bluuebunny/crossref_metadata_2025_split huggingface dataset:
Docking of Velpatasvir to the SARS-CoV-2 Viral Spike Protein-Human ACE2 Complex: repurposing for COVID-19
Authors: Zia Asad , Akhtar Sohail , Khan Mubarak Ali 
Published: October 2021

Abstract
The SARS-CoV-2 outbreak has challenged the world health community and is still out of control. Since there is no clinical drug available for the corona virus therefore the most important and the fastest way of medicines development is to find potential molecules from the marketed drugs. Herein, bioinformatics analysis on the spike protein (S) of CoV and human angiotensin receptor 2 (ACE-2) with already approved anti-HCV approved drug velpatasvir have been reported. We conducted molecular docking to determine the mode of interaction of velpatasvir and RNA dependent RNA polymerase enzyme as well as inhibition of attachment of S-protein with human host receptor ACE-2. We found that, velpatasvir not only binds tightly with S-protein-ACE2 interface but also with 2019-Cov RdRp, can alter the structure and function of the said proteins and hence will results in the eradication of viral infection. The findings of this study further support the idea of drug repurposing and will help to classify the most successful drugs against COVID-19.
Ideal free flows of optimal foragers: Vertical migrations in the ocean
Authors: Thygesen Uffe Høgsbro , Mazuryn Maksim 
Published: October 2021

Abstract
We consider the collective motion of animals in time-varying environments, using as a case diel vertical migration in the ocean. The animals are distributed in space such that each animal moves optimally, seeking regions which offer high growth rates and low mortalities, subject to costs on excessive movements as well as being in regions with high densities of conspecifics. The model applies to repeated scenarios such as diel or seasonal patterns, where the animals are aware of both current and future environmental conditions. We show that this problem can be viewed as a differential game of mean field type, and that the evolutionary stable solution, i.e. the Nash equilibrium, is characterized by partial differential equations, which govern the distributions and migration velocities of animals. These equations have similarities to equations that appear in the fluid dynamics, specifically the Euler equations for compressible inviscid fluids. If the environment is constant, the ideal free distribution emerges as an equilibrium. We illustrate the theory with a numerical example of vertical animal movements in the ocean, where animals are attracted to nutrient-rich surface waters while repulsed from light during daytime due to the presence of visual predators, aiming to reduce both proximity to conspecifics and swimming efforts. For this case, we show that optimal movements are diel vertical migrations in qualitative agreement with observations.
Biomechanical behaviour and hyperelastic model parameters identification of sheep omasum
Authors: Lebea Lebohang , Ngwangwa Harry , Pandelani Thanyani , Nemavhola Fulufhelo 
Published: October 2021

Abstract
The function of the omasum is incompletely understood; however, the omasum plays an important role in the transport of appropriately sized feed particles from the reticulorumen to the abomasum, oesophageal groove closure, fermentation of ingesta, and absorption of water, volatile fatty acids, and minerals. The aim of this study is to evaluate the suitable hyperelastic anisotropic model based on biomechanical properties of sheep omasum. The results show that all five (5) hyperelastic models may be suitable for the evaluation of sheep omasum. The average coefficient of determination (R2) of Fung, Polynomial (Anisotropic), Holzapfel (2000), Holzapfel (2005) and Four-Fiber-Family hyperelastic models were found to be 0.79 ± 0.19, 0.95 ± 0.05, 0.92 ± 0.07, 0.93 ± 0.05 and 0.94 ± 0.03, respectively. Also, it was found that the best hyperelastic model for fitting uniaxial data of the sheep omasum was Polynomial (Anisotropic) with EI of 100.0 followed by the Four-Fiber-Family model with EI of 96.18.
Comparative Effectiveness of Second-Line Biological Therapies for Ulcerative Colitis and Crohn’s Disease in Patients With Prior Failure of Anti-Tumour Necrosis Factor Treatment
Authors: Hyun Hye Kyung , Yu Jongwook , Kang Eun Ae , Park Jihye , Park Soo Jung , Park Jae Jun , Kim Tae Il , Kim Won Ho , Cheon Jae Hee 
Published: October 2021

