bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal dynamics of the fibrotic niche in cardiac repair
Authors: Chan Andy Shing Fung , Greiner Joachim , Brennan Tomas , Agrawal Ankit , Hemmer Helene , Sinning Katrin , Marschhäuser Lisa , Cheung Wing Lam , Iqbal Zafar , Klesen Alexander , Seidel Thomas , Vaeth Martin , Rog-Zielinska Eva , Kohl Peter , Schneider-Warme Franziska , Grün Dominic 
Published: November 2024

SummaryThe heart is one of the least regenerative organs in humans, and ischemic heart disease is the leading cause of death worldwide. Understanding the cellular and molecular processes that occur during cardiac wound healing is an essential prerequisite to reducing health burden and improve cardiac function after myocardial tissue damage. By integrating single-cell RNA-sequencing with imaging-based spatial transcriptomics, we reconstructed the spatio-temporal dynamics of the fibrotic niche after ventricular injury in adult mice. Our analysis reveals dynamic regulation of local cell communication niches over time. We identified interactions that regulate cardiac repair, including fibroblast proliferation silencing byTrem2highmacrophages that prevents excessive fibrosis. Moreover, we discovered a rare population of dedifferentiating cardiomyocytes during early post-lesion stages, which was sustained by signals from myeloid and lymphoid cells. Culturing non-regenerative mouse cardiomyocytes or human heart tissue with these niche factors reactivated progenitor gene expression and cell cycle activity. In summary, this spatio-temporal cell type atlas provides valuable insights into the heterocellular interactions that control cardiac repair.HighlightsscRNA-seq and in situ sequencing reveal spatio-temporal dynamics of heart repairLocal heterocellular communication niches coordinate overall wound responseFibroblast cell cycle silencing byTrem2highmacrophages suppresses excessive fibrosisCardiomyocyte plasticity is promoted by myeloid and lymphoid cells
Prenatal Arsenic Exposure and Gene Expression in Fetal Liver, Heart, Lung, and Placenta
Authors: Rychlik K. A. , Kashiwagi C. , Liao J. , Mathur A. , Illingworth E. J. , Sanchez S. S. , Kleensang A. , Maertens A. , Sillé F. C. M. 
Published: November 2024

AbstractPrenatal arsenic exposure has been linked to a myriad of negative health effects. There is relatively little insight into the mechanisms and signaling alterations across different fetal organs that drive long-term immune-related issues following prenatal arsenic exposure. Therefore, the effects of this exposure window on gene expression in the liver, placenta, heart, and lung of gestation day (GD) 18 C57BL/6 mouse fetuses were investigated. From two weeks prior to mating until tissue collection at GD18, mice were exposed to 0 or 100 ppb sodium (meta) arsenite in drinking water. Genes of interest were analyzed by RT-qPCR, complemented with untargeted Agilent 44K microarray analysis. Data cleanup and analysis was performed in RStudio. Differentially expressed mRNAs were queried in the String Database and using Cytoscape to create interaction networks and identify significantly enriched biological pathways. A total of 251, 165, 158, and 41 genes were significantly altered in the liver, placenta, heart, and lung, respectively, when treated samples were compared to controls. Many altered pathways were immune-related, supporting prior research. Most notably, gene expression of Gbp3, a key player in the cellular response to interferon gamma, was found to be reduced in placentas of female fetuses exposed to arsenic compared to controls (p=0.0762).ImpactThis is the first study comparing alterations in gene expression across multiple organs following prenatal exposure to environmentally relevant levels of arsenic. These findings, elucidating the multi-organ impact of prenatal arsenic exposure on predominantly immune-related pathways, further our mechanistic understanding of the long-term health effects observed in early-life arsenic-exposed populations.
Implication ofTITINVariations in Dilated Cardiomyopathy: Integrating Whole Exome Sequencing With Molecular Dynamics Simulation Study
Authors: Mukhopadhyay Amrita , Devi Bharti , Baidya Anurag TK , Yadav Manohar Lal , Kumar Rajnish , Mohapatra Bhagyalaxmi 
Published: November 2024

