bluuebunny/crossref_metadata_2025_split huggingface dataset:
PubChem 2025 update
Authors: Kim Sunghwan , Chen Jie , Cheng Tiejun , Gindulyte Asta , He Jia , He Siqian , Li Qingliang , Shoemaker Benjamin A , Thiessen Paul A , Yu Bo , Zaslavsky Leonid , Zhang Jian , Bolton Evan E 
Published: November 2024

Abstract
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a large and highly-integrated public chemical database resource at NIH. In the past two years, significant updates were made to PubChem. With additions from over 130 new sources, PubChem contains &gt;1000 data sources, 119 million compounds, 322 million substances and 295 million bioactivities. New interfaces, such as the consolidated literature panel and the patent knowledge panel, were developed. The consolidated literature panel combines all references about a compound into a single list, allowing users to easily find, sort, and export all relevant articles for a chemical in one place. The patent knowledge panels for a given query chemical or gene display chemicals, genes, and diseases co-mentioned with the query in patent documents, helping users to explore relationships between co-occurring entities within patent documents. PubChemRDF was expanded to include the co-occurrence data underlying the literature knowledge panel, enabling users to exploit semantic web technologies to explore entity relationships based on the co-occurrences in the scientific literature. The usability and accessibility of information on chemicals with non-discrete structures (e.g. biologics, minerals, polymers, UVCBs and glycans) were greatly improved with dedicated web pages that provide a comprehensive view of all available information in PubChem for these chemicals.
The Chemical Probes Portal – 2024: update on this public resource to support best-practice selection and use of small molecules in biomedical research
Authors: Sanfelice Domenico , Antolin Albert A , Crisp Alisa , Chen Yi , Bellenie Benjamin , Brennan Paul E , Edwards Aled , Müller Susanne , Al-Lazikani Bissan , Workman Paul 
Published: November 2024

Abstract
The Chemical Probes Portal (www.chemicalprobes.org) is a free, public resource, based on expert-reviews, that supports the assessment, selection and use of small-molecule compounds that qualify as chemical probes. These high-quality reagents are essential for exploring the function of individual proteins in complex biological systems, such as cells and organisms, and for validating proteins as potential therapeutic targets. The use of reliable chemical probes accelerates protein annotation in basic biological studies and informs drug discovery. However, the use of low-quality compounds has historically led to erroneous conclusions in biomedical research, and experience shows that failure to follow best practice continues, an issue which the Portal aims to address. Here, we describe the latest updates to the Chemical Probes Portal in both content and functionality. The number of chemical probes and human protein targets covered has increased significantly, with improvements in the processes for obtaining expert reviews and user engagement. Moreover, new functionalities and enhanced tools have been introduced to better support biological researchers in selecting and using the best chemical probes for their studies.
Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans
Authors: Schiksnis Erin C , Nicastro Ian A , Pasquinelli Amy E 
Published: November 2024

Abstract
Organismal aging is marked by decline in cellular function and anatomy, ultimately resulting in death. To inform our understanding of the mechanisms underlying this degeneration, we performed standard RNA sequencing (RNA-seq) and Oxford Nanopore Technologies direct RNA-seq over an adult time course in Caenorhabditis elegans. Long reads allowed for identification of hundreds of novel isoforms and age-associated differential isoform accumulation, resulting from alternative splicing and terminal exon choice. Genome-wide analysis reveals a decline in RNA processing fidelity. Finally, we identify thousands of inosine and hundreds of pseudouridine edits genome-wide. In this first map of pseudouridine modifications for C. elegans, we find that they largely reside in coding sequences and that the number of genes with this modification increases with age. Collectively, this analysis discovers transcriptomic signatures associated with age and is a valuable resource to understand the many processes that dictate altered gene expression patterns and post-transcriptional regulation in aging.
MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface
Authors: Samarasinghe Kasun W , Kotlyar Max , Vallet Sylvain D , Hayes Catherine , Naba Alexandra , Jurisica Igor , Lisacek Frédérique , Ricard-Blum Sylvie 
Published: November 2024

