bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analyses of transcriptomes induced by Lyme spirochete infection to CNS model system
Authors: Wen Shiyuan , Xu Xin , Kong Jing , Luo Lisha , Yue Peng , Cao Wenjing , Zhang Yu , Liu Meixiao , Fan Yuxin , Chen Jingjing , Ma Mingbiao , Tao Lvyan , Peng Yun , Dong Yan , Li Bingxue , Luo Suyi , Wang Feng , Zhou Guozhong , Chen Taigui , Li Lianbao , Liu Aihua , Bao Fukai 
Published: September 2021

Abstract
Background

Lyme disease is a zoonotic disease caused by infection with Borrelia burgdorferi (Bb), the involvement of the nervous system in Lyme disease is usually referred to as Lyme neuroborreliosis (LNB). LNB has diverse clinical manifestations, most commonly including meningitis, Bell’s palsy, and encephalitis. However, the molecular pathogenesis of neuroborreliosis is still poorly understood. Comprehensive transcriptomic analysis following Bb infection could provide new insights into the pathogenesis of LNB and may identify novel biomarkers or therapeutic targets for LNB diagnosis and treatment.
Methods

In the present study, we pooled transcriptomic datasets (transcriptomic rhesus data from our laboratory and the GSE85143 dataset from the Gene Expression Omnibus database) to screen common differentially expressed genes (DEGs) in the Bb infection group and the control group. Functional and enrichment analyses were conducted using the Database of Annotation Visualization and Integrated Discovery database, Protein-Protein Interaction network, and hub genes were identified using the Search Tool for the Retrieval of Interaction Genes database and the CytoHubba plugin. In addition, in vitro and ex vivo assays were performed to verify the above findings. The mRNA expression levels of these genes were verified by quantitative real-time PCR (qPCR).
Results

A total of 80 upregulated DEGs and 32 downregulated DEGs were identified. Among them, 11 hub genes were selected. Upregulated genes in the Gene Ontology analysis were significantly enriched in cell adhesion processes. The pathway enrichment analyses revealed that the PI3K-Akt signaling pathway was significantly enriched. The mRNA levels of ANGPT1, TLR6, SREBF1, LDLR, TNC, and ITGA2 in U251 cells and/or rhesus brain explants by exposure to Bb were validated by qPCR.
Conclusion

Our study suggested that TLR6, ANGPT1, LDLR, SREBF1, TNC, and ITGA were differentially highly expressed in Bb-infected astrocytes compared to normal controls, and overexpression of LDLR might be a favorable prognostic factor of LNB patients. Further study is needed to explore the value of TLR6, ANGPT1, LDLR, SREBF1, TNC, and ITGA in LNB pathogenesis.
Predicting Stone-Free Status of Percutaneous Nephrolithtomy With Machine Learning System: Comparative Analysis With Guy’s Stone Score and S.T.O.N.E Score System
Authors: Zhao Hong , li Wanling , Li Junsheng , Li Li , Wang Hang , Guo Jianming 
Published: September 2021

Abstract
Purpose
Using machine learning methods (MLMs) to predict stone-free status after percutaneous nephrolithotomy (PCNL). We compared the performance of this system with Guy’s stone score and S.T.O.N.E score system.
Materials and Methods
Data from 222 patients (90 females, 41%) who underwent PCNL at our center were used. Twenty-six parameters, including individual variables, renal and stone factors, surgical factors were used as input data for MLMS. We evaluate the efficacy of four different techniques: Lasso-logistic (LL), random forest (RF), support vector machine (SVM) and Naive Bayes. Model performance was evaluated using area under curve (AUC) and compared with Guy’s stone score and S.T.O.N.E score system.
Results
Overall stone free rate was 50% (111/222). To predict the stone-free status, all receiver operating characteristic curves of the four MLMs were above the curve for the Guy’s stone score. The AUCs of LL, RF, SVM and Naive Bayes were 0.879, 0.803, 0.818, 0.803 respectively. Those values were higher than the AUC of the Guy’s score system, 0.800. The accuracies of the MLMs (0.803–0.818%) were also superior to S.T.O.N.E score system (0.788%). Among the MLMs, Lasso-logistic showed the most favorable AUC.
Conclusion
Machine learning methods can predict stone-free rate with AUCs no inferior to those of Guy’s stone score and S.T.O.N.E score system.
Dysregulation of Alternative Splicing was Associated with the Pathogenesis of Ulcerative Colitis
Authors: Li Daowei , Tan Yue 
Published: September 2021

