Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension.

BACKGROUND: Despite advances in understanding hypertension's genetic structure, how noncoding genetic variants influence it remains unclear. Studying their interaction with DNA methylation is crucial to deciphering this complex disease's genetic mechanisms. METHODS: We investigated the genetic and epigenetic interplay in hypertension using whole-genome bisulfite sequencing. Methylation profiling in 918 males revealed allele-specific methylation and methylation quantitative trait loci. We engineered rs1275988T/C mutant mice using CRISPR/Cas9, bred them for homozygosity, and subjected them to a high-salt diet. Telemetry captured their cardiovascular metrics. Protein-DNA interactions were elucidated using DNA pull-downs, mass spectrometry, and Western blots. A wire myograph assessed vascular function, and analysis of the Kcnk3 gene methylation highlighted the mutation's role in hypertension. RESULTS: We discovered that DNA methylation-associated genetic effects, especially in non-CpG island and noncoding distal regulatory regions, significantly contribute to hypertension predisposition. We identified distinct methylation quantitative trait locus patterns in the hypertensive population and observed that the onset of hypertension is influenced by the transmission of genetic effects through the demethylation process. By evidence-driven prioritization and in vivo experiments, we unearthed rs1275988 in a cell type-specific enhancer as a notable hypertension causal variant, intensifying hypertension through the modulation of local DNA methylation and consequential alterations in Kcnk3 gene expression and vascular remodeling. When exposed to a high-salt diet, mice with the rs1275988C/C genotype exhibited exacerbated hypertension and significant vascular remodeling, underscored by increased aortic wall thickness. The C allele of rs1275988 was associated with elevated DNA methylation levels, driving down the expression of the Kcnk3 gene by attenuating Nr2f2 binding at the enhancer locus. CONCLUSIONS: Our research reveals new insights into the complex interplay between genetic variations and DNA methylation in hypertension. We underscore hypomethylation's potential in hypertension onset and identify rs1275988 as a causal variant in vascular remodeling. This work advances our understanding of hypertension's molecular mechanisms and encourages personalized health care strategies.

PGS-Depot: a comprehensive resource for polygenic scores constructed by summary statistics based methods.

Polygenic score (PGS) is an important tool for the genetic prediction of complex traits. However, there are currently no resources providing comprehensive PGSs computed from published summary statistics, and it is difficult to implement and run different PGS methods due to the complexity of their pipelines and parameter settings. To address these issues, we introduce a new resource called PGS-Depot containing the most comprehensive set of publicly available disease-related GWAS summary statistics. PGS-Depot includes 5585 high quality summary statistics (1933 quantitative and 3652 binary trait statistics) curated from 1564 traits in European and East Asian populations. A standardized best-practice pipeline is used to implement 11 summary statistics-based PGS methods, each with different model assumptions and estimation procedures. The prediction performance of each method can be compared for both in- and cross-ancestry populations, and users can also submit their own summary statistics to obtain custom PGS with the available methods. Other features include searching for PGSs by trait name, publication, cohort information, population, or the MeSH ontology tree and searching for trait descriptions with the experimental factor ontology (EFO). All scores, SNP effect sizes and summary statistics can be downloaded via FTP. PGS-Depot is freely available at http://www.pgsdepot.net.

QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes.

Deciphering the fine-scale molecular mechanisms that shape the genetic effects at disease-associated loci from genome-wide association studies (GWAS) remains challenging. The key avenue is to identify the essential molecular phenotypes that mediate the causal variant and disease under particular biological conditions. Therefore, integrating GWAS signals with context-specific quantitative trait loci (QTLs) (such as different tissue/cell types, disease states, and perturbations) from extensive molecular phenotypes would present important strategies for full understanding of disease genetics. Via persistent curation and systematic data processing of large-scale human molecular trait QTLs (xQTLs), we updated our previous QTLbase database (now QTLbase2, http://mulinlab.org/qtlbase) to comprehensively analyze and visualize context-specific QTLs across 22 molecular phenotypes and over 95 tissue/cell types. Overall, the resource features the following major updates and novel functions: (i) 960 more genome-wide QTL summary statistics from 146 independent studies; (ii) new data for 10 previously uncompiled QTL types; (iii) variant query scope expanded to fit 195 QTL datasets based on whole-genome sequencing; (iv) supports filtering and comparison of QTLs for different biological conditions, such as stimulation types and disease states; (v) a new linkage disequilibrium viewer to facilitate variant prioritization across tissue/cell types and QTL types.

