Category: Statistics

Int J Infect Dis. 2023 Jan 5:S1201-9712(22)00673-7. doi: 10.1016/j.ijid.2022.12.030. Online ahead of print.

ABSTRACT

OBJECTIVES: Investigate risk factors for SARS-CoV-2 infections in schools students and staff.

METHODS: In the 2020/2021 schoolyear, we administered PCR, antibody tests and questionnaires to a sample of primary and secondary schools students and staff, with data linkage to COVID-19 surveillance. We fitted logistic regression models to identify factors associated with infection.

RESULTS: We included 6799 students and 5090 staff in the autumn and 11952 students and 4569 staff in the spring/summer terms. Infections in students in autumn 2020 were related to the percentage of students eligible for free school meals. We found no statistical association between infection risk in primary and secondary schools and reported contact patterns between students and staff in either time period in our study. Using public transports was associated with increased risk in the autumn in students (aOR=1.72 (95%CI 1.31 to 2.25) and staff. One or more infections in the same household during either period was the strongest risk factor for infection in students, and more so among staff.

INTERPRETATION: Deprivation, community and household factors were more strongly associated with infection than contacts patterns at school; this suggests the additional school-based mitigation measures in England’s in 2020/21 likely helped reduce transmission risk in schools.

PMID:36621754 | DOI:10.1016/j.ijid.2022.12.030

Int J Infect Dis. 2023 Jan 5:S1201-9712(23)00001-2. doi: 10.1016/j.ijid.2023.01.001. Online ahead of print.

ABSTRACT

OBJECTIVE: Bloodstream infections (BSIs) caused by ESBL-producing Enterobacteriaceae (ESBL-PE) has become a global public health threat, and beta-lactam/beta-lactamase inhibitor combinations (BLBLIs) are considered as one reliable carbapenem-sparing antibiotic. But it’s still controversial whether BLBLIs is truly non-inferior to carbapenems. Therefore, we conducted this meta-analysis to compare efficacy of BLBLIs with carbapenems for ESBL-PE BSIs.

METHODS: A systematic search of PubMed, Cochrane Library and Embase was conducted until December 2021 to enroll studies comparing BLBLIs with carbapenems for ESBL-PE BSIs. Subgroups analysis was performed based on the choice of therapy (empirical, definitive, and mixed therapy). The protocol was registrated in PROSPERO (#CRD42022316011).

RESULTS: 2,786 patients from one randomized clinical trial (RCT) and 25 cohorts were included. There was no statistically difference between BLBLIs and carbapenems groups in therapeutical response (OR=1.19, P=0.45) and mortality (OR=1.06, P=0.68). Furthermore, although statistical difference was also not found in subgroup analysis, BLBLIs performed better in definitive therapy than empirical therapy when compared with carbapenems, with a numerically higher therapeutical response (OR=1.42 vs 0.89) and a mildly lower mortality (OR=0.85 vs 1.14).

CONCLUSIONS: BLBLIs was non-inferior to carbapenems for ESBL-PE BSIs, especially in definitive therapy. BLBLIs may be a valid alternative to spare the use of carbapenems.

PMID:36621752 | DOI:10.1016/j.ijid.2023.01.001

Clin Gastroenterol Hepatol. 2023 Jan 5:S1542-3565(23)00004-6. doi: 10.1016/j.cgh.2022.12.026. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Multitarget stool DNA (mt-sDNA) testing is a stool-based screening test for colorectal cancer (CRC). In a single instance of testing, the pivotal FDA-approval study (NCT01397747) found that 16% of mt-sDNA tests were positive, and the positive predictive value (PPV) for CRC or advanced precursor lesions (APL) was 27.3%. We aimed to examine real-world longitudinal performance by determining the test positive rate and PPV of mt-sDNA on the 2^nd round of testing.

METHODS: Colonoscopy and pathology reports were retrospectively reviewed for patients with a negative mt-sDNA on the 1^st round of screening and a positive mt-sDNA on the 2^nd round. Test-positivity rate and PPV for CRC, APL, and any colorectal neoplasia (CRN) were calculated for the 2^nd mt-sDNA and compared to baseline PPVs from a previously published cohort of patients from our institution who tested positive on the 1^st round of screening.

RESULTS: 2,758 patients completed a 2^nd test at a median of 3.2 years after the 1^st test. Of these, 422 (15%) had a positive 2^nd mt-sDNA. The PPV was 0.25% for CRC, 24% for APL, and 67% for any CRN. There was no significant difference in PPV on the 2^nd mt-sDNA test compared to the 1^st round (24% vs 28% for APL, P=0.12).

CONCLUSIONS: Mt-sDNA test positive rate and PPV were similar between 1^st and 2^nd rounds of screening. These observations confirm the utility of a second round of mt-sDNA screening and may inform estimates of mt-sDNA effectiveness for CRC screening.

PMID:36621751 | DOI:10.1016/j.cgh.2022.12.026

Environ Pollut. 2023 Jan 5:121021. doi: 10.1016/j.envpol.2023.121021. Online ahead of print.

