Tag: pubmed

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2025 Sep 10;42(9):1039-1044. doi: 10.3760/cma.j.cn511374-20250326-00182.

ABSTRACT

OBJECTIVE: The haplotypes of Killer cell immunoglobulin-like receptors (KIR) can be divided into centromeric and telomeric ones. As the terminal gene at the centromeric end, KIR3DP1 plays an important role in stabilizing the haplotype structure. This study aimed to analyze the distribution of KIR3DP1 gene haplotypes among Han Chinese population in Zhejiang in order provide a basis for further analyzing the role of KIR3DP1 in the KIR haplotypes.

METHODS: A total of 166 unrelated blood donors from Zhejiang were collected (Blood donation period: March 2020 to August 2020), and genotyping was performed by next-generation sequencing based on exon capture. The copy number and allelic frequency of the KIR3DP1 gene and the distribution of centromeric haplotypes were statistically analyzed. This study was approved by the Medical Ethics Committee of Zhejiang Blood Center (Ethics No.: 2023-001).

RESULTS: The KIR3DP1 gene was positive for all individuals but with different copy numbers. Among these, 4 cases (2.4%) had only 1 copy, 156 cases (94.0%) had 2 copies, and 6 cases (3.6%) had 3 copies. A total of 10 KIR3DP1 alleles were found in the population, which could be classified into the KIR3DP1*001-L type, KIR3DP1*003-L type, and KIR3DP1 full deletion type. The KIR3DP1*003 L type allele was linked to the Cen-A01 and Cen-B01 types, and the KIR3DP1*001*L type allele and the KIR3DP1 deletion type were only present in the Cen-B02 type haplotype.

CONCLUSION: This study has derived a high-resolution distribution map of the KIR3DP1 gene in the Han population from Zhejiang, and found that the KIR3DP1 alleles showed different linkage with the centromeric haplotypes, which has provided a basis for further studying the role of KIR3DP1 in genetic immunity.

PMID:41230580 | DOI:10.3760/cma.j.cn511374-20250326-00182

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2025 Sep 10;42(9):1033-1038. doi: 10.3760/cma.j.cn511374-20250707-00410.

ABSTRACT

OBJECTIVE: To explore the detection rate of copy number variations (CNVs) in fetuses with isolated Congenital anomalies of the kidney and urinary tract (CAKUT) and pregnancy outcomes in order to provide a basis for genetic counseling.

METHODS: One hundred and eighty eight fetuses who underwent chromosomal microarray analysis (CMA) due to isolated CAKUT detected by prenatal ultrasonography at Qingdao Women and Children’s Hospital from January 2021 to December 2024 were selected as the study subjects. According to the ultrasound findings, the fetuses were divided into 8 groups, including renal parenchymal dysplasia group, renal cystic dysplasia group, simple renal parenchymal echo enhancement group, abnormal development of renal collecting system group, duplicated kidney group, ectopic kidney group, horseshoe kidney group, and bladder/posterior urethral abnormalities group. The detection of CNVs was retrospectively analyzed, and the pregnant women were followed up to summarize their pregnancy outcomes. 2 test (or Fisher’s exact probability method) was used to compare the CNV detection rates between the groups. This study was approved by the Medical Ethics Committee of the Qingdao Women and Children’s Hospital (Ethics No.: QFELL-YJ-2025-85).

RESULTS: Among the 188 fetuses with isolated CAKUT, 23 CNVs (12.23%) were detected, of which 13 cases (6.91%) were pathogenic and 10 cases were rated as variants of unknown significance (VOUS). Among the 8 groups, the three groups with the highest proportion were renal cystic dysplasia group, renal metaplasia group, and renal parenchymal dysplasia group. The detection rates of pathogenic CNVs in the three groups were 1.79% (1/56), 6.78% (4/59), and 16.67% (5/30), respectively, with statistically significant differences (P < 0.05). Parental verification was conducted on 12 fetuses detected with the CNVs, confirming that 2 cases were de novo and 10 were inherited from parents with a normal phenotype. After genetic counseling, the parents of 9 fetuses opted to terminate the pregnancy, while 11 chose to continue with the pregnancy, and 3 were lost to follow-up. At the time of last follow-up, the youngest offspring was 5 months old and the oldest was 3 years and 11 months old. One child had renal aplasia, and two were born with hydronephrosis, which have been cured through surgery. The remainders had no obvious abnormality with their growth and development.

