bluuebunny/crossref_metadata_2025_split huggingface dataset:
5-Hydroxymethylcytosine in cord blood and associations of DNA methylation with sex in newborns
Authors: Solomon Olivia , Macisaac Julia L , Tindula Gwen , Kobor Michael S , Eskenazi Brenda , Holland Nina 
Published: August 2019

Abstract
DNA methylation has been widely studied for associations with exposures and health outcomes. Both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are epigenetic marks that may function differently to impact gene expression; however, the most commonly used technology to assess methylation for population studies in blood use are the Illumina 450K and EPIC BeadChips, for which the traditional bisulfite conversion does not differentiate 5mC and 5hmC marks. We used a modified protocol originally developed by Stewart et al. to analyse oxidative bisulfite-converted and conventional bisulfite-converted DNA for the same subject in parallel by the EPIC chip, allowing us to isolate the two measures. We measured 5mC and 5hmC in cord blood of 41 newborn participants of the Center for Health Assessment of Mothers and Children of Salinas (CHAMACOS) birth cohort and investigated differential methylation of 5mC + 5hmC, isolated 5mC and isolated 5hmC with sex at birth as an example of a biological variable previously associated with DNA methylation. Results showed low levels of 5hmC throughout the epigenome in the cord blood samples in comparison to 5mC. The concordance of autosomal hits between 5mC + 5hmC and exclusive 5mC analyses were low (25%); however, overlap was larger with increased effect size difference. There were 43 autosomal cytosine nucleotide followed by a guanine nucleotide (CpG) sites where 5hmC was associated with sex, 21 of which were unique to 5hmC after adjustment for cell composition. 5hmC only accounts for a small portion of overall methylation in cord blood; however, it has the potential to impact interpretation of combined 5hmC + 5mC studies in cord blood, especially given that effect sizes of differential methylation analyses are often small. Several significant CpG sites were unique to 5hmC, suggesting some functions distinct from 5mC. More studies of genome-wide 5hmC in children are warranted.
Machine learning-based chemical binding similarity using evolutionary relationships of target genes
Authors: Park Keunwan , Ko Young-Joon , Durai Prasannavenkatesh , Pan Cheol-Ho 
Published: August 2019

Abstract
Chemical similarity searching is a basic research tool that can be used to find small molecules which are similar in shape to known active molecules. Despite its popularity, the retrieval of local molecular features that are critical to functional activity related to target binding often fails. To overcome this limitation, we developed a novel machine learning-based chemical binding similarity score by using various evolutionary relationships of binding targets. The chemical similarity was defined by the probability of chemical compounds binding to identical targets. Comprehensive and heterogeneous multiple target-binding chemical data were integrated into a paired data format and processed using multiple classification similarity-learning models with various levels of target evolutionary information. Encoding evolutionary information to chemical compounds through their binding targets substantially expanded available chemical-target interaction data and significantly improved model performance. The output probability of our integrated model, referred to as ensemble evolutionary chemical binding similarity (ensECBS), was effective for finding hidden chemical relationships. The developed method can serve as a novel chemical similarity tool that uses evolutionarily conserved target binding information.
Fail-safe genetic codes designed to intrinsically contain engineered organisms
Authors: Calles Jonathan , Justice Isaac , Brinkley Detravious , Garcia Alexa , Endy Drew 
Published: August 2019

AbstractOne challenge in engineering organisms is taking responsibility for their behavior over many generations. Spontaneous mutations arising before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such that point mutations in protein-coding sequences are selected against. Synthetic genetic systems so-encoded should fail more safely in response to most spontaneous mutations. We designed fail-safe codes and simulated their expected effects on the evolution of so-encoded proteins. We predict fail-safe codes supporting expression of 20 or 15 amino acids could slow protein evolution to ∼30% or 0% the rate of standard-encoded proteins, respectively. We also designed quadruplet-codon codes that should ensure all single point mutations in protein-coding sequences are selected against while maintaining expression of 20 or more amino acids. We demonstrate experimentally that a reduced set of 21 tRNAs is capable of expressing a protein encoded by only 20 sense codons, whereas a standard 64-codon encoding is not expressed. Our work suggests that biological systems using rationally depleted but otherwise natural translation systems should evolve more slowly and that such hypoevolvable organisms may be less likely to invade new niches or outcompete native populations.
LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA
Authors: Izumikawa Keiichi , Ishikawa Hideaki , Yoshikawa Harunori , Fujiyama Sally , Watanabe Akira , Aburatani Hiroyuki , Tachikawa Hiroyuki , Hayano Toshiya , Miura Yutaka , Isobe Toshiaki , Simpson Richard J , Li Li , Min Jinrong , Takahashi Nobuhiro 
Published: August 2019

AbstractActivation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine–binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.
Robust gene expression control in human cells with a novel universal TetR aptamer splicing module
Authors: Mol Adam A , Groher Florian , Schreiber Britta , Rühmkorff Ciaran , Suess Beatrix 
Published: August 2019

Abstract
Fine-tuning of gene expression is desirable for a wide range of applications in synthetic biology. In this context, RNA regulatory devices provide a powerful and highly functional tool. We developed a versatile, robust and reversible device to control gene expression by splicing regulation in human cells using an aptamer that is recognized by the Tet repressor TetR. Upon insertion in proximity to the 5′ splice site, intron retention can be controlled via the binding of TetR to the aptamer. Although we were able to demonstrate regulation for different introns, the genomic context had a major impact on regulation. In consequence, we advanced the aptamer to develop a splice device. Our novel device contains the aptamer integrated into a context of exonic and intronic sequences that create and maintain an environment allowing a reliable and robust splicing event. The exon-born, additional amino acids will then be cleaved off by a self-cleaving peptide. This design allows portability of the splicing device, which we confirmed by demonstrating its functionality in different gene contexts. Intriguingly, our splicing device shows a high dynamic range and low basal activity, i.e. desirable features that often prove a major challenge when implementing synthetic biology in mammalian cell lines.
High-resolution mapping of brain vasculature and its impairment in the hippocampus of Alzheimer's disease mice
Authors: Zhang Xiaochuan , Yin Xianzhen , Zhang Jingjing , Li Anan , Gong Hui , Luo Qingming , Zhang Haiyan , Gao Zhaobing , Jiang Hualiang 
Published: August 2019

Abstract
Accumulating evidence indicates the critical importance of cerebrovascular dysfunction in the pathogenesis of Alzheimer's disease (AD). However, systematic comparative studies on the precise brain vasculature of wild-type and AD model mice are still rare. Using an image-optimization method for analysing Micro-Optical Sectioning Tomography (MOST) data, we generated cross-scale whole-brain 3D atlases that cover the entire vascular system from large vessels down to smallest capillaries at submicron resolution, for both wild-type mice and a transgenic (APP/PS1) mouse model of AD. In addition to distinct vascular patterns in different brain regions, we found that the main vessels of the molecular layer of the hippocampal dentate gyrus (DG-ml) undergo abrupt changes in both diameter and branch angle, spreading a unique comb-like pattern of capillaries. By using a quantitative analysis workflow, we identified in the hippocampus of AD mice an overall reduction of the mean vascular diameter, volume fraction and branch angle, with most significant impairment in the DG-ml. In addition, virtual endoscopy revealed irregular morphological features in the vessel lumen of the AD mice, potentially contributing to the impairment of blood flow. Our results demonstrate the capability of high-resolution cross-scale evaluation of brain vasculature and underscore the importance of studying hippocampal microcirculation for understanding AD pathogenesis.
Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome
Authors: Sortino Ornella , Phanuphak Nittaya , Schuetz Alexandra , Ortiz Alexandra M , Chomchey Nitiya , Belkaid Yasmine , Davis Jacquice , Mystakelis Harry A , Quiñones Mariam , Deleage Claire , Ingram Brian , Rerknimitr Rungsun , Pinyakorn Suteeraporn , Rupert Adam , Robb Merlin L , Ananworanich Jintanat , Brenchley Jason , Sereti Irini ,   RV254/SEARCH010 Study Group, Teeratakulpisarn Nipat , Pattanachaiwit Supanit , de Souza Mark , Fletcher James , Kroon Eugene , Tantivitayakul Ponpen , Suttichom Duanghathai , Rattanamanee Somprartthana , Poltavee Kultida , Intasan Jintana , Luekasemsuk Tassanee , Savadsuk Hathairat , Tipsuk Somporn , Puttamsawin Suwanna , Benjapornpong Khunthalee , Ratnaratorn Nisakorn , Eamyoung Patcharin , Ubolyam Sasiwimol , O’Connell Robert , Akapirat Siriwat , Nuntapinit Bessara , Tantibul Nantana , Churikanont Nampueng , Getchalarat Saowanit , Vasan Sandhya , Trichavaroj Rapee , Sajiaweerawan Chayada , Phuang-Ngern Yuwadee , Jongrakthaitae Surat , Sukhumvittaya Suchada , Saetun Putida , Chuenarom Weerawan , Michael Nelson , Turk Ellen , McCullough Corinne , Butterworth Oratai , Milazzo Mark 
Published: August 2019

Abstract

Background
Intestinal microbial dysbiosis is evident in chronic HIV-infected individuals and may underlie inflammation that persists even during antiretroviral therapy (ART). It remains unclear, however, how early after HIV infection gut dysbiosis emerges and how it is affected by early ART.

Methods
Fecal microbiota were studied by 16s rDNA sequencing in 52 Thai men who have sex with men (MSM), at diagnosis of acute HIV infection (AHI), Fiebig Stages 1–5 (F1-5), and after 6 months of ART initiation, and in 7 Thai MSM HIV-uninfected controls. Dysbiotic bacterial taxa were associated with relevant inflammatory markers.

Results
Fecal microbiota profiling of AHI pre-ART vs HIV-uninfected controls showed a mild dysbiosis. Transition from F1-3 of acute infection was characterized by enrichment in pro-inflammatory bacteria. Lower proportions of Bacteroidetes and higher frequencies of Proteobacteria and Fusobacteria members were observed post-ART compared with pre-ART. Fusobacteria members were positively correlated with levels of soluble CD14 in AHI post-ART.

Conclusions
Evidence of gut dysbiosis was observed during early acute HIV infection and was partially restored upon early ART initiation. The association of dysbiotic bacterial taxa with inflammatory markers suggests that a potential relationship between altered gut microbiota and systemic inflammation may also be established during AHI.
The Sublimity of Document
Authors: MacDonald Scott 
Published: August 2019

Abstract
The Sublimity of Document: Cinema as Diorama (Avant-Doc 2) is an international collection of in-depth, substantive interviews with moving-image artists working “avant-doc,” that is, making films that explore the territory between documentary and experimental cinema. The Sublimity of Document follows on MacDonald’s earlier Avant-Doc: Intersections of Documentary and Avant-Garde Cinema (Oxford, 2015), though the focus here is on filmmakers who are committed to document itself, willing to go anywhere on the planet (or within film archives or on the internet) to document what they believe we need to see—regardless of whatever political implications the film experiences they create may have for us. The book uses the early history of the museum habitat diorama of animal life, specifically the Akeley Hall of African Mammals at the American Museum of Natural History, as a way of rethinking both early and modern cinema of document—and especially those recent filmmakers and films devoted to providing a panorama of places and events that viewers might never have opportunities to experience in person. The twenty-seven interviews in The Sublimity of Document are organized panoramically within the volume.
Introduction
Authors: MacDonald Scott 
Published: August 2019

Abstract
The introduction creates a context for a wide range of avant-doc films (that is, films that work in the zone between conventional documentary and what has usually been called “avant-garde” filmmaking), locating these films within the tradition established a century ago by the development of the habitat diorama of animal life, specifically the Akeley Hall of African Mammals at the American Museum of Natural History in New York City. The habitat diorama provides precise documentation of the specifics of animal life that is, insofar as possible, devoid of political argument. The aim of the habitat diorama, and of the films discussed throughout the book, is to be as purely educational as cinema can be: the creator of the habitat dioramas and the film documents discussed provide precise visions of what the makers believe we need to see, in order to understand more of the world around us.
Nikolaus Geyrhalter
Authors: MacDonald Scott 
Published: August 2019

Abstract
This is the first career interview with Austrian documentary filmmaker Nikolaus Geyrhalter, whose films, like those of Fred Wiseman, often focus on cultural institutions, though with a radically different sensibility. Geyrhalter’s most widely known film in the United States is Our Daily Bread (2005), his astonishing documentation of mass food production within the European community. Geyrhalter’s films are visually rigorous and formal—he was a photographer before he turned to filmmaking and is his own cinematographer. His films have explored cultural realities far and wide, from the aftermath of the Balkan wars of the 1990s to the plight of workers laid off from an Austrian factory during the years after the factory closed. His most elaborate film is Elsewhere (2000), a global survey of the edges of modern life and cultural transformation at the moment of the new millennium. The recent Homo Sapiens is a panorama of ruined places and landscapes across the planet at the dawn of the Anthropocene.
Brett Story
Authors: MacDonald Scott 
Published: August 2019

Abstract
This interview surveys the career of Canadian filmmaker Brett Story, from her early attempts to evoke dimensions of modern urban life to her feature The Prison in Twelve Landscapes (2016), a panorama of the ways in which the American prison system is visible and audible outside prison walls and away from the remote prison locations across the country, where criminals are housed. Story finds evidence of the prison system hidden in plain sight in New York City’s Washington Square, at an airport built on the flat top of what was once a coal mine in Eastern Kentucky, at Quicken Loans headquarters in downtown Detroit, where a forest fire is being fought in Marin County, California, at a grocery storeroom in the Bronx, at a kids pocket park in LA, in a quiet town outside of St. Louis, in a radio station in Kentucky, and on buses traveling through the night toward rural New York State towns.
Maxim Pozdorovkin on Our New President
Authors: MacDonald Scott 
Published: August 2019

Abstract
Russian-American filmmaker Maxim Pozdorovkin has made a series of films documenting Russia in the age of Putin, including the well-known Pussy Riot (2013), about the radical feminist performance group. This interview focuses specifically on Our New President (2017), which traces the Hillary Clinton/Donald Trump presidential race and the Trump election as depicted in Russian propaganda. Pozdorovkin’s film is a significant contribution to the recent history of recycled cinema. The political weaponizing of media to produce “fake news” is the focus of Our New President. Pozdorovkin demonstrates that in the 2010s propaganda is not so much misinformation carefully embedded in an otherwise informative context, but an attempt to overwhelm by creating total media confusion. He makes clear that in Russia the government controls all major news outlets and hacking into the online networks of other nations is considered patriotism.
What Is Feminist Ethics?
Authors: Lindemann Hilde 
Published: August 2019

Abstract
The chapter explains what is meant by ethics, feminism, and gender, drawing contrasts between feminist and nonfeminist ways of doing ethics. An ethics sketch map shows students the various branches of ethics and how feminists approach them. It is followed by a discussion of power and the moral attention it requires, with a specific focus on gender as an abusive power system that pervades everyday social life.
Intersectionality
Authors: Lindemann Hilde 
Published: August 2019

Abstract
The chapter begins with examples of intersectionality that display how it works. While particular attention is given to the intersections of race and gender, the concept is shown to apply beyond race and gender to cover any social groups against which discrimination is directed. After critiques of intersectionality are addressed, students are introduced to the concept of microaggressions and shown how these too are intersectional.
Standard Moral Theories from a Feminist Perspective
Authors: Lindemann Hilde 
Published: August 2019

Abstract
This chapter focuses on the three moral theories that have long dominated Western philosophy. The overviews of social contract theory, utilitarianism, and Kantian ethics are followed by a criticism, from a feminist point of view, of the failings the theories have in common, described as distorted pictures of the persons who are the moral agents in the theories, the societies these people inhabit, and the understanding of rationality the theories presuppose. It then explains why the theories can’t well be employed to address these failings.
Conclusion
Authors: Bullock Charles S. , MacManus Susan A. , Mayer Jeremy D. , Rozell Mark J. 
Published: August 2019

Abstract
The concluding chapter summarizes key findings of the volume and points the way toward areas of future research and analysis of southern politics. It offers some projections about the future of the region, including its potentially key role in the 2020 elections. The discussion covers the many areas in which change is occurring, including changing demographics, changing partisanship, changing politics of race, and changing politics of religion, all leading up to a discussion of the changing politics of the Trump Era. In its final words, the chapter concludes that the direction of U.S. national politics and governing will continue to be driven substantially by what happens in the South.
How Should Transnational Bribery Law Be Enforced?
Authors: Davis Kevin E. 
Published: August 2019

Abstract
There currently is significant divergence in enforcement of transnational bribery law, and there is little ground for believing there ought to be complete convergence. U.S. enforcement agencies have taken the lead in defining the OECD paradigm’s approach to enforcement and other enforcement agencies have begun to follow. The recent enforcement actions against Odebrecht S.A. are cases in point. The recommended approach favors vigorous investigation and severe sanctions, all aimed primarily at achieving deterrence, and ultimately prevention, with compensation and condemnation as secondary objectives. These methods and objectives are vulnerable to several potent critiques: there might be alternative ways of achieving deterrence, there might be alternatives to deterrence as a form of prevention, and prevention should not be pursued without regard to the associated costs. These objections challenge the effectiveness, efficiency, legitimacy, and fairness of the OECD paradigm’s approach to enforcement.
Concluding Thoughts
Authors: Davis Kevin E. 
Published: August 2019

Abstract
This chapter proposes a path to reconciliation between the OECD paradigm and the anti-imperialist critique. The premises are that: (1) transnational bribery is a significant problem, but (2) reasonable people can and will disagree about the appropriate legal responses. Left unresolved, those disagreements threaten to compromise effectiveness, efficiency, fairness, legitimacy, and due process. This implies that architects of transnational bribery law ought to develop mechanisms that reduce the scope for disagreement about appropriate legal interventions, identify reasonable disagreements that ought to be tolerated, and offer a legitimate process for determining how to overcome disagreements that stem from unreasonable objections.
Mexican American
Authors: Telles Edward , Sue Christina A. 
Published: August 2019

Abstract
This chapter assesses whether U.S.-born Mexican Americans feel American or a part of American society, even though they have been portrayed as threats to Americanism and have had their allegiance questioned. It also considers how their ethnic identity affects their sense of Americanness. For the respondents, they in no way perceive their ethnic and national identities as being mutually exclusive; to the contrary, they find these identities to be highly compatible and complementary. They define Americanness in terms of birthplace, political loyalty, and economic opportunities; they define Mexicanness in terms of culture, family, and ancestral background. Moreover, the vast majority of the respondents view national identity as their primary identity, something that is constant, natural, and unquestioned, whereas their ethnic identities vary in intensity, depending on the individual and the situation.