Towards a metaphorical biology

The metaphorical nature of biological language is examined and the use of metaphors for providing the linguistic context in which similarities and differences are made is described. Certain pervasive metaphors which are characterised by systemic properties are noted, and in order to provide some focus to the study, systemic metaphors associated with machine, text and organism are discussed. Other systemic metaphors such as society and circuit are also reported. Some details concerning interrelations between automaton and organism are presented in the light of the previous discussion.An approach towards the analysis of biosystem metaphors is outlined which relates part-whole, organisational level and systemic metaphors in a single model. Examples are provided throughout the discussion and mainly come from computing. The potential for metaphorical transfers between these domains is considered.     

Walk-weighted subsequence kernels for protein-protein interaction extraction

Background  

The construction of interaction networks between proteins is central to understanding the underlying biological processes. However, since many useful relations are excluded in databases and remain hidden in raw text, a study on automatic interaction extraction from text is important in bioinformatics field.     

Salmon fibrin glue in rats: Antibody studies

Fibrin sealants and topical thrombin preparations are often used for haemostatic and sealing applications in clinical practice. Some of these preparations contain coagulation factors from bovine sources. To minimize the risk of infection and immunogenicity connected with mammalian blood products, proteins derived from the plasma of farmed Atlantic salmon have been considered as an alternative to these mammalian sources. The purpose of this study is to characterize the immunogenicity of salmon fibrin glue in an animal model focusing on crossreactivity of IgG antibodies to host endogenous counterparts. After two immunizations with salmon fibrin glue, rats developed antibodies of IgG and IgM type to both fibrin glue components. Weak crossreactivity to endogenous fibrinogen and thrombin was seen in a subset of rats after the second application of salmon proteins. Coagulation tests showed that salmon fibrin application has no effect on coagulation profiles in mammalian hosts, consistent with previous reports that found no evidence of significant crossreactivity with host proteins. These studies support the potential suitability of salmon fibrin glue for the development of preparations with clinical impact. Before human use can be considered, however, additional data about safety of this preparation in other animal models, including large animal studies, should be obtained.     

Ethnobotany of coniferous trees in Thompson and Lillooet interior salish of British Columbia

All 17 species of conifers (and one taxad) occurring within the traditional territories of the Thompson and Lillooet Interior Salish of British Columbia are known to these peoples and named by them at a restricted level. Of moderate to high cultural significance, most were used many ways in traditional life. Uses included: food—seeds, inner bark, sugar, pitch (for chewing), and boughs (for making beverages); technology—wood for construction and fuel, bark for construction, fibrous materials for weaving, resins for glue and caulking, and, of prime significance, boughs as scents and cleansing agents; and medicine-primarily as tonics, and as remedies for respiratory ailments, stomach and digestive disorders, eye problems, and dermatological complaints. The use of the boughs as scents and agents for cleanliness also made conifers very important in religious and spiritual rituals. Some were also featured in mythology. Thompson and Lillooet peoples continue to use conifers, but to a more limited extent than in the past.     

Towards a semantic lexicon for biological language processing

This paper explores the use of the resources in the National Library of Medicine's Unified Medical Language System (UMLS) for the construction of a lexicon useful for processing texts in the field of molecular biology. A lexicon is constructed from overlapping terms in the UMLS SPECIALIST lexicon and the UMLS Metathesaurus to obtain both morphosyntactic and semantic information for terms, and the coverage of a domain corpus is assessed. Over 77% of tokens in the domain corpus are found in the constructed lexicon, validating the lexicon's coverage of the most frequent terms in the domain and indicating that the constructed lexicon is potentially an important resource for biological text processing.     

Discovery of the canonical Calvin–Benson cycle

It has been 65 years since the Calvin–Benson cycle was first formulated. In this paper, the development of the concepts that are critical to the cycle is traced and the contributions of Calvin, Benson, and Bassham are discussed. Some simplified views often found in text books such as ascending paper chromatography and the use of the “lollipop” for short labeling are discussed and further details given. Key discoveries that underpinned elucidation of the cycle such as the importance of sedoheptulose phosphate and ribulose 1,5-bisphosphate are described. The interchange of ideas between other researchers working on what is now called the pentose phosphate pathway and the development of the ideas of Calvin and Benson are explored while the gluconeogenic aspects of the cycle are emphasized. Concerns raised about anomalies of label distribution in glucose are considered. Other carbon metabolism pathways associated with the Calvin–Benson cycle are also described. Finally, there is a section describing the rift between Calvin and Benson.

