bluuebunny/crossref_metadata_2025_split huggingface dataset:
RADIP technology comprehensively identifies H3K27me3-associated RNA–chromatin interactions
Authors: Shu Xufeng , Kato Masaki , Takizawa Satoshi , Suzuki Yutaka , Carninci Piero 
Published: November 2024

Abstract
Many RNAs associate with chromatin, either directly or indirectly. Several technologies for mapping regions where RNAs interact across the genome have been developed to investigate the function of these RNAs. Obtaining information on the proteins involved in these RNA–chromatin interactions is critical for further analysis. Here, we developed RADIP [RNA and DNA interacting complexes ligated and sequenced (RADICL-seq) with immunoprecipitation], a novel technology that combines RADICL-seq technology with chromatin immunoprecipitation to characterize RNA–chromatin interactions mediated by individual proteins. Building upon the foundational principles of RADICL-seq, RADIP extends its advantages by increasing genomic coverage and unique mapping rate efficiency compared to existing methods. To demonstrate its effectiveness, we applied an anti-H3K27me3 antibody to the RADIP technology and generated libraries from mouse embryonic stem cells (mESCs). We identified a multitude of RNAs, including RNAs from protein-coding genes and non-coding RNAs, that are associated with chromatin via H3K27me3 and that likely facilitate the spread of Polycomb repressive complexes over broad regions of the mammalian genome, thereby affecting gene expression, chromatin structures and pluripotency of mESCs. Our study demonstrates the applicability of RADIP to investigations of the functions of chromatin-associated RNAs.
CAF-1 promotes efficient PrimPol recruitment to nascent DNA for single-stranded DNA gap formation
Authors: Straka Joshua , Khatib Jude B , Pale Lindsey , Nicolae Claudia M , Moldovan George-Lucian 
Published: November 2024

Abstract
Suppression of single-stranded DNA (ssDNA) gap accumulation at replication forks has emerged as a potential determinant of chemosensitivity in homologous recombination (HR)-deficient tumors, as ssDNA gaps are transformed into cytotoxic double-stranded DNA breaks. We have previously shown that the histone chaperone CAF-1’s nucleosome deposition function is vital to preventing degradation of stalled replication forks correlating with HR-deficient cells’ response to genotoxic drugs. Here we report that the CAF-1–ASF1 pathway promotes ssDNA gap accumulation at replication forks in both wild-type and breast cancer (BRCA)-deficient backgrounds. We show that this is independent of CAF-1’s nucleosome deposition function but instead may rely on its proper localization to replication forks. Moreover, we show that the efficient localization to nascent DNA of PrimPol, the enzyme responsible for repriming upon replication stress, is dependent on CAF-1. As PrimPol has been shown to be responsible for generating ssDNA gaps as a byproduct of its repriming function, CAF-1’s role in its recruitment could directly impact ssDNA gap formation. We also show that chemoresistance observed in HR-deficient cells when CAF-1 or ASF1A are lost correlates with suppression of ssDNA gaps rather than protection of stalled replication forks. Overall, this work identifies an unexpected role of CAF-1 in regulating PrimPol recruitment and ssDNA gap generation.
Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes
Authors: Balu Sucharitha , Huget Susie , Medina Reyes Juan Jose , Ragueneau Eliot , Panneerselvam Kalpana , Fischer Samantha N , Claussen Erin R , Kourtis Savvas , Combe Colin W , Meldal Birgit H M , Perfetto Livia , Rappsilber Juri , Kustatscher Georg , Drew Kevin , Orchard Sandra , Hermjakob Henning 
Published: November 2024

Abstract
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It is a unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending the number of manually curated complexes, we have massively extended the coverage of the human complexome through the incorporation of high confidence assemblies predicted by machine-learning algorithms trained on large-scale experimental data. The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0. We have refactored the website to enable easy search and filtering of these different classes of protein complexes and have implemented the Complex Navigator, a visualisation tool to facilitate comparison of related complexes in the context of orthology or paralogy. We have embedded the Rhea reaction visualisation tool into the website to enable users to view the catalytic activity of enzyme complexes.
CAUSALdb2: an updated database for causal variants of complex traits
Authors: Wang Jianhua , Ouyang Liao , You Tianyi , Yang Nianling , Xu Xinran , Zhang Wenwen , Yang Hongxi , Yi Xianfu , Huang Dandan , Zhou Wenhao , Li Mulin Jun 
Published: November 2024

