bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binding affinity improvement analysis of multiple-mutant Omicron on 2019-nCov to human ACE2 by In-silico predictions
Authors: Li Bo , Guo Jindan , Qin Chuan , Liu Jiangning , Hu Wenxiang , Chen Yubao 
Published: March 2022

Abstract
Since the outbreak of COVID-19 in 2019, the 2019-nCov coronavirus has appeared diverse mutational characteristics due to its own flexible conformation. One multiple-mutant strain (Omicron) with surprisingly infective activity outburst, and affected the biological activities of current drugs and vaccines, making the epidemic significantly difficult to prevent and control, and seriously threaten health around the world. Importunately exploration of mutant characteristics for novel coronavirus Omicron can supply strong theoretical guidance for learning binding mechanism of mutant viruses. What’s more, full acknowledgement of key mutated-residues on Omicron strain can provide new methodology of the novel pathogenic mechanism to human ACE2 receptor, as well as the subsequent vaccine development. In this research, 3D structures of 32 single-point mutations of 2019-nCov were firstly constructed, and 32-sites multiple-mutant Omicron were finally obtained based one the wild-type virus by homology modeling method. One total number of 33 2019-nCov/ACE2 complex systems were acquired by protein-protein docking, and optimized by using preliminary molecular dynamics simulations. Binding free energies between each 2019-nCov mutation system and human ACE2 receptor were calculated, and corresponding binding patterns especially the regions adjacent to mutation site were analyzed. The results indicated that one total number of 6 mutated sites on the Omicron strain played crucial role in improving binding capacities from 2019-nCov to ACE2 protein. Subsequently, we performed long-term molecular dynamic simulations and protein-protein binding energy analysis for the selected 6 mutations. 3 infected individuals, the mutants T478K, Q493R and G496S with lower binding energies − 66.36, -67.98 and − 67.09 kcal/mol also presents the high infectivity. These findings indicated that the 3 mutations T478K, Q493R and G496S play the crucial roles in enhancing binding affinity of Omicron to human ACE2 protein. All these results illuminate important theoretical guidance for future virus detection of the Omicron epidemic, drug research and vaccine development.
Identifying the lead angle limit to achieve required surface roughness in ball-end milling
Authors: Pesice Matej , Vavruska Petr , Falta Jiri , Zeman Pavel 
Published: March 2022

Abstract
When milling generally-shaped surfaces with a ball-end milling tool, machined surface roughness and accuracy as well as machining productivity are often monitored. Improving one of these parameters often causes a decrease in the other monitored parameters. Therefore, knowing possible ways of influencing these parameters is important for achieving the optimum result, if possible, in all requirements. A deep understanding of how some technological parameters influence finished surface roughness is still lacking, as well as detailed knowledge of the relationships among some roughness parameters. In response, an experiment entailing machining of planar samples at different orientation angles was carried out to identify the influence of the studied parameters on the transverse roughness of the final surface. A finding was made, that the resulting surface roughness is dependent on the cutting edge geometry of the particular ball-end milling tools used and the achieving of the required surface roughness can be guaranteed by setting the specific lead angles. Furthermore, it was verified that a minimum lead angle limit can be found based on the geometric properties of the specific milling tool, and the relationship between the evaluated roughness parameters Ra and Rz was found as well.
Genome-wide identification of R2R3-MYB gene family and association with anthocyanin biosynthesis in Brassica species
Authors: Chen Daozong , Chen Haidong , Dai Guoqiang , Zhang Haimei , Liu Yi , Shen Wenjie , Zhu Bo , Cui Cheng , Tan Chen 
Published: March 2022

