Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Who Pays for Open Review? Visible Author Reputation and Its Effect on Ratings
arXiv:2609.11983v1 Announce Type: cross Abstract: An OpenReview bug in November 2025 broke anonymity at several conferences and prompted calls for open review, which motivate us to ask what shifting from blind to open would mean for authors. Analyzing over 18,000 reviewed submissions to ICLR 2026, split into de facto open and blind groups by arXiv preprint timing, we find that ratings rise with author reputation under both mechanisms, with a steeper slope under open review that is statistically
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(Multiomics OR Omics) AND (Pancreatic)
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The metastatic spectrum in functional and non-functional NENs: mechanistic insights from multi-omics
Front Endocrinol (Lausanne). 2026 Aug 27;17:1782791. doi: 10.3389/fendo.2026.1782791. eCollection 2026.ABSTRACTNeuroendocrine neoplasms (NENs) are biologically heterogeneous tumors in which differentiation/grade and hormonal functionality are intersecting but non-equivalent axes. This review focuses on functional and non-functional well-differentiated neuroendocrine tumors (NETs), principally gastroenteropancreatic and pancreatic NETs, and critically evaluates how site, lineage, stage, tumor bur
The metastatic spectrum in functional and non-functional NENs: mechanistic insights from multi-omics
Front Endocrinol (Lausanne). 2026 Aug 27;17:1782791. doi: 10.3389/fendo.2026.1782791. eCollection 2026.
ABSTRACT
Neuroendocrine neoplasms (NENs) are biologically heterogeneous tumors in which differentiation/grade and hormonal functionality are intersecting but non-equivalent axes. This review focuses on functional and non-functional well-differentiated neuroendocrine tumors (NETs), principally gastroenteropancreatic and pancreatic NETs, and critically evaluates how site, lineage, stage, tumor burden, genomic and epigenetic alterations, immune-stromal remodeling, metabolic adaptation, microbiome-associated signals, and treatment pressure converge on metastasis and recurrence. Apparent outcome differences by functionality are inconsistent after clinicopathological adjustment: non-functional presentation is often enriched for delayed diagnosis and adverse features, whereas functional subtypes range from typically indolent insulinomas to clinically aggressive hormone-producing tumors. We reconcile these observations through a layered model in which lineage-defining alterations and chromatin/telomere programs establish cellular state; signaling and metabolic plasticity enable stress adaptation; and hypoxia, angiogenesis, immune cells, fibroblasts, extracellular matrix, and therapy create selective niches for dissemination and relapse. We also define computational strategies for heterogeneous multi-omics integration and a staged biomarker-validation pathway. Evidence remains dominated by pancreatic NETs, and causal support is weakest for microbiome-functionality relationships and several proposed cross-omic links. A spectrum-based framework is therefore most useful when it generates testable, site- and grade-specific hypotheses rather than treating functionality as an isolated prognostic variable.
PMID:42724134 | PMC:PMC13559159 | DOI:10.3389/fendo.2026.1782791
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npj Digital Medicine
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Deep learning combined habitat radiomics analysis of central lymph node metastasis in papillary thyroid carcinoma
npj Digital Medicine, Published online: 12 September 2026; doi:10.1038/s41746-026-03203-2Deep learning combined habitat radiomics analysis of central lymph node metastasis in papillary thyroid carcinoma
Deep learning combined habitat radiomics analysis of central lymph node metastasis in papillary thyroid carcinoma
npj Digital Medicine, Published online: 12 September 2026; doi:10.1038/s41746-026-03203-2
Deep learning combined habitat radiomics analysis of central lymph node metastasis in papillary thyroid carcinoma-
Molecular Therapy
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Pan-cancer oncolytic virotherapy through disruption of tumor cell mitochondrial dynamics
Li and colleagues identified RhoA as a “redox rheostat” governing mitochondrial dynamics during oncolytic virotherapy and thereby engineered rNDV-RHOA, an NDV-based oncolytic virus overexpressing RhoA. This tumor-targeted RhoA overexpression synergizes oxidative stress and viral oncolysis, transcending conventional oncolysis by surmounting tumor heterogeneity through exploiting inherent tumor redox dependency.
