Geographic Visualization in Archaeology

Archaeologists are often considered frontrunners in employing spatial approaches within the social sciences and humanities, including geospatial technologies such as geographic information systems (GIS) that are now routinely used in archaeology. Since the late 1980s, GIS has mainly been used to support data collection and management as well as spatial analysis and modeling. While fruitful, these efforts have arguably neglected the potential contribution of advanced visualization methods to the generation of broader archaeological knowledge. This paper reviews the use of GIS in archaeology from a geographic visualization (geovisual) perspective and examines how these methods can broaden the scope of archaeological research in an era of more user-friendly cyber-infrastructures. Like most computational databases, GIS do not easily support temporal data. This limitation is particularly problematic in archaeology because processes and events are best understood in space and time. To deal with such shortcomings in existing tools, archaeologists often end up having to reduce the diversity and complexity of archaeological phenomena. Recent developments in geographic visualization begin to address some of these issues, and are pertinent in the globalized world as archaeologists amass vast new bodies of geo-referenced information and work towards integrating them with traditional archaeological data. Greater effort in developing geovisualization and geovisual analytics appropriate for archaeological data can create opportunities to visualize, navigate and assess different sources of information within the larger archaeological community, thus enhancing possibilities for collaborative research and new forms of critical inquiry.

Simplified PRBMs of spatial compliant multi-beam modules for planar motion

PRBMs (pseudo-rigid-body models) have been becoming important engineering technologies/methods in the field of compliant mechanisms to simplify the design and analysis through the use of the knowledge body of rigid-body mechanisms coupling with springs. This article addresses the PRBMs of spatial multi-beam modules for planar motion, which are composed of three or more symmetrical wire/slender beams parallel to each other where the planar twisting DOF (degree of freedom) is assumed to be very small for specific applications/loading conditions. Simplified PRBMs are firstly proposed through replacing each beam in spatial multi-beam module with a rigid-body link plus two identical spherical joints at its two ends. The characteristics factor, bending stiffness and twisting stiffness for the spherical joint are determined. Load-displacement equations are then derived for a class of spatial multi-beam modules and general spatial multi-beam modules using the virtual work principle and kinematic relationships. Finally, nonlinear FEA (finite element analysis) is employed with comparisons with the PRBMs. The present PRBMs have shown the ability to predict the primary nonlinear constraint characteristics such as load-stiffening effect, cross-axis coupling in the two primary translational directions and buckling load.

Enhancing the Visualization of the Peripheral Retina with Wide Field-of-View Optical Coherence Tomography

The goal of my Ph.D. thesis is to enhance the visualization of the peripheral retina using wide-field optical coherence tomography (OCT) in a clinical setting.

OCT has gain widespread adoption in clinical ophthalmology due to its ability to visualize the diseases of the macula and central retina in three-dimensions, however, clinical OCT has a limited field-of-view of 300. There has been increasing interest to obtain high-resolution images outside of this narrow field-of-view, because three-dimensional imaging of the peripheral retina may prove to be important in the early detection of neurodegenerative diseases, such as Alzheimer's and dementia, and the monitoring of known ocular diseases, such as diabetic retinopathy, retinal vein occlusions, and choroid masses.

Before attempting to build a wide-field OCT system, we need to better understand the peripheral optics of the human eye. Shack-Hartmann wavefront sensors are commonly used tools for measuring the optical imperfections of the eye, but their acquisition speed is limited by their underlying camera hardware. The first aim of my thesis research is to create a fast method of ocular wavefront sensing such that we can measure the wavefront aberrations at numerous points across a wide visual field. In order to address aim one, we will develop a sparse Zernike reconstruction technique (SPARZER) that will enable Shack-Hartmann wavefront sensors to use as little as 1/10th of the data that would normally be required for an accurate wavefront reading. If less data needs to be acquired, then we can increase the speed at which wavefronts can be recorded.

For my second aim, we will create a sophisticated optical model that reproduces the measured aberrations of the human eye. If we know how the average eye's optics distort light, then we can engineer ophthalmic imaging systems that preemptively cancel inherent ocular aberrations. This invention will help the retinal imaging community to design systems that are capable of acquiring high resolution images across a wide visual field. The proposed model eye is also of interest to the field of vision science as it aids in the study of how anatomy affects visual performance in the peripheral retina.

