bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coffee drinking timing and mortality in US adults
Authors: Wang Xuan , Ma Hao , Sun Qi , Li Jun , Heianza Yoriko , Van Dam Rob M , Hu Frank B , Rimm Eric , Manson JoAnn E , Qi Lu 
Published: January 2025

Abstract

Background and Aims
To identify the patterns of coffee drinking timing in the US population and evaluate their associations with all-cause and cause-specific mortality.

Methods
This study included 40 725 adults from the National Health and Nutrition Examination Survey 1999–2018 who had complete information on dietary data and 1463 adults from the Women’s and Men’s Lifestyle Validation Study who had complete data on 7-day dietary record. Clustering analysis was used to identify patterns of coffee drinking timing.

Results
In this observational study, two distinct patterns of coffee drinking timing [morning type (36% of participants) and all-day-type patterns (14% of participants)] were identified in the National Health and Nutrition Examination Survey and were validated in the Women’s and Men’s Lifestyle Validation Study. During a median (interquartile range) follow-up of 9.8 (9.1) years, a total of 4295 all-cause deaths, 1268 cardiovascular disease deaths, and 934 cancer deaths were recorded. After adjustment for caffeinated and decaffeinated coffee intake amounts, sleep hours, and other confounders, the morning-type pattern, rather than the all-day-type pattern, was significantly associated with lower risks of all-cause (hazard ratio: .84; 95% confidential interval: .74–.95) and cardiovascular disease-specific (hazard ratio: .69; 95% confidential interval: .55–.87) mortality as compared with non-coffee drinking. Coffee drinking timing significantly modified the association between coffee intake amounts and all-cause mortality (P-interaction = .031); higher coffee intake amounts were significantly associated with a lower risk of all-cause mortality in participants with morning-type pattern but not in those with all-day-type pattern.

Conclusions
Drinking coffee in the morning may be more strongly associated with a lower risk of mortality than drinking coffee later in the day.
Decoding deception: the binding affinity of cuttlefish ink on shark smell receptors
Authors: Lawless Colleen , Simonitis Lauren E , Finarelli John A , Hughes Graham M 
Published: January 2025

Abstract
Chemical signaling can play a crucial role in predator–prey dynamics. Here, we present evidence that ink from the common cuttlefish (Sepia officinalis) targets olfactory receptor proteins in sharks, potentially acting as a predator deterrent. We apply in silico 3D docking analysis to investigate the binding affinity of various odorant molecules to shark olfactory receptors of 2 shark species: cloudy catshark (Scyliorhinus torazame) and white shark (Carcharodon carcharias). Pavoninin-4 (a known shark repellent compound) displayed selectivity in binding to receptors in the white shark. In contrast, the primary component of cuttlefish ink, melanin, displayed the highest binding affinities to all shark olfactory receptor proteins in both species. Taurine, another important ink component, exhibited standard to strong bindings for both species. Trans-4,5-epoxy-(E)-2-decenal (“blood decenal”), an odorant associated with the smell of blood, displayed strong binding affinities to all shark olfactory receptors, similar to that of melanin. These findings provide new insights into the molecular interplay between cephalopod inking behavior and their shark predators, with cuttlefish ink likely exploiting the narrow band of the shark olfactory repertoire.
An ecosystem for producing and sharing metadata within the web of FAIR Data
Authors: Jacob Daniel , Ehrenmann François , David Romain , Tran Joseph , Mirande-Ney Cathleen , Chaumeil Philippe 
Published: January 2025

Abstract

Background
Descriptive metadata are vital for reporting, discovering, leveraging, and mobilizing research datasets. However, resolving metadata issues as part of a data management plan can be complex for data producers. To organize and document data, various descriptive metadata must be created. Furthermore, when sharing data, it is important to ensure metadata interoperability in line with FAIR (Findable, Accessible, Interoperable, Reusable) principles. Given the practical nature of these challenges, there is a need for management tools that can assist data managers effectively. Additionally, these tools should meet the needs of data producers and be user-friendly, requiring minimal training.