Abstract
Background: Although numerous risk loci of Ulcerative Colitis (UC) in the human genome have been identified, the pathogenesis of UC remains not fully understood. Recently, multiple transcriptomic analyses have shown that aberrant gene expression in UC patients’ colon tissues were associated with the disease progressing. A pioneer study also demonstrated that altered post-transcriptional regulation may be involved in the progression of UC. Methods: Herein, we provided a comprehensive analysis of alternative splicing (AS) signature on UC patients. We analyzed three datasets, which include 74 tissue samples from UC patients in total, and identified over 2,000 significant AS events in these datasets. Results: Skipped Exon (SE) and Alternative first exon (AFE) were found to be the top two significantly altered AS events. Immune response related pathways were significantly enriched. Genes that showed significantly AS events were more likely to be dysregulated at the expression level.Conclusion: Overall, these results suggested that alteration of AS may play crucial roles in the pathogenesis of UC.
Forecast the Supply of General Practitioners in Shanghai: Using an Agent-based Model
Authors: Cheng Jiejie , Yang Yong , Zhang Qingyang , Zhang Guangpeng , Sun Mei 
Published: September 2021

Abstract
BackgroundGeneral practitioners (GPs), as one important human resource for health, is facing a supply shortage in China. The diversity of individual decision-making behaviors of GPs and medical students increases the difficulty of supply forecasting. Agent-based simulation, as a bottom-up approach, has the potential to address this challenge.MethodsAn agent-based model was developed to forecast the supply of GPs in Shanghai, China. Based on the theory of working life cycle, we analyzed the life cycle of GPs and developed the ﻿framework. Publicly available data were used to parameterize the model. Several scenarios were conducted to test hypotheses and examine intervention stratigies. NetLogo 6.1.0 was used for model implemtation. ResultsThe model was run over a nearly 20-year time span from 2016 to 2035 in Shanghai. Simulated results showed that GPs in Shanghai will rise from 8,000 to 15,375 during this period. Sensitivity analysis showed that parameters of the health system had a greater impact on the results than those of the education system. ConclusionsReliable forecasting of the supply and demand is a prerequisite for solving the shortage of GPs. Comprehensive intervention strategies are needed to address the supply shortage. For example, as indiciated by our study, regions should increase their attractiveness to GPs and retain them more effectively, instead of just increasing the number of medical students enrolled.
Metabolic Risk Factors in Patients with Kidney Stones with and without Type 2 Diabetes
Authors: Spivacow Francisco , Valle Elisa Del , Boailchuk Juan , Allo Pablo Martínez , Pailler Martin 
Published: September 2021

Abstract
Background: In the past few decades, the prevalence of kidney stones in Western countries has increased in parallel with the growing overweight/obesity and type 2 diabetes mellitus rates. An increased insulin resistance in these patients explains, in part, the rising prevalence of uric acid stones. The objective of this retrospective study is to evaluate the metabolic abnormalities in type 2 diabetic and non-diabetic patients with kidney stones. All patients were evaluated following an ambulatory protocol for kidney stones. Methods: A total of 104 diabetic patients (age: 57.8 ± 11 years) and 130 non-diabetic (age: 52.1 ± 6.7 years) patients with kidney stones were selected. Higher rates of body mass index, hypertension, urinary tract infection, gout and hyperuricemia were observed in diabetic patients as compared to the non-diabetics, while similar rates were found for their family history of kidney stones. Results: Urinary pH was lower in diabetic patients than in non-diabetic patients. Metabolic abnormalities were detected in 95.2% and 81.5% of diabetic and non-diabetic, respectively. Unduly acidic urine pH was the most frequent abnormality in diabetic patients while hyperuricosuria was the second more common abnormality. On the other hand, in non-diabetics patients idiopathic hypercalciuria was the most common metabolic abnormality followed by hyperuricosuria. Conclusions: The main risk factor for lithogenesis in type 2 diabetes is unduly acidic urine pH, followed by hyperuricosuria and idiopathic hypercalciuria.
Effects of Submerged Convective Cooling In The Turning of AZ31 Magnesium Alloy For Tool Temperature And Wear Improvement
Authors: Zakaria Muhammad Syamil , Mustapha Mazli , Azmi Azwan Iskandar , Ahmad Azlan , Ismail Sikiru Oluwarotimi , Shuaib Norshah Aizat 
Published: September 2021

