bluuebunny/crossref_metadata_2025_split huggingface dataset:
OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers
Authors: Zhang Yangjun , Liu Kai , Xu Zhenzhen , Li Bo , Wu Xiaoliang , Fan Ruixin , Yao Xiangyang , Wu Huahui , Duan Chen , Gong Yan , Chen Ke , Zeng Jin , Li Lu , Xu Hua 
Published: November 2024

Abstract
Alternative splicing (AS) is a crucial mechanism to regulate gene expression and protein complexity. RNA-binding proteins (RBPs) play an important role in regulating abnormal alternative splicing in cancers. However, few resources are available to identify specific RBPs responsible for regulating individual AS event. We have developed the OncoSplicing database for integrative analysis of clinically relevant alternative splicing events in TCGA cancers. Here, we further updated the OncoSplicing database by performing correlation analysis between the splicing and mRNA expression data from the TCGA cancers or GTEx tissues, mapping known RNA-binding motifs and eCLIP-seq peaks to all AS events, conducting splicing analysis for RNA-seq data from RBP perturbation experiments in the ENCODE project, and integrating exon and intron sequences for each AS event. With this updated database, users can easily identify potential RBPs responsible for the queried AS event and obtain sequences to design AS-specific primers and minigene constructs for experiment validation. Overall, compared to the previous version, the substantially updated OncoSplicing database (www.oncosplicing.com) offers a more valuable resource for users to identify RBPs responsible for regulating alternative splicing events in cancers.
The STRING database in 2025: protein networks with directionality of regulation
Authors: Szklarczyk Damian , Nastou Katerina , Koutrouli Mikaela , Kirsch Rebecca , Mehryary Farrokh , Hachilif Radja , Hu Dewei , Peluso Matteo E , Huang Qingyao , Fang Tao , Doncheva Nadezhda T , Pyysalo Sampo , Bork Peer , Jensen Lars J , von Mering Christian 
Published: November 2024

Abstract
Proteins cooperate, regulate and bind each other to achieve their functions. Understanding the complex network of their interactions is essential for a systems-level description of cellular processes. The STRING database compiles, scores and integrates protein–protein association information drawn from experimental assays, computational predictions and prior knowledge. Its goal is to create comprehensive and objective global networks that encompass both physical and functional interactions. Additionally, STRING provides supplementary tools such as network clustering and pathway enrichment analysis. The latest version, STRING 12.5, introduces a new ‘regulatory network’, for which it gathers evidence on the type and directionality of interactions using curated pathway databases and a fine-tuned language model parsing the literature. This update enables users to visualize and access three distinct network types—functional, physical and regulatory—separately, each applicable to distinct research needs. In addition, the pathway enrichment detection functionality has been updated, with better false discovery rate corrections, redundancy filtering and improved visual displays. The resource now also offers improved annotations of clustered networks and provides users with downloadable network embeddings, which facilitate the use of STRING networks in machine learning and allow cross-species transfer of protein information. The STRING database is available online at https://string-db.org/.
GenBank 2025 update
Authors: Sayers Eric W , Cavanaugh Mark , Frisse Linda , Pruitt Kim D , Schneider Valerie A , Underwood Beverly A , Yankie Linda , Karsch-Mizrachi Ilene 
Published: November 2024

Abstract
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public data repository that contains 34 trillion base pairs from over 4.7 billion nucleotide sequences for 581 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. We summarize the content of the database in 2025 and recent updates such as accelerated processing of influenza sequences and the ability to upload feature tables to Submission Portal for messenger RNA sequences. We provide an overview of the web, application programming and command-line interfaces that allow users to access GenBank data. We also discuss the importance of creating BioProject and BioSample records during submissions, particularly for viruses and metagenomes. Finally, we summarize educational materials and recent community outreach efforts.
Yield of Targeted Polymerase Chain Reaction in Probable Early-Onset Sepsis: A Prospective Cohort Study in Term and Near-Term Neonates With Negative Blood Culture Results
Authors: Keij Fleur M , Klaassen Corné H W , Kornelisse René F , van Westreenen Mireille , Tramper-Stranders Gerdien A 
Published: November 2024

Abstract

Background
Discriminating noninfected from infected neonatal cases remains challenging, and subsequently many neonates are treated with antibiotics in the first week of life. We aimed to study the additional value of a targeted polymerase chain reaction (PCR) for group B streptococcus (GBS) and Escherichia coli on leftover blood culture media from term and near-term neonates with probable early-onset sepsis (EOS).

