Tag: statistics

Biostatistics. 2023 Jul 11:kxad012. doi: 10.1093/biostatistics/kxad012. Online ahead of print.

ABSTRACT

Existing methods for fitting continuous time Markov models (CTMM) in the presence of covariates suffer from scalability issues due to high computational cost of matrix exponentials calculated for each observation. In this article, we propose an optimization technique for CTMM which uses a stochastic gradient descent algorithm combined with differentiation of the matrix exponential using a Padé approximation. This approach makes fitting large scale data feasible. We present two methods for computing standard errors, one novel approach using the Padé expansion and the other using power series expansion of the matrix exponential. Through simulations, we find improved performance relative to existing CTMM methods, and we demonstrate the method on the large-scale multiple sclerosis NO.MS data set.

PMID:37433567 | DOI:10.1093/biostatistics/kxad012

J Phys Act Health. 2023 Jul 11:1-9. doi: 10.1123/jpah.2022-0666. Online ahead of print.

ABSTRACT

BACKGROUND: There is little known about physical activity (PA) behaviors and its determinants in Cambodian adolescents, particularly with regard to the home and school settings. Therefore, we aimed to investigate these behaviors and determinants on their PA.

METHODS: The samples collected were from 168 high school students, aged 14-15 years. They were requested to complete the self-report PA questionnaire. Time spent in PA during weekday and weekend by school location and gender, and determinants on PA were analyzed. Differences in the mean values of the PA levels (in minutes) during weekday and the weekend between genders, and between school locations were analyzed using independent sample t tests. The percentage of students’ perceptions on the determinants were calculated. Chi-squared test was used to compare the differences in prevalence of students’ activities during their free time with respect to school location and gender.

RESULTS: The majority of the parents (86.9%-98.2%) demonstrated strong support for their children for academic work. Rural students spent an average time of moderate-to-vigorous PA greater than their counterparts from the urban areas during their weekend days (329.1 vs 239.2 min, respectively). Moderate to vigorous PA was likely to be higher during the weekends compared with weekdays among the boys (387.9 vs 361.4 min, respectively). Girls were more likely to spend their time on moderate to vigorous PA during the weekdays compared with the weekends (205.4 vs 180.5 min, respectively).

CONCLUSION: Consideration should be given to gender, school location, free time, and the environmental setting for the contextualization of more effective PA interventions with Cambodian youths.

PMID:37433521 | DOI:10.1123/jpah.2022-0666

J Natl Compr Canc Netw. 2023 Jul;21(7):715-723.e17. doi: 10.6004/jnccn.2023.7021.

ABSTRACT

BACKGROUND: Adolescents and young adults (AYAs) with advanced cancer often receive intensive end-of-life care, yet it is unclear if this is goal-concordant. Advance care planning (ACP) video tools may promote identification and communication of AYA preferences.

PATIENTS AND METHODS: We conducted a dual-site, 1:1 pilot randomized controlled trial of a novel video-based ACP tool in 50 dyads of AYA patients aged 18 to 39 years with advanced cancer and their caregivers. ACP readiness and knowledge, preferences for future care, and decisional conflict were obtained pre, post, and 3 months after the intervention and compared between groups.

RESULTS: Of the 50 AYA/caregiver dyads enrolled, 25 (50%) were randomized to the intervention. Participants primarily identified as female, white, and non-Hispanic. Most AYAs (76%) and caregivers (86%) identified their overall goal as life-prolonging preintervention; less identified this goal postintervention (42% AYAs; 52% caregivers). There was no significant difference in change in proportion of AYAs or caregivers choosing life-prolonging care, CPR, or ventilation between arms postintervention or at 3 months. The change in participant scores for ACP knowledge (AYAs and caregivers) and ACP readiness (AYAs) from preintervention to postintervention was greater in the video arm compared with the control arm; the difference in caregivers’ scores for decisional conflict from preintervention to postintervention in the video arm was statistically significant (15 vs 7; P=.005). Feedback from the video participants was overwhelmingly positive; of the 45 intervention participants who provided video feedback, 43 (96%) found the video helpful, 40 (89%) were comfortable viewing the video, and 42 (93%) indicated they would recommend the video to other patients facing similar decisions.

CONCLUSIONS: Most AYAs with advanced cancer and their caregivers preferred life-prolonging care in advanced illness, with fewer preferring this type of care postintervention. A brief video-based ACP tool was well-liked by participants and improved caregiver decisional certainty. Videos may be a useful tool to inform AYAs and caregivers about end-of-life care options and promote ACP discussions.

PMID:37433434 | DOI:10.6004/jnccn.2023.7021

Transpl Immunol. 2023 Jul 9:101891. doi: 10.1016/j.trim.2023.101891. Online ahead of print.

