bluuebunny/crossref_metadata_2025_split huggingface dataset:
HMGA2 regulates circular RNA ASPH to promote tumor growth in lung adenocarcinoma
Authors: Xu Li , Ma Ye , Zhang Hua , Lu Qi-Jue , Yang Lie , Jiang Ge-Ning , Liao Wei-Lin 
Published: July 2020

AbstractIn this study, we identified a circular form of ASPH RNA (circASPH), expression of which was upregulated in lung adenocarcinoma and the human lung adenocarcinoma cell lines. We also found a positive correlation between circASPH level and the T and N stages of lung adenocarcinoma patients. Patients with higher levels of circASPH had a shorter overall survival. Moreover, we demonstrated that circASPH was directly regulated by HMGA2 and Twist1. The direct positive regulation of circASPH by Twist1 was dependent on the presence of HMGA2. Functional assays indicated that circASPH promoted the proliferation, migration, and invasion of lung adenocarcinoma cell lines in vitro. The promoting effect of tumor growth by circASPH was also observed in vivo. Mechanistically, circASPH was identified to act as a molecular sponge for miR-370 and abrogate miR-370-mediated inhibition of HMGA2. Finally, we demonstrated that the oncogenic function of circASPH was HMGA2-dependent. These findings reveal the oncogenic functions of the HMGA2-circASPH-HMGA2 axis and may be useful in developing circRNA-based therapeutic strategies for lung adenocarcinoma.
The sugar transporter system of strawberry: genome-wide identification and expression correlation with fruit soluble sugar-related traits in a Fragaria × ananassa germplasm collection
Authors: Liu Hai-Ting , Ji Ying , Liu Ya , Tian Shu-Hua , Gao Qing-Hua , Zou Xiao-Hua , Yang Jing , Dong Chao , Tan Jia-Hui , Ni Di-An , Duan Ke 
Published: July 2020

AbstractSugar from plant photosynthesis is a basic requirement for life activities. Sugar transporters are the proteins that mediate sugar allocation among or within source/sink organs. The transporters of the major facilitator superfamily (MFS) targeting carbohydrates represent the largest family of sugar transporters in many plants. Strawberry (Fragaria × ananassa Duchesne) is an important crop appreciated worldwide for its unique fruit flavor. The involvement of MFS sugar transporters (STs) in cultivated strawberry fruit sugar accumulation is largely unknown. In this work, we characterized the genetic variation associated with fruit soluble sugars in a collection including 154 varieties. Then, a total of 67 ST genes were identified in the v4.0 genome integrated with the v4.0.a2 protein database of F. vesca, the dominant subgenome provider for modern cultivated strawberry. Phylogenetic analysis updated the nomenclature of strawberry ST homoeologs. Both the chromosomal distribution and structural characteristics of the ST family were improved. Semi-RT-PCR analysis in nine tissues from cv. Benihoppe screened 34 highly expressed ST genes in fruits. In three varieties with dramatically differing fruit sugar levels, qPCR integrated with correlation analysis between ST transcript abundance and sugar content identified 13 sugar-correlated genes. The correlations were re-evaluated across 19 varieties, including major commercial cultivars grown in China. Finally, a model of the contribution of the sugar transporter system to subcellular sugar allocation in strawberry fruits was proposed. Our work highlights the involvement of STs in controlling strawberry fruit soluble sugars and provides candidates for the future functional study of STs in strawberry development and responses and a new approach for strawberry genetic engineering and molecular breeding.
High-throughput production of cheap mineral-based two-dimensional electrocatalysts for high-current-density hydrogen evolution
Authors: Zhang Chi , Luo Yuting , Tan Junyang , Yu Qiangmin , Yang Fengning , Zhang Zhiyuan , Yang Liusi , Cheng Hui-Ming , Liu Bilu 
Published: July 2020

