bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus)
Authors: Moorey Sarah E. , Walker Bailey N. , Elmore Michelle F. , Elmore Joshua B. , Rodning Soren P. , Biase Fernando H. 
Published: October 2020

AbstractInfertility is a challenging phenomenon in cattle that reduces the sustainability of beef production worldwide. Here, we tested the hypothesis that gene expression profiles of protein-coding genes expressed in peripheral white blood cells (PWBCs), and circulating micro RNAs in plasma, are associated with female fertility, measured by pregnancy outcome. We drew blood samples from 17 heifers on the day of artificial insemination and analyzed transcript abundance for 10,496 genes in PWBCs and 290 circulating micro RNAs. The females were later classified as pregnant to artificial insemination, pregnant to natural breeding or not pregnant. We identified 1860 genes producing significant differential coexpression (eFDR < 0.002) based on pregnancy outcome. Additionally, 237 micro RNAs and 2274 genes in PWBCs presented differential coexpression based on pregnancy outcome. Furthermore, using a machine learning prediction algorithm we detected a subset of genes whose abundance could be used for blind categorization of pregnancy outcome. Our results provide strong evidence that transcript abundance in circulating white blood cells is associated with fertility in heifers.
Transcriptome sequencing and histology reveal dosage compensation in the liver of triploid pre-smolt Atlantic salmon
Authors: Odei Derrick K. , Hagen Ørjan , Peruzzi Stefano , Falk-Petersen Inger-Britt , Fernandes Jorge M. O. 
Published: October 2020

AbstractTriploid Atlantic salmon (Salmo salar L.) is seen as one of the best solutions to solve key issues in the salmon farming industry, such as the impact of escapees on wild stocks and pre-harvest sexual maturation. However, the effects of triploidy on salmon smoltification are poorly understood at the molecular level, even though smoltification is a very sensitive period that has a major influence on survival rate and performance of farmed salmon. In this study, we have compared the liver transcriptomes of diploid and triploid Atlantic salmon at three ontogeny stages: fry, parr and smolt. In diploid fish, a total of 2,655 genes were differentially expressed between fry and parr, whereas 506 genes had significantly different transcript levels between parr and smolts. In triploids, 1,507 and 974 genes were differentially expressed between fry and parr, and between parr and smolts, respectively. Most of these genes were down-regulated and 34 genes were differentially expressed between ploidies at the same stage. In both ploidy groups, the top differentially expressed genes with ontogeny stage belonged to common functional categories that can be related to smoltification. Nucleotide and energy metabolism were significantly down-regulated in fry when compared to parr, while immune system processes were significantly down-regulated in parr when compared to smolts. The close resemblance of enriched biological processes and pathways between ploidy groups suggests that triploidy is regulated by genome dosage compensation in Atlantic salmon. Histological analysis revealed that areas of vacuolization (steatosis) were present only in fry and parr stages, in contrast to a compact cellular histology with glycogen granules after smoltification. There was no significant difference in vacuolization between ploidy groups at the fry stage but the liver of diploid parr had a 33.5% higher vacuolization area compared to their triploid counterparts. Taken together, our data provide novel insights into the changes that occur at the molecular and histological level in the liver of both diploid and triploid Atlantic salmon prior to and during smoltification.
Modeling the potential of wAu-Wolbachia strain invasion in mosquitoes to control Aedes-borne arboviral infections
Authors: Ogunlade Samson T. , Adekunle Adeshina I. , Meehan Michael T. , Rojas Diana P. , McBryde Emma S. 
Published: October 2020

AbstractArboviral infections such as dengue, Zika and chikungunya are fast spreading diseases that pose significant health problems globally. In order to control these infections, an intracellular bacterium called Wolbachia has been introduced into wild-type mosquito populations in the hopes of replacing the vector transmitting agent, Aedes aegypti with one that is incapable of transmission. In this study, we developed a Wolbachia transmission model for the novel wAu strain which possesses several favourable traits (e.g., enhanced viral blockage and maintenance at higher temperature) but not cyctoplasmic incompatibility (CI)—when a Wolbachia-infected male mosquito mates with an uninfected female mosquito, producing no viable offspring. This model describes the competitive dynamics between wAu-Wolbachia-infected and uninfected mosquitoes and the role of imperfect maternal transmission. By analysing the system via computing the basic reproduction number(s) and stability properties, the potential of the wAu strain as a viable strategy to control arboviral infections is established. The results of this work show that enhanced maintenance of Wolbachia infection at higher temperatures can overcome the lack of CI induction to support wAu-Wolbachia infected mosquito invasion. This study will support future arboviral control programs, that rely on the introduction of new Wolbachia variants.
Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method
Authors: Lim Hocheol , Baek Ayoung , Kim Jongwan , Kim Min Sung , Liu Jiaxin , Nam Ky-Youb , Yoon JeongHyeok , No Kyoung Tai 
Published: October 2020

