Category: Statistics

BMC Pregnancy Childbirth. 2023 Dec 6;23(1):839. doi: 10.1186/s12884-023-06143-x.

ABSTRACT

BACKGROUND: Preeclampsia is the main cause of preterm parturition and maternal-fetal complications. T helper 1 and T helper 2 cytokines balance is a requirement in normal pregnancy and aberrant in this immunologic balance, play an important role in the pathology of preeclampsia. In previous studies single nucleotide polymorphisms have been associated with the alteration of serum cytokine levels.

OBJECTIVE: This study was aimed to discover association between interleukin-13 (rs20541, and rs56035208) and interleukin-19 (rs1028181 (T/C) and rs2243191(T/C)) polymorphisms with susceptibility to preeclampsia.

METHODS: In this case-control study 300 women with and without preeclampsia (n = 150/each) who referred to Zeynabieh Hospital- Shiraz, Iran, from February 2021 to April 2022 were enrolled. For genotyping the interleukin-13 and interleukin-19 polymorphisms, the Allele-specific polymerase chain reaction and direct sequencing method was carried out.

RESULTS: Our statistical results revealed no significant differences in allele and genotype frequencies for interleukin-13 polymorphisms compared to controls. We found that the interleukin-13 polymorphisms are significantly associated with vulnerability to edema at rs20541 position and maternal drinking at rs56035208 position. But it was interesting to note that the differences of both the allele and genotype frequencies of interleukin-19 polymorphisms and their contribution to the risk of preeclampsia susceptibility were significant.

CONCLUSIONS: No risk of preeclampsia was found in all comparisons for interleukin-13 polymorphisms. However, the interleukin-19 polymorphisms were found to confer the risk of preeclampsia in our population.

PMID:38057745 | DOI:10.1186/s12884-023-06143-x

BMC Nephrol. 2023 Dec 6;24(1):362. doi: 10.1186/s12882-023-03407-8.

ABSTRACT

BACKGROUND: Organ measurements derived from magnetic resonance imaging (MRI) have the potential to enhance our understanding of the precise phenotypic variations underlying many clinical conditions.

METHODS: We applied morphometric methods to study the kidneys by constructing surface meshes from kidney segmentations from abdominal MRI data in 38,868 participants in the UK Biobank. Using mesh-based analysis techniques based on statistical parametric maps (SPMs), we were able to detect variations in specific regions of the kidney and associate those with anthropometric traits as well as disease states including chronic kidney disease (CKD), type-2 diabetes (T2D), and hypertension. Statistical shape analysis (SSA) based on principal component analysis was also used within the disease population and the principal component scores were used to assess the risk of disease events.

RESULTS: We show that CKD, T2D and hypertension were associated with kidney shape. Age was associated with kidney shape consistently across disease groups. Body mass index (BMI) and waist-to-hip ratio (WHR) were also associated with kidney shape for the participants with T2D. Using SSA, we were able to capture kidney shape variations, relative to size, angle, straightness, width, length, and thickness of the kidneys, within disease populations. We identified significant associations between both left and right kidney length and width and incidence of CKD (hazard ratio (HR): 0.74, 95% CI: 0.61-0.90, p < 0.05, in the left kidney; HR: 0.76, 95% CI: 0.63-0.92, p < 0.05, in the right kidney) and hypertension (HR: 1.16, 95% CI: 1.03-1.29, p < 0.05, in the left kidney; HR: 0.87, 95% CI: 0.79-0.96, p < 0.05, in the right kidney).

CONCLUSIONS: The results suggest that shape-based analysis of the kidneys can augment studies aiming at the better categorisation of pathologies associated with chronic kidney conditions.

PMID:38057740 | DOI:10.1186/s12882-023-03407-8

BMC Public Health. 2023 Dec 6;23(1):2439. doi: 10.1186/s12889-023-17335-7.

ABSTRACT

BACKGROUND: Child poverty has been gradually rising, and about 12% of all Norwegian children are living in a state of relative poverty. This study was part of the New Patterns project, which recruits low-income families requiring long-term welfare services. Included families receive integrated welfare services, with the help of a family coordinator. The current study objectives were to explore the associations between HRQoL, demographic variables (age, gender, immigration status) and leisure activities in children and adolescents in low-income families.

