bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication
Authors: Aase-Remedios Madeleine E , Janssen Ralf , Leite Daniel J , Sumner-Rooney Lauren , McGregor Alistair P 
Published: November 2023

Abstract
Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.
Opsin Gene Duplication in Lepidoptera: Retrotransposition, Sex Linkage, and Gene Expression
Authors: Mulhair Peter O , Crowley Liam , Boyes Douglas H , Lewis Owen T , Holland Peter W H 
Published: November 2023

Abstract
Color vision in insects is determined by signaling cascades, central to which are opsin proteins, resulting in sensitivity to light at different wavelengths. In certain insect groups, lineage-specific evolution of opsin genes, in terms of copy number, shifts in expression patterns, and functional amino acid substitutions, has resulted in changes in color vision with subsequent behavioral and niche adaptations. Lepidoptera are a fascinating model to address whether evolutionary change in opsin content and sequence evolution are associated with changes in vision phenotype. Until recently, the lack of high-quality genome data representing broad sampling across the lepidopteran phylogeny has greatly limited our ability to accurately address this question. Here, we annotate opsin genes in 219 lepidopteran genomes representing 33 families, reconstruct their evolutionary history, and analyze shifts in selective pressures and expression between genes and species. We discover 44 duplication events in opsin genes across ∼300 million years of lepidopteran evolution. While many duplication events are species or family specific, we find retention of an ancient long-wavelength-sensitive (LW) opsin duplication derived by retrotransposition within the speciose superfamily Noctuoidea (in the families Nolidae, Erebidae, and Noctuidae). This conserved LW retrogene shows life stage–specific expression suggesting visual sensitivities or other sensory functions specific to the early larval stage. This study provides a comprehensive order-wide view of opsin evolution across Lepidoptera, showcasing high rates of opsin duplications and changes in expression patterns.
BloodSpot 3.0: a database of gene and protein expression data in normal and malignant haematopoiesis
Authors: Gíslason Magnús H , Demircan Gül Sude , Prachar Marek , Furtwängler Benjamin , Schwaller Juerg , Schoof Erwin M , Porse Bo Torben , Rapin Nicolas , Bagger Frederik Otzen 
Published: November 2023

Abstract
BloodSpot is a specialised database integrating gene expression data from acute myeloid leukaemia (AML) patients related to blood cell development and maturation. The database and interface has helped numerous researchers and clinicians to quickly get an overview of gene expression patterns in healthy and malignant haematopoiesis. Here, we present an update to our framework that includes protein expression data of sorted single cells. With this update we also introduce datasets broadly spanning age groups, which many users have requested, with particular interest for researchers studying paediatric leukaemias. The backend of the database has been rewritten and migrated to a cloud-based environment to accommodate the growth, and provide a better user-experience for our many international users. Users can now enjoy faster transfer speeds and a more responsive interface. In conclusion, the continuing popularity of the database and emergence of new data modalities has prompted us to rewrite and futureproof the back-end, including paediatric centric views, as well as single cell protein data, allowing us to keep the database updated and relevant for the years to come. The database is freely available at www.bloodspot.eu.
SDRAP for annotating scrambled or rearranged genomes
Authors: Braun Jasper , Neme Rafik , Feng Yi , Landweber Laura F , Jonoska Nataša 
Published: November 2023

Abstract
Genomes sometimes undergo large-scale rearrangements. Programmed genome rearrangements in ciliates offer an extreme example, making them a compelling model system to study DNA rearrangements. Currently, available methods for genome annotation are not adequate for highly scrambled genomes. We present a theoretical framework and software implementation for the systematic extraction and analysis of DNA rearrangement annotations from pairs of genome assemblies corresponding to precursor and product versions. The software makes no assumptions about the structure of the rearrangements, and permits the user to select parameters to suit the data. Compared to previous approaches, this work achieves more complete precursor-product mappings, allows for full transparency and reproducibility, and can be adapted to genomic data from different sources.
Monitoring response to a clinically relevant IDH inhibitor in glioma—Hyperpolarized 13C magnetic resonance spectroscopy approaches
Authors: Hong Donghyun , Kim Yaewon , Mushti Chandrasekhar , Minami Noriaki , Wu Jing , Cherukuri Murali Krishna , Swenson Rolf E , Vigneron Daniel B , Ronen Sabrina M 
Published: November 2023

