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The article presents information on the biography of a well-known scientist, clinician and teacher, a brilliant dentist, Honored Doctor of the Russian Federation, Doctor of Medical Sciences, Professor Sergei Ulitovsky. His contribution to the development of the preventive direction of domestic dentistry, the engineering of basic methods for assessing and dynamically monitoring the dental health of the population depending on the dental and hygienic status of a person, as well as the development of many classifications of means and objects of individual oral hygiene and individual hygienic prevention programs for patients of various ages.

Summary: Artificial intelligence (AI)-driven laboratory automation-combining robotic labware and autonomous software agents-is a powerful trend in modern biology. We developed Genesis-DB, a database system designed to support AI-driven autonomous laboratories by providing software agents access to large quantities of structured domain information. In addition, we present a new ontology for modeling data and metadata from autonomously performed yeast microchemostat cultivations in the framework of the Genesis robot scientist system. We show an example of how Genesis-DB enables the research life cycle by modeling yeast gene regulation, guiding future hypotheses generation and design of experiments. Genesis-DB supports AI-driven discovery through automated reasoning and its design is portable, generic, and easily extensible to other AI-driven molecular biology laboratory data and beyond., Availability and Implementation: Genesis-DB code and installation instructions are available at the GitHub repository https://github.com/TW-Genesis/genesis-database-system.git. The database use case demo code and data are also available through GitHub (https://github.com/TW-Genesis/genesis-database-demo.git). The ontology can be downloaded here: https://github.com/TW-Genesis/genesis-ontology/releases/download/v0.0.23/genesis.owl. The ontology term descriptions (including mappings to existing ontologies) and maintenance standard operating procedures can be found at: https://github.com/TW-Genesis/genesis-ontology., Competing Interests: None declared., (© The Author(s) 2023. Published by Oxford University Press.)

The study consists in studying the state of oral hygiene and periodontal tissues in elderly patients during dynamic follow-up for 12 months. Patients aged 61-74 years with inflammatory periodontal diseases and partial absence of natural teeth in both jaws were under observation. The study showed a significant improvement in oral hygiene and the condition of periodontal tissues in the elderly when using therapeutic and prophylactic products of domestic production for individual intraoral hygiene and professional oral hygiene at least four times a year.

Temporomandibular arthralgia is difficult to treat, painful and often relapses. 48 patients (19 men and 29 women) aged 61-72 years, suffering from the syndrome of pain dysfunction of the temporomandibular joint, were under observation. In 1st (control) group of patients (18 people), NSAIDs indomethacin in tablet form of 25 mg 3 times a day were used for 9 days. In patients of the 2nd (main) group (30 people), the method of invasive carboxytherapy was used, consisting in subcutaneous injection of carbon dioxide with a volume of 3 ml of 5 procedures every other day. On the 3rd, 9th and 15th days of follow-up, invasive carboxytherapy was more effective than the use of a nonsteroidal anti-inflammatory agent by 8.9; 36,5 and 37%, respectively. The high efficiency of the method of invasive carboxytherapy for the elimination of pain symptoms in pain dysfunction was shown, which was 22,86% on day 3; 64,29% on day 9 and 68,16% on day 15 of observation. The method of invasive carboxytherapy can be used in the complex treatment of patients with pain dysfunction of the temporomandibular joint.

The concept of a multidisciplinary approach to the treatment of osteochondrosis in elderly and senile patients by specialists of various profiles using medicinal and non-medicinal methods is especially relevant today, therefore, it is necessary to develop and put into practice various options for the combined use of physical rehabilitation means at different stages of rehabilitation treatment of elderly and senile patients with osteochondrosis of the cervical and thoracic spine. The dynamics of clinical manifestations of osteochondrosis after rehabilitation treatment relative to the age of patients in groups showed that the effectiveness of the technique is much higher in elderly patients, in contrast to senile patients and centenarians. The study revealed no significant complications and side effects when using this technique, which allows us to recommend it as a means of secondary prevention of diseases of the cervical and thoracic osteochondrosis, especially in the presence of contraindications to the use of non-steroidal anti-inflammatory drugs and glucocorticoids. The technique can be recommended for use in fitness clubs, athletic halls and medical and physical education dispensaries.