AbstractDilated cardiomyopathy (DCM) is one of the leading causes of heart failure, characterized by ventricular dilation and impaired systolic function. Variations in theTITIN(TTN)gene, which encodes the giant muscle protein TTN, play a pivotal role in the genetic underpinnings of DCM. We conducted WES on 15 patients (5 familial and 10 sporadic) diagnosed with idiopathic DCM and identified 88 exonic variants including four novel variants. These variants were predominantly located in the A-band region (39 variants) of TTN, a critical region for its mechanical stability and interaction with other sarcomeric proteins, followed by the I-band domain (33 variants), Z-disc domain (7 variants) and M-band region (9 variants). To discern the functional repercussions of these variations, we performed several bioinformatics analyses including pathogenicity prediction, protein stability, and protein-protein docking followed by MD simulations on both wild-type and mutant TTN fragments with their corresponding interacting partners (TCAP, MYH7, LMNA). We revealed that variations in the A-band domain significantly alter the protein’s structural dynamics, leading to decreased mechanical stability and altered protein-protein interactions. These changes are likely to disrupt sarcomere function, thereby elucidating their role in the pathogenesis of DCM.Graphical abstract
A revision of the AfricanRussula radicansand allies in subgen.Heterophyllidiaeprovides an example of a clade that exhibits recent diversification and extensive phenotypic plasticity
Authors: Buyck B , Henkel TW , Manz C , Cao SQ , Amalfi M , Wang XH 
Published: November 2024

AbstractRussulasubsectionRadicantinaeis described forR. radicansand allies, while subsectionAureotactinaeis again restricted toR. aureotacta, the subsectional type species that has never been recollected since its original description.Russula radicans,originally described from Madagascar, as well as the Central AfricanR. brunneoannulata,are epitypified.Russula xylophilais the first confirmed annulate species belonging to Sect.Ingrataeand a close relative toR. oleifera.An ITS sequence has been obtained from theR. xylophilaholotype collection made in 1928, but it is slightly different from those obtained from all new collections. For this reason and some minor morphological differences, we refrained from epitypification.Russula acriannulata, another species attributed toAureotactinaein the past, is now also excluded from the subsection, but needs more sequencing to solve its systematic placement. The MalagasyRussula cibaensisandR. tapiae, as well as the Central AfricanR. cameroonensisandR. afrovinaceaare new species inRadicantinae.At least three more undescribed species are revealed by environmental sequences. The West AfricanR. sankaraeis reduced to a form ofR. radicans. The latter species exhibits an impressive phenotypic plasticity in response to differences in habitat or host associations. It has a very wide distribution covering littoral rain forest in eastern Madagascar (formaradicans), Zambezian woodlands in Central and Eastern Africa (formamiomboensisfo. nov.) and gallery forests in West Africa (formasankarae).
Cell-context dependent in silico organelle localization in label-free microscopy images
Authors: Elmalam Nitsan , Zaritsky Assaf 
Published: November 2024

AbstractIn silico labeling prediction of organelle fluorescence from label-free microscopy images has the potential to revolutionize our understanding of cells as integrated complex systems. However, out-of-distribution data caused by changes in the intracellular organization across cell types, cellular processes or perturbations, can lead to altered label-free images and impaired in silico labeling. We demonstrated that incorporating biological meaningful cell contexts, via a context-dependent model that we call CELTIC, enhanced in silico labeling prediction and enabled downstream analysis of out-of-distribution data such as cells undergoing mitosis, and cells located at the edge of the colony. These results suggest a link between cell context and intracellular organization. Using CELTIC to generate single cell images transitioning between different contexts enabled us to overcome inter-cell variability toward integrated characterization of organelles’ alterations in cellular organization. The explicit inclusion of context has the potential to harmonize multiple datasets, paving the way for generalized in silico labeling foundation models.
Resuscitation-promoting factor (Rpf) terminates dormancy among diverse soil bacteria
Authors: Lennon Jay T. , Lehmkuhl Brent K. , Chen Lingling , Illingworth Melissa , Kuo Venus , Muscarella Mario E. 
Published: November 2024

