Normal view
-
TechCrunch
-
AI companies are building huge natural gas plants to power data centers. What could go wrong?
Meta, Microsoft, and Google are all betting big on new natural gas power plants to run their AI data centers. They may regret it.
-
TechCrunch
-
People would rather have an Amazon warehouse in their backyard than a data center
A new poll shows that the debate over data centers is far from settled.
People would rather have an Amazon warehouse in their backyard than a data center
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
Pan-cancer landscape of protein kinase D3: An integrative TCGA multi-omics analysis of clinical, molecular, and immunological roles
PLoS One. 2026 Apr 3;21(4):e0346173. doi: 10.1371/journal.pone.0346173. eCollection 2026.ABSTRACTCancer remains a leading cause of mortality worldwide and a significant barrier to improving quality of life across all populations. The protein kinase D family, including PRKD3, has been demonstrated to play a crucial role in cancer development through its involvement in regulating key cellular processes. Although growing evidence highlights the role of PRKD3 in the tumorigenesis of certain cancers,
Pan-cancer landscape of protein kinase D3: An integrative TCGA multi-omics analysis of clinical, molecular, and immunological roles
PLoS One. 2026 Apr 3;21(4):e0346173. doi: 10.1371/journal.pone.0346173. eCollection 2026.
ABSTRACT
Cancer remains a leading cause of mortality worldwide and a significant barrier to improving quality of life across all populations. The protein kinase D family, including PRKD3, has been demonstrated to play a crucial role in cancer development through its involvement in regulating key cellular processes. Although growing evidence highlights the role of PRKD3 in the tumorigenesis of certain cancers, a comprehensive pan-cancer analysis of PRKD3 remains unavailable. To address this, we performed an integrative pan-cancer analysis of PRKD3 using multi-omics datasets from The Cancer Genome Atlas, the Genotype-Tissue Expression project, and cBioPortal. We examined PRKD3 expression, copy number variation, mutation, and DNA methylation, and evaluated their associations with clinicopathological features, patient survival, and diagnostic potential across 33 cancer types. Immune relevance was further assessed through correlations with immune infiltration, checkpoint gene expression, and immunotherapy response-related genomic biomarkers. Our results revealed that PRKD3 expression was highly heterogeneous, showing significant upregulation in liver cancer, gastric cancer, and adrenocortical carcinoma, and downregulation in others. Elevated expression was consistently associated with poor prognosis and increased stromal, neutrophil, and cancer-associated fibroblast infiltration in adrenocortical carcinoma, liver cancer, and stomach cancer, whereas paradoxical associations with favorable outcomes were observed in kidney clear cell carcinoma. PRKD3 expression also correlated with immune checkpoint molecules including PD-1, PD-L1, and CTLA-4, supporting an immunosuppressive role, while context-dependent associations with TMB and MSI highlighted its potential influence on tumor immunogenicity and responsiveness to immune checkpoint blockade. Collectively, these findings identify PRKD3 as a potential context-dependent modulator of tumor biology, prognosis, and immune interactions, underscoring its potential as a biomarker of diagnostic, prognostic, and therapeutic relevance in precision oncology.
PMID:41931575 | PMC:PMC13048501 | DOI:10.1371/journal.pone.0346173
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
Immune endotypes in tuberculosis: Keys to decoding disease complexity
J Intern Med. 2026 Apr 3. doi: 10.1111/joim.70092. Online ahead of print.ABSTRACTTuberculosis (TB) remains a major global health challenge, with multi-drug antibiotic regimens as the current standard of care. While effective at killing Mycobacterium tuberculosis, these treatments do not resolve persistent inflammation, prevent lung damage, or reverse immune dysregulation that contribute to poor outcomes and disease recurrence. Precision medicine offers a promising alternative but requires deeper
Immune endotypes in tuberculosis: Keys to decoding disease complexity
J Intern Med. 2026 Apr 3. doi: 10.1111/joim.70092. Online ahead of print.