Methods
Leftover blood culture material from neonates participating in the RAIN study was stored after 5 days of incubation. The RAIN study evaluated intravenous-oral antibiotic switch in probable bacterial infection, defined as risk factors and/or clinical signs and elevated inflammatory parameters but negative blood culture results. We applied 2 targeted PCRs for GBS and E coli, the main pathogens in EOS, and analyzed the samples batchwise in triplicate for each PCR.

Results
PCR was performed in triplicate on blood culture media from 284 neonates. In 23 neonates, the PCR result was positive (3 cycle threshold values &lt;37) for GBS (n = 1) or E coli (n = 22). Inflammatory parameters did not discriminate for positive PCR result, nor did risk factors for sepsis, such as maternal GBS status and prolonged rupture of membranes. However, 96% of neonates with a positive PCR result were born vaginally vs 74% in the PCR-negative group (P = .05); furthermore, 96% vs 81% (P = .21) of neonates had clinical symptoms.

Conclusions
Blood culture–negative “probable” EOS in neonates is accompanied by an 8% rate of PCR positivity, suggesting low-grade bacteriemia after birth with yet unclear clinical consequences. Further research should focus on how PCR can contribute to more targeted antibiotic use of neonates, specifically in those highly suspected of infection but in the absence of a positive blood culture result.
Relapse-free survival with adjuvant dabrafenib/trametinib therapy after relapse on a prior adjuvant CPI in BRAF V600-mutated stage III/IV melanoma
Authors: Weber Jeffrey , Haque Waqas , Markovic Svetomir N , Salama April K S , Mehmi Inderjit , Sullivan Ryan J , Najjar Yana G , van Akkooi Alexander C J , Menzies Alexander M , Long Georgina V , Taylor Amelia M , Haanen John , Zijlker Lisanne P , Davis Keith L , Karanth Siddharth , Norton Deborah , Connolly Lucy 
Published: November 2024

Abstract

Background
In BRAF-mutated high-risk melanoma, targeted therapy (BRAF/MEK inhibitors) and checkpoint inhibitor (CPI) immunotherapy have durable benefits as first-line (1L) adjuvant therapy. Based on differing action mechanisms of BRAF/MEK inhibitors and CPI immunotherapies, there is interest in evaluating the activity of 2L adjuvant targeted therapy in decreasing the risk of subsequent recurrence after repeat resection following relapse on/after 1L adjuvant CPI.

Patients and methods
This was a retrospective review of BRAF V600-mutated resected stage III/IV melanoma patients in the United States, Australia, and The Netherlands who received 1L adjuvant CPI immunotherapy, relapsed locoregionally/distantly, were again resected to no evidence of disease, and received dabrafenib/trametinib (dab/tram) as 2L adjuvant therapy. The primary endpoint was relapse-free survival (RFS) from initiation of 2L adjuvant dab/tram (RFS-2), analyzed via Kaplan-Meier methods.

Results
Thirty-eight patients were included (median age 50 years, 63% male, 87% stage III, median follow-up 19 months from 2L dab/tram initiation). Median dab/tram duration was 10.1 months (range: 1 day–22.7 months), with half discontinuing due to progression or adverse events. Median (95% CI) RFS-2 was 18.9 (14.9–28.1) months, with 91%, 81%, and 58% remaining relapse-free at 6, 12, and 18 months, respectively. Most patients remained distant metastasis-free at 6, 12, and 18 months (97%, 85%, and 71%, respectively). Two patients were deceased at the last follow-up, with 97% alive at 18 months.

Conclusions
Over 80% of patients remained relapse- and metastasis-free at 12 months after 2L dab/tram initiation, with only 2 deaths observed. Dab/tram appears to have activity in the 2L adjuvant setting, although more follow-up is required.
Leptin levels are associated with coronary artery calcification in patients with advanced prostate cancer
Authors: Koutroumpakis Efstratios , Venkatesh Neha , Aparicio Ana , Song Juhee , Panaretakis Theocharis , Deswal Anita , Logothetis Christopher J , Frigo Daniel E , Hahn Andrew W 
Published: November 2024

Abstract

Background
Convergent data suggest that advanced prostate cancer and coronary heart disease (CHD) share biological vulnerabilities that may be linked to adiposity. Here we explore whether leptin, as a marker and mediator of adiposity, could link prostate cancer to CHD.

