Category: Statistics

Discov Oncol. 2024 Mar 31;15(1):92. doi: 10.1007/s12672-024-00955-9.

ABSTRACT

OBJECTIVE: AT-rich interaction domain 1A (ARID1A) mutant tumors show active anti-tumor immune response, which is the potential indication of immunotherapy. However, the relationship between the heterogeneous ARID1A expression and the immune response and immunotherapy efficacy in colorectal cancer (CRC) is still unclear.

METHODS: We collected 1113 cases of patients with stage I-IV CRC who underwent primary resection at Harbin Medical University Cancer Hospital. ARID1A expression in CRC tissues was assessed via immunohistochemistry (IHC). CD8, CD163 and FOXP3 were stained by IHC to identify the immune landscape. Clinicopathological features of patients were compared using statistical tests like the Wilcoxon-Mann-Whitney test or χ2 tests. Kaplan-Meier survival analysis with log-rank tests were employed.

RESULTS: Heterogeneous ARID1A expression was categorized into integrity expression, complete expression deficiency (cd-ARID1A), partial expression deficiency (pd-ARID1A), and clonal expression deficiency (cld-ARID1A). ARID1A-deficient expression was significant association with dMMR (P value < 0.001). Patients with ARID1A deficiency, compared to ARID1A-proficient patients, exhibited increased infiltration levels of CD8 + P value < 0.0001), CD163 + P value < 0.001), and FOXP3 + P value < 0.001).cells within the tumor tissue. However, in different subgroups, only samples with complete or partial deficiency of ARID1A showed a higher abundance of lymphocyte infiltration. In patients with ARID1A-clonal expression deficiency tumor, the infiltration patterns of three immune cell types were comparable to those in ARID1A-proficient patients. Heterogeneous ARID1A expression is related to the different prognosis and immunotherapythe efficacy in CRC patients.

CONCLUSION: Heterogeneous ARID1A expression is accompanied by a different immune landscape. CRC patients with ARID1A-clonal expression deficiency do not benefit from the treatment of immune checkpoint inhibitors (ICIs).

PMID:38555560 | DOI:10.1007/s12672-024-00955-9

Dermatol Ther (Heidelb). 2024 Mar 31. doi: 10.1007/s13555-024-01142-y. Online ahead of print.

ABSTRACT

INTRODUCTION: Androgenetic alopecia (AGA) is a prevalent, multifactorial form of hair loss involving complex aetiological factors, such as altered androgen regulation and energy metabolism. Existing treatments offer limited success, thus highlighting the need for advanced, personalised therapeutic strategies. This study focuses on correlating the genetic mechanisms of AGA with molecular targets involved in the response to current treatment modalities.

METHODS: An anonymised database including 26,607 patients was subjected to analysis. The dataset included information on patients’ genotypes in 26 single nucleotide polymorphisms (SNPs), specifically, and diagnosed AGA grades, representing a broad range of ethnic backgrounds.

RESULTS: In our sample, 64.6% of males and 35.4% of females were diagnosed with female pattern hair loss. This distribution aligns well with prior studies, thus validating the representativeness of our dataset. AGA grading was classified using the Hamilton-Norwood and Ludwig scales, although no association was found to the grade of the disease. SNP association analysis revealed eight SNPs, namely rs13283456 (PTGES2), rs523349 (SRD5A2), rs1800012 (COL1A1), rs4343 (ACE), rs10782665 (PTGFR), rs533116 (PTGDR2), rs12724719 (CRABP2) and rs545659 (PTGDR2), to be statistically significant with a p-value below 0.05.

CONCLUSIONS: The study establishes a preliminary association between eight specific SNPs and AGA. These genetic markers offer insights into the variability of therapeutic responses, thus underlining the importance of personalised treatment approaches. Our findings show the potential for more targeted research to understand these SNPs’ and further roles in AGA pathophysiology and in modulating treatment response.

PMID:38555553 | DOI:10.1007/s13555-024-01142-y

Dev Neurorehabil. 2024 Mar 30:1-9. doi: 10.1080/17518423.2024.2331446. Online ahead of print.

ABSTRACT

PURPOSE: To describe the relationship amongst child and family characteristics (e.g. social relationships, family functioning) and child participation after traumatic brain injury (TBI) an average of 2.65 years post-TBI (SD = 2.12).

