The protective effect of Amitriptyline on experimental colitis through inhibiting TLR4/MD2 signaling pathway.

Amitriptyline, a pleiotropic tricyclic antidepressant, possesses anti-oxidant and anti-inflammatory properties. Despite its diverse benefits, the specific effects of amitriptyline on IBD are not yet well defined. To explore this, we utilized a DSS-induced colitis model to examine the anti-inflammatory effects of amitriptyline and the underlying mechanisms by which it operates. Our research revealed that amitriptyline is effective in alleviating several pathological manifestations associated with colitis. This includes improvements in body weight retention, reductions in DAI, lessening of colon length shortening, and repair of colonic mucosal damage. Treatment with amitriptyline significantly protected mucosal injury by preserving the population of goblet cells and increasing the expression of tight junction proteins. Furthermore, we observed that amitriptyline effectively countered immune cell infiltration, specifically neutrophils and macrophages, while simultaneously lowering the levels of inflammatory cytokines such as TNF-α, IL-1ß, and IL-6. Additionally, RNA sequencing analysis pointed to the potential involvement of the TLR pathway in the anti-colitic effects induced by amitriptyline. Subsequent Western blot analysis indicated that amitriptyline significantly inhibited the TLR4-mediated NF-κB signaling pathway. To bolster our findings, in vitro studies demonstrated that amitriptyline down-regulated the TLR4/NF-κB/MAPK signaling cascades in mouse macrophages stimulated with LPS. Further molecular investigations revealed that amitriptyline was able to suppress the elevated expression of MD-2 that LPS stimulation typically induces. In summary, our findings suggest that amitriptyline effectively mitigates DSS-induced colitis in mice through the inhibition of TLR4/MD-2 pathway signaling, indicating its potential repurposing for IBD treatment. Significance Statement The potential of utilizing amitriptyline in treating IBD appears promising, leveraging its established safety and dosing profile as an antidepressant. Our observations show that amitriptyline can alleviate pathological symptoms, inflammation, and intestinal mucosal damage in mice with colitis induced by DSS. The protective effect observed appear to be linked to the inhibition of the TLR4/MD2 signaling pathway. By exploring novel applications for existing medications, we can optimize amitriptyline's efficacy and broaden its impact in both medical and commercial contexts.

Rethinking Scientific Summarization Evaluation: Grounding Explainable Metrics on Facet-aware Benchmark.

The summarization capabilities of pretrained and large language models (LLMs) have been widely validated in general areas, but their use in scientific corpus, which involves complex sentences and specialized knowledge, has been less assessed. This paper presents conceptual and experimental analyses of scientific summarization, highlighting the inadequacies of traditional evaluation methods, such as $n$-gram, embedding comparison, and QA, particularly in providing explanations, grasping scientific concepts, or identifying key content. Subsequently, we introduce the Facet-aware Metric (FM), employing LLMs for advanced semantic matching to evaluate summaries based on different aspects. This facet-aware approach offers a thorough evaluation of abstracts by decomposing the evaluation task into simpler subtasks.Recognizing the absence of an evaluation benchmark in this domain, we curate a Facet-based scientific summarization Dataset (FD) with facet-level annotations. Our findings confirm that FM offers a more logical approach to evaluating scientific summaries. In addition, fine-tuned smaller models can compete with LLMs in scientific contexts, while LLMs have limitations in learning from in-context information in scientific domains. This suggests an area for future enhancement of LLMs.

Ecological risk of synthetic phenolic antioxidants: A study based on their spatial distribution in water, sediment, and soil from the Yangtze River Delta, China.