AbstractThe high-throughput scalable production of cheap, efficient and durable electrocatalysts that work well at high current densities demanded by industry is a great challenge for the large-scale implementation of electrochemical technologies. Here we report the production of a two-dimensional molybdenum disulfide-based ink-type electrocatalyst by a scalable exfoliation technique followed by a thermal treatment. The catalyst delivers a high current density of 1000 mA cm−2at an overpotential of 412 mV for the hydrogen evolution. Using the same method, we produce a cheap mineral-based catalyst possessing excellent performance for high-current-density hydrogen evolution. Noteworthy, production rate of this catalyst is one to two orders of magnitude higher than those previously reported, and price of the mineral is five orders of magnitude lower than commercial Pt electrocatalysts. These advantages indicate the huge potentials of this method and of mineral-based cheap and abundant natural resources as catalysts in the electrochemical industry.
Discovery of an unrecognized pathway carrying overflow waters toward the Faroe Bank Channel
Authors: Chafik Léon , Hátún Hjálmar , Kjellsson Joakim , Larsen Karin Margretha H. , Rossby Thomas , Berx Barbara 
Published: July 2020

AbstractThe dense overflow waters of the Nordic Seas are an integral link and important diagnostic for the stability of the Atlantic Meridional Overturning Circulation (AMOC). The pathways feeding the overflow remain, however, poorly resolved. Here we use multiple observational platforms and an eddy-resolving ocean model to identify an unrecognized deep flow toward the Faroe Bank Channel. We demonstrate that anticyclonic wind forcing in the Nordic Seas via its regulation of the basin circulation plays a key role in activating an unrecognized overflow path from the Norwegian slope – at which times the overflow is anomalously strong. We further establish that, regardless of upstream pathways, the overflows are mostly carried by a deep jet banked against the eastern slope of the Faroe-Shetland Channel, contrary to previous thinking. This deep flow is thus the primary conduit of overflow water feeding the lower branch of the AMOC via the Faroe Bank Channel.
Preparation of TiH1.924 nanodots by liquid-phase exfoliation for enhanced sonodynamic cancer therapy
Authors: Gong Fei , Cheng Liang , Yang Nailin , Gong Yuehan , Ni Yanwen , Bai Shang , Wang Xianwen , Chen Muchao , Chen Qian , Liu Zhuang 
Published: July 2020

AbstractMetal hydrides have been rarely used in biomedicine. Herein, we fabricate titanium hydride (TiH1.924) nanodots from its powder form via the liquid-phase exfoliation, and apply these metal hydride nanodots for effective cancer treatment. The liquid-phase exfoliation is an effective method to synthesize these metal hydride nanomaterials, and its efficiency is determined by the matching of surface energy between the solvent and the metal hydrides. The obtained TiH1.924 nanodots can produce reactive oxygen species (ROS) under ultrasound, presenting a highly efficient sono-sensitizing effect. Meanwhile, TiH1.924 nanodots with strong near-infrared (NIR) absorbance can serve as a robust photothermal agent. By using the mild photothermal effect to enhance intra-tumoral blood flow and improve tumor oxygenation, a remarkable synergistic therapeutic effect is achieved in the combined photothermal-sonodynamic therapy. Importantly, most of these TiH1.924 nanodots can be cleared out from the body. This work presents the promises of functional metal hydride nanomaterials for biomedical applications.
Long-lasting severe immune dysfunction in Ebola virus disease survivors
Authors: Wiedemann Aurélie , Foucat Emile , Hocini Hakim , Lefebvre Cécile , Hejblum Boris P. , Durand Mélany , Krüger Miriam , Keita Alpha Kabinet , Ayouba Ahidjo , Mély Stéphane , Fernandez José-Carlos , Touré Abdoulaye , Fourati Slim , Lévy-Marchal Claire , Raoul Hervé , Delaporte Eric , Koivogui Lamine , Thiébaut Rodolphe , Lacabaratz Christine , Lévy Yves ,   PostEboGui Study Group, Ayouba Ahidjo , Delaporte Eric , Keita Alpha Kabinet , Koivogui Lamine , Lacabaratz Christine , Marchal Claire Levy , Levy Yves , Raoul Hervé , Touré Abdoulaye 
Published: July 2020