Results
We developed Maggot (Metadata Aggregation on Data Storage), a web-based tool to locally manage a data catalog using high-level metadata. The main goal was to facilitate easy data dissemination and deposition in data repositories. With Maggot, users can easily generate and attach high-level metadata to datasets, allowing for seamless sharing in a collaborative environment. This approach aligns with many data management plans as it effectively addresses challenges related to data organization, documentation, storage, and the sharing of metadata based on FAIR principles within and beyond the collaborative group. Furthermore, Maggot enables metadata crosswalks (i.e., generated metadata can be converted to the schema used by a specific data repository or be exported using a format suitable for data collection by third-party applications).

Conclusion
The primary purpose of Maggot is to streamline the collection of high-level metadata using carefully chosen schemas and standards. Additionally, it simplifies data accessibility via metadata, typically a requirement for publicly funded projects. As a result, Maggot can be utilized to promote effective local management with the goal of facilitating data sharing while adhering to the FAIR principles. Furthermore, it can contribute to the preparation of the future EOSC FAIR Web of Data within the European Open Science Cloud framework.
Q241R mutation of Braf causes neurological abnormalities in a mouse model of cardio-facio-cutaneous syndrome, independent of developmental malformations
Authors: Moriya Akira , Inoue Shin-ichi , Saitow Fumihito , Keitoku Moe , Suzuki Noato , Oike Etsumi , Urano Eriko , Matsumoto Eiko , Suzuki Hidenori , Aoki Yoko , Ohnishi Hiroshi 
Published: January 2025

Abstract
Constitutively active mutants of BRAF cause cardio-facio-cutaneous (CFC) syndrome, characterized by growth and developmental defects, cardiac malformations, facial features, cutaneous manifestations, and mental retardation. An animal model of human CFC syndrome, the systemic BrafQ241R/+ mutant mouse, has been reported to exhibit multiple CFC syndrome-like phenotypes. In this study, we analyzed the effects of Braf mutations on neural function, separately from their effects on developmental processes. To this end, we generated Braf mutant mice expressing BRAFQ241R specifically in mature excitatory neurons (n-BrafQ241R/+). We found no growth retardation or cardiac malformations in n-BrafQ241R/+ mice, indicating normal development. Behavioral analysis revealed that n-BrafQ241R/+ mice exhibited reduced home cage activity and learning disability, which were similar to those of systemic BrafQ241R/+ mice. The active form of ERK was increased in the hippocampus of n-BrafQ241R/+ mice, whereas basal synaptic transmission and synaptic plasticity in hippocampal Schaffer collateral-CA1 synapses seems to be normal. Transcriptome analysis of the hippocampal tissue revealed significant changes in the expression of genes involved in regulation of the RAS/mitogen-activated protein kinase (MAPK) signaling pathway, synaptic function and memory formation. These data suggest that the neuronal dysfunction observed in the systemic CFC mouse model is due to the disruption of homeostasis of the RAS/MAPK signaling pathway by the activated Braf mutant after maturation, rather than abnormal development of the brain. A similar mechanism may be possible in human CFC syndrome.
Difficult Stories that Haunt: Towards Research Otherwise in Transitional Justice
Authors: Lühe Ulrike , Baines Erin 
Published: January 2025

ABSTRACT∞
Stories of suffering, loss and injury encountered in transitional justice research are difficult. They generate affective responses of sadness, guilt, shame and, often, denial of responsibility. Difficult stories are also haunting. They reveal ongoing structural injustices, and in their insistence, challenge claims that the past is over and done with. In this article, we argue that engaging with difficult stories as haunting can propel us towards research otherwise. We first demonstrate how Western modes of research governance silence ghosts through the extraction and translation of difficult stories into data. We consider the possibilities of doing research otherwise when difficult stories refuse, demand return, re-story and claim new ways of seeing, being and doing research. Significantly, in a moment of global reckoning, when the promise of ‘never again’ has become a signifier of ‘ever again,’ the calculus and relevance of scholarship in transitional justice is measured by such ‘ghostly matters.’
Outbreak of Rotavirus Diarrheal Infection Among Adults in King County, Washington, January–June 2023
Authors: Ma Jimmy , Kumbhakar Raaka G , Casto Amanda , Chow Eric J , Englund Janet A , Gautam Rashi , Jaimes Jose , Tate Jacqueline E , Smart Sarah , Mani Nandita S , Cohen Seth A , Hussein Abby , Rietberg Krista , Bryson-Cahn Chloe , Fang Ferric C 
Published: January 2025

