GPS-Net: discovering prognostic pathway modules based on network regularized kernel learning.

The search for prognostic biomarkers capable of predicting patient outcomes, by analyzing gene expression in tissue samples and other molecular profiles, remains largely on single-gene-based or global-gene-search approaches. Gene-centric approaches, while foundational, fail to capture the higher-order dependencies that reflect the activities of co-regulated processes, pathway alterations, and regulatory networks, all of which are crucial in determining the patient outcomes in complex diseases like cancer. Here, we introduce GPS-Net, a computational framework that fills the gap in efficiently identifying prognostic modules by incorporating the holistic pathway structures and the network of gene interactions. By innovatively incorporating advanced multiple kernel learning techniques and network-based regularization, the proposed method not only enhances the accuracy of biomarker and pathway identification but also significantly reduces computational complexity, as demonstrated by extensive simulation studies. Applying GPS-Net, we identified key pathways that are predictive of patient outcomes in a cancer immunotherapy study. Overall, our approach provides a novel framework that renders genome-wide pathway-level prognostic analysis both feasible and scalable, synergizing both mechanism-driven and data-driven for precision genomics.

Epigenome-wide association studies identify novel DNA methylation sites associated with PTSD: A meta-analysis of 23 military and civilian cohorts.

Background: The occurrence of post-traumatic stress disorder (PTSD) following a traumatic event is associated with biological differences that can represent the susceptibility to PTSD, the impact of trauma, or the sequelae of PTSD itself. These effects include differences in DNA methylation (DNAm), an important form of epigenetic gene regulation, at multiple CpG loci across the genome. Moreover, these effects can be shared or specific to both central and peripheral tissues. Here, we aim to identify blood DNAm differences associated with PTSD and characterize the underlying biological mechanisms by examining the extent to which they mirror associations across multiple brain regions. Methods: As the Psychiatric Genomics Consortium (PGC) PTSD Epigenetics Workgroup, we conducted the largest cross-sectional meta-analysis of epigenome-wide association studies (EWASs) of PTSD to date, involving 5077 participants (2156 PTSD cases and 2921 trauma-exposed controls) from 23 civilian and military studies. PTSD diagnosis assessments were harmonized following the standardized guidelines established by the PGC-PTSD Workgroup. DNAm was assayed from blood using either Illumina HumanMethylation450 or MethylationEPIC (850K) BeadChips. A common QC pipeline was applied. Within each cohort, DNA methylation was regressed on PTSD, sex (if applicable), age, blood cell proportions, and ancestry. An inverse variance-weighted meta-analysis was performed. We conducted replication analyses in tissue from multiple brain regions, neuronal nuclei, and a cellular model of prolonged stress. Results: We identified 11 CpG sites associated with PTSD in the overall meta-analysis (1.44e-09 < p < 5.30e-08), as well as 14 associated in analyses of specific strata (military vs civilian cohort, sex, and ancestry), including CpGs in AHRR and CDC42BPB . Many of these loci exhibit blood-brain correlation in methylation levels and cross-tissue associations with PTSD in multiple brain regions. Methylation at most CpGs correlated with their annotated gene expression levels. Conclusions: This study identifies 11 PTSD-associated CpGs, also leverages data from postmortem brain samples, GWAS, and genome-wide expression data to interpret the biology underlying these associations and prioritize genes whose regulation differs in those with PTSD.

Estimating the effectiveness of marked sidewalks: An application of the spatial causality approach.