Methods
Patients with metastatic castration-resistant prostate cancer (mCRPC) enrolled in a phase II trial (NCT02703623) studying androgen deprivation therapy, abiraterone, prednisone, and apalutamide were eligible if they had plasma and a chest CT scan available. Coronary artery calcium (CAC) scores and adipokine levels were measured upon enrollment.

Results
Of 164 patients, 87% were white. The mean age was 65.6 ± 7.5 years, 88% were either overweight or obese, 59% had hypertension, 48% had hyperlipidemia (HLD), 20% had type 2 diabetes mellitus, and 41% were former or current smokers. Coronary calcifications were found in 115 patients (70%). Among 47 patients with non-contrast chest CT scans, the median total CAC score was 133 AU (IQR 22.6-704.6). Four patients (9%) had a score of 0 AU (low risk) and 24 (51%) scores ≥100 AU, associated with high risk for major adverse cardiovascular events. Leptin levels correlated positively with the right coronary artery (RCA) CAC score [Pearson correlation coefficient (ρ) = 0.3715 (P = .0142)]. In a multivariate logistic regression analysis, older age, HLD, and higher leptin levels were independently associated with RCA calcification and a higher number of calcified coronary arteries.

Conclusion
Among men with mCRPC, there was a high burden of CHD, and higher leptin levels were associated with coronary atherosclerosis independently of traditional cardiac risk factors.
Objects in Transit
Authors: Pizzato Fedra A. 
Published: November 2024

Abstract
A widespread view in archaeology holds that, without a systematization in the proper scientific framework, a collection of artifacts is just a bunch of old things. By adopting a novel perspective, which combines science studies and cultural studies, the aim of this chapter is to show that archaeological collecting can be regarded as a form of sociability and therefore imbued with social, political, and cultural values. It is also argued that one of the goals of a historian of archaeology is to decontextualize and recontextualize archaeological objects, that is to address them as scientific, discursive, epistemic, and boundary objects. The importance of the history of collections for subaltern and gender studies applied to archaeology is also explored. Reframing the history of collections in this fashion enables us to better see historical continuities and to appreciate the history of archaeology in a long-durée perspective. Finally, some recent trends in museum practices are considered. One of them—digitalization—suggests new possibilities for the elaboration of a novel history of archaeology throughout the study of historical collections.
International Congresses in the History of Archaeology
Authors: Sommer Ulrike 
Published: November 2024

Abstract
The chapter follows the history of international congresses between 1866 and the present, with a special emphasis on the relationship between the development of international scholarly communication and politics. The Congrès international d’Anthropologie et d’archéologie Préhistoriques was founded in 1865 and met, with decreasing regularity, till 1912. For practical purposes, this predominantly European association ended with World War I among nationalist animosities. The interwar years saw the French-dominated Institut international d’Anthropologie and the foundation of the Congrès international des Sciences pré- et protohistoriques, the latter placing emphasis on political neutrality and the inclusion of scholars from all nations, irrespective of their ideology. This congress is still in existence in the guise of the Union international des Sciences pré- et protohistoriques. The year 1986 saw the foundation of the anglophone World Archaeological Congress, which aimed at inclusivity beyond the First World and academics; which understands itself as a partisan and explicitly political body.
Collecting Antiquities in the Nineteenth Century
Authors: Achim Miruna 
Published: November 2024

