bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells
Authors: Sieg Jacob P , Jolley Elizabeth A , Huot Melanie J , Babitzke Paul , Bevilacqua Philip C 
Published: October 2023

Abstract
We conducted a thermodynamic analysis of RNA stability in Eco80 artificial cytoplasm, which mimics in vivo conditions, and compared it to transcriptome-wide probing of mRNA. Eco80 contains 80% of Escherichia coli metabolites, with biological concentrations of metal ions, including 2 mM free Mg2+ and 29 mM metabolite-chelated Mg2+. Fluorescence-detected binding isotherms (FDBI) were used to conduct a thermodynamic analysis of 24 RNA helices and found that these helices, which have an average stability of –12.3 kcal/mol, are less stable by ΔΔGo37 ∼1 kcal/mol. The FDBI data was used to determine a set of Watson–Crick free energy nearest neighbor parameters (NNPs), which revealed that Eco80 reduces the stability of three NNPs. This information was used to adjust the NN model using the RNAstructure package. The in vivo-like adjustments have minimal effects on the prediction of RNA secondary structures determined in vitro and in silico, but markedly improve prediction of fractional RNA base pairing in E. coli, as benchmarked with our in vivo DMS and EDC RNA chemical probing data. In summary, our thermodynamic and chemical probing analyses of RNA helices indicate that RNA secondary structures are less stable in cells than in artificially stable in vitro buffer conditions.
DNA elements tether canonical Polycomb Repressive Complex 1 to human genes
Authors: Barrasa Juan I , Kahn Tatyana G , Lundkvist Moa J , Schwartz Yuri B 
Published: October 2023

Abstract
Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to repress key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report the identification of several hundreds of DNA elements that tether canonical PRC1 to human developmental genes. We use the term tether to describe a process leading to a prominent presence of canonical PRC1 at certain genomic sites, although the complex is unlikely to interact with DNA directly. Detailed analysis indicates that sequence features associated with PRC1 tethering differ from those that favour PRC2 binding. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 or PRC2 to ones capable of tethering both complexes. The emerging picture is similar to the paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for greater plasticity.
LIPID MAPS: update to databases and tools for the lipidomics community
Authors: Conroy Matthew J , Andrews Robert M , Andrews Simon , Cockayne Lauren , Dennis Edward A , Fahy Eoin , Gaud Caroline , Griffiths William J , Jukes Geoff , Kolchin Maksim , Mendivelso Karla , Lopez-Clavijo Andrea F , Ready Caroline , Subramaniam Shankar , O’Donnell Valerie B 
Published: October 2023

Abstract
LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.
Qualitative Methods in Communication and Media
Authors: Faulkner Sandra L. , Atkinson Joshua D. 
Published: October 2023

Abstract
This book is a learner-centered guide to designing, doing, and evaluating qualitative communication and media research. The book covers method design, analysis, representation, writing, and evaluation of qualitative communication research. It provides key terms, extended examples, discussion questions, student-tested writing and research activities, examples of student work, and lists of suggested resources. The research activities and discussion questions derive from the authors’ years of teaching qualitative research methods. The authors discuss how to perform qualitative and critical communication and media analyses, including arts-based research, using student and research examples from a variety of fields. There is also an extensive discussion of ethics in qualitative research.
Writing and Presenting Qualitative Research
Authors: Faulkner Sandra L. , Atkinson Joshua D. 
Published: October 2023

Abstract
Chapter 6 is devoted to writing and representation, given its importance in qualitative research. In this chapter the authors emphasize that writing is a vital part of qualitative research and make an argument for writing as method. The authors ask readers to think deeply about their writing process, to create a regular writing practice that becomes a habit, and to focus on form, function, style, and audience in their writing. The chapter addresses the typical format of a qualitative research article and notes the importance of considering citational practices. The authors describe various ways in which readers can use arts-based research presentation in their work.
Evaluating Qualitative Research
Authors: Faulkner Sandra L. , Atkinson Joshua D. 
Published: October 2023

Abstract
In this chapter the authors discuss the importance of evaluating qualitative research, as well as different ideas about what counts as quality research. They explain different kinds of criteria for evaluating qualitative research, such as usefulness and saturation, and discuss criteria for evaluating arts-based research. The authors define the terms “rigor” and “vigor” as applied to qualitative research and discuss the disagreements that exist over the use of these terms. They present four frameworks that can be used to assess research ethics in a project. After reading this chapter, the authors hope that readers will be able to articulate what qualitative criteria are most important to them.
Epilogue
Authors: Cox Pamela , Shoemaker Robert , Shore Heather 
Published: October 2023

