bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of loci associated with susceptibility to bovine paratuberculosis and with the dysregulation of the MECOM, eEF1A2, and U1 spliceosomal RNA expression
Authors: Canive Maria , Fernandez-Jimenez Nora , Casais Rosa , Vázquez Patricia , Lavín José Luis , Bilbao José Ramón , Blanco-Vázquez Cristina , Garrido Joseba M. , Juste Ramón A. , Alonso-Hearn Marta 
Published: January 2021

AbstractAlthough genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with the susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infection, only a few functional mutations for bovine paratuberculosis (PTB) have been characterized. Expression quantitative trait loci (eQTLs) are genetic variants typically located in gene regulatory regions that alter gene expression in an allele-specific manner. eQTLs can be considered as functional links between genomic variants, gene expression, and ultimately phenotype. In the current study, peripheral blood (PB) and ileocecal valve (ICV) gene expression was quantified by RNA-Seq from fourteen Holstein cattle with no lesions and with PTB-associated histopathological lesions in gut tissues. Genotypes were generated from the Illumina LD EuroG10K BeadChip. The associations between gene expression levels (normalized read counts) and genetic variants were analyzed by a linear regression analysis using R Matrix eQTL 2.2. This approach allowed the identification of 192 and 48 cis-eQTLs associated with the expression of 145 and 43 genes in the PB and ICV samples, respectively. To investigate potential relationships between these cis-eQTLs and MAP infection, a case–control study was performed using the genotypes for all the identified cis-eQTLs and phenotypical data (histopathology, ELISA for MAP-antibodies detection, tissue PCR, and bacteriological culture) of 986 culled cows. Our results suggested that the heterozygous genotype in the cis-eQTL-rs43744169 (T/C) was associated with the up-regulation of the MDS1 and EVI1 complex (MECOM) expression, with positive ELISA, PCR, and bacteriological culture results, and with increased risk of progression to clinical PTB. As supporting evidence, the presence of the minor allele was associated with higher MECOM levels in plasma samples from infected cows and with increased MAP survival in an ex-vivo macrophage killing assay. Moreover, the presence of the two minor alleles in the cis-eQTL-rs110345285 (C/C) was associated with the dysregulation of the eukaryotic elongation factor 1-α2 (eEF1A2) expression and with increased ELISA (OD) values. Finally, the presence of the minor allele in the cis-eQTL rs109859270 (C/T) was associated with the up-regulation of the U1 spliceosomal RNA expression and with an increased risk of progression to clinical PTB. The introduction of these novel functional variants into marker-assisted breeding programs is expected to have a relevant effect on PTB control.
Southward spreading of the Changjiang Diluted Water in the La Niña spring of 2008
Authors: Chen Chen-Tung Arthur , Bai Yan , Huang Ting-Hsuan , He Xianqiang , Chen Hsien-Wen , Yu Shujie 
Published: January 2021

AbstractThe La Niña of 2007/2008 was particularly strong, so was the southward flow of the cold, nutrient-rich Changjiang (Yangtze River) Diluted Water (CDW) when the winter monsoon started to blow in the fall. Here we use shipboard data in 2008 in two transects, one in the southwestern East China Sea and one in the southern Taiwan Strait, to show that as late as April in 2008 the CDW was still clearly identifiable when the winter monsoon had weakened. Waters as cold as 16 °C with a salinity lower than 30 still occupied the southwestern East China Sea. Waters of 17 °C and S < 32 could also be found off the coast of China in the central Taiwan Strait. The concentration of NO3 + NO2 was higher than 18 μmol L−1 at both places, which was as much as 40 times higher than the northward moving South China Sea (SCS) water to the east. As a result, the Changjiang River plume may be a significant source of nutrients, particularly N, to the oligotrophic, N-poor SCS, especially in the La Niña years. Indeed, colder and more turbid CDW was more intense and went farther south in 2008 compared with the normal springs of 2006, 2007 and 2009.
Biological autoluminescence as a noninvasive monitoring tool for chemical and physical modulation of oxidation in yeast cell culture
Authors: Bereta Martin , Teplan Michal , Chafai Djamel Eddine , Radil Roman , Cifra Michal 
Published: January 2021

