bluuebunny/crossref_metadata_2025_split huggingface dataset:
FlyBase: updates to theDrosophila melanogasterknowledge base
Authors: Larkin Aoife , Marygold Steven J , Antonazzo Giulia , Attrill Helen , dos Santos Gilberto , Garapati Phani V , Goodman Joshua L , Gramates L Sian , Millburn Gillian , Strelets Victor B , Tabone Christopher J , Thurmond Jim ,   FlyBase Consortium, Perrimon Norbert , Gelbart Susan Russo , Agapite Julie , Broll Kris , Crosby Madeline , dos Santos Gilberto , Falls Kathleen , Gramates L Sian , Jenkins Victoria , Longden Ian , Matthews Beverley , Sutherland Carol , Tabone Christopher J , Zhou Pinglei , Zytkovicz Mark , Brown Nick , Antonazzo Giulia , Attrill Helen , Garapati Phani , Larkin Aoife , Marygold Steven , McLachlan Alex , Millburn Gillian , Pilgrim Clare , Ozturk-Colak Arzu , Trovisco Vitor , Kaufman Thomas , Calvi Brian , Goodman Josh , Strelets Victor , Thurmond Jim , Cripps Richard , Lovato TyAnna 
Published: October 2020

AbstractFlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays (‘ribbons’) of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants
Authors: Zhao Lianhe , Wang Jiajia , Li Yanyan , Song Tingrui , Wu Yang , Fang Shuangsang , Bu Dechao , Li Hui , Sun Liang , Pei Dong , Zheng Yu , Huang Jianqin , Xu Mingqing , Chen Runsheng , Zhao Yi , He Shunmin 
Published: October 2020

Abstract
NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. The number of human lncRNAs has increased from 172 216 to 173 112. The number of mouse lncRNAs increased from 131 697 to 131 974. The number of plant lncRNAs is 94 697. The relationship between lncRNAs in human and cancer were updated with transcriptome sequencing profiles. Three important new features were also introduced in NONCODEV6: (i) updated human lncRNA-disease relationships, especially cancer; (ii) lncRNA annotations with tissue expression profiles and predicted function in five common plants; iii) lncRNAs conservation annotation at transcript level for 23 plant species. NONCODEV6 is accessible through http://www.noncode.org/.
The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase
Authors: Cieśla Małgorzata , Turowski Tomasz W , Nowotny Marcin , Tollervey David , Boguta Magdalena 
Published: October 2020

AbstractThe biogenesis of eukaryotic RNA polymerases is poorly understood. The present study used a combination of genetic and molecular approaches to explore the assembly of RNA polymerase III (Pol III) in yeast. We identified a regulatory link between Rbs1, a Pol III assembly factor, and Rpb10, a small subunit that is common to three RNA polymerases. Overexpression of Rbs1 increased the abundance of both RPB10 mRNA and the Rpb10 protein, which correlated with suppression of Pol III assembly defects. Rbs1 is a poly(A)mRNA-binding protein and mutational analysis identified R3H domain to be required for mRNA interactions and genetic enhancement of Pol III biogenesis. Rbs1 also binds to Upf1 protein, a key component in nonsense-mediated mRNA decay (NMD) and levels of RPB10 mRNA were increased in a upf1Δ strain. Genome-wide RNA binding by Rbs1 was characterized by UV cross-linking based approach. We demonstrated that Rbs1 directly binds to the 3′ untranslated regions (3′UTRs) of many mRNAs including transcripts encoding Pol III subunits, Rpb10 and Rpc19. We propose that Rbs1 functions by opposing mRNA degradation, at least in part mediated by NMD pathway. Orthologues of Rbs1 protein are present in other eukaryotes, including humans, suggesting that this is a conserved regulatory mechanism.
Optimized design of antisense oligomers for targeted rRNA depletion
Authors: Phelps Wesley A , Carlson Anne E , Lee Miler T 
Published: October 2020