METHODS: A cross-sectional survey was conducted among low-income families. Participating families had children (N = 214) aged 8-18 years.The family had a household income below 60% of the equivalized median population income for three consecutive years and needed long-term welfare services. HRQoL was measured using the KIDSCREEN-27 self-report instrument. Descriptive statistics, including means, standard deviations, and proportions, were calculated, and ordinary least squares regressions were performed, clustering standard errors at the family level.

RESULTS: Compared with boys, girls reported lower HRQoL on only one out of five dimensions, physical wellbeing. In the regression analysis we found statistically significant positive associations between migrant status and HRQoL on all five dimensions: physical wellbeing, psychological wellbeing, parents and autonomy, peers and social support, and school environment. In addition, age was associated with school environment, and age, gender and participation in leisure activities was associated with better physical wellbeing.

CONCLUSIONS: Baseline results regarding HRQoL among children and adolescents in low-income families indicate that they have overall good HRQoL, though some participants had low HRQoL scores, especially on the physical and social support dimensions. Children with an immigrant background report higher HRQoL than do children without an immigrant background.

PMID:38057731 | DOI:10.1186/s12889-023-17335-7

BMC Bioinformatics. 2023 Dec 7;24(1):459. doi: 10.1186/s12859-023-05578-5.

ABSTRACT

BACKGROUND: Variability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical biases, called batch effects, in, respectively, microarray and RNA-Seq expression data.

RESULTS: In this technical note, we present a new Python implementation of ComBat and ComBat-Seq. While the mathematical framework is strictly the same, we show here that our implementations: (i) have similar results in terms of batch effects correction; (ii) are as fast or faster than the original implementations in R and; (iii) offer new tools for the bioinformatics community to participate in its development. pyComBat is implemented in the Python language and is distributed under GPL-3.0 ( https://www.gnu.org/licenses/gpl-3.0.en.html ) license as a module of the inmoose package. Source code is available at https://github.com/epigenelabs/inmoose and Python package at https://pypi.org/project/inmoose .

CONCLUSIONS: We present a new Python implementation of state-of-the-art tools ComBat and ComBat-Seq for the correction of batch effects in microarray and RNA-Seq data. This new implementation, based on the same mathematical frameworks as ComBat and ComBat-Seq, offers similar power for batch effect correction, at reduced computational cost.

PMID:38057718 | DOI:10.1186/s12859-023-05578-5

BMC Infect Dis. 2023 Dec 6;23(1):858. doi: 10.1186/s12879-023-08682-2.

ABSTRACT

BACKGROUND: To ensure emergency infection prevention and control (IPC) can be fully supervised and monitored in coronavirus disease (COVID-19) epidemic period, a three-level inspector mechanism called “Internal self-check, Departmental cross-check, and Verification of outstanding key and difficult issues” was established in southwest China. The present study aimed to explore the effectiveness of inspector mechanism for the emergency IPC.

METHODS: A self-control real-world study was conducted during COVID-19 epidemic period from 2020 to 2022. An innovative designed mobile phone application was used to realize paperless information transmission and data management. Data were compared between inspection levels using SPSS 19.0 software.

RESULTS: A total of 2,800,132 supervision records were collected, including 149,137 comprehensive epidemic IPC projects, 1,410,093 personal protective equipment (PPE) use, 1,223,595 wearing and removing process of PPE and 17,307 ultraviolet light-detectable fluorescent (UV/F) surface marker. During the study period, the inspectors and subjects explored many optimized IPC measures. The compliance rate of check items has exceeded 98%, and internal self-check has a statistically significant higher rate than departmental cross-check (99.95% versus 98.74%, χ² = 26111.479, P < 0.001). Compare with the failure rate in internal self check, the failure rate of PPE usage and wearing/removing process was statistically higher in departmental cross-check (χ² = 1957.987, P < 0.001, χ² = 465.610, P < 0.001, respectively). The overall clearance rate of UV/F surface markers is 87.88%, but there is no statistically significant difference over the three years of the present study (F = 2.902, P = 0.071).

CONCLUSIONS: Inspector mechanism for the emergency IPC completed an incredible inspection workload and offered creative assistance to combat the COVID-19 outbreak. These methods and accumulated experiences should be helpful for us to strengthen IPC for future epidemic.