Podocyte-specific silencing of acid sphingomyelinase gene to abrogate hyperhomocysteinemia-induced NLRP3 inflammasome activation and glomerular inflammation.

Acid sphingomyelinase (ASM) has been reported to increase tissue ceramide and thereby mediate hyperhomocysteinemia (hHcy)-induced glomerular nucleotide-binding oligomerization domain-like receptor containing pyrin domain 3 (NLRP3) inflammasome activation, inflammation, and sclerosis. In the present study, we tested whether somatic podocyte-specific silencing of Smpd1 gene (mouse ASM gene code) attenuates hHcy-induced NLRP3 inflammasome activation and associated extracellular vesicle (EV) release in podocytes and thereby suppresses glomerular inflammatory response and injury. In vivo, somatic podocyte-specific Smpd1 gene silencing almost blocked hHcy-induced glomerular NLRP3 inflammasome activation in Podocre (podocyte-specific expression of cre recombinase) mice compared with control littermates. By nanoparticle tracking analysis (NTA), floxed Smpd1 shRNA transfection was found to abrogate hHcy-induced elevation of urinary EV excretion in Podocre mice. In addition, Smpd1 gene silencing in podocytes prevented hHcy-induced immune cell infiltration into glomeruli, proteinuria, and glomerular sclerosis in Podocre mice. Such protective effects of podocyte-specific Smpd1 gene silencing were mimicked by global knockout of Smpd1 gene in Smpd1-/- mice. On the contrary, podocyte-specific Smpd1 gene overexpression exaggerated hHcy-induced glomerular pathological changes in Smpd1trg/Podocre (podocyte-specific Smpd1 gene overexpression) mice, which were significantly attenuated by transfection of floxed Smpd1 shRNA. In cell studies, we also confirmed that Smpd1 gene knockout or silencing prevented homocysteine (Hcy)-induced elevation of EV release in the primary cultures of podocyte isolated from Smpd1-/- mice or podocytes of Podocre mice transfected with floxed Smpd1 shRNA compared with WT/WT podocytes. Smpd1 gene overexpression amplified Hcy-induced EV secretion from podocytes of Smpd1trg/Podocre mice, which was remarkably attenuated by transfection of floxed Smpd1 shRNA. Mechanistically, Hcy-induced elevation of EV release from podocytes was blocked by ASM inhibitor (amitriptyline, AMI), but not by NLRP3 inflammasome inhibitors (MCC950 and glycyrrhizin, GLY). Super-resolution microscopy also showed that ASM inhibitor, but not NLRP3 inflammasome inhibitors, prevented the inhibition of lysosome-multivesicular body interaction by Hcy in podocytes. Moreover, we found that podocyte-derived inflammatory EVs (released from podocytes treated with Hcy) induced podocyte injury, which was exaggerated by T cell coculture. Interstitial infusion of inflammatory EVs into renal cortex induced glomerular injury and immune cell infiltration. In conclusion, our findings suggest that ASM in podocytes plays a crucial role in the control of NLRP3 inflammasome activation and inflammatory EV release during hHcy and that the development of podocyte-specific ASM inhibition or Smpd1 gene silencing may be a novel therapeutic strategy for treatment of hHcy-induced glomerular disease with minimized side effect.NEW & NOTEWORTHY In the present study, we tested whether podocyte-specific silencing of Smpd1 gene attenuates hyperhomocysteinemia (hHcy)-induced nucleotide-binding oligomerization domain-like receptor containing pyrin domain 3 (NLRP3) inflammasome activation and associated inflammatory extracellular vesicle (EV) release in podocytes and thereby suppresses glomerular inflammatory response and injury. Our findings suggest that acid sphingomyelinase (ASM) in podocytes plays a crucial role in the control of NLRP3 inflammasome activation and inflammatory EV release during hHcy. Based on our findings, it is anticipated that the development of podocyte-specific ASM inhibition or Smpd1 gene silencing may be a novel therapeutic strategy for treatment of hHcy-induced glomerular disease with minimized side effects.