Using the optical model from aim two, we will design and reduce to practice a clinical OCT system that is capable of imaging a large (800) field-of-view with enhanced visualization of the peripheral retina. A key aspect of this third and final aim is to make the imaging system compatible with standard clinical practices. To this end, we will incorporate sensorless adaptive optics in order to correct the inter- and intra- patient variability in ophthalmic aberrations. Sensorless adaptive optics will improve both the brightness (signal) and clarity (resolution) of features in the peripheral retina without affecting the size of the imaging system.

The proposed work should not only be a noteworthy contribution to the ophthalmic and engineering communities, but it should strengthen our existing collaborations with the Duke Eye Center by advancing their capability to diagnose pathologies of the peripheral retinal.

Housing and Planning in London under the Conservative Government: Spatial impacts, social polarisation, sustainable development and social justice

This paper will be based on my continuing research on planning and housing development in London. It will focus on the proposals in the Government’s Housing and Planning Bill, which are likely to be enacted in Spring 2016. It will review the evidence of potential spatial impacts in terms of the supply of existing affordable homes and the location and affordability of new supply. This will be related to a review of the alternative development options for London’s growth in the context of the Mayor of London’s draft 2050 Infrastructure Plan. The paper will analyse the potential impact of new Government policy and legislation on whether London’s housing requirements can be delivered in accordance with the objectives of sustainable planning and social justice, and will also consider the constraints on the ability of the new Mayor of London, to be elected in May 2016 to achieve manifesto commitments.

Effect of soil structure on temporal and spatial dynamics of bacteria

Soil is a complex heterogeneous system comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota. A question addressed in this research is how soil structure affects the temporal dynamics and spatial distribution of bacteria. Using repacked microcosms, the effect of bulk-density, aggregate sizes and water content on growth and distribution of introduced Pseudomonas fluorescens and Bacillus subtilis bacteria was determined. Soil bulk-density and aggregate sizes were altered to manipulate the characteristics of the pore volume where bacteria reside and through which distribution of solutes and nutrients is controlled. X-ray CT was used to characterise the pore geometry of repacked soil microcosms. Soil porosity, connectivity and soil-pore interface area declined with increasing bulk-density. In samples that differ in pore geometry, its effect on growth and extent of spread of introduced bacteria was investigated. The growth rate of bacteria reduced with increasing bulk-density, consistent with a significant difference in pore geometry. To measure the ability of bacteria to spread thorough soil, placement experiments were developed. Bacteria were capable of spreading several cm’s through soil. The extent of spread of bacteria was faster and further in soil with larger and better connected pore volumes. To study the spatial distribution in detail, a methodology was developed where a combination of X-ray microtopography, to characterize the soil structure, and fluorescence microscopy, to visualize and quantify bacteria in soil sections was used. The influence of pore characteristics on distribution of bacteria was analysed at macro- and microscales. Soil porosity, connectivity and soil-pore interface influenced bacterial distribution only at the macroscale. The method developed was applied to investigate the effect of soil pore characteristics on the extent of spread of bacteria introduced locally towards a C source in soil. Soil-pore interface influenced spread of bacteria and colonization, therefore higher bacterial densities were found in soil with higher pore volumes. Therefore the results in this showed that pore geometry affects the growth and spread of bacteria in soil. The method developed showed showed how thin sectioning technique can be combined with 3D X-ray CT to visualize bacterial colonization of a 3D pore volume. This novel combination of methods is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

Sextant. A spatial data infrastructure for marine environments

At national and European levels, in various projects, data products are developed to provide end-users and stakeholders with homogeneously qualified observation compilation or analysis. Ifremer has developed a spatial data infrastructure for marine environment, called Sextant, in order to manage, share and retrieve these products for its partners and the general public. Thanks to the OGC and ISO standard and INSPIRE compliance, the infrastructure provides a unique framework to federate homogeneous descriptions and access to marine data products processed in various contexts, at national level or European level for DG research (SeaDataNet), DG Mare (EMODNET) and DG Growth (Copernicus MEMS). The discovery service of Sextant is based on the metadata catalogue. The data description is normalized according to ISO 191XX series standards and Inspire recommendations. Access to the catalogue is provided by the standard OGC service, Catalogue Service for the Web (CSW 2.0.2). Data visualization and data downloading are available through standard OGC services, Web Map Services (WMS) and Web Feature Services (WFS). Several OGC services are provided within Sextant, according to marine themes, regions and projects. Depending on the file format, WMTS services are used for large images, such as hyperspectral images, or NcWMS services for gridded data, such as climatology models. New functions are developped to improve the visualization, analyse and access to data, eg : data filtering, online spatial processing with WPS services and acces to sensor data with SOS services.

