Some remarks on information languages, their analysis and comparison.

General remarks on information languages Use of the term "Information Language" (IL) Purposes of an information language-requirements for an information language A general model for the structure of the ensemble of subjects Specializations of the general model Indicative and informative descriptions Analytic vs. synthetic relations Paradigmatic vs. syntagmatic relations Synthetic relations, roles, and categories Comparative list of some schemes given in the literature Principles of construction and state of work Some feature evolving from the comparison of some schemes of role indicators Cumulative and comparative list Sources of relations, role indicators, and categories Reference

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Molecular cloning, structural analysis and expression of a zinc binding protein in cotton

The full-length zinc-binding protein (ZnBP) gene was cloned from a normalized cDNA library constructed from a cotton mutant (Xiangmian-18) during the gland-forming stage. The clone was sequenced and analysed. BLASTP analysis showed that the deduced amino acid sequence of ZnBP in Xiangmian-18 is similar to that in Arabidopsis thaliana (GenBank accession no. EFH46337.1) with an overall similarity of 77%. The cDNA insert comprises 654 base pairs (bp) and 217 amino acid residues. Its molecular weight is 24.6 kDa, and the theoretical pI is 9.33. The cotton ZnBP gene was cloned from the gDNA from Xiangmian-18 leaves. After sequencing the two fragments, a 1731 bp cotton ZnBP gene with three introns was identified. Using pET-28a(+) as a prokaryotic expression vector, the gene was expressed in Escherichia coli BL21(DE3). The conditions for achieving optimal ZnBP expression were 37°C, IPTG 1 mmol/L, 8 h and a shaker speed of 150 rpm. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis confirmed the correct expression of the protein. pCAMBIA2300-35S-OCS was used as a eukaryotic expression vector. The recombinant plasmid pCAMBIA2300-ZnBP was used to transform competent Agrobacterium GV3101 by the freeze-thaw method. Then, A. thaliana plants were transformed by the floral dipping method. Transformed plants were grown to maturity in a growth chamber. After screening on kanamycin-resistant half-strength Murashige and Skoog plates and polymerase chain reaction (PCR) analysis, two transgenic plant strains were obtained. Northern blot analysis showed that ZnBP expression was higher in homozygous plants than in wild-type plants. The differences between the phenotypes of homozygous and wild-type plants indicate that the ZnBP gene affects the growth and development of A. thaliana. The results of prokaryotic expression of ZnBP and overexpression of the ZnBP gene in A. thaliana improve our understanding of the function of this gene. Future studies should investigate the molecular mechanisms involved in gland morphogenesis in cotton.Key words: Gossypium hirsutum, pigment gland, zinc binding protein, prokaryotic expression, overexpression

Pharmacogenomics: Applications in Drug Discovery and Pharmacotherapy

Pharmacogenomics is the scientific study which explains individual variability of drug targets and to explore the genetic basis for such changes. With the completion of human genomic study, clear relation could now be established between the drug response in relation to a person’s genome. Pharmacogenomics, also known as personalized medicine, uses the person’s genome to determine the dose and dosage regimen, so that therapy could be optimized. As with the techniques like DNA microarray technologies person’s response to a therapy can be predicted and new therapies could be assigned. In the present review, the current technologies, and past significance has been discussed

Annotation-based storage and retrieval of models and simulation descriptions in computational biology

This work aimed at enhancing reuse of computational biology models by identifying and formalizing relevant meta-information. One type of meta-information investigated in this thesis is experiment-related meta-information attached to a model, which is necessary to accurately recreate simulations. The main results are: a detailed concept for model annotation, a proposed format for the encoding of simulation experiment setups, a storage solution for standardized model representations and the development of a retrieval concept.Die vorliegende Arbeit widmete sich der besseren Wiederverwendung biologischer Simulationsmodelle. Ziele waren die Identifikation und Formalisierung relevanter Modell-Meta-Informationen, sowie die Entwicklung geeigneter Modellspeicherungs- und Modellretrieval-Konzepte. Wichtigste Ergebnisse der Arbeit sind ein detailliertes Modellannotationskonzept, ein Formatvorschlag für standardisierte Kodierung von Simulationsexperimenten in XML, eine Speicherlösung für Modellrepräsentationen sowie ein Retrieval-Konzept

Research and Applications of the Processes of Performance Appraisal: A Bibliography of Recent Literature, 1981-1989

[Excerpt] There have been several recent reviews of different subtopics within the general performance appraisal literature. The reader of these reviews will find, however, that the accompanying citations may be of limited utility for one or more reasons. For example, the reference sections of these reviews are usually composed of citations which support a specific theory or practical approach to the evaluation of human performance. Consequently, the citation lists for these reviews are, as they must be, highly selective and do not include works that may have only a peripheral relationship to a given reviewer\u27s target concerns. Another problem is that the citations are out of date. That is, review articles frequently contain many citations that are fifteen or more years old. The generation of new studies and knowledge in this field occurs very rapidly. This creates a need for additional reference information solely devoted to identifying the wealth of new research, ideas, and writing that is changing the field

Upbeat and Quirky, With a Bit of a Build: Communicating Meaning and Meeting Information Needs in the Music Industry

Music is widely used to accompany moving images, in films, advertising, television programmes and computer games. The process of choosing and using a piece of pre-existing commercial music for this purpose is known as synchronisation. The addition of music to a piece of film enhances the final work with cultural meaning, and generates additional income for the rights holders. This research examines the information needs of professionals involved in the selection of music, including Users from the advertising and film communities and Owners from the recording and publishing industries. A tentative communications model is developed and proposed from musicological, semiotic and communications literature. Interviews, knowledge organisation systems, queries and observations are identified as rich potential sources of textual data relating to the communications process around satisfying the Users’ information needs. The content of these texts is analysed to identify key musical facets. Mood is found to be an important factor when searching for unknown musical items. Using a Discourse Analytic approach to the interview texts, four discourses, or interpretive repertoires, are identified. These repertoires carry conflicting meanings of music and are employed throughout the community, although relative emphases vary according to the viewpoint of the stakeholder. This is supported by an analysis of the written texts of both the Owners (music search engines) and the Users (written queries, or briefs). A comparison is drawn between the emphasis of the repertoires and the precision of the search engines. The repertoires are applied to the theoretical communications model, which is revised to reflect the findings of the analyses. This is used to make recommendations on how to improve the disintermediated communications process, by emphasising the repertoires employed by the Users rather than those of the Owners

A pilot investigation of Information Extraction in the semantic annotation of archaeological reports

The paper discusses a prototype investigation of semantic annotation, a form of metadata assigning conceptual entities to textual instances; in the case of archaeological grey literature. The use of Information Extraction (IE), a Natural Language Processing (NLP) technique, is central to the annotation process while the use of Knowledge Organization System (KOS) is explored for the association of semantic annotation with both ontological and terminological references. The annotation process follows a rule-based information extraction approach using the GATE NLP toolkit, together with the CIDOC CRM ontology, its CRM-EH archaeological extension and English Heritage thesauri and glossaries. Results are reported from an initial evaluation, which suggest that these information extraction techniques can be applied to archaeological grey literature reports. Further work is discussed drawing on the evaluation and consideration of the characteristics of the archaeology domain. Copyright © 2012 Inderscience Enterprises Ltd