Search results for "76"
showing 10 items of 2584 documents
Analysis of the immune microenvironment in resected non-small cell lung cancer: the prognostic value of different T lymphocyte markers
2016
[EN] The prognosis of non-small cell lung cancer (NSCLC) remains poor and heterogeneous and new biomarkers are needed. As the immune system plays a pivotal role in cancer, the study of immune-related markers may provide valuable prognostic information of NSCLC. In 122 formalin-fixed, paraffin-embedded tumor tissue samples from early-stage NSCLC, tumor and tumor-near stromal areas were microdissected and gene expression levels of conventional and regulatory T cell markers were assessed by quantitative polymerase chain reaction. Also, the presence of infiltrating CD4+, CD8+, and FOXP3+ cells in tumor samples was assessed by immunohistochemistry. The relative proportion of conventional and reg…
A Dirichlet Autoregressive Model for the Analysis of Microbiota Time-Series Data
2021
Growing interest in understanding microbiota dynamics has motivated the development of different strategies to model microbiota time series data. However, all of them must tackle the fact that the available data are high-dimensional, posing strong statistical and computational challenges. In order to address this challenge, we propose a Dirichlet autoregressive model with time-varying parameters, which can be directly adapted to explain the effect of groups of taxa, thus reducing the number of parameters estimated by maximum likelihood. A strategy has been implemented which speeds up this estimation. The usefulness of the proposed model is illustrated by application to a case study.
Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer
2018
Microsatellite instability (MSI) leads to accumulation of an excessive number of mutations in the genome, mostly small insertions and deletions. MSI colorectal cancers (CRCs), however, also contain more point mutations than microsatellite-stable (MSS) tumors, yet they have not been as comprehensively studied. To identify candidate driver genes affected by point mutations in MSI CRC, we ranked genes based on mutation significance while correcting for replication timing and gene expression utilizing an algorithm, MutSigCV. Somatic point mutation data from the exome kit-targeted area from 24 exome-sequenced sporadic MSI CRCs and respective normals, and 12 whole-genome-sequenced sporadic MSI CR…
A Peptidoglycan-Remodeling Enzyme Is Critical for Bacteroid Differentiation in Bradyrhizobium spp. During Legume Symbiosis.
2016
International audience; In response to the presence of compatible rhizobium bacteria, legumes form symbiotic organs called nodules on their roots. These nodules house nitrogen-fixing bacteroids that are a differentiated form of the rhizobium bacteria. In some legumes, the bacteroid differentiation comprises a dramatic cell enlargement, polyploidization, and other morphological changes. Here, we demonstrate that a peptidoglycan-modifying enzyme in Bradyrhizobium strains, a DD-carboxypeptidase that contains a peptidoglycan-binding SPOR domain, is essential for normal bacteroid differentiation in Aeschynomene species. The corresponding mutants formed bacteroids that are malformed and hypertrop…
Centrifugal projections to the main olfactory bulb revealed by trans‐synaptic retrograde tracing in mice
2020
A wide range of evidence indicates that olfactory perception is strongly involved in food intake. However, the polysynaptic circuitry linking the brain areas involved in feeding behavior to the olfactory regions is not well known. The aim of this article was to examine such circuits. Thus, we described, using hodological tools such as transsynaptic viruses (PRV152) transported in a retrograde manner, the long-distance indirect projections (two to three synapses) onto the main olfactory bulb (MOB). The ß-subunit of the cholera toxin which is a monosynaptic retrograde tracer was used as a control to be able to differentiate between direct and indirect projections. Our tracing experiments show…
Wharton’s Jelly Mesenchymal Stromal Cells from Human Umbilical Cord: a Close-up on Immunomodulatory Molecules Featured In Situ and In Vitro
2019
Therapeutic options for end-stage organ failure are often limited to whole organ transplantation. The tolerance or rejection of the transplanted organ is driven by both early non-specific innate and specific adaptive responses. The use of mesenchymal stromal cells (MSCs) is considered a promising tool in regenerative medicine. Human umbilical cord (HUC) is an easily available source of MSCs, without relevant ethical issues. Moreover, Wharton's jelly-derived MSCs (WJ-MSCs), showed consistent immunomodulatory features that may be useful to promote immune tolerance in the host after transplantation. Few data are available on the phenotype of WJ-MSCs in situ. We investigated the expression of i…
Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens.
2016
Background Agrobacterium tumefaciens strain P4 is atypical, as the strain is not pathogenic and produces a for this species unusual quorum sensing signal, identified as N-(3-hydroxy-octanoyl)-homoserine lactone (3OH,C8-HSL). Results By sequence analysis and cloning, a functional luxI-like gene, named cinI, has been identified on the At plasmid of A. tumefaciens strain P4. Insertion mutagenesis in the cinI gene and transcriptome analyses permitted the identification of 32 cinI-regulated genes in this strain, most of them encoding proteins responsible for the conjugative transfer of pAtP4. Among these genes were the avhB genes that encode a type 4 secretion system (T4SS) involved in the forma…
A Basic Architecture of an Autonomous Adaptive System With Conscious-Like Function for a Humanoid Robot.
2018
In developing a humanoid robot, there are two major objectives. One is developing a physical robot having body, hands, and feet resembling those of human beings and being able to similarly control them. The other is to develop a control system that works similarly to our brain, to feel, think, act, and learn like ours. In this article, an architecture of a control system with a brain-oriented logical structure for the second objective is proposed. The proposed system autonomously adapts to the environment and implements a clearly defined “consciousness” function, through which both habitual behavior and goal-directed behavior are realized. Consciousness is regarded as a function for effecti…
How to deal with Haplotype data: An Extension to the Conceptual Schema of the Human Genome
2016
[EN] The goal of this work is to describe the advantages of the application of Conceptual Modeling (CM) in complex domains, such as genomics. Nowadays, the study and comprehension of the human genome is a major challenge due to its high level of complexity. The constant evolution in the genomic domain contributes to the generation of ever larger amounts of new data, which means that if we do not manage it correctly data quality could be compromised (i.e., problems related with heterogeneity and inconsistent data). In this paper, we propose the use of a Conceptual Schema of the Human Genome (CSHG), designed to understand and improve our ontological commitment to the domain and also extend (e…
Machine learning–XGBoost analysis of language networks to classify patients with epilepsy
2017
Our goal was to apply a statistical approach to allow the identification of atypical language patterns and to differentiate patients with epilepsy from healthy subjects, based on their cerebral activity, as assessed by functional MRI (fMRI). Patients with focal epilepsy show reorganization or plasticity of brain networks involved in cognitive functions, inducing ‘atypical’ (compared to ‘typical’ in healthy people) brain profiles. Moreover, some of these patients suffer from drug-resistant epilepsy, and they undergo surgery to stop seizures. The neurosurgeon should only remove the zone generating seizures and must preserve cognitive functions to avoid deficits. To preserve functions, one sho…