Pan-cancer oncolytic virotherapy through disruption of tumor cell mitochondrial dynamics
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Molecular Therapy
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Precise hepatic base editing of ASGR1 enables robust and durable LDLR-independent lipid lowering in vivo
Yang and colleagues demonstrate that lipid nanoparticle-mediated precise hepatic ASGR1 base editing safely produces robust and durable lipid lowering in an LDLR-deficient mouse model of familial hypercholesterolemia. Their work further benchmarks the lipid-lowering effects of ASGR1 and ANGPTL3 editing and supports combined ASGR1/ANGPTL3 targeting for enhanced cholesterol lowering.
Precise hepatic base editing of ASGR1 enables robust and durable LDLR-independent lipid lowering in vivo
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Nature - Issue - nature.com science feeds
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Ancient proteins identify various Denisovan remains from Southwest China
Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-10976-9Identification and proteomic analysis of bone fragments and teeth from an excavation in Southwest China provide insight into the evolution and phenotype of Denisovans and fill a geographical gap in their documented distribution.
Ancient proteins identify various Denisovan remains from Southwest China
Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-10976-9
Identification and proteomic analysis of bone fragments and teeth from an excavation in Southwest China provide insight into the evolution and phenotype of Denisovans and fill a geographical gap in their documented distribution.-
Cell
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Sexual dimorphism in the complete Drosophila male central nervous system connectome
The Drosophila whole male central nervous system connectome enables end-to-end analysis of sensorimotor circuits. Comparison with existing female datasets shows that brain-wide wiring differences between the sexes are concentrated in higher centers.
Sexual dimorphism in the complete Drosophila male central nervous system connectome
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Cell
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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.
Genomics and social practices at Mogou and other Gansu sites during prehistoric trans-Eurasian exchange
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Nature Cancer
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Author Correction: Low-protein diet enhances antitumor immunity in pancreatic cancer through microbiota-derived UDP-galactose
Nature Cancer, Published online: 25 August 2026; doi:10.1038/s43018-026-01241-zAuthor Correction: Low-protein diet enhances antitumor immunity in pancreatic cancer through microbiota-derived UDP-galactose
Author Correction: Low-protein diet enhances antitumor immunity in pancreatic cancer through microbiota-derived UDP-galactose
Nature Cancer, Published online: 25 August 2026; doi:10.1038/s43018-026-01241-z
Author Correction: Low-protein diet enhances antitumor immunity in pancreatic cancer through microbiota-derived UDP-galactose-
cs.AI, q-bio.NC updates on arXiv.org
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Cascade-KDE: Robust Time-Series Restoration under Out-of-Distribution Impulse Corruptions
arXiv:2605.24055v1 Announce Type: cross Abstract: Real-world time-series data in industrial sensing, healthcare, and energy systems is often corrupted by a mixture of Gaussian noise and occasional large-magnitude impulse outliers. For tasks that depend on local shape, such as ECG morphology analysis and battery degradation monitoring, the main requirement is not only low reconstruction error but also preservation of derivative peaks and task-critical features. We propose Cascade-KDE, a training
Cascade-KDE: Robust Time-Series Restoration under Out-of-Distribution Impulse Corruptions
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cs.AI, q-bio.NC updates on arXiv.org
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Treatment Effect Estimation with Differentiated Networked Effect on Graph Data
arXiv:2605.24358v1 Announce Type: cross Abstract: Estimating individual treatment effect (ITE) from observational graph data is crucial for decision-making in the fields such as commerce and medicine. This task is challenging due to interference, where individual outcomes can be influenced by the treatments and covariates of their neighbors. Existing methods attempt to model such interference for accurate ITE estimation. However, a critical issue is often overlooked: differentiated networked ef
Treatment Effect Estimation with Differentiated Networked Effect on Graph Data
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cs.AI, q-bio.NC updates on arXiv.org
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Safety in Embodied AI: A Survey of Risks, Attacks, and Defenses
arXiv:2605.02900v2 Announce Type: replace-cross Abstract: Embodied Artificial Intelligence (Embodied AI) integrates perception, cognition, planning, and interaction into agents that operate in open-world, safety-critical environments. As these systems gain autonomy and enter domains such as transportation, healthcare, and industrial or assistive robotics, ensuring their safety becomes both technically challenging and socially indispensable. Unlike digital AI systems, embodied agents must act un
Safety in Embodied AI: A Survey of Risks, Attacks, and Defenses
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(Multiomics OR Omics) AND (Pancreatic)
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CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection
J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an int
CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection
J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.