Tailoring nondiffracting fields with a non-Markovian phase imprint.

We experimentally generate nondiffracting speckles that carry non-Markovian properties by encoding the wavefront of a monochromatic laser beam with ring-shaped non-Markovian phases. The resulting non-Markovian nondiffracting fields present a ring-shaped pattern and central dark notches, which are analyzed with an expression of the orbital angular momentum spectra of the wavefront possessing ring-shaped non-Markovian phases. Furthermore, we demonstrate that the intensity profiles of these non-Markovian nondiffracting fields exhibit stability over multiple Rayleigh ranges, and their statistical properties could be controlled with the non-Markovianity of the input phase masks. This work presents an approach for simultaneously tailoring the diffracting property and non-Markovianity of optical fields and provides a deeper understanding of non-Markovian processes.

Outcomes of antiretroviral treatment for 0-14-year-old children living with HIV in Ganzhou, China, 2006-2023.

BACKGROUND: Studies on antiretroviral therapy (ART) in children living with HIV (CLHIV) are limited due to the small population and low accession rate of ART. METHODS: All 0-14-year-old CLHIV admitted to the Ganzhou Center for Disease Control and Prevention from January 2006 to June 2023 were included retrospectively. The information of treatment regimens, disease progression, and laboratory tests of the patients under ART were used to explore the outcomes and impacts of long-term ART. The normality of all the data was tested by the Shapiro-Wilk test. RESULTS: From 2006 to 2023, 18 CLHIV were reported in Ganzhou. Among them, 11 received ART and were followed up for 60.0 ± 48.4 months. After receiving ART, the median viral load of them decreased from 89,600 copies/ml to 22 copies/ml (P = 0.007), the median CD4+ T cell count increased from 380.7 cells/µL to 661.9 cells/µL (P = 0.028), and the median CD8+ T cell count decreased from 1065.8 cells/µL to 983.3 cells/µL (P = 0.584). The laboratory test results regarding liver function, renal function, blood cell count, and glucolipid metabolism tended to be within normal reference ranges, and the mean height-for-age z-score and weight-for-age z-score increased. However, all the three CLHIV who received cotrimoxazole developed pneumocystis carinii pneumonia, upper respiratory infection, skin lesions, bacterial pneumonia and/or thrush; the mean body-mass-index-for-age z-score decreased from 0.52 to -0.63. CONCLUSION: For CLHIV, ART could effectively inhibit the replication of HIV and improve the immune function of patients. More studies that focus on ART in CLHIV are urgently needed.

VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases.

Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has following major features: (i) systematically integrates 40 genome-wide variant annotations and prediction scores regarding allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, tissue/cell type-specific epigenome, base-wise functional prediction, allelic imbalance and pathogenicity; (ii) equips with our recent novel index system and parallel random-sweep searching algorithms for efficient management of backend databases and information extraction; (iii) greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps and regulatory profiles (such as EpiMap) across over 33 tissue/cell types; (iv) compiles many genome-scale base-wise prediction scores for regulatory/pathogenic variant classification beyond protein-coding region; (v) enables fast retrieval and direct comparison of functional evidence among linked variants using highly interactive web panel in addition to plain table; (vi) introduces many visualization functions for more efficient identification and interpretation of functional variants in single web page. VannoPortal is freely available at http://mulinlab.org/vportal.

The First High-Quality Genome Assembly of Freshwater Pearl Mussel Sinohyriopsis cumingii: New Insights into Pearl Biomineralization.

China leads the world in freshwater pearl production, an industry in which the triangle sail mussel (Sinohyriopsis cumingii) plays a pivotal role. In this paper, we report a high-quality chromosome-level genome assembly of S. cumingii with a size of 2.90 Gb-the largest yet reported among bivalves-and 89.92% anchorage onto 19 linkage groups. The assembled genome has 37,696 protein-coding genes and 50.86% repeat elements. A comparative genomic analysis revealed expansions of 752 gene families, mostly associated with biomineralization, and 237 genes under strong positive selection. Notably, the fibrillin gene family exhibited gene family expansion and positive selection simultaneously, and it also exhibited multiple high expressions after mantle implantation by transcriptome analysis. Furthermore, RNA silencing and an in vitro calcium carbonate crystallization assay highlighted the pivotal role played by one fibrillin gene in calcium carbonate deposition and aragonite transformation. This study provides a valuable genomic resource and offers new insights into the mechanism of pearl biomineralization.