ABSTRACT

China fully implemented the new emission standards in 2016 to further reduce the emissions of air pollutants from the municipal solid waste (MSW) incineration industry; however, the implementation effect of the new standards remains unknown. This study developed the first nationwide air pollutant emission inventory of MSW incineration plants in China based on the measured concentration data from China’s continuous emissions monitoring systems (CEMS) network, and activity level data from the China Urban Construction Statistical Yearbook, to evaluate the effectiveness of implementing the new emission standards and estimate the future reduction potentials. Our results demonstrated that the overall standard-reaching proportions of particulate matter (PM), sulfur dioxide (SO₂), nitrogen oxide (NO_X), hydrogen chloride (HCl) and carbon monoxide (CO) were 98.8%, 99.3%, 99.4%, 99.4% and 97.6%, respectively, by comparing with the corresponding concentration limits of new emission standards. The total emissions of PM, SO₂, NO_X, HCl and CO from 412 MSW incineration plants in 2019 were 1.9, 6.2, 50.8, 4.3 and 6.6 kt yr^-1, respectively, which is 33.6-75.8% lower than those in 2015, mainly due to the sharp decrease in emission factors. Pollutant emission hotspots were mainly concentrated in eastern and central and southern regions with large populations and well-developed economies. The analysis of future scenario results shows that despite the continuous increase of MSW incineration amount in the future, if the government strengthens pollutant emission standards and comprehensively implements waste sorting, total emissions and emission factors of air pollutants could be further reduced by 25.8-72.7% and 59.8-81.2%, respectively, by 2050. These findings provide helpful insights into future policymaking and technology selection for China and other countries seeking to reduce pollutant emissions from the MSW incineration industry.

PMID:36621718 | DOI:10.1016/j.envpol.2023.121021

Environ Pollut. 2023 Jan 5:120961. doi: 10.1016/j.envpol.2022.120961. Online ahead of print.

ABSTRACT

There are several determinants of a population’s health, including meteorological factors and air pollution. For example, it is well known that low temperatures and air pollution increase mortality rates in infant and elderly populations. With the emergence of SARS-COV-2, it is important to understand what factors contribute to its mitigation and control. There is some research in this area which shows scientific evidence on the virus’s behavior in the face of these variables. This research aims to quantify the impact of climatic factors and environmental pollution on SARS-COV-2 specifically the effect on the number of new infections in different areas of Chile. At the local level, historical information available from the Department of Statistics and Health Information, the Chilean National Air Quality Information System, the Chilean Meteorological Directorate, and other databases will allow the generation of panel data suitable for the analysis. The results show the significant effect of pollution and climate variables measured in lags and will allow us to explain the behavior of the pandemic by identifying the relevant factors affecting health, using heteroskedastic models, which in turn will serve as a contribution to the generation of more effective and timely public policies for the control of the pandemic.

PMID:36621713 | DOI:10.1016/j.envpol.2022.120961

J Equine Vet Sci. 2023 Jan 6:104220. doi: 10.1016/j.jevs.2023.104220. Online ahead of print.

ABSTRACT

BACKGROUND: The TCO₂ (total carbon dioxide) test is performed on the blood of racehorses as a means of combatting the practice of administering alkalizing agents.

OBJECTIVE: This study evaluated serum TCO₂ concentrations and factors influencing concentration of TCO₂ in Thoroughbred and Quarter Horses.

METHODS: The normality of data were evaluated with a Shapiro-Wilk test. Mann-Whitney tests and Kruskal-Wallis tests were used against different effects. When a fixed effect was detected, Dunn’s post-hoc comparisons were performed.

RESULTS: The median pre-race serum TCO₂ concentration (32.20 mmol/L (interquartile range (IQR): 30.80-33.50)) was higher than that of post-race samples (26.70 mmol/L (IQR: 24.55-29.25)) (p<0.0001). The median TCO₂ concentrations in pre-race samples were different between Thoroughbred (32.40 mmol/L (IQR: 30.90-33.60)) and Quarter Horses (31.30 mmol/L (IQR: 30.00-32.50)) (p<0.0001). The median pre-race TCO₂ concentrations were 32.75 (IQR: 31.40-33.90), 31.40 (IQR: 29.80-32.80), 32.50 (IQR: 31.20-33.88), and 31.60 (IQR 30.00-32.70) mmol/L in racehorses at Fair Grounds, Louisiana Downs, Delta Downs, and Evangeline Downs racetracks, respectively (p<0.0001). The total serum TCO₂ concentrations in Thoroughbred and Quarter Horse racehorses were affected by seasonal temperature variation (p<0.0001).

LIMITATIONS OF THE STUDY: A smaller sample size was available for post-race samples (n=205) and Quarter Horse pre-race samples (n=351).

CONCLUSION: The results of this study indicated that the breed, seasonal temperature variation, pre-race or post-race sampling, and track location are strongly correlated to total TCO₂ concentrations. It was not clear whether the statistically significant differences in TCO₂ levels among racetracks in Louisiana were due to location of racetracks and/or seasonal temperature variation.

