The phylogeny of Ureaplasma urealyticum based on the mba gene fragment

Sequencing of mba gene fragments of reference strains of Ureaplasma urealyticum serovars 1, 3, 6, 14, in addition to 33 clinical U. urealyticum isolates is reported. A phylogenetic tree deduced from an alignment of these sequences clearly demonstrates two major clusters (confidence limit 100%), which equate to the parvo and T960 biovars, and five types which we have designated mba 1, 3, 6, 8 and X. These relationships are supported by bootstrap analysis. Polymorphisms within the mba fragment of types mba 1, 3, and 6 were used to define nine subtypes (mba 1a, 1b, 3a, 3b, 3c, 3d, 3e, 6a, and 6b) thus facilitating high resolution typing of U. urealyticum. Inclusion of the reference strains for serovars 1, 3, 6, and 8 in the mba typing scheme showed that the results of this analysis are broadly consistent with currently accepted serotyping. In addition a ure gene fragment from nine of the clinical isolates was amplified and sequenced. Comparisons of the sequences clearly distinguished the two biovars of U. urealyticum; however this fragment was invariant within the parvo biovar. This study has shown that the sequence of the mba can reveal the fine details of the relationships between U. urealyticum isolates and also supports the significant evolutionary gap between the two biovars.

Intratherapist reliability in the rating of scapula posture in multiple planes of reference

Background: Evaluation of scapular posture is a fundamental component in the clinical evaluation of the upper quadrant. This study examined the intrarater reliability of scapular posture ratings. Methods: A test-retest reliability investigation was undertaken with one week between assessment sessions. At each session physical therapists conducted visual assessments of scapula posture (relative to the thorax) in five different scapula postural planes (plane of scapula, sagittal plane, transverse plane, horizontal plane, and vertical plane). These five plane ratings were performed for four different scapular posture perturbating conditions (rest, isometric shoulder; flexion, abduction, and external rotation). Results. A total of 100 complete scapular posture ratings (50 left, 50 right) were undertaken at each assessment. The observed agreement between the test and retest postural plane ratings ranged from 59% to 87%; 16 of the 20 plane-condition combinations exceeded 75% observed agreement. Kappa (and prevalence adjusted bias adjusted kappa) values were inconsistent across the postural planes and perturbating conditions. Conclusions: This investigation generally revealed fair to moderate intrarater reliability in the rating of scapular posture by visual inspection. However, enough disagreement between assessments was present to warrant caution when interpreting perceived changes in scapula position between longitudinal assessments using visual inspection alone.

Polycaprolactone-based scaffold plus recombinant human bone morphogenic protein rhBMP-2) in a sheep thoracic spine fusion model

Adolescent idiopathic scoliosis is a complex three dimensional deformity affecting 2-3% of the general population. The resulting spinal deformity consists of coronal curvature, hypokyphosis of the thoracic spine and vertebral rotation in the axial plane with posterior elements turned into the curve concavity. The potential for curve progression is heightened during the adolescent growth spurt. Success of scoliosis deformity correction depends on solid bony fusion between adjacent vertebrae after the intervertebral (IV) discs have been surgically cleared and the disc spaces filled with graft material. Recently a bioactive and resorbable scaffold fabricated from medical grade polycaprolactone has been developed for bone regeneration at load bearing sites. Combined with rhBMP-2, this has been shown to be successful in acting as a bone graft substitute in a porcine lumbar interbody fusion model when compared to autologous bone graft alone. The study aimed to establish a large animal thoracic spine interbody fusion model, develop spine biodegradable scaffolds (PCL) in combination with biologics (rhBMP-2) and to establish a platform for research into spine tissue engineering constructs. Preliminary results demonstrate higher grades of radiologically evident bony fusion across all levels when comparing fusion scores between the 3 and 6 month postop groups at the PCL CaP coated scaffold level, which is observed to be a similar grade to autograft, while no fusion is seen at the scaffold only level. Results to date suggest that the combination of rhBMP-2 and scaffold engineering actively promotes bone formation, laying the basis of a viable tissue engineered constructs.

