Characterization of genomic diversity in extraintestinal pathogenic Escherichia coli (ExPEC) and development of a diagnostic DNA microarray for the differentiation of ExPEC isolates causing urinary tract infections

Extraintestinal pathogenic Escherichia coli (ExPEC) represent a diverse group of strains of E. coli, which infect extraintestinal sites, such as the urinary tract, the bloodstream, the meninges, the peritoneal cavity, and the lungs. Urinary tract infections (UTIs) caused by uropathogenic E. coli (UPEC), the major subgroup of ExPEC, are among the most prevalent microbial diseases world wide and a substantial burden for public health care systems. UTIs are responsible for serious morbidity and mortality in the elderly, in young children, and in immune-compromised and hospitalized patients. ExPEC strains are different, both from genetic and clinical perspectives, from commensal E. coli strains belonging to the normal intestinal flora and from intestinal pathogenic E. coli strains causing diarrhea. ExPEC strains are characterized by a broad range of alternate virulence factors, such as adhesins, toxins, and iron accumulation systems. Unlike diarrheagenic E. coli, whose distinctive virulence determinants evoke characteristic diarrheagenic symptoms and signs, ExPEC strains are exceedingly heterogeneous and are known to possess no specific virulence factors or a set of factors, which are obligatory for the infection of a certain extraintestinal site (e. g. the urinary tract). The ExPEC genomes are highly diverse mosaic structures in permanent flux. These strains have obtained a significant amount of DNA (predictably up to 25% of the genomes) through acquisition of foreign DNA from diverse related or non-related donor species by lateral transfer of mobile genetic elements, including pathogenicity islands (PAIs), plasmids, phages, transposons, and insertion elements. The ability of ExPEC strains to cause disease is mainly derived from this horizontally acquired gene pool; the extragenous DNA facilitates rapid adaptation of the pathogen to changing conditions and hence the extent of the spectrum of sites that can be infected. However, neither the amount of unique DNA in different ExPEC strains (or UPEC strains) nor the mechanisms lying behind the observed genomic mobility are known. Due to this extreme heterogeneity of the UPEC and ExPEC populations in general, the routine surveillance of ExPEC is exceedingly difficult. In this project, we presented a novel virulence gene algorithm (VGA) for the estimation of the extraintestinal virulence potential (VP, pathogenicity risk) of clinically relevant ExPECs and fecal E. coli isolates. The VGA was based on a DNA microarray specific for the ExPEC phenotype (ExPEC pathoarray). This array contained 77 DNA probes homologous with known (e.g. adhesion factors, iron accumulation systems, and toxins) and putative (e.g. genes predictably involved in adhesion, iron uptake, or in metabolic functions) ExPEC virulence determinants. In total, 25 of DNA probes homologous with known virulence factors and 36 of DNA probes representing putative extraintestinal virulence determinants were found at significantly higher frequency in virulent ExPEC isolates than in commensal E. coli strains. We showed that the ExPEC pathoarray and the VGA could be readily used for the differentiation of highly virulent ExPECs both from less virulent ExPEC clones and from commensal E. coli strains as well. Implementing the VGA in a group of unknown ExPECs (n=53) and fecal E. coli isolates (n=37), 83% of strains were correctly identified as extraintestinal virulent or commensal E. coli. Conversely, 15% of clinical ExPECs and 19% of fecal E. coli strains failed to raster into their respective pathogenic and non-pathogenic groups. Clinical data and virulence gene profiles of these strains warranted the estimated VPs; UPEC strains with atypically low risk-ratios were largely isolated from patients with certain medical history, including diabetes mellitus or catheterization, or from elderly patients. In addition, fecal E. coli strains with VPs characteristic for ExPEC were shown to represent the diagnostically important fraction of resident strains of the gut flora with a high potential of causing extraintestinal infections. Interestingly, a large fraction of DNA probes associated with the ExPEC phenotype corresponded to novel DNA sequences without any known function in UTIs and thus represented new genetic markers for the extraintestinal virulence. These DNA probes included unknown DNA sequences originating from the genomic subtractions of four clinical ExPEC isolates as well as from five novel cosmid sequences identified in the UPEC strains HE300 and JS299. The characterized cosmid sequences (pJS332, pJS448, pJS666, pJS700, and pJS706) revealed complex modular DNA structures with known and unknown DNA fragments arranged in a puzzle-like manner and integrated into the common E. coli genomic backbone. Furthermore, cosmid pJS332 of the UPEC strain HE300, which carried a chromosomal virulence gene cluster (iroBCDEN) encoding the salmochelin siderophore system, was shown to be part of a transmissible plasmid of Salmonella enterica. Taken together, the results of this project pointed towards the assumptions that first, (i) homologous recombination, even within coding genes, contributes to the observed mosaicism of ExPEC genomes and secondly, (ii) besides en block transfer of large DNA regions (e.g. chromosomal PAIs) also rearrangements of small DNA modules provide a means of genomic plasticity. The data presented in this project supplemented previous whole genome sequencing projects of E. coli and indicated that each E. coli genome displays a unique assemblage of individual mosaic structures, which enable these strains to successfully colonize and infect different anatomical sites.