Abstract
MatrixDB, a member of the International Molecular Exchange consortium (IMEx), is a curated interaction database focused on interactions established by extracellular matrix (ECM) constituents including proteins, proteoglycans, glycosaminoglycans and ECM bioactive fragments. The architecture of MatrixDB was upgraded to ease interaction data export, allow versioning and programmatic access and ensure sustainability. The new version of the database includes more than twice the number of manually curated and experimentally-supported interactions. High-confidence predicted interactions were imported from the Integrated Interactions Database to increase the coverage of the ECM interactome. ECM and ECM-associated proteins of five species (human, murine, bovine, avian and zebrafish) were annotated with matrisome divisions and categories, which are used for computational analyses of ECM -omic datasets. Biological pathways from the Reactome Pathway Knowledgebase were also added to the biomolecule description. New transcriptomic and expanded proteomic datasets were imported in MatrixDB to generate cell- and tissue-specific ECM networks using the newly developed in-house Network Explorer integrated in the database. MatrixDB is freely available at https://matrixdb.univ-lyon1.fr.
The Immune Epitope Database (IEDB): 2024 update
Authors: Vita Randi , Blazeska Nina , Marrama Daniel ,   IEDB Curation Team Members, Shackelford Deborah , Zalman Leora , Foos Gabriele , Zarebski Laura , Chan Kenneth , Reardon Brian , Fitzpatrick Sidne , Busse Matthew , Coleman Sara , Sedwick Caitlin , Edwards Lindy , MacFarlane Catriona , Ennis Marcus , Duesing Sebastian , Bennett Jason , Greenbaum Jason , De Almeida Mendes Marcus , Mahita Jarjapu , Wheeler Daniel K , Cantrell Jason R , Overton James A , Natale Darren A , Sette Alessandro , Peters Bjoern 
Published: November 2024

Abstract
Over the past 20 years, the Immune Epitope Database (IEDB, iedb.org) has established itself as the foremost resource for immune epitope data. The IEDB catalogs published epitopes and their contextual experimental data in a freely searchable public resource. The IEDB team manually curates data from the literature into a structured format and spans infectious, allergic, autoimmune, and transplant diseases. Here, we describe the enhancements made since our 2018 paper, capturing user-directed updates to the search interface, advanced data exports, increases in data quality, and improved interoperability across related resources. As we look forward to the next 20 years, we are confident in our ability to meet the needs of our users and to contribute to the broader field of data standardization.
How Psychedelic, Religious, Spiritual, Mystical Experiences Become Effective
Authors: Koch Anne 
Published: November 2024

Abstract
The concept of “efficacy” is dually grounded in theory and in individual experience. On the one hand, it is a key issue in many religious practices, from intercessory prayer to healing rituals. On the other hand, the concept concerns causality, belief, and intentionality and is here localized within recent discussions of predictive mind and embodied cognition and related to the construction of the “really real” within religions. The practices of gaining a new conviction, sensing a healing energy, or synchronizing heart rates raise the important question of how we come to have beliefs or give them up according to apparent evidence. Religions set frameworks for those processes whose underlying cognitive and psychophysiological mechanisms, as well as cultural aesthetic strategies, are elaborated against the background of placebo research, ritual theory, aesthetics of religion, and the cognitive study of religion. Basic aesthetic categories—like aestheticscapes, time perception, absorption, ritual enactment, evaluation, synchronous speech, and tool use—are expounded on to improve our understanding of components of efficacy, like, for example, the role of belief systems as expectations and prediction precision estimates, familiarity with the healing narrative, charisma of the healer, and collective alignment.
Monumental Monsters
Authors: Oswald Simon 
Published: November 2024

Abstract
This chapter examines the form and function of monsters adorning Greek monumental architecture. An overview is provided of the types of monsters encountered and the many places they could manifest themselves in the design of a building. Temples, in particular, provided a meeting place where a multitude of monsters from different myths could mingle across the greater aesthetic programme, though, interestingly, certain monsters, such as gorgons, appeared much more frequently than others, such as satyrs, who are rarely attested at all. While no one theory adequately accounts for all the monsters of monumental architecture, those more narrowly focused offer important insights. The frequent depiction of scenes of Centauromachies and Gigantomachies in sculptural programmes, for example, was likely because the myths were easily identifiable and communicated generic moral messages relating to codes of moral conduct and the consequences of transgressing them.
Spawned from the Nile
Authors: Boychenko Leanna 
Published: November 2024

Abstract
From literature and art to politics and religion, Greeks and Romans incorporated Egyptian monsters into many important cultural institutions, sometimes drawing directly from an Egyptian monster or demon, but at other times, twisting a more benevolent creature and creating a monster. Beginning with the giant snake in the Middle Kingdom’s ‘Tale of the Shipwrecked Sailor’ and its connections to the Odyssey, this chapter examines several anchoring examples of the different ways that Egyptian monsters interact with Greek and Roman culture. A monster-fighting scene from the Book of the Dead becomes Medea’s battle against the bronze man Talos in the Argonautica. Hybrid divinities like the heart-swallowing monster Ammut parallel the Graeco-Roman sphinx. As a result of the power crisis following the break-up of Rome’s Second Triumvirate, Egypt itself becomes monstrous, ruled by the infamous Cleopatra. The land of the Nile provided ample material to stimulate the Greek and Roman imagination, especially in terms of monsters.
Social Movements and International Law in Latin America
Authors: Olarte-Olarte María Carolina , Galvis Castro Felipe 
Published: November 2024

Abstract
This article offers an approach to the relationship between international law (IL) and Latin American social movements (LASM). In the first place, it reminds the two-way interplay of LASM with some international institutions and rules. It then moves to discuss certain LASM experiences with IL ranging from questioning it and using it from an alternative perspective, to deliberately reformulate its terms and seek better ways to use it in daily struggles. It highlights LASM practices regarding institutional arenas and, more importantly, extra-institutional mobilization. Thus, this contribution attempts to show the richness, creative, and pressing value of LASM uses of IL, beyond any pretension of purism or correctness. At the bottom of this chapter is a challenge to the assimilations and institutional registry of social movements as subaltern users of IL, which fits the lack of genuine popular influence in global decision making.
(Un)Governing Assembly
Authors: Hamilton Michael 
Published: November 2024

Abstract
Legal requirements for organizing an assembly often require the submission of prior notification or an application for a permit. But why is the act of assembling with others—one foundational to social and political life (and generally constitutionally protected)—routinely subject to mandatory procedural regulation? This chapter explores why human rights law appears to have so readily conceded the legitimacy of these anticipatory forms of regulatory control. Echoing C. Edwin Baker’s clarion call to fundamentally ‘rethink the issue’, it presents a manifesto for jettisoning mandatory notification requirements in favour of voluntary schemes. Far from ushering in a chaotic system that would render the state incapable of satisfying its obligations to protect the different rights engaged, voluntary notification systems can achieve the purported gains of mandatory requirements while preserving the agency of the assembled people and helping restore some intelligibility to a muddled area of international human rights law.
Emotions and the Visual Representation of Human Suffering
Authors: Auchter Jessica 
Published: November 2024

Abstract
This chapter discusses the connections between emotions and visual representation. It begins by examining how visual representation is often granted a privileged status as the way emotion is rendered accessible. This chapter offers a skeptical view of this notion that the visual is the only, or at least the key, way of accessing emotions, noting that this can reify particular types of representations, especially photographs. It suggests that, through this claim, photographs become reified as truth even more because they purportedly grant access to the unrepresentable “real” of the realm of emotion. Rather than considering specific visual representations such as images or media representations, the chapter instead considers the visual grammar through which emotional encounters occur in international relations (IR), including how emotions become visible to the researcher, particularly in the context of research on human suffering, a key subject of IR study.
Therapeutic Dilemma: Melatonin or not?
Authors: Ratnapalan Savithiri , Rieder Michael 
Published: November 2024

ABSTRACT
Sleep disturbances are common in childhood, especially among neurodivergent children. There are few proven therapeutic options. Melatonin is a hormone that is critical to the normal human sleep cycle. Melatonin therapy has been proven to be effective in adults with jet lag and there is emerging evidence that it may be of value when used in low doses for neurodivergent children. There is however no evidence that melatonin is of utility in addressing sleep problems in otherwise well children.
Deconstructing the Yield Curve
Authors: Crump Richard K , Gospodinov Nikolay 
Published: November 2024

