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1.  Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers 
Briefings in Bioinformatics  2011;13(3):383-389.
Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.
doi:10.1093/bib/bbr064
PMCID: PMC3357490  PMID: 22110242
Bioinformatics; training; end users; bioinformatics courses; learning bioinformatics
2.  Hygrochastic capsule dehiscence supports safe site strategies in New Zealand alpine Veronica (Plantaginaceae) 
Annals of Botany  2010;106(3):405-412.
Background and Aims
Hygrochasy is a capsule-opening mechanism predominantly associated with plants in arid habitats, where it facilitates spatially and temporally restricted dispersal. Recently, hygrochastic capsules were described in detail for the first time in alpine Veronica in New Zealand. The aim of the present study was to investigate whether hygrochastic capsules are an adaptation of alpine Veronica to achieve directed dispersal to safe sites. We expect that by limiting dispersal to rainfall events, distances travelled by seeds are short and confine them to small habitat patches where both seedlings and adults have a greater chance of survival.
Methods
Dispersal distances of five hygrochastic Veronica were measured under laboratory and field conditions and the seed shadow was analysed. Habitat patch size of hygrochastic Veronica and related non-hygrochastic species were estimated and compared.
Key Results
Dispersal distances achieved by dispersal with raindrops did not exceed 1 m but weather conditions could influence the even distribution of seeds around the parent plant. Compared with related Veronica species, hygrochastic Veronica mostly grow in small, restricted habitat patches surrounded by distinctly different habitats. These habitat patches provide safe sites for seeds due to their microtopography and occurrence of adult cushion plants. Non-hygrochastic Veronica can be predominantly found in large habitats without clearly defined borders and can be spread over long distances along rivers.
Conclusions
The results suggest that hygrochasy is a very effective mechanism of restricting seed dispersal to rainfall events and ensuring short-distance dispersal within a small habitat patch. It appears that it is an adaptation for directed dispersal to safe sites that only exist within the parent habitat.
doi:10.1093/aob/mcq136
PMCID: PMC2924830  PMID: 20587583
Dispersal; habitat patch; hygrochasy; New Zealand Alps; ombrohydrochory; safe sites; Veronica
3.  Accuracy of comparing bone quality to chocolate bars for patient information purposes: observational study 
BMJ : British Medical Journal  2007;335(7633):1285-1287.
Objective To test whether standard information for patients using Crunchie and Aero chocolate bars to explain bone health and risk of fracture is robust.
Design Observational study.
Setting Domestic kitchen in rural west Wales.
Participants 10 Crunchie bars and 10 Aero bars.
Main outcome measure Fracture after falls from varying heights.
Results Both Crunchie and Aero bars exhibited the same T and Z scores for bone density. Crunchie bars had a lower chocolate mass index than the Aero bars. Crunchie bars are more liable to fracture.
Conclusions Using Crunchie and Aero chocolate bars to explain bone structure to patients may be visually attractive but oversimplifies the situation.
doi:10.1136/bmj.39413.798472.BE
PMCID: PMC2151161  PMID: 18156229
4.  A multi-compartment vascular model for inferring arteriole dilation and cerebral metabolic changes during functional activation 
Functional hemodynamic responses, measured by methods such as fMRI or optical imaging, are the composite, downstream results of underlying variations in cerebral oxygen consumption and the dilation of arteriole vessels, which follow from changes in neuronal activity. The separation of metabolic and vascular effects is an actively growing area of interest, motivated by increasing evidence of the role of neural-metabolic-vascular coupling in health and disease. However, this coupling cannot be easily or directly observed in vivo. Vascular modeling plays an important role by relating these underlying physiological responses to the hemodynamic variables measured with non-invasive imaging. In this paper, we describe a multi-compartment model of the cerebral vascular and oxygen transport dynamics associated with stimulus driven neuronal activation. The unique formulation of this model allows both the estimation of the dynamic arteriole dilation and metabolic processes associated with the functional response to stimuli, and also enables us to infer details of the structural and baseline properties of the vascular anatomy, such as baseline oxygen consumption, blood flow, and resting hemoglobin concentrations. We apply this model to multimodal optical spectroscopic and laser speckle imaging of the rat somato-sensory cortex during nine conditions of whisker stimulation. We estimate baseline blood flows to be 94(±15) mL/100g/min and baseline oxygen consumption to be 6.7(±1.3) mL O2/100g/min. We calculate parametric, linear increases in the arteriole dilation (R2=0.96) and CMRO2 (R2=0.87) responses over the nine conditions. We find that our model more accurately describes these observed oxygenation changes when compared to a single compartment model.
doi:10.1038/sj.jcbfm.9600435
PMCID: PMC2586902  PMID: 17200678
6.  Introduction of a Carboxyl Group in the First Transmembrane Helix of Escherichia coli F1Fo ATPase Subunit c and Cytoplasmic pH Regulation 
Journal of Bacteriology  2001;183(5):1524-1530.
The multicopy subunit c of the H+-transporting F1Fo ATP synthase of Escherichia coli folds across the membrane as a hairpin of two hydrophobic α helices. The subunits interact in a front-to-back fashion, forming an oligomeric ring with helix 1 packing in the interior and helix 2 at the periphery. A conserved carboxyl, Asp61 in E. coli, centered in the second transmembrane helix is essential for H+ transport. A second carboxylic acid in the first transmembrane helix is found at a position equivalent to Ile28 in several bacteria, some the cause of serious infectious disease. This side chain has been predicted to pack proximal to the essential carboxyl in helix 2. It appears that in some of these bacteria the primary function of the enzyme is H+ pumping for cytoplasmic pH regulation. In this study, Ile28 was changed to Asp and Glu. Both mutants were functional. However, unlike the wild type, the mutants showed pH-dependent ATPase-coupled H+ pumping and passive H+ transport through Fo. The results indicate that the presence of a second carboxylate enables regulation of enzyme function in response to cytoplasmic pH and that the ion binding pocket is aqueous accessible. The presence of a single carboxyl at position 28, in mutants I28D/D61G and I28E/D61G, did not support growth on a succinate carbon source. However, I28E/D61G was functional in ATPase-coupled H+ transport. This result indicates that the side chain at position 28 is part of the ion binding pocket.
doi:10.1128/JB.183.5.1524-1530.2001
PMCID: PMC95036  PMID: 11160082

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