bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a novel victorivirus isolated from the plant-pathogenic fungus Nigrospora chinensis
Authors: Zhong Jie , Sui Wen Wen , Li Ping , Tang Qian Jun , Liu Tian Bo , Xiao Yan Song 
Published: July 2022

Abstract
Here, we characterized a new mycovirus from the Nigrospora chinensis fungus, that was named Nigrospora chinensis victorivirus 1 (NcV1). NcV1 genome was 5, 283 bp in length, containing two overlapping open reading frames (ORFs), ORF1 and ORF2. ORF1 and ORF2 were predicted to encode a putative coat protein and an RNA-dependent RNA polymerase, respectively. The stop codon of ORF1 was overlapped with the start codon of ORF2 by tetranucleotide sequence ATGAG. Phylogenetic analysis based on aa sequences of RdRp indicated that NcRV1 was clustered with members of the genus Victorivirus in the family Totiviridae. To our knowledge, this was the first report of mycovirus infecting N. chinensis.
Designing a Conventional Two-dose mRNA Vaccine for Tuberculosis Comprised of Dormancy-associated Proteins, ESAT6 and a Vault- liposome Vector System
Authors: KOVAČIĆ Dženan , SOFTIĆ Adna , SALIHOVIĆ Adna , JOTANOVIĆ Jovana , HOTIĆ Sarah Maris 
Published: July 2022

Abstract
Human pulmonary tuberculosis represents an unfortunately placed and persistent thorn in global health; asymptomatically infecting nearly a third of the global population, with roughly 10 million new cases and 1.5 million deaths annually. It continues to hold a place among the top ten causes of death in the world and remains the leading infectious cause of death by a single pathogen. Among the numerous reasons for such statistics is the relatively poor efficacy of the near-century-old BCG vaccine. In spite of it being the only approved vaccine for TB, its benefit is predominantly observed in preventing paediatric miliary TB and TB meningitis, whilst it offers considerably limited protection against infection in adults. The advent of mRNA vaccine technologies has passed the critical tribulations for current demand of Coronavirus disease 2019, and in so validating the argument on employing the technology as an effective response to TB as it suggests fulfilment of the necessary criteria: induction of robust, determined innate response with a favourable safety profile across a wider population. To this end, the novel mRNA vaccines were proven to elicit immune responses against bacterial pathogens; by virtue, the technology may be applied in bacterial infection treatment. Meanwhile, no approved mRNA prophylactics for bacterial infections exist yet. Within this work, we propose a novel vaccine design for TB that harvests the potential of mRNA vaccine technology. This was achieved by using a barrage of in silico tools for epitope identification, construct design and rigorous physicochemical evaluation and immune response predictions. The vaccine itself was design for the purpose of immunizing previously unexposed patients, along with individuals that have asymptomatic TB. Additionally, immune response simulations have predicted an immune response relatively in agreement with the natural, beneficial, response to M.tb infection, rather than the detrimental variety.
Identification of Immune and Hypoxia Risk Classifier to Estimate Immune Microenvironment and Prognosis in Cervical Cancer
Authors: Shi Yujing , Chen Hui , Liu Zeyuan , Shen Gefenqiang , Sun Xinchen , Di Xiaoke 
Published: July 2022

Abstract
Background: Cervical cancer (CC) is one of the most common gynecologic neoplasms. Hypoxia is an essential trigger for activating immunosuppressive activity and initiating malignant tumors. However, the determination of the role of immunity and hypoxia on the clinical outcome of CC patients remains unclear.Methods: The CC independent cohort were collected from TCGA database. Consensus cluster analysis was employed to determine a molecular subtype based on immune and hypoxia gene sets. Cox relevant analyses were utilized to set up a risk classifier for prognosis assessment. The underlying pathways of classifier genes were detected by GSEA. Moreover, we conducted CIBERSORT algorithm to mirror the immune status of CC samples.Results: We observed two cluster related to immune and hypoxia status and found the significant difference in outcome of patients between the two clusters. A total of 251 candidate genes were extracted from the two clusters and enrolled into Cox relevant analyses. Then, seven hub genes (CCL20, CXCL2, ITGA5, PLOD2, PTGS2, TGFBI and VEGFA) were selected to create an immune and hypoxia-based risk classifier (IHBRC). The IHBRC can precisely distinguish patient risk and estimate clinical outcomes. In addition, IHBRC was closely bound up with tumor associated pathways such as hypoxia, P53 signaling and TGF β signaling. IHBRC was also tightly associated with numerous types of immunocytes.Conclusion: This academic research revealed that IHBRC can be served as predictor for prognosis assessment and cancer treatment estimation in CC.
Assessment of Earthquake ground motion and Design Response Spectra in Site Response analysis using DEEPSOIL
Authors: Akter Sonia 
Published: July 2022

