bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome sequencing and analysis of the weed pathogen Trichoderma polysporum HZ-31
Authors: He yushan , Zhu haixia 
Published: April 2024

Abstract

In order to resolve the key genes for weed control by Trichoderma polysporum at the genomic level, we extracted the genomic DNA and sequenced the whole genome of T. polysporum strain HZ-31 on the Illumina Hiseq™ platform. The raw data were cleaned up using Trimmomatic and checked for quality using FastQC. The sequencing data were assembled using SPAdes, and GeneMark was used to perform gene prediction on the assembly results. The results showed that the genome size of T. polysporum HZ-31 was 39,325,746 bp, with 48% GC content, and the number of genes encoded was 11,998. A total of 148 tRNAs and 45 rRNAs were predicted. A total of 782 genes were annotated in the Carbohydrase Database, 757 genes were annotated to the Pathogen-Host Interaction Database, and 67 gene clusters were identified. In addition, 1023 genes were predicted to be signal peptide proteins. The annotation and functional analysis of the whole genome sequence of T. polymorpha HZ-31 provide a basis for the in-depth study of the molecular mechanism of its herbicidal action and more effective utilization for weed control.
Non-targeted isomer-sensitive N-glycome analysis reveals new layers of organ-specific diversity in mice.
Authors: Stadlmann Johannes , Helm Johannes , Mereiter Stefan , Oliveira Tiago , Gattinger Anna , Markovitz David , Penninger Josef , Altmann Friedrich 
Published: April 2024

Abstract

N-glycosylation is one of the most common protein modifications in eukaryotes, with immense importance at the molecular, cellular, and organismal level. Accurate and reliable N-glycan analysis is essential to obtain a systems-wide understanding of fundamental biological processes. Due to the structural complexity of glycans, their analysis is still highly challenging. Here we make publicly available a consistent N-glycome dataset of 20 different mouse tissues and demonstrate a multimodal data analysis workflow that allows for unprecedented depth and coverage of N-glycome features. This highly scalable, LC-MS/MS data-driven method integrates the automated identification of N-glycan spectra, the application of non-targeted N-glycome profiling strategies and the isomer-sensitive analysis of glycan structures. Our delineation of critical sub-structural determinants and glycan isomers across the mouse N-glycome uncovered tissue-specific glycosylation patterns, the expression of non-canonical N-glycan structures and highlights multiple layers of N-glycome complexity that derive from organ-specific regulations of glycobiological pathways.
Red blood cell metabolomics identify ergothioneine as a key metabolite in DMARD-naïve rheumatoid arthritis and response to methotrexate
Authors: Sigaux Johanna , Junot Christophe , Boissier Marie-Christophe , Petit Mylène , Breckler Magali , Castelli Florence , Fenaille François , Roméo Paul-Henri , Semerano Luca 
Published: April 2024

Abstract

Using a new red blood cell (RBC) metabolite extraction protocol, we performed a metabolomic analysis on RBCs in rheumatoid arthritis (RA) patients treated or not with methotrexate (MTX), with the two following objectives: to compare the RBC metabolic profiles of MTX-naïve RA patients and healthy controls (HC), and to investigate whether RBC profiles before and after MTX treatment in RA differed between responders and non-responders. Plasma analysis was performed in parallel. Metabolites were extracted and identified in RBCs and plasma by liquid chromatography-mass spectrometry. We compared the metabolomic fingerprints of 31 DMARD-naïve RA patients and 39 HCs. We also compared the RBC and plasma metabolomes of 25 RA patients who responded or not to MTX therapy before (M0) and after a 3-month treatment period (M3). Significance was determined by Storey’s false discovery rate (FDR) q-values to correct for multiple testing. RA patients and HCs differed in the metabolomic signature of RBCs. The signature mainly contained amino acids (AA). Eleven metabolites, including 4 metabolites belonging to the carbohydrate subclass and 2 amino acids (creatine and valine) showed accumulation in RBCs from RA patients. Conversely, citrulline (fold change=0.83; q=0.025), histidine (fold change=0.86; q=0.014) and ergothioneine (EGT) (fold change=0.66; q=0.024), were lower in RA. Among RA patients undergoing MTX treatment pre-treatment (M0), EGT values were significantly lower in non-responders. In conclusion, low RBC levels of EGT, a food-derived AA barely detectable in plasma, characterize DMARD naïve RA patients and lack of response to MTX treatment.
Combining continuous data on soil properties and land use to explore soil carbon changes and soil structure indicators
Authors: Rehn Andreas , Berndes Göran , Cederberg Christel , Englund Oskar 
Published: April 2024

