bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reply to Comment by Poli et al. on “Fragmentation of the Adriatic Promontory: New Chronological Constraints From Neogene Shortening Rates Across the Southern Alps (NE Italy)”
Authors: Moulin Adrien , Benedetti Lucilla 
Published: July 2021

AbstractIn a comment on our manuscript published three years ago (Moulin & Benedetti [2018] https://doi.org/10.1029/2018TC004958), the authors raise concern about so‐called “mis‐interpreted alluvial and tectonic structures,” and conclude that these issues “invalidate all the consequent interpretations on the deformation rates.” Two points raised by the comment are acknowledged, and affect our results only by slightly reducing (by at most 15%) the Late Pleistocene shortening‐rate across the Eastern Southern Alps. The others issues raised by the comment are mainly dealing with the literature review, and alternative interpretations. Herein, we provide additional information to support our interpretations, and to relate our observations to existing data. Most importantly, our results do not call into question the existing consensus on both the crustal architecture of the Eastern Southern Alps, and the rate of recent shortening.
Twelve-month specific IgG response to SARS-CoV-2 receptor-binding domain among COVID-19 convalescent plasma donors in Wuhan
Authors: Li Cesheng , Yu Ding , Wu Xiao , Liang Hong , Zhou Zhijun , Xie Yong , Li Taojing , Wu Junzheng , Lu Fengping , Feng Lu , Mao Min , Lin Lianzhen , Guo Huanhuan , Yue Shenglan , Wang Feifei , Peng Yan , Hu Yong , Wang Zejun , Yu Jianhong , Zhang Yong , Lu Jia , Ning Haoran , Yang Huichuan , Fu Daoxing , He Yanlin , Zhou Dongbo , Du Tao , Duan Kai , Dong Demei , Deng Kun , Zou Xia , Zhang Ya , Zhou Rong , Gao Yang , Zhang Xinxin , Yang Xiaoming 
Published: July 2021

AbstractTo investigate the duration of humoral immune response in convalescent coronavirus disease 2019 (COVID-19) patients, we conduct a 12-month longitudinal study through collecting a total of 1,782 plasma samples from 869 convalescent plasma donors in Wuhan, China and test specific antibody responses. The results show that positive rate of IgG antibody against receptor-binding domain of spike protein (RBD-IgG) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the COVID-19 convalescent plasma donors exceeded 70% for 12 months post diagnosis. The level of RBD-IgG decreases with time, with the titer stabilizing at 35.7% of the initial level by the 9th month. Moreover, male plasma donors produce more RBD-IgG than female, and age of the patients positively correlates with the RBD-IgG titer. A strong positive correlation between RBD-IgG and neutralizing antibody titers is also identified. These results facilitate our understanding of SARS-CoV-2-induced immune memory to promote vaccine and therapy development.
Lack of consideration of sex and gender in COVID-19 clinical studies
Authors: Brady Emer , Nielsen Mathias Wullum , Andersen Jens Peter , Oertelt-Prigione Sabine 
Published: July 2021

AbstractSex and gender differences impact the incidence of SARS-CoV-2 infection and COVID-19 mortality. Furthermore, sex differences influence the frequency and severity of pharmacological side effects. A large number of clinical trials to develop new therapeutic approaches and vaccines for COVID-19 are ongoing. We investigated the inclusion of sex and/or gender in COVID-19 studies on ClinicalTrials.gov, collecting data for the period January 1, 2020 to January 26, 2021. Here, we show that of the 4,420 registered SARS-CoV-2/COVID-19 studies, 935 (21.2%) address sex/gender solely in the context of recruitment, 237 (5.4%) plan sex-matched or representative samples or emphasized sex/gender reporting, and only 178 (4%) explicitly report a plan to include sex/gender as an analytical variable. Just eight (17.8%) of the 45 COVID-19 related clinical trials published in scientific journals until December 15, 2020 report sex-disaggregated results or subgroup analyses.
Neofunctionalisation of the Sli gene leads to self-compatibility and facilitates precision breeding in potato
Authors: Eggers Ernst-Jan , van der Burgt Ate , van Heusden Sjaak A. W. , de Vries Michiel E. , Visser Richard G. F. , Bachem Christian W. B. , Lindhout Pim 
Published: July 2021