The study consists of clinical and radiological parallels between the severity of functional pathology of the temporomandibular joint, bone density of the joint elements and the effect of bioregulatory therapy on it at different ages. Male patients (35-74 years old) with functional pathology of the temporomandibular joint were under observation. The study showed a significant decrease in bone density and correlation of this index with the severity of the disease course in all patients with temporomandibular joint dysfunction compared with the control group of healthy subjects. After a course of bioregulatory therapy the bone density and functional pathology index of the temporomandibular joint indicate a change from the severe course to a form of moderate severity in the group of elderly patients. The correlation correlation between the severity of the course of functional pathology and the decrease in the density of bone structures of the temporomandibular joint has been revealed, increasing with age. Use of bioregulatory therapy in complex treatment of functional pathology has favorable influence on a course of functional pathology of a temporomandibular joint at elderly patients.

Almost all machine learning (ML) is based on representing examples using intrinsic features. When there are multiple related ML problems (tasks), it is possible to transform these features into extrinsic features by first training ML models on other tasks and letting them each make predictions for each example of the new task, yielding a novel representation. We call this transformational ML (TML). TML is very closely related to, and synergistic with, transfer learning, multitask learning, and stacking. TML is applicable to improving any nonlinear ML method. We tested TML using the most important classes of nonlinear ML: random forests, gradient boosting machines, support vector machines, k-nearest neighbors, and neural networks. To ensure the generality and robustness of the evaluation, we utilized thousands of ML problems from three scientific domains: drug design, predicting gene expression, and ML algorithm selection. We found that TML significantly improved the predictive performance of all the ML methods in all the domains (4 to 50% average improvements) and that TML features generally outperformed intrinsic features. Use of TML also enhances scientific understanding through explainable ML. In drug design, we found that TML provided insight into drug target specificity, the relationships between drugs, and the relationships between target proteins. TML leads to an ecosystem-based approach to ML, where new tasks, examples, predictions, and so on synergistically interact to improve performance. To contribute to this ecosystem, all our data, code, and our ∼50,000 ML models have been fully annotated with metadata, linked, and openly published using Findability, Accessibility, Interoperability, and Reusability principles (∼100 Gbytes)., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Traumatic damages to the oral mucosa are the main predisposing factor for the development of the oncostomatological pathology among the old people. The aim of the investigation was to study the occurrence of traumatic lesions of the oral mucosa among people of old age groups and estimate the effectiveness of their treatment using modern domestic remedies. 967 people (569 males and 398 females) from 19 to 82 years old were examined to determine the occurrence of traumatic oral mucosal pathology. Value of effectiveness while treatment of 83 elderly patients using modern domestic agents «ASEPTA® adhesive balm for gums» and «ASEPTA® gel for gums with propolis» was assessed in comparison with vinylin for internal use. It is found that 9,41 and 9,52% of cases are traumatic lesions of the oral mucosa respectively among elderly and senile people respectively. The cause of them in 96,7-97,1% cases are traumatic factors while using removable dental prostheses; the untimely treatment of these factors in 7,9% leads to the formation of prosthetic fibroms. A comparative evaluation of the treatment effectiveness of prosthetic-etiology-traumatic lesions of the oral mucosa showed the advisability of using modern domestic agents like «ASEPTA® adhesive balm for gums» during the first 2 days from the start of therapy and then «ASEPTA® gel for gums with propolis» until complete healing of traumatic injuries, compared to the using of vinylin for internal use for the same purposes, which efficiency remains high. Timely detection and treatment of the traumatic defeats of oral mucosa are an important factors of prevention of oncostomatological pathologies among elderly and senile persons.

