Effects of elevated ozone on winter wheat and potential genetic and physiological mechanisms

Wheat is an ozone-sensitive crop with substantial global yield loss. It is necessary to make assessments of ozone impacts and to investigate the tolerance mechanisms and genetic factors conferring ozone tolerance in wheat. Contrasting wheat cultivars had been pre-selected from a larger wheat population with known ozone tolerance and exposed to season-long ozone fumigation in open-top chambers. Season-long ozone fumigation was conducted at an average ozone concentration of 70 ppb with three additional acute ozone episodes of around 150 ppb. This thesis is structured into three major parts: (1) Based on the large variations of ozone responses in wheat, physiological traits contributing to yield losses or yield stability were identified under ozone stress in eighteen contrasting genotypes for modelling parameterization, that is, foliar chlorophyll content represented by normalized difference vegetation index and net CO2 assimilation rate of young leaves during grain filling. LINTULCC2 crop model was further parametrized for two selected tolerant or sensitive varieties, respectively, with an ozone response routine. Parameters representing the distinct physiological responses of contrasting genotypes were specified to improve the accuracy of modelling simulation. (2) Carbon (C) and nitrogen (N) allocation were analyzed in straw and grains under ozone stress. Elevated ozone exposure reduced the N absorption from soil and allocation from vegetative to reproductive organs, manifested as significantly reduced indicators of N use efficiency (NUE) with the exception of N utilization efficiency (NUtE). In addition, the relationship between harvest index (HI) and nitrogen harvest index (NHI) was changed by ozone stress, and the reduced regression slope between them indicated that ozone exposure significantly affected the relationship of N and biomass allocation into wheat grain. (3) According to genetic backgrounds at ozone tolerant loci, tolerant and sensitive haplotypes represented by two genotypes, respectively, were used for gene expression, physiological and biochemical analyses. Tolerant and sensitive haplotypes showed consistently contrasting responses to ozone in terms of net photosynthetic rate, lipid peroxidation, apoplastic ascorbate, ascorbate peroxidase and peroxidase activity. Among candidate genes located within an ozone tolerant locus on chromosome 5A 592.04 - 593.33 Mb, the gene TraesCS5A01G400500 putatively involved in peroxidase activity was differently regulated in two haplotypes, with consistent sequence polymorphisms in the promoter region. Taken together, this study improved the accuracy of modelling simulation for contrasting genotypes, assessed the C and N allocation and NUE among different genotypes and investigated the potential genetic and physiological mechanisms. Further explorations were warranted to reveal the molecular mechanisms underlying ozone tolerance in wheat

Chinese Fine-Grained Financial Sentiment Analysis with Large Language Models

Entity-level fine-grained sentiment analysis in the financial domain is a crucial subtask of sentiment analysis and currently faces numerous challenges. The primary challenge stems from the lack of high-quality and large-scale annotated corpora specifically designed for financial text sentiment analysis, which in turn limits the availability of data necessary for developing effective text processing techniques. Recent advancements in large language models (LLMs) have yielded remarkable performance in natural language processing tasks, primarily centered around language pattern matching. In this paper, we propose a novel and extensive Chinese fine-grained financial sentiment analysis dataset, FinChina SA, for enterprise early warning. We thoroughly evaluate and experiment with well-known existing open-source LLMs using our dataset. We firmly believe that our dataset will serve as a valuable resource to advance the exploration of real-world financial sentiment analysis tasks, which should be the focus of future research. The FinChina SA dataset is publicly available at https://github.com/YerayL/FinChina-SAComment: FinLLM Symposium at IJCAI 202

Genetic Variants of PTPN2 are Associated with Lung Cancer Risk: a Re-Analysis of Eight GWASs in the TRICL-ILCCO Consortium