AbstractThe prevalence of a novel β-coronavirus (SARS-CoV-2) was declared as a public health emergency of international concern on 30 January 2020 and a global pandemic on 11 March 2020 by WHO. The spike glycoprotein of SARS-CoV-2 is regarded as a key target for the development of vaccines and therapeutic antibodies. In order to develop anti-viral therapeutics for SARS-CoV-2, it is crucial to find amino acid pairs that strongly attract each other at the interface of the spike glycoprotein and the human angiotensin-converting enzyme 2 (hACE2) complex. In order to find hot spot residues, the strongly attracting amino acid pairs at the protein–protein interaction (PPI) interface, we introduce a reliable inter-residue interaction energy calculation method, FMO-DFTB3/D/PCM/3D-SPIEs. In addition to the SARS-CoV-2 spike glycoprotein/hACE2 complex, the hot spot residues of SARS-CoV-1 spike glycoprotein/hACE2 complex, SARS-CoV-1 spike glycoprotein/antibody complex, and HCoV-NL63 spike glycoprotein/hACE2 complex were obtained using the same FMO method. Following this, a 3D-SPIEs-based interaction map was constructed with hot spot residues for the hACE2/SARS-CoV-1 spike glycoprotein, hACE2/HCoV-NL63 spike glycoprotein, and hACE2/SARS-CoV-2 spike glycoprotein complexes. Finally, the three 3D-SPIEs-based interaction maps were combined and analyzed to find the consensus hot spots among the three complexes. As a result of the analysis, two hot spots were identified between hACE2 and the three spike proteins. In particular, E37, K353, G354, and D355 of the hACE2 receptor strongly interact with the spike proteins of coronaviruses. The 3D-SPIEs-based map would provide valuable information to develop anti-viral therapeutics that inhibit PPIs between the spike protein of SARS-CoV-2 and hACE2.
Carotenoid metabolite and transcriptome dynamics underlying flower color in marigold (Tagetes erecta L.)
Authors: Zhang Huali , Zhang Shiya , Zhang Hua , Chen Xi , Liang Fang , Qin Helan , Zhang Yue , Cong Richen , Xin Haibo , Zhang Zhao 
Published: October 2020

AbstractMarigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of flower colors. Despite its economic value, few biochemical and molecular studies have explored the generation of flower color in this species. To study the mechanism underlying marigold petal color, we performed a metabolite analysis and de novo cDNA sequencing on the inbred line ‘V-01’ and its petal color mutant ‘V-01M’ at four flower developmental stages. A total of 49,217 unigenes were identified from 24 cDNA libraries. Based on our metabolites and transcriptomic analyses, we present an overview of carotenoid biosynthesis, degradation, and accumulation in marigold flowers. The carotenoid content of the yellow mutant ‘V-01M’ was higher than that of the orange inbred line ‘V-01’, and the abundances of the yellow compounds lutein, neoxanthin, violaxanthin, zeaxanthin, and antheraxanthin were significantly higher in the mutant. During flower development, the carotenoid biosynthesis genes were upregulated in both ‘V-01’ and ‘V-01M’, with no significant differences between the two lines. By contrast, the carotenoid degradation genes were dramatically downregulated in the yellow mutant ‘V-01M’. We therefore speculate that the carotenoid degradation genes are the key factors regulating the carotenoid content of marigold flowers. Our research provides a large amount of transcriptomic data and insights into the marigold color metabolome.
Efficacy and safety of newer P2Y12 inhibitors for acute coronary syndrome: a network meta-analysis
Authors: Fei Yue , Lam Cheuk Kiu , Cheung Bernard Man Yung 
Published: October 2020

