Multiscaling in Models of Magnetohydrodynamic Turbulence

From a direct numerical simulation of the MHD equations we show, for the first time, that velocity and magnetic-field structure functions exhibit multiscaling, extended self similarity (ESS), and generalized extended self similarity (GESS). We also propose a new shell model for homogeneous and isotropic MHD turbulence, which preserves all the invariants of ideal MHD, reduces to a well-known shell model for fluid turbulence for zero magnetic field, has no adjustable parameters apart from Reynolds numbers, and exhibits the same multiscaling, ESS, and GESS as the MHD equations. We also study dissipation-range asymptotics and the inertial- to dissipation-range crossover.Comment: 5 pages, REVTEX, 4 figures (eps

Inertial- and Dissipation-Range Asymptotics in Fluid Turbulence

We propose and verify a wave-vector-space version of generalized extended self similarity and broaden its applicability to uncover intriguing, universal scaling in the far dissipation range by computing high-order (\leq 20\/) structure functions numerically for: (1) the three-dimensional, incompressible Navier Stokes equation (with and without hyperviscosity); and (2) the GOY shell model for turbulence. Also, in case (2), with Taylor-microscale Reynolds numbers 4 \times 10^{4} \leq Re_{\lambda} \leq 3 \times 10^{6}\/, we find that the inertial-range exponents (\zeta_{p}\/) of the order - p\/ structure functions do not approach their Kolmogorov value p/3\/ as Re_{\lambda}\/ increases.Comment: RevTeX file, with six postscript figures. epsf.tex macro is used for figure insertion. Packaged using the 'uufiles' utilit

Anomalously rough sandpiles in one dimension: exact decimation results

We categorize the possible large-scale behaviors of one-dimensional nearest-neighbor hopping "sandpile" slope models on a circle of N sites with nonconserving noise, via decimation. Defining the height at site i to be hi, we find a continuous infinity of fixed points of the decimation, parametrized by an index n (1≤n≤2) with (h0-hN/2)2~N2/n. The fixed point n=2 corresponds to our ordinary notion of a rough interface, while the others are new and far rougher

[Marco Aur??lio Nunes Ferreira de Queiroz, t??cnico da FJP]

Marco Aur??lio Nunes Ferreira de Queiroz, t??cnico da Funda????o Jo??o Pinheiro (FJP)

Inertial- and Dissipation-Range Asymptotics in Fluid Turbulence

We propose and verify a wave-vector-space version of generalized extended self-similarity [R. Benzi et al., Europhys. Lett. 32, 709 (1995)] and broaden its applicability to uncover intriguing, universal scaling in the far dissipation range by computing high-order ( <= 20) structure functions numerically for (1) the three-dimensional, incompressible Navier-Stokes equation (with and without hyperviscosity) and (2) the Gledzer-Ohkitani-Yamada shell model for turbulence. Also, in case (2), with Taylor-microscale Reynolds numbers 4 x 104 <= Re lambda <= 3 x 106, we find that the inertial-range exponents (zeta p) of the order- p structure functions do not approach their Kolmogorov value p/3 as Re lambda increases

Novel CAF-identifiers via transcriptomic and protein level analysis in HNSC patients

Abstract Cancer-associated fibroblasts (CAFs), a prominent component of the tumor microenvironment, play an important role in tumor development, invasion, and drug resistance. The expression of distinct “CAF-markers” which separates CAFs from normal fibroblasts and epithelial cells, have traditionally been used to identify them. These commonly used CAF-markers have been reported to differ greatly across different CAF subpopulations, even within a cancer type. Using an unbiased -omic approach from public data and in-house RNAseq data from patient derived novel CAF cells, TIMP-1, SPARC, COL1A2, COL3A1 and COL1A1 were identified as potential CAF-markers by differential gene expression analysis using publicly available single cell sequencing data and in-house RNAseq data to distinguish CAF populations from tumor epithelia and normal oral fibroblasts. Experimental validation using qPCR and immunofluorescence revealed CAF-specific higher expression of TIMP-1 and COL1A2 as compared to other markers in 5 novel CAF cells, derived from patients of diverse gender, habits and different locations of head and neck squamous cell carcinoma (HNSC). Upon immunohistochemical (IHC) analysis of FFPE blocks however, COL1A2 showed better differential staining between tumor epithelia and tumor stroma. Similar data science driven approach utilizing single cell sequencing and RNAseq data from stabilized CAFs can be employed to identify CAF-markers in various cancers

Relative quantification of BCL2 mRNA for diagnostic usage needs stable uncontrolled genes as reference.