AbstractNormal or excessive oxidative metabolism in organisms is essential in physiological and pathophysiological processes, respectively. Therefore, monitoring of biological oxidative processes induced by the chemical or physical stimuli is nowadays of extreme importance due to the environment overloaded with various physicochemical factors. Current techniques typically require the addition of chemical labels or light illumination, which perturb the samples to be analyzed. Moreover, the current techniques are very demanding in terms of sample preparation and equipment. To alleviate these limitations, we propose a label-free monitoring tool of oxidation based on biological autoluminescence (BAL). We demonstrate this tool on Saccharomyces cerevisiae cell culture. We showed that BAL can be used to monitor chemical perturbation of yeast due to Fenton reagents initiated oxidation—the BAL intensity changes with hydrogen peroxide concentration in a dose-dependent manner. Furthermore, we also showed that BAL reflects the effects of low-frequency magnetic field on the yeast cell culture, where we observed a disturbance of the BAL kinetics in the exposed vs. control case. Our results contribute to the development of novel techniques for label-free, real-time, noninvasive monitoring of oxidative processes and approaches for their modulation.
Impact of 12-month cryopreservation on endogenous DNA damage in whole blood and isolated mononuclear cells evaluated by the comet assay
Authors: Marino Mirko , Gigliotti Letizia , Møller Peter , Riso Patrizia , Porrini Marisa , Del Bo Cristian 
Published: January 2021

AbstractThe comet assay is an electrophoretic technique used to assess DNA damage, as a marker of genotoxicity and oxidative stress, in tissues and biological samples including peripheral blood mononuclear cells (PBMCs) and whole blood (WB). Although numerous studies are performed on stored samples, the impact of cryopreservation on artifactual formation of DNA damage is not widely considered. The present study aims to evaluate the impact of storage at different time-points on the levels of strand breaks (SBs) and formamidopyrimidine DNA glycosylase (Fpg)-sensitive sites in isolated PBMCs and WB. Samples were collected, aliquoted and stored at − 80 °C. DNA damage was analyzed on fresh samples, and subsequently on frozen samples every 2 months up to a year. Results have shown no changes in DNA damage in samples of PBMCs and WB stored for up to 4 months, while a significant increase in SBs and Fpg-sensitive sites was documented starting from 6-month up to 12-month storage of both the samples. In addition, fresh and frozen WB showed higher basal levels of DNA damage compared to PBMCs. In conclusion, WB samples show high levels of DNA damage compared to PBMCs. One-year of storage increased the levels of SBs and Fpg-sensitive sites especially in the WB samples. Based on these findings, the use of short storage times and PBMCs should be preferred because of low background level of DNA damage in the comet assay.
Pseudomonas aeruginosa OprF plays a role in resistance to macrophage clearance during acute infection
Authors: Moussouni Malika , Berry Laurence , Sipka Tamara , Nguyen-Chi Mai , Blanc-Potard Anne-Béatrice 
Published: January 2021

AbstractWhile considered an extracellular pathogen, Pseudomonas aeruginosa has been reported to be engulfed by macrophages in cellular and animal models. However, the role of macrophages in P. aeruginosa clearance in vivo remains poorly studied. The major outer membrane porin OprF has been recently shown to be involved in P. aeruginosa fate within cultured macrophages and analysis of an oprF mutant may thus provide insights to better understand the relevance of this intramacrophage stage during infection. In the present study, we investigated for the first time the virulence of a P. aeruginosa oprF mutant in a vertebrate model that harbors functional macrophages, the zebrafish (Danio rerio) embryo, which offers powerful tools to address macrophage–pathogen interactions. We established that P. aeruginosa oprF mutant is attenuated in zebrafish embryos in a macrophage-dependent manner. Visualization and quantification of P. aeruginosa bacteria phagocytosed by macrophages after injection into closed cavities suggested that the attenuated phenotype of oprF mutant is not linked to higher macrophage recruitment nor better phagocytosis than wild-type strain. Using cultured macrophages, we showed an intramacrophage survival defect of P. aeruginosa oprF mutant, which is correlated with elevated association of bacteria with acidic compartments. Notably, treatment of embryos with bafilomycin, an inhibitor of acidification, increased the sensibility of embryos towards both wild-type and oprF mutant, and partially suppressed the attenuation of oprF mutant. Taken together, this work supports zebrafish embryo as state-of-the-art model to address in vivo the relevance of P. aeruginosa intramacrophage stage. Our results highlight the contribution of macrophages in the clearance of P. aeruginosa during acute infection and suggest that OprF protects P. aeruginosa against macrophage clearance by avoiding bacterial elimination in acidified phagosomes.
Chemical staining of particulate organic matter for improved contrast in soil X-ray µCT images
Authors: Maenhout Peter , De Neve Stefaan , Wragg Joanna , Rawlins Barry , De Pue Jan , Van Hoorebeke Luc , Cnudde Veerle , Sleutel Steven 
Published: January 2021

