bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny of Arbacia Gray, 1835 (Echinoidea) Reveals Diversification Patterns in the Atlantic and Pacific Oceans
Authors: Courville E. , Mongiardino Koch N. , Jossart Q. , Moreau C. , Mooi R. , Lessios H. A. , Diaz A. , Martinez Salinas A. , Saucède T. , Poulin E. 
Published: December 2024

ABSTRACTAimThe aim of the current study is to conduct a comprehensive phylogenetic analysis of the genus Arbacia to elucidate the evolution and phylogenetic relationships among all extant species and reevaluate the presence of geographic structure within species that have wide, fragmented distributions.LocationSpecimens of Arbacia were collected from 34 localities spanning the Atlantic and Pacific Oceans, and the Mediterranean Sea.MethodsWe obtained sequences from three mitochondrial markers (COI, 16S and the control region and adjacent tRNAs) and two nuclear markers (28S and 18S; the latter ultimately excluded from the final analyses). Phylogenetic trees were constructed using maximum likelihood and Bayesian inference approaches. A time‐calibrated phylogenetic tree was inferred using a relaxed Bayesian molecular clock and three fossil calibration points.ResultsOur analysis supports the monophyly of the genus Arbacia, including the species Arbacia nigra (previously assigned to the monotypic genus Tetrapygus). The new phylogenetic topology suggests an alternative biogeographic scenario of initial divergence between Atlantic and Pacific subclades occurring approximately 9 million years ago. The dispersal and subsequent diversification of the Pacific subclade to the southeast Pacific coincides with the onset of glacial and interglacial cycles in Patagonia. In the Atlantic subclade, the split between A. punctulata and A. lixula occurred 3.01–6.30 (median 3.74 million years ago), possibly associated with the strengthening of the Gulf Stream current connecting the western and eastern Atlantic. Our study also reveals significant genetic and phylogeographic structures within both Atlantic species, indicating ongoing differentiation processes between populations.Main ConclusionOur study provides valuable insights into the evolutionary history and biogeography of the genus Arbacia and highlights the complex interplay between historical climate changes and oceanic currents in shaping the distribution and diversification of echinoids in the Atlantic and Pacific Oceans.
Daily and seasonal changes in steroidogenic markers in the hypothalamus and testes of tree sparrow (Passer montanus)
Authors: Yatung Subu , Trivedi Amit Kumar 
Published: December 2024

AbstractThe population responds to environmental variability largely determined by the dynamic interactions between fitness components within‐ and among‐individual variation in the expression of the environmentally sensitive phenotype. The study was conducted on daily and seasonal changes in the expression of steroidogenic gene markers and corresponding seasonal changes in the physiological characters in adult male tree sparrows. Two experiments were performed. In experiment one, birds (n = 5/time points) were sampled during the breeding season at 6‐time points, i.e., ZT1, ZT5, ZT9, ZT13, ZT17, and ZT21 [Zeitgeber time (ZT) 0 = sun rise time at the respective time of the year], and daily variation in expression of steroidogenic markers was observed in hypothalamus and testes tissues. In experiment two, birds (n = 5/month) were sampled every month at mid‐day for a year. Body mass, bill color, testes size, and molt in feathers were recorded. The hypothalamus and testes tissues were used for gene expression studies. Blood plasma cholesterol and testosterone levels were measured. Higher testicular volumes were recorded from March to May, whereas maximum molt was observed during the post‐breeding phase. Plasma cholesterol levels were highest before the breeding phase. Higher testosterone levels corresponded with the breeding phase. Higher expressions of thyroid‐stimulating hormone subunit beta (tshβ), type 2 deiodinase (dio2), and gonadotropin‐releasing hormone (gnrh) during the breeding phase and higher expression of type 3 deiodinase (dio3) and gonadotropin‐inhibitory hormone (gnih) were observed during the non‐breeding phase. The steroidogenic transcripts showed seasonal changes in their expression in the hypothalamic and testicular tissue and were upregulated either during the pre‐breeding or breeding phase. The study reveals that mRNA levels of steroidogenic enzymes exhibit daily rhythmicity both in the hypothalamus and testis tissues. Further, steroidogenic transcripts show seasonal variations that correspond to the annual reproductive cycle of the tree sparrow (Passer montanus).
Putting cultural mismatch theory to the test: Cultural fit of self‐construal in predicting student outcomes
Authors: Yılmaz Erdem , Phalet Karen , De Leersnyder Jozefien 
Published: December 2024

