Artificial intelligence algorithm for neoplastic cell percentage estimation and its application to copy number variation in urinary tract cancer.

Background: Bladder cancer is characterized by frequent mutations, which provide potential therapeutic targets for most patients. The effectiveness of emerging personalized therapies depends on an accurate molecular diagnosis, for which the accurate estimation of the neoplastic cell percentage (NCP) is a crucial initial step. However, the established method for determining the NCP, manual counting by a pathologist, is time-consuming and not easily executable. Methods: To address this, artificial intelligence (AI) models were developed to estimate the NCP using nine convolutional neural networks and the scanned images of 39 cases of urinary tract cancer. The performance of the AI models was compared to that of six pathologists for 119 cases in the validation cohort. The ground truth value was obtained through multiplexed immunofluorescence. The AI model was then applied to 41 cases in the application cohort that underwent next-generation sequencing testing, and its impact on the copy number variation (CNV) was analyzed. Results: Each AI model demonstrated high reliability, with intraclass correlation coefficients (ICCs) ranging from 0.82 to 0.88. These values were comparable or better to those of pathologists, whose ICCs ranged from 0.78 to 0.91 in urothelial carcinoma cases, both with and without divergent differentiation/ subtypes. After applying AI-driven NCP, 190 CNV (24.2%) were reclassified with 66 (8.4%) and 78 (9.9%) moved to amplification and loss, respectively, from neutral/minor CNV. The neutral/minor CNV proportion decreased by 6%. Conclusions: These results suggest that AI models could assist human pathologists in repetitive and cumbersome NCP calculations.

Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor.

The gut microbiome significantly influences immune responses and the efficacy of immune checkpoint inhibitors. We conducted a clinical trial (NCT04264975) combining an anti-programmed death-1 (PD-1) inhibitor with fecal microbiota transplantation (FMT) from anti-PD-1 responder in 13 patients with anti-PD-1-refractory advanced solid cancers. FMT induced sustained microbiota changes and clinical benefits in 6 of 13 patients, with 1 partial response and 5 stable diseases, achieving an objective response rate of 7.7% and a disease control rate of 46.2%. The clinical response correlates with increased cytotoxic T cells and immune cytokines in blood and tumors. We isolated Prevotella merdae Immunoactis from a responder to FMT, which stimulates T cell activity and suppresses tumor growth in mice by enhancing cytotoxic T cell infiltration. Additionally, we found Lactobacillus salivarius and Bacteroides plebeius may inhibit anti-tumor immunity. Our findings suggest that FMT with beneficial microbiota can overcome resistance to anti-PD-1 inhibitors in advanced solid cancers, especially gastrointestinal cancers.

From laboratory to pilot-scale: Assessing dissolved organic matter, biological stability and per- and polyfluoroalkyl substances removal on managed aquifer recharge performance.

Managed aquifer recharge (MAR) is a promising technique for enhancing groundwater resources and addressing water scarcity. Particularly, this research highlights the novelty and urgent need for MAR facilities in the Chungcheongnam-do region of South Korea as a solution to augment groundwater resources and combat water scarcity. This research encompasses a comprehensive assessment, ranging from laboratory-scale column experiments to pilot-scale tests, focusing on dissolved organic matter (DOM) characterization, natural organic matter (NOM) removal, and water quality improvement, including biological stability. In the laboratory, DOM characteristics of source water and recharged groundwater were analyzed using advanced dissolved organic characteristic tools, and their potential impacts on water quality, as well as per- and polyfluoroalkyl substances (PFASs) were assessed. DOM, total cell counts, and several PFASs with molecular weights >450 Da (particularly long-chain PFASs showing >99.9 % reduction) were effectively reduced in a laboratory-scale experiment. A laboratory-scale column study revealed that most selected PFASs were not effectively removed. Moving to the pilot-scale, a series of experiments were conducted to assess NOM removal during soil passage. Similar to the results of the laboratory-scale experiment, MAR demonstrated significant potential for reducing NOM concentrations, thus improving water quality. Regarding biological stability, assimilable organic carbon in production well (i.e., final produced water by MAR process) was lower than both two sources of surface water (e.g., SW1 and SW2). This suggests that water derived from PW (i.e., production well) exhibited biological stability, undergoing effective biodegradation by aerobic bacteria during soil passage. The findings from this study highlight the critical importance of implementing MAR techniques in regions facing water scarcity, emphasizing its potential to significantly enhance future water security initiatives.