PMID:36621701 | DOI:10.1016/j.jevs.2023.104220

Microb Pathog. 2023 Jan 5:105982. doi: 10.1016/j.micpath.2023.105982. Online ahead of print.

ABSTRACT

BACKGROUND: The pathophysiology of acne is complex and multifactorial. In recent years, fungal infections have increased significantly.

OBJECTIVES: The purpose of this study was to evaluate the role of fungi in the etiopathogenesis of acne vulgaris.

METHODS: This was a prospective case-control study. A total of 200 individuals (100 with acne vulgaris and 100 without acne vulgaris) were enrolled in the study. Direct microscopic investigation and culturing of the samples were done according to Clinical and Laboratory Standards Institute criteria. Descriptive analyses, independent sample t-tests, and chi-squared tests were used for statistical analysis. The subjects in the control group were paired by age and gender with the patients.

RESULTS: Direct microscopic examination revealed hyphae in the samples of all subjects with acne and in the samples of four of the healthy controls. The cultures of 18 of the patients with acne vulgaris were positive for the following: 6 with Aspergillus spp., 7 with Penicillium spp., 3 with Cladosporium spp., 1 with Candida spp., and 1 with Acremonium spp. In addition, Candida spp. was observed in the cultures of two of the healthy controls.

CONCLUSION: We conclude that fungi may be involved in the etiopathogenesis of acne vulgaris.

PMID:36621695 | DOI:10.1016/j.micpath.2023.105982

J Affect Disord. 2023 Jan 5:S0165-0327(23)00020-4. doi: 10.1016/j.jad.2023.01.013. Online ahead of print.

ABSTRACT

BACKGROUND: Mitochondria generate energy through oxidative phosphorylation (OXPHOS). The function of key OXPHOS proteins can be altered by variation in mitochondria-related genes, which may increase the risk of mental illness. We investigated the association of mitochondria-related genes and their genetic risk burden with cognitive performance.

METHODS: We leveraged cross-sectional data from 1320 individuals with a severe psychiatric disorder and 466 neurotypical individuals from the PsyCourse Study. The cognitive tests analyzed were the Trail-Making Test, Verbal Digit Span Test, Digit-Symbol Test, and Multiple Choice Vocabulary Intelligence Test. Association analyses between the cognitive tests, and single-nucleotide polymorphisms (SNPs) mapped to mitochondria-related genes, and their polygenic risk score (PRS) for schizophrenia (SCZ) were performed with PLINK 1.9 and R program.

RESULTS: We found a significant association (FDR-adjusted p < 0.05) in the Cytochrome C Oxidase Assembly Factor 8 (COA8) gene locus of the OXPHOS pathway with the Verbal Digit Span (forward) test. Mitochondrial PRS was not significantly associated with any of the cognitive tests.

LIMITATIONS: Moderate statistical power due to relatively small sample size.

CONCLUSIONS: COA8 encodes a poorly characterized mitochondrial protein involved in apoptosis. Here, this gene was associated with the Verbal Digit Span (forward) test, which evaluates short-term memory. Our results warrant replication and may lead to better understanding of cognitive impairment in mental disorders.

PMID:36621676 | DOI:10.1016/j.jad.2023.01.013

Genomics Inform. 2022 Dec;20(4):e48. doi: 10.5808/gi.22075. Epub 2022 Dec 30.

ABSTRACT

Penalized regression has been widely used in genome-wide association studies for jointanalyses to find genetic associations. Among penalized regression models, the least absolute shrinkage and selection operator (Lasso) method effectively removes some coefficientsfrom the model by shrinking them to zero. To handle group structures, such as genes andpathways, several modified Lasso penalties have been proposed, including group Lasso andsparse group Lasso. Group Lasso ensures sparsity at the level of pre-defined groups, eliminating unimportant groups. Sparse group Lasso performs group selection as in group Lasso,but also performs individual selection as in Lasso. While these sparse methods are useful inhigh-dimensional genetic studies, interpreting the results with many groups and coefficients is not straightforward. Lasso’s results are often expressed as trace plots of regressioncoefficients. However, few studies have explored the systematic visualization of group information. In this study, we propose a multi-level polar Lasso (MP-Lasso) chart, which caneffectively represent the results from group Lasso and sparse group Lasso analyses. An Rpackage to draw MP-Lasso charts was developed. Through a real-world genetic data application, we demonstrated that our MP-Lasso chart package effectively visualizes the resultsof Lasso, group Lasso, and sparse group Lasso.

PMID:36617655 | DOI:10.5808/gi.22075

Genomics Inform. 2022 Dec;20(4):e39. doi: 10.5808/gi.22074. Epub 2022 Dec 30.

ABSTRACT

Various methods of frequent pattern mining have been applied to genetic problems, specifically, to the combined association of two genotypes (a genotype pattern, or diplotype) at different DNA variants with disease. These methods have the ability to come up with a selection of genotype patterns that are more common in affected than unaffected individuals, and the assessment of statistical significance for these selected patterns poses some unique problems, which are briefly outlined here.

PMID:36617647 | DOI:10.5808/gi.22074