CONCLUSION: CMA testing has important value for prenatal diagnosis of isolated CAKUT. In this study, the detection rate of pathogenic CNVs has increased sequentially in fetuses with renal cystic developmental abnormalities, renal collecting system developmental abnormalities, and renal parenchymal dysplasia, while there was no significant difference in the detection rate of CNVs. For fetuses with isolated CAKUT detected by prenatal ultrasound, CMA testing should be considered, and reasonable pregnancy decisions should be made based on the results of prenatal ultrasound and parental verification.

PMID:41230579 | DOI:10.3760/cma.j.cn511374-20250707-00410

Langmuir. 2025 Nov 13. doi: 10.1021/acs.langmuir.5c02750. Online ahead of print.

ABSTRACT

Macroscopic properties of mesoporous metal oxides depend on the mesopore architecture, i.e., the pore size, wall thickness, and pore connectivity. Consequently, rational preparation protocols and deep knowledge of the templating mechanism are required for systematic porosity-property studies and the intentional synthesis of an optimized pore morphology. In this work, we thus prepared a library of 17 poly(ethylene oxide)-block-poly(hexyl acrylate) (PEO-b-PHA) block copolymers of varying PEO and PHA block lengths to quantitatively deduce the effect of the individual block lengths on the mesopore size of the templated silica. The block length of the hydrophobic PHA block in the micelle core showed to enable a pore size tuning between 10 and 80 nm according to electron microscopy, physisorption, and small-angle X-ray scattering. In contrast, varying the PEO block length did not alter the pore size, but revealed that a sufficiently large PEO block is required to ensure ordered spherical mesopores. Electron tomography confirmed a spherical pore geometry and a systematic decrease in pore wall thickness upon increasing the template concentration (i.e., template-to-silica ratio) during soft templating. A statistical in-depth analysis by tomography demonstrated that this wall size decrease is accompanied by an improved pore connectivity (e.g., in terms of the coordination number of adjacent pores) and an increasing pore size. The pore size increase originates from a partial PEO collapse on the micelle core based on a pore volume analysis and occurs only above a certain threshold concentration of block copolymer. We demonstrated that this concentration can be elevated by applying soft templates featuring shorter PEO blocks, which extend the regime of wall size tuning under preservation of pore dimension and shape. Overall, these insights provide a guideline on how to tailor the pore size, wall thickness, and pore connectivity of mesoporous metal oxides and enable systematic studies concerning the optimum porosity, e.g., for electrocatalytic applications to maximize stability and activity.

PMID:41230577 | DOI:10.1021/acs.langmuir.5c02750

Bio Protoc. 2025 Nov 5;15(21):e5491. doi: 10.21769/BioProtoc.5491. eCollection 2025 Nov 5.

ABSTRACT

Sheath blight, caused by Rhizoctonia solani, is a major fungal disease of rice that leads to significant yield losses globally. Conventional inoculation methods often fail to achieve consistent and uniform infection, limiting their applicability in antifungal screening studies. This protocol describes a reliable in planta inoculation method for R. solani using mature sclerotia placed at the internodal region of tillering-stage rice seedlings. The procedure includes step-by-step instructions for seed germination, seedling preparation, pathogen culture, artificial inoculation, and post-infection application of antifungal treatments, including botanical compounds such as Ocimum gratissimum essential oil and thymol. Lesion development is monitored and quantified over time, and data are analyzed statistically to evaluate treatment efficacy. The protocol is optimized for reproducibility, scalability, and compatibility with sustainable disease management approaches. It provides a robust platform for evaluating antifungal agents in a biologically relevant and controlled environment. Key features • Establishes a reliable in planta inoculation method for R. solani in rice, overcoming the common challenge of achieving consistent disease development. • Enables post-inoculation screening of botanicals for antifungal efficacy under realistic plant-pathogen interaction conditions. • Integrates sustainable research practices by detailing botanical extraction and their in planta assessment against R. solani infection.