One of the most challenging tasks in modern science is the development of systems biology models: Existing models are often very complex but generally have low predictive performance. The construction of high-fidelity models will require hundreds/thousands of cycles of model improvement, yet few current systems biology research studies complete even a single cycle. We combined multiple software tools with integrated laboratory robotics to execute three cycles of model improvement of the prototypical eukaryotic cellular transformation, the yeast ( Saccharomyces cerevisiae ) diauxic shift. In the first cycle, a model outperforming the best previous diauxic shift model was developed using bioinformatic and systems biology tools. In the second cycle, the model was further improved using automatically planned experiments. In the third cycle, hypothesis-led experiments improved the model to a greater extent than achieved using high-throughput experiments. All of the experiments were formalized and communicated to a cloud laboratory automation system (Eve) for automatic execution, and the results stored on the semantic web for reuse. The final model adds a substantial amount of knowledge about the yeast diauxic shift: 92 genes (+45%), and 1,048 interactions (+147%). This knowledge is also relevant to understanding cancer, the immune system, and aging. We conclude that systems biology software tools can be combined and integrated with laboratory robots in closed-loop cycles., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

The aim of the study was to estimate dental health of servicemen of young and middle age using PMA index, Schiller-Pisarev assay, iodic number of Svrakov, OHI-S. Hundred and six servicemen were enrolled in the study: control group (n=35) with no orthodontic treatment and groups 2 (n=34) and 3 (n=37) group undergoing orthodontic treatment with bracket-systems. All patients had professional oral hygiene and received standard oral care recommendations. Group 3 participants additionally used dental foam (Splat, Russia) after meal. All patients were examined at baseline and 12 months later. In the presence of orthodontic appliances standard oral care products were not enough to maintain proper oral health. Dental foam improved both periodontal condition and OHI-S.

Oral mucosa reaction of prosthetic bed to the removable acrylic dentures was evaluated in 43 patients (12 male and 31 female) aged 56-69 years with partial and full teeth loss in one or both jaws. Patients of the first (control) group (17 patients) were not using additional tools improving fixation of the removable dentures during adaptation period, while patients of the second (main) group (26 patients) used Corega cream for dentures fixation for 30 days follow-up. Oral mucosa assessment was carried out on 3-4 and 28-30 day of dentures use by 3 end points: pain syndrome, moisture level, inflammation of a prosthetic bed. The results proved Corega cream to improve prosthetic bed mucosa condition reducing inflammatory response to polymeric materials of removable dentures basis.

The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems for Molecular Biology) conference in Boston in 2014. The selected papers span a wide range of topics including the automated re-use and update of ontologies, quality assessment of ontological resources, and the systematic description of phenotype variation, driven by manual, semi- and fully automatic means.

There is an urgent need to make drug discovery cheaper and faster. This will enable the development of treatments for diseases currently neglected for economic reasons, such as tropical and orphan diseases, and generally increase the supply of new drugs. Here, we report the Robot Scientist 'Eve' designed to make drug discovery more economical. A Robot Scientist is a laboratory automation system that uses artificial intelligence (AI) techniques to discover scientific knowledge through cycles of experimentation. Eve integrates and automates library-screening, hit-confirmation, and lead generation through cycles of quantitative structure activity relationship learning and testing. Using econometric modelling we demonstrate that the use of AI to select compounds economically outperforms standard drug screening. For further efficiency Eve uses a standardized form of assay to compute Boolean functions of compound properties. These assays can be quickly and cheaply engineered using synthetic biology, enabling more targets to be assayed for a given budget. Eve has repositioned several drugs against specific targets in parasites that cause tropical diseases. One validated discovery is that the anti-cancer compound TNP-470 is a potent inhibitor of dihydrofolate reductase from the malaria-causing parasite Plasmodium vivax.

Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2)protocols., Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility., Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed., Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.

The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.

Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes.