AbstractDegradability of organic matter (OM) in soil depends on its spatial location in the soil matrix. A recent breakthrough in 3D-localization of OM combined dual-energy X-ray CT-scanning with OsO4 staining of OM. The necessity for synchrotron-based µCT and the use of highly toxic OsO4 severely limit applications in soil biological experiments. Here, we evaluated the potential of alternative staining agents (silver nitrate, phosphomolybdenic acid (PMA), lead nitrate, lead acetate) to selectively enhance X-ray attenuation and contrast of OM in CT volumes of soils containing specific mineral soil particle fractions, obtained via lab-based X-ray µCT. In comparison with OsO4, administration of Ag+ and Pb2+ resulted in insufficient contrast enhancement of OM versus fine silt (< 20 µm) or clay (< 2 µm) mineral particles. The perfusion procedure used in this work induced changes in soil structure. In contrast, PMA staining resulted in a selective increase of OM’s attenuation contrast, which was comparable to OsO4. However, OM discrimination from other soil phases remained a challenge. Further development of segmentation algorithms accounting for grey value patterns and shape of stained particulate OM may enable its automated identification. If successful in undisturbed soils, PMA staining may form an alternative to OsO4 in non-synchrotron based POM detection.
Public perception and awareness of waste management from Benin City
Authors: Adekola P. O. , Iyalomhe F. O. , Paczoski A. , Abebe S. T. , Pawłowska B. , Bąk M. , Cirella G. T. 
Published: January 2021

AbstractPoor waste management is increasingly becoming a major challenge for municipalities, globally. Unlike previous waste management studies in Nigeria, this study examines the implications of waste management to regional greenhouse gas emissions based on awareness levels and perception of urban inhabitants. Benin City was divided into four residential zones: core, intermediate, suburban, and planned estates. Blocking was utilized to collect data from a total of 2720 randomly selected inhabitants through a self-administered survey. Results reveals low awareness level in terms of indiscrimination dumping of waste, thereby promoting sustainable mitigation and adaptation measures region-wide. It is imperative to integrate various aspects of regional government services such as infrastructure, urban planning and development, socioeconomics, public health, and regulation enforcement. Waste management policy is strengthened via working groups, community, and regional authorities.
Data-driven detection of subtype-specific differentially expressed genes
Authors: Chen Lulu , Lu Yingzhou , Wu Chiung-Ting , Clarke Robert , Yu Guoqiang , Van Eyk Jennifer E. , Herrington David M. , Wang Yue 
Published: January 2021

AbstractAmong multiple subtypes of tissue or cell, subtype-specific differentially-expressed genes (SDEGs) are defined as being most-upregulated in only one subtype but not in any other. Detecting SDEGs plays a critical role in the molecular characterization and deconvolution of multicellular complex tissues. Classic differential analysis assumes a null hypothesis whose test statistic is not subtype-specific, thus can produce a high false positive rate and/or lower detection power. Here we first introduce a One-Versus-Everyone Fold Change (OVE-FC) test for detecting SDEGs. We then propose a scaled test statistic (OVE-sFC) for assessing the statistical significance of SDEGs that applies a mixture null distribution model and a tailored permutation test. The OVE-FC/sFC test was validated on both type 1 error rate and detection power using extensive simulation data sets generated from real gene expression profiles of purified subtype samples. The OVE-FC/sFC test was then applied to two benchmark gene expression data sets of purified subtype samples and detected many known or previously unknown SDEGs. Subsequent supervised deconvolution results on synthesized bulk expression data, obtained using the SDEGs detected from the independent purified expression data by the OVE-FC/sFC test, showed superior performance in deconvolution accuracy when compared with popular peer methods.
The TCR repertoire of α-synuclein-specific T cells in Parkinson’s disease is surprisingly diverse
Authors: Singhania Akul , Pham John , Dhanwani Rekha , Frazier April , Rezende Dutra Juliana , Marder Karen S. , Phillips Elizabeth , Mallal Simon , Amara Amy W. , Standaert David G. , Sulzer David , Peters Bjoern , Sette Alessandro , Lindestam Arlehamn Cecilia S. 
Published: January 2021