Various safety enhancements and policies have been proposed to enhance pedestrian safety and minimize vehicle-pedestrian accidents. A relatively recent approach involves marked sidewalks delineated by painted pathways, particularly in Asia's crowded urban centers, offering a cost-effective and space-efficient alternative to traditional paved sidewalks. While this measure has garnered interest, few studies have rigorously evaluated its effectiveness. Current before-after studies often use correlation-based approaches like regression, lacking effective consideration of causal relationships and confounding variables. Moreover, spatial heterogeneity in crash data is frequently overlooked during causal inference analyses, potentially leading to inaccurate estimations. This study introduces a geographically weighted difference-in-difference (GWDID) method to address these gaps and estimate the safety impact of marked sidewalks. This approach considers spatial heterogeneity within the dataset in the spatial causal inference framework, providing a more nuanced understanding of the intervention's effects. The simplicity of the modeling process makes it applicable to various study designs relying solely on pre- and post-exposure outcome measurements. Conventional DIDs and Spatial Lag-DID models were used for comparison. The dataset we utilized included a total of 13,641 pedestrian crashes across Taipei City, Taiwan. Then the crash point data was transformed into continuous probability values to determine the crash risk on each road segment using network kernel density estimation (NKDE). The treatment group comprised 1,407 road segments with marked sidewalks, while the control group comprised 3,097 segments with similar road widths. The pre-development program period was in 2017, and the post-development period was in 2020. Results showed that the GWDID model outperformed the spatial lag DID and traditional DID models. As a local causality model, it illustrated spatial heterogeneity in installing marked sidewalks. The program significantly reduced pedestrian crash risk in 43% of the total road segments in the treatment group. The coefficient distribution map revealed a range from -22.327 to 2.600, with over 95% of the area yielding negative values, indicating reduced crash risk after installing marked sidewalks. Notably, the impact of crash risk reduction increased from rural to urban areas, emphasizing the importance of considering spatial heterogeneity in transportation safety policy assessments.

Parental emotional, social and transitional health in the first 6 months after childhood critical illness: A longitudinal qualitative study.

AIM: To explore the experiences and support needs of parents in the first 6 months after paediatric critical care. DESIGN: Longitudinal qualitative design. METHODS: Sequential semi-structured qualitative interviews were conducted with a sample of 28 parents in succession at 1 month and at 6 months (n = 22) after their child's discharge from paediatric critical care using purposive sampling. Data were analysed using the adapted five-stage framework analysis. RESULTS: Data were developed into eight synthesized themes, three domains and an overarching theme: Regaining Normalcy. Families of children requiring medical treatment at 6 months showed signs of adaption to daily care routines. The two domains were Parental Emotional Health and Parental Social Health. Parental Transitional Health, a third domain, was added to the Post Intensive Care Syndrome-paediatric framework. Parents were forward-looking and discussed emotional health, relating to current caregiving issues. Emotional attention was related to present challenges and concerns about current health and possible readmission to the hospital. In terms of Parental Social Health, families isolated themselves for infection control while remaining connected with families using chat applications. Parents were selective to whom they allowed access to their lives. The impact of parental transitional health was evident and emphasized the daily challenges associated with integration back to home life. Flexible work arrangements allowed working parents to support caregiving needs in the first 6 months after discharge. CONCLUSION: In the first 6 months after paediatric critical illness, most families reported having moved past the experiences while having provoking memories of the admission period. Parents viewed the point of normalcy as child returned to school or when all medications were discontinued. Extension of transitional support can facilitate discharge experiences between paediatric critical care and normalcy. The findings highlight the importance of understanding the medium- and longer-term impact of paediatric critical care. IMPACT: What problem did the study address? ○ Limited understanding of long-term parental experiences and support needs after PICU discharge. What were the main findings? ○ Most families regained normalcy when child returns to school or when medications were discontinued. Some families continued to show signs of adaptations at 6 months after PICU discharge. Where and on whom did the research have an impact? ○ The research has an impact on improving the understanding of long-term parental experiences and support needs after PICU discharge, informing clinical practice, guiding policy development and shaping parental support programs. REPORTING METHOD: We reported this study using the COREQ guidelines. PATIENT OR PUBLIC CONTRIBUTION: Prior to confirming the interview guide, three parents of critically ill children actively participated by reviewing and providing feedback on its content. They provided suggestions to refine the wording and ensure clarity to enhance the participants' understanding. By including the perspectives of these parents, we aimed to improve the overall quality and relevance of the interview guide.

Incidence of Dementia Before Age 65 Years Among World Trade Center Attack Responders.