ABSTRACT
Tuberculosis (TB) remains a major global health challenge, with multi-drug antibiotic regimens as the current standard of care. While effective at killing Mycobacterium tuberculosis, these treatments do not resolve persistent inflammation, prevent lung damage, or reverse immune dysregulation that contribute to poor outcomes and disease recurrence. Precision medicine offers a promising alternative but requires deeper insight into disease mechanisms to enable tailored interventions. This comprehensive review introduces the concept of immune endotyping to define the underlying disease mechanisms as tools to decode clinical and immunological heterogeneity in TB. TB displays a wide spectrum of clinical phenotypes, from latent or asymptomatic infection to mild or severe disease with characteristic non-cavitary or cavitary lung pathology. Instead, distinct immune endotypes capture the diverse biological pathways that shape disease progression and treatment response. Similar clinical presentations may arise from different immune dysfunctions, underscoring the need to move beyond broad phenotypic classifications. Advances in multi-omics and computational analyses uncover immune signatures that enable stratification for host-directed therapies (HDTs) targeting hyperinflammation, immunosuppression, coagulopathy or metabolic exhaustion. Integrating clinical, radiological, and immunological data through multimodal profiling is essential for developing personalized interventions. We also explore how endotyping has transformed treatment in other diseases, offering valuable insights for TB. Additionally, we present examples of how putative immune endotypes may be targeted with appropriate HDTs. In summary, this review underscores the potential of immune endotypes to advance precision medicine in TB, moving beyond one-size-fits-all treatment to improve outcomes, especially in severe and drug-resistant cases.
PMID:41930636 | DOI:10.1111/joim.70092
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
Single-Cell and Multi-Omics-Based Characterization of Gastric Cancer Identifies TPP1 as a Potential Target for Gastric Cancer Progression and Treatment
Oncol Res. 2026 Mar 23;34(4):27. doi: 10.32604/or.2026.070208. eCollection 2026.ABSTRACTBACKGROUND: Cancer-associated fibroblasts (CAFs) play critical roles in tumor progression and immunosuppression; however, their contribution to the functional classification and personalized treatment of gastric cancer remains poorly defined. This study aimed to identify effective therapeutic targets to facilitate individualized treatment strategies for patients with gastric cancer.METHODS: Single-cell and bu
Single-Cell and Multi-Omics-Based Characterization of Gastric Cancer Identifies TPP1 as a Potential Target for Gastric Cancer Progression and Treatment
Oncol Res. 2026 Mar 23;34(4):27. doi: 10.32604/or.2026.070208. eCollection 2026.
ABSTRACT
BACKGROUND: Cancer-associated fibroblasts (CAFs) play critical roles in tumor progression and immunosuppression; however, their contribution to the functional classification and personalized treatment of gastric cancer remains poorly defined. This study aimed to identify effective therapeutic targets to facilitate individualized treatment strategies for patients with gastric cancer.
METHODS: Single-cell and bulk transcriptomic analyses were integrated to characterize gastric cancer fibroblasts. "Seurat", "Slingshot", and "CellChat" were used for dimensionality reduction, trajectory inference, and cell-cell communication analyses, respectively. Key metastasis-associated fibroblast modules were identified using High-dimensional weighted gene co-expression network analysis (hdWGCNA) to construct a prognostic model, which was further evaluated for immune infiltration, therapeutic response, and mutational features. The expression and function of the core gene tripeptidyl peptidase 1 (TPP1) were validated through immunoblotting, PCR, and functional assays.
RESULTS: Eight fibroblast subpopulations associated with gastric cancer metastasis exhibited distinct differentiation trajectories and transcriptional heterogeneity. Prognostic analysis indicated that metastasis-associated fibroblasts correlated with poor clinical outcomes. The high-risk subgroup showed marked immunosuppression, resistance to immunotherapy, and reduced mutational burden, with tumor progression-related pathways significantly enriched in this group. In vitro experiments further confirmed that TPP1 knockdown suppressed gastric cancer cell metastasis, invasion, and clonogenic capacity while inducing apoptosis.
CONCLUSION: This study characterized the heterogeneity of gastric cancer-associated fibroblasts using single-cell transcriptomic analysis and established a prognostic model based on metastasis-related fibroblast markers. The model demonstrated strong predictive performance for patient prognosis, immune landscape, and immunotherapy response. Furthermore, the findings highlighted the pivotal role of TPP1 in gastric cancer progression and its potential as a therapeutic target.