Abstract
In the course of the nineteenth century, pre-Hispanic artifacts became an archaeological category—both plastic enough to adapt to local needs and robust enough to become recognizable and valuable aesthetically, epistemologically, and commercially. Starting from the premise that antiquities do not have intrinsic meanings, but acquire them as they move geographically and conceptually, this chapter draws on an ecological approach to study the connections and follow the trajectories of three collections of a specific case study—Mexican antiquities at the National Museum of Mexico in Mexico City, at the American Philosophical Society in Philadelphia, and at the Louvre (whose collection of Mexican antiquities was later incorporated into the Ethnographic Museum at the Trocadéro, in Paris). The chapter compares the ways in which Mexican antiquities were configured by temporally and spatially situated institutional ecologies, with their specific intellectual traditions, disciplinary practices, political agendas, aesthetic sensibilities, technologies of classification and representation, and social and material infrastructures. Ultimately, the chapter reflects on the tangled, often contingent, processes by which the past matters to the present.
Adorno’s Ethical Materialism
Authors: Whyman Tom 
Published: November 2024

Abstract
When scholars use the word “materialism,” in either a specifically Marxist or generally philosophical sense, the term is not applied in such a way that it would seem to be inclusive of the work of Theodor Adorno: Adorno was not a deterministic historical materialist nor was Adorno a reductionist philosopher of mind. However, Adorno frequently invokes “materialist” motifs at prominent points throughout his work: his philosophical outlook was, at least in terms of his own self-conception, always a “materialist” one. This chapter clears up any mysteries surrounding Adorno’s materialism by explaining that he was an “inclusive” (as opposed to “exclusive”) materialist—and that the main point of his holding the version of materialism that he did, was to make an ethical point, as opposed to a metaphysical one.
The Chimaera
Authors: Smith R. Scott 
Published: November 2024

Abstract
The Chimaera—part lion, part goat, and part serpent—offers an unforgettable image of a monster that remains useful today for exploring hybridity. As is typical, the monster acted as a foil for a Greek hero, in this case Bellerophon from Corinth. After covering the most important early sources and artwork from the Greek period, this chapter will consider the Lycian setting of the myth and assess the theories that assert that the image and myth of the Chimaera developed in the east, even though there is no exact analogy for the Chimaera to be found in Near Eastern art. This chapter takes the position that, whatever the origins of the beast, the Chimaera and the myths that surround it are uniquely Greek. In addition, this chapter recounts the rationalizing and allegorical interpretations that later ancient Greeks brought to bear to explain the creation of this fantastical hybrid.
Image and Monster in Ancient Greek Art
Authors: Winkler-Horaček Lorenz 
Published: November 2024

Abstract
From the seventh century bce on, images of monsters are gradually linked to ancient mythological stories. Examples show to what extent the same myth images can have very different meanings in different eras. Through these images, the myth is rooted in its temporal context and can be connected to the questions, fears, and hopes specific to each period. The monsters differ not only in their physical composition, but also in their respective ability to communicate. As myth images, they play an identity-forming role, whether as part of the development of Greek poleis and the confrontation with the unknown peripheries of the world, or as a visualization of enemies. They stand for the uncivilized and hostile but are not limited to this: the case of the centaurs also shows an ambivalent attitude towards ‘monsters’. Outside the myth images we also find monsters in ancient imagery as part of different taxonomic world views.
Ancient Monsters in Modern Speculative Fiction
Authors: Stevens Benjamin Eldon , Weiner Jesse , Rogers Brett M. 
Published: November 2024

Abstract
This chapter examines how monsters from ancient Greek and Roman materials may be found in every genre and medium of modern speculative fiction: in science fiction, horror, and fantasy, and in formats including print, film and television, and games. It first argues that ancient monsters continue to do what they did in classical sources: they ‘demonstrate’ or reveal the imaginary but consequential boundaries that separate categories of being, especially ‘human’ and ‘natural’ from purported ‘others’, and indicate the limits of human knowledge. Next it describes three examples—the Cyclops, Medusa, and the Minotaur—to suggest the complexity of reception histories and of interrelated definitions of monster/monstrosity and human/humanity. The chapter explores an understanding of modern speculative fiction in terms of Promethean science fiction, Sphinxian horror, and Protean fantasy. It concludes by examining how two modern monsters—Frankenstein’s Creature and the Kraken—in their classical entanglements are suggestive of a potential teratopolitics.
Documentary Forms and Realist Theater
Authors: Kempf Lucie 
Published: November 2024