Environmental occurrence and risks of novel synthetic phenolic antioxidants (SPAs) remain largely unclear. By using a typical algae (Chlorella pyrenoidosa) as model organism, we evaluated the ecological risks of both traditional and novel SPAs, based on their concentrations in water, sediment, and soil collected from the Yangtze River Delta, China. Detection frequencies (DFs) of 10 novel SPAs were 25-100% in water, 3-100% in sediment, and 0-100% in soil, with geometric means (GMs) of 2700 ng/L, 1270 ng/g, and 2440 ng/g, respectively. For 8 traditional SPAs, DFs were 50-100% (GM: 680 ng/L), 3-100% (534 ng/g), and 47-100% (2240 ng/g) in water, sediment, and soil, respectively. AO3114 was the main pollutant in water, while AO1010 dominated in sediment and soil. Notably, low-molecular-weight SPAs showed migration behavior from sediment to water. Four SPAs (AO626, AO1035, AO1098, and AO1076) showed dose- and time-dependent toxicity on Chlorella pyrenoidosa. As time progressed, sediment-released SPAs became more toxic than those in water. Two SPAs (AO1135 and BHT-Q) posed high risks (RQW > 1) to green algae, daphnia, and fish. The SPA mixture exhibited high risks (RQmix > 1) to these organisms, increasing with the trophic level. This research holds valuable guidance for further SPA risk assessments.

Resistant starch confers protection of dietary against diabetic cardiomyopathy.

Long-term dysfunction of glucose metabolism causes cardiac dysfunction called diabetic cardiomyopathy (DCM). To investigate the effect and underlying mechanism of RS on the process of DCM, mouse models induced by a high-fat diet (HFD) and streptozotocin (STZ) were fed RS (2 g/kg/day) and vehicle treatment (by oral gavage) for 14 weeks. Various analyses, including qRT-PCR, western blot, immunofluorescence staining, histology staining, cardiac function, and diversity detection of intestinal microbiota were performed. RS intervention could directly improve myocardial fibrosis, hypertrophy, apoptosis, and cardiac insufficiency in DCM. These beneficial effects may be achieved by elevating the expression of IGF-1, activating the ERK phosphorylation. Furthermore, by carrying out nano LC-MS/MS analyses and 16S rDNA sequencing, we found RS might primarily affect proteins in the cytoplasm involved in post-translational modification, protein conversion, and signal transduction mechanisms. RS altered intestinal microbiota and improved intestinal mucosal permeability towards a favorable direction in DCM. This multidimensional assessment of RS suggests that might be a promising approach towards the treatment of DCM.

Reduced B cell frequencies in cord blood of HIV-exposed uninfected infants: an immunological and transcriptomic analysis.

Introduction: In the course of immune development, HIV-exposed uninfected (HEU) infants exhibit abnormal immune function and increased infectious morbidity compared to HIV-unexposed uninfected (HUU) infants. Yet the specific functional phenotypes and regulatory mechanisms associated with in-utero HIV and/or ART exposure remain largely obscure. Methods: We utilized flow cytometry and RNA-seq technologies to conduct the immunological and transcriptomic profiling in cord blood from 9 HEU mother-infant pairs and 24 HUU pairs. On top of that, we compared the cord blood dataset with the maternal venous blood dataset to characterize unique effects induced by in-utero HIV and/or ART exposure. Results: Flow cytometry immunophenotyping revealed that the level of B lymphocyte subsets was significantly decreased in HEU cord blood as compared to HUU (P < 0.001). Expression profiling-based cell abundance assessment, includes CIBERSORT and ssGSEA algorithm, showed a significantly reduced abundance of naive B cells in HEU cord blood (both P < 0.05), supporting the altered composition of B lymphocyte subsets in HEU. Functional enrichment analysis demonstrated suppressed innate immune responses and impaired immune regulatory function of B cells in HEU cord blood. Furthermore, through differential expression analysis, co-expression network analysis using WGCNA, and feature selection analysis using LASSO, we identified a 4-gene signature associated with HEU status. This signature effectively assesses B cell levels in cord blood, enabling discrimination between HEU and HUU infants. Discussion: Our study provides the first comprehensive immunological and transcriptomic characterization of HEU cord blood. Additionally, we establish a 4-gene-based classifier that holds potential for predict immunological abnormalities in HEU infants.

Site effects in multisite fetal brain MRI: morphological insights into early brain development.