ABSTRACT
BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.
METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8+ T-cell co-culture experiments.
RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR = 1.403, p = 0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8+ T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8+ T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8+ T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.
CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1+ TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.
PMID:42185899 | DOI:10.1186/s12967-026-08301-z
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Omics in Hepatocellular
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CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection
J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an int
CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection
J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.
ABSTRACT
BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.
METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8+ T-cell co-culture experiments.
RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR = 1.403, p = 0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8+ T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8+ T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8+ T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.
CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1+ TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.
PMID:42185899 | DOI:10.1186/s12967-026-08301-z
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection
J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an int
CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection
J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.
ABSTRACT
BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.
METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8+ T-cell co-culture experiments.
RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR = 1.403, p = 0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8+ T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8+ T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8+ T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.
CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1+ TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.
PMID:42185899 | DOI:10.1186/s12967-026-08301-z
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Cell Death Discovery nature.com science feeds
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Cuproptosis causes meiotic metaphase I arrest by disrupting mitochondrial functions in oocytes
Cell Death Discovery, Published online: 23 May 2026; doi:10.1038/s41420-026-03168-xCuproptosis causes meiotic metaphase I arrest by disrupting mitochondrial functions in oocytes
Cuproptosis causes meiotic metaphase I arrest by disrupting mitochondrial functions in oocytes
Cell Death Discovery, Published online: 23 May 2026; doi:10.1038/s41420-026-03168-x
Cuproptosis causes meiotic metaphase I arrest by disrupting mitochondrial functions in oocytes-
Pulmonary nodule
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The 2025 lung cancer landscape: advances in screening, molecular taxonomy and therapeutic strategy: a narrative review
Transl Lung Cancer Res. 2026 Mar 23;15(3):62. doi: 10.21037/tlcr-2025-1-1477. Epub 2026 Mar 18.ABSTRACTBACKGROUND AND OBJECTIVE: In 2025, lung cancer research advanced rapidly across the disease continuum, from population-level risk assessment and screening to mechanistic studies of early carcinogenesis and therapeutic innovation in perioperative and metastatic settings. A key shift moved beyond a smoking-centred paradigm toward a multidimensional risk framework reflecting the growing burden amo
The 2025 lung cancer landscape: advances in screening, molecular taxonomy and therapeutic strategy: a narrative review
Transl Lung Cancer Res. 2026 Mar 23;15(3):62. doi: 10.21037/tlcr-2025-1-1477. Epub 2026 Mar 18.
ABSTRACT
BACKGROUND AND OBJECTIVE: In 2025, lung cancer research advanced rapidly across the disease continuum, from population-level risk assessment and screening to mechanistic studies of early carcinogenesis and therapeutic innovation in perioperative and metastatic settings. A key shift moved beyond a smoking-centred paradigm toward a multidimensional risk framework reflecting the growing burden among never-smokers and the roles of air pollution, occupational exposures, and systemic metabolic-inflammatory states. This narrative review aims to synthesize influential 2025 evidence across prevention, diagnosis, treatment, and survivorship, and to identify convergent themes and translational gaps relevant to clinical practice and policy.