Abstract
Unraveling the causal variants from genome wide association studies (GWASs) is pivotal for understanding genetic underpinnings of complex traits and diseases. Despite continuous efforts, tools to refine and prioritize GWAS signals need enhancement to address the direct causal implications of genetic variations. To overcome challenges related to statistical fine-mapping in identifying causal variants, CAUSALdb has been updated with novel features and comprehensive datasets, morphing into CAUSALdb2. This expanded repository integrates 15 057 updated GWAS summary statistics across 10 839 unique traits and implements both LD-based and LD-free fine-mapping approaches, including innovative applications of approximate Bayes Factor and SuSiE. Additionally, by incorporating larger LD reference panels such as TOPMED and UK Biobank, and integrating functional annotations via PolyFun, CAUSALdb2 enhances the accuracy and context of fine-mapping results. The database now supports interrogation of additional causal signals and offers sophisticated visualizations to aid researchers in deciphering complex genetic architectures. By facilitating a deeper and more precise characterisation of causal variants, CAUSALdb2 serves as a crucial tool for advancing the genetic analysis of complex diseases. Available freely, CAUSALdb2 continues to set benchmarks in the post-GWAS era, fostering the development of targeted diagnostics and therapeutics derived from responsible genetic research. Explore these advancements at http://mulinlab.org/causaldb.
Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation
Authors: Niedner-Boblenz Annika , Monecke Thomas , Hennig Janosch , Klostermann Melina , Hofweber Mario , Davydova Elena , Gerber André P , Anosova Irina , Mayer Wieland , Müller Marisa , Heym Roland Gerhard , Janowski Robert , Paillart Jean-Christophe , Dormann Dorothee , Zarnack Kathi , Sattler Michael , Niessing Dierk 
Published: November 2024

Abstract
RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membraneless organelles. The general function and wide distribution of PUN motifs across species suggest that in an ancient ‘RNA world’ PUN-like motifs may have supported the correct folding of early ribozymes.
Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data
Authors: Hawkins Charles , Xue Bo , Yasmin Farida , Wyatt Gabrielle , Zerbe Philipp , Rhee Seung Y 
Published: November 2024

Abstract
The Plant Metabolic Network (PMN) is a free online database of plant metabolism available at https://plantcyc.org. The latest release, PMN 16, provides metabolic databases representing &gt;1200 metabolic pathways, 1.3 million enzymes, &gt;8000 metabolites, &gt;10 000 reactions and &gt;15 000 citations for 155 plant and green algal genomes, as well as a pan-plant reference database called PlantCyc. This release contains 29 additional genomes compared with PMN 15, including species listed by the African Orphan Crop Consortium and nonflowering plant species. Furthermore, 52 new enzymes with experimentally supported function information have been included in this release. The single-species databases contain a combination of experimental information from the literature and computationally predicted information obtained through PMN’s database generation pipeline for a single species, while PlantCyc contains only experimental information but for any species within Viridiplantae. PMN is a comprehensive resource for querying, visualizing, analyzing and interpreting omics data with metabolic knowledge. It also serves as a useful and interactive tool for teaching plant metabolism.
Incidence and Risk Factors of Ophthalmic Nerve Palsy in Patients With Tuberculous Meningitis: A Retrospective Study and Literature Review
Authors: Fei Zhen-Tao , Xia Lu , Yang Yang , Ye Dan , Liu Hua-Rui , Liu Ping , Huang Wei , Li Feng , Liu Xu-Hui 
Published: November 2024

Abstract

Background
Tuberculous meningitis (TBM) can lead to ophthalmic nerve palsy (ONP), a severe neurological complication. This study aims to evaluates the incidence and risk factors for ONP in TBM patients.

