Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish : Proof of concept for key components of the insulin-like growth factor axis

Acknowledgements This study was funded by a Natural Environment Research Council grant (NERC, project code: NBAF704). FML is funded by a NERC Doctoral Training Grant (Project Reference: NE/L50175X/1). RLS was an undergraduate student at the University of Aberdeen and benefitted from financial support from the School of Biological Sciences. DJM is indebted to Dr. Steven Weiss (University of Graz, Austria), Dr. Takashi Yada (National Research Institute of Fisheries Science, Japan), Dr. Robert Devlin (Fisheries and Oceans Canada, Canada), Prof. Samuel Martin (University of Aberdeen, UK), Mr. Neil Lincoln (Environment Agency, UK) and Prof. Colin Adams/Mr. Stuart Wilson (University of Glasgow, UK) for providing salmonid material or assisting with its sampling. We are grateful to staff at the Centre for Genomics Research (University of Liverpool, UK) (i.e. NERC Biomolecular Analysis Facility – Liverpool; NBAF-Liverpool) for performing sequence capture/Illumina sequencing and providing us with details on associated methods that were incorporated into the manuscript. Finally, we are grateful to the organizers of the Society of Experimental Biology Satellite meeting 'Genome-powered perspectives in integrative physiology and evolutionary biology' (held in Prague, July 2015) for inviting us to contribute to this special edition of Marine Genomics and hosting a really stimulating meeting.

Who Financed the Expansion of the Equity Market? Shareholder Clienteles in Victorian Britain

Who financed the great expansion of the Victorian equity market, and what attracted them to invest? Using data on 453 firm-years and over 172,000 shareholders, we find that the largest providers of capital were rentiers, men with no formal occupation who relied on investment income. We also see a substantial growth in women investors as time progressed. In terms of clientele effects, we find that rentiers invested in large firms, whilst businessmen were the venture capitalists of young, regional enterprises. Women and the middle classes preferred safe investments, whilst financiers and institutional investors were speculators in foreign companies. Our results may help to explain the growth of new types of assets catering for particular clienteles, and the development of managerial policies on dividends and share issues. 

High frequency components of the AE signal as useful features for bond/fibre break discriminators

Abstract not available

Research Monograph: The role of community and lifestyle in the making of a knowledge city

Our brief is to investigate the role of community and lifestyle in the making of a globally successful knowledge city region. Our approach is essentially pragmatic. We start by broadly examining knowledge-based urban development from a number of different perspectives. The first view is historical. In this context knowledge work and knowledge workers are seen as vital parts of a new emergent mode of production reliant on the continual production of abstract knowledge. We briefly develop this perspective to encompass the work of Richard Florida who has, notedly, claimed: “Wherever talent goes, innovation, creativity, and economic growth are sure to follow.” Our next perspective examines concepts of knowledge and modes of its production to discover knowledge is not an unchanging object but a human activity that changes in form and content through history. The suggestion emerges that not only is the production of contemporary ‘knowledge’ organised in a specific (and new) manner but also the output of this networked production is a particular type of knowledge (i.e. techné). The third perspective locates knowledge production and its workers in the contemporary urban context. As such, it co-ordinates the knowledge city in the increasingly global structure of cities and develops a typology of different groups of knowledge workers in their preferred urban environment(s). We see emerging here a distinctive geography of knowledge production. It is an urban phenomenon. There is, in short, something about the nature of cities that knowledge workers find particularly attractive. In the next, essentially anthropological, perspective we start to explore the needs and desires of the individual knowledge worker. Beyond the needs basic to any modern human household an attempt is made to deduce, from a base understanding of knowledge work as mental labour, the compensatory cultural needs of the knowledge worker when not at work - and the expression of these needs in the urban fabric. Our final perspective consists of two case studies. In a review of the experiences of Austin, Texas and Singapore’s one-north precinct we collect empirical data on, respectively, a knowledge city that has sustained itself for over 50 years and an urban precinct newly launched into the global market for knowledge work and knowledge workers. Interwoven The Role of Community and Lifestyle in the Making of a Knowledge City Urban Research Program 8 through all perspectives, in the form of apposite citation, is that of ‘expert opinion’ gathered in a rudimentary poll of academic and industry sources. This opinion appears in text boxes while details of the survey can be found in Appendix A. In the conclusion of the report we interpret the wide range of evidence gathered above in a policy frame. It is our hope this report will leave the reader with a clearer picture of the decisive organisational, infrastructural, aesthetic and social dimensions of a knowledge precinct.

