High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

Transfer factor for carbon monoxide: a glance behind the scene.

The transfer factor for carbon monoxide (TLCO) is widely used in pulmonary function laboratories because it represents a unique non-invasive window on pulmonary microcirculation. The TLCO is the product of two primary measurements, the alveolar volume (VA) and the CO transfer coefficient (KCO). This test is most informative when VA and KCO are examined, together with their product TLCO. In a normal lung, a low VA due to incomplete expansion is associated with an elevated KCO, resulting in a mildly reduced TLCO. Thus, in case of low VA, a seemingly "normal KCO" must be interpreted as an abnormal gas transfer. The most common clinical conditions associated with an abnormal TLCO are characterised by a limited number of patterns for VA and KCO: incomplete lung expansion, discrete loss of alveolar units, diffuse loss of alveolar units, emphysema, pulmonary vascular disorders, high pulmonary blood volume, alveolar haemorrhage.

Diagnostic microbiologique de la pneumonie [Microbiological diagnosis of pneumonia].

Les pneumonies causent une mortalité et une morbidité significatives. De manière simplifiée, deux types de pneumonie sont décrits : la pneumonie communautaire et la pneumonie nosocomiale avec le pneumocoque et l'Haemophilus influenzae comme causes principales pour la première, le Pseudomonas et diverses entérobactéries pour la deuxième. La réalité est cependant plus complexe puisque l'on distingue aussi la pneumonie d'aspiration par exemple. La culture est très importante dans le cas des pneumonies nosocomiales car elle permet de déterminer la sensibilité aux antibiotiques de l'agent infectieux et d'adapter le traitement. Pour les patients immunosupprimés, le diagnostic différentiel est plus large et la recherche par tests moléculaires de certains virus, de champignons filamenteux et du Pneumocystis peut se révéler informative. Pneumonia is an importance cause of mortality and morbidity in adults. Two types of pneumonia are defined: community-acquired and nosocomial pneumonia with their corresponding etiology such as pneumococci or Haemophilus influenzae and Pseudomonas or enterobacteriaceae, respectively. However, the reality is more complex with aspiration pneumonia, pneumonia in immunocompromised patient, and pneumonia in ventilated patients. Culture in the case of nosocomial pneumonia is especially important to obtain the antibiotic susceptibility of the infectious agent and to adjust therapy. Moreover for immunocompromised patients, the differential diagnosis is much wider looking for viruses, filamentous fungi and Pneumocystis can be very informative, using new molecular assays.

A spatial modelling framework for assessing climate change impacts on freshwater ecosystems: Response of brown trout (Salmo trutta L.) biomass to warming water temperature

Mountain regions worldwide are particularly sensitive to on-going climate change. Specifically in the Alps in Switzerland, the temperature has increased twice as fast than in the rest of the Northern hemisphere. Water temperature closely follows the annual air temperature cycle, severely impacting streams and freshwater ecosystems. In the last 20 years, brown trout (Salmo trutta L) catch has declined by approximately 40-50% in many rivers in Switzerland. Increasing water temperature has been suggested as one of the most likely cause of this decline. Temperature has a direct effect on trout population dynamics through developmental and disease control but can also indirectly impact dynamics via food-web interactions such as resource availability. We developed a spatially explicit modelling framework that allows spatial and temporal projections of trout biomass using the Aare river catchment as a model system, in order to assess the spatial and seasonal patterns of trout biomass variation. Given that biomass has a seasonal variation depending on trout life history stage, we developed seasonal biomass variation models for three periods of the year (Autumn-Winter, Spring and Summer). Because stream water temperature is a critical parameter for brown trout development, we first calibrated a model to predict water temperature as a function of air temperature to be able to further apply climate change scenarios. We then built a model of trout biomass variation by linking water temperature to trout biomass measurements collected by electro-fishing in 21 stations from 2009 to 2011. The different modelling components of our framework had overall a good predictive ability and we could show a seasonal effect of water temperature affecting trout biomass variation. Our statistical framework uses a minimum set of input variables that make it easily transferable to other study areas or fish species but could be improved by including effects of the biotic environment and the evolution of demographical parameters over time. However, our framework still remains informative to spatially highlight where potential changes of water temperature could affect trout biomass. (C) 2015 Elsevier B.V. All rights reserved.-

Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance.

