bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Three Hundred project: dynamical state of galaxy clusters and morphology from multiwavelength synthetic maps
Authors: De Luca Federico , De Petris Marco , Yepes Gustavo , Cui Weiguang , Knebe Alexander , Rasia Elena 
Published: April 2021

ABSTRACT
We study the connection between morphology and dynamical state of the simulated galaxy clusters in z ∈ [0, 1.031] from The Three Hundred project. We quantify cluster dynamical state using a combination of dynamical indicators from theoretical measures and compare this combined parameter, χ, with the results from morphological classifications. The dynamical state of the cluster sample shows a continuous distribution from dynamically relaxed, more abundant at lower redshift, to hybrid and disturbed. The dynamical state presents a clear dependence on the radius, with internal regions more relaxed than outskirts. The morphology from multiwavelength mock observation of clusters in X-ray, optical, and Sunyaev–Zel’dovich (SZ) effect images is quantified by M – a combination of six parameters for X-ray and SZ maps and the offsets between the optical position of the brightest cluster galaxy (BCG) and the X-ray/SZ centroids. All the morphological parameters are highly correlated with each other, while they show a moderately strong correlation with the dynamical χ parameter. The X-ray or SZ peaks are less affected by the dynamical state than centroids, which results in reliable tracers of the cluster density peak. The principal source of contamination in the relaxed cluster fraction, inferred from morphological parameters, is due to dynamically hybrid clusters. Compared to individual parameters, which consider only one aspect of cluster property (e.g. only clumping or asymmetry), the combined morphological and dynamical parameters (M and χ) collect more information and provide a single and more accurate estimation of the cluster dynamical state.
Stellar substructures in the periphery of the Magellanic Clouds with the VISTA hemisphere survey from the red clump and other tracers
Authors: El Youssoufi Dalal , Cioni Maria-Rosa L , Bell Cameron P M , de Grijs Richard , Groenewegen Martin A T , Ivanov Valentin D , Matijevĭc Gal , Niederhofer Florian , Oliveira Joana M , Ripepi Vincenzo , Schmidt Thomas , Subramanian Smitha , Sun Ning-Chen , van Loon Jacco Th 
Published: April 2021

ABSTRACT
We study the morphology of the stellar periphery of the Magellanic Clouds in search of substructure using near-infrared imaging data from the Visible and Infrared Survey Telescope for Astronomy Hemisphere Survey. Based on the selection of different stellar populations using the (J − Ks, Ks) colour–magnitude diagram, we confirm the presence of substructures related to the interaction history of the Clouds and find new substructures on the eastern side of the LMC disc, which may be owing to the influence of the Milky Way, and on the northern side of the SMC, which is probably associated with the ellipsoidal structure of the galaxy. We also study the luminosity function of red clump stars in the SMC and confirm the presence of a bi-modal distance distribution, in the form of a foreground population. We find that this bi-modality is still detectable in the eastern regions of the galaxy out to a 10○ distance from its centre. Additionally, a background structure is detected in the North between 7○ and 10○ from the centre that might belong to the Counter Bridge, and a foreground structure is detected in the South between 6○ and 8○ from the centre that might be linked to the Old Bridge.
An HST/STIS view of protoplanetary discs in Upper Scorpius: observations of three young M stars
Authors: Walker Sam , Millar-Blanchaer Maxwell Andrew , Ren Bin , Kalas Paul , Carpenter John 
Published: April 2021

ABSTRACT
We present observations of three protoplanetary discs in visible scattered light around M-type stars in the Upper Scorpius OB association using the Space Telescope Imaging Spectrograph (STIS) instrument on the Hubble Space Telescope (HST). The discs around stars 2MASS J16090075–1908526, 2MASS J16142029–1906481, and 2MASS J16123916–1859284 have all been previously detected with the Atacama Large Millimeter/submillimeter Array (ALMA), and 2MASS J16123916–1859284 has never previously been imaged at scattered light wavelengths. We process our images using reference star differential imaging, comparing and contrasting three reduction techniques – classical subtraction, Karhunen–Loève Image Projection, and non-negative matrix factorization, selecting the classical method as the most reliable of the three for our observations. Of the three discs, two are tentatively detected (2MASS J16142029–1906481 and 2MASS J16123916–1859284), with the third going undetected. Our two detections are shown to be consistent when varying the reference star or reduction method used, and both detections exhibit structure out to projected distances of ≳200 au. Structures at these distances from the host star have never been previously detected at any wavelength for either disc, illustrating the utility of visible-wavelength observations in probing the distribution of small dust grains at large angular separations.
Systematic identification of A-to-I RNA editing in zebrafish development and adult organs
Authors: Buchumenski Ilana , Holler Karoline , Appelbaum Lior , Eisenberg Eli , Junker Jan Philipp , Levanon Erez Y 
Published: April 2021