ABSTRACT

BACKGROUND: We have performed a retrospective analysis of anti-HLA class I MHC and class II MHC antibodies measured using a single antigen bead (SAB) assay and a panel reactive antibody (PRA) assay.

MATERIAL AND METHODS: A group of 256 patients with end-stage renal disease (ESRD) was tested for anti-HLA antibodies in the tissue typing laboratory between 2017 and 2020. In the cohort, the serum samples of patients waiting for transplantation were tested. Both the PRA and SAB tests of these patients were analyzed using the Luminex (Immucor) method. The threshold of positivity was accepted as median fluorescence intensities (MFI) ≥1000 for PRA screening and MFI ≥750 for SAB screening.

RESULTS: Overall, antibodies to HLA antigens were detected in 202 (78.9%) out of 256 patients in the PRA study. Antibodies against both class I/II antigens were detected only in 15.6% of these patients, whereas antibodies against only against class I HLA in 31.3% and only against class II HLA in 32.0%. By comparison, the SAB study found that 66.8% of patients were positive for HLA antigens. Furthermore, donor-specific antibodies (DSA) were detected in 52.0% of PRA-positive patients and 52.6% of SAB-positive patients. It was shown that 168 patients (83.2%) out of 202 PRA-positive patients were found to be SAB-positive. In addition, 51 patients negative in the SAB assay (94.4%) were also negative in the PRA assay. Statistical analysis established a significant correlation between the PRA and SAB positivity (p > 0.001). It was also shown that MFI ≥3000 PRA positivity for class I HLA antigens (p = 0.049) and MFI ≥5000 PRA positivity for class II antigens (p < 0.001) correlated with the SAB positivity in patients.

CONCLUSION: Our results showed the importance of both PRA and SAB assays to define the status of sensitization in patients.

PMID:37433395 | DOI:10.1016/j.trim.2023.101891

J Affect Disord. 2023 Jul 9:S0165-0327(23)00872-8. doi: 10.1016/j.jad.2023.07.042. Online ahead of print.

ABSTRACT

INTRODUCTION: The present article aimed to investigate 1) if mental health problems (depression and burnout including the dimensions; emotional exhaustion, mental distance and cognitive and emotional impairment) differed between nurses and physicians in Sweden, 2) if any differences were explained by differences in sex compositions, and 3) if any sex differences were larger within either of the two professions.

METHOD: Data were derived from a representative sample of nurses (n = 2903) and physicians (n = 2712) in 2022. Two scales were used to assess burnout (KEDS and BAT) and one to assess depression (SCL-6). The BAT scale has four sub-dimensions. Descriptive statistics and logistic regression were used to analyse each scale and dimension separately.

RESULTS: Results showed that 16-28 % of nurses and physicians reported moderate to severe symptoms of burnout. The prevalence differed between occupations across the scales and dimensions used. Nurses reported higher scores on KEDS while physicians reported higher scores on BAT including the four dimensions. Also, 7 % of nurses’ and 6 % of physicians’ score were above the cut-off for major depression. The inclusion of sex in the models changed the odds ratios of differences between doctors and nurses in all mental health dimensions except mental distance and cognitive impairment.

LIMITATIONS: This study was based on cross-sectional survey data which has some limitations.

CONCLUSION: Our study suggests that the prevalence of mental health problems is prominent among nurses and physicians in Sweden. Sex plays an important role in the difference in prevalence of mental health problems between the professions.

PMID:37433382 | DOI:10.1016/j.jad.2023.07.042

Int J Radiat Oncol Biol Phys. 2023 Jul 9:S0360-3016(23)07628-9. doi: 10.1016/j.ijrobp.2023.07.002. Online ahead of print.

ABSTRACT

BACKGROUND: Rectal dose delivered during prostate radiotherapy is associated with gastrointestinal toxicity. Treatment plans are commonly optimised using rectal dose-volume constraints, often whole-rectum relative-volumes (%). We investigate whether improved rectal contouring, use of absolute-volumes (cc) or rectal truncation might improve toxicity prediction.

MATERIALS/METHODS: Patients from the XXXXXX trial (receiving 74Gy/37 fractions (Fr) vs 60Gy/20Fr vs 57Gy/19Fr) were included if radiotherapy plans were available (2350/3216 patients), plus toxicity data for relevant analyses (2170/3216 patients). Whole solid rectum relative-volumes (%) dose-volume-histogram (DVH), as submitted by treating centre (original contour), was assumed standard-of-care. Three investigational rectal DVHs were generated: i) reviewed contour per XXXXXX protocol; ii) original contour absolute volumes (cc); iii) truncated original contour (two versions; ±0 and ±2cm from planning target volume (PTV)). Dose levels of interest (V30,40,50,60,70,74Gy) in 74Gy arm were converted by equivalent-dose-in-2Gy-fractions (EQD2_α/β=3Gy) for 60Gy/57Gy arms. Bootstrapped logistic models predicting late toxicities (frequency G1+/G2+, bleeding G1+/G2+, proctitis G1+/G2+, sphincter control G1+, stricture/ulcer G1+) were compared by area-under-curve (AUC) between standard-of-care and the three investigational rectal definitions.