Biomechanical performance of polycaprolactone (PCL)-based scaffold with rhBMP-2 in a sheep thoracic spine fusion model

Adolescent idiopathic scoliosis is a complex three dimensional deformity affecting 2-3% of the general population. Resulting spine deformities include progressive coronal curvature, hypokyphosis, or frank lordosis in the thoracic spine and vertebral rotation in the axial plane with posterior elements turned into the curve concavity. The potential for curve progression is heightened during the adolescent growth spurt. Success of scoliosis deformity correction depends on solid bony fusion between adjacent vertebrae after the intervertebral discs have been surgically cleared and the disc spaces filled with graft material. Problems with bone graft harvest site morbidity as well as limited bone availability have led to the search for bone graft substitutes. Recently, a bioactive and resorbable scaffold fabricated from medical grade polycaprolactone (PCL) has been developed for bone regeneration at load bearing sites. Combined with recombinant human bone morphogenic protein–2 (rhBMP-2), this has been shown to be successful in acting as a bone graft substitute in acting as a bone graft substitute in a porcine lumbar interbody fusion model when compared to autologous bone graft. This in vivo sheep study intends to evaluate the suitability of a custom designed medical grade PCL scaffold in combination with rhBMP-2 as a bone graft substitute in the setting of mini–thoracotomy surgery as a platform for ongoing research to benefit patients with adolescent idiopathic scoliosis.

Patient-specific simulations of spinal deformity surgery

Adolescent idiopathic scoliosis (AIS) is a three-dimensional spinal deformity involving the side-to-side curvature of the spine in the coronal plane and axial rotation of the vertebrae in the transverse plane. For patients with a severe or rapidly progressing deformity, corrective instrumented fusion surgery is performed. The wide choice of implants and large variability between patients make it difficult for surgeons to choose optimal treatment strategies. This paper describes the patient specific finite element modelling techniques employed and the results of preliminary analyses predicting the surgical outcomes for a series of AIS patients. This report highlights the importance of not only patient-specific anatomy and material parameters, but also patient-specific data for the clinical and physiological loading conditions experienced by the patient who has corrective scoliosis surgery.

Preliminary reliability and validity testing of a self-efficacy questionnaire for Chinese family caregivers

Objectives: To develop and test preliminary reliability and validity of a Self-Efficacy Questionnaire for Chinese Family Caregivers (SEQCFC). Methods: A cross-sectional survey of 196 family caregivers (CGs) of people with dementia (CGs) was conducted to determine the factor structure of a SEQCFC of people with dementia. Following factor analyses, preliminary testing was performed, including internal consistency, 4-week test retest reliability, and construct and convergent validity. Results: Factor analyses with direct oblimin rotation were performed. Eight items were removed and five subscales(selfefficacy for gathering information about treatment, symptoms and health care; obtaining support; responding to behaviour disturbances; managing household, personal and medical care; and managing distress associated with caregiving) were identified. The Cronbach’s alpha coefficients for the whole scale and for each subscale were all over 0.80. The 4-week testretest reliabilities for the whole scale and for each subscale ranged from 0.64 to 0.85. The convergent validity was acceptable. Conclusions: Evidence for the preliminary testing of the SEQCFC was encouraging. A future follow-up study using confirmatory factor analysis with a new sample from different recruitment centres in Shanghai will be conducted. Future psychometric property testings of the questionnaire will be required for CGs from other regions of mainland China.

Fourier Lucas-Kanade Algorithm

In this paper we propose a framework for both gradient descent image and object alignment in the Fourier domain. Our method centers upon the classical Lucas & Kanade (LK) algorithm where we represent the source and template/model in the complex 2D Fourier domain rather than in the spatial 2D domain. We refer to our approach as the Fourier LK (FLK) algorithm. The FLK formulation is advantageous when one pre-processes the source image and template/model with a bank of filters (e.g. oriented edges, Gabor, etc.) as: (i) it can handle substantial illumination variations, (ii) the inefficient pre-processing filter bank step can be subsumed within the FLK algorithm as a sparse diagonal weighting matrix, (iii) unlike traditional LK the computational cost is invariant to the number of filters and as a result far more efficient, and (iv) this approach can be extended to the inverse compositional form of the LK algorithm where nearly all steps (including Fourier transform and filter bank pre-processing) can be pre-computed leading to an extremely efficient and robust approach to gradient descent image matching. Further, these computational savings translate to non-rigid object alignment tasks that are considered extensions of the LK algorithm such as those found in Active Appearance Models (AAMs).