     

Micronucleus formation and DNA damage in buccal epithelial cells of Indian street boys addicted to gasp 'Golden glue'

Genotoxicity of glue sniffing/huffing and tobacco use has been examined in 302 street boys (median age 13 years) and 50 age-matched control school boys who were neither tobacco nor glue users. All the street boys were tobacco users. In addition, 155 were addicted to gasp an industrial adhesive popularly known as 'Golden glue'. Micronucleus (MN) frequency was determined as a measure of chromosomal breakage in exfoliated buccal epithelial cells (BECs) and DNA double strand breaks were quantitatively assessed by counting γ-H2AX foci using immunofluorescence microscopy. Micronucleated cell frequencies (MCFs) in BEC of glue non-addicted (only tobacco) and addicted (tobacco plus glue) street boys were 1.87 ± 1.06‰ and 4.04 ± 2.55‰ respectively, which were significantly higher than that of control (0.32 ± 0.11‰, p<0.0001). Similarly, the numbers γ-H2AX foci in nuclei of BEC were 2.3- and 5.2-times more than control in glue non-addicted and addicted street boys respectively (p<0.0001). Spearman's rank correlation revealed a strong positive association between years of glue addiction with MCFs and γ-H2AX foci numbers, and the association between glue addiction and chromosomal and DNA damage remained positive and significant after controlling income, spending on addiction and loss of appetite as potential confounders in multivariate logistic regression analysis. Thus, addiction to tobacco among the street children in India is associated with chromosomal and DNA damage in BECs and the severity of these changes is significantly increased by the habit of sniffing/huffing of industrial glue.     

Improving subcellular localization prediction using text classification and the gene ontology

MOTIVATION: Each protein performs its functions within some specific locations in a cell. This subcellular location is important for understanding protein function and for facilitating its purification. There are now many computational techniques for predicting location based on sequence analysis and database information from homologs. A few recent techniques use text from biological abstracts: our goal is to improve the prediction accuracy of such text-based techniques. We identify three techniques for improving text-based prediction: a rule for ambiguous abstract removal, a mechanism for using synonyms from the Gene Ontology (GO) and a mechanism for using the GO hierarchy to generalize terms. We show that these three techniques can significantly improve the accuracy of protein subcellular location predictors that use text extracted from PubMed abstracts whose references are recorded in Swiss-Prot.     

New generation tissue sealants and hemostatic agents: innovative urologic applications

Control of blood loss during urologic surgery is paramount to the success of patient recovery. Hemostatic agents and tissue sealants are used routinely to prevent excess blood loss and in reconstruction during surgical repair. Some of the available products include thrombin sealant, fibrin glue, bovine serum/albumin/glutaraldehyde, and gelatin matrix. Each of these agents differs in mechanism, cost, and application. Complications can include allergic reactions or thromboembolism and the risk of contracting bovine spongiform encephalitis or hepatitis. Many new hemostatic agents are being developed and approved. The benefits and risks of use of these agents versus conventional treatment need to be considered on a case-by-case basis by the surgeon.     

Combining literature text mining with microarray data: advances for system biology modeling

A huge amount of important biomedical information is hidden in the bulk of research articles in biomedical fields. At the same time, the publication of databases of biological information and of experimental datasets generated by high-throughput methods is in great expansion, and a wealth of annotated gene databases, chemical, genomic (including microarray datasets), clinical and other types of data repositories are now available on the Web. Thus a current challenge of bioinformatics is to develop targeted methods and tools that integrate scientific literature, biological databases and experimental data for reducing the time of database curation and for accessing evidence, either in the literature or in the datasets, useful for the analysis at hand. Under this scenario, this article reviews the knowledge discovery systems that fuse information from the literature, gathered by text mining, with microarray data for enriching the lists of down and upregulated genes with elements for biological understanding and for generating and validating new biological hypothesis. Finally, an easy to use and freely accessible tool, GeneWizard, that exploits text mining and microarray data fusion for supporting researchers in discovering gene-disease relationships is described.     

Frontiers of biomedical text mining: current progress

It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain. Enormous progress has been made in the areas of information retrieval, evaluation methodologies and resource construction. Some problems, such as abbreviation-handling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon. However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research. In this article we review the current state of the art in biomedical text mining or 'BioNLP' in general, focusing primarily on papers published within the past year.     

esyN: Network Building,Sharing and Publishing

The construction and analysis of networks is increasingly widespread in biological research. We have developed esyN (“easy networks”) as a free and open source tool to facilitate the exchange of biological network models between researchers. esyN acts as a searchable database of user-created networks from any field. We have developed a simple companion web tool that enables users to view and edit networks using data from publicly available databases. Both normal interaction networks (graphs) and Petri nets can be created. In addition to its basic tools, esyN contains a number of logical templates that can be used to create models more easily. The ability to use previously published models as building blocks makes esyN a powerful tool for the construction of models and network graphs. Users are able to save their own projects online and share them either publicly or with a list of collaborators. The latter can be given the ability to edit the network themselves, allowing online collaboration on network construction. esyN is designed to facilitate unrestricted exchange of this increasingly important type of biological information. Ultimately, the aim of esyN is to bring the advantages of Open Source software development to the construction of biological networks.     