AbstractSocioeconomic and ethnicity‐based achievement gaps plague education. Both sociological theories and recent social‐psychological work consider cultural mismatches between schools’ and students’ ways of being and relating (i.e., self‐construal) as a potential mechanism. However, stringent empirical evidence remains lacking. Drawing on a sample of 5076 Belgian adolescents, this study aims to provide rigorous and robust novel evidence by (i) establishing high SES and ethnic majority group average patterns of self in relation to their teacher; (ii) calculating students’ ‘fit’ with these dominant group's patterns; and (iii) linking fit indices to objective and subjective achievement scores. As expected, fit with both high‐SES and ethnic majority self‐patterns were significantly positively related to achievement. Our findings suggest hitherto less visible systemic barriers to equal attainment due to engrained school practices that selectively value and reward majority middle‐class self‐ways. One way to promote equity in education is recognising and reforming such practices in schools.
Using veterinary health records at scale to investigate ageing dogs and their common issues in primary care
Authors: Jackson J. , Radford A. D. , Belshaw Z. , Wallis L. J. , Kubinyi E. , German A. J. , Westgarth C. 
Published: December 2024

ObjectivesThe UK dog population is living longer, raising concerns about their welfare as a result of ageing‐related diseases. Our primary objective was to determine when dogs enter the “old age” life stage based on free‐text clinical narratives in veterinary electronic health records. In addition, to identify common conditions documented during consultations with old dogs.Materials and MethodsRegular expressions were developed for: ageing, elderly, geriatric, senior and old. These were used to search the veterinary clinical narratives within a large database of veterinary electronic health records. A sample of 1000 consultations were then read, and those confirmed as being old age classified according to a modified scheme based on the World Health Organization International Classification of Disease 10th Revision.ResultsA total of 832 old age dogs were identified. The age at which veterinary professionals considered dogs to be in old age was over 7.25 years in 95% of patients (median age 12.5 years). This age varied among the most common breeds, with cocker spaniels being younger (median 11.7 years) compared with Jack Russell terriers (14.1 years). Weight‐related (289/832 consultations, 35%), musculoskeletal (278, 33%), dental (254, 31%), integumentary (235, 28%) and digestive (187, 22%) conditions were most common. The odds of a dental condition were greater (odds ratio: 2.71, 95% confidence interval: 1.38 to 5.31) and musculoskeletal condition less (odds ratio: 0.36, 95% confidence interval: 0.17 to 0.81) in cocker spaniels than in a mixed breeds reference.Clinical SignificanceThis metric applied at scale to identify old patients may provide a novel foundation for timely health interventions targeted to dogs at increased risk of developing various age‐related conditions.
Nitrogen availability in soil controls uptake of different nitrogen forms by plants
Authors: Liu Min , Xu Xingliang , Wanek Wolfgang , Sun Jian , Bardgett Richard D. , Tian Yuqiang , Cui Xiaoyong , Jiang Lili , Ma Zeqing , Kuzyakov Yakov , Ouyang Hua , Wang Yanfen 
Published: December 2024

Summary

Nitrogen (N) uptake by plant roots from soil is the largest flux within the terrestrial N cycle. Despite its significance, a comprehensive analysis of plant uptake for inorganic and organic N forms across grasslands is lacking.

Here we measured in situ plant uptake of 13 inorganic and organic N forms by dominant species along a 3000 km transect spanning temperate and alpine grasslands. To generalize our experimental findings, we synthesized data on N uptake from 60 studies encompassing 148 plant species world‐wide.

Our analysis revealed that alpine grasslands had faster NH4+ uptake than temperate grasslands. Most plants preferred NO3− (65%) over NH4+ (24%), followed by amino acids (11%). The uptake preferences and uptake rates were modulated by soil N availability that was defined by climate, soil properties, and intrinsic characteristics of the N form.