Importance: Reports suggest that the individuals who served in rescue operations following the terrorist attacks on the World Trade Center (WTC) have poorer brain health than expected. Objective: To assess the incidence of dementia before age 65 years in a prospective study of WTC responders and to compare incidence among responders with severe exposures to debris vs responders not exposed to building debris or who wore personalized protective equipment (PPE). Design, Setting, and Participants: This prospective cohort study was conducted from November 1, 2014, to January 1, 2023, in an academic medical monitoring program available to verified WTC responders residing on Long Island, New York. Responders 60 years of age or younger without dementia at the time of their first cognitive assessment were followed up every 18 months, on average, for up to 5 years. Exposures: Exposure severity was based on responses to a detailed questionnaire of WTC exposures and exposure-related activities that included exposures to fine particulate dust and potentially neurotoxic debris, duration of work, and the use of PPE. Exposure level was divided into 5 categories ranging from low to severe. Main Outcomes and Measures: Incidence of all-cause dementia before age 65 years was the primary outcome. Dementia was diagnosed following standard guidelines relying on repeated measures of cognition. Results: Of 9891 responders, 5010 were eligible for inclusion in this study of cognitive function (median [IQR] age, 53 [48-57] years; 4573 [91.3%] male). There were 228 cases of dementia identified during 15 913.1 person-years of follow-up. Increasing WTC exposure severity was associated with incremental increases in the incidence rate of dementia per 1000 person-years (low, 2.95 [95% CI, 1.07-11.18]; mild, 12.16 [95% CI, 10.09-14.79]; moderate, 16.53 [95% CI, 13.30-20.81]; high, 30.09 [95% CI, 21.35-43.79]; and severe, 42.37 [95% CI, 24.86-78.24]). Adjusting for social, demographic, and relevant medical factors, each unit increase in exposure severity was associated with increased incidence of dementia (adjusted hazard ratio, 1.42 [95% CI, 1.18-1.71]; P < .001; mean risk difference, 9.74 [95% CI, 2.94-32.32] per 1000 person-years; P < .001). Conclusions and Relevance: In this cohort study of WTC responders who survived these unique exposures and participated in a longitudinal follow-up study of cognition from 2014 through 2022, when compared with responders with the lowest exposure levels or responders who used PPE, more severe exposure to dust or debris was significantly associated with a higher risk of dementia before 65 years of age. This study suggests that the reliable use of PPE might help prevent the onset of dementia before age 65 years among individuals exposed to an uncontrolled building collapse. Future research is warranted to determine cerebral biomarkers for individuals with exposure-associated dementia.

Psychological Outcomes in Families of PICU Survivors: A Meta-Analysis.

BACKGROUND: Pediatric critical illness exposes family members to stressful experiences that may lead to subsequent psychological repercussions. OBJECTIVE: To systematically review psychological outcomes among PICU survivors' family members. DATA SOURCES: Four medical databases (PubMed, Embase, CINAHL and PsycInfo) were searched from inception till October 2023. STUDY SELECTION: Studies reporting psychological disorders in family members of PICU patients with at least 3 months follow-up were included. Family members of nonsurvivors and palliative care patients were excluded. DATA EXTRACTION: Screening and data extraction was performed according to PRISMA guidelines. Data were pooled using a random-effects model. RESULTS: Of 5360 articles identified, 4 randomized controlled trials, 16 cohort studies, and 2 cross-sectional studies were included (total patients = 55 597; total family members = 97 506). Psychological distress was reported in 35.2% to 64.3% and 40.9% to 53% of family members 3 to 6 months and 1 year after their child's PICU admission, respectively. Post-traumatic stress disorder was diagnosed in 10% to 48% of parents 3 to 9 months later. Parents that experienced moderate to severe anxiety and depression 3 to 6 months later was 20.9% to 42% and 6.1% to 42.6%, respectively. Uptake of mental counseling among parents was disproportionately low at 0.7% to 29%. Risk factors for psychiatric morbidity include mothers, parents of younger children, and longer duration of PICU stay. LIMITATIONS: The majority of studies were on parents with limited data on siblings and second degree relatives. CONCLUSIONS: There is a high burden of psychological sequelae in family members of PICU survivors. Risk stratification to identify high-risk groups and early interventions are needed.

Classification of autonomous vehicle crash severity: Solving the problems of imbalanced datasets and small sample size.

