Multiple human single-stranded DNA binding proteins function in genome maintenance : structural, biochemical and functional analysis

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two singlestranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein–protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.

An assessment system for evaluation of driving competencies

Automobiles have deeply impacted the way in which we travel but they have also contributed to many deaths and injury due to crashes. A number of reasons for these crashes have been pointed out by researchers. Inexperience has been identified as a contributing factor to road crashes. Driver’s driving abilities also play a vital role in judging the road environment and reacting in-time to avoid any possible collision. Therefore driver’s perceptual and motor skills remain the key factors impacting on road safety. Our failure to understand what is really important for learners, in terms of competent driving, is one of the many challenges for building better training programs. Driver training is one of the interventions aimed at decreasing the number of crashes that involve young drivers. Currently, there is a need to develop comprehensive driver evaluation system that benefits from the advances in Driver Assistance Systems. A multidisciplinary approach is necessary to explain how driving abilities evolves with on-road driving experience. To our knowledge, driver assistance systems have never been comprehensively used in a driver training context to assess the safety aspect of driving. The aim and novelty of this thesis is to develop and evaluate an Intelligent Driver Training System (IDTS) as an automated assessment tool that will help drivers and their trainers to comprehensively view complex driving manoeuvres and potentially provide effective feedback by post processing the data recorded during driving. This system is designed to help driver trainers to accurately evaluate driver performance and has the potential to provide valuable feedback to the drivers. Since driving is dependent on fuzzy inputs from the driver (i.e. approximate distance calculation from the other vehicles, approximate assumption of the other vehicle speed), it is necessary that the evaluation system is based on criteria and rules that handles uncertain and fuzzy characteristics of the driving tasks. Therefore, the proposed IDTS utilizes fuzzy set theory for the assessment of driver performance. The proposed research program focuses on integrating the multi-sensory information acquired from the vehicle, driver and environment to assess driving competencies. After information acquisition, the current research focuses on automated segmentation of the selected manoeuvres from the driving scenario. This leads to the creation of a model that determines a “competency” criterion through the driving performance protocol used by driver trainers (i.e. expert knowledge) to assess drivers. This is achieved by comprehensively evaluating and assessing the data stream acquired from multiple in-vehicle sensors using fuzzy rules and classifying the driving manoeuvres (i.e. overtake, lane change, T-crossing and turn) between low and high competency. The fuzzy rules use parameters such as following distance, gaze depth and scan area, distance with respect to lanes and excessive acceleration or braking during the manoeuvres to assess competency. These rules that identify driving competency were initially designed with the help of expert’s knowledge (i.e. driver trainers). In-order to fine tune these rules and the parameters that define these rules, a driving experiment was conducted to identify the empirical differences between novice and experienced drivers. The results from the driving experiment indicated that significant differences existed between novice and experienced driver, in terms of their gaze pattern and duration, speed, stop time at the T-crossing, lane keeping and the time spent in lanes while performing the selected manoeuvres. These differences were used to refine the fuzzy membership functions and rules that govern the assessments of the driving tasks. Next, this research focused on providing an integrated visual assessment interface to both driver trainers and their trainees. By providing a rich set of interactive graphical interfaces, displaying information about the driving tasks, Intelligent Driver Training System (IDTS) visualisation module has the potential to give empirical feedback to its users. Lastly, the validation of the IDTS system’s assessment was conducted by comparing IDTS objective assessments, for the driving experiment, with the subjective assessments of the driver trainers for particular manoeuvres. Results show that not only IDTS was able to match the subjective assessments made by driver trainers during the driving experiment but also identified some additional driving manoeuvres performed in low competency that were not identified by the driver trainers due to increased mental workload of trainers when assessing multiple variables that constitute driving. The validation of IDTS emphasized the need for an automated assessment tool that can segment the manoeuvres from the driving scenario, further investigate the variables within that manoeuvre to determine the manoeuvre’s competency and provide integrated visualisation regarding the manoeuvre to its users (i.e. trainers and trainees). Through analysis and validation it was shown that IDTS is a useful assistance tool for driver trainers to empirically assess and potentially provide feedback regarding the manoeuvres undertaken by the drivers.

