Journal of Translational Medicine
○ Springer Science and Business Media LLC
Preprints posted in the last 7 days, ranked by how well they match Journal of Translational Medicine's content profile, based on 46 papers previously published here. The average preprint has a 0.08% match score for this journal, so anything above that is already an above-average fit.
Escobar, J. S.; Corrales-Agudelo, V.; Ortega-Sierra, O. L.; Villota-Salazar, N. A.; Rivera, D. A.; Pulgarin-Zapata, I. C.; Hernandez-Londono, M.; Lara-Guzman, O. J.; Sierra, J. A.; Alvarez-Quintero, R.; Polanco, J. P.; Munoz-Durango, K.
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Obesity and related cardiometabolic diseases pose significant global health challenges. Konjac glucomannan, a soluble dietary fiber, has shown promise in managing these conditions. However, rigorous studies are necessary to establish its benefits on human health. We designed a parallel-arm, triple-blind, placebo-controlled RCT to test the effects of glucomannan (3 g/day, 12 weeks) on body weight and composition, lipid profile, glucose metabolism, inflammation, adipokines, intestinal permeability, gut microbiota, and fecal metabolites in 40 adults. Participants were randomly assigned to either the glucomannan or placebo group, with both groups adhering to personalized hypocaloric diets and moderate physical activity. Outcomes were analyzed as intention-to-treat using linear mixed-effect models. Irrespective of the treatment, our intervention reduced body weight (mean: -2.39 kg; 95% CI: -3.38, -1.40), BMI (-0.83 kg/m2; -1.15, -0.52), and waist (-2.70 cm; -3.87, -1.53). Glucomannan promoted additional benefits not obtained with the placebo, reducing body fat measured by DEXA (body fat%: -2.16%; -3.04, -1.28; VAT: -20.0 cm2; - 29.2, -10.8; FMI: -0.98 kg/m2; -1.34, -0.62), LDL (-14.1 mg/dL; -23.4, -4.9), and the atherogenic index (-0.50; -0.80, -0.21). It also diminished the Framingham score of 10-year risk of coronary heart disease (-0.370; -0.625, -0.115), C reactive protein (-1.01 mg/L; -2.18, 0.15), leptin (-2.06 ng/mL; -4.48, 0.365), and leptin/adiponectin (-0.282; -0.603, 0.040). The two treatments had similar intakes, physical activity, and adherence to the intervention. There were no adverse effects. This intervention fostered health benefits in a population at high risk of cardiometabolic diseases. Konjac glucomannan was an effective co-adjuvant for further reducing risk factors.
Palmer, M.; Hashiguchi, T.; Arman, A. C.; Shirakata, Y.; Buss, N. E.; Lalezari, J. P.
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BackgroundChemokine receptor type 5 (CCR5) is expressed on hepatic stellate cells (HSCs), which, together with fibroblasts, are major producers of extracellular matrix during liver fibrosis. Leronlimab is a humanized IgG4{kappa} monoclonal antibody that binds to CCR5. The objective of the present study was to evaluate the antifibrotic effects of leronlimab in three independent preclinical studies using two mouse models of liver fibrosis. MethodsIn STAM (Stelic Animal Model) model 1, leronlimab was administered at doses of 5 or 10 mg/kg/week for 3 weeks. STAM model 2 was conducted as a confirmatory study to validate the antifibrotic effect observed with the 10 mg/kg/week dose in STAM model 1. In a third study, a carbon tetrachloride (CCl)-induced liver fibrosis mouse model was used to evaluate leronlimab administered at 10 mg/kg/week for 3 weeks. An isotype-matched control antibody was included in all studies for comparison. Evaluations included liver enzymes and histological assessment of liver fibrosis. ResultsIn STAM model 1, leronlimab at 10 mg/kg/week significantly reduced fibrosis area compared with the isotype control (p = 0.0005). These findings were confirmed in STAM model 2 (p < 0.0001). Consistent antifibrotic effects were also observed in the CCl-induced liver fibrosis model (p = 0.0006). ConclusionsCollectively, these preclinical results demonstrate that CCR5 blockade by leronlimab is associated with a significant reduction of established liver fibrosis in multiple mouse models and support further evaluation of leronlimab as a potential therapeutic option, either as monotherapy or in combination regimens, for chronic liver diseases with fibrosis.
Ng, C. Y.; Liu, M.; Ai, D.; Yao, L.; Yang, M.; Zhong, L. L.
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IntroductionColorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, despite advances in conventional oncological therapies. In recent years, various studies have made advances in integrative oncology, such as investigating the use of Chinese Herbal Medicine (CHM) as a complementary therapy alongside conventional oncological therapies to alleviate treatment-related adverse effects, improve quality of life, and potentially enhance therapeutic outcomes. Despite this, clinical practice in this area remains highly heterogeneous, with limited standardized guidelines on key areas of concern such as (1) optimal intervention, (2) recommended stage and duration of intervention, (3) safety considerations, and (4) possible herb-drug interactions. Hence, this study aims to establish expert consensus on the usage of CHM as a complementary therapy in the management of CRC, to support safe, consistent, and evidence-informed clinical practice. Methods and AnalysisWe will employ a modified Delphi technique to achieve consensus amongst a panel of international experts in various fields related to integrative oncology. Prior to the study, a list of questionnaire items was developed based on a systematic review of existing clinical practice guidelines on CRC. An international panel will be invited based on established international profile in integrative oncology research and clinical practice, and by peer referral. Two rounds of Delphi will be conducted using anonymous online questionnaires. Consensus will be considered reached if at least 50% of the panel strongly agree/disagree that an item should be included or excluded while strong consensus will be set at 76%. Items which achieve strong consensus after Round 1 will be removed, before being sent out for Round 2 with a summary of Round 1 responses for a final consensus. Ethics and DisseminationEthics approval has been obtained from the Institutional Review Board of Nanyang Technological University (IRB-2025-1222). Our findings will be disseminated through peer-reviewed publications and conference presentations. Strengths and limitations of this studyO_LIThis study will develop an expert consensus which aims to guide future integration of Chinese Herbal Medicine (CHM) as a complementary therapy into colorectal cancer (CRC) management. C_LIO_LIKey concerns in areas such as determining the (1) optimal intervention, (2) recommended stage and duration of intervention, (3) safety considerations, and (4) possible herb-drug interactions, thereby laying the groundwork for potential future incorporation of CHM into CRC treatment protocols alongside conventional oncology approaches has been identified, thus limiting implementation in clinical practice. C_LIO_LIDesigning a study e-guide, followed by the consensus rounds study online will facilitate participants responses and the dissemination of information from previous rounds. C_LI
Wolf, C. L.; Ruiz, R. K.; Khou, S.; Cornelison, R.; Stelow, E. B.; Kowalewski, K. M.; Lazzara, M. J.; Poissonnier, A.; Coussens, L. M.; Kelly, K. A.
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BackgroundPancreatic adenocarcinoma (PDAC) is an abysmal disease, with a poor clinical outcome, largely due to limited life-extending treatments for patients. Notoriously, PDAC displays a T cell-suppressive tumor microenvironment where underlying molecular mechanisms that lead to this phenotype remain poorly understood. To unravel specific mechanisms, we utilized bioinformatic analyses with functional studies and revealed the cytolinker protein plectin (PLEC) as a novel player in regulating the T cell-suppressive tumor microenvironment of PDAC. MethodsUtilizing the TCGA-PAAD dataset, tumor samples were separated by PLEC expression to evaluate patient survival, and pathway analyses associated with increased tumorigenesis. Evaluation of immune infiltration and subsequent immune deconvolution was performed using tidyestimate and CIBERSORTx R packages. Single-cell RNA-seq (scRNA-seq) analysis from 229 PDAC patients was analyzed to investigate signaling dynamics and immune cell infiltration in PLECHigh patients. Functional validation was provided using a monoclonal antibody (mAb) against cell surface plectin (CSP) in two murine PDAC models to examine changes in tumor growth and immune cell subset abundance. ResultsOur studies revealed that high plectin expression results in an overall worse survival associated with activation of pro-tumorigenic pathways and decreased anti-tumor immune signature in PDAC patients. Analysis via GSEA indicates PLECHigh patients display an aggressive phenotype and suppressed pro-inflammatory signaling pathways. Immune ESTIMATE scores were significantly decreased in PLECHigh patients, and scRNA-seq analysis revealed that PLECHigh tumors display a decrease in anti-tumor CD8+ T cells. In vivo analyses using an anti-CSP mAb revealed a reduction in tumor growth kinetics compared to IgG control corresponding with a significant increase in proliferating and activated cytotoxic CD8+ T cells. Anti-CSP-mediated tumor suppression was inhibited when CD8+ T cells were depleted, indicating that anti-CSP treatment is contingent on cytotoxic T cell functionality. ConclusionOur findings identify plectin as a biomarker of aggressive disease in PDAC, with high plectin expression associated with decreased T cell infiltration, and that treatment with anti-CSP mAb reinstates anti-tumor immunity and decreases tumor volume in vivo. These findings position plectin as a high-priority therapeutic target, with the potential to fundamentally reshape immune responses in PDAC and improve outcomes for patients with few remaining options.
rani, a.; mishra, s.
