On Some Thermoelastic Problem of a Nonhomogeneous Long Pipe

The paper deals with the thermoelastic problem of a multilayered pipe subjected to normal loadings on its inner surface and temperature differences on its internal and external surfaces. Two types of nonhomogeneous pipe materials of pipe are considered: (1) a ring-layered composite composed of two repeated thermoelastic solids with varying thickness and (2) a functionally graded ring layer. The ring-layered pipe with periodic structure is investigated by using the homogenized model with microlocal parameters. A homogenization approach is proposed for the modelling of the FGM pipe. The analysis of obtained circumferential, radial and axial stress is presented in the form of figures and discussed in detail. It was shown that the proposed approach to the homogenization allows us to correctly calculate the averaged characteristics in the representative cell (the macro-characteristics) and also the characteristics dependent on the choice of the component in the representative cell (the micro-characteristics) for both microperiodic composites and functionally graded materials.

A Generalized Strain Energy-Based Homogenization Method for 2-D and 3-D Cellular Materials with and without Periodicity Constraints

A generalized strain energy-based homogenization method for 2-D and 3-D cellular materials with and without periodicity constraints is proposed using Hill’s Lemma and the matrix method for spatial frames. In this new approach, the equilibrium equations are enforced at all boundary and interior nodes and each interior node is allowed to translate and rotate freely, which differ from existing methods where the equilibrium conditions are imposed only at the boundary nodes. The newly formulated homogenization method can be applied to cellular materials with or without symmetry. To illustrate the new method, four examples are studied: two for a 2-D cellular material and two for a 3-D pentamode metamaterial, with and without periodic constraints in each group. For the 2-D cellular material, an asymmetric microstructure with or without periodicity constraints is analyzed, and closed-form expressions of the effective stiffness components are obtained in both cases. For the 3-D pentamode metamaterial, a primitive diamond-shaped unit cell with or without periodicity constraints is considered. In each of these 3-D cases, two different representative cells in two orientations are examined. The homogenization analysis reveals that the pentamode metamaterial exhibits the cubic symmetry based on one representative cell, with the effective Poisson’s ratio v¯ being nearly 0.5. Moreover, it is revealed that the pentamode metamaterial with the cubic symmetry can be tailored to be a rubber-like material (with v¯ ≅0.5) or an auxetic material (with v¯< 0).

Endoscopic endosonography with fine-needle aspiration biopsy in the diagnosis of pancreatic tumors

Objectives of the study: efficiency assessment of cytological methods in the diagnosis of pancreatic tumors. Material and methods. Our study includes results of 163 pancreatic fine needle aspirations of solid and cystic tumors, from 160 patients of the N.N. Petrov Cancer Research Center for the 4-year period (2016–2020). Results. Representative cell material for morphological studies was obtained in 98.6% of cases. The results of cytological examination of 35 patients with pancreatic tumors were compared with histological data. Malignant process was correctly established in 30 out of 32 patients, benign process- in all three cases. The sensitivity of cytological examination was 93.1%, specificity — 100%. Conclusion. Pancreatic fine-needle aspiration cytology is safe, rapid, accurate and cost‐beneficial modality of investigation of pancreatic mass lesion.

CircVAMP3: A circRNA with a Role in Alveolar Rhabdomyosarcoma Cell Cycle Progression

Circular RNAs (circRNAs), a class of covalently closed RNAs formed by a back-splicing reaction, have been involved in the regulation of diverse oncogenic processes. In this article we describe circVAMP3, a novel circular RNA overexpressed in RH4, a representative cell line of alveolar rhabdomyosarcoma. We demonstrated that circVAMP3 has a differential m6A pattern opposed to its linear counterpart, suggesting that the two isoforms can be differently regulated by such RNA modification. Moreover, we show how circVAMP3 depletion in alveolar rhabdomyosarcoma cells can impair cell cycle progression, through the alteration of the AKT-related pathways, pointing to this non-coding RNA as a novel regulator of the alveolar rhabdomyosarcoma progression and as a putative future therapeutic target.

Elucidating the mechanism of cellular uptake of fullerene nanoparticles

Understanding the molecular interactions between biological cells and engineered nanoparticles is a key to evaluating potential toxicities to humans and the environment. This study developed a method to determine the mechanisms by which fullerene aggregates are distributed into a representative cell line, human intestinal Caco-2 cells. First, we determined that the presence of fetal bovine serum (FBS) in the cell culture media changes the particle characteristics and inhibits particle adsorptions onto cell surfaces. Second, significantly lower amounts of fullerene were internalized at 4°C, a temperature at which active transport mechanisms are effectively impeded, than at 37°C. Third, metabolic inhibitors of active transport and a microtubule transport inhibitor decreased fullerene uptake at 37°C. Fourth, cellular uptake of fullerene increased with increasing fullerene concentration, suggesting that passive diffusion into lipid membranes contributed to uptake over the broad concentration range used in this study. Together, these results indicate fullerene transport into cells occurs via two mechanisms: passive diffusion across the lipid bilayer and active transport including microtubule involved endocytosis. The results also suggest that simple physical-chemical partitioning models do not fully describe fullerene uptake, and instead, active transport models are also required to estimate the cellular uptake and toxicity of fullerene.

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments

Summary scATAC-seq is a powerful approach for characterizing cell-type-specific regulatory landscapes. However, it is difficult to benchmark the performance of various scATAC-seq analysis techniques (such as clustering and deconvolution) without having a priori a known set of gold-standard cell types. To simulate scATAC-seq experiments with known cell-type labels, we introduce an efficient and scalable scATAC-seq simulation method (SCAN-ATAC-Sim) that down-samples bulk ATAC-seq data (e.g., from representative cell lines or tissues). Our protocol uses a consistent but tunable signal-to-noise ratio across cell types in a scATAC-seq simulation for integrating bulk experiments with different levels of background noise, and it independently samples twice without replacement to account for the diploid genome. Because it uses an efficient weighted reservoir sampling algorithm and is highly parallelizable with OpenMP, our implementation in C ++ allows millions of cells to be simulated in less than an hour on a laptop computer. Availability SCAN-ATAC-Sim is available at scan-atac-sim.gersteinlab.org. Supplementary information Supplementary data are available at Bioinformatics online.

Mitochondrial event localiser (MEL) to quantitativelydescribe fission, fusion and depolarisation in the three-dimensional space

Mitochondrial fission and fusion play an important role not only in maintaining mitochondrial homeostasis but also in preserving overall cellular viability. However, quantitative analysis based on the three-dimensional localisation of these highly dynamic mitochondrial events in the cellular context has not yet been accomplished. Moreover, it remains largely uncertain where in the mitochondrial network depolarisation is most likely to occur. We present the mitochondrial event localiser (MEL), a method that allows high-throughput, automated and deterministic localisation and quantification of mitochondrial fission, fusion and depolarisation events in large three-dimensional microscopy time-lapse sequences. In addition, MEL calculates the number of mitochondrial structures as well as their combined and average volume for each image frame in the time-lapse sequence. The mitochondrial event locations can subsequently be visualised by superposition over the fluorescence micrograph z-stack. We apply MEL to both control samples as well as to cells before and after treatment with hydrogen peroxide (H2O2). An average of 9.3/7.2/2.3 fusion/fission/depolarisation events per cell were observed respectively for every 10 sec in the control cells. With peroxide treatment, the rate initially shifted toward fusion with and average of 15/6/3 events per cell, before returning to a new equilibrium not far from that of the control cells, with an average of 6.2/6.4/3.4 events per cell. These MEL results indicate that both pre-treatment and control cells maintain a fission/fusion equilibrium, and that depolarisation is higher in the post-treatment cells. When individually validating mitochondrial events detected with MEL, for a representative cell for the control and treated samples, the true-positive events were 47%/49%/14% respectively for fusion/fission/depolarisation events. We conclude that MEL is a viable method of quantitative mitochondrial event analysis.

Representative Cell Analysis for Damage-Based Failure Model of Polymer Hexagonal Honeycomb Structure under the Out-of-Plane Loadings

The honeycomb (HC) core of sandwich structures undergoes flexural loading and carries the normal compression and shear. The mechanical properties and deformation response of the core need to be established for the design requirements. In this respect, this article describes the development of the smallest possible representative cell (RC) models for quantifying the deformation and failure process of the Nomex polymer-based hexagonal HC core structure under the out-of-plane quasi-static loadings. While the hexagonal single and multi-cell models are suitable for the tension and compression, a six-cell model is the simplest RC model developed for shear in the transverse and ribbon direction. Hashin’s matrix and fiber damage equations are employed in simulating the failure process of the orthotropic cell walls, using the finite element (FE) analysis. The FE-calculated load–displacement curves are validated with the comparable measured responses throughout the loading to failure. The location of the fracture plane of the critical cell wall in the out-of-plane tension case is well predicted. The wrinkling of the cell walls, leading to the structural buckling of the HC core specimen in the compression test, compares well with the observed failure mechanisms. In addition, the observed localized buckling of the cell wall by the induced compressive stress during the out-of-plane shear in both the transverse and ribbon direction is explained. The mesoscale RC models of the polymer hexagonal HC core structure have adequately demonstrated the ability to predict the mechanics of deformation and the mechanisms of failure.

Putative Autoantigen Leiomodin-1 Is Expressed in the Human Brain and in the Membrane Fraction of Newly Formed Neurons

Nodding syndrome is a pediatric epilepsy disorder associated with Onchocerca volvulus infection, but the mechanism driving this relationship is unclear. One hypothesis proposes that parasite-induced immune responses cross-react with human leiomodin-1 resulting in immune-mediated central nervous system (CNS) damage. However, as leiomodin-1 expression and epitope availability in human neurons remains uncharacterized, the relevance of leiomodin-1 autoimmunity is unknown. Leiomodin-1 transcript expression was assessed in silico using publicly available ribonucleic acid (RNA) sequencing databases and in tissue by in situ hybridization and quantitative polymerase chain reaction. Abundance and subcellular localization were examined by cell fractionation and immunoblotting. Leiomodin-1 transcripts were expressed in cells of the CNS, including neurons and astrocytes. Protein was detectable from all brain regions examined as well as from representative cell lines and in vitro differentiated neurons and astrocytes. Leiomodin-1 was expressed on the membrane of newly formed neurons, but not neural progenitor cells or mature neurons. Importantly, leiomodin-1 antibodies were only toxic to cells expressing leiomodin-1 on the membrane. Our findings provide evidence that leiomodin-1 is expressed in human neurons and glia. Furthermore, we show membrane expression mediates leiomodin-1 antibody toxicity, suggesting these antibodies may play a role in pathogenesis.