AbstractMicroorganisms often inhabit environments that are suboptimal for growth and reproduction. To survive when challenged by such conditions, individuals may engage in dormancy where they enter a metabolically inactive state. For this persistence strategy to confer an evolutionary advantage, microorganisms must be able to resuscitate and reproduce when conditions improve. Among bacteria in the phylum Actinomycetota, dormancy can be terminated by resuscitation-promoting factor (Rpf), an exoenzyme that hydrolyzes glycosidic bonds in the peptidoglycan of the cell wall. We characterized Rpf fromMicrococcusKBS0714, a bacterium isolated from agricultural soil. Compared to previous studies, the Rpf elicited activity at relatively high concentrations, yet demonstrated high substrate affinity. Site-directed mutations at conserved catalytic sites significantly reduced or abolished resuscitation, as did the deletion of repeating motifs in a lectin-encoding linker region. We then tested the effects of recombinant Rpf fromMicrococcusKBS0714 on a diverse set of dormant soil bacteria. Patterns of resuscitation mapped onto strain phylogeny, which reflected core features of the cell envelope. Additionally, the direction and magnitude of the Rpf effect were associated with functional traits, in particular, aspects of the moisture niche and biofilm production, which are critical for understanding persistence and resuscitation during dormancy. These findings expand our understanding of how Rpf may affect seed-bank dynamics and have implications for the diversity and functioning of soil ecosystems.
Discordance between biomarkers of iron status in plasma and myocardium across iron replete, iron deficiency, and iron replacement states
Authors: Tomkova Kristina , Cabolis Katerina , Sajic Maria , Wozniak Marcin J , Richards Toby , Murphy Gavin J 
Published: November 2024

AbstractIt is unclear whether plasma measures of iron status reflect iron status in tissues. This study compared the effects of iron deficiency or treatment with intravenous iron on plasma versus myocardial measures of iron metabolism and mitochondrial dysfunction in mice and humans. The human study included 31 people undergoing cardiac surgery. Twenty-two (71%) were iron deficient. The mouse study included 88 mice randomly allocated to iron replete diet group (Controls, n=29), an Iron Deficient diet (n=31) or an iron deficient diet followed by IV Iron administration (n=28). Outcomes included plasma iron and ferritin concentrations, and myocardial total iron, ferritin, IRP1 binding, and mitochondrial complex activity and DNA damage. In the human study, plasma ferritin positively correlated with myocardial ferritin (r2=0.155, p=0.012). People with iron deficiency had significantly lower myocardial ferritin levels than those without iron deficiency. There were no differences or significant correlations for other outcomes. In the mouse study, plasma ferritin negatively correlated with myocardial ferritin (r2=0.113, p=0.004), and iron deficiency reduced myocardial ferritin levels (p=0.018) as well as the binding affinity of myocardial IRP1 to the Ferritin heavy chain mRNA (p=0.033). Intravenous iron had divergent effects on plasma (increased) and myocardial (decreased) ferritin levels, and increased IRP1 binding affinity and mitochondrial respiratory complex activity (p=0.049). These finding suggest that measures of iron metabolism and iron deficiency in plasma do not consistently reflect myocardial iron status across iron replete, iron deficient, and iron replacement states.
Polystyrene nanoplastics promote neurodegeneration by catalyzing TDP43 hyperphosphorylation
Authors: Winanto  , Tan Li-Yi , Chooi Wai Hon , Lee Cheryl Yi-Pin , Ho Wan Yun , Lim Yong Shan , Soh Boon Seng , Sanford Emma , Tan Chong-Lun , Liou Yih-Cherng , Huang Cathy Chia-Yu , Ling Shuo-Chien , Ng Shi-Yan 
Published: November 2024