Making space and place for the knowledge economy : knowledge-based development of Australian cities

The impact of what has been broadly labelled the knowledge economy has been such that, even in the absence of precise measurement, it is the undoubted dynamo of today’s global market, and an essential part of any global city. The socio-economic importance of knowledge production in a knowledge economy is clear, and it is an emerging social phenomenon and research agenda in geographical studies. Knowledge production, and where, how and by whom it is produced, is an urban phenomenon that is poorly understood in an era of strong urbanisation. This paper focuses on knowledge community precincts as the catalytic magnet infrastructures impacting on knowledge production in cities. The paper discusses the increasing importance of knowledge-based urban development within the paradigm of the knowledge economy, and the role of knowledge community precincts as instruments to seed the foundation of knowledge production in cities. This paper explores the knowledge based urban development, and particularly knowledge community precinct development, potentials of Sydney, Melbourne and Brisbane, and benchmarks this against that of Boston, Massachusetts.

The knowledge base of subject-matter experts in teaching : A case study of a professional scientist as a beginning teacher

One method of addressing the shortage of science and mathematics teachers is to train scientists and other science-related professionals to become teachers. Advocates argue that as discipline experts these career changers can relate the subject matter knowledge to various contexts and applications in teaching. In this paper, through interviews and classroom observations with a former scientist and her students, we examine how one career changer used her expertise in microbiology to teach microscopy. These data provided the basis for a description of the teacher’s instruction which was then analysed for components of domain knowledge for teaching. Consistent with the literature, the findings revealed that this career changer needed to develop her pedagogical knowledge. However, an interesting finding was that the teacher’s subject matter as a science teacher differed substantively from her knowledge as a scientist. This finding challenges the assumption that subject matter is readily transferable across professions and provides insight into how to better prepare and support career changers to transition from scientist to science teacher.

Knowledge, attitudes and perceptions of management strategies and regulations of the Florida Keys National Marine Sanctuary by commercial fishers, dive operators, and environmental group members: A baseline characterization and 10-year comparison

This research is part of the Socioeconomic Research & Monitoring Program for the Florida Keys National Marine Sanctuary (FKNMS), which was initiated in 1998. In 1995-96, a baseline study on the knowledge, attitudes and perceptions of proposed FKNMS management strategies and regulations of commercial fishers, dive operators and on selected environmental group members was conducted by researchers at the University of Florida and the University of Miami’s Rosenstiel School of Atmospheric and Marine Science (RSMAS). The baseline study was funded by the U.S. Man and the Biosphere Program, and components of the study were published by Florida Sea Grant and in several peer reviewed journals. The study was accepted into the Socioeconomic Research & Monitoring Program at a workshop to design the program in 1998, and workshop participants recommended that the study be replicated every ten years. The 10-year replication was conducted in 2004-05 (commercial fishers) 2006 (dive operators) and 2007 (environmental group members) by the same researchers at RSMAS, while the University of Florida researchers were replaced by Thomas J. Murray & Associates, Inc., which conducted the commercial fishing panels in the FKNMS. The 10-year replication study was funded by NOAA’s Coral Reef Conservation Program. The study not only makes 10-year comparisons in the knowledge, attitudes and perceptions of FKNMS management strategies and regulations, but it also establishes new baselines for future monitoring efforts. Things change, and following the principles of “adaptive management”, management has responded with changes in the management plan strategies and regulations. Some of the management strategies and regulations that were being proposed at the time of the baseline 1995-96 study were changed before the management plan and regulations went into effect in July 1997. This was especially true for the main focus of the study which was the various types of marine zones in the draft and final zoning action plan. Some of the zones proposed were changed significantly and subsequently new zones have been created. This study includes 10-year comparisons of socioeconomic/demographic profiles of each user group; sources and usefulness of information; knowledge of purposes of FKNMS zones; perceived beneficiaries of the FKNMS zones; views on FKNMS processes to develop management strategies and regulations; views on FKNMS zone outcomes; views on FKNMS performance; and general support for FKNMS. In addition to new baseline information on FKNMS zones, new baseline information was developed for spatial use, investment and costs-and-earnings for commercial fishers and dive operators, and views on resource conditions for all three user groups. Statistical tests were done to detect significant changes in both the distribution of responses to questions and changes in mean scores for items replicated over the 10-year period. (PDF has 143 pages.)