AbstractWhether newer P2Y12 inhibitors are more efficacious and safer than clopidogrel and whether there is a superior one remain uncertain. We compared the effect of P2Y12 inhibitors on clinical outcomes in patients with acute coronary syndrome (ACS). Randomized controlled trials comparing clopidogrel, prasugrel, ticagrelor, or cangrelor, in combination with aspirin were searched. Sixteen trials with altogether 77,896 patients were included. Compared to clopidogrel, cardiovascular mortality was reduced with prasugrel (OR 0.85, 95% CI 0.75–0.97) and ticagrelor (0.82, 0.73–0.93). Myocardial infarction (0.75, 0.63–0.89) and major adverse cardiovascular events (0.80, 0.69–0.94) were reduced by prasugrel. Stent thrombosis was reduced by prasugrel (0.49, 0.38–0.63), ticagrelor (0.72, 0.57–0.90), and cangrelor (0.59, 0.43–0.81). It was reduced more by prasugrel than ticagrelor (0.69, 0.51–0.93). There were more major bleeds with prasugrel (1.24, 1.05–1.48). Thrombolysis in Myocardial Infarction (TIMI) major bleeding was increased with prasugrel compared to clopidogrel (1.36, 1.11–1.66) and ticagrelor (1.33, 1.06–1.67). TIMI minor bleeding was increased with prasugrel (1.44, 1.16–1.77) and cangrelor (1.47, 1.01–2.16) compared to clopidogrel while it was increased with prasugrel compared to ticagrelor (1.32, 1.01–1.72). Prasugrel is preferable to those ACS patients at low bleeding risk to reduce cardiovascular events whereas ticagrelor is a relatively safe antiplatelet drug of choice for most patients.
Study of the heavily p-type doping of cubic GaN with Mg
Authors: Hernández-Gutiérrez C. A. , Casallas-Moreno Y. L. , Rangel-Kuoppa Victor-Tapio , Cardona Dagoberto , Hu Yaoqiao , Kudriatsev Yuri , Zambrano-Serrano M. A. , Gallardo-Hernandez S. , Lopez-Lopez M. 
Published: October 2020

AbstractWe have studied the Mg doping of cubic GaN grown by plasma-assisted Molecular Beam Epitaxy (PA-MBE) over GaAs (001) substrates. In particular, we concentrated on conditions to obtain heavy p-type doping to achieve low resistance films which can be used in bipolar devices. We simulated the Mg-doped GaN transport properties by density functional theory (DFT) to compare with the experimental data. Mg-doped GaN cubic epitaxial layers grown under optimized conditions show a free hole carrier concentration with a maximum value of 6 × 1019 cm−3 and mobility of 3 cm2/Vs. Deep level transient spectroscopy shows the presence of a trap with an activation energy of 114 meV presumably associated with nitrogen vacancies, which could be the cause for the observed self-compensation behavior in heavily Mg-doped GaN involving Mg-VN complexes. Furthermore, valence band analysis by X-ray photoelectron spectroscopy and photoluminescence spectroscopy revealed an Mg ionization energy of about 100 meV, which agrees quite well with the value of 99.6 meV obtained by DFT. Our results show that the cubic phase is a suitable alternative to generate a high free hole carrier concentration for GaN.
Fitting the magnetoresponses of the OLED using polaron pair model to obtain spin-pair dynamics and local hyperfine fields
Authors: Weng Zhichao , Gillin William P. , Kreouzis Theo 
Published: October 2020

AbstractOrganic light-emitting diode (OLED) displays a sign reversal magnetic field effect (MFE) when the applied magnetic field range is reduced to the sub-milliTesla range and the Polaron Pair Model has been successful in explaining the ultra-small MFE. Here, we obtained high resolution (~ 1 µT) magnetoconductance (MC) and magnetoelectroluminescence (MEL) of a tris-(8-hydroxyquinoline)aluminium-based (Alq3) OLED within the magnetic field range of ± 500 µT with the earth magnetic field components cancelled. A clear “W” shaped MC with a dip position of ± 250 µT and a monotonic MEL were observed. We demonstrate a fitting technique using the polaron pair model to the experimentally obtained MC and MEL. The fitting process extracts physically significant parameters within a working OLED: the local hyperfine fields for electron and hole in Alq3: Bhf1 = (0.63 ± 0.01) mT (electron), Bhf2 = (0.24 ± 0.01) mT (hole); the separation rates for singlet and triplet polaron pairs: kS,s = (44.59 ± 0.01) MHz, kT,s = (43.97 ± 0.01) MHz, and the recombination rate for singlet polaron pair kS,r = (88 ± 6) MHz. The yielded parameters are highly reproducible across different OLEDs and are in broad agreement with density functional theory (DFT) calculations and reported experimental observations. This demonstrates the feasibility of this fitting technique to approach any working OLED for obtaining significant microscopic parameters.
Restricted intramolecular rotation of fluorescent molecular rotors at the periphery of aqueous microdroplets in oil
Authors: Kang Jooyoun , Lhee SangMoon , Lee Jae Kyoo , Zare Richard N. , Nam Hong Gil 
Published: October 2020

