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IntroductionThis study investigates the role of Fibroblast Activation Protein (FAP)-positive cancer-associated fibroblasts (FAP+CAF) in shaping the tumor immune microenvironment, focusing on its association with immune cell functionality and cytokine expression patterns.MethodsUtilizing immunohistochemistry, we observed elevated FAP+CAF density in metastatic versus primary renal cell carcinoma (RCC) tumors, with higher FAP+CAF correlating with increased T cell infiltration in RCC, a unique phenomenon illustrating the complex interplay between tumor progression, FAP+CAF density, and immune response.ResultsAnalysis of immune cell subsets in FAP+CAF-rich stromal areas further revealed significant correlations between FAP+ stroma and various T cell types, particularly in RCC and non-small cell lung cancer (NSCLC). This was complemented by transcriptomic analyses, expanding the range of stromal and immune cell subsets interrogated, as well as to additional tumor types. This enabled evaluating the association of these subsets with tumor infiltration, tumor vascularization and other components of the tumor microenvironment. Our comprehensive study also encompassed cytokine, angiogenesis, and inflammation gene signatures across different cancer types, revealing heterogeneous cellular composition, cytokine expressions and angiogenic profiles. Through cytokine pathway profiling, we explored the relationship between FAP+CAF density and immune cell states, uncovering potential immunosuppressive circuits that limit anti-tumor activity in tumor-resident immune cells.ConclusionsThese findings underscore the complexity of tumor biology and the necessity for personalized therapeutic and patient enrichment approaches. The insights gathered from FAP+CAF prevalence, immune infiltration, and gene signatures provide valuable perspectives on tumor microenvironments, aiding in future research and clinical strategy development.

Abstract Approximately 30% of early-stage lung adenocarcinoma patients present with disease progression after successful surgical resection. Despite efforts of mapping the genetic landscape, there has been limited success in discovering predictive biomarkers of disease outcomes. Here we performed a systematic multi-omic assessment of 143 tumors and matched tumor-adjacent, histologically-normal lung tissue with long-term patient follow-up. Through histologic, mutational, and transcriptomic profiling of tumor and adjacent-normal tissue, we identified an inflammatory gene signature in tumor-adjacent tissue as the strongest clinical predictor of disease progression. Single-cell transcriptomic analysis demonstrated the progression-associated inflammatory signature was expressed in both immune and non-immune cells, and cell type-specific profiling in monocytes further improved outcome predictions. Additional analyses of tumor-adjacent transcriptomic data from The Cancer Genome Atlas validated the association of the inflammatory signature with worse outcomes across cancers. Collectively, our study suggests that molecular profiling of tumor-adjacent tissue can identify patients at high risk for disease progression.

IntroductionFibroblast activation protein (FAP) is predominantly upregulated in various tumor microenvironments and scarcely expressed in normal tissues.MethodsWe analyzed FAP across 1216 tissue samples covering 23 tumor types and 70 subtypes.ResultsElevated FAP levels were notable in breast, pancreatic, esophageal, and lung cancers. Using immunohistochemistry and RNAseq, a correlation between FAP gene and protein expression was found. Evaluating FAP’s clinical significance, we assessed 29 cohorts from 12 clinical trials, including both mono and combination therapies with the PD-L1 inhibitor atezolizumab and chemotherapy. A trend links higher FAP expression to poorer prognosis, particularly in RCC, across both treatment arms. However, four cohorts showed improved survival with high FAP, while in four others, FAP had no apparent survival impact.ConclusionsOur results emphasize FAP’s multifaceted role in therapy response, suggesting its potential as a cancer immunotherapy biomarker.

