bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gaussian process modelling for improved resolution in Faraday depth reconstruction
Authors: Ndiritu S W , Scaife A M M , Tabb D L , Cárcamo M , Hanson J 
Published: February 2021

ABSTRACT
The incomplete sampling of data in complex polarization measurements from radio telescopes negatively affects both the rotation measure (RM) transfer function and the Faraday depth spectra derived from these data. Such gaps in polarization data are mostly caused by flagging of radio frequency interference and their effects worsen as the percentage of missing data increases. In this paper we present a novel method for inferring missing polarization data based on Gaussian processes (GPs). GPs are stochastic processes that enable us to encode prior knowledge in our models. They also provide a comprehensive way of incorporating and quantifying uncertainties in regression modelling. In addition to providing non-parametric model estimates for missing values, we also demonstrate that GP modelling can be used for recovering rotation measure values directly from complex polarization data, and that inferring missing polarization data using this probabilistic method improves the resolution of reconstructed Faraday depth spectra.
First light from tidal disruption events
Authors: Bonnerot Clément , Lu Wenbin , Hopkins Philip F 
Published: February 2021

ABSTRACT
When a star comes too close to a supermassive black hole, it gets torn apart by strong tidal forces in a tidal disruption event, or TDE. Half of the elongated stream of debris comes back to the stellar pericentre where relativistic apsidal precession induces a self-crossing shock. As a result, the gas gets launched into an outflow that can experience additional interactions, leading to the formation of an accretion disc. We carry out the first radiation–hydrodynamics simulations of this process, making use of the same injection procedure to treat the self-crossing shock as in our previous adiabatic study. Two sets of realistic parameters of the problem are considered that correspond to different strengths of this initial interaction. In both cases, we find that the injected matter has its trajectories promptly circularized by secondary shocks taking place near the black hole. However, the generated internal energy efficiently diffuses away in the form of radiation, which results in a thin vertical profile of the formed disc. The diffusing photons promptly irradiate the surrounding debris until they emerge with a bolometric luminosity of $L\approx 10^{44} \, \rm erg\, s^{-1}$. Towards the self-crossing shock, diffusion is, however, slowed that results in a shallower luminosity increase, with a potentially significant component in the optical band. Matter launched to large distances continuously gains energy through radiation pressure, which can cause a significant fraction to become unbound. This work provides direct insight into the origin of the early emission from TDEs, which is accessed by a rapidly increasing number of observations.
The tune of the Universe: the role of plasma in tests of strong-field gravity
Authors: Cardoso Vitor , Guo Wen-Di , Macedo Caio F B , Pani Paolo 
Published: February 2021

ABSTRACT
Gravitational-wave (GW) astronomy, together with precise pulsar timing and long baseline interferometry, is changing our ability to perform tests of fundamental physics with astrophysical observations. Some of these tests are based on electromagnetic (EM) probes or electrically charged bodies, and assume an empty Universe. However, the cosmos is filled with plasma, a dilute medium which prevents the propagation of low-frequency, small-amplitude EM waves. We show that the plasma hinders our ability to perform some strong-field gravity tests, in particular: (i) nonlinear plasma effects dramatically quench plasma-driven super-radiant instabilities; (ii) the contribution of EM emission to the inspiral of charged black-hole binaries is strongly suppressed; (iii) EM-driven secondary modes, although present in the spectrum of charged black holes, are excited to negligible amplitude in the GW ringdown signal. The last two effects are relevant also in the case of massive fields that propagate in vacuum and can jeopardize tests of modified theories of gravity containing massive degrees of freedom.
GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues
Authors: Xia Ying , Xia Chun-Qiu , Pan Xiaoyong , Shen Hong-Bin 
Published: February 2021

Abstract
Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this paper, we propose an accurate predictor, GraphBind, for identifying nucleic-acid-binding residues on proteins based on an end-to-end graph neural network. Considering that binding sites often behave in highly conservative patterns on local tertiary structures, we first construct graphs based on the structural contexts of target residues and their spatial neighborhood. Then, hierarchical graph neural networks (HGNNs) are used to embed the latent local patterns of structural and bio-physicochemical characteristics for binding residue recognition. We comprehensively evaluate GraphBind on DNA/RNA benchmark datasets. The results demonstrate the superior performance of GraphBind than state-of-the-art methods. Moreover, GraphBind is extended to other ligand-binding residue prediction to verify its generalization capability. Web server of GraphBind is freely available at http://www.csbio.sjtu.edu.cn/bioinf/GraphBind/.
The Invention of Terrorism in Nineteenth-Century Europe, Russia, and the United States
Authors: Dietze Carola 
Published: February 2021

