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“I Want to Spend My Time Living”—Experiences With a Digital Outpatient Service With a Mobile App for Tailored Care Among Adults With Long-Term Health Service Needs: Qualitative Study Using Thematic Analysis

✇Journal of Medical Internet Research
By: Heidi Holmen · Erik Fosse
16 January 2026 at 05:30
Background: Digital health services are increasingly used in hospital-based outpatient care, offering remote monitoring, patient-reported outcomes, information sharing, and asynchronous communication. While expected to improve self-management, timeliness, and efficiency, the success of digital health interventions relies on patients’ health literacy and digital health literacy. While some research has addressed potential associations between digital health interventions and patients’ health outcomes, research on patients’ experiences remains limited. Objective: The aim of this study was to explore and gain in-depth knowledge about the experiences of patients with chronic or long-term conditions enrolled in a 6-month digital outpatient care intervention for tailored care and health literacy. Methods: We conducted an exploratory qualitative interview study with 17 strategically recruited adult patients with cancer, interstitial lung disease, epilepsy, or complicated pain who used a digital outpatient service for 6 months. Individual telephone interviews were conducted using a semistructured guide, transcribed verbatim, and analyzed with thematic analysis to generate codes and themes. Participants had a median age of 62 years (minimum-maximum 36-83 years), with 8 females and 9 males. Results: The thematic analysis led to 1 main theme “Digital outpatient care as a flexible service supporting patients’ self-management,” informed by 3 subthemes “The ongoing nature of managing a chronic condition and how the digital service meet the patients’ desire for autonomy in their care,” “Digital tools flexibly address the patients’ unique needs, but reliability depends on patient interaction,” and “Digital services enhance the patients’ sense of safety through easy access to a relation with competent healthcare workers.” The themes highlight patients’ appreciation for greater flexibility in their care and their desire to self-manage with the support of easily accessible health care workers, ultimately supporting their health literacy. Patients recognized the importance of actively engaging with the digital solution to fully benefit from its opportunities and emphasized the critical role of health care workers in fostering their sense of security. Conclusions: Digital outpatient care was experienced as flexible and supportive for patients with long-term conditions. The increased possibility of interacting with health care workers was welcomed by the patients, and the combination of flexibility, self-monitoring, and addressing concerns regarding their self-management may increase the patients experience of autonomy. As health literacy likely plays a role in patients’ ability to effectively engage with digital tools and self-manage their conditions, future research should explore how varying levels of health literacy influence these outcomes. In addition, research should address whether such digital outpatient clinics are positive for a wider range of patients, associated health outcomes, and any positive effects on a health system level. Trial Registration: ClinicalTrials.gov NCT05068869; https://clinicaltrials.gov/ct2/show/NCT05068869
  • ✇MIT Technology Review
  • Exclusive eBook: How AGI Became a Consequential Conspiracy Theory MIT Technology Review
    In this exclusive subscriber-only eBook, you’ll learn about how the idea that machines will be as smart as—or smarter than—humans has hijacked an entire industry.by Will Douglas Heaven October 30, 2025 ACCESS EBOOK Table of Contents: How Silicon Valley got AGI-pilled The great AGI conspiracy How AGI hijacked an industry The great AGI conspiracy, concluded Related Stories: How AGI became the most consequential conspiracy theory of our time The New Conspiracy Age
     
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Exclusive eBook: How AGI Became a Consequential Conspiracy Theory

✇MIT Technology Review
By: MIT Technology Review
16 January 2026 at 01:16

In this exclusive subscriber-only eBook, you’ll learn about how the idea that machines will be as smart as—or smarter than—humans has hijacked an entire industry.

by Will Douglas Heaven October 30, 2025

Table of Contents:

  • How Silicon Valley got AGI-pilled
  • The great AGI conspiracy
  • How AGI hijacked an industry
  • The great AGI conspiracy, concluded

Related Stories:

Access all subscriber-only eBooks:

Molecular features of early- vs. late-onset gastric cancer: a systematic review and meta-analysis

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Xinmei Lin · Wenhan Shi · Zitong Zhou · Degang Li · Qiuyuan Yao · Yu Sun
15 January 2026 at 19:00

BMC Cancer. 2026 Jan 14. doi: 10.1186/s12885-026-15567-5. Online ahead of print.

