bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
Authors: Khanum Sofia , Carbone Vincenzo , Gupta Sandeep K. , Yeung Juliana , Shu Dairu , Wilson Tania , Parlane Natalie A. , Altermann Eric , Estein Silvia M. , Janssen Peter H. , Wedlock D. Neil , Heiser Axel 
Published: June 2022

AbstractIn silico prediction of epitopes is a potentially time-saving alternative to experimental epitope identification but is often subject to misidentification of epitopes and may not be useful for proteins from archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigen from the methanogenMethanobrevibacter ruminantiumM1, the Big_1 domain (AdLP-D1, amino acids 19–198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cover the Big_1 domain. Peptide-specific antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specific T-cell responses. Overall, five peptides of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validated epitopes were found in the outside region of the protein, with loop like secondary structures reflecting their flexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identified by in silico predictions were not comparable to those determined empirically.
Absence of causal association between Vitamin D and bone mineral density across the lifespan: a Mendelian randomization study
Authors: Tang Yanchao , Wei Feng , Yu Miao , Zhou Hua , Wang Yongqiang , Cui Zhiyong , Liu Xiaoguang 
Published: June 2022

AbstractVitamin D deficiency is a candidate risk factor for osteoporosis, characterized by decreased bone mineral density (BMD). We performed this two-sample Mendelian randomization (MR) analysis to investigate the causal effect of vitamin D on BMD. We extracted 143 single-nucleotide polymorphisms from a recent GWAS on 417,580 participants of European ancestry as instrumental variables, and used summary statistics for BMD at forearm (n = 10,805), femoral neck (n = 49,988), lumbar spine (n = 44,731) and total-body of different age-stages (< 15, 15–30, 30–45, 45–60, > 60) (n = 67,358). We explored the direct effect of vitamin D on BMD with an adjusted body mass index (BMI) in a multivariable MR analysis. We found no support for causality of 25-hydroxyvitamin D on BMD at forearm, femoral neck, lumbar spine, and total-body BMD across the lifespan. There was no obvious difference between the total and direct effect of vitamin D on BMD after adjusting for BMI. Our MR analysis provided evidence that genetically determined vitamin D was not causally associated with BMD in the general population. Large-scale randomized controlled trials are warranted to investigate the role of vitamin D supplementation in preventing osteoporosis in the high-risk population.
Macaca fascicularis and Macaca nemestrina infected with zoonotic malaria parasites are widely distributed in Sarawak, Malaysian Borneo
Authors: Nada-Raja Thamayanthi , Kadir Khamisah A. , Divis Paul C. S. , Mohamad Dayang S. A. , Matusop Asmad , Singh Balbir 
Published: June 2022

AbstractHuman infections with Plasmodium knowlesi, a malaria parasite of Macaca fascicularis and Macaca nemestrina (long-tailed and pig-tailed macaques respectively), occur throughout Southeast Asia, especially Malaysian Borneo. Other naturally-acquired human infections with malaria parasites from macaques in Southeast Asia are P. cynomolgi, P. inui-like, P. coatneyi and P. simiovale. In Sarawak, Malaysian Borneo, M. fascicularis and M. nemestrina from only the Kapit Division have been examined previously for malaria parasites. In order to determine the distribution of P. knowlesi and other zoonotic malaria parasites, 73 macaque blood samples derived from 7 other administrative divisions in Sarawak were studied. Of 45 blood samples from M. fascicularis and 28 from M. nemestrina tested by nested PCR assays, 23 (51.1%) M. fascicularis and 15 (53.6%) M. nemestrina samples were positive for Plasmodium DNA. Thirty-two of these macaques from 7 divisions sampled, harboured either single (n = 12), double (n = 9), triple (n = 7) or quadruple (n = 4) infections of P. knowlesi, P. inui, P. cynomolgi and P. coatneyi, while the infecting species of Plasmodium could not be identified for 6 samples. P. knowlesi was detected in 15.5% (7/45) M. fascicularis and in 7.1% (2/28) M. nemestrina sampled. Despite the small number of samples analysed from each administrative division, the current study indicates that macaques infected with the zoonotic malaria parasites P. knowlesi, P. cynomolgi, P. inui and P. coatneyi are widely distributed throughout Sarawak, Malaysian Borneo. Travelers to forested areas in Sarawak should be made aware of the potential risk of acquiring zoonotic malaria.
Molecular mechanisms associated with microbial biostimulant-mediated growth enhancement, priming and drought stress tolerance in maize plants
Authors: Lephatsi Motseoa , Nephali Lerato , Meyer Vanessa , Piater Lizelle A. , Buthelezi Nombuso , Dubery Ian A. , Opperman Hugo , Brand Margaretha , Huyser Johan , Tugizimana Fidele 
Published: June 2022

