An IMEX-DG solver for atmospheric dynamics simulations with adaptive mesh refinement

We present an accurate and efficient solver for atmospheric dynamics simulations that allows for non-conforming mesh refinement. The model equations are the conservative Euler equations for compressible flows. The numerical method is based on an $h-$adaptive Discontinuous Galerkin spatial discretization and on a second order Additive Runge Kutta IMEX method for time discretization, especially designed for low Mach regimes. The solver is implemented in the framework of the $deal.II$ library, whose mesh refinement capabilities are employed to enhance efficiency. A number of numerical experiments based on classical benchmarks for atmosphere dynamics demonstrate the properties and advantages of the proposed method

An efficient IMEX-DG solver for the compressible Navier-Stokes equations for non-ideal gases

We propose an efficient, accurate and robust IMEX solver for the compressible Navier-Stokes equation describing non-ideal gases with general equations of state. The method, which is based on an $h-$adaptive Discontinuos Galerkin spatial discretization and on an Additive Runge Kutta IMEX method for time discretization, is tailored for low Mach number applications and allows to simulate low Mach regimes at a significantly reduced computational cost, while maintaining full second order accuracy also for higher Mach number regimes. The method has been implemented in the framework of the $deal.II$ numerical library, whose adaptive mesh refinement capabilities are employed to enhance efficiency. Refinement indicators appropriate for real gas phenomena have been introduced. A number of numerical experiments on classical benchmarks for compressible flows and their extension to real gases demonstrate the properties of the proposed method

The Bio-Molecular Dynamics of Dental Pulp in Different Clinical Scenarios

Dental pulp (DP) is a very dynamic tissue both in health and in disease. When exposed to stressors and pathological conditions. It undergoes a complex series of biological reactions whereby alterations affect the pulp tissue at tissue cellular and molecular levels. The aim of this review is to update the reader on the various bio-molecular alterations in the dental pulp under different clinical conditions: orthodontic treatment (OT), caries, pulpitis and others. The morphological changes in the composition of the DP rang from the reversible remodeling to apoptosis and sometimes necrosis. Many apoptotic factors are involved like Bcl2, Bax and the significant increase in Caspases 9 and 3, as well as, Hsp60, its possible role and its mitochodrial localization. The inflammatory responses in dental pulp and the role of diffusible and cellular factors as well as DP stem cells were highlighted, in particular, where caries was involved in the pulpitis.Recent data report changes in tissue metabolism and homeostasis inside the DP caused by OT leading to increased levels of iNOS reactivity in the nerve fibers of the pulp. Moreover, remodeling of the extra cellular matrix(ECM) is an important feature in clinical scenarios like OT and caries whereby alterations in MMP-2 and MMP-9 expression patterns are reported leading to degradation of type IV and V collagens in the ECM. Furthermore, neurogenic factors are also modified after injuries and OT. Neuropeptides play a significant role not onlyin pain perception but also in vascular responses. Substance P increases in DP and enhances pain perception and so is the increase in CGRP which is correlated with concomitant gain in bone morphogenetic protein expression resulting in more dentin formation. The role of stem cells and the possible molecular mechanisms of dentin genesis are presented in this review. They focus on important signaling proteins and the possible role of various scaffolds in this regeneration process. In conclusion, most alterations inpulpal structure are reversible unless the pulp has a history of caries, restorations, trauma or prolonged heavy orthodontic forces. Pulpal symptoms arising from these clinical conditions should be treated appropriately and swiftly.Otherwise, exacerpation of pulpitis and the interplay of the various bio-molecular factors will lead to inhibition of repair and regeneration

ferret: a Framework for Benchmarking Explainers on Transformers

Many interpretability tools allow practitioners and researchers to explain Natural Language Processing systems. However, each tool requires different configurations and provides explanations in different forms, hindering the possibility of assessing and comparing them. A principled, unified evaluation benchmark will guide the users through the central question: which explanation method is more reliable for my use case? We introduce ferret, an easy-to-use, extensible Python library to explain Transformer-based models integrated with the Hugging Face Hub. It offers a unified benchmarking suite to test and compare a wide range of state-of-the-art explainers on any text or interpretability corpora. In addition, ferret provides convenient programming abstractions to foster the introduction of new explanation methods, datasets, or evaluation metrics

Association between interleukin-10 polymorphisms and Alzheimer's disease: a systematic review and meta-analysis

It has been hypothesized that polymorphisms of interleukin (IL)-10 genes affect the risk of developing late onset Alzheimer's disease (AD). However, results of different studies are often inconsistent. Our aim was to investigate by meta-analysis the association of the common polymorphisms comprehensively defining the genetic variability of the IL-10 gene with AD risk. Fifteen studies investigating the association between IL-10 polymorphisms (-1082,-819,-592) and AD were found and analyzed. The model-free approach was applied to meta-analyze these case-control genetic association studies. Available data suggested an association between-1082 polymorphism and AD risk with a marginal statistical significance (GG versus AG/AA: pooled odds ratio [OR]: 0.82, 95% confidence interval CI: 0.65-1.02) and evidence of a moderate degree of between-study heterogeneity (χ 2 = 27.13, d.f. = 13, p = 0.01, I 2 = 52%). For the-819 and-592 polymorphisms, we did not find an association with AD, but significant between-study heterogeneity made genotype data pooling unacceptable. Analysis by IL-10 haplotype showed that the-1082G/-819C/-592C haplotype is associated with a lower risk of AD, although with a marginal statistical significance, probably due to the low number of studies included (GCC versus other genotypes: OR: 0.61, 95% CI: 0.32-1.15; I 2: 85%). Current findings suggest a possible association between-1082 A > G polymorphism and the risk of developing AD; this effect is more evident in the oldest patients. The high degree of between-study heterogeneity, due to several underpowered studies and to other methodological problems of individual studies underlies the need for further methodologically adequate studies. © 2012-IOS Press and the authors. All rights reserved