Abstract
Background
Therapeutic options for inflammatory bowel disease (IBD) have increased since the introduction of tumour necrosis factor (TNF) inhibitors a few decades ago. However, direct comparisons of the effectiveness of second-line biological agents in patients with ulcerative colitis (UC) and Crohn’s disease (CD) are lacking.
Methods
Patients with UC or CD who experienced anti-TNF treatment failure and subsequently used vedolizumab, ustekinumab, or tofacitinib as a second-line drug were retrospectively recruited. The primary outcomes were the clinical remission rate at week 16 and the cumulative relapse rate 48 weeks after receiving induction therapy.
Results
A total of 94 patients with UC or CD experienced anti-TNF treatment failure and received vedolizumab (UC: 37; CD: 28), ustekinumab (CD: 16), or tofacitinib (UC: 13). The clinical remission rates were not significantly different between the vedolizumab and tofacitinib groups in UC patients (56.8% vs. 46.2%, p = 0.509). In CD patients, the clinical remission rates were not significantly different between the vedolizumab and ustekinumab groups (53.6% vs. 50.0%, p = 0.820). Moreover, the cumulative rates of clinical relapse were not significantly different between the vedolizumab and tofacitinib groups in UC patients and between the vedolizumab and ustekinumab groups in CD patients (p = 0.396 and p = 0.692, respectively). Safety profiles were also similar among the treatment groups in both UC and CD patients.
Conclusions
After prior anti-TNF therapy failure, vedolizumab and tofacitinib in UC patients and vedolizumab and ustekinumab in CD patients showed similarities in terms of the efficacy in inducing and maintaining a clinical response.
Label-Free Quantitative Proteomic Study of The Effect of Dihydrotestosterone (DHT) On Rat Ovarian GCs
Authors: Chen Tairen , Wu Mongjing , Dong Yuting , Kong Bin , Cai Yufang , Hei Changchun , Wu Kai , Zhao Chengjun , Chang Qing 
Published: October 2021

Abstract
Dihydrotestosterone (DHT) is a main androgen in the human body. Previous reports have shown that DHT can affect the proliferation, apoptosis and estrogen and progesterone secretion of ovarian granulosa cells (GCs). An imbalance in DHT secretion leads to GC dysfunction and follicular development disorder.Therefore, exploring the influence of DHT on GCs is necessary. The purpose of this study was to analyze the effect of DHT on GCs through label-free quantitative proteomics (LFQP). After primary cultured rat GCs were treated with DHT (10-8 mol/L), the effect of DHT on GCs was analyzed by LFQP, and some of the differentially expressed proteins (DEPs) were verified by western blotting.A total of 6124.0 proteins were identified, of which 4496.0 were quantifiable. Compared with the control group, 28 proteins were upregulated and 10 were downregulated after DHT intervention. The subcellular localization of DEPs indicates that DHT is involved in the proliferation, migration, molding and metabolism of GCs. Gene Ontology (GO) revealed that DHT downregulated the oxygen transport capacity and oxygen-binding protein of GCs. Orthologous Groups of proteins (COG/KOG) showed that DHT had an important effect on the survival, growth and apoptosis of GCs. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that DHT promotes metabolism, amino acid degradation, chemical carcinogenesis, platelet activation and vasoconstriction in GCs. The western blot results were consistent with the proteomics results. Mark3 and Mre11a are DEPs that were upregulated, and Fth1 and Nqo1 were downregulated, which indicated that DHT could promote the proliferation of GCs.This study comprehensively analyzes the impact of DHT on GCs through LFQP and provides clues for further research.
Decade Long Upsurge In Target Site Pyrethroid Resistance In Bed Bug Populations In The United States
Authors: Lewis Cari D. , Levine Brenna. A. , Schal Coby , Vargo Edward L. , Booth Warren 
Published: October 2021

Abstract
Over the past three decades, the bed bug Cimex lectularius has resurged as a prominent indoor pest on a global scale. Knockdown-associated insecticide resistance (kdr) involving the voltage-gated sodium channel, targeted by organochlorine and pyrethroid insecticides, was first reported in C. lectularius within a few years of the widespread use of Dichlorodiphenyltrichloroethane (DDT) and has been implicated as a significant factor contributing to the species recent resurgence. Since then, selection with pyrethroid insecticides has intensified, yet little is known regarding its short-term impacts on the frequency of kdr-associated mutations. Here, we report temporal changes in the frequencies of three kdr-associated mutations in C. lectularius populations collected across the United States from two time periods, sampled approximately a decade apart. Results reveal a significant increase in the frequencies of kdr-associated mutations over this period, and absence of the insecticide-susceptible genotype in recent collections. Furthermore, a significant transition towards infestations possessing multiple kdr-associated mutations was observed. These results suggest that the persistent use of pyrethroid insecticides over the past decade continues to impose strong selection pressure on C. lectularius populations, driving the proliferation of kdr-associated mutations. They demonstrate that, if unabated, strong anthropogenic selection can drive the rapid evolution of adaptive traits.
Metagenomic Analysis of Lichen Associated Bacterial Community Profiling In Roccella Montagnei
Authors: Vijayakumar Vishnu Raja , Saravanan Karthikeyan , Somasundaram Maharaja , Jayaraj Rajkumar , Annamalai Panneerselvam , Nooruddin Thajuddin , Dharumadurai Dhanasekaran 
Published: October 2021

