bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated approach-based groundwater mapping in sohag governorate, upper Egypt, using remote sensing and aeromagnetic data
Authors: El-Badrawy Hussein T. , Abbas Abbas M. , Massoud Usama , Abu-Alam Tamer , Alrefaee Hamed A. , Abo Khashaba Saif M. , Nagy Mostafa 
Published: September 2024

IntroductionGroundwater demand has been considerably heightened due to rapid urban growth, specifically in arid areas that rely primarily on groundwater. This study aims to utilize remote sensing and aeromagnetic data, combined with the Analytic Hierarchy Process (AHP) based GIS, to evaluate potential groundwater zones in the Sohag area, Egypt.MethodsNine thematic layers, including soil moisture, rainfall, lithology, normalized difference vegetation index (NDVI), drainage density, lineament density, slope, and land use/land cover, were developed using various remote sensing datasets. Besides the remote sensing-derived thematic layers, a geophysics-derived thematic layer represented by the RTP aeromagnetic map was included. The aeromagnetic data were analyzed and interpreted to outline the subsurface structure affecting groundwater storage and flow. Also, the aeromagnetic data analysis helps estimate the basement depth that constitutes the Nubian Aquifer’s base and identifies regions with considerable thick sedimentary deposits and significant water reserves.Results and discussionThe groundwater potentiality map was consistent with production wells in the area, and sites for drilling new wells were predicted, especially in the Nile Valley around the Tahta, El-Hamimia, and west Sohag cities. The most promising sites are clustered along the Nile Valley, and the study area’s northwestern and northeastern parts. The results indicate that the predominant magnetic structural trends are NW-SE, NE-SW, N-S, and E-W, which contribute to the formation of a series of subsurface horsts (H) and grabens (G). Three main basins (A, B, and C) were identified as the most profound areas. These basins represent the most promising areas for groundwater accumulation, making them attractive for future hydrogeological exploration. This integrated approach strongly offers a powerful and effective tool to assist in developing an appropriate plan to manage groundwater in arid regions.
A performance evaluation of random forest, artificial neural network, and support vector machine learning algorithms to predict spatio-temporal land use-land cover dynamics: a case from lusaka and colombo
Authors: Mutale Bwalya , Withanage Neel Chaminda , Mishra Prabuddh Kumar , Shen Jingwei , Abdelrahman Kamal , Fnais Mohammed S. 
Published: September 2024

Reliable information plays a pivotal role in sustainable urban planning. With advancements in computer technology, geoinformatics tools enable accurate identification of land use and land cover (LULC) in both spatial and temporal dimensions. Given the need for precise information to enhance decision-making, it is imperative to assess the performance and reliability of classification algorithms in detecting LULC changes. While research on the application of machine learning algorithms in LULC evaluation is widespread in many countries, it remains limited in Zambia and Sri Lanka. Hence, we aimed to assess the reliability and performance of support vector machine (SVM), random forest (RF), and artificial neural network (ANN) algorithms for detecting changes in land use and land cover taking Lusaka and Colombo City as the study area from 1995 to 2023 using Landsat Thematic Mapper (TM), and Operational Land Imager (OLI). The results reveal that the RF and ANN models exhibited superior performance, both achieving Mean Overall Accuracy (MOA) of 96% for Colombo and 96% and 94% for Lusaka, respectively. Meanwhile, the SVM model yielded Overall Accuracy (OA) ranging between 77% and 94% for the years 1995 and 2023. Further, RF algorithm notably produced slightly higher OA and kappa coefficients, ranging between 0.92 and 0.97, when compared to both the ANN and SVM models, across both study areas. A predominant land use change was observed as the expansion of vegetation by 11,990 ha (60.4%), primarily through the conversion of 1,926 ha of bare lands into vegetation in Lusaka during 1995–2005. However, a noteworthy shift was observed as built-up areas experienced significant growth from 2005 to 2023, with a total increase of 25,110 ha (71%). However, despite the conversion of vegetation to built-up areas during the entire period from 1995 to 2023, there was still a net gain of over 11,000 ha (53.4%) in vegetation cover. In case of Colombo, built-up areas expanded by 1,779 ha (81.5%), while vegetation land decreased by 1,519 ha (62.3%) during concerned period. LULC simulation also indicated a 160-ha expansion of built-up areas during the 2023–2035 period in Lusaka. Likewise, Colombo saw a rise in built-up areas by 337 ha within the same period. Overall, the RF algorithm outperformed the ANN and SVM algorithms. Additionally, the prediction and simulation results indicate an upward trend in built-up areas in both scenarios. The resultant land cover maps provide a crucial baseline that will be invaluable for urban planning and policy development agencies in both countries.
Deciphering the role of tryptophan metabolism-associated genes ECHS1 and ALDH2 in gastric cancer: implications for tumor immunity and personalized therapy
Authors: Wang Lexin , Zhou Xue , Yan Haisheng , Miao Yaping , Wang Binbin , Gu Yuheng , Fan Weining , Xu Ke , Huang Shangke , Liu Jie 
Published: September 2024