Abstract
The behavior of soil like linear in low strain and non-linear in high strain has a significance in the ground motion due to earthquake or volcanic eruption. Ground motion is formed by the propagation of waves that are produced by a sudden movement of earth and long its surface. In seismic hazard study, the appropriate selection of elastic response spectra based on soil classification and earthquake magnitude is the simplest way to account for local site effects. In this research, Bangabandhu Sheikh Mujibur Rahman hall at KUET campus is selected for detailed ground motion analysis. The impact of soil characteristics is evaluated by seismic site response nonlinear analysis using “DEEPSOIL”. The main scheme of this research study is to determine the design response spectra and amplification factor based on shear wave velocity at 30-meter depth. From the SPT value, the average shear wave velocity is found varying 107 (m/s) to 205 (m/s) and the bedrock shear wave velocity increases up to 800 m/s. Four input earthquake motions have been used in this analysis which is scaled based on the zone coefficient. From the analysis, it is evident that with the increase of bedrock properties, the PSA at the surface, the amplification factor of ground motion, and maximum PGA, maximum strain, and maximum stress ratio is increased. The Normalized design response spectrum is compared with the BNBC and EC8 seismic code so that these results could be used for determining seismic hazard assessment or future probable event.
Risk factors for early enteral nutrition feeding intolerance in neurocritical patients: A prospective case-control study
Authors: Sun Panpan , Fan Xiaoning , Jin Yuping , Tang Rui , Chen Xia 
Published: July 2022

Abstract
Background: Determining the factors associated with ENFI in neurocritical patients could be important for better identification of the patients at risk of feeding intolerance.Therefore, this study aimed to identify the risk factors for ENFI in neurocritical patients.Methods: Patients hospitalized in the neurological intensive care unit of the First Affiliated Hospital of University of Science and Technology of China between January 2021 and December 2021 were enrolled in this prospective case-control study.Result: Finally, 250 participants were enrolled. There were 183 patients in the early enteral nutrition feeding tolerance (ENFT) group and 67 patients in the ENFI group respectively. In the multivariable analysis, hypothermia treatment (OR = 2.331, 95% CI: 1.176-4.618, P = 0.015), severity of illness (OR = 2.176, 95% CI: 1.100-4.303, P = 0.025), the levels of sedation (OR = 2.478, 95% CI: 1.182-5.194, P = 0.016) and prealbumin (OR = 1.945, 95% CI: 1.073-3.525, P = 0.028) were independent risk factors of ENFI.Conclusion: Hypothermia treatment, severity of illness, levels of sedation and prealbumin were independent risk factors for ENFI.Chinese Clinical Trial Registry: ChiCTR2100044644
Identification of stable housekeeping genes for induced pluripotent stem cells and -derived endothelial cells for drug testing
Authors: Ong Sheena L. M. , Baelde Hans J. , IJzendoorn David G.P. , Bovée Judith V.M.G. , Szuhai Karoly 
Published: July 2022

Abstract
There are no validated housekeeping genes in induced pluripotent stem cells (iPSC) and derived endothelial iPSC (iPSC-EC). This makes comparison of gene expression levels less reliable especially during drug treatments. Here, we utilized transcriptome sequencing data of iPSC and iPSC-EC with or without CRISPR-Cas9 induced translocation to identify a panel of 15 candidate housekeeping genes. For comparison, five commonly used housekeeping genes (B2M, GAPDH, GUSB, HMBS, and HPRT1) were included in the study. The panel of 20 candidate genes were investigated for their stability as reference genes. This panel was analyzed and ranked based on stability using five algorithms, delta Ct, bestkeeper, geNorm, Normfinder, and Reffinder. Based on the comprehensive ranking of Reffinder, the stability of the top, RPL36AL and TMBIM6, and bottom two genes, UBA1 and B2M, was further studied in iPSC-EC with or without genetic manipulation, and after treatment with telatinib. Using quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR), it was shown that gene expression of the top two housekeeping genes, RPL36AL and TMBIM6, remained stable during drug treatment. We identified a panel of housekeeping genes that could be utilized in various conditions using iPSC and iPSC derived endothelial cells as well as genetically modified iPSC for drug treatment.
Structural Aspects of the Attached Turbulent Boundary Layer Flow Over a Hill
Authors: Duetsch-Patel Julie E , Gargiulo Aldo , Borgoltz Aurelien , Devenport William J , Lowe K Todd 
Published: July 2022

