A survey on computational strategies for genome-resolved gut metagenomics.

Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe-phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.

Deubiquitinating enzyme OTUD4 stabilizes RBM47 to induce ATF3 transcription: a novel mechanism underlying the restrained malignant properties of ccRCC cells.

Dysregulation of deubiquitination contributes to various diseases, including cancer, and aberrant expression of deubiquitinating enzymes is involved in carcinoma progression. As a member of the ovarian tumor (OTU) deubiquitinases, OTUD4 is considered a tumor suppressor in many kinds of malignancies. The biological characteristics and mechanisms of OTUD4 in clear cell renal cell carcinoma (ccRCC) remain unclear. The downregulation of OTUD4 in ccRCC was confirmed based on the TCGA database and a validation cohort of 30-paired ccRCC and para-carcinoma samples. Moreover, OTUD4 expression was detected by immunohistochemistry in 50 cases of ccRCC tissues, and patients with lower levels of OTUD4 showed larger tumor size (p = 0.015). TCGA data revealed that patients with high expression of OTUD4 had a longer overall survival rate. In vitro and in vivo studies revealed that downregulation of OTUD4 was essential for tumor cell growth and metastasis in ccRCC, and OTUD4 overexpression inhibited these malignant phenotypes. We further found that OTUD4 sensitized ccRCC cells to Erastin-induced ferroptosis, and ferrostain-1 inhibited OTUD4-induced ferroptotic cell death. Mechanistic studies indicated that OTUD4 functioned as an anti-proliferative and anti-metastasic factor through the regulation of RNA-binding protein 47 (RBM47)-mediated activating transcription factor 3 (ATF3). OTUD4 directly interacted with RBM47 and promoted its stability via deubiquitination events. RBM47 was critical in ccRCC progression by regulating ATF3 mRNA stability, thereby promoting ATF3-mediated ferroptosis. RBM47 interference abolished the suppressive role of OTUD4 overexpression in ccRCC. Our findings provide mechanistic insight into OTUD4 of ccRCC progression and indicate a novel critical pathway OTUD4/RBM47/ATF3 may serve as a potential therapeutic pathway for ccRCC.

EXPERT: transfer learning-enabled context-aware microbial community classification.

Microbial community classification enables identification of putative type and source of the microbial community, thus facilitating a better understanding of how the taxonomic and functional structure were developed and maintained. However, previous classification models required a trade-off between speed and accuracy, and faced difficulties to be customized for a variety of contexts, especially less studied contexts. Here, we introduced EXPERT based on transfer learning that enabled the classification model to be adaptable in multiple contexts, with both high efficiency and accuracy. More importantly, we demonstrated that transfer learning can facilitate microbial community classification in diverse contexts, such as classification of microbial communities for multiple diseases with limited number of samples, as well as prediction of the changes in gut microbiome across successive stages of colorectal cancer. Broadly, EXPERT enables accurate and context-aware customized microbial community classification, and potentiates novel microbial knowledge discovery.

Association between the American Heart Association's new "Life's Essential 8" metrics and kidney stone.

PURPOSE: The incidence of kidney stone disease has increased worldwide, resulting in high medical costs and social burden. Kidney stone disease shares some common features with the risk factors of cardiovascular diseases (CVDs). We investigated the association between cardiovascular health (CVH) based on the Life's Essential 8 (LE8) score developed by the American Heart Association and the incidence of kidney stone disease. METHODS: We analyzed the data of 29,469 US adults aged 20 years or above from the National Health and Nutrition Examination Survey, 2007-2018. According to the LE8 score, CVH was divided into three categories: poor, intermediate, and ideal. Logistic regression was used to determine the association between CVH and the incidence of kidney stone disease by estimating odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS: The average age of the participants was 48.6 years, and 50% of the participants were women. The numbers of participants with poor, intermediate, and ideal CVH were 4149, 19,782, and 5538, respectively. After adjusting for related confounding factors, ideal CVH was associated with a reduction in the odds of kidney stone occurrence as compared to poor CVH (adjusted OR [aOR]: 0.45, 95% CI: 0.35-0.57, p < 0.001). Moreover, if the ideal CVH metrics was ≥ 6, the odds of kidney stone occurrence decreased by up to 61% (aOR: 0.39, 95% CI: 0.30-0.51). CONCLUSIONS: In the present study, ideal CVH, a factor indicative of a healthy lifestyle, was associated with lower odds of kidney stone occurrence.