PMID:41930144 | PMC:PMC13040347 | DOI:10.32604/or.2026.070208
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
Interpretable Machine Learning to Understand Wildfire Toxicity: Bridging Chemicals, Omics, and Toxicological Outcomes via Symbolic Regression with Novel Feature Scoring
Chem Res Toxicol. 2026 Apr 3. doi: 10.1021/acs.chemrestox.5c00440. Online ahead of print.ABSTRACTWildfire smoke exposures are increasingly common, consisting of complex mixtures of gases and particulates known to cause diverse pulmonary health effects. While health outcomes are regularly studied, quantitative links between smoke chemical composition and toxicological outcomes remain poorly defined, limiting interpretation of wildfire smoke health risks. This study explores symbolic regression (S
Interpretable Machine Learning to Understand Wildfire Toxicity: Bridging Chemicals, Omics, and Toxicological Outcomes via Symbolic Regression with Novel Feature Scoring
Chem Res Toxicol. 2026 Apr 3. doi: 10.1021/acs.chemrestox.5c00440. Online ahead of print.
ABSTRACT
Wildfire smoke exposures are increasingly common, consisting of complex mixtures of gases and particulates known to cause diverse pulmonary health effects. While health outcomes are regularly studied, quantitative links between smoke chemical composition and toxicological outcomes remain poorly defined, limiting interpretation of wildfire smoke health risks. This study explores symbolic regression (SR) as an interpretable artificial intelligence/machine learning method to generate closed-form mathematical models linking chemical exposure to biological responses relevant to wildfire smoke. Prior to application on wildfire-relevant data sets, we benchmarked three Python-based SR packages on simulated data, assessing performance across varying noise levels and operator complexities. Insights from these simulation tests, such as the importance of including necessary operators, were incorporated when applying SR to lab-generated wildland fire exposure-toxicity data. This data set included chemical characterizations of biomass smoke exposures and corresponding pulmonary responses in female CD-1 mice (n = 60). Specifically, we evaluated the ability to predict a lung injury marker using (1) targeted measures of over 80 chemicals measured in smoke (RMSE = 17.57 mg/mL) and (2) lung tissue measures of hundreds of transcripts (RMSE = 15.12 mg/mL). Resulting error metrics were comparable to Random Forest and XGBoost models. To aid model interpretation, we developed directional ensemble contribution scores (DECS), a novel feature importance scoring method that quantifies the direction and magnitude of predictor contributions across top-performing models. Expert toxicologists also contributed to model prioritization, integrating a "biologists-in-the-loop" approach. Results highlighted polycyclic aromatic hydrocarbons as drivers of lung injury and methoxyphenols as suppressors. Transcriptomic analyses highlighted a small set of genes, which have roles in metabolism, cell proliferation, immune regulation, and oncogenic processes, with MYC proto-oncogene (Myc) showing the strongest association. Overall, this study demonstrates SR and associated DECS as practical, interpretable tools for modeling environmental mixtures, such as wildfire smoke, and their toxicological effects.
PMID:41928614 | DOI:10.1021/acs.chemrestox.5c00440
-
Omics in Gastric
-
Pan-cancer landscape of protein kinase D3: An integrative TCGA multi-omics analysis of clinical, molecular, and immunological roles
PLoS One. 2026 Apr 3;21(4):e0346173. doi: 10.1371/journal.pone.0346173. eCollection 2026.ABSTRACTCancer remains a leading cause of mortality worldwide and a significant barrier to improving quality of life across all populations. The protein kinase D family, including PRKD3, has been demonstrated to play a crucial role in cancer development through its involvement in regulating key cellular processes. Although growing evidence highlights the role of PRKD3 in the tumorigenesis of certain cancers,
Pan-cancer landscape of protein kinase D3: An integrative TCGA multi-omics analysis of clinical, molecular, and immunological roles
PLoS One. 2026 Apr 3;21(4):e0346173. doi: 10.1371/journal.pone.0346173. eCollection 2026.
