bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding
Authors: Yperman Klaas , Papageorgiou Anna C. , Merceron Romain , De Munck Steven , Bloch Yehudi , Eeckhout Dominique , Jiang Qihang , Tack Pieter , Grigoryan Rosa , Evangelidis Thomas , Van Leene Jelle , Vincze Laszlo , Vandenabeele Peter , Vanhaecke Frank , Potocký Martin , De Jaeger Geert , Savvides Savvas N. , Tripsianes Konstantinos , Pleskot Roman , Van Damme Daniel 
Published: May 2021

AbstractClathrin-mediated endocytosis (CME) is the gatekeeper of the plasma membrane. In contrast to animals and yeasts, CME in plants depends on the TPLATE complex (TPC), an evolutionary ancient adaptor complex. However, the mechanistic contribution of the individual TPC subunits to plant CME remains elusive. In this study, we used a multidisciplinary approach to elucidate the structural and functional roles of the evolutionary conserved N-terminal Eps15 homology (EH) domains of the TPC subunit AtEH1/Pan1. By integrating high-resolution structural information obtained by X-ray crystallography and NMR spectroscopy with all-atom molecular dynamics simulations, we provide structural insight into the function of both EH domains. Both domains bind phosphatidic acid with a different strength, and only the second domain binds phosphatidylinositol 4,5-bisphosphate. Unbiased peptidome profiling by mass-spectrometry revealed that the first EH domain preferentially interacts with the double N-terminal NPF motif of a previously unidentified TPC interactor, the integral membrane protein Secretory Carrier Membrane Protein 5 (SCAMP5). Furthermore, we show that AtEH/Pan1 proteins control the internalization of SCAMP5 via this double NPF peptide interaction motif. Collectively, our structural and functional studies reveal distinct but complementary roles of the EH domains of AtEH/Pan1 in plant CME and connect the internalization of SCAMP5 to the TPLATE complex.
When timing matters—misdesigned dam filling impacts hydropower sustainability
Authors: Zaniolo Marta , Giuliani Matteo , Sinclair Scott , Burlando Paolo , Castelletti Andrea 
Published: May 2021

AbstractDecades of sustainable dam planning efforts have focused on containing dam impacts in regime conditions, when the dam is fully filled and operational, overlooking potential disputes raised by the filling phase. Here, we argue that filling timing and operations can catalyze most of the conflicts associated with a dam’s lifetime, which can be mitigated by adaptive solutions that respond to medium-to-long term hydroclimatic fluctuations. Our retrospective analysis of the contested recent filling of Gibe III in the Omo-Turkana basin provides quantitative evidence of the benefits generated by adaptive filling strategies, attaining levels of hydropower production comparable with the historical ones while curtailing the negative impacts to downstream users. Our results can inform a more sustainable filling of the new megadam currently under construction downstream of Gibe III, and are generalizable to the almost 500 planned dams worldwide in regions influenced by climate feedbacks, thus representing a significant scope to reduce the societal and environmental impacts of a large number of new hydropower reservoirs.
Molecular insights of exceptionally photostable electron acceptors for organic photovoltaics
Authors: Liu Zhi-Xi , Yu Zhi-Peng , Shen Ziqiu , He Chengliang , Lau Tsz-Ki , Chen Zeng , Zhu Haiming , Lu Xinhui , Xie Zengqi , Chen Hongzheng , Li Chang-Zhi 
Published: May 2021