Methods
This retrospective study included 250 TBM patients from the Shanghai Public Health Clinical Center (2013-2022). Clinical and imaging data were analyzed, with logistic regression identifying risk factors for ONP.

Results
ONP occurred in 6.8% (17/250) of TBM patients. Those with ONP had higher intracranial pressure (ICP) (257.69 ± 68.12 mmH2O vs 191.65 ± 91.58 mmH2O; P = 0.012), cerebrospinal fluid protein levels, and a higher prevalence of tuberculomas (29.4% vs 10.7%; P = 0.039). Logistic regression identified pre-treatment ICP, CD4 percentage, and tuberculomas as significant risk factors. Linezolid use was a protective factor for ONP recovery.

Conclusions
Six point eight percent (17/250) of patients with TBM developed ONP as a complication. ICP, CD4 counts, and tuberculomas are key predictors. Linezolid shows potential as a therapeutic agent for improving outcomes in TBM patients with neurological complications, warranting further study.
HIV Clinical Providers’ Awareness, Attitudes, and Willingness to Support Patient Outreach Efforts for HIV Cure–Directed Research in Philadelphia, United States
Authors: Meanley Steven , Carter William B , Short William R , Metzger David S , Onorato Amy , Montaner Luis J , Dubé Karine 
Published: November 2024

Abstract

Background
Ethical patient outreach is critical for engaging patients with HIV in HIV cure–directed research. We sought to examine HIV clinical providers’ awareness of current HIV cure–directed research strategies investigated through the Martin Delaney Collaboratories (MDC) and providers’ attitudes toward patient outreach for HIV cure–directed research and to identify opportunities for clinical provider education on MDC research strategies.

Methods
We conducted a 1-time, cross-sectional, web-based survey with 64 HIV clinical providers (physicians, physician assistants, and nurses) in Philadelphia. A descriptive analysis was generated to determine clinical providers’ awareness of MDC research strategies and attitudes toward patient outreach. Bivariate analyses were conducted to evaluate differences in awareness and attitudes by provider characteristics.

Results
Most providers were aware of MDC strategies, and nearly three-fourths of providers reported familiarity with 1 of the 2 Philadelphia MDC research programs. Providers overwhelmingly endorsed the need for clinicians to assist with patient outreach for HIV cure–directed research and were willing to recommend patients to participate. Enthusiasm for patient outreach waned if a study required a patient to undergo analytic treatment interruptions (ATIs). Providers identified preferred resources for receiving HIV cure–directed research updates, including webinars with continuing education credit and conferences.

Conclusions
Our study's findings advocate for added investment toward developing resources that better engage clinical providers about HIV cure–directed research updates and ongoing studies, including the importance of ATIs. As gatekeepers to patient participation on HIV cure–directed studies, added efforts to increase provider knowledge of specific HIV cure–directed research will advance patient education and ethical outreach.
Nontuberculous Mycobacterial Infective Endocarditis: A Systematic Review of Clinical Characteristics and Outcomes
Authors: Meena Durga Shankar , Kumar Deepak , Bohra Gopal Krishana , Midha Naresh , Garg Mahendra Kumar 
Published: November 2024

Abstract

Background
Infective endocarditis (IE) due to nontuberculous mycobacteria (NTM) is a rare infection, and several outbreaks have been reported in the last 2 decades. However, the clinical spectrum is still poorly understood. This systematic review aimed to evaluate the clinical characteristics and outcomes in NTM IE.

Methods
We searched the major electronic databases (PubMed, Scopus, and Google Scholar) with appropriate keywords to December 2023. We included studies based on predefined diagnostic criteria, and relevant data were collected on clinical presentation and treatment outcomes. The study was registered with PROSPERO (CRD42023492577).

