Search results for " Embedding"
showing 10 items of 84 documents
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…
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…
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 …
Moduli spaces of rank two aCM bundles on the Segre product of three projective lines
2016
Let P^n be the projective space of dimension n on an algebraically closed field of characteristic 0 and F be the image of the Segre embedding of P^1xP^1xP^1 inside P^7. In the present paper we deal with the moduli spaces of locally free sheaves E on F of rank 2 with h^i(F,E(t))=0 for i=1,2 and each integer t.
Embeddings of a family of Danielewski hypersurfaces and certain \C^+-actions on \C^3
2006
International audience; We consider the family of complex polynomials in \C[x,y,z] of the form x^2y-z^2-xq(x,z). Two such polynomials P_1 and P_2 are equivalent if there is an automorphism \varphi of \C[x,y,z] such that \varphi(P_1)=P_2. We give a complete classification of the equivalence classes of these polynomials in the algebraic and analytic category.
15-prostaglandin dehydrogenase expression alone or in combination with ACSM1 defines a subgroup of the apocrine molecular subtype of breast carcinoma.
2008
Established histopathological criteria divide invasive breast carcinomas into defined groups. Ductal of no specific type and lobular are the two major subtypes accounting for around 75 and 15% of all cases, respectively. The remaining 10% include rarer types such as tubular, cribriform, mucinous, papillary, medullary, metaplastic, and apocrine breast carcinomas. Molecular profiling technologies, on the other hand, subdivide breast tumors into five subtypes, basal-like, luminal A, luminal B, normal breast tissue-like, and ERBB2-positive, that have different prognostic characteristics. An additional subclass termed "molecular apocrine" has recently been described, but these lesions did not ex…
Rank two aCM bundles on the del Pezzo fourfold of degree 6 and its general hyperplane section
2018
International audience; In the present paper we completely classify locally free sheaves of rank 2 with vanishing intermediate cohomology modules on the image of the Segre embedding $\mathbb{P}^2$ x $\mathbb{P}^2 \subseteq \mathbb{P}^8$ and its general hyperplane sections.Such a classification extends similar already known results regarding del Pezzo varieties with Picard numbers 1 and 3 and dimension at least 3.
Dynamic 2- and 3-connectivity on planar graphs
1992
We study the problem of maintaining the 2-edge-, 2-vertex-, and 3-edge-connected components of a dynamic planar graph subject to edge deletions. The 2-edge-connected components can be maintained in a total of O(n log n) time under any sequence of at most O(n) deletions. This gives O(log n) amortized time per deletion. The 2-vertex- and 3-edge-connected components can be maintained in a total of O(n log2n) time. This gives O(log2n) amortized time per deletion. The space required by all our data structures is O(n).
Reproducing kernel hilbert spaces regression methods for genomic assisted prediction of quantitative traits.
2008
Abstract Reproducing kernel Hilbert spaces regression procedures for prediction of total genetic value for quantitative traits, which make use of phenotypic and genomic data simultaneously, are discussed from a theoretical perspective. It is argued that a nonparametric treatment may be needed for capturing the multiple and complex interactions potentially arising in whole-genome models, i.e., those based on thousands of single-nucleotide polymorphism (SNP) markers. After a review of reproducing kernel Hilbert spaces regression, it is shown that the statistical specification admits a standard mixed-effects linear model representation, with smoothing parameters treated as variance components.…