 0.30-0.55) and having more functional support (APR, 0.90 [95% CI, 0.87-0.92] per 1-unit increase in functional social support). In examination of psychological resilience potentially modifying primary exposure associations, no interactions were statistically significant.

CONCLUSIONS AND RELEVANCE: In this cross-sectional study of urban American Indian and Alaska Native peoples, problem-solving coping skills and more social support were associated with better emotional health during the COVID-19 pandemic. These findings can be used to identify strengths-based approaches to support community emotional health during social upheavals.

PMID:39576639 | DOI:10.1001/jamanetworkopen.2024.46901

JAMA Netw Open. 2024 Nov 4;7(11):e2448714. doi: 10.1001/jamanetworkopen.2024.48714.

ABSTRACT

IMPORTANCE: Understanding the association of artificial intelligence (AI) with physician burnout is crucial for fostering a collaborative interactive environment between physicians and AI.

OBJECTIVE: To estimate the association between AI use in radiology and radiologist burnout.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study conducted a questionnaire survey between May and October 2023, using the national quality control system of radiology in China. Participants included radiologists from 1143 hospitals. Radiologists reporting regular or consistent AI use were categorized as the AI group. Statistical analysis was performed from October 2023 to May 2024.

EXPOSURE: AI use in radiology practice.

MAIN OUTCOMES AND MEASURES: Burnout was defined by emotional exhaustion (EE) or depersonalization according to the Maslach Burnout Inventory. Workload was assessed based on working hours, number of image interpretations, hospital level, device type, and role in the workflow. AI acceptance was determined via latent class analysis considering AI-related knowledge, attitude, confidence, and intention. Propensity score-based mixed-effect generalized linear logistic regression was used to estimate the associations between AI use and burnout and its components. Interactions of AI use, workload, and AI acceptance were assessed on additive and multiplicative scales.

RESULTS: Among 6726 radiologists included in this study, 2376 (35.3%) were female and 4350 (64.7%) were male; the median (IQR) age was 41 (34-48) years; 3017 were in the AI group (1134 [37.6%] female; median [IQR] age, 40 [33-47] years) and 3709 in the non-AI group (1242 [33.5%] female; median [IQR] age, 42 [34-49] years). The weighted prevalence of burnout was significantly higher in the AI group compared with the non-AI group (40.9% vs 38.6%; P < .001). After adjusting for covariates, AI use was significantly associated with increased odds of burnout (odds ratio [OR], 1.20; 95% CI, 1.10-1.30), primarily driven by its association with EE (OR, 1.21; 95% CI, 1.10-1.34). A dose-response association was observed between the frequency of AI use and burnout (P for trend < .001). The associations were more pronounced among radiologists with high workload and lower AI acceptance. A significant negative interaction was noted between high AI acceptance and AI use.

CONCLUSIONS AND RELEVANCE: In this cross-sectional study of radiologist burnout, frequent AI use was associated with an increased risk of radiologist burnout, particularly among those with high workload or lower AI acceptance. Further longitudinal studies are needed to provide more evidence.

PMID:39576636 | DOI:10.1001/jamanetworkopen.2024.48714

Invest Ophthalmol Vis Sci. 2024 Nov 4;65(13):48. doi: 10.1167/iovs.65.13.48.

ABSTRACT

PURPOSE: The purpose of this study was to assess fine motor skills and reading proficiency in adults with amblyopia and/or strabismus, and to determine how these relate to clinical measures of vision and self-reported vision-related quality of life.

METHODS: Fine motor skills (Manual dexterity – Bruininks-Oseretsky Test of Motor Proficiency [BOT-2]) and reading performance (International Reading Speed Texts [IReST]) were assessed in 23 adults with non-strabismic amblyopia, 20 with non-amblyopic strabismus, 52 with both amblyopia and strabismus, and 19 with normal visual development. Visual acuity and binocular function score (BFS), obtained from stereoacuity and presence/absence of suppression, were also determined. Vision-related quality of life was assessed with the Amblyopia and Strabismus Questionnaire (A&SQ) in those with amblyopia and/or strabismus. Statistical analysis included ANOVA and multiple regression models.