METHOD: Cross-sectional, secondary analysis of data collected as part of a larger research project.

RESULTS: N = 44 children with TBI. Analysis revealed statistically significant correlations between child participation, family functioning, and child characteristics.

CONCLUSIONS: School-aged children with TBI might experience chronic participation restrictions, associated with challenges in family functioning. Professionals can support children with TBI and their families through follow-up services that include a focus on family-based interventions to better support long-term outcomes for this population.

PMID:38555502 | DOI:10.1080/17518423.2024.2331446

Jpn J Clin Oncol. 2024 Mar 30:hyae043. doi: 10.1093/jjco/hyae043. Online ahead of print.

ABSTRACT

BACKGROUND: Perioperative management methods that reduce surgery-associated invasiveness and improve the quality of postoperative recovery are being promoted as enhanced recovery after surgery programs in various areas. Early enteral nutrition and mobilization are essential elements for enhanced recovery after surgery; however, their safety and feasibility are unclear in head and neck surgery with free tissue transfer reconstruction. This study aimed to clarify these uncertainties.

METHODS: This is a retrospective before-after study. From 2018 to 2022, 187 and 173 patients received conventional management on or before April 2020 and early management on or after May 2020, respectively. The conventional management and early management groups received enteral nutrition and mobilization on postoperative days 2 and 1, respectively. The primary outcome for safety assessment was the incidence of complications. The secondary outcome was the compliance rate of conventional management or early management for feasibility assessment and the length of hospital stay.

RESULTS: The clinical tumour-node-metastasis stage and American Society of Anesthesiologists physical status showed significant differences between the groups. In multivariable analysis, the early management group demonstrated a significantly lower incidence of treatment-required complication classified Clavien-Dindo Grade 2 and above (odds ratio = 0.57; 95% confidence interval = 0.31-0.92) and lower wound infection (odds ratio = 0.53; 95% confidence interval = 0.31-0.92). The early management group had lower compliance rate than the conventional management group; however, no statistically significant difference was observed (79.8% vs. 85.0%, P = 0.21).

CONCLUSION: Early management is safe and feasible following head and neck surgery with free tissue transfer reconstruction. It could reduce the complication rate and is considered a useful postoperative management method.

PMID:38555498 | DOI:10.1093/jjco/hyae043

Radiat Prot Dosimetry. 2024 Mar 30:ncae072. doi: 10.1093/rpd/ncae072. Online ahead of print.

ABSTRACT

Ensuring the safety of healthcare workers in interventional cardiology necessitates effective monitoring of occupational radiation exposure. This study aims to assess the accuracy of the over-apron single dosimetric approach compared with double dosimetric methods and explore the relationship between under-apron and over-apron doses. This investigation showed that the prescribed annual dose constraint of 20 mSv year-1 was not exceeded by the maximum annual occupational doses determined by dosimetric algorithms, which were 0.13 ± 0.02, 0.15 ± 0.02 and 0.27 ± 0.04 mSv, respectively. The study demonstrated excellent statistically significant correlations among single and double dosimetric algorithms and between direct under-apron and over-apron doses. Consequently, single dosimetric algorithms could effectively estimate doses for double dosimetric algorithms, highlighting the limited added value of under-apron measurements. These findings significantly impact the practice of interventional cardiology in Sri Lanka, playing a crucial role in enhancing radiation protection measures.

PMID:38555495 | DOI:10.1093/rpd/ncae072

Brief Funct Genomics. 2024 Mar 30:elae009. doi: 10.1093/bfgp/elae009. Online ahead of print.

ABSTRACT

Genomic data analysis has witnessed a surge in complexity and volume, primarily driven by the advent of high-throughput technologies. In particular, studying chromatin loops and structures has become pivotal in understanding gene regulation and genome organization. This systematic investigation explores the realm of specialized bioinformatics pipelines designed specifically for the analysis of chromatin loops and structures. Our investigation incorporates two protein (CTCF and Cohesin) factor-specific loop interaction datasets from six distinct pipelines, amassing a comprehensive collection of 36 diverse datasets. Through a meticulous review of existing literature, we offer a holistic perspective on the methodologies, tools and algorithms underpinning the analysis of this multifaceted genomic feature. We illuminate the vast array of approaches deployed, encompassing pivotal aspects such as data preparation pipeline, preprocessing, statistical features and modelling techniques. Beyond this, we rigorously assess the strengths and limitations inherent in these bioinformatics pipelines, shedding light on the interplay between data quality and the performance of deep learning models, ultimately advancing our comprehension of genomic intricacies.