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Accurate histopathological differentiation between High-Grade Serous Carcinoma (HGSC) and Low-Grade Serous Carcinoma (LGSC) remains a critical yet challenging aspect of ovarian cancer diagnosis due to their similar morphology and different clinical outcomes. This study presents a deep learning framework that uses custom attention mechanisms, including the Convolutional Block Attention Module (CBAM), Squeeze-and-Excitation (SE) blocks, and a Differential Attention module within five CNN architectures for automated binary classification of ovarian cancer subtypes from H&E WSI patches. Although individual models achieved higher accuracy, the ensemble stacking framework with a shallow MLP meta-learner delivered the best overall performance, with a ROC-AUC of 0.9211, an accuracy of 0.85, and F1-scores of 0.84 and 0.85 across both subtypes. These findings demonstrate that attention-guided feature recalibration combined with ensemble stacking provides robust and clinically interpretable discrimination of ovarian carcinoma subtypes.
Claus, L.; McNamara, M.; Oser, C.; Fogle, C.; Canine, B.
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Cardiovascular disease (CVD) remains the leading cause of mortality in the United States, despite being largely preventable through effective management of risk factors. This study evaluates the impact of Phase II cardiac rehabilitation (CR) on functional capacity and quality of life, using data from the Montana Outcomes Project Cardiac Rehabilitation Registry. Functional capacity improvements were assessed via the six-minute walk test (6MWT) and Dartmouth COOP questionnaire, with statistical analyses exploring the influence of CR session attendance, demographic factors, and referring diagnoses. Results demonstrated significant gains in 6MWT, with a mean improvement of 330.73 feet (p < .0001), and quality of life scores across all subgroups. A dose-response relationship was observed, indicating greater improvements with increased CR sessions (p < .0001), though diminishing returns were observed beyond 24-35 visits. Demographic factors and complex conditions influenced outcomes, underscoring the need for tailored strategies to enhance CR access and effectiveness. These findings highlight the critical role of CR in improving patient outcomes and emphasize the importance of addressing barriers to participation in underserved populations.
Muneer, A.; Showkatian, E.; Kitsel, Y.; Saad, M. B.; Sujit, S. J.; Soto, F.; Shroff, G. S.; Faiz, S. A.; Ghanbar, M. I.; Ismail, S. M.; Vokes, N. I.; Cascone, T.; Le, X.; Zhang, J.; Byers, L. A.; Jaffray, D.; Chang, J. Y.; Liao, Z.; Naing, A.; Gibbons, D. L.; Vaporciyan, A. A.; Heymach, J. V.; Suresh, K. S.; Altan, M.; Sheshadri, A.; Wu, J.
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Background: Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy but can cause serious immune-related adverse events (irAEs), with pneumonitis (ICI-P) being among the most severe. Early identification of high-risk patients before ICI initiation is critical for closer monitoring, timely intervention, and improved outcomes. Purpose: To develop and validate a deep learning foundation model to predict ICI-P from baseline CT scans in patients with lung cancer. Methods: We designed the Checkpoint-Inhibitor Pneumonitis Hazard EstimatoR (CIPHER), a deep learning foundation model that combines contrastive learning with a transformer-based masked autoencoder to predict ICI-P from baseline CT scans in patients with lung cancer. Using self-supervised learning, CIPHER was pre-trained on 590,284 CT slices from 2,500 non-small cell lung cancer (NSCLC) patients to capture heterogeneous lung parenchymal patterns. After pre-training, the model was fine-tuned on an internal NSCLC cohort for ICI-P risk prediction, using images from 254 patients for model development and 93 patients for internal validation. We compared CIPHER with classical radiomic models and further evaluated it on an external NSCLC cohort of 116 patients. Results: In the internal immunotherapy cohort, CIPHER consistently distinguished patients at elevated risk of ICI-P from those without the event, with AUCs ranging from 0.77 to 0.85. In head-to-head benchmarking, CIPHER achieved an AUC of 0.83, outperforming the radiomic models. In the external validation cohort, CIPHER maintained strong performance (AUC = 0.83; balanced accuracy = 81.7%), exceeding the radiomic models (DeLong p = 0.0318) and demonstrating higher specificity without sacrificing sensitivity. By contrast, the radiomic model showed high sensitivity (85.0%) but markedly lower specificity (45.8%). Confusion matrix analysis confirmed the robust classification performance of CIPHER, correctly identifying 80 of 96 non-ICI-P cases and 16 of 20 ICI-P cases. Conclusions: We developed and externally validated CIPHER for predicting future risk of ICI-P from pre-treatment CT scans. With prospective validation, CIPHER may be incorporated into routine patient management to improve outcomes.
Burns, R.; Young, W. J.; Uddin, K.; Petersen, S. E.; Ramirez, J.; Young, A. A.; Munroe, P. B.