ABSTRACT
Cancer remains a leading cause of mortality worldwide and a significant barrier to improving quality of life across all populations. The protein kinase D family, including PRKD3, has been demonstrated to play a crucial role in cancer development through its involvement in regulating key cellular processes. Although growing evidence highlights the role of PRKD3 in the tumorigenesis of certain cancers, a comprehensive pan-cancer analysis of PRKD3 remains unavailable. To address this, we performed an integrative pan-cancer analysis of PRKD3 using multi-omics datasets from The Cancer Genome Atlas, the Genotype-Tissue Expression project, and cBioPortal. We examined PRKD3 expression, copy number variation, mutation, and DNA methylation, and evaluated their associations with clinicopathological features, patient survival, and diagnostic potential across 33 cancer types. Immune relevance was further assessed through correlations with immune infiltration, checkpoint gene expression, and immunotherapy response-related genomic biomarkers. Our results revealed that PRKD3 expression was highly heterogeneous, showing significant upregulation in liver cancer, gastric cancer, and adrenocortical carcinoma, and downregulation in others. Elevated expression was consistently associated with poor prognosis and increased stromal, neutrophil, and cancer-associated fibroblast infiltration in adrenocortical carcinoma, liver cancer, and stomach cancer, whereas paradoxical associations with favorable outcomes were observed in kidney clear cell carcinoma. PRKD3 expression also correlated with immune checkpoint molecules including PD-1, PD-L1, and CTLA-4, supporting an immunosuppressive role, while context-dependent associations with TMB and MSI highlighted its potential influence on tumor immunogenicity and responsiveness to immune checkpoint blockade. Collectively, these findings identify PRKD3 as a potential context-dependent modulator of tumor biology, prognosis, and immune interactions, underscoring its potential as a biomarker of diagnostic, prognostic, and therapeutic relevance in precision oncology.
PMID:41931575 | PMC:PMC13048501 | DOI:10.1371/journal.pone.0346173
-
Omics In Lung
-
Immune endotypes in tuberculosis: Keys to decoding disease complexity
J Intern Med. 2026 Apr 3. doi: 10.1111/joim.70092. Online ahead of print.ABSTRACTTuberculosis (TB) remains a major global health challenge, with multi-drug antibiotic regimens as the current standard of care. While effective at killing Mycobacterium tuberculosis, these treatments do not resolve persistent inflammation, prevent lung damage, or reverse immune dysregulation that contribute to poor outcomes and disease recurrence. Precision medicine offers a promising alternative but requires deeper
Immune endotypes in tuberculosis: Keys to decoding disease complexity
J Intern Med. 2026 Apr 3. doi: 10.1111/joim.70092. Online ahead of print.
ABSTRACT
Tuberculosis (TB) remains a major global health challenge, with multi-drug antibiotic regimens as the current standard of care. While effective at killing Mycobacterium tuberculosis, these treatments do not resolve persistent inflammation, prevent lung damage, or reverse immune dysregulation that contribute to poor outcomes and disease recurrence. Precision medicine offers a promising alternative but requires deeper insight into disease mechanisms to enable tailored interventions. This comprehensive review introduces the concept of immune endotyping to define the underlying disease mechanisms as tools to decode clinical and immunological heterogeneity in TB. TB displays a wide spectrum of clinical phenotypes, from latent or asymptomatic infection to mild or severe disease with characteristic non-cavitary or cavitary lung pathology. Instead, distinct immune endotypes capture the diverse biological pathways that shape disease progression and treatment response. Similar clinical presentations may arise from different immune dysfunctions, underscoring the need to move beyond broad phenotypic classifications. Advances in multi-omics and computational analyses uncover immune signatures that enable stratification for host-directed therapies (HDTs) targeting hyperinflammation, immunosuppression, coagulopathy or metabolic exhaustion. Integrating clinical, radiological, and immunological data through multimodal profiling is essential for developing personalized interventions. We also explore how endotyping has transformed treatment in other diseases, offering valuable insights for TB. Additionally, we present examples of how putative immune endotypes may be targeted with appropriate HDTs. In summary, this review underscores the potential of immune endotypes to advance precision medicine in TB, moving beyond one-size-fits-all treatment to improve outcomes, especially in severe and drug-resistant cases.