OBJECTIVE: To evaluate multisite effects on fetal brain MRI. Specifically, to identify crucial acquisition factors affecting fetal brain structural measurements and developmental patterns, while assessing the effectiveness of existing harmonization methods in mitigating site effects. MATERIALS AND METHODS: Between May 2017 and March 2022, T2-weighted fast spin-echo sequences in-utero MRI were performed on healthy fetuses from retrospectively recruited pregnant volunteers on four different scanners at four sites. A generalized additive model (GAM) was used to quantitatively assess site effects, including field strength (FS), manufacturer (M), in-plane resolution (R), and slice thickness (ST), on subcortical volume and cortical morphological measurements, including cortical thickness, curvature, and sulcal depth. Growth models were selected to elucidate the developmental trajectories of these morphological measurements. Welch's test was performed to evaluate the influence of site effects on developmental trajectories. The comBat-GAM harmonization method was applied to mitigate site-related biases. RESULTS: The final analytic sample consisted of 340 MRI scans from 218 fetuses (mean GA, 30.1 weeks ± 4.4 [range, 21.7-40 weeks]). GAM results showed that lower FS and lower spatial resolution led to overestimations in selected brain regions of subcortical volumes and cortical morphological measurements. Only the peak cortical thickness in developmental trajectories was significantly influenced by the effects of FS and R. Notably, ComBat-GAM harmonization effectively removed site effects while preserving developmental patterns. CONCLUSION: Our findings pinpointed the key acquisition factors in in-utero fetal brain MRI and underscored the necessity of data harmonization when pooling multisite data for fetal brain morphology investigations. KEY POINTS: Question How do specific site MRI acquisition factors affect fetal brain imaging? Finding Lower FS and spatial resolution overestimated subcortical volumes and cortical measurements. Cortical thickness in developmental trajectories was influenced by FS and in-plane resolution. Clinical relevance This study provides important guidelines for the fetal MRI community when scanning fetal brains and underscores the necessity of data harmonization of cross-center fetal studies.

Migration patterns of organophosphate esters from plastic food packaging simulants to foods: Donors, behaviours, and influencing factors.

In recent years, organophosphate esters (OPEs) have been widely produced and used as flame retardants and plasticizer additives, posing significant ecological and health risks. Dietary intake is considered to be the primary route of human exposure to OPEs. Plastic food packaging materials are considered a crucial source for contamination of OPEs in food. However, the migration behaviour of OPEs from plastic food packaging materials into foods has received limited attention. In this study, we employed a novel method to prepare migration donors containing 13 kinds of OPEs. The migration behaviours of OPEs from food packaging simulants (polypropylene) to foods (full-fat milk powder) were simulated, and factors influencing the migration of OPEs were examined, including the properties of the target compounds, migration temperature, fat content of the migration receptors, and mass transfer mode. The results indicated that OPEs exhibited a significant migration tendency. Low molecular weight OPEs (< 300 Da) had faster migration efficiency compared to high molecular weight OPEs. The mean migration efficiencies of various OPEs showed a significant negative correlation with their molecular weights (p < 0.01) and a significant positive correlation with temperature (p < 0.01). Except for resorcinol bis(diphenyl phosphate) (RDP), which showed almost no migration, the mean migration efficiencies of other OPEs at 25 °C, 40 °C, and 60 °C were 3.1-37.5 %, 9.0-60.0 %, and 23.9-80.4 %, respectively. Most of the OPEs demonstrated higher migration efficiency in high-fat content food than low-fat content food. The migration of OPEs from food packaging simulants to foods primarily occurred through contact rather than gas-phase mass transfer. Overall, this study uncovers the migration behaviours of OPEs from food packaging simulants to foods and scrutinized the relevant factors influencing the migration. It is expected that the research in terms of the contamination control of OPEs in food will benefit from this work.

RNA-binding protein LSM7 facilitates breast cancer metastasis through mediating alternative splicing of CD44.

