Using an analytical process to contextualise architectural prototypes for metro stations

In order to meet the pressures of a growing population and employment base, a developing city in the Middle East is planning a new public transport system to allow its sustainable growth. Introducing a new mode of public transport to a city that has a complex urban structure and a dependency on car use necessitates specific design responses to inform the station design process. This paper focuses on a study at the micro scale level that addresses the impact of evidence-based design on contextualised architectural station prototypes. Furthermore, it addresses the processes of working with an architectural design office in creating dynamic design iterations. The research here is presented from a perspective of the process of iterative analytical study to real time projects, reflecting on the balance between academia and practice. In order to construct a set of design principles to station locations, three layers of potential movement patterns are analysed using agents based modelling: movement from station exits; movement towards station entrances and background movement generated through the spatial accessibility values of the surrounding context. In that respect, each prototype station has been contextualised to its unique site. Design proposals developed by architectural teams are informed through fine grain analysis of urban features such as pavement widths and signage locations. The analyses also inform the landscape design process through the positioning of street furniture in relation to potential movement patterns as well as the effect of shading and public realm quality through option testing. To integrate stations within their contexts they must have simple entrances and clear orientation from the points of exit. Overall, the dynamic nature of agent based modelling allows for rapid design feedback to occur permitting an iterative process of design development and optimisation

City planning using integrated urban modeling Jeddah structure plan

This paper explores the use of weighted space syntax models to contribute to the process of integrated urban planning for Jeddah as part of a major planning project in the Saudi Arabia. The Municipality of Jeddah commissioned the production of an integrated suite of planning documents. These plans coordinate Strategic, Sub-Regional, Structural and Local plans across a citywide region and aim to provide a framework for sustainable urban growth and development over the next 20 years. This paper focuses on the space syntax methodologies used to aid urban planners to develop the Structure Plan and builds on the research used to develop the Sub-Regional Plan (Karimi et al, 2015). The Structure Plan studied how the urban structure of the city could accommodate the growth of population by about three million over the next 20 years. This included developing and testing a centres strategy to distribute population, employment and supporting facilities along with a public transport strategy for the city. For analysing the potential and requirements of the city, an Integrated Urban Model (IUM) was constructed to combine the spatial network with land use, population, employment and public transport. The aim of this model was to test the impact of changes in the distribution of population and employment. It also allowed the assessment of public transport alignments. The IUM is a key design tool for planning and optimising the relationships between population, employment and public transport. It was also used to provide a benchmarking methodology to compare options. Because the model links people to employment using the spatial network and public transport, the performance of options can be expressed in terms of benefits to the city's population

Fabrication of AlN/BN bishell hollow nanofibers by electrospinning and atomic layer deposition

Cataloged from PDF version of article.Aluminum nitride (AlN)/boron nitride (BN) bishell hollow nanofibers (HNFs) have been fabricated by successive atomic layer deposition (ALD) of AlN and sequential chemical vapor deposition (CVD) of BN on electrospun polymeric nanofibrous template. A four-step fabrication process was utilized: (i) fabrication of polymeric (nylon 6,6) nanofibers via electrospinning, (ii) hollow cathode plasma-assisted ALD of AlN at 100 degrees C onto electrospun polymeric nanofibers, (iii) calcination at 500 degrees C for 2 h in order to remove the polymeric template, and (iv) sequential CVD growth of BN at 450 degrees C. AlN/BN HNFs have been characterized for their chemical composition, surface morphology, crystal structure, and internal nanostructure using X-ray photoelectron spectroscopy, scanning electron microscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, and selected area electron diffraction. Measurements confirmed the presence of crystalline hexagonal BN and AlN within the three dimensional (3D) network of bishell HNFs with relatively low impurity content. In contrast to the smooth surface of the inner AlN layer, outer BN coating showed a highly rough 3D morphology in the form of BN nano-needle crystallites. It is shown that the combination of electrospinning and plasma-assisted low-temperature ALD/CVD can produce highly controlled multi-layered bishell nitride ceramic hollow nanostructures. While electrospinning enables easy fabrication of nanofibrous template, self-limiting reactions of plasma-assisted ALD and sequential CVD provide control over the wall thicknesses of AlN and BN layers with sub-nanometer accuracy. (C) 2014 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License

HOT or not: examining the basis of high-occupancy target regions

High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and consequently associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solemnly defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed 'hyper-ChIPable' regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers, enrichment of RNA-DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies

Testing timed systems modeled by stream X-machines

Stream X-machines have been used to specify real systems where complex data structures. They are a variety of extended finite state machine where a shared memory is used to represent communications between the components of systems. In this paper we introduce an extension of the Stream X-machines formalism in order to specify systems that present temporal requirements. We add time in two different ways. First, we consider that (output) actions take time to be performed. Second, our formalism allows to specify timeouts. Timeouts represent the time a system can wait for the environment to react without changing its internal state. Since timeous affect the set of available actions of the system, a relation focusing on the functional behavior of systems, that is, the actions that they can perform, must explicitly take into account the possible timeouts. In this paper we also propose a formal testing methodology allowing to systematically test a system with respect to a specification. Finally, we introduce a test derivation algorithm. Given a specification, the derived test suite is sound and complete, that is, a system under test successfully passes the test suite if and only if this system conforms to the specification

PiGx: reproducible genomics analysis pipelines with GNU Guix

In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or for the wider dissemination of workflows. Providing this type of reproducibility and traceability, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally come in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies with GNU Guix. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines called PiGx for the analysis of RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq. All pipelines process raw experimental data, and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own data sets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx

A Brain Phenotype for Stressor‐Evoked Blood Pressure Reactivity

Background Individuals who exhibit large‐magnitude blood pressure (BP) reactions to acute psychological stressors are at risk for hypertension and premature death by cardiovascular disease. This study tested whether a multivariate pattern of stressor‐evoked brain activity could reliably predict individual differences in BP reactivity, providing novel evidence for a candidate neurophysiological source of stress‐related cardiovascular risk. Methods and Results Community‐dwelling adults (N=310; 30–51 years; 153 women) underwent functional magnetic resonance imaging with concurrent BP monitoring while completing a standardized battery of stressor tasks. Across individuals, the battery evoked an increase systolic and diastolic BP relative to a nonstressor baseline period (M ∆systolic BP/∆diastolic BP=4.3/1.9 mm Hg [95% confidence interval=3.7–5.0/1.4–2.3 mm Hg]). Using cross‐validation and machine learning approaches, including dimensionality reduction and linear shrinkage models, a multivariate pattern of stressor‐evoked functional magnetic resonance imaging activity was identified in a training subsample (N=206). This multivariate pattern reliably predicted both systolic BP (r=0.32; P<0.005) and diastolic BP (r=0.25; P<0.01) reactivity in an independent subsample used for testing and replication (N=104). Brain areas encompassed by the pattern that were strongly predictive included those implicated in psychological stressor processing and cardiovascular responding through autonomic pathways, including the medial prefrontal cortex, anterior cingulate cortex, and insula. Conclusions A novel multivariate pattern of stressor‐evoked brain activity may comprise a phenotype that partly accounts for individual differences in BP reactivity, a stress‐related cardiovascular risk factor