bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Subduction Interface and Upper Plate Strength on Back‐Arc Extension: Application to Mediterranean Back‐Arc Basins
Authors: Erdős Zoltán , Huismans Ritske S. , Faccenna Claudio , Wolf Sebastian G. 
Published: July 2021

AbstractWhile there has been a lot of work focusing on improving our understanding of divergent and convergent plate boundaries, the intricate nature of back‐arc extension, where subduction and large‐scale extension occur and interact in close, is yet to be explored properly. It has long been proposed that the strength of the subduction interface, which depends among others on the amount of subducted sediments, plays a pivotal role in subduction dynamics. Here, we investigate the role of back‐arc rheology and subduction interface strength on the deformation style of the overriding plate. Using two‐dimensional thermomechanical model experiments, we demonstrate, that the presence of a weak mantle–lithospheric domain in the overriding plate can result in back‐arc breakup even during the subduction of narrow, land‐locked oceanic basins such as those found in the Mediterranean region. The thinning of the back‐arc mantle–lithosphere results in a weaker overriding plate, hence a lower slab‐pull force is sufficient to initiate back‐arc extension. Convective thinning at the subduction interface also reduces the length of the interface, reducing the portion of slab‐pull lost as energy dissipation. A weak plate interface, can also reduce the energy dissipated along the subduction zone, leading to earlier extension. A detailed analysis of the forces shaping the overriding plate stress field shows that transmission of slab‐pull force has a predominant role while viscous basal drag has a negligible effect in our experiments. Our results compare favorably with large‐scale characteristics of land‐locked Mediterranean back‐arc basins such as the North Tyrrhenian basin and the Pannonian basin.
Acoustic Backscatter and Attenuation Due to River Fine Sediments: Experimental Evaluation of Models and Inversion Methods
Authors: Vergne Adrien , Berni Céline , Le Coz Jérôme , Tencé Florent 
Published: July 2021

AbstractThe hydroacoustic monitoring of suspended sediment concentration (SSC) in rivers is based on the inversion of backscatter and attenuation models. To evaluate such models, acoustic backscatter and attenuation were measured from a homogeneous suspension of fine river sediments (clay) in a laboratory tank at various concentrations in the range 1–18 g/l. Agreement between the modeled and measured acoustic backscatter and attenuation values was found to be relatively poor. The results are highly sensitive to particle size and shape which come with large measurement uncertainties and they can be significantly improved by adjusting plausible particle parameters. Various inversion methods combining single or multiple frequencies, analysis of backscatter and/or attenuation, spherical or oblate shape hypothesis for particles and fixed or estimated lognormal grain size distribution are tested. The most promising inversion methods using both backscatter and attenuation information led to accurate SSC estimates.
Efficient Discretization‐Independent Bayesian Inversion of High‐Dimensional Multi‐Gaussian Priors Using a Hybrid MCMC
Authors: Reuschen Sebastian , Jobst Fabian , Nowak Wolfgang 
Published: July 2021

AbstractIn geostatistics, Gaussian random fields are often used to model heterogeneities of soil or subsurface parameters. To give spatial approximations of these random fields, they are discretized. Then, different techniques of geostatistical inversion are used to condition them on measurement data. Among these techniques, Markov chain Monte Carlo (MCMC) techniques stand out, because they yield asymptotically unbiased conditional realizations. However, standard Markov Chain Monte Carlo (MCMC) methods suffer the curse of dimensionality when refining the discretization. This means that their efficiency decreases rapidly with an increasing number of discretization cells. Several MCMC approaches have been developed such that the MCMC efficiency does not depend on the discretization of the random field. The preconditioned Crank Nicolson Markov Chain Monte Carlo (pCN‐MCMC) and the sequential Gibbs (or block‐Gibbs) sampling are two examples. This paper presents a combination of both approaches with the goal to further reduce the computational costs. Our algorithm, the sequential pCN‐MCMC, will depend on two tuning‐parameters: the correlation parameterof the pCN approach and the block sizeof the sequential Gibbs approach. The original pCN‐MCMC and the Gibbs sampling algorithm are special cases of our method. We present an algorithm that automatically finds the best tuning‐parameter combination (and) during the burn‐in‐phase of the algorithm, thus choosing the best possible hybrid between the two methods. In our test cases, we achieve a speedup factors of 1–5.5 over pCN and of 1–6.5 over Gibbs. Furthermore, we provide the MATLAB implementation of our method as open‐source code.
Protein lysine crotonylation: past, present, perspective
Authors: Jiang Gaoyue , Li Chunxia , Lu Meng , Lu Kefeng , Li Huihui 
Published: July 2021

