An analysis of the prevalence of children with disabilities and disabling chronic illnesses in the Western health sub-district of Cape Town, and the services available for them

Children with disabling chronic illnesses are known to have complex and frequently unmet health care needs. Limited information exists in South Africa regarding the prevalence of children with disability, as well their needs and utilization of services. The purpose of the current study is twofold: (1) identify the number of children known with disability, or disabling chronic illnesses in the western health sub-district of Cape Town; (2) analyse the health services that currently exist for these children. A period prevalence survey was conducted between January 2010 and December 2011. Numerous sources of information were sought to identify as many children with disabling chronic illness as possible. These included the referral hospitals for the Western sub-district, namely Red Cross War Memorial Children's Hospital and New Somerset Hospital, as well as the institutions where children with disability are cared for or educated, and relevant non-profit organisations in the disability sector. Information was gathered between January 2011 and Sept 2012

An investigation of the Eigenvalue Calibration Method (ECM) using GASP for non-imaging and imaging detectors

Polarised light from astronomical targets can yield a wealth of information about their source radiation mechanisms, and about the geometry of the scattered light regions. Optical observations, of both the linear and circular polarisation components, have been impeded due to non-optimised instrumentation. The need for suitable observing conditions and the availability of luminous targets are also limiting factors. GASP uses division of amplitude polarimeter (DOAP) (Compain and Drevillon) to measure the four components of the Stokes vector simultaneously, which eliminates the constraints placed upon the need for moving parts during observation, and offers a real-time complete measurement of polarisation. Results from the GASP calibration are presented in this work for both a 1D detector system, and a pixel-by-pixel analysis on a 2D detector system. Following Compain et al. we use the Eigenvalue Calibration Method (ECM) to measure the polarimetric limitations of the instrument for each of the two systems. Consequently, the ECM is able to compensate for systematic errors introduced by the calibration optics, and it also accounts for all optical elements of the polarimeter in the output. Initial laboratory results of the ECM are presented, using APD detectors, where errors of 0.2% and 0.1{\deg} were measured for the degree of linear polarisation and polarisation angle respectively. Channel-to-channel image registration is an important aspect of 2-D polarimetry. We present our calibration results of the measured Mueller matrix of each sample, used by the ECM. A set of Zenith flat-field images were recorded during an observing campaign at the Palomar 200 inch telescope in November 2012. From these we show the polarimetric errors from the spatial polarimetry indicating both the stability and absolute accuracy of GASP.Comment: Accepted for publication in Experimental Astronom

CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures

We present CATHEDRAL, an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure–based method (using graph theory) to locate known folds within a multidomain context and a residue-based, double-dynamic programming algorithm, which is used to align members of the target fold groups against the query protein structure to identify the closest relative and assign domain boundaries. To increase the fidelity of the assignments, a support vector machine is used to provide an optimal scoring scheme. Once a domain is verified, it is excised, and the search protocol is repeated in an iterative fashion until all recognisable domains have been identified. We have performed an initial benchmark of CATHEDRAL against other publicly available structure comparison methods using a consensus dataset of domains derived from the CATH and SCOP domain classifications. CATHEDRAL shows superior performance in fold recognition and alignment accuracy when compared with many equivalent methods. If a novel multidomain structure contains a known fold, CATHEDRAL will locate it in 90% of cases, with <1% false positives. For nearly 80% of assigned domains in a manually validated test set, the boundaries were correctly delineated within a tolerance of ten residues. For the remaining cases, previously classified domains were very remotely related to the query chain so that embellishments to the core of the fold caused significant differences in domain sizes and manual refinement of the boundaries was necessary. To put this performance in context, a well-established sequence method based on hidden Markov models was only able to detect 65% of domains, with 33% of the subsequent boundaries assigned within ten residues. Since, on average, 50% of newly determined protein structures contain more than one domain unit, and typically 90% or more of these domains are already classified in CATH, CATHEDRAL will considerably facilitate the automation of protein structure classification

Mechanical suppression of osteolytic bone metastases in advanced breast cancer patients: A randomised controlled study protocol evaluating safety, feasibility and preliminary efficacy of exercise as a targeted medicine

Background: Skeletal metastases present a major challenge for clinicians, representing an advanced and typically incurable stage of cancer. Bone is also the most common location for metastatic breast carcinoma, with skeletal lesions identified in over 80% of patients with advanced breast cancer. Preclinical models have demonstrated the ability of mechanical stimulation to suppress tumour formation and promote skeletal preservation at bone sites with osteolytic lesions, generating modulatory interference of tumour-driven bone remodelling. Preclinical studies have also demonstrated anti-cancer effects through exercise by minimising tumour hypoxia, normalising tumour vasculature and increasing tumoural blood perfusion. This study proposes to explore the promising role of targeted exercise to suppress tumour growth while concomitantly delivering broader health benefits in patients with advanced breast cancer with osteolytic bone metastases. Methods: This single-blinded, two-armed, randomised and controlled pilot study aims to establish the safety, feasibility and efficacy of an individually tailored, modular multi-modal exercise programme incorporating spinal isometric training (targeted muscle contraction) in 40 women with advanced breast cancer and stable osteolytic spinal metastases. Participants will be randomly assigned to exercise or usual medical care. The intervention arm will receive a 3-month clinically supervised exercise programme, which if proven to be safe and efficacious will be offered to the control-arm patients following study completion. Primary endpoints (programme feasibility, safety, tolerance and adherence) and secondary endpoints (tumour morphology, serum tumour biomarkers, bone metabolism, inflammation, anthropometry, body composition, bone pain, physical function and patient-reported outcomes) will be measured at baseline and following the intervention. Discussion: Exercise medicine may positively alter tumour biology through numerous mechanical and nonmechanical mechanisms. This randomised controlled pilot trial will explore the preliminary effects of targeted exercise on tumour morphology and circulating metastatic tumour biomarkers using an osteolytic skeletal metastases model in patients with breast cancer. The study is principally aimed at establishing feasibility and safety. If proven to be safe and feasible, results from this study could have important implications for the delivery of this exercise programme to patients with advanced cancer and sclerotic skeletal metastases or with skeletal lesions present in haematological cancers (such as osteolytic lesions in multiple myeloma), for which future research is recommended. Trial registration: anzctr.org.au, ACTRN-12616001368426. Registered on 4 October 2016

