bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning
Authors: Ong Edison , Cooke Michael F , Huffman Anthony , Xiang Zuoshuang , Wong Mei U , Wang Haihe , Seetharaman Meenakshi , Valdez Ninotchka , He Yongqun 
Published: April 2021

Abstract
Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-based vaccine design program using reverse vaccinology with machine learning. Vaxign2 is a comprehensive web server for rational vaccine design, consisting of predictive and computational workflow components. The predictive part includes the original Vaxign filtering-based method and a new machine learning-based method, Vaxign-ML. The benchmarking results using a validation dataset showed that Vaxign-ML had superior prediction performance compared to other RV tools. Besides the prediction component, Vaxign2 implemented various post-prediction analyses to significantly enhance users’ capability to refine the prediction results based on different vaccine design rationales and considerably reduce user time to analyze the Vaxign/Vaxign-ML prediction results. Users provide proteome sequences as input data, select candidates based on Vaxign outputs and Vaxign-ML scores, and perform post-prediction analysis. Vaxign2 also includes precomputed results from approximately 1 million proteins in 398 proteomes of 36 pathogens. As a demonstration, Vaxign2 was used to effectively analyse SARS-CoV-2, the coronavirus causing COVID-19. The comprehensive framework of Vaxign2 can support better and more rational vaccine design. Vaxign2 is publicly accessible at http://www.violinet.org/vaxign2.
Increased expression of tryptophan and tyrosine tRNAs elevates stop codon readthrough of reporter systems in human cell lines
Authors: Beznosková Petra , Bidou Laure , Namy Olivier , Valášek Leoš Shivaya 
Published: April 2021

AbstractRegulation of translation via stop codon readthrough (SC-RT) expands not only tissue-specific but also viral proteomes in humans and, therefore, represents an important subject of study. Understanding this mechanism and all involved players is critical also from a point of view of prospective medical therapies of hereditary diseases caused by a premature termination codon. tRNAs were considered for a long time to be just passive players delivering amino acid residues according to the genetic code to ribosomes without any active regulatory roles. In contrast, our recent yeast work identified several endogenous tRNAs implicated in the regulation of SC-RT. Swiftly emerging studies of human tRNA-ome also advocate that tRNAs have unprecedented regulatory potential. Here, we developed a universal U6 promotor-based system expressing various human endogenous tRNA iso-decoders to study consequences of their increased dosage on SC-RT employing various reporter systems in vivo. This system combined with siRNA-mediated downregulations of selected aminoacyl-tRNA synthetases demonstrated that changing levels of human tryptophan and tyrosine tRNAs do modulate efficiency of SC-RT. Overall, our results suggest that tissue-to-tissue specific levels of selected near-cognate tRNAs may have a vital potential to fine-tune the final landscape of the human proteome, as well as that of its viral pathogens.
Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes
Authors: Yermanos Alexander , Agrafiotis Andreas , Kuhn Raphael , Robbiani Damiano , Yates Josephine , Papadopoulou Chrysa , Han Jiami , Sandu Ioana , Weber Cédric , Bieberich Florian , Vazquez-Lombardi Rodrigo , Dounas Andreas , Neumeier Daniel , Oxenius Annette , Reddy Sai T 
Published: April 2021

Abstract
High-throughput single-cell sequencing (scSeq) technologies are revolutionizing the ability to molecularly profile B and T lymphocytes by offering the opportunity to simultaneously obtain information on adaptive immune receptor repertoires (VDJ repertoires) and transcriptomes. An integrated quantification of immune repertoire parameters, such as germline gene usage, clonal expansion, somatic hypermutation and transcriptional states opens up new possibilities for the high-resolution analysis of lymphocytes and the inference of antigen-specificity. While multiple tools now exist to investigate gene expression profiles from scSeq of transcriptomes, there is a lack of software dedicated to single-cell immune repertoires. Here, we present Platypus, an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. Platypus provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. To showcase the capabilities of Platypus, we use it to analyze and visualize single-cell immune repertoires and transcriptomes from B and T cells from convalescent COVID-19 patients, revealing unique insight into the repertoire features and transcriptional profiles of clonally expanded lymphocytes. Platypus will expedite progress by facilitating the analysis of single-cell immune repertoire and transcriptome sequencing.
Deferring Amputation in Diabetic Foot Osteomyelitis: Doing More Harm Than Good?
Authors: Zhou Shiwei , Schmidt Brian M , Henig Oryan , Kaye Keith S 
Published: April 2021

AbstractIn a cohort of patients with diabetic foot osteomyelitis who were recommended to undergo below-knee amputation, those who deferred amputation and chose medical therapy were more likely to die during the follow-up time compared with those who proceeded with amputation.
In Silico Evaluation of Cyclophilin Inhibitors as Potential Treatment for SARS-CoV-2
Authors: Laurie Kyle , Holcomb David , Kames Jacob , Komar Anton A , DiCuccio Michael , Ibla Juan C , Kimchi-Sarfaty Chava 
Published: April 2021

AbstractBackgroundThe advent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provoked researchers to propose multiple antiviral strategies to improve patients’ outcomes. Studies provide evidence that cyclosporine A (CsA) decreases SARS-CoV-2 replication in vitro and decreases mortality rates of coronavirus disease 2019 (COVID-19) patients. CsA binds cyclophilins, which isomerize prolines, affecting viral protein activity.MethodsWe investigated the proline composition from various coronavirus proteomes to identify proteins that may critically rely on cyclophilin’s peptidyl-proline isomerase activity and found that the nucleocapsid (N) protein significantly depends on cyclophilin A (CyPA). We modeled CyPA and N protein interactions to demonstrate the N protein as a potential indirect therapeutic target of CsA, which we propose may impede coronavirus replication by obstructing nucleocapsid folding.ResultsFinally, we analyzed the literature and protein–protein interactions, finding evidence that, by inhibiting CyPA, CsA may impact coagulation proteins and hemostasis.ConclusionsDespite CsA’s promising antiviral characteristics, the interactions between cyclophilins and coagulation factors emphasize risk stratification for COVID patients with thrombosis dispositions.
Professional Responsibility: Conceptual Rescue and Plea for Reform
Authors: Delacroix Sylvie 
Published: April 2021

Abstract
For as long as knowledge asymmetry continues to be deemed the defining characteristic of the lay-professional relationship, the courts’ delineation of obligations meant to address lay vulnerability will too frequently end up compounding the layperson’s non-epistemic, ‘sense of self’ vulnerability. The proposed re-conceptualisation of professional responsibility calls for reform on several fronts: among these, an expanded ‘duty to consult’ (beyond do-not-resuscitate-orders) is uniquely placed as a justiciable criterion capable of addressing such a situational, ‘sense of self’ vulnerability.
The Resection of a Thalamic Pilocytic Astrocytoma Through the Transchoroidal Fissure, Transcallosal Approach: 2-Dimensional Operative Video
Authors: Kadri Paulo A S , Ibn Essayed Walid , Al-Mefty Ossama 
Published: April 2021

Abstract
Surgical resection is the primary treatment of pilocytic astrocytomas and total removal can be curative. However, these lesions occur in critical areas, such as the thalamus, being surrounded by critical life neurovascular structures, which imposes a surgical challenge.
1–5
Exhaustive acquisition and meticulous interpretation of preoperative radiological exams; reliable surgical orientation based on profound microneurosurgical anatomic knowledge and judicious discernment of the neuroanatomic distortions on the surface and deep-seated structures inflicted by the neuropathological entity; embracing and comprehensive application of the vast scope of available intraoperative guidance imaging and neurophysiological monitoring; in alliance with the mastered carefully microsurgical technique supported by endoscopic visualization are the keystones to the pursed duet “cure with quality of life” in the treatment of these lesions.
We present the case of a 17-yr-old young lady with a progressive motor deficit in her right hemibody for over 2 yr. Her radiological investigation demonstrated a left thalamic lesion displacing the projection fibers (corticospinal tract) within the internal capsule laterally. The patient consented to the surgical procedure. The surgical strategy, intraoperative findings, and microsurgical and endoscopic technique, as well as the postoperative radiological and clinical evaluation are presented.
The patient gave her informed consent for the publication of the case.
The Effect of Changing Political Contexts on Public Opinion in Japan, 1945–2020
Authors: Maeda Yukio 
Published: April 2021

Abstract
The role of public opinion in Japan has changed dramatically in response to major shifts in party politics over the past seventy years. This chapter explains how the creation and disintegration of a dominant pattern in elite political discourse shaped people’s understanding of and response to public affairs. It also describes how polling and the electorate developed side-by-side in a newly democratic Japan. During the early postwar period, Japanese people were preoccupied with achieving economic security. The party system was initially very unstable, but constitutional revision and the security treaty with the US became central issues due to the Korean War and other Cold War conflicts. A bipolar political competition over these issues drove public opinion from 1955 to the mid-1990s. The “conservative” and “progressive” ideologies were diametrically opposed over constitutional revision and the US-Japan Security Treaty. This ideological divide was institutionalized in a decades-long conflict between two political camps in the legislature. Ordinary people understood public affairs through the rhetoric of these two ideologies. In the current post–Cold War, post-reform era that began in the mid-1990s, the conflict between the conservative and progressive ideologies no longer provides signals for understanding politics. Political parties differ mostly in the fact that one group is in government and the others are in opposition. Without guiding principles to organize political discourse, short-term policy concerns and perceptions of incumbent government performance influence public opinion the most. At the same time, whether a government remains in power depends on public approval more than ever before.
Supply Chain Management
Authors: Choi Thomas Y. , Li Julie Juan , Rogers Dale S. , Schoenherr Tobias , Wagner Stephan M. 
Published: April 2021