Moisture dynamics and fungal susceptibility of plywood

Engineered wood products are widely used in construction and transportation. Plywood has one of the best physical and mechanical properties for application under moist conditions in use class 3, i.e. exterior exposure without ground contact. Yet a profound knowledge of their moisture dynamics and fungal susceptibility is a prerequisite for proper use. In this paper the results of more than two years of continuous recording of the moisture content of different plywood types in exterior exposure is presented. Clear differences concerning moisture dynamics are apparent regarding wood species, glue type, and veneer thickness. X-ray tomography scans literally offer insight into the weathering state of the veneer layers and glue lines. Fungal susceptibility of the samples relates primarily to wood species and glue type. Furthermore, edge-sealing for fungal testing is necessary to represent in-service situations and yields distinct differences compared to non-sealed test results. There seems to be a relationship between the accumulated moisture content and layered structure of the plywood, but an unequivocal link with fungal decay is not straightforward.     

The cell theory--history, present state and prospects (on the 150th anniversary of the development of the cell theory)

The main stages of history of this most important biological conception are presented and the state of the modern cell theory and its future prospects are considered. Since 1839, when T. Schwann expounded his conception of the cell, a long pathway in cognition of the cell function and organization has been covered. From the original picture of the complex organism as a "cellular state", made up of relatively independent "elementary organisms", i.e. cells the modern biology has come to the idea of the cell as an integral system either being a part of a complex organism, or living free in the nature (protists). The cell represents certain qualitatively peculiar level in a complex evolutionary established hierarchy of biological systems. Some particular tight relations, existing between cytology, as a fundamental biological science and molecular biology, genetics, ecology and other biological disciplines are considered. The importance of the cell conception is ascertained for practical aims, especially in medicine.     

Analysis of covariance: an alternative to nutritional indices

Some statistical problems are added to the growing list of cautionary tales regarding the use of the conventional, ratio-based nutritional indices (RCR, RGR, ECI, AD and ECD). Analysis of ratios is based on the, probably unrealistic, assumption of an isometric relationship between denominator and numerator variables. Analysis of covariance (ANCOVA) makes less restrictive assumptions, and additionally provides important information about the data which is lost by using ratio variables. We demonstrate, using computer-generated data sets, some of the pitfalls of statistical analysis of ratios and illustrate how these may be avoided using ANCOVA. Some possible consequences of such statistical iniquities for biological interpretations are discussed.     

Two-dimensional supramolecular assemblies involving neoglycoplipids: Self-organization and insertion properties into Langmuir monolayers

In nature, interfacial molecular recognition and chirality are of fundamental significance for the construction of biological assemblies. Lipid monolayers at liquid interface can be used as biomimetic models for studying molecular interactions in such assemblies. In this article, we will focus on the use of Langmuir monolayers for studying self-organization and insertion properties of several neoglycolipids. Two types of glycolipids have been considered, one in the context of the analysis of glycoconjugates of biological relevance, and one dealing with the ability of some glycoprobes to insert into a monolayer in relation with their efficiency for serving as membrane imaging systems.     

Complete Radiofrequency Ablation of Hepatolithiasis-Associated Cholangiocarcinoma and Successful Management of Post-ablation Bronchobiliary Fistula

This report documented the use of radiofrequency ablation (RFA) in the treatment of hepatolithiasis-associated cholangiocarcinoma and cyanoacrylate glue in the management of post-ablation bronchobiliary fistula. A 47-year-old Chinese woman with 20 years history of extrahepatic and intrahepatic cholangiolithiasis and multiple hepatic segmentectomy, developed hepatolithiasis-associated cholangiocarcinoma. The tumor was successfully treated with RFA but patient developed bronchobiliary fistula. Cyanoacrylate glue was used for occluding the bronchobiliary fistula. CT scan at 3 months showed complete restoration of physiological separation between the biliary and bronchial system. Repeat CT scan showed complete tumor ablation with no signs of tumor recurrence 10 months after RFA. In conclusion, RFA may be a safe and effective treatment option for patients with hepatolithiasis-associated cholangiocarcinoma who are poor candidates for surgical resection. Protection of the integrity of the bile duct and diaphragm during RFA can minimize postoperative complications. In case of development of post-ablation bronchobiliary fistula, cyanoacrylate glue can be used to occlude the fistula, before surgical resection is considered.     

Extraction of biological interaction networks from scientific literature

Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, analysis of such networks might shed new light on the function of biological systems. Such biological networks can be obtained from different sources. The extraction of networks from text is an important technique that requires the integration of several different computational disciplines. This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature.     

聚谷氨酸-明胶生物胶生物学评价

考察了聚谷氨酸-明胶生物胶的生物性能。从细胞毒性、急性毒性、皮肤刺激、溶血、热源、皮肤致敏等试验对其进行生物学检测。结果发现：聚谷氨酸-明胶生物胶的细胞毒性、急性毒性、皮肤刺激、溶血、热源、皮肤致敏试验均为阴性。这些结果表明聚谷氨酸-明胶生物胶具有良好的生物性能。     

A Text-Mining System for Extracting Metabolic Reactions from Full-Text Articles

ABSTRACT: BACKGROUND: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway - metabolic pathways - has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein-protein interactions. RESULTS: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. CONCLUSIONS: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein-protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed.