Tag: statistics

JMA J. 2026 Jan 15;9(1):340-349. doi: 10.31662/jmaj.2025-0343. Epub 2026 Jan 14.

ABSTRACT

INTRODUCTION: Malnutrition is common and often goes unrecognized among hospitalized patients, particularly older adults. Early identification and individualized nutritional interventions are essential for improving outcomes. The Nutritional Risk Screening 2002 (NRS-2002) is a validated tool widely used in acute care settings, but its utility in dental and oral surgery remains underexplored. This study aimed to evaluate the clinical utility of NRS-2002 in patients admitted to the Department of Oral and Maxillofacial Surgery (OMFS) at a university-affiliated dental hospital in Japan, and to examine the relationship between nutritional risk and clinical factors such as age, body mass index (BMI), diagnosis, and length of hospital stay.

METHODS: A retrospective observational study was conducted on 548 patients (224 men, 324 women) hospitalized between August 2024 and March 2025. Nutritional screening was performed at admission using NRS-2002. Patients scoring ≥3 were classified as at nutritional risk and further assessed according to the Global Leadership Initiative on Malnutrition criteria.

RESULTS: The overall prevalence of nutritional risk, defined as NRS-2002 ≥3, was 1.6% (n = 9), which was insufficient for robust statistical analysis. Most patients identified as at nutritional risk were elderly women with low BMI and severe conditions, including medication-related osteonecrosis of the jaw and osteomyelitis. These patients experienced prolonged hospital stays and were more likely to require oral nutritional supplements. In contrast, the majority of inpatients were younger adults, accounting for the overall low prevalence of nutritional risk.

CONCLUSIONS: The NRS-2002 effectively identified older, underweight patients who underwent OMFS with severe conditions and longer hospital stays, despite the overall low prevalence of nutritional risk. Early nutritional screening with standardized tools such as NRS-2002 may help optimize perioperative management.

PMID:41676799 | PMC:PMC12889139 | DOI:10.31662/jmaj.2025-0343

JMA J. 2026 Jan 15;9(1):124-133. doi: 10.31662/jmaj.2025-0399. Epub 2025 Nov 21.

ABSTRACT

INTRODUCTION: Japan’s aging population and declining birthrate have intensified the need for foreign workers, with Vietnamese workers now forming the largest group among over 2 million foreign laborers. While statistical studies on their work situations and mental health are increasing, they offer limited direct insight into these workers’ lived experiences. This study aimed to capture their firsthand voices, focusing on differences by residency status.

METHODS: Open-ended responses from 100 Vietnamese workers in Japan, collected through a 2022 survey, were analyzed. Content analysis was used to categorize experiences into positive and negative aspects.

RESULTS: Positive experiences included job satisfaction, adequate salaries, safe environments, supportive colleagues, and personal growth, with workers particularly valuing learning opportunities and workplace relationships that fostered development. Negative experiences, which were more prevalent, encompassed demanding workloads, unfair treatment, inadequate pay, long hours, and insufficient rest. Cultural and language barriers also hindered workplace relationships. Technical Intern Trainees (TIT) more frequently reported dissatisfaction with wages and conditions, while Engineer/Specialist in Humanities/International Services (ESI) workers more often cited interpersonal challenges linked to cultural adaptation.

CONCLUSIONS: Vietnamese workers gain certain benefits from employment in Japan but frequently report dissatisfaction. TIT workers tend to face systemic issues, whereas ESI workers more often experience interpersonal challenges rooted in cultural differences. Addressing both types of challenges with consideration for the distinct situations of foreign workers may improve their mental health and well-being.

PMID:41676797 | PMC:PMC12889150 | DOI:10.31662/jmaj.2025-0399

JMA J. 2026 Jan 15;9(1):160-170. doi: 10.31662/jmaj.2025-0157. Epub 2025 Nov 21.

