bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using twin-pairs to assess potential bias in polygenic prediction of externalising behaviours across development
Authors: Bright Joanna K. , Rayner Christopher , Freeman Ze , Zavos Helena M. S. , Ahmadzadeh Yasmin I. , Viding Essi , McAdams Tom A. 
Published: February 2025

Abstract
Prediction from polygenic scores may be confounded by sources of passive gene-environment correlation (rGE; e.g. population stratification, assortative mating, and environmentally mediated effects of parental genotype on child phenotype). Using genomic data from 10 000 twin pairs, we asked whether polygenic scores from the most recent externalising genome-wide association study predict conduct problems, ADHD symptomology and callous-unemotional traits, and whether these predictions are biased by rGE. We ran regression models including within-family and between-family polygenic scores, to separate the direct genetic influence on a trait from environmental influences that correlate with genes (indirect genetic effects). Findings suggested that this externalising polygenic score is a good index of direct genetic influence on conduct and ADHD-related symptoms across development, with minimal bias from rGE, although the polygenic score predicted less variance in CU traits. Post-hoc analyses showed some indirect genetic effects acting on a common factor indexing stability of conduct problems across time and contexts.
17-beta estradiol prevents cardiac myocyte hypertrophy by regulating mitochondrial E3 ubiquitin ligase 1
Authors: Calle Ximena , Garrido-Moreno Valeria , Becerra Brenda , Troncoso Mayarling F. , Silva-Agüero Juan Francisco , Guajardo-Correa Emanuel , Venegas-Zamora Leslye , Lopez-Gallardo Erik , Muñoz-Córdova Felipe , Fredericksen Fernanda , Aedo-Cares Sebastian , Peñaloza-Otárola Allan , Ortega Angelica , Raya Angel , Maracaja-Coutinho Vinicius , Chiong Mario , Parra Valentina , Lavandero Sergio 
Published: February 2025

Abstract
Cardiac hypertrophy is a cellular process characterized by the increased size of cardiomyocytes in response to a high workload or stress. 17-beta estradiol (E2) has cardioprotective and anti-hypertrophic effects by maintaining mitochondrial network and function. MUL1 is a mitochondrial ubiquitin ligase directly involved in the control of mitochondrial fission and mitophagy. Studies from our group and others have previously shown that cardiomyocyte hypertrophy is associated with mitochondrial fission and dysfunction. These findings led us to study in vitro whether E2 regulates MUL1 to prevent cardiac hypertrophy, mitochondrial fission, and dysfunction induced by the catecholamine norepinephrine (NE). Our results showed that NE induces hypertrophy in cultured rat cardiomyocytes. Pre-treatment with E2 (10-100 nM) prevented the NE-dependent increases in cell perimeter and the hypertrophic stress markers ANP and BNP at both the protein and mRNA levels. NE induced the fragmentation of the mitochondrial network and reduced ATP levels, effects that were both prevented by E2. In silico analysis suggested a putative binding site for estrogen receptors on the MUL1 gene promoter. In accordance with this finding, E2 prevented increases in MUL1 mRNA and protein levels induced by NE. Our data also showed that a siRNA MUL1 knockdown counteracted NE-induced cardiomyocyte hypertrophy and mitochondrial dysfunction, mirroring the protective effect triggered by E2. In contrast, a MUL1 adenovirus did not prevent the E2 protection from cardiomyocyte hypertrophy. Further, in vivo analysis in a transgenic mouse model overexpressing MUL1 revealed that only young male mice overexpressed the protein. Consequently, they exhibited increased levels of the hypertrophic marker ANP, an elevated heart weight, and larger cardiomyocyte size. Therefore, our data demonstrate that 17-beta estradiol prevents cardiac myocyte hypertrophy by regulating MUL1.
Quantifying vitamin D intake among Aboriginal and Torres Strait Islander peoples in Australia
Authors: Neo Belinda , Tilbrook Dale , Nannup Noel , Daly Alison , Dunlop Eleanor , Jacky John , Michie Carol , Prior Cindy , Farrant Brad , Shepherd Carrington C. J. , Lawrence Anita S. , Tescari Edoardo , Black Lucinda J. 
Published: February 2025

Abstract

Background/Objective
Vitamin D deficiency (serum 25-hydroxyvitamin D [25(OH)D] concentration < 50 nmol/L) is prevalent among Aboriginal and Torres Strait Islander peoples in Australia. Alternative to sun exposure (the primary source of vitamin D), vitamin D can also be obtained from food (e.g. fish, eggs, and meat) and supplements. However, the vitamin D intake of this population group is unknown. We aimed to provide the first quantification of vitamin D intake using nationally representative data from Aboriginal and Torres Strait Islander peoples.

Methods
We used food consumption data collected in the 2012–2013 National Aboriginal and Torres Strait Islander Nutrition and Physical Activity Survey (n = 4109) and vitamin D food composition data to quantify vitamin D intake by sex, age group, and remoteness of location. Wilcoxon rank-sum test was used to assess the difference in vitamin D intake between sexes and remoteness of location.

Results
The median (25th, 75th percentile) vitamin D intake among Aboriginal and Torres Strait Islander peoples aged ≥ 2 years was 80 (45, 145) IU/day. Vitamin D intake was statistically significantly different between males and females (p = < 0.001). There was no statistically significant difference between vitamin D intake in non-remote and remote areas (p = 0.292).

Conclusions
Vitamin D intake among Aboriginal and Torres Strait Islander peoples is low. Food-based public health strategies guided by Aboriginal and Torres Strait Islander Elders and communities could be developed to promote higher vitamin D intake among this population.
Parafermions in moiré minibands
Authors: Liu Hui , Perea-Causin Raul , Bergholtz Emil J. 
Published: February 2025

Abstract
Moiré materials provide a remarkably tunable platform for topological and strongly correlated quantum phases of matter. Very recently, the first Abelian fractional Chern insulators (FCIs) at zero magnetic field have been experimentally demonstrated, and it has been theoretically predicted that non-Abelian states with Majorana fermion excitations may be realized in the nearly dispersionless minibands of these systems. Here, we provide telltale evidence based on many-body exact diagonalization for the even more exotic possibility of moiré-based non-Abelian FCIs exhibiting Fibonacci parafermion excitations. In particular, we obtain low-energy quantum numbers, spectral flow, many-body Chern numbers, and entanglement spectra consistent with the

$${{\mathbb{Z}}}_{3}$$

Z

3

Read–Rezayi parafermion phase in an exemplary moiré system with tunable quantum geometry. Our results hint towards the robustness of moiré-based parafermions and encourage the pursuit in moiré systems of these non-Abelian quasiparticles that are superior candidates for topological quantum computing.
Reversible long-range domain wall motion in an improper ferroelectric
Authors: Zahn Manuel , Müller Aaron Merlin , Kelley Kyle P. , Neumayer Sabine , Kalinin Sergei V. , Kézsmarki István , Fiebig Manfred , Lottermoser Thomas , Domingo Neus , Meier Dennis , Schultheiß Jan 
Published: February 2025

Abstract
Reversible ferroelectric domain wall movements beyond the 10 nm range associated with Rayleigh behavior are usually restricted to specific defect-engineered systems. Here, we demonstrate that such long-range movements naturally occur in the improper ferroelectric ErMnO3 during electric-field-cycling. We study the electric-field-driven motion of domain walls, showing that they readily return to their initial position after having traveled distances exceeding 250 nm. By applying switching spectroscopy band-excitation piezoresponse force microscopy, we track the domain wall movement with nanometric spatial precision and analyze the local switching behavior. Phase field simulations show that the reversible long-range motion is intrinsic to the hexagonal manganites, linking it to their improper ferroelectricity and topologically protected structural vortex lines, which serve as anchor point for the ferroelectric domain walls. Our results give new insight into the local dynamics of domain walls in improper ferroelectrics and demonstrate the possibility to reversibly displace domain walls over much larger distances than commonly expected for ferroelectric systems in their pristine state, ensuring predictable device behavior for applications such as tunable capacitors or sensors.
Vernier microcombs for integrated optical atomic clocks
Authors: Wu Kaiyi , O’Malley Nathan P. , Fatema Saleha , Wang Cong , Girardi Marcello , Alshaykh Mohammed S. , Ye Zhichao , Leaird Daniel E. , Qi Minghao , Torres-Company Victor , Weiner Andrew M. 
Published: February 2025

Abstract
Kerr microcombs have drawn substantial interest as mass-manufacturable, compact alternatives to bulk frequency combs. This could enable the deployment of many comb-reliant applications previously confined to laboratories. Particularly enticing is the prospect of microcombs performing optical frequency division in compact optical atomic clocks. Unfortunately, it is difficult to meet the self-referencing requirement of microcombs in these systems owing to the approximately terahertz repetition rates typically required for octave-spanning comb generation. In addition, it is challenging to spectrally engineer a microcomb system to align a comb mode with an atomic clock transition with a sufficient signal-to-noise ratio. Here we adopt a Vernier dual-microcomb scheme for optical frequency division of a stabilized ultranarrow-linewidth continuous-wave laser at 871 nm to an ~235 MHz output frequency. This scheme enables shifting an ultrahigh-frequency (~100 GHz) carrier-envelope offset beat down to frequencies where detection is possible and simultaneously placing a comb line close to the 871 nm laser—tuned so that, if frequency doubled, it would fall close to the clock transition in 171Yb+. Our dual-comb system can potentially combine with an integrated ion trap towards future chip-scale optical atomic clocks.
SPO11 dimers are sufficient to catalyse DNA double-strand breaks in vitro
Authors: Oger Cédric , Claeys Bouuaert Corentin 
Published: February 2025

Abstract
SPO11 initiates meiotic recombination through the induction of programmed DNA double-strand breaks (DSBs)1,2, but this catalytic activity has never been reconstituted in vitro3,4. Here, using Mus musculus SPO11, we report a biochemical system that recapitulates all the hallmarks of meiotic DSB formation. We show that SPO11 catalyses break formation in the absence of any partners and remains covalently attached to the 5′ broken strands. We find that target site selection by SPO11 is influenced by the sequence, bendability and topology of the DNA substrate, and provide evidence that SPO11 can reseal single-strand DNA breaks. In addition, we show that SPO11 is monomeric in solution and that cleavage requires dimerization for the reconstitution of two hybrid active sites. SPO11 and its partner TOP6BL form a 1:1 complex that catalyses DNA cleavage with an activity similar to that of SPO11 alone. However, this complex binds DNA ends with higher affinity, suggesting a potential role after cleavage. We propose a model in which additional partners of SPO11 required for DSB formation in vivo assemble biomolecular condensates that recruit SPO11–TOP6BL, enabling dimerization and cleavage. Our work establishes SPO11 dimerization as the fundamental mechanism that controls the induction of meiotic DSBs.
Reconstitution of SPO11-dependent double-strand break formation
Authors: Zheng Zhi , Zheng Lyuqin , Arter Meret , Liu Kaixian , Yamada Shintaro , Ontoso David , Kim Soonjoung , Keeney Scott 
Published: February 2025

Abstract
Meiotic recombination starts with SPO11 generation of DNA double-strand breaks (DSBs)1. SPO11 is critical for meiosis in most species, but it generates dangerous DSBs with mutagenic2 and gametocidal3 potential. Cells must therefore utilize the beneficial functions of SPO11 while minimizing its risks4—how they do so remains poorly understood. Here we report reconstitution of DNA cleavage in vitro with purified recombinant mouse SPO11 bound to TOP6BL. SPO11–TOP6BL complexes are monomeric (1:1) in solution and bind tightly to DNA, but dimeric (2:2) assemblies cleave DNA to form covalent 5′ attachments that require SPO11 active-site residues, divalent metal ions and SPO11 dimerization. SPO11 can also reseal DNA that it has nicked. Structure modelling with AlphaFold 3 suggests that DNA is bent prior to cleavage5. In vitro cleavage displays a sequence bias that partially explains DSB site preferences in vivo. Cleavage is inefficient on complex DNA substrates, partly because SPO11 is readily trapped in DSB-incompetent (presumably monomeric) binding states that exchange slowly. However, cleavage is improved with substrates that favour dimer assembly or by artificially dimerizing SPO11. Our results inform a model in which intrinsically weak dimerization restrains SPO11 activity in vivo, making it exquisitely dependent on accessory proteins that focus and control DSB formation.
Plasma proteome variation and its genetic determinants in children and adolescents
Authors: Niu Lili , Stinson Sara Elizabeth , Holm Louise Aas , Lund Morten Asp Vonsild , Fonvig Cilius Esmann , Cobuccio Leonardo , Meisner Jonas , Juel Helene Bæk , Fadista Joao , Thiele Maja , Krag Aleksander , Holm Jens-Christian , Rasmussen Simon , Hansen Torben , Mann Matthias 
Published: February 2025

Abstract
Our current understanding of the determinants of plasma proteome variation during pediatric development remains incomplete. Here, we show that genetic variants, age, sex and body mass index significantly influence this variation. Using a streamlined and highly quantitative mass spectrometry-based proteomics workflow, we analyzed plasma from 2,147 children and adolescents, identifying 1,216 proteins after quality control. Notably, the levels of 70% of these were associated with at least one of the aforementioned factors, with protein levels also being predictive. Quantitative trait loci (QTLs) regulated at least one-third of the proteins; between a few percent and up to 30-fold. Together with excellent replication in an additional 1,000 children and 558 adults, this reveals substantial genetic effects on plasma protein levels, persisting from childhood into adulthood. Through Mendelian randomization and colocalization analyses, we identified 41 causal genes for 33 cardiometabolic traits, emphasizing the value of protein QTLs in drug target identification and disease understanding.
Gene expression atlas of the Colorado potato beetle (Leptinotarsa decemlineata)
Authors: Wilhelm Léonore , Wang Yangzi , Xu Shuqing 
Published: February 2025

Abstract
The Colorado potato beetle (CPB) is a major pest of potato crops, known for its remarkable ability to develop resistance to more than 50 pesticides. For decades, CPB has served as a model species for studying insecticide resistance, insect physiology, diapause, reproduction, and evolution. However, research progress on CPB has been hindered by the lack of comprehensive genomic and transcriptomic resources. Here, leveraging a recently established chromosome-level genome assembly, we constructed a gene expression atlas of CPB using transcriptomic data from 61 samples representing major organs and developmental stages. By integrating short- and long-read sequencing technologies, we enhanced the genome annotation and identified 6,623 additional genes that were previously undetected. Furthermore, we developed a web portal to facilitate the search and visualization of the gene expression atlas, providing an accessible resource for the research community. The CPB gene expression atlas offers valuable tools and comprehensive data that will accelerate future research in pest control and insect biology.
High risk of political bias in black box emotion inference models
Authors: Plisiecki Hubert , Lenartowicz Paweł , Flakus Maria , Pokropek Artur 
Published: February 2025

Abstract
This paper investigates the presence of political bias in emotion inference models used for sentiment analysis (SA). Machine learning models often reflect biases in their training data, impacting the validity of their outcomes. While previous research has highlighted gender and race biases, our study focuses on political bias—an underexplored, pervasive issue that can skew the interpretation of text data across many studies. We audit a Polish sentiment analysis model developed in our lab for bias. By analyzing valence predictions for names and sentences involving Polish politicians, we uncovered systematic differences influenced by political affiliations. Our findings suggest that annotations by human raters propagate political biases into the model’s predictions. To prove it, we pruned the training dataset of texts mentioning these politicians and observed a reduction in bias, though not its complete elimination. Given the significant implications of political bias in SA, our study emphasizes caution in employing these models for social science research. We recommend a critical examination of SA results and propose using lexicon-based systems as an ideologically neutral alternative. This paper underscores the necessity for ongoing scrutiny and methodological adjustments to ensure the reliability of the use of machine learning in academic and applied contexts.
Association between breast cancer risk factors and blood microbiome in patients with breast cancer
Authors: An Jeongshin , Kwon Hyungju , Oh Se-Young , Kim Young Ju 
Published: February 2025

Abstract
This study investigated the relationship between risk factors for breast cancer (BC) and the microbiome by comparing the microbiomes of BC patients with fatty liver disease to those with a normal liver. Bacterial extracellular vesicles were collected from each blood sample, and next-generation sequencing was performed. The analysis identified specific microbiome profiles shared among groups with hyperglycaemia, hyperlipidaemia, and high body mass index (BMI), which were then compared with functional biomarkers. In particular, the genus Faecalibacterium was a specific bacterium found in the groups with high concentrations of low-density lipoprotein cholesterol, high BMI, and fatty liver disease. Therefore, when the prognosis of patients with BC was analysed based on Faecalibacterium presence, it was confirmed that patients’ prognoses tended to deteriorate. In this study, BC risk factors, such as hyperglycaemia, hyperlipidaemia, fatty liver, and high BMI, were interconnected through the microbiome. This provides insights into how the risk factors for BC are linked and their impact on the microbiome and human health.
Fecal microbiota and genetics in pediatric-onset orofacial granulomatosis and Crohn´s disease
Authors: Höyhtyä Miikka , Haaramo Anu , Nikkonen Anne , Ventin-Holmberg Rebecka , Agrawal Nitin , Ritari Jarmo , Hickman Brandon , Partanen Jukka , Alapulli Heikki , Tuokkola Jetta , Salonen Anne , de Vos Willem M , Kolho Kaija-Leena 
Published: February 2025

Abstract
Orofacial granulomatosis (OFG) is a rare chronic inflammatory condition. It is under debate, whether it is a condition of its own or merely a subtype of Crohn’s disease (CD). We aimed to search for markers characteristic of patients with pediatric-onset OFG compared to patients with pediatric-onset CD. We recruited young patients with OFG (with or without CD, n = 29), CD (n = 24), and healthy controls (n = 20). All participants provided a fecal sample for microbiota and calprotectin analyses and saliva for DNA analysis of genes associated with OFG and kept a 3-day food diary. Oral disease activity was evaluated using The Oral Disease Activity Score by an otorhinolaryngologist and a dentist. We observed decreased relative abundance in class Clostridia and increased relative abundances of classes Actinobacteria and Bacilli in the feces of patients with OFG when compared to patients with CD and healthy controls. The relative abundances of Bifidobacterium adolescentis increased and Faecalibacterium prausnitzii decreased along with the increase in the Oral Disease Activity Score. We found the NOD2 gene rs8057341 allele A to be enriched in patients with OFG compared to patients with CD. These findings support the theory that OFG is a distinct disease phenotype.
Mastitis-related Staphylococcus aureus-derived extracellular vesicles induce a pro-inflammatory response in bovine monocyte-derived macrophages
Authors: Saenz-de-Juano Mara D. , Silvestrelli Giulia , Buri Samuel , Zinsli Léa V. , Schmelcher Mathias , Ulbrich Susanne E. 
Published: February 2025

Abstract

Staphylococcus aureus (S. aureus) is one of the most common causative agents of mammary gland infection and mastitis, but the specific role of S. aureus-derived extracellular vesicles (SaEVs) in mastitis has been poorly studied to date. Here, we aimed to investigate the response of bovine monocyte-derived macrophages (boMdM) to SaEVs of the genotype B (GTB) mastitis-related strain M5512B. Specifically, we evaluated the effects on the actin cytoskeleton, gene expression, and the SaEV proteomic cargo. Furthermore, we assessed to what extent the cellular and molecular response of boMdM to SaEVs differed from peripheral mononuclear blood cells (PBMCs) used for in vitro derivation of the former. We observed that SaEVs induced morphological changes in boMdM, leading to a pro-inflammatory and pyroptosis-related increased gene expression. Additionally, our study revealed that boMdM and PBMCs exhibited stimulus-specific differing responses. The proteomic analysis of SaEVs identified clusters of proteins related to virulence and antibiotic resistance, supporting the theory that S. aureus might use EVs to evade host defences and colonize the mammary gland. Our results bring new insights into how SaEVs might impact the host during an S. aureus infection, which can be useful for future S. aureus vaccine development.
Core decompression assisted by multi-functional minimally invasive instruments for the treatment of early osteonecrosis of the femoral head
Authors: Yuan Daizhu , Wu Zhanyu , Zhou Yuhu , Teng Jianxiang , Chen Qiuhan , Ye Chuan 
Published: February 2025

Abstract
Core decompression is a common method for treating early osteonecrosis of the femoral head (ONFH). However, the surgical procedure is cumbersome due to the lack of appropriate surgical instruments. This study aims to modify surgical instruments to improve surgery efficiency. A total of 28 patients with early ONFH treated with the core decompression were enrolled. 13 cases were treated with new instruments and the other 15 cases were treated with the traditional methods. The convenience of the new instruments was evaluated by comparing evaluation indicators. The multi-functional instruments reduced the number of fluoroscopy, shorted the operation time, improved the delivery efficiency, reduced the intraoperative blood loss, and reduced the surgical incision compared with the traditional method (p < 0.05). The new instruments removed the healthy bone of the femoral head and neck for reuse, the overall hospitalization cost was lower, and patient satisfaction was higher (p < 0.05). In the postoperative follow-up, the VAS was lower and Harris score was higher compared with the traditional group (p < 0.05). The multi-functional instruments can achieve the advantages of accurate positioning of the necrotic area, removed and reused healthy bone, effective expanded decompression, and efficient implant delivery, which is the effective instrument for the early ONFH.