PMID:38555493 | DOI:10.1093/bfgp/elae009

Brief Bioinform. 2024 Mar 27;25(3):bbae120. doi: 10.1093/bib/bbae120.

ABSTRACT

Digital PCR (dPCR) is a highly accurate technique for the quantification of target nucleic acid(s). It has shown great potential in clinical applications, like tumor liquid biopsy and validation of biomarkers. Accurate classification of partitions based on end-point fluorescence intensities is crucial to avoid biased estimators of the concentration of the target molecules. We have evaluated many clustering methods, from general-purpose methods to specific methods for dPCR and flowcytometry, on both simulated and real-life data. Clustering method performance was evaluated by simulating various scenarios. Based on our extensive comparison of clustering methods, we describe the limits of these methods, and formulate guidelines for choosing an appropriate method. In addition, we have developed a novel method for simulating realistic dPCR data. The method is based on a mixture distribution of a Poisson point process and a skew-$t$ distribution, which enables the generation of irregularities of cluster shapes and randomness of partitions between clusters (‘rain’) as commonly observed in dPCR data. Users can fine-tune the model parameters and generate labeled datasets, using their own data as a template. Besides, the database of experimental dPCR data augmented with the labeled simulated data can serve as training and testing data for new clustering methods. The simulation method is available as an R Shiny app.

PMID:38555473 | DOI:10.1093/bib/bbae120

Cardiovasc Diabetol. 2024 Mar 30;23(1):112. doi: 10.1186/s12933-024-02203-4.

ABSTRACT

BACKGROUND: Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are effective antidiabetic drugs with potential cardiovascular benefits. Despite their well-established role in reducing the risk of major adverse cardiovascular events (MACE), their impact on heart failure (HF) remains unclear. Therefore, our study examined the cardioprotective effects of tirzepatide (TZT), a novel glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide 1 (GLP-1) receptor agonist.

METHODS: A three-steps approach was designed: (i) Meta-analysis investigation with the primary objective of assessing major adverse cardiovascular events (MACE) occurrence from major randomized clinical trials.; (ii) TZT effects on a human cardiac AC16 cell line exposed to normal (5 mM) and high (33 mM) glucose concentrations for 7 days. The gene expression and protein levels of primary markers related to cardiac fibrosis, hypertrophy, and calcium modulation were evaluated. (iii) In silico data from bioinformatic analyses for generating an interaction map that delineates the potential mechanism of action of TZT.

RESULTS: Meta-analysis showed a reduced risk for MACE events by TZT therapy (HR was 0.59 (95% CI 0.40-0.79, Heterogeneity: r² = 0.01, I² = 23.45%, H² = 1.31). In the human AC16 cardiac cell line treatment with 100 nM TZT contrasted high glucose (HG) levels increase in the expression of markers associated with fibrosis, hypertrophy, and cell death (p < 0.05 for all investigated markers). Bioinformatics analysis confirmed the interaction between the analyzed markers and the associated pathways found in AC16 cells by which TZT affects apoptosis, fibrosis, and contractility, thus reducing the risk of heart failure.

CONCLUSION: Our findings indicate that TZT has beneficial effects on cardiac cells by positively modulating cardiomyocyte death, fibrosis, and hypertrophy in the presence of high glucose concentrations. This suggests that TZT may reduce the risk of diabetes-related cardiac damage, highlighting its potential as a therapeutic option for heart failure management clinical trials. Our study strongly supports the rationale behind the clinical trials currently underway, the results of which will be further investigated to gain insights into the cardiovascular safety and efficacy of TZT.

PMID:38555463 | DOI:10.1186/s12933-024-02203-4

Virol J. 2024 Mar 30;21(1):77. doi: 10.1186/s12985-024-02344-8.

ABSTRACT

PURPOSE: The purpose of this study was to investigate immunological variations between a group that received the hepatitis B vaccine and a non-vaccine group. We focused on a cohort that achieved HBsAg seroclearance after Peg-IFNα treatment of CHB.

