bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of PATJ in Stroke Prognosis by modulating Endothelial to Mesenchymal Transition through the Hippo/Notch/PI3K Axis.
Authors: Vives-Bauza Cristofol , Medina-Dols Aina , Cañellas Guillem , Capó Toni , Sole Montserrat , Mola-Caminal Marina , Culell Natalia , Jaume Marina , Nadal Laura , Llinas Jaume , Gomez Lluis , Tur Silvia , Jimenez Carmen , Diaz-Navarro Rosa , Carrera Caty , Muiño Elena , Gallego-Fabriga Cristina , Soriano-Tarraga Carolina , Ruiz-Guerra Laura , Pol-Fuster Josep , Asensio Victor , Muncunill Josep , Fleischer Aarne , Iglesias Amanda , Giralt-Steinhauer Eva , Lazcano Uxue , Fernández-Pérez Isabel , Gabriel-Salazar Marina , Torres-Aguila Nuria , Carcel-Marquez Jara , Llado Jeronia , Olmos Gabriel , Rosell Anna , Montaner Joan , Planas Anna , Rabionet Raquel , Hernández-Guillamón Mar , Jimenez-Conde Jordi , Fernandez-Cadenas Israel 
Published: August 2023

Abstract

Through GWAS studies we identifiedPATJassociated with functional outcome after ischemic stroke (IS). The aim of this study was to determine PATJ role in brain endothelial cells (ECs) in the context of stroke outcome.PATJexpression analyses in patient’s blood revealed that: (i) the risk allele of rs76221407 induces higher expression ofPATJ, (ii)PATJis downregulated 24 hours after IS and (iii) its expression is significantly lower in those patients with functional independence, measured at 3 months with the modified Rankin scale ((mRS) £2), compared to those patients with marked disability (mRS=4-5). In mice brains,PATJwas also downregulated in the injured hemisphere at 24 hours after ischemia, and hypoxia-dependent of Hypoxia Inducible Factor 1a also caused PATJ depletion in ECs. To study the effects ofPATJdownregulation, we generatedPATJ-knockdown human microvascular ECs. Their transcriptomic profile evidenced a complex cell reprogramming involving Notch, TGF-ß, PI3K/Akt and Hippo signaling that translates in morphological and functional changes compatible with endothelial to mesenchymal transition (EndMT). PATJ depletion caused loss of cell-cell adhesion, upregulation of metalloproteases, actin cytoskeleton remodeling, cytoplasmic accumulation of the signal transducer C-terminal transmembrane Mucin 1 (MUC1-C) and downregulation of Notch and Hippo signaling. The EndMT phenotype of PATJ depleted cells was associated with the nuclear recruitment of MUC1-C, YAP/TAZ, b-catenin and ZEB1. Our results suggest thatPATJdownregulation 24 hours after IS promotes EndMT, an initial step prior to secondary activation of a pro-angiogenic program. This effect is associated with functional independence suggesting that activation of EndMT shortly after stroke onset is beneficial for stroke recovery.
The effects of thioredoxin peroxidase from Cysticercus cellulosae excretory-secretory antigens on TGF-β signaling pathway and Th17 cells differentiation in Jurkat cells by transcriptomics
Authors: Sun Xiaoqing , Mu Qianqian , Yang Fengjiao , Liu Meichen , Zhou Biying 
Published: August 2023

Abstract
(1) Background: Thioredoxin peroxidase (TPx) protein from the excretory-secretory antigens (ESAs) of Cysticercus cellulosae (C. cellulosae) has been shown to regulate the differentiation of host Treg and Th17 cells, resulting in an immunosuppressive response dominated by Treg cells. However, the molecular mechanism by which TPx protein from the ESAs of C. cellulosae regulates the imbalance of host Treg/Th17 cell differentiation has not been reported.
(2) Methods: TPx protein from porcine C. cellulosae ESAs was used to stimulate Jurkat cells activated with PMA and Ionomycin at 0, 24, 48, and 72 hours. Transcriptomic analysis was performed to investigate the signaling pathways associated with Jurkat cells differentiation regulated by TPx protein from C. cellulosae ESAs.
(3) Results: Gene Set Enrichment Analysis (GSEA) revealed that TPx protein from porcine C. cellulosae ESAs could induce upregulation of the TGF-β signaling pathway and downregulation of Th17 cell differentiation in Jurkat cells.
(4) Conclusion: TPx protein from porcine C. cellulosae ESAs can activate the TGF-β signaling pathway in Jurkat cells, thereby regulating the differentiation of Treg/Th17 cells and leading to an immunosuppressive response dominated by Treg cells, enabling evasion of the host immune attack. This study provides a foundation for further validation of these pathways and further elucidates the molecular mechanisms underlying immune evasion caused by porcine C. cellulosae.
Testability-Driven Development: An Improvement to the TDD Efficiency
Authors: Parsa Saeed , Zakeri-Nasrabadi Morteza , Turhan Burak 
Published: August 2023