BackgroundTryptophan Metabolism-associated Genes (TMGs), such as ECHS1 and ALDH2, are crucial in cancer progression through immunosuppressive mechanisms, particularly in Gastric Cancer (GC). This study explores their effects on the Tumor Microenvironment (TME). Additionally, it examines their potential as novel immunotherapy targets.MethodsWe utilized single-cell and bulk transcriptomic technologies to analyze the heterogeneity of GC. Non-negative Matrix Factorization (NMF) clustering identified key TMGs, and extensive RNA-seq analyses were performed to pinpoint prognostic genes and potential immunotherapy targets. Furthermore, through PCR analyses we found that ECHS1 and ALDH2 gene expression plays a regulatory role in the migration, invasion and inflammatory factor in AGS and SNU-1 cell lines. The interference effect of si-ECHS1 and ad-ALDH2 was validated using cell scratch assay in AGS and SNU-1 cell line.ResultsWe observed a statistically significant correlation between ECHS1 and ALDH2 expression and increased TME heterogeneity. Our findings also revealed that ECHS1 down-regulation and ALDH2 up-regulation contribute to reduced TME heterogeneity, decreased inflammation, and inhibited AGS and SNU-1 tumor cells migration and proliferation. GSVA enrichment analysis highlighted the NF-kappa B(NF-κB) signaling pathway as specifically regulated by TMGs. Furthermore,ECHS1 and ALDH2 modulated CD8+ and CD4+ T cell activities, impacting GC progression. In vitro experiments further solidified our conclusions by showcasing the inhibitory effects of Si-ECHS1 and ad-ALDH2 on the invasive and proliferative capabilities of AGS and SNU-1 cells. Moreover, Si-ECHS1 and ad-ALDH2 gene expression effectively reduced the expression of inflammatory factors IL-10,IL-7,CXCL8 and IL-6, leading to a remarkable alleviation of chronic inflammation and the heterogeneous nature of the TME.ConclusionThis research highlights the importance of ECHS1 and ALDH2 in GC progression and immune modulation, suggesting that targeted therapies focusing on these genes offer promising avenues for personalized immunotherapy in GC. These findings hold potential for improving patient survival and quality of life. Future studies on the NF-κB signaling pathway’s role in this context are warranted to further elucidate the mechanisms underlying TMG-mediated immune modulation in GC.
Diagnostic challenges in cutaneous leishmaniasis due to atypical Leishmania infantum: pathologists’ insights from re-emergence zones
Authors: Ekemen Suheyla , Nalcaci Muhammed , Toz Seray , Sanjoba Chizu , Demirkesen Cuyan , Cetin Emel D. , Tecimer Tulay , Yildiz Pelin , Gursel Mayda , Ince Umit , Ozbel Yusuf , Coban Cevayir 
Published: September 2024

BackgroundLeishmaniasis, a parasitic infection affecting both humans and animals, is increasingly spreading across Mediterranean and European regions, largely driven by human migration and environmental changes. In countries like Türkiye and across Europe, which have seen large influxes of migrants, the incidence of cutaneous leishmaniasis (CL) is rising, with cases now appearing in cities where the disease was previously undocumented. In these previously non-endemic areas, physicians unfamiliar with the characteristic lesions may misdiagnose CL, particularly in cases with only cutaneous manifestations. This study aims to evaluate the impact of re-emerging CL on the routine diagnostic practices of pathologists in Türkiye, by retrospectively reviewing cases.MethodsWe conducted a retrospective analysis of CL cases diagnosed between 2013 and 2022 at a single pathology center in Türkiye, covering multiple provinces. Twelve cases of CL were identified and analyzed based on clinical presentation, pre-diagnosis, histopathological findings, and molecular diagnostics. DNA extraction and PCR were performed on paraffin-embedded tissue samples to identify the Leishmania species involved.ResultsOut of the twelve CL cases reviewed, seven exhibited morphological findings strongly suggestive of CL (MFSS of CL), warranting further microbiological evaluation. All patients presented with non-healing skin lesions characterized by central ulceration, crater-like formations, or papulonodular lesions. Notably, CL was included in the clinical pre-diagnosis in only 58.3% of cases, while it was not considered in the remaining 41.7% of cases. Clinicians initially pre-diagnosed skin tumors in six cases (50%), four of which led to wide surgical excision. Histopathological examination in all cases revealed chronic or mixed (acute/chronic) inflammation, predominantly rich in histiocytes. To further investigate the role of Leishmania species in the pre-diagnosis, DNA extraction and PCR were performed on paraffin-embedded tissue samples, identifying L. infantum as the causative agent in 10 cases and L. major in two cases. Notably, L. infantum was the causative agent in all five cases initially misdiagnosed as skin tumors, which were also associated with a granulomatous type of chronic inflammation.
Identification of ATRNL1 and WNT9A as novel key genes and drug candidates in hypertrophic cardiomyopathy: integrative bioinformatics and experimental validation
Authors: He Huabin , Liao Yanhui , Chen Yang , Qin Hao , Hu Longlong , Xiao Shucai , Wang Huijian , Yang Renqiang 
Published: September 2024

BackgroundHypertrophic cardiomyopathy (HCM) is a genetic disorder characterized by left ventricular hypertrophy that can lead to heart failure, arrhythmias, and sudden cardiac death. Despite extensive research, the molecular mechanisms underlying HCM are not fully understood, and effective treatments remain limited. By leveraging bioinformatics and experimental validation, this study aims to identify key genes and pathways involved in HCM, uncover novel drug candidates, and provide new insights into its pathogenesis and potential therapeutic strategies.MethodsCommonly upregulated and downregulated genes in hypertrophic cardiomyopathy (HCM) were identified using Gene Expression Omnibus (GEO) datasets, including three mRNA profiling datasets and one miRNA expression dataset. Enrichment analysis and hub-gene exploration were performed using interaction networks and consistent miRNA-mRNA matches. Potential drugs for HCM were screened. HCM cellular and animal models were established using isoproterenol. Key unstudied differentially expressed genes (DEGs) were validated. Animals were treated with novel potential drugs, and improvements in HCM were assessed via ultrasound metrics. Hematoxylin and eosin (H&amp;E) staining was used to assess myocardial fibrosis. Immunohistochemistry was employed to detect DEGs in cellular experiments.ResultWe discovered 145 key upregulated and 149 downregulated DEGs associated with HCM development, among which there are eight core upregulated and seven core downregulated genes. There are 30 upregulated and six downregulated miRNAs. Between the six downregulated miRNAs and 1291 matched miRNAs (against eight core upregulated DEGs), there is one common miRNA, miR-1469. Using the CTD database, drugs that impact the expression/abundance/methylation/metabolic process of core DEGs (after the exclusion of toxic drugs) included acetaminophen, propylthiouracil, methapyrilene, triptolide, tretinoin, etc. In the HCM cell model, only ATRNL1 and WNT9A were significantly increased. In the HCM animal model, propylthiouracil, miR-1469, and triptolide demonstrated varying degrees of therapeutic effects on HCM. Propylthiouracil, but not miR-1469 or triptolide, significantly inhibited the expression of ATRNL1 in the HCM model, and all three drugs suppressed WNT9A expression.ConclusionWe identified several novel genes in HCM development, among which ATRNL1 and WNT9A were validated by cell and animal models. A deficiency of hsa-miR-1469 may be a mechanism behind HCM development. Novel medications for HCM treatment include propylthiouracil and triptolide.
Systemic immune inflammation index and risk of stroke: a cross-sectional study of the National Health and Nutrition Examination Survey 2005–2018
Authors: Xue Hua , Zeng Yuqi , Zou Xinyang , Li Yongkun 
Published: September 2024

BackgroundThe incidence of stroke has increased globally, resulting in medical expenditures and social burdens over the past few decades. We aimed to explore the relationship between systemic immune inflammatory index (SII) and stroke using the National Health and Nutrition Examination Survey (NHANES) from 2005 to 2018.MethodsBased on NHANES data, 902 stroke patients and 27,364 non-stroke patients were included in this study. SII was the independent variable and stroke was the dependent variable. Univariate and multivariate logistic regression analyses were used to explore the association between SII and stroke. Restricted cubic spline (RCS) method was used to test the nonlinear association between SII and stroke.ResultsWeighted logistic regression analysis showed a significant association between SII and stroke (OR: 1.985, 95% CI: 1.245–3.166, p = 0.004). The interaction test showed that the association between SII and stroke was not significant between strata (p &gt; 0.05). A significant positive association between SII and stroke risk (OR &gt;1, p &lt; 0.05) was observed in the crude model, model I and model II. RCS analysis showed no nonlinear positive association between SII and stroke risk after adjusting for all confounders.ConclusionOur study determined that SII is associated with stroke risk. Given the inherent limitations of cross-sectional studies, further research is necessary to validate the causality of this association and to demystify the underlying mechanisms between inflammation and stroke.
Task-dependent neuromuscular adaptations in low back pain: a controlled experimental study
Authors: Ducas Julien , Marineau Emile , Abboud Jacques 
Published: September 2024

IntroductionThis study investigated the variability in lumbar neuromuscular adaptations to pain, the task dependency of pain adaptations and the effect of these adaptations on motor performance.MethodsTwenty-four healthy participants performed isometric back extension contractions at 45° and 90° trunk flexion under pain-free and experimental low back pain conditions induced by electrical stimulation. High-density surface electromyography recorded lumbar muscle activation strategies, and force steadiness was measured using a load cell.ResultsWhile considerable variability in neuromuscular adaptations to lumbar pain was observed among participants, consistent patterns were found between tasks. In the 90° trunk flexion position, both sides exhibited greater magnitudes of pain adaptations for muscle activity redistribution in the mediolateral axis (p &lt; 0.05, 86% increase) and muscle activity amplitude (p &lt; 0.001, 183% increase) compared to the 45° trunk flexion position. A significant negative correlation was found between the magnitude of the mediolateral spatial redistribution of muscle activity and force steadiness on the left side (p = 0.045).DiscussionThese findings highlight the intricate and task-dependent nature of neuromuscular adaptations to pain within lumbar muscles, and points toward a potential trade-off between pain adaptations and performance.
Pickle water ameliorates castor oil-induced diarrhea in mice by regulating the homeostasis of the gut microbiota and intestinal mucosal barrier
Authors: Zhou Tian , Long Dongmei , Zhou Maoting , Hu Xianghong , Wang Yu , Wang Xing 
Published: September 2024

IntroductionDiarrhea is a common clinical condition that can potentially be fatal. Current treatment options often have side effects, such as constipation and vomiting, and there remains a need for more effective therapies. Pickled vegetables, a famous traditional food in China, have been suggested in clinical studies to alleviate diarrhea in children, particularly through the use of pickle water (PW). However, the pharmacological effects and mechanisms of PW on intestinal health remain unclear. This study aimed to explore the protective effects of PW on castor oil-induced diarrhea in ICR mice and to investigate its potential mechanisms.MethodsTo evaluate the antidiarrheal effects of PW, we used a castor oil-induced diarrhea model in ICR mice. Various indices were measured to assess the severity of diarrhea. After euthanizing the mice, oxidative stress markers in the ileum were assessed using biochemical methods, and the expression of tight junction-related proteins in the ileum was analyzed using Western blot. Additionally, 16S rRNA high-throughput sequencing was used to evaluate the diversity and composition of the intestinal flora.ResultsThe results showed that PW supplementation reduced body weight without significantly affecting organ index and liver function in the castor oil-induced diarrhea mice. PW also effectively reduced the dilution rate, diarrhea index, average loose stool grade, propelling distance of carbon powder, and intestinal propulsive rate while improving the pathological abnormality in the ileum. Furthermore, PW enhanced the activities of total antioxidant capacity (T-AOC), glutathione peroxidase (GSH-PX), and catalase (CAT) while reducing malonaldehyde (MDA) levels. PW also increased the expression of tight junction proteins zonula occludens-1 (ZO-1) and occludin in the ileum. Additionally, the analysis of 16S rDNA revealed that PW increased both α and β diversity, improved the composition of the intestinal flora, and restored it to a normal level.DiscussionCollectively, dietary PW administration ameliorates Castor oil-induced diarrhea by restoring tight junctions between intestinal mucosal cells, suppressing oxidative stress, and regulating the composition of intestinal flora. These findings suggest that PW may be a promising strategy for managing diarrhea.
The real-world analysis of adverse events with teduglutide: a pharmacovigilance study based on the FAERS database
Authors: Wang Xiaogan , Chen Hao , Han Shuangshuang , Li Lingbo , Chen Hongjin , Yang Bolin 
Published: September 2024

BackgroundTeduglutide, the first glucagon-like peptide 2 analogue, has been demonstrated to facilitate the absorption of gut nutrient and lessen the need for parenteral assistance in patients with Short Bowel Syndrome (SBS). However, its adverse drug events (AEs) are primarily documented in clinical trials, with a deficit in real-world data. This study evaluates the AEs profile of teduglutide based on Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data.MethodA disproportionality analysis of FAERS data from Quarter 1 (Q1) 2013 to Quarter 3 (Q3) 2023 was conducted to examine the association between teduglutide and adverse events, employing Reporting Odds Ratio (ROR), Proportional Reporting Ratio (PRR), Bayesian Confidence Propagation Neural Network (BCPNN), and Empirical Bayesian Geometric Mean (EBGM) methods.ResultsOut of 13,809,302 reports in the FAERS database, 10,114 reports identified teduglutide as the “primary suspect” in AEs identification. During the dosing observation period, the median occurrence of adverse events was 393 days (interquartile range [IQR] 97–996 days). Teduglutide-associated AEs occurred in 27 System Organ Classes (SOC), of which renal and urinary disorders is not mentioned in the specification. Based on the four algorithms, a total of 260 major disproportionality preferred terms (PTs) were filtered out, including previously unreported AEs including weight decreased (n = 805), vascular device infection (n = 683), dehydration (n = 596) and nephrolithiasis (n = 146).ConclusionOur findings corroborate the AEs listed in the teduglutide prescribing information and additionally unveil new adverse reaction signals such as nephrolithiasis. These discoveries could aid in clinical monitoring and risk identification for teduglutide.
Adjuvant and neoadjuvant therapy with or without CDK4/6 inhibitors in HR+/HER2- early breast cancer: a systematic review and meta-analysis
Authors: Zhang Zhihao , Zhao Xin , Chen Jie 
Published: September 2024

BackgroundThe combination of cyclin-dependent kinases 4/6 (CDK4/6) inhibitors and endocrine therapy is the standard treatment for patients with hormone receptor-positive (HR+)/HER2-negative (HER2-) advanced breast cancer. However, the role of CDK4/6 inhibitors in early breast cancer remains controversial.MethodsThis study aimed to evaluate the efficacy and safety of CDK4/6 inhibitors combined with endocrine therapy versus endocrine therapy alone in patients with HR+, HER2- early breast cancer. A systematic review of Cochrane, PubMed and EMBASE databases was conducted. The efficacy endpoints of adjuvant therapy were invasive disease-free survival (IDFS), overall survival (OS) and distant relapse-free survival (DRFS). The efficacy endpoint included complete cell cycle arrest (CCCA) and complete pathologic response (PCR) with neoadjuvant therapy. Grade 3/4 adverse events (AEs) were assessed as safety outcomes.ResultsEight randomized controlled trials (RCTs) were included in the study. CDK4/6 inhibitors combined with endocrine therapy showed a significant improvement in IDFS (hazard ratio (HR) = 0.81, 95% confidence interval (CI) = 0.68–0.97, P = 0.024), but not DRFS (HR = 0.84, 95% CI = 0.56–1.29, P = 0.106) or OS (HR = 0.96, 95% CI = 0.77–1.19, P = 0.692) in adjuvant therapy. In the neoadjuvant therapy setting, CDK4/6 inhibitors improved CCCA compared with the control group (RR = 2.08, 95% CI = 1.33–3.26, P = 0.001). The risk of 3/4 grade AEs increased significantly with the addition of CDK4/6 inhibitors to endocrine therapy.ConclusionThe addition of CDK4/6 inhibitors in HR+/HER2- early breast cancer patients significantly improved IDFS in adjuvant therapy and CCCA in neoadjuvant. However, CDK4/6 inhibitors also showed significant toxicities during therapy.Systematic Review Registration:Identifier CRD42024530704.