ABSTRACT

BACKGROUND: Early-onset gastric cancer (EOGC), diagnosed before age 50, is characterized by distinct clinicopathological features, though its molecular landscape remains poorly defined.

METHODS: A systematic literature search of PubMed, Embase, and Web of Science identified studies comparing molecular characteristics of EOGC and late-onset gastric cancer (LOGC). Meta-analyses assessed differences in The Cancer Genome Atlas (TCGA) molecular subtypes, gene mutations, therapeutic biomarkers, and serum tumor markers. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated; heterogeneity was assessed using the I2 statistic.

RESULTS: EOGC was associated with a higher prevalence of the genomically stable (GS) subtype (OR = 1.71, 95% CI: 1.37-2.12) and a lower prevalence of the chromosomal instability (CIN) subtype (OR = 0.62, 95% CI: 0.50-0.77). CDH1 mutations were more frequent in EOGC (OR = 3.44, 95% CI: 2.85-4.16), while HER2 expression (OR = 0.54, 95% CI: 0.43-0.67), dMMR/MSI-H status (OR = 0.25, 95% CI: 0.12-0.53), and p53 expression (OR = 0.56, 95% CI: 0.39-0.82) were significantly lower. Serum markers including CEA and CA19-9 were also less frequently elevated in EOGC.

CONCLUSION: EOGC represents a biologically distinct subset of gastric cancer with unique genomic and immunological features. These findings support age-specific diagnostic approaches and emphasize the value of multiomic strategies to uncover the mechanisms driving early-onset disease.

PMID:41535782 | DOI:10.1186/s12885-026-15567-5

ART: Action-based Reasoning Task Benchmarking for Medical AI Agents

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ananya Mantravadi · Shivali Dalmia · Abhishek Mukherji
15 January 2026 at 13:00
arXiv:2601.08988v1 Announce Type: new Abstract: Reliable clinical decision support requires medical AI agents capable of safe, multi-step reasoning over structured electronic health records (EHRs). While large language models (LLMs) show promise in healthcare, existing benchmarks inadequately assess performance on action-based tasks involving threshold evaluation, temporal aggregation, and conditional logic. We introduce ART, an Action-based Reasoning clinical Task benchmark for medical AI agents, which mines real-world EHR data to create challenging tasks targeting known reasoning weaknesses. Through analysis of existing benchmarks, we identify three dominant error categories: retrieval failures, aggregation errors, and conditional logic misjudgments. Our four-stage pipeline -- scenario identification, task generation, quality audit, and evaluation -- produces diverse, clinically validated tasks grounded in real patient data. Evaluating GPT-4o-mini and Claude 3.5 Sonnet on 600 tasks shows near-perfect retrieval after prompt refinement, but substantial gaps in aggregation (28--64%) and threshold reasoning (32--38%). By exposing failure modes in action-oriented EHR reasoning, ART advances toward more reliable clinical agents, an essential step for AI systems that reduce cognitive load and administrative burden, supporting workforce capacity in high-demand care settings

Human-AI Co-design for Clinical Prediction Models

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jean Feng · Avni Kothari · Patrick Vossler · Andrew Bishara · Lucas Zier · Newton Addo · Aaron Kornblith · Yan Shuo Tan · Chandan Singh
15 January 2026 at 13:00
arXiv:2601.09072v1 Announce Type: new Abstract: Developing safe, effective, and practically useful clinical prediction models (CPMs) traditionally requires iterative collaboration between clinical experts, data scientists, and informaticists. This process refines the often small but critical details of the model building process, such as which features/patients to include and how clinical categories should be defined. However, this traditional collaboration process is extremely time- and resource-intensive, resulting in only a small fraction of CPMs reaching clinical practice. This challenge intensifies when teams attempt to incorporate unstructured clinical notes, which can contain an enormous number of concepts. To address this challenge, we introduce HACHI, an iterative human-in-the-loop framework that uses AI agents to accelerate the development of fully interpretable CPMs by enabling the exploration of concepts in clinical notes. HACHI alternates between (i) an AI agent rapidly exploring and evaluating candidate concepts in clinical notes and (ii) clinical and domain experts providing feedback to improve the CPM learning process. HACHI defines concepts as simple yes-no questions that are used in linear models, allowing the clinical AI team to transparently review, refine, and validate the CPM learned in each round. In two real-world prediction tasks (acute kidney injury and traumatic brain injury), HACHI outperforms existing approaches, surfaces new clinically relevant concepts not included in commonly-used CPMs, and improves model generalizability across clinical sites and time periods. Furthermore, HACHI reveals the critical role of the clinical AI team, such as directing the AI agent to explore concepts that it had not previously considered, adjusting the granularity of concepts it considers, changing the objective function to better align with the clinical objectives, and identifying issues of data bias and leakage.