ABSTRACT

INTRODUCTION: The demand for genetic counseling is increasing in Japan owing to rapid advancements in genetic medicine and increased utilization of genetic testing. However, access to genetic counseling remains limited, particularly in rural areas, owing to a shortage of certified professionals. Online genetic counseling (OGC), a form of telemedicine, offers a potential solution to address these disparities. Although OGC is widely practiced in Western countries, its implementation and systemic evaluation in Japan remain limited. To our knowledge, this study represents the first attempt in Japan to systematically assess the effectiveness, challenges, and user satisfaction of OGC compared with in-person genetic counseling (IPGC) in the context of the Japanese health care system.

METHODS: This cross-sectional, single-center study involved 49 participants (15 OGC, 34 IPGC) who received genetic counseling at the NHO Tokyo Medical Center between July 2020 and January 2025. Participants completed anonymous questionnaires assessing demographic characteristics, satisfaction with counseling, and perceived advantages and disadvantages. Statistical analyses included Mann-Whitney U tests, chi-square tests, and Fisher’s exact tests. Free-text responses were analyzed using conventional content analysis and word cloud visualization.

RESULTS: Overall satisfaction was high in both groups, with all participants selecting “Strongly agree” or “Agree” regarding satisfaction. However, the IPGC group scored significantly higher in counselor introduction, responsiveness, and overall satisfaction. OGC participants had significantly longer travel times and were more likely to be in their 20s-30s. Key advantages of OGC included convenience and accessibility, whereas disadvantages included concerns about privacy and technical issues.

CONCLUSIONS: OGC has high potential to improve access to genetic services in Japan, particularly for individuals in remote areas. Despite high satisfaction, challenges such as communication limitations, privacy concerns, and lack of insurance coverage must be addressed. Policy reforms, improved infrastructure, and further large-scale studies are needed to support the widespread implementation of OGC in Japan.

PMID:41676789 | PMC:PMC12889013 | DOI:10.31662/jmaj.2025-0157

Hepatobiliary Surg Nutr. 2026 Feb 1;15(1):7. doi: 10.21037/hbsn-24-417. Epub 2025 Feb 11.

ABSTRACT

BACKGROUND: In the past decade, diabetes prevalence in China increased significantly, with many cases undiagnosed, particularly in rural areas. Despite the limitations of body mass index (BMI) in assessing visceral fat, obesity indices like waist circumference (WC) and waist-to-height ratio (WHtR) have shown stronger associations with the risk of type 2 diabetes mellitus (T2DM). Few cohort studies, especially in rural China, have examined the predictive power of these obesity indices and their changes on T2DM risk. We aimed to assess sex and age difference in the association between obesity, long-term waist circumference and weight changes with the risk of T2DM among rural Chinese adults.

METHODS: Population-based cohort study of 15,076 adult participants was conducted from 2006.08.11 to 2014.07.19 in rural Deqing, China. Participants were annually followed up for the occurrence of major chronic diseases and vital status through the Deqing electronic health records system from enrollment to December 31st, 2021. Cox proportional hazards model was used to estimate adjusted HR (aHR) and 95% confidence intervals (CIs) for the association of obesity indices and their long-term changes with incident T2DM.

RESULTS: A total of 1,888 cases of incident T2DM were found (incidence: 12.35/1,000 person-years) during the mean follow-up of 10.14±3.64 years. Baseline WC (aHR =1.37, 95% CI: 1.31, 1.43), WHtR (aHR =1.38, 95% CI: 1.32, 1.44), BMI (aHR =1.27, 95% CI: 1.21, 1.32), WHtHR (aHR =1.34, 95% CI: 1.25, 1.43) exhibited statistically significant associations with increased risk of T2DM. Per SD increment of WC and weight changes were associated with a 15% and 13% higher risk of incident T2DM, respectively. Stratification analysis revealed that abdominal obesity indices presented stronger associations among males and those under 60 years, while general obesity markers among females and the elderly.

CONCLUSIONS: Obesity, long-term WC and weight changes increase the risk of incident T2DM among rural adults of eastern China, with modification by sex and age.