Abstract
Supply chain management strives to add fundamental value to society by working to provide needed products and services. To facilitate the delivery of these products and services, organizations form relationships, and these relationships represent a valuable managerial resource that give organizations competitive advantage. The Oxford Handbook of Supply Chain Management considers such managerial issues in supply chain management and captures them across the five categories of people and welfare, data and technology, moving goods and services, structure and strategy, and growing and sustaining. As such, this handbook is intended to provide supply chain researchers further motivation to investigate how they can contribute to solving the world’s big and pressing issues.
The Development (and Imagined Reinvention) of Australian Archaeology in the Twentieth Century
Authors: Urwin Chris , Spriggs Matthew 
Published: April 2021

Abstract
Most histories of Australian archaeology written in the past three decades imagine that the discipline came of age in (approximately) the year 1960. We are led to believe that systematic archaeological research, nuanced interpretations, and advocacy for the conservation of Aboriginal cultural heritage all date to the post-1960 era. Yet archaeological research in Australia has a lengthier and more complex genealogy. Here we use a series of case studies to explore the gradual development of the discipline during the twentieth century. We unpack key moments and projects during the early to mid-twentieth century and examine the extent to which the so-called professional archaeologists of the 1960s overlapped with and depended on the work of “amateur” scholars. We conclude by suggesting that the period of most rapid and significant change in archaeological thought and practice was precipitated by Aboriginal activism leading up to the 1980s. Australia’s First Peoples demanded control of research into their cultural heritage, a project that continues today. Our discipline must encourage a culture of reflexivity on its current practices by coming to terms with—rather than silencing—its history, whether good, bad, or ugly.
Ways of the Mind
Authors: Nitzberg Dotan , Bakan Michael B. 
Published: April 2021

Abstract
This chapter proposes a progressive approach to research at the intersection of autism studies and music studies, one through which scientific frames of objectivity-aspiring, anonymizing representation are replaced by ethnographic and phenomenological frames of personhood-aspiring, individual re-presentation. Through a case study of the musical experiences of first author Dotan Nitzberg, a concert pianist on the autism spectrum, and through the re-presentation of dialogues between Nitzberg and the chapter’s second author, ethnomusicologist Michael Bakan, the commonplace practice of objectifying and dehumanizing autistic individuals, including musicians, is challenged. The authors posit that phenomenological approaches, and those informed by a Levinasian philosophy of alterity in particular, have the capacity to leverage this challenge in affirming the agency and humanity of people on the autism spectrum, fostering an appreciation for their difference and contributing to a larger activist agenda of reducing the stigma and marginalization to which they have historically been subjected.
Contemporary Partnerships
Authors: Janzen Russell 
Published: April 2021

Abstract
This chapter seeks to determine what makes for a contemporary partnership on the ballet stage through an examination of gender roles and choreographic invention in three works created for the New York City Ballet in 2017. While choreographers often strive to make new, of-the-moment dances, traditional ballet training still holds strong, turning out dancers whose bodies and abilities adhere to ideals established long ago. This perpetuation of antiquated ideas of masculinity and femininity limits the ways in which ballet partnerships are able to reflect the world of today. After a brief overview of the expectations put on men and women in ballet, with an emphasis on partnering class and partnering techniques, the chapter looks at how Pontus Lidberg, Justin Peck, and Lauren Lovette, each utilizing different approaches, used choreography to craft contemporary partnerships in their new works for the New York City Ballet in 2017.
Performing the Past in the Present
Authors: McLelland Rowan 
Published: April 2021

Abstract
This chapter explores the conscious adoption, reformation, and indigenization of ballet in China in the mid-twentieth century to foreground how this historical development has contributed to the creation of a new genre of ballet unique to China in the contemporary period. Using The Red Detachment of Women (1964, [红色娘子军]) and the more recent Eight Heroines (2015, [八女投江]), the chapter highlights ballet’s contemporaneity in China at the convergence of the unique legacy of the sociopolitical reimagining of the form with tangible links to both the past and the present in ballet in the Global North as a modern transnational practice. It concludes that it is in its very divergence from the style of contemporary ballet more commonly performed in the West that Chinese contemporary ballet embodies the pluralistic cosmopolitan values that contemporary ballet adopts.
Costume
Authors: O’Brien Caroline 
Published: April 2021