PrivacyReasoner: Can LLM Emulate a Human-like Privacy Mind?

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yiwen Tu · Xuan Liu · Lianhui Qin · Haojian Jin
15 January 2026 at 13:00
arXiv:2601.09152v1 Announce Type: new Abstract: This paper introduces PRA, an AI-agent design for simulating how individual users form privacy concerns in response to real-world news. Moving beyond population-level sentiment analysis, PRA integrates privacy and cognitive theories to simulate user-specific privacy reasoning grounded in personal comment histories and contextual cues. The agent reconstructs each user's "privacy mind", dynamically activates relevant privacy memory through a contextual filter that emulates bounded rationality, and generates synthetic comments reflecting how that user would likely respond to new privacy scenarios. A complementary LLM-as-a-Judge evaluator, calibrated against an established privacy concern taxonomy, quantifies the faithfulness of generated reasoning. Experiments on real-world Hacker News discussions show that \PRA outperforms baseline agents in privacy concern prediction and captures transferable reasoning patterns across domains including AI, e-commerce, and healthcare.

Companion Agents: A Table-Information Mining Paradigm for Text-to-SQL

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jiahui Chen · Lei Fu · Jian Cui · Yu Lei · Zhenning Dong
15 January 2026 at 13:00
arXiv:2601.08838v1 Announce Type: cross Abstract: Large-scale Text-to-SQL benchmarks such as BIRD typically assume complete and accurate database annotations as well as readily available external knowledge, which fails to reflect common industrial settings where annotations are missing, incomplete, or erroneous. This mismatch substantially limits the real-world applicability of state-of-the-art (SOTA) Text-to-SQL systems. To bridge this gap, we explore a database-centric approach that leverages intrinsic, fine-grained information residing in relational databases to construct missing evidence and improve Text-to-SQL accuracy under annotation-scarce conditions. Our key hypothesis is that when a query requires multi-step reasoning over extensive table information, existing methods often struggle to reliably identify and utilize the truly relevant knowledge. We therefore propose to "cache" query-relevant knowledge on the database side in advance, so that it can be selectively activated at inference time. Based on this idea, we introduce Companion Agents (CA), a new Text-to-SQL paradigm that incorporates a group of agents accompanying database schemas to proactively mine and consolidate hidden inter-table relations, value-domain distributions, statistical regularities, and latent semantic cues before query generation. Experiments on BIRD under the fully missing evidence setting show that CA recovers +4.49 / +4.37 / +14.13 execution accuracy points on RSL-SQL / CHESS / DAIL-SQL, respectively, with larger gains on the Challenging subset +9.65 / +7.58 / +16.71. These improvements stem from CA's automatic database-side mining and evidence construction, suggesting a practical path toward industrial-grade Text-to-SQL deployment without reliance on human-curated evidence.

Triples and Knowledge-Infused Embeddings for Clustering and Classification of Scientific Documents

✇cs.AI, q-bio.NC updates on arXiv.org
By: Mihael Arcan
15 January 2026 at 13:00
arXiv:2601.08841v1 Announce Type: cross Abstract: The increasing volume and complexity of scientific literature demand robust methods for organizing and understanding research documents. In this study, we explore how structured knowledge, specifically, subject-predicate-object triples, can enhance the clustering and classification of scientific papers. We propose a modular pipeline that combines unsupervised clustering and supervised classification over multiple document representations: raw abstracts, extracted triples, and hybrid formats that integrate both. Using a filtered arXiv corpus, we extract relational triples from abstracts and construct four text representations, which we embed using four state-of-the-art transformer models: MiniLM, MPNet, SciBERT, and SPECTER. We evaluate the resulting embeddings with KMeans, GMM, and HDBSCAN for unsupervised clustering, and fine-tune classification models for arXiv subject prediction. Our results show that full abstract text yields the most coherent clusters, but that hybrid representations incorporating triples consistently improve classification performance, reaching up to 92.6% accuracy and 0.925 macro-F1. We also find that lightweight sentence encoders (MiniLM, MPNet) outperform domain-specific models (SciBERT, SPECTER) in clustering, while SciBERT excels in structured-input classification. These findings highlight the complementary benefits of combining unstructured text with structured knowledge, offering new insights into knowledge-infused representations for semantic organization of scientific documents.