Blended learning in medical imaging pre-clinical skills training – does it work?

Undergraduate Medical Imaging (MI)students at QUT attend their first clinical placement towards the end of semester two. Students undertake two (pre)clinical skills development units – one theory and one practical. Students gain good contextual and theoretical knowledge during these units via a blended learning model with multiple learning methods employed. Students attend theory lectures, practical sessions, tutorial sessions in both a simulated and virtual environment and also attend pre-clinical scenario based tutorial sessions. The aim of this project is to evaluate the use of blended learning in the context of 1st year Medical Imaging Radiographic Technique and its effectiveness in preparing students for their first clinical experience. It is hoped that the multiple teaching methods employed within the pre-clinical training unit at QUT builds students clinical skills prior to the real situation. A quantitative approach will be taken, evaluating via pre and post clinical placement surveys. This data will be correlated with data gained in the previous year on the effectiveness of this training approach prior to clinical placement. In 2014 59 students were surveyed prior to their clinical placement demonstrated positive benefits of using a variety of learning tools to enhance their learning. 98.31%(n=58)of students agreed or strongly agreed that the theory lectures were a useful tool to enhance their learning. This was followed closely by 97% (n=57) of the students realising the value of performing role-play simulation prior to clinical placement. Tutorial engagement was considered useful for 93.22% (n=55) whilst 88.14% (n=52) reasoned that the x-raying of phantoms in the simulated radiographic laboratory was beneficial. Self-directed learning yielded 86.44% (n=51). The virtual reality simulation software was valuable for 72.41% (n=42) of the students. Of the 4 students that disagreed or strongly disagreed with the usefulness of any tool they strongly agreed to the usefulness of a minimum of one other learning tool. The impact of the blended learning model to meet diverse student needs continues to be positive with students engaging in most offerings. Students largely prefer pre -clinical scenario based practical and tutorial sessions where 'real-world’ situations are discussed.

The Rat Trap [Dramaturg]

"The Rat Trap" is a new performance work undertaken as part of Kathryn Kelly's "PhD by Performance" at the University of Queensland: "The Pedagogy of Dramaturgy: A Practice Framework to Train Dramaturgs." Kathryn Kelly worked as dramaturg on each project, which served as case study material for the training program I developed as part of the thesis.

Cities of Light: Two Centuries of Urban Illumination

Cities of Light is the first global overview of modern urban illumination, a development that allows human wakefulness to colonize the night, doubling the hours available for purposeful and industrious activities. Urban lighting is undergoing a revolution due to recent developments in lighting technology, and increased focus on sustainability and human-scaled environments. Cities of Light is expansive in coverage, spanning two centuries and touching on developments on six continents, without diluting its central focus on architectural and urban lighting. Covering history, geography, theory, and speculation in urban lighting, readers will have numerous points of entry into the book, finding it easy to navigate for a quick reference and or a coherent narrative if read straight through. With chapters written by respected scholars and highly-regarded contemporary practitioners, this book will delight students and practitioners of architectural and urban history, area and cultural studies, and lighting design professionals and the institutional and municipal authorities they serve. At a moment when the entire world is being reshaped by new lighting technologies and new design attitudes, the longer history of urban lighting remains fragmentary. Cities of Light aims to provide a global framework for historical studies of urban lighting and to offer a new perspective on the fast-moving developments of lighting today.

