bluuebunny/crossref_metadata_2025 huggingface dataset:
Deficiency in glutathione peroxidase 4 (GPX4) results in abnormal lens development and newborn cataract
Authors: Wei Zongbo , Hao Caili , Radeen Kazi Rafsan , Hao Zheng , Kettimuthu Kavitha , Maner-Smith Kristal , Toyokuni Shinya , Fan Xingjun
Published: November 2024

The human lens is composed of a monolayer of lens epithelial cells (LECs) and elongated fibers that align tightly but are separated by the plasma membrane. The integrity of the lens plasma membrane is crucial for maintaining lens cellular structure, homeostasis, and transparency. Glutathione peroxidase 4 (GPX4), a selenoenzyme, plays a critical role in protecting against lipid peroxidation. This study aims to elucidate the role of GPX4 in lens plasma membrane stability during lens development using in vitro, ex vivo, and in vivo systems. Our findings reveal that GPX4 deficiency triggers lens epithelial apoptosis-independent but ferroptosis-mediated cell death. Blocking lens GPX4 activity during ex vivo culture induces lens opacification, LEC death, and disruption of lens fiber cell arrangement. Deletion of lens-specific Gpx4 results in significant unsaturated phospholipid loss and an increase in oxidized phospholipids. Consequently, lenses with Gpx4 deficiency exhibit massive disruption of lens fiber cell structure, significant loss of LECs via ferroptosis, and formation of newborn cataracts. Remarkably, administering the lipid peroxidation inhibitor, liproxstatin-1, to pregnant mothers at embryonic days 9.5 significantly prevents lipid peroxidation, LEC death, and lens developmental defects. Our study unveils the crucial role of GPX4 in lens development and transparency, and also provides a successful intervention approach to prevent lens developmental defects through lipid peroxidation inhibition.
1.1.3. The eighteenth century
Authors: Ferrand Nathalie
Published: November 2024

The eighteenth century used to enjoy a bad reputation among scholars interested in literary drafts, suffering from its situation between two great moments in the history of the literary manuscript: the medieval period, when the manuscript tradition was the sole possible channel of a work’s dissemination, and the “contemporary” period of the nineteenth and twentieth centuries, when the importance accorded to the manuscript was that of a valuable testimony to “the genius of the author”. Fortunately, new developments in scholarship have changed this situation in the course of the last few decades. The present chapter sets out to analyse the emergence into greater prominence, in the field of eighteenth-century studies, of drafts, sketches and manuscripts. The movement toward a growing interest in such documents has been nourished by textual genetics, an innovative critical approach which has led scholars to ascribe to them greater meaning in the interpretation of the author’s action.
1.3.3. Translation archives
Authors: Cordingley Anthony
Published: November 2024

This chapter details how archives containing literary translation drafts from the early modern period to the present supply evidence that can challenge conventional views of both translatorship and authorship. Three cases are explored in depth. First, two of the oldest known translation drafts in English, Samuel Ward’s (1572–1643) recently discovered draft of apocryphal text 1 Esdras (Ezra) and his partial draft of Wisdom 3–4.6 for the King James Bible provoke a new understanding of the ontology of the translation draft in this period. Second, Percy Bysshe Shelley’s unpublished self-translations of his poems into Italian for the Florentine Contessina, Teresa (Emilia) Viviani della Robbia cast his long poem Epipsychidion (1821) in a different light, revealing Shelley’s cosmopolitan self-fashioning. Third, the archives of the German translator of French nouveau roman authors Elmar Tophoven form a node of significance connecting literary figures and networks across Europe.
1.4.3. Prose
Authors: Beloborodova Olga
Published: November 2024

This chapter addresses and questions the seemingly solitary nature of prose writing, using two cognitive theories (extended mind and distributed cognition) that place cognition outside the boundaries of the human brain and advocate instead an inextricable connection between the brain and the world. Specifically, the tight coupling between the writing mind and literary drafts testifies to the crucial importance of these objects to the writing process, and a number of examples of creative collaborations (the Shelleys, Michael Field, Ilf and Petrov) demonstrate that creativity in prose writing is more often than not distributed and as such is not that different from those genres that are typically considered collaborative (such as drama). This distribution of cognition also applies to works that are not co-authored, as Beckett’s correspondence shows. The conclusion relates the chapter’s main ideas to the future of prose writing, namely the advent of AI and its impact on creativity.
1.5.4. Punctuation
Authors: McCracken Scott
Published: November 2024

All literary drafts manifest the signs of their provisionality. For experimental writers, such as the pioneering modernist writer, Dorothy Richardson, who resist the illusion of the artwork as complete, the improvisatory nature of the draft is a strength, a quality the writer carries over to the published version. This chapter reads the manuscript of Pointed Roofs, the first “chapter-volume” of Richardson’s long modernist novel Pilgrimage, in order to examine three aspects of Richardson’s compositional method: first, its experimental nature, which includes a degree of improvisation; second, her innovative use of punctuation, ellipses, and compression; and third, the relationship between the Richardsonian sentence and the emergence of modernist prose at the beginning of the twentieth century.
2.1.1. Paper
Authors: Honey Andrew
Published: November 2024

