bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of Mixed Multiscale Finite Element Methods for Multiphase Transport in Highly Heterogeneous Media
Authors: Wang Yiran , Chung Eric , Fu Shubin , Huang Zhaoqin 
Published: April 2021

AbstractIn this study, we systemically review and compare two mixed multiscale finite element methods (MMsFEM) for multiphase transport in highly heterogeneous media. In particular, we will consider the mixed multiscale finite element method using limited global information, simply denoted by MMsFEM, and the mixed generalized multiscale finite element method (MGMsFEM) with residual driven online multiscale basis functions. Both methods are within the framework of MMsFEM, where the pressure equation is solved in the coarse grids with carefully constructed multiscale basis functions for the velocity. The multiscale basis functions in both methods include local and global media information. In terms of MsFEM using limited global information, only one multiscale basis function is utilized in each local neighborhood, while multiple bases are used in MGMsFEM. We will test and compare these two methods using the benchmark three‐dimensional SPE10 model. A range of coarse grid sizes and different combinations of basis functions (offline and online) will be considered with CPU time reported for each case. In our numerical experiments, we observe good accuracy by the two above methods. Finally, we will discuss and compare the advantages and disadvantages of the two methods in terms of accuracy and computational costs.
Magnetospheric Multiscale Observations of the Source Region of Energetic Electron Microinjections Along the Duskside, High‐Latitude Magnetopause Boundary Layer
Authors: Nykyri K. , Johnson J. , Kronberg E. , Turner D. , Wing S. , Cohen I. , Sorathia K. , Ma X. , Burkholder B. , Reeves G. , Fennell J. 
Published: April 2021

AbstractThe present paper demonstrates the first observations by the Magnetospheric Multiscale (MMS) mission of the counter‐streaming energetic electrons and trapped energetic protons, localized in the magnetic field depressions between the mirror mode peaks, in the Earth's dusk sector high‐latitude magnetosphere. This region is characterized by high plasma beta, strong ion temperature anisotropy, and intermediate plasma density between magnetospheric and magnetosheath plasma. We show that these plasma conditions are unstable for the drift mirror instability. The counter‐streaming electron feature resembles those of the previously reported energetic electron microinjections, but without the energy‐time dispersion signature. This suggests that MMS is passing through one of the potential microinjection source regions. The energetic ion data in the present study is mainly used to estimate the scale size of the mirror mode structures.
The Dominant Contribution of Southern Ocean Heat Uptake to Time‐Evolving Radiative Feedback in CESM
Authors: Lin Yuan‐Jen , Hwang Yen‐Ting , Lu Jian , Liu Fukai , Rose Brian E. J. 
Published: April 2021

AbstractIn most fully coupled climate models, the net radiative feedback magnitude decreases with time after abruptly quadrupling CO2. Hypotheses have been raised to explain the time dependence of radiative feedbacks, including the influence from surface warming pattern and ocean heat uptake (OHU) pattern. By using the Green's Function derived from pairs of simulations in the atmospheric model (CAM5) coupled with a slab‐ocean, with each simulation being forced by a localized surface heat flux anomaly, we evaluate the influences of regional OHU on transient surface warming pattern, accounting for the changes in radiative feedbacks. The attribution of the time‐evolving net radiative feedback highlights the remote impact from OHU over the Southern Ocean on tropical sea surface temperature. The time‐dependent weakening of OHU over the Southern Ocean gives rise to increasingly enhanced surface warming in southeastern Pacific, which leads to decreasing tropospheric stability and more positive cloud feedback decades after quadrupling CO2.
RNA binding of Hfq monomers promotes RelA-mediated hexamerization in a limiting Hfq environment
Authors: Basu Pallabi , Elgrably-Weiss Maya , Hassouna Fouad , Kumar Manoj , Wiener Reuven , Altuvia Shoshy 
Published: April 2021

