bluuebunny/crossref_metadata_2025 huggingface dataset:
Resimulation-based self-supervised learning for pretraining physics foundation models
Authors: Harris P. , Krupa J. , Kagan M. , Maier B. , Woodward N.
Published: February 2025

Self-supervised learning (SSL) is at the core of training modern large machine learning models, providing a scheme for learning powerful representations that can be used in a variety of downstream tasks. However, SSL strategies must be adapted to the type of training data and downstream tasks required. We propose resimulation-based self-supervised representation learning (RS3L), a novel simulation-based SSL strategy that employs a method of to drive data augmentation for contrastive learning in the physical sciences, particularly, in fields that rely on stochastic simulators. By intervening in the middle of the simulation process and rerunning simulation components downstream of the intervention, we generate multiple realizations of an event, thus producing a set of augmentations covering all physics-driven variations available in the simulator. Using experiments from high-energy physics, we explore how this strategy may enable the development of a foundation model; we show how RS3L pretraining enables powerful performance in downstream tasks such as discrimination of a variety of objects and uncertainty mitigation. In addition to our results, we make the RS3L dataset publicly available for further studies on how to improve SSL strategies.

Published by the American Physical Society
2025
Angular modulation of nonlinear Breit-Wheeler yield by vacuum dichroism
Authors: Chen Jia-Ding , Dai Ya-Nan , Zhuang Kai-Hong , Jiang Jing-Jing , Shen Baifei , Chen Yue-Yue
Published: February 2025

Vacuum polarization is numerically investigated for the interaction between a GeV electron beam and a counterpropagating ultraintense laser pulse in the quantum radiation-dominated regime. We identify a signal of vacuum polarization in pair density using a straightforward one-stage setup, circumventing the challenge of preparations of highly polarized probe photons or precise measurements of photon polarization. In our scheme, most electrons are scattered in the direction of laser propagation while emitting substantial linearly polarized gamma photons. These photons undergo vacuum birefringence and dichroism before decaying into electron-positron pairs via the nonlinear Breit-Wheeler process. We demonstrate that vacuum dichroism enhances the purity of linear polarization, which suppresses the overall yield of electron-positron pairs and allows energetic photons to penetrate deeper into the laser pulse. The pairs produced by these energetic photons are more likely to be deflected into small-angle regions rather than being reflected, leading to an enhancement of pair yield in forward scattering. The difference in positron yield may have potential applications in measuring vacuum polarization effect in future laser-particle experiments.

Published by the American Physical Society
2025
Cross sections and inelasticity distributions of high-energy neutrino deep inelastic scattering
Authors: Weigel Philip L. R. , Conrad Janet M. , Garcia-Soto Alfonso
Published: February 2025

This study presents a comprehensive model for neutrino deep inelastic scattering (DIS) cross sections spanning energies from 50 to 5×1012  GeV with an emphasis on applications to neutrino telescopes. We provide calculations of the total charged-current DIS cross sections and inelasticity distributions up to next-to-next-to-leading order for isoscalar nucleon targets and up to next-to-leading order for nuclear targets. Several modifications to the structure functions are applied to improve the modeling of the cross sections at low energies where perturbative QCD is less accurate and at energies above 104  GeV where there is non-negligible top quark production and small-x logarithms need to be resummed. Using the Fixed-order next-to-leading logarithm (FONLL) general-mass variable-flavor number scheme, we account for heavy quark mass effects and separate the heavy flavor components of the structure functions, obtaining predictions of their relative contributions to the cross sections and the uncertainties arising from the parton distribution functions. Additionally, the effects of final state radiation are implemented in the calculation of the double-differential cross section and discussed in terms of their impact on measurements at neutrino telescopes.

Published by the American Physical Society
2025
Chiral edge states on spheres for lattice domain wall fermions
Authors: Clancy Michael , Kaplan David B.
Published: February 2025

Recently Weyl edge states on manifolds in dimension d+1 with a connected d-dimensional boundary were proposed as candidates for lattice regularization of chiral gauge theories, for even d. The examples considered to date include solid cylinders in any odd dimension, and the 3 ball with boundary S2. Here we consider the general case of a (d+1)-dimensional ball for any even d and show that the theory for the edge states on Sd describe a conventional Weyl fermion on a sphere with half-integer momenta. A possible advantage of such theories is that they can be discretized by a square lattice without breaking the underlying discrete hypercubic symmetry.