Building economic capability to improve the management of marine resources in Australia: Final report

FRDC project 2008/306 Building economic capability to improve the management of marine resources in Australia was developed and approved in response to the widespread recognition and acknowledgement of the importance of incorporating economic considerations into marine management in Australia and of the persistent undersupply of suitably trained and qualified individuals capable of providing this input. The need to address this shortfall received broad based support and following widespread stakeholder consultation and building on previous unsuccessful State-based initiatives, a collaborative, cross-jurisdictional cross-institutional capability building model was developed. The resulting project sits within the People Development Program as part of FRDC’s ‘investment in RD&E to develop the capabilities of the people to whom the industry entrusts its future’, and has addressed its objectives largely through three core activities: 1. The Fisheries Economics Graduate Research Training Program which provides research training in fisheries/marine economics through enrolment in postgraduate higher degree studies at the three participating Universities; 2. The Fisheries Economics Professional Training Program which aims to improve the economic literacy of non-economist marine sector stakeholders and was implemented in collaboration with the Seafood Cooperative Research Centre through the Future Harvest Masterclass in Fisheries Economics; and, 3. The Australian Fisheries Economics Network (FishEcon) which aims to strengthen research in the area of fisheries economics by creating a forum in which fisheries economists, fisheries managers and Ph.D. students can share research ideas and results, as well as news of upcoming research opportunities and events. These activities were undertaken by a core Project team, comprising economic researchers and teachers from each of the four participating institutions (namely the University of Tasmania, the University of Adelaide, Queensland University of Technology and the Commonwealth Scientific and Industrial Research Organisation), spanning three States and the Commonwealth. The Project team reported to and was guided by a project Steering Committee. Commensurate with the long term nature of the project objectives and some of its activities the project was extended (without additional resources) in 2012 to 30th June 2015.

The Edge of Danger: artificial lighting and the dialectics of domestic occupation in Philip Johnson's Glass and Guest Houses

In the first half of the twentieth century the dematerializing of boundaries between enclosure and exposure problematized traditional acts of “occupation” and understandings of the domestic environment. As a space of escalating technological control, the modern domestic interior offered new potential to re-define the meaning and means of habitation. This shift is clearly expressed in the transformation of electric lighting technology and applications for the modern interior in the mid-twentieth century. Addressing these issues, this paper examines the critical role of electric lighting in regulating and framing both the public and private occupation of Philip Johnson’s New Canaan estate. Exploring the dialectically paired transparent Glass House and opaque Guest House (both 1949), this study illustrates how Johnson employed artificial light to control the visual environment of the estate as well as to aestheticize the performance of domestic space. Looking closely at the use of artificial light to create emotive effects as well as to intensify the experience of occupation, this revisiting of the iconic Glass House and lesser-known Guest House provides a more complex understanding of Johnson’s work and the means with which he inhabited his own architecture. Calling attention to the importance of Johnson serving as both architect and client, and his particular interest in exploring the new potential of architectural lighting in this period, this paper investigates Johnson’s use of electric light to support architectural narratives, maintain visual order and control, and to suit the nuanced desires of domestic occupation.

Liberty relighting, 20 years later

Recognized around the world as a powerful beacon for freedom, hope, and opportunity, the Statue of Liberty's light is not just metaphorical: her dramatic illumination is a perfect example of American ingenuity and engineering. Since the statue's installation in New York Harbor in 1886, lighting engineers and designers had struggled to illuminate the 150-foot copper-clad monument in a manner becoming an American icon. It took the thoughtful and creative approach of Howard Brandston-a legend in his own right-to solve this lighting challenge. In 1984, the designer was asked to give the statue a much-needed lighting makeover in preparation for its centennial. In order to avoid the shortcomings of previous attempts, he studied the monument from every angle and in all lighting conditions, discovering that it looked best in the light of dawn. Brandston determined that he would need 'one lamp to mimic the morning sun and one lamp to mimic the morning sky.' Learning that no existing lamps could simulate these conditions, Brandston partnered with General Electric to develop two new metal halide products. With only a short time for R&D, a team of engineers at GE's Nela Park laboratories assembled a 'top secret' testing room dedicated to the Statue of Liberty project. After nearly two years of work to perfect the new lamps, the 'dawn's early light' effect was finally achieved just days before the centennial celebrations were to take place in 1986. 'It was truly a labor of love,' he recalls.