Abstract
A lichen is a composite organism formed of algae or cyanobacteria that live in a mutually advantageous symbiotic relationship with the filaments (hyphae) of fungus. Three lichen samples were obtained from diverse sites at Kuppanasamy temple, Pollachi, a terrestrial habitat located in Coimbatore, Nithiravilai, Nagercoil, and Ramarpatham, Vedaranyam, both coastal habitats located in Kanyakumari and Nagapattinam districts of Tamil Nadu, for this study. Amplification and sequencing of 16S rRNA V3 - V4 regions were used for metagenomic study. Aside from the NGS data, distinct types of lichen microbiome profiles were clearly shown. The bacterial diversity in the lichen genera of Roccella montagnei growing in coastal and terrestrial environments was further investigated using common and unique operational taxonomic units (OTUs) and the QIIME pipeline (1.9.1). By using similarity clustering, the heat map analysis depicts the abundance information of chosen OTUs as well as the similarity and difference between OTUs and lichen samples. Using multiple methods, the Alpha and Beta diversity analysis revealed that there were differences in all of the samples. However, UPGMA tree inference of comparable bacterial community in coastal habitat lichen samples compared to terrestrial habitat validates their evolutionary lineage. As a result, the bacterial population associated with corticolous lichen is dependent on geographic locations, growth substrate, and climatic circumstances of similar lichen genera produced in different habitats and tree substrates.
English Speech Feature Recognition Based On Digital Means
Authors: miao Yuji , Huang Yanan , Da Zhenjing 
Published: October 2021

Abstract
In order to improve the effect of English speech recognition, based on digital means, this paper combines the actual needs of English speech feature recognition to improve the digital algorithm. Moreover, this paper combines fuzzy recognition algorithm to analyze English speech features, and analyzes the shortcomings of traditional algorithms, and proposes the fuzzy digitized English speech recognition algorithm, and builds an English speech feature recognition model on this basis. In addition, this paper conducts time-frequency analysis on chaotic signals and speech signals, eliminates noise in English speech features, improves the recognition effect of English speech features, and builds an English speech feature recognition system based on digital means. Finally, this paper conducts grouping experiments by inputting students' English pronunciation forms, and counts the results of the experiments to test the performance of the system. The research results show that the method proposed in this paper has a certain effect.
Supplemental Hydroxychloroquine Therapy Regulates Adipokines in Patients With Systemic Lupus Erythematosus With Stable Disease
Authors: Wakiya Risa , Ueeda Kiyo , Shimada Hiromi , Nakashima Shusaku , Kameda Tomohiro , Mansour Mai Mahmoud Fahmy , Kato Mikiya , Miyagi Taichi , Sugihara Koichi , Mizusaki Mao , Mino Rina , Kadowaki Norimitsu , Dobashi Hiroaki 
Published: October 2021

Abstract
Background: In patients with systemic lupus erythematosus (SLE), a higher frequency of atherosclerotic lesions is associated with poor prognosis. Hydroxychloroquine (HCQ) has been reported to improve the lifespan and the prognosis of dyslipidaemia in patients with SLE, but the mechanism is unclear. We investigated the effect of supplemental HCQ treatment on the levels of serum cytokines associated with atherosclerosis in patients with stable SLE.Methods: Patients with SLE who received supplemental HCQ and maintained low disease activity between January 2016 and September 2020 were included in this study. Disease activity was assessed by SLE disease activity index, Cutaneous Lupus Erythematous Disease Area and Severity Index and Lupus Low Disease Activity State, and serum complement titres, anti-dsDNA antibodies, serum insulin and serum cytokines (adiponectin, resistin, and leptin) were analyzed before and after HCQ treatment.Results: Forty-one patients (4 males and 37 females, mean age 41.3 ± 13.2 years) were included. Serum adiponectin levels were significantly increased after 3 months of HCQ treatment compared to baseline, and serum resistin levels were significantly reduced. The change in serum resistin level after HCQ administration was correlated with a significant reduction in serum TNF-α, interleukin (IL)-6, IL-8, and IL-1RA levels.Conclusions: Supplemental HCQ treatment in patients with dsDNA antibodies improved lipid levels. HCQ may improve prognosis by controlling disease activity in SLE and reducing risk factors for atherosclerosis.
First Analyses of Lysine Succinylation Proteome and Overlap between Succinylation and Acetylation in Solenopsis Invicta Buren (Hymenoptera: Formicidae)
Authors: Ye Jingwen , Li Jun 
Published: October 2021

