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Background Interferon regulatory factor-1 (IRF-1) is a master regulator of IFN-γ induced gene transcription. Previously we have shown that IRF-1 transcriptionally induces CEACAM1 via an ISRE (Interferon-Stimulated Response Element) in its promoter. CEACAM1 pre-mRNA undergoes extensive alternative splicing (AS) generating isoforms to produce either a short (S) cytoplasmic domain expressed primarily in epithelial cells or as an ITIM-containing long (L) isoform in immune cells. Methods The transcriptional and molecular mechanism of CEACAM1 minigenes AS containing promoter ISREs mutations in the breast epithelial, MDA-MB-468, cell line was detected using flow cytometry. In addition, transcriptome sequencing was utilized to determine whether IRF-1 could direct the AS of other genes as well. Tumor xenografts were used to evaluate CEACAM1 isoform expression on the leading edge of breast tumor cells. Results In the present study, we provide evidence that CEACAM1’s promoter and variable exon 7 cross-talk allowing IRF-1 to direct AS events. Transcriptome sequencing shows that IRF-1 can also induce the global AS of genes involved in regulation of growth and differentiation as well as genes of the cytokine family. Furthermore, MDA-MB-468 cells grown as tumor xenografts exhibit an AS switch to the L-isoform of CEACAM1, demonstrating that an in vivo inflammatory milieu is also capable of generating the AS switch, similar to that found in human breast cancers Mol Cancer 7:46, 2008. Conclusions The novel AS regulatory activities attributed to IRF-1 indicate that the IFN-γ response involves a global change in both gene transcription and AS in breast epithelial cells.

Both the extracellular matrix (ECM) and DNA epigenetic regulation are critical for maintaining stem cell phenotype and cancer progression. Whether and how ECM regulates epigenetic alterations to influence cancer stem cells (CSCs) remain to be explored. Here we report that ECM through laminin-integrin α6 upregulates ten-eleven translocation enzyme 3 (TET3) dioxygenase. TET3 in turn mediates DNA cytosine 5′-hydroxymethylation (5hmC) and upregulates genes critical for maintenance of glioma stem cells (GSCs). Activating integrin α6-FAK pathway increases STAT3 activity, TET3 expression and 5hmC levels in GSCs. Moreover, targeting STAT3 disrupts integrin α6-FAK signaling and inhibits TET3+ GSC maturation in vivo. STAT3 directly regulates TET3 expression and the two proteins are co-localized with 5hmC in GSC clusters. 5hmC is upregulated by STAT3 at the promoters of several tumorigenic genes, including c-Myc, known to be critical for GSCs. In vivo silencing of TET3 in GSC-enriched tumors reduces 5hmC accumulation and expression of the GSC critical genes, leading to tumor growth inhibition. TET3 expression and 5hmC accumulation also co-segregate with integrin α6 in patient malignant glioma. Thus, ECM- integrin α6-STAT3-TET3 axis regulates hydroxymethylation of genes important for GSCs, thereby increasing GSC tumorigenicity and resistance to therapies.

Interferon regulatory factor-1 (IRF-1) is a master regulator of IFN-[gamma] induced gene transcription. Previously we have shown that IRF-1 transcriptionally induces CEACAM1 via an ISRE (Interferon-Stimulated Response Element) in its promoter. CEACAM1 pre-mRNA undergoes extensive alternative splicing (AS) generating isoforms to produce either a short (S) cytoplasmic domain expressed primarily in epithelial cells or as an ITIM-containing long (L) isoform in immune cells. The transcriptional and molecular mechanism of CEACAM1 minigenes AS containing promoter ISREs mutations in the breast epithelial, MDA-MB-468, cell line was detected using flow cytometry. In addition, transcriptome sequencing was utilized to determine whether IRF-1 could direct the AS of other genes as well. Tumor xenografts were used to evaluate CEACAM1 isoform expression on the leading edge of breast tumor cells. In the present study, we provide evidence that CEACAM1's promoter and variable exon 7 cross-talk allowing IRF-1 to direct AS events. Transcriptome sequencing shows that IRF-1 can also induce the global AS of genes involved in regulation of growth and differentiation as well as genes of the cytokine family. Furthermore, MDA-MB-468 cells grown as tumor xenografts exhibit an AS switch to the L-isoform of CEACAM1, demonstrating that an in vivo inflammatory milieu is also capable of generating the AS switch, similar to that found in human breast cancers Mol Cancer 7:46, 2008. The novel AS regulatory activities attributed to IRF-1 indicate that the IFN-[gamma] response involves a global change in both gene transcription and AS in breast epithelial cells.

