bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anticoagulant-related bleeding as a sign of underlying tumoural lesions in patients with atrial fibrillation: a nationwide cohort study
Authors: Proesmans Kristiaan , Grymonprez Maxim , Rottey Sylvie , Lahousse Lies 
Published: September 2024

Abstract

Aims
Bleeding events are a well-known complication of oral anticoagulant (OAC) use in patients with atrial fibrillation (AF). While these are undesirable, bleedings could have a warning potential for underlying tumoural lesions. Therefore, we aimed to investigate the association between anticoagulant-related bleeding and newly diagnosed tumoural lesions in a nationwide cohort study.

Methods and results
Using Belgian nationwide data, AF patients without any tumoural lesions were included when initiating OACs between 2013 and 2019. The absolute and relative risks of newly diagnosed tumoural lesions were investigated in OAC users with vs. without an OAC-related bleeding event. Analyses were additionally stratified by tumoural lesion, location-specific bleeding, and OAC type. A total of 230 386 OAC users were included, among whom 35 192 persons were diagnosed with a tumoural lesion during follow-up. Persons with a clinically relevant bleeding during OAC use had a tumoural lesion incidence of 15.33 per 100 person-years compared to an incidence of 5.22 per 100 person-years in persons without bleeding. Site-specific gastrointestinal, urogenital, respiratory, and intracranial bleeding events were respectively associated with a significantly increased risk of incident gastrointestinal [adjusted hazard ratio (aHR) 8.13 (95% confidence interval (CI): 7.08–9.34)], urological [aHR 12.73 (95% CI: 10.56–15.35)], respiratory [aHR 4.91 (95% CI: 3.24–7.44)], and intracranial tumoural lesions [aHR 27.89 (95% CI: 16.53–47.04)].

Conclusion
Bleeding events in AF patients initiated on OAC were associated with an increased risk of tumoural lesions. Therefore, OAC-related bleeding events could unmask an underlying tumoural lesion.
Local exposure to refugees changed attitudes to ethnic minorities in the Netherlands
Authors: Achard Pascal , Albrecht Sabina , Ghidoni Riccardo , Cettolin Elena , Suetens Sigrid 
Published: September 2024

Abstract
We investigate the effect of exposure to refugees on locals’ preferences with regard to ethnic minorities using individual-level panel data from the Netherlands. The data combine self-reported preferences with administrative data on the residential locations of the locals and the refugees. The study period is marked by a sudden inflow of refugees in some neighbourhoods. We find that individuals living close to newly installed refugee facilities developed a more positive attitude towards ethnic minorities and became less supportive of anti-immigration parties compared to individuals living farther away. An investigation of mechanisms suggests that the local effect is due to contact between residents and refugees.
Don DeLillo’s Falling Man as Cultural Trauma Fiction
Authors: Mullis Courtney 
Published: September 2024

Abstract
The sociological concept of cultural trauma provides a useful lens for understanding large-scale traumatic events and their literary legacies because this concept recognizes the historical, social, and cultural aspects of trauma rather than limiting its scope to the experiences of individuals or small collectives. The terrorist attacks on 11 September 2001 initiated widespread trauma through the spectacle of the planes colliding with the World Trade Center and the Pentagon. Literature after 9/11 is both a product of cultural trauma and a means of exploring the profound effects of that trauma. Some 9/11 novels are part of a subgenre I call Cultural Trauma Fiction, which depicts and explores the effect of a large-scale traumatic event on a culture. Texts within this subgenre represent multiple identities and perspectives, engage with cultural concerns about memorializing the trauma, consider the ethics of representing that trauma through different media, and advance counternarratives that challenge dominant government or media narratives about the trauma. Don DeLillo’s Falling Man constitutes a work of Cultural Trauma Fiction in that its structure and narrative strategies move beyond the scope of the novel’s plot, offering insight into the cultural response to 9/11 and countering hegemonic narratives. Works of Cultural Trauma Fiction like Falling Man highlight the collective hidden transcript of traumatic events and challenge official narratives that oversimplify cultural traumas. Falling Man complicates and enriches the collective understanding of 9/11 by challenging, revising, and reconstructing its cultural narratives.
OfWRKY17-OfC3H49 module responding to high ambient temperature delays flowering via inhibiting OfSOC1B expression in Osmanthus fragrans
Authors: Ye Yong , Lu Xinke , Kong En , Wang Qianqian , Shen Lixiao , Zhong Shiwei , Wang Yiguang , Xiao Zheng , Deng Jinping , Zhao Hongbo , Dong Bin 
Published: September 2024