BackgroundBipolar disorder is a highly heritable polygenic disorder. Recent enrichment analyses suggest that there may be true risk variants for bipolar disorder in the expression quantitative trait loci (eQTL) in the brain.AimsWe sought to assess the impact of eQTL variants on bipolar disorder risk by combining data from both bipolar disorder genome-wide association studies (GWAS) and brain eQTL.MethodTo detect single nucleotide polymorphisms (SNPs) that influence expression levels of genes associated with bipolar disorder, we jointly analysed data from a bipolar disorder GWAS (7481 cases and 9250 controls) and a genome-wide brain (cortical) eQTL (193 healthy controls) using a Bayesian statistical method, with independent follow-up replications. The identified risk SNP was then further tested for association with hippocampal volume (n = 5775) and cognitive performance (n = 342) among healthy individuals.ResultsIntegrative analysis revealed a significant association between a brain eQTL rs6088662 on chromosome 20q11.22 and bipolar disorder (log Bayes factor = 5.48; bipolar disorder P = 5.85×10(-5)). Follow-up studies across multiple independent samples confirmed the association of the risk SNP (rs6088662) with gene expression and bipolar disorder susceptibility (P = 3.54×10(-8)). Further exploratory analysis revealed that rs6088662 is also associated with hippocampal volume and cognitive performance in healthy individuals.ConclusionsOur findings suggest that 20q11.22 is likely a risk region for bipolar disorder; they also highlight the informative value of integrating functional annotation of genetic variants for gene expression in advancing our understanding of the biological basis underlying complex disorders, such as bipolar disorder.

Drivers and Barriers of Collaboration in the Value Chain of Paperboard-Packed Consumer Goods

Value chain collaboration has been a prevailing topic for research, and there is a constantly growing interest in developing collaborative models for improved efficiency in logistics. One area of collaboration is demand information management, which enables improved visibility and decrease of inventories in the value chain. Outsourcing of non-core competencies has changed the nature of collaboration from intra-enterprise to cross-enterprise activity, and this together with increasing competition in the globalizing markets have created a need for methods and tools for collaborative work. The retailer part in the value chain of consumer packaged goods (CPG) has been studied relatively widely, proven models have been defined, and there exist several best practice collaboration cases. The information and communications technology has developed rapidly, offering efficient solutions and applications to exchange information between value chain partners. However, the majority of CPG industry still works with traditional business models and practices. This concerns especially companies operating in the upstream of the CPG value chain. Demand information for consumer packaged goods originates at retailers' counters, based on consumers' buying decisions. As this information does not get transferred along the value chain towards the upstream parties, each player needs to optimize their part, causing safety margins for inventories and speculation in purchasing decisions. The safety margins increase with each player, resulting in a phenomenon known as the bullwhip effect. The further the company is from the original demand information source, the more distorted the information is. This thesis concentrates on the upstream parts of the value chain of consumer packaged goods, and more precisely the packaging value chain. Packaging is becoming a part of the product with informative and interactive features, and therefore is not just a cost item needed to protect the product. The upstream part of the CPG value chain is distinctive, as the product changes after each involved party, and therefore the original demand information from the retailers cannot be utilized as such – even if it were transferred seamlessly. The objective of this thesis is to examine the main drivers for collaboration, and barriers causing the moderate adaptation level of collaborative models. Another objective is to define a collaborative demand information management model and test it in a pilot business situation in order to see if the barriers can be eliminated. The empirical part of this thesis contains three parts, all related to the research objective, but involving different target groups, viewpoints and research approaches. The study shows evidence that the main barriers for collaboration are very similar to the barriers in the lower part of the same value chain; lack of trust, lack of business case and lack of senior management commitment. Eliminating one of them – the lack of business case – is not enough to eliminate the two other barriers, as the operational model in this thesis shows. The uncertainty of the future, fear of losing an independent position in purchasing decision making and lack of commitment remain strong enough barriers to prevent the implementation of the proposed collaborative business model. The study proposes a new way of defining the value chain processes: it divides the contracting and planning process into two processes, one managing the commercial parts and the other managing the quantity and specification related issues. This model can reduce the resistance to collaboration, as the commercial part of the contracting process would remain the same as in the traditional model. The quantity/specification-related issues would be managed by the parties with the best capabilities and resources, as well as access to the original demand information. The parties in between would be involved in the planning process as well, as their impact for the next party upstream is significant. The study also highlights the future challenges for companies operating in the CPG value chain. The markets are becoming global, with toughening competition. Also, the technology development will most likely continue with a speed exceeding the adaptation capabilities of the industry. Value chains are also becoming increasingly dynamic, which means shorter and more agile business relationships, and at the same time the predictability of consumer demand is getting more difficult due to shorter product life cycles and trends. These changes will certainly have an effect on companies' operational models, but it is very difficult to estimate when and how the proven methods will gain wide enough adaptation to become standards.