AbstractGenetic gain in potato is hampered by the heterozygous tetraploid genome of cultivated potato. Converting potato into a diploid inbred-line based F1-hybrid crop provides a promising route towards increased genetic gain. The introduction of a dominant S-locus inhibitor (Sli) gene into diploid potato germplasm allows efficient generation of self-fertilized seeds and thus the development of potato inbred lines. Little is known about the structure and function of theSlilocus. Here we describe the mapping ofSlito a 12.6 kb interval on chromosome 12 using a recombinant screen approach. One of two candidate genes present in this interval shows a unique sequence that is exclusively present in self-compatible lines. We describe an expression vector that converts self-incompatible genotypes into self-compatible and a CRISPR-Cas9 vector that converts SC genotypes into SI. TheSligene encodes an F-box protein that is specifically expressed in pollen from self-compatible plants. A 533 bp insertion in the promotor of that gene leads to a gain of function mutation, which overcomes self-pollen rejection.
Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins
Authors: Liu Zhiwen , Zhao Fanglong , Zhao Boyang , Yang Jie , Ferrara Joseph , Sankaran Banumathi , Venkataram Prasad B. V. , Kundu Biki Bapi , Phillips George N. , Gao Yang , Hu Liya , Zhu Tong , Gao Xue 
Published: July 2021

AbstractPrenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.
Encapsulate α-MnO2 nanofiber within graphene layer to tune surface electronic structure for efficient ozone decomposition
Authors: Zhu Guoxiang , Zhu Wei , Lou Yang , Ma Jun , Yao Wenqing , Zong Ruilong , Zhu Yongfa 
Published: July 2021

AbstractMajor challenges encountered when developing manganese-based materials for ozone decomposition are related to the low stability and water inactivation. To solve these problems, a hierarchical structure consisted of graphene encapsulating α-MnO2 nanofiber was developed. The optimized catalyst exhibited a stable ozone conversion efficiency of 80% and excellent stability over 100 h under a relative humidity (RH) of 20%. Even though the RH increased to 50%, the ozone conversion also reached 70%, well beyond the performance of α-MnO2 nanofiber. Here, surface graphite carbon was activated by capturing the electron from inner unsaturated Mn atoms. The excellent stability originated from the moderate local work function, which compromised the reaction barriers in the adsorption of ozone molecule and the desorption of the intermediate oxygen species. The hydrophobic graphene shells hindered the chemisorption of water vapour, consequently enhanced its water resistance. This work offered insights for catalyst design and would promote the practical application of manganese-based catalysts in ozone decomposition.
Structural basis for chemokine recognition and receptor activation of chemokine receptor CCR5
Authors: Zhang Hui , Chen Kun , Tan Qiuxiang , Shao Qiang , Han Shuo , Zhang Chenhui , Yi Cuiying , Chu Xiaojing , Zhu Ya , Xu Yechun , Zhao Qiang , Wu Beili 
Published: July 2021

AbstractThe chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain elusive. Here we report three cryo-electron microscopy structures of Gi1 protein-coupled CCR5 in a ligand-free state and in complex with the chemokine MIP-1α or RANTES, as well as the crystal structure of MIP-1α-bound CCR5. These structures reveal distinct binding modes of the two chemokines and a specific accommodate pattern of the chemokine for the distal N terminus of CCR5. Together with functional data, the structures demonstrate that chemokine-induced rearrangement of toggle switch and plasticity of the receptor extracellular region are critical for receptor activation, while a conserved tryptophan residue in helix II acts as a trigger of receptor constitutive activation.
Lure-and-kill macrophage nanoparticles alleviate the severity of experimental acute pancreatitis
Authors: Zhang Qiangzhe , Zhou Julia , Zhou Jiarong , Fang Ronnie H. , Gao Weiwei , Zhang Liangfang 
Published: July 2021

AbstractAcute pancreatitis is a disease associated with suffering and high lethality. Although the disease mechanism is unclear, phospholipase A2 (PLA2) produced by pancreatic acinar cells is a known pathogenic trigger. Here, we show macrophage membrane-coated nanoparticles with a built-in ‘lure and kill’ mechanism (denoted ‘MΦ-NP(L&K)’) for the treatment of acute pancreatitis. MΦ-NP(L&K) are made with polymeric cores wrapped with natural macrophage membrane doped with melittin and MJ-33. The membrane incorporated melittin and MJ-33 function as a PLA2 attractant and a PLA2 inhibitor, respectively. These molecules, together with membrane lipids, work synergistically to lure and kill PLA2 enzymes. These nanoparticles can neutralize PLA2 activity in the sera of mice and human patients with acute pancreatitis in a dose-dependent manner and suppress PLA2-induced inflammatory response accordingly. In mouse models of both mild and severe acute pancreatitis, MΦ-NP(L&K) confer effective protection against disease-associated inflammation, tissue damage and lethality. Overall, this biomimetic nanotherapeutic strategy offers an anti-PLA2 treatment option that might be applicable to a wide range of PLA2-mediated inflammatory disorders.
Both microRNA-455-5p and -3p repress hypoxia-inducible factor-2α expression and coordinately regulate cartilage homeostasis
Authors: Ito Yoshiaki , Matsuzaki Tokio , Ayabe Fumiaki , Mokuda Sho , Kurimoto Ryota , Matsushima Takahide , Tabata Yusuke , Inotsume Maiko , Tsutsumi Hiroki , Liu Lin , Shinohara Masahiro , Tanaka Yoko , Nakamichi Ryo , Nishida Keiichiro , Lotz Martin K. , Asahara Hiroshi 
Published: July 2021

AbstractOsteoarthritis (OA), the most common aging-related joint disease, is caused by an imbalance between extracellular matrix synthesis and degradation. Here, we discover that both strands of microRNA-455 (miR-455), -5p and -3p, are up-regulated by Sox9, an essential transcription factor for cartilage differentiation and function. Both miR-455-5p and -3p are highly expressed in human chondrocytes from normal articular cartilage and in mouse primary chondrocytes. We generate miR-455 knockout mice, and find that cartilage degeneration mimicking OA and elevated expression of cartilage degeneration-related genes are observed at 6-months-old. Using a cell-based miRNA target screening system, we identify hypoxia-inducible factor-2α (HIF-2α), a catabolic factor for cartilage homeostasis, as a direct target of both miR-455-5p and -3p. In addition, overexpression of both miR-455-5p and -3p protect cartilage degeneration in a mouse OA model, demonstrating their potential therapeutic value. Furthermore, knockdown of HIF-2α in 6-month-old miR-455 knockout cartilage rescues the elevated expression of cartilage degeneration-related genes. These data demonstrate that both strands of a miRNA target the same gene to regulate articular cartilage homeostasis.
Children’s role in the COVID-19 pandemic: a systematic review of early surveillance data on susceptibility, severity, and transmissibility
Authors: Gaythorpe Katy A. M. , Bhatia Sangeeta , Mangal Tara , Unwin H. Juliette T. , Imai Natsuko , Cuomo-Dannenburg Gina , Walters Caroline E. , Jauneikaite Elita , Bayley Helena , Kont Mara D. , Mousa Andria , Whittles Lilith K. , Riley Steven , Ferguson Neil M. 
Published: July 2021