We present SDialog, an MIT-licensed open-source Python toolkit that unifies dialog generation, evaluation and mechanistic interpretability into a single end-to-end framework for building and analyzing LLM-based conversational agents. Built around a standardized Dialog representation, SDialog provides: (1) persona-driven multi-agent simulation with composable orchestration for controlled, synthetic dialog generation, (2) comprehensive evaluation combining linguistic metrics, LLM-as-a-judge and functional correctness validators, (3) mechanistic interpretability tools for activation inspection and steering via feature ablation and induction, and (4) audio generation with full acoustic simulation including 3D room modeling and microphone effects. The toolkit integrates with all major LLM backends, enabling mixed-backend experiments under a unified API. By coupling generation, evaluation, and interpretability in a dialog-centric architecture, SDialog enables researchers to build, benchmark and understand conversational systems more systematically.

We present SDialog, an MIT-licensed open-source Python toolkit that unifies dialog generation, evaluation and mechanistic interpretability into a single end-to-end framework for building and analyzing LLM-based conversational agents. Built around a standardized Dialog representation, SDialog provides: (1) persona-driven multi-agent simulation with composable orchestration for controlled, synthetic dialog generation, (2) comprehensive evaluation combining linguistic metrics, LLM-as-a-judge and functional correctness validators, (3) mechanistic interpretability tools for activation inspection and steering via feature ablation and induction, and (4) audio generation with full acoustic simulation including 3D room modeling and microphone effects. The toolkit integrates with all major LLM backends, enabling mixed-backend experiments under a unified API. By coupling generation, evaluation, and interpretability in a dialog-centric architecture, SDialog enables researchers to build, benchmark and understand conversational systems more systematically.

We present SDialog, an MIT-licensed open-source Python toolkit that unifies dialog generation, evaluation and mechanistic interpretability into a single end-to-end framework for building and analyzing LLM-based conversational agents. Built around a standardized Dialog representation, SDialog provides: (1) persona-driven multi-agent simulation with composable orchestration for controlled, synthetic dialog generation, (2) comprehensive evaluation combining linguistic metrics, LLM-as-a-judge and functional correctness validators, (3) mechanistic interpretability tools for activation inspection and steering via feature ablation and induction, and (4) audio generation with full acoustic simulation including 3D room modeling and microphone effects. The toolkit integrates with all major LLM backends, enabling mixed-backend experiments under a unified API. By coupling generation, evaluation, and interpretability in a dialog-centric architecture, SDialog enables researchers to build, benchmark and understand conversational systems more systematically.

The fresh water polyp Hydra belongs to the phylum Cnidaria, which diverged from the metazoan lineage before the appearance of bilaterians. In order to understand the evolution of apoptosis in metazoans, we have begun to elucidate the molecular cell death machinery in this model organism. Based on ESTs and the whole Hydra genome assembly, we have identified 15 caspases. We show that one is activated during apoptosis, four have characteristics of initiator caspases with N-terminal DED, CARD or DD domain and two undergo autoprocessing in vitro. In addition, we describe seven Bcl-2-1ike and two Bak-like proteins. For most of the Bcl-2 family proteins, we have observed mitochondrial localization. When expressed in mammalian cells, HyBak-like 1 and 2 strongly induced apoptosis. Six of the Bcl-2 family members inhibited apoptosis induced by camptothecin in mammalian ceils with HyBcl-2-1ike 4 showing an especially strong protective effect. This protein also interacted with HyBak-like 1 in a yeast two-hybrid assay. Mutation of the conserved leucine in its BH3 domain abolished both the interaction with HyBak-like 1 and the anti-apoptotic effect. Moreover, we describe novel Hydra BH-3-only proteins. One of these interacted with Bcl-2-1ike 4 and induced apoptosis in mammalian cells. Our data indicate that the evolution of a complex network for cell death regulation arose at the earliest and simplest level of multicellular organization, where it exhibited a substantially higher level of complexity than in the protostome model organisms Caenorhabditis and Drosophila.