Abstract
Note: Please see pdf for full abstract with equations.Three-dimensional turbulent boundary layers under strong pressure gradients and curvature are the rule in real-world flow applications but are typically not well predicted by turbulence models due to isotropic eddy viscosity or equilibrium assumptions. Validation-quality data in complex 3D flows is necessary for continued efforts to improve simulation accuracy. The BeVERLI (Benchmark Validation Experiments for RANS/LES Investigations) Hill bump model, designed specifically for validation experiments, was tested in the Virginia Tech Stability Wind Tunnel to collect validation experiment data on the three-dimensional (3D) boundary layer flow over a 3D hill. Laser Doppler velocimetry measurements on the bump model were used to study the mean flow and turbulence structure and evaluate the impact of pressure gradient and curvature upon the total shear stress in the boundary layer and evaluate the impact of pressure gradient and curvature upon the total shear stress behavior in the near-wall region. From analysis of the BeVERLI Hill flow, including the boundary layer just upstream of the hill, and comparison with the 3D flow around a wing-body junction of Olcmen et al. (2001), it is shown that none of the stations studied exhibit a constant shear stress region over any significant region of the boundary layer. One station on the hill, located in a region with strong spanwise and streamwise pressure gradients, experiences an apparent return to an equilibrium shear stress for x2+<30 due to significantly increased production of u1'u2' and u2'^2 at this station.
Can additional intravertebral anesthesia improve the intraoperative tolerance to percutaneous kyphoplasty for acute osteoporotic thoracolumbar fractures?
Authors: Wu Xu-Cai , Zou Peng , Yao Ying , Chai Xin , Yang Jun-Song , Wang Ting , Liu Tuan-Jiang , Liu Peng , Liao Bo , Hao Ding-Jun , Zhao Yuan-Ting 
Published: July 2022

Abstract
Purpose: To evaluate the efficacy and safety of different types of anesthesia (LA, LA with IVA, and GA) used during PKP.Patients and methods: A total of 150 patients of single-level OTLF were prospectively included in this study from February 2019 to February 2020. They were randomly divided into three groups of 50 patients each and treated with GA, LA, or LA with IVA. Severity of back pain was measured preoperatively, intraoperatively, and 1 h, 1 day, 1 month, and 1 year postoperatively using VAS scores. The ODI was administered and the AHVB on lateral thoracolumbar radiographs was measured preoperatively and at 1 month and 1 year postoperatively. The MMSE was administered at 1 and 7 days postoperatively to monitor for the development of POCD.Results: 131 patients completed the full postoperative follow-up schedule. The average duration of surgery in the LA group was slightly longer than the other two groups. The intraoperative VAS score of the LA+IVA group was significantly lower than that of the LA group. The MMSE scores at 1 day and 1 week postoperatively were significantly decreased only in the GA group. The incidence of POCD was 45% (18/40) at 1 day and 5% (2/40) and at 1 week postoperatively in the GA group, whereas POCD was not observed in the other two groups. The GA group had the highest incidence of anesthesia-related adverse reactions.Conclusion: IVA with ropivacaine can effectively reduce intraoperative and early postoperative pain, shorten the duration of surgery, reduce surgery-related complications.
Arctic Fe-Mn deposits from the Kara Sea: fast-growing refuges for cosmopolitan marine microorganisms under sharp changes of redox conditions
Authors: Shulga Natalia , Abramov Sergey , Klyukina Alexandra , Ryazantsev Konstantin , Gavrilov Sergey 
Published: July 2022

