bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Evidence of Effectiveness of Digital Contact Tracing for SARS-CoV-2 in Switzerland
Authors: Salathé Marcel , Althaus Christian L. , Anderegg Nanina , Antonioli Daniele , Ballauz Tala , Edouard Bugnion , Čapkun Srdjan , Jackson Dennis , Kim Sang-Il , Larus James R. , Low Nicola , Lueks Wouter , Menges Dominik , Moullet Cédric , Payer Mathias , Riou Julien , Stadler Theresa , Troncoso Carmela , Vayena Effy , Wyl Viktor von 
Published: September 2020

AbstractIn the wake of the pandemic of coronavirus disease 2019 (COVID-19), contact tracing has become a key element of strategies to control the spread of severe acute respiratory syndrome coronavirus 2019 (SARS-CoV-2). Given the rapid and intense spread of SARS-CoV-2, digital contact tracing has emerged as a potential complementary tool to support containment and mitigation efforts. Early modelling studies highlighted the potential of digital contact tracing to break transmission chains, and Google and Apple subsequently developed the Exposure Notification (EN) framework, making it available to the vast majority of smartphones. A growing number of governments have launched or announced EN-based contact tracing apps, but their effectiveness remains unknown. Here, we report early findings of the digital contact tracing app deployment in Switzerland. We demonstrate proof-of-principle that digital contact tracing reaches exposed contacts, who then test positive for SARS-CoV-2. This indicates that digital contact tracing is an effective complementary tool for controlling the spread of SARS-CoV-2. Continued technical improvement and international compatibility can further increase the efficacy, particularly also across country borders.
Seasonal and long-term consequences of esca on grapevine stem xylem integrity
Authors: Bortolami G. , Farolfi E. , Badel E. , Burlett R. , Cochard H. , Ferrer N. , King A. , Lamarque L.J. , Lecomte P. , Marchesseau-Marchal M. , Pouzoulet J. , Torres-Ruiz J.M. , Trueba S. , Delzon S. , Gambetta G.A. , Delmas C.E.L. 
Published: September 2020

ABSTRACTHydraulic failure has been extensively studied during drought-induced plant dieback, but its role in plant-pathogen interactions is under debate. During esca, a grapevine (Vitis vinifera) disease, symptomatic leaves are prone to irreversible hydraulic dysfunctions but little is known about the hydraulic integrity of perennial organs over the short- and long-term. We investigated the effects of esca on stem hydraulic integrity in naturally infected plants within a single season and across season(s). We coupled direct (ks) and indirect (kth) hydraulic conductivity measurements, and tylose and vascular pathogen detection with in vivo X-ray microtomography visualizations. We found xylem occlusions (tyloses), and subsequent loss of stemks, in all of the shoots with severe symptoms (apoplexy) and in more than 60% of the shoots with moderate symptoms (tiger-stripe), and no tyloses in shoots that were currently asymptomatic. In vivo stem observations demonstrated that tyloses were observed only when leaf symptoms appeared, and resulted in more than 50% PLC in 40% of symptomatic stems, unrelated to symptom age. The impact of esca on xylem integrity was only seasonal and no long-term impact of disease history was recorded. Our study demonstrated how and to what extent a vascular disease such as esca, affecting xylem integrity, could amplify plant mortality by hydraulic failure.HighlightOur study reveals that esca can critically affect xylem water movement in grapevine perennial organs, by the presence of plant-derived tyloses.
miR-424(322) is a molecular switch controlling pro-inflammatory vs anti-inflammatory skin DC subset differentiation by modulating TGF-β signaling
Authors: Zyulina Victoria , Yan Koon-Kiu , Ju Bensheng , Passegger Christina , Tam-Amersdorfer Carmen , Pan Qingfei , Sconocchia Tommaso , Pollack Christian , Shaner Bridget , Zebisch Armin , Easton John , Yu Jiyang , Silva Jose M. , Strobl Herbert 
Published: September 2020