Abstract
Brassica species include important oil crops and vegetables in the world. The R2R3-MYB gene participates in a variety of plant functions, including the activation or inhibition of anthocyanin biosynthesis. Although previous studies have reported its phylogenetic relationships, gene structures, and expression patterns in Arabidopsis, the number and sequence variation of this gene family in Brassica crops and its involvement in the natural quantitative variation in anthocyanin biosynthesis regulation are still largely unknown. In this study, by using whole genome sequences and comprehensive genome-wide comparative analysis among the six cultivated Brassica species, 1990 R2R3-MYB genes were identified in six Brassica species, respectively. These R2R3-MYB genes were phylogenetically clustered into 12 groups. The R2R3-MYB family between A and C subgenomes showed better collinearity than between B and C and between A and B. From comparing transcriptional changes of five Brassica species with the purple and green leaves for the detection of the R2R3-MYB genes associated with anthocyanin biosynthesis, 7 R2R3-MYB genes were co-differentially expressed. The promoter and structure analysis of these genes showed that some variations between non-coding region, but they were highly conserved at the protein level and spatial structure. Co-expression analysis of anthocyanin-related genes and R2R3-MYBs indicated that MYB90 was strongly co-expressed with TT8, and they were co-expressed with structural genes F3H, LDOX, ANS and UF3GT at the same time. These results further clarified the roles of the R2R3-MYBs for leaf coloration in Brasica species, which provided new insights into the functions of the R2R3-MYB gene family in Brasica species.
The correlation of serum IGF-1 levels with lower extremity atherosclerotic disease in type 2 diabetes patients
Authors: Liu Fentao , Mai Peipei , Li Xuan , Li Da , Zhao Wenyu , Guo Yiting , Su Jie , Wang Hua , Wang Yunlong , Zhang Yanfang 
Published: March 2022

Abstract
Objective: Clinical and basic studies have indicated the close association between Insulin-like growth factor-1 (IGF-1) and cardiovascular disease, however, the relationship between IGF-1 and lower extremity atherosclerotic disease (LEAD) has rarely been reported. Given that lower extremity arterial disease is the common macrocomplication of type 2 diabetes(T2DM), the purpose of this study was to explore the relationship between serum Insulin-like growth factor-1 levels and the presence of lower extremity atherosclerotic disease in patients with type 2 diabetes mellitus. Methods: A total of 442 hospitalized T2DM patients(371 with LEAD and 71 without LEAD) were enrolled in the study. Serum IGF-1 levels were determined by an automatic chemiluminescence assay. The LEAD was evaluated through color doppler ultrasonography. Results: Compared with patients without LEAD, patients with LEAD exhibited much lower serum IGF-1 levels [115.4 ng/mL (interquartile range = 89.6-145.2 n g/ml) versus 124 ng/mL (interquartile range = 101.3-161.5 ng/mL), repectively, P = 0.03]. Multivariate line regression analysis identified that serum IGF-1 levels were independently and negatively related to age (standardiazed β = -0.208, P <0.001) and gender (standardiazed β = -0.126, P = 0.019). However, multivariate logistic regression analysis revealed that serum IGF-1 level has no significantly relationship with the presense LEAD with OR value of 0.993 in the total population.Conclusion: In T2DM patients, though low serum IGF-1 levels were found in LEAD patients, the IGF-1 may not contribute to the presence of LEAD.
Workflow Task Scheduling Hybrid swarm intelligence in cloud Computing
Authors: Ghafir Shabina , Alam M.Afshar , Siddiqui Farheen , Naaz Sameena 
Published: March 2022

Abstract
Users may access virtual, scalable, and dynamic resources using cloud computing, which is a novel technology that charges them only for the resources they use. This technology is reliant on a network to function. Several services, like as e-commerce apps, use the whole network as a result of the sheer scope of the network. Cloud computing has progressed through three phases in terms of practical development: distributed computing, parallel computing, and grid computing. Cloud computing is a cutting-edge technology that instals networks of computers, many of which are situated in faraway locations, to conduct operations on massive amounts of data in real time. Cloud computing makes use of a workflow model to describe various scientific and web-based applications in the cloud. On the heterogeneous cloud environment, one of the most difficult problems to solve is the scheduling of massive workflows of jobs that adhere to scientific criteria. Other challenges are unique to public cloud computing, such as security and privacy. For example, customers must be happy with quality of service (QoS) metrics such as scalability and dependability, as well as the requirement to maximise end-user resource consumption rates, among other things. This study examines scheduling algorithms that are based on the Water cycle optimization principle. Specifically, it is intended to aid users in determining the most appropriate quality of service consideration for big workflows in infrastructure as a service Shabina Ghafir et al. (IaaS) cloud applications and mapping tasks to available resources. In addition, the scheduling methods are classified based on the variation of the WCA algorithm that is used to implement them. For the purpose of comparing and identifying the potency of the suggested system, the current round-robin (RR), ALO, and PSO approaches have been selected. The results showed that the suggested approach reduces the cost by 9.8 percent for GA-PSO, 10 percent for PSO, 20 percent for ALO, 30 percent for RR, and 12 percent for GA by using a combination of these techniques. The suggested solution decreases load balancing and makespan by 8 percent compared to GA-PSO, 10 percent compared to ALO, 20 percent compared to PSO, 35 percent compared to RR, and 45 percent compared to GA. Furthermore, the performance of energy consumption and reliability are both satisfactory.
Ccq1 restrains Mre11-mediated degradation of short telomeres
Authors: Audry Julien , Runge Kurt 
Published: March 2022