Abstract
RNA sequencing (RNA-seq) is extensively used to quantify gene expression transcriptome-wide. Although often paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA), many applications require alternate approaches to counteract the high proportion of ribosomal RNA (rRNA) in total RNA. Recently, digestion using RNaseH and antisense DNA oligomers tiling target rRNAs has emerged as an alternative to commercial rRNA depletion kits. Here, we present a streamlined, more economical RNaseH-mediated rRNA depletion with substantially lower up-front costs, using shorter antisense oligos only sparsely tiled along the target RNA in a 5-min digestion reaction. We introduce a novel Web tool, Oligo-ASST, that simplifies oligo design to target regions with optimal thermodynamic properties, and additionally can generate compact, common oligo pools that simultaneously target divergent RNAs, e.g. across different species. We demonstrate the efficacy of these strategies by generating rRNA-depletion oligos for Xenopus laevis and for zebrafish, which expresses two distinct versions of rRNAs during embryogenesis. The resulting RNA-seq libraries reduce rRNA to &lt;5% of aligned reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available at https://mtleelab.pitt.edu/oligo to design antisense oligos for any taxon or to target any abundant RNA for depletion.
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis
Authors: Cantelli Gaia , Cochrane Guy , Brooksbank Cath , McDonagh Ellen , Flicek Paul , McEntyre Johanna , Birney Ewan , Apweiler Rolf 
Published: October 2020

Abstract
The European Bioinformatics Institute (EMBL-EBI; https://www.ebi.ac.uk/) provides freely available data and bioinformatics services to the scientific community, alongside its research activity and training provision. The 2020 COVID-19 pandemic has brought to the forefront a need for the scientific community to work even more cooperatively to effectively tackle a global health crisis. EMBL-EBI has been able to build on its position to contribute to the fight against COVID-19 in a number of ways. Firstly, EMBL-EBI has used its infrastructure, expertise and network of international collaborations to help build the European COVID-19 Data Platform (https://www.covid19dataportal.org/), which brings together COVID-19 biomolecular data and connects it to researchers, clinicians and public health professionals. By September 2020, the COVID-19 Data Platform has integrated in excess of 170 000 COVID-19 biomolecular data and literature records, collected through a number of EMBL-EBI resources. Secondly, EMBL-EBI has strived to continue its support of the life science communities through the crisis, with updated Training provision and improved service provision throughout its resources. The COVID-19 pandemic has highlighted the importance of EMBL-EBI’s core principles, including international cooperation, resource sharing and central data brokering, and has further empowered scientific cooperation.
Clinical and Imaging Characteristics of Spinal Dural Arteriovenous Fistulas and Spinal Epidural Arteriovenous Fistulas
Authors: Brinjikji Waleed , Colombo Elisa , Cloft Harry J , Lanzino Giuseppe 
Published: October 2020

Abstract

BACKGROUND
Spinal epidural arteriovenous fistulas (SEDAVFs) are an increasingly recognized form of spinal vascular malformation and are distinct from spinal dural arteriovenous fistulas (SDAVFs). Differentiating between these 2 entities is important as operative strategies often differ based on angioarchitecture.

OBJECTIVE
To compare demographic, clinical, anatomic, and imaging findings of SDAVFs and SEDAVFs.

METHODS
Consecutive patients diagnosed and/or treated for SDAVF or SEDAVF at our institution between January 2000 and November 2018 were included. Data were collected on demographics, clinical presentation, and imaging findings. All cross-sectional and angiographic imaging were reviewed. To compare continuous variables, t-test was used Chi-squared was used for categorical variables.

RESULTS
A total of 169 patients were included. In total 47 patients had SEDAVFs and 122 patients had SDVAFs. Clinical presentation and magnetic resonance imaging (MRI) imaging findings were similar between the 2 groups. SEDAVF patients were significantly more likely to have an epidural venous pouch on gadolinium bolus MR angiography (MRA) (0.0% vs 92.1%, P < .0001). SEDAVFs were more commonly located in the lumbar and sacral spine than SDAVFs (85.1% vs 34.4%, P < .0001). When in the lumbar spine, SEDAVFs unlike SDAVFs were more likely to involve the most caudal segments (L4 and L5, P = .02).

