Search results for "Bedding"

A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations

2016

International audience; A fully polarizable implementation of the hybrid Quantum Mechanics/Molecular Mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. A variational formalism, offering a self-consistent 1 relaxation of both the MM induced dipoles and the QM electronic density is used for ground state energies and extended to electronic excitations in the framework of Time-Dependent Density Functional Theory combined with a state specific response of the classical part. An application to the calculation of the solvatochromism of the pyridinium N-phenolate betaine dye used to define the solvent ET30 scale is presented. Th…

Boulder coastal deposits at Favignana Island rocky coast (Sicily, Italy): Litho-structural and hydrodynamic control

2018

Boulders are frequently dislodged from rock platforms, transported and deposited along coastal zones by high-magnitude storm waves or tsunamis. Their size and shape are often controlled by the thickness of bedding planes as well as by high-angle to bedding fracture network. We investigate these processes along two coastal areas of Favignana Island by integrating geological data for 81 boulders, 49 rupture surfaces (called sockets) and fracture orientation and spacing with four radiocarbon dates, numerical hydrodynamic analysis, and hindcast numerical simulation data. Boulders are scattered along the carbonate platform as isolated blocks or in small groups, which form, as a whole, a disconti…

Effects of arbuscular mycorrhizal fungi on Gazania rigens pot plant cultivation in a Mediterranean environment

2018

Herbaceous plants used in island beds and borders need to be rapid growing, high performing and maintaining good visual quality during the growing season. Arbuscular mycorrhizal (AM) fungi application is acquiring interest for its beneficial effects on ornamental bedding plants. Gazania rigens is a herbaceous ornamental plant grown for its large daisy-like flowers. The species thrives in the coastal areas of the Mediterranean region, particularly in the mild climate of southern Italy and Sicily, where performs well in summer bedding schemes in sea side gardens even in dry and windy conditions. The aim of this study was to evaluate the effect of inoculation with Rhizophagus irregularis on se…

A Novel Intelligent Technique of Invariant Statistical Embedding and Averaging via Pivotal Quantities for Optimization or Improvement of Statistical …

2020

In the present paper, for intelligent constructing efficient (optimal, uniformly non-dominated, unbiased, improved) statistical decisions under parametric uncertainty, a new technique of invariant embedding of sample statistics in a decision criterion and averaging this criterion over pivots’ probability distributions is proposed. This technique represents a simple and computationally attractive statistical method based on the constructive use of the invariance principle in mathematical statistics. Unlike the Bayesian approach, the technique of invariant statistical embedding and averaging via pivotal quantities (ISE&APQ) is independent of the choice of priors and represents a novelty i…

TargetPlex FFPE-Direct DNA Library Preparation Kit for SiRe NGS panel: An international performance evaluation study

2021

AimNext generation sequencing (NGS) represents a key diagnostic tool to identify clinically relevant gene alterations for treatment-decision making in cancer care. However, the complex manual workflow required for NGS has limited its implementation in routine clinical practice. In this worldwide study, we validated the clinical performance of the TargetPlex FFPE-Direct DNA Library Preparation Kit for NGS analysis. Impressively, this new assay obviates the need for separate, labour intensive and time-consuming pre-analytical steps of DNA extraction, purification and isolation from formalin-fixed paraffin embedded (FFPE) specimens in the NGS workflow.MethodsThe TargetPlex FFPE-Direct DNA Libr…

Tissue expansion of lung bronchi due to tissue processing for histology – A comparative analysis of paraffin versus frozen sections in a pig model

2019

Tissue shrinking due to fixation and processing is well known. However, the degree of shrinking varies significantly with the tissue type as well as the processing method and is not well studied in various tissues. In daily pathological routine workflow, histological specimens from frozen and paraffin sections are performed from the same tissue. In the present study we compared the thickness of bronchus walls obtained from paraffin and frozen sections.Pig lungs were frozen in ventilated condition in liquid nitrogen and 36 bronchi were isolated after dissection. Frozen sections of 5 μm thickness were performed and the remaining tissue was fixed and embedded in paraffin after fixation in 4% f…

2016

AbstractThe different factors involved in the growth process of complex networks imprint valuable information in their observable topologies. How to exploit this information to accurately predict structural network changes is the subject of active research. A recent model of network growth sustains that the emergence of properties common to most complex systems is the result of certain trade-offs between node birth-time and similarity. This model has a geometric interpretation in hyperbolic space, where distances between nodes abstract this optimisation process. Current methods for network hyperbolic embedding search for node coordinates that maximise the likelihood that the network was pro…

A clustering package for nucleotide sequences using Laplacian Eigenmaps and Gaussian Mixture Model.

2018

International audience; In this article, a new Python package for nucleotide sequences clustering is proposed. This package, freely available on-line, implements a Laplacian eigenmap embedding and a Gaussian Mixture Model for DNA clustering. It takes nucleotide sequences as input, and produces the optimal number of clusters along with a relevant visualization. Despite the fact that we did not optimise the computational speed, our method still performs reasonably well in practice. Our focus was mainly on data analytics and accuracy and as a result, our approach outperforms the state of the art, even in the case of divergent sequences. Furthermore, an a priori knowledge on the number of clust…

Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue

2018

Abstract Background Gene expression profiling (GEP) studies recognized a prognostic role for tumor microenvironment (TME) in diffuse large B-cell lymphoma (DLBCL), but the routinely adoption of prognostic stromal signatures remains limited. Patients and methods Here, we applied the computational method CIBERSORT to generate a 1028-gene matrix incorporating signatures of 17 immune and stromal cytotypes. Then, we carried out a deconvolution on publicly available GEP data of 482 untreated DLBCLs to reveal associations between clinical outcomes and proportions of putative tumor-infiltrating cell types. Forty-five genes related to peculiar prognostic cytotypes were selected and their expression …

The latent geometry of the human protein interaction network

2017

Abstract Motivation A series of recently introduced algorithms and models advocates for the existence of a hyperbolic geometry underlying the network representation of complex systems. Since the human protein interaction network (hPIN) has a complex architecture, we hypothesized that uncovering its latent geometry could ease challenging problems in systems biology, translating them into measuring distances between proteins. Results We embedded the hPIN to hyperbolic space and found that the inferred coordinates of nodes capture biologically relevant features, like protein age, function and cellular localization. This means that the representation of the hPIN in the two-dimensional hyperboli…