Miracle-dz/UniFAR-FTUs huggingface dataset:
13CO filaments in the Taurus molecular cloud

We have carried out a search for filamentary structures in the Taurus molecular cloud using $\rm^{13}CO$ line emission data from the FCRAO survey of $\rm \sim100 \, deg^2$. We have used the topological analysis tool, DisPerSe, and post-processed its results to include a more strict definition of filaments that requires an aspect ratio of at least 3:1 and cross section intensity profiles peaked on the spine of the filament. In the velocity-integrated intensity map only 10 of the hundreds of filamentary structures identified by DisPerSe comply with our criteria. Unlike Herschel analyses, which find a characteristic width for filaments of $\rm \sim0.1 \, pc$, we find a much broader distribution of profile widths in our structures, with a peak at 0.4 pc. Furthermore, even if the identified filaments are cylindrical objects, their complicated velocity structure and velocity dispersions imply that they are probably gravitationally unbound. Analysis of velocity channel maps reveals the existence of hundreds of `velocity-coherent' filaments. The distribution of their widths is peaked at lower values (0.2 pc) while the fluctuation of their peak intensities is indicative of stochastic origin. These filaments are suppressed in the integrated intensity map due to the blending of diffuse emission from different velocities. Conversely, integration over velocities can cause filamentary structures to appear. Such apparent filaments can also be traced, using the same methodology, in simple simulated maps consisting of randomly placed cores. They have profile shapes similar to observed filaments and contain most of the simulated cores.
The capsule of Bacillus anthracis protects it from the bactericidal activity of human defensins and other cationic antimicrobial peptides

During infection, Bacillus anthracis bacilli encounter potent antimicrobial peptides (AMPs) such as defensins. We examined the role that B. anthracis capsule plays in protecting bacilli from defensins and other cationic AMPs by comparing their effects on a fully virulent encapsulated wild type (WT) strain and an isogenic capsule-deficient capA mutant strain. We identified several human defensins and non-human AMPs that were capable of killing B. anthracis. The human alpha defensins 1–6 (HNP-1-4, HD-5-6), the human beta defensins 1–4 (HBD-1-4), and the non-human AMPs, protegrin, gramicidin D, polymyxin B, nisin, and melittin were all capable of killing both encapsulated WT and non-encapsulated capA mutant B. anthracis. However, non-encapsulated capA mutant bacilli were significantly more susceptible than encapsulated WT bacilli to killing by nearly all of the AMPs tested. We demonstrated that purified capsule bound HBD-2, HBD-3, and HNP-1 in an electrophoretic mobility shift assay. Furthermore, we determined that the capsule layer enveloping WT bacilli bound and trapped HBD-3, substantially reducing the amount reaching the cell wall. To assess whether released capsule might also play a protective role, we pre-incubated HBD-2, HBD-3, or HNP-1 with purified capsule before their addition to non-encapsulated capA mutant bacilli. We found that free capsule completely rescued the capA mutant bacilli from killing by HBD-2 and -3 while killing by HNP-1 was reduced to the level observed with WT bacilli. Together, these results suggest an immune evasion mechanism by which the capsule, both that enveloping the bacilli and released fragments, contributes to virulence by binding to and inhibiting the antimicrobial activity of cationic AMPs.
Multiple Comparisons Using R

Introduction General Concepts Error rates and general concepts Construction methods Methods based on Bonferroni's inequality Methods based on Simes' inequality Multiple Comparisons in Parametric Models General linear models Extensions to general parametric models The multcomp package Applications Multiple comparisons with a control All pairwise comparisons Dose response analyses Variable selection in regression models Simultaneous confidence bands Multiple comparisons under heteroscedasticity Multiple comparisons in logistic regression models Multiple comparisons in survival models Multiple comparisons in mixed-effects models Further Topics Resampling-based multiple comparison procedures Group sequential and adaptive designs Combining multiple comparisons with modeling Bibliography Index
Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus

ABSTRACT Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials – a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of the epidermis, leaf mesophyll and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we applied a pipeline for interspecific single-cell gene expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the principles underlying cell division and differentiation conserved between herbaceous and perennial species while also allowing us to examine species-specific differences at single-cell resolution.
Neuroinflammation: molecular mechanisms and therapeutic perspectives.