AbstractA-to-I RNA editing is a common post transcriptional mechanism, mediated by the Adenosine deaminase that acts on RNA (ADAR) enzymes, that increases transcript and protein diversity. The study of RNA editing is limited by the absence of editing maps for most model organisms, hindering the understanding of its impact on various physiological conditions. Here, we mapped the vertebrate developmental landscape of A-to-I RNA editing, and generated the first comprehensive atlas of editing sites in zebrafish. Tens of thousands unique editing events and 149 coding sites were identified with high-accuracy. Some of these edited sites are conserved between zebrafish and humans. Sequence analysis of RNA over seven developmental stages revealed high levels of editing activity in early stages of embryogenesis, when embryos rely on maternal mRNAs and proteins. In contrast to the other organisms studied so far, the highest levels of editing were detected in the zebrafish ovary and testes. This resource can serve as the basis for understanding of the role of editing during zebrafish development and maturity.
miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale
Authors: Fehlmann Tobias , Kern Fabian , Laham Omar , Backes Christina , Solomon Jeffrey , Hirsch Pascal , Volz Carsten , Müller Rolf , Keller Andreas 
Published: April 2021

Abstract
Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.
mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions
Authors: Rodrigues Carlos H M , Pires Douglas E V , Ascher David B 
Published: April 2021

AbstractProtein–protein interactions play a crucial role in all cellular functions and biological processes and mutations leading to their disruption are enriched in many diseases. While a number of computational methods to assess the effects of variants on protein–protein binding affinity have been proposed, they are in general limited to the analysis of single point mutations and have been shown to perform poorly on independent test sets. Here, we present mmCSM-PPI, a scalable and effective machine learning model for accurately assessing changes in protein–protein binding affinity caused by single and multiple missense mutations. We expanded our well-established graph-based signatures in order to capture physicochemical and geometrical properties of multiple wild-type residue environments and integrated them with substitution scores and dynamics terms from normal mode analysis. mmCSM-PPI was able to achieve a Pearson's correlation of up to 0.75 (RMSE = 1.64 kcal/mol) under 10-fold cross-validation and 0.70 (RMSE = 2.06 kcal/mol) on a non-redundant blind test, outperforming existing methods. Our method is freely available as a user-friendly and easy-to-use web server and API at http://biosig.unimelb.edu.au/mmcsm_ppi.
Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex
Authors: Tran Phong Lan Thao , Rieu Martin , Hodeib Samar , Joubert Alexandra , Ouellet Jimmy , Alberti Patrizia , Bugaut Anthony , Allemand Jean-François , Boulé Jean-Baptiste , Croquette Vincent 
Published: April 2021

Abstract
G-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA metabolic transactions. While many in vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in vivo in double-stranded DNA regions, where their formation is challenged by the complementary strand. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on G4 persistence. To address this, we designed a single-molecule assay allowing to measure G4 folding and persistence times in the presence of the complementary strand. We quantified both folding and unfolding rates of biologically relevant G4 sequences, such as the cMYC and cKIT oncogene promoters, human telomeres and an avian replication origin. We confirmed that G4s are found much more stable in tested replication origin and promoters than in human telomere repeats. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence time increased. Our assay opens new perspectives for the measurement of G4 dynamics in double-stranded DNA mimicking a replication fork, which is important to understand their role in DNA replication and gene regulation at a mechanistic level.
Minimized combinatorial CRISPR screens identify genetic interactions in autophagy
Authors: Diehl Valentina , Wegner Martin , Grumati Paolo , Husnjak Koraljka , Schaubeck Simone , Gubas Andrea , Shah Varun Jayeshkumar , Polat Ibrahim H , Langschied Felix , Prieto-Garcia Cristian , Müller Konstantin , Kalousi Alkmini , Ebersberger Ingo , Brandts Christian H , Dikic Ivan , Kaulich Manuel 
Published: April 2021

