bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design principles and functional basis of enantioselectivity of alanyl-tRNA synthetase and a chiral proofreader during protein biosynthesis
Authors: Sivakumar Koushick , Venkadasamy Vinitha Lakshmi , Amudhan Gurumoorthy , Ann Kezia J , Goud Gadela Karteek , Nayani Kiranmai , Gogoi Jotin , Kuncha Santosh Kumar , Mainkar Prathama S , Kruparani Shobha P , Sankaranarayanan Rajan 
Published: March 2023

Abstract
Homochirality of the cellular proteome is attributed to the L-chiral bias of the translation apparatus. The chiral specificity of enzymes was elegantly explained using the ‘four-location’ model by Koshland two decades ago. In accordance with the model, it was envisaged and noted that some aminoacyl-tRNA synthetases (aaRS) that charge larger amino acids are porous to D-amino acids. However, a recent study showed that alanyl-tRNA synthetase (AlaRS) can mischarge D-alanine and that its editing domain, but not the universally present D-aminoacyl-tRNA deacylase (DTD), is responsible for correcting the chirality-based error. Here, using in vitro and in vivo data coupled with structural analysis, we show that AlaRS catalytic site is a strict D-chiral rejection system and therefore does not activate D-alanine. It obviates the need for AlaRS editing domain to be active against D-Ala-tRNAAla and we show that it is indeed the case as it only corrects L-serine and glycine mischarging. We further provide direct biochemical evidence showing activity of DTD on smaller D-aa-tRNAs that corroborates with the L-chiral rejection mode of action proposed earlier. Overall, while removing anomalies in the fundamental recognition mechanisms, the current study further substantiates how chiral fidelity is perpetuated during protein biosynthesis.
On the dependent recognition of some long zinc finger proteins
Authors: Zuo Zheng , Billings Timothy , Walker Michael , Petkov Petko M , Fordyce Polly M , Stormo Gary D 
Published: March 2023

AbstractThe human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP recognition model asserts longer finger arrays should recognize longer DNA-binding sites. However, recent experimental efforts to identify in vivo ZFP binding sites contradict this assumption, with many exhibiting short motifs. Here we use ZFY, CTCF, ZIM3, and ZNF343 as examples to address three closely related questions: What are the reasons that impede current motif discovery methods? What are the functions of those seemingly unused fingers and how can we improve the motif discovery algorithms based on long ZFPs’ biophysical properties? Using ZFY, we employed a variety of methods and find evidence for ‘dependent recognition’ where downstream fingers can recognize some previously undiscovered motifs only in the presence of an intact core site. For CTCF, high-throughput measurements revealed its upstream specificity profile depends on the strength of its core. Moreover, the binding strength of the upstream site modulates CTCF’s sensitivity to different epigenetic modifications within the core, providing new insight into how the previously identified intellectual disability-causing and cancer-related mutant R567W disrupts upstream recognition and deregulates the epigenetic control by CTCF. Our results establish that, because of irregular motif structures, variable spacing and dependent recognition between sub-motifs, the specificities of long ZFPs are significantly underestimated, so we developed an algorithm, ModeMap, to infer the motifs and recognition models of ZIM3 and ZNF343, which facilitates high-confidence identification of specific binding sites, including repeats-derived elements. With revised concept, technique, and algorithm, we can discover the overlooked specificities and functions of those ‘extra’ fingers, and therefore decipher their broader roles in human biology and diseases.
A library of sensitive position-specific scoring matrices for high-throughput identification of nuclear pore complex subunits
Authors: Ioannides Andreas N , Katsani Katerina R , Ouzounis Christos A , Promponas Vasilis J 
Published: March 2023