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BackgroundGenetic studies using cardiac magnetic resonance (CMR) imaging have identified loci related to cardiac shape, but most focus on static morphology. The value of a dynamic cardiac shape atlas capturing both shape and function remains unknown. MethodsA dynamic shape atlas comprising CMR-derived shape models at end-diastole and end-systole was combined with genetic and outcome data in 36,992 UK Biobank participants. Dynamic shape principal components (PCs) describing >1% of variance were characterized, and tested for associations with prevalent and incident cardiometabolic diseases, including ischemic heart disease (IHD), heart failure (HF), significant atrioventricular block (AVB), and atrial fibrillation (AF), and independent predictive power alongside standard CMR measures. Genome-wide association studies (GWAS) were performed to identify candidate genes and biological pathways, and polygenic risk scores (PRS) were assessed for disease associations. Mendelian randomization (MR) was performed to test causality of observed disease associations. ResultsWe identified 14 dynamic cardiac shape PCs capturing 83.3% of total dynamic cardiac shape variance. These PCs captured distinct functional remodeling patterns such as variation in annular plane systolic excursion, while remaining only modestly correlated with standard CMR measures. All 14 PCs were associated with at least one incident cardiometabolic disease, with the strongest associations observed for incident IHD, HF, and AVB. Notably, incorporating dynamic shape PCs improved the prediction of incident IHD beyond standard CMR measures. GWAS identified 75 genetic loci associated with dynamic shape, including 14 variants previously unreported for cardiac traits, and candidate genes demonstrated enrichment in pathways related to cardiac development and contractile function. PRS derived from dynamic shape loci were significantly associated with multiple outcomes, most prominently HF. MR identified significant causal relationships between several PCs and cardiometabolic disease. ConclusionsDynamic cardiac shape features capture aspects of cardiac structure and function not fully represented by standard CMR measures. These features are strongly associated with incident cardiometabolic disease and provide new insights into the genetic architecture of cardiac remodeling. Clinical perspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIGenetic and outcome relationships with a dynamic statistical shape model capturing both left and right ventricles at end-diastole and end-systole. C_LIO_LIDemonstration of incremental value over existing cardiac shape models, through capture of functional remodeling not represented by standard imaging measures. C_LIO_LIIdentification of genetic susceptibility loci for dynamic cardiac shape, including 14 variants not previously reported for cardiac traits. C_LI What are the clinical implications?O_LIThe results enhance our understanding of the genetic architecture of dynamic cardiac shape and function in the general population and clarify their relationships with other cardiovascular endophenotypes and incident cardiometabolic diseases. C_LIO_LINewly identified candidate genes expand the biological pathways implicated in cardiac remodeling and provide targets for future functional and mechanistic studies. C_LIO_LIThe improved prediction of incident cardiometabolic disease, particularly ischemic heart disease, achieved by adding dynamic shape PCs to traditional CMR measures suggests potential value for their inclusion in evaluation of patients. C_LI
Buzoianu, M. M.; Yu, R.; Assel, M.; Bozkurt, A.; Aghdam, H.; Fine, S.; Vickers, A.
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Objective: To demonstrate the proof of principle that machine learning (ML) can be used to quantify Gleason Pattern (GP) 4 on digitized biopsy slides using multiple measurement approaches, allowing direct comparison of their prognostic performance. Methods: We assembled a convenience sample of 726 patients with grade group 2-4 prostate cancer on systematic biopsy who underwent radical prostatectomy between 2014 and 2023. Digitized biopsy slides were analyzed using a machine-learning algorithm (PAIGE-AI) to quantify GP4 using multiple measurement approaches, particularly with respect to how gaps between cancer foci (interfocal stroma) were handled. GP4 extent was quantified using linear measurements or a pixel-based area metric. Discrimination of each GP4 quantification approach, along with Grade Group (GG), was assessed for adverse radical prostatectomy pathology and biochemical recurrence. Results: We identified 15 different quantification approaches and observed differences between their discrimination. The highest discrimination was in the pixel-counting method (AUC 0.648). GP4 quantification outperformed GG for predicting adverse pathology (AUC 0.627 vs 0.608). Amount of GP3 was non-predictive once GP4 was known. These findings were consistent for BCR. Conclusions: We were able to measure slides using 15 distinct measurement approaches and replicated prior findings using ML to quantify GP4. Our findings support the use of ML as a research tool to compare different GP4 quantification approaches. We intend to use our method on larger cohorts to determine with which measurement approach best predicts oncologic outcome.
Nakaguma, Y.; Kato, Y.; Atef, Y.; Ito, T.; Nishimura, A.; Uesugi, M.; Kanda, Y.; Kunisawa, J.; Nishida, M.
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Vaccine adjuvants are critical for enhancing immune responses and sustaining antibody production. Although their safety profiles are well established, assessments have largely focused on metabolic and excretory organs such as the liver and kidneys, with limited attention to the heart. Here, we systematically evaluated the cardiac effects of five representative adjuvants in mice: alum, MF59, AS03, Sigma Adjuvant Systems, and lipid A. None of the adjuvants impaired baseline cardiac contractile function. Notably, lipid A uniquely enhanced mitochondrial respiratory capacity in rat and human induced pluripotent stem cell-derived cardiomyocytes and promoted mitochondrial membrane hyperpolarization. We next examined its therapeutic potential in a doxorubicin (Dox)-induced heart failure model characterized by mitochondrial dysfunction. Co-administration of lipid A with influenza hemagglutinin (HA) antigen significantly ameliorated cardiac dysfunction. In parallel, lipid A prevented the Dox-induced decline in anti-HA antibody titers, an effect associated with preservation of splenic B cell populations. Collectively, these findings reveal a previously unappreciated cytoprotective dimension of lipid A, demonstrating that it not only potentiates immune responses but also counteracts chemotherapy-induced functional decline by enhancing mitochondrial activity.
