The Climate-G testbed: towards large scale distributed data management for climate change

Climate-G is a large scale distributed testbed devoted to climate change research. It is an unfunded effort started in 2008 and involving a wide community both in Europe and US. The testbed is an interdisciplinary effort involving partners from several institutions and joining expertise in the field of climate change and computational science. Its main goal is to allow scientists carrying out geographical and cross-institutional data discovery, access, analysis, visualization and sharing of climate data. It represents an attempt to address, in a real environment, challenging data and metadata management issues. This paper presents a complete overview about the Climate-G testbed highlighting the most important results that have been achieved since the beginning of this project.

CLSM method for the dynamic observation of pH change within polymer matrices for oral delivery

If acid-sensitive drugs or cells are administered orally, there is often a reduction in efficacy associated with gastric passage. Formulation into a polymer matrix is a potential method to improve their stability. The visualization of pH within these materials may help better understand the action of these polymer systems and allow comparison of different formulations. We herein describe the development of a novel confocal laser-scanning microscopy (CLSM) method for visualizing pH changes within polymer matrices and demonstrate its applicability to an enteric formulation based on chitosan-coated alginate gels. The system in question is first shown to protect an acid-sensitive bacterial strain to low pH, before being studied by our technique. Prior to this study, it has been claimed that protection by these materials is a result of buffering, but this has not been demonstrated. The visualization of pH within these matrices during exposure to a pH 2.0 simulated gastric solution showed an encroachment of acid from the periphery of the capsule, and a persistence of pHs above 2.0 within the matrix. This implies that the protective effect of the alginate-chitosan matrices is most likely due to a combination of buffering of acid as it enters the polymer matrix and the slowing of acid penetration.

Beyond the computer: changing medium from digital to physical

How can organizations use digital infrastructure to realise physical outcomes? The design and construction of London Heathrow Terminal 5 is analysed to build new theoretical understanding of visualization and materialization practices in the transition from digital design to physical realisation. In the project studied, an integrated software solution is introduced as an infrastructure for delivery. The analyses articulate the work done to maintain this digital infrastructure and also to move designs beyond the closed world of the computer to a physical reality. In changing medium, engineers use heterogeneous trials to interrogate and address the limitations of an integrated digital model. The paper explains why such trials, which involve the reconciliation of digital and physical data through parallel and iterative forms of work, provide a robust practice for realizing goals that have physical outcomes. It argues that this practice is temporally different from, and at times in conflict with, building a comprehensive dataset within the digital medium. The paper concludes by discussing the implications for organizations that use digital infrastructures in seeking to accomplish goals in digital and physical media.

Sub-surface terahertz imaging through uneven surfaces: visualizing Neolithic wall paintings in Çatalhöyük

Pulsed terahertz imaging is being developed as a technique to image obscured mural paintings. Due to significant advances in terahertz technology, portable systems are now capable of operating in unregulated environments and this has prompted their use on archaeological excavations. August 2011 saw the first use of pulsed terahertz imaging at the archaeological site of Çatalhöyük, Turkey, where mural paintings dating from the Neolithic period are continuously being uncovered by archaeologists. In these particular paintings the paint is applied onto an uneven surface, and then covered by an equally uneven surface. Traditional terahertz data analysis has proven unsuccessful at sub-surface imaging of these paintings due to the effect of these uneven surfaces. For the first time, an image processing technique is presented, based around Gaussian beam-mode coupling, which enables the visualization of the obscured painting.

Statistical characterization of arctic polar-night jet oscillation events

A novel diagnostic tool is presented, based on polar-cap temperature anomalies, for visualizing daily variability of the Arctic stratospheric polar vortex over multiple decades. This visualization illustrates the ubiquity of extended-time-scale recoveries from stratospheric sudden warmings, termed here polar-night jet oscillation (PJO) events. These are characterized by an anomalously warm polar lower stratosphere that persists for several months. Following the initial warming, a cold anomaly forms in the middle stratosphere, as does an anomalously high stratopause, both of which descend while the lower-stratospheric anomaly persists. These events are characterized in four datasets: Microwave Limb Sounder (MLS) temperature observations; the 40-yr ECMWF Re-Analysis (ERA-40) and Modern Era Retrospective Analysis for Research and Applications (MERRA) reanalyses; and an ensemble of three 150-yr simulations from the Canadian Middle Atmosphere Model. The statistics of PJO events in the model are found to agree very closely with those of the observations and reanalyses. The time scale for the recovery of the polar vortex following sudden warmings correlates strongly with the depth to which the warming initially descends. PJO events occur following roughly half of all major sudden warmings and are associated with an extended period of suppressed wave-activity fluxes entering the polar vortex. They follow vortex splits more frequently than they do vortex displacements. They are also related to weak vortex events as identified by the northern annular mode; in particular, those weak vortex events followed by a PJO event show a stronger tropospheric response. The long time scales, predominantly radiative dynamics, and tropospheric influence of PJO events suggest that they represent an important source of conditional skill in seasonal forecasting.