Only a few researchers have shown how environmental factors and road features relate to Autonomous Vehicle (AV) crash severity levels, and none have focused on the data limitation problems, such as small sample sizes, imbalanced datasets, and high dimensional features. To address these problems, we analyzed an AV crash dataset (2019 to 2021) from the California Department of Motor Vehicles (CA DMV), which included 266 collision reports (51 of those causing injuries). We included external environmental variables by collecting various points of interest (POIs) and roadway features from Open Street Map (OSM) and Data San Francisco (SF). Random Over-Sampling Examples (ROSE) and the Synthetic Minority Over-Sampling Technique (SMOTE) methods were used to balance the dataset and increase the sample size. These two balancing methods were used to expand the dataset and solve the small sample size problem simultaneously. Mutual information, random forest, and XGboost were utilized to address the high dimensional feature and the selection problem caused by including a variety of types of POIs as predictive variables. Because existing studies do not use consistent procedures, we compared the effectiveness of using the feature-selection preprocessing method as the first process to employing the data-balance technique as the first process. Our results showed that AV crash severity levels are related to vehicle manufacturers, vehicle damage level, collision type, vehicle movement, the parties involved in the crash, speed limit, and some types of POIs (areas near transportation, entertainment venues, public places, schools, and medical facilities). Both resampling methods and three data preprocessing methods improved model performance, and the model that used SMOTE and data-balancing first was the best. The results suggest that over-sampling and the feature selection method can improve model prediction performance and define new factors related to AV crash severity levels.

Polygenic risk-stratified screening for nasopharyngeal carcinoma in high-risk endemic areas of China: a cost-effectiveness study.

Background: Nasopharyngeal carcinoma (NPC) has an extremely high incidence rate in Southern China, resulting in a severe disease burden for the local population. Current EBV serologic screening is limited by false positives, and there is opportunity to integrate polygenic risk scores for personalized screening which may enhance cost-effectiveness and resource utilization. Methods: A Markov model was developed based on epidemiological and genetic data specific to endemic areas of China, and further compared polygenic risk-stratified screening [subjects with a 10-year absolute risk (AR) greater than a threshold risk underwent EBV serological screening] to age-based screening (EBV serological screening for all subjects). For each initial screening age (30-34, 35-39, 40-44, 45-49, 50-54, 55-59, 60-64, and 65-69 years), a modeled cohort of 100,000 participants was screened until age 69, and then followed until age 79. Results: Among subjects aged 30 to 54 years, polygenic risk-stratified screening strategies were more cost-effective than age-based screening strategies, and almost comprised the cost-effectiveness efficiency frontier. For men, screening strategies with a 1-year frequency and a 10-year absolute risk (AR) threshold of 0.7% or higher were cost-effective, with an incremental cost-effectiveness ratio (ICER) below the willingness to pay (¥203,810, twice the local per capita GDP). Specifically, the strategies with a 10-year AR threshold of 0.7% or 0.8% are the most cost-effective strategies, with an ICER ranging from ¥159,752 to ¥201,738 compared to lower-cost non-dominated strategies on the cost-effectiveness frontiers. The optimal strategies have a higher probability (29.4-35.8%) of being cost-effective compared to other strategies on the frontier. Additionally, they reduce the need for nasopharyngoscopies by 5.1-27.7% compared to optimal age-based strategies. Likewise, for women aged 30-54 years, the optimal strategy with a 0.3% threshold showed similar results. Among subjects aged 55 to 69 years, age-based screening strategies were more cost-effective for men, while no screening may be preferred for women. Conclusion: Our economic evaluation found that the polygenic risk-stratified screening could improve the cost-effectiveness among individuals aged 30-54, providing valuable guidance for NPC prevention and control policies in endemic areas of China.

Clinical effects and mechanisms of a Chinese patent medicine, Tongxinluo capsule, as an adjuvant treatment in coronary heart disease.

