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Artificial Intelligence-Driven Multiomics and Clinical Investigation Identify Macrophage Migration Inhibitory Factor as a Pan-Cancer Biomarker

Phenomics. 2026 May 20;6(3):213-229. doi: 10.1007/s43657-026-00322-4. eCollection 2026 Jun.

ABSTRACT

Early cancer detection remains challenging due to the lack of reliable pan-cancer screening methods, particularly blood-based biomarkers. Using a novel three-tiered validation framework combining artificial intelligence (AI)-powered literature mining of 180,000 PubMed articles (1950-2024), multiomics integration across major databases, and extensive clinical validation, we identified macrophage migration inhibitory factor (MIF) as a promising blood-based biomarker for pan-cancer detection. Multiomics analysis revealed consistent MIF upregulation across 21 cancer types at the transcriptional level and across 12 cancer types at the protein level. Clinical validation in independent cohorts (n = 4,269) showed that serum MIF protein levels discriminated effectively between cancer patients and healthy controls (median AUC = 0.994) and between cancer and benign conditions (median AUC = 0.881). Notably, comparative analyses showed that MIF demonstrated superior or comparable performance to established cancer-specific markers, including AFP for hepatocellular carcinoma (MIF AUC = 0.885 vs. AFP AUC: 0.744-0.887) and CA125 for ovarian cancer (MIF AUC = 0.831 vs. CA125 AUC: 0.58-0.71). Meta-analysis of 28 cohorts (n = 5,347) confirmed the diagnostic efficacy of MIF (pooled AUC: 0.782). This cost-effective, blood-based ELISA approach establishes MIF as a valuable tool for broad applications in cancer screening.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s43657-026-00322-4.

PMID:42750739 | PMC:PMC13578188 | DOI:10.1007/s43657-026-00322-4

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Spatial proximity sequencing maps developmental dynamics in the germinal center

Sprox-seq enables spatial profiling of protein complexes, surface proteins, and mRNAs in intact tissues by combining proximity ligation with spatial transcriptomics. In human tonsils, Sprox-seq maps germinal center interaction networks, links CD21-CD35 complexes to proliferative programs, reveals interaction-based B cell state transitions, and directly captures B cell-follicular dendritic cell communication.
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Joint impact of pathological burden and cognitive resilience on Alzheimer’s disease risk

Nature Medicine, Published online: 11 September 2026; doi:10.1038/s41591-026-04635-9

A 15-year cohort study shows that Alzheimer’s dementia risk is jointly shaped by Alzheimer’s pathology and cognitive resilience, with high resilience linked to lower risk, even under greater pathology.
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Targeting of the oncogenic fusion EWSR1-FLI1 in Ewing Sarcoma by CRISPR/dCas9 silencers

Blancafort and colleagues describe a non-viral polymeric system for the delivery of dCas9-KRAB silencers as ribonucleoprotein (RNP) payloads for EWSR1-FLI1 repression. They demonstrate highly efficient RNP delivery and robust silencing of EWSR1-FLI1 in both cell line and patient-derived xenografts of Ewing sarcoma, accompanied by potent anti-tumor effects.
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DC vaccine loaded with Bacteroides fragilis elicits functional cross-reactivity and enhances anti-PD-1 immunotherapy

Liu and colleagues develop a dendritic cell vaccine loaded with the gut commensals Bacteroides fragilis (DC-Bf), which triggers CD8+ T cell-dependent antitumor immune responses via MHC-I-mediated cross-presentation and interleukin-12 secretion, and enhances the efficacy of PD-1 antibody by improving the immunosuppressive tumor microenvironment and diversifying the T cell receptor repertoire.
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Efficient Diversity-based Experience Replay for Deep Reinforcement Learning

arXiv:2410.20487v5 Announce Type: replace-cross Abstract: Experience replay is widely used to improve learning efficiency in reinforcement learning by leveraging past experiences. However, existing experience replay methods, whether based on uniform or prioritized sampling, often suffer from low efficiency, particularly in real-world scenarios with high-dimensional state spaces. To address this limitation, we propose a novel approach, Efficient Diversity-based Experience Replay (EDER). EDER employs a determinantal point process to model the diversity between samples and prioritizes replay based on the diversity between samples. To further enhance learning efficiency, we incorporate Cholesky decomposition for handling large state spaces in realistic environments. Additionally, rejection sampling is applied to select samples with higher diversity, thereby improving overall learning efficacy. Extensive experiments are conducted on robotic manipulation tasks in MuJoCo, Atari games, and realistic indoor environments in Habitat. The results demonstrate that our approach not only significantly improves learning efficiency but also achieves superior performance in high-dimensional, realistic environments.
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Genomics and social practices at Mogou and other Gansu sites during prehistoric trans-Eurasian exchange