Published by the American Physical Society
2025
Patterns of link reciprocity in directed, signed networks
Authors: Gallo Anna , Saracco Fabio , Lambiotte Renaud , Garlaschelli Diego , Squartini Tiziano
Published: February 2025

Most of the analyses concerning signed networks have focused on balance theory, hence identifying frustration with undirected, triadic motifs having an odd number of negative edges; much less attention has been paid to their directed counterparts. To fill this gap, we focus on signed, directed connections, with the aim of exploring the notion of frustration in such a context. When dealing with signed, directed edges, frustration is a multifaceted concept, admitting different definitions at different scales: if we limit ourselves to consider cycles of length 2, frustration is related to reciprocity, i.e., the tendency of edges to admit the presence of partners pointing in the opposite direction. As the reciprocity of signed networks is still poorly understood, we adopt a principled approach for its study, defining quantities and introducing models to consistently capture empirical patterns of the kind. In order to quantify the tendency of empirical networks to form either mutualistic or antagonistic cycles of length 2, we extend the exponential random graph framework to binary, directed, signed networks with global and local constraints and then compare the empirical abundance of the aforementioned patterns with the one expected under each model. We find that the (directed extension of the) balance theory is not capable of providing a consistent explanation of the patterns characterizing the directed, signed networks considered in this work. Although part of the ambiguities can be solved by adopting a coarser definition of balance, our results call for a different theory, accounting for the directionality of edges in a coherent manner. In any case, the evidence that the empirical, signed networks can be highly reciprocated leads us to recommend to explicitly account for the role played by bidirectional dyads in determining frustration at higher levels (e.g., the triadic one).

Published by the American Physical Society
2025
Emergent flocking in mixtures of antialigning self-propelled particles
Authors: Kürsten Rüdiger , Mihatsch Jakob , Ihle Thomas
Published: February 2025

We observe a flocking mechanism, the emergence of a state with global polar order, in mixed systems of self-propelled particles with purely antialigning interactions, i.e., the ground state for any pair of particles is to be opposedly oriented. In binary mixtures, we find that flocking can be realized by cross-species antialigning that is dominant compared to intraspecies antialignment. While the key mechanism can be understood within a mean-field description, beyond mean-field we develop an asymptotically exact Boltzmann-scattering theory from first principles. This theory yields analytical predictions for the flocking transition and shows excellent quantitative agreement with simulations of dilute systems. For large systems, we find either microphase separation or static patterns with patches or stripes that carry different polarization orientations.

Published by the American Physical Society
2025
Attraction-Enhanced Emergence of Friction in Colloidal Matter
Authors: van der Meer Berend , Yanagishima Taiki , Dullens Roel P. A.
Published: February 2025

How frictional effects emerge at the microscopic level in particulate materials remains a challenging question, particularly in systems subject to thermal fluctuations due to the transient nature of interparticle contacts. Here, we directly relate particle-level frictional arrest to local coordination in an attractive colloidal model system. We reveal that the orientational dynamics of particles slows down exponentially with increasing coordination number due to the emergence of frictional interactions, the strength of which can be tuned simply by varying the attraction strength. Using a simple computer simulation model, we uncover how the interparticle interactions govern the formation of frictional contacts between particles. Our results establish quantitative relations between friction, coordination, and interparticle interactions. This is a key step toward using interparticle friction to tune the mechanical properties of particulate materials.

Published by the American Physical Society
2025
Cyclic phase transition of substrate-modulated two-dimensional dusty plasma driven by gyroscopic forces
Authors: Xu Ao , Reichhardt C. , Reichhardt C. J. O. , Feng Yan
Published: February 2025

Langevin dynamical simulations are performed to investigate the formation of clusters and voids of a two-dimensional periodic substrate (2DPS)-modulated two-dimensional dusty plasma (2DDP) driven by a gyroscopic force. It is discovered that, as the frequency of the gyroscopic force decreases gradually, the substrate-modulated 2DDP undergoes the cyclic transition between the ordered cluster and void phases. Between the observed ordered cluster and void phases, the studied 2DDP exhibits a more uniform arrangement of particles. The discovered cyclic transition is attributed to the symmetry of the time-averaged potential landscape induced by the 2DPS in the reference frame of the moving particle, as confirmed by superimposing the particle locations on the effective potential landscape under various conditions.

Published by the American Physical Society
2025
Superfluidity and sound propagation in disordered Bose gases
Authors: Geier Kevin T. , Maki Jeff , Biella Alberto , Dalfovo Franco , Giorgini Stefano , Stringari Sandro
Published: February 2025

Superfluidity describes the ability of quantum matter to flow without friction. Due to its fundamental role in many transport phenomena, it is crucial to understand the robustness of superfluid properties to external perturbations. Here, we theoretically study the effects of speckle disorder on the propagation of sound waves in a two-dimensional Bose-Einstein condensate at zero temperature. We numerically solve the Gross-Pitaevskii equation in the presence of disorder and employ a superfluid hydrodynamic approach to elucidate the role of the compressibility and superfluid fraction in the propagation of sound. A key result is that disorder reduces the superfluid fraction and hence the speed of sound; it also introduces damping and mode coupling. In the limit of weak disorder, the predictions for the speed of sound and its damping rate are well reproduced by a quadratic perturbation theory. The hydrodynamic description is valid over a wide range of parameters, while discrepancies become evident if the disorder becomes too strong, the effect being more significant for disorder applied in only one spatial direction. Our predictions are well within the reach of state-of-the-art cold-atom experiments and carry over to more general disorder potentials.