Abstract

Background
Mutant isocitrate dehydrogenase (IDHmut) catalyzes 2-hydroxyglutarate (2HG) production and is considered a therapeutic target for IDHmut tumors. However, response is mostly associated with inhibition of tumor growth. Response assessment via anatomic imaging is therefore challenging. Our goal was to directly detect IDHmut inhibition using a new hyperpolarized (HP) 13C magnetic resonance spectroscopy-based approach to noninvasively assess α-ketoglutarate (αKG) metabolism to 2HG and glutamate.

Methods
We studied IDHmut-expressing normal human astrocyte (NHAIDH1mut) cells and rats with BT257 tumors, and assessed response to the IDHmut inhibitor BAY-1436032 (n ≥ 4). We developed a new 13C Echo Planar Spectroscopic Imaging sequence with an optimized RF pulse to monitor the fate of HP [1-13C]αKG and [5-12C,1-13C]αKG with a 2.5 × 2.5 × 8 mm3 spatial resolution.

Results
Cell studies confirmed that BAY-1436032-treatment leads to a drop in HP 2HG and an increase in HP glutamate detectable with both HP substrates. Data using HP [5-12C,1-13C]αKG also demonstrated that its conversion to 2HG is detectable without the proximal 1.1% natural abundance [5-13C]αKG signal. In vivo studies showed that glutamate is produced in normal brains but no 2HG is detectable. In tumor-bearing rats, we detected the production of both 2HG and glutamate, and BAY-1436032-treatment led to a drop in 2HG and an increase in glutamate. Using HP [5-12C,1-13C]αKG we detected metabolism with an signal-to-noise ratio of 23 for 2HG and 17 for glutamate.

Conclusions
Our findings point to the clinical potential of HP αKG, which recently received FDA investigational new drug approval for research, for noninvasive localized imaging of IDHmut status.
Efficacy of Messenger RNA–1273 Against Severe Acute Respiratory Syndrome Coronavirus 2 Acquisition in Young Adults From March to December 2021
Authors: Stephenson Kathryn E , Marcelin Jasmine R , Pettifor Audrey E , Janes Holly , Brown Elizabeth , Neradilek Moni , Yen Catherine , Andriesen Jessica , Grunenberg Nicole , Espy Nicole , Trahey Meg , Fischer Rebecca S B , DeSouza Christopher A , Shisler Joanna L , Connick Elizabeth , Houpt Eric R , Chu Helen Y , McCulloh Russel J , Becker-Dreps Sylvia , Vielot Nadja A , Kalbaugh Corey A , Cherabuddi Kartik , Krueger Karen M , Rosenberg Molly , Greenberg Richard N , Joaquin Arnel , Immergluck Lilly Cheng , Corey Lawrence , Kublin James G 
Published: November 2023

Abstract

Background
The efficacy of messenger RNA (mRNA)–1273 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is not well defined, particularly among young adults.

Methods
Adults aged 18–29 years with no known history of SARS-CoV-2 infection or prior vaccination for coronavirus disease 2019 (COVID-19) were recruited from 44 US sites from 24 March to 13 September 2021 and randomized 1:1 to immediate vaccination (receipt of 2 doses of mRNA-1273 vaccine at months 0 and 1) or the standard of care (receipt of COVID-19 vaccine). Randomized participants were followed up for SARS-CoV-2 infection measured by nasal swab testing and symptomatic COVID-19 measured by nasal swab testing plus symptom assessment and assessed for the primary efficacy outcome. A vaccine-declined observational group was also recruited from 16 June to 8 November 2021 and followed up for SARS-CoV-2 infection as specified for the randomized participants.