Terahertz pulse imaging of stratified architectural materials for cultural heritage studies

Terahertz pulse imaging (TPI) is a novel noncontact, nondestructive technique for the examination of cultural heritage artifacts. It has the advantage of broadband spectral range, time-of-flight depth resolution, and penetration through optically opaque materials. Fiber-coupled, portable, time-domain terahertz systems have enabled this technique to move out of the laboratory and into the field. Much like the rings of a tree, stratified architectural materials give the chronology of their environmental and aesthetic history. This work concentrates on laboratory models of stratified mosaics and fresco paintings, specimens extracted from a neolithic excavation site in Catalhoyuk, Turkey, and specimens measured at the medieval Eglise de Saint Jean-Baptiste in Vif, France. Preparatory spectroscopic studies of various composite materials, including lime, gypsum and clay plasters are presented to enhance the interpretation of results and with the intent to aid future computer simulations of the TPI of stratified architectural material. The breadth of the sample range is a demonstration of the cultural demand and public interest in the life history of buildings. The results are an illustration of the potential role of TPI in providing both a chronological history of buildings and in the visualization of obscured wall paintings and mosaics.

Assessment of inter-examiner agreement and variability in the manual classification of auditory brainstem response

Abstract Background: The analysis of the Auditory Brainstem Response (ABR) is of fundamental importance to the investigation of the auditory system behaviour, though its interpretation has a subjective nature because of the manual process employed in its study and the clinical experience required for its analysis. When analysing the ABR, clinicians are often interested in the identification of ABR signal components referred to as Jewett waves. In particular, the detection and study of the time when these waves occur (i.e., the wave latency) is a practical tool for the diagnosis of disorders affecting the auditory system. Significant differences in inter-examiner results may lead to completely distinct clinical interpretations of the state of the auditory system. In this context, the aim of this research was to evaluate the inter-examiner agreement and variability in the manual classification of ABR. Methods: A total of 160 ABR data samples were collected, for four different stimulus intensity (80dBHL, 60dBHL, 40dBHL and 20dBHL), from 10 normal-hearing subjects (5 men and 5 women, from 20 to 52 years). Four examiners with expertise in the manual classification of ABR components participated in the study. The Bland-Altman statistical method was employed for the assessment of inter-examiner agreement and variability. The mean, standard deviation and error for the bias, which is the difference between examiners’ annotations, were estimated for each pair of examiners. Scatter plots and histograms were employed for data visualization and analysis. Results: In most comparisons the differences between examiner’s annotations were below 0.1 ms, which is clinically acceptable. In four cases, it was found a large error and standard deviation (>0.1 ms) that indicate the presence of outliers and thus, discrepancies between examiners. Conclusions: Our results quantify the inter-examiner agreement and variability of the manual analysis of ABR data, and they also allows for the determination of different patterns of manual ABR analysis.

An overview of interactive visual data mining techniques for knowledge discovery

n the past decade, the analysis of data has faced the challenge of dealing with very large and complex datasets and the real-time generation of data. Technologies to store and access these complex and large datasets are in place. However, robust and scalable analysis technologies are needed to extract meaningful information from these datasets. The research field of Information Visualization and Visual Data Analytics addresses this need. Information visualization and data mining are often used complementary to each other. Their common goal is the extraction of meaningful information from complex and possibly large data. However, though data mining focuses on the usage of silicon hardware, visualization techniques also aim to access the powerful image-processing capabilities of the human brain. This article highlights the research on data visualization and visual analytics techniques. Furthermore, we highlight existing visual analytics techniques, systems, and applications including a perspective on the field from the chemical process industry.

Visualizing probabilistic flood forecast information: expert preferences and perceptions of best practice in uncertainty communication

The aim of this article is to improve the communication of the probabilistic flood forecasts generated by hydrological ensemble prediction systems (HEPS) by understanding perceptions of different methods of visualizing probabilistic forecast information. This study focuses on interexpert communication and accounts for differences in visualization requirements based on the information content necessary for individual users. The perceptions of the expert group addressed in this study are important because they are the designers and primary users of existing HEPS. Nevertheless, they have sometimes resisted the release of uncertainty information to the general public because of doubts about whether it can be successfully communicated in ways that would be readily understood to nonexperts. In this article, we explore the strengths and weaknesses of existing HEPS visualization methods and thereby formulate some wider recommendations about the best practice for HEPS visualization and communication. We suggest that specific training on probabilistic forecasting would foster use of probabilistic forecasts with a wider range of applications. The result of a case study exercise showed that there is no overarching agreement between experts on how to display probabilistic forecasts and what they consider the essential information that should accompany plots and diagrams. In this article, we propose a list of minimum properties that, if consistently displayed with probabilistic forecasts, would make the products more easily understandable. Copyright © 2012 John Wiley & Sons, Ltd.