Abstract
The notion of realism in theater is fundamentally problematic because even though it tries to recreate the illusion of reality on stage, everything in the performance is in fact based on theatrical conventions. During the performance the spectator agrees to believe in the existence of the “fourth wall,” pretending that what they see is “real life” and not a work of fiction staged by actors: in other words, an attempt to reproduce reality. However, the aim of documentary theater is not to reproduce reality but to immerse the spectator in it. It does not rely on dramatic art, that is, on works of fiction, but on “documents,” whatever their material form. In the documentary theater productions created by two Russian theaters, Teatr.doc and KnAM, the spectator is confronted with testimonies and invited to compare them to their own life experience. This chapter examines the way contemporary documentary theater breaks the theatrical codes of the realist tradition by suppressing mediation: fiction is replaced by documents, theatrical text by journalistic-style investigations; the author disappears behind collective stage composition; characters give way to actors, who sometimes speak in their own name, or even to witnesses who are not professional actors.
Undoing Italy with Ferrante, Sapienza, Scego, and Lahiri
Authors: Bazzoni Alberica 
Published: November 2024

Abstract
This chapter begins with the global success of Elena Ferrante’s tetralogy known as the Neapolitan Novels to sketch an alternative configuration of contemporary Italian literature based on a transnational approach. The author places Ferrante next to case studies of transnational success (Goliarda Sapienza), postcolonial narrative (Igiaba Scego), and translingual authorship (Jhumpa Lahiri) that showcase the porosity of the boundaries of a national canon. Considered together, these authors reveal and institute difference at the very heart of Italian identity, and concomitantly place Italian literature into a transnational network of references and readerships. Reflecting on diverging methodologies and disciplinary confines at play in canon formation in Italian studies in Italy and in Anglophone academia, the chapter foregrounds the categories of trauma, gender, translingualism, hybridity, and multiplicity of identity as central to the definition of a transnational corpus of contemporary literature in Italian. The chapter is divided into two parts: the first addresses a transnational perspective in Italian studies, argues for an enlarged canon that is representative of difference within contemporary literature in Italian, and describes the analytical categories that emerge from the application of a transnational approach to the selected hybrid corpus. The second part introduces works by Ferrante, Sapienza, Scego, and Lahiri, and offers a snapshot of the working of this approach and these categories in these authors’ production.
Lived Buddhism and Mount Wutai, China, in the Northern Dynasties (439–589) and Tang (618–907) Periods
Authors: Andrews Susan 
Published: November 2024

Abstract
This chapter explores how Buddhism and religion more broadly figured in the ordinary lives of humans dwelling nearby Mount Wutai (Wutai shan 五臺山, the Mountain of Five Plateaus) in the sixth and seventh centuries. Focusing on stories compiled in Huixiang’s 慧祥 (ca. seventh century)Ancient Chronicle of Mount Clear and Cool (Gu Qingliang zhuan 古清涼傳)—particularly tales preserved in its less often-studied, final “Miscellaneous Accounts of Branches and Tributaries” (Zhiliu zashu 支流雜述) chapter––the work highlights food’s centrality to lived religion in this setting. It argues that the narratives collected in this fascinating source give voice to tensions surrounding the encounter between long-standing local foodways and Buddhist perspectives and practices related to food’s procurement, distribution, and consumption introduced to the region as part of its reimagining as the center of the Bodhisattva Mañjuśrī cult.
Noli me Tangere in a Reflection on Touch, Taboo, Clergy Child Sexual Abuse, and Pastoral Care
Authors: Demasure Karlijn 
Published: November 2024

Abstract
The phrase “Noli me tangere” (Do not touch me) is the Latin translation of a passage from John 20:17, in which the risen Jesus meets Mary Magdalene, and prohibits her not to touch him “because I have not yet ascended to the Father” (NRSV). Interpretations vary as to why Jesus refused to be touched by Mary Magdalene, and this essay places the passage in the context of clergy sexual abuse within the Catholic Church. “Noli me tangere” is typically uttered in a register of warning before a danger. Physical and sexual touching can cause harm and leave marks on the victim, and victims/survivors feel defiled and have a distorted view of their body and often do not like to be touched. Sexual relations between a child and an adult belong to the realm of taboo. The transgression of a taboo leads to the feeling of defilement and shame. A closer look at the characteristics of the sense of touch explains why the child feels involved in the act of sexual abuse. Provided with these insights, the author explores their implications for the use of touch in the care of victims/survivors of clergy sexual abuse.