Mechanisms of Disease: specialized interstitial cells of the urinary tract--an assessment of current knowledge.

Scientists interested in the smooth muscles of the urinary tract, and their control, have recently been studying cells in the interstitium of tissues that express the c-kit antigen (Kit(+) cells). These cells have morphologic features that are reminiscent of the well-described pacemaker cells in the gut, the interstitial cells of Cajal (ICC). The spontaneous contractile behavior of muscles in the urinary tract varies widely, and it is clear that urinary tract Kit(+) interstitial cells cannot be playing an identical role to that played by the ICC in the gut. Nevertheless, there is increasing evidence that they do play a role in modulating the contractile behavior of adjacent smooth muscle, and might also be involved in mediating neural control. This review outlines the properties of ICC in the gut, and gives an account of the discovery of cells in the interstitium of the main components of the urinary tract. The physiologic properties of such cells and the functional implications of their presence are discussed, with particular reference to the bladder. In this organ, Kit(+) cells are found under the lamina propria, where they might interact with the urothelium and with sensory nerves, and also between and within the smooth-muscle bundles. Confocal microscopy and calcium imaging are being used to assess the physiology of ICC and their interactions with smooth muscles. Differences in the numbers of ICC are seen in smooth muscle specimens obtained from patients with various pathologies; in particular, bladder overactivity is associated with increased numbers of these cells.

What are the components of humanized childbirth in a highly specialized hospital? : an organizational case study

Many studies have focused on the concept of humanization of birth in normal pregnancy cases or at low obstetric risk, but no studies, at our knowledge, have so far specifically focused on the humanization of birth in both high-risk, and low risk pregnancies, in a highly specialized hospital setting. The present study thus aims to: 1) define the specific components of the humanized birth care model which bring satisfaction to women who seek obstetrical care in highly specialized hospitals; and 2) explore the organizational and cultural dimensions which act as barriers or facilitators for the implementation of humanized birth care practices in a highly specialized, university affiliated hospital in Quebec. A single case study design was chosen for this thesis. The data were collected through semi-structured interviews, field notes, participant observations, selfadministered questionnaire, relevant documents, and archives. The samples comprised: 11 professionals from different disciplines, 6 administrators from different hierarchical levels within the hospital, and 157 women who had given birth at the hospital during the study. The performed analysis covered both quantitative descriptive and qualitative deductive and inductive content analyses. The thesis comprises three articles. In the first article, we proposed a conceptual framework, based on Allaire and Firsirotu’s (1984) organizational culture theory. It attempts to examine childbirth patterns as an organizational cultural phenomenon. In our second article, we answered the following specific question: according to the managers and multidisciplinary professionals practicing in a highly specialized hospital as well as the women seeking perinatal care in this hospital setting, what is the definition of humanized care? Analysis of the data collected uncovered the following themes which explained the perceptions of what humanized birth was: personalized care, recognition of women’s rights, humanly care for women, family-centered care,women’s advocacy and companionship, compromise of security, comfort and humanity, and non-stereotyped pregnancies. Both high and low risk women felt more satisfied with the care they received if they were provided with informed choices, were given the right to participate in the decision-making process and were surrounded by competent care providers. These care providers who humanly cared for them were also able to provide relevant medical intervention. The professionals and administrators’ perceptions of humanized birth, on the other hand, mostly focused on personalized and family-centered care. In the third article of the thesis, we covered the dimensions of the internal and external components of an institution which can act as factors that facilitate or barriers that prevent, a specialized and university affiliated hospital in Quebec from adopting a humanized child birthing care. The findings revealed that both the external dimensions of a highly specialized hospital -including its history, society, and contingency-; and its internal dimensions -including culture, structure, and the individuals present in the hospital-, can all affect the humanization of birth care in such an institution, whether separately, simultaneously or in interaction. We thus hereby conclude that the humanization of birth care in a highly specialized hospital setting, should aim to meet all the physiological, as well as psychological aspects of birth care, including respect of the fears, beliefs, values, and needs of women and their families. Integration of competent and caring professionals and the use of obstetric technology to enhance the level of certainty and assurance in both high-risk and low risk women are both positive factors for the implementation of humanized care in a highly specialized hospital. Finally, the humanization of birth care approach in a highly specialized and university affiliated hospital setting demands a new healthcare policy. Such policy must offer a guarantee for women to have the place of birth, and the health care professional of their choice as well as those, which will enable women to make informed choices from the beginning of their pregnancy.