AbstractLysine crotonylation has been discovered in histone and non-histone proteins and found to be involved in diverse diseases and biological processes, such as neuropsychiatric disease, carcinogenesis, spermatogenesis, tissue injury, and inflammation. The unique carbon–carbon π-bond structure indicates that lysine crotonylation may use distinct regulatory mechanisms from the widely studied other types of lysine acylation. In this review, we discussed the regulation of lysine crotonylation by enzymatic and non-enzymatic mechanisms, the recognition of substrate proteins, the physiological functions of lysine crotonylation and its cross-talk with other types of modification. The tools and methods for prediction and detection of lysine crotonylation were also described.
Distinct roles of Fto and Mettl3 in controlling development of the cerebral cortex through transcriptional and translational regulations
Authors: Du Kunzhao , Zhang Zhen , Zeng Zhiwei , Tang Jinling , Lee Trevor , Sun Tao 
Published: July 2021

AbstractProper development of the mammalian cerebral cortex relies on precise gene expression regulation, which is controlled by genetic, epigenetic, and epitranscriptomic factors. Here we generate RNA demethylase Fto and methyltransferase Mettl3 cortical-specific conditional knockout mice, and detect severe brain defects caused by Mettl3 deletion but not Fto knockout. Transcriptomic profiles using RNA sequencing indicate that knockout of Mettl3 causes a more dramatic alteration on gene transcription than that of Fto. Interestingly, we conduct ribosome profiling sequencing, and find that knockout of Mettl3 leads to a more severe disruption of translational regulation of mRNAs than deletion of Fto and results in altered translation of crucial genes in cortical radial glial cells and intermediate progenitors. Moreover, Mettl3 deletion causes elevated translation of a significant number of mRNAs, in particular major components in m6A methylation. Our findings indicate distinct functions of Mettl3 and Fto in brain development, and uncover a profound role of Mettl3 in regulating translation of major mRNAs that control proper cortical development.
Antioxidant and food additive BHA prevents TNF cytotoxicity by acting as a direct RIPK1 inhibitor
Authors: Delanghe Tom , Huyghe Jon , Lee Seungheon , Priem Dario , Van Coillie Samya , Gilbert Barbara , Choi Sze Men , Vandenabeele Peter , Degterev Alexei , Cuny Gregory D. , Dondelinger Yves , Bertrand Mathieu J. M. 
Published: July 2021

AbstractButylate hydroxyanisole (BHA) is a synthetic phenol that is widely utilized as a preservative by the food and cosmetic industries. The antioxidant properties of BHA are also frequently used by scientists to claim the implication of reactive oxygen species (ROS) in various cellular processes, including cell death. We report on the surprising finding that BHA functions as a direct inhibitor of RIPK1, a major signaling hub downstream of several immune receptors. Our in silico analysis predicts binding of 3-BHA, but not 2-BHA, to RIPK1 in an inactive DLG-out/Glu-out conformation, similar to the binding of the type III inhibitor Nec-1s to RIPK1. This predicted superior inhibitory capacity of 3-BHA over 2-BHA was confirmed in cells and using in vitro kinase assays. We demonstrate that the reported protective effect of BHA against tumor necrosis factor (TNF)-induced necroptotic death does not originate from ROS scavenging but instead from direct RIPK1 enzymatic inhibition, a finding that most probably extends to other reported effects of BHA. Accordingly, we show that BHA not only protects cells against RIPK1-mediated necroptosis but also against RIPK1 kinase-dependent apoptosis. We found that BHA treatment completely inhibits basal and induced RIPK1 enzymatic activity in cells, monitored at the level of TNFR1 complex I under apoptotic conditions or in the cytosol under necroptosis. Finally, we show that oral administration of BHA protects mice from RIPK1 kinase-dependent lethality caused by TNF injection, a model of systemic inflammatory response syndrome. In conclusion, our results demonstrate that BHA can no longer be used as a strict antioxidant and that new functions of RIPK1 may emerge from previously reported effects of BHA.
Evolving treatment paradigms for PCV
Authors: Fenner Beau J. , Cheung Chui Ming Gemmy , Sim Shaun S. , Lee Won Ki , Staurenghi Giovanni , Lai Timothy Y. Y. , Ruamviboonsuk Paisan , Kokame Gregg , Yanagi Yasuo , Teo Kelvin Y. C. 
Published: July 2021