CONCLUSION
SEDAVF share clinical and radiological findings similar to SDAVFS, including high T2 cord signal, cord enhancement, and perimedullary flow voids on conventional MRI. However, they have a characteristic appearance on spinal MRA and DSA with a pouch of epidural contrast. SEDAVFs are more commonly located in the lumbosacral spine.
The Intersection Between Adverse Childhood Experiences and Environmental Tobacco Smoke in U.S. Households With Children
Authors: Jackson Dylan B , Testa Alexander 
Published: October 2020

Abstract

Introduction
Environmental tobacco smoke (ETS) is a potent risk factor for secondhand smoke (SHS) exposure. Research reveals, moreover, that children who are exposed to SHS are at an increased risk of disease and premature mortality. Limited research, however, has examined whether households with children experiencing accumulating adverse childhood experiences (ACEs) are also more likely to be characterized by ETS—particularly in the form of family members smoking inside the housing unit.

Aims and Methods
The current study employs a nationally representative sample of 102 341 households with children from the three most recent cohorts of National Survey of Children’s Health. Both multinomial logistic regression and a strategic comparison approach are used to examine the association between ACEs and ETS categories.

Results
A large majority of households characterized by ETS report one or more ACEs, while households without ETS are largely void of ACEs. Findings indicate that this association is not merely a function of general family member smoking, as ACEs are strongly and uniquely associated with family smoking inside the housing unit—above and beyond family members smoking more generally.

Conclusions
Households exhibiting an accumulation of ACEs may benefit from interventions providing resources and education supporting smoke-free home environments. Such families may also be screened and referred through existing family and parenting programs administered in the home environment (eg, home visiting).

Implications
Public health initiatives designed to mitigate child adversities from early life stages may help reduce ETS in housing units—thereby diminishing the risk of secondhand smoke (SHS) exposure among children.
Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis
Authors: Flohr Sarah , Ramette Alban , Agyeman Philipp K A , Duppenthaler Andrea , Scherer Cordula , Keller Peter M , Aebi Christoph 
Published: October 2020

Abstract
Mycobacterium chelonae infections usually resolve with adequate therapy. We report the case of an adolescent with a chronic and progressive M chelonae infection refractory to combined antimicrobial and surgical therapy. Whole genome sequence analysis of consecutive isolates distinguished reinfection from recurrence and contributed to the diagnosis of a factitious disorder.
Chapter 5
Authors: Glancy Mark 
Published: October 2020

Abstract
Archie Leach’s move from vaudeville to Broadway matinee idol is discussed in Chapter 5, which spans the years 1927 to 1931. Under contract first to Arthur Hammerstein and then to the Shubert Organization, Archie appeared in several major shows: Golden Dawn (1927), Polly (1928), Boom Boom (1928), A Wonderful Night (1929), The Street Singer (1930), and Nikki (1931). Spending the summer of 1931 in repertory, with the St Louis Municipal Opera Company, was a sign that his career was not in the ascendant. His most significant asset as a performer was his strikingly handsome appearance. This was often noted by theater critics, but so too were his limitations as an actor and singer. His first film, the Paramount “short” Singapore Sue (1931), demonstrates that he had a lot to learn about screen acting too. His first attempts at creating a public image for himself were also clumsy. His fanciful and largely fictional statements, including the idea that his grandfather was a great Shakespearian actor named Percival Leach, would follow him for many years.
Chapter 10
Authors: Glancy Mark 
Published: October 2020