Juan Valdez in the coffe market of France

El objetivo de este trabajo es presentar un marco organizacional en profundidad de las operaciones de Juan Valdez y sus posibilidades de incursionar en el mercado Francés. El Análisis se presenta en base a una investigación de mercados que tiene como referencia las tendencias de consumo, más exactamente hacía bebidas con alto contenido de cafeína, (Bebidas energizantes, deportivas, café etc.). Igualmente se analizan los socios estratégicos con más fuerza de realizar alianzas con la empresa colombiana, sus posibilidades financieras, así como su experiencia y conocimiento de su mercado local, y la similitud de procesos o cultura organizacional. La investigación de la propuesta nos lleva a generar una aplicación y conocimiento más a fondo de aspectos teóricos relacionados con el estudio del consumidor, la diversidad cultural y su influencia en el momento de realizar estrategias de mercadeo, el concepto de red y complejidad, así como aspectos teóricos relacionados con la organización y desafíos de una empresa al optar el camino de la internacionalización.

The functions of intermediaries in Swedish SMEs internationalization to the Nigerian market

Over the years so many academic literatures has revealed that increased number of firms have seen internationalization as a means to gain and sustain competitive advantage and even increase economic of scale, and this has led many western companies to emerging markets. In this paper we discovered that among the pool of Swedish firms, only the MNEs have seen Nigerian market attractive to internationalize to, but just a few of the Swedish SMEs has expanded to the Nigerian market. This research was conducted by doing a qualitative study with the use of phenomenological research approach, during our investigation on the functions of intermediaries in Swedish SMEs internationalization to Nigeria market.Furthermore, we were able to understand the importance and functions of the different marketing intermediaries’ in Swedish SMEs internationalization to Nigeria market. These intermediaries equip the Swedish firms with the required objective knowledge of the Nigerian market, updating them with recent development of the opportunities and threats involved in the Nigerian marketing environment, and linking these Swedish firms to the required government departments, distributors, agent/broker, customers, middle men etc, thereby impacting them with the experiential knowledge. Moreover, it is important for firms to have objective or pre-market knowledge of a particular market before entering that market, but this knowledge is regarded as non-helpful knowledge to firms. But the experiential knowledge is acquired over time in the market, which is regarded as the helpful knowledge. It is evident that the intermediaries equip these firms with both objective and experiential knowledge.Although the opportunities in some emerging markets are very attractive, but the threats in these markets are other factors firms also put into consideration before internationalizing to these markets. This is why thorough market research has to be done so that firms can create effective marketing strategies when they want to expand their marketing activities to emerging markets. Despite the risk and uncertainties involved in doing business in foreign countries, still yet companies selling global products do not have any choice than to internationalize their marketing operations.

