bluuebunny/crossref_metadata_2025_split huggingface dataset:
BEYOND THE HORIZON: THE DEPICTION OF TIME IN KARLHEINZ STOCKHAUSEN'S KLANG
Authors: Parsons Ian 
Published: December 2020

AbstractKarlheinz Stockhausen's cycle of chamber and electronic music, KLANG – die 24 Stunden des Tages (SOUND – The 24 Hours of the Day) was one of several music cycles, both realised and planned, in which the composer sought to capture the passage and meaning of time. Stockhausen's death in 2007 left KLANG with only 21 of its proposed 24 pieces composed. This article draws on Martin Heidegger's concept of time as ‘the horizon for the understanding of being’ as a lens through which to examine the musical content and imagery of KLANG and as a means of understanding the notion of being that Stockhausen conveyed in these compositions written at the end of his life. It will suggest a significant difference in Stockhausen's thinking about the nature of life and being, moving from the cyclic concepts conveyed in the earlier time-focused works such as SIRIUS and LICHT to a more linear notion of being in KLANG. Finally, the article will use this analysis to suggest that, despite Stockhausen's stated intentions to compose two more time-focused cycles after KLANG, he had begun to confront his own mortality, while continuing to believe in the possibility, if not the knowability, of hope beyond death.
Recent advances in processing negation
Authors: Morante Roser , Blanco Eduardo 
Published: December 2020

AbstractNegation is a complex linguistic phenomenon present in all human languages. It can be seen as an operator that transforms an expression into another expression whose meaning is in some way opposed to the original expression. In this article, we survey previous work on negation with an emphasis on computational approaches. We start defining negation and two important concepts: scope and focus of negation. Then, we survey work in natural language processing that considers negation primarily as a means to improve the results in some task. We also provide information about corpora containing negation annotations in English and other languages, which usually include a combination of annotations of negation cues, scopes, foci, and negated events. We continue the survey with a description of automated approaches to process negation, ranging from early rule-based systems to systems built with traditional machine learning and neural networks. Finally, we conclude with some reflections on current progress and future directions.
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents
Authors: McAllister Sean M , Vandzura Rebecca , Keffer Jessica L , Polson Shawn W , Chan Clara S 
Published: December 2020

Abstract
In principle, iron oxidation can fuel significant primary productivity and nutrient cycling in dark environments such as the deep sea. However, we have an extremely limited understanding of the ecology of iron-based ecosystems, and thus the linkages between iron oxidation, carbon cycling, and nitrate reduction. Here we investigate iron microbial mats from hydrothermal vents at Lōʻihi Seamount, Hawaiʻi, using genome-resolved metagenomics and metatranscriptomics to reconstruct potential microbial roles and interactions. Our results show that the aerobic iron-oxidizing Zetaproteobacteria are the primary producers, concentrated at the oxic mat surface. Their fixed carbon supports heterotrophs deeper in the mat, notably the second most abundant organism, Candidatus Ferristratum sp. (uncultivated gen. nov.) from the uncharacterized DTB120 phylum. Candidatus Ferristratum sp., described using nine high-quality metagenome-assembled genomes with similar distributions of genes, expressed nitrate reduction genes narGH and the iron oxidation gene cyc2 in situ and in response to Fe(II) in a shipboard incubation, suggesting it is an anaerobic nitrate-reducing iron oxidizer. Candidatus Ferristratum sp. lacks a full denitrification pathway, relying on Zetaproteobacteria to remove intermediates like nitrite. Thus, at Lōʻihi, anaerobic iron oxidizers coexist with and are dependent on aerobic iron oxidizers. In total, our work shows how key community members work together to connect iron oxidation with carbon and nitrogen cycling, thus driving the biogeochemistry of exported fluids.
Deubiquitylases in developmental ubiquitin signaling and congenital diseases
Authors: Basar Mohammed A. , Beck David B. , Werner Achim 
Published: December 2020

AbstractMetazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate’s stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
Zero-bias mid-infrared graphene photodetectors with bulk photoresponse and calibration-free polarization detection
Authors: Wei Jingxuan , Li Ying , Wang Lin , Liao Wugang , Dong Bowei , Xu Cheng , Zhu Chunxiang , Ang Kah-Wee , Qiu Cheng-Wei , Lee Chengkuo 
Published: December 2020

AbstractBulk photovoltaic effect (BPVE), featuring polarization-dependent uniform photoresponse at zero external bias, holds potential for exceeding the Shockley-Queisser limit in the efficiency of existing opto-electronic devices. However, the implementation of BPVE has been limited to the naturally existing materials with broken inversion symmetry, such as ferroelectrics, which suffer low efficiencies. Here, we propose metasurface-mediated graphene photodetectors with cascaded polarization-sensitive photoresponse under uniform illumination, mimicking an artificial BPVE. With the assistance of non-centrosymmetric metallic nanoantennas, the hot photocarriers in graphene gain a momentum upon their excitation and form a shift current which is nonlocal and directional. Thereafter, we demonstrate zero-bias uncooled mid-infrared photodetectors with three orders higher responsivity than conventional BPVE and a noise equivalent power of 0.12 nW Hz−1/2. Besides, we observe a vectorial photoresponse which allows us to detect the polarization angle of incident light with a single device. Our strategy opens up alternative possibilities for scalable, low-cost, multifunctional infrared photodetectors.
Organism body size structures the soil microbial and nematode community assembly at a continental and global scale
Authors: Luan Lu , Jiang Yuji , Cheng Menghua , Dini-Andreote Francisco , Sui Yueyu , Xu Qinsong , Geisen Stefan , Sun Bo 
Published: December 2020

AbstractBody size is a key life-history trait that influences community assembly by affecting how ecological processes operate at the organism level. However, the extent to which the relative influences of ecological processes mediate the assembly of differentially sized soil organisms is still unknown. Here, we investigate the community assembly of differentially sized soil microorganisms and microfauna using a continental-scale sampling effort combined with a global-scale meta-analysis. Our results reveal a general relationship between organism body size and the stochastic-deterministic balance operating on community assembly. The smallest microorganisms (bacteria) are relatively more influenced by dispersal-based stochastic processes, while larger ones (fungi, protists and nematodes) are more structured by selection-based deterministic processes. This study elucidates a significant and consistent relationship between an organism life-history trait and how distinct ecological processes operate in mediating their respective community assemblages, thus providing a better understanding of the mechanisms supporting soil biodiversity.
Giant thermoelectric power factor in charged ferroelectric domain walls of GeTe with Van Hove singularities
Authors: Dangić Ðorđe , Fahy Stephen , Savić Ivana 
Published: December 2020

AbstractIncreasing the Seebeck coefficient S in thermoelectric materials usually drastically decreases the electrical conductivity σ, making significant enhancement of the thermoelectric power factor σS2 extremelly challenging. Here we predict, using first-principles calculations, that the extraordinary properties of charged ferroelectric domain walls (DWs) in GeTe enable a five-fold increase of σS2 in the DW plane compared to bulk. The key reasons for this enhancement are the confinement of free charge carriers at the DWs and Van Hove singularities in the DW electronic band structure near the Fermi level. These effects lead to an increased energy dependence of the DW electronic transport properties, resulting in more than a two-fold increase of S with respect to bulk, without considerably degrading the in-plane σ. We propose a design of a nano-thermoelectric device that utilizes the exceptional thermoelectric properties of charged ferroelectric DWs. Our findings should inspire further investigation of ferroelectric DWs as efficient thermoelectric materials.
Nonhuman primate to human immunobridging to infer the protective effect of an Ebola virus vaccine candidate
Authors: Roozendaal Ramon , Hendriks Jenny , van Effelterre Thierry , Spiessens Bart , Dekking Liesbeth , Solforosi Laura , Czapska-Casey Dominika , Bockstal Viki , Stoop Jeroen , Splinter Daniel , Janssen Sarah , Baelen Ben van , Verbruggen Nadia , Serroyen Jan , Dekeyster Eline , Volkmann Ariane , Wollmann Yvonne , Carrion Ricardo , Giavedoni Luis D. , Robinson Cynthia , Leyssen Maarten , Douoguih Macaya , Luhn Kerstin , Pau Maria Grazia , Sadoff Jerry , Vandebosch An , Schuitemaker Hanneke , Zahn Roland , Callendret Benoit 
Published: December 2020