AI Deployment Authorisation: A Global Standard for Machine-Readable Governance of High-Risk Artificial Intelligence

✇cs.AI, q-bio.NC updates on arXiv.org
By: Daniel Djan Saparning
15 January 2026 at 13:00
arXiv:2601.08869v1 Announce Type: cross Abstract: Modern artificial intelligence governance lacks a formal, enforceable mechanism for determining whether a given AI system is legally permitted to operate in a specific domain and jurisdiction. Existing tools such as model cards, audits, and benchmark evaluations provide descriptive information about model behavior and training data but do not produce binding deployment decisions with legal or financial force. This paper introduces the AI Deployment Authorisation Score (ADAS), a machine-readable regulatory framework that evaluates AI systems across five legally and economically grounded dimensions: risk, alignment, externality, control, and auditability. ADAS produces a cryptographically verifiable deployment certificate that regulators, insurers, and infrastructure operators can consume as a license to operate, using public-key verification and transparency mechanisms adapted from secure software supply chain and certificate transparency systems. The paper presents the formal specification, decision logic, evidence model, and policy architecture of ADAS and demonstrates how it operationalizes the European Union Artificial Intelligence Act, United States critical infrastructure governance, and insurance underwriting requirements by compiling statutory and regulatory obligations into machine-executable deployment gates. We argue that deployment-level authorization, rather than model-level evaluation, constitutes the missing institutional layer required for safe, lawful, and economically scalable artificial intelligence.

From Symbolic to Natural-Language Relations: Rethinking Knowledge Graph Construction in the Era of Large Language Models

✇cs.AI, q-bio.NC updates on arXiv.org
By: Kanyao Han · Yushang Lai
15 January 2026 at 13:00
arXiv:2601.09069v1 Announce Type: cross Abstract: Knowledge graphs (KGs) have commonly been constructed using predefined symbolic relation schemas, typically implemented as categorical relation labels. This design has notable shortcomings: real-world relations are often contextual, nuanced, and sometimes uncertain, and compressing it into discrete relation labels abstracts away critical semantic detail. Nevertheless, symbolic-relation KGs remain widely used because they have been operationally effective and broadly compatible with pre-LLM downstream models and algorithms, in which KG knowledge could be retrieved or encoded into quantified features and embeddings at scale. The emergence of LLMs has reshaped how knowledge is created and consumed. LLMs support scalable synthesis of domain facts directly in concise natural language, and prompting-based inference favors context-rich free-form text over quantified representations. This position paper argues that these changes call for rethinking the representation of relations themselves rather than merely using LLMs to populate conventional schemas more efficiently. We therefore advocate moving from symbolic to natural-language relation descriptions, and we propose hybrid design principles that preserve a minimal structural backbone while enabling more flexible and context-sensitive relational representations.

A Marketplace for AI-Generated Adult Content and Deepfakes

✇cs.AI, q-bio.NC updates on arXiv.org
By: Shalmoli Ghosh · Matthew R. DeVerna · Filippo Menczer
15 January 2026 at 13:00
arXiv:2601.09117v1 Announce Type: cross Abstract: Generative AI systems increasingly enable the production of highly realistic synthetic media. Civitai, a popular community-driven platform for AI-generated content, operates a monetized feature called Bounties, which allows users to commission the generation of content in exchange for payment. To examine how this mechanism is used and what content it incentivizes, we conduct a longitudinal analysis of all publicly available bounty requests collected over a 14-month period following the platform's launch. We find that the bounty marketplace is dominated by tools that let users steer AI models toward content they were not trained to generate. At the same time, requests for content that is "Not Safe For Work" are widespread and have increased steadily over time, now comprising a majority of all bounties. Participation in bounty creation is uneven, with 20% of requesters accounting for roughly half of requests. Requests for "deepfake" - media depicting identifiable real individuals - exhibit a higher concentration than other types of bounties. A nontrivial subset of these requests involves explicit deepfakes despite platform policies prohibiting such content. These bounties disproportionately target female celebrities, revealing a pronounced gender asymmetry in social harm. Together, these findings show how monetized, community-driven generative AI platforms can produce gendered harms, raising questions about consent, governance, and enforcement.
  • ✇cs.AI, q-bio.NC updates on arXiv.org
  • Global Benchmark Database Ashlin Iser · Christoph Jabs
    arXiv:2405.10045v3 Announce Type: replace-cross Abstract: This paper presents Global Benchmark Database (GBD), a comprehensive suite of tools for provisioning and sustainably maintaining benchmark instances and their metadata. The availability of benchmark metadata is essential for many tasks in empirical research, e.g., for the data-driven compilation of benchmarks, the domain-specific analysis of runtime experiments, or the instance-specific selection of solvers. In this paper, we introduce t
     