AbstractLong-term follow up studies from Ebola virus disease (EVD) survivors (EBOV_S) are lacking. Here, we evaluate immune and gene expression profiles in 35 Guinean EBOV_S from the last West African outbreak, a median of 23 months (IQR [18–25]) after discharge from treatment center. Compared with healthy donors, EBOV_S exhibit increases of blood markers of inflammation, intestinal tissue damage, T cell and B cell activation and a depletion of circulating dendritic cells. All survivors have EBOV-specific IgG antibodies and robust and polyfunctional EBOV-specific memory T-cell responses. Deep sequencing of the genes expressed in blood reveals an enrichment in ‘inflammation’ and ‘antiviral’ pathways. Integrated analyses identify specific immune markers associated with the persistence of clinical symptoms. This study identifies a set of biological and genetic markers that could be used to define a signature of “chronic Ebola virus disease (CEVD)”.
Li2CO3-affiliative mechanism for air-accessible interface engineering of garnet electrolyte via facile liquid metal painting
Authors: Meng Junwei , Zhang Yang , Zhou Xuejun , Lei Meng , Li Chilin 
Published: July 2020

AbstractGarnet based solid-state batteries have the advantages of wide electrochemical window and good chemical stability. However, at Li-garnet interface, the poor interfacial wettability due to Li2CO3 passivation usually causes large resistance and unstable contact. Here, a Li2CO3-affiliative mechanism is proposed for air-accessible interface engineering of garnet electrolyte via facile liquid metal (LM) painting. The natural LM oxide skin enables a superior wettability of LM interlayer towards ceramic electrolyte and Li anode. Therein the removal of Li2CO3 passivation network is not necessary, in view of its delamination and fragmentation by LM penetration. This dissipation effect allows the lithiated LM nanodomains to serve as alternative Li-ion flux carriers at Li-garnet interface. This mechanism leads to an interfacial resistance as small as 5 Ω cm2 even after exposing garnet in air for several days. The ultrastable Li plating and stripping across LM painted garnet can last for 9930 h with a small overpotential.
Structural basis of RNA cap modification by SARS-CoV-2
Authors: Viswanathan Thiruselvam , Arya Shailee , Chan Siu-Hong , Qi Shan , Dai Nan , Misra Anurag , Park Jun-Gyu , Oladunni Fatai , Kovalskyy Dmytro , Hromas Robert A. , Martinez-Sobrido Luis , Gupta Yogesh K. 
Published: July 2020

AbstractThe severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. In SARS coronaviruses, the non-structural protein 16 (nsp16), in conjunction with nsp10, methylates the 5′-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM). The nsp16/nsp10 heterodimer is captured in the act of 2′-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This induced fit model provides mechanistic insights into the 2′-O methylation of the viral mRNA cap. We also discover a distant (25 Å) ligand-binding site unique to SARS-CoV-2, which can alternatively be targeted, in addition to RNA cap and SAM pockets, for antiviral development.
Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion
Authors: Simon David , Tascilar Koray , Krönke Gerhard , Kleyer Arnd , Zaiss Mario M. , Heppt Franz , Meder Christine , Atreya Raja , Klenske Entcho , Dietrich Peter , Abdullah Abdullah , Kliem Thorsten , Corte Giulia , Morf Harriet , Leppkes Moritz , Kremer Andreas E. , Ramming Andreas , Pachowsky Milena , Schuch Florian , Ronneberger Monika , Kleinert Stefan , Maier Clara , Hueber Axel J. , Manger Karin , Manger Bernhard , Berking Carola , Tenbusch Matthias , Überla Klaus , Sticherling Michael , Neurath Markus F. , Schett Georg 
Published: July 2020

AbstractImmune-mediated inflammatory diseases (IMIDs) of the joints, gut and skin are treated with inhibitors of inflammatory cytokines. These cytokines are involved in the pathogenesis of coronavirus disease 2019 (COVID-19). Investigating anti-SARS-CoV-2 antibody responses in IMIDs we observe a reduced incidence of SARS-CoV-2 seroconversion in IMID patients treated with cytokine inhibitors compared to patients receiving no such inhibitors and two healthy control populations, despite similar social exposure. Hence, cytokine inhibitors seem to at least partially protect from SARS-CoV-2 infection.
The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance
Authors: Ahmed Marwa N. , Abdelsamad Ahmed , Wassermann Tina , Porse Andreas , Becker Janna , Sommer Morten O. A. , Høiby Niels , Ciofu Oana 
Published: July 2020