Abstract
We introduce a novel nonparametric bootstrap for the yield curve that is agnostic to the true factor structure of interest rates. We deconstruct the yield curve into primitive objects, with weak cross-sectional and time-series dependence, that serve as building blocks for resampling the data. We analyze the properties of the bootstrap for mimicking salient features of the data and conducting valid inference. We demonstrate the benefits of our general method by revisiting the predictability of bond returns based on slow-moving fundamentals. We find that trend inflation, but not the equilibrium real rate, has predictive power for future bond returns.
The Occupation Content of Trade
Authors: Kruse Hagen , Timmer Marcel P , de Vries Gaaitzen J , Ye Xianjia 
Published: November 2024

Abstract
This paper develops new data to track the occupation content of trade. These data are based on measuring the value-added exports of workers cross-classified by their industry of work as well as their occupational class, in short by “task.” Countries initially specialize along the extensive margin (shifting exports of value added across industries) and later on along the intensive margin (shifting export income across occupations within industries). Path dependency is strong in the early phase of development, as new task specializations are closely related to the initial task export basket, but this dependence weakens afterwards. Leveraging the new data holds great promise in delivering deeper insights into patterns of trade, structural change, and economic development.
Cardiogenic Shock in Pregnancy
Authors: Greer O.Y.O. , Anandanadesan R. , Shah N.M. , Price S. , Johnson M.R. 
Published: November 2024

(BJOG. 2024; 131:127–139. doi: 10.1111/1471-0528.17645)
Overall, maternal morbidity in developed countries has decreased in recent years; however, data suggests this is mainly due to improved management of conditions, such as preeclampsia (PEC) and postpartum hemorrhage. However, other conditions related to pregnancy, such as cardiac disease, continue to contribute to maternal morbidity. Cardiac death is the leading cause of maternal death in the UK, and the majority of these deaths are due to acquired cardiac disease, not congenital defects.
Knots of the Umbilical Cord: Incidence, Diagnosis, and Management
Authors: Al Qasem M. , Meyyazhagan A. , Tsibizova V. , Clerici G. , Arduini M. , Khader M. , Alkarabsheh A. , Di Renzo G.C. 
Published: November 2024

(Int J Gynecol Obstet. 2024;00:1–8. doi: 10.1002/ijgo.15373)
The umbilical cord is surrounded by Wharton jelly and is frequently referred to as the “lifeline” because of its essential function in transporting nutrients and expelling fetal waste. Factors such as the length and coiling of the cord impact its health and functionality. An essential aspect of umbilical cord function is an arterial anastomosis, known as “Hyrtl anastomosis,” which helps regulate and distribute blood flow to the placenta. This structure, typically located 3 cm before the cord enters the placenta, is vital for fetal well-being, and abnormalities can increase fetal stress or, in severe cases, lead to fetal demise. Umbilical cord knots (UCK) are among the observed abnormalities, often detected accidentally during routine sonography. True knots range from 0.3% to 2.1%, and while usually solitary, multiple knots can occur. Such knots have also been observed in monkey fetuses. The clinical significance of a knot depends on whether it is tight or loose; a tight knot, especially in a hyper-coiled cord, is less flexible and more prone to complications during birth.
Conceptualizing Meaningful Youth Engagement in Adolescent Sexual and Reproductive Health Programming
Authors: Drake Pamela , Marlow Heather , Hinson Laura , Anderson Pamela , Noble Cheryl , Terwilliger Emma , Rosas Scott R. 
Published: November 2024

Background and Objectives:
The Youth Engagement Network (YEN) was a three-year project focused on strengthening meaningful youth engagement in sexual health programs. It sought to answer the question, “What is a useful framework for meaningful youth engagement of vulnerable populations in sexual health programming?”