Abstract
Chapter 10, covering the year 1934, explores the jealousy and insecurity that haunted Cary Grant during his short-lived marriage to Virginia Cherrill, which ended in a drunken fiasco that was reported in the press as a suicide attempt. Grant denied attempting suicide, and the chapter argues that he was likely imitating a scene from one of his recent films, Ladies Should Listen (1934), in which his character attempts to lure his lover to his bedside by faking a suicide attempt. The chapter also considers Paramount’s attempt to remake his screen image, casting him in comedies, including one written by Preston Sturges, Thirty Day Princess (1934), which was his best film of this period. He was also cast as an “art deco dandy” in a string of weak comedies that flopped at the box-office: Kiss and Make Up (1934), Ladies Should Listen, and Enter Madame! (1934). The chapter ends with Cherrill’s courtroom claims that Grant abused her physically and emotionally, and Grant’s explanation, in later years, that her charges were not true but were the legally required “grounds for divorce” in the 1930s.
Chapter 11
Authors: Glancy Mark 
Published: October 2020

Abstract
Chapter 11 reveals that 1935 was a difficult year for Cary Grant both personally and professionally. Stung by the failure of his first marriage, and the humiliating publicity that accompanied it, he withdrew from public life and filmmaking for the first six months of the year. He enjoyed a rare box-office success with Wings in the Dark (1935), but on his return to Paramount he made the shambolic The Last Outpost (1935), a film so bad it was derided by its cast and crew as “The Last Outhouse”. Grant sought loan-outs to other studios without success until director George Cukor, at RKO, cast him in the cross-dressing comedy Sylvia Scarlett (1935). The first of three films Grant made with Cukor and four films that he made with star Katharine Hepburn, Sylvia Scarlett offered him the opportunity to play a Cockney conman. He earned the best reviews of his career, but otherwise the film was a commercial and critical failure. It would be rediscovered in later decades and gradually gain a reputation as a “queer classic”. Later in the year, he also returned to Britain to make the British film The Amazing Quest (1936), and to see his father one last time before his death in December 1935.
Chapter 12
Authors: Glancy Mark 
Published: October 2020

Abstract
By the mid-1930s, Cary Grant was a well-established member of Hollywood’s social set. He and Randolph Scott lived in a rented beach house in Santa Monica and held pool-side parties most Sundays, attracting other filmmakers and stars. The home also featured in the publicity Paramount created for them. The photographer Jerome Zerbe captured them at home, by the pool, and on the beach in a naturalistic style quite different from the studio-bound glamour photography that was still the norm in Hollywood. Grant’s career, meanwhile, continued to suffer as Paramount cast him in feeble comedies such as Big Brown Eyes (1936) and Wedding Present (1936). On a “loan-out” to MGM, he had a rare hit film with Suzy (1936). Although Jean Harlow was the film’s true star, the producers at MGM allowed him to work with the scriptwriter Lenore Coffee, moulding his character into one that suited him. The cooperative, creative environment was a revelation to him. Other loan-outs, to Columbia for When You’re in Love (1937) and to RKO for The Toast of New York (1937), did not prove as successful. By 1936, he was so disillusioned with Paramount and with the direction that his career was taking that he decided not to renew his contract with the studio. Instead, he took the brave decision to become an independent or freelance star.
Chapter 25
Authors: Glancy Mark 
Published: October 2020

Abstract
Cary Grant and Betsy Drake’s marriage limped forward for two years after his affair with Sophia Loren. In the midst of this, Loren arrived in Hollywood and Grant began pursuing her again, asking her to marry him. He was finishing Kiss Them for Me (1957) at the time. Producer Jerry Wald had been trying to film this Second World War story for years, but it was only when Grant signed to star in it that the project got the green light. Grant enjoyed working with the film’s director, Stanley Donen, but he was ill-suited to play a soldier having weekend leave in San Francisco. The film was one of the very few flops in his later career. He then made Houseboat (1958). Drake had written the original screenplay thinking that she and Grant might star in the film together. At Grant’s request, the studio assigned other writers to rewrite it as a vehicle for Sophia Loren. The comedy, about an Italian nanny falling in love with her boss, culminates in their marriage. This was a difficult scene for the stars to film after Loren refused Grant’s own proposal. Indiscreet (1958), directed by Stanley Donen and co-starring Ingrid Bergman, was a happier production. This delightfully sophisticated romantic comedy benefits from Donen’s imaginative direction and from location shooting that captures the glamour of the London setting.
Chapter 26
Authors: Glancy Mark 
Published: October 2020