Long-context audio reasoning is underserved in both training data and evaluation. Existing benchmarks target short-context tasks, and the open-ended generation tasks most relevant to long-context reasoning pose well-known challenges for automatic evaluation. We propose a synthetic data generation pipeline designed to serve both as a training resource and as a controlled evaluation environment, and instantiate it for first-visit doctor-patient conversations with SOAP note generation as the task. The pipeline has three stages, persona-driven dialogue generation, multi-speaker audio synthesis with overlap/pause modeling, room acoustics, and sound events, and LLM-based reference SOAP note production, built entirely on open-weight models. We release 8,800 synthetic conversations with 1.3k hours of corresponding audio and reference notes. Evaluating current open-weight systems, we find that cascaded approaches still substantially outperform end-to-end models.

BackgroundThe duodenum has become a metabolic treatment target through bariatric surgery learnings and the specific observation that bypassing, excluding or altering duodenal nutrient exposure elicits favourable metabolic changes. Duodenal mucosal resurfacing (DMR) is a novel endoscopic procedure that has been shown to improve glycaemic control in people with type 2 diabetes mellitus (T2D) irrespective of body mass index (BMI) changes. DMR involves catheter-based circumferential mucosal lifting followed by hydrothermal ablation of duodenal mucosa. This multicentre study evaluates safety and feasibility of DMR and its effect on glycaemia at 24 weeks and 12 months.MethodsInternational multicentre, open-label study. Patients (BMI 24–40) with T2D (HbA1c 59–86 mmol/mol (7.5%–10.0%)) on stable oral glucose-lowering medication underwent DMR. Glucose-lowering medication was kept stable for at least 24 weeks post DMR. During follow-up, HbA1c, fasting plasma glucose (FPG), weight, hepatic transaminases, Homeostatic Model Assessment for Insulin Resistance (HOMA-IR), adverse events (AEs) and treatment satisfaction were determined and analysed using repeated measures analysis of variance with Bonferroni correction.ResultsForty-six patients were included of whom 37 (80%) underwent complete DMR and 36 were finally analysed; in remaining patients, mainly technical issues were observed. Twenty-four patients had at least one AE (52%) related to DMR. Of these, 81% were mild. One SAE and no unanticipated AEs were reported. Twenty-four weeks post DMR (n=36), HbA1c (−10±2 mmol/mol (−0.9%±0.2%), p<0.001), FPG (−1.7±0.5 mmol/L, p<0.001) and HOMA-IR improved (−2.9±1.1, p<0.001), weight was modestly reduced (−2.5±0.6 kg, p<0.001) and hepatic transaminase levels decreased. Effects were sustained at 12 months. Change in HbA1c did not correlate with modest weight loss. Diabetes treatment satisfaction scores improved significantly.ConclusionsIn this multicentre study, DMR was found to be a feasible and safe endoscopic procedure that elicited durable glycaemic improvement in suboptimally controlled T2D patients using oral glucose-lowering medication irrespective of weight loss. Effects on the liver are examined further.Trial registration number NCT02413567

Sediments cored along the southwestern Iberian margin during Integrated Ocean Drilling Program Expedition 339 provide constraints on Mediterranean Outflow Water (MOW) circulation patterns from the Pliocene epoch to the present day. After the Strait of Gibraltar opened (5.33 million years ago), a limited volume of MOW entered the Atlantic. Depositional hiatuses indicate erosion by bottom currents related to higher volumes of MOW circulating into the North Atlantic, beginning in the late Pliocene. The hiatuses coincide with regional tectonic events and changes in global thermohaline circulation (THC). This suggests that MOW influenced Atlantic Meridional Overturning Circulation (AMOC), THC, and climatic shifts by contributing a component of warm, saline water to northern latitudes while in turn being influenced by plate tectonics.