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cs.AI, q-bio.NC updates on arXiv.org
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DeKeyNLU: Enhancing Natural Language to SQL Generation through Task Decomposition and Keyword Extraction
arXiv:2509.14507v2 Announce Type: replace Abstract: Natural Language to SQL (NL2SQL) provides a new model-centric paradigm that simplifies database access for non-technical users by converting natural language queries into SQL commands. Recent advancements, particularly those integrating Retrieval-Augmented Generation (RAG) and Chain-of-Thought (CoT) reasoning, have made significant strides in enhancing NL2SQL performance. However, challenges such as inaccurate task decomposition and keyword ex
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(Multiomics OR Omics) AND (Pancreatic)
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PIVOT: an open-source tool for multi-omic spatial data registration
bioRxiv [Preprint]. 2025 Jun 8:2025.06.08.658506. doi: 10.1101/2025.06.08.658506.ABSTRACTAdvances in spatial profiling have resulted in the generation of multi-omic atlases that span biological scales. In general, multiple workflows are required for image registration, coordinate registration, and spot deconvolution to integrate modalities. To improve the throughput of registration of multi-omic cohorts, we introduce PIVOT, a user-friendly and open-source interface for streamlined nonlinear regi
PIVOT: an open-source tool for multi-omic spatial data registration
bioRxiv [Preprint]. 2025 Jun 8:2025.06.08.658506. doi: 10.1101/2025.06.08.658506.
ABSTRACT
Advances in spatial profiling have resulted in the generation of multi-omic atlases that span biological scales. In general, multiple workflows are required for image registration, coordinate registration, and spot deconvolution to integrate modalities. To improve the throughput of registration of multi-omic cohorts, we introduce PIVOT, a user-friendly and open-source interface for streamlined nonlinear registration. We demonstrate PIVOT's strengths through registration of three multi-omic datasets, and show comparison of its performance to existing workflows.
PMID:40661390 | PMC:PMC12259011 | DOI:10.1101/2025.06.08.658506
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Spatial Proteomics and Transcriptomics Reveal Early Immune Cell Organization in Pancreatic Intraepithelial Neoplasia
JCI Insight. 2025 Jun 26:e191595. doi: 10.1172/jci.insight.191595. Online ahead of print.ABSTRACTPancreatic ductal adenocarcinoma (PDAC) has a poor survival rate due to late detection. PDAC arises from precursor microscopic lesions, termed pancreatic intraepithelial neoplasia (PanIN), that develop at least a decade before overt disease--this provides an opportunity to intercept PanIN-to-PDAC progression. However, immune interception strategies require full understanding of PanIN and PDAC cellula
Spatial Proteomics and Transcriptomics Reveal Early Immune Cell Organization in Pancreatic Intraepithelial Neoplasia
JCI Insight. 2025 Jun 26:e191595. doi: 10.1172/jci.insight.191595. Online ahead of print.
ABSTRACT
Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate due to late detection. PDAC arises from precursor microscopic lesions, termed pancreatic intraepithelial neoplasia (PanIN), that develop at least a decade before overt disease--this provides an opportunity to intercept PanIN-to-PDAC progression. However, immune interception strategies require full understanding of PanIN and PDAC cellular architecture. Surgical specimens containing PanIN and PDAC lesions from a unique cohort of five treatment-naïve patients with PDAC were surveyed using spatial-omics (proteomic and transcriptomic). Findings were corroborated by spatial proteomics of PanIN and PDAC from tamoxifen-inducible KPC (tiKPC) mice. We uncovered the organization of lymphoid cells into tertiary lymphoid structures (TLSs) adjacent to PanIN lesions. These TLSs lacked CD21+CD23+ B cells compared to more mature TLSs near the PDAC border. PanINs harbored mostly CD4+ T cells with fewer Tregs and exhausted T cells than PDAC. Peri-tumoral space was enriched with naïve CD4+ and central memory T cells. These observations highlight the opportunity to modulate the immune microenvironment in PanINs before immune exclusion and immunosuppression emerge during progression into PDAC.
PMID:40569674 | DOI:10.1172/jci.insight.191595