PMID:41676777 | PMC:PMC12887344 | DOI:10.21037/hbsn-24-417

Hepatobiliary Surg Nutr. 2026 Feb 1;15(1):3. doi: 10.21037/hbsn-24-300. Epub 2024 Dec 17.

ABSTRACT

BACKGROUND: Highly urgent living donor liver transplantation (HU-LDLT) is vital for treating acute liver failure (ALF), acute-on-chronic liver failure (ACLF), and critically ill cirrhotic patients in life-threatening scenarios. The purpose of our study was to identify the characteristics of HU-LDLT patients, compare the outcomes of HU-LDLT patients with those of elective LDLT patients, and determine the risk factors that can influence the outcomes of HU-LDLT.

METHODS: We retrospectively analyzed Korean Network for Organ Sharing (KONOS) data for consecutive HU-LDLT patients between 2017 and 2021. For comparison with the HU-LDLT group, patients who received elective LDLT except HU-LDLT at Samsung Medical Center during the same period were analyzed as the control group.

RESULTS: The most common reasons for HU-LDLT were hepatic encephalopathy, a model for end-stage liver disease (MELD) score ≥35, and uncontrolled varix bleeding. Among the 419 HU-LDLT patients, 53 (12.6%) were pediatric. The cumulative 1-, 3-, and 5-year overall survival rates were 82.4%, 78.3%, and 74.8%, respectively, in the adult HU-LDLT group. The 1-year overall survival rate was 86.1% in the pediatric HU-LDLT group. The presence of chronic kidney disease, pre-transplant ventilator care, high pre-transplant MELD score, and re-transplantation were closely related to mortality in the adult group. Only hepatorenal syndrome (HRS) was a strong risk factor for graft failure in the adult group. The graft and overall survival in the adult HU-LDLT group were significantly lower than those in the control group.

CONCLUSIONS: High MELD scores, hepatic encephalopathy, and bleeding are the main reasons for HU-LDLT applications in Korea. Graft and overall survival curves in the HU-LDLT group are lower than in the elective LDLT group, but the HU-LDLT outcomes are considered acceptable.

PMID:41676776 | PMC:PMC12887345 | DOI:10.21037/hbsn-24-300

Hepatobiliary Surg Nutr. 2026 Feb 1;15(1):2. doi: 10.21037/hbsn-24-276. Epub 2024 Nov 19.

ABSTRACT

BACKGROUND: Postoperative pulmonary complications (PPCs) can impact patient recovery and long-term oncological outcomes after hepatectomy. This study aimed to define whether laparoscopic approach was associated with a reduced incidence of PPCs compared with open approach for patients undergoing hepatectomy for hepatocellular carcinoma (HCC).

METHODS: A multicenter, retrospective cohort study was conducted at 12 Chinese centers between January 2010 and December 2021. Patients underwent either laparoscopic hepatectomy (LH) or open hepatectomy (OH) for HCC. The primary outcome was the incidence of PPCs including symptomatic pleural effusion, respiratory insufficiency, acute respiratory distress syndrome (ARDS), pulmonary infection, and pulmonary embolism. Statistical analysis was performed using propensity score analysis with inverse probability of treatment-weighing (IPTW), multivariable logistic regression, and subgroup analysis to adjust for potential confounders and explore the robustness of the findings.

RESULTS: Among 4,694 patients, 766 (16.3%) patients underwent LH while 3,928 (83.7%) underwent OH for HCC. The overall incidence of PPCs was 10.9%. Among the entire cohort, the incidence of PPCs among patients who underwent LH was significantly lower than individuals who underwent OH (7.3% vs. 11.6%, P=0.001); IPTW analysis demonstrated similar findings (7.4% vs. 11.6%, P=0.01). On multivariable analysis, laparoscopic approach remained independently associated with a lower risk of PPCs [adjusted odds ratio (OR) 0.63, 95% confidence interval (CI): 0.42-0.92, P=0.02]. Subgroup analyses demonstrated similar results relative to different patient and tumor characteristics.