AbstractPolypoidal choroidal vasculopathy (PCV) is a subtype of neovascular AMD (nAMD) that accounts for a significant proportion of nAMD cases worldwide, and particularly in Asia. Contemporary PCV treatment strategies have closely followed those used in typical nAMD, though there are significant gaps in knowledge on PCV management and it remains unclear if these strategies are appropriate. Current clinical trial data suggest intravitreal anti-vascular endothelial growth factor (VEGF) therapy alone or in combination with photodynamic therapy is effective in managing haemorrhage and exudation in PCV, although the optimal treatment interval, including as-needed and treat-and-extend approaches, is unclear. Newer imaging modalities, including OCT angiography and high-resolution spectral domain OCT have enabled characterisation of unique PCV biomarkers that may provide guidance on how and when treatment and re-treatment should be initiated. Treatment burden for PCV is a major focus of future therapeutic research and several newly developed anti-VEGF agents, including brolucizumab, faricimab, and new modes of drug delivery like the port delivery system, offer hope for dramatically reduced treatment burden for PCV patients. Beyond anti-VEGF therapy, recent developments in our understanding of PCV pathophysiology, in particular the role of choroidal anatomy and lipid mediators in PCV pathogenesis, offer new treatment avenues that may become clinically relevant in the future. This article explores the current management of PCV and more recent approaches to PCV treatment based on an improved understanding of this unique disease process.
High-yield parallel fabrication of quantum-dot monolayer single-electron devices displaying Coulomb staircase, contacted by graphene
Authors: Fruhman Joel M. , Astier Hippolyte P.A.G. , Ehrler Bruno , Böhm Marcus L. , Eyre Lissa F. L. , Kidambi Piran R. , Sassi Ugo , De Fazio Domenico , Griffiths Jonathan P. , Robson Alexander J. , Robinson Benjamin J. , Hofmann Stephan , Ferrari Andrea C. , Ford Christopher J. B. 
Published: July 2021

AbstractIt is challenging for conventional top-down lithography to fabricate reproducible devices very close to atomic dimensions, whereas identical molecules and very similar nanoparticles can be made bottom-up in large quantities, and can be self-assembled on surfaces. The challenge is to fabricate electrical contacts to many such small objects at the same time, so that nanocrystals and molecules can be incorporated into conventional integrated circuits. Here, we report a scalable method for contacting a self-assembled monolayer of nanoparticles with a single layer of graphene. This produces single-electron effects, in the form of a Coulomb staircase, with a yield of 87 ± 13% in device areas ranging from < 800 nm2 to 16 μm2, containing up to 650,000 nanoparticles. Our technique offers scalable assembly of ultra-high densities of functional particles or molecules that could be used in electronic integrated circuits, as memories, switches, sensors or thermoelectric generators.
Oil immersed lossless total analysis system for integrated RNA extraction and detection of SARS-CoV-2
Authors: Juang Duane S. , Juang Terry D. , Dudley Dawn M. , Newman Christina M. , Accola Molly A. , Rehrauer William M. , Friedrich Thomas C. , O’Connor David H. , Beebe David J. 
Published: July 2021