This chapter uses Jane Austen as a case study to explore the roles that paper, the underlying support, play within literary drafts. It investigates whether her choice and use of paper within a relatively small surviving corpus reveal methods and habits of writing. It demonstrates the types of evidence that can be drawn by studying the physical marks and characteristics of paper. Examples show that much can be gleaned from careful characterisation and comparison of the physical features of any paper used for literary drafts. Paper might be thought a neutral carrier, but the conscious or unconscious choices of paper by a writer, coupled with their habits and preferences of use, leave material evidence independent of the written text.
2.3.4. Music
Authors: Rink John
Published: November 2024

This chapter begins by acknowledging the impossibility of capturing musical thought in notational form and by highlighting the concomitant provisionality of music scores. It then considers the creative input required of performers when they bring musical notation “to life” in sound and in time. This leads to a case study on the Polish composer Fryderyk Chopin, for whom the act of notation posed innumerable difficulties not least because he continually reimagined and revised his musical ideas. The chapter as a whole thus challenges any assumptions we might have about the identity and stability of the Chopin work and of music more generally, while also raising thorny questions about the best means of representing music’s creative history in editions and performances themselves.
Nanobiochar application and its impact on sustainable agriculture: A concise review
Authors: Salaria Mani , Shobhna Shobhna , Sharma Tarun , Banik Diptanu , Mehta Chandra Mohan , Assouguem Amine , Lahlali Rachid
Published: November 2024

Nanobiochar represents a novel intersection of nanotechnology and sustainable agriculture, holding promise for addressing contemporary challenges in soil health, carbon sequestration, and resource efficiency. Synthesis methods, unique physicochemical properties, and potential applications in various sectors are systematically analysed, contributing to a deeper understanding of this innovative bio-based nanomaterial. The social impact of nanobiochar is investigated, highlighting its role in creating sustainable livelihoods, fostering community engagement, and promoting inclusive agricultural practices. The review also includes the soil-related effects of nanobiochar. Nanobiochar’s role in mitigating soil degradation, enhancing fertility, and promoting sustainable agriculture practices is also studied. The paper evaluates the potential for nanobiochar to sequester carbon effectively and contribute to climate change mitigation efforts. Furthermore, attention is directed towards the environmental considerations and ethical implications associated with the use of nanobiochar. This review paper offers a comprehensive viewpoint on the effects of nanobiochar on environment and agriculture.
Performance study of a new LiCAF:Ce detector developed for high-efficient neutron detection in intense γ-ray fields
Authors: Kaburagi M. , Kamada K. , Ishii J. , Matsumoto T. , Manabe S. , Masuda A. , Harano H. , Kato M. , Shimazoe K.
Published: November 2024

When detecting fast and thermal neutrons in intense
γ-ray fields, it is challenging to discriminate between pulse
signals due to neutron and γ-rays, even when using
pulse-shape-discrimination techniques, because the trailing pulse
signals overlap at high pulse rates. Some nuclear facilities have
faced challenging problems for dispersed nuclear fuel (or nuclear
fuel debris), radioactive wastes, and other radioactive materials
during decommissioning. Particularly, high-efficiency neutron
detection in intense γ-ray fields is required for exploring
dispersed nuclear fuel and for criticality monitoring. LiCaAlF6
(LiCAF):Ce has suitable properties of high 6Li density and fast
decay times for high-efficiency neutron detection in intense
γ-ray fields. A new LiCAF:Ce detector with an ultra-thick (99
μm) crystal and optimized readout was developed. The neutron
detection performance in an intense γ-ray field was
investigated and compared to that using a Li glass (KG2)
detector. The LiCAF:Ce and KG2 detectors were used to detect a
sealed 252Cf neutron source (neutron emission rate of
∼ 4.11 × 105 s-1) using a 5 cm thick high-density
polyethylene (HDPE) block moderator located at the front of the
detector. At the air kerma rates at the front surface of the HDPE
block (Ds
) of up to 1.07 Gy/h, the effective neutron count
rate (n
eff) for the LiCAF:Ce detector was the same
within margins of errors, but it decreased by 5.7 ± 0.8% at
2.97 Gy/h. In contrast, for the KG2 detector, with Ds

increased up to 1.07 Gy/h, n
eff for KG2 increased up
to 20 ± 1.0 % at 1.07 Gy/h. Then, n
eff decreased
by 20 ± 1.0% at 2.97 Gy/h. Therefore, the LiCAF:Ce detector
exhibited a smaller influence on neutron count rates by
γ-rays compared to the KG2 detector because of the faster
decay time and optimization of digital pulse processing.
Excluding a Line from Complex-Representable Matroids
Authors: Geelen Jim , Nelson Peter , Walsh Zach
Published: November 2024

For each positive integer

t
t

and each sufficiently large integer

r
r

, we show that the maximum number of elements of a simple, rank-

r
r

,

C

\mathbb C

-representable matroid with no

U

2
,
t
+
3

U_{2,t+3}

-minor is

t

(

r
2

)

+
r

t{r\choose 2}+r

. We derive this as a consequence of a much more general result concerning matroids on group-labeled graphs.
Lie Pseudogroups à la Cartan
Authors: Crainic Marius , Yudilevich Ori
Published: November 2024

We present a modern formulation of Élie Cartan’s structure theory for Lie pseudogroups and prove a reduction theorem that clarifies the role of Cartan’s systatic system. The monograph is divided into three parts. In part one, using notions coming from the theory of Lie groupoids and algebroids, we introduce the framework of Cartan algebroids and realizations, structures that encode Cartan’s structure equations and notion of a pseudogroup in normal form. In part two, we present a novel proof of Cartan’s Second Fundamental Theorem which states that any Lie pseudogroup is equivalent to a pseudogroup in normal form. In part three, we prove a new reduction theorem that states that, under suitable regularity conditions, a pseudogroup in normal form canonically reduces to a generalized pseudogroup of local solutions of a Lie-Pfaffian groupoid.
Leader Humility and Its Effectiveness in Organizations
Authors: Kelemen Thomas K. , Matthews Michael J. , Matthews Samuel H.
Published: November 2024

As businesses continue to strive for higher standards of morality and researchers’ interest in positive organizational scholarship grows, interest in the construct of humble leadership has accumulated. As a function of this rapid progression, several key findings have emerged. In terms of empirical measures of humble leadership, there exist several psychometrically sound measures and approaches. While there remains some debate on the dimensions of humble leadership, the three dimensions of (a) admitting mistakes and limitations, (b) spotlighting follower strengths and contributions, and (c) modeling teachability consistently appear in most conceptualizations of humble leadership. As such, these three dimensions of humble leadership constitute core elements of humble leadership. Regarding outcomes associated with humble leadership, across levels of analysis, humble leadership generally leads to positive effects for individual followers, teams, and organizations. Likewise, research has generally found that when leaders engage in humble leadership this typically results in improved follower perceptions of the leader and positive career outcomes for the leader, although it can result in some negative effects for the leader. The antecedents of humble leadership are relatively less studied, although research notes that both individual factors such as personality and situational factors contribute to humble leadership. Despite these important findings, additional research that explores the antecedents of humble leadership, better recognizes the nuances and multidimensionality of humble leadership, and applies stronger methodological approaches is warranted.
Game Streaming: Implications for Streamers and Game Creators
Authors: Johnson Mark
Published: November 2024

Since the 2010s, the live streaming—live online video broadcast—of digital gaming has emerged as a significant Internet phenomenon. Millions of people stream their digital gaming for leisure, profit, or some combination, in the process often accumulating large communities of fans and followers who enjoy their streamed content, or simply broadcasting to small but often very dedicated handfuls of viewers. Game live streaming is also plagued by harassment and toxicity, but nevertheless continues to have a significant influence on gaming by generating famous and noteworthy moments within wider gaming culture. Game live streaming is far from a niche practice, and rather one with interest and applicability to a range of media studies, communication studies, game studies, and Internet research agendas.
The Political Economy of News Media and Journalism
Authors: Salamon Errol
Published: November 2024

The political economy of news media and journalism critically examines the structures, processes, and democratic role of journalism within society. It is focused on the power relations that shape the production, distribution, and consumption of online, print, and broadcast news media. The field originated from classical Western political economy in the 17th century. Western media political economies of journalism can be traced back to the early 20th century, with the Frankfurt School’s culture industry approach and Dallas W. Smythe’s radical media approach. Scholars like Armand Mattelart and Jesús Martín-Barbero developed political economy of communication and culture approaches on the Global South. These traditions were informed by Marxian critiques and mainstream economic perspectives. Since the mid-20th century, radical media political economies of journalism have encompassed three key strands:corporate ownership and control; labor and standpoints of resistance; and platform capital and labor. By comparison, the cultural-industries school has analyzed the distinctiveness of individual sectors within journalism, including their structural and creative-labor characteristics. A subset of this school, the infomediation approach, highlights the impact of digital platforms. Unlike the cultural-industries school, radical media political economists often link their research to industry impact. These approaches draw on theoretical perspectives, including liberal pluralism, Marxism, and conflict theories, to analyze the commodification of journalism and social relations. Methodologically, these approaches typically draw on qualitative social science or humanistic methods to analyze media companies, governmental interventions, media production, labor, and resistance. Some political economists also use industry-level statistics to track media ownership concentration, the financial state of media markets, individual companies, and labor market trends. Future research should examine the financialization of journalism, its impact on funding models, the integration of generative artificial intelligence into the labor process, and a wider range of advocacy and activist organizations and practices.
Political Parties and Party Systems in South Asia
Authors: Ziegfeld Adam , Jain Anurag
Published: November 2024