PMID:38057717 | DOI:10.1186/s12879-023-08682-2

Accid Anal Prev. 2023 Dec 4;195:107407. doi: 10.1016/j.aap.2023.107407. Online ahead of print.

ABSTRACT

Driven by advancements in data-driven methods, recent developments in proactive crash prediction models have primarily focused on implementing machine learning and artificial intelligence. However, from a causal perspective, statistical models are preferred for their ability to estimate effect sizes using variable coefficients and elasticity effects. Most statistical framework-based crash prediction models adopt a case-control approach, matching crashes to non-crash events. However, accurately defining the crash-to-non-crash ratio and incorporating crash severities pose challenges. Few studies have ventured beyond the case-control approach to develop proactive crash prediction models, such as the duration-based framework. This study extends the duration-based modeling framework to create a novel framework for predicting crashes and their severity. Addressing the increased computational complexity resulting from incorporating crash severities, we explore a tradeoff between model performance and estimation time. Results indicate that a 15 % sample drawn at the epoch level achieves a balanced approach, reducing data size while maintaining reasonable predictive accuracy. Furthermore, stability analysis of predictor variables across different samples reveals that variables such as Time of day (Early afternoon), Weather condition (Clear), Lighting condition (Daytime), Illumination (Illuminated), and Volume require larger samples for more accurate coefficient estimation. Conversely, Daytime (Early morning, Late morning, Late afternoon), Lighting condition (Dark lighted), Terrain (Flat), Land use (Commercial, Rural), Number of lanes, and Speed converge towards true estimates with small incremental increases in sample size. The validation reveals that the model performs better in highway segments experiencing more frequent crashes (segments where the duration between crashes is less than 100 h, or approximately 4 days).

PMID:38056024 | DOI:10.1016/j.aap.2023.107407

Ann Med. 2023;55(2):2286638. doi: 10.1080/07853890.2023.2286638. Epub 2023 Dec 6.

ABSTRACT

BACKGROUND: The clinical manifestations of maintenance haemodialysis (MHD) outpatients diagnosed with coronavirus disease 2019 (COVID-19) are highly heterogeneous. They are prone to progress to severe conditions, and they often require hospitalization. To better guide the management of MHD outpatients, this retrospective observational study assessed risk factors for hospitalization of MHD patients after a diagnosis of COVID-19.

METHODS: The demographic data, comorbidities, laboratory indicators and imaging data of 128 MHD outpatients at our haemodialysis centre with confirmed COVID-19 infection from December 2022 to January 2023 were collected. The relationships between these factors and hospitalization of patients were analyzed.

RESULTS: Among the 128 patients, 25 (19.53%) were hospitalized. One of the 25 inpatients was mechanically ventilated, and two of them died. Multivariate logistic regression analysis showed that the hospitalization rate was correlated with age, comorbid diabetes and peripheral blood lymphocyte count.

CONCLUSION: Older age, comorbid diabetes and lower lymphocyte count are important risk factors for hospitalization of MHD outpatients after a diagnosis of COVID-19. Focusing on these factors may help in early identification of patients who may need to be admitted due to potential disease progression.

PMID:38056005 | DOI:10.1080/07853890.2023.2286638

Int J Biol Markers. 2023 Dec 6:3936155231217268. doi: 10.1177/03936155231217268. Online ahead of print.

ABSTRACT

BACKGROUND: Gastric cancer is a common cancer developed in a carcinogenesis process from precancerous lesions including chronic gastritis, intestinal metaplasia, and dysplasia. Survivin, an inhibitor-of-apoptosis protein, is associated with the initiation and progression of gastric cancer. The present study aimed to evaluate the immunohistochemical expression patterns of survivin and its relationship with early diagnosis of gastric cancer in Iranian patients.

METHODS: In this retrospective case-control study, immunoexpression of survivin was investigated on sections obtained from formalin-fixed paraffin-embedded tissue blocks of 38 chronic gastritis, 32 intestinal metaplasia, 20 dysplasia, 28 gastric adenocarcinoma, and 22 controls.