Computational fluid dynamics modelling of the air movement in an environmental test chamber with a respiring manikin

In recent years, computational fluid dynamics (CFD) has been widely used as a method of simulating airflow and addressing indoor environment problems. The complexity of airflows within the indoor environment would make experimental investigation difficult to undertake and also imposes significant challenges on turbulence modelling for flow prediction. This research examines through CFD visualization how air is distributed within a room. Measurements of air temperature and air velocity have been performed at a number of points in an environmental test chamber with a human occupant. To complement the experimental results, CFD simulations were carried out and the results enabled detailed analysis and visualization of spatial distribution of airflow patterns and the effect of different parameters to be predicted. The results demonstrate the complexity of modelling human exhalation within a ventilated enclosure and shed some light into how to achieve more realistic predictions of the airflow within an occupied enclosure.

AmalgamScope: merging annotations data across the human genome

The past years have shown an enormous advancement in sequencing and array-based technologies, producing supplementary or alternative views of the genome stored in various formats and databases. Their sheer volume and different data scope pose a challenge to jointly visualize and integrate diverse data types. We present AmalgamScope a new interactive software tool focusing on assisting scientists with the annotation of the human genome and particularly the integration of the annotation files from multiple data types, using gene identifiers and genomic coordinates. Supported platforms include next-generation sequencing and microarray technologies. The available features of AmalgamScope range from the annotation of diverse data types across the human genome to integration of the data based on the annotational information and visualization of the merged files within chromosomal regions or the whole genome. Additionally, users can define custom transcriptome library files for any species and use the file exchanging distant server options of the tool.

Gaussian processes autoencoder for dimensionality reduction

Learning low dimensional manifold from highly nonlinear data of high dimensionality has become increasingly important for discovering intrinsic representation that can be utilized for data visualization and preprocessing. The autoencoder is a powerful dimensionality reduction technique based on minimizing reconstruction error, and it has regained popularity because it has been efficiently used for greedy pretraining of deep neural networks. Compared to Neural Network (NN), the superiority of Gaussian Process (GP) has been shown in model inference, optimization and performance. GP has been successfully applied in nonlinear Dimensionality Reduction (DR) algorithms, such as Gaussian Process Latent Variable Model (GPLVM). In this paper we propose the Gaussian Processes Autoencoder Model (GPAM) for dimensionality reduction by extending the classic NN based autoencoder to GP based autoencoder. More interestingly, the novel model can also be viewed as back constrained GPLVM (BC-GPLVM) where the back constraint smooth function is represented by a GP. Experiments verify the performance of the newly proposed model.

Helium ion microscopy visualizes lipid nanodomains in mammalian cells

Cell membranes are composed of two-dimensional bilayers of amphipathic lipids, which allow a lateral movement of the respective membrane components. These components are arranged in an inhomogeneous manner as transient micro- and nanodomains, which are believed to be crucially involved in the regulation of signal transduction pathways in mammalian cells. Because of their small size (diameter 10-200 nm), membrane nanodomains cannot be directly imaged using conventional light microscopy. Here, we present direct visualization of cell membrane nanodomains by helium ion microscopy (HIM). We show that HIM is capable to image biological specimens without any conductive coating, and that HIM images clearly allow the identification of nanodomains in the ultrastructure of membranes with 1.5 nm resolution. The shape of these nanodomains is preserved by fixation of the surrounding unsaturated fatty acids while saturated fatty acids inside the nanodomains are selectively removed. Atomic force microscopy, fluorescence microscopy, 3D structured illumination microscopy and direct stochastic optical reconstruction microscopy provide additional evidence that the structures in the HIM images of cell membranes originate from membrane nanodomains. The nanodomains observed by HIM have an average diameter of 20 nm and are densely arranged with a minimal nearest neighbor distance of ~15 nm.

Phase 1

Exhibition investigating the role of different methods of drawing in the visualization of architectural space

Characteristics of the equine embryo and fetus from days 15 to 107 of pregnancy

In spite of numerous, substantial advances in equine reproduction, many stages of embryonic and fetal morphological development are poorly understood, with no apparent single source of comprehensive information. Hence, the objective of the present study was to provide a complete macroscopic and microscopic description of the equine embryo/fetus at various gestational ages. Thirty-four embryos/fetuses were aged based on their crown rump length (CRL), and submitted to macroscopic description, biometry, light and scanning microscopy, as well as the alizarin technique. All observed developmental changes were chronologically ordered and described. As examples of the main observed features, an accentuated cervical curvature was observed upon macroscopic examination in all specimens. In the nervous system, the encephalic fourth ventricle and the encephalic vesicles forebrain, midbrain, and hindbrain, were visualized from Day 19 (ovulation = Day 0). The thoracic and pelvic limbs were also visualized; their extremities gave rise to the hoof during development from Day 27. Development of other structures such as pigmented optical vesicle, liver, tail, cardiac area, lungs, and dermal vascularization started on Days 25, 25, 19, 19, 34, and 35, respectively. Light and scanning microscopy facilitated detailed examinations of several organs, e.g., heart, kidneys, lungs, and intestine, whereas the alizarin technique enabled visualization of ossification. Observations in this study contributed to the knowledge regarding equine embryogenesis, and included much detailed data from many specimens collected over a long developmental interval. (C) 2011 Elsevier Inc. All rights reserved.