Miracle-dz/UniFAR-FTUs huggingface dataset:
Revealing Heavy Metal Resistances in the Yanomami Microbiome

BACKGROUND The Amazon hosts invaluable and unique biodiversity as well as mineral resources. As a consequence, there are large illegal and artisanal gold mining areas in indigenous territories. Mercury has been used in gold mining, and some are released into the environment and atmosphere, primarily affecting indigenous as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region. OBJECTIVE Investigation of the Yanomami gut microbiome focusing on metal resistance. METHODS Metagenomic data from the Yanomami gut microbiome were assembled into contigs, and their putative proteins were matched to a database of metal resistance proteins. FINDINGS Most identified proteins have the potential to confer resistance to multiple metals (two or more), followed by mercury, copper, zinc, chromium, arsenic, and others. Operons with potential resistance to mercury, arsenic, chromium, nickel, zinc, copper, copper/silver, and cobalt/nickel were identified. Mercury resistance operon was the most abundant, even though a diversity of operons in the Yanomami microbiome was observed to have the potential to confer resistance to various metals CONCLUSION The Yanomami gut microbiome gene composition shows that these people have been exposed directly or indirectly to mercury and other heavy metals. Sponsorships This study was partly financed by the Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ); and PAEF (IOC-023-FIO-18-2-47).
Computational insights into the conformational transition of STING: mechanistic, energetic considerations, and the influence of crucial mutations

STING (stimulator of interferon genes) is a crucial protein in the innate immune system’s response to viral and bacterial infections. In this study, we investigated the mechanistic and energetic mechanism of the conformational transition process of STING activated by cGAMP binding. We found that the STING connector region undergoes an energetically unfavorable transition during this process, which is compensated by the favorable interaction between cGAMP and the STING ligand binding domain. We utilized enhanced sampling methods to study STING’s rotation and finds that several disease-causing mutations, such as N154S and V155L, can result in a smoother transition process, while V147L exhibits unfavorable conformational transition energy. These findings indicate that V147L may not be a gain-of-function mutation, as previously thought, and are further supported by an evolutionary analysis of the STING connector region. Overall, our study provides detailed insights into the mechanism of STING’s rotation and has implications for the development of treatments for STING-related diseases.
Development and internal validation of a novel nomogram for predicting lymph node invasion for prostate cancer patients undergoing extended pelvic lymph node dissection

Background Few studies have focused on the performance of Briganti 2012, Briganti 2017 and MSKCC nomograms in the Chinese population in assessing the risk of lymph node invasion(LNI) in prostate cancer(PCa) patients and identifying patients suitable for extended pelvic lymph node dissection(ePLND). We aimed to develop and validate a novel nomogram based on Chinese PCa patients treated with radical prostatectomy(RP) and ePLND for predicting LNI. Methods We retrospectively retrieved clinical data of 631 patients with localized PCa receiving RP and ePLND at a Chinese single tertiary referral center. All patients had detailed biopsy information from experienced uropathologist. Multivariate logistic-regression analyses were performed to identify independent factors associated with LNI. The discrimination accuracy and net-benefit of models were quantified using the area under curve(AUC) and Decision curve analysis(DCA). The nonparametric bootstrapping were used to internal validation. Results A total of 194(30.7%) patients had LNI. The median number of removed lymph nodes was 13(range, 11-18). In univariable analysis, preoperative prostate-specific antigen(PSA), clinical stage, biopsy Gleason grade group, maximum percentage of single core involvement with highest-grade PCa, percentage of positive cores, percentage of positive cores with highest-grade PCa and percentage of cores with clinically significant cancer on systematic biopsy differed significantly. The multivariable model that included preoperative PSA, clinical stage, biopsy Gleason grade group, maximum percentage of single core involvement with highest-grade PCa and percentage of cores with clinically significant cancer on systematic biopsy represented the basis for the novel nomogram. Based on a 12% cutoff, our results showed that 189(30%) patients could have avoided ePLND while only 9(4.8%) had LNI missing ePLND. Our proposed model achieved the highest AUC (proposed model vs Briganti 2012 vs Briganti 2017 vs MSKCC model: 0.83 vs 0.8 vs 0.8 vs 0.8, respectively) and highest net-benefit via DCA in the Chinese cohort compared with previous nomograms. In internal validation of proposed nomogram, all variables had a percent inclusion greater than 50%. Conclusion We developed and validated a nomogram predicting the risk of LNI based on Chinese PCa patients, which demonstrated superior performance compared with previous nomograms.
Super-V-shaped structure on 3C-SiC grown on the C-face of 4H-SiC