Abstract
Low melting point and material adhesion attributed by the magnesium alloy led to extreme built-up edge (BUE) and built-up layer (BUL) formations. Dry machining is favourable for machining magnesium alloy; however, this strategy inflicts excessive adhesive wear on the cutting tool. Therefore, this current work focuses on innovative cooling technique known as submerged convective cooling (SCC) for the turning of the AZ31 magnesium alloy. Prior to cutting experiment, a computational fluid dynamics (CFD) simulation was conducted to evaluate internal structure of cooling module. Based on the CFD simulation, small inlet/outlet diameter significantly contribute to reduction of tool temperature because of effective heat transfer coefficient of cooling fluid in the SCC. Experimental results revealed that SCC has effectively reduced the tool temperature by 50% and contributed to 37% improvement in surface roughness when compared to dry cutting. Finally, both BUE and BUL were observed in dry and SCC conditions, but the severity of these wear mechanisms improved or decreased remarkably under SCC conditions.
Designing Chickpea For a Hotter Drier World
Authors: Akinlade Oluwaseun Johnson , Voss-Fels Kai , Costilla Roy , Kholova Jana , Choudhary Sunita , Varshney Rajeev K , Hickey Lee , Smith Millicent R 
Published: September 2021

Abstract
Chickpea (Cicer arietinum L.) is one of the most important grain legumes in the world, but its current and future production is threatened due to the increased incidence of drought and heat stress. To address this challenge, an integrated crop improvement strategy encompassing breeding, genomics, physiology and agronomy is required. Here, we review the physiological traits known to confer drought and heat adaptation in chickpea and identify areas of drought and heat adaptation research that should be prioritised in the future. Furthermore, we underscore approaches to efficiently phenotype chickpea adaptation traits and highlight the significant challenges and importance of understanding the nexus between canopy and root development. Finally, we present the opportunity to adopt multi-trait genomic prediction approaches to efficiently utilise key physiological traits, that can be assayed using high-throughput phenotyping platforms, to accelerate genetic gain in drought and heat prone environments.
miR-208a-3p promotes NSCLC proliferation and migration by suppressing lncRNA-MEG3 expression
Authors: Yang Linfei , Li Qian , Zhong Hai , Ye Liang , Fang Surong , Gu Wei , Qian Yingying 
Published: September 2021

Abstract
Background The disordered expression of maternally expressed gene 3 (MEG3) has been observed in non-small-cell lung cancer (NSCLC). However, the molecular mechanism accounting for this abnormal expression is not fully understood. Methods MEG3 expression was detected by qRT-PCR in 51 cases of NSCLC and adjacent normal tissues. Then, the relationship between MEG3 and miR-208a-3p was assessed in vitro by cell viability assay, cell migration assay, protein extraction and western blot analysis. Resoults We observed that MEG3 expression was decreased in NSCLC tissues. And MEG3 expression was negatively related to lymph node metastasis and differentiation. Moreover, MEG3 expression is regulated by miR-208a-3p expression by overexpression and knockout experiments. Furthermore, we focused on the underlying mechanism of MEG3 downregulation. We found that the overexpression of miR-208a-3p reduced the level of MEG3 expression based on computational predictions and in vitro assays. Using CCK-8 and transwell migration assays, we found that the overexpression of miR-208a-3p can increased proliferation and apoptosis in NSCLC cells. Moreover, the depletion of MEG3 rescued the proliferation and migration induced by miR-208a-3p knockdown. Conclusion Taken together, the results of this study reveal that miR-208a-3p promotes NSCLC tumorigenesis by negatively regulating MEG3 expression and functions as an oncogenic miRNA in NSCLC.
A Chelation-Enhanced Fluorescence Assay Using Thiourea Capped Carbonaceous Fluorescent Nanoparticles For As (III) Detection In Water Samples
Authors: Mohammadi Susan , Mohammadi Somayeh , Salimi Abdollah , Ahmadi Rezgar 
Published: September 2021