Abstract
Rotavirus is a leading cause of diarrhea among children but less known as a cause among adults. We describe clinical, epidemiologic, and genotypic characteristics of a rotavirus outbreak among adults in King County, Washington, occurring during January–June 2023. Adult rotavirus incidence in 2023 was 10 times higher than the same period in 2022 (5% vs 0.5% of samples). Disease severity was mild. G9P[4], an uncommon, nonvaccine strain in the United States, was the predominant genotype. Genotyping suggested spillover from children with subsequent spread among adults. Our study highlights benefits of routine testing and genotyping during outbreaks for surveillance, tracking, and understanding implications on vaccination.
GTF2I acts as a novel tumor suppressor transcription factor and shows Favorable prognosis in renal cancer
Authors: Dakal Tikam Chand , Thakur Mony , George Nancy , Singh Tiratha Raj , Yadav Vinod , Kumar Abhishek 
Published: January 2025

Abstract
The role of GTF2I (General Transcription Factor2I) alteration has already been reported in thymic cancer as a valuable biomarker. However, the association of GTF2I mutation with renal cancer for prognosis of immunotherapy is not yet examined. The biologic and oncologic significance of GTF2I in renal cancer was examined at multiomics level such as mutation, copy number alteration, structural variants. The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA) were used to retrieve the omics data. The expression of GTF2I mRNA was quite significant in case of renal caner. Correlation among the GTF2I mRNA, mutation, CNA and structural variants was also studied. Interactome of GTF2I was also constructed using STRING database. Gain, amplification, and missense mutation exhibited a positive correlation between GTF2I mRNA expression and non-structural variants. Similarly, GTF2I mRNA expression and copy number alterations from GISTIC were positively correlated. High expression of GTF2I was associated with better overall survival indicating the less aggressive clinical features.
Insight Box Investigating GTF2I's complex function as a tumor suppressor transcription factor in renal carcinoma provides fresh insights into its biologic and oncologic importance, especially when considering the prognosis of immunotherapy. Little is known about its possible use as a biomarker for renal cancer. Using a multiomics approach and utilizing information from the Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA), our study clarifies the intricate relationship between mRNA expression, GTF2I changes, and clinical outcomes in renal cancer. Our results indicate that GTF2I expression may be used as a prognostic indicator because it is positively correlated with favorable survival outcomes. Furthermore, the molecular interactions behind GTF2I's functional significance in renal cancer are revealed by interactome analysis utilizing the STRING database, providing important information for further study and treatment approaches.
Early differentiation of committed erythroid cells defined by miR-144/451 expression
Authors: Li Xiaohong , Dong Yong , Xu Pan , Sun Wencui , Xue Yuan , Zhou Ya , Lai Mowen , Zhang Yonggang , Ma Feng 
Published: January 2025

Abstract
Before committing to an erythroid cell lineage, hematopoietic stem cells differentiate along a myeloid cell pathway to generate megakaryocyte–erythroid biopotential progenitor cells in bone marrow. Recent studies suggest that erythroid progenitors (EryPs) could be generated at the level of common myeloid progenitors (CMPs). However, due to a lack of suitable markers, little is known about the early differentiation of these committed EryP cells during CMP development. Herein, using miR-144/451-eGFP knock-in mice, we found that early differentiation of committed erythroid cells could be defined by miR-144/451 expression within CMPs. Single-cell RNA sequencing showed that miR-144/451+ progenitors had obvious differentiation characteristics of erythroid lineage cells and diverged from megakaryocyte and other myeloid cell lineages. These progenitors exclusively gave rise to erythroid cells, both in vitro and in vivo, and the commitment to an erythroid cell lineage was accompanied by loss of CD53 expression. Our findings will facilitate further understanding of the molecular mechanisms governing erythroid development and support the identification of therapeutic targets for diseases related to erythrocyte development.
Forced displacement and utilization of maternal health care services in host communities: micro-level evidence from Sub-Saharan Africa, 1986–2016
Authors: Østby Gudrun , Tollefsen Andreas Forø 
Published: January 2025