Brave new green world : consequences of a carbon economy for the conservation of Australian biodiversity

Pricing greenhouse gas emissions is a burgeoning and possibly lucrative financial means for climate change mitigation. Emissions pricing is being used to fund emissions-abatement technologies and to modify land management to improve carbon sequestration and retention. Here we discuss the principal land-management options under existing and realistic future emissions-price legislation in Australia, and examine them with respect to their anticipated direct and indirect effects on biodiversity. The main ways in which emissions price-driven changes to land management can affect biodiversity are through policies and practices for (1) environmental plantings for carbon sequestration, (2) native regrowth, (3) fire management, (4) forestry, (5) agricultural practices (including cropping and grazing), and (6) feral animal control. While most land-management options available to reduce net greenhouse gas emissions offer clear advantages to increase the viability of native biodiversity, we describe several caveats regarding potentially negative outcomes, and outline components that need to be considered if biodiversity is also to benefit from the new carbon economy. Carbon plantings will only have real biodiversity value if they comprise appropriate native tree species and provide suitable habitats and resources for valued fauna. Such plantings also risk severely altering local hydrology and reducing water availability. Management of regrowth post-agricultural abandonment requires setting appropriate baselines and allowing for thinning in certain circumstances, and improvements to forestry rotation lengths would likely increase carbon-retention capacity and biodiversity value. Prescribed burning to reduce the frequency of high-intensity wildfires in northern Australia is being used as a tool to increase carbon retention. Fire management in southern Australia is not readily amenable for maximising carbon storage potential, but will become increasingly important for biodiversity conservation as the climate warms. Carbon price-based modifications to agriculture that would benefit biodiversity include reductions in tillage frequency and livestock densities, reductions in fertiliser use, and retention and regeneration of native shrubs; however, anticipated shifts to exotic perennial grass species such as buffel grass and kikuyu could have net negative implications for native biodiversity. Finally, it is unlikely that major reductions in greenhouse gas emissions arising from feral animal control are possible, even though reduced densities of feral herbivores will benefit Australian biodiversity greatly.

Cross-calbration of push-broom 2D LIDARs and cameras in natural scenes

This paper addresses the problem of automatically estimating the relative pose between a push-broom LIDAR and a camera without the need for artificial calibration targets or other human intervention. Further we do not require the sensors to have an overlapping field of view, it is enough that they observe the same scene but at different times from a moving platform. Matching between sensor modalities is achieved without feature extraction. We present results from field trials which suggest that this new approach achieves an extrinsic calibration accuracy of millimeters in translation and deci-degrees in rotation.

Intern underperformance is detected more frequently in emergency medicine rotations

Objective: To determine the frequency and nature of intern underperformance as documented on in-training assessment forms. Methods: A retrospective review of intern assessment forms from a 2 year period (2009–2010) was conducted at a tertiary referral hospital in Brisbane, Queensland. The frequency of interns assessed as ‘requiring substantial assistance’ and/or ‘requires further development’ on mid- or end-of-term assessment forms was determined. Forms were analysed by the clinical rotation, time of year and domain(s) of clinical practice in which underperformance was documented. Results: During 2009 and 2010 the overall documented incidence of intern underperformance was 2.4% (95% CI 1.5–3.9%). Clinical rotation in emergency medicine detected significantly more underperformance compared with other rotations (P < 0.01). Interns predominantly had difficulty with ‘clinical judgment and decision-making skills’, ‘time management skills’ and ‘teamwork and colleagues’ (62.5%, 55% and 32.5% of underperforming assessments, respectively). Time of the year did not affect frequency of underperformance. A proportion of 13.4% (95% CI 9.2–19.0%) of interns working at the institution over the study period received at least one assessment in which underperformance was documented. Seventy-six per cent of those interns who had underperformance identified by mid-term assessment successfully completed the term following remediation. Conclusion: The prevalence of underperformance among interns is low, although higher than previously suggested. Emergency medicine detects relatively more interns in difficulty than other rotations.

Hydrogen bonding in two ammonium salts of 5-sulfosalicylic acid : ammonium 3-carboxy-4-hydroxybenzenesulfonate monohydrate and triammonium 3-carboxy-4-hydroxybenzenesulfonate 3-carboxylato-4-hydroxybenzenesulfonate