AbstractCiprofloxacin (CIP) is used to treat Pseudomonas aeruginosa biofilm infections. We showed that the pathways of CIP-resistance development during exposure of biofilms and planktonic P. aeruginosa populations to subinhibitory levels of CIP depend on the mode of growth. In the present study, we analyzed CIP-resistant isolates obtained from previous evolution experiments, and we report a variety of evolved phenotypic and genotypic changes that occurred in parallel with the evolution of CIP-resistance. Cross-resistance to beta-lactam antibiotics was associated with mutations in genes involved in cell-wall recycling (ftsZ, murG); and could also be explained by mutations in the TCA cycle (sdhA) genes and in genes involved in arginine catabolism. We found that CIP-exposed isolates that lacked mutations in quorum-sensing genes and acquired mutations in type IV pili genes maintained swarming motility and lost twitching motility, respectively. Evolved CIP-resistant isolates showed high fitness cost in planktonic competition experiments, yet persisted in the biofilm under control conditions, compared with ancestor isolates and had an advantage when exposed to CIP. Their persistence in biofilm competition experiments in spite of their fitness cost in planktonic growth could be explained by their prolonged lag-phase. Interestingly, the set of mutated genes that we identified in these in vitro-evolved CIP-resistant colonies, overlap with a large number of patho-adaptive genes previously reported in P. aeruginosa isolates from cystic fibrosis (CF) patients. This suggests that the antibiotic stress is contributing to the bacterial evolution in vivo, and that adaptive laboratory evolution can be used to predict the in vivo evolutionary trajectories.
European maize genomes highlight intraspecies variation in repeat and gene content
Authors: Haberer Georg , Kamal Nadia , Bauer Eva , Gundlach Heidrun , Fischer Iris , Seidel Michael A. , Spannagl Manuel , Marcon Caroline , Ruban Alevtina , Urbany Claude , Nemri Adnane , Hochholdinger Frank , Ouzunova Milena , Houben Andreas , Schön Chris-Carolin , Mayer Klaus F. X. 
Published: July 2020

AbstractThe diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.
Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Authors: Petek Marko , Zagorščak Maja , Ramšak Živa , Sanders Sheri , Tomaž Špela , Tseng Elizabeth , Zouine Mohamed , Coll Anna , Gruden Kristina 
Published: July 2020

AbstractAlthough the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.
Gait asymmetry, and bilateral coordination of gait during a six-minute walk test in persons with multiple sclerosis
Authors: Plotnik Meir , Wagner Joanne M. , Adusumilli Gautam , Gottlieb Amihai , Naismith Robert T. 
Published: July 2020

AbstractGait impairments in persons with multiple sclerosis (pwMS) leading to decreased ambulation and reduced walking endurance remain poorly understood. Our objective was to assess gait asymmetry (GA) and bilateral coordination of gait (BCG), among pwMS during the six-minute walk test (6MWT), and determine their association with disease severity. We recruited 92 pwMS (age: 46.6 ± 7.9; 83% females) with a range of clinical disability, who completed the 6MWT wearing gait analysis system. GA was assessed by comparing left and right swing times, and BCG was assessed by the phase coordination index (PCI). Several functional and subjective gait assessments were performed. Results show that gait is more asymmetric and less coordinated as the disease progresses (p < 0.0001). Participants with mild MS showed significantly better BCG as reflected by lower PCI values in comparison to the other two MS severity groups (severe: p = 0.001, moderate: p = 0.02). GA and PCI also deteriorated significantly each minute during the 6MWT (p < 0.0001). GA and PCI (i.e., BCG) show weaker associations with clinical MS status than associations observed between functional and subjective gait assessments and MS status. Similar to other neurological cohorts, GA and PCI may be important parameters to assess and target in interventions among pwMS.
Ollivier Ricci curvature of directed hypergraphs
Authors: Eidi Marzieh , Jost Jürgen 
Published: July 2020

