bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutrophil microvesicles drive atherosclerosis by delivering miR-155 to atheroprone endothelium
Authors: Gomez Ingrid , Ward Ben , Souilhol Celine , Recarti Chiara , Ariaans Mark , Johnston Jessica , Burnett Amanda , Mahmoud Marwa , Luong Le Anh , West Laura , Long Merete , Parry Sion , Woods Rachel , Hulston Carl , Benedikter Birke , Niespolo Chiara , Bazaz Rohit , Francis Sheila , Kiss-Toth Endre , van Zandvoort Marc , Schober Andreas , Hellewell Paul , Evans Paul C. , Ridger Victoria 
Published: January 2020

AbstractNeutrophils are implicated in the pathogenesis of atherosclerosis but are seldom detected in atherosclerotic plaques. We investigated whether neutrophil-derived microvesicles may influence arterial pathophysiology. Here we report that levels of circulating neutrophil microvesicles are enhanced by exposure to a high fat diet, a known risk factor for atherosclerosis. Neutrophil microvesicles accumulate at disease-prone regions of arteries exposed to disturbed flow patterns, and promote vascular inflammation and atherosclerosis in a murine model. Using cultured endothelial cells exposed to disturbed flow, we demonstrate that neutrophil microvesicles promote inflammatory gene expression by delivering miR-155, enhancing NF-κB activation. Similarly, neutrophil microvesicles increase miR-155 and enhance NF-κB at disease-prone sites of disturbed flow in vivo. Enhancement of atherosclerotic plaque formation and increase in macrophage content by neutrophil microvesicles is dependent on miR-155. We conclude that neutrophils contribute to vascular inflammation and atherogenesis through delivery of microvesicles carrying miR-155 to disease-prone regions.
Midwinter Arctic leads form and dissipate low clouds
Authors: Li Xia , Krueger Steven K. , Strong Courtenay , Mace Gerald G. , Benson Sally 
Published: January 2020

AbstractLeads are a key feature of the Arctic ice pack during the winter owing to their substantial contribution to the surface energy balance. According to the present understanding, enhanced heat and moisture fluxes from high lead concentrations tend to produce more boundary layer clouds. However, described here in our composite analyses of diverse surface- and satellite-based observations, we find that abundant boundary layer clouds are associated with low lead flux periods, while fewer boundary layer clouds are observed for high lead flux periods. Motivated by these counterintuitive results, we conducted three-dimensional cloud-resolving simulations to investigate the underlying physics. We find that newly frozen leads with large sensible heat flux but low latent heat flux tend to dissipate low clouds. This finding indicates that the observed high lead fractions likely consist of mostly newly frozen leads that reduce any pre-existing low-level cloudiness, which in turn decreases downwelling infrared flux and accelerates the freezing of sea ice.
ADAR1 mediated regulation of neural crest derived melanocytes and Schwann cell development
Authors: Gacem Nadjet , Kavo Anthula , Zerad Lisa , Richard Laurence , Mathis Stephane , Kapur Raj P. , Parisot Melanie , Amiel Jeanne , Dufour Sylvie , de la Grange Pierre , Pingault Veronique , Vallat Jean Michel , Bondurand Nadege 
Published: January 2020

AbstractThe neural crest gives rise to numerous cell types, dysfunction of which contributes to many disorders. Here, we report that adenosine deaminase acting on RNA (ADAR1), responsible for adenosine-to-inosine editing of RNA, is required for regulating the development of two neural crest derivatives: melanocytes and Schwann cells. Neural crest specific conditional deletion ofAdar1in mice leads to global depigmentation and absence of myelin from peripheral nerves, resulting from alterations in melanocyte survival and differentiation of Schwann cells, respectively. Upregulation of interferon stimulated genes precedes these defects, which are associated with the triggering of a signature resembling response to injury in peripheral nerves. Simultaneous extinction of MDA5, a key sensor of unedited RNA, rescues both melanocytes and myelin defects in vitro, suggesting that ADAR1 safeguards neural crest derivatives from aberrant MDA5-mediated interferon production. We thus extend the landscape of ADAR1 function to the fields of neural crest development and disease.
Gate controlled anomalous phase shift in Al/InAs Josephson junctions
Authors: Mayer William , Dartiailh Matthieu C. , Yuan Joseph , Wickramasinghe Kaushini S. , Rossi Enrico , Shabani Javad 
Published: January 2020

