Category: Statistics

J Health Organ Manag. 2021 Sep 2;ahead-of-print(ahead-of-print). doi: 10.1108/JHOM-12-2020-0479.

ABSTRACT

PURPOSE: This study examines the relationship between workplace bullying (WPB) and the turnover intentions (TIs) of nurses, both directly and indirectly, i.e. through serial mediation of psychological contract violation (PCV) and poor employee wellbeing (EWB). And that with the moderating effect of servant leadership (SL) on its final path to TIs of nurses.

DESIGN/METHODOLOGY/APPROACH: A total of 285 nurses voluntarily participated in the survey through convenient sampling from 13 different district hospitals. The authors performed partial least squares structural equation modeling (PLS-SEM) to test the study’s measurement and structural models.

FINDINGS: Overall, results indicated 62% prevalence rate of WPB and TIs of nurses had 67% variance explained by the exogenous factors. Workplace bullying was found to have direct as well as indirect relationship with TIs of nurses. For the latter, PCV and poor EWB were found to have partially mediated, both singly and serially. The moderating effect of SL on the serial mediation pathway was negative and significant.

ORIGINALITY/VALUE: Drawing on a tripartite theoretical perspective, this study illuminates the mechanism underlying WPB-TIs relationship with an advanced multivariate statistical technique in the nursing work setting in a developing country.

PMID:34469664 | DOI:10.1108/JHOM-12-2020-0479

Int J Cancer. 2021 Sep 1. doi: 10.1002/ijc.33790. Online ahead of print.

ABSTRACT

Lynch syndrome (LS), Lynch-like syndrome (LLS), and familial colorectal cancer type X (FCCX) are different entities of familial cancer predisposition leading to an increased risk of colorectal cancer (CRC). The aim of this prospective study was to characterize and to compare the risks for adenoma and CRC in these three risk groups. Data was taken from the registry of the German Consortium for Familial Intestinal Cancer. Patients were prospectively followed up in an intensified colonoscopic surveillance programme that included annual examinations. Cumulative risks for adenoma and CRC were calculated separately for LS, LLS, and FCCX, and then for males and females. Multivariate Cox regression was used to analyse the independent contributions of risk group, mismatch repair gene (within LS), sex, and previous adenoma. The study population comprised 1448 individuals (103 FCCX, 481 LLS and 864 LS). The risks were similar for colorectal adenomas, but different for first and metachronous CRC between the three risk groups. CRC risk was highest in LS, followed by LLS, and lowest in FCCX. Male sex and a prevalent adenoma in the index colonoscopy were associated with a higher risk for incident adenoma and CRC. In patients with LS, CRC risks were particularly higher in female MSH2 than MLH1 carriers. This study may support the development of risk-adapted surveillance policies in LS, LLS and FCCX. This article is protected by copyright. All rights reserved.

PMID:34469588 | DOI:10.1002/ijc.33790

Acta Paediatr. 2021 Sep 1. doi: 10.1111/apa.16084. Online ahead of print.

ABSTRACT

AIM: We investigated timing of survival differences and effects on morbidity for fetuses alive at maternal admission to hospital delivered at 22 to 26 weeks’ gestational age (GA).

METHODS: Data for from the EXPRESS (Sweden, 2004-07), EPICure-2 (England, 2006), and EPIPAGE- 2 (France, 2011) cohorts were harmonised. Survival, stratified by GA, was analysed to 112 days using Kaplan-Meier analyses and Cox regression adjusted for population and pregnancy characteristics; neonatal morbidities, survival to discharge and follow-up, and outcomes at 2-3 years of age were compared.

RESULTS: Among 769 EXPRESS, 2310 EPICure-2 and 1359 EPIPAGE-2 fetuses, 112-day survival was, respectively, 28.2%, 10.8% and 0.5% at 22-23 weeks’ GA; 68.5%, 40.0% and 23.6% at 24 weeks; 80.5%, 64.8% and 56.9% at 25 weeks; and 86.6%, 77.1% and 74.4% at 26 weeks. Deaths were most marked in EPIPAGE-2 before 1 day at 22-23 and 24 weeks GA. At 25 weeks, survival varied before 28 days; differences at 26 weeks were minimal. Cox analyses were consistent with the Kaplan-Meier analyses. Variations in morbidities were not clearly associated with survival.

CONCLUSION: Differences in survival and morbidity outcomes for extremely preterm births are evident despite adjustment for background characteristics. No clear relationship was identified between early mortality and later patterns of morbidity.

