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A statistical physics approach to integrating multi-omics data for disease-module detection

Cell Rep Methods. 2025 Sep 19:101183. doi: 10.1016/j.crmeth.2025.101183. Online ahead of print.

ABSTRACT

Genes associated with the same disease frequently engage in mutual biological interactions, e.g., perturbation within a specific neighborhood in the molecular interactome, often referred to as the disease module. This has propelled the advancement of network-based approaches toward elucidating the molecular bases of human diseases. Although many computational methods have been developed to integrate the molecular interactome and omics profiles to extract such context-dependent disease modules, approaches that leverage multi-omics for disease-module detection are still lacking. Here, we developed a statistical physics approach based on the random-field O(n) model (RFOnM) to fill this gap. We applied the RFOnM approach to integrate gene-expression data and genome-wide association studies or mRNA data and DNA methylation for several complex diseases with the human interactome. We found that the RFOnM approach outperforms existing single omics methods in most of the complex diseases considered in this study.

PMID:40975055 | DOI:10.1016/j.crmeth.2025.101183

Implementation of a Virtual Hospital in the Home Service for Patients With COVID-19 in Queensland, Australia: Mixed Methods Evaluation Using the RE-AIM Framework

Background: Hospital in the home (HITH) provides home-based care as an alternative to traditional hospitalization. In response to the COVID-19 Omicron wave, a public hospital in the rural Western portion of Southeast Queensland implemented a virtual HITH service to support adults, maternity patients, and children with moderate COVID-19 symptoms and additional health concerns. Although the pandemic accelerated the uptake of virtual care within HITH models, existing literature has focused on clinical outcomes, with limited evidence on key implementation outcomes. Objective: Using the RE-AIM (reach, effectiveness, adoption, implementation, and maintenance) framework, this study evaluated the implementation of the virtual COVID-19 HITH service and identified factors influencing its implementation, to inform ongoing service development and support potential scaling of this model of care. Methods: The RE-AIM implementation science framework was selected to guide the evaluation, capturing both clinical and contextual dimensions of implementation at both individual and organizational levels. Quantitative data on service usage and costs were retrospectively extracted from electronic medical records and finance records, while patient experience data were drawn from patient-reported experience measures surveys. Qualitative data were collected through one-on-one interviews with patients and staff. All data sources were analyzed separately and then triangulated within the RE-AIM framework to understand what occurred, how, and why. Results: The service admitted 3192 patients, most of whom were female (2027/3192, 63.5%), English-speaking (3140/3192, 98.4%), and residing in socioeconomically disadvantaged areas (1879/3192, 58.9%) (reach). The model was feasible and safe to implement, managing 3240 admissions with no reported deaths. Patients valued continuous access to care and described better recovery experiences at home (effectiveness). Staff viewed the model as appropriate for identifying and managing high-risk patients in the community, easing pressure on hospital beds (adoption). The service cost Aus $ 5.4 million (US $3.5 million) over 11 months. Implementation barriers included the urgency of the pandemic scenario, limited infrastructure and human resources, and changing requirements in relation to COVID-19. These were mitigated by several people factors that were critical to its successful implementation, including a consultant-led structure, staff commitment, and adaptability (implementation). The service saved 16,651 inpatient bed days before being integrated into core HITH operations. The experience strengthened staff capabilities in emergency response, virtual care delivery, and strategic planning. The model shows promise for broader application into pediatric care, though further work is needed to enhance interdepartmental collaboration and staff recognition (maintenance). Conclusions: This study demonstrated that a virtual HITH model can be implemented effectively and safely at scale. Findings support its potential for integration into routine care, provided that adequate resource planning, a skilled and multidisciplinary workforce, well-defined care pathways, and equity-focused strategies are in place.
  • ✇36氪
  • 交通运输部印发《交通运输行业高质量数据集建设方案》
    36氪获悉,近日,交通运输部印发了《交通运输行业高质量数据集建设方案》(以下简称《建设方案》),系统部署交通运输行业高质量数据集建设任务。《建设方案》以数据为中心,应用为牵引,遵循急用先行、系统推进的原则,优先解决行业人工智能应用最迫切的场景,着力提高数据集供给数量和质量,完善行业高质量数据集服务体系,健全行业高质量数据集标准规范,营造行业高质量数据集建设生态,加快构建行业高质量数据集供给体系,培育壮大交通运输新质生产力,支撑打造智能综合立体交通网。到2030年底,建成一批服务于不同应用场景的高质量数据集,形成一批高质量数据集驱动交通运输行业模型应用的典型案例,基本满足世界领先模型的训练需求。
     

