Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are ...computationally intensive. To address this problem, a strategy consisting of sieving (pre-selecting closely related genomes) followed by alignment and calculation has been proposed.
Here, we initially test a published approach called "genome-wide tetranucleotide frequency correlation coefficient" (TETRA), which is specially tailored for sieving. Our results show that sieving by TETRA requires > 40% completeness for both genomes of a pair to yield > 95% sensitivity, indicating that TETRA is completeness-dependent. Accordingly, we develop a novel algorithm called "fragment tetranucleotide frequency correlation coefficient" (FRAGTE), which uses fragments rather than whole genomes for sieving. Our results show that FRAGTE achieves ~ 100% sensitivity and high specificity on simulated genomes, real genomes and metagenome-assembled genomes, demonstrating that FRAGTE is completeness-independent. Additionally, FRAGTE sieved a reduced number of total genomes for subsequent alignment and calculation to greatly improve computational efficiency for the process after sieving. Aside from this computational improvement, FRAGTE also reduces the computational cost for the sieving process. Consequently, FRAGTE extremely improves run efficiency for both the processes of sieving and after sieving (subsequent alignment and calculation) to together accelerate genome-wide species delineation.
FRAGTE is a completeness-independent algorithm for sieving. Due to its high sensitivity, high specificity, highly reduced number of sieved genomes and highly improved runtime, FRAGTE will be helpful for whole-genome approaches to facilitate taxonomic studies in prokaryotes.
Tumor-infiltrating lymphocytes (TILs) by routine hematoxylin and eosin staining (H&E-TILs) are a robust prognostic biomarker in various cancers. However, the role of H&E-TILs in esophageal squamous ...cell carcinoma (ESCC) treated with concurrent chemoradiotherapy (CCRT) has not been reported. The purpose of this study was to assess the prognostic value of H&E-TILs in ESCC treated with CCRT.
The clinical data of 160 patients with ESCC treated with CCRT in our center between Jan. 2014 and Dec. 2021 were collected and retrospectively reviewed, and propensity score matching (PSM) analyses were performed. The H&E-TILs sections before CCRT were reassessed by two experienced pathologists independently. The H&E-TILs sections were classified into a positive group (+, > 10%) and a negative group (-, ≤ 10%) using 10% as the cutoff. The effects of H&E-TILs on overall survival (OS), progression-free survival (PFS), distant metastasis-free survival (DMFS), and locoregional recurrence-free survival (LRFS) were explored using the Kaplan‒Meier method, and the log-rank test was used to test the differences. Multivariable analysis was performed using the Cox proportion hazards model.
The short-term response to CCRT and the OS (P < 0.001), DMFS (P = 0.001), and LRFS (P < 0.001) rates were significantly different between the H&E-TILs (+) and H&E-TILs (-) groups. Subgroup analysis showed that H&E-TILs(+) with CR + PR group had a longer survival than H&E-TILs(-) with CR + PR, H&E-TILs(+) with SD + PD and H&E-TILs(-) with SD + PD group, respectively(P < 0.001). Furthermore, based on TCGA data, patients in the high TILs group had a better prognosis than those in the low TILs group. Multivariate analyses indicated that H&E-TILs and the short-term response to CCRT were the only two independent factors affecting OS, PFS, DMFS, and LRFS simultaneously, and H&E-TILs expression was associated with an even better prognosis for those patients with CR + PR.
H&E-TILs may be an effective and beneficial prognostic biomarker for ESCC patients treated with CCRT. Patients with H&E-TILs (+) with PR + CR would achieve excellent survival. Further prospective studies are required to validate the conclusions.