Immunohistochemical expression and distribution of orexin, orphanin and leptin in the major salivary glands of some mammals

Abstract: The aim of the study was to assess the involvement of apoptotic factors, cytokeratins and metalloproteinase- 9 in the histogenesis of both Epithelialized Gingival Lesions (EGL) and Periapical Lesions (PAL). 55 consecutive patients, 30 with PAL and 25 with EGL, were selected for the study after clinical and radiological examinations. The PAL patients had severe periapical lesions and tooth decay with exposure of the pulp chamber. All PAL and EGL biopsies were surgically extracted, fixed in 10% buffered formalin, and processed for routine light microscopy. Ten biopsies of each category were processed for immunohistochemistry (IHC). Serial paraffin sections were stained by IHC with appropriate antibodies to detect cytokeratins (CKs) 1, 5, 8, 10 and 14, caspase-3 and -9, metalloproteinase-9, and for PCNA and TUNEL assays. Both PAL and EGL showed a high expression of the cytokeratin 1, 5 and 8 with higher expression in EGL. Moreover, CK10 was markedly less intense expressed in EGL compared to PAL, while CK14 was almost three times stronger expressed in EGL. The expression of caspase-3 and -9 was stronger in PAL compared to EGL, however, the difference was only significant for caspase-9. In PAL apoptosis detected by TUNNEL method and the expression of MMP-9 were higher than in EGL, whereas PCNA was significantly more expressed in EGL. The results clearly suggest that both lesions have exclusively an epithelial origin and that epithelial proliferation was correlated with the degree of apoptosis in both entities. PAL and EGL presented mostly similar cytokeratin expression except for CK10 and CK14, though with marked differences in the distribution and intensity of IHC reactions. Finally, the degradation of extracellular matrix in both lesions could be partially attributed to the strong presence of MMP-9. (Folia Histochemica et Cytobiologica 2012, Vol. 50, No. 4, 497–503)The aim of the study was to determine by immunochemistry the expression of leptin, orexin A and orphanin FQ in the major salivary glands (parotid, submandibular and sublingual) of rat, sheep and cow. These peptides, originally synthesized in central nervous system, adipose tissue and peripheral tissues including gastrointestinal tract, play an orexigenic (orphanin and orexin) or anorexigenic (leptin) roles in the intricate neuronal network appointed to the control of nutritional homeostasis. Peptide-specific immunoreactivity was present in the studied salivary glands with various intensities in different species, in the ductal epithelium, sometimes in the acinar epithelium, and in nervous trunks spread in connective tissue stroma. The obtained data show that salivary glands present an unexpected source of orexigenic and anorexigenic peptides which with their autocrine, paracrine, and endocrine mechanisms of action may participate in the control of salivary gland function

Histopathology of Skeletal Muscle in a Distal Motor Neuropathy Associated with a Mutant CCT5 Subunit: Clues for Future Developments to Improve Differential Diagnosis and Personalized Therapy

Genetic chaperonopathies are rare but, because of misdiagnosis, there are probably more cases than those that are recorded in the literature and databases. This occurs because practitioners are generally unaware of the existence and/or the symptoms and signs of chaperonopathies. It is necessary to educate the medical community about these diseases and, with research, to unveil their mechanisms. The structure and functions of various chaperones in vitro have been studied, but information on the impact of mutant chaperones in humans, in vivo, is scarce. Here, we present a succinct review of the most salient abnormalities of skeletal muscle, based on our earlier report of a patient who carried a mutation in the chaperonin CCT5 subunit and suffered from a distal motor neuropathy of early onset. We discuss our results in relation to the very few other published pertinent reports we were able to find. A complex picture of multiple muscle-tissue abnormalities was evident, with signs of atrophy, apoptosis, and abnormally low levels and atypical distribution patterns of some components of muscle and the chaperone system. In-silico analysis predicts that the mutation affects CCT5 in a way that could interfere with the recognition and handling of substrate. Thus, it is possible that some of the abnormalities are the direct consequence of defective chaperoning, but others may be indirectly related to defective chaperoning or caused by other different pathogenic pathways. Biochemical, and molecular biologic and genetic analyses should now help in understanding the mechanisms underpinning the histologic abnormalities and, thus, provide clues to facilitate diagnosis and guide the development of therapeutic tools

Non Monotonous Effects of Noncovalently Functionalized Graphene Addition on the Structure and Sound Absorption Properties of Polyvinylpyrrolidone (1300 kDa) Electrospun Mats

Graphene is an attractive component for high-performance stimuli-responsive or 'smart' materials, shape memory materials, photomechanical actuators, piezoelectric materials and flexible strain sensors. Nanocomposite fibres were produced by electrospinning high molecular weight Polyvinylpyrrolidone (PVP-1300 kDa) in the presence of noncovalently functionalised graphene obtained through tip sonication of graphite alcoholic suspensions in the presence of PVP (10 kDa). Bending instability of electrospun jet appears to progressively increase at low graphene concentrations with the result of greater fibre stretching that leads to lower fibre diameter and possibly conformational changes of PVP. Further increase of graphene content seams having the opposite effect leading to greater fibre diameter and Raman spectra similar to the pure PVP electrospun mats. All this has been interpreted on the basis of currently accepted model for bending instability of electrospun jets. The graphene addition does not lower the very high sound absorption coefficient, α, close to unity, of the electrospun PVP mats in the frequency range 200⁻800 Hz. The graphene addition affects, in a non-monotonous manner, the bell shaped curves of α versus frequency curves becoming sharper and moving to higher frequency at the lower graphene addition. The opposite is observed when the graphene content is further increased