Inflammatory meditated mechanisms of cisplatin resistance in non-small cell lung cancer

The majority of non-small cell lung cancer (NSCLC) patients present with advanced stage disease, where chemotherapy is usually the most common treatment option. While somewhat effective, patients treated with cisplatin-based chemotherapy will eventually develop resistance. Multiple pathways have been implicated in chemo-resistance, however the critical underlying mechanisms have yet to be elucidated. The aim of this project is to determine the role of inflammatory mediators in cisplatin resistance.

Characterisation of the impact of open biomass burning on urban air quality in Brisbane, Australia

Open biomass burning from wildfires and the prescribed burning of forests and farmland is a frequent occurrence in South-East Queensland (SEQ), Australia. This work reports on data collected from 10-30 September 2011, which covers the days before (10-14 September), during (15-20 September) and after (21-30 September) a period of biomass burning in SEQ. The aim of this project was to comprehensively quantify the impact of the biomass burning on air quality in Brisbane, the capital city of Queensland. A multi-parameter field measurement campaign was conducted and ambient air quality data from 13 monitoring stations across SEQ were analysed. During the burning period, the average concentrations of all measured pollutants increased (from 20% to 430%) compared to the non-burning period (both before and after burning), except for total xylenes. The average concentration of O3, NO2, SO2, benzene, formaldehyde, PM10, PM2.5 and visibility-reducing particles reached their highest levels for the year, which were up to 10 times higher than annual average levels, while PM10, PM2.5 and SO2 concentrations exceeded the WHO 24-hour guidelines and O3 concentration exceeded the WHO maximum 8-hour average threshold during the burning period. Overall spatial variations showed that all measured pollutants, with the exception of O3, were closer to spatial homogeneity during the burning compared to the non-burning period. In addition to the above, elevated concentrations of three biomass burning organic tracers (levoglucosan, mannosan and galactosan), together with the amount of non-refractory organic particles (PM1) and the average value of f60 (attributed to levoglucosan), reinforce that elevated pollutant concentration levels were due to emissions from open biomass burning events, 70% of which were prescribed burning events. This study, which is the first and most comprehensive of its kind in Australia, provides quantitative evidence of the significant impact of open biomass burning events, especially prescribed burning, on urban air quality. The current results provide a solid platform for more detailed health and modelling investigations in the future.

Insights from stimulating creative behaviours in a project-based organization team

Novel and useful ideas and creative behaviours originate in varied work environments, yet the characteristics of work environments that stimulate and foster such creative behaviours are not well defined. The aim of this study was to identify the influences that contribute to creative behaviours in the work environment of a global project-based professional service organization. This article is based on an investigation of the work environment of one project team undertaking interdisciplinary work in the construction of a processing plant in a remote location. This multi-disciplinary team encouraged creative behaviours through regular team meetings, ensuring the presentation of diverse views and commitments to regular interaction and collaboration in co-located environments. In addition, a technology manager dedicated to identifying potential opportunities for patenting and commercialization further extended the creative behaviours of the team by focusing on the best solution for each situation. The study contributes new knowledge to research regarding work environments that facilitate creative behaviours.

Constructing Fair Tourism in Ecuador: The Case of Asoguabo

Tämän pro gradu-tutkielman tarkoitus on tutkia, miten reilun kaupan banaania tuottavan El Guabon pienten banaaninviljelijöiden järjestön Asoguabon reilun turismin projekti on rakennettu. Projektin muotoutumista tutkitaan tässä työssä kahdesta eri näkökulmasta: siitä, miksi ja miten Asoguabo on monipuolistanut viljelystä turismiin, sekä siitä, millainen kuva projektista on rakennettu markkinoinnin kautta ja miten reilun kaupan mainonnasta tuttuja ilmiöitä on hyödynnetty reilun turismin rakentamisessa. Tutkielman teoreettisena taustana on maaseudun muutoksia tarkasteleva uuden ruraliteetin käsite. Turismi on viime vuosikymmenten aikana muuttunut, ja matkailijat etsivät yhä enemmän aitoja ja autenttisia matkailukokemuksia. Samanaikaisesti turismia on tuotteistettu korostamalla sen tiettyjä, kestävän kehityksen mukaisia piirteitä, ja erityisesti kehittyvissä maissa turismia markkinoidaan usein vaihtoehtoisena, yhteisöpohjaisena tai ekoturismina. Reilu turismi on uutena käsitteenä tullut mukaan tähän laajaan kirjoon, ja tämä tutkielma käsitteleekin Asoguabon projektia nimenomaan reilun turismin näkökulmasta. Tämä tutkielma on tapaustutkimus Asoguabon turismiprojektista, ja pohjautuu kuukauden pituiseen kenttätyöhön Ecuadorissa tammikussa 2010 sekä kirjoittajan aiempiin kokemuksiin Asoguabosta. Aineisto koostuu 21 puoli-strukturoidusta laadullisesta haastattelusta kuudentoista informantin kanssa, joista suurin osa oli hyvin läheisesti tekemisissä projektin kanssa. Tämän lisäksi aineistonkeruussa on käytetty havainnointia sekä projektin markkinointimateriaalien sisällönanalyysia. Tutkielma osoittaa reilun turismin projektin sisältävän monia haasteita ennen kuin se voi saavuttaa tavoitteensa tuottaa lisätuloja Asoguabon toimintaan. Tutkimushetkellä projekti hyödytti suoraan pääasiassa muutamia järjestön viljelijöitä, lähinnä niitä, jotka toimivat projektissa oppaina. Nämä oppaat hyötyvät projektista saamalla pieniä lisätuloja, kasvattamalla sosiaalista pääomaansa, sekä saamalla mahdollisuuden oppia muun muassa osallistumalla kursseille. Tutkimuksen keskeiset tulokset osoittavat myös, kuinka vuorovaikutus-ongelmat projektin eri toimijoiden välillä vaikeuttavat tiedonkulkua ja täten reilun turismin toimintaa. Nämä ongelmat myös lisäävät epätietoisuutta Asoguabon muiden viljelijöiden parissa. Lisäksi tutkimus osoittaa, kuinka reilun turismin projektin mainonnassa käytetään osittain samoja keinoja kuin reilun kaupan tuotteiden mainonnassa, joskin tuottajia on kuvattu mainosmateriaaleissa yllättävän vähän ja pääosassa ovat usein eurooppalaiset turistit.

End-User Attitudes Towards EDM Use in Construction Project Work: Case Study

This article reports on a cross-sectional case study of a large construction project in which Electronic document management (EDM) was used. Attitudes towards EDM from the perspective of individual end users were investigated. Responses from a survey were combined with data from system usage log files to obtain an overview of attitudes prevalent in different user segments of the total population of 334 users. The survey was followed by semi-structured interviews with representative users. A strong majority of users from all segments of the project group considered EDM as a valuable aid in their work processes, despite certain functional limitations of the system used and the complexity of the information mass. Based on the study a model describing the key factors affecting end user EDM adoption is proposed. The model draws on insight from earlier studies of EDM enabled projects and theoretical frameworks on technology acceptance and success of information systems, as well as the insights gained from the case study.

Managing Project Business Development: an Inter-Organizational and Intra-Organizational Perspective (summary section only)

The driving force behind this study is the gap between the reality of the firms engaged in project business and the available studies covering project management and business process development. Previous studies show that project-based organizations were ‘immature’ in terms of the project-management ‘maturity model’, as few firms were found to be optimizing processes. Even within those, very little attention was paid to combine inter-organizational and intra-organizational perspectives. In this study an effort is made to elaborate some thoughts and views on project management, which interrelate firms’ external and internal activities. In line with the integration, the dissertation uses an approach to the management of project-business interdependencies in the networks of actors, activities and resources. Firstly, the study develops an understanding for inter-organizational perspectives by exploring the complementarities of process activities in the basic development of project business. It presents a framework that is elaborated on the basis of the reciprocal interactions of activities within and outside the organization—thus providing a coherent basis for continuous business-process improvement. In addition, the study presents new tools that can be used to develop project-business processes in each of its functional areas. The research demonstrates how project-business activities can be optimized using the right resources at the right time with the right actors and the right actions. The selected five articles included in this dissertation explain the basic framework for the development of project business. Each paper covers various aspects of inter-organizational and intra-organizational perspectives for project management. The study develops a valuable and procedural model for business-process improvement using the Delphi method that can be used not only in academia but also as a guide for practitioners that takes them through a series of well-defined steps when making informed, consistent and efficient changes to their business processes.