ABSTRACTThe ubiquity of polystyrene nanoplastics (PS-NPs) in our environment raises substantial concerns about their potential impact on human health. Recent studies have shown that PS-NPs cross the blood-brain-barrier and accumulate in the central nervous system (CNS), raising the concerns on the causal role of PS-NP exposure and neurodegenerative diseases. In this study, we utilized human-induced pluripotent stem cell-derived neurons to examine the effects of PS-NPs on neuronal function and health. Our results revealed that PS-NPs penetrate neuronal cells in a size-dependent manner, and are bound by various cellular proteins, including TDP43, a key protein implicated in amyotrophic lateral sclerosis (ALS). Interestingly, CK1 and GSK3β kinases that are known to phosphorylate TDP-43 were found to be associated with PS-NPs. This observation suggests that PS-NPs may play a role in facilitating conditions that lead to TDP43 phosphorylation. We further demonstrate that exposure to healthy motor neurons with PS-NPs resulted in ALS-like phenotypes, characterized by hyperphosphorylated TDP-43, disrupted neuronal morphology, impaired mitochondrial respiration, and accelerated motor neuron death. These findings suggest that PS-NPs contribute to the pathogenesis of neurodegenerative diseases such as ALS and highlight the urgent need for strategies to limit human exposure to nanoplastics.
More with less: Simulation-based inference enables accurate diffusion-weighted MRI with minimal acquisition time
Authors: Eggl Maximilian F. , De Santis Silvia 
Published: November 2024

AbstractDiffusion-weighted magnetic resonance imaging (dw-MRI) is an essential tool in neuroimaging, providing non-invasive insights into brain microstructure. However, obtaining reproducible and accurate maps requires lengthy acquisition due to the need to massively oversample the parameter space. This means that tensor-based dw-MRI accessibility is still relatively low in daily practice, and more advanced approaches with increased sensitivity and specificity to microstructure are seldom applied in research and clinical contexts. Motivated by recent advances in simulation-based inference (SBI) methods, this work uses neural networks to model the posterior distribution of key diffusion parameters when provided experimental data, allowing accurate estimation with fewer measurements and without the need to train on real data. We find that SBI outperforms standard non-linear least squares fitting under noisy and sparse data conditions in both diffusion tensor and kurtosis imaging, reducing imaging time by 90% while maintaining high accuracy and robustness. Demonstrated on simulated and real data in healthy and pathological brains, this approach can substantially impact radiology by:i)increasing dw-MRI access to more patients, including those unable to undergo long exams;ii)promoting advanced dw-MRI protocols for greater microstructure sensitivity; andiii)rescuing older data where noise hindered analysis. Combining SBI with dw-MRI could greatly improve clinical MRI workflows by reducing patient discomfort, enhancing scan efficiency, and enabling advanced imaging approaches in a data and privacy friendly way.
Evaluating the relationship between visual privacy and work-process interactions in open-plan offices: a space syntax approach
Authors: Yenel Güler Gizem , Demirkan Halime 
Published: November 2024

PurposePrevious studies on privacy in offices have primarily focused on the characteristics of generic visibility, examining the entire visible space from each workspace in 360 degrees. Nevertheless, employees in their workspaces investigate the visual targets within their binocular vision at 120 degrees. Therefore, by adopting the affordances perspective, this study aims to examine deeply generic and targeted visibility in open-plan offices and their relationship to interactions.Design/methodology/approachThe study consisted of two phases utilizing space syntax techniques. Initially, work-process interactions of the employees were determined through the survey. The survey data underwent spatial analysis to calculate the number of work-process interactions. Subsequently, DepthMapX software was used for visibility analyses. A new Python script for DepthMapX was developed to analyse the targeted visibility ratio. Multiple regression analyses were conducted to examine the relationship between the number of work-process interactions with generic and targeted visibility parameters.FindingsThe findings revealed that a higher number of visible employees within the 120-degree and 360-degree fields of vision corresponded to a lower number of work-process interactions in open-plan offices. Furthermore, the study establishes a direct link between visual privacy and interaction, indicating that increased visibility leads to decreased visual privacy.Originality/valueThe current research concluded that the relationship between visual privacy and interaction in open-plan offices differs from the previous studies, as employees with low visual privacy and high visibility tend to engage in fewer interactions. Overall, this study highlights that increased employee visibility is not directly associated with increased interaction in open-plan offices unless adequate visual privacy is provided.
Engaging tourists through destination social responsibility: the moderating role of self-congruence
Authors: Kumar Vikas , Kaushal Vikrant , Sharma Mohit 
Published: November 2024

