A Genetic Programming Framework for Two Data Mining Tasks: Classification and Generalized Rule Induction

This paper proposes a genetic programming (GP) framework for two major data mining tasks, namely classification and generalized rule induction. The framework emphasizes the integration between a GP algorithm and relational database systems. In particular, the fitness of individuals is computed by submitting SQL queries to a (parallel) database server. Some advantages of this integration from a data mining viewpoint are scalability, data-privacy control and automatic parallelization

Conceptual information processing: A robust approach to KBS-DBMS integration

Integrating the respective functionality and architectural features of knowledge base and data base management systems is a topic of considerable interest. Several aspects of this topic and associated issues are addressed. The significance of integration and the problems associated with accomplishing that integration are discussed. The shortcomings of current approaches to integration and the need to fuse the capabilities of both knowledge base and data base management systems motivates the investigation of information processing paradigms. One such paradigm is concept based processing, i.e., processing based on concepts and conceptual relations. An approach to robust knowledge and data base system integration is discussed by addressing progress made in the development of an experimental model for conceptual information processing

Legal and Policy Framework for Promoting Equitable Access to Documentary Heritage

The National Mission for Manuscripts of India, in association with UNESCO, completed a research study to assist in the development of legal and policy framework and protocols for promoting equitable access to documentary heritage, relevant to India and other South Asian countries. This study report seeks to accurately identify and critically examine the legal and policy framework for promoting equitable access to our documentary heritage. The National Mission for Manuscripts is the most important institution in India creating bibliographic databases of manuscripts and engaged in the conservation and preservation of valuable manuscripts. This report engages with the legal and policy framework which envelops the lifecycle of the Mission’s work: the process of access to manuscripts, digitization of manuscripts and the creation of databases. By critically examining the legal rules in the practical context of the Mission’s work, the research team has put together the first such review of any such initiative in the protection of traditional knowledge in the country. The conclusions of the report are in the form of draft legal agreements and policy recommendations located in the discussion on various parts of the Mission’s work. While this report does not set out to be the final word on these significant policy initiatives, the report definitely makes significant progress in the policy debate and legal literature in this field. This report illustrates working patterns of the Mission within the legal and policy framework in the Country. This report will be a valuable sourcebook for understanding South Asian legal and policy framework for accessing documentary heritage collections. The draft legal agreements and policy recommendations, presented in this report, will also be valuable intervention tools for South Asian countries that share similar legal and policy framework within the sub-region

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism

Rational methods for the selection of diverse screening compounds.

Traditionally a pursuit of large pharmaceutical companies, high-throughput screening assays are becoming increasingly common within academic and government laboratories. This shift has been instrumental in enabling projects that have not been commercially viable, such as chemical probe discovery and screening against high-risk targets. Once an assay has been prepared and validated, it must be fed with screening compounds. Crafting a successful collection of small molecules for screening poses a significant challenge. An optimized collection will minimize false positives while maximizing hit rates of compounds that are amenable to lead generation and optimization. Without due consideration of the relevant protein targets and the downstream screening assays, compound filtering and selection can fail to explore the great extent of chemical diversity and eschew valuable novelty. Herein, we discuss the different factors to be considered and methods that may be employed when assembling a structurally diverse compound collection for screening. Rational methods for selecting diverse chemical libraries are essential for their effective use in high-throughput screens.We are grateful for financial support from the MRC, Wellcome Trust, CRUK, EPSRC, BBSRC and Newman Trust.This is the author accepted manuscript. The final version is available from American Chemical Society via http://dx.doi.org/10.1021/cb100420

Toward integrated conservation of North America's crop wild relatives

North America harbors a rich native flora of crop wild relatives—the progenitors and closely related species of domesticated plants—as well as a range of culturally significant wild utilized plants. Despite their current and potential future value, they are rarely prioritized for conservation efforts; thus many species are threatened in their natural habitats, and most are underrepresented in plant genebanks and botanical gardens. Further coordination of efforts among land management, botanical, and agricultural science organizations will improve conservation and general public awareness with regard to these species. We present examples of productive collaborations focused on wild cranberries (Vaccinium macrocarpon and Vaccinium oxycoccos) and chile peppers (Capsicum annuum var. glabriusculum). We then discuss five shared priorities for further action: (1) understand and document North America's crop wild relatives and wild utilized plants, (2) protect threatened species in their natural habitats, (3) collect and conserve ex situ the diversity of prioritized species, (4) make this diversity accessible and attractive for plant breeding, research, and education, and (5) raise public awareness of their value and the threats to their persistence

Recent trends in molecular diagnostics of yeast infections : from PCR to NGS

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside

Applications and Challenges of Real-time Mobile DNA Analysis

The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA sequencing outside of laboratory, leading to faster and more accessible DNA-based diagnostics. However, portable DNA sequencing and analysis are challenging for mobile systems, owing to high data throughputs and computationally intensive processing performed in environments with unreliable connectivity and power. In this paper, we provide an analysis of the challenges that mobile systems and mobile computing must address to maximize the potential of portable DNA sequencing, and in situ DNA analysis. We explain the DNA sequencing process and highlight the main differences between traditional and portable DNA sequencing in the context of the actual and envisioned applications. We look at the identified challenges from the perspective of both algorithms and systems design, showing the need for careful co-design

Audiovisual research collections and their preservation

The basic problem of primary audio and video research materials is clearly shown by the survey: A great and important part of the entire heritage is still outside archival custody in the narrower sense, scattered over many institutions in fairy small collections, and even in private hands. reservation following generally accepted standards can only be carried out effectively if collections represent critical mass. Specialised audiovisual archives will solve their problems, as they will sooner or later succeed in getting appropriate funding to achieve their aims. A very encouraging example is the case of the Netherlands. The larger audiovisual research archives will also manage, more or less autonomously, the transfer of contents in time. For a considerable part of the research collections, however, the concept of cooperative models and competence centres is the only viable model to successfullly safeguard their holdings. Their organisation and funding is a considerable challenge for the scientific community. TAPE has significantly raised awareness of the fact that, unless action is swiftly taken, the loss of audiovisual materials is inevitable. TAPE’s international and regional workshops were generally overbooked. While TAPE was already underway, several other projects for the promotion of archives have received grants from organisations other than the European Commission, inter alia support for the St. Petersburg Phonogram Archive, and the Folklore Archive in Tirana, obviously as a result of a better understanding of the need for audiovisual preservation. When the TAPE project started its partners assumed that cooperative projects would fail because of the notorious distrust of researchers, specifically in the post-communist countries. One of the most encouraging surprises was to learn that, at least in the most recent survey, it became apparent that this social obstacle is fading out. TAPE may have contributed to this important development