Abstract
Ambient temperature is a pivotal factor in the regulation of the flowering process in plants. In this study, we found that high ambient temperature exerts an inhibitory effect on the flowering of Osmanthus fragrans “Sjigui”. However, the underlying molecular mechanisms remain not fully understood. Through transcriptome analysis, a differently expressed C3H gene OfC3H49 was identified, which is induced by high ambient temperature. OfC3H49 was demonstrated to delay the flowering process of Arabidopsis and downregulate the expression of flowering-related genes in O. fragrans calli. Further investigation indicates that OfC3H49 as a transcriptional repressor directly suppresses the expression of the OfSOC1B thereby causing a delay in flowering time. Furthermore, a WRKY transcription factor, OfWRKY17, was identified to be responsive to high ambient temperature, directly binding to the OfC3H49 promoter and enhance OfC3H49 expression. Overexpression of OfWRKY17 in Arabidopsis resulted in a significant delay in flowering and induced the expression of OfC3H49 in O. fragrans calli. Collectively, our findings delineate a regulatory module, OfWRKY17-OfC3H49, which is activated by high ambient temperature and functions as a negative regulator of flowering by suppressing the expression of OfSOC1B in O. fragrans. This study provides novel insights into the molecular mechanisms involved in ambient temperature-mediated flowering control and contributes to the development of molecular breeding strategies for O. fragrans.
Opportunities and Challenges in Applying AI to Evolutionary Morphology
Authors: He Y , Mulqueeney J M , Watt E C , Salili-James A , Barber N S , Camaiti M , Hunt E S E , Kippax-Chui O , Knapp A , Lanzetti A , Rangel-de Lázaro G , McMinn J K , Minus J , Mohan A V , Roberts L E , Adhami D , Grisan E , Gu Q , Herridge V , Poon S T S , West T , Goswami A 
Published: September 2024

Synopsis
Artificial intelligence (AI) is poised to revolutionize many aspects of science, including the study of evolutionary morphology. While classical AI methods such as principal component analysis and cluster analysis have been commonplace in the study of evolutionary morphology for decades, recent years have seen increasing application of deep learning to ecology and evolutionary biology. As digitized specimen databases become increasingly prevalent and openly available, AI is offering vast new potential to circumvent long-standing barriers to rapid, big data analysis of phenotypes. Here, we review the current state of AI methods available for the study of evolutionary morphology, which are most developed in the area of data acquisition and processing. We introduce the main available AI techniques, categorizing them into 3 stages based on their order of appearance: (1) machine learning, (2) deep learning, and (3) the most recent advancements in large-scale models and multimodal learning. Next, we present case studies of existing approaches using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, and phylogenetics. We then discuss the prospectus for near-term advances in specific areas of inquiry within this field, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. In particular, we note key areas where AI remains underutilized and could be used to enhance studies of evolutionary morphology. This combination of current methods and potential developments has the capacity to transform the evolutionary analysis of the organismal phenotype into evolutionary phenomics, leading to an era of “big data” that aligns the study of phenotypes with genomics and other areas of bioinformatics.
Organelles in the ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses
Authors: Sonett Dylan , Brown Tanya , Bengtsson-Palme Johan , Padilla-Gamiño Jacqueline L , Zaneveld Jesse R 
Published: September 2024

