bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative omics provide new insights on association of RNA splicing with the tumorigenesis of Wilms’ Tumor
Authors: Lin Yang , Lin Lin , chen shan , Li Bing , zhang lin , wang jianbin , Qiu Xinyi , He Shiwei , Xu Di , Li Lizhi 
Published: July 2024

Abstract

Background The tumorigenesis of Wilms’ tumor (WT) or nephroblastoma is still unclear. The alteration of RNA splicing and EMT is the manifestation of tumorigenesis. Therefore, this study aims to study the association between RNA splicing and epithelial-mesenchymal transition (EMT), for better understanding on the tumorigenesis of WT.
Methods Using the high-resolution mass spectrometry to collect the peptide information in WT and control kidney (CK) after the pre-treatment (extraction, purification and digestion) of protein, intending to find out the protein profiles of WT via database alignment. Then a label-free quantification method based on the SWATH-MSALL proteomic technology was performed to identify differentially expressed proteins (DEPs) between WT and CK. The bioinformatics analysis employs the GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, and PPI (protein-protein interaction) analysis. Integrated with the data from single cell RNA-sequencing (scRNA-seq) and bulk RNA-seq transcriptomicss, aiming to further annotation of DEGs enrichment in WT tumorigenesis via GO, KEGG and Gene Set Enrichment Analysis (GSEA).
Results In our study, 2005 proteins were identified from Wilms’ tumor with a global false discovery rate (FDR) of 1% (FDR threshold, 84%), followed by 330 DEPs between WT and CK (P＜0.05, |log2fold-change (FC)| ≥ 1). Integrated with the data of scRNA-seq and bulk RNA-seq transcriptomicss, the function enrichment of DEGs represented RNA splicing and epigenetic modification. The validation assays also revealed the over-expression of the transcription factors heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and poly(ADP-ribose) polymerase 1 (PARP1) in WT, compared with CK tissue. Further investigation revealed the aberrant accumulation of hnRNP A1 and PARP1 in the mesenchymal compartment of WT, indicative of the critical roles in the dysregulation of EMT.
Conclusions There were amounts of DEPs between WT/CK engaging in RNA splicing, indicative of the complicated transcription regulatory in tumorigenesis of nephroblastoma. Integrated with data from multi-omics and validation assay, hnRNP A1 and PARP1 could play role of the tumor-enriched biomarkers. However, the possibility of hnRNP A1 and PARP1 in targeted therapy for WT remained to consideration. It’s necessary to further investigate the role of hnRNP A1 and PARP1 on the alternative splicing (AS) and EMT for tumorigenesis of WT.
Genotyping of cocoa trees (Theobroma cacao L.) from first and second cycle of reccurent and reciprocal selection program in Côte d'Ivoire
Authors: GUIRAUD Boguinard Sahin , TAHI Gnion Mathias , POKOU Désiré , TREBISSOU Inago Caudou , COULIBALY Klotioloma , N’GUESSAN Walet Pierre , MINAKOU Okayo Sandrine , ASSI Evelyne Maryse , GOGBE-DIBI Françoise , KOTAIX Jacques Alain , KOUAME Norbert N’Dri , N’GUESSAN Kouamé François 
Published: July 2024

Abstract

The recurrent and reciprocal cocoa breeding program in Côte d'Ivoire is in its 2nd cycle of crossing High Amazon Forastero (HA)2 and a mixture of Low Amazon Forastero and Trinitario (LA + T)2. It was created with the aim of improving the characteristics of these genetic groups. This study was carried out to evaluate the identity and genetic structure of cocoa trees selected on index for production and rotted pod rate, with a view to better assessing the genetic conformity of individuals within each genetic group. 152 cocoa trees were genotyped with 99 SNPs markers. These samples included 53 HA2 genotypes, 26 (BA + T)2 genotypes, 30 parents genotypes and 43 progenies from crosses between HA2 and (BA + T)2. Results indicate that observed heterozygosity (Ho = 0.35) is higher than expected heterozygosity (He = 0.31), showing an excess of heterozygotes. Strong genetic differentiation (Fst = 0.90) was revealed between HA2 and (BA + T)2 and weak genetic differentiation between these groups and their offspring (Fst = 0.03). Multivariate analysis revealed two main phylogenetic groups. Group 1 containing almost all HA2 individuals and group 2 comprising almost all (BA + T)2 genotypes. Indeed, genetic conformity of individuals was revealed within each group, with 94% of HA2 genotypes and 81% of (BA + T)2 genotypes. These results are a good indicator for avoiding errors when selecting the best cocoa trees within each genetic group, with a view to starting a new selection cycle.
Enhancing Urban Resilience to Flooding in Hydrogeological Risk Areas Through Big Data Analytics Using Deep Neuro-Fuzzy System
Authors: Malik Varun , Martin R. John , Mittal Ruchi , Ravali Ravula Sahithya , Almalki Khalid Jaber , Ramakrishnan Jayabrabu , Swapna SL , Mavaluru Dinesh , Goyal SB , Kumar Manoj 
Published: July 2024