Abstract
Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale.
Recurrent Chordoma Resection in the Advanced Multimodality Image Guided Operating Suite: 2-Dimensional Operative Video
Authors: Ibn Essayed Walid , Almefty Kaith K , Al-Mefty Ossama 
Published: April 2021

Abstract
Recurrent skull base chordomas are challenging lesions. They already had maximum radiation, and in the absence of any effective medical treatment, surgical resection is the only treatment.
1,2
Surgery on recurrent previously radiated chordomas, however, carries much higher risk and the likelihood of subtotal resection. Maximizing tumor resection allows longer tumor control.
3-5
The Advanced Multimodality Image Guided Operating Suite developed at the Brigham and Women's Hospital, Harvard Medical School, with the support of the National Institutes of Health, provides an optimal environment to manage these tumors. It offers the capability to obtain and integrate multiple modalities during surgery, including magnetic resonance imaging (MRI), positron emission tomography-computed tomography (PET-CT), endoscopy, ultrasound, fluoroscopy, and the ability to perform emergent endovascular procedures.
5-7

The patient is a 39-yr-old male, presenting after 19 yr follow-up of a surgical resection and proton beam treatment for a skull base chordoma. He developed progressive ophthalmoplegia due to recurrence of his chordoma at the right petrous apex and cavernous sinus. Preoperative angiography demonstrated narrowing of the petrous segment of the right carotid artery suspect of radiation-induced angiopathy. The presence of radiation-induced angiopathy increases the risk of intraoperative carotid rupture, and the availability of endovascular intervention in the operative suite added favorable preparedness to deal with such complications if they happen. Given the clinical and radiological progression, surgical intervention was carried out through the prior zygomatic approach with the goal of performing maximum resection.
8
The patient had an uneventful postoperative course and remained stable until he had a second recurrence 4 yr later. The patient consented to the procedure.
On the Theory of Instrumentation (1985)
Authors: Dahlhaus Carl 
Published: April 2021

Abstract
In this essay, originally published in 1985, Carl Dahlhaus addresses the problem of how to integrate timbre into our understanding of music while honoring its resistance to description and quantification. In particular, he explores the history of orchestration in terms of an opposition between “coloristic” and “structural instrumentation,” the latter defined as that which “actively intervenes in the compositional logic [Tonsatz] of the music, rather than being merely dependent on it.” Dahlhaus’ essay is grounded squarely in the common-practice era: his compositional points of reference span from Haydn to Richard Strauss, and he is particularly concerned with how instrumentation can reveal structural patterns that stand athwart the formal trajectories suggested by tonal analyses.
Research with Human Participants in the European Union
Authors: Shaw David , Townend David 
Published: April 2021

Abstract
This chapter examines research with human participants in the European Union. In the EU, the driving force for legislation is the creation of the single market. Research with human participants is both a response to the urgent demand to advance the health of EU citizens through the efficiencies of the single market, and to the commitment of the EU to act in accordance with the shared social and cultural values of the Member States. One might expect, therefore, that EU legislation on research with human participants would be clear, creating a harmonized framework within the single market both for internal consistency and to enhance external competitiveness. However, each of the 27 Member States of the EU operates with a large amount of independence in relation to the governance of research with human participants. The chapter then describes the EU legislation on clinical trials and considers the protection of privacy through the General Data Protection Regulation.
Meaning and Value Across the Generations
Authors: Scheffler Samuel 
Published: April 2021