AbstractPhoto-degradation of organic semiconductors remains as an obstacle preventing their durable practice in optoelectronics. Herein, we disclose that volume-conserving photoisomerization of a unique series of acceptor-donor-acceptor (A-D-A) non-fullerene acceptors (NFAs) acts as a surrogate towards their subsequent photochemical reaction. Among A-D-A NFAs with fused, semi-fused and non-fused backbones, fully non-fused PTIC, representing one of rare existing samples, exhibits not only excellent photochemical tolerance in aerobic condition, but also efficient performance in solar cells. Along with a series of in-depth investigations, we identify that the structural confinement to inhibit photoisomerization of these unique A-D-A NFAs from molecular level to macroscopic condensed solid helps enhancing the photochemical stabilities of molecules, as well as the corresponding OSCs. Although other reasons associating with the photostabilities of molecules and devices should not excluded, we believe this work provides helpful structure-property information toward new design of stable and efficient photovoltaic molecules and solar cells.
Modifying redox properties and local bonding of Co3O4 by CeO2 enhances oxygen evolution catalysis in acid
Authors: Huang Jinzhen , Sheng Hongyuan , Ross R. Dominic , Han Jiecai , Wang Xianjie , Song Bo , Jin Song 
Published: May 2021

AbstractDeveloping efficient and stable earth-abundant electrocatalysts for acidic oxygen evolution reaction is the bottleneck for water splitting using proton exchange membrane electrolyzers. Here, we show that nanocrystalline CeO2 in a Co3O4/CeO2 nanocomposite can modify the redox properties of Co3O4 and enhances its intrinsic oxygen evolution reaction activity, and combine electrochemical and structural characterizations including kinetic isotope effect, pH- and temperature-dependence, in situ Raman and ex situ X-ray absorption spectroscopy analyses to understand the origin. The local bonding environment of Co3O4 can be modified after the introduction of nanocrystalline CeO2, which allows the CoIII species to be easily oxidized into catalytically active CoIV species, bypassing the potential-determining surface reconstruction process. Co3O4/CeO2 displays a comparable stability to Co3O4 thus breaks the activity/stability tradeoff. This work not only establishes an efficient earth-abundant catalysts for acidic oxygen evolution reaction, but also provides strategies for designing more active catalysts for other reactions.
Cryo-EM structure of the mature and infective Mayaro virus at 4.4 Å resolution reveals features of arthritogenic alphaviruses
Authors: Ribeiro-Filho Helder V. , Coimbra Lais D. , Cassago Alexandre , Rocha Rebeca P. F. , Guerra João Victor da Silva , de Felicio Rafael , Carnieli Carolina Moretto , Leme Luiza , Padilha Antonio Cláudio , Paes Leme Adriana F. , Trivella Daniela B. B. , Portugal Rodrigo Villares , Lopes-de-Oliveira Paulo Sérgio , Marques Rafael Elias 
Published: May 2021

AbstractMayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related arthritogenic alphaviruses. Here, we present the structure of MAYV at 4.4 Å resolution, obtained from a preparation of mature, infective virions. MAYV presents typical alphavirus features and organization. Interactions between viral proteins that lead to particle formation are described together with a hydrophobic pocket formed between E1 and E2 spike proteins and conformational epitopes specific of MAYV. We also describe MAYV glycosylation residues in E1 and E2 that may affect MXRA8 host receptor binding, and a molecular “handshake” between MAYV spikes formed by N262 glycosylation in adjacent E2 proteins. The structure of MAYV is suggestive of structural and functional complexity among alphaviruses, which may be targeted for specificity or antiviral activity.
Ecology and molecular targets of hypermutation in the global microbiome
Authors: Roux Simon , Paul Blair G. , Bagby Sarah C. , Nayfach Stephen , Allen Michelle A. , Attwood Graeme , Cavicchioli Ricardo , Chistoserdova Ludmila , Gruninger Robert J. , Hallam Steven J. , Hernandez Maria E. , Hess Matthias , Liu Wen-Tso , McAllister Tim A. , O’Malley Michelle A. , Peng Xuefeng , Rich Virginia I. , Saleska Scott R. , Eloe-Fadrosh Emiley A. 
Published: May 2021

AbstractChanges in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.
Fast widefield scan provides tunable and uniform illumination optimizing super-resolution microscopy on large fields
Authors: Mau Adrien , Friedl Karoline , Leterrier Christophe , Bourg Nicolas , Lévêque-Fort Sandrine 
Published: May 2021

