Category: Statistics

Cancer Med. 2022 Apr 1. doi: 10.1002/cam4.4696. Online ahead of print.

ABSTRACT

BACKGROUND: Bereavement after the death of a child is devastating and associated with worse physical and psychosocial well-being in parents. Evidence suggests that parents desire and benefit from support provided by other bereaved parents. To foster this peer support, an institutional peer-to-peer mentorship program for bereaved parents was established, through which trained bereaved parent mentors offer support for newly bereaved parents.

METHODS: Using a retrospective cohort design, we describe the characteristics of participants of the Bereaved Parent Mentorship program. Trained bereaved parent mentors documented encounters with newly bereaved parent mentees using a secure internet-based form. Mentors summarized each encounter including any concerns or need for professional psychosocial support. Descriptive statistics were used to describe mentor and mentee characteristics; free text from encounter summaries was qualitatively analyzed using content analysis.

RESULTS: A total of 1368 documented encounters occurred between 150 mentees and 39 mentors from January 1, 2014 to February 29, 2020. Only seven encounters (0.5%) were flagged as serious concern necessitating professional psychosocial support. Four key themes in the encounters between mentors and mentees emerged, including: descriptions of the grief experience, ways in which a mentor supported their mentee, challenges the mentor experienced in supporting the mentee, and personal benefit gained by the mentor from supporting their mentee.

CONCLUSION: This structured Bereaved Parent Mentorship program fostered rich interactions between bereaved parent participants, with very few encounters requiring professional assistance. Future research will assess the impact of bereaved mentor programs on resilience and psychosocial, physical, and functional well-being of parents.

PMID:35362669 | DOI:10.1002/cam4.4696

Se Pu. 2022 Apr;40(4):372-383. doi: 10.3724/SP.J.1123.2021.09005.

ABSTRACT

Early diagnosis of Epstein-Barr virus (EBV) can reduce the risk of major illnesses. Disadvantages of EBV antibody detection methods that are commonly used clinically include lengthy assay time, need for a lot of reagent, and low efficiency. Compared with traditional detection methods, microfluidics technology offers high throughput, low reagent consumption, less bio-contamination, and a higher degree of automation. Advantages of magnetic immunofluorescence technology include high detection efficiency and a strong signal. The combined advantages of the two methods can compensate for the shortcomings of traditional methods. In the present study, polymethyl methacrylate (PMMA) as the raw material was subjected to laser cutting and vacuum hot pressing to quickly obtain chips. Magnetic beads labeled with antigen and fluorescent microspheres labeled with anti-human antibody were then rapidly lyophilized into microspheres by freeze-drying and embedded into the chips. After incubation and cleaning, the last step was detection. Image J software was used to analyze the mean fluorescence intensity and obtain negative or positive test results. To determine the precision of the chip, high- and low-value samples of each item were retested 10 times. The mean values were calculated to obtain the relative standard deviation (RSD) for several common pathogens. Furthermore, the coincidence rate of clinical samples was tested using a chemiluminescence immunoassay (CLIA) to determine the potential clinical application value. The RSD of the precision test for each item was <10%, indicating good precision. The precision of the accelerated stability test was not verified. Specificity test results revealed no cross-reaction with some common pathogen antibodies, indicating good specificity. It remains to be verified whether the antibodies detected by this method cross-react with other herpes simplex viruses, such as types 1 and 2, Kaposi’s sarcoma-associated virus, and human herpes virus type 6 and 7. Of the 121 clinical samples tested, statistical analysis of the data indicated good agreement with the chemiluminescence immunoassay in clinical trials. EB viral capsid antigen (EB VCA) IgG positive coincidence rate was 95.77% (68/71), the negative coincidence rate was 86% (43/50) (Kappa=0.828, P<0.05), the limit of detection (LOD) was 1.92 U/mL, and the linear range was 1.92 to 200 U/mL. The EB VCA IgA positive coincidence rate was 92% (46/50), negative coincidence rate was 92.96% (66/71) (Kappa=0.847, P<0.05), LOD was 2.79 U/mL, and the linear range was 2.79 to 200 U/mL. The positive coincidence rate of EB nuclear antigen 1 (EB NA1) IgG was 92.96% (66/71), the negative coincidence rate was 92% (46/50) (Kappa=0.847, P<0.05), the LOD was 3.13 U/mL, and the linear range was 3.13 to 200 U/mL. The positive coincidence rate of EB NA1 IgA was 90% (45/50), the negative coincidence rate was 91.55% (65/71) (Kappa=0.813, P<0.05), the LOD was 1.53 U/mL, and the linear range was 1.53 to 200 U/mL. Compared with the traditional enzyme-linked immunosorbent assay, the novel method featured a shorter detection time, reduced use of reagent, high degree of automation, and less bio-contamination. Compared with CLIA, advantages of the novel method include multi-item combined detection, long luminescence time, and simple use as a basic health service. Compared with silicon and ceramic microfluidic chips, advantages of the selected PMMA material include low processing cost, short processing time, simple processing technology, and easy industrialization. A refinement that can still be made include the use of molding instead of laser cutting technology, which can further shorten the chip processing time. In summary, a microfluidic detection platform was initially built to provide a rapid, sensitive, simple, highly automated, and easy to be used by basic health service for the quantitative combined detection of EBV VCA and EB NA1 IgG and IgA.

PMID:35362685 | DOI:10.3724/SP.J.1123.2021.09005

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

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

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

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