AbstractIt has been proven challenging to conduct traditional efficacy trials for Ebola virus (EBOV) vaccines. In the absence of efficacy data, immunobridging is an approach to infer the likelihood of a vaccine protective effect, by translating vaccine immunogenicity in humans to a protective effect, using the relationship between vaccine immunogenicity and the desired outcome in a suitable animal model. We here propose to infer the protective effect of the Ad26.ZEBOV, MVA-BN-Filo vaccine regimen with an 8-week interval in humans by immunobridging. Immunogenicity and protective efficacy data were obtained for Ad26.ZEBOV and MVA-BN-Filo vaccine regimens using a fully lethal EBOV Kikwit challenge model in cynomolgus monkeys (nonhuman primates [NHP]). The association between EBOV neutralizing antibodies, glycoprotein (GP)-binding antibodies, and GP-reactive T cells and survival in NHP was assessed by logistic regression analysis. Binding antibodies against the EBOV surface GP were identified as the immune parameter with the strongest correlation to survival post EBOV challenge, and used to infer the predicted protective effect of the vaccine in humans using published data from phase I studies. The human vaccine-elicited EBOV GP-binding antibody levels are in a range associated with significant protection against mortality in NHP. Based on this immunobridging analysis, the EBOV GP-specific-binding antibody levels elicited by the Ad26.ZEBOV, MVA-BN-Filo vaccine regimen in humans will likely provide protection against EBOV disease.
Plasma-MDS, a metadata schema for plasma science with examples from plasma technology
Authors: Franke Steffen , Paulet Lucian , Schäfer Jan , O’Connell Deborah , Becker Markus M. 
Published: December 2020

AbstractA metadata schema, named Plasma-MDS, is introduced to support research data management in plasma science. Plasma-MDS is suitable to facilitate the publication of research data following the FAIR principles in domain-specific repositories and with this the reuse of research data for data driven plasma science. In accordance with common features in plasma science and technology, the metadata schema bases on the concept to separately describe the source generating the plasma, the medium in which the plasma is operated in, the target the plasma is acting on, and the diagnostics used for investigation of the process under consideration. These four basic schema elements are supplemented by a schema element with various attributes for description of the resources, i.e. the digital data obtained by the applied diagnostic procedures. The metadata schema is first applied for the annotation of datasets published in INPTDAT—the interdisciplinary data platform for plasma technology.
Herpes simplex virus 1 targets IRF7 via ICP0 to limit type I IFN induction
Authors: Shahnazaryan David , Khalil Rana , Wynne Claire , Jefferies Caroline A. , Ní Gabhann-Dromgoole Joan , Murphy Conor C. 
Published: December 2020

AbstractHerpes simplex keratitis (HSK), caused by herpes simplex virus type 1 (HSV-1) infection, is the commonest cause of infectious blindness in the developed world. Following infection the virus is initially suspended in the tear film, where it encounters a multi-pronged immune response comprising enzymes, complement, immunoglobulins and crucially, a range of anti-viral and pro-inflammatory cytokines. However, given that HSV-1 can overcome innate immune responses to establish lifelong latency throughout a susceptible individual’s lifetime, there is significant interest in understanding the mechanisms employed by HSV-1 to downregulate the anti-viral type I interferon (IFN) mediated immune responses. This study aimed to investigate the interactions between infected cell protein (ICP)0 and key elements of the IFN pathway to identify possible novel targets that contribute to viral immune evasion. Reporter gene assays demonstrated the ability of ICP0 to inhibit type I IFN activity downstream of pathogen recognition receptors (PRRs) which are known to be involved in host antiviral defences. Further experiments identified interferon regulatory factor (IRF)7, a driver of type I IFN, as a potential target for ICP0. These findings increase our understanding of the pathogenesis of HSK and suggest IRF7 as a potential therapeutic target.
Noise representations of open system dynamics
Authors: Szańkowski Piotr , Cywiński Łukasz 
Published: December 2020