Developments in the Agricultural and Rural Capital Market of the Former Yugoslav Republic of Macedonia. Factor Markets Working Paper No. 9, October 2011

The undeveloped rural capital market in the Former Yugoslav Republic of Macedonia is constrained by an urban–rural development gap, with limited capacities for rural development and imperfections in the rural capital market. Among the most striking hindrances are the illegal status of a large share of agricultural buildings and other real estate in rural areas, particularly on the individual family farms that prevail in the country, and the insufficient knowledge and abilities of individual farmers in applying for credit. National, EU and other donor funds are being used to improve knowledge, skills and other human resources, and to address the illegal status of buildings and facilities. In recent years, government support for agricultural, rural and regional development has been introduced to promote good agricultural practices, production and economic activity in rural areas. The elimination of imperfections and improvements to the functioning of the capital market – making access to credit and funds easier, especially for small-scale family farms and for rural development – are seen as measures contributing to agriculture and more balanced rural and regional development.

Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.

The role of organisational capacity in the knowledge-based transformation of Brisbane, Australia

Purpose - The cumulative impacts of the knowledge economy together with the emerging dominance of knowledge-intensive sectors, have led to an unprecedented period of socio-economic and spatial restructuring. As a result, the paradigm of knowledge-based urban development (KBUD) has emerged as a development strategy to guide knowledge-based economic transformation (Knight, 1995; Yigitcanlar, 2007). Notwithstanding widespread government commitment and financial investment, in many cases providing the enabling circumstances for KUBUD has proven a complicated task as institutional barriers remain. Researchers and practitioners advocate that the way organisations work and their institutional relationships, policies and programs, will have a significant impact on a regions capacity to achieve KBUD (Savitch, 1998; Savitch and Kantor, 2002; Keast and Mandell, 2009). In this context, building organisational capacity is critical to achieving institutional change and bring together all of the key actors and sources, for the successful development, adoption, and implementation of knowledge-based development of a city (Yigitcanlar, 2009). Design/methodology/approach - There is a growing need to determine the complex inter-institutional arrangements and intra-organisational interactions required to advance urban development within the knowledge economy. In order to design organisational capacity-building strategies, the associated attributes of good capacity must first be identified. The paper, with its appraisal of knowledge-based urban development, scrutinises organisational capacity and institutional change in Brisbane. As part of the discussion of the case study findings, the paper describes the institutional relationships, policies, programs and funding streams, which are supporting KBUD in the region. Originality/value - In consideration that there has been limited investigation into the institutional lineaments required to provide the enabling circumstances for KBUD, the broad aim of this paper is to discover some good organisational capacity attributes, achieved through a case study of Brisbane. Practical implications - It is anticipated that the findings of the case study will contribute to moving the discussion on the complex inter-institutional arrangements and intra-organisaational interactions required for KBUD, beyond a position of rhetoric.

The lifecycle of the fashion garment : voices of mass market designers

For the Australian fashion industry to move towards a more socially and environmentally ethical industry, change to existing processes would need to occur in all market levels. Change is particularly needed in the mass market, where larger volumes inevitably lead to greater environmental impact. Recent trends in eco fashion have waxed and waned, with only minor impact on the methodology of the mass market design process, with greenwashing and confusion of concepts being common problems. In the mass market, the product lifecycle begins in the design room and ends on the retail floor. A design process for sustainability necessarily expands this lifecycle, assessing the impact of every stage in the life of a fashion garment from the fibre and textiles through to consumer use, to eventual disposal and beyond disposal to fibre recycling and reuse or resale. However, how easy is it for designers to consider a wider view of the product lifecycle in their design process? How much autonomy do they have over their design process, and where do they believe their responsibility begins and ends for the garments they design? This paper will present some preliminary findings from interviews with designers in the Australian women’s wear mass market, revealing their concerns and views on the challenges of a sustainability for their industry.