Search results for "bioinformatics"
showing 10 items of 1632 documents
Virus diversity in a winter epidemic of acute diarrhea in France.
2002
ABSTRACT In France, an epidemic peak of acute diarrhea is observed each winter. Previous results suggested a viral etiology for these winter epidemics. We investigated the role of enteric viruses in acute diarrhea and their molecular diversity. One hundred sixty-one patients with acute diarrhea and 45 healthy patients (controls) from the general population were given a standardized questionnaire between December 1998 and May 1999. Stool specimens were screened for group A and C rotaviruses, human caliciviruses, astroviruses, and adenovirus types 40 and 41 by reverse transcription-PCR and/or enzyme immunoassay. Virologic analysis was positive for 63 cases (39%). Caliciviruses and group A rot…
Differential occurrence of S100A7 in breast cancer tissues: A proteomic-based investigation
2012
Purpose The present study reports for the first time a large-scale proteomic screening of the occurrence, subcellular localization and relative quantification of the S100A7 protein among a group of 100 patients, clinically grouped for the diagnosis of infiltrating ductal carcinoma (IDC). Experimental design To this purpose, the methods of differential proteomics, Western blotting, and immunohistochemistry were used. Results The identity of two isoforms of the protein was assessed by mass spectrometry and immunologically confirmed. Moreover, we proved by immunocytochemical applications the exclusive localization of the protein within the neoplastic cells. The correlation of S100A7 expression…
AP5Z1/SPG4 8 frequency in autosomal recessive and sporadic spastic paraplegia
2014
Hereditary spastic paraplegias (HSP) constitute a rare and highly heterogeneous group of neurodegenerative disorders, defined clinically by progressive lower limb spasticity and pyramidal weakness. Autosomal recessive HSP as well as sporadic cases present a significant diagnostic challenge. Mutations in AP5Z1, a gene playing a role in intracellular membrane trafficking, have been recently reported to be associated with spastic paraplegia type 48 (SPG48). Our objective was to determine the relative frequency and clinical relevance of AP5Z1 mutations in a large cohort of 127 HSP patients. We applied a targeted next-generation sequencing approach to analyze all coding exons of the AP5Z1 gene. …
Interest of studying the saliva metabolome, transcriptome and microbiome in screening for pancreatic cancer
2019
Abstract Introduction Pancreatic cancer is a public health problem because its mortality rate is close to its incidence rate. If it were possible to detect this cancer before the onset of symptoms, 5-year survival could reach 75%. Numerous studies have attempted to accelerate the diagnosis to improve survival. Saliva presents interesting characteristics as a fluid for screening and diagnosis. Its many components provide a promising source of constitutive biomarkers with a specific signature of the disease. The aim of this work was to determine the interest of studying the metabolome, the transcriptome and the microbiome of saliva in screening for pancreatic cancer. Materials and methods A r…
Estimation of Pyruvic acid in serum and saliva among healthy and potentially malignant disorder subjects – a stepping stone for cancer screening?
2014
Background: According to Warburg’s effect, the rate of glycolysis increases in cancerous cells. This will increase overall levels of pyruvic acid. The present on-going study was conducted to estimate the levels of pyruvic acid in saliva and serum in normal, oral PMD subjects. Material and Methods: A total of 50 subjects in healthy, PMD of the oral cavity individuals were selected based on clinical and histological criteria. Collected saliva and serum samples were subjected to pyruvic acid level estimation using biochemical analysis. Results: Of the 50 participants 25 (13: Males; 12: Females) & 25 (16: Males; 9: Females) were PMD group. Independent samples t test showed statistically signifi…
MPP1 links the Usher protein network and the Crumbs protein complex in the retina.
2007
Contains fulltext : 53571.pdf (Publisher’s version ) (Closed access) The highly ordered distribution of neurons is an essential feature of a functional mammalian retina. Disruptions in the apico-basal polarity complexes at the outer limiting membrane (OLM) of the retina are associated with retinal patterning defects in vertebrates. We have analyzed the binding repertoire of MPP5/Pals1, a key member of the apico-basal Crumbs polarity complex, that has functionally conserved counterparts in zebrafish (nagie oko) and Drosophila (Stardust). We show that MPP5 interacts with its MAGUK family member MPP1/p55 at the OLM. Mechanistically, this interaction involves heterodimerization of both MAGUK mo…
“ One Ring to Bind Them All ”—Part I: The Efficiency of the Macrocyclic Scaffold for G-Quadruplex DNA Recognition
2010
International audience; Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the "standard" B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding …
Curcumin as Scaffold for Drug Discovery against Neurodegenerative Diseases
2021
Neurodegenerative diseases (NDs) are one of major public health problems and their impact is continuously growing. Curcumin has been proposed for the treatment of several of these pathologies, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) due to the ability of this molecule to reduce inflammation and aggregation of involved proteins. Nevertheless, the poor metabolic stability and bioavailability of curcumin reduce the possibilities of its practical use. For these reasons, many curcumin derivatives were synthetized in order to overcome some limitations. In this review will be highlighted recent results on modification of curcumin scaffold in the search of new effective therap…
Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model
2015
[Abstract] Detecting epistasis, such as 2-SNP interactions, in genome-wide association studies (GWAS) is an important but time consuming operation. Consequently, GPUs have already been used to accelerate these studies, reducing the runtime for moderately-sized datasets to less than 1 hour. However, single-GPU approaches cannot perform large-scale GWAS in reasonable time. In this work we present multiEpistSearch, a tool to detect epistasis that works on GPU clusters. While CUDA is used for parallelization within each GPU, the workload distribution among GPUs is performed with Unified Parallel C++ (UPC++), a novel extension of C++ that follows the Partitioned Global Address Space (PGAS) model…
On Obtaining Classification Confidence, Ranked Predictions and AUC with Tsetlin Machines
2020
Tsetlin machines (TMs) are a promising approach to machine learning that uses Tsetlin Automata to produce patterns in propositional logic, leading to binary (hard) classifications. In many applications, however, one needs to know the confidence of classifications, e.g. to facilitate risk management. In this paper, we propose a novel scheme for measuring TM confidence based on the logistic function, calculated from the propositional logic patterns that match the input. We then use this scheme to trade off precision against recall, producing area under receiver operating characteristic curves (AUC) for TMs. Empirically, using four real-world datasets, we show that AUC is a more sensitive meas…