Abstract
This chapter examines the emergence of terrorism. It argues that five men invented terrorist tactics in a transnational learning process between 1858 and 1866 in Europe, the United States, and Russia. After a systematic reflection on terrorism’s sociopolitical logic and its preconditions, the chapter analyzes Felice Orsini’s attempt to assassinate Napoleon III and the media reactions. This case is interpreted as the beginning of the invention of terrorism. News of Orsini’s deed traveled to America and had inspired John Brown, who changed his tactics from guerilla war to terrorism when he planned his raid on Harpers Ferry. Oskar Wilhelm Becker, John Wilkes Booth, and Dmitrii Vladimirovich Karakozov were the three most significant imitators of both Orsini’s and Brown’s deeds. They finalized the tactic by universalizing it politically and developing the claim of responsibility (Bekennerschreiben). With these developments the terrorist tactic as we know it today was fully developed.
A Mobile Phone in One Hand and Erskine May in the Other: The European Research Group’s Parliamentary Revolution
Authors: Murray C R G , Armstrong Megan A 
Published: February 2021

Abstract
It has become axiomatic that backbench Members of Parliament (MPs) at Westminster have limited the capacity for independent action under the burdens of constituency business and whipped votes. Even the limited avenues available for such MPs to shine, such as select committees, are often illusory because parliamentarians have little time to prepare the materials or brief themselves on any but the highest profile witnesses. The political parties have benefitted from this state of affairs; docile MPs make for reliable votes. The rise of the European Research Group (ERG) as a parliamentary force disrupts this narrative. Galvanised by single-issue opposition to the UK’s involvement in ‘Europe’, encompassing both the European Union (EU) and the European Convention on Human Rights (ECHR), the Group successfully exploited the balance of power in the Commons during the 2017–2019 Parliamentary Session. This article analyses the methods by which the Group’s members magnified their influence over Brexit debates.
Loss, grief and healing: accompaniment in time of COVID-19
Authors: Corpuz Jeff Clyde G 
Published: February 2021

Abstract
This paper is a response to the recent correspondence published in this journal where the author rightly stated that need to redirect one’s perception on the different realities of life such as death. This paper discusses the difficulties associated with loss, grief and healing in the time of COVID-19 pandemic. This paper further adds the importance of accompaniment to people experiencing the complicated grief process. The COVID-19 pandemic is affecting the way one overcome grief where the bereaved are required to grieve without the support of usual social, cultural and religious rituals.
Local R&D support as a driver of network diversification: A cross-regional comparison in Japan
Authors: Takano Keisuke , Okamuro Hiroyuki 
Published: February 2021

AbstractThis study compares the effects of local research and development (R&D) support programs on firm performance in three neighboring prefectures in the same district in Japan. Particularly, we focus on the regional and industrial diversification of transaction networks as the outcome to evaluate regional innovation policies for higher competitiveness. One of these prefectures has a large industrial agglomeration around world-leading manufacturers, which is not applicable to the other two prefectures. Empirical evaluation based on a firm-level dataset confirms only weak and partial effects of local R&D support on business diversification, but provides evidence of different consequences of local innovation policies, reflecting the differences in industrial structure, geographical positions, and policy schemes.
Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data
Authors: Adams Richard H , Blackmon Heath , DeGiorgio Michael 
Published: February 2021

Abstract
Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing two phylogenies in terms of their induced probability distributions that are functions of many model parameters, these distances can be more informative than traditional approaches that rely strictly on differences in topology or branch lengths alone. Currently, however, these approaches are designed for comparing models of nucleotide substitution and gene tree distributions, and thus, are unable to address other classes of traits and associated models that may be of interest to evolutionary biologists. Here, we expand the principles of probabilistic phylogenetic distances to compute tree distances under models of continuous trait evolution along a phylogeny. By explicitly considering both the degree of relatedness among species and the evolutionary processes that collectively give rise to character traits, these distances provide a foundation for comparing models and their predictions, and for quantifying the impacts of assuming one phylogenetic background over another while studying the evolution of a particular trait. We demonstrate the properties of these approaches using theory, simulations, and several empirical data sets that highlight potential uses of probabilistic distances in many scenarios. We also introduce an open-source R package named PRDATR for easy application by the scientific community for computing phylogenetic distances under models of character trait evolution.[Brownian motion; comparative methods; phylogeny; quantitative traits.]
Observing Plasticity of the Auditory System: Volumetric Decreases Along with Increased Functional Connectivity in Aspiring Professional Musicians
Authors: Wenger Elisabeth , Papadaki Eleftheria , Werner André , Kühn Simone , Lindenberger Ulman 
Published: February 2021