Abstract
Despite a growing literature on refugee health challenges, the effects of inflows of refugees on the utilization of health services in host communities remain largely ignored. Linking data on the location of displaced populations and geo-referenced survey data on the use of maternal health services in 30 sub-Saharan African countries, we explore whether geographical proximity to refugee- and internally displaced person (IDP) camps and settlements affects the utilization of maternal health care among women in host communities. More specifically, we apply a mother fixed-effects analysis isolating the effect of hosting refugees and IDPs on the probability of delivering at a health facility. We find that living within 25 km of displaced population significantly increases the likelihood of institutional births. This effect is stronger for the poorest mothers. Our study disproves the common misconception that refugees and IDPs have a negative impact on their host communities. Rather, we find a positive effect of hosting displaced populations.
Chemical characterization and evaluation of antiviral activity of two fucoidans extracted from Mediterranean brown seaweeds, Padina pavonica and Dictyopteris membranacea
Authors: Amri Safa , Bouslama Lamjed , Mzoughi Zeineb , Nouira Fatma , Majdoub Hatem , Bouraoui Abderrahman 
Published: January 2025

Abstract
Brown seaweeds are known for their bioactive compounds, particularly sulfated polysaccharides such as fucoidans, which have demonstrated antiviral properties. However, limited studies have focused on the antiviral potential of fucoidans extracted from Mediterranean brown seaweeds. In this study, two brown seaweeds Padina pavonica and Dictyopteris membranacea (Fuc-Pad and Fuc-Dic, respectively) were collected from monastir coasts, Tunisia, and a specific extraction protocol was employed to obtain fucoidans. The main objective of this study was to evaluate their antiviral activity against Herpes simplex virus type 2 (HSV-2) and coxsackievirus B3 (CVB-3). Fuc-Pad and Fuc-Dic exhibited potent antiviral activity with high selectivity indexes (&gt;158 780 and 3125 for Fuc-Pad and 6101 and 84 for Fuc-Dic against HSV-2 and CVB-3, respectively). On the other hand, the two brown algae demonstrated different mechanisms of antiviral action according to virus type since they inhibited HSV-2 during the adsorption and penetration stages likely through interaction with cellular receptors that block viral binding while directly inhibiting CVB-3 by blocking specific viral ligands, preventing their attachment to host cell receptors. This antiviral activity seems to be associated with the high degree of sulfating of the fucoidans. These results may suggest the possibility of developing new antiviral drugs.
Migrant people, (in)mobility and art on a borderland: Tijuana, Mexico
Authors: Montes Veronica , Busse Erika , Cantú Nelly 
Published: January 2025

Abstract
By examining the border town of Tijuana, Mexico, we explore the artistic production in this distinctive migratory landscape. We seek to answer a central question: What insights does art provide about migration that traditional social sciences do not? Due to its geopolitical location, Tijuana serves as a crossroads for thousands of individuals who confront the stark contrast between their aspirations to enter the United States and the harsh realities of border securitization that impede their access. These contradictions create a fertile environment for diverse and rich artistic expression. We highlight three key moments that establish Tijuana as a vibrant hub attracting artists from around the globe. Among these moments, we focus more deeply on one that emphasizes the active participation of migrants in artistic projects initiated by Civil Society Organizations and migrant shelters. Notably, we examine the project “Jugamos a Leer” (Let’s Play to Read), which employs reading and playful, creative writing as pedagogical tools. This project aims to foster peace, identity, belonging, and memory among groups facing vulnerable circumstances, especially within migrant communities. We believe these projects enable individuals to present themselves as whole persons rather than being confined to a single identity, such as “deported,” “asylum seeker,” or “economic migrant.” These inclusive spaces allow participants to temporarily set aside their everyday challenges. Furthermore, by appealing to a fundamental aspect of humanity—creativity—participants, including those migrating without proper documents and those awaiting immigration procedures, can recognize and connect with each other’s humanity.
Quiescent or dusty? Unveiling the nature of extremely red galaxies at z &gt; 3
Authors: Barrufet L , Oesch P A , Marques-Chaves R , Arellano-Cordova K , Baggen J F W , Carnall A C , Cullen F , Dunlop J S , Gottumukkala R , Fudamoto Y , Illingworth G D , Magee D , McLure R J , McLeod D J , Michałowski M J , Stefanon M , van Dokkum P G , Weibel A 
Published: January 2025