Background. Systemic inflammation may be involved in the entire cancer process as a promoter and is associated with antitumor immunity. The systemic immune-inflammation index (SII) has been shown to ...be a promising prognostic factor. However, the relationship between SII and tumor-infiltrating lymphocytes (TIL) have not been established in esophageal cancer (EC) patients receiving concurrent chemoradiotherapy (CCRT). Methods. Retrospective analysis of 160 patients with EC was performed, peripheral blood cell counts were collected, and TIL concentration was assessed in H&E-stained sections. Correlations of SII and clinical outcomes with TIL were analyzed. Cox proportional hazard model and Kaplan–Meier method were used to perform survival outcomes. Results. Compared with high SII, low SII had longer overall survival (OS) (P=0.036, hazard ratio (HR) = 0.59) and progression-free survival (PFS) (P=0.041, HR = 0.60). Low TIL showed worse OS (P<0.001, HR = 2.42) and PFS (P<0.001, HR = 3.05). In addition, research have shown that the distribution of SII, platelet-to-lymphocyte ratio, and neutrophil-to-lymphocyte ratio were negatively associated with the TIL state, while lymphocyte-to-monocyte ratio presented a positive correlation. Combination analysis observed that SIIlow + TILhigh had the best prognosis of all combinations, with a median OS and PFS of 36 and 22 months, respectively. The worst prognosis was identified as SIIhigh + TILlow, with a median OS and PFS of only 8 and 4 months. Conclusion. SII and TIL as independent predictors of clinical outcomes in EC receiving CCRT. Furthermore, the predictive power of the two combinations is much higher than a single variable.
As a novel and environmentally friendly energy source, thermoelectric (TE) materials are receiving more and more attention because of their unique capability to directly convert heat into ...electricity. Chalcogenide-based materials have been extensively explored as promising TE candidates in the past years, primarily attributed to their unique properties in accommodating diverse compositions and structures, resulting in exceptional TE performance. Enhancing the TE properties of such materials typically involves a series of strategies: optimizing carrier concentration, harnessing energy band engineering to decouple the Seebeck coefficient and electric conductivity, and lowering the lattice thermal conductivity via nanostructuing. These approaches collectively hold the potential to significantly boost the overall performance of chalcogenide materials. This review provides a comprehensive overview of several classical chalcogenide-based TE material systems, such as SnQ (Q = S, Se, Te), PbQ (Q = S, Se, Te), GeTe, and Bi2Te3, focusing on their structures, and elucidates strategies for enhancing their thermoelectric performance.
This article offers a comprehensive overview of commonly used chalcogenide-based thermoelectric Materials, including SnQ (Q = S, Se, Te), PbQ (Q = S, Se, Te), GeTe, and Bi2Te3. The crystal structures and energy band structures of these materials are introduced. Furthermore, the optimization methods for enhancing the thermoelectric properties of chalcogenide-based thermoelectric Materials are detailed and summarized, focusing on three key aspects: carrier concentration, energy band engineering, and lattice thermal conductivity. Towards the conclusion of the article, a thorough discussion is presented on the application potential of these materials, along with insights into future research priorities. Display omitted
•Chalcogenides, including materials like SnTe, PbTe, Bi2Te3, etc., exhibit a notably high thermoelectric figure of merit.•The carrier concentration and conductivity of chalcogenide thermoelectric materials can be optimized by doping and alloying.•Optimizing carrier concentration and engineering energy bands enhances thermoelectric performance.•The manipulation of multiscale microstructures offers a promising means to reduce lattice thermal conductivity.
Pyroptosis is an exceptional mode of inflammation and programmed cell death involved in inflammasomes and Caspase-1 activation and inflammatory cytokines releasing. Our goal is to explore whether ...uranium (U)-intoxication could induce NRK-52
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cells pyroptosis in vitro and its underlying molecular mechanism. Rat NRK-52
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cells were intoxicated with U concentrations (400-500 μM) for 24 h. The results indicate that the cells showed characteristic features of pyroptosis, which were identified through augmented NLRP3 and cleaved Caspase-1 proteins expression, GSDMD mRNA level, mature interleukin IL-18 and IL-1β contents, LDH leakage, and the number of double-positive cells. But, administration of glycine (an inhibitor of pyroptosis) effectively attenuated U-induced pyroptosis, LDH releasing and cytotoxicity. Pretreatment of CRID3 (an inhibitor of NLRP3 inflammasome) evidently abrogated NLRP3 and cleaved Caspase-1 proteins and GSDMD mRNA expression which all were up-regulated by U exposure. Simultaneously, CRID3 significantly reversed U-increased pyroptosis rate and active interleukin IL-18 and IL-1β contents. NAC application (an ROS scavenger) effectively decreased U-increased ROS content and NLRP3 expression and restored U-induced pyroptosis. Taken together, our results suggest that U-treatment can trigger NRK-52
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cells pyroptosis which is involvement of ROS/NLRP3/Caspase-1 pathway. Targeting ROS/NLRP3/Caspase-1-mediated pyroptosis may be a novel approach for attenuating U nephrotoxicity.