Significant Increase in Ammonia Emissions in China: Considering Nonagricultural Sectors Based on Isotopic Source Apportionment.

Isotopic source apportionment results revealed that nonagricultural sectors are significant sources of ammonia (NH3) emissions, particularly in urban areas. Unfortunately, nonagricultural sources have been substantially underrepresented in the current anthropogenic NH3 emission inventories (EIs). Here, we propose a novel approach to develop a gridded EI of nonagricultural NH3 in China for 2016 using a combination of isotopic source apportionment results and the emission ratios of carbon monoxide (CO) and NH3. We estimated that isotope-corrected nonagricultural NH3 emissions were 4370 Gg in China in 2016, accounting for an increase in the total NH3 emissions from 7 to 31%. As a result, compared to the original NH3 EI, the annual emissions of total NH3 increased by 35%. Thus, in comparison to the simulation driven by the original NH3 EI, the WRF-Chem model driven by the isotope-corrected NH3 EI has reduced the model biases in the surface concentrations and dry deposition flux of reduced nitrogen (NHx = gaseous NH3 + particulate NH4+) by 23 and 31%, respectively. This study may have wide-ranging implications for formulating targeted strategies for nonagricultural NH3 emissions controls, making it facilitate the achievement of simultaneously alleviating nitrogen deposition and atmospheric pollution in the future.

mBodyMap: a curated database for microbes across human body and their associations with health and diseases.

mBodyMap is a curated database for microbes across the human body and their associations with health and diseases. Its primary aim is to promote the reusability of human-associated metagenomic data and assist with the identification of disease-associated microbes by consistently annotating the microbial contents of collected samples using state-of-the-art toolsets and manually curating the meta-data of corresponding human hosts. mBodyMap organizes collected samples based on their association with human diseases and body sites to enable cross-dataset integration and comparison. To help users find microbes of interest and visualize and compare their distributions and abundances/prevalence within different body sites and various diseases, the mBodyMap database is equipped with an intuitive interface and extensive graphical representations of the collected data. So far, it contains a total of 63 148 runs, including 14 401 metagenomes and 48 747 amplicons related to health and 56 human diseases, from within 22 human body sites across 136 projects. Also available in the database are pre-computed abundances and prevalence of 6247 species (belonging to 1645 genera) stratified by body sites and diseases. mBodyMap can be accessed at: https://mbodymap.microbiome.cloud.

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.

GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs/samples, which are significantly increased from the previous version. Among these runs/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project/phenotype comparison. We first identified disease markers between two phenotypes (e.g. health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https://gmrepo.humangut.info.

Risk factors on surgical compliance and its impact on survival outcomes in meningioma patients: a SEER-based retrospective propensity-score matched analysis.

BACKGROUND: This study aimed to analyze the effect of surgical compliance on the survival outcome of patients with meningioma and explore the factors affecting surgical compliance. METHODS: We selected data from the Surveillance, Epidemiology, and End Results database for 122,632 meningioma patients diagnosed between 2004 and 2018. The effect of surgical compliance on patients' overall survival (OS) was analyzed through Cox regression and Kaplan-Meier curves. Independent risk factors for surgical compliance were identified through multifactorial logistic regression analyses to construct diagnostic nomograms, further assessed by receiver operating characteristic curves. Furthermore, we used univariate and multivariate logistic regression analyses to evaluate relevant variables linked to adherence with meningioma surgery. Moreover, 1:1 propensity score matching was applied to assess the validity of the results in patients with favorable and poor surgical compliance. RESULTS: A total of 48,735 were eligible from the initial cohort of 122,632 patients with meningioma. Among them, 45,038 (92.40%) exhibited good surgical compliance, while 3697 (7.60%) had poor surgical compliance. The rate of patients with good surgical compliance was significantly higher than that of patients with inadequate surgical compliance (p < 0.001). Moreover, surgical compliance is an independent prognostic factor for OS in meningioma patients. Univariate Cox regression analysis indicated that individuals with poor surgical compliance demonstrated lower OS rates than those with good surgical compliance (hazard ratio [HR 2.404; 95% confidence interval [CI] 2.276-2.54, p < 0.001], consistent with the observation in the multivariate analysis (HR 1.564; 95% CI 1.471-1.663, p < 0.001). We developed a prediction model using seven variables: age, sex, race, tumor behavior recode, tumor size, family income, and residential setting (p < 0.05). Surgical compliance was associated with patient age, sex, race, tumor behavior recode, tumor size, family income, and residential setting by logistic regression analysis. CONCLUSIONS: Surgical compliance emerged as an independent prognostic factor for survival in patients with meningioma. Poor surgical compliance was associated with older age, black and other races, females, advanced-stage tumors, larger tumor size, lower household income, and rural residence. When patients experienced these conditions, OS was shorter, requiring more aggressive treatment.

Interface-Compatible Gel-Polymer Electrolyte Enabled by NaF-Solubility-Regulation toward All-Climate Solid-State Sodium Batteries.

Gel-polymer electrolyte (GPE) is a pragmatic choice for high-safety sodium batteries but still plagued by interfacial compatibility with both cathode and anode simultaneously. Here, salt-in-polymer fibers with NaF salt inlaid in polylactide (PLA) fiber network was fabricated via electrospinning and subsequent in situ forming gel-polymer electrolyte in liquid electrolytes. The obtained PLA-NaF GPE achieves a high ion conductivity (2.50×10-3 S cm-1) and large Na+ transference number (0.75) at ambient temperature. Notably, the dissolution of NaF salt occupies solvents leading to concentrated-electrolyte environment, which facilitates aggregates with increased anionic coordination (anion/Na+ >1). Aggregates with higher HOMO realize the preferential oxidation on the cathode so that inorganic-rich and stable CEI covers cathode' surface, preventing particles' breakage and showing good compatibility with different cathodes (Na3V2(PO4)3, Na2+2xFe2-x(SO4)3, Na0.72Ni0.32Mn0.68O2, NaTi2(PO4)3). While, passivated Na anode induced by the lower LUMO of aggregates, and the lower surface tension between Na anode and PLA-NaF GPE interface, leading to the dendrites-free Na anode. As a result, the assembled Na || Na3V2(PO4)3 cells display excellent electrochemical performance at all-climate conditions.

Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial.

OBJECTIVE: We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis. DESIGN: Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups. RESULTS: Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like Fusobacterium nucleatum and Streptococcus anginosus. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users. CONCLUSION: Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use. TRIAL REGISTRATION NUMBER: ChiCTR2300072310.

zPoseScore model for accurate and robust protein-ligand docking pose scoring in CASP15.

We introduce a deep learning-based ligand pose scoring model called zPoseScore for predicting protein-ligand complexes in the 15th Critical Assessment of Protein Structure Prediction (CASP15). Our contributions are threefold: first, we generate six training and evaluation data sets by employing advanced data augmentation and sampling methods. Second, we redesign the "zFormer" module, inspired by AlphaFold2's Evoformer, to efficiently describe protein-ligand interactions. This module enables the extraction of protein-ligand paired features that lead to accurate predictions. Finally, we develop the zPoseScore framework with zFormer for scoring and ranking ligand poses, allowing for atomic-level protein-ligand feature encoding and fusion to output refined ligand poses and ligand per-atom deviations. Our results demonstrate excellent performance on various testing data sets, achieving Pearson's correlation R = 0.783 and 0.659 for ranking docking decoys generated based on experimental and predicted protein structures of CASF-2016 protein-ligand complexes. Additionally, we obtain an averaged local distance difference test (lDDT pli = 0.558) of AIchemy LIG2 in CASP15 for de novo protein-ligand complex structure predictions. Detailed analysis shows that accurate ligand binding site prediction and side-chain orientation are crucial for achieving better prediction performance. Our proposed model is one of the most accurate protein-ligand pose prediction models and could serve as a valuable tool in small molecule drug discovery.

Reductive Competition Effect-Derived Solid Electrolyte Interphase with Evenly Scattered Inorganics Enabling Ultrahigh Rate and Long-Life Span Sodium Metal Batteries.

Constructing an inorganic-rich and robust solid electrolyte interphase (SEI) is one of the crucial approaches to improving the electrochemical performance of sodium metal batteries (SMBs). However, the low conductivity and distribution of common inorganics in SEI disturb Na+ diffusion and induce nonuniform sodium deposition. Here, we construct a unique SEI with evenly scattered high-conductivity inorganics by introducing a self-sacrifice LiTFSI into the sodium salt-base carbonate electrolyte. The reductive competition effect between LiTFSI and FEC facilitates the formation of the SEI with evenly scattered inorganics. In which the high-conductive Li3N and inorganics provide fast ions transport domains and high-flux nucleation sites for Na+, thus conducive to rapid sodium deposition at a high rate. Therefore, the SEI derived from LiTFSI and FEC enables the Na∥Na3V2(PO4)3 cell to show 89.15% capacity retention (87.62 mA h g-1) at an ultrahigh rate of 60 C after 10,000 cycles, while the cell without LiTFSI delivers only 48.44% capacity retention even after 8000 cycles. Moreover, the Na∥Na3V2(PO4)3 pouch cell with the special SEI presents a stable capacity retention of 92.05% at 10 C after 2000 cycles. This unique SEI design elucidates a new strategy to propel SMBs to operate under extreme high-rate conditions.

Liquid Template Assisted Activation for "Egg Puff"-Like Hard Carbon toward High Sodium Storage Performance.

The slow solid diffusion dynamics of sodium ions and the side-reaction of sodium metal plating at low potential in the hard carbon anode of sodium ion batteries (SIBs) pose significant challenges to the safety manipulation of high-rate batteries. Herein, a simple yet powerful fabricating method is reported on for "egg puff"-like hard carbon with few N doping using rosin as a precursor via liquid salt template-assisted and potassium hydroxide dual activation. The as-synthesized hard carbon delivers promising electrochemical properties in the ether-based electrolyte especially at high rates, based on the absorption mechanism of fast charge transfer. The optimized hard carbon exhibits a high specific capacity of 367 mAh g-1 at 0.05 A g-1 and 92.9% initial coulombic efficiency (ICE), 183 mAh g-1 at 10 A g-1 , and ultra-long cycle stability of reversible discharge capacity of 151 mAh g-1 after 12,000 cycles at 5 A g-1 with the average coulombic efficiency of ≈99% and the decay of 0.0026% per cycle. These studies will undoubtedly provide an effective and practical strategy for advanced hard carbon anode of SIBs based on adsorption mechanism.

Suppression of YTHDF2 attenuates autoimmune hepatitis by expansion of myeloid-derived suppressor cells.

BACKGROUND & AIMS: The N6-methyladenosine (m6A) reader YTH domain-containing family protein 2 (YTHDF2) is critically involved in a multiplicity of biological processes by mediating the degradation of m6A modified mRNAs. Based on our current understanding of this process, we hypothesized that YTHDF2 will play a role in the natural history and function of myeloid-derived suppressor cells (MDSC) and in particular in AIH. APPROACH & RESULTS: We took advantage of YTHDF2 conditional knock-out mice to first address the phenotype and function of MDSCs by flow cytometry. Importantly, the loss of YTHDF2 resulted in a gradual elevation of MDSCs including PMN-MDSCs both in liver and ultimately in the BM. Notably, YTHDF2 deficiency in myeloid cells attenuated concanavalin (ConA)-induced liver injury, with enhanced expansion and chemotaxis to liver. Furthermore, MDSCs from Ythdf2CKO mice had a greater suppressive ability to inhibit the proliferation of T cells. Using multi-omic analysis of m6A RNA immunoprecipitation (RIP) and mRNA sequencing, we noted RXRα as potential target of YTHDF2. Indeed YTHDF2-RIP-qPCR confirmed that YTHDF2 directly binds RXRα mRNA thus promoting degradation and decreasing gene expression. Finally, by IHC and immunofluorescence, YTHDF2 expression was significantly upregulated in the liver of patients with AIH which correlated with the degree of inflammation. CONCLUSION: Suppression of YTHDF2 enhances the expansion, chemotaxis and suppressive function of MDSCs and our data reveals a unique therapeutical target in immune mediated hepatitis.

