Dynamic data retrieval on the world wide web

Methods for accessing data on the Web have been the focus of active research over the past few years. In this thesis we propose a method for representing Web sites as data sources. We designed a Data Extractor data retrieval solution that allows us to define queries to Web sites and process resulting data sets. Data Extractor is being integrated into the MSemODB heterogeneous database management system. With its help database queries can be distributed over both local and Web data sources within MSemODB framework. Data Extractor treats Web sites as data sources, controlling query execution and data retrieval. It works as an intermediary between the applications and the sites. Data Extractor utilizes a two-fold "custom wrapper" approach for information retrieval. Wrappers for the majority of sites are easily built using a powerful and expressive scripting language, while complex cases are processed using Java-based wrappers that utilize specially designed library of data retrieval, parsing and Web access routines. In addition to wrapper development we thoroughly investigate issues associated with Web site selection, analysis and processing. Data Extractor is designed to act as a data retrieval server, as well as an embedded data retrieval solution. We also use it to create mobile agents that are shipped over the Internet to the client's computer to perform data retrieval on behalf of the user. This approach allows Data Extractor to distribute and scale well. This study confirms feasibility of building custom wrappers for Web sites. This approach provides accuracy of data retrieval, and power and flexibility in handling of complex cases.

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.

An integrated psychology virtual research ethics committee

Research and professional ethics are an integral part of every Psychology degree, as this is seen as a key graduate learning outcome for students leaving to become clinicians working with clients and patients. The development of these skills is embedded in teaching, but they culminate in the final year of a degree when final year students must gain formal ethical approval for their final research project. Decision as to the ethical appropriateness of research are made by a Departmental Research Ethics Committee, which considers all research project proposals submitted by staff and students within the department. One of the challenges of this practice is the scale of work involved for committee members (Doyle & Buckley, 2014) who are all faculty members, and the tracking of applications and decisions, alongside the quality assurance required to ensure that all applications are treated fairly and equally. The time involved in performing this work is often underestimated by Universities, and the variety and complexity of decisions requires extensive discussion and negotiation. Traditionally, these decisions are reached by committee discussions, however this presents logistical difficulties as it requires meetings with quorate attendance. The University of Westminster launched a virtual tool in 2014 to facilitate the management of the Research Ethics Committee, to help track the progress of applications and to allow discussions to occur and be managed virtually. The Department of Psychology adopted the tools in September 2014 to deal with all ethics applications. Here we report on how this virtual committee has affected the role and practices of a working committee that deals with over 300 applications per year, and how an online ethics procedure has facilitated an integrated developmental approach to ethical education.

La ética hacker frente al capitalismo netárquíco: software libre y peer production en las iniciativas de Economía Colaborativa en Andalucía

En los últimos años el término Economía Colaborativa se ha popularizado sin que, hasta el momento, haya sido definido de manera inequívoca. Bajo esta denominación se engloban experiencias tan diversas como bancos de tiempo, huertos urbanos, startups o grandes plataformas digitales. La proliferación de este tipo de iniciativas puede relacionarse con una multiplicidad de factores tales como el desarrollo tecnológico, la recesión económica y otras crisis superpuestas (medioambiental, de cuidados, de valores, de lo político) y un cierto cambio en los valores sociales. Entre 2014-2015 se han realizado dos investigaciones en Andalucía de manera casi paralela y con una metodología similar. La primera de ellas pretendía identificar prácticas de Economía Colaborativa en el entorno universitario. La segunda investigación identificaba experiencias de emprendimiento a nivel autonómico. A luz de los resultados obtenidos se plantea la siguiente cuestión sobre la naturaleza misma de la Economía Colaborativa: ¿nos encontramos ante prácticas postcapitalistas que abren el camino a una sociedad más justa e igualitaria o, más bien, estamos ante una respuesta del capital para, una vez más, seguir extrayendo de manera privada el valor que se genera socialmente? Este artículo, partiendo del análisis del conjunto de iniciativas detentadas en Andalucía, se centra en aquellas basadas en el software libre y la producción digital concluyendo cómo, gracias a la incorporación de ciertos aspectos de la ética hacker y las lógicas del conocimiento abierto, éstas pueden situarse dentro de un escenario de fomento de los comunes globales frente a las lógicas imperantes del capitalismo netárquico. 