AbstractMicrobial-based biostimulants are emerging as effective strategies to improve agricultural productivity; however, the modes of action of such formulations are still largely unknown. Thus, herein we report elucidated metabolic reconfigurations in maize (Zea mays) leaves associated with growth promotion and drought stress tolerance induced by a microbial-based biostimulant, a Bacillus consortium. Morphophysiological measurements revealed that the biostimulant induced a significant increase in biomass and enzymatic regulators of oxidative stress. Furthermore, the targeted metabolomics approach revealed differential quantitative profiles in amino acid-, phytohormone-, flavonoid- and phenolic acid levels in plants treated with the biostimulant under well-watered, mild, and severe drought stress conditions. These metabolic alterations were complemented with gene expression and global DNA methylation profiles. Thus, the postulated framework, describing biostimulant-induced metabolic events in maize plants, provides actionable knowledge necessary for industries and farmers to confidently and innovatively explore, design and fully implement microbial-based formulations and strategies into agronomic practices for sustainable agriculture and food production.
A piecewise sine waveguide for terahertz traveling wave tube
Authors: Zhang Luqi , Jiang Yi , Lei Wenqiang , Hu Peng , Guo Jun , Song Rui , Tang Xianfeng , Ma Guowu , Chen Hongbin , Wei Yanyu 
Published: June 2022

AbstractIn this paper, a piecewise sine waveguide (PWSWG) is proposed as the slow-wave structure (SWS) to develop high-power terahertz (THz) traveling wave tubes (TWTs). The PWSWG is an improvement over the rectangular waveguide wherein its two E-planes simultaneously oscillate up and down along the longitudinal direction. The oscillation curve in the H-plane is a piecewise sine curve formed by inserting line segments into the peaks and troughs of the sine curve. The simulation analysis and experimental verification show that the PWSWG offers the advantages of large interaction impedance and excellent electromagnetic transmission performance. Furthermore, the calculation results of beam–wave interaction show that the TWT based on PWSWG SWS can generate a radiated power of 253.1 W at the typical frequency of 220 GHz, corresponding to a gain of 37.04 dB and an interaction efficiency of 6.92%. Compared with the conventional SWG TWTs, the PWSWG TWT has higher interaction efficiency and shorter saturation tube length. In conclusion, the PWSWG proposed in this paper can be considered a suitable SWS for high-power THz radiation sources.
Modeling and characterization of the electrical conductivity on metal nanoparticles/carbon nanotube/polymer composites
Authors: Wang Yang , Lu Sijian , He Wenke , Gong Shen , Zhang Yunqian , Zhao Xinsi , Fu Yuanyuan , Zhu Zhenghong 
Published: June 2022

AbstractFlexible conductive films have good deformability and conductivity, and are expected to be used in flexible electronic devices. In this paper, four kinds of flexible conductive films were successfully prepared by compounding nano-sized metal (Ni, Cu, Au or AuCu alloy) particles to CNT surface and then dispersing to polydimethylsiloxane matrix. Experiment results show that the conductivity of these prepared films are almost two orders of magnitude higher than that of CNT/polydimethylsiloxane films with the same CNT loadings. A simulation model based on percolation network theory and Monte Carlo technology is introduced to study the influence of nanoparticles on the composite conductivity. Results confirmed that the introduction of nanoparticles effectively reduces the effective resistance of CNT and the tunnelling resistance at CNT junctions. The intrinsic conductivity and the length diameter ratio of CNT, the intrinsic conductivity, the size and the coverage ratio of nanoparticles are the core parameters affecting the conductivity of composite. Compared with CNT/polydimethylsiloxane films, the optimized theoretical conductivity of these nano-sized particles enhanced composites can be further improved.
Optimization and prediction of tribological behaviour of filled polytetrafluoroethylene composites using Taguchi Deng and hybrid support vector regression models
Authors: Ibrahim Musa Alhaji , Çamur Hüseyin , Savaş Mahmut A. , Abba S. I. 
Published: June 2022