Independent effects of the triglyceride-glucose index on all-cause mortality in critically ill patients with coronary heart disease: analysis of the MIMIC-III database.

BACKGROUND: The triglyceride-glucose (TyG) index is a reliable alternative biomarker of insulin resistance (IR). However, whether the TyG index has prognostic value in critically ill patients with coronary heart disease (CHD) remains unclear. METHODS: Participants from the Medical Information Mart for Intensive Care III (MIMIC-III) were grouped into quartiles according to the TyG index. The primary outcome was in-hospital all-cause mortality. Cox proportional hazards models were constructed to examine the association between TyG index and all-cause mortality in critically ill patients with CHD. A restricted cubic splines model was used to examine the associations between the TyG index and outcomes. RESULTS: A total of 1,618 patients (65.14% men) were included. The hospital mortality and intensive care unit (ICU) mortality rate were 9.64% and 7.60%, respectively. Multivariable Cox proportional hazards analyses indicated that the TyG index was independently associated with an elevated risk of hospital mortality (HR, 1.71 [95% CI 1.25-2.33] P = 0.001) and ICU mortality (HR, 1.50 [95% CI 1.07-2.10] P = 0.019). The restricted cubic splines regression model revealed that the risk of hospital mortality and ICU mortality increased linearly with increasing TyG index (P for non-linearity = 0.467 and P for non-linearity = 0.764). CONCLUSIONS: The TyG index was a strong independent predictor of greater mortality in critically ill patients with CHD. Larger prospective studies are required to confirm these findings.

More light components and less light damage on rats' eyes: evidence for the photobiomodulation and spectral opponency.

The blue-light hazard (BLH) has raised concerns with the increasing applications of white light-emitting diodes (LEDs). Many researchers believed that the shorter wavelength or more light components generally resulted in more severe retinal damage. In this study, based on the conventional phosphor-coated white LED, we added azure (484 nm), cyan (511 nm), and red (664 nm) light to fabricate the low-hazard light source. The low-hazard light sources and conventional white LED illuminated 68 Sprague-Dawley (SD) rats for 7 days. Before and after light exposure, we measured the retinal function, thickness of retinal layers, and fundus photographs. The expression levels of autophagy-related proteins and the activities of oxidation-related biochemical indicators were also measured to investigate the mechanisms of damaging or protecting the retina. With the same correlated color temperature (CCT), the low-hazard light source results in significantly less damage on the retinal function and photoreceptors, even if it has two times illuminance and blue-light hazard-weighted irradiance ([Formula: see text]) than conventional white LED. The results illustrated that [Formula: see text] proposed by IEC 62471 could not exactly evaluate the light damage on rats' retinas. We also figured out that more light components could result in less light damage, which provided evidence for the photobiomodulation (PBM) and spectral opponency on light damage.

Association between the insulin resistance marker TyG index and subsequent adverse long-term cardiovascular events in young and middle-aged US adults based on obesity status.

