bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immune correlates of protection following Rift Valley fever virus vaccination
Authors: Doyle Joshua D. , Barbeau Dominique J. , Cartwright Haley N. , McElroy Anita K. 
Published: October 2022

AbstractRift Valley fever virus (RVFV) is a hemorrhagic fever virus with the potential for significant economic and public health impact. Vaccination with an attenuated strain, DelNSsRVFV, provides protection from an otherwise lethal RVFV challenge, but mechanistic determinants of protection are undefined. In this study, a murine model was used to assess the contributions of humoral and cellular immunity to DelNSsRVFV-mediated protection. Vaccinated mice depleted of T cells were protected against subsequent challenge, and passive transfer of immune serum from vaccinated animals to naïve animals was also protective, demonstrating that T cells were dispensable in the presence of humoral immunity and that humoral immunity alone was sufficient. Animals depleted of B cells and then vaccinated were protected against challenge. Total splenocytes, but not T cells alone, B cells alone, or B + T cells harvested from vaccinated animals and then transferred to naïve animals were sufficient to confer protection, suggesting that multiple cellular interactions were required for effective cellular immunity. Together, these data indicate that humoral immunity is sufficient to confer vaccine-mediated protection and suggests that cellular immunity plays a role in protection that requires the interaction of various cellular components.
Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways
Authors: Xu Ke , Shi Xingyi , Husted Christopher , Hong Rui , Wang Yichen , Ning Boting , Sullivan Travis B. , Rieger-Christ Kimberly M. , Duan Fenghai , Marques Helga , Gower Adam C. , Xiao Xiaohui , Liu Hanqiao , Liu Gang , Duclos Grant , Platt Michael , Spira Avrum E. , Mazzilli Sarah A. , Billatos Ehab , Lenburg Marc E. , Campbell Joshua D. , Beane Jennifer E. 
Published: October 2022

AbstractSARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in the airway epithelium. The similarities and differences of VE gene expression (ACE2, TMPRSS2, and CTSL) across nasal and bronchial compartments have not been fully characterized using matched samples from large cohorts. Gene expression data from 793 nasal and 1673 bronchial brushes obtained from individuals participating in lung cancer screening or diagnostic workup revealed that smoking status (current versus former) was the only clinical factor significantly and reproducibly associated with VE gene expression. The expression of ACE2 and TMPRSS2 was higher in smokers in the bronchus but not in the nose. scRNA-seq of nasal brushings indicated that ACE2 co-expressed genes were highly expressed in club and C15orf48+ secretory cells while TMPRSS2 co-expressed genes were highly expressed in keratinizing epithelial cells. In contrast, these ACE2 and TMPRSS2 modules were highly expressed in goblet cells in scRNA-seq from bronchial brushings. Cell-type deconvolution of the gene expression data confirmed that smoking increased the abundance of several secretory cell populations in the bronchus, but only goblet cells in the nose. The association of ACE2 and TMPRSS2 with smoking in the bronchus is due to their high expression in goblet cells which increase in abundance in current smoker airways. In contrast, in the nose, these genes are not predominantly expressed in cell populations modulated by smoking. In individuals with elevated lung cancer risk, smoking-induced VE gene expression changes in the nose likely have minimal impact on SARS-CoV-2 infection, but in the bronchus, smoking may lead to higher viral loads and more severe disease.
How dynamic adsorption controls surfactant-enhanced boiling
Authors: Mata Mario R. , Ortiz Brandon , Luhar Dhruv , Evereux Vesper , Cho H. Jeremy 
Published: October 2022

AbstractImproving boiling is challenging due to the unpredictable nature of bubbles. One way to enhance boiling is with surfactants, which alter the solid–liquid and liquid–vapor interfaces. The conventional wisdom established by previous studies suggests that heat transfer enhancement is optimized near the critical micelle concentration (CMC), which is an equilibrium property that depends on surfactant type. However, these studies only tested a limited number of surfactants over small concentration ranges. Here, we test a larger variety of nonionic and anionic surfactants over the widest concentration range and find that a universal, optimal concentration range exists, irrespective of CMC. To explain this, we show that surfactant-enhanced boiling is controlled by two competing phenomena: (1) the dynamic adsorption of surfactants to the interfaces and (2) the increase in liquid dynamic viscosity at very high surfactant concentrations. This dynamic adsorption is time-limited by the millisecond-lifetime of bubbles on the boiling surface—much shorter than the timescales required to see equilibrium behaviors such as CMC. At very high concentrations, increased viscosity inhibits rapid bubble growth, reducing heat transfer. We combine the effects of adsorption and viscosity through a simple proportionality, providing a succinct and useful understanding of this enhancement behavior for boiling applications.
Theoretical and numerical analysis of COVID-19 pandemic model with non-local and non-singular kernels
Authors: Cui Ting , Liu Peijiang , Din Anwarud , Ali Fawad 
Published: October 2022