Abstract

Increasing crop rotational diversity, e.g., by including grass-clover ley crops, can increase soil organic carbon (SOC) and support climate change mitigation and adaptation, with economic and environmental co-benefits. Here, we apply a method for using large and continuously updated geospatial datasets on (i) agricultural land use and (ii) soil properties, from the Swedish national soil inventory, to analyze how grass-clover (ley) cultivation in rotation with annual crops influences SOC content and soil structure quality (SOC/clay ratio). The results suggest a positive correlation between the occurrence of ley in crop rotations and SOC content. The method used in this study can build on and complement long-term field experiments and can enable the use of spatially explicit soil structure indicators for mapping and analyzing effects of land management, providing input to inform development and implementation of policies for land-based climate change mitigation.
GZMA Suppressed GPX4-mediated Ferroptosis to Improve Intestinal Mucosal Barrier Function in Inflammatory Bowel Disease
Authors: Niu Rongwei , Lan Jiaoli , Xiang Li , Wu Jiaxin , Zhang Xiaoyan , Li Zhiling , Xu Wanfu , Gong Sitang , Yang Min 
Published: April 2024

Abstract

Background
Intestinal epithelial cells (IECs) is a critical component in maintaining intestinal homeostasis. Our previous study demonstrated a decreased population of colonic CD8+CD39+ T cells in pediatric-onset colitis and inflammatory bowel disease (IBD), and further revealed an enrichment of granzyme A (GZMA) in CD8+CD39+ T cells. However, the function of GZMA in IECs remained to be identified.
Methods
ELISA was performed to detect GZMA expression. WB, q-PCR and IF were performed to detect the expression of CDX2, OCLN, ZO-1 and ferroptosis-related genes expression. In vitro permeability assay was performed to assess the impact of GZMA in intestinal permeability. Intestinal organoid assay was used to explore the effect of GZMA on intestinal organoid differentiation. Luciferase and a subcellular fractionation approach were applied to reveal the mechanism underlying GZMA mediated ferroptosis in vitro. In vivo experiment in mice was conducted to validate the role of GZMA in alleviating ferroptosis in IECs, thereby promoting cell differentiation.
Results
Herein, we, for the first time, demonstrated that GZMA contributed to IECs differentiation characterized by enhanced CDX2 expression, leading to induce Occludin(OCLN) and Zonula Occludens-1(ZO-1) expression, which was attributed to ferroptosis inhibition caused by GZMA. Mechanically, GZMA activated cAMP/PKA/CREB pathway in IECs, leading to CREB nuclear translocation and initiate GPX4 transactivity. Most importantly, treatment of GZMA could alleviate DSS-induced colitis in mice confirmed by immunofluorescence.
Conclusion
These findings suggested that GZMA contributed to intestinal epithelial cell differentiation through ferroptosis via the PDE4/PKA/CREB signaling pathway, targeting GZMA could be a promising strategy to patients with IBD.
Expression and role of CNIH2 in prostate cancer
Authors: Zhang Wei , li Zhenhua , Zhang Yunmeng , Wang Shen , Jiang Xin , Ma Yuepeng , Hu Caoyang , Ma Zhifang , Wang Xin 
Published: April 2024