Gerontostomatology is one of the most important interdisciplinary sections of the medicine, studying mechanisms of aging of the chewing device of a person, and also carrying-out search of decisions in treatment of stomatologic diseases in persons of the senior age groups, at the same time increasing quality of their life. The article covers actual problems of modern gerontostomatology in Russia.

Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data.

The results of dynamic supervision over application a peptide bioregulator of "Sigumir" in complex treatment of 62 patients of the senior age groups with various diseases of a temporomandibular joint are presented. It is shown that application of a complex of treatment-and-prophylactic actions, including rational tooth prosthetics, functional and pharmacotherapy (including accompanying diseases), and also use a peptide bioregulator of cartilaginous and bone tissues "Sigumir" in complex therapy of patients with diseases of a temporomandibular joint of a various etiology, enables to stop in short-terms a painful syndrome in such patients, to increase amplitude of opening of a mouth, to improve chewing function, to reduce terms of treatment and to provide preventive maintenance of relapses of TMJ's pathology during all period of supervision.

The reuse of scientific knowledge obtained from one investigation in another investigation is basic to the advance of science. Scientific investigations should therefore be recorded in ways that promote the reuse of the knowledge they generate. The use of logical formalisms to describe scientific knowledge has potential advantages in facilitating such reuse. Here, we propose a formal framework for using logical formalisms to promote reuse. We demonstrate the utility of this framework by using it in a worked example from biology: demonstrating cycles of investigation formalization [F] and reuse [R] to generate new knowledge. We first used logic to formally describe a Robot scientist investigation into yeast (Saccharomyces cerevisiae) functional genomics [f(1)]. With Robot scientists, unlike human scientists, the production of comprehensive metadata about their investigations is a natural by-product of the way they work. We then demonstrated how this formalism enabled the reuse of the research in investigating yeast phenotypes [r(1) = R(f(1))]. This investigation found that the removal of non-essential enzymes generally resulted in enhanced growth. The phenotype investigation was then formally described using the same logical formalism as the functional genomics investigation [f(2) = F(r(1))]. We then demonstrated how this formalism enabled the reuse of the phenotype investigation to investigate yeast systems-biology modelling [r(2) = R(f(2))]. This investigation found that yeast flux-balance analysis models fail to predict the observed changes in growth. Finally, the systems biology investigation was formalized for reuse in future investigations [f(3) = F(r(2))]. These cycles of reuse are a model for the general reuse of scientific knowledge.

Background: Hypotheses are now being automatically produced on an industrial scale by computers in biology, e.g. the annotation of a genome is essentially a large set of hypotheses generated by sequence similarity programs; and robot scientists enable the full automation of a scientific investigation, including generation and testing of research hypotheses., Results: This paper proposes a logically defined way for recording automatically generated hypotheses in machine amenable way. The proposed formalism allows the description of complete hypotheses sets as specified input and output for scientific investigations. The formalism supports the decomposition of research hypotheses into more specialised hypotheses if that is required by an application. Hypotheses are represented in an operational way - it is possible to design an experiment to test them. The explicit formal description of research hypotheses promotes the explicit formal description of the results and conclusions of an investigation. The paper also proposes a framework for automated hypotheses generation. We demonstrate how the key components of the proposed framework are implemented in the Robot Scientist "Adam"., Conclusions: A formal representation of automatically generated research hypotheses can help to improve the way humans produce, record, and validate research hypotheses., Availability: http://www.aber.ac.uk/en/cs/research/cb/projects/robotscientist/results/

Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks.