Coronary heart disease (CHD) is the leading cause of death globally, posing a serious threat to human health. However, the current treatment approaches available for CHD fall short of the ideal results. Tongxinluo (TXL) is a traditional Chinese medicine (TCM) that has been employed in the clinical treatment of cardiovascular and cerebrovascular diseases (such as angina pectoris, stroke, etc.) in China for many years and holds great potential as a prospective treatment. TXL either as a standalone treatment or in combination with interventions recommended in CHD guidelines has been shown to be effective and well tolerated in clinical trials for CHD. Drawing on the evidence from clinical trials and experimental studies, this review will focus on the cardiovascular protective properties and related mechanisms of TXL. By searching 8 Chinese and English databases, more than 4000 articles were retrieved. These articles were categorized, then read, and finally written into this review. In this review, the pharmacological properties of TXL include regulation of blood lipids, improvement of endothelial function, anti-inflammatory, antioxidant, inhibition of apoptosis and regulation of autophagy, anti-fibrosis, promotion of angiogenesis, and modulation of exosome communication. The information provided in this review will help the reader to comprehend better the insights that TCM has developed over time in practice and provide new perspectives for the treatment of CHD.

Exploring the spatial relationship of e-bike and motorcycle crashes: Implications for risk reduction.

INTRODUCTION: Electric bicycles, or e-bikes, have become very popular over the past decade. In order to reduce the risk of crashes, it is necessary to understand the contributing factors. While several researchers have examined these elements, few have considered the spatial heterogeneity between crashes and environmental variables, such as Points of Interest (POI). In addition, there is a scarcity of studies comparing the crash-related factors of e-bikes and motorcycles. Despite their differing speed and range capabilities, different POIs also tend to impact area/bandwidths differently because e-bikes cannot cover the same range that motorcycles can. METHOD: In this study, we compared e-bike and motorcycle crashes at 11 different types of POIs in Taipei from 2016 to 2020. Since crashes are sparse events and easily affected by the Modifiable Areal Unit Problem (MAUP), Kernel Density Estimation (KDE) was employed to transform crash points (count data) to crash risk surfaces (continuous data). Additionally, an advanced variant of Geographical Weighted Regression (GWR), Multiscale Geographically Weighted Regression (MGWR) utilized to predict crash risk because each predictor is allowed to have a different bandwidth. RESULTS: The results showed: (a) For e-bike crashes, the MGWR model outperformed the GWR and OLS models in terms of AIC values, while the MGWR and GWR performed similarly with regard to motorcycle crashes; (b) The analysis revealed e-bike and motorcycle crash risk to be associated with various types of POIs. E-bike crashes tended to occur more frequently in areas with more schools, supermarkets, intersections, and elderly people. Meanwhile, motorcycle crashes were more likely to occur in areas with a high number of restaurants and intersections. The search bandwidths of e-bikes are inconsistent and narrower than those of motorcycles.

The METTL3-m6A-YTHDC1-AMIGO2 axis contributes to cell proliferation and migration in esophageal squamous cell carcinoma.

The upregulation of methyltransferase-like 3 (METTL3) has been associated with the progression of esophageal cancer. However, METTL3-induced N6-methyladenosine (m6A) alterations on the downstream target mRNAs in esophageal squamous cell carcinoma (ESCC) are not yet fully understood. Our study revealed that silencing METTL3 resulted in a significant decrease in ESCC cell proliferation and metastasis in vitro and in vivo. Additionally, the adhesion molecule with Ig like domain 2 (AMIGO2) was identified as a potential downstream target of both METTL3 and YTH Domain-Containing Protein 1 (YTHDC1) in ESCC cells. Functionally, AMIGO2 augmented the malignant behaviors of ESCC cells in vitro and in vivo, and its overexpression can rescue the inhibition of the proliferation and migration in ESCC cells induced by METTL3 or YTHDC1 knockdown. Furthermore, our findings revealed that knockdown of METTL3 decreased m6A modification in the 5'-untranslated regions (5'UTR) of AMIGO2 precursor mRNA (pre-mRNA), and YTHDC1 interacted with AMIGO2 pre-mRNA to regulate AMIGO2 expression by modulating the splicing process of AMIGO2 pre-mRNA in ESCC cells. These findings highlighted a novel role of the METTL3-m6A-YTHDC1-AMIGO2 axis in regulating ESCC cell proliferation and motility, suggesting its potential as a therapeutic target for ESCC.

The middle-aged and older Chinese adults' health using actigraphy in Taiwan (MOCHA-T): protocol for a multidimensional dataset of health and lifestyle.

