bluuebunny/crossref_metadata_2025_split huggingface dataset:
Usability: comparison of DataONE on four university LibGuides
Authors: Cannon Leah , Volentine Rachel 
Published: February 2025

PurposeA 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/approachThe 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.FindingsWith people leaning more towards images than text, the idea of people preferring scanning to reading seems to be outdated thinking.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/implicationsOur 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/valueUntil 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

AbstractDeoxynivalenol (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 ApplicationThe 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

ABSTRACTCultivation 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

ABSTRACTIntroductionExposure 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.MethodsIn 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.ResultsfMRI 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.ConclusionThese 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

ABSTRACTBackground and PurposeFerroptosis 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.MethodsSprague 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.ResultsPhosphorylated 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.ConclusionsOur 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

ABSTRACTType 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

ABSTRACTFish 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

ABSTRACTThe 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

ABSTRACTSex 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

AbstractThis 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

ABSTRACTNuclease 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

AbstractRespiration 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.
imageKey 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.