AbstractFluorescent molecular rotor dyes, including Cy3, Cy5, and Alexa Fluor 555, dissolved in micron-sized aqueous droplets (microdroplets) in oil were excited, and the fluorescence intensity was recorded as function of time. We observed lengthening of the fluorescence lifetime of these dyes at the water–oil periphery, which extended several microns inward. This behavior shows that intramolecular rotation is restricted at and near the microdroplet interface. Lengthened lifetimes were observed in water microdroplets but not in microdroplets composed of organic solvents. This lifetime change was relatively insensitive to added glycerol up to 60%, suggesting that solution viscosity is not the dominant mechanism. These restricted intramolecular rotations at and near the microdroplet periphery are consistent with the reduced entropy observed in chemical reactions in microdroplets compared to the same reaction conditions in bulk solution and helps us further understand why microdroplet chemistry differs so markedly from bulk-phase chemistry.
Aeromonas salmonicida activates rainbow trout IgM+ B cells signalling through Toll like receptors
Authors: Soleto Irene , Morel Esther , Muñoz-Atienza Estefanía , Díaz-Rosales Patricia , Tafalla Carolina 
Published: October 2020

AbstractAs B cells are singularly equipped with a B cell receptor (BCR) and a range of innate receptors, they are able to integrate both antigen-specific and innate signals, with the latter being essential to reach an adequate level of activation. Whether teleost B cells sense pathogens through innate mechanisms has not yet been explored, despite the fact that fish B cells display a wider array of innate receptors than many mammalian B cell subsets. Hence, in the current study, we have investigated the effects of inactivated Aeromonas salmonicida, a Gram negative rainbow trout pathogen, on trout splenic IgM+ B cells in vitro in the presence or absence of different inhibitors of Toll-like receptor (TLR) signalling, to establish to what degree innate signals are contributing to the activation of B cells in teleosts. Our results demonstrate that most of the effects that A. salmonicida exerts on trout IgM+ B cells are significantly blocked in the presence of inhibitors of MyD88 and TRIF, important nodes in TLR signal pathways. Thus, the data presented demonstrates that, also in teleost, TLR signalling is essential for the activation of IgM+ B cells. These results will be useful for the future optimization of novel vaccines and adjuvants.
Endocrine disruption of vitamin D activity by perfluoro-octanoic acid (PFOA)
Authors: Di Nisio Andrea , Rocca Maria Santa , De Toni Luca , Sabovic Iva , Guidolin Diego , Dall’Acqua Stefano , Acquasaliente Laura , De Filippis Vincenzo , Plebani Mario , Foresta Carlo 
Published: October 2020

AbstractPerfluoroalkyl substances (PFAS) are a class of compounds used in industry and consumer products. Perfluorooctanoic acid (PFOA) is the predominant form in human samples and has been shown to induce severe health consequences, such as neonatal mortality, neurotoxicity, and immunotoxicity. Toxicological studies indicate that PFAS accumulate in bone tissues and cause altered bone development. Epidemiological studies have reported an inverse relationship between PFAS and bone health, however the associated mechanisms are still unexplored. Here, we present computational, in silico and in vitro evidence supporting the interference of PFOA on vitamin D (VD). First, PFOA competes with calcitriol on the same binding site of the VD receptor, leading to an alteration of the structural flexibility and a 10% reduction by surface plasmon resonance analysis. Second, this interference leads to an altered response of VD-responsive genes in two cellular targets of this hormone, osteoblasts and epithelial cells of the colorectal tract. Third, mineralization in human osteoblasts is reduced upon coincubation of PFOA with VD. Finally, in a small cohort of young healthy men, PTH levels were higher in the exposed group, but VD levels were comparable. Altogether these results provide the first evidence of endocrine disruption by PFOA on VD pathway by competition on its receptor and subsequent inhibition of VD-responsive genes in target cells.
Low Antarctic continental climate sensitivity due to high ice sheet orography
Authors: Singh Hansi A. , Polvani Lorenzo M. 
Published: October 2020