Abstract

Urban areas worldwide are increasingly at risk from hydrogeological hazards, leading to severe consequences. Urban flooding and mismanagement of water resources, resulting in riverine flooding, are primary contributors to this risk. Utilizing big data, including mobile phone signals collected at high frequencies, alongside administrative data, is essential for developing risk exposure indicators in smaller urban regions. Accurately assessing human traffic flows and movements is crucial for mitigating the impacts of natural disasters and ensuring a high quality of life in smart cities. However, comprehensive solutions to these challenges are lacking in many countries. Therefore, this study focuses on analyzing the impact of traffic data flow analysis in hydrogeological risk areas. The study employs mobile phone signals as big data to analyze traffic flows and forecast exposure risks to aid decision-making. To ensure data reliability, a circle search integrated fully connected conditional neural network (CS-ConNN) is used for data cleaning, categorizing mobile phone signal data into normal, empty, and garbage. Additionally, the study uses a deep recurrent neuro fuzzy system (DRNFS) to analyze the compound seasonality of circulation flow data and forecast risks, providing alerts to individuals transiting through affected areas. The model is validated through a case study of "Mandolossa," and developed area prone to inundating near Brescia, using hourly data from September 2020 to August 2021. Experimental results and cross-validation demonstrate a forecasting accuracy of 98.975%.
Cost-benefit Analysis on the Implementation of Treated Wastewater Reuse: Case of Sekem Farm El-wahat, Egypt
Authors: WAHID Nadya , KHAIRY Wael , KRAUSE Regina 
Published: July 2024

Abstract

In a context of increasing pressure on water resources and severe aridity; expansion in the reuse of naturally treated wastewater can be a viable and low-cost solution particularly for irrigation forests, green non-fruit trees, fabric crops, industrial oils, and non-edible raw crops. Wastewater treatment is increasingly recognized as a potential means in El-Wahat El-Bahariya in Egypt. However, investment decisions concerning the reuse of treated wastewater in irrigation needs to be justified in terms of financial and economic feasibility and profitability. Therefore, this research study aims to conduct a cost-benefit analysis (CBA) of an investment project “reuse treated wastewater in irrigation compared to other modes of water irrigation projects. The CBA results revealed that the cost of the initial investment for the production of treated water used for irrigating green non-fruit trees, Bamboo trees, and Cactus in Sekem El-Wahat, is economically efficient with 88% compared to the exploitation of aquifer groundwater for irrigating the same crops. That project allows for an economic gain of about 4,428.5 €/ha compared to the cost of producing aquifer ground water in Sekem Farm El-Wahat is estimated at 10,800 €/year. Substituting the use of aquifer ground water for irrigating crops with reuse of treated wastewater helps reducing energy consumption and offers great financial benefits to the beneficial communities. A net benefit of the reuse of treated wastewater project is largely positive with NPV equivalent to 4599 €/year with a medium economic efficiency (BCR) of about 0.44.
Synergistic Influence of Surface Sanding Technique and Multi-Walled Carbon Nanotube Incorporation on the Mode I Fracture Behavior of Glass Composite Laminates
Authors: Nazari Roohollah , Hakimi Rashid , Daneshfar Mohammad , Talebi Behnam 
Published: July 2024

