Addressing non-motorised transport movement along and across railway lines in the city of Cape Town

Paper presented at the 33rd Annual Southern African Transport Conference 7-10 July 2014 "Leading Transport into the Future", CSIR International Convention Centre, Pretoria, South Africa.There are numerous reasons why pedestrians choose to cross railway tracks in South Africa and in Cape Town in particular. Whilst this behavior generally forms part of their desire line and is often part of their journey, the crossing of railway lines is illegal and unsafe and is causing a significant amount of injuries and fatalities within the rail network in the City. Such incidents occurring along railway lines cause a great disruption to the railway operational service with a resultant negative effect on the economic growth of the City. In this paper, an investigation into the Non-Motorised Transport (NMT) movements along and across all railway lines, within the jurisdictional area of the City of Cape Town, has been undertaken using innovative video-based techniques and assessed using GIS-mapping methods. The investigation identified several “hotspot” locations where various types of recommendations and/or intervention strategies are urgently needed to enhance public (pedestrian) safety and ensure uninterrupted train service. Intervention strategies proposed have been drawn from international best practice tailored to suit the unique South African pedestrian culture. The paper highlights the “Nomzamo rail crossing” as a special case study as it demonstrates the failure of town planning processes to consider the impacts of locating developments next to railway lines. The Nomzamo case study is an example of a large-scale, low-income urban development that has been allowed to develop alongside a rail line without due consideration of NMT desire lines that have materialised across the rail line. Currently, approx. 3,000 pedestrians cross the railway line at the Nomzamo location in the 2½-hour morning peak period, which include scholars and cyclists.This paper was transferred from the original CD ROM created for this conference. The material was published using Adobe Acrobat 10.1.0 Technology. The original CD ROM was produced by CE Projects cc. Postal Address: PO Box 560 Irene 0062 South Africa. Tel.: +27 12 667 2074 Fax: +27 12 667 2766 E-mail: [email protected]

Molecular and Structural Discrimination of Proline Racemase and Hydroxyproline-2-Epimerase from Nosocomial and Bacterial Pathogens

The first eukaryotic proline racemase (PRAC), isolated from the human Trypanosoma cruzi pathogen, is a validated therapeutic target against Chagas' disease. This essential enzyme is implicated in parasite life cycle and infectivity and its ability to trigger host B-cell nonspecific hypergammaglobulinemia contributes to parasite evasion and persistence. Using previously identified PRAC signatures and data mining we present the identification and characterization of a novel PRAC and five hydroxyproline epimerases (HyPRE) from pathogenic bacteria. Single-mutation of key HyPRE catalytic cysteine abrogates enzymatic activity supporting the presence of two reaction centers per homodimer. Furthermore, evidences are provided that Brucella abortus PrpA [for ‘proline racemase’ virulence factor A] and homologous proteins from two Brucella spp are bona fide HyPREs and not ‘one way’ directional PRACs as described elsewhere. Although the mechanisms of aminoacid racemization and epimerization are conserved between PRAC and HyPRE, our studies demonstrate that substrate accessibility and specificity partly rely on contraints imposed by aromatic or aliphatic residues distinctively belonging to the catalytic pockets. Analysis of PRAC and HyPRE sequences along with reaction center structural data disclose additional valuable elements for in silico discrimination of the enzymes. Furthermore, similarly to PRAC, the lymphocyte mitogenicity displayed by HyPREs is discussed in the context of bacterial metabolism and pathogenesis. Considering tissue specificity and tropism of infectious pathogens, it would not be surprising if upon infection PRAC and HyPRE play important roles in the regulation of the intracellular and extracellular amino acid pool profiting the microrganism with precursors and enzymatic pathways of the host

Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci

Background DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach. Methods The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear mixed models adjusting for age, sex, smoking, and study-specific and technical variables. Summary results were meta-analyzed within and across ethnicities. Findings were assessed using integrative epigenomics methods and pathway analyses. Results We identified 93 DMPs associated with eGFR at an FDR of 0.05 and replicated 13 and 1 DMPs across independent samples in trans-ethnic and African American meta-analyses, respectively. The study also validated 6 previously published DMPs. Identified DMPs showed significant overlap enrichment with DNase I hypersensitive sites in kidney tissue, sites associated with the expression of proximal genes, and transcription factor motifs and pathways associated with kidney tissue and kidney development. Conclusions We uncovered trans-ethnic and ethnic-specific DMPs associated with eGFR, including DMPs enriched in regulatory elements in kidney tissue and pathways related to kidney development. These findings shed light on epigenetic mechanisms associated with kidney function, bridging the gap between population-specific eGFR-associated DNAm and tissue-specific regulatory context

Review article: AntArchitecture – building an age–depth model from Antarctica's radiostratigraphy to explore ice-sheet evolution

Radio-echo sounding (RES) has revealed an internal architecture within both the West and East Antarctic ice sheets that records their depositional, deformational and melting histories. Crucially, RES-imaged internal-reflecting horizons, tied to ice-core age–depth profiles, can be treated as isochrones that record the age–depth structure across the Antarctic ice sheets. These enable the reconstruction of past climate and ice dynamical processes on large scales, which are complementary to but more spatially extensive than commonly used proxy records (e.g. former ice limits constrained by cosmogenic dating or offshore sediment sequences) around Antarctica. We review the progress towards building a pan-Antarctic age–depth model from these data by first introducing the relevant RES datasets that have been acquired across Antarctica over the last 6 decades (focussing specifically on those that detected internal-reflecting horizons) and outlining the processing steps typically undertaken to visualise, trace and date (by intersection with ice cores or modelling) the RES-imaged isochrones. We summarise the scientific applications for which Antarctica's internal architecture has been used to date and present a pathway to expanding Antarctic radiostratigraphy across the continent to provide a benchmark for a wider range of investigations: (1) identification of optimal sites for retrieving new ice-core palaeoclimate records targeting different periods; (2) reconstruction of surface mass balance on millennial or historical timescales; (3) estimation of basal melting and geothermal heat flux from radiostratigraphy and comprehensive mapping of basal-ice units to complement inferences from other geophysical and geological methods; (4) advancement of the knowledge of volcanic activity and fallout across Antarctica; and (5) refinement of numerical models that leverage radiostratigraphy to tune time-varying accumulation, basal melting and ice flow, firstly to reconstruct past behaviour and then to reduce uncertainties in projecting future ice-sheet behaviour

Structural Stability of Transparent Conducting Films Assembled from Length Purified Single-Wall Carbon Nanotubes

Single-wall carbon nanotube (SWCNT) films show significant promise for transparent electronics applications that demand mechanical flexibility, but durability remains an outstanding issue. In this work, thin membranes of length purified single-wall carbon nanotubes (SWCNTs) are uniaxially and isotropically compressed by depositing them on prestrained polymer substrates. Upon release of the strain, the topography, microstructure, and conductivity of the films are characterized using a combination of optical/fluorescence microscopy, light scattering, force microscopy, electron microscopy, and impedance spectroscopy. Above a critical surface mass density, films assembled from nanotubes of well-defined length exhibit a strongly nonlinear mechanical response. The measured strain dependence reveals a dramatic softening that occurs through an alignment of the SWCNTs normal to the direction of prestrain, which at small strains is also apparent as an anisotropic increase in sheet resistance along the same direction. At higher strains, the membrane conductivities increase due to a compression-induced restoration of conductive pathways. Our measurements reveal the fundamental mode of elasto-plastic deformation in these films and suggest how it might be suppressed