Association of computed tomography measures of muscle and adipose tissue and progressive changes throughout treatment with clinical endpoints in patients with advanced lung cancer treated with immune checkpoint inhibitors

To investigate the association between skeletal muscle mass and adiposity measures with disease-free progression (DFS) and overall survival (OS) in patients with advanced lung cancer receiving immunotherapy, we retrospectively analysed 97 patients (age: 67.5 ± 10.2 years) with lung cancer who were treated with immunotherapy between March 2014 and June 2019. From computed tomography scans, we assessed the radiological measures of skeletal muscle mass, and intramuscular, subcutaneous and visceral adipose tissue at the third lumbar vertebra. Patients were divided into two groups based on specific or median values at baseline and changes throughout treatment. A total number of 96 patients (99.0 %) had disease progression (median of 11.3 months) and died (median of 15.4 months) during follow-up. Increases of 10 % in intramuscular adipose tissue were significantly associated with DFS (HR: 0.60, 95 % CI: 0.38 to 0.95) and OS (HR: 0.60, 95 % CI: 0.37 to 0.95), while increases of 10 % in subcutaneous adipose tissue were associated with DFS (HR: 0.59, 95 % CI: 0.36 to 0.95). These results indicate that, although muscle mass and visceral adipose tissue were not associated with DFS or OS, changes in intramuscular and subcutaneous adipose tissue can predict immunotherapy clinical outcomes in patients with advanced lung cancer

Posterior Malleolar Ankle Fractures: An Effort at Improving Outcomes.

BackgroundThere is increasing acceptance that the clinical outcomes following posterior malleolar fractures are less than satisfactory. We report our results of posterior malleolar fracture management based on the classification by Mason and Molloy.MethodsAll fractures were classified on the basis of computed tomographic (CT) scans obtained preoperatively. This dictated the treatment algorithm. Type-1 fractures underwent syndesmotic fixation. Type-2A fractures underwent open reduction and internal fixation through a posterolateral incision, type-2B fractures underwent open reduction and internal fixation through either a posteromedial incision or a combination of a posterolateral with a medial-posteromedial incision, and type-3 fractures underwent open reduction and internal fixation through a posteromedial incision.ResultsPatient-related outcome measures were obtained in 50 patients with at least 1-year follow-up. According to the Mason and Molloy classification, there were 17 type-1 fractures, 12 type-2A fractures, 10 type-2B fractures, and 11 type-3 fractures. The mean Olerud-Molander Ankle Score was 75.9 points (95% confidence interval [CI], 66.4 to 85.3 points) for patients with type-1 fractures, 75.0 points (95% CI, 61.5 to 88.5 points) for patients with type-2A fractures, 74.0 points (95% CI, 64.2 to 83.8 points) for patients with type-2B fractures, and 70.5 points (95% CI, 59.0 to 81.9 points) for patients with type-3 fractures.ConclusionsWe have been able to demonstrate an improvement in the Olerud-Molander Ankle Score for all posterior malleolar fractures with the treatment algorithm applied using the Mason and Molloy classification. Mason classification type-3 fractures have marginally poorer outcomes, which correlates with a more severe injury; however, this did not reach significance.Level of evidenceTherapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43 229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616 470 domain sequences classified into 23 876 sequence families. This results in the significant expansion of the CATHHMMmodel library to include models built from the CATH sequence relatives, giving a10%increase in coveragefor detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned

Clinical implications of circulating tumor cells of breast cancer patients: role of epithelial-mesenchymal plasticity

There is increasing interest in circulating tumor cells (CTCs) due to their purported role in breast cancer metastasis, and their potential as a “liquid biopsy” tool in breast cancer diagnosis and management. There are, however, questions with regards to the reliability and consistency of CTC detection and to the relationship between CTCs and prognosis, which is limiting their clinical utility. There is increasing acceptance that the ability of CTCs to alter from an epithelial to mesenchymal phenotype plays an important role in determining the metastatic potential of these cells. This review examines the phenotypic and genetic variation, which has been reported within CTC populations. Importantly, we discuss how the detection and characterization of CTCs provides additional and often differing information from that obtained from the primary tumor, and how this may be utilized in determining prognosis and treatment options. It has been shown for example that hormone receptor status often differs between the primary tumor and CTCs, which may help to explain failure of endocrine treatment. We examine how CTC status may introduce alternative treatment options and also how they may be used to monitor treatment. Finally, we discuss the most interesting current clinical trials involving CTC analysis and note further research that is required before the breast cancer “liquid biopsy” can be realized