Tag: statistics

Orthod Craniofac Res. 2022 Apr 1. doi: 10.1111/ocr.12576. Online ahead of print.

ABSTRACT

OBJECTIVE: To assess nasolabial esthetics in patients with complete unilateral cleft lip, with or without cleft palate (UCL±P) using two scoring systems.

DESIGN: A cross-sectional study conducted in a tertiary care government hospital.

PATIENTS: Photographic records of 91 patients with complete UCL±P from the age group of 5-18 years (mean age = 13.2±3.14 years) were included.

METHOD: A panel of three orthodontists with varying experience in cleft management rated nasolabial esthetics using two scoring systems i.e. Asher Mc-Dade index (AMAI) and Cleft Aesthetic Rating Scale (CARS). Intraclass correlation coefficient, Fleiss’ kappa and Cronbach’s alpha were used to measure the internal consistency among three raters and Spearman Brown formula was used for measuring overall reliability. Time required for assessment of each photograph was compared with ANOVA.

RESULTS: Overall, both AMAI and CARS showed high reliability and outcome assessment with good inter-rater reliability and internal consistency, when used independently by orthodontists having varied experience. Statistically significant difference was present in time taken for assessment of nasolabial esthetics with CARS index (8.75±1.65 seconds) as compared to AMAI (18.62±3.49 seconds).

CONCLUSION: AMAI and CARS are equally reliable and consistent for the assessment of nasolabial esthetics in patients with UCL±P. However, considerably less time was taken for assessment using CARS index as compared to AMAI. The use of CARS index is recommended for initial assessment and screening of patients by orthodontists using two dimensional photographs.

PMID:35362657 | DOI:10.1111/ocr.12576

Suicide Life Threat Behav. 2022 Apr 1. doi: 10.1111/sltb.12860. Online ahead of print.

ABSTRACT

OBJECTIVES: Veterans who decline to provide information on their history of self-injurious thoughts and behaviors (SITBs) may be at elevated suicide risk. We examined associations between non-response to a question assessing lifetime SITBs and proxy variables of suicide risk.

METHODS: In this population-based cross-sectional study of 4069 US veterans, responses to the Suicidal Behaviors Questionnaire-Revised were examined to group veterans into one of three categories: (1) denied lifetime SITBs, (2) reported lifetime SITBs, or (3) declined to respond.

RESULTS: Overall, 69.5% of veterans denied a SITB history, 29.5% reported a SITB history, and 1.0% declined to provide information regarding SITBs. In adjusted analyses, veterans who declined to provide information on SITBs were significantly more likely than veterans who explicitly denied lifetime SITBs to screen positive for posttraumatic stress disorder; report lifetime non-suicidal self-injury; and report elevated levels of total trauma burden, externalizing behaviors, loneliness, received social support, and provided social support. Across these constructs, veterans who declined to provide SITB information were statistically indistinguishable from veterans who explicitly reported lifetime SITBs.

CONCLUSIONS: Veterans who decline to provide information about suicidal thoughts and behaviors may represent a covert group at elevated risk for suicide.

PMID:35362636 | DOI:10.1111/sltb.12860

Environ Microbiol. 2022 Apr 1. doi: 10.1111/1462-2920.15984. Online ahead of print.

ABSTRACT

Biological nitrogen fixation performed by diazotrophs forms a cornerstone of Earth’s terrestrial ecosystem productivity. However, the composition, diversity and distribution of soil diazotrophs are poorly understood across different soil ecosystems. Furthermore, the biological potential of the key diazotroph species in relation to key environmental parameters is unknown. To address this, we used meta-analysis approach to merge together 39 independent diazotroph amplicon sequencing (nifH gene) datasets consisting of 1988 independent soil samples. We then employed multiple statistical analyses and machine-learning approaches to compare diazotroph community differences and indicator species between terrestrial ecosystems on a global scale. The distribution, composition and structure of diazotroph communities varied across seven different terrestrial ecosystems, with community composition exhibiting an especially clear effect. The Cyanobacteria were the most abundant taxa in crust ecosystems (accounting for ~45% of diazotrophs), while other terrestrial ecosystems were dominated by Proteobacteria, including Alpha-, Beta- and Gamma-Proteobacteria (accounting for ~70% of diazotrophs). Farmland ecosystems harboured the highest and crust ecosystems the lowest alpha and phylogenetic diversities. Azospirillum zeae, Skermanella aerolata and four Bradyrhizobium species were identified as key indicator species of potential diazotroph activity. Overall, diazotroph abundances and distribution were affected by multiple environmental parameters, including soil pH, nitrogen, organic carbon, C:N ratio and annual mean precipitation and temperature. Together, our findings suggest that based on the relative abundance and diversity of nifH marker gene, diazotrophs have adapted to a range of environmental niches globally.

PMID:35362656 | DOI:10.1111/1462-2920.15984

Community Dent Oral Epidemiol. 2022 Apr 1. doi: 10.1111/cdoe.12747. Online ahead of print.

ABSTRACT

OBJECTIVES: To estimate the socioeconomic disparities in untreated dental caries in early childhood according to socioeconomic characteristics in three birth cohorts in Southern Brazil.

METHODS: The socioeconomic data to this study were collected at the 48-month follow-up and oral health studies of 1993, 2004 and 2015 Pelotas birth cohort studies. The outcome was untreated dental caries in children aged 6 (1993 cohort), 5 (2004 cohort) and 4 years (2015 cohort), dichotomized into absence/presence. Analyses were stratified by maternal skin colour/race, maternal education and family income. For statistical purposes, the prevalence difference, relative risk and absolute and relative indices of health inequality (Slope Index of Inequality-SII and Concentration Index-CIX) were used.

RESULTS: The prevalence of untreated dental caries in primary dentition was 63.4%, 45.5% and 15.6%, in 1993, 2004 and 2015 cohorts, respectively. The prevalence of untreated dental caries was concentrated in the poorest quintile and lower maternal education group in both absolute (SII) and relative (CIX) measures of inequality, being characterized as a pro-poor event. A higher risk of untreated caries was found in the poorest quintile of family income compared with the richest quintile in the 1993 cohort (RR 1.44 [95% CI 1.05; 1.98]). That risk was higher considering the 2004 Cohort (RR 1.78 [95% CI 1.42; 2.23]) and 2015 cohort (RR 4.20 [95% CI 2.97; 5.94]) data.

CONCLUSIONS: Over the course of two decades, a higher prevalence of untreated dental caries is concentrated among the most socioeconomically deprived children.

PMID:35362631 | DOI:10.1111/cdoe.12747

J Clin Periodontol. 2022 Apr 1. doi: 10.1111/jcpe.13620. Online ahead of print.

ABSTRACT

AIM: Observational research suggests that periodontitis affects psoriasis. However, observational studies are prone to reverse causation and confounding, which hampers drawing causal conclusions and the effect direction. We applied the Mendelian randomization (MR) method to comprehensively assess the potential bi-directional association between periodontitis and psoriasis.

MATERIALS AND METHODS: We used genetic instruments from the largest available genome-wide association study of European descent for periodontitis (17,353 cases, 28,210 controls) to investigate the relationship with psoriasis (13,229 cases, 21,543 controls), and vice versa. Causal Analysis Using Summary Effect (CAUSE) estimates and inverse variance-weighted (IVW) MR analyses were used for the primary analysis. Robust MR approaches were used for sensitivity analyses.

RESULTS: Both univariable methods, CAUSE and IVW MR analyses, did not reveal any impact of periodontitis on psoriasis (CAUSE odds ratio [OR] = 1.00, p = 1.00; IVW OR = 1.02, p = .6247), or vice versa (CAUSE OR = 1.01, p = .5135; IVW OR = 1.00, p = .7070). The null association was corroborated by pleiotropy-robust methods with ORs close to 1 and p-values >.59. Overall, MR analyses did not suggest any effect of periodontitis on psoriasis. Similarly, there was no evidence to support an effect of psoriasis on periodontitis.

CONCLUSIONS: Within the limitations of this MR study, the outcomes supported neither periodontitis affecting psoriasis nor psoriasis affecting periodontitis.

PMID:35362630 | DOI:10.1111/jcpe.13620

Brief Bioinform. 2022 Mar 31:bbac088. doi: 10.1093/bib/bbac088. Online ahead of print.

ABSTRACT

Characterizing the molecular identity of a cell is an essential step in single-cell RNA sequencing (scRNA-seq) data analysis. Numerous tools exist for predicting cell identity using single-cell reference atlases. However, many challenges remain, including correcting for inherent batch effects between reference and query data andinsufficient phenotype data from the reference. One solution is to project single-cell data onto established bulk reference atlases to leverage their rich phenotype information. Sincast is a computational framework to query scRNA-seq data by projection onto bulk reference atlases. Prior to projection, single-cell data are transformed to be directly comparable to bulk data, either with pseudo-bulk aggregation or graph-based imputation to address sparse single-cell expression profiles. Sincast avoids batch effect correction, and cell identity is predicted along a continuum to highlight new cell states not found in the reference atlas. In several case study scenarios, we show that Sincast projects single cells into the correct biological niches in the expression space of the bulk reference atlas. We demonstrate the effectiveness of our imputation approach that was specifically developed for querying scRNA-seq data based on bulk reference atlases. We show that Sincast is an efficient and powerful tool for single-cell profiling that will facilitate downstream analysis of scRNA-seq data.