PMID:41230549 | PMC:PMC12602175 | DOI:10.21769/BioProtoc.5491

Front Hum Neurosci. 2025 Oct 28;19:1652773. doi: 10.3389/fnhum.2025.1652773. eCollection 2025.

ABSTRACT

BACKGROUND: Sporadic Creutzfeldt-Jakob disease (sCJD) is a rapidly progressive and fatal neurodegenerative disorder. Early diagnosis remains challenging due to nonspecific initial symptoms. Although electroencephalography (EEG) is a key diagnostic tool, particularly through the detection of periodic sharp wave complexes (PSWCs), the longitudinal evolution of EEG features and their correlation with clinical and neuroimaging progression are not fully characterized.

METHODS: This retrospective cohort study analyzed 37 patients diagnosed with probable and very probable sCJD according to the 2021 Chinese diagnostic guidelines. All patients underwent at least one EEG examination. One representative patient was followed for 23 weeks with serial EEG and MRI studies to document dynamic electrophysiological and structural changes. EEG background activity was graded as mild, moderate, or severe, and PSWCs were identified based on standardized criteria. MRI analyses focused on the spatial and temporal progression of hyperintense lesions on DWI and FLAIR sequences.

RESULTS: Among the 37 patients, 46% underwent initial EEG within 1 month of symptom onset, and 49% exhibited severe background abnormalities. PSWCs were present in 84% of patients at first EEG, with a high prevalence (82%) even in those examined within 4 weeks of onset. Longitudinal analysis in the index case revealed a progressive EEG deterioration: from slowed and disorganized background rhythms and emerging triphasic waves at 8 weeks, to widespread PSWCs with increasing periodicity (9-16 weeks), and finally to a burst-suppression pattern near electrical silence by week 23. Concurrent MRI showed a parallel expansion of hyperintense lesions from unilateral cortical and basal ganglia regions to bilateral involvement, closely correlated with the EEG progression. Statistical analysis showed no significant correlation between survival time and age, time to first EEG, CSF 14-3-3 protein status, or initial EEG background grade. Furthermore, neither the presence of typical PSWCs nor the severity of background activity was associated with survival outcomes.

CONCLUSION: EEG, especially the early and highly prevalent presence of PSWCs, offers high diagnostic value in sCJD but does not serve as prognostic predictors. The close correlation between EEG decline and MRI progression supports multimodal monitoring. Serial EEG should be integrated into sCJD diagnosis and follow-up.

PMID:41230545 | PMC:PMC12602467 | DOI:10.3389/fnhum.2025.1652773

J R Stat Soc Series B Stat Methodol. 2025 May 27;87(5):1508-1527. doi: 10.1093/jrsssb/qkaf028. eCollection 2025 Nov.

ABSTRACT

When an exposure of interest is confounded by unmeasured factors, an instrumental variable (IV) can be used to identify and estimate certain causal contrasts. Identification of the marginal average treatment effect (ATE) from IVs relies on strong untestable structural assumptions. When one is unwilling to assert such structure, IVs can nonetheless be used to construct bounds on the ATE. Famously, Alexander Balke and Judea Pearl proved tight bounds on the ATE for a binary outcome, in a randomized trial with noncompliance and no covariate information. We demonstrate how these bounds remain useful in observational settings with baseline confounders of the IV, as well as randomized trials with measured baseline covariates. The resulting bounds on the ATE are nonsmooth functionals, and thus standard nonparametric efficiency theory is not immediately applicable. To remedy this, we propose (1) under a novel margin condition, influence function-based estimators of the bounds that can attain parametric convergence rates when the nuisance functions are modelled flexibly, and (2) estimators of smooth approximations of these bounds. We propose extensions to continuous outcomes, explore finite sample properties in simulations, and illustrate the proposed estimators in an observational study targeting the effect of higher education on wages.

PMID:41230541 | PMC:PMC12602419 | DOI:10.1093/jrsssb/qkaf028

Front Neurosci. 2025 Oct 28;19:1638503. doi: 10.3389/fnins.2025.1638503. eCollection 2025.