Abstract

Test-first development (TFD) is a software development approach involving automated tests before writing the actual code. TFD offers many benefits, such as improving code quality, reducing debugging time, and enabling easier refactoring. However, TFD also poses challenges and limitations, requiring more effort and time to write and maintain test cases, especially for large and complex projects. Refactoring for testability is improving the internal structure of source code to make it easier to test. Refactoring for testability can reduce the cost and complexity of software testing and speed up the test-first life cycle. However, measuring testability is a vital step before refactoring for testability, as it provides a baseline for evaluating the current state of the software and identifying the areas that need improvement. This paper proposes a mathematical model for calculating class testability based on test effectiveness and effort and a machine-learning regression model that predicts testability using source code metrics. It also introduces a testability-driven development (TsDD) method that conducts the TFD process toward developing testable code. TsDD focuses on improving testability and reducing testing costs by measuring testability frequently and refactoring to increase testability without running the program. Our testability prediction model has a mean squared error of 0.0311 and an R2 score of 0.6285. We illustrate the usefulness of TsDD by applying it to 50 Java classes from three open-source projects. TsDD achieves an average of 77.81% improvement in the testability of these classes. Experts’ manual evaluation confirms the potential of TsDD in accelerating the TDD process.
Combined used of long-lasting insectiticidal nets and Bacillus thuringiensis israelensis larviciding, a promising integrated approach against malaria transmission in northern Côte d'Ivoire
Authors: Tia Jean-Philippe B. , Tchicaya Emile S.F. , Zahouli Julien Z. B. , Ouattara Alassane F. , Vavassori Laura , Assamoi Jean-Baptiste , Small Graham , Koudou Benjamin G. 
Published: August 2023

Abstract
Background The recent reduction in malaria burden in Côte d’Ivoire is largely attributable to use of long-lasting insecticidal nets (LLINs). However, this progress is threatened by insecticide resistance and behavioral changes in Anopheles gambiae sensu lato (s.l.) populations and residual malaria transmission, and complementary tools are required. Thus, this study aimed to assess the efficacy of the combined use of LLINs and Bacillus thuringiensis israelensis (Bti), in comparison with LLINs.Methods This study was conducted in the health district of Korhogo, northern Côte d'Ivoire, within two study arms (LLIN + Bti arm and LLIN-only arm) from March 2019 to February 2020. In the LLIN + Bti arm, Anopheles larval breeding sites were treated every fortnight with Bti in addition to the use of LLINs. Mosquito larvae and adults were sampled and identified morphologically to genus and species using standard methods. An. gambiae s.l. complex members were determined using a polymerase chain reaction technique. Plasmodium infection in An. gambiae s.l. and malaria incidence in local people was also assessed.Results Overall, Anopheles spp. larval density was lower in the LLIN + Bti arm 0.61 [95% CI: 0.41–0.81] larva/dipper (l/d)) compared with the LLIN-only arm 3.97 [95% CI: 3.56–4.38] l/d (OR = 6.50; 95% CI: 5.81–7.29; P < 0.001). The overall biting rate of An. gambiae s.l. was 0.59 [95% CI: 0.43–0.75] biting/person/night in the LLIN + Bti arm against 2.97 [95% CI: 2.02–3.93] biting/person/night in LLIN-only arm (P < 0.001). An. gambiae s.l. was dominated by An. gambiae sensu stricto (s.s.) (95.1%, n = 293), followed by An. coluzzii (4.9%; n = 15). The high human-blood index was 80.5% (n = 389) in study area. EIR was 1.36 infected bites/person/year (ib/p/y) in the LLIN + Bti arm against 47.71 ib/p/y in the LLIN-only arm. Malaria incidence dramatically declined from 40.5‰ (n = 765) to 15‰ (n = 292) in LLIN + Bti arm (P < 0.001).Conclusions The combined use of LLINs with Bti significantly reduced the incidence of malaria. The LLINs and Bti duo could be a promising integrated approach for effective vector control of An. gambiae s.l for elimination of malaria.
Lipid Metabolism related Gene Expression is correlated with Immune-metabolic Microenvironment and Predicts Prognosis in Hepatocellular Carcinoma
Authors: Zhao Shuang , Xiong Haofeng , Hou Fei , Zhang Yizhi , Kang Qian , Sun Liying 
Published: August 2023