Ancient DNA from 149 individuals at 11 sites in Gansu, China, dated to around 4,700–3,000 years ago, reveals human population history during early transcontinental exchanges of agriculture and technology, as well as contemporary social practices, at the large Mogou cemetery.
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Skin-innervating glutamatergic neurons modulate aging

Within the skin, glutamatergic neurons expressing neurofilament heavy chain (Nefh) play a role in aging. Loss of Nefh during aging drives skin fibroblast senescence and collagen loss, whereas glutamate supplementation improves skin aging phenotypes.
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Pulmonary nodule prediction in the multi-omics era: Integrating radiomics, AI, liquid biopsy, and airway classifiers

Crit Rev Oncol Hematol. 2026 Sep;225:105483. doi: 10.1016/j.critrevonc.2026.105483. Epub 2026 Jul 10.

ABSTRACT

Low-dose CT (LDCT) lung cancer screening significantly reduces mortality but has dramatically increased the detection of pulmonary nodules. Most of these nodules are benign, leading to a high false-positive rate that triggers unnecessary invasive procedures and patient anxiety, underscoring the need for more precise noninvasive diagnostic tools. Critically, single-modality liquid biopsy biomarkers, including circulating tumor cells, cell-free DNA mutations, or individual microRNAs, have demonstrated insufficient sensitivity or specificity for independent clinical deployment when used in isolation. This necessitates a paradigm shift toward multimodal molecular integration, wherein complementary biomarker classes are combined to overcome the inherent limitations of any single analyte. Traditional clinical prediction models (Mayo, VA, Brock, Herder) assist in estimating malignancy risk, yet their accuracy remains modest. Emerging approaches harness radiomics and artificial intelligence (AI) to extract high-dimensional imaging features from chest CT scans, improving risk stratification beyond human assessment alone. In parallel, minimally invasive liquid biopsy biomarkers offer complementary avenues to detect occult malignancy signals. Additionally, bronchial airway gene expression classifiers leverage the "field-of-injury" effect in normal respiratory epithelium to help identify lung cancer even when the nodule itself cannot be directly sampled via biopsy. Integrating these radiologic and molecular data streams into a multi-omics framework has the potential to enhance diagnostic precision for indeterminate pulmonary nodules, enabling more confident discrimination between benign and malignant lesions. However, most of these emerging tools have not yet been validated in large prospective trials and face technological barriers as well as challenges in real-world implementation. This review focuses primarily on LDCT screening detected pulmonary nodules, while incorporating evidence from incidentally detected and other indeterminate nodule cohorts when relevant to broader CT based management. By synthesizing advances in radiomics, AI, liquid biopsy, airway classifiers, and multi-omics integration, we highlight the need for prospective validation and multidisciplinary collaboration to translate these approaches into clinically useful pathways that improve early lung cancer detection, reduce unnecessary interventions, and enhance patient outcomes.

PMID:42431477 | DOI:10.1016/j.critrevonc.2026.105483

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CyBOKClaw: Human-in-the-Loop CyBOK Mapping for Cybersecurity Curriculum

arXiv:2605.24663v1 Announce Type: cross Abstract: This paper presents CyBOKClaw, an interpretable human-in-the-loop retrieval framework for mapping cybersecurity keywords or phrases (KWoPs) to the Cyber Security Body of Knowledge (CyBOK). Rather than treating the task as strict exact classification, the framework is designed as a top-k candidate generator for expert review. It combines query normalization, curated term expansion, concept-level boosts, topic-description enrichment, and domain-sensitive ranking rules. Because educational KWoPs are often broad, ambiguous, and only approximately aligned with CyBOK terminology, strict exact matching provides only a partial account of practical utility. We therefore evaluate the framework using both structural retrieval metrics and an expert-guided top-5 usefulness metric, ECA-5 (Exact or Closest Acceptable Match at top-5), which records whether the returned candidates contain at least one mapping that an expert would judge exact or accept as the nearest practical CyBOK placement. On the development dataset, CyBOKClaw achieves 64.73% EXA-5 (Exact Match at top-5), 84.18% structural semantic alignment, and 91.88% ECA-5; on the validation dataset, it achieves 81.19% EXA-5, 93.32% structural semantic alignment, and 98.00% ECA-5. These results show that expert-guided top-k usefulness provides a more faithful account of practical CyBOK mapping utility than exact structural matching alone, and that CyBOKClaw is effective as a CyBOK-specific expert-support retrieval system.
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IPR-1: Interactive Physical Reasoner