Abstract
Telomeres cap chromosome ends with specialized chromatin composed of DNA repeats bound by a multiprotein complex called shelterin. Fission yeast telomeres can be formed by cleaving a “proto-telomere” bearing 48 bp of telomere repeats to form a new stable chromosomal end that prevents the rapid degradation seen at similar DNA double-strand breaks (DSBs). This end-protection was investigated in viable mutants lacking telomere-associated proteins. Telomerase, the shelterin components Taz1, Rap1, or Poz1 or the telomere-associated protein Rif1 were not required to form a stable chromosome end after cleavage of the proto-telomere. However, cells lacking the fission yeast shelterin component Ccq1 converted the cleaved telomere repeat-capped end to a rapidly degraded DSB. Degradation was greatly reduced by eliminating the nuclease activity of Mre11, a component of the Mre11-Rad50-Nbs1/Xrs2 complex that processes DSBs. These results demonstrate a novel function for Ccq1 to effect end-protection by restraining Mre11-dependent degradation.
Identification of cryptic neoepitopes generated by chimeric transcripts in ovarian cancer
Authors: Dixit Vaishnavi M , Wagle Arpita K , Bapat Sharmila A 
Published: March 2022

Abstract
Background: Considerable recent interest lies in the immunogenicity of non-canonical neoantigens generated by alternative ORFs emerging from non-synonymous mutations or nucleotide insertions and deletions, exonization of untranslated regions of the genome, non-coding transcripts, transposable elements, etc. Amongst these ‘cryptic’ epitopes, those derived from chimeric transcripts which harbor sequences derived from more than one gene remain undefined, since the translational potential and immunogenicity of these transcripts is relatively unexplored.Methods: The present study was hence designed to predict and assess the neoepitopes generated by chimeric transcripts in ovarian cancer. Peptides identified in a customized targeted database were assessed for antigenicity. Further docking of peptide – MHC as well as peptide-MHC-TCR complexes provided proof-of-concept of antigenicity.Results: We identified peptides uniquely generated by chimeric transcripts, expressed by reading-frame as well as sense/anti-sense isoforms. Further assessment of the antigenicity of these peptides identified a small number of putative neoepitopes that are likely to be presented to MHC-I in an allele-specific manner, and further recognized by specific TCRs.Conclusions:Such generation of chimeric molecules by relaxed rigidity of canonical transcription and translation may present opportunities in immunotherapy.
Evaluation of the practice of antibiotic prophylaxis in a surgical setting in Mbujimayi, Democratic Republic of the Congo
Authors: Mbuyamba Hervé Tshikomba , Muamba Crispin Mukendi , Binene Séraphin Katulondi , Uwonda Séverin Akinja 
Published: March 2022

Abstract
Background: Antibiotic prophylaxis is helpful to prevent patients from developping surgical site infections. In Mbujimayi, the issue is not documented at all. The known study on the subject was conducted more than five years ago. This study aims to assess the compliance of the practice of antibiotic prophylaxis in the surgery and gyneco-obstetrics departments of the Bonzola General Reference Hospital compared to the international standard.Methods: We conducted a prospective observational study from March 2020 to March 2021 of operated patients who had been subjected to antibiotic prophylaxis.Results: Three hundred and twenty-four patients were selected for this study. Compliance for each of the criteria was 87.35% for the indication ; 0.31% for the choice of molecule ; 3.65% for the time of the first administration ; nil for the duration of antibiotic prophylaxis. So overall compliance was nil.This study shows a significant gap between the recommendations of international societies and the actual practice in Mbujimayi. It is therefore necessary to conduct further studies to identify the determinants in order to reverse the trend.Conclusion: Compliance of the practice of antibiotic prophylaxis in Mbujimayi is zero. It is therefore important to take steps to improve antibiotic prophylaxis practice to maximize harms for the benefits of patients and practitioners.
A tungsten enzyme using hydrogen as an electron donor to reduce carboxylic acids and NAD+
Authors: Winiarska Agnieszka , Hege Dominik , Gemmecker Yvonne , Kryściak-Czerwenka Joanna , Seubert Andreas , Heider Johann , Szaleniec Maciej 
Published: March 2022

