bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures
Authors: Ban Yuki , Ando Yuka , Terai Yuma , Matsumura Risa , Nakane Keita , Iwai Shigenori , Sato Shinichi , Yamamoto Junpei 
Published: November 2024

Abstract
Non-canonical DNA structures, such as the G-quadruplex (G4) and i-motif (iM), are formed at guanine- and cytosine-rich sequences, respectively, in living cells and involved in regulating various biological processes during the cell cycle. Therefore, the formation and resolution of these non-canonical structures must be dynamically regulated by physiological conditions or factors that can bind G4 and iM structures. Although many G4 binding proteins responsible for tuning the G4 structure have been discovered, the structural regulation of iM by iM-binding proteins remains enigmatic. In this study, we developed a protein-labeling DNA probe bearing an alkyne moiety through a reactive linker, for proximity-labeling of nucleic acid-binding proteins, and searched for new iM-binding proteins. Alkyne-modified proteins in the nuclear extract of HeLa cells were labeled with biotin via a click reaction and then captured with streptavidin-coated magnetic beads. This fingerprint-targeting enrichment, followed by proteome analyses, identified new candidate proteins that potentially bind to the iM structure, in addition to the reported iM-binding proteins. Among the newly identified candidates, we characterized a nucleolar protein, nucleolin, that binds to the iM structure and relaxes it, while nucleolin stabilizes the G4 structure.
The rice genome annotation project: an updated database for mining the rice genome
Authors: Hamilton John P , Li Chenxin , Buell C Robin 
Published: November 2024

Abstract
Rice (Oryza sativa L.) is a major cereal crop that provides calories across the world. With a small genome, rice has been used extensively as a model for genetic and genomic studies in the Poaceae. Since the release of the first rice genome sequence in 2002, an improved reference genome assembly, multiple whole genome assemblies, extensive gene expression profiles, and resequencing data from over 3000 rice accessions have been generated. To facilitate access to the rice genome for plant biologists, we updated the Rice Genome Annotation Project database (RGAP; https://rice.uga.edu) with new datasets including 16 whole genome rice assemblies and sequence variants generated from multiple rice pan-genome projects including the 3000 Rice Genomes Project. We updated gene expression abundance data with 80 RNA-sequencing datasets and to facilitate gene function discovery, performed gene coexpression resulting in 39 coexpression modules that capture highly connected sets of co-regulated genes. To facilitate comparative genome analyses, 32 335 syntelogs were identified between the Nipponbare reference genome and other rice genomes and 19 371 syntelogs were identified between Nipponbare and four other Poaceae genomes. Infrastructure improvements to the RGAP database include an upgraded genome browser and data access portals, enhanced website security and increased performance of the website.
GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes
Authors: Herrera Luis P Taracena , Andreassen Søren N , Caroli Jimmy , Rodríguez-Espigares Ismael , Kermani Ali A , Keserű György M , Kooistra Albert J , Pándy-Szekeres Gáspár , Gloriam David E 
Published: November 2024

Abstract
G protein-coupled receptors (GPCRs) are membrane-spanning transducers mediating the actions of numerous physiological ligands and drugs. The GPCR database GPCRdb supports a large global research community with reference data, analysis, visualization, experiment design and dissemination. Here, we describe our sixth major GPCRdb release starting with an overview of all resources for receptors and ligands. As a major addition, all ∼400 human odorant receptors and their orthologs in major model organisms can now be studied across the various data and tool resources. For the first time, a Data mapper page enables users to map their own data onto receptors visualized as a GPCRome wheel, tree, clusters, list or heatmap. The structure model data have been expanded with models of physiological ligand complexes and updated with new state-specific structure models of all human GPCRs (built using AlphaFold, RoseTTAFold and AlphaFold-Multistate). Furthermore, a structure or model (pdb file) can now be queried against GPCRdb’s entire structure/model collection through a Structuresimilarity search page implementing FoldSeek. Finally, for ligands, new search tools can query names, database identifiers, similarities or substructures against integrated entries from the ChEMBL, Guide to Pharmacology, PDSP Ki, PubChem, DrugCentral and DrugBank databases. GPCRdb is available at https://gpcrdb.org.
NASA open science data repository: open science for life in space
Authors: Gebre Samrawit G , Scott Ryan T , Saravia-Butler Amanda M , Lopez Danielle K , Sanders Lauren M , Costes Sylvain V 
Published: November 2024