AbstractWe analyze the conditions under which the dynamics of a quantum system open to a given environment can be simulated with an external noisy field that is a surrogate for the environmental degrees of freedom. We show that such a field is either a subjective or an objective surrogate; the former is capable of simulating the dynamics only for the specific system–environment arrangement, while the latter is an universal simulator for any system interacting with the given environment. Consequently, whether the objective surrogate field exists and what are its properties is determined exclusively by the environment. Thus, we are able to formulate the sufficient criterion for the environment to facilitate its surrogate, and we identify a number of environment types that satisfy it. Finally, we discuss in what sense the objective surrogate field representation can be considered classical and we explain its relation to the formation of system–environment entanglement, and the back-action exerted by the system onto environment.
Cross-testing of major molecular markers indicates distinct pathways of tumorigenesis in gastric adenocarcinomas and synchronous gastrointestinal stromal tumors
Authors: Kocsmár Éva , Kocsmár Ildikó , Szalai Luca , Lendvai Gábor , Szijártó Attila , Schaff Zsuzsa , Kiss András , Kovalszky Ilona , Papp Gergő , Lotz Gábor 
Published: December 2020

AbstractSmall subtype of the gastrointestinal stromal tumor (micro-GIST, MG) is usually asymptomatic and is frequently found incidentally in association with gastric adenocarcinoma (GAC). The background of this coincidence is still an open question. This study comprehensively characterized nine MGs and GACs present in the same surgical specimen by cross-testing the markers of the major pathogenetic pathways of both tumor types. All of the MGs were immunohistochemically positive for CD117/KIT, CD34, and DOG1. DOG1 was also detected in four GACs. Four MGs carried mutations in c-KIT (exons 9, 11, and 13) and two cases in PDGFRα (exon 18). None of the GACs carried activating mutations in c-KIT or PDGFRα. MMR immunopanel identified one GAC as microsatellite unstable tumor. No EBV-positive tumor was found. According to the TCGA molecular classification, one GAC was categorized in the MSI subgroup, three GACs in the genomically stable subgroup, and the rest into the chromosomal instability subgroup. Although a common carcinogenic effect cannot be ruled out, our data suggest a distinct molecular background in the evolvement of the synchronous MGs and GACs. The presence of a MG in gastric resection specimens may be indicative of the development of synchronous malignant tumors in or outside the stomach.
Expression of transgenes enriched in rare codons is enhanced by the MAPK pathway
Authors: Peterson Jackson , Li Siqi , Kaltenbrun Erin , Erdogan Ozgun , Counter Christopher M. 
Published: December 2020

AbstractThe ability to translate three nucleotide sequences, or codons, into amino acids to form proteins is conserved across all organisms. All but two amino acids have multiple codons, and the frequency that such synonymous codons occur in genomes ranges from rare to common. Transcripts enriched in rare codons are typically associated with poor translation, but in certain settings can be robustly expressed, suggestive of codon-dependent regulation. Given this, we screened a gain-of-function library for human genes that increase the expression of a GFPrare reporter encoded by rare codons. This screen identified multiple components of the mitogen activated protein kinase (MAPK) pathway enhancing GFPrare expression. This effect was reversed with inhibitors of this pathway and confirmed to be both codon-dependent and occur with ectopic transcripts naturally coded with rare codons. Finally, this effect was associated, at least in part, with enhanced translation. We thus identify a potential regulatory module that takes advantage of the redundancy in the genetic code to modulate protein expression.
Analysis of mutant and total huntingtin expression in Huntington’s disease murine models
Authors: Fodale Valentina , Pintauro Roberta , Daldin Manuel , Altobelli Roberta , Spiezia Maria Carolina , Bisbocci Monica , Macdonald Douglas , Bresciani Alberto 
Published: December 2020