Genome-wide association study reveals greater polygenic loading for schizophrenia in cases with a family history of illness

Genome-wide association studies (GWAS) of schizophrenia have yielded more than 100 common susceptibility variants, and strongly support a substantial polygenic contribution of a large number of small allelic effects. It has been hypothesized that familial schizophrenia is largely a consequence of inherited rather than environmental factors. We investigated the extent to which familiality of schizophrenia is associated with enrichment for common risk variants detectable in a large GWAS. We analyzed single nucleotide polymorphism (SNP) data for cases reporting a family history of psychotic illness (N = 978), cases reporting no such family history (N = 4,503), and unscreened controls (N = 8,285) from the Psychiatric Genomics Consortium (PGC1) study of schizophrenia. We used a multinomial logistic regression approach with model-fitting to detect allelic effects specific to either family history subgroup. We also considered a polygenic model, in which we tested whether family history positive subjects carried more schizophrenia risk alleles than family history negative subjects, on average. Several individual SNPs attained suggestive but not genome-wide significant association with either family history subgroup. Comparison of genome-wide polygenic risk scores based on GWAS summary statistics indicated a significant enrichment for SNP effects among family history positive compared to family history negative cases (Nagelkerke's R(2 ) = 0.0021; P = 0.00331; P-value threshold <0.4). Estimates of variability in disease liability attributable to the aggregate effect of genome-wide SNPs were significantly greater for family history positive compared to family history negative cases (0.32 and 0.22, respectively; P = 0.031). We found suggestive evidence of allelic effects detectable in large GWAS of schizophrenia that might be specific to particular family history subgroups. However, consideration of a polygenic risk score indicated a significant enrichment among family history positive cases for common allelic effects. Familial illness might, therefore, represent a more heritable form of schizophrenia, as suggested by previous epidemiological studies.

Product and Process Innovation: Antecedents and Performance outcomes in small IT firms in India

Innovation is a strategic necessity for the survival of today’s organizations. The wide recognition of innovation as a competitive necessity, particularly in dynamic market environments, makes it an evergreen domain for research. This dissertation deals with innovation in small Information Technology (IT) firms in India. The IT industry in India has been a phenomenal success story of the last three decades, and is today facing a crucial phase in its history characterized by the need for fundamental changes in strategies, driven by innovation. This study, while motivated by the dynamics of changing times, importantly addresses the research gap on small firm innovation in Indian IT.This study addresses three main objectives: (a) drivers of innovation in small IT firms in India (b) impact of innovation on firm performance (c) variation in the extent of innovation adoption in small firms. Product and process innovation were identified as the two most contextually relevant types of innovation for small IT firms. The antecedents of innovation were identified as Intellectual Capital, Creative Capability, Top Management Support, Organization Learning Capability, Customer Involvement, External Networking and Employee Involvement.Survey method was adopted for data collection and the study unit was the firm. Surveys were conducted in 2014 across five South Indian cities. Small firm was defined as one with 10-499 employees. Responses from 205 firms were chosen for analysis. Rigorous statistical analysis was done to generate meaningful insights. The set of drivers of product innovation (Intellectual Capital, Creative Capability, Top Management Support, Customer Involvement, External Networking, and Employee Involvement)were different from that of process innovation (Creative Capability, Organization Learning Capability, External Networking, and Employee Involvement). Both product and process innovation had strong impact on firm performance. It was found that firms that adopted a combination of product innovation and process innovation had the highest levels of firm performance. Product innovation and process innovation fully mediated the relationship between all the seven antecedents and firm performance The results of this study have several important theoretical and practical implications. To the best of the researcher’s knowledge, this is the first time that an empirical study of firm level innovation of this kind has been undertaken in India. A measurement model for product and process innovation was developed, and the drivers of innovation were established statistically. Customer Involvement, External Networking and Employee Involvement are elements of Open Innovation, and all three had strong association with product innovation, and the latter twohad strong association with process innovation. The results showed that proclivity for Open Innovation is healthy in the Indian context. Practical implications have been outlined along how firms can organize themselves for innovation, the human talent for innovation, the right culture for innovation and for open innovation. While some specific examples of possible future studies have been recommended, the researcher believes that the study provides numerous opportunities to further this line of enquiry.

