bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons
Authors: Li Hao , Ding Zhan , Fang Zhuo-Ya , Long Ni , Ang Hao-Yang , Zhang Yu , Fan Yu-Jie , Xu Yong-Zhen 
Published: March 2024

Abstract
Alternative splicing (AS) generates multiple RNA isoforms and increases the complexities of transcriptomes and proteomes. However, it remains unclear how RNA structures contribute to AS regulation. Here, we systematically search transcriptomes for secondary structures with concealed branch sites (BSs) in the alternatively spliced introns and predict thousands of them from six organisms, of which many are evolutionarily conserved. Intriguingly, a highly conserved stem–loop structure with concealed BSs is found in animal SF3B3 genes and colocalizes with a downstream poison exon (PE). Destabilization of this structure allows increased usage of the BSs and results in enhanced PE inclusion in human and Drosophila cells, leading to decreased expression of SF3B3. This structure is experimentally validated using an in-cell SHAPE-MaP assay. Through RNA interference screens of 28 RNA-binding proteins, we find that this stem–loop structure is sensitive to U2 factors. Furthermore, we find that SF3B3 also facilitates DNA repair and protects genome stability by enhancing interaction between ERCC6/CSB and arrested RNA polymerase II. Importantly, both Drosophila and human cells with the secondary structure mutated by genome editing exhibit altered DNA repair in vivo. This study provides a novel and common mechanism for AS regulation of PEs and reveals a physiological function of SF3B3 in DNA repair.
Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori
Authors: Åberg Anna , Gideonsson Pär , Bhat Abhayprasad , Ghosh Prachetash , Arnqvist Anna 
Published: March 2024

Abstract
Adaptation to variations in pH is crucial for the ability of Helicobacter pylori to persist in the human stomach. The acid responsive two-component system ArsRS, constitutes the global regulon that responds to acidic conditions, but molecular details of how transcription is affected by the ArsR response regulator remains poorly understood. Using a combination of DNA-binding studies, in vitro transcription assays, and H. pylori mutants, we demonstrate that phosphorylated ArsR (ArsR-P) forms an active protein complex that binds DNA with high specificity in order to affect transcription. Our data showed that DNA topology is key for DNA binding. We found that AT-rich DNA sequences direct ArsR-P to specific sites and that DNA-bending proteins are important for the effect of ArsR-P on transcription regulation. The repression of sabA transcription is mediated by ArsR-P with the support of Hup and is affected by simple sequence repeats located upstream of the sabA promoter. Here stochastic events clearly contribute to the fine-tuning of pH-dependent gene regulation. Our results reveal important molecular aspects for how ArsR-P acts to repress transcription in response to acidic conditions. Such transcriptional control likely mediates shifts in bacterial positioning in the gastric mucus layer.
Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein
Authors: Rodríguez-Vargas Anthony , Collins Kathleen 
Published: March 2024

Abstract
Eukaryotic retrotransposons encode a reverse transcriptase that binds RNA to template DNA synthesis. The ancestral non-long terminal repeat (non-LTR) retrotransposons encode a protein that performs target-primed reverse transcription (TPRT), in which the nicked genomic target site initiates complementary DNA (cDNA) synthesis directly into the genome. The best understood model system for biochemical studies of TPRT is the R2 protein from the silk moth Bombyx mori. The R2 protein selectively binds the 3′ untranslated region of its encoding RNA as template for DNA insertion to its target site in 28S ribosomal DNA. Here, binding and TPRT assays define RNA contributions to RNA–protein interaction, template use for TPRT and the fidelity of template positioning for TPRT cDNA synthesis. We quantify both sequence and structure contributions to protein–RNA interaction. RNA determinants of binding affinity overlap but are not equivalent to RNA features required for TPRT and its fidelity of template positioning for full-length TPRT cDNA synthesis. Additionally, we show that a previously implicated RNA-binding protein surface of R2 protein makes RNA binding affinity dependent on the presence of two stem-loops. Our findings inform evolutionary relationships across R2 retrotransposon RNAs and are a step toward understanding the mechanism and template specificity of non-LTR retrotransposon mobility.
Clinical and Demographic Factors Associated With Kaposi Sarcoma–Associated Herpesvirus Shedding in Saliva or Cervical Secretions in a Cohort of Tanzanian Women
Authors: Mertelsmann Anna M , Mukerebe Crispin , Miyaye Donald , Shigella Peter , Mhango Loyce , Lutonja Peter , Corstjens Paul L A M , de Dood Claudia , van Dam Govert J , Colombe Soledad , Maganga Jane K , Aristide Christine , Kalluvya Samuel E , Ward Maureen M , Cordeiro Alexandra A , Lee Myung Hee , Changalucha John M , Downs Jennifer A 
Published: March 2024