AbstractTGF-β family ligands are key regulators of dendritic cell (DC) differentiation and activation. Epidermal Langerhans cells (LCs) require TGF- β family signaling for their differentiation and canonical TGF-β1 signaling secures a non-activated LC state. LCs reportedly control skin inflammation and are replenished from peripheral blood monocytes, which also give rise to pro-inflammatory monocyte-derived DCs (moDCs). Among all the miRNAs differentially expressed in LC vs moDCs, we observed miR-424 to be strongly induced during moDC differentiation from monocytes. We discovered that miR-424 is required for moDC differentiation from human and murine precursor cellsin vitroand for inflammation-associated moDCin vivo. Mechanistically we found that low levels of miR-424 facilitate TGF-β1-dependent LC differentiation at the expense of moDC differentiation. Loss of miR-424 in monocyte/DC precursors resulted in the induction of TGF-β pathway. Therefore, miR-424 plays a decisive role in anti-inflammatory LC vs pro-inflammatory moDC differentiation from monocytes, and its repression allows TGF-β ligands to promote LC differentiation.Short summaryMonocytes give rise to two distinct DC subsets in skin inflammation, exhibiting opposite roles in inflammation. This study identified miR-424(322) as a molecular switch controlling pro-inflammatory (moDC) vs anti-inflammatory LC subset differentiation by modulating TGF-β signaling.
Micro-XRF study of the troodontid dinosaurJianianhualong tengireveals new biological and taphonomical signals
Authors: Li Jinhua , Pei Rui , Teng Fangfang , Qiu Hao , Tagle Roald , Yan Qiqi , Wang Qiang , Chu Xuelei , Xu Xing 
Published: September 2020

AbstractJianianhualong tengiis a key taxon for understanding the evolution of pennaceous feathers as well as troodontid theropods, and it is known by only the holotype, which was recovered from the Lower Cretaceous Yixian Formation of western Liaoning, China. Here, we carried out a large-area micro-X-Ray fluorescence (micro-XRF) analysis on the holotypic specimen ofJianianhualong tengivia a Brucker M6 Jetstream mobile XRF scanner. The elemental distribution measurements of the specimen show an enrichment of typical bones couponing elements such as S, P and Ca allowing to visualize the fossil structure. Additionally, to this, the bones are enriched in several heavier elements such as Sr, Th, Y and Ce over the surrounding rocks. The enrichment is most likely associated to secondary mineralization and the phosphates from the bones. Interestingly the plumage shape correlates with an enrichment in elements such as Cu, Ni and Ti, consistent with a previous study [1] onArchaeopteryxusing synchrotron imaging. The analysis presented here provide new biological and taphonomic information of this fossil. Anin-situand nondestructive micro-XRF analysis is currently the most ideal way to map the chemistry of fossils, so far this is manly restricted to small samples. Larger samples usually required a synchrotron facility for analysis. Our study demonstrated that laboratory-based large-area micro-XRF scanner can provides a practical tool for the study of large large-sized specimens allowing collect full chemical data for a better understanding of evolutionary and taphonomic processes.
InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network
Authors: Johansson-Åkhe Isak , Mirabello Claudio , Wallner Björn 
Published: September 2020

AbstractMotivationPeptide-protein interactions between a smaller or disordered peptide stretch and a folded receptor make up a large part of all protein-protein interactions. A common approach for modelling such interactions is to exhaustively sample the conformational space by fast-fourier-transform docking, and then refine a top percentage of decoys. Commonly, methods capable of ranking the decoys for selection in short enough time for larger scale studies rely on first-principle energy terms such as electrostatics, Van der Waals forces, or on pre-calculated statistical pairwise potentials.ResultsWe present InterPepRank for peptide-protein complex scoring and ranking. InterPepRank is a machine-learning based method which encodes the structure of the complex as a graph; with physical pairwise interactions as edges and evolutionary and sequence features as nodes. The graph-network is trained to predict the LRMSD of decoys by using edge-conditioned graph convolutions on a large set of peptide-protein complex decoys. InterPepRank is tested on a massive independent test set with no targets sharing CATH annotation nor 30% sequence identity with any target in training or validation data. On this set, InterPepRank has a median AUC of 0.86 for finding coarse peptide-protein complexes with LRMSD<4Å. This is an improvement compared to other state-of-the-art ranking methods that have a median AUC of circa 0.69. When included as selection-method for selecting decoys for refinement in a previously established peptide docking pipeline, InterPepRank improves the number of Medium and High quality models produced by 80% and 40%, respectively.AvailabilityThe program is available from:http://wallnerlab.org/InterPepRankContactBjörn Wallnerbjorn.wallner@liu.seSupplementary informationSupplementary data are available atBioRxivonline.
The influence of stimulus duration on olfactory identity
Authors: Kuruppath Praveen , Belluscio Leonardo 
Published: September 2020

AbstractDuration of a stimulus plays an important role in coding of sensory information. The role of stimulus duration is extensively studied in tactile, visual and auditory system. In the olfactory system, how the stimulus duration influences the identity of an olfactory information is not well understood. To test this, we activated the olfactory bulbs with blue light in mice expressing channelrhodopsin and behaviorally assessed the relevance of stimulus duration on olfactory identity. Our behavior data demonstrate that stimulus duration changes the olfactory information and the associated behavior.
Reconstitution of prospermatogonial specificationin vitrofrom human induced pluripotent stem cells
Authors: Hwang Young Sun , Suzuki Shinnosuke , Seita Yasunari , Ito Jumpei , Sakata Yuka , Aso Hirofumi , Sato Kei , Hermann Brian P. , Sasaki Kotaro 
Published: September 2020

ABSTRACTEstablishment of spermatogonia throughout the fetal and postnatal period is essential for production of spermatozoa and male fertility. Here, we established a protocol forin vitroreconstitution of human prospermatogonial specification whereby human primordial germ cell (PGC)-like cells (hPGCLCs) differentiated from human induced pluripotent stem cells were further induced into M-prospermatogonia-like cells (MLCs) and T1 prospermatogonia-like cells (T1LCs) using long-term cultured xenogeneic reconstituted testes. Single cell RNA-sequencing was used to delineate the lineage trajectory leading to T1LCs, which closely resemble human T1-prospermatogoniain vivoand exhibited gene expression related to spermatogenesis and diminished proliferation, a hallmark of quiescent T1 prospermatogonia. Notably, this system enabled us to visualize the dynamic and stage-specific regulation of transposable elements during human prospermatogonial specification. Together, our findings pave the way for understanding and reconstructing human male germline developmentin vitro.
McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation
Authors: Hajdusits Bence , Suskiewicz Marcin J. , Hundt Nikolas , Meinhart Anton , Kurzbauer Robert , Leodolter Julia , Kukura Philipp , Clausen Tim 
Published: September 2020

AbstractIn Gram-positive bacteria, the McsB protein arginine kinase is central to protein quality control, labelling aberrant molecules for degradation by the ClpCP protease. Despite its importance for stress response and pathogenicity, it is still elusive how the bacterial degradation labelling is regulated. Here, we delineate the mechanism how McsB targets aberrant proteins during stress conditions. Structural data reveal a self-compartmentalized kinase, in which the active sites are sequestered in a molecular cage. The “closed” octamer interconverts with other oligomers in a phosphorylation-dependent manner and, contrary to these “open” forms, preferentially labels unfolded proteins.In vivodata show that heat-shock triggers accumulation of higher-order oligomers, of which the octameric McsB is essential for surviving stress situations. The interconversion of open and closed oligomers represents a distinct regulatory mechanism of a degradation labeler, allowing the McsB kinase to adapt its potentially dangerous enzyme function to the needs of the bacterial cell.
Antibody binding to SARS-CoV-2 S glycoprotein correlates with, but does not predict neutralization
Authors: Ding Shilei , Laumaea Annemarie , Gasser Romain , Medjahed Halima , Pancera Marie , Stamatatos Leonidas , McGuire Andrew , Bazin Renée , Finzi Andrés 
Published: September 2020