It's always been about the links

Abstract The World Wide Web Consortium, W3C, is known for standards like HTML and CSS but there's a lot more to it than that. Mobile, automotive, publishing, graphics, TV and more. Then there are horizontal issues like privacy, security, accessibility and internationalisation. Many of these assume that there is an underlying data infrastructure to power applications. In this session, W3C's Data Activity Lead, Phil Archer, will describe the overall vision for better use of the Web as a platform for sharing data and how that translates into recent, current and possible future work. What's the difference between using the Web as a data platform and as a glorified USB stick? Why does it matter? And what makes a standard a standard anyway? Speaker Biography Phil Archer Phil Archer is Data Activity Lead at W3C, the industry standards body for the World Wide Web, coordinating W3C's work in the Semantic Web and related technologies. He is most closely involved in the Data on the Web Best Practices, Permissions and Obligations Expression and Spatial Data on the Web Working Groups. His key themes are interoperability through common terminology and URI persistence. As well as work at the W3C, his career has encompassed broadcasting, teaching, linked data publishing, copy writing, and, perhaps incongruously, countryside conservation. The common thread throughout has been a knack for communication, particularly communicating complex technical ideas to a more general audience.

Beyond the Acronyms: Sport Diplomacy and the Classification of the International Olympic Committee

Diplomacy often finds itself reduced to actions centred on states. However, after the Cold War, international relations and diplomacy have expanded with different actors growing into significant roles, particularly in the increase of diplomatic relations in the context of sport. The classification and significance of other actors remains under-researched in relation to sport, with literature focusing more on the growth of new and varying practices of diplomacy. This analysis contends that there is a need to interrogate fundamental components of modern diplomacy—with the actor being the focus—more specifically the classification of sports organisations in diplomacy. It is relevant as a more accurate understanding of sports organisations will contribute to how diplomatic studies can analyse and evaluate modern diplomacy within the context of sport. The International Olympic Committee is the actor used to illustrate how problematic classifications currently in the academic literature translate into weak and reduced analysis and evaluation of its role and significance in diplomacy. As counterpoint, this analysis proposes an analytical framework of socio-legal theory that harnesses legal regulation as a benchmark to classify an actor’s capacity within a society. In consequence, the IOC is as an active and significant contributor to the ever expanding and complex diplomatic environment and wider society.

Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Development and application of sensitive genome-wide platforms to study the genetic and epigenetic (DNA methylation) makeup of gametes and early bovine embryos