Methods:
The YEN chose Group Concept Mapping (GCM) as the approach to answer their learning question. GCM is a mixed-methods process that can be used to integrate the unique perspectives of a group of individuals. The approach entails 1) brainstorming ideas related to a prompt, 2) individual sorting and rating of the ideas, and 3) the application of multi-dimensional scaling (MDS) and hierarchical cluster analysis to integrate the individual sorting information and develop a series of concept maps.

Results:
Seventy-four young people and adults generated 141 responses to our prompt. These were pared down to 82 statements that were then sorted and/or rated on importance by 113 participants. Our final cluster map focused on 9 concepts: Facilitators, Diversity, Relevance, Access, Connection, Comprehensive Sex Ed, Co-development, and Space.

Conclusions:
We found GCM to be useful for identifying potential components of a framework to move the field toward more meaningful engagement of young people in sexual health programming.
Illustrating How Health Policy May Perpetuate Coverage and Access Disparities for Undocumented Immigrants
Authors: Pourat Nadereh , Martinez Ana E. 
Published: November 2024

Background and Objectives:
Evidence indicates significant disparities in access to health care for immigrants, but few studies have focused on changes in patterns of access to care by immigration status over time. We examined patterns of change in access and health indicators before and after the Affordable Care Act (ACA) for the undocumented and compared to US-born, naturalized, and documented residents.

Methods:
We examined indicators of usual source of care, service use, delays and self-reported health from 2005 to 2018 using a California Health Interview Survey sample of non-elderly adults (n = 207,652). We used multinomial and logistic regression models to assess changes in access and health status within each immigration category and across ACA periods.

Results:
From early- to post-ACA periods, we found a widening gap in insurance coverage of undocumented vs. US-born residents, and a shift toward use of public settings as usual source of care for both groups. From the pre- to early-ACA periods, there was a greater reduction of delayed medical care, and an increase in any mental health visits for US-born vs. undocumented residents.

Discussion:
Findings portend exacerbation of disparities in access for undocumented residents due to the economic consequences of events such as the pandemic and continued exclusion of undocumented residents from federally-funded coverage.
Diagnosis and prognosis of different methods of tongue base mucosectomy for occult head and neck cancer: A systematic review and meta-analysis
Authors: Wang Dengshun , Zou Teng , Gao Tong , Yao Yuan , Liu Changfu , Wang Yu’e , Lu Haibin , Yu Hongwei , Wang Qiuxu , Song Jianmin 
Published: November 2024

Background:
Trans-oral robotic surgery (TORS) and trans-oral laser microsurgery (TLM) have been increasingly employed for the diagnosis and identification of primary occult cancers in the head and neck region. This systematic review and meta-analysis aimed to evaluate the application and effectiveness of tonsillectomy with TORS and TLM in detecting these cancers.

Methods:
We searched PubMed, EMBASE, and the Cochrane Library for eligible studies using TORS or TLM in identifying the unknown primary sites of occult head and neck cancer, published from inception to September 2023. Two investigators independently screened articles based on inclusion and exclusion criteria.

Results:
From 2282 articles identified, 20 individual studies meeting the inclusion criteria were included in this meta-analysis. Primary tumors were identified by TORS/TLM in 65% (364/561) of patients. The initial identification rates of lingual tonsillectomy (n = 219) and palatine tonsillectomy (n = 83) were 39% and 15%, respectively. The identification rates of primary sites for trans-oral surgical techniques were 60.7% (95% CI, 49.4–72%) for TORS and 75.7% (95% CI, 60.7–90.7%) for TLM. Seventy-nine point six percent (467/587) of the tumors were associated with human papilloma virus (HPV). The detection rate of HPV+ tumors was 79% (173/220) and the detection rate of HPV− tumors was 10% (5/52). The most common complication was nasogastric/gastrostomy, accounting for 6% (29/481). The length of hospital stay reported varied from 1 to more than 7 days.

Conclusion:
This is a latest systematic review of the detection rates of head and neck squamous cell carcinoma of unknown primary sites by tongue base mucosectomy (TBM) via TORS and TBM via TLM. This study confirmed that TBM via TLM performed better than TBM–TORS in the detection rate of the primary. In particular, TBM via TLM showed significant advantages in detecting primary lesions in HPV-positive head and neck squamous cell carcinoma of unknown primary patients.