Published by the American Physical Society
2025
An assessment model for socio-cultural sustainability of campus outdoor environments using physical and satisfaction indicators
Authors: Manahasa Odeta , Logli Manjola , Manahasa Edmond
Published: February 2025

Purpose

This study aims to identify the physical properties of the outdoor campus planning and its components in the development of a sustainable campus, regarding the socio-cultural dimension.

Design/methodology/approach

Studying the under-theorized concept of socio-cultural sustainability in a university campus context and exploring their fundamental role in societies can contribute to generating socio-cultural sustainability on a broader scale. As a case study is taken, the Agricultural University campus of Tirana, where a meta-analysis and an observation of the campus components through a checklist are done. An online questionnaire with campus users brought their view about campus usage. The physical design and the experiences of the building users are all considered when comparing the socio-cultural sustainability of the campus’s outdoor environments qualitatively.

Findings

Findings conclude a common attitude towards most of the campus components by the users. In addition, the main properties of the physicality of a campus environment that contribute to a socio-cultural sustainable campus design are found to be the adequacy of outdoor components, the quality of outdoor environments, accessibility, safety and comfort, all elements that refine the assessment model.

Originality/value

This study’s novelty relies on proposing a socio-cultural sustainability model that works as a matrix to improve future assessment of campus outdoor spaces.
Supply chain resilience and soft organizational factors – a bibliometric analysis and systematic literature review
Authors: Ahmed Quba , Sumbal Muhammad Saleem , Lee Carman , Tsui Eric
Published: February 2025

Purpose

The advent of a dynamic and uncertain environment has shifted organizational focus from reactive to proactive approaches to develop resilience against disruptions. Organizations can strengthen their supply chain networks through strategic changes in structure and processes. In this connection, this study explores the extant literature on supply chain resilience (SCRE) concerning soft organizational factors (leadership, organizational culture and knowledge management) to analyse recent trends in this domain and propose future research directions.

Design/methodology/approach

It is a bibliometric analysis and systematic literature review of research articles from 2004 to 2024, collected from ISI Web of Science with keywords searches such as “knowledge management and supply chain resilience,” “leadership and supply chain resilience” and “organizational culture and supply chain resilience.” “VOS viewer” and “ATLAS.ti” were utilized for the co-occurrence and co-authorship analysis of the articles along with focusing on aspects such as theoretical and practical implications, the collaboration institutions and the countries involved in relation to the topic of interest.

Findings

The review shows that the development of studies on SCRE was slow from 2004 to 2015 but grew significantly from 2015 onwards and rose exponentially after 2020. Most studies were published in 2023. Results reveal the development of proactive strategies for SCRE in the recent literature by focusing on organizational factors. The study highlights exploring the contextual interplay between environmental, social and governance (ESG) and soft organizational factors for mitigation of supply chain risk and resilience in large-scale projects.

Originality/value

The COVID-19 pandemic became the precursor to highlighting the antecedents of SCRE, but the study of soft organizational drivers is still an ongoing area of research. There is a need to map the nascent literature on the link between organizational soft drivers and SCRE.
Agency costs in family firms: state of the art and future directions for emerging countries
Authors: Dote-Pardo Jairo , Contreras-Henríquez José Miguel , Espinosa Jaramillo Maria Teresa
Published: February 2025

Purpose

This paper analyzes the dynamics of agency costs in family firms through a systematic literature review, focusing on the interplay of governance mechanisms, institutional contexts and socioemotional wealth.

Design/methodology/approach

A systematic literature review of 91 articles published between 2010 and 2024 was made. The data was sourced from the Web of Science and Scopus databases using a search strategy emphasizing agency theory, family enterprises and emerging economies. Quantitative analysis identified key themes, influential authors and emerging trends, while qualitative synthesis provided deeper insights into governance practices and agency dynamics.

Findings

The study highlights the dual nature of family ownership as both a stabilizing force and a source of agency conflicts. While concentrated ownership aligns family and firm interests, it can lead to principal–principal conflicts, such as earnings management and minority shareholder expropriation, particularly in weak institutional contexts. Governance mechanisms, including board independence, external directors and professional management, are critical for mitigating agency costs but are often constrained by socioemotional wealth considerations.

Originality/value

The findings underscore the pivotal role of institutional environments in shaping governance practices and the performance of family firms. The study offers actionable insights for family business leaders, policymakers and practitioners.
Transforming asset recovery offices (AROs) to enhance their role in combating money laundering
Authors: Pavlidis Georgios
Published: February 2025

Purpose

This paper critically examines the recent legislative initiative of the European Union (EU) – the new Directive 2024/1260 on asset recovery and confiscation. It focuses particularly on the provisions that revamp Asset Recovery Offices (AROs) as part of the EU’s anti-money laundering and countering the financing of terrorism (AML/CFT) strategy. This paper aims to explore why the reform of AROs was considered necessary; highlight the key objectives, rules and principles governing AROs; and discusses the challenges and opportunities that arise as AROs are strengthened.