We investigate a unique super-V-shaped structure (SVSS) on the C-face of 3C/4H-SiC heteroepitaxial films. Atomic force microscopy (AFM) and optical images reveal that two low protruding straight lines of an SVSS join at a common higher protruding point. Transmission electron microscopy images determine that the protruding point is induced by polycrystalline nucleation, and straight lines are found to be 3C crystals without any specific defects. High-resolution AFM reveals that the directions of the SVSSs are strongly related to step-flow. It is believed that the straight lines are caused by redundant adatoms gathering and crystallizing when they meet and deviate around the protruding point defect on their original migration path. The effects of step-flow and anti-step-flow in the formation of SVSSs are discussed.
Gut microbial profile of treatment-naive patients with primary biliary cholangitis

Background and aims The pathogenesis of primary biliary cholangitis (PBC) is associated with alterations of gut microbiota. We compared the gut microbiota of PBC patients and healthy controls from Zhejiang Province and assessed the use of these data for the diagnosis of PBC. Methods First, 16S rRNA gene sequencing was used to characterize the gut microbiota of treatment-naive PBC patients (n=25) and matched healthy controls (n=25). Then, the value of gut microbiota composition for the diagnosis of PBC and assessment of PBC severity was determined. Results The gut microbiota of PBC patients had lower diversity based on three different metrics of alpha-diversity (ace, Chao1, and observed features) and fewer overall genera (all p<0.01). PBC patients had significant enrichment of four genera and significant depletion of eight genera. We identified six amplicon sequence variants (Serratia, Oscillospirales, Ruminococcaceae, Faecalibacterium, Sutterellaceae, and Coprococcus) as optimal biomarkers to distinguish PBC patients from controls based on receiver operating characteristic analysis (area under the curve [AUC] = 0.824). PBC patients who were anti-gp210-positive had lower levels of Oscillospiraceae than those who were anti-gp210-negative. KEGG functional annotation suggested the major changes in the gut microbiota of PBC patients were related to lipid metabolism and biosynthesis of secondary metabolites. Conclusion We characterized the gut microbiota of treatment-naive PBC patients and healthy controls from Zhejiang Province. The PBC patients had significant alterations in their gut microbiota, suggesting that gut microbiota composition could be useful as a non-invasive tool for the diagnosis of PBC.
What is the potential impact of genetic divergence of plastid ribosomal genes between Silene nutans lineages in hybrids? An in silico approach using the 3D structure of the plastid ribosome

Introduction Following the integration of cyanobacteria into the eukaryotic cells, many genes were transferred from the plastid to the nucleus. As a result, plastid complexes are encoded both by plastid and nuclear genes. Tight co-adaptation is required between these genes as plastid and nuclear genomes differ in several characteristics, such as mutation rate and inheritance patterns. Among these are complexes from the plastid ribosome, composed of two main subunits: a large and a small one, both composed of nuclear and plastid gene products. This complex has been identified as a potential candidate for sheltering plastid–nuclear incompatibilities in a Caryophyllaceae species, Silene nutans. This species is composed of four genetically differentiated lineages, which exhibit hybrid breakdown when interlineage crosses are conducted. As this complex is composed of numerous interacting plastid–nuclear gene pairs, in the present study, the goal was to reduce the number of gene pairs that could induce such incompatibilities. Method We used the previously published 3D structure of the spinach ribosome to further elucidate which of the potential gene pairs might disrupt plastid–nuclear interactions within this complex. After modeling the impact of the identified mutations on the 3D structure, we further focused on one strongly mutated plastid–nuclear gene pair: rps11–rps21. We used the centrality measure of the mutated residues to further understand if the modified interactions and associated modified centralities might be correlated with hybrid breakdown. Results and discussion This study highlights that lineage-specific mutations in essential plastid and nuclear genes might disrupt plastid–nuclear protein interactions of the plastid ribosome and that reproductive isolation correlates with changes in residue centrality values. Because of this, the plastid ribosome might be involved in hybrid breakdown in this system.
Water status and macronutrient concentrations, but not carbon status, of Viscum album ssp. album are determined by its hosts: a study across nine mistletoe–host pairs in central Switzerland

Introduction European mistletoe, Viscum album L. , is a hemiparasite that can infect various tree species, yet our understanding of its physiological interactions with host species is limited. Methods Nine mistletoe–host pairs (i.e. V. album ssp. album growing on nine different broadleaf tree species) under different growth conditions in central Switzerland were selected to examine the carbon, water and nutrient relationships between mistletoe and its hosts. We measured leaf morphological traits, isotopic compositions (δ13C and δ15N), concentrations of non-structural carbohydrates (NSC) and specific compounds (i.e. mobile sugars and starch), and macronutrients (i.e. N, P, K, Ca, Mg, S) in leaf and xylem tissues of both mistletoe and its hosts. Results and Discussion There were only non-significant relationships between NSC concentrations in mistletoe and in its host species across the nine mistletoe–host pairs, suggesting the carbon condition of V. album ssp. album is determined by both the heterotrophic carbon transfer and self-photosynthetic capacity among different mistletoe-host pairs. However, mistletoe leaf morphological traits (single leaf area and mass, and leaf mass per unit leaf area) did not change across the nine mistletoe–host pairs, and mistletoe leaf δ13C, water content and macronutrient concentrations were linearly correlated with those in the host leaves. Macronutrients showed accumulations in mistletoe across the nine pairs. Further, tissue N concentrations were significantly higher in mistletoe grown on N-fixing hosts than on non-N-fixing hosts. Finally, leaf N:P in mistletoe was significantly correlated with the ratio in the host across the nine mistletoe–host pairs. Overall, our results indicate strong relationships between mistletoe and its hosts for water- and nutrient-related traits, but not for carbon-related traits, which demonstrates that V. album ssp. album can adjust its physiology to survive on different deciduous tree species hosts and under different site conditions.
Mesophyll conductance and N allocation co-explained the variation in photosynthesis in two canola genotypes under contrasting nitrogen supply

The application of nitrogen fertilizer within a normal range has been found to increase the leaf nitrogen content and photosynthetic rate of canola plants (Brassica napus L.). Despite numerous studies on the separate effects of CO2 diffusion limitation and nitrogen allocation trade-off on photosynthetic rate, few have examined both these factors in relation to the photosynthetic rate of canola. In this study, two genotypes of canola with varying leaf nitrogen content were analyzed to determine the impact of nitrogen supply on leaf photosynthesis, mesophyll conductance, and nitrogen partitioning. The results showed that the CO2 assimilation rate (A), mesophyll conductance (g m), and photosynthetic nitrogen content (N psn) increased with an increase in nitrogen supply in both genotypes. The relationship between nitrogen content and A followed a linear-plateau regression, while A had linear relationships with both photosynthetic nitrogen content and g m, indicating that the key to enhancing A is increasing the distribution of leaf nitrogen into the photosynthetic apparatus and g m, rather than just increasing nitrogen content. Under high nitrogen treatment, the genotype (QZ) with high nitrogen content had 50.7% more nitrogen than the other genotype (ZY21), but had similar A, which was primarily due to ZY21’s higher photosynthetic nitrogen distribution ratio and stomatal conductance (g sw). On the other hand, QZ showed a higher A than ZY21 under low nitrogen treatment as QZ had higher N psn and g m compared to ZY21. Our results indicate that, in selecting high PNUE rapeseed varieties, it is important to consider the higher photosynthetic nitrogen distribution ratio and CO2 diffusion conductance.
Quantifying changes in soil organic carbon density from 1982 to 2020 in Chinese grasslands using a random forest model

China has the second-largest grassland area in the world. Soil organic carbon storage (SOCS) in grasslands plays a critical role in maintaining carbon balance and mitigating climate change, both nationally and globally. Soil organic carbon density (SOCD) is an important indicator of SOCS. Exploring the spatiotemporal dynamics of SOCD enables policymakers to develop strategies to reduce carbon emissions, thus meeting the goals of “emission peak” in 2030 and “carbon neutrality” in 2060 proposed by the Chinese government. The objective of this study was to quantify the dynamics of SOCD (0–100 cm) in Chinese grasslands from 1982 to 2020 and identify the dominant drivers of SOCD change using a random forest model. The results showed that the mean SOCD in Chinese grasslands was 7.791 kg C m−2 in 1982 and 8.525 kg C m−2 in 2020, with a net increase of 0.734 kg C m−2 across China. The areas with increased SOCD were mainly distributed in the southern (0.411 kg C m−2), northwestern (1.439 kg C m−2), and Qinghai–Tibetan (0.915 kg C m−2) regions, while those with decreased SOCD were mainly found in the northern (0.172 kg C m−2) region. Temperature, normalized difference vegetation index, elevation, and wind speed were the dominant factors driving grassland SOCD change, explaining 73.23% of total variation in SOCD. During the study period, grassland SOCS increased in the northwestern region but decreased in the other three regions. Overall, SOCS of Chinese grasslands in 2020 was 22.623 Pg, with a net decrease of 1.158 Pg since 1982. Over the past few decades, the reduction in SOCS caused by grassland degradation may have contributed to soil organic carbon loss and created a negative impact on climate. The results highlight the urgency of strengthening soil carbon management in these grasslands and improving SOCS towards a positive climate impact.
Metabolome analysis reveals flavonoid changes during the leaf color transition in Populus × euramericana ‘Zhonghuahongye’

Introduction To investigate the mechanism of leaf color change at different stages in Populus × euramericana ‘Zhonghuahongye’ (‘Zhonghong’ poplar). Methods Leaf color phenotypes were determined and a metabolomic analysis was performed on leaves at three stages (R1, R2 and R3). Results The a*, C* and chromatic light values of the leaves decreased by 108.91%, 52.08% and 113.34%, while the brightness L values and chromatic b* values gradually increased by 36.01% and 13.94%, respectively. In the differential metabolite assay, 81 differentially expressed metabolites were detected in the R1 vs. R3 comparison, 45 were detected in the R1 vs. R2 comparison, and 75 were detected in the R2 vs. R3 comparison. Ten metabolites showed significant differences in all comparisons, which were mostly flavonoid metabolites. The metabolites that were upregulated in the three periods were cyanidin 3,5-O-diglucoside, delphinidin, and gallocatechin, with flavonoid metabolites accounting for the largest proportion and malvidin 3- O-galactoside as the primary downregulated metabolite. The color shift of red leaves from a bright purplish red to a brownish green was associated with the downregulation of malvidin 3-O-glucoside, cyanidin, naringenin, and dihydromyricetin. Discussion Here, we analyzed the expression of flavonoid metabolites in the leaves of ‘Zhonghong’ poplar at three stages and identified key metabolites closely related to leaf color change, providing an important genetic basis for the genetic improvement of this cultivar.
Increased meso-striatal connectivity mediates trait impulsivity in FTO variant carriers

Objective While variations in the first intron of the fat mass and obesity-associated gene (FTO, rs9939609 T/A variant) have long been identified as a major contributor to polygenic obesity, the mechanisms underlying weight gain in risk allele carriers still remain elusive. On a behavioral level, FTO variants have been robustly linked to trait impulsivity. The regulation of dopaminergic signaling in the meso-striatal neurocircuitry by these FTO variants might represent one mechanism for this behavioral alteration. Notably, recent evidence indicates that variants of FTO also modulate several genes involved in cell proliferation and neuronal development. Hence, FTO polymorphisms might establish a predisposition to heightened trait impulsivity during neurodevelopment by altering structural meso-striatal connectivity. We here explored whether the greater impulsivity of FTO variant carriers was mediated by structural differences in the connectivity between the dopaminergic midbrain and the ventral striatum. Methods Eighty-seven healthy normal-weight volunteers participated in the study; 42 FTO risk allele carriers (rs9939609 T/A variant, FTO + group: AT, AA) and 39 non-carriers (FTO − group: TT) were matched for age, sex and body mass index (BMI). Trait impulsivity was assessed via the Barratt Impulsiveness Scale (BIS-11) and structural connectivity between the ventral tegmental area/substantia nigra (VTA/SN) and the nucleus accumbens (NAc) was measured via diffusion weighted MRI and probabilistic tractography. Results We found that FTO risk allele carriers compared to non-carriers, demonstrated greater motor impulsivity (p = 0.04) and increased structural connectivity between VTA/SN and the NAc (p< 0.05). Increased connectivity partially mediated the effect of FTO genetic status on motor impulsivity. Conclusion We report altered structural connectivity as one mechanism by which FTO variants contribute to increased impulsivity, indicating that FTO variants may exert their effect on obesity-promoting behavioral traits at least partially through neuroplastic alterations in humans.
Axl promotes intracranial aneurysm rupture by regulating macrophage polarization toward M1 via STAT1/HIF-1α

