Statistical properties of microphase and bubbly phase-separated active fluids.

In phase-separated active fluids, the Ostwald process can go into reverse, leading to either microphase separation or bubbly phase separation. We show that the latter is formed of two macroscopic regions that are occupied by the homogeneous fluid and by the microphase separated one. Within the microphase-separated fluid, the relative rate of the Ostwald process, coalescence, and nucleation determines whether the size distribution of mesoscopic domains is narrowly peaked or displays a broad range of sizes before attaining a cutoff independent of system size.

tidysbml: R/Bioconductor package for SBML extraction into dataframes.

Summary: We present , an R package able to perform , , and data extraction from Systems Biology Markup Language (SBML) documents (up to Level 3) in tabular data structures (i.e. R dataframes) to easily access and handle the richness of the biological information.

Differential Anti-Inflammatory Effects of Electrostimulation in a Standardized Setting.

The therapeutic usage of physical stimuli is framed in a highly heterogeneous research area, with variable levels of maturity and of translatability into clinical application. In particular, electrostimulation is deeply studied for its application on the autonomous nervous system, but less is known about the anti- inflammatory effects of such stimuli beyond the . Further, reproducibility and meta-analyses are extremely challenging, owing to the limited rationale on dosage and experimental standardization.

Hyperuniformity in phase ordering: the roles of activity, noise, and non-constant mobility.

Hyperuniformity emerges generically in the coarsening regime of phase-separating fluids. Numerical studies of active and passive systems have shown that the structure factor() behaves asfor → 0, with hyperuniformity exponent = 4. For passive systems, this result was explained in 1991 by a qualitative scaling analysis of Tomita, exploiting isotropy at scales much larger than the coarsening length.

Spindle Cell Lesions with Oncogenic EGFR Kinase Domain Aberrations: Expanding the Spectrum of Protein Kinase-Related Mesenchymal Tumors.

EGFR aberrations are reported in a subset of myofibroblastic lesions with kinase domain duplication (EGFR-KDD) and exon 20 mutations being assigned to infantile fibrosarcomas (IFS), mesoblastic nephroma, and fibrous hamartoma of infancy (FHI), respectively. In this retrospective study, we correlated molecular findings with the histomorphology of 14 myofibroblastic lesions harboring such genetic changes identified by NGS. We additionally performed DNA methylation profiling (DNAmp) and immunohistochemistry.

Evaluating cell culture reliability in pediatric brain tumor primary cells through DNA methylation profiling.

In vitro models of pediatric brain tumors (pBT) are instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; thus, ideally, they should recapitulate the original tumor. We applied DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples, including 155 tumors and 86 pBT-derived cell cultures, considering serum vs serum-free conditions, late vs early passages, and dimensionality (2D vs 3D cultures). We performed a t-SNE classification and identified differentially methylated regions in tumors compared to cell models.

Where are we in the implementation of tissue-specific epigenetic clocks?

DNA methylation clocks presents advantageous characteristics with respect to the ambitious goal of identifying very early markers of disease, based on the concept that accelerated ageing is a reliable predictor in this sense. Such tools, being epigenomic based, are expected to be conditioned by sex and tissue specificities, and this work is about quantifying this dependency as well as that from the regression model and the size of the training set. Our quantitative results indicate that elastic-net penalization is the best performing strategy, and better so when-unsurprisingly-the data set is bigger; sex does not appear to condition clocks performances and tissue specific clocks appear to perform better than generic blood clocks.

Responding to threat: Associations between neural reactivity to and behavioral avoidance of threat in pediatric anxiety.

Background: Despite broad recognition of the central role of avoidance in anxiety, a lack of specificity in its operationalization has hindered progress in understanding this clinically significant construct. The current study uses a multimodal approach to investigate how specific measures of avoidance relate to neural reactivity to threat in youth with anxiety disorders.

Methods: Children with anxiety disorders (ages 6-12 years; n = 65 for primary analyses) completed laboratory task- and clinician-based measures of avoidance, as well as a functional magnetic resonance imaging task probing neural reactivity to threat.

CNS tumor with CREBBP::BCORL1 Fusion and pathogenic mutations in BCOR and CREBBP: expanding the spectrum of BCOR-altered tumors.

The fifth edition of the World Health Organization (WHO) classification of central nervous system (CNS) tumors introduced the new tumor type CNS tumor with BCOR internal tandem duplication (ITD), characterized by a distinct DNA methylation profile and peculiar histopathological features, including a circumscribed growth pattern, ependymoma-like perivascular pseudorosettes, microcystic pattern, absent or focal GFAP immunostaining, OLIG2 positivity, and BCOR immunoreactivity. We describe a rare case of a CNS tumor in a 45-year-old man with histopathological and immunohistochemical features overlapping the CNS tumor with BCOR internal tandem duplication (ITD) but lacking BCOR immunostaining and BCOR ITD. Instead, the tumor showed CREBBP::BCORL1 fusion and pathogenic mutations in BCOR and CREBBP, along with a DNA methylation profile matching the "CNS tumor with EP300:BCOR(L1) fusion" methylation class.

methyLImp2: faster missing value estimation for DNA methylation data.