Results
A total of 97 studies were reviewed, encompassing 167 patients with NTM IE. The earliest cases were reported in 1975, involving M chelonae and M fortuitum. M chimaera was the most prevalent species (38.9%), though rapidly growing NTM (RGM) were more common than slow-growing NTM (SGM; 59.3% vs 40.7%). Disseminated NTM infection occurred in 84% of cases, with bone marrow infiltration and osteomyelitis as frequent manifestations. Prosthetic valves were the main risk factor, present in 63.5% of cases. In native valve IE, nearly all cases (n = 27, 96%) were attributed to RGM. The overall mortality rate was 44.9%, with conservative management without surgery associated with poorer outcomes (66.7% vs 30.6%). Mortality was comparable between SGM and RGM IE, although relapses were more common in SGM IE (17.6% vs 1.9%).

Conclusions
This review highlights the changing epidemiology of NTM IE with the emergence of RGM IE. Disseminated infections in the setting of prosthetic valves warrant NTM evaluation. The high mortality rate necessitates the role of early surgery.
Ancient Bogeys
Authors: Kucharski Janek 
Published: November 2024

Abstract
That Lamia, Mormo, Empousa, and Gello—as well as a host of other, less well-known creatures such as Alphito, Kerko, and Ephialtes—constituted a distinct category of supernatural beings is already intimated in some ancient sources and explicitly acknowledged in a number of modern works. They are usually grouped under one common banner such as that of bogeys, untimely dead, or snake daimones. Yet none of these criteria can do full justice to each of these beings, their attested traits, functions, and backstories. This chapter therefore begins with a catalogue of differences which distinguish one creature from another. It is argued that there is no single criterion shared by all members of this category, and that their association with one another is based on the principle of family resemblances as described by Ludwig Wittgenstein.
Ghosts
Authors: Doroszewska Julia 
Published: November 2024

Abstract
This chapter begins with a distinction between ghosts that could be considered monsters and other kinds of ghostly creatures, providing the background for a firm delimitation of its subject matter. The chapter concerns ghosts understood as the dead who interact with the living in an unpleasant way, with an emphasis on their spontaneous apparitions rather than cases of their intentional or artificial provocation by the living (such as necromantic practices or katabaseis). The main steps in the discussion that follows include (1) the relevant vocabulary, with particular attention given to the overlapping and criss-crossing notions of daimon, phasma, larva, etc.; (2) the crucial distinction between the disembodied and embodied ghosts (revenants); (3) ancient ideas about their background: aoroi, agamoi, ataphoi, bi(ai)othanatoi (i.e. those who died prematurely, unmarried, unburied, or violently, respectively)—a discussion largely based on Tertullian’s De anima.
Gods and Monsters
Authors: Larson Jennifer 
Published: November 2024

Abstract
A common component in definitions of the monster is its challenge to categories. Yet not every category violation yields a monster. Deviation from the essential norm of a living kind (or perfect adherence to an essential norm) is what allows animals to function symbolically. Like gods and ‘perfect’ animals, monsters perform symbolic work. Human cognition helps to shape what we find monstrous: innate attentional biases sharpen our awareness of missing or misshapen body parts, while large predators of all kinds are impossible to ignore. Pascal Boyer’s theory of minimally counterintuitive concepts explains why monster body plans follow predictable patterns, and why their deviations tend to be limited in number and degree, simple enough to transmit accurately. Finally, the work of Dan Sperber on the ‘epidemiology of representations’ can help to illuminate the transmission of monster representations from the ancient Near East to the Greek world.
The Revival of Classical Monsters in the Italian Renaissance
Authors: Freedman Luba 
Published: November 2024

Abstract
This chapter emphasizes the intellectual contributions of the Italian Renaissance (between 1445 and 1550) to post-antique depiction of classical monsters, including centaurs, sirens, sphinxes, harpies, satyrs, Tritons, Nereids, Pegasus, Cerberus, the Gorgon Medusa, Argus, and Polyphemus. Apart from Tritons and Nereids, these are all monsters mentioned in Dante’s Commedia and glossed in the commentaries to the poem. Renaissance humanists studied Greek and Latin texts with an eye to the classical authors’ historical reality. They revealed both the role played by classical monsters in the poetry of myths and the placement of their sculpted images in sacred precincts. Working in collaboration with humanists, artists restored classical monsters to their classical forms. They did so while adapting them to the new reality, imbuing their images with ethical interpretations. Renaissance innovations not only reintroduced classical monsters into contemporary culture, but also established new marvellous models for subsequent generations.
Classical Monsters in Modern Popular Culture
Authors: Gloyn Liz 
Published: November 2024