Design/methodology/approach

This paper draws on reports, legislation, legal scholarship and other open-source data on the EU legislative initiative to enhance the role and effectiveness of AROs in AML/CFT.

Findings

The new Directive 2024/1260 on asset recovery and confiscation establishes a comprehensive framework for AROs, aimed at improving their effectiveness and cooperation. If organizational challenges are properly addressed, AROs will greatly strengthen the EU’s capabilities in the field of AML/CFT.

Originality/value

To the best of the author’s knowledge, this study is the first to explore the new roles and powers of AROs under Directive 2024/1260 on asset recovery and confiscation, providing a critical analysis of how the Directive addresses longstanding inefficiencies in asset recovery. It examines the harmonization of AROs’ powers, enhanced mechanisms for cross-border cooperation and improved access to data resources. The study assesses the challenges and opportunities related to AROs operation, offering insights into the Directive’s transformative potential for combating crime within the EU.
Enhancing academic access: evaluating integrated ICT-based library services at IIT from users' perspectives
Authors: Faizan Mohd , Munshi Shamim Aktar
Published: February 2025

Purpose

The purpose of this study is to investigate the integrated ICT-based library services at the Indian Institute of Technology (IIT) from the users' perspectives. By evaluating these services, the study seeks to know how ICT integration enhances academic access, user satisfaction and overall library functionality.

Design/methodology/approach

The research employed a survey approach with a questionnaire as the primary data collection tool, involving a sample of 277 participants, determined through the Cochran sample size formula, with a 95% confidence level and a ±5% margin of error, drawing upon 25% of the population using a stratified random sampling technique. The collected data were analyzed using SPSS software version 23, applying statistical tests including T-tests, ANOVA and multivariate MANOVA, along with Tukey’s post hoc analysis.

Findings

The findings revealed that the library is equipped with a state-of-the-art ICT infrastructure facility, which significantly impacts users' academic performance. Research scholars (RS) perceived the highest impact with a mean score of 60.01, followed by postgraduates at 50.04 and undergraduates at 39.83. In terms of ICT-based library services, RS exhibit the highest usage. Additionally, the results indicate a high overall satisfaction level among users regarding library resources and services, with a mean satisfaction score of 4.10. However, 28.5% (N = 79) of respondents reported issue “in locating specific information.”

Practical implications

The study demonstrates how the integration of ICT can significantly enhance service delivery, support academic advancement and improve user satisfaction in an increasingly digital and networked environment. These findings and strategies are valuable for libraries around the world, providing a roadmap for using technology to satisfy their users' changing requirements and encouraging an atmosphere of innovation and constant development for library services.

Originality/value

By focusing on user perspectives, the study provides actionable recommendations for library administrators and policymakers aiming to optimize library services in the digital age. The findings can serve as a benchmark for similar academic institutions striving to enhance academic access through technological advancements.
Usability: comparison of DataONE on four university LibGuides
Authors: Cannon Leah , Volentine Rachel
Published: February 2025

Purpose

A usability eye-tracking study was conducted to examine how users interact with university LibGuides to find scientific data resources. During a study of DataONE’s Google Analytics, we found a high number of referrals from several university LibGuides. We wondered, “Does the high referral rate indicate that those LibGuides are more useable?”

Design/methodology/approach

The study was conducted at the User-eXperience Lab at the University of Tennessee. Four LibGuides were selected for the study: Two had high referral rates, and two did not but included references to DataONE.

Findings

With people leaning more towards images than text, the idea of people preferring scanning to reading seems to be outdated thinking. Instead, people want to look at as little text as possible. Blending website design to match people’s preference for images over text while still conveying your message is becoming increasingly important. Design features such as collapsible boxes and using images to break up text blocks could be configured to help LibGuides become more modern to match the textless Internet that people seemingly prefer.

Research limitations/implications

Our study does not provide recommendations for a specific LibGuide but hopes to inform the general usability of all LibGuide interfaces. Individual universities should conduct their own usability studies when redesigning their interface. One potential limitation of the study is that our participants were not representative users of any of the university libraries’ LibGuides. We did not recruit for discipline or familiarity with any of the four universities we examined.

Originality/value

Until recently there has not been a wide range of published studies about the usability of LibGuides; however, there is a growing body of literature on the subject.
Deoxynivalenol modulated mucin expression and proinflammatory cytokine production, affecting susceptibility to enteroinvasive Escherichia coli infection in intestinal epithelial cells
Authors: Wan Murphy Lam Yim , Co Vanessa Anna , Turner Paul C , Nagendra Shah P , El‐Nezami Hani
Published: February 2025

Deoxynivalenol (DON) is a common mycotoxin in crops that could induce intestinal inflammation, affecting the susceptibility of intestinal epithelial cells (IECs) to pathogen infection. This study aimed to investigate DON's effects on mucin and cytokine production as part of the local immune system and how it affected intestinal susceptibility to pathogen infection. Caco‐2 cells were exposed to DON followed by acute enteroinvasive Escherichia coli (EIEC) infection. An increase in EIEC attachment to DON‐exposed cells was observed, probably in part, mediated by secretory MUC5AC mucins and membrane‐bound MUC4 and MUC17 mucins. Additionally, DON with EIEC posttreatment led to significant changes in the gene expression of several proinflammatory cytokines (IL1α, IL1β, IL6, IL8, TNFα, and MCP‐1), which may be in part, mediated by NK‐κB and/or MAPK signaling pathways. These data suggested DON may exert immunomodulatory effects on IECs, altering the IEC susceptibility to bacterial infection.