Abstract
The impact of biomineralization and redox processes on the formation and growth of ferromanganese deposits in the World Ocean remains understudied. This problem is particularly relevant for the Arctic marine environment where sharp seasonal variations of temperature, redox conditions and organics inflow significantly impact the biogenic and abiotic pathways of ferromanganese deposits formation. The microbial communities of the fast-growing Arctic Fe-Mn deposits have not been reported so far. Here, we describe the microbial diversity, structure and chemical composition of nodules, crust and their underlying sediments collected from three different sites of the Kara Sea. Scanning electron microscopy revealed a high abundance of microfossils and biofilm-like structures within the nodules. Phylogenetic profiling together with redundancy and correlation analyses revealed a positive selection for putative metal-reducers (Desulfobacterota), iron oxidizers (Hyphomicrobiaceae and Scalinduaceae), and Fe-scavenging Nitrosopumilaceae or Magnetospiraceae in the microenvironments of the Fe-Mn deposits from their surrounding benthic microbial populations. We hypothesize that in the Kara Sea, the nodules provide unique redox-stable microniches for cosmopolitan benthic marine metal-cycling microorganisms in an unsteady environment, thus focusing the overall geochemical activity of nodule-associated microbial communities and accelerating processes of ferromanganese deposits formation to uniquely high rates.
Correlation between Optical Coherence Tomography Angiography (OCT- A) findings at three to six weeks and functional outcome (modified Rankin Scale – mRS) at three months of onset of acute ischemic stroke due to Extracranial Carotid Artery Atherosclerotic Disease (ECAD)
Authors: Mishra Biswamohan , Pandit Awadh Kishor , Chawla Rohan , Aalok Swati Phuljhele , Srivast M Vasantha Padma , Nayak Manoj Kumar , PM Yogeesh , Salunkhe Manish , Garg Ajay , Srivast Achal Kumar , Vishnu Venugopalan Y , Bhatia Rohit , Misra Shubham , Upadhyay Ashish Datt , Molla Kabiruddin 
Published: July 2022

Abstract
Background and Aims Optical Coherence Tomography Angiography (OCTA) images retinal vasculature without the need of contrast injection. In the present study we aim to determine whether OCTA findings can predict functional outcomes (mRS, modified Rankin Score) in patients with ECAD -stroke.Material and Methods This Exploratory study enrolled was performed on adults with acute ischemic stroke due to ECAD at 3-6 weeks of stroke onset and risk factors matched controls without carotid artery stenosis. Results: Twenty-three ECAD stroke patients (cases) and twenty-three risk factor matched controls were enrolled. There was a significant difference between cases and controls in the Deep Vessel Density (DVD) at macula (p = 0.0007). Statistically significant difference was noted in the total superficial vessel density (SVD) at macula [SVD within 1 standard deviation (SD) of control data vs SVD beyond 1 SD of control data) in the ipsilateral eye and functional outcome at 3 months (Poor vs very good outcome, mRS 0-1 vs mRS 2-6, respectively ( p= 0.0361). There was statistically insignificant correlation between the RPCPD at ONH and National Institutes of Health Stroke Scale (NIHSS) at admission, mRS at discharge, and functional outcome (mRS) at 3 months of stroke onset (r =0.33, r=0.35, r=0.39; p=0.11, p=0.09, p=0.06, respectively).Conclusions: The findings of this exploratory study led us to hypothesize that OCTA findings may predict three-month outcomes in cases of ECAD associated stroke and this could be useful in decision making in intervention studies as to whether intervene or not in patients having critical or non-critical ECAD for preventing future stroke.
Humic substances from composted fennel residues control the inflammation induced by Helicobacter pylori infection in AGS cells
Authors: Verrillo Mariavittoria , Cuomo Paola , Montone Angela Michela Immacolata , Savy Davide , Spaccini Riccardo , Capparelli Rosanna , Piccolo Alessandro 
Published: July 2022

Abstract
Helicobacter pylori (H. pylori) is a common human pathogen causing inflammation. Recent studies have suggested a sophisticated interplay between mitochondria, innate immunity and inflammatory response, thus proposing mitochondrial disfunction as the hallmark of severe inflammatory disorders. In this study, humic substances isolated from composted fennel residues (HS-FEN) were tested as potential therapeutical strategy to restore the mitochondrial physiology and control the inflammation associated with H. pylori infection. The molecular features of HS-FEN were characterized by infrared spectrometry, thermochemolysis-GC/MS, NMR spectroscopy, and high-performance size-exclusion chromatography (HPSEC), which revealed the presence of aromatic polyphenolic components arranged in a rather stable conformation. In vitro results showed antioxidant and anti-inflammatory properties of HS-FEN, that was found to increase the expression level of OPA-1 and SOD-2 genes in AGS cells stimulated with H. pylori culture filtrate (Hpcf) and concomitantly decrease the expression of IL-12, IL-17 and G-CSF. The hydrophobic features of HS, their conformational arrangement and large content of bioactive molecules may explain the beneficial effects of HS-FEN, that may potentially become an interesting source of anti-inflammatory agents capable to counteract or prevent the H. pylori-related inflammatory disorders.
A machine learning model for improving virtual machine migration in cloud computing
Authors: Belgacem Ali , Mahmoudi Said , Ferrag Mohamed Amine 
Published: July 2022