AbstractNon-uniform illumination limits quantitative analyses of fluorescence imaging techniques. In particular, single molecule localization microscopy (SMLM) relies on high irradiances, but conventional Gaussian-shaped laser illumination restricts the usable field of view to around 40 µm × 40 µm. We present Adaptable Scanning for Tunable Excitation Regions (ASTER), a versatile illumination technique that generates uniform and adaptable illumination. ASTER is also highly compatible with optical sectioning techniques such as total internal reflection fluorescence (TIRF). For SMLM, ASTER delivers homogeneous blinking kinetics at reasonable laser power over fields-of-view up to 200 µm × 200 µm. We demonstrate that ASTER improves clustering analysis and nanoscopic size measurements by imaging nanorulers, microtubules and clathrin-coated pits in COS-7 cells, and β2-spectrin in neurons. ASTER’s sharp and quantitative illumination paves the way for high-throughput quantification of biological structures and processes in classical and super-resolution fluorescence microscopies.
Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis
Authors: Moradali M. Fata , Davey Mary E. 
Published: May 2021

AbstractOur understanding of how the oral anaerobe Porphyromonas gingivalis can persist below the gum line, induce ecological changes, and promote polymicrobial infections remains limited. P. gingivalis has long been described as a highly proteolytic and asaccharolytic pathogen that utilizes protein substrates as the main source for energy production and proliferation. Here, we report that P. gingivalis displays a metabolic plasticity that enables the exploitation of non-proteinaceous substrates, specifically the monocarboxylates pyruvate and lactate, as well as human serum components, for colonization and biofilm formation. We show that anabolism of carbohydrates from pyruvate is powered by catabolism of amino acids. Concomitantly, the expression of fimbrial adhesion is upregulated, leading to the enhancement of biofilm formation, stimulation of multispecies biofilm development, and increase of colonization and invasion of the primary gingival epithelial cells by P. gingivalis. These studies provide the first glimpse into the metabolic plasticity of P. gingivalis and its adaptation to the nutritional condition of the host niche. Our findings support the model that in response to specific nutritional parameters, P. gingivalis has the potential to promote host colonization and development of a pathogenic community.
Quantum Zeno effects across a parity-time symmetry breaking transition in atomic momentum space
Authors: Chen Tao , Gou Wei , Xie Dizhou , Xiao Teng , Yi Wei , Jing Jun , Yan Bo 
Published: May 2021

AbstractWe experimentally study quantum Zeno effects in a parity-time (PT) symmetric cold atom gas periodically coupled to a reservoir. Based on the state-of-the-art control of inter-site couplings of atoms in a momentum lattice, we implement a synthetic two-level system with passive PT symmetry over two lattice sites, where an effective dissipation is introduced through repeated couplings to the rest of the lattice. Quantum Zeno (anti-Zeno) effects manifest in our experiment as the overall dissipation of the two-level system becoming suppressed (enhanced) with increasing coupling intensity or frequency. We demonstrate that quantum Zeno regimes exist in the broken PT symmetry phase, and are bounded by exceptional points separating the PT symmetric and PT broken phases, as well as by a discrete set of critical coupling frequencies. Our experiment establishes the connection between PT-symmetry-breaking transitions and quantum Zeno effects, and is extendable to higher dimensions or to interacting regimes, thanks to the flexible control with atoms in a momentum lattice.
Multimodal assessment of communicative-pragmatic features in schizophrenia: a machine learning approach
Authors: Parola Alberto , Gabbatore Ilaria , Berardinelli Laura , Salvini Rogerio , Bosco Francesca M. 
Published: May 2021