Nauman, R. W.; Greer, P. A.; Craig, A. W.; Cotechini, T.; Siemens, D. R.; Graham, C. H.
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In recent years, immunotherapy of patients with higher-risk non-muscle invasive bladder cancer (NMIBC) in North America has relied on the use of the TICE strain of BCG. However, limitations in the supply chain have warranted investigation of the therapeutic benefit of other strains of BCG, such as BCG-Russia. Trained immunity, a form of innate immune memory, is now widely believed to be an important component of the therapeutic benefit of BCG. Therefore, in the present study we compared the effects of BCG-TICE and BCG-Russia on the acquisition of trained immunity and related secondary immune responses. C57BL/6 mice received a single intravenous injection of BCG-Russia or BCG-TICE. Four weeks later, bone marrow was collected for flow cytometric analysis of hematopoietic stem and progenitor cell (HSPC) populations, generation of bone marrow-derived macrophages, functional assessment of trained immunity, and transcriptomic profiling. Compared with BCG-Russia, BCG-TICE elicited stronger levels of trained immunity, characterized by higher production of several proinflammatory cytokines upon secondary activation. BCG promoted the expansion of HSPCs independent of strain. BCG-TICE was linked to upregulation of key inflammation-related genes and enrichment of functionally relevant pathways. The results of this study reveal strain-dependent differences in the ability of BCG to induce innate immune memory and inflammatory pathways that could ultimately determine efficacy of immunotherapy of patients with NMIBC.
Crystal, O.; Farina, J. M. M.; Scalia, I. G.; Ayoub, C.; Park, H.-B.; Kim, K. A.; Arsanjani, R.; Lester, S. J.; Banerjee, I.
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BackgroundAccurate assessment of left ventricular outflow tract (LVOT) gradients is critical for hypertrophic cardiomyopathy (HCM) management, yet Doppler-based measurements are technically demanding and require expertise. ObjectiveTo develop a multi-view deep learning model capable of classifying LVOT obstruction (> 20mmHg) using routine 2D echocardiographic windows without reliance on Doppler imaging. MethodsWe trained and externally validated a cross-attention-based video-to-video fusion framework that integrated EchoPrime-derived video representations from three standard transthoracic echocardiographic views to classify LVOT gradients. ResultsTraining was performed on a derivation cohort (N = 1833) from a tertiary care system in the United States, with model performance evaluated on an internal held-out test set (N = 275) and a Korean external validation cohort (N = 46). Single-view baselines showed limited discrimination (external AUROCs 0.47-0.70). Conversely, domain-specific foundational model (EchoPrime) achieved superior single-view performance (AUROCs 0.75-0.80 internal; 0.79-0.83 external), highlighting the importance of echo-specific pretraining and temporal modeling. The proposed multi-view fusion further enhanced predictive performance, with the late fusion model reaching an AUROC of 0.84 on the external cohort with significant population-shift. ConclusionsThese results suggest LVOT physiology is encoded in routine 2D imaging and can be leveraged for clinically relevant gradient classification without Doppler input- proposed AI-guided strategy demonstrates substantial cost savings compared with the screen-all approach. By integrating complementary spatial-temporal information across multiple views, our approach generalizes robustly across populations and may enable real-time decision support, extend LVOT assessment to portable or resource-limited settings, and complement Doppler-based evaluation for longitudinal HCM management.
Kwon, C.-Y.; Lee, B.; Kim, M.; Mun, J.-h.; Seo, M.-G.; Yoon, D.