RESULTS: Survivin immunoexpression in chronic gastritis was higher than controls, but this difference was not statistically significant (P > 0.05). However, survivin immunoexpression had a steady significant increase from control and chronic gastritis to intestinal metaplasia to dysplasia to gastric adenocarcinoma (P < 0.05). Sensitivity, specificity, and area under the curve of survivin immunohistochemical test for the diagnosis of gastric cancer were 87.5%, 74.4%, and 0.85, respectively. Males had a significantly higher survivin expression than females (P < 0.001). Also, survivin expression was significantly higher in older patients than in younger ones (P < 0.001).

CONCLUSION: It seems that the steady increase in survivin expression from different precancerous lesions to gastric adenocarcinoma suggests that survivin can be used as a potential biomarker for the prevention and early diagnosis of gastric cancer.

PMID:38055975 | DOI:10.1177/03936155231217268

J Insect Sci. 2023 Nov 1;23(6):21. doi: 10.1093/jisesa/iead094.

ABSTRACT

European foulbrood (EFB) is a severe disease of honey bee (Apis mellifera) larvae caused by the bacterium Linnaeus [Hymenoptera: Apidae]) Melissococcus plutonius (ex White) Bailey and Collins (Lactobacillales: Enterococcaceae). Many beekeepers in North America report severe EFB following blueberry pollination, but it is not clear what factors during pollination are related to clinical disease. Additionally, the impact that other factors such as viral load and hygienic behavior have on EFB has not been studied. In Spring of 2020 we enrolled 60 commercial honey bee colonies in a prospective cohort study. Colonies were inspected 3 times over the season with hive metrics and samples taken for viral testing. Each colony was tested for hygienic behavior twice and the score was averaged. Viral loads were determined by qPCR for deformed wing virus (DWV) A and B. We found no statistical difference in the EFB prevalence or severity between the 2 yards at any timepoint; 50% (n = 16) of the colonies in the holding yard and 63% (n = 17) in blueberry developed moderate to severe EFB over the study period. When colonies from both yards were pooled, we found no relationship between viral load or hygienic behavior and development of EFB. These results suggest that other factors may be responsible for driving EFB virulence and hygienic behavior is not likely helpful in managing this disease.

PMID:38055945 | DOI:10.1093/jisesa/iead094

Ocul Immunol Inflamm. 2023 Dec 6:1-7. doi: 10.1080/09273948.2023.2280709. Online ahead of print.

ABSTRACT

BACKGROUND: Immunoglobulin G4-related ophthalmic disease (IgG4-ROD) poses clinical challenges due to its heterogeneous ocular and systemic manifestations. We aim to report the systemic involvement and the clinical, serological and radiological associations of a cohort of Chinese patients.

METHODS: A territory-wide, biopsy-proven, Chinese cohort. A retrospective, masked chart review of medical records, orbital images, and histopathology reports.

RESULTS: A total of 122 (65 male) patients with a follow-up of 81 ± 49 (24 to 84) months were reviewed. Ninety (74%) patients presented bilaterally. Subacute upper eyelid swelling was the commonest presentation (82/122, 67%). During follow-up, 91/122 patients (75%) underwent extra-orbital imaging including computer tomography (692 films), ultrasonography (182 films), magnetic resonance imaging (76 films) and whole body FDG-PET scan (33 films). Eighty-six (95%) of these 91 patients had extra-orbital involvement radiologically (2.7 ± 1.6 regions, range: 0 to 9). Lymph node was the most prevalent (N = 60,66%), followed by salivary gland (N = 51,56%), lung (N = 49,54%), kidney (N = 22, 24%), hepatobiliary tree (N = 18, 20%) and pancreas (N = 17, 19%). Other organs include thyroid, aorta, meninges/brain and skin. Twenty-eight (23%) patients had allergic diseases (19 asthma, 16 allergic rhinitis, and 6 eczemas). Fifty-seven (48%) patients had paranasal sinusitis. Serum eosinophilia was associated with a higher number (3.24 versus 2.52, P = 0.0304) of organ involvement. Patients with deep organ involvement was associated with a higher age of IgG4-ROD onset (70 ± 12 versus 56 ± 13, P < 0.0001).

CONCLUSIONS: 95% of the patients who underwent systemic imaging in our cohort had systemic organ involvement. An early physicians’ assessment and radiological imaging are recommended after the diagnosis of IgG4-ROD.

PMID:38055933 | DOI:10.1080/09273948.2023.2280709