Pour ce projet, nous avons développé une plateforme pour l’analyse pangénomique de la méthylation de l’ADN chez le bovin qui est compatible avec des échantillons de petites tailles. Cet outil est utilisé pour étudier les caractéristiques génétiques et épigénétiques (méthylation de l’ADN) des gamètes soumis aux procédures de procréation médicalement assisitée et des embryons précoces. Dans un premier temps, une plateforme d’analyse de biopuces spécifiques pour l’étude de la méthylation de l’ADN chez l’espèce bovine a été développée. Cette plateforme a ensuite été optimisée pour produire des analyses pangénomiques de méthylation de l’ADN fiables et reproductibles à partir d’échantillons de très petites tailles telle que les embryons précoces (≥ 10 ng d’ADN a été utilisé, ce qui correspond à 10 blastocystes en expansion). En outre, cet outil a permis d’évaluer de façon simultanée la méthylation de l’ADN et le transcriptome dans le même échantillon, fournissant ainsi une image complète des profils génétiques et épigénétiques (méthylation de l’ADN). Comme preuve de concept, les profils comparatifs de méthylation de l’ADN spermatique et de blastocystes bovins ont été analysés au niveau de l’ensemble du génome. Dans un deuxième temps, grâce à cette plateforme, les profils globaux de méthylation de l’ADN de taureaux jumeaux monozygotes (MZ) ont été analysés. Malgré qu’ils sont génétiquement identiques, les taureaux jumeaux MZ ont des descendants avec des performances différentes. Par conséquent, l’hypothèse que le profil de méthylation de l’ADN spermatique de taureaux jumeaux MZ est différent a été émise. Dans notre étude, des différences significatives entre les jumeaux MZ au niveau des caractéristiques de la semence ainsi que de la méthylation de l’ADN ont été trouvées, chacune pouvant contribuer à l’obtention de performances divergentes incongrues des filles engendrées par ces jumeaux MZ. Dans la troisième partie de ce projet, la même plateforme a été utilisée pour découvrir les impacts d’une supplémentation à forte concentration en donneur de méthyle universel sur les embryons précoces bovins. La supplémentation avec de grandes quantités d’acide folique (AF) a été largement utilisée et recommandée chez les femmes enceintes pour sa capacité bien établie à prévenir les malformations du tube neural chez les enfants. Cependant, plus récemment, plusieurs études ont rapporté des effets indésirables de l’AF utilisé à des concentrations élevées, non seulement sur le développement de l’embryon, mais aussi chez les adultes. Au niveau cellulaire, l’AF entre dans le métabolisme monocarboné, la seule voie de production de S-adénosyl méthionine (SAM), un donneur universel de groupements méthyles pour une grande variété de biomolécules, y compris l’ADN. Par conséquent, pour résoudre cette controverse, une forte dose de SAM a été utilisée pour traiter des embryons produits in vitro chez le bovin. Ceci a non seulement permis d’influencer le phénotype des embryons précoces, mais aussi d’avoir un impact sur le transcriptome et le méthylome de l’ADN. En somme, le projet en cours a permis le développement d’une plateforme d’analyse de la méthylation de l’ADN à l’échelle du génome entier chez le bovin à coût raisonnable et facile à utiliser qui est compatible avec les embryons précoces. De plus, puisque c’est l’une des premières études de ce genre en biologie de la reproduction bovine, ce projet avait trois objectifs qui a donné plusieurs nouveaux résultats, incluant les profils comparatifs de méthylation de l’ADN au niveau : i) blastocystes versus spermatozoïdes ; ii) semence de taureaux jumeaux MZ et iii) embryons précoces traités à de fortes doses de SAM versus des embryons précoces non traités.

Phylum-wide transcriptome analysis of oogenesis and early embryogenesis in selected nematode species

Oogenesis is a prerequisite for embryogenesis in Metazoa. During both biological processes important decisions must be made to form the embryo and hence ensure the next generation: (1) Maternal gene products (mRNAs, proteins and nutrients) must be supplied to the embryo. (2) Polarity must be established and axes must be specified. While incorporation of maternal gene products occurs during oogenesis, the time point of polarity establishment and axis specification varies among species, as it is accomplished either prior, during, or after fertilisation. But not only the time point when these events take place varies among species but also the underlying mechanisms by which they are triggered. For the nematode model Caenorhabditis elegans the underlying pathways and gene regulatory networks (GRNs) are well understood. It is known that there the sperm entry point initiates a primary polarity in the 1-celled egg and with it the establishment of the anteroposterior axis. However, studies of other nematodes demonstrated that polarity establishment can be independent of sperm entry (Goldstein et al., 1998; Lahl et al., 2006) and that cleavage patterns, symmetry formation and cell specification also differ from C. elegans. In contrast to the studied Chromadorea (more derived nematodes including C. elegans), embryos of some marine Enoplea (more basal representatives) even show no discernible early polarity and blastomeres can adopt variable cell fates (Voronov and Panchin 1998). The underlying pathways controlling the obviously variant embryonic processes in non-Caenorhabditis nematodes are essentially unknown. In this thesis I addressed this issue by performing a detailed unbiased comparative transcriptome analysis based on microarrays and RNA sequencing of selected developmental stages in a variety of nematodes from different phylogenetic branches with C. elegans as a reference system and a nematomorph as an outgroup representative. In addition, I made use of available genomic data to determine the presence or absence of genes for which no expression had been detected. In particular, I focussed on components of selected pathways or GRNs which are known to play essential roles during C. elegans development and/or other invertebrate or vertebrate model systems. Oogenesis must be regulated differently in non-Caenorhabditis nematodes, as crucial controlling components of Wnt and sex determination signaling are absent in these species. In this respect, I identified female-specific expression of potential polarity associated genes during gonad development and oogenesis in the Enoplean nematode Romanomermis culicivorax. I could show that known downstream components of the polarity complexes PAR-3/-6/PKC-3 and PAR-1/-2 are absent in non-Caenorhabditis species. Even PAR-2 as part of the polarity complex does not exist in these nematodes. Instead, transcriptomes of nematodes (including C. elegans), show expression of other polarity-associated complexes such as the Lgl (Lethal giant larvae) complex. This result could pose an alternative route for nematodes and nematomorphs to initiate polarity during early embryogenesis. I could show that crucial pathways of axis specification, such as Wnt and BMP are very different in C. elegans compared to other nematodes. In the former, Wnt signaling, for instance, is mediated by four paralogous beta-catenins, while other Chromadorea have fewer and Enoplea only one beta-catenin. The transcriptomes of R. culicivorax and the nematomorph show that regulators of BMP (e.g. Chordin), are specifically expressed during early embryogenesis only in Enoplea and the close outgroup of nematomorphs. In conclusion, my results demonstrate that the molecular machinery controlling oogenesis and embryogenesis in nematodes is unexpectedly variable and C. elegans cannot be taken as a general model for nematode development. Under this perspective, Enoplean nematodes show more similarities with outgroups than with C. elegans. It appears that certain pathway components were lost or gained during evolution and others adopted new functions. Based on my findings I can conjecture, which pathway components may be ancestral and which were newly acquired in the course of nematode evolution.

