Farm Boundaries as Agroecological Systems

Agricultural boundaries as fence lines, hedgerows, tractor paths, stone walls, forest edges, or field breaks are historically and ecologically significant. In South-Central Pennsylvania where the author lives and works, pollinator conservation depends upon agricultural history

Ontology-Based MEDLINE Document Classification

An increasing and overwhelming amount of biomedical information is available in the research literature mainly in the form of free-text. Biologists need tools that automate their information search and deal with the high volume and ambiguity of free-text. Ontologies can help automatic information processing by providing standard concepts and information about the relationships between concepts. The Medical Subject Headings (MeSH) ontology is already available and used by MEDLINE indexers to annotate the conceptual content of biomedical articles. This paper presents a domain-independent method that uses the MeSH ontology inter-concept relationships to extend the existing MeSH-based representation of MEDLINE documents. The extension method is evaluated within a document triage task organized by the Genomics track of the 2005 Text REtrieval Conference (TREC). Our method for extending the representation of documents leads to an improvement of 17% over a non-extended baseline in terms of normalized utility, the metric defined for the task. The SVMlight software is used to classify documents

Ecology of Pilgrimage: Building Socio-Ecological Community on the Way

A developed sense of interdependence with the socio-ecological landscapes of pilgrimage can serve as a path for accepting and reducing the impact we have in our sacred travels. Developing ecological habits of mind allows the pilgrim to draw deeper meanings from and thus greater affinity with the natural world. Raising awareness of environmental issues and appreciating the interaction of humans and the natural world helps modern pilgrims play an important role in conservation and restoration of pilgrimage landscapes

Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)

Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.

Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. 

Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. 

MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers.

MTB is supported by NCI grant CA089713

Aberration Correction with Aspheric Intraocular Lenses

The shape of the normal human cornea induces positive spherical aberration (SA) which causes image blur. In the young phakic eye, the crystalline lens compensates for a certain amount of this corneal aberration. However, the compensation slowly decreases with the aging lens and is fully lost after cataract extraction and implantation of a standard intraocular lens (IOL). Conventional spherical IOLs add their intrinsic positive SA to the positive SA of the cornea increasing the image blur. As a useful side effect, this also increases the depth of focus—often referred to as pseudo-accommodation. Aspheric intraocular lenses have been introduced to be either neutral to SA or to compensate for a certain amount of corneal SA. A customized correction for the individual eye seems to be the most promising solution for tailored correction of SA. In this chapter we will provide detailed information on the various concepts of aspheric intraocular lenses to elucidate that the term “aspheric intraocular lens” is being used for a large amount of different lens designs

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data

Imaging the Cornea, Anterior Chamber, and Lens in Corneal and Refractive Surgery

Anterior segment OCT (AS-OCT) is an optical and noncontact imaging technology, which has numerous fields of application in the imaging of the cornea, anterior chamber, and the lens. In this chapter, we will present some of the application fields of AS-OCT in corneal, cataract, and refractive surgery. We will emphasize the potential of AS-OCT by several clinical examples including corneal imaging (keratoconus, keratoplasty, and refractive surgery) and intraocular lens imaging after refractive surgery. AS-OCT shows special potential for corneal imaging in case of corneal edema and for postoperative control after Descemet’s membrane endothelial keratoplasty (DMEK). The postoperative follow-up of a posterior chamber Collamer lens’ses vault and measuring the anterior chamber angle could be identified as another promising field of application for AS-OCT

The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the authoritative source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) resource. MGD contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. Major improvements to the Mouse Genome Database include comprehensive update of genetic maps, implementation of new classification terms for genome features, development of a recombinase (cre) portal and inclusion of all alleles generated by the International Knockout Mouse Consortium (IKMC)