South Asia’s five largest countries—Bangladesh, India, Nepal, Pakistan, and Sri Lanka—have had very different experiences with democracy. In spite of these differences, their party systems exhibit several common features. First, two leading parties have tended to dominate politics over long periods of time in most South Asian countries. Second, these two parties typically anchor fragmented bipolar systems in which many very small parties combine to win substantial vote shares. Third, parties are seldom tied to voters through strong programmatic linkages. Fourth, parties tend to be more starkly differentiated from one another on the basis of ethnicity, though the type of ethnic identity that structures party systems varies across South Asia. Fifth, political dynasties dominate many of the region’s main parties. Of the main South Asian countries, India’s party system has received the most attention, with many arguing that its party system fundamentally changed with the rise of the Bharatiya Janata Party in 2014. However, in terms of many key indicators (competitiveness, number and size of major parties, importance of regional parties, party system nationalization), the 2014 national election largely resembled prior elections. The 2019 election represented a much starker departure from prior patterns. But, it is arguably still too soon to know whether India has fully transitioned to a durable new party system and what the characteristics of a new party system might be.
Ottoman-Safavid Relations: A Religious or Political Rivalry
Authors: Ates-Vural Genç Sabri
Published: November 2024

The Safavid state (1501–1722) spent considerable portions of its early history in conflict with its neighbor, the Ottoman Empire. The transformation of the Safavid order into a temporal state and the declaration of Shiʿism as the state religion by its first ruler, Shah Ismaʿil, posed significant challenges to the Ottomans. Faced with the threat of losing eastern Anatolia and adjacent territories to the rapidly expanding Safavids, the Ottoman establishment swiftly took action. As the self-proclaimed champions of Sunni Islam and the protectors of the abode of Islam, the Ottoman religious and scholarly circles initiated a theological debate in response to the emerging Shia threat from the East. They issued fatwas to excommunicate the Safavids and their followers, the Qezelbash. Empowered by these fatwas, the Ottoman sultans Selim I and his son Suleiman the Magnificent carried out four campaigns aimed at eliminating the new state, which posed challenges to their religious and temporal claims. The campaigns of 1514, 1533–1534, 1548–1549, and 1553–1554 were motivated more by religious concerns than political ones. However, unable to eliminate the Safavids, who remained on the defensive and did not issue anti-Sunni fatwas to reciprocate the Ottoman attacks, the Ottomans agreed to the 1555 Amasya Treaty, recognizing the Safavids as a legitimate political entity.

The Amasya Treaty halted but did not end the conflict. However, by the end of the 16th century, the nature of the Ottoman–Safavid confrontations had changed. Protracted wars driven by geopolitical and strategic concerns replaced seasonal campaigns. The first cycle of wars extended from 1578 to 1590, and the second cycle began in 1603 and ended with the Treaty of Zohab in 1639. Imperial and expansionist ambitions, such as the rivalry over the Caucasus and Baghdad and the Ottoman strategy of capturing the rich Caspian provinces, played a more significant role than the sectarian differences in these conflicts. Nonetheless, the rivalry was often framed in religio-ideological terms, and sectarian contention remained an important component of the Ottoman–Iranian rivalry until the end of the Safavids in 1722.
World War I in West and Equatorial Africa
Authors: Lunn Joe
Published: November 2024

The First World War was likely the most destructive war in African history prior to the comparable catastrophe of 1935 to 1945. It was also not the African peoples’ war to fight. Instead, it was a by-product of the recent subjugation and subdivision of the continent by a handful of West and Central European industrial powers, their internal nationalist rivalries, and their exploitation of their African colonial subjects for imperial ends, and, in the case of France, for national defense.

The war’s impact on West and Central Africans may be assessed from two different vantage points. On the continent, French and British colonial armies, comprised largely of African troops accompanied by supporting carriers (noncombatant laborers), invaded the German colonies of Togoland (Togo) and Kamerun (Cameroon), before the British West Africans were redeployed in 1916 to fight and labor during the Allied conquest German East Africa (Tanzania, Burundi, and Rwanda). Meanwhile, the French also introduced West African combat troops into Europe on a massive scale. This uniquely French policy, little more than a controversial contingency plan until heavy losses prompted its implementation in 1915, provoked widespread resistance and rebellion in West Africa. Thereafter, deployed as “shock troops” on the Western Front and in the Balkans, African combatants interpreted their wartime experience in various ways. A few believed it to be personally transformative and in retrospect, a harbinger of the political quest for equality with Europeans to come; most, who received little in recompense for their sacrifice and suffering, returned to their homelands and resumed their former lives much as before.