Abstract

This study sequentially investigates the enhancement of fracture behavior in adhesive joints. Initially, mechanical sanding techniques were explored, revealing significant improvements of 55% in fracture energy and 38% in load-bearing capacity with optimal 240-grit sanding. Subsequently, in a second stage, Multi-Walled Carbon Nanotubes (MWCNTs) were introduced at varying weight percentages (0.1%, 0.3%, and 0.5% by weight) into the adhesive joints. This combined approach aimed to synergistically examine the impact of surface pretreatments and nanoparticle integration on fracture behavior. Results highlight the potential for fracture resistance and enhanced load-carrying capabilities in reinforced specimens, with maximum load and fracture energy improvements of up to 92% and 50%, respectively, compared to unreinforced specimens and those subjected solely to sanding treatments. Furthermore, the fracture mode shifted from adhesive failure to cohesive substrate failure in reinforced specimens. This comprehensive investigation underscores the intricate interplay between mechanical preparation and nanomaterial incorporation in significantly improving adhesive joint performance
Association between triglyceride glucose body mass index and left ventricular systolic synchronicity in patients with type 2 diabetes
Authors: Yan Fei-fan , Lu Chun-feng , Wang Xiao-hua , Huang Hua-xing 
Published: July 2024

Abstract

Background: The triglyceride glucose-body mass index (TyG-BMI) is considered to be an alternative indicator of insulin resistance (IR) with greater clinical value in terms of cardiovascular risk. However, the relationship between TyG-BMI and left ventricular asynchrony, which determines heart function, is unclear. The purpose of this study was to explore the association between the TyG-BMI and left ventricular asynchrony in patients with type 2 diabetes.
Methods: This cross-sectional study included 614 patients with type 2 diabetes between September 2021 and June 2023. All patients initially screened with conventional echocardiography underwent subsequent evaluations, including speck-tracking echocardiography and real-time three-dimensional echocardiography. The systolic dyssynchrony index (SDI) was automatically derived from real-time three-dimensional echocardiography in order to assess the degree of left ventricular asynchrony among patients. The TyG-BMI was calculated, and the included patients were stratified according to TyG-BMI quartiles.
Results: The analysis of the 614 patients with type 2 diabetes who were ultimately included revealed that the SDI tended to increase as the TyG-BMI increased, with the SDI corresponding to the highest quartile being the highest. According to multiple linear regression analysis, the TyG-BMI is independently related to the SDI. Further exploratory subgroup analysis revealed that the TyG-BMI was more likely to be associated with SDI in patients ≤55 years of age with type 2 diabetes.
Conclusions: Our research revealed that the TyG-BMI of patients with type 2 diabetes was positively correlated with the SDI, and this correlation was more obvious in patients with type 2 diabetes who were ≤55 years old.
SentiLexIT: Advancing Italian Sentiment Analysis through Automated Lexicon Generation
Authors: de Melo Tiago , Merialdo Paolo 
Published: July 2024

Abstract

The proliferation of digital platforms has exponentially increased the volume of user-generated content, providing rich data sources for sentiment analysis. This study introduces SentiLexIT, a novel methodology for automatically constructing domain-specific sentiment lexicons for the Italian language using an unsupervised approach. We analyzed 321,817 user reviews from diverse categories such as Amazon.it and Google Reviews, applying Bayes' Theorem to derive sentiment scores that effectively categorize review sentiments into distinct polarities. Our methodology significantly outperforms existing Italian sentiment lexicons and two versions of ChatGPT, achieving an average F1-score of 0.92 across various domains. The paper highlights the method's effectiveness in handling linguistic nuances specific to Italian, providing a robust tool for sentiment analysis. This research contributes to the field by offering a scalable, precise methodology for sentiment lexicon construction without the need for manual annotation, addressing the gap in non-English sentiment analysis resources.
Parameter estimation and model selection for stochastic differential equations for biological growth
Authors: Baltazar-Larios Fernando , Delgado-Vences Francisco , Ornelas Arelly 
Published: July 2024