Results
The study enrolled 1149 in the randomized arms and 311 in the vaccine-declined group and collected &gt;122 000 nasal swab samples. Based on randomized participants, the efficacy of 2 doses of mRNA-1273 vaccine against SARS-CoV-2 infection was 52.6% (95% confidence interval, −14.1% to 80.3%), with the majority of infections due to the Delta variant. Vaccine efficacy against symptomatic COVID-19 was 71.0% (95% confidence interval, −9.5% to 92.3%). Precision was limited owing to curtailed study enrollment and off-study vaccination censoring. The incidence of SARS-CoV-2 infection in the vaccine-declined group was 1.8 times higher than in the standard-of-care group.

Conclusions
mRNA-1273 vaccination reduced the incidence of SARS-CoV-2 infection from March to September 2021, but vaccination was only one factor influencing risk.

Clinical Trials Registration
NCT04811664.
Clinical Characteristics and Outcomes of Patients With Mpox Who Received Tecovirimat in a New York City Health System
Authors: Vo Christopher , Zomorodi Rustin , Silvera Richard , Bartram Logan , Lugo Luz Amarilis , Kojic Erna , Urbina Antonio , Aberg Judith , Sigel Keith , Chasan Rachel , Patel Gopi 
Published: November 2023

Abstract

Background
The 2022 global mpox outbreak was notable for transmission between persons outside of travel and zoonotic exposures and primarily through intimate contact. An understanding of the presentation of mpox in people with human immunodeficiency virus (HIV) and other immunocompromising conditions and knowledge of the efficacy of tecovirimat continue to evolve.

Methods
This retrospective study describes clinical features and outcomes of persons with mpox who received tecovirimat. Data were obtained via medical record review of patients prescribed tecovirimat in a health system in New York City during the height of the outbreak in 2022.

Results
One hundred thirty people received tecovirimat between 1 July and 1 October 2022. People with HIV (n = 80) experienced similar rates of recovery, bacterial superinfections, and hospitalization compared to patients without immunocompromising conditions. Individuals determined to be severely immunocompromised (n = 14) had a higher risk of hospitalization than those without severe immunocompromise (cohort inclusive of those with well-controlled HIV, excluding those without virologic suppression, n = 101): 50% versus 9% (P &lt; .001). Hospitalized patients (n = 18 [13% of total]) were primarily admitted for bacterial superinfections (44.4%), with a median hospital stay of 4 days. Of those who completed follow-up (n = 85 [66%]), 97% had recovery of lesions at time of posttreatment assessment. Tecovirimat was well tolerated; there were no reported severe adverse events attributed to therapy.

Conclusions
There were no significant differences in outcomes between people with HIV when evaluated as a whole and patients without immunocompromising conditions. However, mpox infection was associated with higher rates of hospitalization in those with severe immunocompromise, including patients with HIV/AIDS. Treatment with tecovirimat was well tolerated.
Key Points: In our mpox cohort, people with HIV had similar rates of recovery and complications as those without HIV or other immunocompromising conditions. Severe immunocompromise was associated with a higher hospitalization rate. Tecovirimat was well tolerated, with minimal side effects.
Italian Opera in Late Eighteenth-Century London
Authors: Milhous Judith , Dideriksen Gabridla , Hume Robert D 
Published: November 2023

Abstract
Following on from the volume on the King’s Theatre, Haymarket (published by OUP in 1995), this interdisciplinary study of opera and ballet now turns to London’s Pantheon Opera during the period 1789-98. The discovery of six cartons of previously unknown manuscripts in the possession of the Duke of Bedford makes possible the rewriting of a hitherto dark and little understood chapter in the history of opera in London. The King’s Theatre, Haymarket, burnt down in 1789. To replace it, the fifth Duke of Bedford and the Marquis of Salisbury secretly backed a new opera company, to be housed in the Pantheon, an elegant exhibition hall hastily converted to house the venture. Part 1 of this book tells a tale of intrigue, blackmail, bankruptcy, arson, and high-society infighting against a background of exalted artistic aspirations and genuine love of opera. The Pantheon tried to engage Mozart to compete against Haydn, and hired some of the most notable singers and dancers in Europe. Mismanagement led to huge losses, and the theatre burnt in highly suspicious circumstances in 1792. The backers tried to impose an artistic vision and financial controls on the management of the rebuilt King’s Theatre, Haymarket, when opera returned there in 1793, but by 1795 their failure was evident. The second part of the book is a detailed analysis of the opera and ballet repertoire, personnel, management, costumes, staging practices, and finances of the company, based on the Bedford archive and a wealth of hitherto unused sources. What emerges is the fullest operational analysis ever published of any pre-nineteenth-century English theatre or opera company.
The Fire and the Little Haymarket Season, I79I-92
Authors: Milhous Judith , Dideriksen Gabridla , Hume Robert D 
Published: November 2023