AbstractThe COVID-19 pandemic exposed difficulties in scaling current quantitative PCR (qPCR)-based diagnostic methodologies for large-scale infectious disease testing. Bottlenecks include lengthy multi-step processes for nucleic acid extraction followed by qPCR readouts, which require costly instrumentation and infrastructure, as well as reagent and plastic consumable shortages stemming from supply chain constraints. Here we report an Oil Immersed Lossless Total Analysis System (OIL-TAS), which integrates RNA extraction and detection onto a single device that is simple, rapid, cost effective, and requires minimal supplies and infrastructure to perform. We validated the performance of OIL-TAS using contrived SARS-CoV-2 viral particle samples and clinical nasopharyngeal swab samples. OIL-TAS showed a 93% positive predictive agreement (n = 57) and 100% negative predictive agreement (n = 10) with clinical SARS-CoV-2 qPCR assays in testing clinical samples, highlighting its potential to be a faster, cheaper, and easier-to-deploy alternative for infectious disease testing.
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity
Authors: Bui Linh T. , Winters Nichelle I. , Chung Mei-I , Joseph Chitra , Gutierrez Austin J. , Habermann Arun C. , Adams Taylor S. , Schupp Jonas C. , Poli Sergio , Peter Lance M. , Taylor Chase J. , Blackburn Jessica B. , Richmond Bradley W. , Nicholson Andrew G. , Rassl Doris , Wallace William A. , Rosas Ivan O. , Jenkins R. Gisli , Kaminski Naftali , Kropski Jonathan A. , Banovich Nicholas E. ,   Human Cell Atlas Lung Biological Network, Misharin Alexander V. , Tsankov Alexander M. , Spira Avrum , Barbry Pascal , Brazma Alvis , Samakovlis Christos , Shepherd Douglas P. , Rawlins Emma L. , Theis Fabian J. , Griffonnet Jennifer , Lee Haeock , Schiller Herbert B. , Hofman Paul , Powell Joseph E. , Schultze Joachim L. , Whitsett Jeffrey , Choi Jiyeon , Lundeberg Joakim , Kaminski Naftali , Kropski Jonathan A. , Banovich Nicholas E. , Ordovas-Montanes Jose , Rajagopal Jayaraj , Meyer Kerstin B. , Krasnow Mark A. , Saeb‐Parsy Kourosh , Zhang Kun , Lafyatis Robert , Leroy Sylvie , Haniffa Muzlifah , Nawijn Martijn C. , Nikolić Marko Z. , van den Berge Maarten , Kuhnemund Malte , Marquette Charles-Hugo , Von Papen Michael , Eickelberg Oliver , Rosenblatt-Rosen Orit , Reyfman Paul A. , Pe’er Dana , Horvath Peter , Tata Purushothama Rao , Regev Aviv , Rojas Mauricio , Seibold Max A. , Shalek Alex K. , Spence Jason R. , Teichmann Sarah A. , Quake Stephen , Duong Thu Elizabeth , Biancalani Tommaso , Desai Tushar , Sun Xin , Zaragosi Laure Emmanuelle 
Published: July 2021

AbstractPatients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyze the transcriptomes of 611,398 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observe a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD AT2 cells express higher levels of genes linked directly to the efficiency of viral replication and the innate immune response. Additionally, we identify basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.
Coordination of biradial-to-radial symmetry and tissue polarity by HD-ZIP II proteins
Authors: Carabelli Monica , Turchi Luana , Morelli Giorgio , Østergaard Lars , Ruberti Ida , Moubayidin Laila 
Published: July 2021

AbstractSymmetry establishment is a critical process in the development of multicellular organs and requires careful coordination of polarity axes while cells actively divide within tissues. Formation of the apical style in the Arabidopsis gynoecium involves a bilateral-to-radial symmetry transition, a stepwise process underpinned by the dynamic distribution of the plant morphogen auxin. Here we show that SPATULA (SPT) and the HECATE (HEC) bHLH proteins mediate the final step in the style radialisation process and synergistically control the expression of adaxial-identity genes, HOMEOBOX ARABIDOPSIS THALIANA 3 (HAT3) and ARABIDOPSIS THALIANA HOMEOBOX 4 (ATHB4). HAT3/ATHB4 module drives radialisation of the apical style by promoting basal-to-apical auxin flow and via a negative feedback mechanism that finetune auxin distribution through repression of SPT expression and cytokinin sensitivity. Thus, this work reveals the molecular basis of axes-coordination and hormonal cross-talk during the sequential steps of symmetry transition in the Arabidopsis style.
A prometaphase mechanism of securin destruction is essential for meiotic progression in mouse oocytes
Authors: Thomas Christopher , Wetherall Benjamin , Levasseur Mark D. , Harris Rebecca J. , Kerridge Scott T. , Higgins Jonathan M. G. , Davies Owen R. , Madgwick Suzanne 
Published: July 2021

