bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leukaemia inhibitory factor modulates the differentiation of granulosa cells during sheep in vitro preantral to antral follicle development and improves oocyte meiotic competence
Authors: Cadoret V , Jarrier-Gaillard P , Papillier P , Monniaux D , Guérif F , Dalbies-Tran R 
Published: August 2021

Abstract
In vitro follicle development from cryopreserved ovarian tissue could become an invaluable assisted reproduction technology for women with early ovarian failure. The challenge lies in producing, from small follicles present in the ovarian cortex, high-quality mature oocytes able to sustain embryo development. In vivo, an optimal combination of hormones and other factors coordinates the development of follicles and their enclosed oocyte. We have investigated the effect of the leukaemia inhibitory factor (LIF) cytokine, alone or in combination with FSH, on sheep in vitro follicle development from the preantral stage onwards. LIF did not alter follicle growth or antrum formation, but it modulated the differentiation of granulosa cells, as revealed by decreased production of anti-Müllerian hormone and abolished FSH-induced stimulation of oestradiol secretion. This modulatory role was also reflected in the abundance of mRNA from 35 genes, analysed by reverse-transcription coupled to microfluidic quantitative PCR. LIF stimulated or at least maintained the expression of genes involved in the dialogue between the oocyte and granulosa cells, through gap junctions (GJA4 encoding connexin 37) or paracrine signalling (Bone morphogenetic protein 15, KIT ligand and their receptors). Finally, the presence of both LIF and FSH during follicle growth strongly improved oocyte meiotic competence: most oocytes (56%) underwent subsequent nuclear maturation, a significant increase compared with their counterparts from follicles of similar size (550–900 µm) cultured with FSH only (28%) or developed in vivo (9%). Their ability to sustain embryo development remains to be evaluated. Combined supplementation with FSH and LIF certainly merits investigation with human follicles.
Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation
Authors: Sklias Athena , Halaburkova Andrea , Vanzan Ludovica , Jimenez Nora Fernandez , Cuenin Cyrille , Bouaoun Liacine , Cahais Vincent , Ythier Victor , Sallé Aurélie , Renard Claire , Durand Geoffroy , Le Calvez-Kelm Florence , Khoueiry Rita , Murr Rabih , Herceg Zdenko 
Published: August 2021

Abstract
Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins
Authors: Zhao Weihao , Zhang Shang , Zhu Yumin , Xi Xiaochen , Bao Pengfei , Ma Ziyuan , Kapral Thomas H , Chen Shuyuan , Zagrovic Bojan , Yang Yucheng T , Lu Zhi John 
Published: August 2021

AbstractRNA-binding proteins (RBPs) play key roles in post-transcriptional regulation. Accurate identification of RBP binding sites in multiple cell lines and tissue types from diverse species is a fundamental endeavor towards understanding the regulatory mechanisms of RBPs under both physiological and pathological conditions. Our POSTAR annotation processes make use of publicly available large-scale CLIP-seq datasets and external functional genomic annotations to generate a comprehensive map of RBP binding sites and their association with other regulatory events as well as functional variants. Here, we present POSTAR3, an updated database with improvements in data collection, annotation infrastructure, and analysis that support the annotation of post-transcriptional regulation in multiple species including: we made a comprehensive update on the CLIP-seq and Ribo-seq datasets which cover more biological conditions, technologies, and species; we added RNA secondary structure profiling for RBP binding sites; we provided miRNA-mediated degradation events validated by degradome-seq; we included RBP binding sites at circRNA junction regions; we expanded the annotation of RBP binding sites, particularly using updated genomic variants and mutations associated with diseases. POSTAR3 is freely available at http://postar.ncrnalab.org.
3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues
Authors: Cui Ya , Peng Fanglue , Wang Dan , Li Yumei , Li Jason Sheng , Li Lei , Li Wei 
Published: August 2021

Abstract
Genome-wide association studies (GWAS) have identified thousands of non-coding single-nucleotide polymorphisms (SNPs) associated with human traits and diseases. However, functional interpretation of these SNPs remains a significant challenge. Our recent study established the concept of 3′ untranslated region (3′UTR) alternative polyadenylation (APA) quantitative trait loci (3′aQTLs), which can be used to interpret ∼16.1% of GWAS SNPs and are distinct from gene expression QTLs and splicing QTLs. Despite the growing interest in 3′aQTLs, there is no comprehensive database for users to search and visualize them across human normal tissues. In the 3′aQTL-atlas (https://wlcb.oit.uci.edu/3aQTLatlas), we provide a comprehensive list of 3′aQTLs containing ∼1.49 million SNPs associated with APA of target genes, based on 15,201 RNA-seq samples across 49 human Genotype-Tissue Expression (GTEx v8) tissues isolated from 838 individuals. The 3′aQTL-atlas provides a ∼2-fold increase in sample size compared with our published study. It also includes 3′aQTL searches by Gene/SNP across tissues, a 3′aQTL genome browser, 3′aQTL boxplots, and GWAS-3′aQTL colocalization event visualization. The 3′aQTL-atlas aims to establish APA as an emerging molecular phenotype to explain a large fraction of GWAS risk SNPs, leading to significant novel insights into the genetic basis of APA and APA-linked susceptibility genes in human traits and diseases.
Factors associated with sickness absence in a large NHS Trust
Authors: Grime P , McElvenny D M , Madan I 
Published: August 2021

Abstract

Background
Sickness absence rates vary widely across a large acute NHS Trust, with the highest rates in some of the largest directorates.

Aims
This study was aimed to identify factors associated with sickness absence in teams and to inform interventions to improve staff health and well-being.

Methods
Using 2018 data from the electronic staff record and NHS Staff Survey, we examined variables associated with cost centre sickness absence rates, perceived abuse and staff engagement scores using multivariable linear regression.

Results
Data were available for 9362/15 423 (61%) of staff. Cost centre sickness absence was significantly positively associated with predominance of nursing and midwifery staff (β = 0.28 [0.012–0.55]) and significantly inversely associated with predominance of medical and dental staff (β = −0.94 [−1.2 to −0.65]) and proportion white (β = −1.11 [−1.9 to −0.37]). Cost centre sickness absence was not significantly associated with staff engagement, reported abuse, age or higher headcount. Cost centre staff engagement was significantly positively associated with proportion white (β = 0.98 [0.42–1.6]). Reported abuse by managers (β = −13 [−22 to −4.2]) and by colleagues (β = −24 [−35 to −12]) was significantly inversely associated with proportion white. Reported abuse by colleagues was significantly associated with predominance of medical and dental (β = 7.6 [2.3–13]) and nursing and midwifery staff (β = 9.1 [4.4–14]).

Conclusions
These observed associations of sickness absence, staff engagement and perceived abuse with job mix and ethnicity should be further explored. Individual or team-level data, rather than cost centre-level data, might more meaningfully elucidate why sickness absence rates vary between groups of staff.
The Soul of the American University Revisited
Authors: Marsden George M. 
Published: August 2021

Abstract
The Soul of the American University Revisited traces the role of Protestantism in shaping American higher education from the founding of Harvard in the 1630s to the present. It offers a critical analysis of the changing ways in which Protestantism intersected with collegiate life, intellectual inquiry, and broader cultural developments. In accounts that have been edited and somewhat abridged for this second edition, it looks at pace-setting colleges and universities as they coped with modern society, post-Darwinian science, new secular philosophies, and increasing diversity in American life. Until the mid-twentieth century most leading American schools remained nominally Protestant, but their Protestantism was typically of a liberal variety that emphasized the broad ethical ideals of the Western and Judeo-Christian heritage. After the attacks in the 1960s on the “WASP” privilege, the vestiges of that establishment in higher education were soon largely dismantled. By the late twentieth century exclusive secular viewpoints were often considered the normative standard in higher education. Originally published in 1994 as The Soul of the American University, this new edition carries the story into the twenty-first-century culture. In the disarray and diversity of the intellectual life of this arguably “postsecular” age there is increasing room in the academy for varieties of intellectually responsible religious viewpoints. Indeed, as a concluding chapter recounts, more traditionalist Christian scholars and institutions, Protestant as well as Catholic, have developed substantially in recent decades.
The New Queen of the Sciences and the New Republic
Authors: Marsden George M. 
Published: August 2021

Abstract
In the eighteenth century Christian higher education faced several new challenges. Most notable is the Enlightenment. American schools generally incorporated moderate Enlightenment ideas into their teaching, especially the new moral philosophy growing out of the tradition of John Locke and Scottish Common Sense Philosophy. The religious dimensions of higher education were intensified by the Great Awakening and the associated New Light Movement. Yale College, founded in 1701, became by mid-century a leading New Light school. So was the College of New Jersey (Princeton), founded in 1746. A number of other new colleges had New Light connections. Thomas Clap at Yale, Jonathan Edwards, and Ezra Stiles each illustrate efforts to relate the new thought of the era to Christian teachings. The era of the American Revolution brought a new synthesis of Christian concerns and concerns for the right ordering of society, as best illustrated by the work of President John Witherspoon at Princeton.
Liberal Protestantism at Michigan
Authors: Marsden George M. 
Published: August 2021

Abstract
In the later nineteenth century the University of Michigan under President James Angell was often seen as a model of a modern university friendly to Christianity. Early in his tenure the university was accused of discrimination in preferring Protestant Christianity to Roman Catholicism, Judaism, or atheism. Angell responded to the satisfaction of a state investigating committee that while the school was Christian, it was not sectarian in the sense of teaching any one theology in preference to another. The emphasis was on building moral character rather than relating theology directly to other learning. Throughout the rest of the century this was the prevailing resolution of the tension between the Christian heritage and modern scientific research ideals. Characteristic was a volume, Religious Thought at the University of Michigan (1893), published by the Student Christian Association at Michigan. It represented a broad Christian ethical emphasis and included a presentation by John Dewey.
Outsiders
Authors: Marsden George M. 
Published: August 2021

Abstract
Groups were underrepresented in the mainstream either because they chose a separate identity or were discriminated against, or both. Roman Catholics were the largest outsider religious group, mainly by choice. A major Catholic Foundation at the University of Illinois drew rebuke from authorities for undercutting Catholic schools. Among Protestants, many supported smaller denominational colleges. Fundamentalists mostly chose their own institutions. Women remained in ambiguous positions; they were included in state universities, but not in the Ivy League, and often had their own colleges. African Americans were strongly discriminated against. Howard was the only true African American university. Christianity played a considerable role at most African American colleges and universities. Jews founded Yeshiva College and Brandeis University, but most were eager to assimilate into mainstream American schools, where they faced quotas; anti-Semitism also played a role in faculty hiring, especially in the humanities.
Epilogue
Authors: Marsden George M. 
Published: August 2021

Abstract
In the mid-twentieth century leading scholars such as Reinhold Niebuhr or David Riesman wrote off conservative evangelical education as fading. William McLoughlin also saw the new revival movements as ephemeral. Billy Graham and Carl Henry had ambitions to start a major university around 1960 but did not have the resources. Wheaton College in Illinois, the leading ex-fundamentalist college, began to rise academically despite the anti-intellectualism of its tradition. Calvin College had been an ideologically isolated Reformed school but by the 1960s had produced leading Christian philosophers. Intervarsity Christian Fellowship helped raise consciousness regarding strong scholarship, and by 2000 the Council for Christian Colleges and Universities had grown to over one hundred schools with well-trained faculties. Like-minded Christian scholars founded their own academic societies. Baylor University became an intentionally Christian research university. Evangelical Protestant and Catholic scholars often cooperated. Despite many challenges, distinctly Christian scholars could hold their own in twenty-first-century academia.
The Concentrated and Hybrid Models of Judicial Review
Authors: Calabresi Steven Gow 
Published: August 2021

Abstract
This chapter examines the two models of judicial review that exist in the civil law countries: the Concentrated Model and the Hybrid Model. The Concentrated Model of judicial review is built around the idea that what judges do when they enforce constitutions and Bills of Rights is inherently political and nonjudicial. For this reason, a separate Constitutional Court is created outside the ordinary judicial system, and is the only entity with the power of judicial review. The power of judicial review of Constitutional Courts is conceived as being a power to make the law and not simply to interpret it. Hence, a Constitutional Court in a civil law country is, essentially, a fourth branch of the government. Meanwhile, many countries, especially in Latin America, have developed distinct Hybrid Models of judicial review. The country of Brazil can be considered as the archetypal Hybrid Model. Brazil’s Hybrid Model of judicial review consists of a very complex system full of institutional mechanisms that are meant to enforce the Constitution. The Brazilian system combines features from both the Concentrated and the Diffuse Models hence the term Hybrid Model.
Mexico
Authors: Calabresi Steven Gow 
Published: August 2021

Abstract
This chapter explores the origins and growth of Mexican judicial review. Mexico borrowed the idea of a Supreme Court with the power of a Constitutional Court from Brazil in 1994. In addition, the rise of independent judicial review, after 2000, coincided with the rise of different parties controlling the presidency, the two houses of Congress, and the state governorships and legislatures. This created a need in Mexico for a constitutional umpire, which was filled by the emergence of independent judicial review. It also created a political environment in which governmental power was checked and balanced enough to leave political space for an active Supreme Court. There is, in addition, a rights from wrongs element to the emergence of Mexican judicial review after the end of the often-brutal PRI dictatorship.
Indonesia
Authors: Calabresi Steven Gow 
Published: August 2021

Abstract
This chapter highlights the origins and growth of Indonesian judicial review. Indonesia today is a constitutional democracy that has attained surprising success in eliminating hyper-presidentialism by implementing important checks and balances on presidential power; by separating executive, legislative, and judicial power; and by attaining rapidly an astonishing amount of decentralization since 1998. That degree of checks and balances and of decentralization has undoubtedly made Indonesians much freer than they were under President Suharto’s dictatorship. The Indonesian Constitutional Court seems to function well and enjoys the confidence of the people. Looked at from an American perspective, however, Indonesia is a constitutional democracy, which does not yet fully protect freedom of expression, freedom of religion, or economic freedoms to the extent that those freedoms are protected by the U.S. Supreme Court. Indonesia’s Bill of Rights and its system of judicial review originated for rights from wrongs reasons, because of borrowing, and because power is sufficiently divided in Indonesia, as a result of the separation of powers and federalism, so that there is political space in which the Supreme Court can operate.
The European Union and the Council of Europe
Authors: Calabresi Steven Gow 
Published: August 2021

Abstract
This chapter discusses two final supranational mixed civil law and common law jurisdictions, which are comparable in size, population, and GDP to the United States of America, to India, to the former British Empire, and to Brazil. These jurisdictions had two common law members prior to Brexit becoming a reality in 2020: the United Kingdom and Ireland. These two supranational jurisdictions are, of course, the European Union (EU) and the Council of Europe. The origins and growth of the power of judicial review in the EU is a very complicated tale of federalism umpiring giving rise to judicial power. The European Court of Justice (ECJ) successfully asserted its power between 1963 and 1989 to hear individual rights claims, as it enlisted the member courts of the EU over that period of time in the project of enforcing EU law as being supreme over the later-in-time law of the EU nation-states. The ECJ persuaded the national courts of the EU’s member states that (1) EU law had a direct effect in the member nations, and (2) that EU law was supreme over the post-1958 laws enacted by the EU member nations. The chapter then explains the origins and growth in power of the Council of Europe’s European Court of Human Rights (ECHR). This enterprise began for rights from wrongs reasons and has grown in power for supranational umpiring reasons.
Business Ethics for Better Behavior
Authors: Brennan Jason , English William , Hasnas John , Jaworski Peter 
Published: August 2021

Abstract
Business Ethics for Better Behavior concisely answers the three most pressing ethical questions business professionals face: 1. What makes business practices right or wrong? 2. Why do normal, decent businesspeople of goodwill sometimes do the wrong thing? 3. How can we use the answer to these questions to get ourselves, our coworkers, our bosses, and our employees to behave better? Bad behavior in business rarely results from bad will. Most people mean well much of the time. But most of us are vulnerable. We all fall into moral traps, usually without even noticing. Business Ethics for Better Behavior teaches business professionals, students, and other readers how to become aware of those traps, how to avoid them, and how to dig their way out if they fall in. It integrates the best work in psychology, economics, management theory, and normative philosophy into a simple action plan for ensuring the best ethical performance at all levels of business practice. This is a book anyone in business, from an entry-level employee to CEO, can use.
The Effect of Incentives
Authors: Brennan Jason , English William , Hasnas John , Jaworski Peter 
Published: August 2021

Abstract
Even if cooperating will make everyone better off, cooperation won’t happen if people lack certain kinds of knowledge and motivation. In group settings, individuals will often have incentives to promote their own interest at the expense of the group, either by exploiting others or by failing to contribute to public goods. There are two ways to overcome these “collective action” problems: (1) the incentives that individuals face can be changed so that individual and group interest no longer conflict, and/or (2) group members can embrace norms that enable them to exercise self-restraint and forego opportunities to get ahead at the expense of others. The rule of law, property rights, and proper firm structure can help overcome collective action problems. However, these same structures can also create new opportunities for rent seeking.
Sacrifice in Service to Truth
Authors: Bellon Richard 
Published: August 2021

Abstract
Victorian men of science struggled to address a central question of nineteenth-century British thought: how do fallible human beings recognize truth? Their solution, embodied within the principles establishing the British Association for the Advancement of Science, focused on a stable set of selfless epistemic virtues—patience, humility, diligence, disinterest, self-control—that provided moral stability amid the relentless advance of new and revised theories of physical reality. But if well-founded ideas flow from virtuous practices, did it not follow that dangerously unsound ideas stem from vice? For this reason, a widely shared commitment to virtuous conduct meant that intellectual disagreements often degenerated into accusations of immoral behavior. This essay explores the complicated role of epistemic virtue in Victorian science by examining three towering products of the University of Cambridge: John Herschel, Adam Sedgwick, and William Whewell.