Abstract
Cloud Computing is a paradigm allowing access to physical and application resources online via the Internet. These resources are virtualized using virtualization software to make them available to users as a service. In this environment, the migration of virtual machines (VMs) is a significant concern these days. This technique provided by virtualization technology impacts the performance of the cloud. When allocating resources, the distribution of VMs is unbalanced, and their migration from one server to another can increase energy consumption and network overhead, necessitating an improvement in VM migrations. This paper presents a machine learning model for migrating virtual machines. The goal is to improve the selection of virtual machines and migration processes by reducing energy consumption and the number of VMs migrations. Numerical results demonstrate that the proposed solution can significantly enhance the goals addressed.
Assessment of recent methods for determination of soil final settlement using field data
Authors: Dali Mohamed Aymen , Benamghar Ahcène 
Published: July 2022

Abstract
The problem of soil consolidation was first studied by Terzaghi who formulated the well-known one-dimensional consolidation theory. However, this widely used method was found to provide poorly accurate estimations, since Terzaghi considered the assumption of constant permeability and consolidation coefficient. The poor accuracy is also due to the low resemblance between laboratory results and field actual measurements. In order to overcome this issue, many researchers proposed new approaches to estimate and predict soil settlement more accurately. Among these approaches, field-based methods are particularly promising. For instance, the Asaoka method (1978), Sridharan (1987) method, Tan (1995) method, Chunlin’s method (2014), and recent methods of Guo et al. (2017, 2018b) and Guo et al. 2018(a). This paper aims to assess and discuss the results of some recent methods using a field consolidation monitoring data set.
L-arginine application triggered soil hydrolytic activity for protein hydrolysis
Authors: Khosrozade Sajedeh , Nourbakhsh Farshid 
Published: July 2022

Abstract
Application of amino acids to soils is reportedly associated with controversial responses in soil enzyme activities. After a lag time, protease and fluorescein diacetate (FDA) hydrolysis increased in L-arginine-amended soils. After 30 days, the ratio of protease and FDA hydrolysis in L-arginine-amended soil samples to those in the control reached 3.7 and 2.0, respectively. It was concluded that L-arginine was able to stimulate protease and FDA hydrolysis, thereby making the soil hydrolytic system capable of facing more complicated substrates.
Transcriptome-wide association study identiﬁes new susceptibility genes and pathways for spondyloarthritis
Authors: Su Xiaochen , Chen Anfa , Teng Menghao , Lou Xiaoxiao , Zhao Xiaoming , Han Hao , Ma Hongyun , Zhang Yingang 
Published: July 2022

Abstract
Background: Spondyloarthritis (SpA) is a group of multifactorial bone diseases influenced by genetic factors, the environment and lifestyle. However, current studies have found a limited number of SpA-related genes, and the genetic and pathogenic mechanism of SpA is still unclear. Methods: A tissue-specific transcriptome-wide association study (TWAS) of SpA was performed by using genome-wide association study (GWAS, including 3966 SpA patients and 452264 controls) summary data and gene expression weights of whole blood and skeletal muscle. The SpA-associated genes identified by TWAS were further compared with the differentially expressed genes (DEGs) identified in the SpA gene expression profile acquired from the Gene Expression Omnibus database (GEO, GSE58667). Finally, FUMA and Metascape were used to perform functional enrichment and annotation analysis.Results: The TWAS detected 28 significant genes associated with SpA in whole blood and skeletal muscle, such as CTNNAL1 (PSM=0.0304, PWB=0.0096). The gene expression profile of SpA identified 20 candidate genes that overlapped in the TWAS data, such as MCM4 (PTWAS=0.0132, PDEG=0.0275) and KIAA1109 (PTWAS=0.0371, PDEG =0.0467). Enrichment analysis of the genes identified by TWAS identified 93 significant GO terms 33 and KEGG pathways, such as mitochondrion organization (GO:0007005) and axon guidance (hsa04360).Conclusion: We identified multiple candidate genes that were genetically related to SpA. Our study may provide novel clues of the genetic mechanism, diagnosis, and treatment of SpA.