AIMS: The RNA-binding protein LSM7 is essential for RNA splicing, acting as a key component of the spliceosome complex; however, its specific role in breast cancer (BC) has not been extensively investigated. MATERIALS AND METHODS: LSM7 expression in BC samples was evaluated through bioinformatics analysis and immunohistochemistry. The impact of LSM7 on promoting metastatic tumor characteristics was examined using transwell and wound healing assays, as well as an orthotopic xenograft model. Additionally, the involvement of LSM7 in alternative splicing of CD44 was explored via RNA immunoprecipitation and third-generation sequencing. The regulatory role of TCF3 in modulating LSM7 gene expression was further elucidated using luciferase reporter assays and chromatin immunoprecipitation. KEY FINDINGS: Our findings demonstrate that LSM7 was significantly overexpressed in metastatic BC tissues and was associated with poor prognostic outcomes in patients with BC. LSM7 overexpression markedly increased the migratory and invasive capabilities of BC cells in vitro and significantly promoted spontaneous lung metastasis in vivo. Furthermore, RIP-seq analysis revealed that LSM7 binded to CD44 RNA, enhancing the expression of its alternatively spliced isoform CD44s, thereby driving BC metastasis and invasion. Additionally, the transcription factor TCF3 was found to activate LSM7 transcription by directly binding to its promoter. SIGNIFICANCE: In summary, this study highlights the pivotal role of LSM7 in the production of the CD44s isoform and the promotion of breast cancer metastasis. Targeting the TCF3/LSM7/CD44s axis may offer a promising therapeutic strategy for breast cancer treatment.

Additional EBUS-guided intralesional amphotericin B injection combined systemic intravenous therapy in pulmonary mucormycosis: a case report.

Mucormycosis is an invasive fungal infection that can result in severe lung infections, with pulmonary mucormycosis (PM) being one of the most prevalent manifestations. Prompt diagnosis is crucial for patient survival, as PM often exhibits rapid clinical progression and carries a high fatality rate. Broncho-alveolar lavage fluid or endobronchial biopsy (EBB) has been commonly employed for diagnosing PM, although there is limited mention of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) in the literature. In this report, we present a case of PM in a patient with diabetes. While EBB did not yield evidence of Rhizopus infection, a definitive diagnosis was obtained through EBUS-TBNA. The patient underwent combination therapy, including oral medication, nebulization, and EBUS-guided intrafocal amphotericin B injection, which resulted in significant improvement following the failure of initial therapy with amphotericin B injection cholesterol sulfate complex. Our case highlights the potential of EBUS-TBNA not only for mediastinal lymphadenopathy but also for obtaining extraluminal lesion specimens. Furthermore, for patients with an inadequate response to mono-therapy and no access to surgical therapy, the addition of EBUS-guided intralesional amphotericin B injection to systemic intravenous therapy may yield unexpected effects.

Nationwide Investigation on Organophosphate Flame Retardants in Tea from China: Migration from Packaging Materials and Implications for Global Risk Assessment.

In this study, we measured 15 common organophosphate flame retardants (OPFRs) in six categories of tea samples across China. OPFRs were found in all the tea samples, with the total concentrations of OPFRs (∑OPFRs) at 3.44-432 ng/g [geometric mean (GM): 17.6 ng/g]. Triphenyl phosphate (TPhP) was the dominant OPFR, accounting for 39.0-76.2% of ∑OPFRs across all tea categories. The potential factors influencing the residual OPFRs in tea were thoroughly examined, including the agricultural environment, fermentation, and packaging of teas. Tea packaging materials (TPMs) were then identified as the primary sources of OPFRs in teas. The migration test revealed that OPFRs with lower molecular weights and log Kow values exhibited a higher propensity for facilitating the migration of OPFRs from TPMs to teas. The estimated daily intakes of OPFRs from teas were relatively higher for the general populations in Mauritania, Gambia, Togo, Morocco, and Senegal (3.18-9.79 ng/kg bw/day) than China (3.12 ng/kg bw/day). The health risks arising from OPFRs in Chinese teas were minor. This study established a baseline concentration and demonstrated the contamination sources of OPFRs in Chinese tea for the first time, with an emphasis on enhancing the hygiene standards for TPMs.