Background Macrophage infiltration and polarization are crucial for the pathogenesis of intracranial aneurysm (IA) rupture. Axl, a receptor tyrosine kinase, is involved in inflammation and efferocytosis in multiple organs. Upregulated soluble Axl in cerebrospinal fluid (CSF) and plasma is correlated with intracranial aneurysm rupture. This study aimed to investigate the role of Axl in IA rupture and macrophage polarization. Methods Male C57BL/6J mice were used to induce IA. The level of Axl from control vessels and unruptured and ruptured IA samples was detected. In addition, the relationship between Axl and macrophages was confirmed. The pathway of Axl-mediated macrophage polarization was explored after IA induction in vivo and in bone marrow-derived macrophages (BMDMs) stimulated by LPS/IFN-γ in vitro. The animals were randomized into three groups and treated intraperitoneally with the vehicle, selective AXL antagonist R428, and recombinant mouse growth arrest-specific 6 (rmGas6) for 21 consecutive days. Then, we evaluated the influence of Axl on IA rupture by administrating R428 to inhibit or rmGas6 to activate the Axl receptor in vivo. Results Compared with that in normal vessels, Axl expression was significantly upregulated in unruptured IA samples. The ruptured IA tissue exhibited significantly higher expression of Axl than the unruptured IA tissue. Axl and F4/80 were coexpressed in IA tissue and LPS/IFN-γ-stimulated BMDMs. R428 treatment significantly reduced the rate of M1-like macrophage infiltration and IA rupture. In contrast, rmGas6 treatment promoted M1 macrophage infiltration and IA rupture. Mechanistically, R428 inhibited the phosphorylation of Axl and STAT1 and the expression of hypoxia-inducible factor-1α (HIF-1α) and decreased the levels of IL-1β, NOS2, and MMP9 in LPS/IFN-γ-stimulated BMDMs. rmGas6 promoted the phosphorylation of Axl and STAT1 and the expression of HIF-1α. In addition, STAT1 knockdown abolished Axl-mediated M1 macrophage polarization. Conclusion The inhibition of Axl reduced macrophage polarization toward the M1 phenotype via the STAT1/HIF-1α signaling pathway and prevented IA rupture in mice. This finding suggests that pharmacological inhibition of Axl might be used to prevent the progression and rupture of IA.
Two new species of

Two new species of Sarcomyxa from China were described and illustrated based on morphological features and multi-locus (ITS, nrLSU, RPB2, and TEF1-α) phylogeny. Sarcomyxa baishanzuensis has a basidiome without a bitter taste, a purple to purplish yellow pileus surface, clavate cheilocystidia with broadly rounded apex or with short outgrowths, and clavate to nearly fusiform pleurocystidia, while S. ochracea usually has an ochraceous yellow pileus surface, clavate cheilocystidia often with apical outgrowths, and subfusiform pleurocystida usually with a broadly rounded apex. A key to the known species of Sarcomyxa is provided.
Number Type Recognition of Chinese Personal Noun Phrase

Number type is absolutely a necessary feature for co-reference resolution.Different from English,Chinese, belonging to Sino-Tibetan language family,cannot reflect number information directly by nouns themselves.However,the problem can be tackled by virtue of noun phrase.This paper presents two methods of number type recognition of Chinese personal noun phrase and their tests on ACE 2005 corpus.The first one is rule-based,which defines the template rules based on some knowledge resources,employing some slots and slot values.The other one is machine learning method,with maximum entropy model on features of word,pos,word sense,and quantitative relation.The two methods reached total accuracies of 48.24% and 87.48%,respectively.Experimental results showed that the rule based method could ensure the precision but the recall,while the machine learning method managed the number type recognition task.