AbstractPlaying music relies on several sensory systems and the motor system, and poses strong demands on control processes, hence, offering an excellent model to study how experience can mold brain structure and function. Although most studies on neural correlates of music expertise rely on cross-sectional comparisons, here we compared within-person changes over time in aspiring professionals intensely preparing for an entrance exam at a University of the Arts to skilled amateur musicians not preparing for a music exam. In the group of aspiring professionals, we observed gray-matter volume decrements in left planum polare, posterior insula, and left inferior frontal orbital gyrus over a period of about 6 months that were absent among the amateur musicians. At the same time, the left planum polare, the largest cluster of structural change, showed increasing functional connectivity with left and right auditory cortex, left precentral gyrus, left supplementary motor cortex, left and right postcentral gyrus, and left cingulate cortex, all regions previously identified to relate to music expertise. In line with the expansion–renormalization pattern of brain plasticity (Wenger et al., 2017a. Expansion and renormalization of human brain structure during skill acquisition. Trends Cogn Sci. 21:930–939.), the aspiring professionals might have been in the selection and refinement period of plastic change.
Protection of apigenin against acrylonitrile-induced sperm and testis injury in rats: involvement of activation of ASK1-JNK/p38 signaling pathway
Authors: Shi Ying , Bai Jin , Dang Yuhui , Bai Qingli , Zheng Rong , Chen Jia , Li Zhilan 
Published: February 2021

Abstract
This study aims to clarify if apigenin (AP) could play a pivotal role in attenuating acrylonitrile (ACN)-induced sperm and testis injury by inhibiting ASK1-JNK/p38 signaling pathway. Male Sprague–Dawley rats were randomly divided into five groups: a control group (corn oil), an ACN group (ACN 46 mg kg−1), an ACN + AP1 group (ACN + AP 117 mg kg−1), an ACN + AP2 group (ACN + AP 234 mg kg−1) and an ACN + AP3 group (ACN + AP 351 mg kg−1). The ACN + AP groups were given ACN by gavage after a pretreatment with different dosages of AP for 30 min, whereas the rats in the control group received an equivalent volume of corn oil. The gavage was conducted for 6 days per week in 4 weeks. The results showed that AP reduced sperm deformity rate and DNA fragment index and attenuated the testicular injury induced by ACN. AP could also alleviate oxidative stress, downregulate ASK1-JNK/p38 signaling pathway and eventually inhibit mitochondria-mediated testicular apoptosis. In brief, AP could dampen oxidative stress thereby inhibiting testicular apoptosis mediated by ASK1-JNK/p38 signaling pathway, alleviating ACN-induced sperm and testis injury and exerting a protective effect on male reproductive system.
Don't Hold Your Breath—A Video-Based Study of Procedural Intervals During Pediatric Rapid Sequence Intubation
Authors: Shah Ashish , Edmunds Katherine , Dean Preston , Frey Mary , Boyd Stephanie , Ahaus Karen , Zhang Yin , Varadarajan Kartik , Kerrey Benjamin T. 
Published: February 2021

Objective
Develop a framework for data collection to determine the contributions of both laryngoscopy and tube delivery intervals to the apneic period in unsuccessful and successful attempts among patients undergoing rapid sequence intubation (RSI) in a pediatric emergency department (PED).

Design
This was a retrospective, observational study of RSI.

Setting
An academic PED.

Patients
A consecutive sample of all intubations attempts of first provider physicians performing RSI in the shock trauma suite over a 10-month period in 2018–2019.

Measurement and Main Results
Data were collected by structured video review. The main outcome was the duration of the laryngoscopy and tube delivery intervals per attempt. We compared interval duration between successful and unsuccessful attempts, adjusting for age, accounting for repeated measures, and clustering by provider. There were 69 patients with 89 total intubation attempts. Sixty-three patients were successfully intubated by the first provider (91%). Pediatric emergency medicine fellows performed 54% of the attempts. The median duration of the apneic period per attempt was longer in unsuccessful attempts (57 vs 44 seconds; median of difference, −10.5; 95% confidence interval [CI], −17.0 to −4.0). The duration of laryngoscopy was similar (18 vs 13 seconds; median of difference, −3.5; 95% CI, −8.0 to 1.0), but tube delivery was longer in unsuccessful attempts (25.5 vs. 11 seconds; median of difference, −12.5; 95% CI, −17.0 to −4.0). These results did not change when adjusting for age or clustering by provider.