METHODS: We performed a narrative synthesis of influential lung cancer studies published in major international journals in 2025. Evidence was organized along a clinically oriented pathway spanning carcinogenesis and screening, precision diagnosis, treatment optimization in resectable and advanced disease, and survivorship, emphasizing practice-informing trials, high-impact translational research, and implementation-relevant technologies.
KEY CONTENT AND FINDINGS: Lineage tracing, single-cell and spatial omics, and evolutionary inference refined concepts of field cancerization, clonal selection, and copy-number-driven fitness. In small-cell lung cancer, evidence further supported neuronal coupling and synapse-like programs as potentially tractable vulnerabilities. Clinically, low-dose computed tomography (CT) strategies and data-informed nodule thresholds aimed to balance under-detection against over-surveillance harms. In diagnostics, artificial intelligence (AI) models increasingly inferred molecular features from routine histopathology ("virtual molecular testing") and should be regarded as decision support requiring prospective validation, population calibration, and explicit failure-mode reporting. Multimodal approaches integrating imaging with circulating tumor DNA (ctDNA) improved feasibility in tissue-limited settings, but clinical utility remains contingent on assay standardization and pathway-level implementation. In resectable disease, longer follow-up consolidated neoadjuvant chemo-immunotherapy for selected patients, while ctDNA kinetics emerged as a candidate biomarker for response-adaptive escalation and de-escalation. In advanced non-small cell lung cancer (NSCLC), phase III evidence for antibody-drug conjugates and bispecific antibodies began reshaping sequencing, while highlighting challenges in toxicity, access, affordability, and immature overall survival in several programs.
CONCLUSIONS: The 2025 landscape reflects coordinated progress in risk conceptualization, biology, diagnostics, and therapeutics, yet gaps in validation, standardization, and real-world deliverability persist. Priorities include prospective evaluation of AI- and ctDNA-enabled pathways, toxicity-informed sequencing, and equitable implementation aligned with health-system capacity.
PMID:41982682 | PMC:PMC13071762 | DOI:10.21037/tlcr-2025-1-1477
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cs.AI, q-bio.NC updates on arXiv.org
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TABQAWORLD: Optimizing Multimodal Reasoning for Multi-Turn Table Question Answering
arXiv:2604.03393v1 Announce Type: new Abstract: Multimodal reasoning has emerged as a powerful framework for enhancing reasoning capabilities of reasoning models. While multi-turn table reasoning methods have improved reasoning accuracy through tool use and reward modeling, they rely on fixed text serialization for table state readouts. This introduces representation errors in table encoding that significantly accumulate over multiple turns. Such accumulation is alleviated by tabular grounding
TABQAWORLD: Optimizing Multimodal Reasoning for Multi-Turn Table Question Answering
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cs.AI, q-bio.NC updates on arXiv.org
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ActionNex: A Virtual Outage Manager for Cloud
arXiv:2604.03512v1 Announce Type: new Abstract: Outage management in large-scale cloud operations remains heavily manual, requiring rapid triage, cross-team coordination, and experience-driven decisions under partial observability. We present \textbf{ActionNex}, a production-grade agentic system that supports end-to-end outage assistance, including real-time updates, knowledge distillation, and role- and stage-conditioned next-best action recommendations. ActionNex ingests multimodal operationa
ActionNex: A Virtual Outage Manager for Cloud
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cs.AI, q-bio.NC updates on arXiv.org
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Combating Data Laundering in LLM Training
arXiv:2604.01904v1 Announce Type: cross Abstract: Data rights owners can detect unauthorized data use in large language model (LLM) training by querying with proprietary samples. Often, superior performance (e.g., higher confidence or lower loss) on a sample relative to the untrained data implies it was part of the training corpus, as LLMs tend to perform better on data they have seen during training. However, this detection becomes fragile under data laundering, a practice of transforming the