Abstract Challenges in social communication is one of the core symptom domains in autism spectrum disorder (ASD). Novel therapies are under development to help individuals with these challenges, however the ability to show a benefit is dependent on a sensitive and reliable measure of treatment effect. Currently, measuring these deficits requires the use of time-consuming and subjective techniques. Objective measures extracted from natural conversations could be more ecologically relevant, and administered more frequently—perhaps giving them added sensitivity to change. While several studies have used automated analysis methods to study autistic speech, they require manual transcriptions. In order to bypass this time-consuming process, an automated speaker diarization algorithm must first be applied. In this paper, we are testing whether a speaker diarization algorithm can be applied to natural conversations between autistic individuals and their conversational partner in a natural setting at home over the course of a clinical trial. We calculated the average duration that a participant would speak for within their turn. We found a significant correlation between this feature and the Vineland Adaptive Behaviour Scales (VABS) expressive communication score (r = 0.51, p = 7 × 10–5). Our results show that natural conversations can be used to obtain measures of talkativeness, and that this measure can be derived automatically, thus showing the promise of objectively evaluating communication challenges in ASD.

Summary: Epigenetics underpins the regulation of genes known to play a key role in the adaptive and innate immune system (AIIS). We developed a method, EpiNN, that leverages epigenetic data to detect AIIS-relevant genomic regions and used it to detect 2,765 putative AIIS loci. Experimental validation of one of these loci, DNMT1, provided evidence for a novel AIIS-specific transcription start site. We built a genome-wide AIIS annotation and used linkage disequilibrium (LD) score regression to test whether it predicts regional heritability using association statistics for 176 traits. We detected significant heritability effects (average |τ∗|=1.65) for 20 out of 26 immune-relevant traits. In a meta-analysis, immune-relevant traits and diseases were 4.45× more enriched for heritability than other traits. The EpiNN annotation was also depleted of trans-ancestry genetic correlation, indicating ancestry-specific effects. These results underscore the effectiveness of leveraging supervised learning algorithms and epigenetic data to detect loci implicated in specific classes of traits and diseases.

Abstract Digital health technologies enable remote and therefore frequent measurement of motor signs, potentially providing reliable and valid estimates of motor sign severity and progression in Parkinson’s disease (PD). The Roche PD Mobile Application v2 was developed to measure bradykinesia, bradyphrenia and speech, tremor, gait and balance. It comprises 10 smartphone active tests (with ½ tests administered daily), as well as daily passive monitoring via a smartphone and smartwatch. It was studied in 316 early-stage PD participants who performed daily active tests at home then carried a smartphone and wore a smartwatch throughout the day for passive monitoring (study NCT03100149). Here, we report baseline data. Adherence was excellent (96.29%). All pre-specified sensor features exhibited good-to-excellent test–retest reliability (median intraclass correlation coefficient = 0.9), and correlated with corresponding Movement Disorder Society–Unified Parkinson's Disease Rating Scale items (rho: 0.12–0.71). These findings demonstrate the preliminary reliability and validity of remote at-home quantification of motor sign severity with the Roche PD Mobile Application v2 in individuals with early PD.

This paper introduces the works of two Vietnamese Buddhist nuns in Taiwan. They both envision a permanent or long-term stay in Taiwan and have purchased properties to function as their temples. They provide services to the Vietnamese diaspora. Special attention will be given to the discussion of gender role in the transmission of Vietnamese Buddhism to Taiwan and an assessment of what Buddhist feminist Rita Gross calls “the prison of gender role” in the works the nuns conduct.

This paper will use the case study of a Chinese Mahayana Buddhist nun in a border town in Shan state, Myanmar, to explore the importance of identity in transnational Buddhism. Three life stories related to the Chinese Mahayana Buddhist nun will be told; that is, stories of her mother, her tonsure grandmaster, and herself. The main discussion of this paper is on the analysis of three dimensions of the nun’s identity, which are overseas Chinese, Mahayana monastic, and Buddhist nun. This paper will argue that identity is a crucial factor in transnational Buddhism, for identity helps an individual to communicate, interact, and take actions with others transnationally.

Obesity is a major public health concern worldwide with a rising prevalence. Diets containing whole grains have been demonstrated to benefit body composition and inflammatory conditions in individuals at a high risk of metabolic disorders. This study investigated the effects of dehulled adlay on blood lipids and inflammation in overweight and obese adults. We recruited 21 individuals with abdominal obesity to participate in a 6-week experiment, providing them 60 g of dehulled adlay powder per day as a substitute for their daily staple. Before and after the 6-week intervention, we performed anthropometric analyses and measured blood lipid profiles, adipokines, and markers of inflammation. At the end of the study, the percentage of body fat mass, blood total cholesterol, and triglyceride levels were significantly decreased compared with the baseline. Plasma tumor necrosis factor alpha, interleukin-6, leptin, and malondialdehyde levels were also reduced. In addition, participants with higher basal blood lipid levels exhibited enhanced lipid lowering effects after the dehulled adlay intervention. These results suggest that a dietary pattern containing 60 g of dehulled adlay per day may have a beneficial effect on lipid profiles and inflammatory markers in individuals that are overweight and obese.

BackgroundWe aimed to develop a Human Activity Recognition (HAR) model using a wrist-worn device to assess patient activity in relation to negative symptoms of schizophrenia.MethodsData were analyzed in a randomized, three-way cross-over, proof-of-mechanism study (ClinicalTrials.gov: NCT02824055) comparing two doses of RG7203 with placebo, given as adjunct to stable antipsychotic treatment in patients with chronic schizophrenia and moderate levels of negative symptoms. Baseline negative symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS) and Brief Negative Symptom Scale (BNSS). Patients were given a GeneActiv™ wrist-worn actigraphy device to wear over a 15-week period. For this analysis, actigraphy data and behavioral and clinical assessments obtained during placebo treatment were used. Motivated behavior was evaluated with a computerized effort-choice task. A trained HAR model was used to classify activity and an activity–time ratio was derived. Gesture events and features were inferred from the HAR-detected activities and the acceleration signal.ResultsThirty-three patients were enrolled: mean (±SD) age 36.6 ± 7 years; mean (±SD) baseline PANSS negative symptom factor score 23.0 ± 3.5; and mean (±SD) baseline BNSS total score 36.0 ± 11.5. Activity data were collected for 31 patients with a median monitoring time of 1,859 h per patient, equating to ~11 weeks or 74% monitoring ratio. The trained HAR model demonstrated >95% accuracy in separating ambulatory and stationary activities. A positive correlation was seen between the activity–time ratio and the percent of high-effort choices (Spearman r = 0.58; P = 0.002) in the effort-choice task. Median daily gesture counts correlated negatively with the BNSS total score (Spearman r = −0.44; P = 0.03), specifically with the diminished expression sub-score (Spearman r = −0.42; P = 0.03). Gesture features also correlated negatively with the BNSS total score and diminished expression sub-scores. Activity measures showed similar correlations with PANSS negative symptom factor but did not reach significance.ConclusionOur findings support the use of wrist-worn devices to derive activity and gesture-based digital outcome measures for patients with schizophrenia with negative symptoms in a clinical trial setting.

Abstract Physical mechanisms that are key to observed convective clustering in 2‐day rain events are examined. Previous analysis of the 2‐day rain events during the Atmospheric Radiation Measurement Madden‐Julian Oscillation Investigation Experiment (AMIE)/Dynamics of the Madden‐Julian Oscillation (DYNAMO) field campaign data revealed two distinct phases of convective clustering. Using a cloud‐system‐resolving model, we perform a series of intervention experiments to investigate the underlying mechanisms for convective clustering in each phase. In the developing phase, in addition to previously emphasized processes such as the cold pool‐updraft interaction and moisture‐convection feedbacks, our results show that the vertical wind shear in the lower free troposphere is a critical factor for convective clustering. Stronger lower free‐tropospheric wind shear increases the entrainment of environmental air into updrafts and prevents convective clouds from being omnipresent. This result suggests that stronger vertical wind shear in the lower free troposphere can help spatially organize the convection, even for non–squall‐line‐type convective systems. In the decaying phase, the cold pool‐updraft interaction becomes less effective in aggregating convective clouds because the boundary layer is widely cooled by stratiform precipitation. Instead, the mesoscale downdraft driven by the stratiform precipitation becomes the dominant factor to maintain the relatively aggregated convection. Additionally, removing horizontal variations in radiative heating has no impact on convective clustering on this 2‐day time scale, even in the decaying phase when stratiform clouds are widespread. The implication of these results for improving the representation of mesoscale convective organization in convection schemes is discussed.