交通运输部印发《交通运输行业高质量数据集建设方案》

19 September 2025 at 15:46
36氪获悉,近日,交通运输部印发了《交通运输行业高质量数据集建设方案》(以下简称《建设方案》),系统部署交通运输行业高质量数据集建设任务。《建设方案》以数据为中心,应用为牵引,遵循急用先行、系统推进的原则,优先解决行业人工智能应用最迫切的场景,着力提高数据集供给数量和质量,完善行业高质量数据集服务体系,健全行业高质量数据集标准规范,营造行业高质量数据集建设生态,加快构建行业高质量数据集供给体系,培育壮大交通运输新质生产力,支撑打造智能综合立体交通网。到2030年底,建成一批服务于不同应用场景的高质量数据集,形成一批高质量数据集驱动交通运输行业模型应用的典型案例,基本满足世界领先模型的训练需求。
  • ✇STAT
  • STAT+: Fresh data on hospital AI use & Califf dishes on tech Mario Aguilar
    You’re reading the web edition of STAT’s Health Tech newsletter, our guide to how technology is transforming the life sciences. Sign up to get it delivered in your inbox every Tuesday and Thursday. Califf warns AI in health care ‘overhyped’ On a makeshift stage in a Midtown Manhattan office earlier this week,former Food and Drug Administration Commissioner Robert Califf struck a measured tone about the potential for artificial intelligence in health care. Asked whether the technology was o
     

STAT+: Fresh data on hospital AI use & Califf dishes on tech

18 September 2025 at 22:18

You’re reading the web edition of STAT’s Health Tech newsletter, our guide to how technology is transforming the life sciences. Sign up to get it delivered in your inbox every Tuesday and Thursday.

Califf warns AI in health care ‘overhyped’

On a makeshift stage in a Midtown Manhattan office earlier this week,former Food and Drug Administration Commissioner Robert Califf struck a measured tone about the potential for artificial intelligence in health care. Asked whether the technology was overhyped he said it was. “I hear way too much about the money. I’m not hearing a lot of human values coming through discussions,” he said. Adding:

“Almost all of the technology is being applied to optimizing the financial status of healthcare delivery entities or companies that are making medical products and that’s not aligned with equitable, better patient outcomes. So until someone puts a soul back in the system, I think it’s going to get worse and worse.”

Continue to STAT+ to read the full story…

© Adobe

Opinion: Four reasons why generative AI chatbots could lead to psychosis in vulnerable people

18 September 2025 at 16:30

Three scholars discovered a strange mirror deep in the forest. It spoke to them in a soothing voice and answered all their questions warmly, knowledgeably, and eloquently.

The captivated scholars became obsessed, whispering one secret after another to the mirror. It replied with affection, promise, and meaning that kept them returning to it. They began ignoring one another, each convinced the mirror “understood” them best.

Read the rest…

© Adobe

From frameworks to finance: how sharing benefits from the use of digital sequence information can evolve to contribute to biodiversity conservation

Nature Biotechnology, Published online: 18 September 2025; doi:10.1038/s41587-025-02820-8

The COP16 decision established a multilateral mechanism for digital sequence information (DSI) benefit-sharing. This Comment brings together insights from academia and commercial DSI researchers to assess what has been accomplished so far, identify remaining challenges and describe elements under discussion to support collective goals.

Diagnostic Performance of Computed Tomography–Based Artificial Intelligence for Early Recurrence of Cholangiocarcinoma: Systematic Review and Meta-Analysis

Background: Despite artificial intelligence (AI) models demonstrating high predictive accuracy for early cholangiocarcinoma recurrence, their clinical application faces challenges, such as reproducibility, generalizability, hidden biases, and uncertain performance across diverse datasets and populations, raising concerns about their practical applicability. Objective: This meta-analysis aims to systematically assess the diagnostic performance of AI models using computed tomography (CT) imaging to predict early recurrence of cholangiocarcinoma. Methods: A systematic search was conducted in PubMed, Embase, and Web of Science for studies published up to May 2025. Studies were selected based on the Participants, Index test, Target condition, Reference standard, Outcomes, and Setting (PITROS) framework. Participants included patients diagnosed with cholangiocarcinoma (including intrahepatic and extrahepatic locations). The index test was AI techniques applied to CT imaging for early recurrence prediction (defined as within 1 year), while the target condition was early recurrence of cholangiocarcinoma (positive group: recurrence; negative group: no recurrence). The reference standard was pathological diagnosis or imaging follow-up confirming recurrence. Outcomes included sensitivity, specificity, diagnostic odds ratio (DOR), and area under the receiver operating characteristic curve (AUC), assessed in both internal and external validation cohorts. The setting comprised retrospective or prospective studies using hospital datasets. Methodological quality was assessed using an optimized version of the revised Quality Assessment of Diagnostic Accuracy Studies-2 tool. Heterogeneity was assessed using the I² statistic. Pooled sensitivity, specificity, DOR, and AUC were calculated using a bivariate random-effects model. Results: A total of 9 studies with 30 datasets involving 1537 patients were included. In internal validation cohorts, CT-based AI models showed a pooled sensitivity of 0.87 (95% CI 0.81-0.92), specificity of 0.85 (95% CI 0.79-0.89), DOR of 37.71 (95% CI 18.35-77.51), and AUC of 0.93 (95% CI 0.90-0.94). In external validation cohorts, pooled sensitivity was 0.87 (95% CI 0.81-0.91), specificity was 0.82 (95% CI 0.77-0.86), DOR was 30.81 (95% CI 18.79-50.52), and AUC was 0.85 (95% CI 0.82-0.88). The AUC was significantly lower in external validation cohorts compared to internal validation cohorts (P<.001). Conclusions: Our results show that CT-based AI models predict early cholangiocarcinoma recurrence with high performance in internal validation sets and moderate performance in external validation sets. However, the high heterogeneity observed may impact the robustness of these results. Future research should focus on prospective studies and establishing standardized gold standards to further validate the clinical applicability and generalizability of AI models.