Investigation into the introduction of clonal strains of Pseudomonas aeruginosa to the cystic fibrosis population by consumption of raw salad vegetables

Most salad vegetables are eaten fresh by consumers. However, raw vegetables may pose a risk of transmitting opportunistic bacteria to immunocompromised people, including cystic fibrosis (CF) patients. In particular, CF patients are vulnerable to chronic Pseudomonas aeruginosa lung infections and this organism is the primary cause of morbidity and mortality in this group. Clonal variants of P. aeruginosa have been identified as emerging threats to people afflicted with CF; however it has not yet been proven from where these clones originate or how they are transmitted. Due to the organisms‟ aquatic environmental niche, it was hypothesised that vegetables may be a source of these clones. To test this hypothesis, lettuce, tomatoes, mushrooms and bean sprout packages (n = 150) were analysed from a green grocer, supermarket and farmers‟ market within the Brisbane region, availability permitting. The internal and external surfaces of the vegetables were separately analysed for the presence of clonal strains of P. aeruginosa using washings and homogenisation techniques, respectively. This separation was in an attempt to establish which surface was contaminated, so that recommendations could be made to decrease or eliminate P. aeruginosa from these foods prior to consumption. Soil and water samples (n = 17) from local farms were also analysed for the presence of P. aeruginosa. Presumptive identification of isolates recovered from these environmental samples was made based on growth on Cetrimide agar at 42°C, presence of the cytochrome-oxidase enzyme and inability to ferment lactose. P. aeruginosa duplex real-time polymerase chain reaction assay (PAduplex) was performed on all bacterial isolates presumptively identified as P. aeruginosa. Enterobacterial repetitive intergenic consensus strain typing PCR (ERIC-PCR) was subsequently performed on confirmed bacterial isolates. Although 72 P. aeruginosa were isolated, none of these proved to be clonal strains. The significance of these findings is that vegetables may pose a risk of transmitting sporadic strains of P. aeruginosa to people afflicted with CF and possibly, other immunocompromised people.

Bis(guanidinium) 4,5-dichlorophthalate monohydrate

In the structure of the title hydrate salt 2(CH6N3)+ C8H2Cl2O42- . H2O, the planes of the carboxylate groups of the dianion are rotated out of the plane of the benzene ring [dihedral angles 48.42(10) and 55.64(9)deg.]. A duplex-sheet structure is formed through guanidinium-carboxylate N-H...O, guanidinium-water N-H...O, and water-carboxylate O-H..O hydrogen-bonding associations.

Real-time volume estimation of a dragline payload

This paper presents a method for measuring the in-bucket payload volume on a dragline excavator for the purpose of estimating the material's bulk density in real-time. Knowledge of the payload's bulk density can provide feedback to mine planning and scheduling to improve blasting and therefore provide a more uniform bulk density across the excavation site. This allows a single optimal bucket size to be used for maximum overburden removal per dig and in turn reduce costs and emissions in dragline operation and maintenance. The proposed solution uses a range bearing laser to locate and scan full buckets between the lift and dump stages of the dragline cycle. The bucket is segmented from the scene using cluster analysis, and the pose of the bucket is calculated using the Iterative Closest Point (ICP) algorithm. Payload points are identified using a known model and subsequently converted into a height grid for volume estimation. Results from both scaled and full scale implementations show that this method can achieve an accuracy of above 95%.

A biomechanical investigation of vertebral staples for fusionless scoliosis correction

Background: Fusionless scoliosis surgery is an early-stage treatment for idiopathic scoliosis which claims potential advantages over current fusion-based surgical procedures. Anterior vertebral stapling using a shape memory alloy staple is one such approach. Despite increasing interest in this technique, little is known about the effects on the spine following insertion, or the mechanism of action of the staple. The purpose of this study was to investigate the biomechanical consequences of staple insertion in the anterior thoracic spine, using in vitro experiments on an immature bovine model. Methods: Individual calf spine thoracic motion segments were tested in flexion, extension, lateral bending and axial rotation. Changes in motion segment rotational stiffness following staple insertion were measured on a series of 14 specimens. Strain gauges were attached to three of the staples in the series to measure forces transmitted through the staple during loading. A micro-CT scan of a single specimen was performed after loading to qualitatively examine damage to the vertebral bone caused by the staple. Findings: Small but statistically significant decreases in bending stiffness occurred in flexion,extension, lateral bending away from the staple, and axial rotation away from the staple. Each strain-gauged staple showed a baseline compressive loading following insertion which was seen to gradually decrease during testing. Post-test micro-CT showed substantial bone and growth plate damage near the staple. Interpretation: Based on our findings it is possible that growth modulation following staple insertion is due to tissue damage rather than sustained mechanical compression of the motion segment.

Assessment of corneal dynamics with high-speed swept source optical coherence tomography combined with an air puff system

We present a novel method and instrument for in vivo imaging and measurement of the human corneal dynamics during an air puff. The instrument is based on high-speed swept source optical coherence tomography (ssOCT) combined with a custom adapted air puff chamber from a non-contact tonometer, which uses an air stream to deform the cornea in a non-invasive manner. During the short period of time that the deformation takes place, the ssOCT acquires multiple A-scans in time (M-scan) at the center of the air puff, allowing observation of the dynamics of the anterior and posterior corneal surfaces as well as the anterior lens surface. The dynamics of the measurement are driven by the biomechanical properties of the human eye as well as its intraocular pressure. Thus, the analysis of the M-scan may provide useful information about the biomechanical behavior of the anterior segment during the applanation caused by the air puff. An initial set of controlled clinical experiments are shown to comprehend the performance of the instrument and its potential applicability to further understand the eye biomechanics and intraocular pressure measurements. Limitations and possibilities of the new apparatus are discussed.