AbstractThe global consequences of Coronavirus (COVID-19) have been evident by several hundreds of demises of human beings; hence such plagues are significantly imperative to predict. For this purpose, the mathematical formulation has been proved to be one of the best tools for the assessment of present circumstances and future predictions. In this article, we propose a fractional epidemic model of coronavirus (COVID-19) with vaccination effects. An arbitrary order model of COVID-19 is analyzed through three different fractional operators namely, Caputo, Atangana-Baleanu-Caputo (ABC), and Caputo-Fabrizio (CF), respectively. The fractional dynamics are composed of the interaction among the human population and the external environmental factors of infected peoples. It gives an extra description of the situation of the epidemic. Both the classical and modern approaches have been tested for the proposed model. The qualitative analysis has been checked through the Banach fixed point theory in the sense of a fractional operator. The stability concept of Hyers-Ulam idea is derived. The Newton interpolation scheme is applied for numerical solutions and by assigning values to different parameters. The numerical works in this research verified the analytical results. Finally, some important conclusions are drawn that might provide further basis for in-depth studies of such epidemics.
Biosynthetic regulatory network of flavonoid metabolites in stems and leaves of Salvia miltiorrhiza
Authors: Yang Hanting , Li Hongyan , Li Qian 
Published: October 2022

AbstractFlavonoid secondary metabolites can treat and prevent many diseases, but systematic studies on regulation of the biosynthesis of such metabolites in aboveground parts of Salvia miltiorrhiza are lacking. In this study, metabonomic and transcriptomic analyses of different S. miltiorrhiza phenotypes were conducted to explore pathways of synthesis, catalysis, accumulation, and transport of the main flavonoid secondary metabolites regulating pigment accumulation. Tissue localization and quantitative analysis of flavonoid secondary metabolites were conducted by laser scanning confocal microscopy (LSCM). A total 3090 differentially expressed genes were obtained from 114,431 full-length unigenes in purple and green phenotypes, and 108 functional genes were involved in flavonoid biosynthesis. Five key phenylpropane structural genes (PAL, 4CL, ANS, 3AT, HCT) were highly differentially expressed, and four transcription factor genes (MYB, WRKY, bHLH, bZiP) were identified. In addition, six GST genes, nine ABC transporters, 22 MATE genes, and three SNARE genes were detected with key roles in flavonoid transport. According to LSCM, flavonoids were mainly distributed in epidermis, cortex, and collenchyma. Thus, comprehensive and systematic analyses were used to determine biosynthesis, accumulation, and transport of flavonoids in stems and leaves of different S. miltiorrhiza phenotypes. The findings will provide a reference for flavonoid production and cultivar selection.
Performance evaluation of a preclinical SPECT/CT system for multi-animal and multi-isotope quantitative experiments
Authors: Prieto Elena , Irazola Leticia , Collantes María , Ecay Margarita , Cuenca Teresa , Martí-Climent Josep Mª , Peñuelas Iván 
Published: October 2022