The structures of two ammonium salts of 3-carboxy-4-hydroxybenzenesulfonic acid (5-sulfosalicylic acid, 5-SSA) have been determined at 200 K. In the 1:1 hydrated salt, ammonium 3-carboxy-4-hydroxybenzenesulfonate monohydrate, NH4+·C7H5O6S-·H2O, (I), the 5-SSA- monoanions give two types of head-to-tail laterally linked cyclic hydrogen-bonding associations, both with graph-set R44(20). The first involves both carboxylic acid O-HOwater and water O-HOsulfonate hydrogen bonds at one end, and ammonium N-HOsulfonate and N-HOcarboxy hydrogen bonds at the other. The second association is centrosymmetric, with end linkages through water O-HOsulfonate hydrogen bonds. These conjoined units form stacks down c and are extended into a three-dimensional framework structure through N-HO and water O-HO hydrogen bonds to sulfonate O-atom acceptors. Anhydrous triammonium 3-carboxy-4-hydroxybenzenesulfonate 3-carboxylato-4-hydroxybenzenesulfonate, 3NH4+·C7H4O6S2-·C7H5O6S-, (II), is unusual, having both dianionic 5-SSA2- and monoanionic 5-SSA- species. These are linked by a carboxylic acid O-HO hydrogen bond and, together with the three ammonium cations (two on general sites and the third comprising two independent half-cations lying on crystallographic twofold rotation axes), give a pseudo-centrosymmetric asymmetric unit. Cation-anion hydrogen bonding within this layered unit involves a cyclic R33(8) association which, together with extensive peripheral N-HO hydrogen bonding involving both sulfonate and carboxy/carboxylate acceptors, gives a three-dimensional framework structure. This work further demonstrates the utility of the 5-SSA- monoanion for the generation of stable hydrogen-bonded crystalline materials, and provides the structure of a dianionic 5-SSA2- species of which there are only a few examples in the crystallographic literature.

The effect of testing protocol on immature bovine thoracic spine segment stiffness

Introduction. In vitro spine biomechanical testing has been central to many advances in understanding the physiology and pathology of the human spine. Owing to the difficulty in obtaining sufficient numbers of human samples to conduct these studies, animal spines have been accepted as a substitute model. However, it is difficult to compare results from different studies, as they use different preparation, testing and data collection methods. The aim of this study was to identify the effect of repeated cyclic loading on bovine spine segment stiffness. It also aimed to quantify the effect of multiple freeze-thaw sequences, as many tests would be difficult to complete in a single session [1-3]. Materials and Methods. Thoracic spines from 6-8 week old calves were used. Each spine was dissected and divided into motion segments including levels T4-T11 (n=28). These were divided into two equal groups. Each segment was potted in polymethylemethacrylate. An Instron Biaxial materials testing machine with a custom made jig was used for testing. The segments were tested in flexion/extension, lateral bending and axial rotation at 37 degrees C and 100% humidity, using moment control to a maximum plus/minus 1.75 Nm with a loading rate of 0.3 Nm per second. Group (A) were tested with continuous repeated cyclic loading for 500 cycles with data recorded at cycles 3, 5, 10, 25, 100, 200, 300, 400 and 500. Group (B) were tested with 10 load cycles after each of 5 freeze thaw sequences. Data was collected from the tenth load cycle after each sequence. Statistical analysis of the data was performed using paired samples t-tests, ANOVA and generalized estimating equations. Results. The data were confirmed as having a normal distribution. 1. There were significant reductions in mean stiffness in flexion/extension (-20%; P=0.001) and lateral bending (-17%; P=0.009) over the 500 load cycles. However, there was no statistically significant change in axial rotation (P=0.152) 2. There was no statistically significant difference between mean stiffness over the five freeze-thaw sequences in flexion/extension (p=0.879) and axial rotation (p=0.07). However, there was a significant reduction in stiffness in lateral bending (-26%; p=0.007) Conclusion. Biomechanical testing of immature bovine spine motion segments requires careful interpretation. The effect of the number of load cycles as well as the number of freeze-thaw cycles on the stiffness of the motion segments depends on the axis of main movement.

Segmental torso masses and coronal plane joint torques in the adolescent scoliotic spine

Introduction. Calculating segmental (vertebral level-by-level) torso masses in Adolescent Idiopathic Scoliosis (AIS) patients allows the gravitational loading on the scoliotic spine during relaxed standing to be determined. This study used CT scans of AIS patients to measure segmental torso masses and explores how joint moments in the coronal plane are affected by changes in the position of the intervertebral joint’s axis of rotation; particularly at the apex of a scoliotic major curve. Methods. Existing low dose CT data from the Paediatric Spine Research Group was used to calculate vertebral level-by-level torso masses and joint torques occurring in the spine for a group of 20 female AIS patients (mean age 15.0 ± 2.7 years, mean Cobb angle 53 ± 7.1°). Image processing software, ImageJ (v1.45 NIH USA) was used to threshold the T1 to L5 CT images and calculate the segmental torso volume and mass corresponding to each vertebral level. Body segment masses for the head, neck and arms were taken from published anthropometric data. Intervertebral (IV) joint torques at each vertebral level were found using principles of static equilibrium together with the segmental body mass data. Summing the torque contributions for each level above the required joint, allowed the cumulative joint torque at a particular level to be found. Since there is some uncertainty in the position of the coronal plane Instantaneous Axis of Rotation (IAR) for scoliosis patients, it was assumed the IAR was located in the centre of the IV disc. A sensitivity analysis was performed to see what effect the IAR had on the joint torques by moving it laterally 10mm in both directions. Results. The magnitude of the torso masses from T1-L5 increased inferiorly, with a 150% increase in mean segmental torso mass from 0.6kg at T1 to 1.5kg at L5. The magnitudes of the calculated coronal plane joint torques during relaxed standing were typically 5-7 Nm at the apex of the curve, with the highest apex joint torque of 7Nm being found in patient 13. Shifting the assumed IAR by 10mm towards the convexity of the spine, increased the joint torque at that level by a mean 9.0%, showing that calculated joint torques were moderately sensitive to the assumed IAR location. When the IAR midline position was moved 10mm away from the convexity of the spine, the joint torque reduced by a mean 8.9%. Conclusion. Coronal plane joint torques as high as 7Nm can occur during relaxed standing in scoliosis patients, which may help to explain the mechanics of AIS progression. This study provides new anthropometric reference data on vertebral level-by-level torso mass in AIS patients which will be useful for biomechanical models of scoliosis progression and treatment. However, the CT scans were performed in supine (no gravitational load on spine) and curve magnitudes are known to be smaller than those measured in standing.

Inter-vertebral rotational deformity after endoscopic anterior scoliosis correction may contribute to rib hump recurrence after two years

Introduction. Endoscopic anterior scoliosis correction has been employed recently as a less invasive and level-sparing approach compared with open surgical techniques. We have previously demonstrated that during the two-year post-operative period, there was a mean loss of rib hump correction by 1.4 degrees. The purpose of this study was to determine whether intra- or inter-vertebral rotational deformity during the post-operative period could account for the loss of rib hump correction. Materials and Methods. Ten consecutive patients diagnosed with adolescent idiopathic scoliosis were treated with an endoscopic anterior scoliosis correction. Low-dose computed tomography scans of the instrumented segment were obtained post-operatively at 6 and 24 months following institutional ethical approval and patient consent. Three-dimensional multi-planar reconstruction software (Osirix Imaging Software, Pixmeo, Switzerland) was used to create axial slices of each vertebral level, corrected in both coronal and sagittal planes. Vertebral rotation was measured using Ho’s method for every available superior and inferior endplate at 6 and 24 months. Positive changes in rotation indicate a reduction and improvement in vertebral rotation. Intra-observer variability analysis was performed on a subgroup of images. Results. Mean change in rotation for vertebral endplates between 6 and 24 months post-operatively was -0.26˚ (range -3.5 to 4.9˚) within the fused segment and +1.26˚ (range -7.2 to 15.1˚) for the un-instrumented vertebrae above and below the fusion. Mean change in clinically measured rib hump for the 10 patients was -1.6˚ (range -3 to 0˚). The small change in rotation within the fused segment accounts for only 16.5% of the change in rib hump measured clinically whereas the change in rotation between the un-instrumented vertebrae above and below the construct accounts for 78.8%. There was no clear association between rib hump recurrence and intra- or inter-vertebral rotation in individual patients. Intra-rater variability was ± 3˚. Conclusions. Intra- and inter-vertebral rotation continues post-operatively both within the instrumented and un-instrumented segments of the immature spine. Rotation between the un-instrumented vertebrae above and below the fusion was +1.26˚, suggesting that the un-instrumented vertebrae improved and de-rotated slightly after surgery. This may play a role in rib hump recurrence, however this remains clinically insignificant.

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

Background Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study. Results In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender information (GenCall, GenoSNP). We observe that CRLMM and GenoSNP are more accurate at calling SNPs with low minor allele frequency than GenCall or Illuminus. The sample quality metrics from each of the four methods were found to have a high level of agreement at flagging samples with unusual signal characteristics. Conclusions CRLMM, GenoSNP and GenCall can be applied with confidence in studies of any size, as their performance was shown to be invariant to the number of samples available. Illuminus on the other hand requires a larger number of samples to achieve comparable levels of accuracy and its use in smaller studies (50 or fewer individuals) is not recommended.