AbstractThis study presents optimization and prediction of tribological behaviour of filled polytetrafluoroethylene (PTFE) composites using hybrid Taguchi and support vector regression (SVR) models. To achieve the optimization, Taguchi Deng was employed considering multiple responses and process parameters relevant to the tribological behaviour. Coefficient of friction (µ) and specific wear rate (Ks) were measured using pin-on-disc tribometer. In this study, load, grit size, distance and speed were the process parameters. An L27orthogonal array was applied for the Taguchi experimental design. A set of optimal parameters were obtained using the Deng approach for multiple responses of µ and KS. Analysis of variance was performed to study the effect of individual parameters on the multiple responses.To predict µ and Ks, SVR was coupled with novel Harris Hawks’ optimization (HHO) and swarm particle optimization (PSO) forming SVR-HHO and SVR-PSO models respectively, were employed. Four model evaluation metrics were used to appraise the prediction accuracy of the models. Validation results revealed enhancement under optimal test conditions. Hybrid SVR models indicated superior prediction accuracy to single SVR model. Furthermore, SVR-HHO outperformed SVR-PSO model. It was found that Taguchi Deng, SVR-PSO and SVR-HHO models led to optimization and prediction with low cost and superior accuracy.
The Pseudomonas aeruginosa DksA1 protein is involved in H2O2 tolerance and within-macrophages survival and can be replaced by DksA2
Authors: Fortuna Alessandra , Collalto Diletta , Schiaffi Veronica , Pastore Valentina , Visca Paolo , Ascenzioni Fiorentina , Rampioni Giordano , Leoni Livia 
Published: June 2022

AbstractIn Gram-negative pathogens, the stringent response regulator DksA controls the expression of hundreds of genes, including virulence-related genes. Interestingly, Pseudomonas aeruginosa has two functional DksA paralogs: DksA1 is constitutively expressed and has a zinc-finger motif, while DksA2 is expressed only under zinc starvation conditions and does not contain zinc. DksA1 stimulates the production of virulence factors in vitro and is required for full pathogenicity in vivo. DksA2 can replace these DksA1 functions. Here, the role of dksA paralogs in P. aeruginosa tolerance to H2O2-induced oxidative stress has been investigated. The P. aeruginosa dksA1 dksA2 mutant showed impaired H2O2 tolerance in planktonic and biofilm-growing cultures and increased susceptibility to macrophages-mediated killing compared to the wild type. Complementation with either dksA1 or dksA2 genes restored the wild type phenotypes. The DksA-dependent tolerance to oxidative stress involves, at least in part, the positive transcriptional control of both katA and katE catalase-encoding genes. These data support the hypothesis that DksA1 and DksA2 are eco-paralogs with indistinguishable function but optimal activity under different environmental conditions, and highlight their mutual contribution to P. aeruginosa virulence.
Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome
Authors: Ishihara Shinya , Kumagai Masahiko , Arakawa Aisaku , Taniguchi Masaaki , Cuc Ngo Thi Kim , Pham Lan Doan , Mikawa Satoshi , Kikuchi Kazuhiro 
Published: June 2022

AbstractThe Vietnamese native pig (VnP)—a porcine breed with a small body—has proven suitable as a biomedical animal model. Here, we demonstrate that, compared to other breeds, VnPs have fewer copies of porcine endogenous retroviruses (PERVs), which pose a risk for xenotransplantation of pig organs to humans. More specifically, we sought to characterize non-reference PERVs (nrPERVs) that were previously unidentified in the reference genome. To this end, we used whole-genome sequencing data to identify nrPERV loci with long terminal repeat (LTR) sequences in VnPs. RetroSeq was used to estimate nrPERV loci based on the most current porcine reference genome (Sscrofa11.1). LTRs were detected using de novo sequencing read assembly near the loci containing the target site duplication sequences in the inferred regions. A total of 21 non-reference LTR loci were identified and separated into two subtypes based on phylogenetic analysis. Moreover, PERVs within the detected LTR loci were identified, the presence of which was confirmed using conventional PCR and Sanger sequencing. These novel loci represent previously unknown PERVs as they have not been identified in the porcine reference genome. Thus, our RetroSeq method accurately detects novel PERV loci, and can be applied for development of a useful biomedical model.
Optimization design of the large area Dynode-MCP-PMT
Authors: Chen Lin , Wang Xingchao , He Jianli , Tian Liping , Tian Jinshou , Wang Qilong , Wang Yunji , Yang Jie , Qian Junshuo , Zhang Fan 
Published: June 2022