AbstractThe RNA chaperone Hfq, acting as a hexamer, is a known mediator of post-transcriptional regulation, expediting basepairing between small RNAs (sRNAs) and their target mRNAs. However, the intricate details associated with Hfq-RNA biogenesis are still unclear. Previously, we reported that the stringent response regulator, RelA, is a functional partner of Hfq that facilitates Hfq-mediated sRNA–mRNA regulation in vivo and induces Hfq hexamerization in vitro. Here we show that RelA-mediated Hfq hexamerization requires an initial binding of RNA, preferably sRNA to Hfq monomers. By interacting with a Shine–Dalgarno-like sequence (GGAG) in the sRNA, RelA stabilizes the initially unstable complex of RNA bound-Hfq monomer, enabling the attachment of more Hfq subunits to form a functional hexamer. Overall, our study showing that RNA binding to Hfq monomers is at the heart of RelA-mediated Hfq hexamerization, challenges the previous concept that only Hfq hexamers can bind RNA.
Activation of von Willebrand factor via mechanical unfolding of its discontinuous autoinhibitory module
Authors: Arce Nicholas A. , Cao Wenpeng , Brown Alexander K. , Legan Emily R. , Wilson Moriah S. , Xu Emma-Ruoqi , Berndt Michael C. , Emsley Jonas , Zhang X. Frank , Li Renhao 
Published: April 2021

AbstractVon Willebrand factor (VWF) activates in response to shear flow to initiate hemostasis, while aberrant activation could lead to thrombosis. Above a critical shear force, the A1 domain of VWF becomes activated and captures platelets via the GPIb-IX complex. Here we show that the shear-responsive element controlling VWF activation resides in the discontinuous autoinhibitory module (AIM) flanking A1. Application of tensile force in a single-molecule setting induces cooperative unfolding of the AIM to expose A1. The AIM-unfolding force is lowered by truncating either N- or C-terminal AIM region, type 2B VWD mutations, or binding of a ristocetin-mimicking monoclonal antibody, all of which could activate A1. Furthermore, the AIM is mechanically stabilized by the nanobody that comprises caplacizumab, the only FDA-approved anti-thrombotic drug to-date that targets VWF. Thus, the AIM is a mechano-regulator of VWF activity. Its conformational dynamics may define the extent of VWF autoinhibition and subsequent activation under force.
Ordered clustering of single atomic Te vacancies in atomically thin PtTe2 promotes hydrogen evolution catalysis
Authors: Li Xinzhe , Fang Yiyun , Wang Jun , Fang Hanyan , Xi Shibo , Zhao Xiaoxu , Xu Danyun , Xu Haomin , Yu Wei , Hai Xiao , Chen Cheng , Yao Chuanhao , Tao Hua Bing , Howe Alexander G. R. , Pennycook Stephen J. , Liu Bin , Lu Jiong , Su Chenliang 
Published: April 2021

AbstractExposing and stabilizing undercoordinated platinum (Pt) sites and therefore optimizing their adsorption to reactive intermediates offers a desirable strategy to develop highly efficient Pt-based electrocatalysts. However, preparation of atomically controllable Pt-based model catalysts to understand the correlation between electronic structure, adsorption energy, and catalytic properties of atomic Pt sites is still challenging. Herein we report the atomically thin two-dimensional PtTe2 nanosheets with well-dispersed single atomic Te vacancies (Te-SAVs) and atomically well-defined undercoordinated Pt sites as a model electrocatalyst. A controlled thermal treatment drives the migration of the Te-SAVs to form thermodynamically stabilized, ordered Te-SAV clusters, which decreases both the density of states of undercoordinated Pt sites around the Fermi level and the interacting orbital volume of Pt sites. As a result, the binding strength of atomically defined Pt active sites to H intermediates is effectively reduced, which renders PtTe2 nanosheets highly active and stable in hydrogen evolution reaction.
Distance to native climatic niche margins explains establishment success of alien mammals
Authors: Broennimann Olivier , Petitpierre Blaise , Chevalier Mathieu , González-Suárez Manuela , Jeschke Jonathan M. , Rolland Jonathan , Gray Sarah M. , Bacher Sven , Guisan Antoine 
Published: April 2021

