Mapping the Gene Ontology Into the Unified Medical Language System

We have recently mapped the Gene Ontology (GO), developed by the Gene Ontology Consortium, into the National Library of Medicine's Unified Medical Language System (UMLS). GO has been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for integrating large numbers of disparate terminologies, primarily for the purpose of providing better access to biomedical information sources. The mapping of GO to UMLS highlighted issues in both terminology systems. After some initial explorations and discussions between the UMLS and GO teams, the GO was integrated with the UMLS. Overall, a total of 23% of the GO terms either matched directly (3%) or linked (20%) to existing UMLS concepts. All GO terms now have a corresponding, official UMLS concept, and the entire vocabulary is available through the web-based UMLS Knowledge Source Server. The mapping of the Gene Ontology, with its focus on structures, processes and functions at the molecular level, to the existing broad coverage UMLS should contribute to linking the language and practices of clinical medicine to the language and practices of genomics

Nga iwi o Ngapuhi membership system: relationship management and relational design

This paper reviews a capstone project undertaken by Auckland University of Technology (AUT) students to develop a tribal membership register for Te Runanga a Iwi o Ngapuhi. The initial scope of the project incorporated a database to record details of people, land, and their common history. As the project unfolded complex issues related to land, genealogical and historical relationships had to be addressed. The paper discusses the relationship between the clients and developers and the partnership model that was adopted. Research conducted to develop a suitable data model uncovered the GENTECH genealogical data model originated by genealogists in Texas. This model was adapted for this project to suit the unique needs of Maori. The paper describes the initial implementation of an online membership register and concludes with a critique of this model proposing further extensions to address the interactions between people, land and history

Ginkgo leaf cuticle chemistry across changing pCO2 regimes

Cuticles have been a key part of palaeobotanical research since the mid-19th Century. Recently, cuticular research has moved beyond morphological traits to incorporate the chemical signature of modern and fossil cuticles, with the aim of using this as a taxonomic and classification tool. For this approach to work, cuticle chemistry would have to maintain a strong taxonomic signal, with a limited input from the ambient environment in which the plant grew. Here, we use attenuated total reflectance Fourier Transform infrared (ATR-FTIR) spectroscopy to analyse leaf cuticles from Ginkgo biloba plants grown in experimentally enhanced CO2 conditions, to test for the impact of changing CO2 regimes on cuticle chemistry. We find limited evidence for an impact of CO2 on the chemical signature of Ginkgo cuticles, with more pronounced differences demonstrated between the abaxial (lower leaf surface) and adaxial (upper leaf surface) cuticles. These findings support the use of chemotaxonomy for plant cuticular remains across geological timescales, and the concomitant large-scale variations in CO2 concentrations

The impact of oxidation on spore and pollen chemistry

Sporomorphs (pollen and spores) have an outer wall composed of sporopollenin. Sporopollenin chemistry contains both a signature of ambient ultraviolet-B flux and taxonomic information, but it is currently unknown how sensitive this is to standard palynological processing techniques. Oxidation in particular is known to cause physical degradation to sporomorphs, and it is expected that this should have a concordant impact on sporopollenin chemistry. Here, we test this by experimentally oxidizing Lycopodium (clubmoss) spores using two common oxidation techniques: acetolysis and nitric acid. We also carry out acetolysis on eight angiosperm (flowering plant) taxa to test the generality of our results. Using Fourier Transform infrared (FTIR) spectroscopy, we find that acetolysis removes labile, non-fossilizable components of sporomorphs, but has a limited impact upon the chemistry of sporopollenin under normal processing durations. Nitric acid is more aggressive and does break down sporopollenin and reorganize its chemical structure, but when limited to short treatments (i.e. ≤10 min) at room temperature sporomorphs still contain most of the original chemical signal. These findings suggest that when used carefully oxidation does not adversely affect sporopollenin chemistry, and that palaeoclimatic and taxonomic signatures contained within the sporomorph wall are recoverable from standard palynological preparations

A treatment planning intercomparison of proton and intensity modulated photon radiotherapy.

peer reviewedAbstract Purpose: A comparative treatment planning study has been undertaken between standard photon delivery techniques,b intensity modulated photon methods and spot scanned protons in order to investigate the merits and limitations of each of these treatment approaches. Methods: Plans for each modality were performed using CT scans and planning information for nine patients with varying indications and lesion sites and the results have been analysed using a variety of dose and volume based parameters. Results: Over all cases, it is predicted that the use of protons could lead to a reduction of the total integral dose by a factor three compared to standard photon techniques and a factor two compared to IM photon plans. In addition, in all but one Organ at Risk (OAR) for one case, protons are predicted to reduce both mean OAR dose and the irradiated volume at the 50% mean target dose level compared to both photon methods. However, when considering the volume of an OAR irradiated to 70% or more of the target dose, little difference could be shown between proton and intensity modulated photon plans. On comparing the magnitude of dose hot spots in OARs resulting from the proton and IM photon plans, more variation was observed, and the ranking of the plans was then found to be case and OAR dependent. Conclusions: The use of protons has been found to reduce the medium to low dose load (below about 70% of the target dose) to OARs and all non-target tissues compared to both standard and inversely planned photons, but that the use of intensity modulated photons can result in similar levels of high dose conformation to that afforded by protons. However, the introduction of inverse planning methods for protons is necessary before general conclusions on the relative efficacy of photons and protons can be drawn