RESULTS: The alternative dose/volume parameters were compared with the original relative-volume (%) DVH of the whole rectal contour, itself fitted as a weak predictor of toxicity (AUC range 0.57-0.65, across the 8 toxicity measures). There were no significant differences in toxicity prediction for: i) original vs reviewed rectal contours (AUCs 0.57-0.66, p-values 0.21-0.98); ii) relative- vs absolute-volumes (AUCs 0.56-0.63, p-values 0.07-0.91) iii) whole-rectum vs truncation at PTV±2cm (AUCs 0.57-0.65, p-values 0.05-0.99), nor PTV±0cm (AUCs 0.57-0.66, p-values 0.27-0.98).

CONCLUSIONS: We used whole-rectum relative-volume DVH, submitted by the treating centre, as the standard-of-care dosimetric predictor for rectal toxicity. There were no statistically significant differences in prediction performance when using central rectal contour review, use of absolute-volume dosimetry, nor rectal truncation relative to PTV. Whole-rectum relative-volumes were not improved upon for toxicity prediction and should remain standard-of-care.

PMID:37433374 | DOI:10.1016/j.ijrobp.2023.07.002

J Equine Vet Sci. 2023 Jul 9:104892. doi: 10.1016/j.jevs.2023.104892. Online ahead of print.

ABSTRACT

Accumulating high-speed exercise has been identified as a significant risk factor for catastrophic injuries in racing Thoroughbreds. Injuries, regardless of severity, are a main cause of withdrawal from the racing industry, raising animal welfare concerns and resulting in significant economic losses. While most of the current literature focuses on injuries incurred during racing rather than training, the present study aims to help fill this gap. As such, peripheral blood was collected weekly, prior to exercise or administration of medication, from eighteen, two-year-old Thoroughbreds throughout their first season of race training. Messenger RNA (mRNA) was isolated and used to analyze the expression of 34 genes via RT-qPCR. Statistical analysis of the non-injured horses (n=6) showed that 13 genes were significantly correlated with increasing average weekly furlong performance. Additionally, there was a negative correlation for CXCL1, IGFBP3, and MPO with both cumulative high-speed furlongs and week of training for all horses. Comparison of both groups showed opposing correlations between the anti-inflammation index (IL1RN, IL-10, and PTGS1) and average weekly furlong performance. Furthermore, evaluation of training effects on mRNA expression during the weeks surrounding injury, showed differences between groups in IL-13 and MMP9 at -3 and -2 weeks prior to injury. While some previously reported relationships between exercise adaptation and mRNA expression were not noted in this study, this may have been due to the small sample size. Several novel correlations, however, were identified and warrant further investigation as markers of exercise adaptation or potential risk for injury.

PMID:37433342 | DOI:10.1016/j.jevs.2023.104892

Sci Total Environ. 2023 Jul 9:165393. doi: 10.1016/j.scitotenv.2023.165393. Online ahead of print.

ABSTRACT

This study presents the development of a SARS-CoV-2 detection method for domestic wastewater and river water in Costa Rica, a middle-income country in Central America. Over a three-year period (November to December 2020, July to November 2022, and June to October 2022), 80 composite wastewater samples (43 influent and 37 effluent) were collected from a Wastewater Treatment Plant (SJ-WWTP) located in San José, Costa Rica. Additionally, 36 river water samples were collected from the Torres River near the SJ-WWTP discharge site. A total of three protocols for SARS-CoV-2 viral concentration and RNA detection and quantification were analyzed. Two protocols using adsorption-elution with PEG precipitation (Protocol A and B, differing in the RNA extraction kit; n = 82) were used on wastewater samples frozen prior to concentration, while wastewater (n = 34) collected in 2022 were immediately concentrated using PEG precipitation. The percent recovery of Bovine coronavirus (BCoV) was highest using the Zymo Environ Water RNA (ZEW) kit with PEG precipitation executed on the same day as collection (mean 6.06 % ± 1.37 %). It was lowest when samples were frozen and thawed, and viruses were concentrated using adsorption-elution and PEG concentration methods using the PureLink™ Viral RNA/DNA Mini (PLV) kit (protocol A; mean 0.48 % ± 0.23 %). Pepper mild mottle virus and Bovine coronavirus were used as process controls to understand the suitability and potential impact of viral recovery on the detection/quantification of SARS-CoV-2 RNA. Overall, SARS-CoV-2 RNA was detected in influent and effluent wastewater samples collected in 2022 but not in earlier years when the method was not optimized. The burden of SARS-CoV-2 at the SJ-WWTP decreased from week 36 to week 43 of 2022, coinciding with a decline in the national COVID-19 prevalence rate. Developing comprehensive nationwide surveillance programs for wastewater-based epidemiology in low-middle-income countries involves significant technical and logistical challenges.