AbstractBackgroundReasons for the high prevalence of Kaposi sarcoma–associated herpesvirus (KSHV) in sub-Saharan Africa, and risk factors leading to viral reactivation and shedding, remain largely undefined. Preliminary studies have suggested that schistosome infection, which has been associated with impaired viral control, is associated with KSHV. In this study we sought to determine the relationship between active Schistosoma mansoni or Schistosoma haematobium infection and KSHV shedding.MethodsWe quantified KSHV DNA in saliva and cervical swabs from 2 cohorts of women living in northwestern Tanzanian communities endemic for S mansoni or S haematobium by real-time polymerase chain reaction. χ2 and Fisher exact tests were used to determine differences in clinical and demographic factors between those who were and were not shedding KSHV.ResultsAmong 139 total women, 44.6% were KSHV seropositive. Six percent of those with S mansoni and 17.1% of those with S haematobium were actively shedding KSHV in saliva and none in cervical samples. Women from the S mansoni cohort who were shedding virus reported infertility more frequently (80% vs 19.5%, P = .009). There was no difference in frequency of KSHV salivary shedding between schistosome-infected and -uninfected women.ConclusionsIn an area with high KSHV seroprevalence and endemic schistosome infections, we provide the first report with data demonstrating no association between schistosome infection and salivary or cervical herpesvirus shedding. KSHV salivary shedding was associated with infertility, a known effect of another herpesvirus, human herpesvirus 6.
Shared Decision-Making for Partial Oral Antibiotic Treatment of Infective Endocarditis: A Case Series
Authors: El-Dalati Sami , Castillo Marice Ruiz Conejo , Strnad Luke , Reda Hassan , London Tessa , Sekela Michael , Stoner Bobbi Jo 
Published: March 2024

Abstract
Although literature has demonstrated the noninferiority of oral antibiotics in the treatment of infectious endocarditis, widespread adoption of this practice has yet to occur in the United States. We report on 32 patients with infectious endocarditis treated by a multidisciplinary endocarditis team and a standardized approach to partial oral antibiotic therapy with a high rate of clinical success.
Edith Landmann-Kalischer (1877–1951)
Authors: Dahlstrom Daniel O. 
Published: March 2024

Abstract
This chapter aims to begin remedying the lamentable neglect of the philosophical contributions of Edith Landmann-Kalischer (1877–1951). The first part introduces readers to her life and major works before 1925. The second part reviews central insights in three of those works: her attempt to demonstrate “the cognitive value of aesthetic judgments” by paralleling them with sensory judgments, her argument for “artistic truth” consisting in the representation of the life of the mind, and her account of “the essence of the poet” as the true educator of a people, thanks to verses that, through an inspired and harmonious marriage of form and content, fashion the ideal of a complete humanity. The final part chronicles her work during the last twenty-five years of her life, including her responses to the tragic events in Germany as the Jewish “evangelist” for Stefan George, deemed by some the prophet of the National Socialist revolution.
The Emergence of a Phenomenology of Spirit: 1910–1922
Authors: Tolley Clinton 
Published: March 2024

Abstract
This chapter charts out the contributions by Margarete Calinich, Else Voigtländer, Edith Stein, and Gerda Walther to the transformation of “early phenomenology” from a philosophy of “consciousness” and to a philosophy of “spirit.” The first two sections focus on how Calinich and Voigtländer broadened phenomenology to incorporate aesthetic and affective dimensions through their investigations of various forms of feeling. The later sections trace the path from the phenomenology of feeling to the emergence, in Stein and Walther, of a phenomenology of intersubjectivity and sociality. This was achieved via reflection on the nature and function of “Einfühlung” (“feeling into,” often translated as “empathy”), which was crucial for the foundations of “objective spirit” within phenomenology. The chapter concludes with remarks on the ways in which Stein and Walther expanded phenomenology in the early 1920s to include explicit reflection on the relation between consciousness and “absolute” spirit.
Spinozism around 1800 and Beyond
Authors: Yonover Jason Maurice 
Published: March 2024

Abstract
The main purpose of this chapter is to show that the engagement with Spinozism among modern women philosophers in the German tradition is as strong as in the case of canonical figures. More specifically, the chapter explores the apparent significance of the ethical, liberatory dimension of Spinoza’s thought among several women thinkers in the long nineteenth century. It begins with brief discussions of Elise Reimarus and Charlotte von Stein. It then proceeds to more in-depth treatments of Caroline Michaelis-Böhmer-Schlegel-Schelling and Karoline von Günderrode, in both cases stressing not only that we may learn about each in drawing out the link to Spinoza, but likewise that we may learn about Spinoza in bringing him into dialogue with each (regarding, for instance, the importance of others for self-understanding, as well as the metaphysical and ethical status of death, respectively). The chapter concludes with shorter treatments of several later nineteenth century (or earlier twentieth century) philosophers: Lou Salomé, Resa von Schirnhofer, Anna Tumarkin, and especially Elisabeth Schmitt.
Two Female Pessimists
Authors: Beiser Frederick C. 
Published: March 2024

Abstract
This chapter treats two female philosophers who were active in the pessimism controversy in late nineteenth-century Germany: Agnes Taubert (1844–1877) and Olga Plümacher, née Hünerwadel (1839–1895). In this controversy Taubert and Plümacher defended the pessimism of Eduard von Hartmann, which he had developed in his Philosophie des Unbewussten (1869). They defended Hartmann’s contentions that the value of life should be measured in the quantitative terms of pleasure and pain; their pessimism was founded on their claim that suffering in life far outweighs its pleasures. Their main contribution to the controversy was extending the topics it covered; they maintained that the controversy should consider such topics as love, work, beauty, and nature. Taubert was especially important as the historian of the controversy.
The American Reception of German Women Philosophers in the Nineteenth Century
Authors: Rogers Dorothy 
Published: March 2024

Abstract
This chapter explores the impact of women in German philosophical thought on the development of women’s philosophy in the United States. Margaret Fuller introduced German romantic thinkers to the American reading public in the 1840s. This was followed by explorations of then-new developments in pedagogical theories between German and American women, largely in a process of mutual exchange and adaptation in the last half of the century. Concurrently, German progressives influenced and were influenced by the American feminist movement, also in the second half of the century. In the last decades of the century, a number of American women explored German philosophy, idealist thought in particular. This development helped shape academic philosophy, particularly among women, in the early twentieth century. The century closed with an increasing number of collaborations among women, for political rights, social concerns, and peace.
Karoline von Günderrode (1780–1806)
Authors: Ezekiel Anna 
Published: March 2024

Abstract
This chapter considers philosophical contributions by Karoline von Günderrode (1780–1806) to German Idealist and Romantic traditions. Günderrode’s work adds to debates regarding free will, the nature of the self and consciousness, what happens to us after we die, the human vocation, the relationship between the self and nature and between these and the Absolute or divine, gender roles, politics, and the pursuit of virtue and beauty. Her writings provide a rich and relatively unexplored perspective on these topics. After a biography and overview of Günderrode’s work, the chapter summarizes key areas of Günderrode’s thought. These include Günderrode’s metaphysics, accounts of love, death, consciousness and identity, political theory (especially regarding revolution), thought on gender, and nascent ethics and aesthetics. The last section considers how Günderrode might have influenced nineteenth-century thinkers including Clemens Brentano, Georg Friedrich Creuzer, and Bettina Brentano von Arnim—and, through the latter, the Young Hegelians and American transcendentalism.
Worker Health in Modern Agriculture
Authors: Aso Michitake 
Published: March 2024

Abstract
From 1800 to the present, agriculture has grown increasingly reliant on chemicals, machines, and capital. Adopting the lens of structural vulnerability, this chapter gives an overview of the health risks, from malaria infection to pesticides exposure, that farm workers face in modern agriculture. Drawing on primary sources and secondary literature on worker health ranging from Southeast Asian plantations to California family farms, the chapter argues that as agricultural labor has become a more specialized job it has also become a more hazardous occupation. Farm worker vulnerability to occupational hazards has depended on many factors, including race, class, gender, nationality, and environment. Worker activism and at times government regulation have mitigated some of the greatest dangers to worker health, while agricultural medicine has played an ambiguous role as it has mostly served the needs of capital. Climate change will most likely exacerbate the insecurities inherent in agricultural labor.
Making Sense of Land
Authors: Uekötter Frank 
Published: March 2024

Abstract
The chapter argues that the history of agricultural land requires a multitude of perspectives. It begins with an outline of Indigenous soil knowledge, knowledge in settler societies, and the crucial differences to modern expertise. The chapter stresses that science-based understandings provided a clearer idea of elements of soil fertility while at the same time running a risk of a reductionist approach. This was particularly significant for agrochemistry, which viewed soils as little more than a store of nutrients. Organic farming was an outgrowth of controversies over an exceedingly chemical approach to soil fertility. The chapter also discusses the rise of the concept of land ownership, the rise and fall of land reform in Western societies, and the persistence of land reform in the Global South. In sum, the multiple trends that define the modern history of lands imply tensions and contradictions that will shape agricultural challenges in the future.
Potatoes
Authors: Shepherd Christopher 
Published: March 2024

Abstract
This chapter explores the most prolific tuber, the potato, from its early history to the present. The discussion moves from the potato in its original pre-Columbian Andean setting, through the Spanish colonial and republican periods in Peru, and then to Europe before returning to modern-day Peru. It looks at the potato’s domestication and its attributes, and its place in state-making and state expansion, in warfare and peasant resistance, in demographic growth and industrialization, in scientific agronomy and Third World development, and, finally, in the national and cultural politics of Indigenous agricultural practice and agrobiodiversity conservation. Arguing that the potato was never a couch potato, but rather a most ambitious and enthusiastic little tubérculo, the chapter addresses the question of how history, social science, and ethnography position and explain the potato’s political, sociocultural, and economic agency over the longue durée.
Cotton
Authors: Robins Jonathan 
Published: March 2024

Abstract
Cotton agriculture emerged independently in at least four places across the tropics. Cotton became a versatile and highly valued fiber for making textiles, spreading across the Old and New Worlds. The American South became the world’s leading exporter of cotton in the nineteenth century, relying on slave labor. Colonial states forced peasants across Africa and Asia to grow cotton in competition with the South during and after the US Civil War, but the United States remained a dominant exporter into the twentieth century. Large-scale irrigation projects brought cotton agriculture to arid regions in Africa, America, and Asia, but the most cotton continued to be rain-fed, grown by small-scale farmers. Mechanization gradually drove small producers out in the United States, but small-scale cotton cultivation remains viable in many parts of the world.
Wet Rice in East Asia
Authors: Bray Francesca 
Published: March 2024

Abstract
In the history of many Asian civilizations, from medieval Angkor to early modern China and modern Japan, wet-rice farming could be considered a “killer app”: once established as the mainstay of the economy, its requirements and affordances structured long-term patterns of social organization and material growth. This chapter analyzes the role of intensive rice farming in shaping “industrious revolutions” in China and Japan. In the East Asian rice economies, rice not only nourished local communities and the state but circulated as the lifeblood of internal and external trading circuits, establishing first China, then Japan as leading players in the global economy. Yet rice farming need not be intensive to perform this linking function, as we learn from the hitherto hidden histories of Asian swidden farmers’ engagement in commodity markets and global trade circuits. The chapter concludes with some thoughts on how Asia’s rice-based histories challenge established paradigms of historical change and future progress.
A History of Livestock and People
Authors: Strom Claire 
Published: March 2024

Abstract
This chapter offers a global overview of the history of livestock. It focuses exclusively on ungulates (hoofed mammals), as the most significant livestock throughout history, and, more specifically, on cattle and hogs as the most important livestock in terms of meat production and global presence. It argues that the animality of livestock was initially a benefit to humans, as animals could feed and reproduce themselves as well as move independently to market. However, with advances in technology and science, these advantages have largely disappeared. By the twenty-first century, the animality of livestock is more of a liability, contributing to environmental and climatic degradation.
Wheat
Authors: Isern Thomas D. 
Published: March 2024

Abstract
Wheat is a cultivar with agency in world history. Gluten as well as other nutritional and agronomic virtues commended early wheats to humankind. Out of its Neolithic origins, wheat achieved a unity with human agriculturalists; was disseminated across Europe, Asia, and North Africa; spread globally as a participant in settler colonialism; established identifiable wheat belts; and was implicated in environmental catastrophes on the order the Dust Bowl of the Great Plains of North America. Established wheat belts such as the Great Plains developed coherent commodity cultures by which production practices were related to the environment. A direct historical relationship tied the wheat culture of the Great Plains to that of the Russian steppe. In the late twentieth century, wheat culture rose to new prominence in Asian nations as a result of the Green Revolution.
Mechanization in Agriculture
Authors: Hurt R. Douglas 
Published: March 2024

Abstract
The mechanization of American agriculture depended on cumulative knowledge, perceived need, and affordability. Inventors and agricultural engineers built on previous knowledge, farmers had specific technological needs that required mechanized implements, and these machines had to be affordable. Environment and geography also influenced the development and adoption of mechanized implements, that is, equipment with moving parts. The dry, level terrain of the Great Plains and Far West proved more satisfactory for mechanization than the humid Midwest. The mechanization of cotton farming in the South remained a difficult problem until the mid-twentieth century. The two most important developments in the mechanization of American agriculture on a national scale are the gasoline tractor and grain harvesting implements. Henry Ford built the first commercially and operationally successful tractor, called the Fordson, and the International Harvester Company improved this implement with the Farmall. Obed Hussy and Cyrus Hall McCormick built the first successful reapers. Combine innovations began with Hiram Moore. Threshing machines and fanning or winnowing mills also contributed to the mechanization of the grain harvest. The mechanization of American agriculture with these implements saved farmers time and labor, enabling the cultivation of more acres and greater productivity. Mechanized implements also contributed to overproduction, the elimination of farm workers, and the consolidation of farms, as well as the loss of farm population.
The Growing Power of Agricultural Science
Authors: Anderson J. L. 
Published: March 2024

Abstract
The story of agricultural science is one of growing power; power to increase production and the enhanced authority of scientists. Eighteenth-century farmers and rural elites were interested in agricultural reforms, paying attention to scientists who articulated theories about chemistry and breeding in an attempt to solve production problems. Those elites established laboratories and experimental farms that were the progenitors of state-sponsored agricultural science. Scientists built educational and research institutions that ultimately provided producers with useful knowledge to boost production. They subsequently fought with other scientists for power and for a place of influence in public life. The scientific solutions they offered often cut both ways, solving old problems even as they created new ones, ranging from environmental degradation to the de-skilling of labor. Furthermore, science was yoked to colonial authority, constructing a landscape of commodity production and the social control required to sustain it. Agricultural science has been commodified and deployed with mixed success in the fight against hunger and poverty, most famously in what became known as the Green Revolution. Scientists’ success in developing solutions to the problems of agricultural production, despite some notable shortcomings, has given them unprecedented power over people and the land.