Abstract
This chapter brings this story into the present and summarizes the value of historicizing both victims’ participation and their increasing politicization over three centuries. Historically, the state did not care explicitly about victims. It cared about the peace of the realm and it cared that victims took action to enforce it. Victims were displaced within the higher courts as a result of efforts to construct a more effective English criminal justice system to maintain that peace. Today, however, influential segments of British public opinion demand that the state must care, and be seen to care. As a result, the state has taken on legal duties in relation to victims and also seeks to be seen by the public as performing that care. The political price of apparent indifference is too high. Victim groups, and indeed other constituencies, who can mobilize around the claim that the state ‘doesn’t care’ have a powerful card to play in today’s political arena. But within the adversarial trial and its historic delegation of powers to police, counsel and public prosecutors, there are clear limits to what can be achieved through wider policy measures—simply because a criminal trial cannot prioritize the interests of victims. In this sense, the victims’ rights agenda is incompatible with adversarialism as currently framed. Rather than implying that it is possible to restore aspects of victims’ historically central role in the prosecution process, the state needs to develop a more explicit justification of why this would not serve the current public interest.
Introduction
Authors: Lewis David 
Published: October 2023

Abstract
This is the introduction chapter of Confirmation Theory. Confirmation Theory is a book manuscript that Lewis wrote in 1969 on the basis of a course he’d given at UCLA. He submitted the manuscript to Harvard University Press who expressed an interest. It consists of seven chapters covering intensional semantics, probability measures, rational belief, principles of indifference and Carnap and Hintikka’s inductive systems. The work was intended to be accessible to students with, as Lewis put it, ‘hairy high-school algebra’. He described the manuscript to Richard Jeffrey as ‘Mathematically self-contained, with proofs for the major theorems’. Lewis originally envisaged that Carnap’s The Continuum of Inductive Methods (1952) be used as an accompanying text. Lewis focused on Carnap and Hintikka in particular because he believed that their work constituted the attractive core of what competing theories of confirmation had in common.
Intensional Semantics
Authors: Lewis David 
Published: October 2023

Abstract
This is the zero chapter of Confirmation Theory. Confirmation Theory is a book manuscript that Lewis wrote in 1969 on the basis of a course he’d given at UCLA. He submitted the manuscript to Harvard University Press who expressed an interest. It consists of seven chapters covering intensional semantics, probability measures, rational belief, principles of indifference and Carnap and Hintikka’s inductive systems. The work was intended to be accessible to students with, as Lewis put it, ‘hairy high-school algebra’. He described the manuscript to Richard Jeffrey as ‘Mathematically self-contained, with proofs for the major theorems’. Lewis originally envisaged that Carnap’s The Continuum of Inductive Methods (1952) be used as an accompanying text. Lewis focused on Carnap and Hintikka in particular because he believed that their work constituted the attractive core of what competing theories of confirmation had in common.
Scientific Method
Authors: Lewis David 
Published: October 2023

Abstract
This is the fourth chapter of Confirmation Theory. Confirmation Theory is a book manuscript that Lewis wrote in 1969 on the basis of a course he’d given at UCLA. He submitted the manuscript to Harvard University Press who expressed an interest. It consists of seven chapters covering intensional semantics, probability measures, rational belief, principles of indifference and Carnap and Hintikka’s inductive systems. The work was intended to be accessible to students with, as Lewis put it, ‘hairy high-school algebra’. He described the manuscript to Richard Jeffrey as ‘Mathematically self-contained, with proofs for the major theorems’. Lewis originally envisaged that Carnap’s The Continuum of Inductive Methods (1952) be used as an accompanying text. Lewis focused on Carnap and Hintikka in particular because he believed that their work constituted the attractive core of what competing theories of confirmation had in common.
Carnap’s λ-System: Many Families
Authors: Lewis David 
Published: October 2023

Abstract
This is the seventh chapter of Confirmation Theory. Confirmation Theory is a book manuscript that Lewis wrote in 1969 on the basis of a course he’d given at UCLA. He submitted the manuscript to Harvard University Press who expressed an interest. It consists of seven chapters covering intensional semantics, probability measures, rational belief, principles of indifference and Carnap and Hintikka’s inductive systems. The work was intended to be accessible to students with, as Lewis put it, ‘hairy high-school algebra’. He described the manuscript to Richard Jeffrey as ‘Mathematically self-contained, with proofs for the major theorems’. Lewis originally envisaged that Carnap’s The Continuum of Inductive Methods (1952) be used as an accompanying text. Lewis focused on Carnap and Hintikka in particular because he believed that their work constituted the attractive core of what competing theories of confirmation had in common.
Hintikka’s λ-α-System
Authors: Lewis David 
Published: October 2023