AbstractAn impairment in pragmatic communication is a core feature of schizophrenia, often associated with difficulties in social interactions. The pragmatic deficits regard various pragmatic phenomena, e.g., direct and indirect communicative acts, deceit, irony, and include not only the use of language but also other expressive means such as non-verbal/extralinguistic modalities, e.g., gestures and body movements, and paralinguistic cues, e.g., prosody and tone of voice. The present paper focuses on the identification of those pragmatic features, i.e., communicative phenomena and expressive modalities, that more reliably discriminate between individuals with schizophrenia and healthy controls. We performed a multimodal assessment of communicative-pragmatic ability, and applied a machine learning approach, specifically a Decision Tree model, with the aim of identifying the pragmatic features that best separate the data into the two groups, i.e., individuals with schizophrenia and healthy controls, and represent their configuration. The results indicated good overall performance of the Decision Tree model, with mean Accuracy of 82%, Sensitivity of 76%, and Precision of 91%. Linguistic irony emerged as the most relevant pragmatic phenomenon in distinguishing between the two groups, followed by violation of the Gricean maxims, and then extralinguistic deceitful and sincere communicative acts. The results are discussed in light of the pragmatic theoretical literature, and their clinical relevance in terms of content and design of both assessment and rehabilitative training.
The inhibition of ABCB1/MDR1 or ABCG2/BCRP enables doxorubicin to eliminate liver cancer stem cells
Authors: Yin Wang , Xiang Dongxi , Wang Tao , Zhang Yumei , Pham Cuong V. , Zhou Shufeng , Jiang Guoqin , Hou Yingchun , Zhu Yimin , Han Yinglu , Qiao Liang , Tran Phuong H.-L. , Duan Wei 
Published: May 2021

AbstractTwo ATP-binding cassette transporters, ABCB1/MDR1 and ABCG2/BCRP, are considered the most critical determinants for chemoresistance in hepatocellular carcinoma. However, their roles in the chemoresistance in liver cancer stem cells remain elusive. Here we explored the role of inhibition of MDR1 or ABCG2 in sensitizing liver cancer stem cells to doxorubicin, the most frequently used chemotherapeutic agent in treating liver cancer. We show that the inhibition of MDR1 or ABCG2 in Huh7 and PLC/PRF/5 cells using either pharmacological inhibitors or RNAi resulted in the elevated level of intracellular concentration of doxorubicin and the accompanied increased apoptosis as determined by confocal microscopy, high-performance liquid chromatography, flow cytometry, and annexin V assay. Notably, the inhibition of MDR1 or ABCG2 led to the reversal of the chemoresistance, as evident from the enhanced death of the chemoresistant liver cancer stem cells in tumorsphere-forming assays. Thus, the elevation of effective intracellular concentration of doxorubicin via the inhibition of MDR1 or ABCG2 represents a promising future strategy that transforms doxorubicin from a traditional chemotherapy agent into a robust killer of liver cancer stem cells for patients undergoing transarterial chemoembolization.
Improved methods for RNAseq-based alternative splicing analysis
Authors: Halperin Rebecca F. , Hegde Apurva , Lang Jessica D. , Raupach Elizabeth A. ,   C4RCD Research Group, Narayanan Vinodh , Huentelman Matt , Belnap Newell , Aziz Anne-Marie , Ramsey Keri , Legendre Christophe , Liang Winnie S. , LoRusso Patricia M. , Sekulic Aleksandar , Sosman Jeffrey A. , Trent Jeffrey M. , Rangasamy Sampathkumar , Pirrotte Patrick , Schork Nicholas J. 
Published: May 2021

AbstractThe robust detection of disease-associated splice events from RNAseq data is challenging due to the potential confounding effect of gene expression levels and the often limited number of patients with relevant RNAseq data. Here we present a novel statistical approach to splicing outlier detection and differential splicing analysis. Our approach tests for differences in the percentages of sequence reads representing local splice events. We describe a software package called Bisbee which can predict the protein-level effect of splice alterations, a key feature lacking in many other splicing analysis resources. We leverage Bisbee’s prediction of protein level effects as a benchmark of its capabilities using matched sets of RNAseq and mass spectrometry data from normal tissues. Bisbee exhibits improved sensitivity and specificity over existing approaches and can be used to identify tissue-specific splice variants whose protein-level expression can be confirmed by mass spectrometry. We also applied Bisbee to assess evidence for a pathogenic splicing variant contributing to a rare disease and to identify tumor-specific splice isoforms associated with an oncogenic mutation. Bisbee was able to rediscover previously validated results in both of these cases and also identify common tumor-associated splice isoforms replicated in two independent melanoma datasets.
Distributed abstraction and verification of an installed optical fibre network
Authors: Ives D. J. , Yan S. , Galdino L. , Wang R. , Elson D. J. , Wakayama Y. , Vaquero-Caballero F. J. , Saavedra G. , Lavery D. , Nejabati R. , Bayvel P. , Simeonidou D. , Savory S. J. 
Published: May 2021