AbstractThe aim was to study the performance of the U-SPECT6/CT E-class system for preclinical imaging, to later demonstrate the viability of simultaneous multi-animal and multi-isotope imaging with reliable quantitative accuracy. The performance of the SPECT was evaluated for two collimators dedicated for mouse (UHS-M) and rat imaging (UHR-RM) in terms of sensitivity, energy resolution, uniformity and spatial resolution. Point sources, hot‑rod and uniform phantoms were scanned, and additional tests were carried out to evaluate singular settings such as simultaneous multi-isotope acquisition and imaging with a multi-bed system. For in-vivo evaluation, simultaneous triple-isotope and multi-animal studies were performed on mice. Sensitivity for 99mTc was 2370 cps/MBq for the UHS-M collimator and 493 cps/MBq for the UHR-RM. Rods of 0.6 mm and 0.9 mm were discernible with the UHS-M and UHR-RM collimators respectively, with optimized reconstruction. Uniformity in low counting conditions has proven to be poor (> 75%). Multi-isotope and multi-bed phantom acquisitions demonstrated accurate quantification. In mice, simultaneous multi-isotope imaging provided the separate distribution of 3 tracers and image quality of the multi-mouse bone scan was adequate. The U-SPECT6/CT E-class has shown good sensitivity and spatial resolution. This system provides quantitative images with suitable image quality for multi-mouse and multi-isotope acquisitions.
Prevalence and clinical association of sarcopenia among Thai patients with systemic sclerosis
Authors: Sangaroon Arthitaya , Foocharoen Chingching , Theerakulpisut Daris , Srichompoo Kannikar , Mahakkanukrauh Ajanee , Suwannaroj Siraphop , Seerasaporn Patpiya , Pongchaiyakul Chatlert 
Published: October 2022

AbstractPatients with systemic sclerosis (SSc) have some potential factors associated with an increased risk of sarcopenia. There has been currently no study to examine such associations in SSc patients. We aimed to determine the prevalence of sarcopenia among SSc patients and examine its association with clinical manifestations and laboratory tests. A cross-sectional study was conducted in 180 adult SSc patients at the Scleroderma Clinic, Khon Kaen University, Thailand, between July 2019 and April 2020. Clinical data, laboratory tests for inflammatory markers, serology, hormone, body composition by dual-energy X-ray absorptiometry, handgrip strength, functional lower extremity strength, and usual gait speed were collected and measured. Sarcopenia was defined according to the criteria of the Asian Working Group for Sarcopenia. One hundred and eighty patients were recruited. Ninety-four cases (52.2%) were the diffuse cutaneous SSc subset. The respective mean age and duration of disease was 58.8 ± 9.4 and 6.2 ± 5.3 years. Sarcopenia was revealed in 41 SSc patients for a prevalence of 22.8% (95% CI 12.1–34.8), while the prevalence was higher in patients with the diffuse cutaneous SSc (dcSSc) compared to the limited cutaneous SSc. BMI at the onset of SSc and C-reactive protein > 5 mg/dL were significantly associated with sarcopenia with a respective OR of 0.60 (95% CI 0.48–0.75) and 3.18 (1.06–9.54). Sarcopenia is common in patients with SSc, but the prevalence is more pronounced in the dcSSc. Inflammatory markers, particularly the CRP level, are strongly associated. BMI at the onset had a negative association with sarcopenia among SSc patients.
Phylogeny explains capture mortality of sharks and rays in pelagic longline fisheries: a global meta-analytic synthesis
Authors: Gilman Eric , Chaloupka Milani , Benaka Lee R. , Bowlby Heather , Fitchett Mark , Kaiser Michel , Musyl Michael 
Published: October 2022

AbstractApex and mesopredators such as elasmobranchs are important for maintaining ocean health and are the focus of conservation efforts to mitigate exposure to fishing and other anthropogenic hazards. Quantifying fishing mortality components such as at-vessel mortality (AVM) is necessary for effective bycatch management. We assembled a database for 61 elasmobranch species and conducted a global meta-synthesis to estimate pelagic longline AVM rates. Evolutionary history was a significant predictor of AVM, accounting for up to 13% of variance in Bayesian phylogenetic meta-regression models for Lamniformes and Carcharhiniformes clades. Phylogenetically related species may have a high degree of shared traits that explain AVM. Model-estimated posterior mean AVM rates ranged from 5% (95% HDI 0.1%–16%) for pelagic stingrays and 76% (95% HDI 49%–90%) for salmon sharks. Measures that reduce catch, and hence AVM levels, such as input controls, bycatch quotas and gear technology to increase selectivity are appropriate for species with higher AVM rates. In addition to reducing catchability, handling-and-release practices and interventions such as retention bans in shark sanctuaries and bans on shark finning and trade hold promise for species with lower AVM rates. Robust, and where applicable, phylogenetically-adjusted elasmobranch AVM rates are essential for evidence-informed bycatch policy.
Tracking footprints of artificial and natural selection signatures in breeding and non-breeding cats
Authors: Zhang Xuying , Jamwal Kokila , Distl Ottmar 
Published: October 2022

