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Nevin Manimala Statistics

The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets

Mol Ecol Resour. 2021 Oct 1. doi: 10.1111/1755-0998.13522. Online ahead of print.

ABSTRACT

The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the ΔK method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of K and is sensitive to uneven sampling. If this finding holds for empirical datasets, conclusions about the scale of gene flow may have to be revised for a large number of studies. To determine the impact of method choice, we applied recently described estimators of K to re-estimate genetic structure in 41 empirical microsatellite datasets; 15 from a broad range of taxa and 26 focused on a diverse phylogenetic group, coral. We compared alternative estimates of K (Puechmaille statistics) with traditional (ΔK and posterior probability) estimates and found widespread disagreement of estimators across datasets. Thus, one estimator alone is insufficient for determining the optimal number of clusters regardless of study organism or evenness of sampling scheme. Subsequent analysis of molecular variance (AMOVA) between clustering solutions did not necessarily clarify which solution was best. To better infer population structure, we suggest a combination of visual inspection of STRUCTURE plots and calculation of the alternative estimators at various thresholds in addition to ΔK. Differences between estimators could reveal patterns with important biological implications, such as the potential for more population structure than previously estimated, as was the case for many studies reanalyzed here.

PMID:34597471 | DOI:10.1111/1755-0998.13522

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Nevin Manimala Statistics

Epithelial-mesenchymal transition in gingival tissues from chronic periodontitis patients: A case-control study

Dent Med Probl. 2021 Jul-Sep;58(3):311-319. doi: 10.17219/dmp/133514.

ABSTRACT

BACKGROUND: It has been proposed that epithelial-mesenchymal transition (EMT) is responsible for the pathogenesis of several diseases. However, the relationship between the EMT process and the severity of periodontitis has not been previously investigated.

OBJECTIVES: This study aimed to localize and quantitatively assess the expression of transforming growth factor-beta 1 (TGF-β1), vimentin and E-cadherin in correlation with the EMT process in human gingiva of periodontally diseased patients in comparison with halthy individuals.

MATERIAL AND METHODS: Gingival tissue samples from 36 participants were divided into 2 groups: the healthy (control) group (n = 9); and the periodontitis group (n = 27). The periodontitis group was further subclassified into mild, moderate and severe periodontitis subgroups (9 patients in each subgroup). The samples were subjected to histological staining, the histomorphometric analysis and the quantitative real-time polymerase chain reaction (RT‑PCR) analysis for TGF-β, vimentin and E-catherin. Statistical and correlation analyses were performed.

RESULTS: The hematoxylin and eosin (H&E) stain sections from both the moderate and severe periodontitis subgroups showed epithelial hyperplasia, perinuclear haloing and a marked increase in the inflammatory cell count as compared to the control group. The highest mean TGF-β1 and vimentin expression values were recorded in the severe periodontitis subgroup, whereas the lowest mean values were recorded in the control gingiva. On the contrary, the expression of E-catherin had the highest mean value in the control gingiva, whereas the lowest mean value was recorded in the severe periodontitis subgroup. All results were found to be statistically significant. The correlation analysis revealed a statistically significant positive correlation between the severity of periodontitis and the expression of TGF-β and vimentin, while a statistically significant inverse correlation was found between the expression of E-catherin and the severity of periodontitis.

CONCLUSIONS: There is a direct correlation between the severity of periodontitis and the expression of the EMT process markers (TGF-β and vimentin). This correlation indicates that EMT plays an important role in the pathogenesis and prognosis of periodontal disease. The data presented in this study could open the door for using anti-EMT agents in treating periodontal disease.

PMID:34597477 | DOI:10.17219/dmp/133514

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Nevin Manimala Statistics

Patient-reported symptoms and experience following Guillain-Barré syndrome and related conditions: Questionnaire development and validation

Health Expect. 2021 Oct 1. doi: 10.1111/hex.13367. Online ahead of print.

ABSTRACT

BACKGROUND: Guillain-Barré syndrome (GBS) is a rare inflammatory peripheral nerve disorder with variable recovery. Evidence is lacking on experiences of people with GBS and measurement of these experiences.

OBJECTIVE: We aimed to develop and validate an instrument to measure experiences of people with GBS.

DESIGN: We used a cross-sectional design and online self-administered questionnaire survey. Question domains, based on a previous systematic review and qualitative study, covered experiences of GBS, symptom severity at each stage, healthcare and factors supporting or hindering recovery. Descriptive, exploratory factor and reliability analyses and multivariable regression analysis were used to investigate the relationships between variables of interest, explore questionnaire reliability and validity and identify factors predicting recovery.

SETTING AND PARTICIPANTS: People with a previous diagnosis of GBS were recruited through a social media advert.

RESULTS: A total of 291 responders, of different sexes, and marital statuses, were included, with most diagnosed between 2015 and 2019. Factor analysis showed four scales: symptoms, information provided, factors affecting recovery and care received. Positive social interactions, physical activity including physiotherapy and movement, changes made at home and immunoglobulin treatment were important for recovery. Multivariable models showed that immunoglobulin and/or plasma exchange were significant predictors of recovery. Employment and recovery factors (positive interactions, work support and changes at work or home, physical activity and therapy), though associated with recovery, did not reach statistical significance.

CONCLUSION: The questionnaire demonstrated good internal reliability of scales and subscales and construct validity for people following GBS.

PATIENT CONTRIBUTION: Patients were involved in developing and piloting the questionnaire.

PMID:34597442 | DOI:10.1111/hex.13367

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Nevin Manimala Statistics

Clinical characteristics of and antibody response to spotted fever group rickettsial infections in South India: case series and serological cohort study

Trop Med Int Health. 2021 Oct 1. doi: 10.1111/tmi.13682. Online ahead of print.

ABSTRACT

OBJECTIVE: The clinical and serological characteristics of spotted fever group rickettsial (SFGR) infections in South Asia are poorly understood. We studied the clinical presentation and the IgM/IgG response in cases enrolled at two health care centres in South India.

METHOD: We enrolled 77 patients. 57 of these were recruited at a tertiary care centre, the remaining 20 at a community hospital (secondary care level). Diagnostic tests included IgM and IgG ELISA, and PCR. Over a period of one year, 41 cases were followed up for repeated sero-analysis.

RESULTS: Median age was 9 years (range 1 to 79). A rash was present in 74% of cases (57/77). In cases aged <15 years rash was present in 94% (44/47) vs 43% (13/30) in cases aged ≥15 years. An eschar was found in two cases (3%). Severe infection or complications occurred in 10 cases (13%). These included central nervous system infection (6/77, 8%), kidney injury (3/77, 4%), shock (3/77, 4%), lung involvement (2/77, 3%) and peripheral gangrene (2/77, 3%). IgM antibody levels increased faster after fever onset than IgG antibodies, peaking at 50 and 60 days respectively. After the peak, IgM and IgG levels showed a slow decline over one year with less than 50% of cases showing persistent IgG antibody levels.

CONCLUSION: SFGR infections in South India may be under-diagnosed, as many cases may not develop a rash. The proportion of cases developing severe infection seems lower than for scrub typhus in this region. IgG sero-prevalence may substantially under-estimate the proportion in a population with past SFGR infection.

PMID:34597443 | DOI:10.1111/tmi.13682

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Nevin Manimala Statistics

Prevalence of hearing protection device non-use among noise-exposed US workers in 2007 and 2014

Am J Ind Med. 2021 Oct 1. doi: 10.1002/ajim.23291. Online ahead of print.

ABSTRACT

BACKGROUND: This study estimated the prevalence of hearing protection device (HPD) non-use among US workers exposed to hazardous workplace noise and provided risk estimates.