Methane removal efficiencies of biochar-mediated landfill soil cover with reduced depth.

Biochar amendment for landfill soil cover has the potential to enhance methane removal efficiency while minimizing the soil depth. However, there is a lack of information on the response of biochar-mediated soil cover to the changes in configuration and operational parameters during the methane transport and transformation processes. This study constructed three biochar-amended landfill soil covers, with reduced soil depths from 75 cm (C2) to 55 cm (C3) and 45 cm (C4), and the control group (C1) with 75 cm and no biochar. Two operation phases were conducted under two soil moisture contents and three inlet methane fluxes in each phase. The methane removal efficiency increased for all columns along with the increase in methane flux. However, increasing moisture content from 10% to 20% negatively influenced the methane removal efficiency due to mass transfer limitation when at a low inlet methane flux, especially for C1; while this adverse effect could be alleviated by a high flux. Except for the condition with low moisture content and flux combination, C3 showed comparable methane removal efficiency to C2, both dominating over C1. As for C4 with only 45 cm, a high moisture content combined with a high methane flux enabled its methane removal efficiency to be competitive with other soil depths. In addition to the geotechnical reasons for gas transport processes, the evolution in methanotroph community structure (mainly type I methanotrophs) induced by biochar amendment and variations in soil properties supplemented the biological reasons for the varying methane removal efficiencies.

Novel TCF21high pericyte subpopulation promotes colorectal cancer metastasis by remodelling perivascular matrix.

OBJECTIVE: Haematogenous dissemination is a prevalent route of colorectal cancer (CRC) metastasis. However, as the gatekeeper of vessels, the role of tumour pericytes (TPCs) in haematogenous metastasis remains largely unknown. Here, we aimed to investigate the heterogeneity of TPCs and their effects on CRC metastasis. DESIGN: TPCs were isolated from patients with CRC with or without liver metastases and analysed by single-cell RNA sequencing (scRNA-seq). Clinical CRC specimens were collected to analyse the association between the molecular profiling of TPCs and CRC metastasis. RNA-sequencing, chromatin immunoprecipitation-sequencing and bisulfite-sequencing were performed to investigate the TCF21-regulated genes and mechanisms underlying integrin α5 on TCF21 DNA hypermethylation. Pericyte-conditional Tcf21-knockout mice were constructed to investigate the effects of TCF21 in TPCs on CRC metastasis. Masson staining, atomic force microscopy, second-harmonic generation and two-photon fluorescence microscopy were employed to observe perivascular extracellular matrix (ECM) remodelling. RESULTS: Thirteen TPC subpopulations were identified by scRNA-seq. A novel subset of TCF21high TPCs, termed 'matrix-pericytes', was associated with liver metastasis in patients with CRC. TCF21 in TPCs increased perivascular ECM stiffness, collagen rearrangement and basement membrane degradation, establishing a perivascular metastatic microenvironment to instigate colorectal cancer liver metastasis (CRCLM). Tcf21 depletion in TPCs mitigated perivascular ECM remodelling and CRCLM, whereas the coinjection of TCF21high TPCs and CRC cells markedly promoted CRCLM. Mechanistically, loss of integrin α5 inhibited the FAK/PI3K/AKT/DNMT1 axis to impair TCF21 DNA hypermethylation in TCF21high TPCs. CONCLUSION: This study uncovers a previously unidentified role of TPCs in haematogenous metastasis and provides a potential diagnostic marker and therapeutic target for CRC metastasis.

Kruppel-like factor 14 ameliorated obesity and related metabolic disorders by promoting adipose tissue browning.