BACKGROUND AND OBJECTIVES: Older adults keep transforming with Baby Boomers and Gen Xers being the leading older population. Their lifestyle, however, is not well understood. The middle-aged and older Chinese adults' health using actigraphy in Taiwan (MOCHA-T) collected both objective and subjective data to depict the health and lifestyle of this population. The objectives, design, and measures of the MOCHA-T study are introduced, and the caveats and future directions related to the use of the data are presented. METHODS: People aged 50 and over were recruited from the community, with a subset of women aged 45-49 invited to supplement data on menopause and aging. Four instruments (i.e., self-reported questionnaires, diary, wrist actigraphy recorder, and GPS) were used to collect measures of sociodemographic, health, psychosocial, behavioral, temporal, and spatial data. RESULTS: A total of 242 participants who returned the informed consent and questionnaires were recruited in the MOCHA-T study. Among them, 94.6%, 95.0%, and 25.2% also completed the diary, actigraphy, and GPS data, respectively. There was almost no difference in sociodemographic characteristics between those with and without a completed diary, actigraphy, and GPS data, except for age group and educational level for those who returned completed actigraphy data. CONCLUSION: The MOCHA-T study is a multidimensional dataset that allows researchers to describe the health, behaviors, and lifestyle patterns, and their interactions with the environment of the newer generation of middle-aged and older adults in Taiwan. It can be compared with other countries with actigraphy and GPS-based lifestyle data of middle-aged and older adults in the future.

The rapid access eye clinic's playbook: how to cut eye casualty attendance by 50.

BACKGROUND: Moorfields Eye Unit at the London Borough of Croydon sees over 47,000 outpatient attendances each year, 5894 of which attended the eye walk-in Urgent Care in the 2017- 2018 year, which has become unsustainable. METHODS: A recent audit found that referrers and patients had limited experience in managing ophthalmic conditions. If triaged according to clinical need only 22% patients attended required same-day hospital eye care. As such the service needed to be reconfigured. This was achieved through extensive collaboration with our local Clinical commissioning groups (CCG), General Practitioner (GP) body, Optometrists and host hospital at the Croydon University Hospital. The Rapid Access Clinic (RAC) was set up in November 2018 to replace the old-style walk-in pathway and provide a streamlined emergency eye care service for patients. RESULTS: RAC demonstrated an efficient and safe triage system which can improve patient flow. Since the launch date of RAC on the 1st November 2018, a 50% sustained decrease in attendances to urgent care was noted. This was achieved without impacting other eye services, by advising the referrers and redirecting referrals appropriately. At the same time the appropriateness of the attendances to our emergency clinic improved from 32% to 68%. Using a digital platform for referrals and data collection allowed up to continuously perform service evaluation. CONCLUSION: The forward-online triage and our close relationship with community enabled a safe continuation of providing emergency eye care locally. The controlled booked attendance as well as the advice and guidance system enabled us to prioritise true emergencies.

A comprehensive predictive model for radiation-induced brain injury in risk stratification and personalized radiotherapy of nasopharyngeal carcinoma.

BACKGROUND AND PURPOSE: Radiation-induced brain injury (RBI) is a severe radiotoxicity for nasopharyngeal carcinoma (NPC) patients, greatly affecting their long-term life quality and survival. We aim to establish a comprehensive predictive model including clinical factors and newly developed genetic variants to improve the precision of RBI risk stratification. MATERIALS AND METHODS: By performing a large registry-based retrospective study with magnetic resonance imaging follow-up on RBI development, we conducted a genome-wide association study and developed a polygenic risk score (PRS) for RBI in 1189 NPC patients who underwent intensity-modulated radiotherapy. We proposed a tolerance dose scheme for temporal lobe radiation based on the risk predicted by PRS. Additionally, we established a nomogram by combining PRS and clinical factors for RBI risk prediction. RESULTS: The 38-SNP PRS could effectively identify high-risk individuals of RBI (P = 1.42 × 10-34). Based on genetic risk calculation, the recommended tolerance doses of temporal lobes should be 57.6 Gy for individuals in the top 10 % PRS subgroup and 68.1 Gy for individuals in the bottom 50 % PRS. Notably, individuals with high genetic risk (PRS > P50) and receiving high radiation dose in the temporal lobes (D0.5CC > 65 Gy) had an approximate 50-fold risk over individuals with low PRS and receiving low radiation dose (HR = 50.09, 95 %CI = 24.27-103.35), showing an additive joint effect (Pinteraction < 0.001). By combining PRS with clinical factors including age, tumor stage, and radiation dose of temporal lobes, the predictive accuracy was significantly improved with C-index increased from 0.78 to 0.85 (P = 1.63 × 10-2). CONCLUSIONS: The PRS, together with clinical factors, could improve RBI risk stratification and implies personalized radiotherapy.