AbstractOne key hypothesis explaining the fate of exotic species introductions posits that the establishment of a self-sustaining population in the invaded range can only succeed within conditions matching the native climatic niche. Yet, this hypothesis remains untested for individual release events. Using a dataset of 979 introductions of 173 mammal species worldwide, we show that climate-matching to the realized native climatic niche, measured by a new Niche Margin Index (NMI), is a stronger predictor of establishment success than most previously tested life-history attributes and historical factors. Contrary to traditional climatic suitability metrics derived from species distribution models, NMI is based on niche margins and provides a measure of how distant a site is inside or, importantly, outside the niche. Besides many applications in research in ecology and evolution, NMI as a measure of native climatic niche-matching in risk assessments could improve efforts to prevent invasions and avoid costly eradications.
Efficacy of induction regimens for cryptococcal meningitis in HIV-infected adults: a systematic review and network meta-analysis
Authors: Chen Chang-Hua , Li Hua , Chen Hsien-Meng , Chen Yu-Min , Chang Yu-Jun , Lin Pao-Yen , Hsu Chih-Wei , Tseng Ping-Tao , Lin Kai-Huang , Tu Yu-Kang 
Published: April 2021

AbstractCryptococcal meningitis (CM) is the most fatal adult meningitis in patients with human immunodeficiency virus (HIV). There is no conclusive evidence for the superiority of 1-week amphotericin B deoxycholate (AmphB) + flucytosine (5-FC) regimen over other antifungals in the management of HIV patients with CM (HIV–CM patients). We aimed to evaluate the differences in efficacy and tolerability of different antifungal agents in HIV–CM patients by conducting a current network meta-analysis NMA. Overall, 19 randomized controlled trials were included with 2642 participants. A regimen indicated a possibly lower early mortality rate, namely, AmphB + 5-FC + Azole (OR = 1.1E−12, 95% CIs = 1.3E−41 to 0.06) comparing to AmphB + 5-FC. The current NMA provides evidence that AmphB + 5-FC + Azole are superior to all the investigated treatments for induction regimen in HIV–CM patients.
The construction and visualization of the transmission networks for COVID-19: A potential solution for contact tracing and assessments of epidemics
Authors: Luo Caiying , Ma Yue , Jiang Pei , Zhang Tao , Yin Fei 
Published: April 2021

AbstractThe WHO has described coronavirus disease 2019 (COVID-19) as a pandemic due to the speed and scale of its transmission. Without effective interventions, the rapidly increasing number of COVID-19 cases would greatly increase the burden of clinical treatments. Identifying the transmission sources and pathways is of vital importance to block transmission and allocate limited public health resources. According to the relationships among cases, we constructed disease transmission network graphs for the COVID-19 epidemic through a visualization technique based on individual reports of epidemiological data. We proposed an analysis strategy of the transmission network with the epidemiological data in Tianjin and Chengdu. The transmission networks showed different transmission characteristics. In Tianjin, an imported case of COVID-19 can produce an average of 2.9 secondary infections and ultimately produce as many as 4 generations of infections, with a maximum of 6 cases being generated before the imported case is identified. In Chengdu, 45 noninformative cases and 24 cases with vague exposure information made accurate information about the transmission network difficult to provide. The proposed analysis framework of visualized transmission networks can trace the transmission source and contacts, assess the current situation of transmission and prevention, and provide evidence for the global response and control of the COVID-19 pandemic.
Potent sialic acid inhibitors that target influenza A virus hemagglutinin
Authors: Chang Yu-Jen , Yeh Cheng-Yun , Cheng Ju-Chien , Huang Yu-Qi , Hsu Kai-Cheng , Lin Yu-Feng , Lu Chih-Hao 
Published: April 2021

AbstractEradicating influenza A virus (IAV) is difficult, due to its genetic drift and reassortment ability. As the infectious cycle is initiated by the influenza glycoprotein, hemagglutinin (HA), which mediates the binding of virions to terminal sialic acids moieties, HA is a tempting target of anti-influenza inhibitors. However, the complexity of the HA structure has prevented delineation of the structural characterization of the HA protein–ligand complex. Our computational strategy efficiently analyzed > 200,000 records of compounds held in the United States National Cancer Institute (NCI) database and identified potential HA inhibitors, by modeling the sialic acid (SA) receptor binding site (RBS) for the HA structure. Our modeling revealed that compound NSC85561 showed significant antiviral activity against the IAV H1N1 strain with EC50 values ranging from 2.31 to 2.53 µM and negligible cytotoxicity (CC50 > 700 µM). Using the NSC85561 compound as the template to generate 12 derivatives, robust bioassay results revealed the strongest antiviral efficacies with NSC47715 and NSC7223. Virtual screening clearly identified three SA receptor binding site inhibitors that were successfully validated in experimental data. Thus, our computational strategy has identified SA receptor binding site inhibitors against HA that show IAV-associated antiviral activity.
Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree
Authors: Sebastiana M. , Gargallo-Garriga A. , Sardans J. , Pérez-Trujillo M. , Monteiro F. , Figueiredo A. , Maia M. , Nascimento R. , Silva M. Sousa , Ferreira A. N. , Cordeiro C. , Marques A. P. , Sousa L. , Malhó R. , Peñuelas J. 
Published: April 2021

AbstractMycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungusPisolithus tinctoriuswere compared with non-colonized roots. Results show that compounds putatively corresponding to carbohydrates, organic acids, tannins, long-chain fatty acids and monoacylglycerols, were depleted in ectomycorrhizal cork oak colonized roots. Conversely, non-proteogenic amino acids, such as gamma-aminobutyric acid (GABA), and several putative defense-related compounds, including oxylipin-family compounds, terpenoids and B6 vitamers were induced in mycorrhizal roots. Transcriptomic analysis suggests the involvement of GABA in ectomycorrhizal symbiosis through increased synthesis and inhibition of degradation in mycorrhizal roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such asP. tinctoriusbenefit their host plants.
Pre-existing depression in patients with coronary artery disease undergoing percutaneous coronary intervention
Authors: Park Jangho , Park Sangwoo , Kim Yong-Giun , Ann Soe Hee , Park Hyun Woo , Suh Jon , Roh Jae-Hyung , Cho Young-Rak , Han Seungbong , Park Gyung-Min 
Published: April 2021

AbstractThe impact of pre-existing depression on mortality in individuals with established coronary artery disease (CAD) remains unclear. We evaluate the clinical implications of pre-existing depression in patients who underwent percutaneous coronary intervention (PCI). Based on National Health Insurance claims data in Korea, patients without a known history of CAD who underwent PCI between 2013 and 2017 were enrolled. The study population was divided into patients with angina (n = 50,256) or acute myocardial infarction (AMI; n = 40,049). The primary endpoint, defined as all-cause death, was compared between the non-depression and depression groups using propensity score matching analysis. After propensity score matching, there were 4262 and 2346 matched pairs of patients with angina and AMI, respectively. During the follow-up period, there was no significant difference in the incidence of all-cause death in the angina (hazard ratio [HR] of depression, 1.013; 95% confidence interval [CI] 0.893–1.151) and AMI (HR, 0.991; 95% CI 0.865–1.136) groups. However, angina patients less than 65 years of age with depression had higher all-cause mortality (HR, 1.769; 95% CI 1.240–2.525). In Korean patients undergoing PCI, pre-existing depression is not associated with poorer clinical outcomes. However, in younger patients with angina, depression is associated with higher all-cause mortality.
Investigation of random telegraph signal in two junction layouts of proton irradiated CMOS SPADs
Authors: Capua F. Di , Campajola M. , Fiore D. , Gasparini L. , Sarnelli E. , Aloisio A. 
Published: April 2021

AbstractThis paper focuses on the understanding of the Random Telegraph Signal (RTS) in Single-Photon Avalanche Diodes (SPAD). We studied the RTS of two different SPAD layouts, designed and implemented in a 150-nm CMOS process, after proton irradiation. The two structures are characterized by different junction types: the first structure is constituted by a P+/Nwell junction, while the second is formed by a Pwell/Niso junction. RTS occurrence has been measured in about one thousand SPAD pixels and the differences addressed in two layouts are motivated and discussed. Hypotheses on the RTS origin are drawn by analyzing the RTS time constants and the RTS occurrence evolution as a function of the annealing temperature.
Characterization of a Bowman–Birk type trypsin inhibitor purified from seeds of Solanum surattense
Authors: Herwade Abhijeet P. , Kasar Sainath S. , Rane Niraj R. , Ahmed Shadab , Maras Jaswinder Singh , Pawar Pankaj K. 
Published: April 2021

AbstractA Bowman–Birk type trypsin inhibitor protein (SSTI) from seeds of the medicinal plant Solanum surattense was isolated, purified and characterized. SSTI showed a single band on SDS-PAGE corresponding to 11.4 kDa molecular weight. It is a glycoprotein (2.8% glycosylation) that differentially interacted with trypsin and chymotrypsin in a concentration-dependent manner. Its peptide sequence is similar to other Bowman–Birk type protease inhibitors found in Glycine max and Phaseolus acutifolius. The inhibitory activity was stable over a wide range of pH (1–10) and temperatures (10–100° C). Far-UV Circular Dichroism (CD) studies showed that SSTI contains β sheets (~ 23%) and α helix (~ 6%) and demonstrated structural stability at wide pH and high temperature. The kinetic analysis revealed a noncompetitive (mixed) type nature of SSTI and low inhibitor constant (Ki) values (16.6 × 10−8 M) suggested strong inhibitory activity. Isothermal titration calorimetric analysis revealed its high affinity towards trypsin with dissociation constant (Kd) 2.28 µM.
RANDGAN: Randomized generative adversarial network for detection of COVID-19 in chest X-ray
Authors: Motamed Saman , Rogalla Patrik , Khalvati Farzad 
Published: April 2021

AbstractCOVID-19 spread across the globe at an immense rate and has left healthcare systems incapacitated to diagnose and test patients at the needed rate. Studies have shown promising results for detection of COVID-19 from viral bacterial pneumonia in chest X-rays. Automation of COVID-19 testing using medical images can speed up the testing process of patients where health care systems lack sufficient numbers of the reverse-transcription polymerase chain reaction tests. Supervised deep learning models such as convolutional neural networks need enough labeled data for all classes to correctly learn the task of detection. Gathering labeled data is a cumbersome task and requires time and resources which could further strain health care systems and radiologists at the early stages of a pandemic such as COVID-19. In this study, we propose a randomized generative adversarial network (RANDGAN) that detects images of an unknown class (COVID-19) from known and labelled classes (Normal and Viral Pneumonia) without the need for labels and training data from the unknown class of images (COVID-19). We used the largest publicly available COVID-19 chest X-ray dataset, COVIDx, which is comprised of Normal, Pneumonia, and COVID-19 images from multiple public databases. In this work, we use transfer learning to segment the lungs in the COVIDx dataset. Next, we show why segmentation of the region of interest (lungs) is vital to correctly learn the task of classification, specifically in datasets that contain images from different resources as it is the case for the COVIDx dataset. Finally, we show improved results in detection of COVID-19 cases using our generative model (RANDGAN) compared to conventional generative adversarial networks for anomaly detection in medical images, improving the area under the ROC curve from 0.71 to 0.77.
Evolving in islands of mud: old and structured hidden diversity in an endemic freshwater crayfish from the Chilean hotspot
Authors: Victoriano Pedro F. , D’Elía Guillermo 
Published: April 2021

AbstractParastacus is a genus of South American freshwater crayfishes disjunctively distributed in southern Chile, Northern Argentina, Uruguay and Southeastern Brazil. Parastacus pugnax is a Chilean endemic distributed along 700 km of latitude in central-southern Chile from the Pacific coast to the Andean piedmont, which is intensively captured for consumption for local communities. Considering the habitat (wet meadows) and natural history (primary burrower, non-migrant) of the species, we tested a hypothesis of highly structured genetic diversity using mtDNA of 465 specimens gathered at 56 localities across the species range. The crown age of P. pugnax was estimated at 38 Ma, predating the main Andean uplift. The genetic variation of P. pugnax is large and geographically structured. In some cases, genetic groups do not match basin limits, suggesting a previous to current dynamic of basin evolution. The uncovered intraspecific main lineages have different demographic histories. A latitudinal cline in past effective population size reduction suggests environmental singularities with a glacial effect in the southern populations. We suggest adding morphologic and more genetic data in order to assess species limits. Our results contribute to improve future conservation actions for this taxon, providing basic information to delimit conservation units.