Abstract

Background & AimsHepatocellular Carcinoma (HCC)is a leading cause of cancer mortality worldwide. This study was aimed at exploring the prognosis predictive ability of lipid metabolism related genes (LMRGs) in HCC and constructing a reliable risk model for clinical management.MethodsBioinformatics analysis of transcription data obtained from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and the International Cancer Genome Consortium (ICGC) database was utilized in this study. COX regression and consensus clustering were performed to identify two molecular subgroups based on LMRGs. Immune infiltrating analysis, KEGG, GSVA, and GO pathway analysis was applied to clarify the underlying mechanisms of LMRGs participated in the prognosis of HCC. We then performed LASSO-COX regression analysis to build the risk model and validate the model in an external HCC cohort from the ICGC database.ResultsWe identified two molecular subgroups with distinct overall survival based on the different expression profiles of LMRGs. The increased immune score and expression of immune checkpoints, altered immune cell subtypes, and dysregulated metabolic pathways were involved in the worse overall survival of the molecular subgroup with higher expression of the majority of LMRGs. The risk model based on four LMRGs including SRD5A3, PPARGC1A, HSD17B12, AKR1B15 and the integrated nomogram established with the four LMRGs and TNM stage performed reliable predictive ability of HCC prognosis both in the train set and validation set.ConclusionLMRG dysregulation is correlated with the immune microenvironment and various metabolic pathways in HCC. The risk model developed based on the expression of LMRGs could act as a potent predictor of HCC prognosis.
Comparison of Adsorption Capacity of Amine Modified Activated Carbon from Stone Apple for CO2 Capture
Authors: Das Dipa 
Published: August 2023

Abstract
Increase in atmospheric Carbon dioxide concentration due to industrial activity of more than a century has led to the problem of global warming, which hints at a catastrophic climatic consequence for the whole world. The reduction in the emissions of greenhouse gases possesses a challenge in addressing the issue of climate change. Adsorption is considered as a competitive solution. This present research focus separation of post combustion capture carbon dioxide from flue gas by adsorption mechanism as it needs less energy and amine modified activated carbon prepared from stone apple can be used as solid adsorbents. Two different amine solution i.e Ethylene Diamine(EDA) and Tetra Ethylene Penta Amine(TEPA) solution were used as impregnating agent for activated carbon with impregnation ratio 0.4 (EDA-AC(0.4) and TEPA-AC(0.4). Further the amine impregnated activated carbons were characterized using various techniques such as Proximate Analysis, Ultimate Analysis, Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy(EDS), Fourier Transform Infrared spectroscopy(FTIR), BET surface area analyser, Thermo Gravimetric Analysis (TGA), X-Ray Diffraction(XRD). A remarkable increase in the adsorption capacity was observed and the maximum adsorption (36.05 mg/g) is found in Ethylene diamine impregnated activated carbon having impregnation ratio 0.4(EDA-AC(0.4) at 25°C and 1 atm and break through time of 214 min.
The core symptom in gastric cancer patients undergoing chemotherapy: a network analysis
Authors: Wang Xiao-Qing , Zou Yan-Ling , Li Yi , Li Xun , Zhang Zi-Yan , Yang Li-Hua , Gao Juan , Guan Hui Yun , Duan Pei-Bei 
Published: August 2023