ABSTRACT
The advent of the JWST has revolutionized our understanding of high-redshift galaxies. In particular, the NIRCam instrument on-board JWST has revealed a population of red galaxies that had largely evaded detection with Hubble Space Telescope (HST), potentially due to significant dust obscuration, quiescence, or extreme redshift. Here, we present the first NIRSpec spectra of 23 red, HST faint or dark galaxies ($\mathrm{H-F444W\gt 1.75}$), unveiling their nature and physical properties. This sample includes both dusty and quiescent galaxies with spectroscopic data from NIRSpec/PRISM, providing accurate spectroscopic redshifts with $\mathrm{\overline{z}_{spec} = 4.1 \pm 0.7}$. The spectral features demonstrate that, while the majority of red galaxies are dusty, a substantial fraction, $\mathrm{13^{+9}_{-6} \%}$, are quiescent. For the dusty galaxies, we have quantified the dust attenuation using the Balmer decrement ($\mathrm{H\,\alpha / H\,\beta }$), finding attenuations $\mathrm{A_{V} \gt 2\ mag}$. We find that red dusty galaxies are $\mathrm{H\,\alpha }$ emitters with equivalent widths spanning the range $\mathrm{ 68 \mathring{\rm A}\lt EW_{H\alpha } \lt 550 \mathring{\rm A}}$, indicative of a wide range of recent star-formation activity. Whether dusty or quiescent, we find that red galaxies are predominantly massive, with 85 per cent of the galaxies in the sample having masses $\mathrm{log({\it M}_{*}/{\rm M}_{\odot }) \gt 9.8}$. This pilot NIRSpec programme reveals the diverse nature of HST-dark galaxies and highlights the effectiveness of NIRSpec/PRISM spectroscopic follow-up in distinguishing between dusty and quiescent galaxies and properly quantifying their physical properties. Upcoming research utilizing higher-resolution NIRSpec data and combining JWST with ALMA observations will enhance our understanding of these enigmatic and challenging sources.
A critical evaluation of the elemental abundances and evolutionary status of 15 Vul (HD 189849): the first identification of an evolved Am star
Authors: Çay M Taşkın , Çay İpek H , Civelekler Betül 
Published: January 2025

ABSTRACT
Understanding the evolution of metallic-line (${\rm A}_{\rm m}$) stars requires well-determined atmospheric parameters and abundance patterns of the selected candidates. In this study, we present a detailed abundance analysis of 15 Vul (HD 189849), identified as a marginal ${\rm A}_{\rm m}$ star, using a combination of equivalent width and spectrum synthesis techniques, under the local thermodynamic equilibrium assumption. We compare our findings with previous analyses of the star, providing critique on both their results and our own. Our results suggest that, although 15 Vul exhibits some underabundances of calcium and scandium, which are typically associated with ${\rm A}_{\rm m}$ stars, it might more accurately be identified as a normal A star in terms of its abundance pattern of all other elements and microturbulence velocity. The star’s position on the Hertzsprung–Russell diagram, along with our findings, may indicate that it is potentially a classical ${\rm A}_{\rm m}$ star that has evolved into the subgiant phase as a ‘quasi-normal’ star. This may be the first identification of an evolved ${\rm A}_{\rm m}$ star.
Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution
Authors: Kim Jun , Park Jong Lyul , Yang Jin Ok , Kim Sangok , Joe Soobok , Park Gunwoo , Hwang Taeyeon , Cho Mun-Jeong , Lee Seungjae , Lee Jong-Eun , Park Ji-Hwan , Yeo Min-Kyung , Kim Seon-Young 
Published: January 2025

Abstract
Given the presence of highly repetitive genomic regions such as subtelomeric regions, understanding human genomic evolution remains challenging. Recently, long-read sequencing technology has facilitated the identification of complex genetic variants, including structural variants (SVs), at the single-nucleotide level. Here, we resolved SVs and their underlying DNA damage–repair mechanisms in subtelomeric regions, which are among the most uncharted genomic regions. We generated ∼20 × high-fidelity long-read sequencing data from three Korean individuals and their partially phased high-quality de novo genome assemblies (contig N50: 6.3–58.2 Mb). We identified 131 138 deletion and 121 461 insertion SVs, 41.6% of which were prevalent in the East Asian population. The commonality of the SVs identified among the Korean population was examined by short-read sequencing data from 103 Korean individuals, providing the first comprehensive SV set representing the population based on the long-read assemblies. Manual investigation of 19 large subtelomeric SVs (≥5 kb) and their associated repair signatures revealed the potential repair mechanisms leading to the formation of these SVs. Our study provides mechanistic insight into human telomere evolution and can facilitate our understanding of human SV formation.