Abstract
Background: Lysine succinylation (Ksu) exists in both eukaryotes and prokaryotes, and influences a variety of metabolism processes. However, little attention has been paid to Ksu in insects, especially the notorious invasive pest Solenopsis invicta. Results: In this study, the first analyses of Ksu proteome and overlap between Ksu and lysine acetylation (Kac) in S. invicta were presented. 3,753 succinylated sites in 893 succinylated proteins were tested. The dihydrolipoyl dehydrogenase, V-type proton ATPase subunit G, and tubulin alpha chain all had evolutionary conservatism among diverse ant or bee species. Immunoblotting validation showed that there were many Ksu protein bands with a wide range of molecular mass. In addition, 1,230 sites in 439 proteins were highly overlapped between Ksu and Kac. 54.05% of Ksu proteins in cytoplasm were acetylated. The results demonstrated that Ksu may play a vital part in the allergization, redox metabolism, sugar, fat, and protein metabolism, energy production, immune response, and biosynthesis of various secondary metabolites.Conclusions: Ksu and Kac were two ubiquitous protein post-translational modifications participated in a variety of biological processes. Our results may supply rich resources and a starting point for the molecular basic research of regulation on metabolic pathways and other biological processes by succinylation and acetylation.
Spatial Evaluation of Earthquake Disaster Based On Correlation Characteristics And BP Neural Network
Authors: Zhou Hanxu , Che Ailan , Shuai Xianghua 
Published: October 2021

Abstract
Rapid spatial evaluation of disaster after earthquake occurrence is required in the emergency rescue management, due to its significant support for decreasing casualties and property losses. The earthquake-hit population is taken as an example of earthquake disaster to construct the evaluation model using the data from the 2013 Ms7.0 Lushan earthquake. Ten influencing factors are classified into environmental factors and seismic factors. The correlation analysis reveals characteristics that there is a nonlinear relationship between the earthquake-hit population and various factors, and per capita GDP and PGA factor have a stronger correlation with earthquake-hit population. Moreover, the spatial variability of influencing factors would affect the distribution of earthquake-hit population. The earthquake-hit population is evaluated using BP neural network with optimizing training samples based on the spatial characteristics of per capita GDP and PGA factors. Different number of sample points are generated in areas with different value intervals of influencing factors, instead of the random distribution of sample points. The minimum value of RMSE (Root Mean Square Error) from testing set is 18 people/km2, showing good accuracy in the spatial evaluation of earthquake-hit population. Meanwhile, the optimizing samples considering spatial characteristics could improve the convergence speed and generalization capability comparing to random samples. The trained network was generalized to the 2017 Ms7.0 Jiuzhaigou earthquake to verify the prediction accuracy. The evaluation results indicate that BP neural network considering the correlation characteristics of factors has the capability to evaluate the seismic disaster information in space, providing more detailed information for emergency service and rescue operation.
Multi-omics Analysis of the Biomarkers and Molecular Mechanism of Rheumatoid Arthritis With Bone Destruction
Authors: Huang Qian , Su Jiang , Zhang Weihua , Chang Shengjia , Li Silin , Zhou Jun , Zhang Jie , Li Xue , Wang Tingting , Jiang Xuejun , Wu Jianhong , Zhu Jing , Zeng Fanxin 
Published: October 2021