AbstractHuntington’s disease (HD) is a monogenetic neurodegenerative disorder that is caused by the expansion of a polyglutamine region within the huntingtin (HTT) protein, but there is still an incomplete understanding of the molecular mechanisms that drive pathology. Expression of the mutant form of HTT is a key aspect of diseased tissues, and the most promising therapeutic approaches aim to lower expanded HTT levels. Consequently, the investigation of HTT expression in time and in multiple tissues, with assays that accurately quantify expanded and non-expanded HTT, are required to delineate HTT homeostasis and to best design and interpret pharmacodynamic readouts for HTT lowering therapeutics. Here we evaluate mutant polyglutamine-expanded (mHTT) and polyglutamine-independent HTT specific immunoassays for validation in human HD and control fibroblasts and use to elucidate the CSF/brain and peripheral tissue expression of HTT in preclinical HD models.
Identification of hnRNP-A1 as a pharmacodynamic biomarker of type I PRMT inhibition in blood and tumor tissues
Authors: Noto Paul B. , Sikorski Timothy W. , Zappacosta Francesca , Wagner Craig D. , Montes de Oca Rocio , Szapacs Matthew E. , Annan Roland S. , Liu Yan , McHugh Charles F. , Mohammad Helai P. , Piccoli Steven P. , Creasy Caretha L. 
Published: December 2020

AbstractArginine methylation has been recognized as a post-translational modification with pleiotropic effects that span from regulation of transcription to metabolic processes that contribute to aberrant cell proliferation and tumorigenesis. This has brought significant attention to the development of therapeutic strategies aimed at blocking the activity of protein arginine methyltransferases (PRMTs), which catalyze the formation of various methylated arginine products on a wide variety of cellular substrates. GSK3368715 is a small molecule inhibitor of type I PRMTs currently in clinical development. Here, we evaluate the effect of type I PRMT inhibition on arginine methylation in normal human peripheral blood mononuclear cells and utilize a broad proteomic approach to identify type I PRMT substrates. This work identified heterogenous nuclear ribonucleoprotein A1 (hnRNP-A1) as a pharmacodynamic biomarker of type I PRMT inhibition. Utilizing targeted mass spectrometry (MS), methods were developed to detect and quantitate changes in methylation of specific arginine residues on hnRNP-A1. This resulted in the development and validation of novel MS and immune assays useful for the assessment of GSK3368715 induced pharmacodynamic effects in blood and tumors that can be applied to GSK3368715 clinical trials.
Piezoelectric and dielectric properties of Bi3TiNbO9 prepared by hot pressing from powders activated using the serial dilution method
Authors: Spitsin A. I. , Bush A. A. , Kamentsev K. E. 
Published: December 2020

AbstractBi-based layer structure ferroelectrics are the most promising compounds for the fabrication of high-temperature piezoelectric materials. Studies aiming to develop and optimize the techniques to produce efficient high-density piezoelectric ceramics, and to investigate the effects of ceramics production conditions on their structure and functional properties, have become high-priority objectives of modern piezo-engineering. We applied ultra high dilution (UHD) technology to pre-treat Bi3TiNbO9 powders and used hot pressing to prepare perovskite-layer structured ceramic specimens. Main characteristics of the synthesized piezoelectric ceramic specimens (the dimensions of the Bi3TiNbO9 orthorhombic unit cell, dielectric permittivity, dielectric loss, piezoelectric coefficient d33 and pyroelectric coefficient pσ) and their temperature-dependent variations were studied using piezoelectric, dielectric, and pyroelectric measurements. X-ray diffraction studies demonstrated that the prepared ceramics were single phased, and highly textured, as their plate-like crystallites were preferentially aligned perpendicularly to the pressure axis on hot pressing. For d33, an increase in values of more than 20% was found for samples obtained using a combined modification of the UHD technology and hot pressing (12 pC/N) relative to intact samples, and more than two times relative to unmodified Bi3TiNbO9 ceramics (6 pC/N). Due to their characteristics, the obtained ceramics are promising materials for high-temperature applications; of particular interest is potential use, as electroacoustic transducers and sensors for operation at high temperatures. Thus, the UHD technology can modify the properties of ceramics and is relatively easy to implement. This makes it attractive for use in various fields of science and technology.