AbstractThe self-antigen α-synuclein (α-syn) was recently shown to be associated with Parkinson’s disease (PD). Here we mapped the T cell receptor (TCR) repertoire of α-syn-specific T cells from six PD patients. The self-antigen α-syn-specific repertoire was compared to the repertoire of T cells specific for pertussis (PT), as a representative foreign antigen that most individuals are exposed to, revealing that the repertoire for α-syn was as diverse as the repertoire for PT. The diversity of PT-specific clonotypes was similar between individuals with PD diagnosis and age-matched healthy controls. We found that the TCR repertoire was specific to each PD patient, and no shared TCRs among patients were defined, likely due to differences in HLA expression that select for different subsets of epitope-specific TCR rearrangements. This study provides the first characterization of α-syn-specific TCR clonotypes in individuals with PD. Antigen-specific TCRs can serve as immunotherapeutics and diagnostics, and means to track longitudinal changes in specific T cells, and disease progression.
Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer’s Disease
Authors: Johnson Travis S. , Xiang Shunian , Dong Tianhan , Huang Zhi , Cheng Michael , Wang Tianfu , Yang Kai , Ni Dong , Huang Kun , Zhang Jie 
Published: January 2021

AbstractAlzheimer’s disease (AD) brains are characterized by progressive neuron loss and gliosis. Previous studies of gene expression using bulk tissue samples often fail to consider changes in cell-type composition when comparing AD versus control, which can lead to differences in expression levels that are not due to transcriptional regulation. We mined five large transcriptomic AD datasets for conserved gene co-expression module, then analyzed differential expression and differential co-expression within the modules between AD samples and controls. We performed cell-type deconvolution analysis to determine whether the observed differential expression was due to changes in cell-type proportions in the samples or to transcriptional regulation. Our findings were validated using four additional datasets. We discovered that the increased expression of microglia modules in the AD samples can be explained by increased microglia proportions in the AD samples. In contrast, decreased expression and perturbed co-expression within neuron modules in the AD samples was likely due in part to altered regulation of neuronal pathways. Several transcription factors that are differentially expressed in AD might account for such altered gene regulation. Similarly, changes in gene expression and co-expression within astrocyte modules could be attributed to combined effects of astrogliosis and astrocyte gene activation. Gene expression in the astrocyte modules was also strongly correlated with clinicopathological biomarkers. Through this work, we demonstrated that combinatorial analysis can delineate the origins of transcriptomic changes in bulk tissue data and shed light on key genes and pathways involved in AD.
The application of a biostimulant based on tannins affects root architecture and improves tolerance to salinity in tomato plants
Authors: Campobenedetto Cristina , Mannino Giuseppe , Beekwilder Jules , Contartese Valeria , Karlova Rumyana , Bertea Cinzia M. 
Published: January 2021

AbstractRoots have important roles for plants to withstand adverse environmental conditions, including salt stress. Biostimulant application was shown to enhance plant resilience towards abiotic stresses. Here, we studied the effect of a tannin-based biostimulant on tomato (Solanum lycopersicum L.) grown under salt stress conditions. We investigated the related changes at both root architecture (via imaging and biometric analysis) and gene expression (RNA-Seq/qPCR) levels. Moreover, in order to identify the main compounds potentially involved in the observed effects, the chemical composition of the biostimulant was evaluated by UV/Vis and HPLC-ESI-Orbitrap analysis. Sixteen compounds, known to be involved in root development and having a potential antioxidant properties were identified. Significant increase of root weight (+ 24%) and length (+ 23%) was observed when the plants were grown under salt stress and treated with the biostimulant. Moreover, transcriptome analysis revealed that the application of the biostimulant upregulated 285 genes, most of which correlated to root development and salt stress tolerance. The 171 downregulated genes were mainly involved in nutrient uptake. These data demonstrated that the biostimulant is able not only to restore root growth in salty soils, but also to provide the adequate plant nourishment by regulating the expression of essential transcription factors and stress responsive genes.
A quantum circuit simulator and its applications on Sunway TaihuLight supercomputer
Authors: Wang Zhimin , Chen Zhaoyun , Wang Shengbin , Li Wendong , Gu Yongjian , Guo Guoping , Wei Zhiqiang 
Published: January 2021