Abstract

In this paper, we consider stochastic versions of three classical growth models given by ordinary differential equations (ODEs). Indeed we use stochastic versions of Von Bertalanffy, Gompertz, and Logistic differential equations as models. We assume that each stochastic differential equation (SDE) has some crucial parameters to be estimated and we use the Maximum Likelihood Estimator (MLE) to estimate them. For estimating the diffusion parameter, we use the MLE for two cases and the quadratic variation of the data for one of the SDEs. We apply the Akaike information criterion (AIC) to choose the best model for the simulated data. We consider that the AIC is a function of the drift parameter. We conduct numerical experiments to validate our selection method. Subsequently, we also apply it to actual data.
The proposed methodology could be applied to datasets with discrete observations including highly sparse data. Indeed, we can use this method even in the extreme case where we have observed only one point for each path, under the condition that we observed a sufficient number of trajectories. For the last two cases, the data can be viewed as incomplete observations of a model with a tractable likelihood function; then, we propose a version of the Expectation Maximiza- tion (EM) algorithm to estimate these parameters. This type of dataset typically appears in fishery, for instance.
Bioactive Compounds Derived from Sargassum wightii Exhibit Antibacterial Activity against Multi-Drug Resistant Acinetobacter baumannii
Authors: Suvaithenamudhan Suvaiyarasan , Kumar Sundarraj Dinesh , Thirugnanasambandam Rajendran , Ponmalar Esaki Muthu , Ganesh Pitchaipillai Sankar , Mariappan Vanitha , Shankar Esaki M. , Rudrapathy Parthiban 
Published: July 2024

Abstract

Acinetobacter baumannii (A. baumannii) is a notorious nosocomial pathogen known for its ability to form biofilms, rendering it highly resistant to conventional antibiotics and immune clearance. In this study, the minimum inhibitory concentration (MIC) ranged from 70 µg/mL to 100 µg/mL remarkably, the tested ethanolic extracts inhibited A. baumannii biofilm development in a concentration-dependent manner. Epifluorescence microscopic analysis revealed a significant reduction in treated biofilm formation compared to the control. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis of the ethanol extract of Sargassum wightii (S. wightii) identified 10 major compounds. Molecular docking studies were conducted to explore the interaction of small molecules from S. wightii with the BfmR protein of A. baumannii. The molecular docking of three ligand molecules (CAS No. 002302-12-7, 015120-94-2, and 146397-91-3) with the target BfmR-Ab revealed the lowest binding energies (∆Gbind) of -42.26 and − 50.49 (kcal/mol) for the ligands CAS No. 002302-12-7 and 146397-91-3, respectively, and the lowest Glide score of -4.067 (kcal/mol) for the ligand CAS No. 015120-94-2. These top three hit molecules exhibited the highest affinity as efficient ligands against BfmR of A. baumannii. Nevertheless, S. wightii demonstrated antibiofilm activities against the multidrug-resistant (MDR) pathogen A. baumannii, with bioactive compounds exhibiting promising drug-likeness and pharmacokinetic signatures.
Functional characterization of malate dehydrogenase gene, HcMDH1 in enhancing abiotic stress tolerance in kenaf (Hibiscus cannabinus L.)
Authors: Luo Dengjie , Li Zengqiang , Mubeen Samavia , Rehman Muzammal , Cao Shan , Wang Caijin , Yue Jiao , Pan Jiao , Jin Gang , Li Ru , Chen Tao , Chen Peng 
Published: July 2024

Abstract

Drought and salt stress are two important environmental factors that significantly restrict plant growth and production. Malate dehydrogenase is essential to life as it is engaged in numerous physiological processes in cells, particularly those related to abiotic stress reactions. However, a complete understanding on MDH family members in kenaf is not clear yet. In this study, subcellular localization analysis and a yeast transcriptional activation assay revealed that HcMDH1 was localized in chloroplasts but had no transcriptional activation activity. When exposed to salt or drought, yeast cells that express the HcMDH1 gene have a greater survival rate. Overexpression of HcMDH1 in Arabidopsisincreased seed germination rate and root growth when transgenic lines were exposed to varying concentrations of mannitol and NaCl. Subsequent physiological studies revealed that transgenic lines had higher concentrations of soluble carbohydrates, proline, and chlorophyll and lower concentrations of malondialdehyde (MDA) and reactive oxygen species (ROS). Furthermore, inhibiting HcMDH1 in kenaf using virus-induced gene silencing (VIGS) decreased salt and drought tolerance due to elevated ROS and MDA levels. In these silenced lines, the expression of six essential genes engaged in stress-resistance and photosynthesis, namely HcGAPDH, HcGLYK, HcFBA, HcFBPase, HcPGA, and HcLSD, is significantly altered under salt and drought stress. In summary, HcMDH1 is a positive regulator of salt and drought tolerance in kenaf, which may have implications for transgenic breeding.
Examining Preferences for Weight Loss Interventions Among Black Men and Women Experiencing Overweight or Obesity: A Qualitative Approach
Authors: Ray Snehaa , Idiong Christie I. , Anderson Rachel , Killion Kate , Antrum Curtis , Puglisi Michael , Kalinowski Jolaade , Stowers Kristen Cooksey , Carr Loneke T. Blackman 
Published: July 2024