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Global Benchmark Database

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ashlin Iser · Christoph Jabs
15 January 2026 at 13:00
arXiv:2405.10045v3 Announce Type: replace-cross Abstract: This paper presents Global Benchmark Database (GBD), a comprehensive suite of tools for provisioning and sustainably maintaining benchmark instances and their metadata. The availability of benchmark metadata is essential for many tasks in empirical research, e.g., for the data-driven compilation of benchmarks, the domain-specific analysis of runtime experiments, or the instance-specific selection of solvers. In this paper, we introduce the data model of GBD as well as its interfaces and provide examples of how to interact with them. We also demonstrate the integration of custom data sources and explain how to extend GBD with additional problem domains, instance formats and feature extractors.

Mitigating Gender Bias via Fostering Exploratory Thinking in LLMs

✇cs.AI, q-bio.NC updates on arXiv.org
By: Kangda Wei · Hasnat Md Abdullah · Ruihong Huang
15 January 2026 at 13:00
arXiv:2505.17217v3 Announce Type: replace-cross Abstract: Large Language Models (LLMs) often exhibit gender bias, resulting in unequal treatment of male and female subjects across different contexts. To address this issue, we propose a novel data generation framework that fosters exploratory thinking in LLMs. Our approach prompts models to generate story pairs featuring male and female protagonists in structurally identical, morally ambiguous scenarios, then elicits and compares their moral judgments. When inconsistencies arise, the model is guided to produce balanced, gender-neutral judgments. These story-judgment pairs are used to fine-tune or optimize the models via Direct Preference Optimization (DPO). Experimental results show that our method significantly reduces gender bias while preserving or even enhancing general model capabilities. We will release the code and generated data. We release the code and generated data at: https://github.com/WeiKangda/LLMs-Exploratory-Bias-Mitigation/tree/main.

GI-Bench: A Panoramic Benchmark Revealing the Knowledge-Experience Dissociation of Multimodal Large Language Models in Gastrointestinal Endoscopy Against Clinical Standards

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yan Zhu · Te Luo · Pei-Yao Fu · Zhen Zhang · Zi-Long Wang · Yi-Fan Qu · Zi-Han Geng · Jia-Qi Xu · Lu Yao · Li-Yun Ma · Wei Su · Wei-Feng Chen · Quan-Lin Li · Shuo Wang · Ping-Hong Zhou
15 January 2026 at 13:00
arXiv:2601.08183v2 Announce Type: replace-cross Abstract: Multimodal Large Language Models (MLLMs) show promise in gastroenterology, yet their performance against comprehensive clinical workflows and human benchmarks remains unverified. To systematically evaluate state-of-the-art MLLMs across a panoramic gastrointestinal endoscopy workflow and determine their clinical utility compared with human endoscopists. We constructed GI-Bench, a benchmark encompassing 20 fine-grained lesion categories. Twelve MLLMs were evaluated across a five-stage clinical workflow: anatomical localization, lesion identification, diagnosis, findings description, and management. Model performance was benchmarked against three junior endoscopists and three residency trainees using Macro-F1, mean Intersection-over-Union (mIoU), and multi-dimensional Likert scale. Gemini-3-Pro achieved state-of-the-art performance. In diagnostic reasoning, top-tier models (Macro-F1 0.641) outperformed trainees (0.492) and rivaled junior endoscopists (0.727; p>0.05). However, a critical "spatial grounding bottleneck" persisted; human lesion localization (mIoU >0.506) significantly outperformed the best model (0.345; p