Abstract
ObjectivesOur study aimed to elucidate the role of metabolites, bacteria, and fungi in rheumatoid arthritis (RA) patients with bone destruction (BD(+)) and find some biomarkers to predicate bone progression of RA.MethodsWe conducted plasma metabolites of the 127 RA patients and 69 healthy control by using nontargeted liquid chromatography-mass spectrometry (LC-MS), and the gut bacteria and fungi were assessed by 16S rRNA and internal transcribed spacer (ITS).ResultsCompared with RA patients without bone destruction (BD(-)), some metabolites, bacteria, and fungi altered in BD(+). Sever metabolites were selected as key metabolites for classifying the BD(+) and BD(-) groups with moderate accuracy (AUC=0.71). Metabolites-groups, metabolites-metabolites, and metabolites-clinical factors had a certain correlation, and 7 metabolites were enriched in glycerophospholipid metabolism and L-arginine and proline metabolism pathways. The bacteria and fungi of the BD(+) group showed significant differences in composition and function compared with BD(-) group. The changed 4 bacteria and 12 fungi yielded accuracy (AUC=0.74 and AUC=0.87, respectively) for the two groups. Taken 7 metabolites, 4 bacteria and 12 fungi as a panel for AUC analysis, an improved AUC of 0.99 significantly discriminated the two groups. The changed metabolites, gut bacteria, and fungi may affected the pathway related to L-arginine.ConclusionsOur nontargeted LC-MS, 16S rRNA, and ITS highlight a novel link among the metabolites, bacteria, fungi, and pathology of BD(+), which contributed to our understanding of the role of metabolites, bacteria, and fungi in BD(+) aetiology and offers some novel biomarkers to predict the bone progression of RA.
Efficacy of Sigmoidoscopy for Evaluating Disease Activity in Patients With Ulcerative Colitis
Authors: Park Su Bum , Kim Seong-Jung , Lee Jun , Lee Yoo Jin , Baek Dong Hoon , Seo Geom Seog , Kim Eun Soo , Kim Sang-Wook , Kim So Yeong 
Published: October 2021

Abstract
Background: Endoscopic assessment of disease activity is a key parameter in the management of ulcerative colitis. Whether sigmoidoscopy alone is sufficient to evaluate the disease activity in ulcerative colitis lacks studies. Methods: We retrospectively analyzed the medical records and endoscopic results of patients with ulcerative colitis followed by colonoscopy in seven tertiary hospitals between January 2012 and December 2018. Endoscopic disease activity was scored using the Mayo Endoscopic Score (MES) and Ulcerative Colitis Endoscopic Index of Severity (UCEIS) for each segment from the colonoscopy images. Concordance was evaluated by comparing the highest MES and UCEIS in the rectosigmoid and proximal regions to confirm the usefulness of sigmoidoscopy. Results: A total of 500 colonoscopic examinations from 333 patients were enrolled. Only in 7.6% [k(kappa): 0.893, r(Spearman): 0.906, p<0.001] and 8.6% [k(kappa): 0.890, r(Spearman): 0.914; p<0.001] of cases, MES and UCEIS scored more severely in the proximal colon. Comparison of active disease (MES ≥2) in the rectosigmoid area and the entire colon showed a high concordance rate [k(kappa): 0.899, r(Spearman): 0.904, p<0.001]. Endoscopic healing (MES=0) also showed a high concordance rate [k(kappa): 0.882, r(Spearman): 0.887, p<0.001]. In 38 cases (7.6%) of patients with a higher MES in the proximal area, it was significantly higher in patients with previous extensive colitisConclusions: Sigmoidoscopy and colonoscopy showed a high concordance rate. Therefore, sigmoidoscopy is considered a sufficient substitute for colonoscopy. However, colonoscopy should be considered in patients with previous extensive colitis
Effect of Human Mobility On The Spatial Spread of Airborne Diseases: An Epidemic Model With Indirect Transmission
Authors: David Jummy Funke , Iyaniwura Sarafa A. 
Published: October 2021

Abstract
We extended a class of coupled PDE-ODE models for studying the spatial spread of airborne diseases by incorporating human mobility. Human populations are modeled with patches, and a Lagrangian perspective is used to keep track of individuals’ places of residence. The movement of pathogens in the air is modeled with linear diffusion and coupled to the SIR dynamics of each human population through an integral of the density of pathogen around the population patch. In the limit of fast diffusion pathogens, the method of matched asymptotic analysis is used to reduce the coupled PDE-ODE model to a nonlinear system of ODEs for the average density of pathogens in the air. The reduced system of ODEs is used to derive the basic reproduction number and the final size relation for the model. Numerical simulations of the full PDE-ODE model and the reduced system of ODEs are used to assess the impact of human mobility, together with the diffusion of pathogens on the dynamics of the disease. Results from the two models are consistent and show that human mobility significantly affects disease dynamics. In addition, we show that an increase in the diffusion rate of pathogen leads to a smaller epidemic.