Conclusions
We successfully developed a specific, time-based framework for the contributors to prolonged apnea in RSI. Prolonged tube delivery accounted for more of the apneic period. Future studies and improvement should focus on problems during tube delivery in the PED.
Interactions between auditory statistics processing and visual experience emerge only in late development
Authors: Berto Martina , Pietrini Pietro , Ricciardi Emiliano , Bottari Davide 
Published: February 2021

ABSTRACTThe human auditory system relies on both detailed and summarized representations to recognize different sounds. As local features can exceed the storage capacity, average statistics are computed over time to generate more compact representations at the expense of temporal details availability. This study aimed to identify whether these fundamental sound analyses develop and function exclusively under the influence of the auditory system or interact with other modalities, such as vision. We employed a validated computational synthesis approach allowing to control directly statistical properties embedded in sounds. To address whether the two modes of auditory representation (local features processing and statistical averaging) are influenced by the availability of visual input in different phases of development, we tested samples of sighted controls (SC), congenitally blind (CB), and late-onset (> 10 years of age) blind (LB) individuals in two separate experiments which uncovered auditory statistics computations from behavioral performances. In experiment 1, performance relied on the availability of local features at specific time points; in experiment 2, performance benefited from computing average statistics over longer durations. As expected, when sound duration increased, detailed representation gave way to summary statistics in SC. In both experiments, the sample of CB individuals displayed a remarkably similar performance revealing that both local and global auditory processes are not altered by blindness since birth. Conversely, LB individuals performed poorly compared to the other groups when relying on local features, with no impact on statistical averaging. The dampening in the performance was not associated with the onset and duration of visual deprivation. Results provide clear evidence that vision is not necessary for the development of the auditory computations tested here. Remarkably, a functional interplay between acoustic details processing and vision emerges at later developmental phases. Findings are consistent with a model in which the efficiency of local auditory processing is vulnerable in case sight becomes unavailable. Ultimately results are in favor of a shared computational framework for auditory and visual processing of local features, which emerges in late development.
In vitroevolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2
Authors: Szemiel Agnieszka M. , Merits Andres , Orton Richard J. , MacLean Oscar , Pinto Rute Maria , Wickenhagen Arthur , Lieber Gauthier , Turnbull Matthew L. , Wang Sainan , Mair Daniel , da Silva Filipe Ana , Willett Brian J. , Wilson Sam J. , Patel Arvind H. , Thomson Emma C. , Palmarini Massimo , Kohl Alain , Stewart Meredith E. 
Published: February 2021

AbstractRemdesivir (RDV) is used widely for COVID-19 patients despite varying results in recent clinical trials. Here, we show how serially passaging SARS-CoV-2in vitroin the presence of RDV selected for drug-resistant viral populations. We determined that the E802D mutation in the RNA-dependent RNA polymerase was sufficient to confer decreased RDV sensitivity without affecting viral fitness. Analysis of more than 200,000 sequences of globally circulating SARS-CoV-2 variants show no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we also observed changes in the Spike (i.e., H69 E484, N501, H655) corresponding to mutations identified in emerging SARS-CoV-2 variants indicating that they can arisein vitroin the absence of immune selection. This study illustrates SARS-CoV-2 genome plasticity and offers new perspectives on surveillance of viral variants.One Sentence SummarySARS-CoV-2 drug resistance & genome plasticity
Detection Of Genomic Variants Of SARS-CoV-2 Circulating In Wastewater By High-Throughput Sequencing
Authors: Pérez-Cataluña Alba , Chiner-Oms Álvaro , Cuevas-Ferrando Enric , Díaz-Reolid Azahara , Falcó Irene , Randazzo Walter , Girón-Guzmán Inés , Allende Ana , Bracho María A. , Comas Iñaki , Sánchez Gloria 
Published: February 2021

The use of SARS-CoV-2 metagenomics in wastewater can allow the detection of variants circulating at community level. After comparing with clinical databases, we identified three novel variants in the spike gene, and six new variants in the spike detected for the first time in Spain. We finally support the hypothesis that this approach allows the identification of unknown SARS-CoV-2 variants or detected at only low frequencies in clinical genomes.Abstract Figure