Exploring Road Incident Data with Heat Maps

This research seeks to determine whether heat mapping is an effective technique for the visual exploration of road incident data. Four software prototypes, which adopted map, treemap and spatial treemap layouts, were developed using open source software. Whilst the visualization process described by Fry (2007) informed the development effort, the evaluation methodology was based on the Nested Process Model (Munzner, 2009). The results of two evaluation methods-a design study and the presentation and discussion of results with domain experts-confirm heat mapping's validity and provide requirements for further software development

Opening of DNA double strands by helicases. Active versus passive opening

Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA). We describe helicase opening of dsNA, based on helicases which bind single NA strands and move towards the double-stranded region, using a discrete ``hopping'' model. The interaction between the helicase and the junction where the double strand opens is characterized by an interaction potential. The form of the potential determines whether the opening is active or passive. We calculate the rate of passive opening for the helicase PcrA, and show that the rate increases when the opening is active. Finally, we examine how to choose the interaction potential to optimize the rate of strand separation. One important result is our finding that active opening can increase the unwinding rate by 7 fold compared to passive opening.Comment: 13 pages, 3 figure

Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub

Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products

X-Ray photoelectron spectroscopy and mass spectrometry studies of X-ray-processed solid CO2

Solid CO2 films have been grown on a stainless steel substrate and processed by X-ray bombardment for up to 6 hr.. The reactions induced were monitored using X-ray photoelectron spectroscopy (XPS) and mass spectrometry. The XPS results are twofold: direct X-ray photolysis of the CO2 ice produced CO and an unidentified O product, possibly atomic O; secondary effects resulting from surface reactions between CO, O, and residual H from the vacuum environment produced H2CO, CH3OH, and a water ice cap on the CO2 film. The rate of production of CO from direct X-ray photolysis of CO2 is measured to be 5.4 × 102 molecule photon-1, corresponding to a formation cross section of 4.7 × 10-20 cm2. The growth rate for the water cap is calculated to be 2.6 × 10-4 monolayers s-1 for a partial pressure of H equal to 2 × 10-10 Torr. The appearance of gas-phase products from the film showed a time lag which indicates that the diffusion of the product species in the bulk CO2 is affected by some time-dependent process, possibly the creation of defects in the film. A model for the observed time dependence of the dissociation products in the gas phase yields diffusion coefficients in the CO2 of 5 × 10-12 and 1 × 10-12 cm2 s-1, for O and CO, respectively

Implications of Arm Restraint on Lower Extremity Kinetics During Gait

Background Literature indicates the importance of the upper extremities in providing stability and propulsion for the body during ambulation. However, the kinetic implications of upper extremity restraint during gait are not as well documented. Aim The objective of this study was to examine the effect of arm restraint (unilateral and bilateral) on lower extremity joint kinetics during walking. Methods Twenty-three healthy young participants were instrumented for three dimensional motion analysis, and tested in four randomly ordered upper extremity restraint conditions (unrestrained, bilateral restraint, right side restraint, and left side restraint). Temporal spatial parameters and gait/phase-specific lower extremity kinetics and kinematics were measured. For each restraint condition, pointwise differences from the unrestrained condition were compared using a two-way ANOVA model of restraint condition (“Condition”) and gait cycle phase (“Timing”). Results Decreases in walking speed and stride length were observed for all restraint conditions. Differences in kinetic demands were also noted, primarily at the hip and knee. Conclusion Upper extremity restraint in healthy young adults leads to significant changes in temporal-spatial parameters and proximal joint kinetics, most prominently during periods of load accommodation and balance

Insights into Chi recognition from the structure of an AddAB-type helicase–nuclease complex

Homologous recombination DNA repair requires double-strand break resection by helicase–nuclease enzymes. The crystal structure of bacterial AddAB in complex with DNA substrates shows that it employs an inactive helicase site to recognize ‘Chi' recombination hotspot sequences that regulate resection

Chi hotspots trigger a conformational change in the helicase-like domain of AddAB to activate homologous recombination

In bacteria, the repair of double-stranded DNA breaks is modulated by Chi sequences. These are recognised by helicase-nuclease complexes that process DNA ends for homologous recombination. Chi activates recombination by changing the biochemical properties of the helicase-nuclease, transforming it from a destructive exonuclease into a recombination-promoting repair enzyme. This transition is thought to be controlled by the Chi-dependent opening of a molecular latch, which enables part of the DNA substrate to evade degradation beyond Chi. Here, we show that disruption of the latch improves Chi recognition efficiency and stabilizes the interaction of AddAB with Chi, even in mutants that are impaired for Chi binding. Chi recognition elicits a structural change in AddAB that maps to a region of AddB which resembles a helicase domain, and which harbours both the Chi recognition locus and the latch. Mutation of the latch potentiates the change and moderately reduces the duration of a translocation pause at Chi. However, this mutant displays properties of Chi-modified AddAB even in the complete absence of bona fide hotspot sequences. The results are used to develop a model for AddAB regulation in which allosteric communication between Chi binding and latch opening ensures quality control during recombination hotspot recognition

Anaemia among clinically well under-fives attending a community health centre in Venda, Limpopo Province

Background. Anaemia has been reported to affect 20 - 75% of children in South Africa. The range suggests the effects that geography, health, and socio-economic status can have on the observed prevalence of anaemia within a specific community. Our objective was to investigate the prevalence of anaemia in children aged under 5 presenting for well-child examinations at a community health centre in Thohoyandou, Limpopo Province. Design. A cross-sectional observational study was carried out in June and July 2007. Caregivers participated in a brief interview where demographic, health and nutritional information was collected. A blood sample was collected from each child, and haemoglobin levels were assessed with a point-of-care haemoglobin testing system. Anaemia was defined as having a haemoglobin valu

Atmospheric pressure plasma hydrophilic modification of a silicone surface

Presented in part at the 1st International Conference on Structural Adhesive Bonding (AB2011), Porto, Portugal, 7-8 July 2011.The aim of this study was the creation of a silicone hydrophilic surface prior to bonding. Modifications in wettability and adhesion properties of silicone were performed with an atmospheric plasma torch (APPT). Surface energy variations of the substrate, both pristine and APPT-treated, were evaluated through contact angle measurements, studying the hydrophobic recovery of the samples up to 24 hours of aging. Compositional and topographical changes induced by APPT and aging were studied by attenuated total multiple reflection mode infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), mechanical profilometry, scanning electron microscopy (SEM), and atomic force microscopy (AFM), respectively. Adhesion pull-off tests were performed on silicone-aluminium stud joints using three commercial adhesives, which were Sikaflex®-252, polyurethane-based, Loctite®-330, urethane methacrylate ester-based acrylic, and Terostat®-922, modified silicone. Although experimental data of all the bonding specimens led to an undesired adhesive failure, it was found that APPT-treated samples gave higher adhesive strength than the pristine ones, which was explained by the higher surface energy, thus more wettable material, after APPT. This effect remained stable for just 1 h, when the substrate began its hydrophobic recovery, reaching the original surface energy values after 24 h of aging.Financial support from the Universidad Carlos III de Madrid Foundation and Chemistry and Materials Technological Institute ‘‘Álvaro Alonso Barba’’ are acknowledged, as well as from the Universidad Pontificia Comillas (ICAI) (Spain)