As an endogenous gaseous mediator, H2S exerts anti-oxidative, anti-inflammatory and cytoprotective effects in kidneys. This study was designed to investigate the protective effect of H2S against ...uranium-induced nephrotoxicity in adult SD male rats after in vivo effect of uranium on endogenous H2S formation was explored in kidneys. The levels of endogenous H2S and H2S-producing enzymes (CBS and CSE) were measured in renal homogenates from rats intoxicated by an intraperitoneally (i.p.) injection of uranyl acetate at a single dose of 2.5, 5 or 10 mg/kg. In rats injected i.p. with uranyl acetate (5 mg/kg) or NaHS (an H2S donor, 28 or 56 μmol/kg) alone or in combination, we determined biochemical parameters and histopathological alteration to assess kidney function, examined oxidative stress markers, and investigated Nrf2 and NF-κB pathways in kidney homogenates. The results suggest that uranium intoxication in rats decreased endogenous H2S generation as well as CBS and CSE protein expression. NaHS administration in uranium-intoxicated rats ameliorated the renal biochemical indices and histopathological effects, lowered MDA accumulation, and restored GSH level and anti-oxidative enzymes activities like SOD, CAT, GPx and GST. NaHS treatment in uranium-intoxicated rats activated uranium-inhibited protein expression and nuclear translocation of transcription factor Nrf2, which increased protein expression of downstream target-Nrf2 genes HO-1, NQO-1, GCLC, and TXNRD-1. NaHS administration in uranium-intoxicated rats inhibited uranium-induced nuclear translocation and phosphorylation of transcription factor κB/p65, which decreased protein expression of target-p65 inflammatory genes TNF-α, iNOS, and COX-2. Taken together, these data implicate that H2S can afford protection to rat kidneys against uranium-induced adverse effects through induction of antioxidant defense by activating Nrf2 pathway and reduction of inflammatory response by suppressing NF-κB pathway.
•Uranium (U)-intoxication in rats decreased endogenous H2S level in kidneys.•H2S supplement in rats improved U-induced renal structure and function injuries.•H2S supplement alleviated U-induced oxidative stress in kidney homogenates.•H2S supplement induced antioxidant defense by activating U-inhibited Nrf2 pathway.•H2S addition reduced inflammatory response by inhibiting U-activated NF-κB pathway.
Propylphosphonic anhydride (T3P)-mediated condensation and intramolecular cyclization of 1-hydroxyanthraquinone with various active methylene acetates in the presence of Et3N was efficiently ...accomplished, affording oxaperylenone derivatives. The in situ generated propylphosphate derivatives were confirmed as reactive intermediates, which were produced by acylation from 1-hydroxyanthraquinone with T3P. The reaction mechanism was investigated theoretically using density functional theory, and a plausible reaction mechanism was proposed. This method is useful for the synthesis of the core structure of oxaperylenone derivatives.
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•One-pot synthesis of naptho 1,2,3-dechromene-2,7-dione skeleton.•Improved the synthesis method of oxaperylenone derivatives.•The mechanism relies on stabilization changes of anthraquinone-4-phosphoryl ester intermediates.