From the traditional verification approach to the spatial methods: a study of applicability of the SAL metric in the framework of the WMO project MesoVICT

Increasing in resolution of numerical weather prediction models has allowed more and more realistic forecasts of atmospheric parameters. Due to the growing variability into predicted fields the traditional verification methods are not always able to describe the model ability because they are based on a grid-point-by-grid-point matching between observation and prediction. Recently, new spatial verification methods have been developed with the aim of show the benefit associated to the high resolution forecast. Nested in among of the MesoVICT international project, the initially aim of this work is to compare the newly tecniques remarking advantages and disadvantages. First of all, the MesoVICT basic examples, represented by synthetic precipitation fields, have been examined. Giving an error evaluation in terms of structure, amplitude and localization of the precipitation fields, the SAL method has been studied more thoroughly respect to the others approaches with its implementation in the core cases of the project. The verification procedure has concerned precipitation fields over central Europe: comparisons between the forecasts performed by the 00z COSMO-2 model and the VERA (Vienna Enhanced Resolution Analysis) have been done. The study of these cases has shown some weaknesses of the methodology examined; in particular has been highlighted the presence of a correlation between the optimal domain size and the extention of the precipitation systems. In order to increase ability of SAL, a subdivision of the original domain in three subdomains has been done and the method has been applied again. Some limits have been found in cases in which at least one of the two domains does not show precipitation. The overall results for the subdomains have been summarized on scatter plots. With the aim to identify systematic errors of the model the variability of the three parameters has been studied for each subdomain.

Mixed Spatial and Nonspatial Problems in Location Based Services

With hundreds of millions of users reporting locations and embracing mobile technologies, Location Based Services (LBSs) are raising new challenges. In this dissertation, we address three emerging problems in location services, where geolocation data plays a central role. First, to handle the unprecedented growth of generated geolocation data, existing location services rely on geospatial database systems. However, their inability to leverage combined geographical and textual information in analytical queries (e.g. spatial similarity joins) remains an open problem. To address this, we introduce SpsJoin, a framework for computing spatial set-similarity joins. SpsJoin handles combined similarity queries that involve textual and spatial constraints simultaneously. LBSs use this system to tackle different types of problems, such as deduplication, geolocation enhancement and record linkage. We define the spatial set-similarity join problem in a general case and propose an algorithm for its efficient computation. Our solution utilizes parallel computing with MapReduce to handle scalability issues in large geospatial databases. Second, applications that use geolocation data are seldom concerned with ensuring the privacy of participating users. To motivate participation and address privacy concerns, we propose iSafe, a privacy preserving algorithm for computing safety snapshots of co-located mobile devices as well as geosocial network users. iSafe combines geolocation data extracted from crime datasets and geosocial networks such as Yelp. In order to enhance iSafe's ability to compute safety recommendations, even when crime information is incomplete or sparse, we need to identify relationships between Yelp venues and crime indices at their locations. To achieve this, we use SpsJoin on two datasets (Yelp venues and geolocated businesses) to find venues that have not been reviewed and to further compute the crime indices of their locations. Our results show a statistically significant dependence between location crime indices and Yelp features. Third, review centered LBSs (e.g., Yelp) are increasingly becoming targets of malicious campaigns that aim to bias the public image of represented businesses. Although Yelp actively attempts to detect and filter fraudulent reviews, our experiments showed that Yelp is still vulnerable. Fraudulent LBS information also impacts the ability of iSafe to provide correct safety values. We take steps toward addressing this problem by proposing SpiDeR, an algorithm that takes advantage of the richness of information available in Yelp to detect abnormal review patterns. We propose a fake venue detection solution that applies SpsJoin on Yelp and U.S. housing datasets. We validate the proposed solutions using ground truth data extracted by our experiments and reviews filtered by Yelp.