Obesity has been identified as a serious and debilitating disease that threatens human health, but the current treatment strategies still have some shortcomings. Exercise and dieting are difficult for many people to adhere to, and a series of surgical risks and pain brought about by volume reduction have made it difficult for the current weight loss effect to meet human expectations. In this study, we first found that mice with overexpression of the transcription factor Kruppel-like factor 14 (KLF14) in subcutaneous adipose tissue gained weight more slowly while consuming a high-fat diet than did control mice, and these mice also showed reduced insulin resistance and liver lipid deposition abnormalities. Mechanistically, the browning of white adipose tissue was promoted in adipose tissue with KLF14 overexpression; therefore, we preliminarily concluded that KLF14 can improve obesity by promoting the browning of white adipose tissue and energy consumption, thus ameliorating obesity and related metabolic disturbances. In summary, our results revealed that KLF14 may promote white adipose tissue browning, thus ameliorating high-fat diet-induced obesity and hepatic steatosis, as well as serum lipid levels and insulin resistance, thereby achieving a positive effect on metabolism.NEW & NOTEWORTHY Our study first explored the role of KLF14 in the development and progression of HFD-induced obesity in male mice. Its beneficial effect on adipose browning and metabolic disorders suggests that KLF14 may provide us a new therapeutic strategy for obesity and related metabolic complications. This health problem is of global concern and needs to be addressed.

NFE2L3 drives hepatocellular carcinoma cell proliferation by regulating the proteasome-dependent degradation of ISGylated p53.

Nuclear factor erythroid 2-like 3 (NFE2L3) is a member of the cap 'n' collar basic-region leucine zipper (CNC-bZIP) transcription factor family that plays a vital role in modulating oxidation-reduction steady-state and proteolysis. Accumulating evidence suggests that NFE2L3 participates in cancer development; however, little is known about the mechanism by which NFE2L3 regulates hepatocellular carcinoma (HCC) cell growth. Here, we confirmed that NFE2L3 promotes HCC cell proliferation by acting as a transcription factor, which directly induces the expression of proteasome and interferon-stimulated gene 15 (ISG15) to enhance the proteasome-dependent degradation of ISGylated p53. Post-translational ISGylation abated the stability of p53 and facilitated HCC cell growth. In summary, we uncovered the pivotal role of NFE2L3 in promoting HCC cell proliferation during proteostasis. This finding may provide a new target for the clinical treatment of HCC.

Ultrafast and scalable variant annotation and prioritization with big functional genomics data.

The advances of large-scale genomics studies have enabled compilation of cell type-specific, genome-wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole-genome sequencing variants against a huge database with billions of genomic features. Here, we develop VarNote to rapidly annotate genome-scale variants in large and complex functional annotation resources. Equipped with a novel index system and a parallel random-sweep searching algorithm, VarNote shows substantial performance improvements (two to three orders of magnitude) over existing algorithms at different scales. It supports both region-based and allele-specific annotations and introduces advanced functions for the flexible extraction of annotations. By integrating massive base-wise and context-dependent annotations in the VarNote framework, we introduce three efficient and accurate pipelines to prioritize the causal regulatory variants for common diseases, Mendelian disorders, and cancers.

Development and validation of postoperative circulating tumor DNA combined with clinicopathological risk factors for recurrence prediction in patients with stage I-III colorectal cancer.

BACKGROUND: Circulating tumor DNA (ctDNA) detection following curative-intent surgery could directly reflect the presence of minimal residual disease, the ultimate cause of clinical recurrence. However, ctDNA is not postoperatively detected in ≥ 50% of patients with stage I-III colorectal cancer (CRC) who ultimately recur. Herein we sought to improve recurrence risk prediction by combining ctDNA with clinicopathological risk factors in stage I-III CRC. METHODS: Two independent cohorts, both consisting of early-stage CRC patients who underwent curative surgery, were included: (i) the discovery cohort (N = 124) with tumor tissues and postoperative plasmas for ctDNA determination; and (ii) the external validation cohort (N = 125) with available ctDNA results. In the discovery cohort, somatic variations in tumor tissues and plasmas were determined via a 733-gene and 127-gene next-generation sequencing panel, respectively. RESULTS: In the discovery cohort, 17 of 108 (15.7%) patients had detectable ctDNA. ctDNA-positive patients had a significantly high recurrence rate (76.5% vs. 16.5%, P < 0.001) and short recurrence-free survival (RFS; P < 0.001) versus ctDNA-negative patients. In addition to ctDNA status, the univariate Cox model identified pathologic stage, lymphovascular invasion, nerve invasion, and preoperative carcinoembryonic antigen level associated with RFS. We combined the ctDNA and clinicopathological risk factors (CTCP) to construct a model for recurrence prediction. A significantly higher recurrence rate (64.7% vs. 8.1%, P < 0.001) and worse RFS (P < 0.001) were seen in the high-risk patients classified by the CTCP model versus those in the low-risk patients. Receiver operating characteristic analysis demonstrated that the CTCP model outperformed ctDNA alone at recurrence prediction, which increased the sensitivity of 2 year RFS from 49.6% by ctDNA alone to 87.5%. Harrell's concordance index, calibration curve, and decision curve analysis also suggested that the CTCP model had good discrimination, consistency, and clinical utility. These results were reproduced in the validation cohort. CONCLUSION: Combining postoperative ctDNA and clinical risk may better predict recurrence than ctDNA alone for developing a personalized postoperative management strategy for CRC.