Though varied and often incomplete, casualty assessments for soldiers, carriers, and civilians during the conflict suggest grievous losses by West and Central Africans between 1914 and 1918. Indeed, while very modest changes in postwar colonial society occurred because of Africans’ participation in the war, they were incommensurate with the scale of violence endured. Moreover, the territorial changes occurring in Africa because of the conflict would likely have taken place even if the destructive campaigns on the continent and abroad had never been waged. Largely forgotten by European authorities immediately after the conflict, the memory of the veterans’ wartime ordeal and contribution to the nation nevertheless endures and is cited, especially by African immigrants, as justification for their civic inclusion in European societies, particularly in France. Unfortunately, so too do the centuries-old racist stereotypes about Africans’ being invariably subordinate to Europeans persist in contemporary societies, denying their acceptance.
Enslaved African Muslims in the Americas
Authors: Véras Bruno R. , Elzeiny Mariam
Published: November 2024

Throughout the slave trade era, wars and raids in the hinterlands of West Africa brought captives into different ports of the Atlantic coast, many of whom were Muslims. Various political and social factors in Africa influenced the nature of the transatlantic slave trade, including the identities of those involved in exporting enslaved Muslims, the number of people transported, their ethnic origins, and the colonies and countries to which they were shipped. These dynamics shaped the trade’s complexity across different regions. Following the literary developments in Europe, the collection of individual histories of slavery began in North America in the first decades of the 18th century. Abolitionist biographical accounts were written about the enslaved (overwhelmingly about male individuals) as well as autobiographies in Arabic and English produced by freed Muslim Africans in Maryland, South Carolina, North Carolina, Georgia, Alabama, and Mississippi, as well as Québec and Canada West (present-day Ontario). In the Caribbean, Arabic and Hausa-Ajami manuscripts were produced both on the islands and on the shores of Central America. Freed and enslaved Muslim Africans in Brazil, particularly those from Central Sudan, created long-standing and rebellious communities. The Malê Uprising of 1835 was a cornerstone event for slave resistance and marked the strengthening of the bonds of a transnational community of Muslim Africans in different parts of Brazil that had an enduring impact until the early 20th century. Community practices as well as religious and cultural pluralisms marked the histories of these diverse diasporas.
Islamic Bioethics: Ijtihad
Authors: Mavani Hamid
Published: November 2024

In the context of Islamic jurisprudence, ijtihad refers to the process of legal reasoning and hermeneutics undertaken by a qualified jurist (mujtahid or faqih) to extract or infer a fresh probable legal ruling (fatwa) based on a particular set of principles and procedures. In principle, ijtihad remains a perpetual obligation that must be undertaken by a qualified jurist because it enables Muslims to resolve contemporary ethical issues. To implement appropriate legal norms addressing contemporary bioethical issues, jurists are required to formulate a legal theory and articulate new principles and procedures. Organ donation demonstrates the evolution of a legal ruling (tatawwur al-fiqh) within a revitalized ijtihad and in light of new information. The ever-increasing complexity and ever-widening scope of issues cropping up in Islamic bioethics demand a collective and a contextual ijtihad functioning at an institutional level (majmaʻ al-fiqhiyyah).
Islamic Bioethics: Afterlife
Authors: Rustomji Nerina
Published: November 2024

The Islamic afterlife (al-ākhirah) refers to the final, everlasting stage of life where Muslims will be rewarded with the Garden (al-jannah) or the Fire (al-nār). Essentially, Muslims will be transformed from their earthly selves into their reformed bodies and experience an eternal phase of life through enhanced bodily experiences and sense perception. In the modern period, the belief in the afterlife affects the issues of human dignity and euthanasia. Belief in the afterlife entails an expectation that death is a transformative passage. Since many of the advents of modern medicine were unknown during the early years of Islamic history, there is room for jurists and theologians to interpret the quality of life and its connection to the afterlife for contemporary Islam.
Aniconism
Authors: Gaifman Milette
Published: November 2024

In scholarship on religion and religious art, the term aniconism describes the absence of a figural representation of a deity (whether anthropomorphic or theriomorphic), primarily in the context of ritual veneration of one deity or more, but also within a visual tradition more broadly. Aniconic worship may take on a variety of forms, including veneration centered around a standing stone, open fire, vacant space, or no independent physical focal point at all. In religious art and visual culture, aniconism may also be manifested in a range of ways, such as adherence to the usage of ornament, calligraphy, or geometric forms. Although it is often treated as synonymous with iconoclasm, the word aniconism does not refer to the destruction of religious images. It may be adopted without an articulated reason or coherent doctrine, or it may be connected with an explicit theology.

Worship of deities without figural representations has been widely attested for millennia in both polytheistic traditions (Greco-Roman, Phoenician) and monotheistic ones (Jewish, Islamic). The concept of aniconism, however, is modern. It was introduced by Johannes Adolph Overbeck (1826–1895) for the particular purpose of describing the presumed earliest phases in the development of Greek religion, which were construed as imageless. In the 20th century, aniconism has come to describe the absence of the figural image of a deity in worship and has been applied more broadly to certain artistic traditions such as early Buddhist, Islamic, and Jewish art. Since the manifestations of aniconism differ widely, it is vitally important to apply the concept contextually, with clear criteria for what is considered aniconic within a particular framework.

Among the religions in the West from the Renaissance to the present, aniconism is notable in its emergence in certain strands of Protestantism, particularly in Calvinist houses of worship. Worship with no figural image is also often linked with primeval religions and is seen either negatively, as the practice of a less advanced culture, or positively, as a marker of higher spirituality. Claims of a complete absence of imagery and figural art in various religious traditions (e.g., Jewish, Islamic) have often been disproven, as further examination of those traditions has revealed the occurrence of figuration alongside some form of aniconism. The wide range of forms of aniconism and its coexistence with semi-figural and fully figural forms in worship and within broader visual traditions suggest that the concept is best applied through a nuanced approach which considers the nature and frequency of its occurrence rather than seeing it as an absolute negation of the figural image.
Revolts and Rebellions in Colonial Brazil
Authors: Figueiredo Luciano
Published: November 2024

In the context of the political instability that characterized the Portuguese conquest and colonization of America, disputes often took the extreme form of rebellions, as rivals took up arms in defense of the principles of justice and law. These uprisings were numerous and varied widely in their social composition, causes, and duration, as well as in the responses and repression they provoked. There were a variety of rebellions from the earliest days of Brazil’s conquest in the 16th century until 1808, when Brazil’s colonial status was altered by the relocation of the seat of the Portuguese monarchy to Rio de Janeiro. Rather than classifying revolts by their typology, conjunctures, regions, or dominant political ideas that has become common in historiography, it may be instructive to view these events through an interpretation that draws together the diverse political cultures that were mobilized in the rebels’ discourses and practices, such as indigenous beliefs, Central African traditions, Islamic religion, Iberian contractualism (natural law), and the Enlightenment. Certain social groups tended to adhere progressively to the moral arguments of contractualist ideas; an examination of rebel languages and political practices shows a dynamic in which protagonists acted in defense of rights over the course of advances and retreats during the colonial conquest, affirming principles, and establishing exchanges and interactions between political cultures.
Theoretical Issues in Planning the Articulation of Spoken Utterances
Authors: Turk Alice
Published: November 2024

Theories of speech articulation planning must account for the coordinated movements of speech articulators that produce contrastive lexical items, as well as the ways these vary systematically in different contexts both within and across utterances. The systematic phonetic variability of phonologically equivalent forms relates to many factors including adjacent segmental context, rate and style of speech, local contextual factors, such as position in prosodic structure. This variability has been proposed to contribute to the transmission of meaning and to communicative efficiency.

Theories proposed to account for speech articulation behaviors differ in many key respects. Theoretical controversies relate to the nature of phonological representations used to distinguish words in the mental lexicon, as well as the processing components, representations, and mechanisms involved in planning and producing speech.

One of the most fundamental theoretical distinctions relates to assumptions about the spatiotemporal vs. symbolic nature of phonological representations. Distinctions in system architecture, including the number and type of processing components, derive from these assumptions. Other differences among theories relate to assumptions about the nature of speech production goals, movement targets, timekeeping mechanisms, dynamic parametric models of movement, movement coordination, the separate vs. integrated representation for spatial and temporal characteristics of movement, as well as proposed mechanisms to account for systematic phonetic variability in different contexts (coupled oscillators, optimization-based, vs. dynamic field theory approaches).
Neoclassical Compounding in the Romance Languages
Authors: Montermini Fabio
Published: November 2024

The label “neoclassical compounds” (NC) encompasses a set of phenomena found in, but not limited to, Romance languages. They can be roughly characterized as the emergence, in the lexicon of a language, of lexical units totally or partially made up of elements borrowed from ancient (classical) languages, namely Greek and Latin, and constructed by means of processes not (or not necessarily) corresponding to the “canonical” morphological processes at work in the language in question. Historically, the existence of NC in Romance languages is linked, on the one side, to the role played by Latin, and partly Greek, in the intellectual history of Europe; and, on the other side, to the various waves of relatinization Romance languages were subject to at different times, with two major turning points, in the 15th and 16th centuries, with the revival of classical authors advocated by Humanism and the Renaissance, and from the 18th century onward, with the development and democratization of scientific and technical knowledge. Progressively, NC have served as models for the emergence of productive word formation patterns which are, today, perfectly integrated into the derivational systems of Romance languages. However, rather than constituting a clearly delimited and homogeneous class, the label NC encompasses a constellation of phenomena sharing some characteristics that can globally be attributed to their common origin in the lexicon of neoclassical descent that has been transferred to Romance languages across the centuries.
Social Isolation
Authors: Crewe Sandra Edmonds , Cosby Robert
Published: November 2024

Social isolation is both a social and public health problem that is lethal across the life span. Its harmful effects have both psychological and physiological impact and is recognized by social workers and allied health professionals as a major barrier to quality of life for individuals and groups. The effects of social isolation have been reported to be as harmful as smoking 15 cigarettes a day and four times as harmful as obesity. These facts have galvanized the social work profession around eradicating social isolation with a focus on defining social isolation and identifying its causes, strategies for eradication and prevention, and addressing the differences between perceived isolation (loneliness) and objective isolation. Additionally, social isolation is examined through a cultural lens using both micro- and macroperspectives giving attention to social exclusion as well as to groups who have higher risks such as older persons, at-risk youth, prisoners, stigmatized groups, and historically oppressed populations.
Comparative effects of topiramate and naltrexone on neural activity during anticipatory anxiety in individuals with alcohol use disorder
Authors: Dali Gezelle , Logge Warren , Kranzler Henry R , Hurzeler Tristan , Gallagher Hugh , Haber Paul S , Morley Kirsten C
Published: November 2024

Topiramate has been found to be effective in reducing alcohol use and may also attenuate anxiety severity in patients with alcohol use disorder (AUD). This study compared the neural response of treatment-seeking patients with AUD on either topiramate or naltrexone during an anticipatory anxiety task. Participants were 42 patients with AUD who were randomized to receive either topiramate (n = 23; titrated dose up to 200 mg/day) or naltrexone (n = 19; 50 mg/day) for 12-weeks as part of a larger randomized controlled trial. Following 6 weeks of treatment, participants completed an anticipatory anxiety task during a functional magnetic resonance imaging (fMRI) session. The task presented a series of high-threat and low-threat stimuli followed by an unpleasant or pleasant image, respectively. Primary whole-brain analyses revealed no significant differences in neural activation between the topiramate and naltrexone groups. Deactivation for safe cues relative to threat cues was observed within the precuneus, inferior parietal lobule and the cingulate gyrus. In the precentral and middle frontal gyri, threat cues elicited greater activation. Exploratory analyses revealed an effect of change in anxiety from baseline to week 6, with a greater reduction associated with a reduced response to threat cues relative to safe cues in the cuneus and lingual gyrus. The current study is the first to examine and compare neural activation during anticipatory anxiety in treatment-seeking individuals on topiramate and naltrexone. This preliminary research contributes to our understanding of the therapeutic mechanisms of these alcohol pharmacotherapies.
Interplay of physical and social drivers of movement in male African savanna elephants
Authors: Wiśniewska Maggie , O’Connell-Rodwell Caitlin E , Kilian J Werner , Garnier Simon , Russell Gareth J
Published: November 2024

Despite extensive research into the behavioral ecology of free-ranging animal groups, questions remain about how group members integrate information about their physical and social surroundings. This is because (1) tracking of multiple group members is limited to a few easily manageable species and (2) the tools to simultaneously quantify physical and social influences on an individual’s movement remain challenging, especially across large geographic scales. A relevant example of a widely ranging species with complex social structure and of conservation concern is the African savanna elephant. We evaluate highly synchronized GPS tracks from 5 male elephants in Etosha National Park in Namibia by incorporating their dynamic social landscape into an established resource selection model. The fitted model predicts movement patterns based simultaneously on the physical landscape (e.g. repeated visitation of waterholes) and the social landscape (e.g. avoidance of a dominant male). Combining the fitted models for multiple focal individuals produces landscape-dependent social networks that vary over space (e.g. with distance from a waterhole) and time (e.g. as the seasons change). The networks, especially around waterholes, are consistent with dominance patterns determined from previous behavioral studies. Models that combine physical landscape and social effects, based on remote tracking, can augment traditional methods for determining social structure from intensive behavioral observations. More broadly, these models will be essential to effective, in-situ conservation and management of wide-ranging social species in the face of anthropogenic disruptions to their physical surroundings and social connections.
Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation
Authors: Alshammari Maytha , He Jing , Wriggers Willy
Published: November 2024

Motivation

This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results

We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 to 0.64), cation diffusion facilitator YiiP (TM-score increased from 0.76 to 0.83), and Sulfolobus islandicus pilus (TM-score increased from 0.77 to 0.85). We explored the effect of three different mode ranges (modes 1–9, 7–9, and 1–12), masked or box-cropped density maps, numerical optimization methods, and two similarity measures (Pearson correlation and inner product). The best results were achieved for the widest mode range (modes 1–12), masked maps, inner product, and local Powell optimization. These optimal parameters were implemented in the flexible fitting utility elforge.py in version 1.4 of our Python-based ModeHunter package.