arXiv:2511.15407v4 Announce Type: replace Abstract: Humans learn by observing, interacting with environments, and internalizing physics and causality. Here, we aim to ask whether an agent can similarly acquire human-like reasoning from interaction and keep improving with more experience. To study this, we introduce a Game-to-Unseen (G2U) benchmark of 1,000+ heterogeneous games that exhibit significant visual domain gaps. Existing approaches, including VLMs and world models, struggle to capture underlying physics and causality since they are not focused on core mechanisms and overfit to visual details. VLM/VLA agents reason but lack look-ahead in interactive settings, while world models imagine but imitate visual patterns rather than analyze physics and causality. We therefore propose IPR (Interactive Physical Reasoner), using world-model rollouts to score and reinforce a VLM's policy, and introduce PhysCode, a physics-centric action code aligning semantic intent with dynamics to provide a shared action space for prediction and reasoning. Pretrained on 1,000+ games, our IPR performs robustly on levels from primitive intuition to goal-driven reasoning, and even surpasses GPT-5 overall. We find that performance improves with more training games and interaction steps, and that the model also zero-shot transfers to unseen games. These results support physics-centric interaction as a path to steadily improving physical reasoning. Further demos and project details can be found at https://mybearyzhang.github.io/ipr-1.
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SkillOpt: Executive Strategy for Self-Evolving Agent Skills

arXiv:2605.23904v2 Announce Type: replace Abstract: Agent skills today are hand-crafted, generated one-shot, or evolved through loosely controlled self-revision, none of which behaves like a deep-learning optimizer for the skill, and none of which reliably improves over its starting point under feedback. We argue the skill should instead be trained as the external state of a frozen agent, with the same discipline that makes weight-space optimization reproducible. SkillOpt is, to our knowledge, the first systematic controllable text-space optimizer for agent skills: a separate optimizer model turns scored rollouts into bounded add/delete/replace edits on a single skill document, and an edit is accepted only when it strictly improves a held-out validation score. A textual learning-rate budget, rejected-edit buffer, and epoch-wise slow/meta update make skill training stable while adding zero inference-time model calls at deployment. Across six benchmarks, seven target models, and three execution harnesses (direct chat, Codex, Claude Code), SkillOpt is best or tied on all 52 evaluated (model, benchmark, harness) cells and beats every per-cell competitor among human, one-shot LLM, Trace2Skill, TextGrad, GEPA, and EvoSkill skills. On GPT-5.5 it lifts the average no-skill accuracy by +23.5 points in direct chat, by +24.8 inside the Codex agentic loop, and by +19.1 inside Claude Code. Transfer experiments further show that optimized skill artifacts retain value when moved across model scales, between Codex and Claude Code execution environments, and to a nearby math benchmark without further optimization. Code: https://aka.ms/skillopt
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Bridging the Semantic-Action Gap in Visual Token Pruning for Efficient VLA Inference

arXiv:2511.16449v5 Announce Type: replace-cross Abstract: Vision-Language-Action (VLA) models have shown great potential for embodied AI by integrating visual perception, language understanding, and action execution. In real-time deployment, these models must process continuous visual streams, incurring substantial computational overhead. Visual token pruning -- a mainstream technique for accelerating Vision-Language Models (VLMs) by retaining salient tokens while discarding redundant ones -- offers a natural candidate solution to this challenge. However, directly applying VLM-oriented pruning methods to VLA inference can cause severe degradation in manipulation performance. Our analysis attributes this degradation to a key mismatch: VLA inference exhibits distinct attention patterns between the vision-language prefill stage and the action-decode stage, so pruning based only on context-prefill semantic salience is biased toward semantic cues and may remove action-critical visual tokens. Motivated by this observation, we propose VLA-Pruner, an effective plug-and-play token pruning method grounded in the visual requirements of VLA inference, further exploiting the temporal continuity of robot manipulation. Specifically, VLA-Pruner estimates visual-token importance from both semantic prefilling and temporally smoothed action relevance, and then applies a Combine-then-Filter strategy to retain compact, non-redundant tokens under the compute budget. Experiments show that VLA-Pruner outperforms state-of-the-art approaches across multiple VLA architectures, achieving up to 1.99x speedup with comparable manipulation quality.
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Deubiquitinase USP35 regulates MDM4 degradation to promote endothelial ferroptosis and renal injury progression

Cell Death Discovery, Published online: 25 May 2026; doi:10.1038/s41420-026-03128-5

Deubiquitinase USP35 regulates MDM4 degradation to promote endothelial ferroptosis and renal injury progression
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A pathogen lncRNA secreted into rice sequesters a host miRNA for virulence

Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10572-x

A fungal long non-coding RNA from Magnaporthe oryzae translocates into rice cells to sequester a host microRNA that normally represses PKR1, a negative immunity regulator, thereby facilitating infection and revealing a widespread RNA-based pathogen–host interaction mechanism.
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Quantifying Trust: Financial Risk Management for Trustworthy AI Agents

arXiv:2604.03976v1 Announce Type: new Abstract: Prior work on trustworthy AI emphasizes model-internal properties such as bias mitigation, adversarial robustness, and interpretability. As AI systems evolve into autonomous agents deployed in open environments and increasingly connected to payments or assets, the operational meaning of trust shifts to end-to-end outcomes: whether an agent completes tasks, follows user intent, and avoids failures that cause material or psychological harm. These risks are fundamentally product-level and cannot be eliminated by technical safeguards alone because agent behavior is inherently stochastic. To address this gap between model-level reliability and user-facing assurance, we propose a complementary framework based on risk management. Drawing inspiration from financial underwriting, we introduce the \textbf{Agentic Risk Standard (ARS)}, a payment settlement standard for AI-mediated transactions. ARS integrates risk assessment, underwriting, and compensation into a single transaction framework that protects users when interacting with agents. Under ARS, users receive predefined and contractually enforceable compensation in cases of execution failure, misalignment, or unintended outcomes. This shifts trust from an implicit expectation about model behavior to an explicit, measurable, and enforceable product guarantee. We also present a simulation study analyzing the social benefits of applying ARS to agentic transactions. ARS's implementation can be found at https://github.com/t54-labs/AgenticRiskStandard.
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Your Agent, Their Asset: A Real-World Safety Analysis of OpenClaw

arXiv:2604.04759v1 Announce Type: cross Abstract: OpenClaw, the most widely deployed personal AI agent in early 2026, operates with full local system access and integrates with sensitive services such as Gmail, Stripe, and the filesystem. While these broad privileges enable high levels of automation and powerful personalization, they also expose a substantial attack surface that existing sandboxed evaluations fail to capture. To address this gap, we present the first real-world safety evaluation of OpenClaw and introduce the CIK taxonomy, which unifies an agent's persistent state into three dimensions, i.e., Capability, Identity, and Knowledge, for safety analysis. Our evaluations cover 12 attack scenarios on a live OpenClaw instance across four backbone models (Claude Sonnet 4.5, Opus 4.6, Gemini 3.1 Pro, and GPT-5.4). The results show that poisoning any single CIK dimension increases the average attack success rate from 24.6% to 64-74%, with even the most robust model exhibiting more than a threefold increase over its baseline vulnerability. We further assess three CIK-aligned defense strategies alongside a file-protection mechanism; however, the strongest defense still yields a 63.8% success rate under Capability-targeted attacks, while file protection blocks 97% of malicious injections but also prevents legitimate updates. Taken together, these findings show that the vulnerabilities are inherent to the agent architecture, necessitating more systematic safeguards to secure personal AI agents. Our project page is https://ucsc-vlaa.github.io/CIK-Bench.
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Pyruvate is a natural suppressor of interferon signaling by inducing STAT1 protein pyruvylation

Yibo et al. identify protein pyruvylation as a post-translational modification that can modulate immune signaling and host antiviral response.
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The neonatal lung microbiome: a dynamic determinant of respiratory health, disease, and novel therapeutics

Front Pediatr. 2026 Mar 16;14:1770578. doi: 10.3389/fped.2026.1770578. eCollection 2026.

ABSTRACT

The neonatal lung, once considered sterile, is now recognized to harbor a dynamic and complex microbiome that plays a critical role in respiratory health and disease. This review synthesizes current evidence on the composition, development, and functional impact of the lung microbiome in neonates, with a focus on its involvement in key respiratory disorders such as bronchopulmonary dysplasia, respiratory syncytial virus infection, neonatal acute respiratory distress syndrome, cystic fibrosis, and asthma predisposition. We place particular emphasis on the bidirectional communication along the gut-lung axis as a central mechanism, wherein intestinal microbiota and their metabolites modulate pulmonary immunity and inflammation. Emerging multi-omics studies that integrate microbial data with host metabolomic and immune profiles are highlighted for their role in deciphering disease-specific dysbiotic signatures and mechanistic pathways. Critically, this review advances the discussion beyond association by evaluating the translational potential of the microbiome as both a diagnostic biomarker and a therapeutic target. We provide a critical appraisal of innovative microbiome-targeted strategies-including probiotics, postbiotics, phage therapy, and bacterial lysates-and discuss the unique challenges and future directions for translating these approaches into safe, effective clinical interventions for vulnerable neonates. By bridging foundational science with clinical implications, this work aims to inform the development of novel, ecology-informed therapeutics to prevent and mitigate neonatal respiratory diseases.

PMID:41918694 | PMC:PMC13033698 | DOI:10.3389/fped.2026.1770578

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