BACKGROUND Neuroinflammation is a key component in the etiopathogenesis of neurological diseases and brain aging. This process involves the brain immune system that modulates synaptic functions and protects neurons from infection or damage. Hence, the knowledge of neuroinflammation related-pathways and modulation by drugs or natural compounds is functional to the development of therapeutic strategies aimed at preserving, maintaining and restoring brain health. OBJECTIVE This review article summarizes the basics in neuroinflammation and related signaling pathways, the success of dietary intervention in clinical practice and the possible development of RNA-based strategies for the treatment of neurological diseases. METHODS Pubmed search (2012-2022); keywords: neuroinflammation and molecular mechanisms in combination with diet, miRNA and non-coding RNA. RESULTS Glial cells play a crucial role in neuroinflammation, but several pathways can be activated in response to different inflammatory stimuli, inducing cell death by apoptosis, pyroptosis or necroptosis. Dietary intervention has immunomodulatory effects and could limit the inflammatory process induced by microglia and astrocytes. Thus by ihibiting neuroinflammation and improving the symptoms of a variety of neurological diseases, diet exerts pleiotropic neuroprotective effects independently from the spectrum of pathophysiological mechanisms underlying the specific disorder. Furthermore, data from animal models revealed that altered expression of specific non-coding RNAs, in particular microRNAs, contributes to neuroinflammatory diseases; consequently, RNA-based strategies may be promising to alleviate the consequences of neuroinflammation. CONCLUSION Further studies are needed to identify the molecular pathways and the new pharmacological targets in neuroinflammation to lay the basis for more effective and selective therapies to be applied, in parallel to dietary intervention, in the treatment of neuroinflammation-based diseases.
The functions of SID1 transmembrane family, member 2 (Sidt2)

The SID1 transmembrane family, member 2, namely, Sidt2, is a highly glycosylated multichannel lysosomal transmembrane protein, but its specific physiological function remains unknown. Lysosomal membrane proteins are very important for the executive functioning of lysosomes. As an important part of the lysosomal membrane, Sidt2 can maintain the normal morphology of lysosomes and help stabilize them from the acidic pH environment within. As a receptor/transporter, it binds and transports nucleic acids and mediates the uptake and degradation of RNA and DNA by the lysosome. During glucose metabolism, deletion of Sidt2 can cause an increase in fasting blood glucose and the impairment of grape tolerance, which is closely related to the secretion of insulin. During lipid metabolism, the loss of Sidt2 can cause hepatic steatosis and lipid metabolism disorders and can also play a role in signal regulation and transport. Here, we review the function of the lysosomal membrane protein Sidt2, and focus on its role in glucose and lipid metabolism, autophagy and nucleotide (DNA/RNA) transport.
The emerging microbiome‐based approaches to IBD therapy: From SCFAs to urolithin A

Inflammatory bowel disease (IBD) is a group of chronic gastrointestinal inflammatory conditions which can be life‐threatening, affecting both children and adults. Crohn's disease and ulcerative colitis are the two main forms of IBD. The pathogenesis of IBD is complex and involves genetic background, environmental factors, alteration in gut microbiota, aberrant immune responses (innate and adaptive), and their interactions, all of which provide clues to the identification of innovative diagnostic or prognostic biomarkers and the development of novel treatments. Gut microbiota provide significant benefits to its host, most notably via maintaining immunological homeostasis. Furthermore, changes in gut microbial populations may promote immunological dysregulation, resulting in autoimmune diseases, including IBD. Investigating the interaction between gut microbiota and immune system of the host may lead to a better understanding of the pathophysiology of IBD as well as the development of innovative immune‐ or microbe‐based therapeutics. In this review we summarized the most recent findings on innovative therapeutics for IBD, including microbiome‐based therapies such as fecal microbiota transplantation, probiotics, live biotherapeutic products, short‐chain fatty acids, bile acids, and urolithin A.
Atomistic-continuum modeling of short laser pulse melting of Si targets

We present an atomistic-continuum model to simulate ultrashort laser-induced melting processes in semiconductor solids on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with a Molecular Dynamics method at atomic level, whereas the laser light absorption, strong generated electron-phonon non-equilibrium, fast diffusion and heat conduction due to photo-excited free carriers are accounted for in the continuum. We give a detailed description of the model, which is then applied to study the mechanism of short laser pulse melting of free standing Si films. The effect of laser-induced pressure and temperature of the lattice on the melting kinetics is investigated. Two competing melting mechanisms, heterogeneous and homogeneous, were identified. Apart of classical heterogeneous melting mechanism, the nucleation of the liquid phase homogeneously inside the material significantly contributes to the melting process. The simulations showed, that due to the open diamond structure of the crystal, the laser-generated internal compressive stresses reduce the crystal stability against the homogeneous melting. Consequently, the latter can take a massive character within several picoseconds upon the laser heating. Due to negative volume of melting of modeled Si material, -7.5%, the material contracts upon the phase transition, relaxes the compressive stresses and the subsequent melting proceeds heterogeneously until the excess of thermal energy is consumed. The threshold fluence value, at which homogeneous nucleation of liquid starts contributing to the classical heterogeneous propagation of the solid-liquid interface, is found from the series of simulations at different laser input fluences. On the example of Si, the laser melting kinetics of semiconductors was found to be noticeably different from that of metals with fcc crystal structure.
Tactics of evasion: strategies used by signallers to deter eavesdropping enemies from exploiting communication systems