Regulatory gray areas of LLM Terms

✇cs.AI, q-bio.NC updates on arXiv.org
By: Brittany I. Davidson · Kate Muir · Florian A. D. Burnat · Adam N. Joinson
15 January 2026 at 13:00
arXiv:2601.08415v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) are increasingly integrated into academic research pipelines; however, the Terms of Service governing their use remain under-examined. We present a comparative analysis of the Terms of Service of five major LLM providers (Anthropic, DeepSeek, Google, OpenAI, and xAI) collected in November 2025. Our analysis reveals substantial variation in the stringency and specificity of usage restrictions for general users and researchers. We identify specific complexities for researchers in security research, computational social sciences, and psychological studies. We identify `regulatory gray areas' where Terms of Service create uncertainty for legitimate use. We contribute a publicly available resource comparing terms across platforms (OSF) and discuss implications for general users and researchers navigating this evolving landscape.

Circulating metabolites, genetics and lifestyle factors in relation to future risk of type 2 diabetes

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Jun Li · Jie Hu · Huan Yun · Zhendong Mei · Xingyan Wang · Kai Luo · Marta Guasch-Ferré · Xikun Han · Buu Truong · Jordi Merino · Chengyong Jia · Miguel Ruiz-Canela · Casey M Rebholz · Eun Hye Moon · Taryn Alkis · Guning Liu · Jie Yao · Xiyuan Zhang · Bianca C Porneala · Jordi Salas-Salvadó · Thomas J Wang · Josée Dupuis · Elizabeth Selvin · Xiuqing Guo · Shilpa N Bhupathiraju · Jennifer A Brody · Yongmei Liu · Alexis C Wood · Kari E North · Su Yon Jung · Ching-Ti Liu · Nona Sotoodehnia · Simin Liu · Lesley F Tinker · A Heather Eliassen · JoAnn E Manson · Jose C Florez · Robert E Gerszten · Clary B Clish · Liming Liang · Rozenn N Lemaitre · Katherine L Tucker · Stephen S Rich · Jerome I Rotter · Miguel Angel Martínez-González · Kathryn M Rexrode · James B Meigs · Eric Boerwinkle · Robert C Kaplan · Frank B Hu · Bing Yu · Qibin Qi
14 January 2026 at 19:00

Nat Med. 2026 Jan 14. doi: 10.1038/s41591-025-04105-8. Online ahead of print.

ABSTRACT

The human metabolome reflects complex metabolic states affected by genetic and environmental factors. However, metabolites associated with type 2 diabetes (T2D) risk and their determinants remain insufficiently characterized. Here we integrated blood metabolomic, genomic and lifestyle data from up to 23,634 initially T2D-free participants from ten cohorts. Of 469 metabolites examined, 235 were associated with incident T2D during up to 26 years of follow-up, including 67 associations not previously reported across bile acid, lipid, carnitine, urea cycle and arginine/proline, glycine and histidine pathways. Further genetic analyses linked these metabolites to signaling pathways and clinical traits central to T2D pathophysiology, including insulin resistance, glucose/insulin response, ectopic fat deposition, energy/lipid regulation and liver function. Lifestyle factors-particularly physical activity, obesity and diet-explained greater variations in T2D-associated versus non-associated metabolites, with specific metabolites revealed as potential mediators. Finally, a 44-metabolite signature improved T2D risk prediction beyond conventional factors. These findings provide a foundation for understanding T2D mechanisms and may inform precision prevention targeting specific metabolic pathways.

PMID:41535386 | DOI:10.1038/s41591-025-04105-8

Multi-omics to study chronic respiratory diseases and viral infections

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Sobia Idrees · Hao Chen · Tayyaba Sadaf · Saima Firdous Rehman · Matt D Johansen · Keshav Raj Paudel · Gang Liu · Yuting Wang · Malte D Luecken · Elinor Hortle · Ashleigh S Philp · Kurtis F Budden · Matthew O'Rourke · Gerard E Kaiko · Sionne E M Lucas · Joanne L Dickinson · Peter C Allen · Joseph E Powell · Lai-Ying Zhang · Daniel C Chambers · Tamera Corte · Gaetano Caramori · Maor Sauler · Peter A Wark · Janine Gote-Schniering · Mareike Lehmann · Thomas M Conlon · Theodore S Kapellos · Ali Önder Yildirim · Rosa Faner · Shyamali C Dharmage · Craig E Wheelock · Maarten van den Berge · Martijn C Nawijn · Francesca Polverino · Gabrielle T Belz · Sanjay H Chotirmall · Leopoldo N Segal · Alen Faiz · Philip M Hansbro
14 January 2026 at 19:00

Eur Respir Rev. 2026 Jan 14;35(179):240286. doi: 10.1183/16000617.0286-2024. Print 2026 Jan.

ABSTRACT

Despite recent advances, the underlying mechanisms of the development and progression of many chronic respiratory diseases remain to be elucidated. Factors such as heterogeneity and complexity of human diseases and difficulty interpreting large datasets hinder research into chronic respiratory diseases. Omics assesses the changes in specific biological entities, such as mRNA expression, epigenetics/epigenomics, genomics, proteomics, metagenomics and metabolomics, and provides valuable insights into the roles of these processes in chronic respiratory diseases. High-throughput omics at bulk, single-cell and spatial levels empower the exploration of disease-related changes through untargeted data-driven statistical methods. Multi-omics is the exploration and integration of multiple biological processes, which compared to a single-omics, can provide a substantially greater and more holistic overview of the pathogenic mechanisms that underpin complex diseases. Multi-omics analysis can comprehensively characterise the mechanisms that drive chronic respiratory diseases, capturing unique biological signatures and cellular interactions at different omics levels. Use of these methods has begun to identify key factors and biomarkers in chronic respiratory diseases. Here, we review current omics approaches and highlight recent advances in respiratory research achieved using multi-omics and integrative methods. Our review provides a valuable resource for researchers and clinicians in this area.

PMID:41534886 | DOI:10.1183/16000617.0286-2024

Complement-secreting CAFs are associated with better prognosis in pancreatic cancer: single-cell multiomics

✇(Multiomics OR Omics) AND (Pancreatic)
By: Kai Chen · Yongsu Ma · Liling Huang · Pengfei Wu · Heng-Chung Kung · Bohan Yang · Jixin Zhang · Robert A Anders · Jacquelyn W Zimmerman · Qingfeng Zhu · Xiaodong Tian · Jin He · Yinmo Yang
14 January 2026 at 19:00

Gut. 2026 Jan 13:gutjnl-2025-335683. doi: 10.1136/gutjnl-2025-335683. Online ahead of print.

ABSTRACT

BACKGROUND: Accumulating evidence has demonstrated that distinct tumour-promoting and tumour-restraining cancer-associated fibroblast (CAF) subtypes coexist in pancreatic ductal adenocarcinoma.

OBJECTIVE: To develop targeted CAF therapeutic strategies by reprogramming tumour-promoting CAF subtypes.

DESIGN: We leveraged multiomics technologies to systematically identify and characterise CAF subtypes transcriptionally, epigenetically and spatially and correlate them with clinicopathological features.

RESULTS: We found that complement-secreting CAFs (csCAFs), initially identified by our group and inflammatory CAFs (iCAFs) share significant overlap in their transcriptional profiles and chromatin accessibility. iCAFs specifically express transcription factors from the heme and oxidative homeostasis pathway and the activator protein 1 family, which are both involved in cellular response to oxidative stress. Notably, the composition of csCAFs among all CAFs declined during pancreatic carcinogenesis, while trajectory analysis showed that csCAFs could potentially differentiate into iCAFs. Spatially resolved analysis indicated that tumour regions with a higher csCAF composition were associated with lower levels of TGF-β ligands, fewer M2 tumour-associated macrophages and increased levels of lipid mediators. Additionally, we identified a spatially defined CXCL12-CXCR4 ligand-receptor interaction between csCAFs and T cells, but in distinct patterns between different metastatic organs. Patients with a higher composition of csCAFs have significantly longer overall survival and recurrence-free survival through multiplex immunohistochemistry and bulk RNA-seq deconvolution.

CONCLUSION: Our study demonstrates that csCAFs may represent an early-stage iCAF subtype and suggests a promising strategy for reprogramming iCAFs into csCAFs.

PMID:41534892 | DOI:10.1136/gutjnl-2025-335683

Artificial intelligence tools expand scientists’ impact but contract science’s focus

✇Nature - Issue - nature.com science feeds
By: Qianyue Hao · Fengli Xu · Yong Li · James Evans
14 January 2026 at 08:00

Nature, Published online: 14 January 2026; doi:10.1038/s41586-025-09922-y

Artificial intelligence boosts individual scientists’ output, citations and career progression, but collectively narrows research diversity and reduces collaboration, concentrating work in data-rich areas and potentially limiting broader scientific exploration.
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