AbstractIn a standard Josephson junction the current is zero when the phase difference between superconducting leads is zero. This condition is protected by parity and time-reversal symmetries. However, the combined presence of spin–orbit coupling and magnetic field breaks these symmetries and can lead to a finite supercurrent even when the phase difference is zero. This is the so called anomalous Josephson effect—the hallmark effect of superconducting spintronics—which can be characterized by the corresponding anomalous phase shift. Here we report the observation of a tunable anomalous Josephson effect in InAs/Al Josephson junctions measured via a superconducting quantum interference device. By gate controlling the density of InAs, we are able to tune the spin–orbit coupling in the Josephson junction. This gives us the ability to tune the anomalous phase, and opens new opportunities for superconducting spintronics, and new possibilities for realizing and characterizing topological superconductivity.
Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
Authors: Thöming Janne G. , Tomasch Jürgen , Preusse Matthias , Koska Michal , Grahl Nora , Pohl Sarah , Willger Sven D. , Kaever Volkhard , Müsken Mathias , Häussler Susanne 
Published: January 2020

AbstractStudying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.
DNA extraction approaches substantially influence the assessment of the human breast milk microbiome
Authors: Douglas Chloe A. , Ivey Kerry L. , Papanicolas Lito E. , Best Karen P. , Muhlhausler Beverly S. , Rogers Geraint B. 
Published: January 2020

AbstractIn addition to providing nutritional and bioactive factors necessary for infant development, human breast milk contains bacteria that contribute to the establishment of commensal microbiota in the infant. However, the composition of this bacterial community differs considerably between studies. We hypothesised that bacterial DNA extraction methodology from breast milk samples are a substantial contributor to these inter-study differences. We tested this hypothesis by applying five widely employed methodologies to a mock breast milk sample and four individual human breast milk samples. Significant differences in DNA yield and purity were observed between methods (P < 0.05). Microbiota composition, assessed by 16S rRNA gene amplicon sequencing, also differed significantly with extraction methodology (P < 0.05), including in the contribution of contaminant signal. Concerningly, many of the bacterial taxa identified here as contaminants have been reported as components of the breast milk microbiome in other studies. These findings highlight the importance of using stringent, well-validated, DNA extraction methodologies for analysis of the breast milk microbiome, and exercising caution interpreting microbiota data from low-biomass contexts.
Optimizing High-Efficiency Quantum Memory with Quantum Machine Learning for Near-Term Quantum Devices
Authors: Gyongyosi Laszlo , Imre Sandor 
Published: January 2020

AbstractQuantum memories are a fundamental of any global-scale quantum Internet, high-performance quantum networking and near-term quantum computers. A main problem of quantum memories is the low retrieval efficiency of the quantum systems from the quantum registers of the quantum memory. Here, we define a novel quantum memory called high-retrieval-efficiency (HRE) quantum memory for near-term quantum devices. An HRE quantum memory unit integrates local unitary operations on its hardware level for the optimization of the readout procedure and utilizes the advanced techniques of quantum machine learning. We define the integrated unitary operations of an HRE quantum memory, prove the learning procedure, and evaluate the achievable output signal-to-noise ratio values. We prove that the local unitaries of an HRE quantum memory achieve the optimization of the readout procedure in an unsupervised manner without the use of any labeled data or training sequences. We show that the readout procedure of an HRE quantum memory is realized in a completely blind manner without any information about the input quantum system or about the unknown quantum operation of the quantum register. We evaluate the retrieval efficiency of an HRE quantum memory and the output SNR (signal-to-noise ratio). The results are particularly convenient for gate-model quantum computers and the near-term quantum devices of the quantum Internet.
Unraveling Asian Soybean Rust metabolomics using mass spectrometry and Molecular Networking approach
Authors: Silva Evandro , da Graça José Perez , Porto Carla , Martin do Prado Rodolpho , Hoffmann-Campo Clara Beatriz , Meyer Mauricio Conrado , de Oliveira Nunes Estela , Pilau Eduardo Jorge 
Published: January 2020

AbstractAsian Soybean Rust (ASR), caused by the biotrophic fungus Phakopsora pachyrhizi, is a devastating disease with an estimated crop yield loss of up to 90%. Yet, there is a nerf of information on the metabolic response of soybean plants to the pathogen Untargeted metabolomics and Global Natural Products Social Molecular Networking platform approach was used to explore soybean metabolome modulation to P. pachyrhizi infection. Soybean plants susceptible to ASR was inoculated with P. pachyrhizi spore suspension and non-inoculated plants were used as controls. Leaves from both groups were collected 14 days post-inoculation and extracted using different extractor solvent mixtures. The extracts were analyzed on an ultra-high performance liquid chromatography system coupled to high-definition electrospray ionization-mass spectrometry. There was a significant production of defense secondary metabolites (phenylpropanoids, terpenoids and flavonoids) when P. pachyrhizi infected soybean plants, such as putatively identified liquiritigenin, coumestrol, formononetin, pisatin, medicarpin, biochanin A, glyoceollidin I, glyoceollidin II, glyoceollin I, glyoceolidin II, glyoceolidin III, glyoceolidin IV, glyoceolidin VI. Primary metabolites (amino acids, peptides and lipids) also were putatively identified. This is the first report using untargeted metabolomics and GNPS-Molecular Networking approach to explore ASR in soybean plants. Our data provide insights into the potential role of some metabolites in the plant resistance to ASR, which could result in the development of resistant genotypes of soybean to P. pachyrhizi, and effective and specific products against the pathogen.
Diagnosis of Bovine Respiratory Disease in feedlot cattle using blood 1H NMR metabolomics
Authors: Blakebrough-Hall C. , Dona A. , D’occhio M. J. , McMeniman J. , González L. A 
Published: January 2020

AbstractCurrent diagnosis methods for Bovine Respiratory Disease (BRD) in feedlots have a low diagnostic accuracy. The current study aimed to search for blood biomarkers of BRD using 1H NMR metabolomics and determine their accuracy in diagnosing BRD. Animals with visual signs of BRD (n = 149) and visually healthy (non-BRD; n = 148) were sampled for blood metabolomics analysis. Lung lesions indicative of BRD were scored at slaughter. Non-targeted 1H NMR metabolomics was used to develop predictive algorithms for disease classification using classification and regression trees. In the absence of a gold standard for BRD diagnosis, six reference diagnosis methods were used to define an animal as BRD or non-BRD. Sensitivity (Se) and specificity (Sp) were used to estimate diagnostic accuracy (Acc). Blood metabolomics demonstrated a high accuracy at diagnosing BRD when using visual signs of BRD (Acc = 0.85), however was less accurate at diagnosing BRD using rectal temperature (Acc = 0.65), lung auscultation score (Acc = 0.61) and lung lesions at slaughter as reference diagnosis methods (Acc = 0.71). Phenylalanine, lactate, hydroxybutyrate, tyrosine, citrate and leucine were identified as metabolites of importance in classifying animals as BRD or non-BRD. The blood metabolome classified BRD and non-BRD animals with high accuracy and shows potential for use as a BRD diagnosis tool.
In silico analysis of alternative splicing on drug-target gene interactions
Authors: Ji Yanrong , Mishra Rama K. , Davuluri Ramana V. 
Published: January 2020

AbstractIdentifying and evaluating the right target are the most important factors in early drug discovery phase. Most studies focus on one protein ignoring the multiple splice-variant or protein-isoforms, which might contribute to unexpected therapeutic activity or adverse side effects. Here, we present computational analysis of cancer drug-target interactions affected by alternative splicing. By integrating information from publicly available databases, we curated 883 FDA approved or investigational stage small molecule cancer drugs that target 1,434 different genes, with an average of 5.22 protein isoforms per gene. Of these, 618 genes have ≥5 annotated protein-isoforms. By analyzing the interactions with binding pocket information, we found that 76% of drugs either miss a potential target isoform or target other isoforms with varied expression in multiple normal tissues. We present sequence and structure level alignments at isoform-level and make this information publicly available for all the curated drugs. Structure-level analysis showed ligand binding pocket architectures differences in size, shape and electrostatic parameters between isoforms. Our results emphasize how potentially important isoform-level interactions could be missed by solely focusing on the canonical isoform, and suggest that on- and off-target effects at isoform-level should be investigated to enhance the productivity of drug-discovery research.
Natural convection of Nanoliquid from a Cylinder in Square Porous Enclosure using Buongiorno’s Two-phase Model
Authors: Alhashash Abeer 
Published: January 2020

AbstractNatural convection of nanoliquid in a square porous enclosure has been studied using non homogeneous two-phase Buongiorno’s model. The outer of enclosure has cold temperature and a circular cylinder is put at the center. A finite heated segment is located on the top cylinder surface which is otherwise insulated. The momentum in the porous layer is modeled applying the Brinkman-Forchheimer equations. The analysis are conducted in the following interval of the associated groups: the portion of heated surface (5% ≤ H ≤ 100%), the concentration (0.0 ≤ ϕ ≤ 0.04), the Darcy number, 10−5 ≤ Da ≤ 10−2 and the cylinder size, (0.15 ≤ R ≤ 0.25). The minimum heat transfer rate of the active surface were obtained at location ξ = 90°. In general, the ratio of the heat transfer per unit area of the heat source decreases as the length of the heated surface increases. The heat transfer rate is intensified for the half thermally active surface and high value of Darcy number at higher nanoparticles concentration.
Molecular Simulation Elaborating the Mechanism of 1β-Hydroxy Alantolactone Inhibiting Ubiquitin-Conjugating Enzyme UbcH5s
Authors: Xu Youdong , Meng Xianli 
Published: January 2020

Abstract1β-hydroxy alantolactone, a sesquiterpene lactone, exhibits potent anti-inflammatory and anticancer activities. Recently, it has been found to target UbcH5s by covalently bonding with Cys85 specifically, but the exact molecular basis remains unclear. Here, we analyzed the structural specificity of the catalytic site of UbcH5s by comparing them with other E2 proteins. Molecular dynamics was performed to detect the structural stability of the catalytic site. Docking method was then used to predict conformations of ligand docked at the catalytic site of UbcH5s. The electrostatic surface and charge distribution of ligand and proteins were analyzed by quantitative calculation. Molecular dynamics was used to detect the stability of docking complexes of 1β-hydroxy alantolactone and UbcH5s, the covalently bonded intermediates and the products. The QM/MM methodology was used to calculate the free energy barrier of hydrogen transfer and formation of covalent bond between 15-position carbon of ligand and Cys85. Results revealed that the structure of the catalytic site is stable, and 1β-hydroxy alantolactone can dock at the catalytic site with correct conformation. Molecular dynamics further demonstrates that 1β-hydroxy alantolactone can steadily combine with UbcH5s. Intermediate and product of catalytic reaction are also certified to be stable. Besides, Asp112 and Asn114 function as anchors to fix ligand, ensuring it steadily docked at catalytic site to complete covalent reaction. More importantly, we have found that Cys85 of UbcH5c is more efficient to form a covalent bond with the ligand in comparison with UbcH5a and UbcH5b. Our results successfully explained the mechanism of 1β-hydroxy alantolactone covalently bonding with UbcH5s. Such molecular mechanism may provide a better insight into the molecular development or modification for ubiquitin-related drugs.
Down-regulation of placental Cdc42 and Rac1 links mTORC2 inhibition to decreased trophoblast amino acid transport in human intrauterine growth restriction
Authors: Jansson Thomas , Castillo-Castrejon Marisol , Gupta Madhulika B. , Powell Theresa L. , Rosario Fredrick J. 
Published: January 2020

Abstract
Intrauterine growth restriction (IUGR) increases the risk for perinatal complications and metabolic and cardiovascular disease later in life. The syncytiotrophoblast (ST) is the transporting epithelium of the human placenta, and decreased expression of amino acid transporter isoforms in the ST plasma membranes is believed to contribute to IUGR. Placental mechanistic target of rapamycin Complex 2 (mTORC2) signaling is inhibited in IUGR and regulates the trafficking of key amino acid transporter (AAT) isoforms to the ST plasma membrane; however, the molecular mechanisms are unknown. Cdc42 and Rac1 are Rho-GTPases that regulate actin-binding proteins, thereby modulating the structure and dynamics of the actin cytoskeleton. We hypothesized that inhibition of mTORC2 decreases AAT expression in the plasma membrane and amino acid uptake in primary human trophoblast (PHT) cells mediated by down-regulation of Cdc42 and Rac1. mTORC2, but not mTORC1, inhibition decreased the Cdc42 and Rac1 expression. Silencing of Cdc42 and Rac1 inhibited the activity of the System L and A transporters and markedly decreased the trafficking of LAT1 (System L isoform) and SNAT2 (System A isoform) to the plasma membrane. mTORC2 inhibition by silencing of rictor failed to decrease AAT following activation of Cdc42/Rac1. Placental Cdc42 and Rac1 protein expression was down-regulated in human IUGR and was positively correlated with placental mTORC2 signaling. In conclusion, mTORC2 regulates AAT trafficking in PHT cells by modulating Cdc42 and Rac1. Placental mTORC2 inhibition in human IUGR may contribute to decreased placental amino acid transfer and reduced fetal growth mediated by down-regulation of Cdc42 and Rac1.
Research and design of automatic alternation between constant‐current and constant‐voltage modes on the secondary side in wireless charging systems
Authors: Ji Li , Wang Lifang , Liao Chenglin , Li Shufan , Ma Jing 
Published: January 2020

During wireless charging, the constant‐current (CC) mode must be quickly and stably changed to constant‐voltage (CV) mode to ensure battery safety. This switch often requires communication between the primary side and the secondary side along with complex control methods on the primary side. The authors propose a method for automatically and rapidly switching from CC mode to CV mode by changing the resonant compensation network on the secondary side without requiring communication or any complex control processes. Additionally, a method for designing the parameters of the secondary side is presented to ensure battery voltage stability at the transition point. By examining two examples of revised circuitry for the different power levels needed in industry applications, the proposed design methods are analysed and verified, two sets of experiments with a 20 cm coil spacing are conducted, and two systems with output powers of 1 and 2.7 kW and average efficiencies of 90.8 and 93% are implemented. Experimental results show that as the load varies, the output current and voltage obtained using the proposed methods essentially remain constant. In addition, the process of changing from CC mode to CV mode is stable, which satisfies battery‐charging requirements.