The T-cell protein tyrosine phosphatase (TCPTP) pathway consists of signaling events mediated by TCPTP. Mutations and genetic variants of some genes in the TCPTP pathway are associated with lung cancer risk and survival. In the present study, we first investigated associations of 5,162 single nucleotide polymorphisms (SNPs) in 43 genes of this TCPTP pathway with lung cancer risk by using summary data of six published genome-wide association studies (GWAS) of 12,160 cases and 16,838 controls. We identified 11 independent SNPs in eight genes after correction for multiple comparisons by a false discovery rate \u3c 0.20. Then, we performed in silico functional analyses for these 11 SNPs by eQTL analysis, two of which, PTPN2 SNPs rs2847297 and rs2847282, were chosen as tagSNPs. We further included two additional GWAS datasets of Harvard University (984 cases and 970 controls) and deCODE (1,319 cases and 26,380 controls), and the overall effects of these two SNPs among all eight GWAS studies remained significant (OR = 0.95, 95% CI = 0.92–0.98, and P = 0.004 for rs2847297; OR = 0.95, 95% CI = 0.92–0.99, and P = 0.009 for rs2847282). In conclusion, the PTPN2 rs2847297 and rs2847282 may be potential susceptible loci for lung cancer risk

Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly.

Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we report the first crystal structure of the pre-fusion form of the NiV-F glycoprotein ectodomain. Interestingly this structure also revealed a hexamer-of-trimers encircling a central axis. Electron tomography of Nipah virus-like particles supported the hexameric pre-fusion model, and biochemical analyses supported the hexamer-of-trimers F assembly in solution. Importantly, structure-assisted site-directed mutagenesis of the interfaces between F trimers highlighted the functional relevance of the hexameric assembly. Shown here, in both cell-cell fusion and virus-cell fusion systems, our results suggested that this hexamer-of-trimers assembly was important during fusion pore formation. We propose that this assembly would stabilize the pre-fusion F conformation prior to cell attachment and facilitate the coordinated transition to a post-fusion conformation of all six F trimers upon triggering of a single trimer. Together, our data reveal a novel and functional pre-fusion architecture of a paramyxoviral fusion glycoprotein

Efficient and durable uranium extraction from uranium mine tailings seepage water via a photoelectrochemical method

Current photocatalytic uranium (U) extraction methods have intrinsic obstacles, such as the recombination of charge carriers, and the deactivation of catalysts by extracted U. Here we show that, by applying a bias potential on the photocatalyst, the photoelectrochemical (PEC) method can address these limitations. We demonstrate that, owing to efficient spatial charge-carriers separation driven by the applied bias, the PEC method enables efficient and durable U extraction. The effects of multiple operation conditions are investigated. The U extraction proceeds via single-step one-electron reduction, resulting in the formation of pentavalent U, which can facilitate future studies on this often-overlooked U species. In real seepage water the PEC method achieves an extraction capacity of 0.67 gU m(-3).h(-1) without deactivation for 156 h continuous operation, which is 17 times faster than the photocatalytic method. This work provides an alternative tool for U resource recovery and facilitates future studies on U(V) chemistry

Genetic testing and prognosis of sarcomatoid hepatocellular carcinoma patients

BackgroundSarcomatoid hepatocellular carcinoma (SHC) is a rare epithelial malignancy with high invasiveness and poor prognosis. However, the molecular characteristics and main driver genes for SHC have not been determined. The aim of this study is to explore the potentially actionable mutations of driver genes, which may provide more therapeutic options for SHC.MethodsIn this study, DNA extraction and library preparation were performed using tumor tissues from 28 SHC patients. Then we used Miseq platform (Illumina) to sequence the target-enriched library, and we aligned and processed the sequencing data. The gene groups were tested for SNVs/Indels/CNVs. Tumor mutation burden (TMB) was assessed by the 425-cancer-relevant gene panel. Multivariate analysis of COX’s model was used for survival analysis (OS) of patients’ clinical characteristics.ResultThe median overall survival (OS) of the patients was only 4.4 months. TP53, TERT, and KRAS were the top three frequently mutated genes, with frequencies of 89.3%, 64.3%, and 21.4%, respectively. A considerable number of patients carried mutations in genes involved in the TP53 pathway (96%) and DNA Damage Repair (DDR) pathway (21%). Multiple potentially actionable mutations, such as NTRK1 fusions and BRCA1/2 mutations, were identified in SHCs.ConclusionsThis study shows a landscape of gene mutations in SHC. SHC has high mutation rates in TP53 pathway and DDR pathway. The potentially actionable mutations of driver genes may provide more therapeutic options for SHC. Survival analysis found that age, smoking, drinking, and tumor diameter may be independent prognostic predictors of SHC