Abstract
The present chapter moves from the reorganization at the end of the Pan the ones disastrous first season to the termination of the venture in the summer of 1792. The season of 1791--92 itself is virtually an epilogue, con ducted at the Little Haymarket after the Pantheon burnt down just four nights into the new season. The only reason that Italian opera did not instantly return to the King’s Theatre, Haymarket, in January 1792 was that William Taylor had rented it out to the Drury Lane actors while their theatre was being rebuilt.
The Ballet
Authors: Milhous Judith , Dideriksen Gabridla , Hume Robert D 
Published: November 2023

Abstract
The Nature of the Pantheon ballet company and the expectations it had to meet were established by the extraordinary changes that had occurred in the world of dance in London during the preceding decade. Ballet had become an increasingly important part of the opera company’s offerings during the 1770s, and large salaries were paid to obtain Continental stars, but dance made little effort to tell stories in detail.
African Countries
Authors: Harding Jeremy 
Published: November 2023

Abstract
Introducing a collection of African oral literature in 1988, the Nigerian polemicist and poet Chinweizu warned against any approach to the subject that reinforces ‘an Africa which European racism is flattered to imagine’. Instead, he suggests that ‘we [Africans] should listen to Africans talking to Africans about the world’. Writers like Chinweizu are concerned that the encounter between Africa and Europe is neither innocent nor symmetrical: slavery and the colonial past tilt this uneasy exchange in favour of non Africans. As outsiders, Europeans face a central problem when considering contemporary African writing: to think of it sui genms is to condescend to it; to compare it with other traditions-English, American, Indian, or French-is to disregard its specificity.
Australia
Authors: Craven Peter 
Published: November 2023

Abstract
There is no real substance in the belief that Australian writing only got going when national publishing began to sever itself from the essentially derivative, post-colonial, British variety in the 1970s. Australia’s three most formidable writers of fiction (four if one includes the short-story writer and memoirist Hal Porter) were active long before that date: Patrick White (1912-90) wrote three of his most ambitious novels in the 1950s, and Martin Boyd’s (1893-1972) Langton Quartet was largely composed during this same period. Christina Stead (1902-83) wrote her masterpiece in the 1940s though it was not discovered by her compatriots until 1966.
Brazil
Authors: Gledson John 
Published: November 2023

Abstract
Brazilian literature since 1960 has been dominated by political and social changes of great depth and, at times, violence. The military coup of 1964, and the subsequent ‘coup within a coup’ in 1968, which brought the pro-American Right to power, extended the practice of torture of political dissidents, and instituted severe censorship, delivering a traumatic shock to intellectuals as well as many others; and the ‘economic miracle’ of the late 1960s and early 1970s led to a sudden and massive urbanization, and the growth, in the south of the country above all, of a huge working class.
Czech Republic And Slovakia
Authors: Hájek Igor 
Published: November 2023

Abstract
When, in late December 1958, two weeks after its publication, Josef Škvorecký’s (b. 1924) first novel, The Cowards, was withdrawn from the bookshops and its author banned, it looked like the end of an all too brief period of grace in Czechoslovakia. Over the previous two years a remarkable thaw had occurred after the Stalinist freeze, enlivening both the Czech and the Slovak cultural scenes. In literature, quite a few new names had been introduced, some of whom were to stay in the forefront of interest for the next forty years: notably Miroslav Holub (b. 1923), Ivan Klima (b. 1931), and Milan Kundera (b. 1929).
England
Authors: Wood James 
Published: November 2023

