Challenges for automatically extracting molecular interactions from full-text articles

Background  

The increasing availability of full-text biomedical articles will allow more biomedical knowledge to be extracted automatically with greater reliability. However, most Information Retrieval (IR) and Extraction (IE) tools currently process only abstracts. The lack of corpora has limited the development of tools that are capable of exploiting the knowledge in full-text articles. As a result, there has been little investigation into the advantages of full-text document structure, and the challenges developers will face in processing full-text articles.     

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms

Background  

Microarray technology produces gene expression data on a genomic scale for an endless variety of organisms and conditions. However, this vast amount of information needs to be extracted in a reasonable way and funneled into manageable and functionally meaningful patterns. Genes may be reasonably combined using knowledge about their interaction behaviour. On a proteomic level, biochemical research has elucidated an increasingly complete image of the metabolic architecture, especially for less complex organisms like the well studied bacterium Escherichia coli.     

Isolation of a human-like antibody fragment (scFv) that neutralizes ricin biological activity

Background  

Ricin is a lethal toxin that inhibits protein synthesis. It is easily extracted from a ubiquitously grown plant, Ricinus communis, and thus readily available for use as a bioweapon (BW). Anti-ricin antibodies provide the only known therapeutic against ricin intoxication.     

Washing scaling of GeneChip microarray expression

Background  

Post-hybridization washing is an essential part of microarray experiments. Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities.     

Thesaurus-based disambiguation of gene symbols

Background  

Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.     

Antimicrobial resistance and virulence factors in <Emphasis Type="Italic">Escherichia coli</Emphasis> from swedish dairy calves

Background  

In Sweden, knowledge about the role of enteropathogenic Escherichia coli in neonatal calf diarrhea and the occurrence of antimicrobial resistance in E. coli from young calves is largely unknown. This has therapeutic concern and such knowledge is also required for prudent use of antimicrobials.     

Identifying biological concepts from a protein-related corpus with a probabilistic topic model

Background  

Biomedical literature, e.g., MEDLINE, contains a wealth of knowledge regarding functions of proteins. Major recurring biological concepts within such text corpora represent the domains of this body of knowledge. The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE^? titles and abstracts by applying a probabilistic topic model.     

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

Background  

To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted.     

Styrylpyrone Derivative (SPD) induces apoptosis in a caspase-7-dependent manner in the human breast cancer cell line MCF-7

Background  

Styrylpyrone derivative (SPD) is a plant-derived pharmacologically active compound extracted from Goniothalamus sp. Previously, we have reported that SPD inhibited the proliferation of MCF-7 human breast cancer cells by inducing apoptotic cell death, while having minimal effects on non-malignant cells. Here, we attempt to further elucidate the mode of action of SPD.     

Biomechanical analysis of rollator walking

Background  

The rollator is a very popular walking aid. However, knowledge about how a rollator affects the walking patterns is limited. Thus, the purpose of the study was to investigate the biomechanical effects of walking with and without a rollator on the walking pattern in healthy subjects.     

Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in <Emphasis Type="Italic">Lolium perenne</Emphasis>

Background  

Association analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium in ryegrass is lacking, which is essential for the efficiency of association analyses.     

Skeletal muscle contraction. The thorough definition of the contractile event requires both load acceleration and load mass to be known

Background  

The scope of this work is to show that the correct and complete definition of the system of muscle contraction requires the knowledge of both the mass and the acceleration of the load.     

Generation and analysis of 9792 EST sequences from cold acclimated oat, <Emphasis Type="Italic">Avena sativa</Emphasis>

Background  

Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required.     

TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis

Background  

Computational enzyme design is far from being applicable for the general case. Due to computational complexity and limited knowledge of the structure-function interplay, heuristic methods have to be used.     

Word add-in for ontology recognition: semantic enrichment of scientific literature

Background  

In the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely necessary and new media are allowing information and knowledge to be more interactive and immediate. One approach to making knowledge more accessible is the addition of machine-readable semantic data to scholarly articles.     

Optimising the Use of TRIzol-extracted Proteins in Surface Enhanced Laser Desorption/ Ionization (SELDI) Analysis

Background  

Research with clinical specimens is always hampered by the limited availability of relevant samples, necessitating the use of a single sample for multiple assays. TRIzol is a common reagent for RNA extraction, but DNA and protein fractions can also be used for other studies. However, little is known about using TRIzol-extracted proteins in proteomic research, partly because proteins extracted from TRIzol are very resistant to solubilization.     

Cell-specific expression of tryptophan decarboxylase and 10-hydroxygeraniol oxidoreductase,key genes involved in camptothecin biosynthesis in <Emphasis Type="Italic">Camptotheca acuminata</Emphasis> Decne (Nyssaceae)

Background  

Camptotheca acuminata is a major natural source of the terpenoid indole alkaloid camptothecin (CPT). At present, little is known about the cellular distribution of the biosynthesis of CPT, which would be useful knowledge for developing new strategies and technologies for improving alkaloid production.     

Iterative approach to model identification of biological networks

Background  

Recent advances in molecular biology techniques provide an opportunity for developing detailed mathematical models of biological processes. An iterative scheme is introduced for model identification using available system knowledge and experimental measurements.     

<Emphasis Type="Italic">Rhodococcus erythropolis</Emphasis> ATCC 25544 as a suitable source of cholesterol oxidase: cell-linked and extracellular enzyme synthesis,purification and concentration

Background  

The suitability of the strain Rhodococcus erythropolis ATCC 25544 grown in a two-liter fermentor as a source of cholesterol oxidase has been investigated. The strain produces both cell-linked and extracellular cholesterol oxidase in a high amount, that can be extracted, purified and concentrated by using the detergent Triton X-114.     

HaploRec: efficient and accurate large-scale reconstruction of haplotypes

Background  

Haplotypes extracted from human DNA can be used for gene mapping and other analysis of genetic patterns within and across populations. A fundamental problem is, however, that current practical laboratory methods do not give haplotype information. Estimation of phased haplotypes of unrelated individuals given their unphased genotypes is known as the haplotype reconstruction or phasing problem.