Large Language Models’ Clinical Decision-Making on When to Perform a Kidney Biopsy: Comparative Study

Background: Artificial intelligence (AI) and Large Language models (LLMs) are increasing in sophistication and are being integrated into many disciplines. The potential for LLMs to augment clinical decisions is an evolving area of research. Objective: This study compared the responses of over 1000 kidney specialist physicians (nephrologists) to outputs of commonly used LLMs using a questionnaire determining when a kidney biopsy should be performed. Methods: This research group completed a large online questionnaire for nephrologists to determine when a kidney biopsy should be performed. The questionnaire was co-designed with patient participation, refined through multiple iterations, then piloted locally before international dissemination. It was the largest international study in the field and demonstrated variation between human clinicians in biopsy propensity relating to human factors such as sex and age, as well as systemic factors such as country, job seniority and technical proficiency. The same questions were put to both human doctors and LLMs in an identical order in a single session. Eight commonly used LLMs were interrogated: Chat GPT 3.5, Mistral Hugging Face, Perplexity, Microsoft Co-pilot, Llama 2, GPT 4.0, MedLM and Claude 3. The most common response given by clinicians (human mode) to each question was taken as the baseline for comparison. Questionnaire responses to the indications and contraindications for biopsy generated a score (0-44) reflecting biopsy propensity, in which a higher score was used as a surrogate marker for an increased tolerance of potential associated risks. Results: The ability of LLMs to reproduce human expert consensus varied widely with some models demonstrating a balanced approach to risk in a similar manner to humans, whilst other models reported outputs at either end of the spectrum for risk tolerance. In terms of agreement with the human mode, Chat GPT 3.5 and GPT 4.0 (Open AI) had the highest levels of alignment, with the human mode selected in 6/11 questions. The total biopsy propensity score generated from the human mode was 23/44. Both Open AI models produced similar propensity scores between 22 and 24, however Llama 2 and MS Co-pilot also reported scores within this range, but with poorer response alignment to the human mode at only 2/11 questions. The most risk averse model in this study was MedLM with a propensity score of 11 and the least risk averse model was Claude 3 with a score of 34. Conclusions: LLM outputs demonstrated a modest ability to replicate human clinical decision making in this study, however the performance varied widely between LLM models. Questions with more uniform human responses produced LLM outputs with greater alignment, whereas in questions with low levels of human consensus there was poor output alignment. This may limit the practical use of LLMs in real world clinical practice.

Navigating the Boundaries of Teleconsultation—Capabilities, Limitations, and Pathways for Improvement: Qualitative Study of the Experiences of Patients With Stroke

Background: Survivors of stroke often face persistent challenges accessing postdischarge care due to mobility limitations, transportation burdens, and inflexible scheduling. Teleconsultation has emerged as a potential solution to improve continuity of care, but its perceived strengths and limitations from the patient perspective remain insufficiently understood. Objective: This study aimed to explore the experiences of survivors of stroke with a nurse-led teleconsultation program to (1) identify perceived capabilities; (2) understand limitations in usability, accessibility, and clinical function; and (3) generate patient-informed recommendations for improvement. Methods: A qualitative study was embedded within a 3-month nurse-led teleconsultation intervention delivered by advanced practice nurses. A total of 21 survivors of ischemic stroke (aged 45-76 y; female: n=11, 52%) who had preserved cognitive function (Montreal Cognitive Assessment score ≥22) and smartphone access participated in 6 focus groups conducted via Zoom. Data were analyzed thematically using an established framework. Data saturation was achieved. Results: Participants widely valued teleconsultation for reducing logistical burdens; enhancing access; and offering a more comfortable, emotionally supportive setting for follow-up care. Many reported increased awareness and motivation for self-monitoring. However, limitations included an inability to perform physical assessments or respond to emergencies; digital and usability barriers, especially among older users; and scheduling inflexibility. Participants emphasized the need for patient-initiated follow-up mechanisms, physician collaboration for medication management, and greater support for users considered digitally marginalized. They also highlighted the potential of teleconsultation to serve as a triage tool, reserving in-person care for complex cases. Conclusions: Nurse-led teleconsultation was perceived as a convenient and supportive modality for poststroke care, particularly for stable follow-ups and psychosocial support. However, its long-term viability depends on addressing clinical and technical limitations, enhancing user autonomy, and integrating interdisciplinary input. By centering the lived experiences of survivors of stroke, this study offers concrete recommendations to guide the development of more inclusive, responsive, and patient-centered teleconsultation models.