The microbiocenosis of periodontal recesses was studied and an assessment of the innate immunity mechanisms, as well as profiles of inflammatory cytokines were carried out in 114 people of middle, elderly and senile age with chronic generalized periodontitis (CGP). It was found that periodontal recesses mikrobiocenosis of patients with CGP of various ages was mainly presented by conditionally pathogenic bacterial and fungal microflora. There were identified the inefficient mechanisms of immune inflammation in case of conditionally pathogenic microflora, the reduction of neutrophils functional properties, and the increasing part of destructed phagocytazing neutrophils in patients of elderly and senile age. The immunosuppression in patients of elderly and senile age appears in insufficient production of IL-1beta, IL-8, resulting in reduced activity of phagocytosis mechanisms and lymphoid cells functional activity. Thus, the differences in etiopatogenetic microflora, immune homeostasis status in patients with CGP in middle, elderly and senile age, complexity in the application of antibacterial drugs require the development of new criteria for the selection of antibacterial drugs.

A comprehensive treatment with Likopid of chronic generalized parodontitis in 114 elderly and senile patients was carried out. The state of mechanisms of innate immunity (phagocytosis mechanisms) as well as the profile of proinflammatory cytokines was assessed. The effect of antibiotic-resistant strains of prior microflora on the combined therapy of patients of different age with chronic generalized parodontitis was studied. It is established that due to presence of various types of opportunistic pathogens in patients of different age with parodontitis using the prophylactic antibiotics for the empirical (to determine the antibiotic resistance), a combination of Metronidazole and Lincomycin with the mandatory appointment of immunomodulatory drugs for activation of monocyte-phagocytic system of the patient elderly is most advisable. Use of the drug , "Likopid" significantly improves the results of treatment the elderly and old patients with chronic generalized parodonthitis.

Background: Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval., Results: The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI., Conclusion: We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components., Availability: OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl.

The paper presents an ontology for the description of Drug Discovery Investigation (DDI).This has been developed through the use of a Robot Scientist "Eve", and in consultation with industry. DDI aims to define the principle entities and the relations in the research and development phase of the drug discovery pipeline. DDI is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. This enables DDI to be integrated with such related ontologies as the Vaccine Ontology, the Advancing Clinico-Genomic Trials on Cancer Master Ontology, etc. DDI is available at http://purl.org/ddi/wikipedia or http://purl.org/ddi/home.

We review the main components of autonomous scientific discovery, and how they lead to the concept of a Robot Scientist. This is a system which uses techniques from artificial intelligence to automate all aspects of the scientific discovery process: it generates hypotheses from a computer model of the domain, designs experiments to test these hypotheses, runs the physical experiments using robotic systems, analyses and interprets the resulting data, and repeats the cycle. We describe our two prototype Robot Scientists: Adam and Eve. Adam has recently proven the potential of such systems by identifying twelve genes responsible for catalysing specific reactions in the metabolic pathways of the yeast Saccharomyces cerevisiae. This work has been formally recorded in great detail using logic. We argue that the reporting of science needs to become fully formalised and that Robot Scientists can help achieve this. This will make scientific information more reproducible and reusable, and promote the integration of computers in scientific reasoning. We believe the greater automation of both the physical and intellectual aspects of scientific investigations to be essential to the future of science. Greater automation improves the accuracy and reliability of experiments, increases the pace of discovery and, in common with conventional laboratory automation, removes tedious and repetitive tasks from the human scientist.

This article presents the data of epidemiological inspection of 1000 persons of average, elderly and senile age. Prevalence and intensity of a current of the basic stomatologic diseases (caries, pathology of a paradont and a mucous membrane of an oral cavity, a temporal-mandibular joint and chewing muscles) have been studied. Indicators of need of people of various age groups in tooth prosthetics are established. Level of rendering the stomatologic help is defined to be insufficient in groups of people of elderly and senile age. Recommendations aimed at improvement of stomatologic help to people of elderly and senile age are made.

The basis of science is the hypothetico-deductive method and the recording of experiments in sufficient detail to enable reproducibility. We report the development of Robot Scientist "Adam," which advances the automation of both. Adam has autonomously generated functional genomics hypotheses about the yeast Saccharomyces cerevisiae and experimentally tested these hypotheses by using laboratory automation. We have confirmed Adam's conclusions through manual experiments. To describe Adam's research, we have developed an ontology and logical language. The resulting formalization involves over 10,000 different research units in a nested treelike structure, 10 levels deep, that relates the 6.6 million biomass measurements to their logical description. This formalization describes how a machine contributed to scientific knowledge.

Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being made worse by the increasing complexity of high-throughput/automated methods. There is therefore a growing need to represent experiment protocols in an efficient and unambiguous way., Results: We have developed the Experiment ACTions (EXACT) ontology as the basis of a method of representing biological laboratory protocols. We provide example protocols that have been formalized using EXACT, and demonstrate the advantages and opportunities created by using this formalization. We argue that the use of EXACT will result in the publication of protocols with increased clarity and usefulness to the scientific community., Availability: The ontology, examples and code can be downloaded from http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/.

Honeybee venom hyaluronidase (Api m 2) is a major glycoprotein allergen. Previous studies have indicated that recombinant Api m 2 expressed in insect cells has enzyme activity and IgE binding comparable with that of native Api m 2. In contrast, Api m 2 expressed in Escherichia coli does not. In this study, we characterized the carbohydrate side chains of Api m 2 expressed in insect cells, and compared our data with the established carbohydrate structure of native Api m 2. We assessed both the monosaccharide and the oligosaccharide content of recombinant Api m 2 using fluorophore-assisted carbohydrate electrophoresis and HPLC. To identify the amino acid residues at which glycosylation occurs, we digested recombinant Api m 2 with endoproteinase Glu-C and identified the fragments that contained carbohydrate by specific staining. Recombinant Api m 2 expressed in insect cells contains N-acetylglucosamine, mannose, and fucose, as well as trace amounts of glucose and galactose, and the oligosaccharide analysis is consistent with heterogeneous oligosaccharide chains consisting of two to seven monosaccharides. No sialic acid or N-acetylgalactosamine were detected. These results are similar to published data for native Api m 2, although some monosaccharide components appear to be absent in the recombinant protein. Analysis of proteolytic digests indicates that of the four candidate N-glycosylation sites, carbohydrate chains are attached at asparagines 115 and 263. Recombinant Api m 2 expressed in insect cells has enzymic activity and IgE binding comparable with the native protein, and its carbohydrate composition is very similar.

The formal description of experiments for efficient analysis, annotation and sharing of results is a fundamental part of the practice of science. Ontologies are required to achieve this objective. A few subject-specific ontologies of experiments currently exist. However, despite the unity of scientific experimentation, no general ontology of experiments exists. We propose the ontology EXPO to meet this need. EXPO links the SUMO (the Suggested Upper Merged Ontology) with subject-specific ontologies of experiments by formalizing the generic concepts of experimental design, methodology and results representation. EXPO is expressed in the W3C standard ontology language OWL-DL. We demonstrate the utility of EXPO and its ability to describe different experimental domains, by applying it to two experiments: one in high-energy physics and the other in phylogenetics. The use of EXPO made the goals and structure of these experiments more explicit, revealed ambiguities, and highlighted an unexpected similarity. We conclude that, EXPO is of general value in describing experiments and a step towards the formalization of science.

Motivation: A Robot Scientist is a physically implemented robotic system that can automatically carry out cycles of scientific experimentation. We are commissioning a new Robot Scientist designed to investigate gene function in S. cerevisiae. This Robot Scientist will be capable of initiating >1,000 experiments, and making >200,000 observations a day. Robot Scientists provide a unique test bed for the development of methodologies for the curation and annotation of scientific experiments: because the experiments are conceived and executed automatically by computer, it is possible to completely capture and digitally curate all aspects of the scientific process. This new ability brings with it significant technical challenges. To meet these we apply an ontology driven approach to the representation of all the Robot Scientist's data and metadata., Results: We demonstrate the utility of developing an ontology for our new Robot Scientist. This ontology is based on a general ontology of experiments. The ontology aids the curation and annotating of the experimental data and metadata, and the equipment metadata, and supports the design of database systems to hold the data and metadata., Availability: EXPO in XML and OWL formats is at: http://sourceforge.net/projects/expo/. All materials about the Robot Scientist project are available at: http://www.aber.ac.uk/compsci/Research/bio/robotsci/.