Availability and implementation

https://modehunter.biomachina.org.
Tiberius: end-to-end deep learning with an HMM for gene prediction
Authors: Gabriel Lars , Becker Felix , Hoff Katharina J , Stanke Mario
Published: November 2024

Motivation

For more than 25 years, learning-based eukaryotic gene predictors were driven by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently, Holst et al. demonstrated with their program Helixer that the accuracy of ab initio eukaryotic gene prediction can be improved by combining deep learning layers with a separate HMM postprocessor.

Results

We present Tiberius, a novel deep learning-based ab initio gene predictor that end-to-end integrates convolutional and long short-term memory layers with a differentiable HMM layer. Tiberius uses a custom gene prediction loss and was trained for prediction in mammalian genomes and evaluated on human and two other genomes. It significantly outperforms existing ab initio methods, achieving F1 scores of 62% at gene level for the human genome, compared to 21% for the next best ab initio method. In de novo mode, Tiberius predicts the exon−intron structure of two out of three human genes without error. Remarkably, even Tiberius’s ab initio accuracy matches that of BRAKER3, which uses RNA-seq data and a protein database. Tiberius’s highly parallelized model is the fastest state-of-the-art gene prediction method, processing the human genome in under 2 hours.

Availability and implementation

https://github.com/Gaius-Augustus/Tiberius
DeepDR: a deep learning library for drug response prediction
Authors: Jiang Zhengxiang , Li Pengyong
Published: November 2024

Accurate drug response prediction is critical to advancing precision medicine and drug discovery. Recent advances in deep learning (DL) have shown promise in predicting drug response; however, the lack of convenient tools to support such modeling limits their widespread application. To address this, we introduce DeepDR, the first DL library specifically developed for drug response prediction. DeepDR simplifies the process by automating drug and cell featurization, model construction, training, and inference, all achievable with brief programming. The library incorporates three types of drug features along with nine drug encoders, four types of cell features along with nine cell encoders, and two fusion modules, enabling the implementation of up to 135 DL models for drug response prediction. We also explored benchmarking performance with DeepDR, and the optimal models are available on a user-friendly visual interface.

Availability and implementation

DeepDR can be installed from PyPI (https://pypi.org/project/deepdr). The source code and experimental data are available on GitHub (https://github.com/user15632/DeepDR).
APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data
Authors: Sousa Bruno , Bessa Maria , de Mendonça Filipa L , Ferreira Pedro G , Moreira Alexandra , Pereira-Castro Isabel
Published: November 2024

APAtizer is a tool designed to analyze alternative polyadenylation events on RNA-sequencing data. The tool handles different file formats, including BAM, htseq, and DaPars bedGraph files. It provides a user-friendly interface that allows users to generate informative visualizations, including Volcano plots, heatmaps, and gene lists. These outputs allow the user to retrieve useful biological insights such as the occurrence of polyadenylation events when comparing two biological conditions. In addition, it can perform differential gene expression, gene ontology analysis, visualization of Venn diagram intersections, and correlation analysis.

Availability and implementation

Source code and example case studies for APAtizer are available at https://github.com/GeneRegulationi3S/APAtizer/.
M2ara: unraveling metabolomic drug responses in whole-cell MALDI mass spectrometry bioassays
Authors: Enzlein Thomas , Geisel Alexander , Hopf Carsten , Schmidt Stefan
Published: November 2024

Fast computational evaluation and classification of concentration responses for hundreds of metabolites represented by their mass-to-charge (m/z) ratios is indispensable for unraveling complex metabolomic drug actions in label-free, whole-cell Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI MS) bioassays. In particular, the identification of novel pharmacodynamic biomarkers to determine target engagement, potency, and potential polypharmacology of drug-like compounds in high-throughput applications requires robust data interpretation pipelines. Given the large number of mass features in cell-based MALDI MS bioassays, reliable identification of true biological response patterns and their differentiation from any measurement artefacts that may be present is critical. To facilitate the exploration of metabolomic responses in complex MALDI MS datasets, we present a novel software tool, M2ara. Implemented as a user-friendly R-based shiny application, it enables rapid evaluation of Molecular High Content Screening (MHCS) assay data. Furthermore, we introduce the concept of Curve Response Score (CRS) and CRS fingerprints to enable rapid visual inspection and ranking of mass features. In addition, these CRS fingerprints allow direct comparison of cellular effects among different compounds. Beyond cellular assays, our computational framework can also be applied to MALDI MS-based (cell-free) biochemical assays in general.

Availability and implementation

The software tool, code, and examples are available at https://github.com/CeMOS-Mannheim/M2ara and https://dx.doi.org/10.6084/m9.figshare.25736541.