Abstract
This chapter turns away from mainstream commercial receptions of classical monsters to explore their rich afterlife in a more democratic form of popular culture, namely fan fiction. The rise of the internet, fan culture, and freely accessible technology has meant that ‘fans’ of classical monsters can now create their own versions of their favourite creatures which may remain ephemeral or (appropriately enough) go viral. These monsters are characterized by multiple manifestations and interpretations unaffected by interventions from creative and economic gatekeepers. Through analysis of sample case studies taken from the fan fiction website Archive of Our Own, including Medusa and the Minotaur, this chapter argues that fanfic allows classical monsters to connect to broader social patterns of deploying monstrosity, particularly around LGBT+ identity. It also reflects on the potential productivity of seeing ancient myth as a fandom in its own right.
Ancient Monsters in Modern Science
Authors: Felton Debbie 
Published: November 2024

Abstract
The monsters of ancient myth made their way into modern science principally through the method of taxonomic nomenclature developed by Linnaeus as part of his biological classification system, but also via general surviving knowledge of and interest in the ancient stories. This chapter, focusing mainly on the natural and applied sciences, discusses how and why these mythical monsters remain relevant. Examples from astronomy, various biological sciences (e.g. botany, entomology, herpetology, genetics), and computer science, demonstrate how scholarship in STEM fields frequently draws upon the monsters of classical and other mythologies, drawing connections between current living organisms or inventions and the monsters’ unusual physical features, odd behaviours, and even their geological habitats. Appreciation of ancient myth is not limited to students of the humanities.
The ‘Monster-Harbouring Sea’
Authors: Ingemark Dominic , Ingemark Camilla Asplund 
Published: November 2024

Abstract
Views of the sea in antiquity were ambivalent. There can be little doubt that the societies were dependent on seafaring; moreover, it offered many opportunities. Equally, however, the sea was associated with death and hence evoked a sense of dread. What was feared was not only the violent nature of the sea itself, but also the dreadful creatures that were thought to dwell in its depths. Indeed, the notion of the sea teeming with monsters is frequently found in ancient literature, for instance Homer wrote about the ‘monster-harbouring sea’. This chapter focuses on that aspect: on the one hand, sea monsters and sea-serpents found in mythical accounts, such as those threatening Andromeda, Hesione, and Laocoön; on the other, the monstrous beasts featuring in various legends, such as giant octopuses and killer whales. A common theme is how the aforementioned ambivalent views of the sea came to influence these narratives.
Sentimentalism and the Gendered Aesthetics of Global Realisms
Authors: Hoogenboom Hilde 
Published: November 2024

Abstract
Only in the twentieth century did realism come to dominate our understanding of nineteenth-century arts. A historical approach to realism reveals that in the nineteenth-century debates about aesthetics, realism was the underdog, while sentimentalism remained dominant, led by George Sand. A renewed appreciation of sentimentalism shows that its power lay in the struggle over virtue and the restraint of passions, for the greater good. The debate between these opposing aesthetics was often the subject of European, American, and later Russian novels, which deployed a hybrid aesthetic called “sentimental realism.” Sentimentalism’s ruthless pursuit of virtue found a worthy opponent in realism’s ruthless pursuit of truth. In this debate, women were denigrated as insipid sentimental novelists, while men sought their market success by adapting sentimentalism’s struggle over virtue to realism. The recovery of this global gendered debate reveals the importance of women writers, translations, and global bestsellers and transforms our understanding of the career of George Sand and literature in Russia, which lay at the frontier of the globalization of novels. Through 1850, Russia initially imported and translated 90% of the novels that Russians read. Russians translated Sand’s novels more quickly and in greater quantities than other countries. Once Russians began to export their novels in the 1880s, Sand’s influence was key to their branding as profound and humane, as they made their way to Europe, America, Asia, and beyond. Finally, global sentimental realist novels created rich and contradictory national and international communities, both including and excluding people.