METHODS: Self-reported data from the National Health Interview Survey in 2007 (15,852 workers) and 2014 (23,656 workers) were examined. Weighted prevalence and adjusted prevalence ratios of HPD non-use (using HPDs half the time or less when exposed to hazardous noise) were estimated by demographic, industry, and occupation. Differences in the prevalences of non-use were estimated and compared.

RESULTS: The prevalence of HPD non-use was 53% among all noise-exposed workers in 2014. Workers in the Accommodation and Food Services industry had the highest prevalence (90%) and risk (PR: 2.47, 95% confidence interval: 1.54-3.96) of HPD non-use. The industries with the lowest prevalences of noise exposure, including Finance and Insurance (2%) and Health Care and Social Assistance (4%), had some of the highest prevalences of HPD non-use (80% and 83%, respectively). There were no statistically significant changes in HPD non-use among industries between 2007 and 2014. Among occupations, HPD non-use increased 37% in Arts, Design, Entertainment, Sports and Media, and decreased 39% in Architecture and Engineering.

CONCLUSION: The prevalence of HPD non-use remains high; especially within industries and occupations with fewer noise-exposed workers. These groups need targeted attention to increase awareness and compliance. Employers should require HPD use and trainings among noise-exposed workers and provide an assortment of HPDs tailored to noise level and type, workplace environment, communication and audibility needs, and individual comfort and convenience.

PMID:34597431 | DOI:10.1002/ajim.23291

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Nevin Manimala Statistics

Taxonomic Chauvinism in Pesticide Ecotoxicology

Environ Toxicol Chem. 2021 Oct 1. doi: 10.1002/etc.5227. Online ahead of print.

NO ABSTRACT

PMID:34597437 | DOI:10.1002/etc.5227

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Nevin Manimala Statistics

Dissecting genomic determinants of positive selection with an evolution-guided regression model

Mol Biol Evol. 2021 Oct 1:msab291. doi: 10.1093/molbev/msab291. Online ahead of print.

ABSTRACT

In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald-Kreitman test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the McDonald-Kreitman test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their non-metabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation.

PMID:34597406 | DOI:10.1093/molbev/msab291

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Nevin Manimala Statistics

The effectiveness of an educational intervention to enhance undergraduate nursing students’ competence with interprofessional collaboration

Nurs Forum. 2021 Oct 1. doi: 10.1111/nuf.12655. Online ahead of print.

ABSTRACT

BACKGROUND: Interprofessional collaboration and teamwork have been identified as priorities for delivering quality client care. Improved teamwork, communication, and collaboration among healthcare professionals improve client outcomes. Nurse professionals are challenged to be equally engaged with other healthcare professionals to develop a culturally competent client-centered plan of care.

PURPOSE: The purpose of the current project was to examine the effectiveness of a multifaceted educational intervention on prelicensure nursing students’ development of interprofessional competencies with teams and teamwork, communication, roles and responsibility, values, and ethics.

METHODS: Metrics used included the Interprofessional Collaboration Competency Attainment (ICCAS) and the Assessment of Collaborative Environments (ACE-15) surveys.

RESULTS: The results support practical and statistical significance in the students’ self-reported collaborative competence across all items of the ICCAS at p < 0.000 level, and across each individual item.

CONCLUSIONS: The multifaceted educational strategy effectively engaged prelicensure nursing students with other healthcare disciplines to develop a client-centered plan of care and achieve interprofessional competencies.

PMID:34597424 | DOI:10.1111/nuf.12655

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Nevin Manimala Statistics

Interactions of Age and Blood Immune Factors and Non-Invasive Prediction of Glioma Survival

J Natl Cancer Inst. 2021 Oct 1:djab195. doi: 10.1093/jnci/djab195. Online ahead of print.

ABSTRACT

BACKGROUND: Tumor-based classification of human glioma portends patient prognosis; however, considerable unexplained survival variability remains. Host factors (eg, age) also strongly influence survival times, partly reflecting a compromised immune system. How blood epigenetic measures of immune characteristics and age augment molecular classifications in glioma survival has not been investigated. We assess the prognostic impact of immune-cell fractions and epigenetic age in archived blood across glioma molecular subtypes for the first time.