Closed-Loop Control of Melt Pool Temperature during Laser Metal Deposition.

Laser metal deposition (LMD) is a technology for the production of near-net-shape components. It is necessary to control the manufacturing process to obtain good geometrical accuracy and metallurgical properties. In the present study, a closed-loop control method of melt pool temperature for the deposition of small Ti6Al4V blocks in open environment was proposed. Based on the developed melt pool temperature sensor and deposition height sensor, a closed-loop control system and proportional-integral (PI) controller were developed and tested. The results show that with a PI temperature controller, the melt pool temperature tends to the desired value and remains stable. Compared to the deposition block without the controller, a flatter surface and no oxidation phenomenon are obtained with the controller.

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports.

In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging. Current metrics, such as Conventional Natural Language Generation (NLG) and Clinical Efficacy (CE), often fall short in capturing the semantic intricacies of clinical contexts or overemphasize clinical details, undermining report clarity. To overcome these issues, our proposed method synergizes the expertise of professional radiologists with Large Language Models (LLMs), like GPT-3.5 and GPT-4. Utilizing In-Context Instruction Learning (ICIL) and Chain of Thought (CoT) reasoning, our approach aligns LLM evaluations with radiologist standards, enabling detailed comparisons between human and AI-generated reports. This is further enhanced by a Regression model that aggregates sentence evaluation scores. Experimental results show that our "Detailed GPT-4 (5-shot)" model achieves a 0.48 score, outperforming the METEOR metric by 0.19, while our "Regressed GPT-4" model shows even greater alignment with expert evaluations, exceeding the best existing metric by a 0.35 margin. Moreover, the robustness of our explanations has been validated through a thorough iterative strategy. We plan to publicly release annotations from radiology experts, setting a new standard for accuracy in future assessments. This underscores the potential of our approach in enhancing the quality assessment of AI-driven medical reports.

RANKL/RANK signaling recruits Tregs via the CCL20-CCR6 pathway and promotes stemness and metastasis in colorectal cancer.

TNF receptor superfamily member 11a (TNFRSF11a, RANK) and its ligand TNF superfamily member 11 (TNFRSF11, RANKL) are overexpressed in many malignancies. However, the clinical importance of RANKL/RANK in colorectal cancer (CRC) is mainly unknown. We examined CRC samples and found that RANKL/RANK was elevated in CRC tissues compared with nearby normal tissues. A higher RANKL/RANK expression was associated with a worse survival rate. Furthermore, RANKL was mostly produced by regulatory T cells (Tregs), which were able to promote CRC advancement. Overexpression of RANK or addition of RANKL significantly increased the stemness and migration of CRC cells. Furthermore, RANKL/RANK signaling stimulated C-C motif chemokine ligand 20 (CCL20) production by CRC cells, leading to Treg recruitment and boosting tumor stemness and malignant progression. This recruitment process was accomplished by CCL20-CCR6 interaction, demonstrating a connection between CRC cells and immune cells. These findings suggest an important role of RANKL/RANK in CRC progression, offering a potential target for CRC prevention and therapy.

Band Gap Engineering and Lattice Distortion for Synergetic Tuning Optical Properties of NaNbO3 toward Enhanced Piezo-photocatalytic Activity.

Piezo-photocatalytic efficiency is severely constrained by the wide band gap and bad piezoelectric properties. Herein, La(Mn0.5Ni0.5)O3 was successfully introduced into NaNbO3 lattices (referred to as 0LMN, 0.05LMN, 0.10LMN, and 0.15LMN) through a water-based sol-gel method. The piezo-photocatalytic degradation ratio for Rhodamine B (RhB) is enhanced from 59.7% (0LMN) to 89.7% (0.10LMN) within 100 min, and the kinetic rate constant (k) is increased from 0.009 to 0.022 min-1. The enhanced performance is attributed to (i) the narrowed band gap (from 3.40 to 2.84 eV), which is conducive to the generation of photogenerated electrons and holes, and (ii) the enhanced piezoelectric properties, which can strengthen the piezoelectric polarization, thereby accelerating the separation of the photogenerated electrons and holes. And we also found that the synergetic effect of photocatalysis and piezocatalysis was superior to that of photocatalysis and piezocatalysis alone. This study could provide new perspectives for the reasonable construction of an efficient catalyst in the piezo-photocatalytic field.