These findings pave the way toward more fully understanding of N cycling in terrestrial ecosystems, provide novel insights into the N form‐specific mechanisms of plant N uptake, and highlight ecological consequences of chemical niche differentiation to reduce competition between coexisting plant species.
A systematic review of longitudinal risk and protective factors for loneliness in youth
Authors: Buecker Susanne , Petersen Kimberly , Neuber Anne , Zheng Yixuan , Hayes Daniel , Qualter Pamela 
Published: December 2024

AbstractTo effectively tackle loneliness in youth, prevention and intervention strategies should be based on solid evidence regarding risk and protective factors in this age group. This systematic literature review identifies and narratively synthesizes longitudinal studies of risk and protective factors for loneliness in children and adolescents aged below 25 years. A systematic literature search was conducted in October 2023 using PsycINFO and MEDLINE, resulting in n = 398 articles, with n = 105 articles meeting the inclusion criteria. The examined factors included demographic (e.g., gender), socioeconomic (e.g., income sufficiency), social (e.g., peer acceptance), mental health (e.g., depression), physical health (e.g., disabilities), health behavior (e.g., sport participation), and psychological factors (e.g., shyness). Additionally, adverse childhood experiences (e.g., child maltreatment) and environmental factors (e.g., neighborhood characteristics) were investigated. Despite the wide range of potential risk and protective factors examined, relatively few studies provided strong evidence for a prospective association with loneliness. Risk factors that were consistently identified across multiple longitudinal studies included low peer acceptance and peer victimization, depression, social anxiety, internalizing symptoms, low self‐esteem, shyness, and neuroticism. Additional replication is required to evaluate factors that have shown significant associations with loneliness in only a limited number of longitudinal studies (e.g., aggression).
Improving the Likelihood of Positive Outcomes for Survivors of Sexual Violence, Considering Intersections Between Justice, Gender, and Trauma
Authors: Bond Kim , Davis Kate 
Published: December 2024

ABSTRACTThis paper explores the complex impacts of childhood abuse on survivors, emphasising how these experiences shape both individual and societal outcomes. It acknowledges the extensive and enduring effects of abuse, which extend beyond immediate physical and psychological harm to broader social and economic repercussions. The paper critically examines the difficulties of holding perpetrators accountable within the criminal justice system, where low reporting rates, high attrition, and re‐traumatization are significant challenges. Using a gendered lens, the analysis situates these issues within a broader social, cultural, and historical context, highlighting how abuse, particularly sexual abuse, is perceived and managed. A key focus is on the issue of disclosure, essential for survivors to access support and justice. However, disclosure is often hindered by fears of disbelief, stigma, and retaliation, which are exacerbated by socioeconomic factors. Even when support systems are available, low conviction rates and ongoing re‐victimisation significantly impede justice and healing, undermining the criminal justice system and support structures. The paper also discusses the wider implications of childhood abuse for public health, social services, and education. The trauma affects not only survivors' mental and physical health but also their ability to engage fully in society, impacting relationships, employment, and educational outcomes. These personal challenges lead to broader societal costs, including increased demand for healthcare and lost productivity. The paper advocates for an integrated approach that improves prevention, enhances safeguarding, and develops effective support systems, addressing both the immediate needs of survivors and systemic barriers to recovery and justice.
Effect of Radial Clearance on Static and Dynamic Performances of Single-Structured Hybrid Gas-Magnetic Bearing Rotor System
Authors: Liu Qing , Wu Mingdi , Ge Ruihuan , He Weipei , Cheng Ziyu 
Published: December 2024

Abstract
As the demand for ultrahigh-speed bearings grows, hybrid gas-magnetic bearings (HGMBs) have emerged as a research focus due to the ability to integrate the merits of active magnetic bearings (AMBs) and gas bearings (GBs). However, HGMBs face challenges related to complex structure and manufacturing. This study emphasizes the critical role of radial clearance in HGMB design, as excessive clearance reduces GB load capacity and stability. In contrast, insufficient clearance increases the risk of rotor–stator contact and is prone to thermal runaway failure or bearing seizure. This work investigates the comprehensive performance of HGMBs with varying clearances. The results show that radial clearance significantly influences GB and HGMB load capacities, with a 30-μm clearance increasing GB capacity up to 16.8 times compared to 150 μm at 46 krpm. Increasing radial clearance also reduces total losses in AMB, GB, and HGMB, notably decreasing GB air friction loss by up to 80.1%. The AMB/HGMB total loss increases tremendously with rotor eccentricity, especially in larger radial clearances. In addition, higher clearances lead to increased instability and vibration, with GB being the most sensitive. HGMBs exhibit superior startup stability, while zero-bias HGMBs and AMBs face challenges with increasing radial clearance. These findings highlight the importance of considering radial clearance effects and provide valuable insights for HGMB design, promoting advancements in this technology and engineering applications.
De novo-
assembled long-read genomes of
Saccharomyces cerevisiae
strains in commerce
Authors: Shwed P. S. , Anoop V. , Leveque G. 
Published: December 2024

ABSTRACT

Saccharomyces cerevisiae
strains NRRL Y-1646, Red Star, and VL3 are commercial yeast strains for baking and fermentation. These long-read genome assemblies will serve to better understand structural variation and biological properties of these strains.
Supplemental Material: Inception of ridge-ridge-ridge triple junctions: Morphostructural analysis and dynamics in the early back-arc extension of the northern Okinawa Trough
Authors: Koge Hiroaki , al. et 
Published: December 2024

<p>Detailed bathymetric images, explanations of the analytical methods and processing steps, and selected seismic reflection profiles aligned with the bathymetry. </p>
Thermal control on the updip and downdip extents of megathrust earthquake rupture: revisiting Dr. Roy Hyndman's seminal contributions 30 years later
Authors: Wang Kelin 
Published: December 2024

How far earthquake ruptures extend updip and downdip along subduction megathrusts has important science and hazard implications. In the Hyndman hypothesis proposed in the 1990s, the updip limit was set by a change in clay mineralogy at 100–150 °C, and the downdip limit by a temperature of ∼350 °C or the serpentinized mantle wedge corner (MWC), whichever was shallower. These limits were based on reported changes in fault friction behaviour with temperature and petrology. Many recent megathrust ruptures extended much beyond these limits, but the core idea of the hypothesis is still of great scientific value. Here, I highlight advances in earthquake science over the past three decades relevant to this subject and explain how the Hyndman hypothesis should be accordingly revised. The key point is that the clayey shallow segment of the megathrust and the MWC segment that is rich in lizardite serpentinite can act as “soft barriers” to seismic slip instead of hard limits. They impede seismic slip but may still participate in the slip while undergoing rate-strengthening, or they may even facilitate the slip by exhibiting dynamic weakening at high enough slip rates. In most subduction zones, antigorite serpentinites exhibit seismic behaviour to allow rupture to occur 10–20 km deeper than the MWC while radiating high-frequency seismic energy. In very warm subduction zones, seismic rupture is limited to be shallower than the MWC by thermally activated creep, and the ∼350 °C limit approximately holds. In this situation, the thermal and petrologic conditions at the MWC harbour Episodic Tremor and Slip.
Sacituzumab Govitecan in Patients with Relapsed/Refractory Advanced Head and Neck Squamous Cell Carcinoma: Results from the Phase II TROPiCS-03 Basket Study
Authors: Michel Loren , Jimeno Antonio , Sukari Ammar , Beck J. Thaddeus , Chiu Joanne , Ahern Elizabeth , Hilton John , Even Caroline , Zanetta Sylvie , Mekan Sabeen , Patel Jilpa , Wu Tia , Dumbrava Ecaterina E. 
Published: December 2024

Abstract

Purpose:
Treatment options for advanced head and neck squamous cell carcinoma (HNSCC) previously treated with platinum-based chemotherapy and a PD-1 inhibitor are limited. Trophoblast cell-surface antigen 2 (Trop-2) is highly expressed in HNSCC. Sacituzumab govitecan (SG) is a Trop-2–directed antibody-drug conjugate approved for patients with certain previously treated solid tumors.

Patients and Methods:
TROPiCS-03 (NCT03964727) is an open-label, multicohort, phase II study evaluating SG in advanced solid tumors, including HNSCC. Adults with locally advanced or metastatic HNSCC that progressed following platinum-based chemotherapy and anti–PD-(L)1 therapy [given sequentially (either order) or in combination] were administered SG 10 mg/kg on days 1 and 8 of a 21-day cycle. The primary endpoint was the investigator-assessed objective response rate. Secondary endpoints included duration of response, clinical benefit rate, progression-free survival, overall survival, and safety.

Results:
Patients (N = 43) received a median of 3 (range, 2–9) prior anticancer regimens. The objective response rate was 16% [95% confidence interval (CI), 7%–31%], with seven confirmed partial responses. The clinical benefit rate was 28% (95% CI, 15%–44%). The median (95% CI) duration of response, progression-free survival, and overall survival were 4.2 (2.6–not reached), 4.1 (2.6–5.8), and 9.0 (7.1–10.5) months, respectively. The most common treatment-emergent adverse events (TEAE) were diarrhea (47%), nausea (47%), and neutropenia (47%). Grade ≥3 TEAE occurred in 58% of patients. Three patients died from TEAE, with one event (septic shock) considered related to SG.

Conclusions:
These data demonstrate the clinical potential of Trop-2–directed therapy in managing heavily pretreated patients with advanced HNSCC.
Mathematical Modeling Predicts Optimal Immune Checkpoint Inhibitor and Radiotherapy Combinations and Timing of Administration
Authors: Sakai Shunsuke A. , Saeki Koichi , Chi SungGi , Hamaya Yamato , Du Junyan , Nakamura Masaki , Hojo Hidehiro , Kojima Takashi , Nakamura Yoshiaki , Bando Hideaki , Kojima Motohiro , Suzuki Ayako , Suzuki Yutaka , Akimoto Tetsuo , Tsuchihara Katsuya , Haeno Hiroshi , Yamashita Riu , Kageyama Shun-Ichiro 
Published: December 2024

Abstract
Radiotherapy (RT) combined with immune checkpoint inhibitor (ICI) therapy has attracted substantial attention due to its potential to improve outcomes for patients with several types of cancer. However, the optimal administration timepoints and drug combinations remain unclear because the mechanisms underlying RT-induced changes in immune checkpoint molecule expression and interaction with their ligand(s) remain unclear. In this study, we demonstrated the dynamics of lymphocyte-mediated molecular interactions in tissue samples from patients with esophageal cancer throughout RT schedules. Single-cell RNA sequencing and spatial transcriptomic analyses were performed to investigate the dynamics of these interactions. The biological signal in lymphocytes transitioned from innate to adaptive immune reaction, with increases in ligand–receptor interactions, such as PD-1–PD-L1, CTLA4–CD80/86, and TIGIT–PVR interactions. A mathematical model was constructed to predict the efficacy of five types of ICIs when administered at four different timepoints. The model suggested that concurrent anti–PD-1/PD-L1 therapy or concurrent/adjuvant anti-CTLA4/TIGIT therapy would exert a maximal effect with RT. This study provides rationale for clinical trials of RT combined with defined ICI therapy, and these findings will support future studies to search for more effective targets and timing of therapy administration.
Decreased Adipose Lipid Turnover Associates With Cardiometabolic Risk and the Metabolic Syndrome
Authors: Andersson Daniel P. , Arner Peter 
Published: December 2024

BACKGROUND:
Disturbed white adipose tissue function is important for cardiometabolic risk and metabolic syndrome (MetS). Whether this involves adipose lipid turnover (lipolysis and synthesis of triglycerides) is unknown and was presently investigated in subcutaneous adipose tissue, the body’s largest fat depot.

METHODS:

In cross-sectional studies in 78 subjects, adipose lipid age, representing overall lipid turnover (mobilization and storage), and lipid storage capacity were assessed by the incorporation of atmospheric
14
C into adipose lipids. Adipose lipid age from an algorithm of adipocyte lipolysis and clinical parameters was also determined in 185 subjects. Adult Treatment Panel III (ATPIII) scoring defined MetS (scores 3–5) or healthy (score 0). ANOVA or ANCOVA and
t
test were used for statistical comparison. Because there was no method interaction to determine lipid age, the 2 groups were combined.

RESULTS:

Lipid age increased by incremental ATPIII score (F=42;
P
<0.0001) and was 2-fold advanced in MetS (t=11.3;
P
<0.0001). The correlation with lipid age was independent of age, sex, body mass index, waist-to-hip ratio, sedentary lifestyle, absence of obesity, and adipose insulin resistance (F=10.7;
P
<0.0001). Lipid storage capacity was not related to the ATPIII score (F=1.0;
P
=0.44) or MetS (t=−0.9;
P
=0.35). Adipocyte lipolysis activation was decreased in MetS and inversely related to incremental ATPIII score, suggesting that decreased lipid mobilization is the major factor behind high lipid age in these conditions.

CONCLUSIONS:
Despite normal lipid assimilation capacity, abdominal subcutaneous adipose lipid turnover is decreased in MetS and high ATPIII score because of impaired ability to mobilize lipids involving low adipocyte lipolysis activation.