AbstractThe Antarctic continent has not warmed in the last seven decades, despite a monotonic increase in the atmospheric concentration of greenhouse gases. In this paper, we investigate whether the high orography of the Antarctic ice sheet (AIS) has helped delay warming over the continent. To that end, we contrast the Antarctic climate response to CO2-doubling with present-day orography to the response with a flattened AIS. To corroborate our findings, we perform this exercise with two different climate models. We find that, with a flattened AIS, CO2-doubling induces more latent heat transport toward the Antarctic continent, greater moisture convergence over the continent and, as a result, more surface-amplified condensational heating. Greater moisture convergence over the continent is made possible by flattening of moist isentropic surfaces, which decreases humidity gradients along the trajectories on which extratropical poleward moisture transport predominantly occurs, thereby enabling more moisture to reach the pole. Furthermore, the polar meridional cell disappears when the AIS is flattened, permitting greater CO2-forced warm temperature advection toward the Antarctic continent. Our results suggest that the high elevation of the present AIS plays a significant role in decreasing the susceptibility of the Antarctic continent to CO2-forced warming.
Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice
Authors: Yang Long , Geng Tingting , Yang Guang , Ma Jinzhu , Wang Leilei , Ketkar Harshada , Yang Duomeng , Lin Tao , Hwang Jesse , Zhu Shu , Wang Yanlin , Dai Jianfeng , You Fuping , Cheng Gong , Vella Anthony T. , Flavell Richard. A. , Fikrig Erol , Wang Penghua 
Published: October 2020

AbstractMacrophage scavenger receptor 1 (MSR1) mediates the endocytosis of modified low-density lipoproteins and plays an important antiviral role. However, the molecular mechanism underlying MSR1 antiviral actions remains elusive. We report that MSR1 activates autophagy to restrict infection of Chikungunya virus (CHIKV), an arthritogenic alphavirus that causes acute and chronic crippling arthralgia. Msr1 expression was rapidly upregulated after CHIKV infection in mice. Msr1 knockout mice had elevated viral loads and increased susceptibility to CHIKV arthritis along with a normal type I IFN response. Induction of LC3 lipidation by CHIKV, a marker of autophagy, was reduced in Msr1−/− cells. Mechanistically, MSR1 interacted with ATG12 through its cytoplasmic tail and this interaction was enhanced by CHIKV nsP1 protein. MSR1 repressed CHIKV replication through ATG5-ATG12-ATG16L1 and this was dependent on the FIP200-and-WIPI2-binding domain, but not the WD40 domain of ATG16L1. Our results elucidate an antiviral role for MSR1 involving the autophagic function of ATG5-ATG12-ATG16L1.
Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism
Authors: Chaguza Chrispin , Yang Marie , Cornick Jennifer E. , du Plessis Mignon , Gladstone Rebecca A. , Kwambana-Adams Brenda A. , Lo Stephanie W. , Ebruke Chinelo , Tonkin-Hill Gerry , Peno Chikondi , Senghore Madikay , Obaro Stephen K. , Ousmane Sani , Pluschke Gerd , Collard Jean-Marc , Sigaùque Betuel , French Neil , Klugman Keith P. , Heyderman Robert S. , McGee Lesley , Antonio Martin , Breiman Robert F. , von Gottberg Anne , Everett Dean B. , Kadioglu Aras , Bentley Stephen D. 
Published: October 2020

AbstractHyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation in serotype 1 strains modulates tropism into cerebrospinal fluid to cause central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal serotype 1 isolates collected from CNS and non-CNS human samples. By controlling for host age, geography, and strain population structure, we identify genome-wide statistically significant genotype-phenotype associations in surface-exposed choline-binding (P = 5.00 × 10−08) and helicase proteins (P = 1.32 × 10−06) important for invasion, immune evasion and pneumococcal tropism to CNS. The small effect sizes and negligible heritability indicated that causation of CNS infection requires multiple genetic and other factors reflecting a complex and polygenic aetiology. Our findings suggest that certain pathogen genetic variation modulate pneumococcal survival and tropism to CNS tissue, and therefore, virulence for meningitis.