PMID:34469604 | DOI:10.1111/apa.16084

J Natl Cancer Inst. 2021 Sep 1:djab169. doi: 10.1093/jnci/djab169. Online ahead of print.

ABSTRACT

BACKGROUND: Tumors with homologous recombination (HR) deficiency (HRD) show high sensitivity to platinum salts and PARP-inhibitors in several malignancies. In colorectal cancer (CRC), the role of HRD alterations is mostly unknown.

METHODS: Next generation sequencing, whole transcriptome sequencing and whole exome sequencing were conducted using CRC samples submitted to a commercial Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Tumors with pathogenic/presumed pathogenic mutations in 33 genes involved in the HR pathway were considered HRD, the others HR proficient (HRP). Furthermore, tumor samples from patients enrolled in the phase III TRIBE2 study comparing upfront FOLFOXIRI/bevacizumab versus FOLFOX/bevacizumab were analyzed with next generation sequencing. The analyses were separately conducted in microsatellite stable/proficient mismatch repair (MSS/pMMR) and microsatellite instable-high/deficient mismatch repair (MSI-H/dMMR) groups. All statistical tests were 2-sided.

RESULTS: Of 9321 CRC tumors, 1270 (13.6%) and 8051 (86.4%) were HRD and HRP, respectively. HRD tumors were more frequent among MSI-H/dMMR than MSS/pMMR tumors (73.4% vs 9.5%, p and q < 0.001). In MSS/pMMR group, HRD tumors were more frequently tumor mutational burden high (8.1% vs 2.2% P and q < 0.001) and PD-L1 positive (5.0% vs 2.4%, P and q = 0.001), enriched in all immune cell and fibroblast populations, and genomic loss of heterozygosity-high (16.2% vs 9.5%, P = .03). In the TRIBE2 study, patients with MSS/pMMR and HRD tumors (10.7%) showed longer overall survival compared to MSS/pMMR and HRP ones (40.2 vs 23.8 months; hazard ratio = 0.66; 95% confidence interval = 0.45-0.98, P = .04). Consistent results were reported in the multivariable model (hazard ratio = 0.67; 95% confidence ratio = 0.45-1.02, P = .07). No interaction effect was evident between HR groups and treatment arm.

CONCLUSIONS: HRD tumors are a distinctive subgroup of MSS/pMMR CRCs with specific molecular and prognostic characteristics. The potential efficacy of agents targeting the HR system and immune check-point inhibitors in this subgroup is worth of clinical investigation.

PMID:34469533 | DOI:10.1093/jnci/djab169

Syst Biol. 2021 Sep 1:syab073. doi: 10.1093/sysbio/syab073. Online ahead of print.

ABSTRACT

Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the Effective Sequence Length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set of equal size, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification.

PMID:34469581 | DOI:10.1093/sysbio/syab073

Bioinformatics. 2021 Sep 1:btab629. doi: 10.1093/bioinformatics/btab629. Online ahead of print.

ABSTRACT

MOTIVATION: Each year, the number of published bulk and single-cell RNA-seq data sets is growing exponentially. Studies analyzing such data are commonly looking at gene-level differences, while the collected RNA-seq data inherently represents reads of transcript isoform sequences. Utilizing transcriptomic quantifiers, RNA-seq reads can be attributed to specific isoforms, allowing for analysis of transcript-level differences. A differential transcript usage (DTU) analysis is testing for proportional differences in a gene’s transcript composition, and has been of rising interest for many research questions, such as analysis of differential splicing or cell type identification.

RESULTS: We present the R package DTUrtle, the first DTU analysis workflow for both bulk and single-cell RNA-seq data sets, and the first package to conduct a ‘classical’ DTU analysis in a single-cell context. DTUrtle extends established statistical frameworks, offers various result aggregation and visualization options and a novel detection probability score for tagged-end data. It has been successfully applied to bulk and single-cell RNA-seq data of human and mouse, confirming and extending key results. Additionally, we present novel potential DTU applications like the identification of cell type specific transcript isoforms as biomarkers.

AVAILABILITY: The R package DTUrtle is available at https://github.com/TobiTekath/DTUrtle with extensive vignettes and documentation at https://tobitekath.github.io/DTUrtle/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34469510 | DOI:10.1093/bioinformatics/btab629

Mol Biol Evol. 2021 Sep 1:msab266. doi: 10.1093/molbev/msab266. Online ahead of print.