Abstract
Herein, we designed a sensitive and selective “Turn-On” fluorescence nanosensor using water-soluble carbonaceous fluorescent nanomaterials (CFNs) functionalized with thiourea (CFNs-thiourea) for efficient detection of trace amounts of arsenic (III) in aqueous samples. The CFNs and CFNs-Thiourea were characterized by transmission electron microscopy (TEM), UV–Visible spectroscopy (UV-vis) and Fourier transformed infrared spectroscopy (FTIR). The emission peak intensity of proposed nanosensor at 425 nm was gradually enhanced on arsenite addition in wide detection range (3.3–828.5 µg L-1) attributed to the binding of arsenite species with sulfur groups of CFNs-thiourea. The limit of detection (LOD) was 0.48 µg L-1 being much lower than the World Health Organization (WHO) recommended threshold value of 10 µg L-1. Furthermore, the as prepared thiourea -CFNs exhibited an superb selectivity for As (III) compared various cations and anions such as; NO3−, NO2−, F−, Ni2+, Fe3+, Cu2+, Ca2+, Mg2+, Zn2+, Fe2+, Hg2+, Pb2+, F-, Cl-, Mn2+, Cr3+, Co2+, Cd2+, Bi3+, Al3+ and As (V) at 100 folds concentration of As (III). The turn on fluorescence nanosensor was successfully exploited for quantification of arsenic in spiked water samples with acceptable efficiencies.
Thermal-Induced Dielectric Response In Mechanically Durable Polyvinylidene Fluoride/Tubular Kapok Fiber Encapsulated Polyethylene Glycol Composite Films
Authors: Wu Wenqi , Pei Xianglin , Li Hairong , Tu Junyang , Li Qiong , Zhou Weijie , Gong Yutie , Jiang Ming , Gong Wei 
Published: September 2021

Abstract
Dielectric materials with thermally responsive property are being pursued in fields such as next-generation sensors, smart switches, and novel actuators. These applications require that the dielectric materials have mechanical durability and stable serviceability besides thermally responsive dielectric behavior. Herein, we report a novel thermally responsive, mechanically durable, and low-cost dielectric composite simply fabricated by vacuum impregnating polyethylene glycol (PEG) into Kapok fiber (KF) and compounding them with polyvinylidene fluoride (PVDF). A remarkable dielectric susceptibility, controlled dielectric transition temperature and obvious thermal hysteresis of the composite films induced by the solid-liquid phase transition of PEG are demonstrated. The effect of molecular weights of PEG on the dielectric response behaviors is evaluated. Such thermally responsive dielectric materials with satisfactory mechanical durability will offer a chance toward constructing thermally responsive systems for safe and stable operation.
Synthesis, Spectral Characterization and Antimicrobial Evaluation of New Metal Complexes of Novel Schiff Base Derived from 4,6-dihydroxy-1,3-phenylenediethanone
Authors: Ahmed Yasmin mamdoh hussien , Mohamed Gehad G. 
Published: September 2021

Abstract
A new tetradentate Schiff base ligand was prepared from condensation of 4,6-dihydroxy-1,3-phenylenediethanone with ethane-1,2-diylbis(oxy)diethanamine. The ligand forms complexes in good yield. The Schiff base and its complexes were characterized by analytical (CHN elemental analyses, solubility, melting point, conductivity) measurements, spectral (IR, UV-vis, 1H NMR and MS) and magnetic measurements. The elemental analyses, Uv-vis spectra, and room temperature magnetic moment data and theoretically through density function theory were used as characterizing techniques in supporting of further interpretation of the complexes structures. The results of elemental analyses, EI-mass and conductivity measurements confirmed the stoichiometry of the ligand and its complexes while the characteristic absorption bands and resonance peaks in IR and NMR spectra confirmed the formation of the ligand frameworks around the metal ions. The octahedral environment for complexes derived from Schiff base ligand have been confirmed on the basis of results of electronic and diffused reflectance spectral studies and magnetic moment measurements. Detailed studies of the thermal properties of the Schiff base ligand and complexes were investigated by thermogravimetric technique. Moreover, the molecular docking into (PDB: 6NE0) was the DNA binding and supports the experimental finding and 6IY0 Crystal structure of conserved hypothetical protein SAV0927 from Staphylococcus aureus subsp. aureus Mu50. The synthesized ligand and its complexes were tested for in vitro antimicrobial activity against Candida albicans, Bacillus subtilis, Aspergillus flavus, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus by using agar-well diffusion method.
Non-Obligate Pairwise Metabolite Cross-Feeding Suggests Ammensalic Interactions Between Bacillus and Aspergillus Species
Authors: Singh Digar , Lee Sang Hee , Lee Choong 
Published: September 2021

