Search results for "SIGNATURE"

Stable isotope fractionation in speleothems: Laboratory experiments

2010

Abstract In recent years, stalagmites have become important archives for paleoclimate. Several studies applying carbon and oxygen isotopes of stalagmites show a simultaneous increase of δ 13 C and δ 18 O along individual growth layers, which is interpreted as being indicative of isotope fractionation under disequilibrium conditions. In order to obtain robust paleoclimatic information from calcite precipitated under these non-equilibrium conditions it is important to improve the quantitative understanding of the corresponding isotope fractionation processes. Here we present laboratory experiments simulating calcite precipitation under cave-analogue conditions. The major focus was the investi…

Characterization of disease-specific cellular abundance profiles of chronic inflammatory skin conditions from deconvolution of biopsy samples

2019

Background Psoriasis and atopic dermatitis are two inflammatory skin diseases with a high prevalence and a significant burden on the patients. Underlying molecular mechanisms include chronic inflammation and abnormal proliferation. However, the cell types contributing to these molecular mechanisms are much less understood. Recently, deconvolution methodologies have allowed the digital quantification of cell types in bulk tissue based on mRNA expression data from biopsies. Using these methods to study the cellular composition of the skin enables the rapid enumeration of multiple cell types, providing insight into the numerical changes of cell types associated with chronic inflammatory skin c…

Hyperspectral Image Classification with Kernels

2007

The information contained in hyperspectral images allows the characterization, identification, and classification of land covers with improved accuracy and robustness. However, several critical problems should be considered in the classification of hyperspectral images, among which are (a) the high number of spectral channels, (b) the spatial variability of the spectral signature, (c) the high cost of true sample labeling, and (d) the quality of data. Recently, kernel methods have offered excellent results in this context. This chapter reviews the state-of-the-art hyperspectral image classifiers, presents two recently proposed kernel-based approaches, and systematically discusses the specif…

An expression signature characterizes cancer stem cells from lung adenocarcinoma patients

2018

The genetic tumor background is an important determinant for heterogeneous MYCN ‐amplified neuroblastoma

2016

Amplification of MYCN is the signature genetic aberration of 20–25% of neuroblastoma and a stratifying marker associated with aggressive tumor behavior. The detection of heterogeneous MYCN amplification (hetMNA) poses a diagnostic dilemma due to the uncertainty of its relevance to tumor behavior. Here, we aimed to shed light on the genomic background which permits hetMNA in neuroblastoma and tied the occurrence to other stratifying markers and disease outcome. We performed SNP analysis using Affymetrix Cytoscan HD arrays on 63 samples including constitutional DNA, tumor, bone marrow and relapse samples of 26 patients with confirmed hetMNA by MYCN‐FISH. Tumors of patients ≤18m were mostly an…

Distinct immune evasion in APOBEC ‐enriched, HPV ‐negative HNSCC

2020

Immune checkpoint inhibition leads to response in some patients with head and neck squamous cell carcinoma (HNSCC). Robust biomarkers are lacking to date. We analyzed viral status, gene expression signatures, mutational load and mutational signatures in whole exome and RNA-sequencing data of the HNSCC TCGA dataset (n = 496) and a validation set (DKTK MASTER cohort, n = 10). Public single-cell gene expression data from 17 HPV-negative HNSCC were separately reanalyzed. APOBEC3-associated TCW motif mutations but not total single nucleotide variant burden were significantly associated with inflammation. This association was restricted to HPV-negative HNSCC samples. An APOBEC-enriched, HPV-negat…

Mantle-cell lymphoma genotypes identified with CGH to BAC microarrays define a leukemic subgroup of disease and predict patient outcome

2005

To identify recurrent genomic changes in mantle cell lymphoma (MCL), we used high-resolution comparative genomic hybridization (CGH) to bacterial artificial chromosome (BAC) microarrays in 68 patients and 9 MCL-derived cell lines. Array CGH defined an MCL genomic signature distinct from other B-cell lymphomas, including deletions of 1p21 and 11q22.3-ATM gene with coincident 10p12-BMI1 gene amplification and 10p14 deletion, along with a previously unidentified loss within 9q21-q22. Specific genomic alterations were associated with different subgroups of disease. Notably, 11 patients with leukemic MCL showed a different genomic profile than nodal cases, including 8p21.3 deletion at tumor necr…

Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese prod…

2020

Reggiana is an autochthonous cattle breed reared mainly in the province of Reggio Emilia, located in the North of Italy. Reggiana cattle (originally a triple-purpose population largely diffused in the North of Italy) are characterised by a typical solid red coat colour. About 2500 cows of this breed are currently registered to its herd book. Reggiana is now considered a dual-purpose breed even if it is almost completely dedicated to the production of a mono-breed branded Protected Designation of Origin Parmigiano-Reggiano cheese, which is the main driver of the sustainable conservation of this local genetic resource. In this study, we provided the first overview of genomic footprints that c…

Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets

2012

PLoS one 7(11), e49831 (2012). doi:10.1371/journal.pone.0049831

Signatures of selection in the genome of Swedish warmblood horses selected for sport performance

2019

Abstract Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85%…