Practical Application

The results suggested that DON might modulate immune responses by affecting mucus and cytokine production, which may affect the susceptibility of intestinal epithelial cells to pathogen infection.
A Molecular Survey of the Occurrence of Coffee Berry Disease Resistant Coffee Cultivars Near the Wild Gene Pool of Arabica Coffee in Its Region of Origin in Southwest Ethiopia
Authors: Bawin Yves , Zewdie Beyene , Ayalew Biruk , Roldán‐Ruiz Isabel , Janssens Steven B. , Tack Ayco J. M. , Nemomissa Sileshi , Tesfaye Kassahun , Hylander Kristoffer , Honnay Olivier , Ruttink Tom
Published: February 2025

Cultivation of crops close to their wild relatives may jeopardise the integrity of wild genetic resources. Detecting cultivars among wild plants is necessary to characterise crop‐wild gene flow, but can be challenging if cultivars and wild plants are phenotypically highly similar. Genomics tools can be used instead, but the selection of diagnostic loci for cultivar identification can be difficult if the wild and cultivated genepools are closely related. In Ethiopia, Arabica coffee cultivars resistant to coffee berry disease (CBD) occur near wild Coffea arabica plants and local landraces. However, the abundance and distribution of these cultivars across coffee sites remains unclear. Here, we present a new module of the SMAP package called SMAP relatedness pairwise to characterise pairwise genetic relationships between individuals based on haplotype calls and to identify diagnostic loci that distinguish (sets of) individuals from each other. Next, we estimate the relative abundance of CBD‐resistant cultivars across 60 Ethiopian Arabica coffee sites using a genome‐wide fingerprinting approach. We confirm the presence of these cultivars in around 75% of the coffee sites with a high agreement between a field survey and our DNA fingerprinting approach. At least 20 out of 60 sites with supposedly wild C. arabica individuals contain signatures of the cultivated genepool. Overall, we conclude that CBD‐resistant cultivars are widespread in Ethiopian coffee sites. The development of SMAP relatedness pairwise opens opportunities to assess the distribution of coffee cultivars in other regions in Ethiopia and to apply similar screenings near wild relatives from other crops.
The Impact of Childhood Maltreatment on Central Pain Processing in Individuals With Psychosis
Authors: Cay Mariesa , van Gool Raquel , Berry Camryn , Golden Emma , Cao Amanda , van der Heijden Hanne , Westbrook Anthony , Gonzalez‐Heydrich Joseph , Shinn Ann K. , Upadhyay Jaymin
Published: February 2025

Introduction

Exposure to childhood maltreatment can contribute to multiple behavioral and clinical manifestations, including the development of psychotic illnesses and pain‐related abnormalities. Aberrant pain perception in individuals with psychosis may be associated with the worsening psychiatric symptoms, including an increase in mood episodes and a higher risk for suicidality. Despite the multiple connections between psychosis, pain, and childhood maltreatment, the combined investigation of these three domains remains limited.

Methods

In this study, patients with schizophrenia (SZ, n = 20) or bipolar I disorder (BD, n = 24) and healthy controls (HC, n = 24) underwent a comprehensive clinical evaluation followed by quantitative sensory testing (QST), where behavioral sensitivity to thermal stimuli was quantified. Central pain circuitry was probed using a combination of functional and structural magnetic resonance imaging. Neuroimaging analyses focused on thermal stimulation fMRI responses, resting‐state connectivity, and gray matter morphological properties.

Results

fMRI demonstrated diminished sensorimotor activation during an evoked pain state for both SZ and BD patients, where reduced activity in thalamic subdivisions (i.e., pulvinar nucleus) in BD patients negatively correlates with the severity of childhood maltreatment. Resting‐state connectivity analyses revealed altered connectivity of various cortical regions with the postcentral gyri and thalamic nuclei, suggesting potential altered neural mechanisms underlying pain perception in patients with SZ and BD. Morphological analysis identified reduced gray matter thickness in the postcentral sulcus of BD patients, which correlated with the severity of childhood maltreatment.

Conclusion

These findings provide insight into the multidimensional nature of clinical presentations in SZ and BD and contribute to our understanding of the complex relationship between childhood maltreatment and central pain processing in patients with psychotic illnesses.
Metrnl/C‐KIT Axis Attenuates Early Brain Injury Following Subarachnoid Hemorrhage by Inhibiting Neuronal Ferroptosis
Authors: Zhou You , Li Jiani , Yuan Ye , Zhang Hao , Luo Xu , Wang Feng , Tao Yihao , Yue Jianhe , Huang Luyi , Wu Lei , Cao Yunxing , Yu Qian , He Qiuguang
Published: February 2025

Background and Purpose

Ferroptosis is a distinct form of cell death characterized by iron‐dependent lipid peroxidation and plays a crucial role in the early brain injury (EBI) following subarachnoid hemorrhage (SAH). As a newly discovered endogenous ligand for the C‐KIT receptor tyrosine kinase, meteorin‐like protein (Metrnl) exerts regulatory functions in oxidative stress and protects against various diseases. However, the specific role of the Metrnl/C‐KIT axis in neuronal ferroptosis during EBI following SAH remains to be elucidated.

Methods

Sprague Dawley rats were used to establish the SAH model through endovascular perforation. r‐Metrnl was administered intranasally 1 h after SAH. Metrnl shRNA, C‐KIT inhibitor ISCK03, AMPK inhibitor dorsomorphin, and Nrf2 inhibitor ML385 were administered intracerebroventricularly or intraperitoneally before r‐Metrnl treatment to explore the underlying mechanisms. Neurobehavioral assessments, immunofluorescence, western blot, ELISA, Fluoro‐Jade C staining, transmission electron microscopy, and Nissl staining were conducted to evaluate the effects. Additionally, primary neuron culture with hemoglobin (Hb) stimulation was used for in vitro studies.

Results

Phosphorylated C‐KIT and endogenous Metrnl levels were upregulated after SAH. Knockdown of Metrnl aggravated neurobehavioral deficits and neuronal ferroptosis, whereas r‐Metrnl treatment showed a protective effect. Mechanistically, r‐Metrnl significantly increased the protein levels of SLC7A11, GPX4, FTH, FSP1, and GSH, whereas it decreased the levels of ACSL4, 4HNE, and MDA in the ipsilateral hemisphere 24 h after SAH. Also, r‐Metrnl reduced mitochondrial shrinkage, increased mitochondrial crista, and decreased membrane density. However, the beneficial effects of r‐Metrnl were partially reversed by ISCK03, dorsomorphin, or ML385 treatment both in vivo and in vitro.

Conclusions

Our study demonstrated that r‐Metrnl reduced neuronal ferroptosis and improved neurological outcomes after SAH by modulating the C‐KIT/AMPK/Nrf2 signaling pathway.
Tissue‐Resident Th2 Cells in Type 2 Immunity and Allergic Diseases
Authors: Mannion Jenny M. , Rahimi Rod A.
Published: February 2025

Type 2 immunity represents a unique immune module that provides host protection against macro‐parasites and noxious agents such as venoms and toxins. In contrast, maladaptive type 2 immune responses cause allergic diseases. While multiple cell types play important roles in type 2 immunity, recent studies in humans and murine models of chronic allergic diseases have shown that a distinct population of tissue‐resident, CD4+ T helper type 2 (Th2) cells play a critical role in chronic allergic inflammation. The rules regulating Th2 cell differentiation have remained less well defined than other T cell subsets, but recent studies have shed new light into the specific mechanisms controlling Th2 cell biology in vivo. Here, we review our current understanding of the checkpoints regulating the development and function of tissue‐resident Th2 cells with a focus on chronic allergic diseases. We discuss evidence for a barrier tissue checkpoint in initial Th2 cell priming, including the role of neuropeptides, damage‐associated molecular patterns, and dendritic cell macro‐clusters. Furthermore, we review the evidence for a second barrier tissue checkpoint that instructs the development of multi‐cytokine producing, tissue‐resident Th2 cells that orchestrate allergic inflammation. Lastly, we discuss potential approaches to therapeutically target tissue‐resident Th2 cells in chronic allergic diseases.
Dynamics of Reinfection by Neobenedenia sp. (Monogenea, Capsalidae) in Almaco Jack, Seriola rivoliana, Kept in a Cultivation System
Authors: Mera‐Loor Geormery Belén , Alcívar‐Mendoza Limber José , Cruz‐Quintana Yanis , Santana‐Piñeros Ana María , Caña‐Bozada Víctor Hugo
Published: February 2025

Fish susceptibility to parasitic infection is a crucial issue in aquaculture, where the density of captive fish increases the intensity of parasitic infections. Monogeneans are a group of parasitic flatworms that include pathogenic species for fish, among them Neobenedenia spp., which pose significant challenges for fish health in farming systems. Understanding the dynamics of parasitism in fish and how they may vary according to host susceptibility or environmental conditions is essential for the development of effective management strategies in aquaculture. Therefore, the aim of this study was to investigate the individual susceptibility of Almaco jack (Seriola rivoliana) to infections by Neobenedenia sp. and examine how reinfection affects parasite load in an aquaculture setting. Our findings unveiled an aggregated distribution of parasites in the fish population, indicating a non‐random pattern influenced by specific host factors. Furthermore, our results revealed that even minor temperature variations, such as an increase of just 1°C, were associated with a noticeable rise in parasite abundance. These results underscore the importance of regular monitoring in S. rivoliana tank‐maintained systems, as even minor temperature fluctuations can cause a substantial increase in Neobenedenia sp. infections, particularly in more susceptible individuals.
MicroRNA gatekeepers: Orchestrating rhizospheric dynamics
Authors: Fahad Muhammad , Tariq Leeza , Li Wanchang , Wu Liang
Published: February 2025

The rhizosphere plays a crucial role in plant growth and resilience to biotic and abiotic stresses, highlighting the complex communication between plants and their dynamic rhizosphere environment. Plants produce a wide range of signaling molecules that facilitate communication with various rhizosphere factors, yet our understanding of these mechanisms remains elusive. In addition to protein‐coding genes, increasing evidence underscores the critical role of microRNAs (miRNAs), a class of non‐coding single‐stranded RNA molecules, in regulating plant growth, development, and responses to rhizosphere stresses under diverse biotic and abiotic factors. In this review, we explore the crosstalk between miRNAs and their target mRNAs, which influence the development of key plant structures shaped by the belowground environment. Moving forward, more focused studies are needed to clarify the functions and expression patterns of miRNAs, to uncover the common regulatory mechanisms that mediate plant tolerance to rhizosphere dynamics. Beyond that, we propose that using artificial miRNAs and manipulating the expression of miRNAs and their targets through overexpression or knockout/knockdown approaches could effectively investigate their roles in plant responses to rhizosphere stresses, offering significant potential for advancing crop engineering.
Evidence for evolution of a new sex chromosome within the haploid‐dominant Marchantiales plant lineage
Authors: Fu Yuan , Zhang Xiaoxia , Zhang Tian , Sun Wenjing , Yang Wenjun , Shi Yajing , Zhang Jian , He Qiang , Charlesworth Deborah , Jiao Yuannian , Chen Zhiduan , Xu Bo
Published: February 2025

Sex chromosomes have evolved independently in numerous lineages across the Tree of Life, in both diploid‐dominant species, including many animals and plants, and the less studied haploid‐dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self‐fertilize. Here, we studied dioicy–monoicy transitions in the ancient liverwort haploid‐dominant plant lineage, using three telomere‐to‐telomere gapless chromosome‐scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re‐evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that micro‐chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.
Parent‐adolescent emotional communication patterns and adolescent depressive symptoms: A dyadic, mixed methods study
Authors: Zhou Ting , Liu Lingjia , Chen Kan , Hu Jennifer , Shang Zhe
Published: February 2025

This study aimed to explore the characteristics of parent–adolescent emotional communication patterns from the perspectives of both parents and adolescents and to further examine their relationships with adolescent depressive symptoms. A mixed methods exploratory sequential design was used. In the qualitative phase, 21 parent–adolescent dyads (adolescents aged 15.1 years, with 11 reporting high depressive symptoms and 10 reporting low depressive symptoms) were interviewed, and the data were analyzed via inductive thematic analysis. The quantitative phase surveyed 369 parent–adolescent dyads (adolescents aged 13.5, 48.5% female). Emotional communication patterns were identified via latent profile analyses, and adolescent depressive symptoms were compared across patterns. The qualitative phase identified six parent–adolescent emotional communication patterns depending on parental behaviors, adolescents’ needs, and family arrangements. Different patterns were observed between groups with high and low depressive symptoms. In the quantitative phase, five patterns emerged from both adolescent and parent reports. Adolescents’ depressive symptoms significantly differed across patterns regardless of the data source, with the lowest in the adaptive communication pattern and the highest in maladaptive or limited communication patterns. Reporting concordance/discordance was also associated with adolescent depressive symptoms. Parent–adolescent emotional communication patterns differ in frequency and quality. Adolescent depressive symptoms varied across patterns. Concordance/discordance in reporting was associated with depressive symptoms in adolescents.
A Conserved Endonuclease From Rust Fungi Suppresses Plant Extracellular DNA‐Triggered Immunity
Authors: Zhang Ying , Hao Zhenkai , Nian Jiting , Zhang Yanfei , Tian Song , Xu Yiqian , Duan Wanlu , Kang Zhensheng , Zhao Jing
Published: February 2025

Nuclease 1 (NUC1) is a highly conserved nonspecific endonuclease present in vertebrates, fungi, and a few plant species. While the involvement of yeast NUC1p in apoptotic cell death independent of metacaspase or apoptosis‐inducing factors is documented, its function in other fungi, particularly pathogenic ones, remains elusive. In this study, we identified and characterised the homologue of yeast NUC1p, termed PstNUC1, in Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust. PstNUC1 was induced during infection and was secreted to the extracellular space of the host. Silencing of PstNUC1 significantly attenuated the virulence of Pst, suggesting its critical role in pathogenicity. Exogenous treatment of PstNUC1 diminished the extracellular DNA (exDNA)‐triggered plant immune response, including cell death, oxygen peroxide production, and upregulation of Pathogenesis‐related genes. Notably, overexpression of wild‐type PstNUC1, but not a signal peptide‐deficient mutant (PstNUC1ΔSP), in wheat compromised exDNA‐triggered immunity, resulting in enhanced susceptibility to Pst infection. These finding collectively highlight the contribution of PstNUC1 to virulence through degradation of exDNA, thereby dampening the exDNA‐induced plant immune response.
The pupillary respiratory‐phase response: pupil size is smallest around inhalation onset and largest during exhalation
Authors: Schaefer Martin , Mathôt Sebastiaan , Lundqvist Mikael , Lundström Johan N. , Arshamian Artin
Published: February 2025