AbstractThe nuclear pore complex exhibits different manifestations across eukaryotes, with certain components being restricted to specific clades. Several studies have been conducted to delineate the nuclear pore complex composition in various model organisms. Due to its pivotal role in cell viability, traditional lab experiments, such as gene knockdowns, can prove inconclusive and need to be complemented by a high-quality computational process. Here, using an extensive data collection, we create a robust library of nucleoporin protein sequences and their respective family-specific position-specific scoring matrices. By extensively validating each profile in different settings, we propose that the created profiles can be used to detect nucleoporins in proteomes with high sensitivity and specificity compared to existing methods. This library of profiles and the underlying sequence data can be used for the detection of nucleoporins in target proteomes.
The Four Evangelical Theologies of Work
Authors: Lynn Andrew 
Published: March 2023

Abstract
This chapter begins with an account of an Evangelical seminary course on meaning and vocation, bringing out the degree to which such courses seek to relocate notions of sacred activity among evangelical laity. A review of texts targeting religious laity from 1940 to 1980 suggests the emergence of four different “theologies of work” within the American evangelical cultural space. All four approaches seek to identify and repudiate a Sunday-Monday gap that threatens to compartmentalize and sequester religious life to the world of “Sunday.” A final assessment lays out how faith and work has changed since the 1980s: leaders have incorporated Romantic-inspired notions of purposeful work that emphasize beauty, harmony, fulfillment of purpose, and personal integration. A final assessment of these trends argues that these efforts ultimately recover something previously laid claim to by the Puritans: a theology that could affirm the day-to-day life of the laity and the various non-ecclesial activities that make up the textures of everyday life.
Black is a Church
Authors: Sorett Josef 
Published: March 2023

Abstract
Across four chapters that proceed as chronologically organized episodes, Black is a Church maps the ways in which black American culture and identity have been animated by a particular set of often unmarked Protestant logics. In doing so, it tracks the entangled discourses of racial authenticity and religious orthodoxy as Christianity was made constitutive of the content and forms of black subjectivity and facilitated the emergence of black social life in North America. Chapter 1 argues that Afro-Protestantism relied upon literary strategies to enunciate itself since the earliest years of its formation. As seen in slave narratives, Protestant Christianity was essential to the establishment of the earliest black literary forms. Chapter 2 follows Afro-Protestantism’s heterodox history in the convergence of literature, politics, and religion at the end of the nineteenth century. This chapter tracks a set of social movements, revealing how religious aspirations animated early calls for a “race literature” and the “the color line” provided an organizing logic for religious innovations as divergent as the practices of pluralism and Pentecostalism at the century’s close. Chapter 3 surveys historical, sociological, and anthropological work during the 1930s and 1940s—focusing especially on the launch of Phylon: The Atlanta University Review of Race and Culture—at a key moment in the study of African American culture. Finally, chapter 4 presents three recent episodes, across the spheres of scholarship, literature, and politics, to illustrate the persistence—that is, the afterlives—of Afro-Protestantism at the turn of the twenty-first century.
The Assyrian Empire in Contact with the World
Authors: Novotny Jamie 
Published: March 2023

Abstract
This chapter discusses the history of the Assyrian Empire between the ninth and seventh centuries bc, principally through the lens of Assyria’s contacts with its contemporaries. In addition to providing a brief overview of the primary source material—in particular royal inscriptions and correspondence, two genres of texts that record some details about Assyria’s numerous interactions with the outside world—this contribution examines certain key events in order to highlight the empire’s complex relationship with its neighbors, rivals, and allies. These include Ashurnasirpal II’s lavish festivities that inaugurated his newly constructed palace and capital at Kalhu; the Battle of Qarqar between Shalmaneser III and a coalition of twelve Levantine kings; Esarhaddon’s public nomination of his royal successors on the thrones of Assyria and Babylon; the “brother war” between Ashurbanipal and Šamaš-šumu-ukin; and the fall of Assyria. The chapter also addresses external influences on Assyria, in particular the incorporation of Anatolian architectural features into Assyrian royal residences; Babylon’s function as a model for Sargon II’s new capital Dur-Šarrukin; and that city’s influence on the cult and temple of the god Aššur during the reign of Sennacherib.
The Persian Empire under the Teispid Dynasty
Authors: Waters Matt 
Published: March 2023