Geospatial Data Indexing Analysis and Visualization via Web Services with Autonomic Resource Management

With the exponential growth of the usage of web-based map services, the web GIS application has become more and more popular. Spatial data index, search, analysis, visualization and the resource management of such services are becoming increasingly important to deliver user-desired Quality of Service. First, spatial indexing is typically time-consuming and is not available to end-users. To address this, we introduce TerraFly sksOpen, an open-sourced an Online Indexing and Querying System for Big Geospatial Data. Integrated with the TerraFly Geospatial database [1-9], sksOpen is an efficient indexing and query engine for processing Top-k Spatial Boolean Queries. Further, we provide ergonomic visualization of query results on interactive maps to facilitate the user’s data analysis. Second, due to the highly complex and dynamic nature of GIS systems, it is quite challenging for the end users to quickly understand and analyze the spatial data, and to efficiently share their own data and analysis results with others. Built on the TerraFly Geo spatial database, TerraFly GeoCloud is an extra layer running upon the TerraFly map and can efficiently support many different visualization functions and spatial data analysis models. Furthermore, users can create unique URLs to visualize and share the analysis results. TerraFly GeoCloud also enables the MapQL technology to customize map visualization using SQL-like statements [10]. Third, map systems often serve dynamic web workloads and involve multiple CPU and I/O intensive tiers, which make it challenging to meet the response time targets of map requests while using the resources efficiently. Virtualization facilitates the deployment of web map services and improves their resource utilization through encapsulation and consolidation. Autonomic resource management allows resources to be automatically provisioned to a map service and its internal tiers on demand. v-TerraFly are techniques to predict the demand of map workloads online and optimize resource allocations, considering both response time and data freshness as the QoS target. The proposed v-TerraFly system is prototyped on TerraFly, a production web map service, and evaluated using real TerraFly workloads. The results show that v-TerraFly can accurately predict the workload demands: 18.91% more accurate; and efficiently allocate resources to meet the QoS target: improves the QoS by 26.19% and saves resource usages by 20.83% compared to traditional peak load-based resource allocation.

The Effects of Visual Discriminability and Rotation Angle on 30-Month-Olds’ Search Performance in Spatial Rotation Tasks

Tracking objects that are hidden and then moved is a crucial ability related to object permanence, which develops across several stages in early childhood. In spatial rotation tasks, children observe a target object that is hidden in one of two or more containers before the containers are rotated around a fixed axis. Usually, 30-month-olds fail to find the hidden object after it was rotated by 180°. We examined whether visual discriminability of the containers improves 30-month-olds’ success in this task and whether children perform better after 90° than after 180° rotations. Two potential hiding containers with same or different colors were placed on a board that was rotated by 90° or 180° in a within-subjects design. Children (N D 29) performed above chance level in all four conditions. Their overall success in finding the object did not improve by differently colored containers. However, different colors prevented children from showing an inhibition bias in 90° rotations, that is, choosing the empty container more often when it was located close to them than when it was farther away: This bias emerged in the same colors condition but not in the different colors condition. Results are discussed in view of particular challenges that might facilitate or deteriorate spatial rotation tasks for young children.

Distraction by task-irrelevant stimuli: the effects of endogenous spatial attention and visual working memory load

Salient stimuli, like sudden changes in the environment or emotional stimuli, generate a priority signal that captures attention even if they are task-irrelevant. However, to achieve goal-driven behavior, we need to ignore them and to avoid being distracted. It is generally agreed that top-down factors can help us to filter out distractors. A fundamental question is how and at which stage of processing the rejection of distractors is achieved. Two circumstances under which the allocation of attention to distractors is supposed to be prevented are represented by the case in which distractors occur at an unattended location (as determined by the deployment of endogenous spatial attention) and when the amount of visual working memory resources is reduced by an ongoing task. The present thesis is focused on the impact of these factors on three sources of distraction, namely auditory and visual onsets (Experiments 1 and 2, respectively) and pleasant scenes (Experiment 3). In the first two studies we recorded neural correlates of distractor processing (i.e., Event-Related Potentials), whereas in the last study we used interference effects on behavior (i.e., a slowing down of response times on a simultaneous task) to index distraction. Endogenous spatial attention reduced distraction by auditory stimuli and eliminated distraction by visual onsets. Differently, visual working memory load only affected the processing of visual onsets. Emotional interference persisted even when scenes occurred always at unattended locations and when visual working memory was loaded. Altogether, these findings indicate that the ability to detect the location of salient task-irrelevant sounds and identify the affective significance of natural scenes is preserved even when the amount of visual working memory resources is reduced by an ongoing task and when endogenous attention is elsewhere directed. However, these results also indicate that the processing of auditory and visual distractors is not entirely automatic.