Abstract
Dress is integral to the performance of ballet, carefully considered in the collaboration between the choreographer and the designer. This chapter offers a broad introduction to thinking about “costume” as a term that is reserved for and relates to garments used for performance. It examines contemporary ballet costume through the conventions evidenced in the component parts of garments while emphasizing a tradition of making. Uniform is used in the training of a dancer so that dress is embedded in bodily practice, becoming a symbiotic partner in the dance. Contemporary ballet abandoned the form of the classical tutu and features leotards, bare legs, and pointe shoes or canvas slippers, flattening the hierarchy and blurring the gender lines.
Justin Peck
Authors: Aloff Mindy 
Published: April 2021

Abstract
Justin Peck, barely thirty, not only is the resident choreographer at New York City Ballet (NYCB) but also is in demand by dance companies throughout the United States and in Europe. He received a Tony Award for his choreography for the 2018 Broadway production of Carousel, and Steven Spielberg hired him to choreograph Spielberg’s new film of West Side Story. This chapter focuses on Everywhere We Go, the spectacular “epic” that Peck and indie composer Sufjan Stevens made for NYCB in 2014, including discussions of Peck’s musicality, his composition of duets and use of sneakers in some dances, and influences he acknowledges from the works of George Balanchine and Jerome Robbins. At the end is an essay by Peck from 2008, “How to Become an Artist.”
Digitalisation and Administrative Justice: An Access to Justice Perspective
Authors: Sossin Lorne , Thompson Darin 
Published: April 2021

Abstract
This chapter examines the impact of digitalisation on access to justice and administrative justice. It discusses the significant potential of digitalisation to enhance access to justice as well as the accompanying risks, and argues for a more contextualized approach to the subject. It advocates for a focus on user needs as well as design and administrative justice architecture. The chapter concludes that the relationships between digitalisation and access to justice must not be over-simplified. Increased reliance on technology is often thought to increase access to justice based on assumptions that digital legal services will be less expensive and easier to use. Poorly designed digital interfaces and processes, however, can add unnecessary complexity to simple justice transactions. Perspectives on digitalisation and access should recognize the nuance of this evolving landscape. The chapter sketches out a more holistic approach to access to justice in a digital age that places considerable emphasis on the importance of design with an intention to benefit administrative justice users. The analysis is divided into five sections. The first section examines key frameworks and perspectives on access to administrative justice in the digital age. The second section considers the ‘digital divide’ and the importance of careful design. The third section considers the impact of digital access to various forms of legal supports. The fourth section reviews the digital architecture of administrative justice specifically. Finally, the fifth section explores online dispute resolution in administrative justice and its potential for enhancing access to justice.
Courtroom Workgroups
Authors: Heumann Milton , Kavin Rick , Chugh Anu 
Published: April 2021

Abstract
“Courtroom workgroup” is a term used to describe the ongoing relationships between judges, prosecutors, and defense attorneys. These three interrelated relationships define how the central figures operate and indeed how a case progresses. The authors survey the existing literature on such workgroups and conduct twelve interviews with key stakeholders in the workgroup structure at both the state and federal levels. Such interviews allow the authors to compare the literature—often decades old—to the experiences of judges and attorneys in today’s courtrooms. The authors examine how the relationships in the three courtroom roles explain some case outcomes, but also examine the host of other variables which arguably sometimes individually, and more often collectively, contribute to a richer, more nuanced, and more comprehensive understanding of court outputs and outcomes, including the nature of workgroups themselves. The authors caution against “concept hagiography”—i.e. too enthusiastically touting the explanatory power of the concept being studied, while giving shorter shrift to underlying explanatory variables. Finally, note is taken of how the recent election of exceptionally progressive prosecutors in several major jurisdictions may lead to opportunities for quasi-experimental testing of how changes in workgroups affect case outcomes.
The Relationship between Prosecutors and Defenders
Authors: Yaroshefsky Ellen 
Published: April 2021

Abstract
The interactions between prosecutors and defense attorneys in any given legal system depends on a number of factors. The most important is the power differential between the two positions, and the difference between the two is greatest in the United States. The deep-seated differences between adversarial and inquisitorial legal systems has an important influence on the gap in power between prosecutors and defenders. The nature of the relationship between prosecutors and defense lawyers also depends on professional and office culture within both the prosecutor’s office and the defender’s office. Individual characteristics of the attorneys, including experience, age, race, ethnicity, gender, and personalities, also shape the relationship. This chapter summarizes the effects of these structural and individual qualities, while describing the limited empirical research on the topic and the challenge of drawing generalizable lessons from studies that focus on institutions in only a few locations.