Eavesdropping predators, parasites and parasitoids exploit signals emitted by their prey and hosts for detection, assessment, localization and attack, and in the process impose strong selective pressures on the communication systems of the organisms they exploit. Signallers have evolved numerous anti‐eavesdropper strategies to mitigate the trade‐off between the costs imposed from signal exploitation and the need for conspecific communication. Eavesdropper strategies fall along a continuum from opportunistic to highly specialized, and the tightness of the eavesdropper–signaller relationship results in differential pressures on communication systems. A wide variety of anti‐eavesdropper strategies mitigate the trade‐off between eavesdropper exploitation and conspecific communication. Antagonistic selection from eavesdroppers can result in diverse outcomes including modulation of signalling displays, signal structure, and evolutionary loss or gain of a signal from a population. These strategies often result in reduced signal conspicuousness and in decreased signal ornamentation. Eavesdropping enemies, however, can also promote signal ornamentation. While less common, this alternative outcome offers a unique opportunity to dissect the factors that may lead to different evolutionary pathways. In addition, contrary to traditional assumptions, no sensory modality is completely ‘safe’ as eavesdroppers are ubiquitous and have a broad array of sensory filters that allow opportunity for signal exploitation. We discuss how anthropogenic change affects interactions between eavesdropping enemies and their victims as it rapidly modifies signalling environments and community composition. Drawing on diverse research from a range of taxa and sensory modalities, we synthesize current knowledge on anti‐eavesdropper strategies, discuss challenges in this field and highlight fruitful new directions for future research. Ultimately, this review offers a conceptual framework to understand the diverse strategies used by signallers to communicate under the pressure imposed by their eavesdropping enemies.
From approachables on the sidelines to dedicated sensitives: developing a leadership typology among healthcare leaders utilizing grounded theory

Purpose Based on a resulting typing model, this paper focuses on four types of leaders (Approachables on the sidelines, Distanced overseers, Realistic succeeders and Dedicated sensitives), who differ in the analytical core category of “development of awareness. ” Design/methodology/approach Internal team coaching is intended to strengthen leaders in the health care system. The Team Leader Coaching Programme (TLCP) was implemented as an internal coaching instrument at rehabilitation centers using a train-the-trainer format. Twenty-one team leaders were surveyed on their experience of the coaching process they implemented in their teams. The interviews were analyzed using the grounded theory method (GTM) as theoretically discussed by representatives of second-generation GTM (Charmaz, 2014). Findings Use of the TLCP proved to be an intervention for initiating and enhancing an awareness development process regarding team leaders' reflections on their own position and leadership role, regardless of their profession. This process was found to be a prerequisite for implementing the learned content. The typing model is discussed given current contextual conditions in the rehabilitation system and their connectivity in practice for integrating coaching elements into daily management. Originality/value This article presents a typology of healthcare leaders. Thanks to the reconstructive approach using grounded theory methodology, this article presents an in-depth analysis of the implementation process of a coaching program. The findings are both connectable to applied leadership research and useable for further development of training and interventions to strengthen team leaders in clinical settings.
Evolution of basic human values orientations: An application of monitoring changes in cluster solutions

This study enumerates the evolution of basic human values orientations and the dynamic relationship between them, computed from Schwartz’s value survey conducted in European nations. For this purpose, eight datasets related to the human value scale were extracted from the European Social Survey; each corresponds to a single round conducted cross-sectionally every two years since 2001. Change detection algorithm was implemented to the cluster solutions of temporal datasets, and the evolution of important clusters was traced. Finding of the study reveals that Universalism and Benevolence values are on the rise in European societies in the last couple of decades. Most of the European inhabitants believe in the smooth group functioning and form the organismic needs of cooperation. The people prefer anxiety-free life, and love for nature, environment, humanity, and kindness to other beings in society are essential constructs for them. They avoid self-centred behaviour and prefer social physiognomies.
IL-4, IL-10, CCL2 and TGF-β as potential biomarkers for severity in Plasmodium vivax malaria