AbstractThe optimization work of a newly proposed 20-in. photomultiplier tube based on dynode and microchannel plates (Dynode-MCP-PMT) are conducted in this paper. Three-dimensional models are developed in CST STUDIO SUITE to systematically investigate the effects of the size and bias voltage of the two focusing electrodes, dynode and the glass envelop handle based on the Finite Integral Technique and Monte Carlo method. Results predict that the collection efficiency and the transit time spread of the optimized design are substantially improved which are 100% and 3.7 ns.
Association of national and regional lockdowns with COVID-19 infection rates in Pune, India
Authors: Mave Vidya , Shaikh Arsh , Monteiro Joy Merwin , Bogam Prasad , Pujari Bhalchandra S. , Gupte Nikhil 
Published: June 2022

AbstractAssessing the impact of lockdowns on COVID-19 incidence may provide important lessons for management of pandemic in resource-limited settings. We examined growth of incident confirmed COVID-19 patients before, during and after lockdowns during the first wave in Pune city that reported the largest COVID-19 burden at the peak of the pandemic. Using anonymized individual-level data captured by Pune’s public health surveillance program between February 1st and September 15th 2020, we assessed weekly incident COVID-19 patients, infection rates, and epidemic curves by lockdown status (overall and by sex, age, and population density) and modelled the natural epidemic using the compartmental model. Effect of lockdown on incident patients was assessed using multilevel Poisson regression. We used geospatial mapping to characterize regional spread. Of 241,629 persons tested for SARS-CoV-2, 64,526 (26%) were positive, contributing to an overall rate of COVID-19 disease of 267·0 (95% CI 265·3–268·8) per 1000 persons. The median age of COVID-19 patients was 36 (interquartile range [IQR] 25–50) years, 36,180 (56%) were male, and 9414 (15%) were children < 18 years. Epidemic curves and geospatial mapping showed delayed peak of the patients by approximately 8 weeks during the lockdowns as compared to modelled natural epidemic. Compared to a subsequent unlocking period, incident COVID-19 patients were 43% lower (IRR 0·57, 95% CI 0·53–0·62) during India’s nationwide lockdown and were 22% lower (IRR 0·78, 95% CI 0.73–0.84) during Pune’s regional lockdown and was uniform across age groups and population densities. Both national and regional lockdowns slowed the COVID-19 infection rates in population dense, urban region in India, underscoring its impact on COVID-19 control efforts.
Impact of Navier’s slip and chemical reaction on the hydromagnetic hybrid nanofluid flow and mass transfer due to porous stretching sheet
Authors: Mahabaleshwar U. S. , Anusha T. , Bég O. Anwar , Yadav Dhananjay , Botmart Thongchai 
Published: June 2022

AbstractHybrid nanofluids (HNFs) comprise combinations of different nanoparticles suspended in base fluid. Applications of such nanofluids are rising in the areas of energy and biomedical engineering including smart (functional) coatings. Motivated by these developments, the present article examines theoretically the magnetohydrodynamic coating boundary layer flow of HNFs from a stretching sheet under the transverse magnetic field in porous media with chemically reactive nanoparticles. Darcy’s law is deployed. Momentum slips of both first and second order are included as is solutal slip. The transformed boundary value problem is solved analytically. Closed form solutions for velocity are derived in terms of exponential functions and for the concentration field in terms of incomplete Gamma functions by the application of the Laplace transformation technique. The influence of selected parameters e.g. suction/injection, magnetic field and slips on velocity and concentration distributions are visualized graphically. Concentration magnitudes are elevated with stronger magnetic field whereas they are suppressed with greater wall solutal slip. Magnetic field suppresses velocity and increases the thickness of the hydrodynamic boundary layer. The flow is accelerated with reduction in inverse Darcy number and stronger suction direct to reduce in skin friction. The concentration magnitudes are boosted with magnetic field whereas they are depleted with increasing solutal slip. The analysis provides a good foundation for further investigations using numerical methods.
Spatial distribution and source apportionment of heavy metal(loid)s in urban topsoil in Mianyang, Southwest China
Authors: Du Huaming , Lu Xinwei 
Published: June 2022