Exosome Biogenesis and Lysosome Function Determine Podocyte Exosome Release and Glomerular Inflammatory Response during Hyperhomocysteinemia.

Nucleotide-binding oligomerization domain-like receptor containing pyrin domain 3 (NLRP3) inflammasome activation in podocytes is reportedly associated with enhanced release of exosomes containing NLRP3 inflammasome products from these cells during hyperhomocysteinemia (hHcy). This study examined the possible role of increased exosome secretion during podocyte NLRP3 inflammasome activation in the glomerular inflammatory response. Whether exosome biogenesis and lysosome function are involved in the regulation of exosome release from podocytes during hHcy in mice and upon stimulation of homocysteine (Hcy) in podocytes was tested. By nanoparticle tracking analysis, treatments of mice with amitriptyline (acid sphingomyelinase inhibitor), GW4869 (exosome biogenesis inhibitor), and rapamycin (lysosome function enhancer) were found to inhibit elevated urinary exosomes during hHcy. By examining NLRP3 inflammasome activation in glomeruli during hHcy, amitriptyline (but not GW4869 and rapamycin) was shown to have an inhibitory effect. However, all treatments attenuated glomerular inflammation and injury during hHcy. In cell studies, Hcy treatment stimulated exosome release from podocytes, which was prevented by amitriptyline, GW4869, and rapamycin. Structured illumination microscopy revealed that Hcy inhibited lysosome-multivesicular body interactions in podocytes, which was prevented by amitriptyline or rapamycin but not GW4869. Thus, the data from this study shows that activation of exosome biogenesis and dysregulated lysosome function are critically implicated in the enhancement of exosome release from podocytes leading to glomerular inflammation and injury during hHcy.

Supramolecular-Interactions-Modulated Photoluminescence in Indium Bromide-Based Isomers.

Here, two isomeric ionic zero-dimensional indium bromide crystals of α (1)/ß (2)-[OPy][InBr4(Phen)] (OPy = N-octylpyridinium; Phen = 1,10-phenanthroline) have been isolated simply by changing the cooling conditions in solvothermal syntheses. Structural comparisons indicate their different supramolecular interactions, which can be confirmed by Hirshfeld surface analyses. The crystal 2 has additional hydrogen bonds and π-π interactions; as a result, the more compact stacking of 2 could result in a 10-fold higher photoluminescence (PL) quantum yield (PLQY) than that of 1. Density functional theory calculations confirm the electron transition from the inorganic moiety to the organic ligand, which provides a further understanding of the optical process. This work provides a new idea for designing PL indium-based halides by understanding the structure-PL relationship.

Predicting Atmospheric Particle Phase State Using an Explainable Machine Learning Approach Based on Particle Rebound Measurements.

The particle phase state plays a vital role in the gas-particle partitioning, multiphase reactions, ice nucleation activity, and particle growth in the atmosphere. However, the characterization of the atmospheric phase state remains challenging. Herein, based on measured aerosol chemical composition and ambient relative humidity (RH), a machine learning (ML) model with high accuracy (R2 = 0.952) and robustness (RMSE = 0.078) was developed to predict the particle rebound fraction, f, which is an indicator of the particle phase state. Using this ML model, the f of particles in the urban atmosphere was predicted based on seasonal average aerosol chemical composition and RH. Regardless of seasons, aerosols remain in the liquid state of mid-high latitude cities in the northern hemisphere and in the semisolid state over semiarid regions. In the East Asian megacities, the particles remain in the liquid state in spring and summer and in the semisolid state in other seasons. The effects of nitrate, which is becoming dominant in fine particles in several urban areas, on the particle phase state were evaluated. More nitrate led the particles to remain in the liquid state at an even lower RH. This study proposed a new approach to predict the particle phase state in the atmosphere based on RH and aerosol chemical composition.