PMID:41930636 | DOI:10.1111/joim.70092
-
InfoQ

-
Presentation: Panel: Taking Architecture Out of the Echo Chamber
Andrew Harmel-Law and a panel of expert architects discuss the shifting practice of architecture in 2025. They explain strategies for communicating technical debt to stakeholders, the benefits of decentralized decision-making through ADRs, and the career paths of modern leaders. The panel shares insights on bridging the gap between mobile and backend teams to ensure a holistic system. By Andrew Harmel-Law, Cat Morris, Diana Montalion, Shana Dacres-Lawrence, Vanessa Formicola, Elena Stojmilova, P
Presentation: Panel: Taking Architecture Out of the Echo Chamber
Andrew Harmel-Law and a panel of expert architects discuss the shifting practice of architecture in 2025. They explain strategies for communicating technical debt to stakeholders, the benefits of decentralized decision-making through ADRs, and the career paths of modern leaders. The panel shares insights on bridging the gap between mobile and backend teams to ensure a holistic system.
By Andrew Harmel-Law, Cat Morris, Diana Montalion, Shana Dacres-Lawrence, Vanessa Formicola, Elena Stojmilova, Peter Hunter-
cs.AI, q-bio.NC updates on arXiv.org
-
Runtime Burden Allocation for Structured LLM Routing in Agentic Expert Systems: A Full-Factorial Cross-Backend Methodology
arXiv:2604.01235v1 Announce Type: new Abstract: Structured LLM routing is often treated as a prompt-engineering problem. We argue that it is, more fundamentally, a systems-level burden-allocation problem. As large language models (LLMs) become core control components in agentic AI systems, reliable structured routing must balance correctness, latency, and implementation cost under real deployment constraints. We show that this balance is shaped not only by prompts or schemas, but also by how st
Runtime Burden Allocation for Structured LLM Routing in Agentic Expert Systems: A Full-Factorial Cross-Backend Methodology
-
cs.AI, q-bio.NC updates on arXiv.org
-
Parallelized Hierarchical Connectome: A Spatiotemporal Recurrent Framework for Spiking State-Space Models
arXiv:2604.01295v1 Announce Type: new Abstract: This work presents the Parallelized Hierarchical Connectome (PHC), a general framework that upgrades temporal-only State-Space Models (SSMs) into spatiotemporal recurrent networks. Conventional SSMs achieve high-speed sequence processing through parallel scans, yet are limited to temporal recurrence without lateral or feedback interactions within a single timestep. PHC maps the diagonal SSM core to a shared Neuron Layer and inter-neuronal communic
Parallelized Hierarchical Connectome: A Spatiotemporal Recurrent Framework for Spiking State-Space Models
-
cs.AI, q-bio.NC updates on arXiv.org
-
IDEA2: Expert-in-the-loop competency question elicitation for collaborative ontology engineering
arXiv:2604.01344v1 Announce Type: new Abstract: Competency question (CQ) elicitation represents a critical but resource-intensive bottleneck in ontology engineering. This foundational phase is often hampered by the communication gap between domain experts, who possess the necessary knowledge, and ontology engineers, who formalise it. This paper introduces IDEA2, a novel, semi-automated workflow that integrates Large Language Models (LLMs) within a collaborative, expert-in-the-loop process to ad
IDEA2: Expert-in-the-loop competency question elicitation for collaborative ontology engineering
-
cs.AI, q-bio.NC updates on arXiv.org
-
Crashing Waves vs. Rising Tides: Preliminary Findings on AI Automation from Thousands of Worker Evaluations of Labor Market Tasks
arXiv:2604.01363v1 Announce Type: new Abstract: We propose that AI automation is a continuum between: (i) crashing waves where AI capabilities surge abruptly over small sets of tasks, and (ii) rising tides where the increase in AI capabilities is more continuous and broad-based. We test for these effects in preliminary evidence from an ongoing evaluation of AI capabilities across over 3,000 broad-based tasks derived from the U.S. Department of Labor O*NET categorization that are text-based and
Crashing Waves vs. Rising Tides: Preliminary Findings on AI Automation from Thousands of Worker Evaluations of Labor Market Tasks
-
cs.AI, q-bio.NC updates on arXiv.org
-
CogBias: Measuring and Mitigating Cognitive Bias in Large Language Models