AbstractStray non-breeding cats (stray) represent the largest heterogeneous cat population subject to natural selection, while populations of the Siamese (SIAM) and Oriental Shorthair (OSH) breeds developed through intensive artificial selection for aesthetic traits. Runs of homozygosity (ROH) and demographic measures are useful tools to discover chromosomal regions of recent selection and to characterize genetic diversity in domestic cat populations. To achieve this, we genotyped 150 stray and 26 household non-breeding cats (household) on the Illumina feline 63 K SNP BeadChip and compared them to SIAM and OSH. The 50% decay value of squared correlation coefficients (r2) in stray (0.23), household (0.25), OSH (0.24) and SIAM (0.25) corresponded to a mean marker distance of 1.12 Kb, 4.55 Kb, 62.50 Kb and 175.07 Kb, respectively. The effective population size (Ne) decreased in the current generation to 55 in stray, 11 in household, 9 in OSH and 7 in SIAM. In the recent generation, the increase in inbreeding per generation (ΔF) reached its maximum values of 0.0090, 0.0443, 0.0561 and 0.0710 in stray, household, OSH and SIAM, respectively. The genomic inbreeding coefficient (FROH) based on ROH was calculated for three length categories. The FROH was between 0.014 (FROH60) and 0.020 (FROH5) for stray, between 0.018 (FROH60) and 0.024 (FROH5) for household, between 0.048 (FROH60) and 0.069 (FROH5) for OSH and between 0.053 (FROH60) and 0.073 (FROH5) for SIAM. We identified nine unique selective regions for stray through genome-wide analyses for regions with reduced heterozygosity based on FST statistics. Genes in these regions have previously been associated with reproduction (BUB1B), motor/neurological behavior (GPHN, GABRB3), cold-induced thermogenesis (DIO2, TSHR), immune system development (TSHR), viral carcinogenesis (GTF2A1), host immune response against bacteria, viruses, chemoattractant and cancer cells (PLCB2, BAHD1, TIGAR), and lifespan and aging (BUB1B, FGF23). In addition, we identified twelve unique selective regions for OSH containing candidate genes for a wide range of coat colors and patterns (ADAMTS20, KITLG, TYR, TYRO3—a MITF regulator, GPNMB, FGF7, RAB38) as well as congenital heart defects (PDE4D, PKP2) and gastrointestinal disorders (NLGN1, ALDH1B1). Genes in stray that represent unique selective events indicate, at least in part, natural selection for environmental adaptation and resistance to infectious disease, and should be the subject of future research. Stray cats represent an important genetic resource and have the potential to become a research model for disease resistance and longevity, which is why we recommend preserving semen before neutering.
A pilot study of microRNA assessment as a means to identify novel biomarkers of spontaneous osteoarthritis in dogs
Authors: Yamazaki Atsushi , Tomo Yuma , Eto Hinano , Tanegashima Koji , Edamura Kazuya 
Published: October 2022

AbstractMicroRNAs (miRNAs) are important regulators of intercellular signaling and are promising biomarkers in osteoarthritis (OA). In this study, comprehensive analysis was performed to identify miRNAs involved in the pathogenesis of spontaneous OA in dogs. Dogs diagnosed with OA based on radiography and arthroscopy of the stifle joint were included in the OA group. Dogs without any evidence of orthopedic disease were included in the unaffected group. To investigate miRNA expression levels, RNA sequencing analysis (RNA-seq) was performed in synovial tissue (OA group: n = 3, Unaffected group: n = 3) and RT-qPCR was performed in synovial tissue, synovial fluid and serum (OA group: n = 17, Unaffected group: n = 6), and compared between the two groups. The RNA-seq results showed that 57 miRNAs were significantly upregulated and 42 were significantly downregulated in the OA group. Specifically, miR-542 and miR-543 expression levels in the synovial tissue, synovial fluid, and serum were consistently higher in the OA group than in the unaffected group, suggesting that these miRNAs may be used as biomarkers for detecting canine OA. This is the first report to comprehensively analyze the expression patterns of miRNAs in the synovial tissue of dogs with spontaneous OA.
Global genomic methylation related to the degree of parasitism in cattle
Authors: de Soutello Ricardo Velludo Gomes , Rodrigues Maria Gabriela Fontanetti , Gonçalves Juliana Alencar , Bello Hornblenda Joaquina Silva , Pavan Bruno Ettore , Ramos Ester Silveira 
Published: October 2022

