On the persistence of supplementary resources in biomedical publications

Background  

Providing for long-term and consistent public access to scientific data is a growing concern in biomedical research. One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers.     

Discovery of protein-protein interactions using a combination of linguistic,statistical and graphical information

Background  

The rapid publication of important research in the biomedical literature makes it increasingly difficult for researchers to keep current with significant work in their area of interest.     

Natural Language Processing in aid of FlyBase curators

Background  

Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.     

The structural and content aspects of abstracts versus bodies of full text journal articles are different

Background  

An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research.     

Clique-based data mining for related genes in a biomedical database

Background  

Progress in the life sciences cannot be made without integrating biomedical knowledge on numerous genes in order to help formulate hypotheses on the genetic mechanisms behind various biological phenomena, including diseases. There is thus a strong need for a way to automatically and comprehensively search from biomedical databases for related genes, such as genes in the same families and genes encoding components of the same pathways. Here we address the extraction of related genes by searching for densely-connected subgraphs, which are modeled as cliques, in a biomedical relational graph.     

Engineering of a multi-functional extracellular matrix protein for immobilization to bone mineral hydroxyapatite

Purpose of Work  

We have developed a strategy of designing multi-functional extracellular matrix proteins for functionalizing bone tissue engineering scaffolds and other biomedical surfaces to achieve improvements in bone grafting, bone repair and bone regeneration.     

Synthesis and characterization of core-shell Fe<Subscript>3</Subscript>O<Subscript>4</Subscript>-gold-chitosan nanostructure

Background  

Fe₃O₄-gold-chitosan core-shell nanostructure can be used in biotechnological and biomedical applications such as magnetic bioseparation, water and wastewater treatment, biodetection and bioimaging, drug delivery, and cancer treatment.     

Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque

Background  

Rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate animal in biomedical research. A global map of genetic variations in rhesus macaque is valuable for both evolutionary and functional studies.     

A micro-fluidic study of whole blood behaviour on PMMA topographical nanostructures

Background  

Polymers are attractive materials for both biomedical engineering and cardiovascular applications. Although nano-topography has been found to influence cell behaviour, no established method exists to understand and evaluate the effects of nano-topography on polymer-blood interaction.     

Identifying functional relationships among human genes by systematic analysis of biological literature

Background  

The availability of biomedical literature in electronic format has made it possible to implement automatic text processing methods to expose implicit relationships among different documents, and more importantly, the functional relationships among the molecules and processes that these documents describe.     

The textual characteristics of traditional and Open Access scientific journals are similar

Background  

Recent years have seen an increased amount of natural language processing (NLP) work on full text biomedical journal publications. Much of this work is done with Open Access journal articles. Such work assumes that Open Access articles are representative of biomedical publications in general and that methods developed for analysis of Open Access full text publications will generalize to the biomedical literature as a whole. If this assumption is wrong, the cost to the community will be large, including not just wasted resources, but also flawed science. This paper examines that assumption.     

A realistic assessment of methods for extracting gene/protein interactions from free text

Background  

The automated extraction of gene and/or protein interactions from the literature is one of the most important targets of biomedical text mining research. In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users. Hence we have specifically avoided methods that are complex to install or require reimplementation, and we coupled our chosen extraction methods with a state-of-the-art biomedical named entity tagger.     

BioInfer: a corpus for information extraction in the biomedical domain

Background  

Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora.     

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.     

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat

Background  

Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult to study AS evolution in mammals and its biomedical implications.     

PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

Background  

Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts.     

The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature

Background  

One of the most neglected areas of biomedical Text Mining (TM) is the development of systems based on carefully assessed user needs. We have recently investigated the user needs of an important task yet to be tackled by TM -- Cancer Risk Assessment (CRA). Here we take the first step towards the development of TM technology for the task: identifying and organizing the scientific evidence required for CRA in a taxonomy which is capable of supporting extensive data gathering from biomedical literature.     

Molecular mechanistic associations of human diseases

Background  

The study of relationships between human diseases provides new possibilities for biomedical research. Recent achievements on human genetic diseases have stimulated interest to derive methods to identify disease associations in order to gain further insight into the network of human diseases and to predict disease genes.     

Identification of restriction endonuclease with potential ability to cleave the HSV-2 genome: Inherent potential for biosynthetic versus live recombinant microbicides

Background  

Herpes Simplex virus types 1 and 2 are enveloped viruses with a linear dsDNA genome of ~120–200 kb. Genital infection with HSV-2 has been denoted as a major risk factor for acquisition and transmission of HIV-1. Developing biomedical strategies for HSV-2 prevention is thus a central strategy in reducing global HIV-1 prevalence. This paper details the protocol for the isolation of restriction endunucleases (REases) with potent activity against the HSV-2 genome and models two biomedical interventions for preventing HSV-2.     

Biocompatible hydroxyapatite nanoparticles as a redox luminescence switch

Abstract  

A redox luminescence switch was prepared by doping hydroxyapatite nanoparticles with CePO₄:Tb. The resulting multifunctional material exhibits good biocompatibility, biological affinity, and potential drug-carrying capability. The luminescent hydroxyapatite nanoparticles may find important applications in biomedical diagnostics, drug delivery, and biological sensors.