Laser doppler imaging in a paediatric burns population

Objective Laser Doppler imaging (LDI) was compared to wound outcomes in children's burns, to determine if the technology could be used to predict these outcomes. Methods Forty-eight patients with a total of 85 burns were included in the study. Patient median age was 4 years 10 months and scans were taken 0–186 h post-burn using the fast, low-resolution setting on the Moor LDI2 laser Doppler imager. Wounds were managed by standard practice, without taking into account the scan results. Time until complete re-epithelialisation and whether or not grafting and scar management were required were recorded for each wound. If wounds were treated with Silvazine™ or Acticoat™ prior to the scan, this was also recorded. Results The predominant colour of the scan was found to be significantly related to the re-epithelialisation, grafting and scar management outcomes and could be used to predict those outcomes. The prior use of Acticoat™ did not affect the scan relationship to outcomes, however, the use of Silvazine™ did complicate the relationship for light blue and green scanned partial thickness wounds. Scans taken within the 24-h window after-burn also appeared to be accurate predictors of wound outcome. Conclusion Laser Doppler imaging is accurate and effective in a paediatric population with a low-resolution fast-scan.

Towards automated and in-situ, near-real time 3-D reconstruction of coral reef environments

Coral reefs are biologically complex ecosystems that support a wide variety of marine organisms. These are fragile communities under enormous threat from natural and human-based influences. Properly assessing and measuring the growth and health of reefs is essential to understanding impacts of ocean acidification, coastal urbanisation and global warming. In this paper, we present an innovative 3-D reconstruction technique based on visual imagery as a non-intrusive, repeatable, in situ method for estimating physical parameters, such as surface area and volume for efficient assessment of long-term variability. The reconstruction algorithms are presented, and benchmarked using an existing data set. We validate the technique underwater, utilising a commercial-off-the-shelf camera and a piece of staghorn coral, Acropora cervicornis. The resulting reconstruction is compared with a laser scan of the coral piece for assessment and validation. The comparison shows that 77% of the pixels in the reconstruction are within 0.3 mm of the ground truth laser scan. Reconstruction results from an unknown video camera are also presented as a segue to future applications of this research.

A pilot study assessing the feasibility of a home-based progressive resistance exercise program and trend toward healing rates for patients with venous leg ulcers

Venous leg ulceration is a serious condition affecting 1 – 3% of the population. Decline in the function of the calf muscle pump is correlated with venous ulceration. Many previous studies have reported an improvement in the function of the calf muscle pump, endurance of the calf muscle and increased range of ankle motion after structured exercise programs. However, there is a paucity of published research that assesses if these improvements result in an improvement in the healing rates of venous ulcers. The primary purpose of this pilot study was to establish the feasibility of a homebased progressive resistance exercise program and examine if there was any clinical significance or trend toward healing. The secondary aims were to examine the benefit of a home-based progressive resistance exercise program on calf muscle pump function and physical parameters. The methodology used was a randomised controlled trial where eleven participants were randomised into an intervention (n = 6) or control group (n = 5). Participants who were randomised to receive a 12-week home-based progressive resistance exercise program were instructed through weekly face-to-face consultations during their wound clinic appointment by the author. Control group participants received standard wound care and compression therapy. Changes in ulcer parameters were measured fortnightly at the clinic (number healed at 12 weeks, percentage change in area and pressure ulcer score healing score). An air plethysmography test was performed at baseline and following the 12 weeks of training to determine changes in calf muscle pump function. Functional measures included maximum number of heel raises (endurance), maximal isometric plantar flexion (strength) and range of ankle motion (ROAM); these tests were conducted at baseline, week 6 and week 12. The sample for the study was drawn from the Princess Alexandra Hospital in Brisbane, Australia. Participants with venous leg ulceration who met the inclusion criteria were recruited. The participants were screened via duplex scanning and ankle brachial pressure index (ABPI) to ensure they did not have any arterial complications. Participants were excluded if there was evidence of cellulitis. Demographic data were obtained from each participant and details regarding medical history, quality of life and geriatric depression scores were collected at baseline. Both the intervention and control group were required to complete a weekly exercise diary to monitor activity levels between groups. To test for the effect of the intervention over time, a repeated measures analysis of variance was conducted on the major outcome variables. Group (intervention versus control) was the between subject factor and time (baseline, week 6, week 12) was the within subject or repeated measures factor. Due to the small sample size, further tests were conducted to check the assumptions of the statistical test to be used. The results showed that Mauchly.s Test, the Sphericity assumptions of repeated measures for ANOVA were met. Further tests of homogeneity of variance assumptions also confirmed that this assumption was met. Data analysis was conducted using the software package SPSS for Windows Release 17.0. The pilot study proved feasible with all of the intervention (n=6) participants continuing with the resistance program for the 12 week duration and no deleterious effects noted. Clinical significance was observed in the intervention group with a 32% greater change in ulcer size (p= 0.26) than the control group, and a 10% (p = 0.74) greater difference between the numbers healed compared to the control group. Statistical significance was observed for the ejection fraction (p = 0.05), residual volume fraction (p = 0.04) and ROAM (p = 0.01), which all improved significantly in the intervention group over time. These results are encouraging, nevertheless, further investigations seem warranted to examine the effect exercise has on the healing rates of venous leg ulcers, with a multistudy site, larger sample size and longer follow up period.

Improved image quality for x-ray CT imaging of gel dosimeters

Purpose: This study provides a simple method for improving precision of x-ray computed tomography (CT) scans of irradiated polymer gel dosimetry. The noise affecting CT scans of irradiated gels has been an impediment to the use of clinical CT scanners for gel dosimetry studies. Method: In this study, it is shown that multiple scans of a single PAGAT gel dosimeter can be used to extrapolate a ‘zero-scan’ image which displays a similar level of precision to an image obtained by averaging multiple CT images, without the compromised dose measurement resulting from the exposure of the gel to radiation from the CT scanner. Results: When extrapolating the zero-scan image, it is shown that exponential and simple linear fits to the relationship between Hounsfield unit and scan number, for each pixel in the image, provides an accurate indication of gel density. Conclusions: It is expected that this work will be utilised in the analysis of three-dimensional gel volumes irradiated using complex radiotherapy treatments.

Optical waveguide and cavity effects on whispering-gallery mode resonances in a ZnO nanonail

Spatially resolved cathodoluminescence (CL) study of a ZnO nanonail, having thin shank, tapered neck, and hexagonal head sections, is reported. Monochromatic imaging and line scan profiling indicate that the wave guiding and leaking from growth imperfections in addition to the oxygen deficiency variation determine the spatial contrast of CL emissions. Occurrence of resonance peaks at identical wavelengths regardless of CL-excitation spots is inconsistent with the whispering-gallery mode (WGM) resonances of a two-dimensional cavity in the finite difference time domain simulation. However, three dimensioanl cavity simulation produced WGM peaks that are consistent with the experimental spectra, including transverse-electric resonances that are comparable to transverse-magnetic ones.

Letter to the editor : likelihood of tetraplegia after CT clearance of the cervical spine in obtunded blunt trauma patients

...the probabilistic computer simulation study by Dunham and colleagues evaluating the impact of different cervical spine management (CSM) strategies on tetraplegia and brain injury outcomes.1 Based on literature findings, expert opinion and with use of advances programming techniques the authors conclude that early collar removal without cervical spine magnetic resonance imaging (MRI) is a preferable CSM strategy for comatose, blunt trauma patients with extremity movement and a negative cervical spine computed tomography(CT) scan. Although we do not have the required expertise to comment on the applied statistical approach, we would like to comment on one of the medical assumptions raised by the authors, namely the likelihood of tetraplegia in this specific population....

Technical note : a technique for measuring the surface area of articular cartilage in acetabular fractures

The aim of this study was to develop a reliable technique for measuring the area of a curved surface from an axial computed tomography (CT) scan and to apply this clinically in the measurement of articular cartilage surface area in acetabular fractures. The method used was a triangulation algorithm. In order to determine the accuracy of the technique, areas of hemispheres of known size were measured to give the percentage error in area measurement. Seven such hemispheres were machined into a Perspex block and their area measured geometrically, and also from CT scans by means of the triangulation algorithm. Scans of 1, 2 and 4 mm slice thickness and separation were used. The error varied with slice thickness and hemisphere diameter. It was shown that the 2 mm slice thickness provides the most accurate area measurement, while 1 mm cuts overestimate and 4 mm cuts underestimate the area. For a hemisphere diameter of 5 cm, which is of similar size to the acetabulum, the error was -11.2% for 4 mm cuts, +4.2% for 2 mm cuts and + 5.1% for 1 mm cuts. As expected, area measurement was more accurate for larger hemispheres. This method can be applied clinically to quantify acetabular fractures by measuring the percentage area of intact articular cartilage. In the case of both column fractures, the percentage area of secondary congruence can be determined. This technique of quantifying acetabular fractures has a potential clinical application as a prognostic factor and an indication for surgery in the long term.