ABSTRACT

INTRODUCTION: Alzheimer’s disease involves progressive white matter microstructural degeneration that may precede clinical symptoms by decades. While polygenic risk scores (PRS) quantify cumulative genetic liability for AD, genome-wide PRS lack mechanistic specificity. We tested whether pathway-specific PRS, targeting areas of biology including tau binding, lipid metabolism, and immune response, are differentially associated with diffusion MRI measures across the lifespan.

METHODS: We analyzed two population-based cohorts: the Avon Longitudinal Study of Parents and Children (ALSPAC; mean age = 19.8 years, n = 517) and UK Biobank (mean age = 64.2 years, n = 18,172). Genome-wide and nine pathway-specific PRS for Alzheimer’s disease were constructed using GWAS summary statistics and a clumping threshold of r² < 0.2 at p < 0.001. Diffusion MRI data were processed separately within each cohort: in ALSPAC, tract-based fractional anisotropy (FA) and mean diffusivity (MD) were extracted using probabilistic tractography from native-space regions of interest; in UK Biobank, diffusion metrics were derived from TBSS-aligned skeletons and standard atlas-based ROIs. Analyses focused on three tracts vulnerable to early AD pathology: the dorsal cingulum, parahippocampal cingulum, and fornix. Multiple linear regression models were used to assess PRS associations with FA and MD, adjusting for demographic, scanner, and genetic ancestry covariates. False discovery rate correction addressed multiple comparisons, and sensitivity analyses were performed excluding the APOE region.

RESULTS: In UK Biobank, higher PRS for protein-lipid complex assembly and tau protein binding were robustly associated with lower fractional anisotropy and higher mean diffusivity in both dorsal and parahippocampal cingulum segments (False discovery rate-corrected p < 0.05), explaining more variance than APOE alone; no significant effects emerged in the fornix. Genome-wide PRS showed weaker, non-significant associations. In ALSPAC, no PRS metric survived FDR correction, though nominal trends appeared in the dorsal cingulum. Sensitivity analyses confirmed that key cingulum associations in older adults persisted after omitting APOE.

CONCLUSION: Pathway-specific polygenic risk for Alzheimer’s disease manifests in white matter microstructure by mid- to late adulthood but not in early adulthood, suggesting an age-dependent emergence of genetic effects. dMRI phenotypes may thus serve as intermediate biomarkers for dissecting mechanistic pathways of preclinical Alzheimer’s disease vulnerability.

PMID:41230509 | PMC:PMC12602405 | DOI:10.3389/fnins.2025.1638503

Bioinform Adv. 2025 Nov 4;5(1):vbaf255. doi: 10.1093/bioadv/vbaf255. eCollection 2025.

ABSTRACT

SUMMARY: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria and archaea or ITS for fungi. zAMP is complemented by two modules: one to process databases to optimize taxonomy assignment, and the second to benchmark primers, databases and classifier performances. Coupled with zAMPExplorer, an interactive R Shiny application that provides an intuitive interface for quality control, diversity analysis, and statistical testing, this complete toolbox addresses both research and clinical needs in microbiota profiling.

AVAILABILITY AND IMPLEMENTATION: Comprehensive documentation and tutorials are provided alongside the source code of zAMP and zAMPExplorer software to facilitate installation and use. zAMP is implemented as a Snakemake workflow, ensuring reproducibility by running within Singularity or Docker containers, and is also easily installable via Bioconda. The zAMPExplorer application, designed for visualization and statistical analysis, can be installed using either a Docker image or from R-universe.

PMID:41230489 | PMC:PMC12603355 | DOI:10.1093/bioadv/vbaf255

Cureus. 2025 Nov 10;17(11):e96486. doi: 10.7759/cureus.96486. eCollection 2025 Nov.

ABSTRACT

INTRODUCTION: Perforation of a duodenal ulcer is a severe complication of peptic ulcer disease that requires prompt resuscitation and appropriate surgical intervention to minimize morbidity and mortality. This study aimed to compare the outcomes and complications of Graham’s patch versus modified Graham’s patch repair in patients with perforated duodenal ulcers admitted to a tertiary care hospital in Bangladesh.