A field investigation was conducted for the vegetation composition and 226Ra uptake by native plant species at a uranium mill tailings impoundment in South China. 80 species belonging to 67 genera in ...32 families were recorded in the sampling sites. The Poaceae and Asteraceae were the dominant families colonizing the impoundment. The number of the plant species and vegetation community composition in the sampling sites seemed most closely related to the activities of 226Ra and the pH value of the uranium tailings. The plant species in the sampling sites with relatively low activities of 226Ra and relatively high pH value formed a relatively stable vegetation community. The plant species in the sampling sites with medium activities of 226Ra and medium pH value formed the transitional vegetation community. The plant species in the sampling sites with relatively high activities of 226Ra and relatively low pH value formed a simple unstable vegetation community that was similar to that on the unused grassland. The activities of 226Ra and transfer factors (TFs) varied greatly with the plant species. The high activities of 226Ra and TFs were found in the leaves of Pteris multifida (150.6 Bq/g of AW; 9.131), Pteridium aquilinum (122.2 Bq/g of AW; 7.409), and Dryopteris scottii (105.7 Bq/g of AW; 6.408). They satisfied the criteria for a hyperaccumulator for 226Ra. They may be the candidates for phytoremediation of 226Ra in the uranium mill tailings impoundment areas and the contaminated soils around.
•Vegetation composition of native plant species at an impoundment was analyzed.•226Ra uptake by native plant species at the impoundment was investigated.•Poaceae and Asteraceae were the dominated families colonizing this impoundment.•The plant species and composition were related to activities of 226Ra and pH.•Three plant species were found to be hyperaccumulators for 226Ra.
Hydrogen sulfide (H
2
S) shows antioxidative, anti-inflammatory, antiapoptotic, and cytoprotective effects in kidneys. Recently, H
2
S has been reported to alleviate uranium-induced rat ...nephrotoxicity through oxidative stress and inflammatory response via Nrf2-NF-κB pathways. Here, the protective effect and molecular mechanism of H
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S on uranium-induced apoptosis were examined in normal rat kidney proximal cells (NRK-52
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) in vitro. The results indicate that NaHS (an H
2
S donor) administration in uranium-intoxicated kidney cells ameliorated uranium-induced reactive oxygen species generation, caspase-3-dependent apoptosis, and endoplasmic reticulum (ER) stress identified through several key markers including GRP78, C/EBP homologous protein (CHOP), and caspase-12. NaHS treatment in uranium-intoxicated kidney cells abolished the effects of uranium on Akt phosphorylation, GSK-3β activation, increased Fyn nuclear expression, and concomitantly decreased Nrf2 nuclear expression. NaHS administration in uranium-treated kidney cells resorted uranium-decreased the expression of two key subunit PSMA6 and PSMB7 in 20S proteasome. But, DRB (an Nrf2 inhibitor) administration abrogated the effects of NaHS on PSMA6 and PSMB7 expression in uranium-contaminated kidney cells. Bortezomib (a proteasome inhibitor) treatment in NaHS pulsing uranium cotreated kidney cells reversed the effects of NaHS on not only PSMA6 and PSMB7 but also GRP78 and CHOP. Taken together, all data suggest that H
2
S can attenuate uranium-induced kidney cell apoptosis mediated by ER stress via 20S proteasome involving in Akt/GSK-3β/Fyn-Nrf2 signaling axis.
Plant, soil, and sediment samples were taken from the Fuqiao area within the Huayuan River basin in South China. Concentrations of manganese, zinc, cadmium, and lead in the samples were measured, and ...the characteristics of the plant samples to absorb, transfer, and accumulate the target metals were analyzed. It was indicated that the concentrations of target metals in 13 plant samples greatly exceeded the background values of target metals in plants over the world, and that the plant species might evolve to the accumulating ecotypes for the target metals under the long-term stress from the contaminated environment. Among 13 plant species, Alternanthera philoxeroides exhibited the highest accumulation capacities for the target metals, amounting to 6511, 13,784, 155, and 104 mg/kg in its shoots for manganese, zinc, cadmium, and lead, respectively. Its bioaccumulation coefficients for manganese, zinc, cadmium, and lead were 5.08, 49.23, 36.78, and 34.81, respectively, and its transfer factors for manganese, zinc, cadmium, and lead were 7.53, 3.19, 7.38, and 1.29, respectively. The results showed that Alternanthera philoxeroides satisfied the criteria for the hyperaccumulator for zinc and cadmium, and that it might be a potential native plant species for phytoremediation of the contaminated soil, sediment, and river water by the target metals within the basin.
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