RESULTS: Participants with amblyopia and/or strabismus exhibited poorer performance in all five manual dexterity sub-items and the overall standardized score (P < 0.05). The reading rate was significantly slower across all amblyopia/strabismus groups (P < 0.05). Poorer fine motor skills and slower reading performance were associated with each other (R = 0.29). Clinical visual characteristics (visual acuity [VA], BFS, and presence of strabismus) explained 39% of the variance in fine motor skills score (R2 = 0.39), however, these explained only 6% of the variance in reading speed (R2 = 0.06). Self-report of functional ability related most to BFS, whereas psychosocial impact related to the presence of strabismus. The clinical and functional characteristics predicted 4% of the variance in functional impact score (R2 = 0.038) and explained 16% of the variance in psychosocial impact score (R2 = 0.16).

CONCLUSIONS: The functional and psychosocial effects of amblyopia and strabismus are common and persist into adulthood, with outcomes inadequately accounted for by clinical measures of vision.

PMID:39576625 | DOI:10.1167/iovs.65.13.48

JAMA Health Forum. 2024 Nov 1;5(11):e244156. doi: 10.1001/jamahealthforum.2024.4156.

ABSTRACT

IMPORTANCE: Telemedicine is an increasingly used yet understudied vehicle to deliver pediatric primary care. Evidence detailing downstream health care utilization after telemedicine visits is needed.

OBJECTIVE: To compare pediatric primary care conducted via telemedicine (video or telephone) with in-person office visits with regard to physician medication prescribing and imaging and laboratory ordering and downstream follow-up office visits, emergency department (ED) visits, and hospitalizations.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study included all patients younger than 18 years who had scheduled primary care appointments with a pediatrician from January 1 to December 31, 2022, in the Kaiser Permanente Northern California health system, a large integrated health care delivery system offering in-person office visits, video visits, or telephone visits for pediatric primary care.

EXPOSURE: Pediatric primary care in-person visit, telephone visit, or video visit.

MAIN OUTCOME AND MEASURES: Rates of physician medication prescribing and imaging and laboratory ordering during an index telemedicine or office visit and rates of in-person office visits, ED visits, and hospitalizations within 7 days after the visit, adjusted for patient and clinical characteristics.

RESULTS: Of 782 596 total appointments (51.1% male) among 438 638 patients, telemedicine was used for 332 153 visits (42.4%). After adjustment, there was more medication prescribing for in-person visits (39.8%) compared with video visits (29.5%; adjusted difference, -10.3%; 95% CI, -10.6% to -10.0%) or telephone visits (27.3%; adjusted difference, -12.5%; 95% CI, -12.5% to -12.7%). There was also more laboratory ordering for in-person visits (24.6%) compared with video visits (7.8%; adjusted difference, -16.8%; 95% CI, -17.0% to -16.6%) or telephone visits (8.5%; adjusted difference, -16.2%; 95% CI, -16.3% to -16.0%). There was more imaging ordering for in-person visits (8.5%) compared with video visits (4.0%; adjusted difference, -4.5%; 95% CI, -4.6% to -4.4%) and telephone visits (3.5%; adjusted difference, -5.0%; 95% CI, -5.1% to -4.9%). After adjustment, fewer in-person follow up visits occurred for index visits that were in-person (4.3%) compared with video (14.4%; adjusted difference, 10.1%; 95% CI, 9.9%-10.3%) or telephone (15.1%; adjusted difference, 10.8%; 95% CI, 10.7%-11.0%) visits. The rate of ED visits following an in-person visit was slightly lower (1.75%) compared with after video visits (2.04%; adjusted difference, 0.29%; 95% CI, 0.21%-0.38%) or telephone visits (2.00%; adjusted difference, 0.25%; 95% CI, 0.18%-0.33%). There was no statistically significant difference in the 7-day rate of hospitalizations.

CONCLUSIONS AND RELEVANCE: In this cohort study, telephone and video visits for pediatric primary care were associated with less prescribing and ordering than in-person visits. Telemedicine visits were associated with modestly higher rates of subsequent in-person visits and slightly higher rates of ED visits, and there was no difference in hospitalizations. Telemedicine appears to be a useful vehicle for health care delivery in the pediatric population, although it is not a universal substitute for in-person visits.

PMID:39576615 | DOI:10.1001/jamahealthforum.2024.4156