Direct Visualization Of The Action Of Triton X-100 On Giant Vesicles Of Erythrocyte Membrane Lipids.

The raft hypothesis proposes that microdomains enriched in sphingolipids, cholesterol, and specific proteins are transiently formed to accomplish important cellular tasks. Equivocally, detergent-resistant membranes were initially assumed to be identical to membrane rafts, because of similarities between their compositions. In fact, the impact of detergents in membrane organization is still controversial. Here, we use phase contrast and fluorescence microscopy to observe giant unilamellar vesicles (GUVs) made of erythrocyte membrane lipids (erythro-GUVs) when exposed to the detergent Triton X-100 (TX-100). We clearly show that TX-100 has a restructuring action on biomembranes. Contact with TX-100 readily induces domain formation on the previously homogeneous membrane of erythro-GUVs at physiological and room temperatures. The shape and dynamics of the formed domains point to liquid-ordered/liquid-disordered (Lo/Ld) phase separation, typically found in raft-like ternary lipid mixtures. The Ld domains are then separated from the original vesicle and completely solubilized by TX-100. The insoluble vesicle left, in the Lo phase, represents around 2/3 of the original vesicle surface at room temperature and decreases to almost 1/2 at physiological temperature. This chain of events could be entirely reproduced with biomimetic GUVs of a simple ternary lipid mixture, 2:1:2 POPC/SM/chol (phosphatidylcholine/sphyngomyelin/cholesterol), showing that this behavior will arise because of fundamental physicochemical properties of simple lipid mixtures. This work provides direct visualization of TX-100-induced domain formation followed by selective (Ld phase) solubilization in a model system with a complex biological lipid composition.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Fracture Of Distal Humerus: Mipo Technique With Visualization Of The Radial Nerve.

To evaluate the outcomes in patients treated for humerus distal third fractures with MIPO technique and visualization of the radial nerve by an accessory approach, in those without radial palsy before surgery. The patients were treated with MIPO technique. The visualization and isolation of the radial nerve was done by an approach between the brachialis and the brachiorradialis, with an oblique incision, in the lateral side of the arm. MEPS was used to evaluate the elbow function. Seven patients were evaluated with a mean age of 29.8 years old. The average follow up was 29.85 months. The radial neuropraxis after surgery occurred in three patients. The sensorial recovery occurred after 3.16 months on average and also of the motor function, after 5.33 months on average, in all patients. We achieved fracture consolidation in all patients (M=4.22 months). The averages for flexion-extension and prono-supination were 112.85° and 145°, respectively. The MEPS average score was 86.42. There was no case of infection. This approach allowed excluding a radial nerve interposition on site of the fracture and/or under the plate, showing a high level of consolidation of the fracture and a good evolution of the range of movement of the elbow. Level of Evidence IV, Case Series.

Non-gaussian Spatial Correlations Dramatically Weaken Localization.

We perform variational studies of the interaction-localization problem to describe the interaction-induced renormalizations of the effective (screened) random potential seen by quasiparticles. Here we present results of careful finite-size scaling studies for the conductance of disordered Hubbard chains at half-filling and zero temperature. While our results indicate that quasiparticle wave functions remain exponentially localized even in the presence of moderate to strong repulsive interactions, we show that interactions produce a strong decrease of the characteristic conductance scale g^{*} signaling the crossover to strong localization. This effect, which cannot be captured by a simple renormalization of the disorder strength, instead reflects a peculiar non-Gaussian form of the spatial correlations of the screened disordered potential, a hitherto neglected mechanism to dramatically reduce the impact of Anderson localization (interference) effects.