Spatial-temporal analysis of hepatitis E in Hainan Province, China (2013-2022): insights from four major hospitals

ObjectiveExploring the Incidence, Epidemic Trends, and Spatial Distribution Characteristics of Sporadic Hepatitis E in Hainan Province from 2013 to 2022 through four major tertiary hospitals in the Province.MethodsWe collected data on confirmed cases of hepatitis E in Hainan residents admitted to the four major tertiary hospitals in Haikou City from January 2013 to December 2022. We used SPSS software to analyze the correlation between incidence rate and economy, population density and geographical location, and origin software to draw a scatter chart and SAS 9.4 software to conduct a descriptive analysis of the time trend. The distribution was analyzed using ArcMap 10.8 software (spatial autocorrelation analysis, hotspot identification, concentration, and dispersion trend analysis). SAS software was used to build an autoregressive integrated moving average model (ARIMA) to predict the monthly number of cases in 2023 and 2024.ResultsFrom 2013 to 2022, 1,922 patients with sporadic hepatitis E were treated in the four hospitals of Hainan Province. The highest proportion of patients (n = 555, 28.88%) were aged 50–59 years. The annual incidence of hepatitis E increased from 2013 to 2019, with a slight decrease in 2020 and 2021 and an increase in 2022. The highest number of cases was reported in Haikou, followed by Dongfang and Danzhou. We found that there was a correlation between the economy, population density, latitude, and the number of cases, with the correlation coefficient |r| value fluctuating between 0.403 and 0.421, indicating a linear correlation. At the same time, a scatter plot shows the correlation between population density and incidence from 2013 to 2022, with r2 values fluctuating between 0.5405 and 0.7116, indicating a linear correlation. Global Moran’s I, calculated through spatial autocorrelation analysis, showed that each year from 2013 to 2022 all had a Moran’s I value >0, indicating positive spatial autocorrelation (p < 0.01). Local Moran’s I analysis revealed that from 2013 to 2022, local hotspots were mainly concentrated in the northern part of Hainan Province, with Haikou, Wenchang, Ding’an, and Chengmai being frequent hotspot regions, whereas Baoting, Qiongzhong, and Ledong were frequent cold-spot regions. Concentration and dispersion analysis indicated a clear directional pattern in the average density distribution, moving from northeast to southwest. Time-series forecast modeling showed that the forecast number of newly reported cases per month remained relatively stable in 2023 and 2024, fluctuating between 17 and 19.ConclusionThe overall incidence of hepatitis E in Hainan Province remains relatively stable. The incidence of hepatitis E in Hainan Province increased from 2013 to 2019, with a higher clustering of cases in the northeast region and a gradual spread toward the southwest over time. The ARIMA model predicted a relatively stable number of new cases each month in 2023 and 2024

Demulsification mechanism of asphaltene-stabilized water-in-oil emulsions by a polymeric ethylene oxide-propylene oxide demulsifier

The demulsification mechanism of asphaltene-stabilized water-in-toluene emulsions by an ethylene-oxide-propylene oxide (EO-PO) based polymeric demulsifier was studied. Demulsification efficiency was determined by bottle tests and correlated to the physicochemical properties of asphaltene interfacial films after demulsifier addition. From bottle tests and droplet coalescence experiments, the demulsifier showed an optimal performance at 2.3 ppm (mass basis) in toluene. At high concentrations, the demulsification performance deteriorated due to the intrinsic stabilizing capacity of the demulsifier, which was attributed to steric repulsion between water droplets. Addition of demulsifier was shown to soften the asphaltene film (i.e., reduce the viscoelastic moduli of asphaltene films) under both shear and compressional interfacial deformations. Study of the macrostructures and the chemical composition of asphaltene film at the toluene-water interface after demulsifier addition demonstrated gradual penetration of the demulsifier into the asphaltene film. Demulsifier penetration in the asphaltene film changed the asphaltene interfacial mobility and morphology, as probed with Brewster angle and atomic force microscopy

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe