bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple analytical model for bamboo-reinforced slopes using modified Bishop method
Authors: Chakrabortty Pradipta , Srivastava Lokesh Sharan , Kumar Pintu 
Published: May 2023

Introduction: Embankments are constructed in many places for transportation purposes such as railways and roads. The stability of slopes in embankments has always been a concern, especially in cohesionless soils. There are many methods to increase the safety factor of cohesionless soil slopes using geogrids, geocells, concrete piles, and so on. The conventional material used to stabilize slopes has a huge impact on the environment. Nowadays, researchers are using natural fibers such as bamboo and coir fiber for stabilization purposes.Methods: In this paper, bamboo piles are used to stabilize slopes. The bamboo piles are inserted vertically on the slope face to increase the shear strength and stability against slope failure. A limit equilibrium method has been developed to estimate the stability of a slope improved by friction piles after modifying the Bishop method of slices. The stability of the slope is analyzed for both the reinforced conditions and the unreinforced conditions using the developed analytical formula.Results and Discussion: The analytical equations were developed by considering three modes of slope failure: shear failure of the bamboo piles along the failure surface, movement of the upper part of the soil, leaving the bamboo pile embedded in the base soil, and pulling out of the bamboo along with the upper part of the soil mass. Further validation of the results is carried out with the limit equilibrium method-based software SLOPE/W using a modified Bishop method. The factor of safety increased after reinforcing the slope with bamboo piles for all three modes.
Seminal cadmium affects human sperm motility through stable binding to the cell membrane
Authors: Pappalardo Claudia , Cosci Ilaria , Moro Giulia , Stortini Angela Maria , Sandon Annalisa , De Angelis Cristina , Galdiero Giacomo , Trifuoggi Marco , Pivonello Rosario , Pedrucci Federica , Di Nisio Andrea , Foresta Carlo , Ferlin Alberto , De Toni Luca 
Published: May 2023

Environmental pollutants are claimed to be major factors involved in the progressive decline of the fertility rate worldwide. Exposure to the heavy metal Cadmium (Cd) has been associated with reproductive toxicity due to its ionic mimicry. However, the possible direct accumulation of Cd in human sperm cells has been poorly investigated. In this study, we aimed to clarify the possible direct effect of Cd exposure on sperm function through the analysis of its cell accumulation. Semen samples from 30 male subjects residing in high environmental impact areas and adhering to the “Exposoma e Plurifocalità nella Prevenzione Oncologica” campaign for testis cancer prevention were compared with semen samples from 15 males residing in low exposure areas. Semen levels and cell Cd content were quantified by inductively coupled plasma (ICP) spectroscopy. Cell Cd distribution was assessed by scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS). The impact of Cd on sperm function was evaluated by the in vitro exposure to the heavy metal, whilst possible scavenging approaches/agents were assessed. In addition to higher values of semen Cd, exposed subjects showed a reduction in total motile sperm fraction compared to not-exposed controls (59.6% ± 13.6% vs. 66.3% ± 7.3%, p = 0.037). Semen Cd levels were also significantly correlated with SEM-EDS signals of Cd detected on the head and neck of sperm (respectively p = 0.738, p &lt; 0.001 and ρ = 0.465, p &lt; 0.001). A total of 2 h of in vitro exposure to 0.5 μM Cd was associated with a significant reduction of sperm progressive motility. Scavenging approaches with either hypo-osmotic swelling or 10 μM reduced glutathione were ineffective in blunting cell Cd and restoring motility. The reduction of exposure levels appears to be the main approach to reducing the reproductive issues associated with Cd.
Analysis of flood control risk in floodwater utilization considering the uncertainty of flood volume and peak
Authors: Du Huihua , Wang Zongzhi , Yin Jun 
Published: May 2023

Introduction: A design flood is a hypothetical flood used for the design of reservoirs and other hydrologic engineering infrastructures. Among many hydrological properties of a design flood, flood volume and peak can significantly affect the safety of reservoir operation. However, the uncertainty of flood volume and peak has rarely been considered in the risk analysis of reservoir operation regarding floodwater utilization.Methods: In this paper, a general risk analysis framework that integrates the Monte Carlo sampling method and the most likely event selection method is proposed to calculate the risk of operating a single reservoir. By generating a large amount of stochastic bivariate flood data, the most likely design values were selected for a given return period. The probability of the maximum water level exceeding the current design flood level was calculated based on the simulation of flood control operation under various floodwater utilization schemes.Results: The model is applied to the Shagou reservoir in the Shuhe River basin, China. The results show that the design flood volume and flood peak obtained by the bivariate joint return are 7.59% and 8.22% higher than those from univariate frequency analysis, respectively; the joint return period of bivariate design value spans from 10a to 1000a compared to the historical data; and the flood control risk at Shagou reservoir is 0.29 under current flood control operations based on the uncertainty of flood volume and peak.Discussion: Moreover, the marginal benefit may contain floodwater utilization and a transmission risk effect between different node projects in the flood control system.
Systematic evaluation of combined herbal adjuvant therapy for proliferative diabetic retinopathy
Authors: Huai Baogeng , Huai Baosha , Su Zhenghua , Song Min , Li Changling , Cao Yingjuan , Xin Tao , Liu Deshan 
Published: May 2023

ObjectiveTo evaluate the efficacy and safety of combined traditional Chinese medicine in the adjuvant treatment of proliferative diabetic retinopathy (PDR) by Meta-analysis.MethodsPubMed, Embase, Web of Science, Cochrane Library, China National Knowledge Infrastructure (CNKI), Wanfang databases were searched by computer. Random controlled clinical trials (RCTS) using traditional Chinese medicine as adjuvant therapy for proliferative diabetic retinopathy were screened, and Stata16.0 software was used to perform meta-analysis on the final included literatures.ResultsA total of 18 studies involving 1392 patients were included. Meta-analysis showed that the clinical effective rate OR=2.99 (CI: 2.18-4.10, I2 = 42.7%, P&lt;0.05); Visual acuity MD=0.10(CI: 0.06-0.13, I2 = 0%, P&lt;0.05); Fundus efficacy OR=5.47 (CI: 1.33-22.51, I2 = 71.4%, P&lt;0.05); Neovascularisation regression rate OR=8 (CI: 3.83-16.71, I2 = 30.1%, P&lt;0.05); Macular foveal thickness MD=-44.24 (CI: -84.55–3.93, I2 = 95.6%, P&lt;0.05); Absorption of vitreous hemorrhage OR=4.7 (CI: 2.26-9.77, I2 = 0%, P&lt;0.05); Fasting blood glucose MD=-0.23, (CI: -0.38–0.07, I2 = 0%, P&lt;0.05); 2h postprandial blood glucose MD=-0.19 (CI: -0.52-0.14, I2 = 0%, P=0.25). From the results, the combined Chinese medicine adjuvant therapy showed better efficacy than the control group. A total of 69 kinds of traditional Chinese medicine were involved in 18 studies, among which the top four applied frequencies were Panax notoginseng, Rehmannia rehmannii, Astragalus membranaceus and Poria cocos. Most of the medicines were sweet and bitter in taste, the qi tended to be slight cold and cold, and the meridian tropism belongs to the liver meridian.ConclusionThe combination of traditional Chinese medicine adjuvant therapy has a good curative effect on PDR patients. However, the relevant clinical trials are few and more high-quality clinical trials are still needed, what’s more the attention should be paid to the exploration of its safety.
Depressive and anxiety symptoms, and neural correlates of reward and punishment anticipation in female athletes with amenorrhea
Authors: Baskaran Charumathi , Kumar Poornima , Plessow Franziska , Nimmala Supritha , Ackerman Kathryn E. , Eddy Kamryn T. , Pizzagalli Diego A. , Misra Madhusmita 
Published: May 2023

ObjectiveStudies in estrogen deficiency states such as primary ovarian insufficiency and Turner syndrome suggest that estrogen status may be an important modulator of mood and emotions. In this study we compared depressive and anxiety symptoms between adolescent and young adult female oligo-amenorrheic athletes (AA) and eumenorrheic females (EM), and explored structural, and functional changes in related brain areas during reward processing, a behavioral construct that is altered in depression and anxiety.MethodsWe included (i) 24 AA participating in ≥4 hours/week of aerobic exercise or running ≥20 miles/week for ≥6 months in the preceding year, with lack of menstrual cycles for ≥3 months within at least 6 preceding months of oligo-amenorrhea, OR in premenarchal girls, absence of menses at &gt;15 years), and (ii) 27 EM aged 14-25 years. Participants completed the Beck Depression Inventory-II (BDI-II), State and Trait Anxiety Inventory (STAI), and Mood and Anxiety Symptoms Questionnaire (MASQ). Structural MRI and brain activation during a functional MRI (fMRI) task that probes reward and punishment processing was examined in a subset of 10 AA and 23 EM.ResultsMedian (IQR) age and BMI of AA and EM groups were 20.6 (19.0-22.6) vs. 20.6 (19.2-23.7) years, p=0.6 and v 20.3 (18.8-21.5) vs. 21.9 (19.6-23.5) kg/m2, p=0.005, respectively. While groups did not differ for BDI-II scores, AA had higher anhedonic depression MASQ scores (p=0.04), and STAI (p=0.03) scores vs. EM. In the fMRI subset, AA had higher caudate volumes vs. EM [F(1, 29)=9.930, p=0.004]. Lower activation observed in the right caudate during reward anticipation in AA compared with EM (p=0.036) suggests blunted reward processing in the striatum in estrogen deficient states.ConclusionAthletes with amenorrhea had higher depressive and anxiety symptomatology compared to eumenorrheic young women. Exploratory analyses demonstrated increased caudate volumes and decreased caudate activation during reward processing in athletes with amenorrhea suggesting that estrogen may play a role in reward processing.
Retrieval of particle size distribution based on a multi-objective genetic algorithm for multi-wavelength lidar
Authors: Bao Jun , Qi Liangliang , Mao Jiandong , Gong Xin 
Published: May 2023

Introduction: Aerosols affect the radiation budget of the Earth’s atmospheric system. The aerosol particle size distribution (PSD) is one of the main parameters for characterizing the effect of aerosol on radiative forcing.Methods: The extinction coefficient and backscattering coefficient at 355 and 532 nm and backscattering coefficient at 1064 nm of aerosol particles over Yinchuan area, China, which measured by a multi-wavelength lidar developed by North Minzu University, were used to retrieve the aerosol PSD. In view of the disadvantages of traditional regularization methods, the elitist Non-Dominated Sorting Genetic Algorithm (NSGA-II) is selected to retrieve PSD.Results and Discussion: To verify the feasibility for retrieval of aerosol PSD, the NSGA-II with different errors in the input optical signal was simulated, in which the errors of the inverted PSD are still in the acceptable range when 35% error added into the optical parameters. Moreover, some experiments were carried out under different atmospheric conditions, including background sunny, cloudy and dusty days, and comparisons were performed with Multiple Population Genetic Algorithm (MPGA) and Simple Genetic Alogrithm (SGA) method. The results show that the retrieval effect of NSGA-II was better than that of MPGA and SGA, and the NSGA-II is very suitable for retrieve PSD by using the multi-wavelength lidar data.
Genome-wide search identified DNA methylation sites that regulate the metabolome
Authors: Nikpay Majid 
Published: May 2023

Background: Identifying DNA methylation sites that regulate the metabolome is important for several purposes. In this study, publicly available GWAS data were integrated to find methylation sites that impact metabolome through a discovery and replication scheme and by using Mendelian randomization.Results: The outcome of analyses revealed 107 methylation sites associated with 84 metabolites at the genome-wide significance level (p&lt;5e−8) at both the discovery and replication stages. A large percentage of the observed associations (85%) were with lipids, significantly higher than expected (p = 0.0003). A number of CpG (methylation) sites showed specificity e.g., cg20133200 within PFKP was associated with glucose only and cg10760299 within GATM impacted the level of creatinine; in contrast, there were sites associated with numerous metabolites e.g., cg20102877 on the 2p23.3 region was associated with 39 metabolites. Integrating transcriptome data enabled identifying genes (N = 82) mediating the impact of methylation sites on the metabolome and cardiometabolic traits. For example, PABPC4 mediated the impact of cg15123755-HDL on type-2 diabetes. KCNK7 mediated the impact of cg21033440-lipids on hypertension. POC5, ILRUN, FDFT1, and NEIL2 mediated the impact of CpG sites on obesity through metabolic pathways.Conclusion: This study provides a catalog of DNA methylation sites that regulate the metabolome for downstream applications.
Identification of DLL3-related genes affecting the prognosis of patients with colon adenocarcinoma
Authors: Xiang Jinyu , Gong Wenjing , Liu Jiannan , Zhang Huijuan , Li Ming , Wang Rujian , Lv Yaodong , Sun Ping 
Published: May 2023

Background: Delta-like ligand 3 (DLL3) is one of the NOTCH family of ligands, which plays a pro- or anti-carcinogenic role in some cancers. But the role of DLL3 in colon adenocarcinoma (COAD) has not been studied in depth.Materials and methods: First, we used Kaplan-Meier (K-M) curve to evaluate the effect of DLL3 on the prognosis of COAD in The Cancer Genome Atlas (TCGA), which was further validated in clinical samples for immunohistochemistry. Then we screened for differentially expressed genes (DEGs) of DLL3 by analyzing datasets of COAD samples from Gene Expression Omnibus (GEO) and TCGA. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and Gene Set Enrichment Analysis (GSEA) were conducted to explore the underlying mechanisms of DLL3-related in the development and prognosis of COAD. On the basis of DLL3-related signature genes, a prognostic model and a nomogram were constructed. Finally, CIBERSORT was applied to assess the proportion of immune cell types in COAD sample.Results: Survival analysis showed a significant difference in overall survival between high- and low-expression group (p = 0.0092), with COAD patients in the high-group having poorer 5-year survival rate. Gene functional enrichment analysis revealed that DLL3-related DEGs were mainly enriched in tumor- and immunity-related signaling pathways, containing AMPK pathway and mitophagy-animal. The comparison of COAD tumor and normal, DLL3 high- and low-expression groups by GSEA found that AMPK signaling pathway and mitophagy-animal were inhibited. Nomogram constructed from DLL3-related signature genes had a good predictive effect on the prognosis of COAD. We found the highest correlation between DLL3 and interstitial dendritic cell (iDC), natural killer (NK) cell and Interstitial dendritic cell (Tem). DLL3 was also revealed to be diagnostic for COAD. In clinical sample, we identified higher DLL3 expression in colon cancer tissue than in adjacent control (p &lt; 0.0001) and in metastasis than in primary lesion (p = 0.0056). DLL3 expression was associated with stage and high DLL3 expression was observed to predict poorer overall survival (p = 0.004).Conclusion: It suggested that DLL3 may offer prognostic value and therapeutic potential for individualized treatment of COAD, and that it may has a diagnostic role in COAD.
SPARTIN: a Bayesian method for the quantification and characterization of cell type interactions in spatial pathology data
Authors: Osher Nathaniel , Kang Jian , Krishnan Santhoshi , Rao Arvind , Baladandayuthapani Veerabhadran 
Published: May 2023

Introduction: The acquisition of high-resolution digital pathology imaging data has sparked the development of methods to extract context-specific features from such complex data. In the context of cancer, this has led to increased exploration of the tumor microenvironment with respect to the presence and spatial composition of immune cells. Spatial statistical modeling of the immune microenvironment may yield insights into the role played by the immune system in the natural development of cancer as well as downstream therapeutic interventions.Methods: In this paper, we present SPatial Analysis of paRtitioned Tumor-Immune imagiNg (SPARTIN), a Bayesian method for the spatial quantification of immune cell infiltration from pathology images. SPARTIN uses Bayesian point processes to characterize a novel measure of local tumor-immune cell interaction, Cell Type Interaction Probability (CTIP). CTIP allows rigorous incorporation of uncertainty and is highly interpretable, both within and across biopsies, and can be used to assess associations with genomic and clinical features.Results: Through simulations, we show SPARTIN can accurately distinguish various patterns of cellular interactions as compared to existing methods. Using SPARTIN, we characterized the local spatial immune cell infiltration within and across 335 melanoma biopsies and evaluated their association with genomic, phenotypic, and clinical outcomes. We found that CTIP was significantly (negatively) associated with deconvolved immune cell prevalence scores including CD8+ T-Cells and Natural Killer cells. Furthermore, average CTIP scores differed significantly across previously established transcriptomic classes and significantly associated with survival outcomes.Discussion: SPARTIN provides a general framework for investigating spatial cellular interactions in high-resolution digital histopathology imaging data and its associations with patient level characteristics. The results of our analysis have potential implications relevant to both treatment and prognosis in the context of Skin Cutaneous Melanoma. The R-package for SPARTIN is available at https://github.com/bayesrx/SPARTIN along with a visualization tool for the images and results at: https://nateosher.github.io/SPARTIN.
Clinical value of anoikis-related genes and molecular subtypes identification in bladder urothelial carcinoma and in vitro validation
Authors: Dong Ying , Xu Chaojie , Su Ganglin , Li Yanfeng , Yan Bing , Liu Yuhan , Yin Tao , Mou Shuanzhu , Mei Hongbing 
Published: May 2023

BackgroundAnoikis is a programmed cell death process that was proven to be associated with cancer. Uroepithelial carcinoma of the bladder (BLCA) is a malignant disease of the urinary tract and has a strong metastatic potential. To determine whether anoikis-associated genes can predict the prognosis of BLCA accurately, we evaluated the prognostic value of anoikis-associated genes in BLCA and constructed the best model to predict prognosis.MethodThe BLCA transcriptome data were downloaded from TCGA and GEO databases, and genes with differential expression were selected and then clustered using non-negative matrix factorization (NMF). The genes with the most correlation with anoikis were screened and identified using univariate Cox regression, lasso regression, and multivariate Cox regression. The GEO dataset was used for external validation. Nomograms were created based on risk characteristics in combination with clinical variants and the performance of the model was validated with receiver operating characteristic (ROC) curves. The immunotherapeutic significance of this risk score was assessed using the immune phenomenon score (IPS). IC50 values of predictive chemotherapeutic agents were calculated. Finally, we used RT-qPCR to determine the mRNA expression of four genes, CALR, FASN, CASP6, and RAD9A.ResultWe screened 406 tumor samples and 19 normal tissue samples from the TCGA database. Based on anoikis-associated genes, we classified patients into two subtypes (C1 and C2) using NMF method. Subsequently, nine core genes were screened by multiple methods after analysis, which were used to construct risk profiles. The design of nomograms based on risk profiles and clinical variables, ROC, and calibration curves confirmed that the model could well have the ability to predict the survival of BLCA patients at 1, 3, and 5 years. By predicting the IC50 values of chemotherapeutic drugs, it was learned that the high-risk group (HRG) was more susceptible to paclitaxel, gemcitabine, and cisplatin, and the low-risk group (LRG) was more susceptible to veriparib and afatinib.ConclusionIn summary, the risk score of anoikis-associated genes can be applied as a predictor to predict the prognosis of BLCA in clinical practice.
The genetically predicted causal relationship of inflammatory bowel disease with bone mineral density and osteoporosis: evidence from two-sample Mendelian randomization
Authors: Xu Dengyong , Chen Yao , Gao Xing , Xie Weidong , Wang Ya , Shen Jiaying , Yang Guang , Xie Binbin 
Published: May 2023

BackgroundMany existing studies indicated that patients with inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), tend to have the risk of low total body bone mineral density (BMD), and are more likely to have osteoporosis (OS). To determine the causal relationship between IBD and bone metabolic disorders, we herein performed a two-sample Mendelian randomization analysis (TSMR) using publicly available summary statistics.MethodsSummary statistics of total body BMD, OS and IBD were downloaded from the Open Genome-Wide Association Study (GWAS), FinnGen consortium and International Inflammatory Bowel Disease Genetics Consortium (IIBDGC). The European and East Asian populations have consisted in this Mendelian Randomization (MR) work. A range of quality control procedures were taken to select eligible instrument SNPs closely associated with total body BMD, OS and IBD. To make the conclusions more reliable, we applied five robust analytical methods, among which the inverse variance weighting (IVW) method acted as the major method. Besides, heterogeneity, pleiotropy and sensitivity were evaluated.ResultsIn the European population, the genetic association of UC on total body BMD (OR=0.97, 95%CI=0.96,0.99, P&lt;0.001) and overall IBD on total body BMD (OR=0.98, 95%CI=0.97,1.00, P=0.013) were significant, while the effect of CD on total body BMD was not significant enough (OR=0.99, 95%CI=0.98,1.00, P=0.085). All of UC, CD and overall IBD can be the genetic risk factor of having OS with pathological fracture (UC: OR=1.13, 95%CI=1.02,1.26, P=0.024, CD: OR=1.14, 95%CI=1.05,1.25, P=0.003, overall IBD: OR=1.13, 95%CI=1.02,1.24, P=0.015). In East Asian groups, only CD had a causal relationship with OS (OR=1.04, 95% CI=1.01,1.07, P=0.019).ConclusionOur study revealed genetically predicted associations between IBD on total body BMD and OS in European and East Asian populations. This work supplemented the results of previous retrospective studies and demonstrated the necessity of BMD monitoring in patients with IBD.