Abstract
Cyrus the Great founded the Persian Empire in roughly 550 bc. His conquests of the kingdoms of the Medes, Lydians, Babylonians, and others by the time of his death in 530 bc made this state the most expansive and durable empire until Roman times. His impact as a transformational figure in world history remains to be fully appreciated. The disparate but sporadic evidence for the period testifies to an underlying Elamite-Iranian acculturation that was formative to the rise of Cyrus’s predecessors, the Teispid dynasty, in Fars (Parsa). After the reigns of Cyrus’s sons Cambyses and Bardiya, Darius I joined Cyrus’s line to his own through marriages to Cyrus’s daughters, Atossa and Artystone. These women were important historical figures in their own right, as manifest not only in the Greek traditions but also, and primarily, in the Persepolis Fortification Archive.
The Satrapies of the Persian Empire
Authors: Bedford Peter R. 
Published: March 2023

Abstract
According to Herodotus, the Levant and Cyprus constituted the “fifth satrapy” of the Persian Empire, known as Ebir-nari, “Across-the-River,” in Akkadian texts. This chapter discusses the region of Across-the-River, briefly examining its constituent districts and comparing the urbanism, population density, and economic activity on the Levantine coast with less developed inland territories. The chapter also reviews aspects of the administration of Across-the-River, including evidence for the history of satrapal leadership, the various forms of sub-provincial organization, the role of Phoenician cities in Persian imperial politics, tribute/taxes and their collection, lower-level bureaucrats, the administration of law, and the place of Judah (Yehud) among sub-provinces in the southern Levant.
The Persian Empire in Contact with the World
Authors: Rollinger Robert 
Published: March 2023

AbstractThe chapter argues that the Persian Empire became the center of an entangled Afro-Asian world and offered one of the very first conceptions of the world as being diverse and variegated. This concept of diversity was consciously and officially propagated. It was not inserted into a dichotomized world view of “we” and “they,” “inside” and “outside,” but was equated with the world as such, a diversified world ruled by the Persian king. Moreover, the Persian Empire introduced a novel conception of empire that was both self-contained and universalistic at the same time. From an outside perspective, the concept was self-contained since it defined an imperial space that pretended to represent the world but evidently did not match this claim. From an official, interior perspective, the concept was universalistic since it professed to constitute the world, but less obviously did not reflect “reality.” The dynamic between these two concepts became especially manifest in imperial border zones that created a hotbed for specific developments of adaptations and adoptions but also propelled processes of delimitation and alienation, identity-shaping, and binary worldviews. The Persian Empire’s reach into an outside world far beyond its rulers’ direct control was the essential trigger and ingredient for these dynamic developments. Contacts and transfers were intense throughout the empire’s entire existence, pushing forward integration as well as disintegration.
After the Prophet
Authors: Matthiesen Toby 
Published: March 2023

Abstract
This chapter discusses the aftermath of Prophet Muhammad’s death. It notes how the sources for the early period of Islam were contested on whether it was based on Muhammad’s life and the immediate aftermath. While Muslim scholars working within the Islamic tradition do not necessarily share similar scepticism, everyone still acknowledges that early history is significant because Muslims structured their life according to the precedents set by the Prophet and his Companions (for Sunnis), and the Prophet and the Imams (for Shia). The chapter explains that the problematic nature of the sources doubts the linear narratives of the Umayyad period (661–750). It then elaborates on the divide between Sunnism and Shiism.
The Religion of Martyrdom
Authors: Matthiesen Toby 
Published: March 2023

Abstract
This chapter looks into the reformulation towards a religion of protest and mass mobilisation. The reformulation involved activist clerics and lay intellectuals from across the Shii worlds, and an appropriation of ideas from Marxism and Sunni Islamism. The Shi experience was one of marginality fit for lamentation and quiet survival instead of political rule. Moreover, Shii history was reinterpreted and formed the basis of an activist Shii ideology. The chapter explains how Iran tried to be accepted by Sunnis but relied heavily on Shii symbolism. It cites that the aspect of self-sacrifice and the iconography of activist Shiism became propaganda tools in a major war effort, and influenced global Shiism.
What does God know?
Authors: Jong Jonathan 
Published: March 2023