Dysregulation of BCL2 is a pathophysiology observed in haematological malignancies. For implementation of available treatment-options it is preferred to know the relative quantification of BCL2 mRNA with appropriate reference genes. For the choice of reference genes-(i) Reference Genes were selected by assessing variation of >60,000 genes from 4 RNA-seq datasets of haematological malignancies followed by filtering based on their GO biological process annotations and proximity of their chromosomal locations to known disease translocations. Selected genes were experimentally validated across various haematological malignancy samples followed by stability comparison using geNorm, NormFinder, BestKeeper and RefFinder. (ii) 43 commonly used Reference Genes were obtained from literature through extensive systematic review. Levels of BCL2 mRNA was assessed by qPCR normalized either by novel reference genes from this study or GAPDH, the most cited reference gene in literature and compared. The analysis showed PTCD2, PPP1R3B and FBXW9 to be the most unregulated genes across lymph-nodes, bone marrow and PBMC samples unlike the Reference Genes used in literature. BCL2 mRNA level shows a consistent higher expression in haematological malignancy patients when normalized by these novel Reference Genes as opposed to GAPDH, the most cited Reference Gene. These reference genes should also be applicable in qPCR platforms using Taqman probes and other model systems including cell lines and rodent models. Absence of sample from healthy-normal individual in diagnostic cases call for careful selection of Reference Genes for relative quantification of a biomarker by qPCR.BCL2 can be used as molecular diagnostics only if normalized with a set of reference genes with stable yet low levels of expression across different types of haematological malignancies

Estimation of ALU Repetitive Elements in Plasma as a Cost-Effective Liquid Biopsy Tool for Disease Prognosis in Breast Cancer

Background: Liquid biopsy is widely recognized as an efficient diagnostic method in oncology for disease detection and monitoring. Though the examination of circulating tumor cells (CTC) is mostly implemented for the assessment of genomic aberrations, the need of complex methodologies for their detection has impeded its acceptance in low-resource settings. We evaluated cell-free DNA (cfDNA) as a liquid biopsy tool and investigated its utility in breast cancer patients. Methods: Total cell-free DNA was extracted from the plasma of breast cancer patients (n = 167) with a median follow-up of more than 5 years, at various stages of the disease. Quantitative PCR was performed to estimate the copy numbers of two fractions of ALU repetitive elements (ALU 115 and ALU 247), and DNA integrity (DI) was calculated as the ratio of ALU 247/115. Mutations in TP53 and PIK3CA in the cfDNA were estimated by next-gen sequencing (NGS) in a subset of samples. Associations of the levels of both the ALU fragments with various clinico-pathological factors and disease-free survival at various stages were examined. Nomogram models were constructed with clinical variables and ALU 247 levels to predict disease-free survival and the best performing model was evaluated by decision curve analysis. Results: DI and ALU 247 levels were significantly lower (p p p = 0.005). Higher levels of ALU 247 in the circulation also correlated with low tumor-infiltrating lymphocytes (TIL) within their primary tumors in the ER-negative breast cancer subtype (p = 0.01). Cox proportional hazard analysis confirmed ALU 247 as an independent variable of disease-free survival both in univariate and multivariate analysis [HR 1.3 (95% CI 1.047 to 1.613, p = 0.017)]. The nomogram model showed that the addition of ALU 247 with other variables significantly improved (C-index 0.823) the predictive ability of the model. Conclusion: Our results confirm the utility of cfDNA as an evolving liquid biopsy tool for molecular analysis. Evaluation of larger fragments of cfDNA estimated through ALU 247 can provide vital information concurrent with the pathological process of disease evolution in breast cancer and warrants expansion to other cancer types