METHODS: This comparative observational study was conducted in the Department of Surgery at Dhaka Medical College Hospital (DMCH) in Dhaka, Bangladesh, over a six-month period in 2018. Patients diagnosed with duodenal ulcer perforation were selected based on pre-defined inclusion criteria. Informed written consent was obtained from all participants prior to enrollment. A total of 60 patients (30 in each group) were included using a systematic sampling method. Data on post-operative outcomes and complications, such as leakage and wound infection, were collected using a pre-designed data sheet. Data analysis was performed using IBM SPSS Statistics for Windows, V. 24.0 (IBM Corp., Armonk, NY, USA).

RESULTS: The study included 60 participants with a mean age of 34.22±8.59 years (range: 16-53 years) and a male-to-female ratio of 2:1. In the Graham’s patch group, 90% of patients had pus in the intraperitoneal cavity, compared to 67% in the modified Graham’s patch group. Wound infection and post-operative fever were the most common complications observed in both groups, with no statistically significant differences (p=0.59; p=0.78). The average hospital stay was six days for the Graham’s patch group and eight days for the modified Graham’s patch group, also showing no significant difference between the groups (p=0.145).

CONCLUSION: This study compared the short-term outcomes of traditional versus modified Graham’s patch repairs for perforated duodenal ulcers and found no significant differences in post-operative complications or hospital stay. Both techniques were safe and effective, allowing surgeons to choose based on experience and intra-operative factors, with the modified patch potentially offering easier handling for certain cases. However, due to limitations like small sample size and short follow-up, larger multi-center trials are needed to better assess long-term outcomes and guide surgical practice.

PMID:41230479 | PMC:PMC12603592 | DOI:10.7759/cureus.96486

Cureus. 2025 Nov 10;17(11):e96494. doi: 10.7759/cureus.96494. eCollection 2025 Nov.

ABSTRACT

Introduction Seroma formation is a frequent complication after simple mastectomy due to the creation of a large dead space. Multiple aspirations are required to manage patients’ symptoms. At present, breast surgeons lack consensus on effective preventative strategies. To address this issue, we have implemented a technique called quilting, which involves suturing the mastectomy flap to the chest wall muscle to convert the dead space into smaller compartments, thereby reducing the possibility of seroma. Method An audit was carried out from April 2020 to June 2021 to establish postoperative seroma rates for patients undergoing simple mastectomy without reconstruction. A subsequent evaluation was completed between October 2023 and December 2024 following the adoption of quilting as standard practice. After each stage, results were shared with UK breast surgeons along with a survey to assess perceptions of quilting and other preventive strategies. An analysis was then done to examine the relationship between sharing audit data and the decision to quilt. This study seeks to outline the effectiveness of quilting in the prevention of seroma formation while also assessing current and alternative practices of UK surgeons in managing seromas. The insights gained from the quilting audit were shared in a follow-up survey to challenge the perception surgeons held of quilting and to consider incorporating this technique into their future practices. Results A total of 66 simple mastectomies were performed, with 32 patients receiving quilting and 34 undergoing conventional closure. On average, each patient in the quilting group received 13 sutures, taking an average of nine minutes for suturing. Among the 32 patients in the quilting group, there were no failed day cases due to postoperative haematomas or complications such as pain, wound breakdown, or long-term disfigurement of the flap. Only one case developed a seroma, but the volume was not clinically significant enough to require drainage. The non-quilting group showed a 70% seroma rate, with patients averaging three aspirations each, averaging 230 ml of fluid. Sixty UK-based surgeons responded to the first survey and 48 to the second. The first survey revealed that only 11.6% of surgeons offered quilting, 48% relied on drains, and 35% took no measures to prevent seroma formation. After sharing the quilting audit results, 79% of respondents indicated they would consider implementing quilting, while 20% remained resistant to the idea. The changes to response were statistically significant (p<0.00001). Conclusion The feedback from the surveys indicates a lack of consensus among UK surgeons regarding the prevention of seromas post-mastectomy. Nonetheless, there is a significant willingness to explore quilting. Our findings demonstrate that quilting is both safe and effective in reducing seroma formation, leading to improved patient outcomes. We recommend that future research focus on establishing comprehensive national evidence and guidelines aimed at decreasing seroma rates, thus addressing the current variability in approach across the country.

PMID:41230474 | PMC:PMC12603609 | DOI:10.7759/cureus.96494