PMID:35362513 | DOI:10.1093/bib/bbac088

Acta Crystallogr D Struct Biol. 2022 Apr 1;78(Pt 4):410-423. doi: 10.1107/S2059798322001978. Epub 2022 Mar 16.

ABSTRACT

Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters.

PMID:35362465 | DOI:10.1107/S2059798322001978

J Neurogastroenterol Motil. 2022 Apr 30;28(2):320-326. doi: 10.5056/jnm19040.

ABSTRACT

BACKGROUND/AIMS: Sixty-eight percent of multiple sclerosis (MS) patients suffer from neurogenic bowel dysfunction (NBD). Transanal irrigation (TAI) is part of the therapeutic strategy. This retrospective study aims to assess the efficacy of TAI in MS population.

METHODS: Twenty-eight MS patients who underwent TAI after a learning period were included. We collected several demographic data: MS disease characteristics, treatments, urinary and bowel dysfunction characteristics, urodynamic parameters, results of the NBD score, the Urinary Symptom Profile (USP) score, and the Patient Global Impression of Severity score, completed by patients before the learning and during the follow-up consultation. We defined 4 specific groups depending on the NBD score severity: very minor, minor, moderate, and severe.

RESULTS: Mean follow-up was 124 days, 85.0% were initially constipated and 36% had fecal incontinence. After TAI, improvement of NBD score was higher in initial Moderate NBD score group with 75.0% of patients decreasing their NBD score into lower severity categories. Few modifications were observed for baseline Very minor and Severe NBD score groups with 60.0% and 87.5% of patients staying in the same category. Statistical improvement of USP voiding dysfunction score was observed (95% CI, -6.13–1.19; P = 0.005) without improvement of overactive bladder USP sub-score.

CONCLUSIONS: TAI is effective in NBD, especially in MS patients with initial Moderate NBD score. Improvement of voiding dysfunction following TAI confirms the pelvic organ cross-talk and the need to systematically consider and treat bowel dysfunction in MS to also improve urinary symptoms.

PMID:35362457 | DOI:10.5056/jnm19040

Health Econ. 2022 Mar 31. doi: 10.1002/hec.4490. Online ahead of print.

ABSTRACT

There is a growing but mixed literature on the health effects of minimum wages. If minimum wage changes have a statistically significant impact on health, this suggests health effects should be incorporated into cost-benefit analyses to capture wider policy impacts. Whilst most existing UK based literature examines the introduction of a minimum wage, this paper exploits the 2016, 2017 and 2018 UK National Minimum Wage (NMW) increases as natural experiments using a series of difference-in-differences models. Short Form-12 (SF-12) mental and physical component summary scores are used as dependent variables. In the base case and all sensitivity analyses, the estimated impact of NMW increases on mental and physical health are insignificant. The policy implication is that health effects should not be included in cost-benefit analyses examining the NMW.

PMID:35362225 | DOI:10.1002/hec.4490

Diagn Cytopathol. 2022 Apr 1. doi: 10.1002/dc.24959. Online ahead of print.

ABSTRACT

BACKGROUND: Adequacy criteria of pleural fluid volume for optimal reporting are contentious, and very little literature is available to date. This problem has not been addressed in the novel International System for Reporting Serous Fluid Cytology.

MATERIALS AND METHODS: A retrospective analysis was performed on 939 pleural fluid samples. Five volume bins were created: 0-9.9 ml, 10-19.9 ml, 20-34.9 ml, 35-69.9 ml, and > 70 ml and included 203, 222, 314, 174, and 26 samples, respectively. Volume bins were compared across various categories using a Chi-square test. A malignancy fraction was used to assess diagnostic accuracy. Descriptive statistics for categorical variables were done with median and interquartile range. A ROC curve was constructed to find if pleural fluid volume can be used to detect malignancy. A cut-off volume was found which can detect malignancy with optimum sensitivity.

RESULTS: The area under the Receiver Operating Characteristic curve showed that 55% of the time, the pleural volume can detect malignancy correctly. From the coordinates of the curve it was found that for a sensitivity of 81% and specificity of 40%, a cut-off volume of 13.5 ml of pleural fluid is sufficient to detect malignancy.

CONCLUSIONS: We recommend 13.5 ml as the minimum volume cut-off for a satisfactory pleural effusion cytology report. Below this volume, the false-negative rates increase, and the specimen may be deemed as limited for a conclusive diagnosis. As the volume rises above this threshold volume, the false negativity rate decreases but does not significantly improve malignant cells’ detection.

PMID:35362266 | DOI:10.1002/dc.24959