Respiration shapes brain activity and synchronizes sensory and exploratory motor actions, with some evidence suggesting that it also affects pupil size. However, evidence for a coupling between respiration and pupil size remains scarce and inconclusive, hindered by small sample sizes and limited controls. Given the importance of pupil size in visual perception and as a reflection of brain state, understanding its relationship with respiration is essential. In five experiments using a pre‐registered protocol, we systematically investigated how respiratory phase affects pupil size across different conditions. In Experiment 1 (n = 50), we examined nasal and oral breathing at rest under dim lighting with nearby fixation points, then replicated these results under identical conditions in Experiment 2 (n = 53). Experiment 3 (n = 112) extended this to active visual tasks, while Experiment 4 (n = 57) extended this to controlled breathing at different paces under ambient lighting with distant fixation. Finally, in Experiment 5 (n = 34), individuals with isolated congenital anosmia (born without olfactory bulbs) were used as a lesion‐type model during visual–auditory tasks to assess whether the respiratory–pupil link depends on olfactory bulb‐driven oscillations.

Across all conditions – free and controlled breathing; different tasks, lighting and fixation distances; and with and without olfactory bulbs – we consistently found that pupil size is smallest around inhalation onset and largest during exhalation. We term this effect the pupillary respiratory‐phase response, the fourth known mechanism influencing pupil size, alongside the pupillary light, near fixation and psychosensory responses.

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Key points

The influence of respiration on pupil size dynamics has long been debated.

In this study, we systematically investigated how pupil size changes across the breathing cycle through a series of five experiments, while varying tasks, lighting, fixation distance and brain region involvement.

We show that pupil size is smallest around inhalation onset and largest during exhalation, with pupil dilatation occurring through most of inhalation and the early phase of exhalation, and pupil constriction occurring primarily during the latter part of exhalation.

This pattern was consistent across all experimental conditions, demonstrating that it is robust and likely controlled by brainstem circuits.

We term this effect the pupillary respiratory‐phase response, the fourth known mechanism influencing pupil size.
¿Influye el bienestar social en las actitudes hacia la reconciliación? Análisis desde la experiencia de la población civil cuatro años después del Acuerdo de Paz en Colombia
Authors: Martinez Perez Melissa
Published: February 2025

Este artículo analizó las relaciones funcionales entre el bienestar social y la disposición hacia la reconciliación entre miembros de la población civil colombiana. Se estudió una muestra de 320 personas, de las cuales un 55.9% fueron mujeres y un 43.8% hombres con edades entre los 18 y 68 años. Se construyeron Modelos de Ecuaciones Estructurales para evaluar las relaciones entre el bienestar social como variable independiente, y la disposición hacia la reconciliación como variable dependiente, obteniendo índices satisfactorios para todos los parámetros calculados en el modelo. Los resultados demostraron que existe una relación funcional directa y positiva del bienestar social con respecto a la disposición hacia la reconciliación; a partir de la cual se concluye, en primer lugar, que el bienestar social es un factor determinante de la disposición hacia la reconciliación, y en segundo lugar, que un componente esencial de cualquier proceso reconciliatorio es la recuperación social y emocional de las comunidades que vivieron la situación de conflicto.
Behavioral reactions of harbor porpoises to impact pile driving noise are predicted by the auditory frequency weighted sound pressure level
Authors: Tougaard Jakob
Published: February 2025

Offshore impact pile driving is a major source of high level underwater noise that can disturb marine mammal behavior tens of kilometers away. Projects involving pile driving are therefore subject to environmental impact assessments, which include modelling of the spatial extent of the behavioral disturbance. Reliable predictions about behavioral reaction distances require robust estimates of the minimum received levels of noise above which animals are likely to respond. Studies of reactions of harbor porpoises to pile driving noise in the wild and playback in captivity were identified, and reaction thresholds were extracted. Thresholds were weighted with the auditory frequency weighting function for VHF-cetaceans, the functional hearing group to which porpoises belong. The thresholds derived from playback studies to animals in captivity could be frequency weighted directly, whereas thresholds from exposure to noise from actual pile driving activities were weighted via a range-dependent weighting factor. Seven studies of porpoise reactions provided a first estimate of a behavioral reaction threshold as a VHF-weighted received level (Lp,125 ms,VHF) in the range 95–115 dB re 1 μPa.