CONCLUSIONS: Laparoscopic approach was associated with improved postoperative pulmonary outcomes and a lower incidence of PPCs than open approach the following hepatectomy for HCC. These findings have potentially important implications in selecting optimal surgical management for HCC.

PMID:41676768 | PMC:PMC12887286 | DOI:10.21037/hbsn-24-276

bioRxiv [Preprint]. 2026 Feb 6:2026.02.04.703681. doi: 10.64898/2026.02.04.703681.

ABSTRACT

Point process generalized linear models (GLMs) have been a major tool for studying coordinated activity across populations of neurons. These models typically quantify how the spiking of a single neuron depends on the past activity of other neurons at multiple time lags, and the resulting neuron-to-neuron interactions are then aggregated to obtain population-coupling effects. However, when neurons within the same population exhibit similar spiking patterns, explicitly modeling individual interactions can be redundant and can unnecessarily increase model complexity. In such cases, population-level formulations may offer a more efficient alternative. For example, biophysical population models often characterize circuit dynamics using the average firing rate across neurons within a population, and recent data-driven approaches have similarly demonstrated the utility of population-level statistics for capturing cross-population interactions. Motivated by this consideration, we reformulate the GLM framework to operate directly at the population level. The resulting model, which we call pop-GLM, provides a computationally efficient method for estimating coupling between populations. In a simulated dataset, we show that pop-GLM achieves greater sensitivity in detecting coupling effects and can account for trial-to-trial variation in stimulus drive, which would otherwise introduce bias. We also note that moving from single-neuron to population-level modeling requires a specific modification of the traditional GLM framework. We then apply pop-GLM to real data and find reduced functional connectivity from primary visual cortex (V1) to a higher visual area during locomotion, a change not detected by single-neuron GLMs.

AUTHOR SUMMARY: A central goal of systems neuroscience is to understand how multiple populations of neurons across different brain areas interact as a coordinated circuit to produce perception and behavior. We formulated and investigated a new method for estimating functional interactions between two populations of spiking neurons, and we show that it can be more sensitive and robust than previous approaches. To illustrate, we discovered decreased interaction between two mouse visual areas during locomotion, a result that previous techniques did not detect. The method should aid investigators in searching for important functional relationships across populations of neurons, with precise time scale resolution.

PMID:41676710 | PMC:PMC12889648 | DOI:10.64898/2026.02.04.703681

bioRxiv [Preprint]. 2026 Feb 2:2026.01.30.702623. doi: 10.64898/2026.01.30.702623.

ABSTRACT

Synapses are fundamental building blocks of cortical circuits, yet their geometry is typically regarded as a local property, independent of mesoscale architecture. The prevailing assumption is that synaptic clefts are isotropically oriented in space. Here, this assumption was tested by analyzing approximately 117 million synaptic clefts from two independent 1 mm ³ electron microscopy datasets: the human H01 middle temporal gyrus and the mouse MICrONS primary visual cortex. Across both volumes, synaptic cleft orientations are not randomly distributed, but instead show statistically significant and spatially coherent directional biases across cortical layers. This mesoscale anisotropy is conserved across species, yet is stronger and more consistent in human association cortex than in mouse sensory cortex. These findings reveal an unrecognized dimension of cortical microarchitecture and suggest that synaptic geometry contributes to circuit organization, mesoscale connectivity, and interactions with endogenous or externally applied electric fields.

PMID:41676682 | PMC:PMC12889479 | DOI:10.64898/2026.01.30.702623

bioRxiv [Preprint]. 2026 Feb 6:2026.02.04.703700. doi: 10.64898/2026.02.04.703700.