O marketing em um hospital universitário na relação com o trabalho da enfermagem: um estudo de caso

No setor hospitalar, o marketing compõe um grupo interdependente de serviços e tem como objetivo principal aproximar clientes - externos, internos e corpo gestor -, através de estratégias específicas que promovem satisfação e qualidade. Esta organização possui uma larga diversidade de profissionais da saúde e o marketing, neste sentido, auxilia no processamento de seus serviços de forma a lapidá-los sob a ótica do cliente, buscando efetividade e produtividade. Neste cenário encontra-se o enfermeiro, cujo trabalho é composto pelas dimensões cuidar, gerenciar, educar/pesquisar, que se entrelaçam e caracterizam o serviço deste profissional. No entanto, costumeiramente, a enfermagem não declara o marketing como uma ferramenta estratégica ao seu processo de trabalho – fato verificável na exploração de publicações científicas -, e, paralelamente, depara-se com empecilhos na execução de seu trabalho que podem comprometer a sua excelência. Assim, este estudo busca analisar a relação do marketing com o trabalho do enfermeiro nas dimensões cuidar, gerenciar, ensinar/pesquisar. Para sua efetivação, optou-se pelo referencial metodológico Estudo de Caso, onde o fenômeno é verificado como ocorre em seu cenário real. Assim, a coleta, caracterizada por pesquisador e unidade únicos, ocorreu em um hospital universitário, geral e público no sul do país que declara publica e virtualmente o marketing institucional. Como fontes de evidência, foram utilizadas: entrevista focada com quatro sujeitos de áreas estratégicas para esta pesquisa; análise de documentação criada pela assessoria de marketing e observação direta. O tratamento e a análise dos dados ocorreram por meio da Análise Temática, que possibilitou a exposição dos resultados através de dois artigos: “A relação do marketing com o processo de trabalho do enfermeiro na dimensão cuidar” e “A relação do marketing com o processo de trabalho do enfermeiro nas dimensões gerenciar e educar/pesquisar”. Os resultados evidenciaram que o marketing no cuidar - auxilia a efetividade do cuidado através de novas estratégias de comunicação com o usuário, produz materiais elucidativos, lúdicos para sua continuação e manutenção e o divulga no meio intra e extra-hospitalar; no gerenciar - auxilia a o enfermeiro a ter um método mais inovador e criativo, a focar no cliente e no bom relacionamento interpessoal com a equipe; no educar/pesquisar - cria canais de comunicação interna e campanhas únicas que, além de auxiliar na realização da educação permanente e na atualização de enfermeiros, propicia meios para transmitir novos achados científicos à prática da enfermagem hospitalar. Através deste estudo, percebeu-se que ações de marketing podem contribuir para a efetividade do trabalho do enfermeiro em suas facetas dimensionais, aproximando este agente de saúde do usuário ao qual seu serviço é destinado e da gestão da organização, propiciando a este profissional maior visibilidade e valorização no espaço hospitalar e social.