Abstract
Background
​During chemotherapy for gastric cancer, patients may experience symptoms associated with both the disease and chemotherapy. There have been limited studies exploring the relationship between these symptoms. Network analysis can identify the core symptoms in the symptom network.
Objective
The purpose of this research was to investigate the core symptoms and contributing factors in gastric cancer patients undergoing chemotherapy.
Methods
A cross-sectional study of convenient samples of patients with gastric cancer undergoing chemotherapy was conducted. A total of 616 gastric cancer patients undergoing chemotherapy were enrolled between January 2021 and November 2022.​ The symptom network and node characteristics were analyzed using network analysis, and the factors affecting the symptom network were investigated using multivariate linear regression analysis.
Results
The findings indicated that 89% of gastric cancer patients undergoing chemotherapy experienced lack of appetite. Taste alteration was the most prominent symptom in the network analysis, with the strongest correlation between taste alteration and lack of appetite in patients. Multiple linear regression analysis showed that gender, history of tobacco use and chemotherapy cycles were the factors affecting taste alteration.
Conclusion
Taste alteration was the core symptom in gastric cancer patients undergoing chemotherapy. Interventions are likely to be most effective if symptom management focuses on taste alteration. Additionally, lack of appetite should be treated together in a clinical setting to ensure accurate symptom management.
Quantifying the Flooding Regime and Vegetation Zone in Riparian Wetlands
Authors: Lee Hoyong , Kwak Jaewon , Lee Junhyeong , Kim Hung Soo , Kim Soojun 
Published: August 2023

Abstract
Wetlands play an important role in cycling water resources, organic matter, water purification, and ecosystem conservation. Understanding flood regimes is essential for effective wetland management because it significantly influences wetland succession and circulation. This study aims to develop a methodology for quantifying flood regimes of the Jangdan Wetland (Imjin River) and the Binae Wetland (Namhan River). This study analyzed the hydrologic regime of these wetlands using the water level duration curve (LDC) based on the flow duration curve (FDC). Flood regime diagrams describing the inundation characteristics over time, were then constructed using the LDC and the digital elevation models (DEM) of the wetlands. To understand the relationship between vegetation communities and hydrologic regime in the wetland, this study classified nine vegetation zones based on the tolerance of associated plant species to inundation. The study revealed that the Jangdan Wetland were dry primarily on most days but experienced complete inundation during flooding events. In contrast, the Binae Wetlands were found to be frequently inundated, with approximately 40% of the area experiencing regular flooding, while 20% of the higher elevation areas were only inundated once every few years.
Practice Dimension Analysis of Activities in Physical Education Class and Teaching Methods——A Study Based on 56 Award-Winning Lessons
Authors: Xia Xiaohui , Zhu Yixuan , Guo Wenqian , Yang Jiadong 
Published: August 2023

Abstract
Backgrounds: The purpose of this study was to analysis the PE class activities and teachers' teaching methods after the promulgation of the new curriculum standards in China and to provide guidance for curriculum reform practices.
Methods: A total of 56 award-winning PE lesson videos from Gansu province in 2022 were used to study class activities and teaching methods. The SOFIT (The System for Observing Fitness Instruction Time system) was used to encode class activities, and the students’ participation in MVPA (moderate-to-vigorous-intensity physical activity), lesson context, and teacher’s intervention behavior were analyzed. The Likert five-point scale method was used to evaluate the teaching design and implementation that promote students' active learning and practice, including lesson activities, lesson context, teaching methods, exercise load and information technology education means. Differences between lessons from different grade level and school location were compared, and multiple regression analysis was conducted to examine the relationship between MVPA time and class activities, and teaching methods.
Results: The SOFIT analysis showed that the MVPA time for students was 52.5%, with class management, knowledge explanation, practice for fitness, and skill practice accounting for 8.3%, 32.2%, 27.7%, and 31.9%, respectively. Teacher intervention’s time for inside and outside of the class to promotion of PA accounted for 18.6% and 3.2%, respectively. In terms of teaching methods, the group exercise density was 62.5%, and the scores for student learning activities and sport scenario design were relatively high, at 4.3 and 4.0, respectively. The scores for practice for fitness and information technology education design were relatively low, at 2.9 and 2.3, respectively. There were no significant differences between different groups. Linear regression analysis showed that MVPA time was negatively correlated with class management time and positively correlated with physical fitness exercise time, skill practice time, and group movement density (P<0.05).
Conclusions and Suggestions: In high-quality lessons after the implementation of the new curriculum standards in China, students had a higher level of PA (physical activity). However, there was a phenomenon of excessive time spent on knowledge explanation and insufficient time for practice, highlighting the need for emphasizing intensive explanation and more practice. The design of group movement density in instructional design needs further improvement, as well as the strengthening of information technology education methods and practice for fitness. Measures such as reducing class management time, increasing physical and skill practice time, and enhancing exercise density can improve the effective time for physical exercise in the class.
Objective evaluation of cough and diaphragmatic ultrasound improve the predictive capacity of spontaneous breathing test for extubation success - COBRE-US trial
Authors: Varón-Vega Fabio Andrés , Giraldo-Cadavid Luis F. , Uribe Ana María , Rincon Adriana , Palacios Jhonatan , Crevoiser Stephanie , Tuta-Quintero Eduardo , Ordoñez Lina , Boada Natalia , Rincon Paola , Poveda Marcela , Monedero Pablo 
Published: August 2023