Impacts of digestate-based compost on soil property and nutrient availability.

The treatment of digestate from food waste (DFW) has emerged as the bottleneck for food waste anaerobic digestion. DFW generally contains abundant nutrients that can be recycled by composting. However, the effect of DFW-based compost on soil improvement has not been extensively explored. In this study, soil properties were improved by adding various amounts of DFW-based compost, and the growth conditions of Pak choi were monitored. The results indicated that the DFW-based compost could provide nitrogen, calcium, magnesium, and organic matter, thereby enhancing the growth of Pak choi, accumulating chlorophyll, and improving photosynthesis efficiency. As the amount of added DFW-based compost increased from 0% to 20%, the fresh biomass, leaf weight, and root weight of Pak choi increased by 242%, 262%, and 99%, respectively. The total chlorophyll content was 2.62 mg g-1 in control and increased to 12.45 mg g-1 in the group with 20% DFW-based compost, benefiting the photochemical efficiency of Pak choi. However, the growth was inhibited when the addition amount exceeded 20%, potentially due to excessive nutrient supplementation. Overall, the addition of 20% of DFW-based compost was suggested to promote the growth of Pak choi by providing proper nutrients.

Clinicopathological analysis of a type of "low grade" poorly cohesive gastric adenocarcinoma not otherwise specified with a good prognosis.

Poorly cohesive carcinoma not otherwise specified (PCGCA-NOS) is regarded in the most recent WHO classification as a high-grade malignancy; however, some cases may be associated with a relatively good prognosis. We have studied a series of 115 cases of PCGCA-NOS and were able to identify low-grade features in 14 cases based on three morphological manifestations. Immunohistochemical staining, EBER in situ hybridization, Feulgen staining and flow cytometry were employed. Among the 115 cases of PCGAC-NOS, 14 cases met the criteria of "low grade", accounting for 12.2 %. The "low grade" cases exhibited more shallow invasion and less lymph node metastasis (both P < 0.05); showed less frequent expression of MUC5AC, E-cadherin and p53 (all P < 0.05). Moreover, "low grade" PCGAC-NOS had a lower proliferative index(P < 0.001). We also found that the DNA content was lower in the "low grade" group, and aneuploidy was not detected in the "low grade" group, which was sharply different from the control group (50 %). Last, "low grade" PCGAC-NOS had a more favorable prognosis. A small subset of PCGAC-NOS cases have a low grade nature, and the clinicopathological features, immunophenotypes, and cytogenetics of these "low grade" cases differ from those of traditional PCGAC-NOS.

Effects of Exogenous Nitric Oxide Treatment on Grape Berries Against Botrytis cinerea and Alternaria alternata Related Enzymes and Metabolites.

Postharvest losses of grape berries caused by the pathogenic fungi Botrytis cinerea and Alternaria alternata have been widely reported, and nitric oxide (NO) as a plant signaling molecule to control postharvest diseases has recently become an active research topic. This study aimed to investigate the regulatory effect of NO on the interaction between grape berries and fungi. During interactions between grape berries and pathogenic fungi, treatment with 10 mM sodium nitroprusside (SNP, an NO donor) delayed the decline of the physiological quality of the grape berries and had positive effects on the weight loss rate, firmness, and respiration intensity. SNP treatment increased the activities of superoxide dismutase (SOD) and polyphenol oxidase (PPO) and inhibited the activities of peroxidase (POD) and catalase (CAT) of grape berries during the resistance to fungal pathogen infection. In addition, the increase in browning degree and the accumulation of hydrogen peroxide were inhibited by SNP treatment. In the phenylpropane metabolic pathway, the activities of phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), and 4-coumaric acid coenzyme A ligase (4CL) were increased during the activation of grape berries during the resistance to pathogen infection by SNP, and the intermediate metabolites lignin, flavonoids, and total phenols were accumulated. In addition, SNP treatment had a regulatory effect on the gene expression levels of SOD, POD, PPO, PAL, and 4CL. These results suggested that SNP treatment was effective for the preservation and disease reduction of grape berries.