Abstract
Metabolite trade-offs at bacterial-fungal interfaces determine their ecological interactions. We designed a non-obligate pairwise metabolite cross-feeding (MCF) between Bacillus and Aspergillus. Cross-feeding Aspergillus metabolites (MCF-1) affected higher growth and biofilm formation in Bacillus. LC-MS-based multivariate analyses (MVA) showed marked variations in the endogenous metabolite profiles between the cross-fed and control Bacillus. We observed and validated that Aspergillus-derived oxylipins were rapidly depleted in Bacillus cultures concomitant with lowered secretion of cyclic lipopeptides (CLPs). Conversely, Bacillus extracts cross-fed to Aspergillus (MCF-2) diminished its mycelial growth and conidiation. Fungistatic effects of Bacillus-derived cyclic surfactins were temporally reduced following their hydrolytic linearization. MVA highlighted disparity between the cross-fed (MCF-2) and control Aspergillus cultures with marked variations in the oxylipin levels. We conclude that the pairwise MCF selectively benefitted Bacillus while suppressing Aspergillus, which suggests their ammensalic interaction. Widening this experimental pipeline across tailored communities may help model and simulate BFIs in more complex microbiomes.
Evaluation of Four Methods to Identify the Homozygotic Sex Chromosome in Small Populations
Authors: Hansen Charles Christian Riis , Westfall Kristen M. , Pálsson Snaebjörn 
Published: September 2021

Abstract
BackgroundWhole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types differ in effective population size and can have highly disparate evolutionary histories, it is imperative to take this information into account when analysing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome in a small population using two whole genome sequences (WGS) and 133 RAD sequences of white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold in a male and a female, ii) heterozygosity per scaffold in a male and a female, iii) mapping to a reference genome of a related species (chicken) with identified sex chromosomes, and iv) analysis of SNP-loadings from a principal components analysis (PCA), based on the low-depth RADseq data. ResultsThe best performing approach was the reference mapping (method iii), which identified 98.12% of the expected homogametic sex chromosome (Z). The read depth per scaffold (method i) identified 86.41% of the homogametic sex chromosome with few false positives. The SNP-loading scores (method iv) found 78.6% of the Z-chromosome and had a false positive discovery rate of more than 10%. The heterozygosity per scaffold (method ii) did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W). The evaluation of these methods also revealed 10 Mb of likely PAR and gametologous regions.ConclusionIdentification of the homogametic sex chromosome in a small population is best accomplished by reference mapping or examining read depth differences between sexes.
Fear of COVID-19 Among Elderly Patients with a Chronic Physical or Mental Disease
Authors: Holeva Vasiliki , Nikopoulou Vasiliki Aliki , Parlapani Eleni , Karkaletsis Konstantinos , Kokkoni Styliani , Nouvakis Dimitrios , Theocharis Patroklos , Diakogiannis Ioannis 
Published: September 2021

Abstract
Older age renders individuals vulnerable during public emergency crises. Considering that older adults are a highly heterogeneous and continuously growing demographic subgroup, this study aimed to assess the mental health impact of COVID-19 on two groups of older patients: a group of chronic physical disease and a group of chronic mental disease. A total of 102 patients completed the Fear of COVID-19 Scale, the Generalized Anxiety Disorder scale, the Brief Patient Health Questionnaire (PHQ-9) and several questions regarding demographic characteristics. Suicidality was assessed by the 9th item of the PHQ-9.According to the results, older chronic disease patients showed higher levels of fear, whereas anxiety and depressive symptoms were present mainly in the group of older psychiatric patients. Suicidality was reported from a subtotal of 25.4% that was composed of 7.8% chronic disease patients and 17.6% psychiatric patients. Chronic physical disease and higher anxiety predicted more severe COVID-19-related fear.