Abstract
Tungsten-dependent aldehyde oxidoreductases (AOR) catalyse the oxidation of aldehydes to acids and are the only known enzymes reducing non-activated acids using electron donors with low redox potentials. We report here that AOR from Aromatoleum aromaticum (AORAa) catalyses the reduction of organic acids not only with low-potential Eu(II) or Ti(III) complexes but also with H2 as an electron donor. Additionally, AORAa catalyzes the H2-dependent reduction of NAD+ or benzyl viologen. The rate of H2 dependent NAD+ reduction equals to 10% of that of aldehyde oxidation, representing the highest H2 turnover rate observed among the Mo/W enzymes. As AORAa simultaneously catalyzes the reduction of acids and NAD+ we designed a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase to reduce organic acids to the corresponding alcohols with H2 as the only reductant. The newly discovered W-hydrogenase side-activity of AORAa may find applications in either NADH-recycling or conversion of carboxylic acids to more useful biochemicals.
Branching Pattern of the Internal Iliac Artery Accompanied by a Venous Anastomosis: Rare Vascular Variations
Authors: Kula Maciej , Olewnik Łukasz , Ruzik Kacper , Tubbs Richard Shane , Balcerzak Adrian , Zielinska Nicol 
Published: March 2022

Abstract
The ability to navigate the complex and often deceptive branching patterns of the internal iliac artery can be decisive in planning and performing surgeries within the lesser pelvis. The following case report presents a peculiar quadruple division of the internal iliac artery, accompanied by a venous anastomotic structure. Apart from the posterior and anterior trunks, the superior vesicle and iliolumbar arteries arose independently from the internal iliac artery. The division was surrounded by a venous oval, compressing certain branches and potentially complicating surgical access. Clinical significance of the case is discussed. Knowledge of this anatomical variation is significant for both diagnosis and surgery.Level of Evidence – II Basic Science Research﻿
Clinicians’ perceived quality of laboratory services provided at public hospitals and primary health centres in northeast Ethiopia
Authors: Abebe Daniel Dagne , Temesgen Minwuyelet Maru , Abozin Addisu Tesfie 
Published: March 2022

Abstract
Background
Satisfaction is a key measure of quality performance and an important tool for continual improvement. This study aimed to assess clinicians’ satisfaction with laboratory services delivered at public hospitals and health centres.
Methods
A facility-based cross-sectional study was conducted in northeast Ethiopia from May to June 2019. A total of 224 clinicians were randomly selected from 8 public hospitals and 24 health centres. Satisfaction with multiple aspects of laboratory services was assessed using a self-administered questionnaire, on a rating scale of 1 (very dissatisfied) to 5 points (very satisfied). Laboratory quality assessment was performed using WHO-AFRO’s stepwise accreditation checklist. Multivariable logistic regression model was fitted to determine the association of factors with clinicians’ overall satisfaction level using STATA ver14.1. A p- value < 0.05 was considered significant.
Results
Overall, the majority (72.8%) of clinicians were satisfied. A higher percentage of clinicians were satisfied in hospitals than in primary health centres (56.0% vs. 76.8%, p = 0.003). The lowest mean ratings were obtained for the helpfulness of the user handbook (3.3), provision of STAT/urgent services (3.7) and adequacy of the test menu provided (3.8). The clinicians’ timely receipt of results, notification of panic results and perceived reliability of results, as well as the laboratories’ concordance rate of malaria microscopy results (based on blinded slide rechecking), were significantly associated with clinicians’ satisfaction (all, p ≤ 0.036). There were no associations with socio-demographic characteristics, stepwise accreditation level or star grade of the laboratories (p- values > 0.05).
Conclusions
More clinicians were dissatisfied with the services of the larger hospital laboratories than those of the primary health centres. Improvements need to emphasize the identified specific gaps related to both users’ experiences and technical quality aspects.
Risk factors of nosocomial Covid-19 in a French university hospital: a case- control study
Authors: Dinh Claire , Gallouche Meghann , Terrisse Hugo , Gam Kamal , Giner Céline , Nemoz Benjamin , Larrat Sylvie , Giai Joris , Bosson Jean-Luc , Landelle Caroline 
Published: March 2022