Prediction of evapotranspiration variance in the Budyko framework with the incorporation of soil storage and runoff.

Water availability needs to be accurately assessed to understand and effectively manage hydrologic environments. However, the estimation of evapotranspiration (ET) is prone to errors due to the complex interactions that occur between the atmosphere, the Earth's surface, and vegetation cover. This paper proposes a novel approach for analyzing the sources of inaccuracy in estimating the annual ET using the Budyko framework (BF), particularly temporal variability in precipitation (P), potential evapotranspiration (EP), runoff (R), and the change in soil storage (ΔS). Error decomposition is employed to determine the individual contributions of P, R, EP, and ΔS to the ET error variance at 12 locations in the state of Illinois using a dataset covering a 22-year period. To the best of our knowledge, this study represents the first BF-based investigation that considers R in the error decomposition of the predicted ET variance. The ET error variance increases with the variance in the P and R in Illinois and decreases with the covariance between these two variables. In addition, when accounting for ΔS in the BF, the scenario in which ΔS affects the total available water (i.e., P) is reliable, with a low prediction error and a 13.87 % lower root mean square error compared with the scenario in which the effect of ΔS is negligible. We thus recommend the inclusion of ΔS and R as key variables in the BF to improve water budget estimations.

Hypothalamic astrocyte NAD+ salvage pathway mediates the coupling of dietary fat overconsumption in a mouse model of obesity.

Nicotinamide adenine dinucleotide (NAD)+ serves as a crucial coenzyme in numerous essential biological reactions, and its cellular availability relies on the activity of the nicotinamide phosphoribosyltransferase (NAMPT)-catalyzed salvage pathway. Here we show that treatment with saturated fatty acids activates the NAD+ salvage pathway in hypothalamic astrocytes. Furthermore, inhibition of this pathway mitigates hypothalamic inflammation and attenuates the development of obesity in male mice fed a high-fat diet (HFD). Mechanistically, CD38 functions downstream of the NAD+ salvage pathway in hypothalamic astrocytes burdened with excess fat. The activation of the astrocytic NAMPT-NAD+-CD38 axis in response to fat overload induces proinflammatory responses in the hypothalamus. It also leads to aberrantly activated basal Ca2+ signals and compromised Ca2+ responses to metabolic hormones such as insulin, leptin, and glucagon-like peptide 1, ultimately resulting in dysfunctional hypothalamic astrocytes. Our findings highlight the significant contribution of the hypothalamic astrocytic NAD+ salvage pathway, along with its downstream CD38, to HFD-induced obesity.

Characterization of lymphocyte-rich hepatocellular carcinoma and the prognostic role of tertiary lymphoid structures.

BACKGROUND & AIMS: Lymphocyte-rich hepatocellular carcinoma (LR-HCC) is largely unknown and a rare subtype of HCC with immune-rich stroma. Tertiary lymphoid structures (TLS), frequently observed in LR-HCC, are known to be prognostically significant in various malignancies; however, their significance in HCC remains unevaluated. METHODS: Clinicopathologic data of 191 cases of surgically resected conventional HCC (C-HCC, n = 160) and LR-HCC (n = 31) were retrieved. Immunohistochemistry, multiplex immunofluorescence staining, RNA sequencing and proteomic analysis were conducted. Differences between the subtypes were statistically evaluated. RESULTS: LR-HCC was significantly correlated to larger tumour size, higher Edmondson-Steiner grade, presence of TLS and higher CD3-, CD8- and FOXP3-positive T cell, high PD-1 and PD-L1 expression (p < .001 for all) compared to C-HCC. Patients with LR-HCC exhibited significantly better overall survival (OS) (p = .044) and recurrence-free survival (RFS) (p = .025) than C-HCC. LR-HCC demonstrated TLS signatures with significantly higher proteomic-based immune scores in 14 of 17 types of tumour-infiltrating immune cells. Furthermore, C-HCC with secondary follicles, the most mature form of TLS, exhibited significantly better OS (p = .031) and RFS (p = .033) than those without. Across the global proteome, LR-HCC was well-differentiated from C-HCC and a map of protein-protein interactions between tumour-infiltrating lymphocytes and HCC in tumour microenvironment was completed. CONCLUSION: LR-HCC is clinicopathologically and molecularly distinct and shows better prognosis compared to C-HCC. Also, the presence of secondary follicle can be an important prognostic marker for better prognosis in both LR-HCC and C-HCC.