Developing an Evaluation System for Quality of Health Educational Short Videos on Social Media (LassVQ) Using Nominal Group Technique and Analytic Hierarchy Process: Qualitative Study

Background: With the increasing use of social media platforms for health communication, the quality of health educational short videos (HESVs) has become a key concern. However, no standardized framework exists to evaluate the quality of health videos on social media, highlighting the need for a comprehensive evaluation system. Objective: The aim of this study is to develop a valid and structured evaluation tool for assessing the quality of HESVs on social media. Methods: The initial evaluation indicators obtained from the literature review and brainstorming undertaken in the study group were provided to the nominal group reference Lasswell’s 5W communication model, and two rounds of nominal group technique (NGT) were carried out to screen, add, revise, and adjust indicators, and reach a consensus of evaluation system. The indicators were then ranked based on their significance, as scored by the experts using the analytic hierarchy process. The content validity was assessed by experts who rated the relevance of each indicator on a 4-point Likert scale. Results: The primary indicators include communicator, communication content, communication channel, and communication effect, along with 13 secondary indicators and 34 tertiary indicators. 11 experts were enrolled in the NGT, 45% of experts had a doctoral degree, 80% of them were ranked associate professor or professor. The average familiarity coefficient of each key indicator of the NGT was 0.85. The average values of the expert judgment coefficient and authority coefficient were 0.93 and 0.85, respectively. In Round 1 of NGT, the “Communication target” of 5 primary indicators, 7 of 20 secondary indicators, and 66 of 94 tertiary indicators did not reach a consensus, and therefore, they were not deleted and will proceed to the next round of NGT. In Round 2 NGT, 1 primary indicator, 7 secondary indicators, and 59 tertiary indicators were deleted based on the consensus criteria. After the two rounds of NGT, 4 primary indicators, 13 secondary indicators, and 34 tertiary indicators finally reached a consensus. Among primary indicators, communication content was found to be the most influential, accounting for 45.68%. Among secondary indicators, credibility, scientificity, availability, and social attention were the most influential indicators, with priorities of 56.67%, 24.26%, 74.62%, and 39.89% in their respective categories. Among tertiary indicators, ‘Become a hot search recommended by the platform’ was the most influential indicator with a weight of 0.07. The content validity of all the evaluation indicators were 0.73 – 1.0, and the scale-level content validity index (average) was 0.87, which was indicated as acceptable. Conclusions: The evaluation system for the quality of HESVs on social media (LassVQ) was developed, and its validity was acceptable. The proposed evaluation system can be used in conjunction with qualitative methods to gain a holistic perspective on the multidimensional quality of HESVs on social media.
  • ✇Cell
  • Multi-adjuvant personalized neoantigen vaccines: Fine-tuning anti-cancer T cells Hejia Henry Wang · Neeha Zaidi
    Personalized cancer vaccines aim to broaden the anti-tumor T cell repertoire by targeting neoantigens unique to each patient’s tumor, but immunogenicity has been inconsistent. In this issue of Cell, Blass, Keskin, Tu et al. evaluate NeoVaxMI, a multi-adjuvant personalized synthetic long-peptide vaccine administered with nivolumab in patients with melanoma. NeoVaxMI elicited stronger CD4+ and CD8+ responses than earlier iterations, and vaccine-induced T cells trafficked to regressing metastatic l
     

Multi-adjuvant personalized neoantigen vaccines: Fine-tuning anti-cancer T cells

18 September 2025 at 08:00
Personalized cancer vaccines aim to broaden the anti-tumor T cell repertoire by targeting neoantigens unique to each patient’s tumor, but immunogenicity has been inconsistent. In this issue of Cell, Blass, Keskin, Tu et al. evaluate NeoVaxMI, a multi-adjuvant personalized synthetic long-peptide vaccine administered with nivolumab in patients with melanoma. NeoVaxMI elicited stronger CD4+ and CD8+ responses than earlier iterations, and vaccine-induced T cells trafficked to regressing metastatic lesions.
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