Reklamsvenska i Finland speglad genom varuhuset Stockmanns tidningsannonser under det 20e seklet - Swedish Advertising Language in Finland Mirrored by the Newspaper Advertisements of the Stockmanns Department Store during the 20th Century

Reklam sägs använda ett modernt, gärna ett nyskapande språk. Detta är ett påstående som inte så lätt kan verifieras. Tidningsannonsen är troligen den skriftspråksgenre som har fått minst uppmärksamhet av språkforskare. De som skriver texten i en tidningsannons är personer som representerar det samtida språkbruket. Annonser som representerar olika tidsepoker skiljer sig därför från varandra inte bara genom att annonsen förändras i fråga om stil och form. Annonsens språk avspeglar också den språkliga förändringsprocess som kontinuerligt pågår i varje språksamhälle. Annonser, och marknadsföringsmaterial över huvud taget, läses också av många människor som i övrigt läser mycket litet eller kanske inte alls. Marknadsföraren, reklamskribenten (copywriter) och AD:n producerar m.a.o. texter som på ett omedvetet sätt kommer att vara språkmodeller för sina läsare. Förändringar i språket kreeras inte och drivs inte på av språkforskare, utan av vanliga språkbrukare i interaktion med andra språkbrukare. Sett ur ett sociolingvistiskt perspektiv har det vitt spridda reklamspråket därför inflytande på språket i samhället. Syftet med det reklamspråksprojekt som presenteras i föreliggande rapport är att analysera hur och när förändringar i svenskan som uppträder i Sverige dyker upp i annonser som skrivs på svenska i Finland. Reklam på svenska Finland under 1900-talet står i fokus, och tidningsannonser för Stockmanns varuhus i Helsingfors utgör primärmaterialet. Tidningsannonser för varuhuset Nordiska Kompaniet (NK) i Stockholm under motsvarande tid tjänar som jämförelsematerial. I denna rapport presenteras projektets syfte, de uppställda forskningsfrågorna, och resonemanget illustreras med exempel ur projektmaterialet. Rapporten innehåller också en beskrivning av projektets reklamdatabas och basfakta om material och metoder. -

Jac. Ahrenberg ja historian perintö : Restaurointisuunnitelmat Viipurin ja Turun linnoihin 1800-luvun lopussa

Jac. Ahrenberg and Patrimony Restoration Plans for Viipuri and Turku Castles at the End of the 19th Century This dissertation examines the unrealized restoration plans for two castles in the Grand Duchy of Finland one located at Viipuri (Vyborg, nowadays in Russia), the other at Turku (in Swedish, Åbo) during the last decades of the 19th century. Both castles were used as prisons, barracks and warehouses. From the middle of the 19th century on, their restoration and transformation into museums and "national monuments" were demanded in the newspapers. The prison reform in the 1860s stimulated the documentation and debate concerning their future, but it was only at the beginning of the 1880s when their restoration became an official state-run project. The undertaking was carried out by Johan Jacob (Jac.) Ahrenberg (1847 1914), architect of the National Board of Public Buildings. By combining written sources with drawings and photographs, this dissertation examines the restoration projects, the two castles' significance and the ways in which they were investigated by scholars. The plans are analyzed in connection with restoration practices in France and Sweden and in the context of contemporary discussions concerning national art and patrimony. The thesis argues that these former castles of the Swedish crown were used to manifest the western roots of Finnish law and order, the lineage of power and the capacity of the nation to defend itself. However, because of their symbolism, their restoration became a politically delicate question concerning the role of the Swedish heritage in Finland's nation-building process. According to Jac. Ahrenberg's plans, the two castles were to be restored to their assumed appearance at the time of the Vasa dynasty. Consequently, the structures would have resembled castles in Sweden. It is suggested that one aim of the restoration plans was to transform the two buildings into monuments testifying to the common history of Sweden and Finland. They were meant to consolidate the Swedish basis of Finnish culture and autonomy and thus to secure them against the threatening implications of Russian imperialism. It seems that along with the changing ideals of architectural restoration and the need for an original Finnish architectural heritage, the political connotations associated with the castles were one reason why Jac. Ahrenberg's restoration plans were never realized.