Fast Structural Search in Phylogenetic Databases

As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P. The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

A review on data stream classification

At this present time, the significance of data streams cannot be denied as many researchers have placed their focus on the research areas of databases, statistics, and computer science. In fact, data streams refer to some data points sequences that are found in order with the potential to be non-binding, which is generated from the process of generating information in a manner that is not stationary. As such the typical tasks of searching data have been linked to streams of data that are inclusive of clustering, classification, and repeated mining of pattern. This paper presents several data stream clustering approaches, which are based on density, besides attempting to comprehend the function of the related algorithms; both semi-supervised and active learning, along with reviews of a number of recent studies

Project SEMACODE : a scale-invariant object recognition system for content-based queries in image databases

For the efficient management of large image databases, the automated characterization of images and the usage of that characterization for searching and ordering tasks is highly desirable. The purpose of the project SEMACODE is to combine the still unsolved problem of content-oriented characterization of images with scale-invariant object recognition and modelbased compression methods. To achieve this goal, existing techniques as well as new concepts related to pattern matching, image encoding, and image compression are examined. The resulting methods are integrated in a common framework with the aid of a content-oriented conception. For the application, an image database at the library of the university of Frankfurt/Main (StUB; about 60000 images), the required operations are developed. The search and query interfaces are defined in close cooperation with the StUB project “Digitized Colonial Picture Library”. This report describes the fundamentals and first results of the image encoding and object recognition algorithms developed within the scope of the project

Immunophenotype of Atypical Polypoid Adenomyoma of the Uterus: Diagnostic Value and Insight on Pathogenesis

Atypical polypoid adenomyoma (APA) is a rare uterine lesion constituted by atypical endometrioid glands, squamous morules, and myofibromatous stroma. We aimed to assess the immunophenotype of the 3 components of APA, with regard to its pathogenesis and its differential diagnosis. A systematic review was performed by searching electronic databases from their inception to January 2019 for immunohistochemical studies of APA. Thirteen studies with 145 APA cases were included. APA glands appeared analogous to atypical endometrial hyperplasia (endometrioid cytokeratins pattern, Ki67≤50%, common PTEN loss, and occasional mismatch repair deficiency); the prominent expression of hormone receptors and nuclear β-catenin suggest that APA may be a precursor of "copy number-low," CTNNB1-mutant endometrial cancers. Morules appeared as a peculiar type of hyperdifferentiation (low KI67, nuclear β-catenin+, CD10+, CDX2+, SATB2+, p63-, and p40-), analogous to morular metaplasia in other lesions and distinguishable immunohistochemically from both conventional squamous metaplasia and solid cancer growth. Stroma immunphenotype (low Ki67, α-smooth-muscle-actin+, h-caldesmon-, CD10-, or weak and patchy) suggested a derivation from a metaplasia of normal endometrial stroma. It was similar to that of nonatypical adenomyoma, and different from adenosarcoma (Ki67 increase and CD10+ in periglandular stroma) and myoinvasive endometrioid carcinoma (h-caldesmon+ in myometrium and periglandular fringe-like CD10 pattern)

Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

Graph theoretic methods for the analysis of structural relationships in biological macromolecules

Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and an efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Examples are provided of the use of graph theory to analyze proteins for which three-dimensional crystallographic or NMR structures are available, focusing on the use of the Bron-Kerbosch clique detection algorithm to identify common folding motifs and of the Ullmann subgraph isomorphism algorithm to identify patterns of amino acid residues. Our methods are also applicable to other types of biological macromolecule, such as carbohydrate and nucleic acid structures

The Signal Data Explorer: A high performance Grid based signal search tool for use in distributed diagnostic applications

We describe a high performance Grid based signal search tool for distributed diagnostic applications developed in conjunction with Rolls-Royce plc for civil aero engine condition monitoring applications. With the introduction of advanced monitoring technology into engineering systems, healthcare, etc., the associated diagnostic processes are increasingly required to handle and consider vast amounts of data. An exemplar of such a diagnosis process was developed during the DAME project, which built a proof of concept demonstrator to assist in the enhanced diagnosis and prognosis of aero-engine conditions. In particular it has shown the utility of an interactive viewing and high performance distributed search tool (the Signal Data Explorer) in the aero-engine diagnostic process. The viewing and search techniques are equally applicable to other domains. The Signal Data Explorer and search services have been demonstrated on the Worldwide Universities Network to search distributed databases of electrocardiograph data

A neural network for mining large volumes of time series data

Efficiently mining large volumes of time series data is amongst the most challenging problems that are fundamental in many fields such as industrial process monitoring, medical data analysis and business forecasting. This paper discusses a high-performance neural network for mining large time series data set and some practical issues on time series data mining. Examples of how this technology is used to search the engine data within a major UK eScience Grid project (DAME) for supporting the maintenance of Rolls-Royce aero-engine are presented