Abstract

Prostate cancer is one of the most common cancers in men and poses a significant threat to global male health. Traditional prostate cancer assessment methods have certain limitations, necessitating the identification of new prognostic factors and treatment targets. Our study revealed that low expression of the CNIH2 gene was associated with a better progression-free survival rate in prostate cancer patients. The area under the ROC curve (AUC) showed that the prognostic ability of the CNIH2 gene was high at 1, 3, and 5 years. The gene was an independent prognostic factor according to multivariate analysis. Functional verification experiments showed that knocking down the CNIH2 gene could inhibit the proliferation, migration and invasion of prostate cancer cells and could also inhibit tumor growth in nude mice. Our study is the first to reveal the important role of the CNIH2 gene in prostate cancer. This discovery provides a new research direction for individualized treatment and prognostic evaluation of prostate cancer.
A Parallel Program for the Simulation of Flooding
Authors: Busaman Anurak , MCNEIL RHYSA , Chuai-Aree Somporn , Eso Mayuening 
Published: April 2024

Abstract
Flood simulation reduces computational time, which is essential for timely prevention. It needs numerical algorithms for reducing computation times without losing much accuracy in the results of flood simulation. This study presents a parallel algorithm by applying the automatic domain updating method for solving the shallow water equation with the well-balanced positivity-preserving first-order finite volume scheme. The developed parallel program was tested by simulating the water flow, compared with the results obtained in the literature, and applied to the Bang Lang dam break simulation to create information on flooding. The computational times obtained by the proposed parallel program were compared with those of the serial program, which used only the automatic domain updating method without the parallel technique. The results show that the parallel program outperforms the serial program by reducing the computational time.
Nasal Dominance Potentiates Intranasal Oxytocin’s Anxiolytic Effects
Authors: Julius Nikita Catalina , Nicholls Dasha , Nowell Joseph , Burmester Victoria 
Published: April 2024

Abstract
The nasal cycle is a phenomenon whereby alterations in airflow alternate between left and right nostrils. During a nostril’s decongested – or dominant – state, the contralateral nostril is congested, or non-dominant. Intranasal oxytocin may elicit anxiolytic effects. To date, no study has investigated whether there is an optimal nasal pathway for oxytocin’s effects. Forty-four female adolescents aged 16 to 17 years were included in this exploratory study investigating effects of nasal dominance on intranasal oxytocin delivery. We show that intranasal oxytocin significantly reduces stress relative to placebo (p = 0.019, ηp2 = 0.129) and greater stress reduction occurs when oxytocin is delivered to the dominant, rather than non-dominant, nostril (p = 0.045, ηp2 = 0.102). We postulate that oxytocin administration may reduce stress and be most effective in the context of anxiolysis when administered to the dominant nostril. Further research investigating whether other intranasal psychotropic drugs have nostril-specific effects might benefit clinical practice.
Nutrition and dietary inflammatory indices of the eight major cuisines of China
Authors: Zhao Wehzhi , Jia Zhongwei , Shi Hanping 
Published: April 2024

Abstract
Background
Chinese cuisines are famous for excellence in color, aroma, and taste. There are eight major styles, and each cuisine has its unique flavors. Dietary inflammatory index (DII) is a comprehensive parameter of diet-derived inflammatory capacity and designed to be universally applicable across all human studies for dietary assessment.
Methods
Food materials, food composition, and DII of dishes from the eight major cuisines of China were analyzed based on two cookbooks. The usage rate and dosage of food components were calculated for each cuisine. The energy and nutrient content of every dish was measured based on China Food Composition Tables. Then, DII was calculated. Continuous variables were presented as quartiles. Mann–Whitney U test or Kruskal–Wallis H test for non-normally distributed data was applied.
Results
A total of 980 dishes belonging to the 8 cuisines were included. Condiments were the most popular food material in different cuisines. For standard serves (per 500g) of a dish, energy (calories) and fat contained in Sichuan cuisine was the highest. The carbohydrate contained in Zhejiang cuisine and Sichuan cuisine were the highest and lowest, respectively. For each energy equivalent serve (per 500kcal) of a dish, the total fat of dishes contained in Sichuan cuisine was the highest. The content of carbohydrate and protein of dishes contained in Fujian cuisine and Sichuan cuisine was the highest and lowest, respectively. There was a significant difference between cuisines in the distribution of DII. The percentage of pro-inflammatory dishes was the highest in Cantonese cuisine (47.4%) whereas the lowest in Hunan cuisine (11.6%), regardless measured by standard serve or energy equivalent serve.
Conclusions
Different Chinese cuisines exhibited different prior selections of food materials, which was partly explained by the taste of local cuisine. The energy and nutrient content of different cuisines significantly varied. The percentage of pro-inflammatory dishes was the highest in Cantonese cuisine whereas the lowest in Hunan cuisine, unanticipatedly.
Unraveling the phenomenon of supply-demand feedback in agricultural water interventions
Authors: Alam Mohammad Faiz , McClain Michael , Sikka Alok , Sena Dipaka , Pande Saket 
Published: April 2024