Cytokines and chemokines are immune response molecules that display diverse functions, such as inflammation and immune regulation. In Plasmodium vivax infections, the uncontrolled production of these molecules is thought to contribute to pathogenesis and has been proposed as a possible predictor for disease complications. The objective of this study was to evaluate the cytokine profile of P. vivax malaria patients with different clinical outcomes to identify possible immune biomarkers for severe P. vivax malaria. The study included patients with non-severe (n = 56), or severe (n = 50) P. vivax malaria and healthy controls (n = 50). Patient plasma concentrations of IL-4, IL-2, CXCL10, IL-1β, TNF-α, CCL2, IL-17A, IL-6, IL-10, IFN-γ, IL-12p70, CXCL8 and active TGF-β1 were determined through flow cytometry. The levels of several cytokines and chemokines, CXCL10, IL-10, IL-6, IL-4, CCL2 and IFN-γ were found to be significantly higher in severe, compared to non-severe P. vivax malaria patients. Severe thrombocytopenia was positively correlated with IL-4, CXCL10, IL-6, IL-10 and IFN-γ levels, renal dysfunction was related to an increase in IL-2, IL-1β, IL-17A and IL-8, and hepatic impairment with CXCL10, MCP-1, IL-6 and IFN-γ. A Lasso regression model suggests that IL-4, IL-10, CCL2 and TGF-β might be developed as biomarkers for severity in P. vivax malaria. Severe P. vivax malaria patients present specific cytokine and chemokine profiles that are different from non-severe patients and that could potentially be developed as biomarkers for disease severity.
Risk Factors and Characteristics of the Recurrence of Juvenile Nasopharyngeal Angiofibroma: A 22-Year Experience With 123 Cases at a Tertiary Center

Objectives. Despite the efficacy of surgical treatments, the high rate of recurrence in juvenile nasopharyngeal angiofibroma (JNA) after surgery remains an unresolved problem. The present study comprehensively analyzed the risk factors and characteristics of JNA recurrence, providing clinical guidance for reducing recurrence. Methods. A total of 123 patients who underwent surgery for JNA between 1997 and 2019 at a single hospital were analyzed retrospectively. Univariate and multivariate analyses were used to assess the clinical risk factors for the recurrence of JNA. The relapse-free survival and annual cumulative recurrence rates were analyzed for subgroups defined according to clinical parameters. Results. After screening, 78 of the 123 patients were included in the present study. The main risk factors associated with JNA recurrence included the year of diagnosis, tumor size, sphenoid bone invasion, Radkowski stage, surgical approach, and intraoperative bleeding. Importantly, the surgical approach and sphenoid bone invasion were independent prognostic factors affecting recurrence. Patients who underwent endoscopic surgery without sphenoid bone invasion exhibited longer relapse-free survival. In the present study, the overall cumulative recurrence rate of JNA was 38.7%, and recurrence occurred mainly in the first year after the initial surgery. Conclusion. Endoscopic surgery achieved better relapse-free survival in JNA patients, and patients with sphenoid bone invasion should be carefully explored to avoid residual JNA. The recurrence rate of JNA differed among subgroups defined based on clinical parameters and was highest in the first year after surgery. Computed tomography or magnetic resonance imaging, along with close follow-up, should be performed strictly within 1 year after the primary operation.
A RECOLLIMATION SHOCK 80 mas FROM THE CORE IN THE JET OF THE RADIO GALAXY 3C 120: OBSERVATIONAL EVIDENCE AND MODELING

We present Very Long Baseline Array observations of the radio galaxy 3C 120 at 5, 8, 12, and 15 GHz designed to study a peculiar stationary jet feature (hereafter C80) located ∼80 mas from the core, which was previously shown to display a brightness temperature ∼600 times larger than expected at such distances. The high sensitivity of the images—obtained between 2009 December and 2010 June—has revealed that C80 corresponds to the eastern flux density peak of an arc of emission (hereafter A80), downstream of which extends a large (∼20 mas in size) bubble-like structure that resembles an inverted bow shock. The linearly polarized emission closely follows that of the total intensity in A80, with the electric vector position angle distributed nearly perpendicular to the arc-shaped structure. Despite the stationary nature of C80/A80, superluminal components with speeds up to 3 ± 1 c have been detected downstream from its position, resembling the behavior observed in the HST-1 emission complex in M87. The total and polarized emission of the C80/A80 structure, its lack of motion, and brightness temperature excess are best reproduced by a model based on synchrotron emission from a conical shock with cone opening angle η = 10°, jet viewing angle θ = 16°, a completely tangled upstream magnetic field, and upstream Lorentz factor γu = 8.4. The good agreement between our observations and numerical modeling leads us to conclude that the peculiar feature associated with C80/A80 corresponds to a conical recollimation shock in the jet of 3C 120 located at a de-projected distance of ∼190 pc downstream from the nucleus.