Search results for "Database"
showing 10 items of 2136 documents
Proteomic analysis of the acid-soluble nacre matrix of the bivalve Unio pictorum: detection of novel carbonic anhydrase and putative protease inhibit…
2010
10 pages; International audience; The matrix extracted from mollusc shell nacre is a mixture of proteins and glycoproteins that is thought to play a major role in controlling biomineral synthesis and in increasing its mechanical properties. We investigated the nacreous shell of the freshwater mussel Unio pictorum, to which we applied a proteomics approach adapted to mollusc shell proteins. On one hand, the acid-soluble nacre matrix was fractionated by SDS-PAGE and the five main protein bands (P95, P50, P29, P16, and P12) were digested with trypsin and analyzed by nanoLC-MS/MS followed by de novo sequencing. On the other hand, the acid-soluble nacre matrix was analyzed in a similar manner, w…
Reconfigurable Accelerator for the Word-Matching Stage of BLASTN
2013
BLAST is one of the most popular sequence analysis tools used by molecular biologists. It is designed to efficiently find similar regions between two sequences that have biological significance. However, because the size of genomic databases is growing rapidly, the computation time of BLAST, when performing a complete genomic database search, is continuously increasing. Thus, there is a clear need to accelerate this process. In this paper, we present a new approach for genomic sequence database scanning utilizing reconfigurable field programmable gate array (FPGA)-based hardware. In order to derive an efficient structure for BLASTN, we propose a reconfigurable architecture to accelerate the…
Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone.
2013
T-cell protein tyrosine phosphatase (TCPTP) is a ubiquitously expressed non-receptor protein tyrosine phosphatase. It is involved in the negative regulation of many cellular signaling pathways. Thus, activation of TCPTP could have important therapeutic applications in diseases such as cancer and inflammation. We have previously shown that the α-cytoplasmic tail of integrin α1β1 directly binds and activates TCPTP. In addition, we have identified in a large-scale high-throughput screen six small molecules that activate TCPTP. These small molecule activators include mitoxantrone and spermidine. In this study, we have investigated the molecular mechanism behind agonist-induced TCPTP activation.…
Grover’s Search with Faults on Some Marked Elements
2016
Grover's algorithm is a quantum query algorithm solving the unstructured search problem of size N using $$O\sqrt{N}$$ queries. It provides a significant speed-up over any classical algorithm [2]. The running time of the algorithm, however, is very sensitive to errors in queries. Multiple authors have analysed the algorithm using different models of query errors and showed the loss of quantum speed-up [1, 4]. We study the behavior of Grover's algorithm in the model where the search space contains both faulty and non-faulty marked elements. We show that in this setting it is indeed possible to find one of marked elements in $$O\sqrt{N}$$ queries.
Genome-wide association analysis identifies six new loci associated with forced vital capacity
2014
Forced vital capacity (FVC), a spirometric measure of pulmonary function, reflects lung volume and is used to diagnose and monitor lung diseases. We performed genome-wide association study meta-analysis of FVC in 52,253 individuals from 26 studies and followed up the top associations in 32,917 additional individuals of European ancestry. We found six new regions associated at genome-wide significance (P <5 x 10(-8)) with FVC in or near EFEMP1, BMP6, MIR129-2-HSD17B12, PRDM11, WWOX and KCNJ2. Two loci previously associated with spirometric measures (GSTCD and PTCH1) were related to FVC. Newly implicated regions were followed up in samples from African-American, Korean, Chinese and Hispani…
The reaction enthalpy of hydrogen dissociation calculated with the Small System Method from simulation of molecular fluctuations.
2014
We show how we can find the enthalpy of a chemical reaction under non-ideal conditions using the Small System Method to sample molecular dynamics simulation data for fluctuating variables. This method, created with Hill's thermodynamic analysis, is used to find properties in the thermodynamic limit, such as thermodynamic correction factors, partial enthalpies, volumes, heat capacities and compressibility. The values in the thermodynamic limit at (T,V, μj) are then easily transformed into other ensembles, (T,V,Nj) and (T,P,Nj), where the last ensemble gives the partial molar properties which are of interest to chemists. The dissociation of hydrogen from molecules to atoms was used as a conve…
Incompleteness in Conceptual Data Modelling
2013
Although conceptual data modelers can ”get creative” when designing entities and relationships to meet business requirements, they are highly constrained by the business rules which determine the details of how the entities and relationships combine. Typically, there is a delay in realising which business rules might be relevant and a further delay in obtaining an authoritative statement of these rules. We identify circumstances under which viable database designs can be constructed from conceptual data models which are incomplete in the sense that they lack this “infrastructural” detail normally obtained from the business rules. As such detail becomes available, our approach allows the con…
Using Chemical Structural Indicators for Periodic Classification of Local Anaesthetics
2011
Algorithms for classification and taxonomy based on criteria as information entropy and its production are proposed. Some local anaesthetics, currently in use, are classified using five characteristic chemical properties of different portions of their molecules. Many classification algorithms are based on information entropy. When applying the procedures to sets of moderate size, an excessive number of results appear compatible with data and the number suffers a combinatorial explosion. However, after the equipartition conjecture one has a selection criterion between different variants resulting from classification between hierarchical trees. Information entropy and principal component anal…
Traitpedia: a collaborative effort to gather species traits
2018
Abstract Summary Traitpedia is a collaborative database aimed to collect binary traits in a tabular form for a growing number of species. Availability and implementation Traitpedia can be accessed from http://cbdm-01.zdv.uni-mainz.de/~munoz/traitpedia. Supplementary information Supplementary data are available at Bioinformatics online.
A Three-Dimensional Object Point Process for Detection of Cosmic Filaments
2007
Summary We propose to apply an object point process to delineate filaments of the large scale structure in red shift catalogues automatically. We illustrate the feasibility of the idea on an example of the recent 2dF Galaxy Redshift Survey, describe the procedure and characterize the results.