Abstract
This chapter takes us to the Tyva Republic, in Southern Siberia. The gods there are said to be broadly unconcerned with human moral behavior; they are even said by Tuvans to be morally indifferent. But Ben Purzycki wondered if they genuinely believed that. So, he went out there, bringing with him a combination tools, including questionnaires, response time measures, and vignettes. What he discovers is that local deities are much more like so-called “big gods” than scholars assume: they too both know and care about human shenanigans. This research is a good example of a recent development in the social sciences that combines quantitative research methods from psychology with the deep fieldwork characteristic of anthropology.
Role Obligations to Alter Role Obligations
Authors: Collins Stephanie 
Published: March 2023

Abstract
Many roles are situated within organizations. The occupants of these roles often confront a dilemma between (i) the occupancy conditions, performance conditions, and functions of the role, as bestowed upon the role by the organization’s decision-making procedures, and (ii) the occupancy conditions, performance conditions, and function that the role should ideally have. This chapter argues that this dilemma should be resolved in favour of (ii). Yet this does not require forgoing role-based considerations in favour of extra-role considerations. Instead, we should conceptualize organizationally specified roles as being one token of an underlying role-type. The underlying role-type provides the organizational role-token with its fundamental occupancy conditions, performance conditions, and function. When the token is a poor instance of its type, organizational role-occupants have obligations—grounded in the fundamental aspects of the role—to challenge this. These are role obligations that call upon one to alter one’s role obligations.
Two-dimensional spectroscopy of semiconductor quantum dots
Authors: Li Hebin , Lomsadze Bachana , Moody Galan , Smallwood Christopher L. , Cundiff Steven T. 
Published: March 2023

Abstract
Two-dimensional spectroscopy of a variety of semiconductor quantum dots is discussed in this chapter. The chapter begins with the optical and electronic properties of quantum dots. Experiments on three specific types of quantum dots are discussed, including GaAs interfacial fluctuation dots, self-assembled In(Ga)As dots including coherent control experiments, and colloidal dots.
Introduction
Authors: Chadha Monima 
Published: March 2023

Abstract
This book sets forth a revisionary conceptual scheme envisaged by the ancient Indian Buddhist philosopher Vasubandhu. The book describes his revisionary no-self and no-person metaphysics and its normative implications as an alternative vantage point to challenge what we ordinarily assume and intuit. I argue that we can account for the phenomenology and the subjective character of our ordinary conscious experience in the absence of selves and persons. The no-person view, however, leaves us without a basis for our person-related concerns and interpersonal practices. A wholesale rejection of our ordinary practices is practically impossible. The best way forward is to build theories of “what we are” and “how we should live” that are mutually constrained by some forms of reflective equilibrium.
Historical Introduction to Abhidharma Buddhist Philosophy
Authors: Chadha Monima 
Published: March 2023

Abstract
The scene is set with placing Abhidharma philosophy in the context of the history of Buddhism followed by a short introduction to the Abhidharma tradition mentioning some key divisions, seminal texts, and philosophers in this scholastic tradition. This is not an exhaustive list. The purpose is to give the reader a flavor of the complexity and evolution of the Abhidharma tradition and to introduce our protagonist, Vasubandhu. This is followed by a discussion of their distinctive theses and the role of meditation in Abhidharma Buddhist philosophy. The Abhidharma tradition is known for providing the first systematic account of conscious experiences without a self within the Buddhist tradition.
Self/No-Self in Abhidharma Philosophy
Authors: Chadha Monima 
Published: March 2023

Abstract
This chapter locates Vasubandhu’s no-self view in the contemporary landscape of the self/no-self debate. After placing the no-self view in this analytical framework, the chapter presents Vasubandhu’s argument for his claim that there is no need to posit a self because it is causally impotent. The argument reveals Vasubandhu’s strategy which is to show that different components of the “mental” do all the causal work. He also argues against persons using the same strategy. In order to be true to the spirit and argumentative strategy employed by Vasubandhu we should reject selves and persons. Vasubandhu would not approve of positing conventional persons to do the work of the self.
The Abhidharma Buddhist Account of Conscious Experience
Authors: Chadha Monima 
Published: March 2023