Abstract
Chapter 26 is devoted entirely to Cary Grant’s most famous and frequently revived film, North by Northwest (1959). It argues that North by Northwest is not just a great Cary Grant film, it is the Cary Grant film; that is, a summation of his entire career. The chapter discusses the making of the film, beginning with Ernest Lehmann’s screenplay. Lehmann set out to write “the Hitchcock film to end all Hitchcock films”, and this evidently included many elements of the three previous Hitchcock-Grant collaborations: Suspicion (1941), Notorious (1946), and To Catch a Thief (1955). Each of the five acts of North by Northwest, it is argued, puts the star through the paces of a single Cary Grant film. At the beginning of each act, his character is initially debonair and nonchalant, but then steadily becomes more tense, alarmed and threatened. This is brilliantly realized in the film’s climactic third act, when Roger O. Thornhill is chased across an empty prairie by a crop dusting plane. Both absurdly excessive and genuinely thrilling at the same time, the scene is now one of the most iconic moments in cinema history. The chapter details the film’s extensive location shooting, including time at Mount Rushmore for the final scene. It considers Eve Marie Saint as the quintessential Hitchcock blonde, and it discusses the film’s reception from its first release in 1959 to its modern reputation as a highly influential, classic film.
How Children Invented Humanity
Authors: Bjorklund David F. 
Published: October 2020

Abstract
Infants and children are the often-ignored heroes when it comes to understanding human evolution. Evolutionary pressures acted upon the young of our ancestors more powerfully than on adults. Changes over the course of development in our ancestors were primarily responsible for the species and the people we have become. This book takes an evolutionary developmental perspective, emphasizing that developmental plasticity—the ability to change our physical and psychological selves early in life—is the creative force in evolution, with natural selection serving primarily as the Grim Reaper, or a filter, eliminating novel developmental outcomes that did not benefit the survival of those individuals who possessed them, while letting the more successful outcomes through. Over generations as embryos, infants, and children continued to change and to produce slightly different adults, a new species was born—Homo sapiens. This book is about becoming—of becoming human and of becoming mature adults. One theme of this book is about how an understanding of our species’ evolution can help us better understand current development and how to better rear successful and emotionally healthy children. The second theme turns the relation between evolution and development on its head: How can an understanding of human development help us better understand human evolution? The short answer to this second question is that children invented humanity, and that human evolution can be seen as children setting the stage and leading the way to species innovation.
The Adaptive Value of Immaturity (or The Benefits of Being Young at Heart)
Authors: Bjorklund David F. 
Published: October 2020

Abstract
There are many aspects of young children’s thinking that are immature on the surface but have adaptive value for the young learner, a form of cognitive neoteny. These include young children’s self-centered, or egocentric, perspective; inefficient aspects of memory; tendencies to copy all relevant and irrelevant actions of adult models (overimitation); tendencies to overestimate their abilities; and strong propensity to play. Also included are special abilities to learn, and even create, language, due, in part, to aspects of immature cognition. Ancient human adults retained many youthful characteristics including behavioral plasticity, curiosity, play, imagination, and optimism. These characteristics, coupled with enhanced reasoning and executive function, have led to advances in material and intellectual culture far surpassing anything achieved by other species and to the evolution of the modern human mind.
The Twentieth Century
Authors: Fesko J. V. 
Published: October 2020

Abstract
In the twentieth century, critics of the covenant works rejected it for several reasons. First, the doctrine had a faulty understanding of the nature of a covenant. A covenant is promise not agreement. Second, they believed there was scant, if any, biblical evidence for the doctrine. Third, they believed that Reformed scholasticism was an unhelpful development in the Reformed tradition. Conversely, proponents of the doctrine held diametrically opposed views. A covenant is an agreement but context and parties determines the precise nature of the covenant. There were a host of biblical texts that teach the doctrine. And, Reformed scholasticism was a good resource. Especially in the twentieth century, the rise of biblicism marks the period as well as the influx of Idealist-influenced methods.