Search results for " Computer Science"
showing 10 items of 3983 documents
Detecting global and local hippocampal shape changes in Alzheimer's disease using statistical shape models.
2012
Item does not contain fulltext The hippocampus is affected at an early stage in the development of Alzheimer's disease (AD). With the use of structural magnetic resonance (MR) imaging, we can investigate the effect of AD on the morphology of the hippocampus. The hippocampal shape variations among a population can be usually described using statistical shape models (SSMs). Conventional SSMs model the modes of variations among the population via principal component analysis (PCA). Although these modes are representative of variations within the training data, they are not necessarily discriminative on labeled data or relevant to the differences between the subpopulations. We use the shape des…
Metallothionein Gene Family in the Sea Urchin Paracentrotus lividus: Gene Structure, Differential Expression and Phylogenetic Analysis
2017
Metallothioneins (MT) are small and cysteine-rich proteins that bind metal ions such as zinc, copper, cadmium, and nickel. In order to shed some light on MT gene structure and evolution, we cloned seven Paracentrotus lividus MT genes, comparing them to Echinodermata and Chordata genes. Moreover, we performed a phylogenetic analysis of 32 MTs from different classes of echinoderms and 13 MTs from the most ancient chordates, highlighting the relationships between them. Since MTs have multiple roles in the cells, we performed RT-qPCR and in situ hybridization experiments to understand better MT functions in sea urchin embryos. Results showed that the expression of MTs is regulated throughout de…
What place does molecular topology have in today’s drug discovery?
2020
Introduction: Most methods in molecular and drug design are currently based on physicochemical descriptors. However, molecular topology, which relies on topological descriptors, has also shown value for molecular design even if it does not take into account the physical or chemical properties of ligands and receptors, including the ligand-receptor interaction itself. Areas covered: Herein, the authors provide new insights into the importance of molecular topology according to some of the latest discoveries in physics and chemistry. Furthermore, the authors report on the most significant achievements in drug design using molecular topology over the last 5 years and give their expert perspect…
On the contribution of molecular topology to drug design and discovery.
2010
Abstract The role of molecular topology (MT) in the design and selection of new drugs is discussed. After an overview of the different in silico molecular design current technologies, the QSAR analysis is dealt in detail with particular emphasis in the use of topological indices as molecular descriptors. The results of the application of MT in drug design and discovery are described and finally a possible explanation is given about some of the key reasons explaining it's the extraordinary performance.
Exploiting a list of protein sequences
2007
Abstract: We describe a software program to help exploit a database of aligned protein sequences. In addition to the classical lists of sequences, a graphical representation is used to get a better overview of the information. As natural parameters, the type of amino acid and sequence position are used. Various plots or 3D representations are then updated. Examples are shown based on globin sequences from various species and on the abnormal human hemoglobins. The software should be of interest to protein engineers who need to know what variants are already known.
General topological patterns of known drugs.
2001
Abstract Discriminating “drug-like” from “non-drug-like” compounds is a relatively emerging topic within the drug research. The basic assumption is that it is possible to obtain relevant information from structural features common to the known drugs, in order to discard a huge number of candidate chemical structures with low probability of becoming drugs. A graph-theoretical contribution to this subject is reported in this paper, by making exclusive use of linear relationships. The results suggest that it is possible to achieve a pattern of general pharmacological activity based on molecular topology. Conclusions are tentative pending verification of the results with larger compound librari…
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
Posets That Locally Resemble Distributive Lattices
2000
Abstract Let P be a graded poset with 0 and 1 and rank at least 3. Assume that every rank 3 interval is a distributive lattice and that, for every interval of rank at least 4, the interval minus its endpoints is connected. It is shown that P is a distributive lattice, thus resolving an issue raised by Stanley. Similar theorems are proven for semimodular, modular, and complemented modular lattices. As a corollary, a theorem of Stanley for Boolean lattices is obtained, as well as a theorem of Grabiner (conjectured by Stanley) for products of chains. Applications to incidence geometry and connections with the theory of buildings are discussed.
Distributed evolutionary approach to data clustering and modeling
2014
In this article we describe a framework (DEGA-Gen) for the application of distributed genetic algorithms for detection of communities in networks. The framework proposes efficient ways of encoding the network in the chromosomes, greatly optimizing the memory use and computations, resulting in a scalable framework. Different objective functions may be used for producing division of network into communities. The framework is implemented using open source implementation of MapReduce paradigm, Hadoop. We validate the framework by developing community detection algorithm, which uses modularity as measure of the division. Result of the algorithm is the network, partitioned into non-overlapping co…
Bɪ-CомDᴇт: Community Detection in Bipartite Networks
2019
Abstract Extracting hidden communities from bipartite networks witnessed a determined effort. In this respect, different streams of research relied on bipartite networks to unveil communities. In this paper, we introduce a new approach, called Bi-Comdet, that aims to an efficient community detection in bipartite networks. The main trust of the introduced approach is that it stresses on the importance of grouping two types of nodes in communities having a full connection between its nodes. The quality of the unveiled communities, is assessed through some metrics borrowed from the FCA community, to wit modularity, overlapping and stability. These metrics are then aggregated through the use of…