Abstract
Background: During the Covid-19 pandemic, prevention strategies implemented by hospitals to reduce nosocomial transmission sometimes failed and determining transmission risk factors remains crucial. Our objective was to determine the risk factors of nosocomial Covid-19.Methods: A case-control study was conducted in a French hospital between 09/01/2020 and 01/31/2021. Adult patients hospitalized in medical or surgical units were included. Infants or patients hospitalized in ICU were excluded. Cases were patients with a nosocomial Covid-19 (clinical symptoms and RT-PCR positive for SARS-CoV-2 or RT-PCR positive for SARS-CoV-2 with Ct ≤28 more than five days after admission); controls were patients without infection (RT-PCR negative for SARS-CoV-2 more than 5 days after admission). They were matched according to length of stay before diagnosis and period of admission. Analyses were performed with a conditional logistic regression.Results: A total of 281 cases and 441 controls were included. In the bivariate analysis, cases were older (OR per 10 years: 1.22; CI95% [1.10; 1.36]), had more often shared a room (OR: 1.74; CI95% [1.25; 2.43]), had more often a risk factor of severe Covid-19 (OR: 1.94; CI95% [1.09; 3.45]), were more often hospitalized in medical units [OR: 1.59; CI95% [1.12; 2.25]), had a higher exposure to contagious health care workers (HCW; OR per 1 person.days: 1.12; CI95% [1.08; 1.17]) and contagious patients (OR per 1 person.days: 1.11; CI95% [1.08; 1.14]) than controls. In an adjusted model, risk factors of nosocomial Covid-19 were exposure to contagious HCW (aOR per 1 person.days: 1.08; CI95% [1.03; 1.14]) and exposure to contagious patients (aOR per 1 person.days: 1.10; CI95% [1.07; 1.13]).Conclusions: Exposure to contagious professionals and contagious patients are the main risk factors for nosocomial Covid-19, outweighing all other potential risk factors including the hospitalisation in double room. Prevention strategies need to be adjusted according to these results to decrease the risk of nosocomial COVID-19.Trial registrationStudy ethics approval was obtained retrospectively on 22 December 2021 (CECIC Rhône-Alpes-Auvergne, Clermont-Ferrand, IRB 5891).
HDAC10-mediated acetylation of COX5A promotes inflammatory responses of silica- treated macrophages in silicosis via the ROS/NF-κβ/TNF-α pathway
Authors: Li Shao-min , Zhao Feng , Zhu Min-xia , Zhao Wen , Xie Rong-xing , Shi Hong-yang , Li Jian-zhong 
Published: March 2022

Abstract
BackgroundSilicosis is pneumoconiosis of the lung, which usually results from prolonged exposure to and inhalation of silicon dioxide. Currently an effective treatment for silicosis is lacking. The hallmark of silicosis is chronic inflammation of silica-treated macrophages. However, the detailed molecular mechanism underlying silicosis remains elusive. MethodsSilicotic rats were established by a single intratracheal instillation of silica suspension. The lung tissues from silicotic and control rats were obtained for pathological observation, transcriptome sequencing, tandem mass tag quantitative proteomic analysis and quantitative proteome detection by acetylation modification. We further examined silica-treated macrophage-derived inflammation and the underlying molecular mechanism using siRNAs and overexpression plasmids in vitro.Results Transcriptome sequencing revealed downregulated expression of histone deacetylase 10 (HDAC10) in lungs from silicotic rats. Knockdown of HDAC10 enhanced the acetylation level of cytochrome oxidase 5A(COX5A) in rat silicosis tissue and increased reactive oxygen species (ROS), which led to increased secretion of inflammatory factors and chemokines from silica-treated macrophages. High acetylation of COX5A aggravated silica-treated macrophage-derived inflammation by the ROS/NF-κb/TNF-α pathway.ConclusionOur results indicate that HDAC10 mediates silica-treated macrophage-derived inflammation by the ROS/NF-κb/TNF-α pathway. Targeting this pathway may help improve silicosis and represents a potential therapeutic strategy to reduce inflammation and potentially treat silicosis.