Abstract
This is the eighth chapter of Confirmation Theory. Confirmation Theory is a book manuscript that Lewis wrote in 1969 on the basis of a course he’d given at UCLA. He submitted the manuscript to Harvard University Press who expressed an interest. It consists of seven chapters covering intensional semantics, probability measures, rational belief, principles of indifference and Carnap and Hintikka’s inductive systems. The work was intended to be accessible to students with, as Lewis put it, ‘hairy high-school algebra’. He described the manuscript to Richard Jeffrey as ‘Mathematically self-contained, with proofs for the major theorems’. Lewis originally envisaged that Carnap’s The Continuum of Inductive Methods (1952) be used as an accompanying text. Lewis focused on Carnap and Hintikka in particular because he believed that their work constituted the attractive core of what competing theories of confirmation had in common.
On the Nature of Certain Nonidentities: A Reply to Montague (1968)
Authors: Lewis David 
Published: October 2023

Abstract
In this paper, dating from 1968, Lewis argues against an objection Montague had made to Lewis’s 1966 paper ‘An Argument for the Identity Theory’. Montague had argued that Lewis’s paper implied the negation of a principle Montague wanted to endorse, namely, ‘Every experience is identical with the attribute of having that experience’. Lewis argues that there are readings of Montague’s principle on which they are compatible with his identity theory.
Contagion without Rigidity
Authors: Lewis David 
Published: October 2023

Abstract
In this short paper, dating from 1971, Lewis argues, against Kripke, that rigid designation is less important for names and name-like expressions than what Lewis calls ‘contagion’. By ‘contagion’ of names Lewis means the phenomenon of learning a name from others who use it to refer, and wanting it to have the same meaning it had for those other people. The doctrine of contagion without rigidity also makes a brief appearance in footnote 9 of ‘Truth in Fiction’ (Lewis 1978: 41) but is here defended in some more detail.
Reply to Davidson (1972)
Authors: Lewis David 
Published: October 2023

Abstract
In this short paper, dating from 1972, Lewis discusses Davidson’s contention that, following Tarskian principles, there is no one general notion of word-reference for all languages, but rather reference-in-L for each language L. Lewis expresses agreement with Davidson, but goes on to point out that a Tarskian approach is sufficient for giving us a general schematic approach for determining word-reference for each language.
Counterfactual and Objective Probability (1973)
Authors: Lewis David 
Published: October 2023

Abstract
In this short paper, dating from 1973, Lewis proposes that given a set of worlds, a probability function over them, and a system of spheres of similarity around each world, we can think of the objective probability of A at i as the counterfactual probability of A if I, where I is the set of all worlds. He raises, but does not answer, the question what further technical assumptions are necessary to make the proposal come out right for propositions about objective probability.
Mass and Value (1985)
Authors: Lewis David 
Published: October 2023

Abstract
In this short paper, dating from 1985, Lewis explores an analogy between the theoretical term ‘mass’, which ambiguously denotes multiple equally good candidate fillers for the mass role, and the term ‘value’ considered as a theoretical term of a folk theory of value. Lewis argues that the latter can be seen as ambiguously denoting the alleged fillers of the value role for meta-ethical naturalism, non-cognitivism, and even error theory.
De Se Detectivism (1986)
Authors: Lewis David 
Published: October 2023

Abstract
In this short paper, dating from 1986, Lewis adds to the view expressed in his 1989 paper ‘Dispositional Theories of Value’. In the present short paper Lewis considers a new type of detectivism about value according to which states of affairs are egocentric, not agent-neutral. Lewis expounds this de se variety of detectivism but does not endorse it.
A Fifth Solution to the Problem of Temporary Intrinsics (c.1987)
Authors: Lewis David 
Published: October 2023

Abstract
This short paper, dated to ca. 1987, appears to have been cut from Lewis’s 1988 reply to E.J. Lowe. In his published reply, Lewis had considered four solutions to the problem of temporary intrinsics; here he considers, and rebuts, a fifth, according to which an enduring individual is wholly present at each stage of its perduring trajectory and takes part in intrinsic changes vicariously.
Introduction
Authors: Oksamytna Kseniya 
Published: October 2023