AbstractClassical simulation of quantum computation is vital for verifying quantum devices and assessing quantum algorithms. We present a new quantum circuit simulator developed on the Sunway TaihuLight supercomputer. Compared with other simulators, the present one is distinguished in two aspects. First, our simulator is more versatile. The simulator consists of three mutually independent parts to compute the full, partial and single amplitudes of a quantum state with different methods. It has the function of emulating the effect of noise and support more kinds of quantum operations. Second, our simulator is of high efficiency. The simulator is designed in a two-level parallel structure to be implemented efficiently on the distributed many-core Sunway TaihuLight supercomputer. Random quantum circuits can be simulated with 40, 75 and 200 qubits on the full, partial and single amplitude, respectively. As illustrative applications of the simulator, we present a quantum fast Poisson solver and an algorithm for quantum arithmetic of evaluating transcendental functions. Our simulator is expected to have broader applications in developing quantum algorithms in various fields.
Clinical efficacy of high-flow nasal oxygen in patients undergoing ERCP under sedation
Authors: Cha Boram , Lee Man-Jong , Park Jin-Seok , Jeong Seok , Lee Don Haeng , Park Tae Gyu 
Published: January 2021

AbstractHypoxemia can occur during endoscopic retrograde cholangiography (ERCP) and it is difficult to achieve adequate ventilation with the prone position. High-flow nasal oxygen (HFNO) has been recommended to be more effectively help ventilation than conventional low flow oxygen. The aim of this study was to evaluate the effect of HFNO during sedated ERCP and to identify predictors of desaturation during ERCP. The investigated variables were age, gender, American Society of Anesthesiologists classes (ASA), duration of exam, and sedative used for midazolam or/and propofol of 262 patients with sedated ERCP. The differences between categorical and continuous variables were analyzed using the Student’s t test and the chi-square test. Desaturation (SpO2 ≤ 90%) occurred in 9(3.4%) patients among 262 patients during sedated ERCP. The variables found to predict desaturation were older age (p < 0.01), higher sedation dose for midazolam or propofol (p < 0.01), and use of midazolam (p < 0.01). Desaturation rate was lower during sedated ERCP with HFNO compared to the preliminary study with conventional low flow nasal oxygen. Patients with older age, higher sedation dose, or the use of midazolam might require close monitoring for desaturation and hypoventilation by nursing staff. The study shows the use of high-flow nasal oxygen reduces the incidence of desaturation during ERCP.
Mathematical simulation of tumour angiogenesis: angiopoietin balance is a key factor in vessel growth and regression
Authors: Yanagisawa Hayato , Sugimoto Masahiro , Miyashita Tomoyuki 
Published: January 2021

AbstractExcessive tumour growth results in a hypoxic environment around cancer cells, thus inducing tumour angiogenesis, which refers to the generation of new blood vessels from pre-existing vessels. This mechanism is biologically and physically complex, with various mathematical simulation models proposing to reproduce its formation. However, although temporary vessel regression is clinically known, few models succeed in reproducing this phenomenon. Here, we developed a three-dimensional simulation model encompassing both angiogenesis and tumour growth, specifically including angiopoietin. Angiopoietin regulates both adhesion and migration between vascular endothelial cells and wall cells, thus inhibiting the cell-to-cell adhesion required for angiogenesis initiation. Simulation results showed a regression, i.e. transient decrease, in the overall length of new vessels during vascular network formation. Using our model, we also evaluated the efficacy of administering the drug bevacizumab. The results highlighted differences in treatment efficacy: (1) earlier administration showed higher efficacy in inhibiting tumour growth, and (2) efficacy depended on the treatment interval even with the administration of the same dose. After thorough validation in the future, these results will contribute to the design of angiogenesis treatment protocols.