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BackgroundHwa-byung (HB) is a Korean culture-bound syndrome characterised by prolonged suppression of anger and somatic complaints. No evidence-based digital therapeutic (DTx) has been developed for HB. We evaluated the feasibility, user experience (UX), and preliminary clinical effect of an acceptance and commitment therapy (ACT)-based DTx application, Hwa-free, for HB. MethodsAdults aged 19-80 years diagnosed with HB were enrolled in a four-week app-based intervention with assessment at baseline (Week 0), Week 2, Week 4, and Week 8 follow-up. The primary outcome was UX assessed via a 22-item survey at Week 4. Secondary outcomes included HB-related symptom and personality scales, depression, anxiety, anger expression, psychological flexibility, health-related quality of life, and heart rate variability. ResultsOf 45 screened, 30 were enrolled and 28 constituted the modified intention-to-treat population. Mean app use was 19.9 {+/-} 7.9 days (71.2% adherence over 28 days). Adverse events were infrequent and unrelated to the intervention. Positive response rates exceeded 80% for video content (items 2-4: 82.8-89.7%), HB self-assessment (86.2%), meditation therapy (86.2%), and in-app guidance (85.7%). Pre-post improvements from baseline to Week 4 were observed in 11 of 18 clinical scales, including HB Symptom Scale ({Delta} = -9.8, Cohens d = -0.92), Beck Depression Inventory-II ({Delta} = -13.3, d = -1.11), and state anger ({Delta} = -7.8, d = -0.96). The HB screening-positive rate declined from 100% at baseline to 55.6% at Week 8. ConclusionsHwa-free demonstrated adequate feasibility, acceptable UX, and preliminary evidence of clinically meaningful improvement in HB-related symptoms. Future randomised controlled trial is warranted. Trial registrationCRIS, KCT0011105
Pizzagalli, M.; Sasipalli, S.; Leary, O.; Tran, L.; Haas, B.; Tapinos, N.
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BackgroundTransposable elements (TEs) account for over half of the human genome and are often derepressed in cancer. TEs can add cryptic splice sites, undergo exonization, and generate gene-TE fusion transcripts, but the combined effects of TEs on RNA processing and translation in glioblastoma stem cells (GSCs) remains incompletely elucidated. ResultsWe combined long-read RNA sequencing with polysome profiling in four patient-derived GSCs and two neural stem cell (NSC) controls to resolve TE-associated transcript diversity and its relationship to ribosomal engagement. Across GSCs, we identified 13,421 alternative splicing (AS) events, 3,077 of which contained TEs within 150 bp of splice junctions. AS sites proximal to TEs were associated with increased isoform switching compared to non-TE-associated AS sites (odds ratio 2.9 - 4.3). Moreover, AS isoforms generated from TE-proximal sites were more likely to exhibit altered ribosomal association (odds ratio 2.54). Directional shifts were observed, with shorter isoforms associating with monosome fractions and longer isoforms with polysome fractions. To enable systematic detection of gene - TE chimeric transcripts, we developed FuTER (Fusion TE Reporter), a long-read-based framework for identifying TE-associated fusions. Application to GSC datasets identified 78 GSC enriched fusion transcripts, several supported by breakpoint-spanning reads in polysome fractions, consistent with ribosome association. ConclusionsOur data suggest that TEs correlate with abnormal splicing activity and altered ribosome engagement in glioblastoma stem cells. By integrating long-read sequencing with polysome profiling and fusion detection, we establish a framework for analysis of TE-induced transcript diversity and its effects on cancer evolution and plasticity.
Wang, V.; Deng, S.; Aguilar, R.
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BackgroundThe retired antigen hypothesis, introduced by Tuohy and colleagues, proposes that tissue-specific proteins expressed conditionally during early life or reproductive stages, then silenced in normal aging tissue, represent safe and effective cancer vaccine targets when re-expressed in tumors. To date, discovery of retired antigens has relied entirely on hypothesis-driven wet lab work, limiting throughput. MethodsHere we present RADAR (Retired Antigen Discovery and Ranking), a multi-omics computational pipeline implemented on a standard server that systematically identifies retired antigen candidates. RADAR comprises four core discovery layers integrating: 1) The Genotype-Tissue Expression Portal (GTEx) normal tissue expression, 2) TCGA tumor re-expression, 3) DNA methylation, and 4) miRNA regulatory networks, each applied sequentially to identify genes exhibiting the epigenetic and post-transcriptional hallmarks of tissue-specific retirement followed by tumor re-activation. Candidate characterization is further supported by three automated modules: 1) protein-level safety screening via the Human Protein Atlas, 2) molecular subtype enrichment analysis, and 3) cross-cancer confirmation, which execute automatically when the relevant data are available for the selected cancer type. ResultsThe pipeline independently validated known targets including alpha-lactalbumin (LALBA, the basis of the Tuohy Phase 1 triple-negative breast cancer vaccine trial) and anti-Mullerian hormone (AMH), consistent with Tuohys ovarian cancer vaccine program targeting AMHR2, and rediscovered multiple known cancer-testis antigens (MAGEA1, MAGEC1, SSX1) as positive controls. Among 4,664 initial candidates derived from GTEx, the pipeline identified 20 high-confidence retired antigen candidates passing all filters. DCAF4L2, COX7B2, TEX19, and CT83 emerge as the highest-priority novel candidates for experimental validation, demonstrating zero expression in critical somatic organs, strong epigenetic silencing, and significant re-expression across multiple cancer types. ConclusionRADAR provides the first systematic computational framework for retired antigen discovery, offering a reproducible and scalable approach to expanding the cancer immunoprevention pipeline beyond individually characterized targets. The pipeline is fully reproducible, requires no specialized hardware, and is immediately extensible to additional TCGA cancer types.
Armstrong, M.; Williams, H.; Fernandez Faith, E.; Ni, A.; Xiang, H.
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BackgroundLasers have wide applications in medicine and dermatology, but are associated with pain and anxiety, particularly in younger patients. Pain mitigation is often limited to topical anesthetics in the outpatient setting. Distraction techniques are limited by the need for ocular protection, which can include adhesive eye patches that can completely occlude vision. Virtual reality is effective at managing procedural pain and anxiety under other short medical procedures and is a promising tool for this population. ObjectiveThis trial aims to assess the safety, feasibility, and efficacy of Virtual Reality Pain Alleviation Therapeutic (VR-PAT) for pain management during outpatient laser procedures. Methods40 patients requiring outpatient laser therapy for at least two sessions will be recruited from a pediatric hospital in the midwestern United States for this crossover randomized, two-arm clinical trial with a 1:1 allocation ratio. During the first laser visit, the participant will be randomly assigned to either play the VR-PAT game during their procedure or wear the headset with a dark screen. Participants will answer questions about their pain (Numeric Rating Scale (NRS) 0-10), anxiety (State Trait Anxiety Inventory for Children, NRS 0-10, Modified Yale Preoperative Anxiety Scale (mYPAS)), and pain medication usage. Those playing the VR-PAT will additionally report simulator sickness symptoms and their experience playing the game. At their second laser visit, participants will crossover to the opposite intervention from their first visit. The primary outcomes are the difference in self-reported pain and anxiety between the two interventions. Feasibility outcomes include the proportion of screened patients who are eligible, consent, and complete both visits and adverse events reported. To evaluate the efficacy of pain reduction, composite scores of pain score, pain medication will be calculated for each laser visit. To evaluate the efficacy of anxiety reduction, the change of mYPAS scores will be compared between control and VR groups at each visit using Wilcoxon rank sum tests. All statistical analyses will follow the intention-to-treat principle in regard to intervention assignment at each visit. ResultsThe study was funded in January 2023 and began enrollment at that time. A total of n=44 participants were recruited and data collection was completed in November 2025, with n=40 subjects completing both visits. The sample was balanced with n=40 subjects using the intervention and participating in the control condition. The age range of the complete sample was 6 to 21 years at recruitment and was 55% female sex. Data analysis is in progress with final results planned for June 2026. ConclusionsFindings from this innovative randomized clinical trial will provide early evidence on the efficacy of the VR-PAT for reducing self-reported pain and anxiety during outpatient laser procedures. The results from this trial will inform a large-scale, multisite study. Trial RegistrationClinicalTrials.gov: NCT05645224 [https://clinicaltrials.gov/study/NCT05645224]
Dehghani, A.; Gantz, D. M.; Murphy, E. K.; Halter, R. J.; Wager, T. D.
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Background: Transcranial temporal interference stimulation (tTIS) is an emerging noninvasive neuromodulation approach that enables focal, frequency-specific modulation of deep brain regions, offering a novel method for investigating therapeutic mechanisms underlying brain and mental health disorders. Pain is a key target because it is a feature of multiple disorders and is increasingly understood to depend on brain circuits. Here, we tested the effects of tTIS on bilateral evoked pain, capitalizing on converging evidence from human and animal studies indicating that the primary motor cortex (M1) contains body-wide inter-effector regions and has descending projections to regions implicated in nociceptive, motivational, and autonomic processing, making it a key cortical target for pain modulation. Methods: We conducted a pre-registered, triple-blind, randomized crossover study (N = 32, 160 study sessions), investigating frequency-dependent effects of tTIS applied to the left M1 on experimentally evoked thermal pain in healthy adults. We tested four stimulation frequencies (10 Hz, 20 Hz, 70 Hz, and sham) on separate days (>10,000 pain trials total). Noxious heat was applied to both the right and left forearms using individually calibrated temperatures both pre- and post-stimulation. Results: Active tTIS produced significant analgesia at all stimulation frequencies (10 Hz, 20 Hz, and 70 Hz) relative to sham (Cohens d = 0.46-0.82, all p < 0.05). 10 Hz produced the greatest reduction (d = 0.82), and both 10 Hz and 20 Hz produced more analgesia than 70 Hz (d = 0.44 and 0.38, respectively; p < 0.05). Stimulation-related sensations were equivalent across frequencies, and participants were blind to condition. Pain reductions remained stable over a [~]40-min post-stimulation period and were bilateral, consistent with stimulation of body-wide inter-effector regions. Conclusions: These results provide the first evidence that tTIS can reliably reduce experimental pain perception in humans in a frequency-dependent manner, providing a foundation for noninvasive pain modulation with tTIS.
Yang, D.; Li, G.; Song, J.; Shi, X.; Xu, X.; Ma, J.; Guo, C.; Liu, C.; Yang, J.; Li, F.; Zhu, Y.; Zi, W.; Ding, Q.; Chen, Y.