High blood pressure is a crucial risk factor for many cardiovascular diseases, and a diet rich in whole-grain foods may modulate blood pressure. This study investigated the effects of dehulled adlay consumption on blood pressure in vivo. We initially fed spontaneous hypertensive rats diets without (SHR group) or with 12 or 24% dehulled adlay (SHR + LA and SHR + HA groups), and discovered that it could limit blood pressure increases over a 12-week experimental period. Although we found no significant changes in plasma, heart, and kidney angiotensin-converting enzyme activities, both adlay-consuming groups had lower endothelin-1 and creatinine concentrations than the SHR group; the SHR + HA group also had lower aspartate aminotransferase and uric acid levels than the SHR group did. We later recruited 23 participants with overweight and obesity, and they consumed 60 g of dehulled adlay daily for a six-week experimental period. At the end of the study, we observed a significant decrease in the group’s systolic blood pressure (SBP), and the change in SBP was even more evident in participants with high baseline SBP. In conclusion, our results suggested that daily intake of dehulled adlay had beneficial effects in blood-pressure management. Future studies may further clarify the possible underlying mechanisms for the consuming of dehulled adlay as a beneficial dietary approach for people at risk of hypertension.

Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude that they represent a universal biological mechanism shared among multiple cancer types. Here we present a computational method for generating signatures using an iterative process that converges to one of several precise attractors defining signatures representing biomolecular events, such as cell transdifferentiation or the presence of an amplicon. By analyzing rich gene expression datasets from different cancer types, we identified several such biomolecular events, some of which are universally present in all tested cancer types in nearly identical form. Although the method is unsupervised, we show that it often leads to attractors with strong phenotypic associations. We present several such multi-cancer attractors, focusing on three that are prominent and sharply defined in all cases: a mesenchymal transition attractor strongly associated with tumor stage, a mitotic chromosomal instability attractor strongly associated with tumor grade, and a lymphocyte-specific attractor.

A stage-associated gene expression signature of coordinately expressed genes, including the transcription factor Slug (SNAI2) and other epithelial-mesenchymal transition (EMT) markers has been found present in samples from publicly available gene expression datasets in multiple cancer types, including nonepithelial cancers. The expression levels of the co-expressed genes vary in a continuous and coordinate manner across the samples, ranging from absence of expression to strong co-expression of all genes. These data suggest that tumor cells may pass through an EMT-like process of mesenchymal transition to varying degrees. Here we show that, in glioblastoma multiforme (GBM), this signature is associated with time to recurrence following initial treatment. By analyzing data from The Cancer Genome Atlas (TCGA), we found that GBM patients who responded to therapy and had long time to recurrence had low levels of the signature in their tumor samples (P = 3×10(-7)). We also found that the signature is strongly correlated in gliomas with the putative stem cell marker CD44, and is highly enriched among the differentially expressed genes in glioblastomas vs. lower grade gliomas. Our results suggest that long delay before tumor recurrence is associated with absence of the mesenchymal transition signature, raising the possibility that inhibiting this transition might improve the durability of therapy in glioma patients.