AbstractThe management of wavelength routed optical mesh networks is complex with many potential light path routes and numerous physical layer impairments to transmission performance. This complexity can be reduced by applying the ideas of abstraction from computer science where different equipment is described in the same basic terms. The noise-to-signal ratio can be used as a metric to describe the quality of transmission performance of a signal propagated through a network element and accumulates additively through a sequence of such elements allowing the estimation of end-to-end performance. This study aims to explore the robustness of the noise-to-signal ratio metric in an installed fibre infrastructure. We show that the abstracted noise-to-signal ratio is independent of the observers and their location. We confirm that the abstracted noise-to-signal ratio can reasonably predict the performance of light-paths subsequently set in our network. Having a robust network element abstraction that can be incorporated into routeing engines allows the network management controller to make decisions on the most effective way to use the network resources in terms of the routeing and data coding format.
The pest kill rate of thirteen natural enemies as aggregate evaluation criterion of their biological control potential of Tuta absoluta
Authors: van Lenteren Joop C. , Lanzoni Alberto , Hemerik Lia , Bueno Vanda H. P. , Bajonero Cuervo Johanna G. , Biondi Antonio , Burgio Giovanni , Calvo Francisco J. , de Jong Peter W. , López Silvia N. , Luna M. Gabriela , Montes Flavio C. , Nieves Eliana L. , Aigbedion-Atalor Pascal Osa , Riquelme Virgala Maria B. , Sánchez Norma E. , Urbaneja Alberto 
Published: May 2021

AbstractEcologists study how populations are regulated, while scientists studying biological pest control apply population regulation processes to reduce numbers of harmful organisms: an organism (a natural enemy) is used to reduce the population density of another organism (a pest). Finding an effective biological control agent among the tens to hundreds of natural enemies of a pest is a daunting task. Evaluation criteria help in a first selection to remove clearly ineffective or risky species from the list of candidates. Next, we propose to use an aggregate evaluation criterion, the pest kill rate, to compare the pest population reduction capacity of species not eliminated during the first selection. The pest kill rate is the average daily lifetime killing of the pest by the natural enemy under consideration. Pest kill rates of six species of predators and seven species of parasitoids of Tuta absoluta were calculated and compared. Several natural enemies had pest kill rates that were too low to be able to theoretically reduce the pest population below crop damaging densities. Other species showed a high pest reduction capacity and their potential for practical application can now be tested under commercial crop production conditions.
The limit of tolerable micromotion for implant osseointegration: a systematic review
Authors: Kohli Nupur , Stoddart Jennifer C. , van Arkel Richard J. 
Published: May 2021

AbstractMuch research effort is being invested into the development of porous biomaterials that enhance implant osseointegration. Large micromotions at the bone-implant interface impair this osseointegration process, resulting in fibrous capsule formation and implant loosening. This systematic review compiled all the in vivo evidence available to establish if there is a universal limit of tolerable micromotion for implant osseointegration. The protocol was registered with the International Prospective Register for Systematic Reviews (ID: CRD42020196686). Pubmed, Scopus and Web of Knowledge databases were searched for studies containing terms relating to micromotion and osseointegration. The mean value of micromotion for implants that osseointegrated was 32% of the mean value for those that did not (112 ± 176 µm versus 349 ± 231 µm, p < 0.001). However, there was a large overlap in the data ranges with no universal limit apparent. Rather, many factors were found to combine to affect the overall outcome including loading time, the type of implant and the material being used. The tables provided in this review summarise these factors and will aid investigators in identifying the most relevant micromotion values for their biomaterial and implant development research.