AbstractSARS-CoV-2 infections have been reported in all age groups including infants, children, and adolescents. However, the role of children in the COVID-19 pandemic is still uncertain. This systematic review of early studies synthesises evidence on the susceptibility of children to SARS-CoV-2 infection, the severity and clinical outcomes in children with SARS-CoV-2 infection, and the transmissibility of SARS-CoV-2 by children in the initial phases of the COVID-19 pandemic. A systematic literature review was conducted in PubMed. Reviewers extracted data from relevant, peer-reviewed studies published up to July 4th 2020 during the first wave of the SARS-CoV-2 outbreak using a standardised form and assessed quality using the NIH Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. For studies included in the meta-analysis, we used a random effects model to calculate pooled estimates of the proportion of children considered asymptomatic or in a severe or critical state. We identified 2775 potential studies of which 128 studies met our inclusion criteria; data were extracted from 99, which were then quality assessed. Finally, 29 studies were considered for the meta-analysis that included information of symptoms and/or severity, these were further assessed based on patient recruitment. Our pooled estimate of the proportion of test positive children who were asymptomatic was 21.1% (95% CI: 14.0–28.1%), based on 13 included studies, and the proportion of children with severe or critical symptoms was 3.8% (95% CI: 1.5–6.0%), based on 14 included studies. We did not identify any studies designed to assess transmissibility in children and found that susceptibility to infection in children was highly variable across studies. Children’s susceptibility to infection and onward transmissibility relative to adults is still unclear and varied widely between studies. However, it is evident that most children experience clinically mild disease or remain asymptomatically infected. More comprehensive contact-tracing studies combined with serosurveys are needed to quantify children’s transmissibility relative to adults. With children back in schools, testing regimes and study protocols that will allow us to better understand the role of children in this pandemic are critical.
Metabolic and enzymatic elucidation of cooperative degradation of red seaweed agarose by two human gut bacteria
Authors: Yun Eun Ju , Yu Sora , Park Na Jung , Cho Yoonho , Han Na Ree , Jin Yong-Su , Kim Kyoung Heon 
Published: July 2021

AbstractVarious health beneficial outcomes associated with red seaweeds, especially their polysaccharides, have been claimed, but the molecular pathway of how red seaweed polysaccharides are degraded and utilized by cooperative actions of human gut bacteria has not been elucidated. Here, we investigated the enzymatic and metabolic cooperation between two human gut symbionts, Bacteroides plebeius and Bifidobacterium longum ssp. infantis, with regard to the degradation of agarose, the main carbohydrate of red seaweed. More specifically, B. plebeius initially decomposed agarose into agarotriose by the actions of the enzymes belonging to glycoside hydrolase (GH) families 16 and 117 (i.e., BpGH16A and BpGH117) located in the polysaccharide utilization locus, a specific gene cluster for red seaweed carbohydrates. Then, B. infantis extracted energy from agarotriose by the actions of two agarolytic β-galactosidases (i.e., Bga42A and Bga2A) and produced neoagarobiose. B. plebeius ultimately acted on neoagarobiose by BpGH117, resulting in the production of 3,6-anhydro-l-galactose, a monomeric sugar possessing anti-inflammatory activity. Our discovery of the cooperative actions of the two human gut symbionts on agarose degradation and the identification of the related enzyme genes and metabolic intermediates generated during the metabolic processes provide a molecular basis for agarose degradation by gut bacteria.
Feature-based attention enables robust, long-lasting location transfer in human perceptual learning
Authors: Hung Shao-Chin , Carrasco Marisa 
Published: July 2021

AbstractVisual perceptual learning (VPL) is typically specific to the trained location and feature. However, the degree of specificity depends upon particular training protocols. Manipulating covert spatial attention during training facilitates learning transfer to other locations. Here we investigated whether feature-based attention (FBA), which enhances the representation of particular features throughout the visual field, facilitates VPL transfer, and how long such an effect would last. To do so, we implemented a novel task in which observers discriminated a stimulus orientation relative to two reference angles presented simultaneously before each block. We found that training with FBA enabled remarkable location transfer, reminiscent of its global effect across the visual field, but preserved orientation specificity in VPL. Critically, both the perceptual improvement and location transfer persisted after 1 year. Our results reveal robust, long-lasting benefits induced by FBA in VPL, and have translational implications for improving generalization of training protocols in visual rehabilitation.
Leaf scale quantification of the effect of photosynthetic gas exchange on Δ47 of CO2
Authors: Adnew Getachew Agmuas , Hofmann Magdalena E. G. , Pons Thijs L. , Koren Gerbrand , Ziegler Martin , Lourens Lucas J. , Röckmann Thomas 
Published: July 2021

AbstractThe clumped isotope composition (Δ47, the anomaly of the mass 47 isotopologue relative to the abundance expected from a random isotope distribution) of CO2has been suggested as an additional tracer for gross CO2fluxes. However, the effect of photosynthetic gas exchange on Δ47has not been directly determined and two indirect/conceptual studies reported contradicting results. In this study, we quantify the effect of photosynthetic gas exchange on Δ47of CO2using leaf cuvette experiments with one C4and two C3plants. The experimental results are supported by calculations with a leaf cuvette model. Our results demonstrate the important roles of the Δ47value of CO2entering the leaf, kinetic fractionation as CO2diffuses into, and out of the leaf and CO2–H2O isotope exchange with leaf water. We experimentally confirm the previously suggested dependence of Δ47of CO2in the air surrounding a leaf on the stomatal conductance and back-diffusion flux. Gas exchange can enrich or deplete the Δ47of CO2depending on the Δ47of CO2entering the leaf and the fraction of CO2exchanged with leaf water and diffused back to the atmosphere, but under typical ambient conditions, it will lead to a decrease in Δ47.
Multi-frequency passive and active microrheology with optical tweezers
Authors: Kumar Randhir , Vitali Valerio , Wiedemann Timo , Meissner Robert , Minzioni Paolo , Denz Cornelia 
Published: July 2021

AbstractOptical tweezers have attracted significant attention for microrheological applications, due to the possibility of investigating viscoelastic properties in vivo which are strongly related to the health status and development of biological specimens. In order to use optical tweezers as a microrheological tool, an exact force calibration in the complex system under investigation is required. One of the most promising techniques for optical tweezers calibration in a viscoelastic medium is the so-called active–passive calibration, which allows determining both the trap stiffness and microrheological properties of the medium with the least a-priori knowledge in comparison to the other methods. In this manuscript, we develop an optimization of the active–passive calibration technique performed with a sample stage driving, whose implementation is more straightforward with respect to standard laser driving where two different laser beams are required. We performed microrheological measurements over a broad frequency range in a few seconds implementing an accurate multi-frequency driving of the sample stage. The optical tweezers-based microrheometer was first validated by measuring water, and then exemplarily applied to more viscous medium and subsequently to a viscoelastic solution of methylcellulose in water. The described method paves the way to microrheological precision metrology in biological samples with high temporal- and spatial-resolution allowing for investigation of even short time-scale phenomena.
Enhancement of the thermoelectric properties in bilayer graphene structures induced by Fano resonances
Authors: Briones-Torres J. A. , Pérez-Álvarez R. , Molina-Valdovinos S. , Rodríguez-Vargas I. 
Published: July 2021

AbstractFano resonances of bilayer graphene could be attractive for thermoelectric devices. The special profile presented by such resonances could significantly enhance the thermoelectric properties. In this work, we study the thermoelectric properties of bilayer graphene single and double barrier structures. The barrier structures are typically supported by a substrate and encapsulated by protecting layers, reducing considerably the phonon thermal transport. So, we will focus on the electronic contribution to the thermal transport. The charge carriers are described as massive chiral particles through an effective Dirac-like Hamiltonian. The Hybrid matrix method and the Landauer–Büttiker formalism are implemented to obtain the transmission, transport and thermoelectric properties. The temperature dependence of the Seebeck coefficient, the power factor, the figure of merit and the efficiency is analyzed for gapless single and double barriers. We find that the charge neutrality point and the system resonances shape the thermoelectric response. In the case of single barriers, the low-temperature thermoelectric response is dominated by the charge neutrality point, while the high-temperature response is determined by the Fano resonances. In the case of double barriers, Breit–Wigner resonances dominate the thermoelectric properties at low temperatures, while Fano and hybrid resonances become preponderant as the temperature rises. The values for the figure of merit are close to two for single barriers and above three for double barriers. The system resonances also allows us to optimize the output power and the efficiency at low and high temperatures. By computing the density of states, we also corroborate that the improvement of the thermoelectric properties is related to the accumulation of electron states. Our findings indicate that bilayer graphene barrier structures can be used to improve the response of thermoelectric devices.