Introduction: This study investigates the role of Fibroblast Activation Protein (FAP)-positive cancer-associated fibroblasts (FAP+CAF) in shaping the tumor immune microenvironment, focusing on its association with immune cell functionality and cytokine expression patterns. Methods: Utilizing immunohistochemistry, we observed elevated FAP+CAF density in metastatic versus primary renal cell carcinoma (RCC) tumors, with higher FAP+CAF correlating with increased T cell infiltration in RCC, a unique phenomenon illustrating the complex interplay between tumor progression, FAP +CAF density, and immune response. Results: Analysis of immune cell subsets in FAP+CAF-rich stromal areas further revealed significant correlations between FAP+ stroma and various T cell types, particularly in RCC and non-small cell lung cancer (NSCLC). This was complemented by transcriptomic analyses, expanding the range of stromal and immune cell subsets interrogated, as well as to additional tumor types. This enabled evaluating the association of these subsets with tumor infiltration, tumor vascularization and other components of the tumor microenvironment. Our comprehensive study also encompassed cytokine, angiogenesis, and inflammation gene signatures across different cancer types, revealing heterogeneous cellular composition, cytokine expressions and angiogenic profiles. Through cytokine pathway profiling, we explored the relationship between FAP+CAF density and immune cell states, uncovering potential immunosuppressive circuits that limit anti-tumor activity in tumor-resident immune cells. Conclusions: These findings underscore the complexity of tumor biology and the necessity for personalized therapeutic and patient enrichment approaches. The insights gathered from FAP+CAF prevalence, immune infiltration, and gene signatures provide valuable perspectives on tumor microenvironments, aiding in future research and clinical strategy development. [ABSTRACT FROM AUTHOR]

Introduction: Fibroblast activation protein (FAP) is predominantly upregulated in various tumor microenvironments and scarcely expressed in normal tissues. Methods: We analyzed FAP across 1216 tissue samples covering 23 tumor types and 70 subtypes. Results: Elevated FAP levels were notable in breast, pancreatic, esophageal, and lung cancers. Using immunohistochemistry and RNAseq, a correlation between FAP gene and protein expression was found. Evaluating FAP's clinical significance, we assessed 29 cohorts from 12 clinical trials, including both mono and combination therapies with the PD-L1 inhibitor atezolizumab and chemotherapy. A trend links higher FAP expression to poorer prognosis, particularly in RCC, across both treatment arms. However, four cohorts showed improved survival with high FAP, while in four others, FAP had no apparent survival impact. Conclusions: Our results emphasize FAP's multifaceted role in therapy response, suggesting its potential as a cancer immunotherapy biomarker. [ABSTRACT FROM AUTHOR]

Background: Although the incidence of adenocarcinoma of the esophagogastric junction (AEG) has been increasing since the past decade, the proportion of AEG cases in two previous clinical trials (ACTS-GC and CLASSIC) that investigated the efficacy of adjuvant chemotherapy was relatively small. Therefore, whether AEG patients can benefit from adjuvant chemotherapy remains unclear. Methods: Patients who were diagnosed with pathological stage II/III, Siewert II/III AEG, and underwent curative surgery at three high-volume institutions were assessed. Clinical outcomes were analyzed by using Kaplan-Meier curves, log-rank test, and Cox regression model. Propensity score matching (PSM) was used to reduce the selection bias. Results: A total of 927 patients were included (the chemotherapy group: 696 patients; the surgery-only group: 231 patients). The median follow-up was 39.0 months. The 5-year overall survival was 63.1% (95% confidence interval [CI]: 59.0-67.6%) for the chemotherapy group and 50.2% in the surgery-only group (hazard ratio [HR] = 0.69, 95% CI: 0.54-0.88; p = 0.003). The 5-year, disease-free survival was 35.4% for the chemotherapy group and 16.6% for the surgery-only group (HR = 0.66, 95% CI: 0.53-0.83; p < 0.001). After PSM, the survival benefit of adjuvant chemotherapy for AEG was maintained. Multivariate analysis for overall survival and disease-free survival further demonstrated the survival benefit of adjuvant chemotherapy, with HRs of 0.63 (p < 0.001) and 0.52 (p < 0.001), respectively. Conclusions: Postoperative adjuvant chemotherapy was associated with improved overall survival and disease-free survival in patients with operable stage II or III AEG after D2 gastrectomy. [ABSTRACT FROM AUTHOR]