ABSTRACT

Insertions and deletions (indels) are common molecular evolutionary events. However, probabilistic models for indel evolution are under-developed due to their computational complexity. Here we introduce several improvements to indel modeling: (1) While previous models for indel evolution assumed that the rates and length distributions of insertions and deletions are equal, here we propose a richer model that explicitly distinguishes between the two; (2) We introduce numerous summary statistics that allow Approximate Bayesian Computation (ABC) based parameter estimation; (3) We develop a method to correct for biases introduced by alignment programs, when inferring indel parameters from empirical datasets; (4) Using a model-selection scheme we test whether the richer model better fits biological data compared to the simpler model. Our analyses suggest that both our inference scheme and the model-selection procedure achieve high accuracy on simulated data. We further demonstrate that our proposed richer model better fits a large number of empirical datasets and that, for the majority of these datasets, the deletion rate is higher than the insertion rate.

PMID:34469521 | DOI:10.1093/molbev/msab266

PLoS One. 2021 Sep 1;16(9):e0256896. doi: 10.1371/journal.pone.0256896. eCollection 2021.

ABSTRACT

Determining the level of customer satisfaction in cleanliness regarding a product or service is a significant aspect of businesses. However, the availability of feedback tools for consumers to evaluate the cleanliness of a restaurant is a crucial issue as several aspects of cleanliness need to be evaluated collectively. To overcome this issue, this study designed a survey instrument based on the standard form used for grading the food premises and transformed it into a seven Likert scale questionnaire and consists of seven questions. This study employed fuzzy conjoint analysis to measure the level of satisfaction in cleanliness in food premises. This pilot study recruited 30 students in Universiti Teknologi MARA (UiTM) Seremban 3. The student’s perception was represented by the scores calculated based on their degree of similarities and corresponding levels of satisfaction, whereby, only scores with the highest degree of similarity were selected. Furthermore, this study identified the aspects of hygiene that assessed based on the customers’ satisfaction upon visiting the premises. The results indicated that the fuzzy conjoint analysis produced a similar outcome as the statistical mean, thus, was useful for the evaluation of customer satisfaction on the cleanliness of food premises.

PMID:34469489 | DOI:10.1371/journal.pone.0256896

PLoS One. 2021 Sep 1;16(9):e0257146. doi: 10.1371/journal.pone.0257146. eCollection 2021.

ABSTRACT

[This corrects the article DOI: 10.1371/journal.pone.0206033.].

PMID:34469490 | DOI:10.1371/journal.pone.0257146

PLoS One. 2021 Sep 1;16(9):e0256814. doi: 10.1371/journal.pone.0256814. eCollection 2021.

ABSTRACT

BACKGROUND &OBJECTIVES: Though there are studies to evaluate the effectiveness of blended learning in pharmacy education, most of them originate from USA and have used previous year students’ scores as control. Also there is less research in comparing use of self -regulated learning strategies between blended and other learning strategies. Primary aim was to evaluate the effectiveness of blended learning on knowledge score using clinical research modules. Secondary objective was designed to compare the use of self-regulated learning strategies between blended learning, web-based e-learning and didactic teaching.

MATERIALS AND METHODS: A prospective cluster randomized trial was conducted with didactic teaching as control and web-based e-learning and blended learning as interventions. The target population was final year Pharm D students. Outcome was assessed using a validated knowledge questionnaire, a motivated strategies for learning questionnaire and a feedback form. All statistical analyses were carried out using Statistical Package for Social Science (SPSS) Version 20.

RESULTS: A total of 241 students from 12 colleges completed the study. Mean knowledge score of students in blended learning group was higher than those in the didactic teaching and web- based e- learning program (64.26±18.19 Vs 56.65±8.73 Vs 52.11±22.06,p<0.001).Frequency of use of learning strategies namely rehearsal, elaboration, organization and critical thinking was statistically significantly higher in the blended learning group compared to those of didactic and web-based e-learning group (p<0.05) But there were no statistically significant difference of motivational orientations between didactic and blended learning group except strategies of extrinsic goal orientation and self-efficacy. Students preferred blended learning (86.5%) over didactic and web-based e-learning.

CONCLUSION: Blended learning approach is an effective way to teach clinical research module. Students of blended learning group employed all motivational and learning strategies more often than students of the didactic and web- based e-learning groups except strategies of intrinsic goal orientation, task value, control of learning belief and help seeking.

PMID:34469484 | DOI:10.1371/journal.pone.0256814