Purpose
Engaging tourists with a destination brand can offer innumerable benefits. Based on stakeholder and social exchange theories, this study aims to comprehend destination social responsibility’s (DSR) role in inducing destination brand engagement (DBE) and favorable behavioral intentions, i.e. destination advocacy and revisit intentions. Further, the study examines self-congruence as a boundary condition to DSR’s impact on DBE.

Design/methodology/approach
Data were collected through an online survey of individuals in India and analyzed using structural equation modeling.

Findings
Findings highlight the importance of stakeholder and social exchange theories for socially responsible destinations by establishing a link between DSR and DBE, which adds to scholarship and holds practical relevance. Results confirm the moderating effects of self-congruence.

Research limitations/implications
The study did not assume the variation of tourists based on their characteristics and types while examining the moderation effects.

Originality/value
Research adds value by establishing the importance of DSR in engaging tourists with a destination. Furthermore, the study demonstrates how engaged tourists can showcase favorable responses toward the destination.
Leadership canvas: towards a leadership meta-theory
Authors: Bagchi Soumendra N. , Sharma Rajeev 
Published: November 2024

Purpose
The voluminous research on leadership, along with multiple theories, makes it challenging for organizational leaders, managers, and trainers to keep track of and reconcile the different theories of leadership to derive benefits from them. We propose a leadership canvas as a meta-theory of leadership theories, integrating the major existing theories by highlighting the unifying principles that underpin these theories.

Design/methodology/approach
This paper has been triggered by students’ and executives’ questions regarding leadership theories and how they choose one over the other. In this paper, we have coded the leadership theories and plotted them on the two-dimensional framework using two dimensions: (1) the collaboration between leader and followers engrained in the theories, and (2) the leader focus, as implied by the different theorists.

Findings
Our proposed two-dimensional leadership canvas reveals that concepts in theories lower on the canvas are necessary conditions for theories higher on the leadership canvas. Thus, our framework illustrates how different leadership theories are part of a continuum rather than distinct from each other.

Originality/value
The proposed framework ensures a bird’s eye view of the theories, facilitating rapid comprehension of existing leadership theories regardless of readers’ prior knowledge. It also incorporates environmental complexity and leader focus in a single framework.
Students' thinking dispositions and teacher's approaches in conflict situations: a case study of a secondary school mathematics class in Japan
Authors: Toyoshima Marie 
Published: November 2024

PurposeThis study aims to depict the process of creating a culture of thinking in relation to developing thinking dispositions, focusing on conflicts between students and teachers at the beginning of the school year.Design/methodology/approachThis study conducted a year-long fieldwork in a secondary school in Tokyo, Japan, including participatory observation of a mathematics class and a semi-structured interview with a teacher. The classroom discourse is analyzed to interpret the students’ thinking dispositions and the teacher's approaches in context using eight lessons. A situation in which the teacher attempts to change the method or direction of students’ thinking is defined as a conflict.FindingsFive conflict situations are found, namely (1) listening, (2) mathematical explanation, (3) disclosure, (4) giving up and (5) examining ideas. They reveal three characteristics about students’ thinking dispositions: closed-minded, correct answer-ism and mathematical immaturity. Against such students’ thinking, the teacher tried to make them listen carefully to, understand and examine peer ideas, aiming to discuss mathematically. Through these conflicts, the classroom culture moves toward a community of thinking and discussing mathematically.Originality/valueThis study emphasizes the cultural and contextual aspects of thinking dispositions as shaped by a classroom culture. By depicting “conflict” as a new analysis unit, this study reveals students’ thinking dispositions and how they are enacted in what situations and how teacher’s approaches to them create a culture of thinking.