METHODS: We evaluated immune-cell fractions and epigenetic age in archived blood from the University of California San Francisco Adult Glioma Study, including a training set of 197 IDH-wildtype, 1p19q intact, TERT wildtype (IDH/1p19q/TERT-WT) glioma patients, an evaluation set of 350 patients with other subtypes of glioma, and 454 subjects without glioma.

RESULTS: IDH/1p19q/TERT-WT patients had lower lymphocyte fractions (CD4+T, CD8+T, natural killer, and B cells) and higher neutrophil fractions than subjects without glioma. Recursive partitioning analysis delineated four statistically significantly different survival groups for IDH/1p19q/TERT-WT patients based on an interaction between chronological age and two blood immune factors, CD4+T cells, and neutrophils with median overall survival ranging from 0.76 years [95% confidence intervaI = 0.55 to 0.99] for the worst survival group (n = 28) to 9.72 years [95% confidence intervaI = 6.18 to NA] for the best (n = 33). The Recursive partitioning analysis also statistically significantly delineated four risk groups in patients with other glioma subtypes.

CONCLUSION: The delineation of different survival groups in the training and evaluation sets based on an interaction between chronological age and blood immune characteristics suggests that common host immune factors among different glioma types may impact survival. The ability of DNA methylation-based markers of immune status to capture diverse, clinically relevant information may facilitate non-invasive personalized patient evaluation in the neuro-oncology clinic.

PMID:34597382 | DOI:10.1093/jnci/djab195

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Nevin Manimala Statistics

Prospective Cohort Study of Pre- and Post-Diagnosis Obesity and Endometrial Cancer Survival

J Natl Cancer Inst. 2021 Oct 1:djab197. doi: 10.1093/jnci/djab197. Online ahead of print.

ABSTRACT

BACKGROUND: Disease-free and overall survival associations with anthropometric measures of obesity and changes in these exposures remain unknown among endometrial cancer survivors.

METHODS: Endometrial cancer survivors diagnosed between 2002-2006 completed direct anthropometric measurements and self-reported lifetime weight history during in-person interviews approximately 4 months after diagnosis (peri-diagnosis) and approximately 3 years after diagnosis (follow-up). Participants were followed until death or March 20, 2019. Cox proportional regression estimated multivariable-adjusted hazard ratios (HR) and 95% confidence intervals (CI) for body mass index (BMI), weight, waist circumference, and waist-hip ratio with disease-free survival (DFS) and overall survival (OS). Statistical tests were two-sided.

RESULTS: 540 and 425 cancer survivors were assessed peri-diagnosis and follow-up, respectively. During the median 14.2 years of follow-up (range = 0.3-16.5 years), 132 participants had a recurrence and/or died (DFS) with 111 deaths overall (OS). Reduced DFS was noted with greater recalled weight one-year before-diagnosis (HR = 1.88, 95% CI = 1.15 to 3.07), BMI one-year before-diagnosis (HR = 1.88, 95% CI = 1.09 to 3.22), and measured peri-diagnosis BMI (HR = 2.04, 95% CI = 1.18 to 3.53). Measured peri-diagnosis waist circumference ≥88 cm was associated with decreased DFS (HR = 1.94, 95% CI = 1.24 to 3.03) and OS (HR = 1.90, 95% CI = 1.16 to 3.13). A two-fold decrease in DFS and OS was associated with ≥5% BMI or weight change from one-year before diagnosis to peri-diagnosis. No associations were observed for the assessment during follow-up.

CONCLUSION: One-year before- and peri-diagnosis anthropometric measures of obesity were associated with reduced survival among endometrial cancer survivors. Anthropometric changes from one-year before- to peri-diagnosis may provide an important indication of future survival in this population.

PMID:34597394 | DOI:10.1093/jnci/djab197