arXiv:2604.01366v1 Announce Type: new Abstract: Large Language Models (LLMs) are increasingly deployed in high-stakes decision-making contexts. While prior work has shown that LLMs exhibit cognitive biases behaviorally, whether these biases correspond to identifiable internal representations and can be mitigated through targeted intervention remains an open question. We define LLM cognitive bias as systematic, reproducible deviations from correct answers in tasks with computable ground-truth ba
CogBias: Measuring and Mitigating Cognitive Bias in Large Language Models
-
cs.AI, q-bio.NC updates on arXiv.org
-
RIFT: A RubrIc Failure Mode Taxonomy and Automated Diagnostics
arXiv:2604.01375v1 Announce Type: new Abstract: Rubric-based evaluation is widely used in LLM benchmarks and training pipelines for open-ended, less verifiable tasks. While prior work has demonstrated the effectiveness of rubrics using downstream signals such as reinforcement learning outcomes, there remains no principled way to diagnose rubric quality issues from such aggregated or downstream signals alone. To address this gap, we introduce RIFT: RubrIc Failure mode Taxonomy, a taxonomy for sy
RIFT: A RubrIc Failure Mode Taxonomy and Automated Diagnostics
-
cs.AI, q-bio.NC updates on arXiv.org
-
Leveraging the Value of Information in POMDP Planning
arXiv:2604.01434v1 Announce Type: new Abstract: Partially observable Markov decision processes (POMDPs) offer a principled formalism for planning under state and transition uncertainty. Despite advances made towards solving large POMDPs, obtaining performant policies under limited planning time remains a major challenge due to the curse of dimensionality and the curse of history. For many POMDP problems, the value of information (VOI) - the expected performance gain from reasoning about observa
Leveraging the Value of Information in POMDP Planning
-
cs.AI, q-bio.NC updates on arXiv.org
-
ClawSafety: "Safe" LLMs, Unsafe Agents
arXiv:2604.01438v1 Announce Type: new Abstract: Personal AI agents like OpenClaw run with elevated privileges on users' local machines, where a single successful prompt injection can leak credentials, redirect financial transactions, or destroy files. This threat goes well beyond conventional text-level jailbreaks, yet existing safety evaluations fall short: most test models in isolated chat settings, rely on synthetic environments, and do not account for how the agent framework itself shapes s
ClawSafety: "Safe" LLMs, Unsafe Agents
-
cs.AI, q-bio.NC updates on arXiv.org
-
When AI Gets it Wong: Reliability and Risk in AI-Assisted Medication Decision Systems
arXiv:2604.01449v1 Announce Type: new Abstract: Artificial intelligence (AI) systems are increasingly integrated into healthcare and pharmacy workflows, supporting tasks such as medication recommendations, dosage determination, and drug interaction detection. While these systems often demonstrate strong performance under standard evaluation metrics, their reliability in real-world decision-making remains insufficiently understood. In high-risk domains such as medication management, even a singl
When AI Gets it Wong: Reliability and Risk in AI-Assisted Medication Decision Systems
-
cs.AI, q-bio.NC updates on arXiv.org
-
A Multi-Agent Human-LLM Collaborative Framework for Closed-Loop Scientific Literature Summarization
arXiv:2604.01452v1 Announce Type: new Abstract: Scientific discovery is slowed by fragmented literature that requires excessive human effort to gather, analyze, and understand. AI tools, including autonomous summarization and question answering, have been developed to aid in understanding scientific literature. However, these tools lack the structured, multi-step approach necessary for extracting deep insights from scientific literature. Large Language Models (LLMs) offer new possibilities for
A Multi-Agent Human-LLM Collaborative Framework for Closed-Loop Scientific Literature Summarization
-
cs.AI, q-bio.NC updates on arXiv.org
-
Infeasibility Aware Large Language Models for Combinatorial Optimization
arXiv:2604.01455v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly explored for NP-hard combinatorial optimization problems, but most existing methods emphasize feasible-instance solution generation and do not explicitly address infeasibility detection. We propose an infeasibility-aware framework that combines certifiable dataset construction, supervised fine-tuning, and LLM-assisted downstream search. For the minor-embedding problem, we introduce a new mathematical p