BACKGROUND: A lthough the triglyceride-glucose (TyG) index has been shown to closely correlate with cardiometabolic outcomes and predict cardiovascular events in many groups, it remains unclear whether obese status in young and middle-aged adults is associated with long-term unfavorable cardiovascular events. This warrants further investigation. METHODS: This retrospective cohort study analyzed data from the National Health and Nutrition Examination Survey spanning the years 1999-2018, with follow-up for mortality status until December 31, 2019. To categorize participants based on the TyG level, the optimal critical value was determined through restricted cubic spline function analysis, dividing them into high and low TyG groups. The study assessed the relationship between TyG and cardiovascular events and all-cause mortality in young and middle-aged adults stratified by obesity status. Kaplan‒Meier and Cox proportional risk models were used to analyze the data. RESULTS: During a follow-up period of 123 months, a high TyG index increased the risk of cardiovascular events by 63% (P = 0.040) and the risk of all-cause mortality by 32% (P = 0.010) in individuals after adjusting for all covariates. High TyG was shown to be linked to cardiovascular events in obese people (Model 3: HR = 2.42, 95% CI = 1.13-5.12, P = 0.020); however, there was no significant difference in TyG groups for nonobese adults in Model 3 (P = 0.08). CONCLUSIONS: TyG was independently associated with harmful long-term cardiovascular events in young and middle-aged US populations, with a stronger association observed in those who were obese.

Influence of renal function on the ability of TyG Index to predict all-cause mortality.

BACKGROUND: The association between triglyceride-glucose (TyG) index and poor prognosis remains controversial. Whether renal function status affects the ability of the TyG index to predict poor prognosis has not yet been elucidated and merits further studies. METHODS: This retrospective cohort study included 22,031 participants from communities in the U.S. By juxtaposing the TyG categories with the estimated glomerular filtration rate (eGFR, either < 60 mL/min/1.73m2 or ≥ 60 mL/min/1.73m2), participants were categorized into four distinct groups: (1) TyG_L/eGFR_H; (2) TyG_H/eGFR_H; (3) TyG_L/eGFR_L; and (4) TyG_H/eGFR_L. The endpoint was the all-cause mortality rate. Standard Kaplan-Meier plots were constructed and multifactor Cox regression analyses were carried out and restricted cubic spline regression analysis was utilized to assess the association between death and the TyG index for different renal function statuses. RESULTS: No statistical differences were found in the TyG groups in participants with normal renal function after adjustment for all covariates (P = 0.070). However, in the high TyG index group with renal insufficiency, the risk of all-cause mortality rates was reduced by 18%. (HR, 0.82; CI, 0.69-0.98). The TyG index (high vs. low) and renal function (eGFR < 60 vs. eGFR ≥ 60) had statistically significant interactions with death (P < 0.001). When all covariates were adjusted, the risk of mortality for the TyG_L combined with eGFR_L group was 56% higher than that for the TyG_L combined with eGFR_H group (HR, 1.56; CI, 1.33-1.82). In the renal insufficiency population, a nonlinear relationship was observed between mortality and the TyG index, albeit with a differing pattern (P for nonlinearity < 0.001). CONCLUSIONS: While it has been known that TyG index was a prognosis marker of CVD, this research highlights that higher TyG index was associated with higher all-cause mortality rates for all participants. Furthermore, renal function status significantly moderates the effect of the TyG index on all-cause mortality in community-dwelling adults.

STAB: a spatio-temporal cell atlas of the human brain.

The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available. Here, we present STAB (a Spatio-Temporal cell Atlas of the human Brain), a database consists of single-cell transcriptomes across multiple brain regions and developmental periods. Right now, STAB contains single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With STAB, the landscape of cell types and their regional heterogeneity and temporal dynamics across the human brain can be clearly seen, which can help to understand both the development of the normal human brain and the etiology of neuropsychiatric disorders. STAB is available at http://stab.comp-sysbio.org.

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements.

Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution and shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes. Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples. About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below). We provide extensive annotations of the identified eMGEs including sequence characteristics, taxonomy affiliation, gene contents and their prokaryotic hosts. We also calculate the prevalence, both within and across samples for each eMGE and eMGE cluster, enabling users to see putative associations of eMGEs with human phenotypes or their distribution preferences. All eMGE records can be browsed or queried in multiple ways, such as eMGE clusters, metagenomic samples and associated hosts. The mMGE is equipped with a user-friendly interface and a BLAST server, facilitating easy access/queries to all its contents easily. mMGE is freely available for academic use at: https://mgedb.comp-sysbio.org.