Three dimensional visualization of the World Wide Web

Although large-scale public hypermedia structures such as the World Wide Web are popularly referred to as "cyberspace", the extent to which they constitute a space in the everyday sense of the word is questionable. This paper reviews recent work in the area of three dimensional (3D) visualization of the Web that has attempted to depict it in the form of a recognizable space; in other words, as a navigable landscape that may be visibly populated by its users. Our review begins by introducing a range of visualizations that address different aspects of using the Web. These include visualizations of Web structure, especially of links, that act as 3D maps; browsing history; searches; evolution of the Web; and the presence and activities of multiple users. We then summarize the different techniques that are employed by these visualizations. We conclude with a discussion of key challenges for the future.

Genome Wide Association Studies of Phagocytosis and the Cellular Immune Response in Drosophila melanogaster.

Phagocytosis of bacteria by specialized blood cells, known as hemocytes, is a vital component of Drosophila cellular immunity. To identify novel genes that mediate the cellular response to bacteria, we conducted three separate genetic screens using the Drosophila Genetic Reference Panel (DGRP). Adult DGRP lines were tested for the ability of their hemocytes to phagocytose the Gram-positive bacteria Staphylococcus aureus or the Gram-negative bacteria Escherichia coli. The DGRP lines were also screened for the ability of their hemocytes to clear S. aureus infection through the process of phagosome maturation. Genome-wide association analyses were performed to identify potentially relevant single nucleotide polymorphisms (SNPs) associated with the cellular immune phenotypes. The S. aureus phagosome maturation screen identified SNPs near or in 528 candidate genes, many of which have no known role in immunity. Three genes, dpr10, fred, and CG42673, were identified whose loss-of-function in blood cells significantly impaired the innate immune response to S. aureus. The DGRP S. aureus screens identified variants in the gene, Ataxin 2 Binding Protein-1 (A2bp1) as important for the cellular immune response to S. aureus. A2bp1 belongs to the highly conserved Fox-1 family of RNA-binding proteins. Genetic studies revealed that A2bp1 transcript levels must be tightly controlled for hemocytes to successfully phagocytose S. aureus. The transcriptome of infected and uninfected hemocytes from wild type and A2bp1 mutant flies was analyzed and it was found that A2bp1 negatively regulates the expression of the Immunoglobulin-superfamily member Down syndrome adhesion molecule 4 (Dscam4). Silencing of A2bp1 and Dscam4 in hemocytes rescues the fly’s immune response to S. aureus indicating that Dscam4 negatively regulates S. aureus phagocytosis. Overall, we present an examination of the cellular immune response to bacteria with the aim of identifying and characterizing roles for novel mediators of innate immunity in Drosophila. By screening panel of lines in which all genetic variants are known, we successfully identified a large set of candidate genes that could provide a basis for future studies of Drosophila cellular immunity. Finally, we describe a novel, immune-specific role for the highly conserved Fox-1 family member, A2bp1.

Finite difference calculations of permeability in large domains in a wide porosity range.

Determining effective hydraulic, thermal, mechanical and electrical properties of porous materials by means of classical physical experiments is often time-consuming and expensive. Thus, accurate numerical calculations of material properties are of increasing interest in geophysical, manufacturing, bio-mechanical and environmental applications, among other fields. Characteristic material properties (e.g. intrinsic permeability, thermal conductivity and elastic moduli) depend on morphological details on the porescale such as shape and size of pores and pore throats or cracks. To obtain reliable predictions of these properties it is necessary to perform numerical analyses of sufficiently large unit cells. Such representative volume elements require optimized numerical simulation techniques. Current state-of-the-art simulation tools to calculate effective permeabilities of porous materials are based on various methods, e.g. lattice Boltzmann, finite volumes or explicit jump Stokes methods. All approaches still have limitations in the maximum size of the simulation domain. In response to these deficits of the well-established methods we propose an efficient and reliable numerical method which allows to calculate intrinsic permeabilities directly from voxel-based data obtained from 3D imaging techniques like X-ray microtomography. We present a modelling framework based on a parallel finite differences solver, allowing the calculation of large domains with relative low computing requirements (i.e. desktop computers). The presented method is validated in a diverse selection of materials, obtaining accurate results for a large range of porosities, wider than the ranges previously reported. Ongoing work includes the estimation of other effective properties of porous media.