AbstractSpatial distributions and sources of some commonly concerned heavy metal(loid)s (HMs, As, Ba, Cr, Co, Cu, Ni, Pb, Mn, Zn, and V) in topsoil of Mianyang city, a typical medium-sized emerging industrial city in Southwest China, were determined to explore the influences of anthropogenic activities on the urban environment. The contents of the 10 HMs in 101 topsoil samples were analyzed using an X-ray fluorescence spectrometer, and their sources were analyzed by positive matrix factorization and statistical analysis. The spatial distributions of the HMs and the source contributions were mapped using GIS technology. The results showed that the mean contents of Ba, Cr, Cu, and Zn in the topsoil were significantly higher than their background values. Industrial activities resulted in high contents of Ba, Zn, Cu, and Cr. As, Co, Ni, and V that primarily came from natural sources; Pb, Cr, Cu, and Zn were chiefly derived from a mixed source of industry and traffic; and Ba and Mn primarily originated from industrial sources. Natural sources, mixed sources, and industrial sources contributed 32.6%, 34.4%, and 33.0% of the total HM contents, respectively. Industrial sources and mixed sources of industry and traffic were the main anthropogenic sources of HMs in the urban topsoil and should be the focus of pollution control.
Secular trends in physical fitness of Slovenian boys and girls aged 7 to 15 years from 1989 to 2019: a population-based study
Authors: Radulović Ana , Jurak Gregor , Leskošek Bojan , Starc Gregor , Blagus Rok 
Published: June 2022

AbstractUsing the population-based data we aim to estimate the general population trends of multiple components of physical fitness of children, identify critical structural changes in these trends, and evaluate the potential changes in differences in the test scores between the children. During the entire study period, 1989–2019, median body mass index and triceps skinfold increased in both genders and all age groups. Muscular fitness, in general, showed negative trends, with some exceptions: during the post-2010 period, children were mostly experiencing the improvement of isometric strength of the upper body. The neuromuscular components of physical fitness showed positive trends, especially in girls. Cardiorespiratory fitness has been declining in all age groups until the last decade, with the largest decreases occurring before 2000. In the last decade, the trends reversed. The flexibility indicator revealed the largest differences between boys and girls, with boys mainly experiencing negative and girls mostly positive trends. The variability of the test scores mostly increased during the study period. This increasing variance suggests that—despite generally favourable trends in the last decade—children in Slovenia have been facing increasing inequalities in their development, which can potentially lead to future inequalities in health.
Biological approach synthesis and characterization of iron sulfide (FeS) thin films from banana peel extract for contamination of environmental remediation
Authors: Saka Abel , Jule Leta Tesfaye , Soressa Shuma , Gudata Lamessa , Nagaprasad N. , Seenivasan Venkatesh , Ramaswamy Krishnaraj 
Published: June 2022

AbstractBiological approach synthesis and characterization of Iron Sulfide (FeS) thin films from banana peel extract for contamination remediation of environment studied. Iron chloride, Sodium thiosulfate and Ethylene-di-amine-tetra acetate (EDTA) were used as precursor solutions without further purification. The nanoparticle of banana peel was extracted and prepared with synthesized FeS thin films and analyzed by X ray-diffraction for structural examination, Scanning electron microscope (SEM) for surface morphological analysis, Ultra-violet-visible-spectrometer (UV–Vis) and photo-luminescence spectro-photo-meter (P-L) for optical characterizations. XRD peaks are shown with recognized to (110), (200), (310), and (301) crystalline planes. The occurrence of this deflection peak are recognised the FeS crystal segment of the tetragonal crystalline systems. SEM micrographs of the films prepared biological method show the distribution of grains, which cover the surface of the substrate completely and are uniform and films deposited purely have defects. The photo-luminescence, absorbance, and transmittance strength of banana peel extract FeS thin film is greater than pure FeS thin films in which wide-ranging and symmetries groups were perceived. In the present study, the comparison of pure FeS thin films and Nano synthesized banana peel extract with FeS thin films was studied. It is observed that Nano synthesized banana fibre absorbs higher than pure FeS thin films in solar cell application. Finally, green synthesis is an ecofriendly, easy and cheap promising method for the fabrication of thin films for solar cell applications.