AbstractConvalescent plasma from SARS-CoV-2 infected individuals and monoclonal antibodies were shown to potently neutralize viral and pseudoviral particles carrying the S glycoprotein. However, a non-negligent proportion of plasma samples from infected individuals as well as S-specific monoclonal antibodies were reported to be non-neutralizing despite efficient interaction with the S glycoprotein in different biochemical assays using soluble recombinant forms of S or when expressed at the cell surface. How neutralization relates to binding of S glycoprotein in the context of viral particles remains to be established. Here we developed a pseudovirus capture assay (VCA) to measure the capacity of plasma samples or antibodies immobilized on ELISA plates to bind to membrane-bound S glycoproteins from SARS-CoV-2 expressed at the surface of lentiviral particles. By performing VCA and neutralization assays we observed a strong correlation between these two parameters. However, while we found that plasma samples unable to capture viral particles did not neutralize, capture did not guarantee neutralization, indicating that the capacity of antibodies to bind to the S glycoprotein at the surface of viral particles is required but not sufficient to mediate neutralization. Altogether, our results highlights the importance of better understanding the inactivation of S by plasma and neutralizing antibodies.
Characterization and Prediction of ISRE Binding Patterns Across Cell Types Under Type I Interferon Stimulation
Authors: Leviyang Sivan 
Published: September 2020

AbstractStimulation of cells by type I interferons (IFN) leads to the differential expression of 100s of genes known as interferon stimulated genes, ISGs. The collection of ISGs differentially expressed under IFN stimulation, referred to as the IFN signature, varies across cell types. Non-canonical IFN signaling has been clearly associated with variation in IFN signature across cell types, but the existence of variation in canonical signaling and its impact on IFN signatures is less clear. The canonical IFN signaling pathway involves binding of the transcription factor ISGF3 to IFN-stimulated response elements, ISREs. We examined ISRE binding patterns under IFN stimulation across six cell types using existing ChIPseq datasets available on the GEO and ENCODE databases. We find that ISRE binding is cell specific, particularly for ISREs distal to transcription start sites, potentially associated with enhancer elements, while ISRE binding in promoter regions is more conserved. Given variation of ISRE binding across cell types, we investigated associations between the cell type, homeostatic state and ISRE binding patterns. Taking a machine learning approach and using existing ATACseq and ChIPseq datasets available on GEO and ENCODE, we show that the epigenetic state of an ISRE locus at homeostasis and the DNA sequence of the ISRE locus are predictive of the ISRE’s binding under IFN stimulation in a cell type, specific manner, particularly for ISRE distal to transcription start sites.
β-catenin dependent axial patterning in Cnidaria and Bilateria uses similar regulatory logic
Authors: Bagaeva Tatiana , Aman Andrew J. , Graf Thomas , Niedermoser Isabell , Zimmermann Bob , Kraus Yulia , Schatka Magdalena , Demilly Adrien , Technau Ulrich , Genikhovich Grigory 
Published: September 2020

AbstractIn animals, body axis patterning is based on the concentration-dependent interpretation of graded morphogen signals, which enables correct positioning of the anatomical structures. The most ancient axis patterning system acting across animal phyla relies on β-catenin signaling, which directs gastrulation, and patterns the main body axis. However, within Bilateria, the patterning logic varies significantly between protostomes and deuterostomes. To deduce the ancestral principles of β-catenin dependent axial patterning, we investigated the oral-aboral axis patterning in the sea anemoneNematostella- a member of the bilaterian sister group Cnidaria. Here we elucidate the regulatory logic by which more orally expressed β-catenin targets repress more aborally expressed β- catenin targets, and progressively restrict the initially global, maternally provided aboral identity. Similar regulatory logic of β-catenin-dependent patterning inNematostellaand deuterostomes suggests a common evolutionary origin of these processes.
No evidence of impaired sensorimotor adaptation in Complex Regional Pain Syndrome
Authors: Vittersø Axel D. , Buckingham Gavin , Ten Brink Antonia F. , Halicka Monika , Proulx Michael J. , Bultitude Janet H. 
Published: September 2020