Abstract
The Abhidharma account of conscious experience faces some serious challenges not only because of the absence of selves or persons, but also because of its commitment to mereological nihilism and the doctrine of momentariness. This chapter presents the account of conscious experience and notes the challenges that arise due to the latter commitments. These challenges question the reality, coherence, and empirical viability of the Abhidharma view of conscious experience and thought. On behalf of Vasubandhu and Abhidharma philosophers the author develops the Abhidharma interpretation of conscious experience and shows that the account can withstand these challenges and deserves serious consideration.
Classical Equilibrium Theory: Particles to Fields
Authors: Delaney Fredrickson , Delaney Kris T. 
Published: March 2023

AbstractStarting with the simplest classical monatomic fluid, Chapter 2 discusses an “auxiliary field” technique that can be used to exactly convert equilibrium models of fluids framed in particle coordinates to statistical field theory models. The technique is applied to a variety of polymer and soft material models, including bonded, non-bonded, and electrostatic interactions among polymer segments. Field operators are identified that yield important structural and thermodynamic properties. A second “coherent states” field theory representation is introduced and shown to be useful in modeling polymers that can reversibly react
The Necessity of Young Adult Fiction
Authors: Williams Deborah Lindsay 
Published: March 2023

AbstractThe Necessity of Young Adult Literature argues that young adult (YA) fiction helps readers to think about some of the most pressing problems of the twenty-first century by offering imaginative reconceptualizations about identity, nation, family, and the human relationship to the planet. Using examples from YA fiction that range from the Harry Potter series to Nnedi Okorafor’s trilogy set in contemporary Nigeria, the book argues that the cultural work of YA fiction shapes readers’ perceptions, making them receptive to—and invested in—the possibility of positive social change. Speculative YA fiction shows how a cosmopolitan world-view can help to form communities that are not threatened by difference but instead see diversity and dissent as sources of strength and knowledge. YA literature opens up conversations about cosmopolitanism and climate change, suggesting that cosmopolitanism is not just a subject for theoretical debate but an ongoing practice that could radically restructure readers’ relationships with one another and the planet. The novels examined in this book could all be considered “fantastical,” but they offer insights into the real world that all readers—and particularly young adult readers—might draw on to reimagine social structures and the well-being of the planet. In different ways, these novels also illustrate the dangers inherent in fundamentalist visions of the world. The cultural work they perform and their engagement with important social and political issues demonstrate not only the power of literature to shape understandings of the world but also the ongoing relevance of “the book.”
Introduction: Why “Kids’ Books?”
Authors: Williams Deborah Lindsay 
Published: March 2023

AbstractThis chapter maps out the book’s overall trajectory and highlights its central focus on how the adolescent characters in the novels under discussion learn to be good readers who see the world with compassion and flexibility, rather than dogmatism and fear. “Good readers,” as introduced in this chapter, refers to the concept of “cosmopolitan reading,” an idea that is central to the argument of this book. With brief reference to each chapter, the introduction charts the book’s engagements with cosmopolitan reading, monstrosity, and the relationship between local and global, ideas that create crucial interventions in thinking about the threat of climate crisis and the fate of the human species.
Introduction
Authors: Howell Robert J. 
Published: March 2023

Abstract
Chapter 1 introduces readers to the puzzle of the elusive subject. On the one hand, it seems certain that there is a subject of experience. Not only does Descartes’ cogito, “I am thinking,” appear indubitable, but there are compelling metaphysical reasons to believe that conscious states must have subjects. Nevertheless, in some sense the subject of experience is elusive. As Hume observed, introspection doesn’t reveal a thing that has conscious states: it just reveals the conscious states themselves. After introducing readers to the basics of this puzzle, this introduction provides a roadmap of the argument in the rest of the book.