The failure of many bio-ontologies to follow international standards for ontology design and description is hampering their application and threatens to restrict their future use.

Background: Mite allergen vaccines are important diagnostic and immunotherapeutic reagents. Previous studies on mite allergen stability under different storage conditions have yielded contradictory results., Objective: We sought to compare, over a 12-month period, the stability of mite allergens reconstituted in 50% glycerol and stored at different temperatures and to examine the role of protease inhibitors in enhancing allergen stability., Methods: Lyophilized allergen extracts were reconstituted in 50% glycerol, with and without protease inhibitors, and stored at -70 degrees C, -20 degrees C, 4 degrees C, or 37 degrees C for 12 months. At 6 and 12 months, the extracts were compared with freshly dissolved extracts by competition ELISA with pooled allergic sera, 2-site ELISA with mite-specific mAbs, and immunoblot analyses., Results: The overall potencies of the stored extracts measured by competition ELISA were stable at -20 degrees C and 4 degrees C. As determined by means of the immunoblot and 2-site ELISA, Der f 1 levels decreased at 4 degrees C. Levels of Der f 2, Der p 1, and Der p 2 decreased in at least one of the allergen-specific assays. Storage at 37 degrees C led to overall loss of potency and allergen content, whereas storage at -70 degrees C was associated with a moderate loss of potency that increased with multiple freeze-thaw cycles. Protease inhibitors had no effect on allergen stability., Conclusion: Although overall potency of the extracts, as measured by competition ELISA, was preserved at -20 degrees C and 4 degrees C, allergen-specific assays indicated loss of allergens. These findings suggest that the competition ELISA is insensitive to decreases in the concentrations of individual allergens.

Background: Hyaluronidase (Hya) is one of several allergens in honeybee venom. Its cDNA sequence was recently described., Objective: We sought to express recombinant Hya in prokaryotic and eukaryotic systems and to compare it with natural (n)Hya for biologic activity., Methods: In Escherichia coli Hya was produced as inclusion body 6 x His-fusion protein. In baculovirus-infected insect cells expression was obtained by cotransfection of linearized Bac-N-Blue DNA and pMelBac transfer vector into Spodoptera frugiperda cells., Results: Enzymatic activity of Hya from the baculovirus system was equal to nHya, and that of the enzyme expressed in E. coli was only 20% to 30% of nHya. In vitro IgE binding was similar in nHya and the enzyme from baculovirus but markedly lower in Hya expressed in E. coli., Conclusions: Biologic activity of Hya expressed in baculovirus-infected insect cells was comparable with that of the natural enzyme, indicating a native-like conformation of the recombinant protein. In contrast, the enzyme expressed in E. coli as an inclusion-body protein and reconstituted in vitro reached only 20% to 30% of the activity of nHya.

Immunization of mice with a pure preparation of the ganglioside adsorbed on Salmonella typhimurium and hybridization of splenocytes with myeloma P3-X63-Ag 8.653 have resulted in hybridomas producing monoclonal antibodies against ganglioside Fuc GM1, a marker of human small cell lung carcinoma. Characterization of four hybridomal clones and data on the antigenic specificity of the monoclonal antibodies are given. All four monoclonal antibodies reacted only with Fuc GM1 in an enzyme-linked immunosorbent assay. In radioimmunodetection of the antigen on thin-layer plates, two of the four monoclonal antibodies gave cross-reactions with Fuc GD1b. The obtained monoclonal antibodies have revealed the presence of Fuc GM1 in all seven cases of small cell lung carcinoma we have studied and the absence of Fuc GM1 in the normal human lung tissue and in lung adenocarcinomas.