Abstract
This chapter argues that our relations to our successors are richer, more varied, and more complex than is sometimes recognized. Although we cannot in any straightforward sense interact or form personal relationships with people who will live long after we have died, future generations nevertheless matter greatly to us and in a variety of ways. These facts, which reflect our underappreciated historicist sensibility, must be taken into account in developing an adequate theory of intergenerational ethics. They are also facts of great motivational significance. To ensure the survival of humanity, sufficient numbers of people must be strongly and stably motivated to solve the problems that threaten future generations, and people’s sense of moral obligation may not, by itself, be sufficiently robust or reliable to provide all the necessary motivational support. So one challenge we face, in seeking to address problems like climate change and nuclear proliferation, is to overcome this potentially disabling motivational deficit. Yet once one appreciates the complexity of our attitudes toward future generations, one can see that we have a variety of reasons for caring about the fate of our successors. These reasons provide additional motivational resources that may complement and cooperate with our distinctively moral motivations for addressing threats to future generations.
Rethinking Representations of Trade Unionism in South Africa
Authors: Naicker Camalita 
Published: April 2021

Abstract
This essay reviews the literature on trade unions in South Africa in the last century. It points to some of its limitations seeking to challenge narrow conceptions and worn binaries of worker resistance and trade unionism, spontaneity and organization, that still plague some histories of labor and labor unions. It therefore attempts to review the literature in a way that opens up new readings and theoretical perspectives on labor and trade unions. It seeks to show how migrant and women’s organizing continue to be two areas that the literature has not adequately grasped. That women have often organized themselves outside of unions and dominant political structures implies that there is broad scope for theoretical perspectives that challenge masculine notions of organizing and institutional culture. In addition, there needs to be more attention paid to the issue that migrant members of unions themselves are finding more expression for their grievances outside of trade union bureaucratic structures. Moreover, in a country such as South Africa, with extremely high unemployment in a global economy of fewer and fewer jobs, it is necessary to ask whether the notion of industrial unionism, which has for so long excluded those on the margins of the so-called formal economy, is still viable, or whether new forms of organizing that are more cognizant of the local and global interconnectedness of all spheres of the economy, beyond the public/private divide, must be sought. In order for these perspectives to emerge, however, it is necessary to rethink the categories that people impose on history and how it limits future possibilities.
Digital Youth Politics
Authors: Earl Jennifer , Scovill Sam , Ramo Elliot 
Published: April 2021

Abstract
The authors examine the debate over youth engagement as it has developed since 1990, especially the role of digital and social media. Despite panics over youth disengagement and the pervasiveness of the youth deficit model, contemporary research largely finds that young people are politically engaged, that new media facilitate youth engagement, and that new media usage tends to reduce inequalities between youth in political engagement. Beyond these general findings, the authors also examine how youth use digital and social media in the development of political knowledge and interest and when participating in campaigns and elections, social movements and protest, political consumption (e.g., boycotts and buycotts), and participatory politics (i.e., traditional and new forms of engagement such as making cultural interventions and circulating information and opinions). For each form of engagement, the authors also assess the role of digital and social media usage in making engagement more inclusive and equitable. The authors close by introducing evidence-based resources that young people have access to online to aid their engagement and thoughts about future research.
Normative and Legal Pluralism: A Global Perspective
Authors: Twining William 
Published: April 2021

Abstract
This chapter sets out to demystify the topic of legal pluralism by examining the relationship between legal pluralism, normative pluralism, and general normative theory from a global perspective. The central theme is that treating legal pluralism as a species of normative pluralism decenters the state, links legal pluralism to a rich body of literature, and helps to show that some of the central puzzlements surrounding the topic can usefully be viewed as much broader issues in the general theory of norms and legal theory. A second theme is that so-called “global legal pluralism” is in several respects qualitatively different from the older anthropological and sociolegal accounts of legal pluralism and is largely based on a different set of concerns. Following the introduction in section I, section II considers normative pluralism. It explores the ambiguity of “pluralism” and some themes in general normative theory. Section III introduces the heritage of literature on legal pluralism. It presents an ideal type of social fact legal pluralism to which much, but by no means all, of the mainstream literature approximates. Some brief case studies illustrate some distinctions that are increasingly under attack. Section III suggests that social fact pluralism has achieved much in raising awareness of nonstate normative orders, but provides little guidance on issues of state policy and institutional design. Section IV considers the implications of adopting a global perspective in this context. It questions how far social fact legal pluralism is helpful in addressing a wide range of concerns raised by “globalization” and argues that the radically ambiguous idea of “global legal pluralism” is being applied to such a variety of phenomena and concerns as to be virtually meaningless.