Abstract
The genomes of mitochondria and chloroplasts contain ribosomal RNA (rRNA) genes, reflecting their ancestry as free-living bacteria. These organellar rRNAs are often amplified in microbiome studies of animals and plants. If identified, they can be discarded, merely reducing sequencing depth. However, we identify certain high-abundance organeller RNAs not identified by common pipelines, which may compromise statistical analysis of microbiome structure and diversity. We quantified this by reanalyzing 7459 samples from seven 16S rRNA studies, including microbiomes from 927 unique animal genera. We find that under-annotation of cryptic mitochondrial and chloroplast reads affects multiple of these large-scale cross-species microbiome comparisons, and varies between host species, biasing comparisons. We offer a straightforward solution: supplementing existing taxonomies with diverse organelle rRNA sequences. This resolves up to 97% of unique unclassified sequences in some entire studies as mitochondrial (14% averaged across all studies), without increasing false positive annotations in mitochondria-free mock communities. Improved annotation decreases the proportion of unknown sequences by ≥10-fold in 2262 of 7459 samples (30%), spanning five of seven major studies examined. We recommend leveraging organelle sequence diversity to better identify organelle gene sequences in microbiome studies, and provide code, data resources and tutorials that implement this approach.
Prescribing Information: Elizabeth B. Connell, the Pill, and the (Woman) Patient’s Peace of Mind
Authors: Wei Jiemin Tina 
Published: September 2024

Abstract
Throughout the 1970s and 1980s, commercialized reproductive technologies experienced a reputational crisis as news about the hormonal birth control pill’s possible side effects reportedly caused 18–30% of women to stop taking it. While secondary literature has followed patients’ and legislatures’ actions, few histories have focused on physicians’ responses. How did physicians manage this public crisis of confidence? This article contributes to existing literature through a backstage look at the work of Elizabeth B. Connell (1925–2018), whose wide-ranging career in medicine, academia, government, industry consulting, and popular writing embroiled her at the center of these controversies. To counter critique from legislatures and consumer reformers, Connell became a mediator for medicine in the public sphere, dispensing select information and arguing for limits on others — for the patient’s sake. If legislative inquiry’s primary havoc was unleashing information, Connell would help the profession moderate it. Because Connell was a woman doctor whom health feminists who were her contemporaries denied was a feminist doctor, the existing scholarship has occluded her. This article reconstructs the contributions of this important and flawed doctor, illuminating how she contorted herself to suit her various public messages, constrained by her conflicting, dual identities as woman and doctor.
Benchmarking the spectroscopic masses of 249 evolved stars using asteroseismology with TESS
Authors: Malla Sai Prathyusha , Stello Dennis , Montet Benjamin T , Huber Daniel , Hon Marc , Bedding Timothy R , Reyes Claudia , Hey Daniel R 
Published: September 2024

ABSTRACT
One way to understand planet formation is through studying the correlations between planet occurrence rates and stellar mass. However, measuring stellar mass in the red giant regime is very difficult. In particular, the spectroscopic masses of certain evolved stars, often referred to as ‘retired A-stars’, have been questioned in the literature. Efforts to resolve this mass controversy using spectroscopy, interferometry, and asteroseismology have so far been inconclusive. A recent ensemble study found a mass-dependent mass offset, but the result was based on only 16 stars. With NASA’s Transiting Exoplanet SurveySatellite (TESS), we expand the investigation of the mass discrepancy to a total of 92 low-luminosity stars, synonymous with the retired A-stars. We measure their characteristic oscillation frequency, $\mathrm{\nu }_{\mathrm{max}}$, and the large frequency separation, $\mathrm{\Delta \nu }$, from their TESS photometric time series. Using these measurements and asteroseismic scaling relations, we derive asteroseismic masses and compare them with spectroscopic masses from five surveys, to comprehensively study the alleged mass-dependent mass offset. We find a mass offset between spectroscopy and seismology that increases with stellar mass. However, we note that adopting the seismic mass scale does not have a significant effect on the planet occurrence-mass-metallicity correlation for the so-called retired A-stars. We also report seismic measurements and masses for 157 higher luminosity giants (mostly helium-core-burning) from the spectroscopic surveys.
INSPIRE: INvestigating Stellar Population In RElics – VII. The local environment of ultra-compact massive galaxies
Authors: Scognamiglio Diana , Spiniello Chiara , Radovich Mario , Tortora Crescenzo , Napolitano Nicola R , Li Rui , Maturi Matteo , Maksymowicz-Maciata Michalina , Cappellari Michele , Arnaboldi Magda , Bevacqua Davide , Coccato Lodovico , D’Ago Giuseppe , Feng Hai-Cheng , Ferré-Mateu Anna , Hartke Johanna , Martín-Navarro Ignacio , Pulsoni Claudia 
Published: September 2024

ABSTRACT
Relic galaxies, the oldest ultra-compact massive galaxies (UCMGs), contain almost exclusively ‘pristine’ stars formed during an intense star formation (SF) burst at high redshift. As such, they allow us to study in detail the early mechanism of galaxy assembly in the Universe. Using the largest catalogue of spectroscopically confirmed UCMGs for which a degree of relicness (DoR) had been estimated, the INSPIRE catalogue, we investigate whether or not relics prefer dense environments. The objective of this study is to determine if the DoR, which measures how extreme the SF history was, and the surrounding environment are correlated. In order to achieve this goal, we employ the AMICO galaxy cluster catalogue to compute the probability for a galaxy to be a member of a cluster, and measure the local density around each UCMG using machine learning-based photometric redshifts. We find that UCMGs can reside both in clusters and in the field, but objects with very low DoR ($\lt 0.3$, i.e. a relatively extended SF history) prefer underdense environments. We additionally report a correlation between the DoR and the distance from the cluster centre: more extreme relics, when located in clusters, tend to occupy the more central regions of them. We finally outline potential evolution scenarios for UCMGs at different DoR to reconcile their presence in both clusters and field environments.
ExoMol line lists–LIX. High-temperature line list for N2O
Authors: Yurchenko Sergei N , Mellor Thomas M , Tennyson Jonathan 
Published: September 2024

ABSTRACT
New hot line lists for five isotopologues of N$_2$O called TYM are presented, for the parent $^{14}$N$_2$$^{16}$O and 4 singly substituted species $^{14}$N$_2$$^{17}$O, $^{14}$N$_2$$^{18}$O, $^{14}$N$^{15}$N$^{16}$O and $^{15}$N$^{14}$N$^{16}$O. The line lists have been computed with the variational program TROVE (Theoretical ROVibrational Energies) using a new empirical potential energy surface (PES) and an accurate ab initio dipole moment surface of N$_2$O Ames-1. The PES was obtained by fitting to experimentally derived energies of N$_2$O compiled using the well established measured active rotation vibration energy levels (MARVEL) procedure. Here we also introduce an ‘artificial symmetry group’ $C_{n \text{s}}(\text{AEM})$ for an efficient construction of rotation-vibrational basis set of a linear non-symmetric triatomic molecule of the XYZ type. The line lists cover the rotational excitations up to $J=160$ and the wavenumber range up to 20000 cm$^{-1}$. MARVEL energies are also used to improve predicted line positions resulting in excellent agreement with the available experimental spectra, as demonstrated. An extensive comparison with existing line lists for N$_2$O HITRAN, HITEMP, NOSL-296, NOSD-1000, and Ames-296K is provided. The TYM line lists are freely accessible from www.exomol.com.
The chemical diversity of the metal-poor Milky Way
Authors: Buckley Nicole , Das Payel , Jofré Paula , Yates Robert M , Hawkins Keith 
Published: September 2024

ABSTRACT
We present a detailed study of the chemical diversity of the metal-poor Milky Way using data from the GALAH DR3 survey. Considering 17 chemical abundances relative to iron ([X/Fe]) for 9923 stars, we employ principal component analysis (PCA) and extreme deconvolution (XD) to identify 10 distinct stellar groups. This approach, free from chemical or dynamical cuts, reveals known populations, including the accreted halo, thick disc, thin disc, and in situ halo. The thick disc is characterized by multiple substructures, suggesting it comprises stars formed in diverse environments. Our findings highlight the limited discriminatory power of magnesium in separating accreted and disc stars. Elements such as Ba, Al, Cu, and Sc are critical in distinguishing disc from accreted stars, while Ba, Y, Eu, and Zn differentiate disc and accreted stars from the in situ halo. This study demonstrates the potential power of combining a latent space representation of the data (PCA) with a clustering algorithm (XD) in Galactic archaeology, in providing new insights into the Galaxy’s assembly and evolutionary history.
Electron microscopy evidence of gadolinium toxicity being mediated through cytoplasmic membrane dysregulation
Authors: Arino Trevor , Faulkner David , Bustillo Karen C , An Dahlia D , Jorgens Danielle , Hébert Solène , McKinley Carla , Proctor Michael , Loguinov Alex , Vulpe Christopher , Abergel Rebecca J 
Published: September 2024