AbstractAdvocacy is a crucial but overlooked source of change in international organizations. The advocacy-focused framework explains why some actors succeed at promoting change whereas others fail. The framework pairs advocacy strategies (social pressure, persuasion, and ‘authority talk’) with strategy-specific favourable conditions (characteristics of advocates, targets, issues, and context). The transformation of UN peacekeeping is an illustrative example of organizational change. Three elements of UN peacekeeping’s transformation are the focus of this book: strategic communications, protection of civilians, and quick impact projects. The three case studies exhibit variation in several important respects. First, they differ in salience, from the fundamental question of protection of human life to a seemingly technical issue of quick impact projects. Second, protection of civilians, strategic communications, and quick impact projects represent top-down, bottom-up, and outside-in pathways to change in international organizations: the top-down pathway entails issue construction in intergovernmental bodies, the bottom-up pathway is driven by experimentation by international bureaucrats, and the outside-in pathway relies on input from external actors. Third, the three issues emerged due to different advocacy strategies: persuasion in the case of strategic communications, social pressure and persuasion in the case of protection of civilians, and ‘authority talk’ in the case of quick impact projects. Finally, the three issues achieved varying degrees of institutionalization at different speeds. This book investigates their emergence through comparative process tracing based on archives, memoirs, UN policy and budgetary documents, and elite interviews.
The Essence of Biology
Authors: Braun Veit 
Published: October 2023

Abstract
Focusing on recent decisions at the European Patent Office dealing with the patentability of modified vegetables (the Tomato/Broccoli I and II cases), the chapter explores the role and place that biology plays within patent law. In doing so, the chapter shows how patent law’s appeal to ‘biology’ raises important questions about ‘life’ and ‘nature’ and how these concepts have been implicated in the way that patent law embraces plant innovations.
Conceptualizing Nature as Information
Authors: Fish Allison 
Published: October 2023

Abstract
This chapter examines efforts by the Indian central government to protect South Asian genetic resources and associated knowledge from biopiracy. Specifically, the chapter explores the information technology-related innovations that the National Biodiversity Authority is developing and testing in order to effect compliance with the country’s obligations under the Nagoya Protocol. In developing these new tools the NBA is relying on machine learning systems and blockchain technology to draw together and search across a suite of already-existing informational resources - including some that have been developed specifically around the problem of biopiracy, such as the Traditional Knowledge Digital Library, and others which have been developed for different purposes, such as the Web of Science and Global Biodiversity Information Facility. The purpose of these new systems is to assist the NBA in distinguishing between permissible and legitimate bioprospecting activities versus unauthorized and illegitimate biopiracy. In tracing the accretion of techno-legal tools designed to combat biopiracy, the chapter explores the problems that occur when natural resources and their related utilization is not legible or accessible to the law. It also highlights some of the unexpected consequences that arise when, in attempting to respond to these problems, governmental authorities set out to render nature visible using technological solutions.
Introduction
Authors: Davenport Caillan , McEvoy Meaghan 
Published: October 2023

AbstractThis introductory chapter by the editors provides a methodological foundation for the volume as a whole. It first considers the definition of a court and Roman perceptions of the court using ancient literary sources and modern historical and sociological scholarship. It then reviews scholarly investigations of the Roman imperial court as an institution in the Principate and Late Antiquity across the nineteenth and twentieth centuries. The chapter concludes by considering the three major themes of the volume—ritual and spatial dynamics; individual and community at court; and the politics of access—and places the individual chapters in their historical and scholarly contexts
The Court in Constantinople Facing the Death of the Emperor
Authors: Becker Audrey 
Published: October 2023

AbstractThe aim of this chapter is to show the role played by the courtiers in the imperial investiture process from the death of the previous emperor to the coronation ceremony of the new one. During this process, the future emperor was more vulnerable than any other member of the court, because he absolutely needed his power to be recognized by the courtiers. The courtiers accomplished this by manipulating and modifying the protocol to suit their own political context and interest, simultaneously re-establishing and re-ensuring their own prominent place within the court. From this perspective, protocol can be studied not only as a tool employed by the emperor to manipulate the courtiers, but also as a tool employed by the courtiers themselves to maintain a balance of power with the emperor. This chapter will discuss the period in between the death of one emperor and the coronation of the next one in four significant cases: the emperors Constantine, Zeno, Anastasius, and Justinian.
Mathematical tools
Authors: Maggiore Michele 
Published: October 2023

Abstract
Classical electrodynamics requires a good familiarity with a set of mathematical tools, which will then find applications basically everywhere in physics. We begin by recalling some of these concepts so that, later, the understanding of the physics will not be obscured by the mathematical manipulations. We discuss differential operators (curl and gradient, Gauss theorem, and Stokes theorem) the use of Dirac delta for point-like for modeling point charges, the Fourier transform., vector and tensors. We also introduce more advanced concepts related to group theory and group representations (that will not be needed for the more elementary parts of the book)