ABSTRACT

Protein-protein interactions governed by conformationally heterogeneous domains remain difficult to drug because ligand-competent states are often absent from single static structures. Here, we present AtlasNMR, a statistical framework that transforms multi-model NMR ensembles into screening-ready conformational hypotheses for small molecule discovery. Using the neuronal nitric oxide synthase (nNOS) PDZ domain that engages the adaptor protein CAPON (NOS1AP) as a model system, AtlasNMR identified two representative conformational states capturing the dominant and minor populations of the NMR ensemble. Ensemble-based virtual screening followed by consensus ranking yielded MC-3 , a small molecule modulator that disrupts the NOS1-NOS1AP interaction in live cells and directly engages the nNOS PDZ domain. MC-3 produced convergent neuroprotective effects in disease-relevant neuronal models by reducing amyloid-β-induced cytotoxicity, suppressing NMDA-driven nitrosative stress, and attenuating pathological tau phosphorylation, while exhibiting a balanced early lead-like ADME and safety profile. Together, this work establishes a generalizable strategy for exploiting NMR ensemble heterogeneity to enable small molecule discovery against dynamic protein-protein interfaces.

PMID:41676628 | PMC:PMC12889626 | DOI:10.64898/2026.02.04.703700

bioRxiv [Preprint]. 2026 Feb 8:2026.02.05.704068. doi: 10.64898/2026.02.05.704068.

ABSTRACT

Kinase family proteins constitute the second largest protein class targeted in drug development efforts, most prominently to treat cancer, but also several other diseases associated with kinase dysfunction. In this work we focus on type II kinase inhibitors which bind to the “classical” inactive conformation of the protein kinase catalytic domain where the DFG motif has a ″DFG-out″ orientation and the activation loop is folded. Many Tyrosine kinases (TKs) exhibit strong binding affinity with a wide spectrum of type II inhibitors while serine/threonine kinases (STKs) often bind more weakly. Recent work suggests this difference is largely due to differences in the folded to extended conformational equilibrium of the activation loop between TKs vs. STKs. The binding affinity of a type II inhibitor to its kinase target can be decomposed into a sum of two contributions: (1) the free energy cost to reorganize the protein from the active to inactive state, and (2) the binding affinity of the type II inhibitor to the inactive kinase conformation. In previous work we used a Potts statistical energy potential based on sequence co variation to thread sequences over ensembles of active and inactive kinase structures. The threading function was used to estimate the free energy cost to reorganize kinases from the active to classical inactive conformation, and we showed that this estimator is consistent with the results of molecular dynamics free energy simulations for a small set of STKs and TKs. In the current study, we analyze the results of a large-scale study of the binding affinities of 50 type II inhibitors to 348 kinases, of which the results for 16 of the 50 type II inhibitors were reported in an earlier study (the “Davis dataset”). The binding data for the remaining 34 type II inhibitors to the panel of 348 kinases were recently obtained (the “Schrödinger dataset”). We use the Potts statistical energy model to investigate the contribution of protein reorganization to the selectivity of the large kinase panel against the set of 50 type II inhibitors, and find that protein reorganization makes a significant contribution to the selectivity. The AUC of the receiver operator characteristic curve is ≈0.8. We report the results of an internal “blind test”, that shows how Potts threading energies can provide more accurate estimates of kinase selectivity than corresponding predictions using experimental results of small sample size. We discuss why two STK phylogenetic kinase families, STE and CMGC, appear to contain many outliers, and how to improve the ability to predict kinase selectivity with a more complete analysis of the kinase conformational landscape. We compare the performance of Potts threading for predicting binding properties of the large set of (50) Type II inhibitors to 348 kinases, with those of a sequence-based purely machine learning model, DeepDTAGen, a publicly available machine learning model that was trained on the complete Davis dataset, including both Type I and Type II kinase inhibitors. We observe that DeepDTAGen performs well on binding predictions for the 16 type II inhibitors in the Davis dataset, but performs poorly on binding predictions for the 34 type II inhibitors against 348 kinases in the Schrödinger dataset.

PMID:41676586 | PMC:PMC12889613 | DOI:10.64898/2026.02.05.704068