Abstract
Space biology and health data are critical for the success of deep space missions and sustainable human presence off-world. At the core of effectively managing biomedical risks is the commitment to open science principles, which ensure that data are findable, accessible, interoperable, reusable, reproducible and maximally open. The 2021 integration of the Ames Life Sciences Data Archive with GeneLab to establish the NASA Open Science Data Repository significantly enhanced access to a wide range of life sciences, biomedical-clinical and mission telemetry data alongside existing ‘omics data from GeneLab. This paper describes the new database, its architecture and new data streams supporting diverse data types and enhancing data submission, retrieval and analysis. Features include the biological data management environment for improved data submission, a new user interface, controlled data access, an enhanced API and comprehensive public visualization tools for environmental telemetry, radiation dosimetry data and ‘omics analyses. By fostering global collaboration through its analysis working groups and training programs, the open science data repository promotes widespread engagement in space biology, ensuring transparency and inclusivity in research. It supports the global scientific community in advancing our understanding of spaceflight's impact on biological systems, ensuring humans will thrive in future deep space missions.
The European Nucleotide Archive in 2024
Authors: O’Cathail Colman , Ahamed Alisha , Burgin Josephine , Cummins Carla , Devaraj Rajkumar , Gueye Khadim , Gupta Dipayan , Gupta Vikas , Haseeb Muhammad , Ihsan Maira , Ivanov Eugene , Jayathilaka Suran , Kadhirvelu Vishnukumar , Kumar Manish , Lathi Ankur , Leinonen Rasko , McKinnon Jasmine , Meszaros Lili , Pauperio Joana , Pesant Stephane , Rahman Nadim , Rinck Gabriele , Selvakumar Sandeep , Suman Swati , Sunthornyotin Yanisa , Ventouratou Marianna , Waheed Zahra , Woollard Peter , Yuan David , Zyoud Ahmad , Burdett Tony , Cochrane Guy 
Published: November 2024

Abstract
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Outlined here are changes to and updates on the ENA service in 2024, aligning with the broad goals of enhancing interoperability, globalisation of the service and scaling the platform to meet current and future needs.
Stratigraphy in the History of Archaeology
Authors: Tarantini Massimo 
Published: November 2024

Abstract
This chapter deals with the history of stratigraphy in archaeology in the last two centuries. It focuses on some key moments and issues: the origin of the principles of stratigraphy; the debate on the antiquity of man and the Three-Age System; the difficulties and specificities of classical archaeology; the relations between typology, stratigraphy, and chronological sequences; the contrast between (and the combination of) the vertical and horizontal dimensions; as well as the debate on formation processes and the new perspectives opened by soil micromorphology. The chapter aims to overcome a view focused on the role of individual precursors by analyzing methodological and conceptual innovations in their historical context and in relation to intellectual networks. It highlights how stratigraphy changes its meaning according to the perspectives, issues, and tools applied to it. Special attention is given to interdisciplinarity, in particular to the role of geologists and architects.
From Stunning Solitaires to Creative Clusters
Authors: Arwill-Nordbladh Elisabeth 
Published: November 2024

Abstract
Based on the assumption that archaeological knowledge and the subject of knowledge production is inextricably bound to the period of history within which it was generated, this chapter discusses some of the conditions surrounding women in early European antiquarianism and early archaeology. It is proposed that the historiography of antiquarianism has underestimated the role of women within the discipline, in part because historiographers have neglected some sources that in their historical era of creation fell, and indeed continue to fall today, outside the commonly accepted and gendered definitions of what constitutes the practice of antiquarianism or archaeology. Many women actively participated in, and contributed significantly to, the transition from antiquarianism to the discipline of professional archaeology during the nineteenth century, even though their professional conditions were very different to those of men. In particular, these women’s paths were full of obstacles that men did not encounter. This essay examines lives and circumstances of a few of these women, as well as their impact on the practice of antiquarianism, archaeological scholarship, and the road towards emancipation.
The History of Public Archaeology
Authors: Moshenska Gabriel 
Published: November 2024

Abstract
This chapter provides an outline of the development of public archaeology, focusing primarily on the Anglophone world. The history of public archaeology is a dynamic and significant strand within the history of the discipline. Like public science, public archaeology is a field of both practice and scholarship, touching upon many other aspects of the wider discipline. The chapter considers the historiography of public archaeology, examines some of the main themes and milestones in its development, and sets out a provisional agenda for future studies. In surveying this rich and complicated history, the chapter draws on case studies from nineteenth-century Britain and twentieth-century Japan—as well as on a wealth of international research—to illuminate the key themes and events in the emergence of public archaeology as a global discipline.
Violence, Armies, and Archaeological Research from the Nineteenth to the Twenty-First Century
Authors: Gracia Alonso Francisco 
Published: November 2024

Abstract
This chapter analyzes the profound relationship between armies and archaeological research from the mid-nineteenth to the twenty-first century. Among other questions, it examines the development and technical advances of aerial and underwater archaeology; the protection of historical and archaeological heritage in wartime since the mid-twentieth century, including the utilization of prisoners of war; the links between the army, political systems, and archaeology in the definition of the state’s historical narratives; the development of conflict archaeology as a basis for the reassessment of armed conflicts, with special emphasis on the excavation and study of mass graves from prehistory to the present day; the recovery of movable and immovable heritage related to conflicts; and the study of the archaeologies of genocide and the Holocaust.
Amateur Archaeology in the Nineteenth and Twentieth Centuries
Authors: Richard Nathalie 
Published: November 2024

Abstract
This chapter demonstrates that amateurs have played and continue to play a significant role in the development of archaeology. It challenges the idea that the professionalization of archaeology has led to the demise or marginalization of amateurs. The chapter highlights the role they played in collecting data on the field, in carrying out inventories, and, more generally, in the production and circulation of knowledge. Analyzing the process that rendered amateurs almost invisible in the general histories of archaeology, this chapter also suggests that taking them into account could enrich our view of the past of the discipline and help us better understand its present state.
“Governed by Legislation”
Authors: Carman John 
Published: November 2024

Abstract
This chapter charts the development of laws, with a view to understanding why archaeologists rely so heavily upon them and what having those laws in place means for us. The chapter raises questions as to why we have laws at all and how the idea of legal regulation of our material and our practices spread across the globe. The connection between ancient material and legal regulation begins in the distant past, long before the emergence of anything we can identify as “archaeology.” In more recent times, that body of regulation has grown to encompass the practices of archaeology as well as the material with which we deal. It is a global phenomenon which differs in form and specifics from place to place and context to context; and yet the theme of legal regulation of archaeology is common to every nation of the world.
Race, Racialism, and Racism in European Archaeology, 1800–1960
Authors: Link Fabian 
Published: November 2024

Abstract
This chapter explores racial thinking and racism in German and European archaeology from 1800 to 1960, discussing several archaeological subfields, such as classical archaeology, national archaeology, Near Eastern archaeology, colonial archaeology, and prehistory. It will be argued that a distinction is needed between racial thinking and racism. Racial thinking was widely established in archaeology and was reinforced by the rise of racial anthropology and evolutionary theory during the nineteenth century. In contrast, racism developed from racial interpretations through their connection with nationalism and chauvinism. This was the case in many European countries in the late nineteenth century, but most prominently in those that became nation-states at a very late date, such as Germany and Italy. Notions of race in archaeology were strongly radicalized in Nazi Germany and in other fascist countries during the 1930s and ’40s. The chapter ends in the early 1960s, when archaeologists increasingly dismissed racial interpretations.
Photo Archives and the History of Archaeology
Authors: Mallart Lucila 
Published: November 2024

Abstract
This chapter explores the role of photo archives in the making of archaeological knowledge from the mid-nineteenth century to the present day. It discusses, among other topics, their role in the pursuit of objectivity, their connections to nation-building processes, and the challenges and opportunities posed by the digital age. To do so, the chapter draws on a series of conceptual tools developed by several scholars, such as the notion of the “total photo archive,” the “documentary impulse” prompted by the emergence of photography, the conceptualization of photographs as “facts,” and the understanding of archival practices as “collective undertakings.” The chapter analyzes archaeological photo archives in Europe, the United States, and the rest of the world.
The History of Gender Archaeology
Authors: Díaz-Andreu Margarita , Pope Rachel 
Published: November 2024

Abstract
In this chapter, the history of gender archaeology is traced, focusing primarily on Western academia. A clear link is demonstrated with waves of feminist action. We begin with the antecedents, the first studies on women undertaken amid first-wave feminism by nineteenth-century women travelers and Egyptologists, alongside considerations of the changing social role of prehistoric women in Victorian evolutionary perspectives, until these were superseded by culture-historical perspectives in the 1920s. In the second period, we recognize the impact of 1960s–1970s social movements that developed feminist theory, to the early years of gender archaeology in the 1980s, with an apex of interest in the early 1990s. In the final section, we discuss a move from theory to practice and the application of contextual method and scientific techniques to large data sets, the recognition of the possibility of different genders in the archaeological record, and new feminist archaeologies.
The History of Commercial Archaeology
Authors: Aitchison Kenneth 
Published: November 2024

Abstract
The majority of archaeological investigations in the Global North are undertaken as commercial, development-led archaeology that is facilitating the requirements of construction or other development. This chapter describes how this is undertaken in Europe, where a major driver has been the Council of Europe’s 1992 Valletta Convention, which established the requirement for archaeology to be undertaken ahead of development. In most, but not all, of these countries such investigations are undertaken commercially, by private enterprises being paid by commercial clients for these services. The chapter discusses how, elsewhere in the world, commercial archaeology is either also an established or an emerging practice that has become increasingly common in Global North countries, with regional differences in terms of delivery and funding norms. The chapter examines the different nature of practice in developing countries, where this is not widely practiced, except when required by the World Bank or other development finance institutions as conditions on funding of major projects.
Writing the History of Archaeology
Authors: Díaz-Andreu Margarita 
Published: November 2024

Abstract
This article offers a review of how the history of archaeology has been written. The earliest accounts are found at the time of the institutionalization of archaeology by intellectuals and professional archaeologists connected to any of the first institutions dealing with archaeology in western Europe and North America. After World War II, there was a marked increase in the number and depth of publications and a widening of the number of countries in which the history of archaeology became a research topic. In the 1970s, interest in the subject led to the establishment of a specialist commission, the organization of conferences, and edited books. There were also new generations who paid attention to the effects of previously unheeded external factors in the history of archaeology, with special consideration given to politics, and in particular to totalitarianism of the 1930s and 1940s. The last section is a brief overview of how the history of archaeology has been written in the last two decades.
Fakes in the History of Archaeology
Authors: Podgorny Irina 
Published: November 2024

Abstract
Proliferation of forgeries is part of the history of archaeology and archaeological methods. Archaeologists have always been attentive to questions of provenance, and they learned from forgers (i.e., expert and knowledgeable artisans). From this point of view, archaeological fakes acted as catalyzers of new methods and provided heuristics for modern archaeology, just as they were pieces in the games of wealth and prestige. Counterfeits also illustrate the process of “scientific acculturation,” namely how lay people acquired the skills and knowledge for evaluating objects presented to them by archaeologists, museum curators, and collectors. Fakes reveal the porosity of boundaries between the true and the false, and especially how these borders relate to the fears of the deceived.
Introduction
Authors: Topper Keith 
Published: November 2024

Abstract
The resurgence of interest in rhetoric among political theorists is one of the more remarkable developments in the field over the past few decades. The publication of this Handbook, which constitutes the most ambitious effort to date to display the range and vitality of work that encompasses the “rhetorical turn” in political theory, represents a landmark in the development of this branch of inquiry. The following introduction provides a brief genealogy of the changing status of rhetoric in political theory and philosophy, exploring disputes that emerged in ancient Athens and have continued to the present day. It also explicates the different understandings of rhetoric that have animated recent scholarship and identifies key issues and approaches that have fueled the multidisciplinary renaissance of interest in rhetoric and political thought. Finally, it sketches the structure and aims of this Handbook. Having been maligned since the term “rhetoric” was first coined, this Handbook demonstrates that an adequate understanding of political affairs cannot be attained without taking account of the impact of rhetoric on political thought and conduct.
Sirens and Harpies
Authors: Denson Ryan 
Published: November 2024

Abstract
Associated through a similar blend of human women and avian bodies, the Sirens and Harpies were two classical monsters whose physical forms were closely related. Yet despite their corporeal similarities, these monsters had distinct traditions in the ancient world, each with their own traits and roles within the narratives they inhabit. The Sirens, songstresses known for the enchanting quality of their words and the potential danger associated therein, were most famously tied to Odysseus’ voyage. Meanwhile, the Harpies, did not typically exhibit such an alluring nature, and were prominently attached to the myth of Phineus as the creatures that perpetually snatch away and befoul his food as part of his divine punishment. This chapter sets forth the major literary instances and iconographic repertoires of these classical monsters, while also underscoring the dominant attributes of each in the ancient imagination.
Monstrous Metamorphoses
Authors: Liveley Genevieve 
Published: November 2024

Abstract
Ovid’s Metamorphoses represents a virtual bestiary of narratives about ancient monsters, hybrids, and uncanny creatures of all kinds. Indeed, the poem itself is a monstrous chimera, fusing different genres and confusing different aesthetics—in direct transgression of the poetic precepts set out in the Ars Poetica of Ovid’s Augustan near contemporary, Horace. As this chapter sets out to explore, Ovid is particularly interested in the making of monsters—not only in their backstories but also in their transformations and deformations. Focusing upon the metamorphoses of some of Ovid’s most memorable monsters—Scylla, Glaucus, and Lycaon—this chapter examines the troubling mixture of narrative bathos and pathos employed in his reworking of these myths. Drawing upon some of the insights of both ancient and modern narratology, it shows how the Ovidian transformations of these stories are carefully plotted so as to elicit not only pity and fear but also horror and humour.