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Abstract Background: Acute ischemic stroke (AIS) remains a significant cause of disability worldwide. Current treatments, primarily intravenous thrombolysis (IVT), are limited by narrow time windows and reperfusion injury, leading to suboptimal outcomes for many patients. Chuanzhi Tongluo (CZTL), a traditional Chinese medicine, has been preliminarily recognized as a novel cerebral protection agent in animal models. Objectives: This trial investigates the efficacy and safety of CZTL capsule in patients with AIS who are not eligible for IVT or who experience early neurological deterioration after IVT. Methods and design: The CONCERN trial is an investigator-initiated, prospective, multicenter, double-blind, parallel-control, randomized clinical study in China. An estimated 1,208 eligible participants will be consecutively randomized to receive CZTL capsule therapy or placebo in 1:1 ratio across approximately 70 stroke centers in China. All enrolled patients are orally administered 2 capsules of CZTL or placebo 3 times a day together with antiplatelet agents for 3 months. Outcomes: The primary endpoint is an excellent functional outcome, defined as a score of 0 or 1 on the mRS at 90 days. Lead safety endpoints included 90-day mortality and symptomatic intracranial hemorrhage within 48 hours. Conclusions: Results of CONCERN trial will determine the clinical efficacy and safety of the traditional Chinese medicine CZTL capsule in the treatment of AIS patients. Trial registry number: ChiCTR2300074147 (www.chictr.org.cn).
Adegbosin, O. T.; Patel, H.
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BackgroundMicrosatellite stability status determination is important for prognostication and therapeutic decision making in colorectal cancer management, but the conventional methods for this assessment are not readily available, especially in low- and middle-income countries. Deep learning (DL) models have been proposed for addressing this problem; however, potential computational cost due to model complexity and inadequate explainability may limit their adoption in low-resource settings. This study explored the potential of explainable lightweight models for detection of microsatellite instability in colorectal cancer. MethodsDL models were trained using a public dataset of colorectal cancer histology images and then used to classify a set of test images into one of two classes: microsatellite instability or microsatellite stability. The models were compared for efficiency. Gradient-weighted class activation mapping (Grad-CAM) was used to interpret the models decision making. ResultsThe simpler convolutional neural network (CNN) trained from scratch had modest performance (accuracy=0.757, area under receiver-operating characteristic curve [AUROC]=0.840). With an attention mechanism added, these values increased, but specificity and sensitivity reduced. Pretrained models performed better than the ones trained from scratch, and EfficientNet_B0 had the best balance of high performance and low computational requirements (accuracy=0.936, AUROC=0.990, negative predictive value=0.923, specificity=0.953, 4,010,000 trainable parameters, 0.38 gigaFLOPs). However, a simple CNN model with attention mechanism had the best interpretability based on Grad-CAM. ConclusionThis study demonstrated that DL models that are lightweight when compared to previously proposed ones can be useful for colorectal cancer microsatellite instability screening in resource-limited settings while balancing performance and computational efficiency.
Wang, P.; Song, Y.; Zhang, B.; Yang, J.
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Abstract Background: Hypertrophic (HCM) and dilated (DCM) cardiomyopathy constitute the principal phenotypes of primary cardiomyopathy, yet both lack sufficient therapeutic options. Integrating genetic insights with detailed cardiac phenotyping offers a promising strategy to prioritize targets and elucidate their mechanisms of action. Methods: We conducted an three-stage analysis. First, drug-target Mendelian randomization (MR) was performed using cis-acting protein (pQTL) and expression (eQTL) quantitative trait loci as genetic instruments for potential drug targets. Second, we examined causal associations between 82 cardiac magnetic resonance (CMR)-derived imaging traits and HCM/DCM risk in a CMR-based MR analysis. Third, mediation MR was employed to quantify the proportion of the genetic effect of prioritized drug targets on cardiomyopathy risk that was mediated through specific CMR phenotypes. Results: Our analyses identified 19 and 13 potential therapeutic targets for HCM and DCM, respectively. CMR-based MR revealed that HCM risk was causally associated with increased right ventricular ejection fraction (RVEF) and greater left ventricular wall thickness, whereas DCM risk was linked to ventricular dilation, impaired myocardial strain, and altered aortic dimensions. Critically, mediation analysis established that these CMR traits served as significant intermediate pathways. The protective effect of ALPK3 on HCM risk was mediated through a reduction in myocardial wall thickness. Conversely, the effects of PDLIM5, HSPA4, and FBXO32 on DCM risk were exerted in part via alterations in aortic dimensions. Conclusion: This integrative genetic and imaging study systematically identify candidate therapeutic targets for HCM and DCM and delineates the specific CMR phenotypes through which they likely exert their causal effects. Our findings advance the understanding of disease pathogenesis and highlight new possibilities for improving the diagnosis and management of cardiomyopathy.