Abstract

Background Behavioral interventions aiming to modify dietary habits and physical activity have been less effective in achieving clinically significant weight loss in Black adults. Weight loss needs vary by race and gender, so different strategies are needed to engage individuals in healthy behaviors. While there have been some research efforts focused on weight loss in Black women, participation rates of Black men in weight loss interventions are lower. This may perpetuate the development of obesity-related conditions such as diabetes, heart disease, and other cardiovascular problems. This qualitative study investigated the barriers and facilitators to healthy eating and physical activity and the weight loss desires among Black adults with overweight or obesity.Methods Black adults mainly residing in Hartford, Connecticut were recruited for the study. Semi-structured interviews were conducted with Black males and females who self-reported being overweight or obese. Preferences for weight loss specific to each gender, barriers, and facilitators for weight-related behaviors such as diet and physical activity, were examined through thematic analysis to inform the development of a culturally relevant behavioral weight loss intervention.Results The sample consisted of Black adults from diverse racial and ethnic backgrounds. Black females (n = 16) and Black males (n = 8) were mostly non-Hispanic Black Americans. The key themes that emerged were: 1. the creation of a weight loss program for Black adults, 2. healthy eating barriers, 3. physical activity barriers, 4. healthy living facilitators, and social support. Both Black females and Black males identified unique weight loss preferences. Community and personalization were preferred by Black females while Black males preferred personalized diet and exercise regimes for diverse health conditions, not limited to weight loss. While both genders referred to digital devices and apps for recording weight, diet and physical activity as a major facilitator to adopting healthy habits, social support in the form of culturally relevant information from healthcare providers was highly desired to be incorporated into the intervention.Conclusion The findings of this study hold relevance for designing and developing of weight loss programs that promote behavior change for Black adults and help reduce obesity-related health inequities within this population.
Adverse events of pegvaliase in the treatment of phenylketonuria: A pharmacovigilance study based on the FAERS database
Authors: Liu Junfa , Chen Zhe , Liu Xiongfei , Li Xiangyang , Dong Zhitao 
Published: July 2024

Abstract

Pegvaliase was approved by the FDA in 2018 for the treatment of phenylketonuria(PKU).However, the long-term safety of pegvaliase in a large sample population is unclear. The purpose of this study was to investigate the adverse events associated with pegvaliase in the real world by mining data from the FAERS database. We extract adverse event data on pegvaliase from the FAERS database and perform a disproportionality analysis utilizing ROR，PRR，BCPNN and MGPS. A total of 82 preferred terms (PTs) simultaneously met the criteria of all four algorithms. Common PTs include reactions at the injection site，joint pain, sensitivity reactions, headaches, skin reactions, injection site pruritus, and rash pruritic, corresponding to adverse events reported in clinical trials. Unexpected significant adverse events were identified, such as amino acid level decreased or increased, panic attacks, self-injurious ideation, disturbances in attention, tunnel vision, and so on. The median onset time for adverse events to pegvaliase is 15 days(IQR = 9-42 days), with the majority occurring within 30 days (n=509, 67.78%). The top three drugs most commonly prescribed in conjunction with pegvaliase are famotidine, cetirizine, and sapropterin. When pegvaliase is used in combination with these drugs, it is associated with an increase or decrease in the risk of certain adverse events. Our study provides crucial insights for the safer and more effective use of pegvaliase.