Abstract
Past functional toxicogenomic studies have indicated that genes relevant to membrane lipid synthesis are important for tolerance to the lanthanides. Moreover, previously reported imaging of patient's brains following administration of gadolinium-based contrast agents shows gadolinium lining the vessels of the brain. Taken together, these findings suggest the disruption of cytoplasmic membrane integrity as a mechanism by which lanthanides induce cytotoxicity. In the presented work we used scanning transmission electron microscopy and spatially resolved elemental spectroscopy to image the morphology and composition of gadolinium, europium, and samarium precipitates that formed on the outside of yeast cell membranes. In no sample did we find that the lanthanide contaminant had crossed the cell membrane, even in experiments using yeast mutants with disrupted genes for sphingolipid synthesis—the primary lipids found in yeast cytoplasmic membranes. Rather, we have evidence that lanthanides are co-located with phosphorus outside the yeast cells. These results lead us to hypothesize that the lanthanides scavenge or otherwise form complexes with phosphorus from the sphingophospholipid head groups in the cellular membrane, thereby compromising the structure or function of the membrane, and gaining the ability to disrupt membrane function without entering the cell.
Bile from the hemojuvelin-deficient mouse model of iron excess is enriched in iron and ferritin
Authors: Prajapati Milankumar , Chiu Lauren , Zhang Jared Z , Chong Grace S , DaSilva Nicholas A , Bartnikas Thomas B 
Published: September 2024

Abstract
Iron is an essential nutrient but is toxic in excess. Iron deficiency is the most prevalent nutritional deficiency and typically linked to inadequate intake. Iron excess is also common and usually due to genetic defects that perturb expression of hepcidin, a hormone that inhibits dietary iron absorption. Our understanding of iron absorption far exceeds that of iron excretion, which is believed to contribute minimally to iron homeostasis. Prior to the discovery of hepcidin, multiple studies showed that excess iron undergoes biliary excretion. We recently reported that wild-type mice raised on an iron-rich diet have increased bile levels of iron and ferritin, a multi-subunit iron storage protein. Given that genetic defects leading to excessive iron absorption are much more common causes of iron excess than dietary loading, we set out to determine if an inherited form of iron excess known as hereditary hemochromatosis also results in bile iron loading. We employed mice deficient in hemojuvelin, a protein essential for hepcidin expression. Mutant mice developed bile iron and ferritin excess. While lysosomal exocytosis has been implicated in ferritin export into bile, knockdown of Tfeb, a regulator of lysosomal biogenesis and function, did not impact bile iron or ferritin levels. Bile proteomes differed between female and male mice for wild-type and hemojuvelin-deficient mice, suggesting sex and iron excess impact bile protein content. Overall, our findings support the notion that excess iron undergoes biliary excretion in genetically determined iron excess.
Evolving Escherichia coli to use a tRNA with a non-canonical fold as an adaptor of the genetic code
Authors: Edelmann Martin P , Couperus Sietse , Rodríguez-Robles Emilio , Rivollier Julie , Roberts Tania M , Panke Sven , Marlière Philippe 
Published: September 2024

Abstract
All known bacterial tRNAs adopt the canonical cloverleaf 2D and L-shaped 3D structures. We aimed to explore whether alternative tRNA structures could be introduced in bacterial translation. To this end, we crafted a vitamin-based genetic system to evolve Escherichia coli toward activity of structurally non-canonical tRNAs. The system reliably couples (escape frequency &lt;10−12) growth with the activities of a novel orthogonal histidine suppressor tRNA (HisTUAC) and of the cognate ARS (HisS) via suppression of a GTA valine codon in the mRNA of an enzyme in thiamine biosynthesis (ThiN). Suppression results in the introduction of an essential histidine and thereby confers thiamine prototrophy. We then replaced HisTUAC in the system with non-canonical suppressor tRNAs and selected for growth. A strain evolved to utilize mini HisT, a tRNA lacking the D-arm, and we identified the responsible mutation in an RNase gene (pnp) involved in tRNA degradation. This indicated that HisS, the ribosome, and EF-Tu accept mini HisT ab initio, which we confirmed genetically and through in vitro translation experiments. Our results reveal a previously unknown flexibility of the bacterial translation machinery for the accepted fold of the adaptor of the genetic code and demonstrate the power of the vitamin-based suppression system.