PMID:37433341 | DOI:10.1016/j.scitotenv.2023.165393

Sci Total Environ. 2023 Jul 9:165423. doi: 10.1016/j.scitotenv.2023.165423. Online ahead of print.

ABSTRACT

The contribution of bio-based plastics in the global market is gradually growing and diversifying. Therefore, it is necessary to assess their environmental impact including the biotic parts of ecosystems. Earthworms are regarded as functionally essential and useful bioindicators of ecological disturbances in the terrestrial ecosystems. The purpose of this study was to evaluate the impact of three innovative bio-based plastics on earthworms Eisenia andrei in the long-term experiments. It comprised the mortality, body mass and reproduction ability of earthworms as well as the oxidative stress response. Regarding the latter the activities of catalase (CAT) and superoxide dismutase (SOD) involved in the antioxidant system of earthworms were determined. Two out of three bio-based materials tested were polylactic acid-based (PLA-based) plastics, while one was poly(hydroxybutyrate-co-valerate)-based (PHBV-based) plastic. Neither mortality nor weight of adult earthworms was affected even at high concentration of the bio-based plastics up to 12.5 % w/w in the soil. Reproduction ability occurred to be more sensitive endpoint than mortality or body mass. At the concentration of 12.5 % w/w each of the studied bio-based plastics contributed to the decrease of the earthworm reproduction at statistically significant level. PLA-based plastics exerted stronger effect on earthworm reproduction ability than PHBV-based plastic did. CAT activity turned out to be a good indicator of the cellular response against oxidative stress induced by bio-based plastics in earthworms. The activity of this enzyme increased in the response to the exposure to the bio-based plastics compared to the level achieved in the control tests. It was from 16 % to about 84 % dependent on the material tested and its concentration in the soil. Finally, the reproduction ability and catalase activity are recommended to be used in the evaluation of the potential impacts of bio-based plastics on earthworms.

PMID:37433336 | DOI:10.1016/j.scitotenv.2023.165423

J Integr Complement Med. 2023 Jul 11. doi: 10.1089/jicm.2022.0701. Online ahead of print.

ABSTRACT

Background: Several clinical trials support the efficacy of music therapy (MT) for improving outcomes in hospitalized patients, but few studies have evaluated the real-world delivery and integration of MT across multiple medical centers. This article describes the rationale, design, and population characteristics of a retrospective study examining the delivery and integration of MT within a large health system. Methods: A retrospective electronic health record (EHR) review was conducted of hospitalized patients seen by and/or referred to MT between January 2017 and July 2020. MT was provided across ten medical centers, including an academic medical center, a freestanding cancer center, and eight community hospitals. Discrete demographic, clinical, and MT treatment and referral characteristics were extracted from the EHR, cleaned, and organized using regular expressions functions, and they were summarized using descriptive statistics. Results: The MT team (average 11.6 clinical fulltime equivalent staff/year) provided 14,261 sessions to 7378 patients across 9091 hospitalizations. Patients were predominantly female (63.7%), White (54.3%) or Black/African American (44.0%), 63.7 ± 18.5 years of age at admission, and insured under Medicare (51.1%), Medicaid (18.1%), or private insurance (14.2%). Patients’ hospitalizations (median length of stay: 5 days) were primarily for cardiovascular (11.8%), respiratory (9.9%), or musculoskeletal (8.9%) conditions. Overall, 39.4% of patients’ hospital admissions included a mental health diagnosis, and 15.4% were referred to palliative care. Patients were referred by physicians (34.7%), nurses (29.4%), or advanced practice providers (24.7%) for coping (32.0%), anxiety reduction (20.4%), or pain management (10.1%). Therapists provided sessions to patients discharged from medical/surgical (74.5%), oncology (18.4%), or intensive care (5.8%) units. Conclusions: This retrospective study indicates that MT can be integrated across a large health system for addressing the needs of socioeconomically diverse patients. However, future research is needed to assess MT’s impact on health care utilization (i.e., length of stay and rates of readmission) and immediate patient-reported outcomes.

PMID:37433198 | DOI:10.1089/jicm.2022.0701