Motivation: methyLImp, a method we recently introduced for the missing value estimation of DNA methylation data, has demonstrated competitive performance in data imputation compared to the existing, general-purpose, approaches. However, imputation running time was considerably long and unfeasible in case of large datasets with numerous missing values.

Results: methyLImp2 made possible computations that were previously unfeasible.

Malignant peripheral nerve sheath tumor (MPNST) and MPNST-like entities are defined by a specific DNA methylation profile in pediatric and juvenile population.

Background: Malignant peripheral nerve sheath tumors (MPNSTs) account for 3-10% of pediatric sarcomas, 50% of which occur in neurofibromatosis type 1 (NF1). Sporadic MPNSTs diagnosis may be challenging due to the absence of specific markers, apart from immunohistochemical H3K27me3 loss. DNA methylation (DNAm) profiling is a useful tool for brain and mesenchymal neoplasms categorization, and MPNSTs exhibit a specific DNAm signature.

A retrospective observational study on cutaneous adverse events induced by immune checkpoint inhibitors.

Background: Cutaneous adverse events (CAEs) related to oncological therapies are a common scenario in daily clinical practice.

Methods: This is a retrospective observational study collecting the data regarding CAEs of patients treated with immune checkpoints inhibitors (ICIs) in four different Italian centers.

Results: Of 323 patients included, 305 were evaluable for this analysis; 182 patients (59.

Identification of a robust DNA methylation signature for Fanconi anemia.

Fanconi anemia (FA) is a clinically variable and genetically heterogeneous cancer-predisposing disorder representing the most common bone marrow failure syndrome. It is caused by inactivating predominantly biallelic mutations involving >20 genes encoding proteins with roles in the FA/BRCA DNA repair pathway. Molecular diagnosis of FA is challenging due to the wide spectrum of the contributing gene mutations and structural rearrangements.

Interface Roughening in Nonequilibrium Phase-Separated Systems.

Interfaces of phase-separated systems roughen in time due to capillary waves. Because of fluxes in the bulk, their dynamics is nonlocal in real space and is not described by the Edwards-Wilkinson or Kardar-Parisi-Zhang (KPZ) equations, nor their conserved counterparts. We show that, in the absence of detailed balance, the phase-separated interface is described by a new universality class that we term |q|KPZ.

Classical Nucleation Theory for Active Fluid Phase Separation.

Classical Nucleation Theory (CNT), linking rare nucleation events to the free-energy landscape of a growing nucleus, is central to understanding phase-change kinetics in passive fluids. Nucleation in nonequilibrium systems is much harder to describe because there is no free energy, but instead a dynamics-dependent quasipotential that typically must be found numerically. Here we extend CNT to a class of active phase-separating systems governed by a minimal field-theoretic model (Active Model B+).

Affective language spreads between anxious children and their mothers during a challenging puzzle task.

Humans influence each other's emotions. The spread of emotion is well documented across behavioral, psychophysiological, and neuroscientific levels of analysis, but might this influence also be evident in language (e.g.

Semi-automated socio-anthropologic analysis of the medical discourse on rheumatoid arthritis: Potential impact on public health.

Background: The debilitating effects of noncommunicable diseases (NCDs) and the accompanying chronic inflammation represent a significant obstacle for the sustainability of our development, with efforts spreading worldwide to counteract the diffusion of NCDs, as per the United Nations Sustainable Development Goals (SDG 3). In fact, despite efforts of varied intensity in numerous directions (from innovations in biotechnology to lifestyle modifications), the incidence of NCDs remains pandemic. The present work wants to contribute to addressing this major concern, with a specific focus on the fragmentation of medical approaches, via an interdisciplinary analysis of the medical discourse, i.

Living in endemic area for infectious diseases accelerates epigenetic age.

Inflammaging is a low-grade inflammatory state generated by the aging process that can contribute to frailty and age-related diseases in the elderly. However, it can have distinct effects in the elderly living in endemic areas for infectious diseases. An increased inflammatory response may confer protection against infectious agents in these areas, although this advantage can cause accelerating epigenetic aging.

Explainable Drug Repurposing Approach From Biased Random Walks.

Drug repurposing is a highly active research area, aiming at finding novel uses for drugs that have been previously developed for other therapeutic purposes. Despite the flourishing of methodologies, success is still partial, and different approaches offer, each, peculiar advantages. In this composite landscape, we present a novel methodology focusing on an efficient mathematical procedure based on gene similarity scores and biased random walks which rely on robust drug-gene-disease association data sets.

Evaluation of different computational methods for DNA methylation-based biological age.

In recent years there has been a widespread interest in researching biomarkers of aging that could predict physiological vulnerability better than chronological age. Aging, in fact, is one of the most relevant risk factors for a wide range of maladies, and molecular surrogates of this phenotype could enable better patients stratification. Among the most promising of such biomarkers is DNA methylation-based biological age.