METHODS: We enrolled twenty-eight individuals who achieved HBsAg seroclearance after Peg-IFNα treatment. They were divided into two groups: a vaccine group (n = 14) and a non-vaccine group (n = 14). We assessed lymphocyte subpopulations, B cell- and T cell-surface costimulatory/inhibitory factors, cytokines and immunoglobulin levels were detected at different time points to explore immune-function differences between both groups.

RESULTS: The seroconversion rate in the vaccine group at 24 weeks post-vaccination was 100%, which was significantly higher (p = 0.006) than that of the non-vaccine group (50%). Additionally, more individuals in the vaccine group exhibited anti-HBs levels exceeding 100 IUs/L and 300 IUs/L compared to the non-vaccine group (p < 0.05). The vaccine group demonstrated significantly increase total B cells and class-switched B cells at 24 weeks and plasma cells, CD80⁺B cells, Tfh cells, and ICOS⁺Tfh cell at 12 weeks, compared with baseline levels (p < 0.05). Conversely, Bregs (CD24⁺CD27⁺ and CD24⁺CD38^high) decreased significantly at 24 weeks (p < 0.05). None of the above changes were statistically significance in the non-vaccine group (p > 0.05). Total IgG increased significantly in the vaccine group, and IL-2, IL-5, and IL-6 concentrations increased significantly at week 24 (p < 0.05). Differences in various types of cytokines and immunoglobulins in the plasma of the non-vaccine group were not significant (p > 0.05). Anti-HBs titers positively correlated with Th1/Th2 cells at 24 weeks (r = 0.448 and 0.458, respectively, p = 0.022 and 0.019, respectively), and negatively with CD24⁺CD38^highBreg cells (r = -0.402, p = 0.042).

CONCLUSIONS: After achieving HBsAg seroclearance through Peg-IFNα treatment for CHB, administering the hepatitis B vaccine significantly increased anti-HBs-seroconversion rates and antibody levels. We also observed significant immunological differences between the vaccine and non-vaccine groups. Specifically, the vaccine group exhibited significant increases in B cells, plasma cells, and Tfh cells, while Breg levels was significantly lower. These immunological changes are likely conducive to the production of anti-HBs antibodies. However, in the non-vaccine group, the observed changes were not significantlly significant.

PMID:38555445 | DOI:10.1186/s12985-024-02344-8

Cardiovasc Diabetol. 2024 Mar 30;23(1):115. doi: 10.1186/s12933-024-02194-2.

ABSTRACT

BACKGROUND: Diabetes mellitus (DM) duration affects incident atrial fibrillation (AF) risk; the effect of physical activity on mitigating AF risk related to varying DM duration remains unknown. We assessed the effect of physical activity on incident AF in patients with DM with respect to known DM duration.

METHODS: Patients with type 2 DM who underwent the Korean National Health Insurance Service health examination in 2015-2016 were grouped by DM duration: new onset and < 5, 5-9, and ≥ 10 years. Physical activity was classified into four levels: 0, < 500, 500-999, 1,000-1,499, and ≥ 1,500 metabolic equivalent task (MET)-min/week, with the primary outcome being new-onset AF.

RESULTS: The study enrolled 2,392,486 patients (aged 59.3 ± 12.0 years, 39.8% female) with an average follow-up of 3.9 ± 0.8 years and mean DM duration of 5.3 ± 5.1 years. Greater physical activity was associated with a lower AF risk. Lowering of incident AF risk varied with different amounts of physical activity in relation to known DM duration. Among patients with new-onset DM, DM duration < 5 years and 5-9 years and 1,000-1,499 MET-min/week exhibited the lowest AF risk. Physical activity ≥ 1,500 MET-min/week was associated with the lowest incident AF risk in patients with DM duration ≥ 10 years (by 15%), followed DM duration of 5-9 years (12%) and < 5 years (9%) (p-for-interaction = 0.002).

CONCLUSIONS: Longer DM duration was associated with a high risk of incident AF, while increased physical activity generally reduced AF risk. Engaging in > 1,500 MET-min/week was associated with the greatest AF risk reduction in patients with longer DM duration, highlighting the potential benefits of higher activity levels for AF prevention.

PMID:38555442 | DOI:10.1186/s12933-024-02194-2