Shape-based classification of 3D head data

Abstract. Craniofacial disorders are one of the most common category of birth defects worldwide, and are an important topic of biomedical research. In order to better understand these disorders and correlate them with genetic patterns and life outcomes, researchers need to quantify the craniofacial anatomy. In this paper we introduce several different craniofacial descriptors that are being used in research studies for two craniofacial disorders: the 22q11.2 deletion syndrome (a genetic disorder) and plagiocephaly/brachycephaly, disorders caused by pressure on the head. Experimental results show that our descriptors show promise for quantifying craniofacial shape. Key words: 3D shape, shape-based classification, craniofacial data

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance

An ontology-based comparative anatomy information system

Introduction: This paper describes the design, implementation, and potential use of a comparative anatomy information system (CAIS) for querying on similarities and differences between homologous anatomical structures across species, the knowledge base it operates upon, the method it uses for determining the answers to the queries, and the user interface it employs to present the results. The relevant informatics contributions of our work include (1) the development and application of the structural difference method, a formalism for symbolically representing anatomical similarities and differences across species; (2) the design of the structure of a mapping between the anatomical models of two different species and its application to information about specific structures in humans, mice, and rats; and (3) the design of the internal syntax and semantics of the query language. These contributions provide the foundation for the development of a working system that allows users to submit queries about the similarities and differences between mouse, rat, and human anatomy; delivers result sets that describe those similarities and differences in symbolic terms; and serves as a prototype for the extension of the knowledge base to any number of species. Additionally, we expanded the domain knowledge by identifying medically relevant structural questions for the human, the mouse, and the rat, and made an initial foray into the validation of the application and its content by means of user questionnaires, software testing, and other feedback

A Graphical User Interface for a Comparative Anatomy Information System: Design, Implementation and Usage Scenarios

Building on our previous design work in the development of the Structural Difference Method (SDM) for describing anatomical similarities and differences across species, we describe the design and implementation of the associated comparative anatomy information system (CAIS) interface and provide scenarios from the literature for its use by research scientists

A graphical user interface for a comparative anatomy information system: design, implementation and usage scenarios

ABSTRAC