bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twist-angle dependence of moiré excitons in WS2/MoSe2 heterobilayers
Authors: Zhang Long , Zhang Zhe , Wu Fengcheng , Wang Danqing , Gogna Rahul , Hou Shaocong , Watanabe Kenji , Taniguchi Takashi , Kulkarni Krishnamurthy , Kuo Thomas , Forrest Stephen R. , Deng Hui 
Published: November 2020

AbstractMoiré lattices formed in twisted van der Waals bilayers provide a unique, tunable platform to realize coupled electron or exciton lattices unavailable before. While twist angle between the bilayer has been shown to be a critical parameter in engineering the moiré potential and enabling novel phenomena in electronic moiré systems, a systematic experimental study as a function of twist angle is still missing. Here we show that not only are moiré excitons robust in bilayers of even large twist angles, but also properties of the moiré excitons are dependant on, and controllable by, the moiré reciprocal lattice period via twist-angle tuning. From the twist-angle dependence, we furthermore obtain the effective mass of the interlayer excitons and the electron inter-layer tunneling strength, which are difficult to measure experimentally otherwise. These findings pave the way for understanding and engineering rich moiré-lattice induced phenomena in angle-twisted semiconductor van der Waals heterostructures.
Multilayer stabilization for fabricating high-loading single-atom catalysts
Authors: Zhou Yazhou , Tao Xiafang , Chen Guangbo , Lu Ruihu , Wang Ding , Chen Ming-Xi , Jin Enquan , Yang Juan , Liang Hai-Wei , Zhao Yan , Feng Xinliang , Narita Akimitsu , Müllen Klaus 
Published: November 2020

AbstractMetal single-atom catalysts (M-SACs) have emerged as an attractive concept for promoting heterogeneous reactions, but the synthesis of high-loading M-SACs remains a challenge. Here, we report a multilayer stabilization strategy for constructing M-SACs in nitrogen-, sulfur- and fluorine-co-doped graphitized carbons (M = Fe, Co, Ru, Ir and Pt). Metal precursors are embedded into perfluorotetradecanoic acid multilayers and are further coated with polypyrrole prior to pyrolysis. Aggregation of the metals is thus efficiently inhibited to achieve M-SACs with a high metal loading (~16 wt%). Fe-SAC serves as an efficient oxygen reduction catalyst with half-wave potentials of 0.91 and 0.82 V (versus reversible hydrogen electrode) in alkaline and acid solutions, respectively. Moreover, as an air electrode in zinc–air batteries, Fe-SAC demonstrates a large peak power density of 247.7 mW cm−2 and superior long-term stability. Our versatile method paves an effective way to develop high-loading M-SACs for various applications.
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site
Authors: Lee Jaeyong , Worrall Liam J. , Vuckovic Marija , Rosell Federico I. , Gentile Francesco , Ton Anh-Tien , Caveney Nathanael A. , Ban Fuqiang , Cherkasov Artem , Paetzel Mark , Strynadka Natalie C. J. 
Published: November 2020

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (Mpro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on Mpro inhibition.
Genome-enabled discovery of anthraquinone biosynthesis in Senna tora
Authors: Kang Sang-Ho , Pandey Ramesh Prasad , Lee Chang-Muk , Sim Joon-Soo , Jeong Jin-Tae , Choi Beom-Soon , Jung Myunghee , Ginzburg Daniel , Zhao Kangmei , Won So Youn , Oh Tae-Jin , Yu Yeisoo , Kim Nam-Hoon , Lee Ok Ran , Lee Tae-Ho , Bashyal Puspalata , Kim Tae-Su , Lee Woo-Haeng , Hawkins Charles , Kim Chang-Kug , Kim Jung Sun , Ahn Byoung Ohg , Rhee Seung Yon , Sohng Jae Kyung 
Published: November 2020

AbstractSenna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.
Endogenous antisense RNA curbs CD39 expression in Crohn’s disease
Authors: Harshe Rasika P. , Xie Anyan , Vuerich Marta , Frank Luiza Abrahão , Gromova Barbora , Zhang Haohai , Robles Rene’ J. , Mukherjee Samiran , Csizmadia Eva , Kokkotou Efi , Cheifetz Adam S. , Moss Alan C. , Kota Satya K. , Robson Simon C. , Longhi Maria Serena 
Published: November 2020

AbstractCD39 is an ectonucleotidase that initiates conversion of extracellular nucleotides into immunosuppressive adenosine. CD39 is expressed by regulatory T (Treg)-cells, where it mediates immunosuppression, and by a subset of T-helper (Th) 17-cells, where it limits pathogenicity. CD39 is regulated via single-nucleotide-polymorphisms and upon activation of aryl-hydrocarbon-receptor and oxygen-mediated pathways. Here we report a mechanism of CD39 regulation that relies on the presence of an endogenous antisense RNA, transcribed from the 3′-end of the human CD39/ENTPD1 gene. CD39-specific antisense is increased in Treg and Th17-cells of Crohn’s disease patients over controls. It largely localizes in the cell nucleus and regulates CD39 by interacting with nucleolin and heterogeneous-nuclear-ribonucleoprotein-A1. Antisense silencing results in CD39 upregulation in vitro and amelioration of disease activity in a trinitro-benzene-sulfonic-acid model of colitis in humanized NOD/scid/gamma mice. Inhibition/blockade of antisense might represent a therapeutic strategy to restore CD39 along with immunohomeostasis in Crohn’s disease.
Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease
Authors: Bowerman Kate L. , Rehman Saima Firdous , Vaughan Annalicia , Lachner Nancy , Budden Kurtis F. , Kim Richard Y. , Wood David L. A. , Gellatly Shaan L. , Shukla Shakti D. , Wood Lisa G. , Yang Ian A. , Wark Peter A. , Hugenholtz Philip , Hansbro Philip M. 
Published: November 2020

AbstractChronic obstructive pulmonary disease (COPD) is the third commonest cause of death globally, and manifests as a progressive inflammatory lung disease with no curative treatment. The lung microbiome contributes to COPD progression, but the function of the gut microbiome remains unclear. Here we examine the faecal microbiome and metabolome of COPD patients and healthy controls, finding 146 bacterial species differing between the two groups. Several species, includingStreptococcus sp000187445,Streptococcus vestibularisand multiple members of the familyLachnospiraceae, also correlate with reduced lung function. Untargeted metabolomics identifies a COPD signature comprising 46% lipid, 20% xenobiotic and 20% amino acid related metabolites. Furthermore, we describe a disease-associated network connectingStreptococcus parasanguinis_Bwith COPD-associated metabolites, including N-acetylglutamate and its analogue N-carbamoylglutamate. While correlative, our results suggest that the faecal microbiome and metabolome of COPD patients are distinct from those of healthy individuals, and may thus aid in the search for biomarkers for COPD.
DNA synthesis for true random number generation
Authors: Meiser Linda C. , Koch Julian , Antkowiak Philipp L. , Stark Wendelin J. , Heckel Reinhard , Grass Robert N. 
Published: November 2020

AbstractThe volume of securely encrypted data transmission required by today’s network complexity of people, transactions and interactions increases continuously. To guarantee security of encryption and decryption schemes for exchanging sensitive information, large volumes of true random numbers are required. Here we present a method to exploit the stochastic nature of chemistry by synthesizing DNA strands composed of random nucleotides. We compare three commercial random DNA syntheses giving a measure for robustness and synthesis distribution of nucleotides and show that using DNA for random number generation, we can obtain 7 million GB of randomness from one synthesis run, which can be read out using state-of-the-art sequencing technologies at rates of ca. 300 kB/s. Using the von Neumann algorithm for data compression, we remove bias introduced from human or technological sources and assess randomness using NIST’s statistical test suite.
Immunogenicity, safety, and efficacy of sequential immunizations with an SIV-based IDLV expressing CH505 Envs
Authors: Blasi Maria , Negri Donatella , Saunders Kevin O. , Baker Erich J. , Stadtler Hannah , LaBranche Celia , Mildenberg Benjamin , Morton Georgeanna , Ciarla Andrew , Shen Xiaoying , Wang Yunfei , Rountree Wes , Balakumaran Bala , Santra Sampa , Haynes Barton F. , Moody Anthony M. , Cara Andrea , Klotman Mary E. 
Published: November 2020

AbstractA preventative HIV-1 vaccine is an essential intervention needed to halt the HIV-1 pandemic. Neutralizing antibodies protect against HIV-1 infection in animal models, and thus an approach toward a protective HIV-1 vaccine is to induce broadly cross-reactive neutralizing antibodies (bnAbs). One strategy to achieve this goal is to define envelope (Env) evolution that drives bnAb development in infection and to recreate those events by vaccination. In this study, we report the immunogenicity, safety, and efficacy in rhesus macaques of an SIV-based integrase defective lentiviral vector (IDLV) expressing sequential gp140 Env immunogens derived from the CH505 HIV-1-infected individual who made the CH103 and CH235 bnAb lineages. Immunization with IDLV expressing sequential CH505 Envs induced higher magnitude and more durable binding and neutralizing antibody responses compared to protein or DNA +/− protein immunizations using the same sequential envelopes. Compared to monkeys immunized with a vector expressing Envs alone, those immunized with the combination of IDLV expressing Env and CH505 Env protein demonstrated improved durability of antibody responses at six months after the last immunization as well as lower peak viremia and better virus control following autologous SHIV-CH505 challenge. There was no evidence of vector mobilization or recombination in the immunized and challenged monkeys. Although the tested vaccines failed to induce bnAbs and to mediate significant protection following SHIV-challenge, our results show that IDLV proved safe and successful at inducing higher titer and more durable immune responses compared to other vaccine platforms.
From gangue to the fuel-cells application
Authors: El-Eskandarany M. Sherif , Al-Salem Sultan Majed , Ali Naser , Banyan Mohammad , Al-Ajmi Fahad , Al-Duweesh Ahmed 
Published: November 2020

AbstractHydrogen, which is a new clean energy option for future energy systems possesses pioneering characteristics making it a desirable carbon-free energy carrier. Hydrogen storage plays a crucial role in initiating a hydrogen economy. Due to its low density, the storage of hydrogen in the gaseous and liquids states had several technical and economic challenges. Despite these traditional approaches, magnesium hydride (MgH2), which has high gravimetric and volumetric hydrogen density, offers an excellent potential option for utilizing hydrogen in automobiles and other electrical systems. In contrast to its attractive properties, MgH2 should be mechanically and chemically treated to reduce its high activation energy and enhance its modest hydrogen sorption/desorption kinetics. The present study aims to investigate the influence of doping mechanically-treated Mg metal with 5 wt% amorphous Zr2Cu abrasive nanopowders in improving its kinetics and cyclability behaviors. For the first time, solid-waste Mg, Zr, and Cu metals were utilized for preparing MgH2 and amorphous Zr2Cu alloy (catalytic agent), using hydrogen gas-reactive ball milling, and arc melting techniques, respectively. This new nanocomposite system revealed high-capacity hydrogen storage (6.6 wt%) with superior kinetics and extraordinary long cycle-life-time (1100 h) at 250 °C.
Benefits and constrains of covalency: the role of loop length in protein stability and ligand binding
Authors: Linse Sara , Thulin Eva , Nilsson Hanna , Stigler Johannes 
Published: November 2020

AbstractProtein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.
A new generation of direct X-ray detectors for medical and synchrotron imaging applications
Authors: Datta A. , Zhong Z. , Motakef S. 
Published: November 2020

AbstractLarge-area X-ray imaging is one of the most widely used imaging modalities that spans several scientific and technological fields. Currently, the direct X-ray conversion materials that are being commercially used for large-area (> 8 cm × 4 cm without tiling) flat panel applications, such as amorphous selenium (a-Se), have usable sensitivities of up to only 30 keV. Although there have been many promising candidates (such as polycrystalline HgI2 and CdTe), none of the semiconductors were able to assuage the requirement for high energy (> 40 keV) large-area X-ray imaging applications due to inadequate cost, manufacturability, and long-term performance metrics. In this study, we successfully demonstrate the potential of the hybrid Methylammonium lead iodide (MAPbI3) perovskite-based semiconductor detectors in satisfying all the requirements for its successful commercialization in synchrotron and medical imaging. This new generation of hybrid detectors demonstrates low dark current under electric fields needed for high sensitivity X-ray imaging applications. The detectors have a linear response to X-ray energy and applied bias, no polarization effects at a moderate bias, and signal stability over long usage durations. Also, these detectors have demonstrated a stable detection response under BNL’s National Synchrotron Light Source II (NSLS-II) 70 keV monochromatic synchrotron beamline.
Water warming increases aggression in a tropical fish
Authors: Kua Zi Xun , Hamilton Ian M. , McLaughlin Allison L. , Brodnik Reed M. , Keitzer S. Conor , Gilliland Jake , Hoskins Elizabeth A. , Ludsin Stuart A. 
Published: November 2020

AbstractOur understanding of how projected climatic warming will influence the world’s biota remains largely speculative, owing to the many ways in which it can directly and indirectly affect individual phenotypes. Its impact is expected to be especially severe in the tropics, where organisms have evolved in more physically stable conditions relative to temperate ecosystems. Lake Tanganyika (eastern Africa) is one ecosystem experiencing rapid warming, yet our understanding of how its diverse assemblage of endemic species will respond is incomplete. Herein, we conducted a laboratory experiment to assess how anticipated future warming would affect the mirror-elicited aggressive behaviour of Julidochromis ornatus, a common endemic cichlid in Lake Tanganyika. Given linkages that have been established between temperature and individual behaviour in fish and other animals, we hypothesized that water warming would heighten average individual aggression. Our findings support this hypothesis, suggesting the potential for water warming to mediate behavioural phenotypic expression through negative effects associated with individual health (body condition). We ultimately discuss the implications of our findings for efforts aimed at understanding how continued climate warming will affect the ecology of Lake Tanganyika fishes and other tropical ectotherms.
Similarity-based link prediction in social networks using latent relationships between the users
Authors: Zareie Ahmad , Sakellariou Rizos 
Published: November 2020

AbstractSocial network analysis has recently attracted lots of attention among researchers due to its wide applicability in capturing social interactions. Link prediction, related to the likelihood of having a link between two nodes of the network that are not connected, is a key problem in social network analysis. Many methods have been proposed to solve the problem. Among these methods, similarity-based methods exhibit good efficiency by considering the network structure and using as a fundamental criterion the number of common neighbours between two nodes to establish structural similarity. High structural similarity may suggest that a link between two nodes is likely to appear. However, as shown in the paper, the number of common neighbours may not be always sufficient to provide comprehensive information about structural similarity between a pair of nodes. To address this, a neighbourhood vector is first specified for each node. Then, a novel measure is proposed to determine the similarity of each pair of nodes based on the number of common neighbours and correlation between the neighbourhood vectors of the nodes Experimental results, on a range of different real-world networks, suggest that the proposed method results in higher accuracy than other state-of-the-art similarity-based methods for link prediction.
The effect of refractive error on optokinetic nystagmus
Authors: Doustkouhi Soheil M. , Turnbull Philip R. K. , Dakin Steven C. 
Published: November 2020

AbstractSubjective refraction is the gold-standard for prescribing refractive correction, but its accuracy is limited by patient’s subjective judgment about their clarity of vision. We asked if an involuntary eye movement, optokinetic nystagmus (OKN), could serve as an objective measure of visual-clarity, specifically measuring the dependence of OKN—elicited by drifting spatial-frequency filtered noise—on mean spherical equivalent (MSE) refractive error. In Experiment 1 we quantified OKN score—a measure of consistency with stimulus-direction—for participants with different MSEs. Estimates of MSE based on OKN scores correlate well with estimates of MSE made using autorefraction (r = 0.878, p < 0.001, Bland–Altman analysis: mean difference of 0.00D (95% limits of agreement: − 0.85 to + 0.85D). In Experiment 2, we quantified the relationship between OKN gain (ratio of tracking eye-movement velocity to stimulus velocity) and MSEs (− 2.00, − 1.00, − 0.50, 0.00 and + 1.00D) induced with contact lenses for each participant. The mean difference between measures of MSE based on autorefraction or on OKN gain was + 0.05D (− 0.90 to + 1.01D), and the correlation of these measures across participants was r = 0.976, p < 0.001. Results indicate that MSE attenuates OKN gain so that OKN can be used as an objective proxy for patient response to select the best corrective lens.
Spen modulates lipid droplet content in adult Drosophila glial cells and protects against paraquat toxicity
Authors: Girard Victor , Goubard Valérie , Querenet Matthieu , Seugnet Laurent , Pays Laurent , Nataf Serge , Dufourd Eloïse , Cluet David , Mollereau Bertrand , Davoust Nathalie 
Published: November 2020

AbstractGlial cells are early sensors of neuronal injury and can store lipids in lipid droplets under oxidative stress conditions. Here, we investigated the functions of the RNA-binding protein, SPEN/SHARP, in the context of Parkinson’s disease (PD). Using a data-mining approach, we found that SPEN/SHARP is one of many astrocyte-expressed genes that are significantly differentially expressed in the substantia nigra of PD patients compared with control subjects. Interestingly, the differentially expressed genes are enriched in lipid metabolism-associated genes. In a Drosophila model of PD, we observed that flies carrying a loss-of-function allele of the ortholog split-ends (spen) or with glial cell-specific, but not neuronal-specific, spen knockdown were more sensitive to paraquat intoxication, indicating a protective role for Spen in glial cells. We also found that Spen is a positive regulator of Notch signaling in adult Drosophila glial cells. Moreover, Spen was required to limit abnormal accumulation of lipid droplets in glial cells in a manner independent of its regulation of Notch signaling. Taken together, our results demonstrate that Spen regulates lipid metabolism and storage in glial cells and contributes to glial cell-mediated neuroprotection.