Serum IGFBP5 as a predictor of major adverse cardiac events in patients with acute myocardial infarction.

BACKGROUND: Acute myocardial infarction (AMI) is a serious condition with high mortality rates. Early risk stratification is of significant importance to assess the prognosis. Insulin-like growth factor-binding protein 5 (IGFBP5) levels in AMI patients and its potential as a prognosis biomarker were unclear. OBJECTIVE: To investigate serum IGFBP5 levels in AMI and its prognostic value for short-term major adverse cardiovascular events (MACE). METHODS: We collected serum IGFBP5 levels from 200 patients with new-onset AMI and 71 coronary heart disease (CAD) patients without AMI. Linear regression was used to analyze the relationship between IGFBP5 and baseline variables. AMI patients were followed up, and the risk of major adverse cardiovascular events (MACE) was assessed using Kaplan-Meier curve, multivariate Cox models and restricted cubic spline (RCS) analysis. RESULTS: During a median follow-up of 217 days, 40 patients developed MACE. Serum IGFBP5 was associated with serum cardiac troponin T (cTnT) and C-reactive protein (CRP) (P = 0.013 and P = 0.013). In multivariable survival analyses, higher IGFBP5 was associated with an increased risk of MACE [HR = 1.183, 95%CI (1.104, 1.268), P < 0.001)]. There was a positive and linear association between IGFBP5 levels and the occurrence of MACE (P for nonlinearity = 0.283). The positive association between IGFBP5 and MACE risk consist across subgroups characterized by demographics and comorbidities. CONCLUSION: Serum IGFBP5 was highly expressed in patients with AMI and positively associated with the short-term risk of MACE. Circulating IGFBP5 may be a diagnostic and prognostic indicator for AMI, and further studies with larger sample and longer follow-up are warranted.

The Feasibility and Reliability of Sentinel Lymph Node Biopsy After Neoadjuvant Chemotherapy in Breast Cancer Patients With Negative Axillary Lymph Nodes-A Meta-analysis.

Background: The application of sentinel lymph node biopsy (SLNB) has expanded from early breast cancer to locally advanced breast cancer with neoadjuvant chemotherapy (NAC). For patients with negative axillary lymph nodes, performing SLNB before or after NAC remains controversial. Objectives: To evaluate the diagnostic feasibility and reliability of SLNB after NAC in breast cancer patients with negative axillary nodes at initial diagnosis. Design: To calculate pooled identification rate (IR) and false negative rate (FNR) of SLNB after NAC on breast cancer patients with initially negative axillary nodes by enrolling relevant studies and perform subgroup analysis by the type of tracer and the number of biopsied sentinel lymph nodes in average. Data sources and methods: The PubMed, Embase, Cochrane, Web of Science, and Scopus databases from January 1, 2002, to March 1, 2022, were searched for studies. The QUADAS-2 tool and MINORS item were employed to evaluate the quality of the included studies. I2 and Q tests were used to evaluate the heterogeneity among the studies. Random-effects model and fixed-effects model were employed to calculate the pooled IR, FNR, and 95% confidence interval (CI). Publication bias was evaluated, and sensitivity analysis was performed. Subgroup analysis was performed according to the type of tracer (single/double) and the number of biopsied sentinel lymph nodes in average (⩽2/>2). Results: A total of 21 studies covering 1716 patients were enrolled in this study (IR = 93%, 95% CI = 90-96; FNR = 8%, 95% CI = 6-11). Conclusion: The SLNB after NAC can serve as a feasible and reliable approach in breast cancer patients with negative axillary lymph node. In our study, no significant impact of tracer was found on the IR and FNR of SLNB, and the number of biopsy nodes >2 leads to the decreased FNR of SLNB.

Cognition of diet quality and dietary management in elderly patients with coronary and other atherosclerotic vascular disease in western China, a qualitative research study.

BACKGROUND: Healthy eating is one of the most important nonpharmacologic treatments for patients with atherosclerosis(AS). However, it is unclear how elderly AS patients in western China perceive their dietary status and which type of nutritional assistance they would be willing to receive. Therefore, the primary purpose of this study was to understand the level of knowledge about current dietary habits and healthy eating habits among elderly AS patients in western China, and the secondary purpose was to identify acceptable nutritional assistance measures or pathways for those patients to help them manage disease progression. METHODS: An implementation study approach was used to recruit elderly patients with AS-related diseases in western China for semistructured interviews. RESULTS: 14 participants were included in the study, and the following three themes were identified from the interviews:(1) the diet with regional characteristics; (2) low nutrition-related health literacy; (3) complex attitudes towards nutritional assistance. Most participants had misconceptions about healthy eating, and the sources of their knowledge might not be trustworthy. Participants expressed a preference for personalized nutritional assistance, especially that provided by medical-nursing combined institutions. CONCLUSION: Patients in western China need nutritional assistance for their regional dietary habits; therefore, healthy dietary patterns consistent with the regional culture are proposed to improve the prevailing lack of knowledge about healthy diets, improve the dietary structure of patients, and control the development of the disease.

GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases.

Gene set knowledge discovery is essential for advancing human functional genomics. Recent studies have shown promising performance by harnessing the power of Large Language Models (LLMs) on this task. Nonetheless, their results are subject to several limitations common in LLMs such as hallucinations. In response, we present GeneAgent, a first-of-its-kind language agent featuring self-verification capability. It autonomously interacts with various biological databases and leverages relevant domain knowledge to improve accuracy and reduce hallucination occurrences. Benchmarking on 1,106 gene sets from different sources, GeneAgent consistently outperforms standard GPT-4 by a significant margin. Moreover, a detailed manual review confirms the effectiveness of the self-verification module in minimizing hallucinations and generating more reliable analytical narratives. To demonstrate its practical utility, we apply GeneAgent to seven novel gene sets derived from mouse B2905 melanoma cell lines, with expert evaluations showing that GeneAgent offers novel insights into gene functions and subsequently expedites knowledge discovery.

Cholesterol 25-Hydroxylase Protects Against Diabetic Kidney Disease by Regulating ADP Ribosylation Factor 4.

Cholesterol 25-hydroxylase (CH25H), an enzyme involved in cholesterol metabolism, regulates inflammatory responses and lipid metabolism. However, its role in kidney disease is not known.  The author found that CH25H transcript is expressed mostly in glomerular and peritubular endothelial cells and that its expression increased in human and mouse diabetic kidneys.  Global deletion of Ch25h in Leprdb/db mice aggravated diabetic kidney disease (DKD), which is associated with increased endothelial cell apoptosis. Treatment of 25-hydroxycholesterol (25-HC), the product of CH25H, alleviated kidney injury in Leprdb/db mice. Mechanistically, 25-HC binds to GTP-binding protein ADP-ribosylation factor 4 (ARF4), an essential protein required for maintaining protein transport in the Golgi apparatus. Interestingly, ARF4's GTPase-activating protein ASAP1 is also predominantly expressed in endothelial cells and its expression increased in DKD. Suppression of ARF4 activity by deleting ARF4 or overexpressing ASAP1 results in endothelial cell death. These results indicate that 25-HC binds ARF4 to inhibit its interaction with ASAP1, and thereby resulting in enhanced ARF4 activity to confer renoprotection. Therefore, treatment of 25-HC improves kidney injury in DKD in part by restoring ARF4 activity to maintain endothelial cell survival. This study provides a novel mechanism and a potential new therapy for DKD.