Abstract
English writing in the 1960s and 1970s resembles a Victorian house whose windows have all been smashed: a solid structure timidly vandalized. Tom between nostalgia and rebellion, tradition and experiment, English writing of this period often lapsed into symmetrical failures: its Victorian solidity seems uninspiring and its experimentation only wanly successful. The Dickensian robustness of Angus Wilson’s (1913-82) novels, for instance, is not robust enough; but neither is his attempt to modernize or Post-Modernize the Dickensian tradition; Iris Murdoch’s (b. 1919) twentieth-century version of Tolstoyan realism has not been realized, nor could it have been, perhaps; but her philosophical dance around that realism has not been springy enough, and has attracted no partners; A. S. Byatt’s (b. 1936) desire to write what she calls ‘self-conscious realism’ seems too self-conscious and not real enough.
France
Authors: Taylor John 
Published: November 2023

Abstract
As the twentieth century draws to a close, French literature seems in a confusing state. The lamenters most often attribute this to the absence of ‘great writers’ who, having captured the international limelight, would compensate for the deaths of, say, Albert Camus (1913-60), Andre Breton (1896-1966), Francois Mauriac (1885-1970), Andre Malraux (1910-76), Jean-Paul Sartre (1905-80), and Simone de Beauvoir (1908-86). Other commentators add that no literary avant-gardes have stirred up world-wide excitement as intense as that created by the surrealists before the Second World War, by the existentialists after that war, or by the practitioners of the New Novel during the 1950s and early 1960s.
India
Authors: Cronin Richard 
Published: November 2023

Abstract
V. S. Naipaul pointed out in 1964 that Indian literature in English had ceased to exist: ‘The only writer who, while working from within the society, is yet able to impose on it a vision which is an acceptable type of comment, is R. Prawer Jhabvala. And she is European.’ He ought to have been right. That Indians had chosen to write in English must then have seemed simply a historical accident, a product of the Raj that would not long survive its passing. The government of India had committed itself to Hindi as the national language, and those who wrote in one of India’s twelve other major languages felt themselves engaged in a struggle against, not the pretensions of English, but the encroachments of Hindi. English remained as the first language of only one tiny and sadly disadvantaged Indian community, the Anglo-Indians.
Israel
Authors: Cheyette Bryan 
Published: November 2023

Abstract
In a typical contribution to the Hebrew Writers’ Association conference in 1968, Hayim Hazaz (1893-1972), a doyen of Hebrew literature, voiced his dissatisfaction with contemporary Israeli writing: ‘It goes without saying that Israeli literature should be a responsible literature ... Above all, books shouldn’t be mere books, writers shouldn’t be anonymous, shouldn’t be lukewarm, comfortable people ... they should be heroes of a national struggle, of a class-war, of culture; people of conviction and responsibility.’ Hazaz’s own contrived, overly rhetorical fiction, especially his novels of ideas, often bears out this programmatic statement, and contrasts unfavourably with the enigmatic modernism of his contemporary S. Y. Agnon (1888-1970). Agnon won the Nobel Prize for literature in 1966 for an oeuvre which, in its use of parables and its pervasive if unexplained Angst, is closely akin to Kafka. Much of Agnon’s fiction was published posthumously and, because of this, has continued to influence a good deal of contemporary Israeli literature.
Japan
Authors: Morris Mark 
Published: November 2023

Abstract
The most respected writer at work in Japan today is Oe Kenzaburo* (b. 1935), who in 1994 received the Nobel Prize for literature. Since the late 1950s, as part of a generation of talented writer-intellectuals, he has produced millions of words in the form of fiction, criticism, political essays, journalism, and several genres yet to be classified. Still this side of 60, Oe has hinted strongly all the same that he will one day probably stop writing fiction altogether..