AbstractThe objective of the present study was to characterize a herd of 72 ½ Angus × ½ Nellore heifers, identify the resistant, resilient and susceptible animals to parasites, relate the overall DNA methylation of these animals with the degree of parasitism, evaluated by the egg count per gram of feces (EPG), Haematobia irritans count (horn fly) and Rhipicephalus microplus count (bovine tick). The experiment was carried out in a completely randomized design, containing 72 treatments, with each animal considered a treatment, and 11 repetitions, with each collection within a year considered a repetition. The data obtained from the counts of the evaluated parasites were subjected to statistical analysis using the SISVAR program, to classify heifers according to the degree of parasitism in low (resistant), intermediary (resilient) and high (susceptible) parasite load for infection by nematodes, infestation by ticks and flies. Addition the animals in these three groups, by hierarchical grouping using the GENES program, heifers were classified as to the degree of parasitism by the three parasites along with the DNA methylation content of the animals in each group. A negative relationship was observed between resistance and methylated DNA content in both classifications, with the resistant, resilient, and susceptible animals showing the highest, intermediate, and lowest methylated DNA quantifications, respectively. Thus, the methodologies used herein enabled the classification of 72 heifers according to the degree of collective infection by gastrointestinal nematodes and infestation by ticks and horn flies, thereby establishing a link between the degree of parasitic resistance in cattle and the global methylated DNA quantification.
Growth characteristics of Cunninghamia lanceolata in China
Authors: Jiang Yangao , Hu Zhe , Han Zhiguang , Zhang Junhui , Han Shijie , Hao Lin 
Published: October 2022

AbstractChinese fir (Cunninghamia lanceolata) is one of southern China's most important native tree species, which has experienced noticeable climate-induced changes. Published papers (1978–2020) on tree growth of Chinese fir forests in China were collected and critically reviewed. After that, a comprehensive growth data set was developed from 482 sites, which are distributed between 102.19° and 130.07°E in longitude, between 21.87° and 37.24°N in latitude and between 5 and 2260 m in altitude. The dataset consists of 2265 entries, including mean DBH (cm), mean H (m), volume (m3), biomass (dry weight) (kg) (stem (over bark) biomass, branches biomass, leaves biomass, bark biomass, aboveground biomass, roots biomass, total trees biomass) and related information, i.e. geographical location (Country, province, study site, longitude, latitude, altitude, slope, and aspect), climate (mean annual precipitation-MAP and mean annual temperature-MAT), stand description (origin, age, canopy density and stand density), and sample regime (plot size, number and investigation year). Our results showed that (1) the best prediction of height was obtained using nonlinear composite model Height = $$1.3 + 34.23*(1 - {\text{e}}^{{\left( { - 0.01025*{\text{DBH}}^{1.347} } \right)}} )$$

1.3
+
34.23

∗
(
1
-

e

-
0.01025

∗

DBH

1.347

)

, (R2 = 0.8715, p < 0.05), (2) the equation Volume = DBH2/(387.8 + 19,190/Height) (R2 = 0.9833, p < 0.05) was observed to be the most suitable model for volume estimation. Meanwhile, when the measurements of the variables are difficult to carry out, the volume model Volume = 0.03957 − 0.01215*DBH + 0.00118*DBH2 (R2 = 0.9573, p < 0.05) is determined from DBH only has a practical advantage, (3) the regression equations of component biomass against DBH explained more significant than 86% variability in almost all biomass data of woody tissues, which were ranked as total trees (97.25%) > aboveground (96.55%) > stems (with bark) (96.17%) > barks (88.95%) > roots (86.71%), and explained greater than 64% variability in branch biomass. The foliage biomass equation was the poorest among biomass components (R2 = 0.6122). The estimation equations derived in this study are particularly suitable for the Chinese fir forests in China. This dataset can provide a theoretical basis for predicting and assessing the potential of carbon sequestration and afforestation activities of Chinese fir forests on a national scale.