Abstract
Background
Use of clinical tests and ventilator weaning tests in conjunction with the spontaneous breathing test (SBT) can increase the predictive capacity of extubation success. Therefore, we assessed the predictive ability of SBT, cuff leak test, rapid-shallow-breathing-index, cough intensity, and velocity of diaphragmatic contraction (VDC) in successful weaning of mechanically ventilated patients.
Methods
A prospective multicenter observational study from in which consecutive adult patients admitted to 4 intensive care units. The performance of tests in discriminating between success and failure of the weaning process was assessed at different time points using ROC-curve in which the dependent variable was successful extubation.
Results
A total of 367 subjects who received invasive mechanical ventilation, 456 SBT were performed, with a success rate of 76.5%. The ROC curve of this model (0.52xCough)-(0.12xVDC) + 0.3 to predict a successful SBT was 0.63 (95%CI:0.60–0.65), a cut-off point > 0.84 had a sensitivity of 90.1% and a specificity of 25.3%. The ROC-curve of the model (5.7xSBT)+(0.75xCough)–(0.25xVDC)–4.5 to predict a successful extubation was 0.89 (95%CI:0.85–0.94), a cut-off point > 5.97 had a sensitivity of 98.9% and a specificity of 73.2%. The Hosmer-Lemeshow test showed no significant differences between observed and predicted values (p = 0.92).
Conclusion
Objective measures of cough and diaphragmatic function demonstrate excellent discriminatory ability to predict successful extubation with a cutoff of 5.97. The probability of having a successful extubation could be evaluated using the proposed model.
Surrogate model for CFD based on machine learning
Authors: Rahman Ashfaqur , Pereira Gerald , Kilby Phil , Lahur Paulus 
Published: August 2023

Abstract
The paper presents the results of a data-driven surrogate modelling effort to reproduce the results of a Computational Fluid Dynamics (CFD) model. The CFD model considered here simulates a scenario where air containing CO2 flows through a tube. A metal scaffold (that are highly selective in adsorbing Co2 from air) is placed inside the tube that absorbs CO2 from the fluid as it flows through. The CFD model computes two important quantities: (i) the amount of transportation (a measure of CO2 absorbed by the metal scaffold) and (ii) the amount of fluid mixing. Given the shape features of the metal scaffold as input, the CFD model (a) produces a 3D lattice filling part of it with the metal scaffold, (b) uses Lattice-Boltzmann equation to solve the CFD, and (c) compute amount of transportation and fluid mixing. The CFD model is time consuming. To reduce the computation time, we have investigated surrogate models for this CFD based on a machine learning (ML) method. The ML model takes as input the shape features of the metal scaffold and predicts amount of CO2 absorption and fluid mixing. The objective is to come up with a ML model that produces the above quantities with reasonably low error. We investigated several ML models to find their effectiveness to produce reasonably accurate results for predicting the two quantities above. The data for training and testing the ML model was generated from the CFD based on different shape features of the metal scaffold. The underlying objective of the project was to produce an optimal design of the metal scaffold that maximises absorption (of CO2) and fluid mixing. The optimization was done using an evolutionary algorithm (EA). EA starts with a set (population) of random shapes and modifies the shapes over generations based on feedback from CFD. In each generation the CFD computes the absorption and mixing for each of the shapes in the population. The best of the shapes from the population goes through some transformations (crossover and mutation) to generate the population for next generation. The process continues until the optimization converges. The shape features and their fitness (absorption and mixing) of the population from the several generations are combined into one large dataset where the shape features are input, and the fitness values are target. This constitutes the data used for training and testing the ML models. Given a total of n generations, we trained ML models on data up to k–th generation and tested the model on the data from last n–k generations. We present the CFD model, the surrogate models, and some preliminary results in this paper.