Autoantibody repertoire profiling in tissue and blood identifies colorectal cancer-specific biomarkers.

Autoantibodies (AAbs) in the blood of colorectal cancer (CRC) patients have been evaluated for tumor detection. However, it remains uncertain whether these AAbs are specific to tumor-associated antigens. In this study, we explored the IgG and IgM autoantibody repertoires in both the in situ tissue microenvironment and peripheral blood as potential tumor-specific biomarkers. We applied high-density protein arrays to profile AAbs in the tumor-infiltrating lymphocyte supernatants and corresponding serum from four patients with CRC, as well as in the serum of three noncancer controls. Our findings revealed that there were more reactive IgM AAbs than IgG in both the cell supernatant and corresponding serum, with a difference of approximately 3-5 times. Immunoglobulin G was predominant in the serum, while IgM was more abundant in the cell supernatant. We identified a range of AAbs present in both the supernatant and the corresponding serum, numbering between 432 and 780, with an average of 53.3% shared. Only 4.7% (n = 23) and 0.2% (n = 2) of reactive antigens for IgG and IgM AAbs, respectively, were specific to CRC. Ultimately, we compiled a list of 19 IgG AAb targets as potential tumor-specific AAb candidates. Autoantibodies against one of the top candidates, p15INK4b-related sequence/regulation of nuclear pre-mRNA domain-containing protein 1A (RPRD1A), were significantly elevated in 53 CRC patients compared to 119 controls (p < 0.0001). The project revealed that tissue-derived IgG AAbs, rather than IgM, are the primary source of tumor-specific AAbs in peripheral blood. It also identified potential tumor-specific AAbs that could be applied for noninvasive screening of CRC.

intCC: An efficient weighted integrative consensus clustering of multimodal data.

High throughput profiling of multiomics data provides a valuable resource to better understand the complex human disease such as cancer and to potentially uncover new subtypes. Integrative clustering has emerged as a powerful unsupervised learning framework for subtype discovery. In this paper, we propose an efficient weighted integrative clustering called intCC by combining ensemble method, consensus clustering and kernel learning integrative clustering. We illustrate that intCC can accurately uncover the latent cluster structures via extensive simulation studies and a case study on the TCGA pan cancer datasets. An R package intCC implementing our proposed method is available at https://github.com/candsj/intCC.

The interaction and mediation effects between the host genetic factors and Epstein-Barr virus VCA-IgA in the risk of nasopharyngeal carcinoma.

Previous studies have demonstrated strong associations between host genetic factors and Epstein-Barr virus (EBV) VCA-IgA with the risk of nasopharyngeal carcinoma (NPC). However, the specific interplay between host genetics and EBV VCA-IgA on NPC risk is not well understood. In this two-stage case-control study (N = 4804), we utilized interaction and mediation analysis to investigate the interplay between host genetics (genome-wide association study-derived polygenic risk score [PRS]) and EBV VCA-IgA antibody level in the NPC risk. We employed a four-way decomposition analysis to assess the extent to which the genetic effect on NPC risk is mediated by or interacts with EBV VCA-IgA. We consistently found a significant interaction between the PRS and EBV VCA-IgA on NPC risk (discovery population: synergy index [SI] = 2.39, 95% confidence interval [CI] = 1.85-3.10; replication population: SI = 3.10, 95% CI = 2.17-4.44; all pinteraction < 0.001). Moreover, the genetic variants included in the PRS demonstrated similar interactions with EBV VCA-IgA antibody. We also observed an obvious dose-response relationship between the PRS and EBV VCA-IgA antibody on NPC risk (all ptrend < 0.001). Furthermore, our decomposition analysis revealed that a substantial proportion (approximately 90%) of the genetic effects on NPC risk could be attributed to host genetic-EBV interaction, while the risk effects mediated by EBV VCA-IgA antibody were weak and statistically insignificant. Our study provides compelling evidence for an interaction between host genetics and EBV VCA-IgA antibody in the development of NPC. These findings emphasize the importance of implementing measures to control EBV infection as a crucial strategy for effectively preventing NPC, particularly in individuals at high genetic risk.

Lower HbA1C of glycemic control is associated with higher risk of depressive symptoms in elderly with type 2 diabetes mellitus-A Nationwide Community-based study.

OBJECTIVE: We investigated the correlation between glycemic control status and depressive symptoms in type 2 diabetes elderly. METHODS: A total of 1527 participants with type 2 diabetes aged 55 years and older from the Healthy Aging Longitudinal Study in Taiwan study were included in this cross-sectional study. The Center for Epidemiologic Studies Depression Scale (CESD) (20 items) score of ≥16 was indicative of depressive symptoms. The participants were divided into HbA1c ≥ 6.5% and < 6.5% representing the glycemic control. Multiple logistic regression (MLR) and Generalized linear model (GLM) were used. RESULTS: The MLR analysis showed that the low HbA1c group had significant two-fold increased odds of depressive symptoms compared to the high HbA1c group (OR 1.89, 95% CI 1.17-3.05). The risk of depressive symptoms was lower among males (OR 0.49, 95% CI 0.30-0.80) and those with higher BMI (OR 0.93, 95% CI 0.86-1.00); whereas the risk was higher among those who lived alone (OR 2.37, 95% CI 1.31-4.27) and with ADL disability (OR 3.01, 95% CI 1.85-4.89). The GLM showed that the dimension of depressive affect reached statistical significance with lower HbA1c. CONCLUSION: This nationwide community-based study shows that depressive symptoms are associated with lower HbA1C, reminding us that more attention should be paid to the presence of depressive symptoms in those with lower HbA1C. Further research is needed to clarify the causal relationship.

Pathogenesis and novel therapeutics of regulatory T cell subsets and interleukin-2 therapy in systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a heterogeneous multisystem inflammatory disease with wide variability in clinical manifestations. Natural arising CD4+ regulatory T cells (Tregs) play a critical role in maintaining peripheral tolerance by suppressing inflammation and preventing autoimmune responses in SLE. Additionally, CD8+ regulatory T cells, type 1 regulatory T cells (Tr1), and B regulatory cells also have a less well-defined role in the pathogenesis of SLE. Elucidation of the roles of various Treg subsets dedicated to immune homeostasis will provide a novel therapeutic approach that governs immune tolerance for the remission of active lupus. Diminished interleukin (IL)-2 production is associated with a depleted Treg cell population, and its reversibility by IL-2 therapy provides important reasons for the treatment of lupus. This review focuses on the pathogenesis and new therapeutics of human Treg subsets and low-dose IL-2 therapy in clinical benefits with SLE.

Deforestation within breeding ranges may still drive population trends of migratory forest birds in the East Asian Flyway.

The East Asian Flyway (EAF) is the most species diverse of global flyways, with deforestation in its migratory landbird's non-breeding range suspected to be the main driver of population decline. Yet range-wide habitat loss impact assessments on EAF migratory landbirds are scarce, and seasonal variation in habitat preference of migratory species further increases the complexity for conservation strategies. In this study, we reviewed population trends of migratory forest breeding birds in the EAF along with their seasonal habitat preference from the literature and assessed the impact of forest cover change in species' breeding and non-breeding ranges on population trends. We found that 41.3% of the bird species with trend data available are declining, and most have higher forest preference in the breeding season. Despite 93.4% of the species experienced deforestation throughout their annual cycle, forest cover change in the non-breeding range was not identified as the main driver of population trend. However, forest cover change in species' regional breeding range interacts positively with the degree of breeding season forest preference in predicting population trends. We therefore stress that regional breeding habitat protection may still be important while following the call for cross-border collaboration to fill the information gap for flyway conservation.