AbstractMany empirical networks incorporate higher order relations between elements and therefore are naturally modelled as, possibly directed and/or weighted, hypergraphs, rather than merely as graphs. In order to develop a systematic tool for the statistical analysis of such hypergraph, we propose a general definition of Ricci curvature on directed hypergraphs and explore the consequences of that definition. The definition generalizes Ollivier’s definition for graphs. It involves a carefully designed optimal transport problem between sets of vertices. While the definition looks somewhat complex, in the end we shall be able to express our curvature in a very simple formula, $$\kappa =\mu _0-\mu _2-2\mu _3$$κ=μ0-μ2-2μ3. This formula simply counts the fraction of vertices that have to be moved by distances 0, 2 or 3 in an optimal transport plan. We can then characterize various classes of hypergraphs by their curvature.
Near field excited state imaging via stimulated electron energy gain spectroscopy of localized surface plasmon resonances in plasmonic nanorod antennas
Authors: Collette Robyn , Garfinkel David A. , Hu Zhongwei , Masiello David J. , Rack Philip D. 
Published: July 2020

AbstractContinuous wave (cw) photon stimulated electron energy loss and gain spectroscopy (sEELS and sEEGS) is used to image the near field of optically stimulated localized surface plasmon resonance (LSPR) modes in nanorod antennas. An optical delivery system equipped with a nanomanipulator and a fiber-coupled laser diode is used to simultaneously irradiate plasmonic nanostructures in a (scanning) transmission electron microscope. The nanorod length is varied such that the m = 1, 2, and 3 LSPR modes are resonant with the laser energy and the optically stimulated near field spectra and images of these modes are measured. Various nanorod orientations are also investigated to explore retardation effects. Optical and electron beam simulations are used to rationalize the observed patterns. As expected, the odd modes are optically bright and result in observed sEEG responses. The m = 2 dark mode does not produce a sEEG response, however, when tilted such that retardation effects are operative, the sEEG signal emerges. Thus, we demonstrate that cw sEEGS is an effective tool in imaging the near field of the full set of nanorod plasmon modes of either parity.
Impact of an active lifestyle on heart rate variability and oxidative stress markers in offspring of hypertensives
Authors: Santa-Rosa F. A. , Shimojo G. L. , Dias D. S. , Viana A. , Lanza F. C. , Irigoyen M. C. , De Angelis K. 
Published: July 2020

AbstractFamilial history of hypertension is associated with autonomic dysfunction and increase in blood pressure (BP). However, an active lifestyle has been found to improve a number of health outcomes and reduce all-cause mortality. The aim of the present study was to investigate the effects of an active lifestyle on hemodynamics, heart rate variability (HRV) and oxidative stress markers in offspring of hypertensive parents. One hundred twenty-seven subjects were assigned into four groups: sedentary offspring of normotensives (S-ON) or hypertensives (S-OH); and physically active offspring of normotensives (A-ON) or hypertensives (A-OH). Diastolic BP and heart rate were reduced in the physically active groups when compared to S-OH group. A-ON and A-OH groups presented increased values of RR total variance when compared to the sedentary ones (A-ON: 4,912 ± 538 vs. S-ON: 2,354 ± 159; A-OH: 3,112 ± 236 vs. S-OH: 2,232 ± 241 ms2). Cardiac sympato-vagal balance (LF/HF), systemic hydrogen peroxide and superoxide anion were markedly increased in S-OH group when compared to all other studied groups. Additionally, important correlations were observed between LF/HF with diastolic BP (r = 0.30) and hydrogen peroxide (r = 0.41). Thus, our findings seem to confirm an early autonomic dysfunction in offspring of hypertensive parents, which was associated with a systemic increase in reactive oxygen species and blood pressure. However, our most important finding lies in the attenuation of such disorders in offspring of physically active hypertensives, thus emphasizing the importance of a physically active lifestyle in the prevention of early disorders that may be associated with onset of hypertension.