AbstractSensorimotor conflict is theorised to contribute to the maintenance of some pathological pain conditions, such as Complex Regional Pain Syndrome (CRPS). We therefore tested whether sensorimotor adaptation is impaired in people with CRPS by characterising their adaption to lateral prismatic shifts in vision. People with unilateral upper limb CRPS Type I (n = 17), and pain-free individuals (n = 18; matched for age, sex, and handedness) completed prism adaptation with their affected/non-dominant and non-affected/dominant arm, in a counterbalanced order. We examined 1) the rate at which participants compensated for the optical shift during prism exposure (i.e. strategic recalibration), 2) endpoint errors made directly after prism adaptation (sensorimotor realignment) and their retention, and 3) kinematic markers associated with feedforward motor control and sensorimotor realignment. We found no evidence that strategic recalibration was different between people with CRPS and controls, including no evidence for differences in a kinematic marker associated with trial-by-trial changes in movement plans. Participants made significant endpoint errors in the prism adaptation after-effect phase, which are indicative of sensorimotor realignment. Overall, the magnitude of this realignment was not found to differ between people with CRPS and pain-free controls. However, people with CRPS made greater endpoint errors when using their affected hand than their non-affected hand, whereas no such difference was seen in controls. Taken together, these findings suggest that strategic control and sensorimotor realignment were not impaired for either arm in people with CRPS. In contrast, they provide some evidence that there is a greater propensity for sensorimotor realignment in CRPS, consistent with more flexible representations of the body and peripersonal space. Our study challenges the theory that sensorimotor conflict might underlie pathological pain that is maintained in the absence of tissue pathology.
Global supply chains after COVID-19: the end of the road for neoliberal globalisation?
Authors: Free Clinton , Hecimovic Angela 
Published: September 2020

PurposeThrough its impact on both demand and supply, the outbreak of novel coronavirus disease 2019 (COVID-19) has profoundly disrupted supply chains throughout the world. The purpose of this paper is to explore the underlying drivers of the supply chain vulnerability exposed by COVID-19 and considers potential future directions for global supply.Design/methodology/approachThis paper adopts a case study approach, reviewing the automotive manufacturing sector in Australia to illustrate how neoliberal globalisation policy settings have shifted large tracts of manufacturing from the global north to the global south.FindingsThe authors demonstrate the way that neoliberal globalisation policies, facilitated by certain accounting rhetorics and technologies, have consolidated manufacturing in China and Southeast Asia in ways that embed vulnerabilities in global supply chains. The authors present three scenarios for post-COVID-19 supply chains and the accounting techniques likely to garner stronger attention as a result of the pandemic.Research limitations/implicationsThe paper illustrates how certain accounting rhetorics and technologies facilitate neoliberal globalisation, embedding supply chain vulnerability that has been exposed by COVID-19. It also suggests how supply chain accounting may develop more robust supply chains in a post-COVID-19 world and sets out an agenda for future research in this area.Practical implicationsA number of practical supply chain accounting and planning technologies are suggested to facilitate more robust supply chains.Originality/valueThis paper draws attention to the neoliberal globalisation policies that have shaped global supply chains as well as how COVID-19, in concert with other geopolitical trajectories, may represent a watershed moment for global supply chains.
Ownership concentration in the Gulf Cooperation Council
Authors: Martinez-Garcia Irma , Basco Rodrigo , Gomez-Anson Silvia , Boubakri Narjess 
Published: September 2020

PurposeThis article attempts to answer the following questions: Who ultimately owns firms listed in the Gulf Cooperation Council (GCC) countries? Does ownership structure depend on the institutional context? How does ownership affect firm performance? Do institutional factors influence the ownership–performance relationship?Design/methodology/approachWe apply univariate analyses and generalised methods of moments estimations for a sample of 692 GCC listed firms during 2009–2015.FindingsOur results reveal that corporations are mainly controlled by the state or families, the ownership structure is highly concentrated and pyramid structures are common in the region. Ownership is more concentrated in non-financial than financial firms, and ownership concentration and shareholder identity differ by institutional country setting. Finally, ownership concentration does not influence performance, but formal institutions play a moderating role in the relationship.Practical implicationsAs our findings reveal potential type II agency problems due to ownership concentration, policymakers should raise awareness of professional corporate governance practices and tailor them to GCC countries’ institutional contexts.Social implicationsEven with the introduction of new regulations by some GCC states to protect minority investors and promote corporate governance practices, ownership concentration is a rigid structure, and its use by investors to protect their economic endowment and power is culturally embedded.Originality/valueAlthough previous studies have analysed ownership concentration and large shareholders’ identities across countries, this study fills a research gap investigating this phenomenon in-depth in emerging economies.