Abstract

The human-water feedbacks associated with agricultural water interventions may result in unintended and adverse externalities such as the phenomenon of supply-demand feedback, i.e. of increasing water demand in response to measures that enhance water supply. By integrating a spatially explicit hydrological model with a farmer’s behavioral module, simulated using Risks-Attitudes-Norms-Abilities-Self-regulation (RANAS) behavioral theory based on household surveys and rules derived from observed data, this paper emulates the phenomenon of supply-demand feedback. The Kamadhiya catchment in India is studied, where the decisions of 38,447 farmers in response to the intensive development of check dams (CDs) are simulated. The results show that the perceived increase in water supply from CDs has led nearby farmers to increase their cotton and wheat cultivation areas by 11.9% and 36.1%, respectively. This increase in demand has nullified the expected benefits from CD recharge with approximately 54.0% of the additional recharge being used for expanding irrigation for cotton and wheat, and lowering groundwater levels by 1.0 m. These findings underscore the need to critically understand human-water feedbacks that lead to unintended consequences and inform future investments in agricultural water interventions.
Utilising Dimensionality Reduction for Improved Data Analysis with Quantum Feature Learning
Authors: Sihare Shyam R. 
Published: April 2024

Abstract
This research explores the potential of quantum computing in data analysis, focusing on the efficient analysis of high-dimensional quantum datasets using dimensionality reduction techniques. The study aims to fill the knowledge gap by developing robust quantum dimensionality reduction techniques that can mitigate noise and errors. The research methodology involved a comprehensive review and analysis of existing quantum dimensionality reduction techniques, such as quantum principal component analysis, quantum linear discriminant analysis and quantum generative models. The study also explored the limitations imposed by NISQ devices and proposed strategies to adapt these techniques to work efficiently within these constraints. The key results demonstrate the potential of quantum dimensionality reduction techniques to effectively reduce the dimensionality of high-dimensional quantum datasets while preserving critical quantum information. The evaluation of quantum principal component analysis, quantum linear discriminant analysis and quantum generative models showed their effectiveness in improving quantum data analysis, particularly in improving simulation speed and predicting properties. Despite the challenges posed by noise and errors, robust quantum dimensionality reduction methods showed promise in mitigating these effects and preserving quantum information. Finally, this research contributes to the advancement of quantum data analysis by presenting a comprehensive analysis of quantum dimensionality reduction techniques and their applications. It highlights the importance of developing robust quantum feature learning methods that can operate efficiently in noisy quantum environments, especially in the NISQ era.
Effect of continuous cropping on bacterial and fungal communities in Glehnia littoralis soil
Authors: Rong Zhengpu , Zhao Jingqiao , Shang Xiaoying , Shi Weihong , Zheng Yuguang , Sun Huigai , Han Xiaowei 
Published: April 2024

Abstract

Rhizosphere soil microorganisms are critical in the plant's growth and soil health. Continuous crop cropping had significant effects on rhizosphere soil microbial community. To figure out the effects of continuous cropping of Glehnia littoralis on the composition, structure and diversity of rhizosphere soil microbial communities, this study brings to G. littoralis of 1 year (first cropping soil, FS), 2 years (continuous cropping soil, CS), and 0 years (Layland, control soil, CK) soil as the materials. The composition, structure, and diversity of soil fungi and bacteria in different planting years were analyzed by the Illumina high-throughput sequencing technology. The α-diversity of fungi in CS was significantly lower than that in other rotation systems. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacteria, and Ascomycota, Basidiomycota, and Zygomycota were dominant phylum fungi. The relative abundance of Actinobacteria and Acidobacteria in the bacterial community decreased with the increase of stubbles, which may significantly reduce the microbial diversity and remedy the negative effects of continuous cropping of G. littoralis. The pH value, urease activity, and total nitrogen content were higher in the continuous cropping soil. Redundancy analysis showed that soil nutrients, pH value, and urease activity had significant effects on soil fungal and bacterial communities. Significant correlations were detected between soil total nitrogen and urease, and between soil total phosphorus and total potassium. In conclusion, continuous cropping changes soil nutrients, pH value, and urease activity, which, in turn, shifts the soil microbial community. The interaction and mutual influence of these factors may be the main cause of continuous cropping obstacle of G. littoralis.
Synthetic Generation and Detection of Crown-of-Thorns Starfish Instances retrival in Underwater Image
Authors: Sekar pavithra , mohan Jyothimurugan 
Published: April 2024

Abstract

Crown-of-thorns starfish (COTS), which eats coral is becoming increasingly common. Coral reefs, which are highly valued for their aesthetic appeal and ecological importance, are seriously threatened. This collection of carefully shot underwater photo sequences covering the whole Great Barrier Reef at different times and places is an invaluable resource for understanding and mitigating the negative effects of commercial overfishing (COTS) on these fragile ecosystems. Due to the predatory nature of the crown-of-thorns starfish coral reefs face significant threats necessitating urgent innovation in methods to control their population.
Impact of Gasoline and Renewable Energy Consumption on Manufacturing Sector Output in Nigeria: New Evidence From ARDL Model
Authors: EZE UCHECHUKWU , CHIDUMEBI MBA COLLINS 
Published: April 2024

Abstract
This research examined how gasoline and renewable energy use affects output in Nigeria’s manufacturing sector from 1990 to 2022, using data from the Central Bank of Nigeria’s Statistical Bulletin and the World Development Indicators. It employed the Auto-Regressive Distributed Lag (ARDL) model for its analysis. The Bounds co-integration test revealed the presence of a long-term relationship among the variables selected for the study. The findings reveal that in the short term, gasoline consumption marginally boosts manufacturing output, but it significantly hampers it over the long term. On the other hand, renewable energy’s influence on manufacturing output is negligible yet positive in both the short and long term. The study suggests that by shifting focus from gasoline to renewable energy sources, Nigeria can enhance the resilience, sustainability, and innovation of its manufacturing sector, thus aligning with international environmental objectives and boosting economic growth.
Comparative analysis of FWTPET welded austenitic alloy steel samples using transition fit approach: An investigation of mechanical, morphological, and microstructural properties
Authors: A Daniel Das , Manivannan S. 
Published: April 2024

Abstract
FWTPET (Friction Welding of Tube-to-tube plate using an External Tool) is the modified FSW process that has been enhanced and verified mechanical and metallurgical properties in all base metals. To assess the welding strength, samples with and without a hole on the perimeter were compared utilizing a backing block and same experimental is repeated and compared without utilizing a backing block. Maximum tensile strength is employed as the output parameter for determining the optimal combination of rotational tool speed, extrusion of tube (tube projection) and impression on tube plate (depth of cut) for achieving the desired joint strength. Under a Transition fit scenario, the experiment was conducted when heat from the tool pin was transferred to the Tube and tube plate. Taguchi's L9 Orthogonal Array technique and Analysis of Variance (ANOVA) are used as optimization approaches for finding the best joint strength (tensile strength). A microstructural study was conducted to determine the grain size in the weld zone. At the study's end, welding strength was found to be exceptionally high, at 831.8 MPa for samples with a hole (WH) and 784.35 MPa for samples without a hole and utilizing backing block (WBB) respectively. The computed tensile strength values for samples with and without a hole (WoH) were 757.2 MPa and 700.8 MPa, for the value without utilizing backing block (WoBB) respectively. Later, special characterization technique is used to evaluate the joint strength at the weld interface (WI).