AbstractSuccessful cell division relies on the timely removal of key cell cycle proteins such as securin. Securin inhibits separase, which cleaves the cohesin rings holding chromosomes together. Securin must be depleted before anaphase to ensure chromosome segregation occurs with anaphase. Here we find that in meiosis I, mouse oocytes contain an excess of securin over separase. We reveal a mechanism that promotes excess securin destruction in prometaphase I. Importantly, this mechanism relies on two phenylalanine residues within the separase-interacting segment (SIS) of securin that are only exposed when securin is not bound to separase. We suggest that these residues facilitate the removal of non-separase-bound securin ahead of metaphase, as inhibiting this period of destruction by mutating both residues causes the majority of oocytes to arrest in meiosis I. We further propose that cellular securin levels exceed the amount an oocyte is capable of removing in metaphase alone, such that the prometaphase destruction mechanism identified here is essential for correct meiotic progression in mouse oocytes.
Engineered macrophages as near-infrared light activated drug vectors for chemo-photodynamic therapy of primary and bone metastatic breast cancer
Authors: Huang Yanjuan , Guan Zilin , Dai Xiuling , Shen Yifeng , Wei Qin , Ren Lingling , Jiang Jingwen , Xiao Zhanghong , Jiang Yali , Liu Di , Huang Zeqian , Xu Xiaoyu , Luo Yong , Zhao Chunshun 
Published: July 2021

AbstractPatients with primary and bone metastatic breast cancer have significantly reduced survival and life quality. Due to the poor drug delivery efficiency of anti-metastasis therapy and the limited response rate of immunotherapy for breast cancer, effective treatment remains a formidable challenge. In this work, engineered macrophages (Oxa(IV)@ZnPc@M) carrying nanomedicine containing oxaliplatin prodrug and photosensitizer are designed as near-infrared (NIR) light-activated drug vectors, aiming to achieve enhanced chemo/photo/immunotherapy of primary and bone metastatic tumors. Oxa(IV)@ZnPc@M exhibits an anti-tumor M1 phenotype polarization and can efficiently home to primary and bone metastatic tumors. Additionally, therapeutics inside Oxa(IV)@ZnPc@M undergo NIR triggered release, which can kill primary tumors via combined chemo-photodynamic therapy and induce immunogenic cell death simultaneously. Oxa(IV)@ZnPc@M combined with anti-PD-L1 can eliminate primary and bone metastatic tumors, activate tumor-specific antitumor immune response, and improve overall survival with limited systemic toxicity. Therefore, this all-in-one macrophage provides a treatment platform for effective therapy of primary and bone metastatic tumors.
Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases
Authors: Vieira Marcos C. , Donato Celeste M. , Arevalo Philip , Rimmelzwaan Guus F. , Wood Timothy , Lopez Liza , Huang Q. Sue , Dhanasekaran Vijaykrishna , Koelle Katia , Cobey Sarah 
Published: July 2021

AbstractHow a history of influenza virus infections contributes to protection is not fully understood, but such protection might explain the contrasting age distributions of cases of the two lineages of influenza B, B/Victoria and B/Yamagata. Fitting a statistical model to those distributions using surveillance data from New Zealand, we found they could be explained by historical changes in lineage frequencies combined with cross-protection between strains of the same lineage. We found additional protection against B/Yamagata in people for whom it was their first influenza B infection, similar to the immune imprinting observed in influenza A. While the data were not informative about B/Victoria imprinting, B/Yamagata imprinting could explain the fewer B/Yamagata than B/Victoria cases in cohorts born in the 1990s and the bimodal age distribution of B/Yamagata cases. Longitudinal studies can test if these forms of protection inferred from historical data extend to more recent strains and other populations.
Three-dimensional atomic mapping of ligands on palladium nanoparticles by atom probe tomography
Authors: Jang Kyuseon , Kim Se-Ho , Jun Hosun , Jung Chanwon , Yu Jiwon , Lee Sangheon , Choi Pyuck-Pa 
Published: July 2021

AbstractCapping ligands are crucial to synthesizing colloidal nanoparticles with functional properties. However, the synergistic effect between different ligands and their distribution on crystallographic surfaces of nanoparticles during colloidal synthesis is still unclear despite powerful spectroscopic techniques, due to a lack of direct imaging techniques. In this study, atom probe tomography is adopted to investigate the three-dimensional atomic-scale distribution of two of the most common types of these ligands, cetrimonium (C19H42N) and halide (Br and Cl) ions, on Pd nanoparticles. The results, validated using density functional theory, demonstrate that the Br anions adsorbed on the nanoparticle surfaces promote the adsorption of the cetrimonium cations through electrostatic interactions, stabilizing the Pd {111} facets. In contrast, the Cl anions are not strongly adsorbed onto the Pd surfaces. The high density of adsorbed cetrimonium cations for Br anion additions results in the formation of multiple-twinned nanoparticles with superior oxidation resistance.