Behavioural characteristics in phylogenetics : a case study using black fly (Diptera: Simuliidae) cocoon spinning behaviour

1-1 is torically, the predominan t method of reconstructing phylogenies has been through the use of morphological characters. There are new techniques now gaining acceptance, including molecular techniques al1d chromosomal information. Altl10ugh the study of behaviour has been used in a comparative framework, these analyses have, historically, been based on intuition. Hennig (1966) devised a neV\' method of reconstructing phylogenies which provided a 110ncircular method for formulating, testing and refining phylogenies. Subsequent s)Tstematists had virtually abandoned ecological and beha\lioural data as primary indicators of phylogenetic relationships (Brooks and McLennan 1991). Therefore, in a modern cladistic framework (sensu Hennig) the analysis of behavioural traits remains underrepresented as a method of reconstructing phylogenies. This thesis will reconstruct the phylogeny for species of black flies (Diptera: Simuliidae), using two steps. The first step is to thoroughl)' understand and explain the cocoon spinning in black fly larvae. There have bee115 previous descriptions of cocoon spinning, but all were incomplete or erroneous. The advances in technology, including video recorders and VCRs, have allowed this behaviour to be analyzed in great detail in 20 different species. A complete description of the cocoon spinning of Simulium \littatum is given. This description will be used as a template for the other species observed. The description and understanding of cococ)n spinning was the first step in undertaking a phylogenetic analysis using this behaviour. The behaviour was then broken down and analyzed, revealing 23 characters, 3 either qualitative and quantitative in nature. These characters were assessed in a cladistic framework (sensu Hennig) and a phylogenetic tree was reconstructed with a e.I of 0.91 and an R.I. of 0.96. This phylogenetic tree closely resembles a previously established pllylogenetic tree produced from morphological and cytological information. The importance of this result is the indication that, contrary to some authors, behavioural characters, if used properly, can add very informative characters to a data set.

Fast atom bombardment mass spectrometry of the coordination complexes of the ligand 5, 5, 7, 12, 12, 14- hexamenthyl-1, 4, 8, 11-tetraazacycloteradecane

A number of metal complexes containing the ligand 5,5,7,12,12,14-hexamethyl-l,4,8,11-tetra-azatetradecane were synthesized and analyzed using electron impact (EI) and fast atom bombardment (FAB). The FAB mass spectra were obtained in positive and negative ion mode. FAB in the positive ion mode proved to be the most successful technique for the identification of these compounds. In the majority of cases the spectra obtained using positive ion FAB were structurally informative, although not all showed molecular (M+) or quasimolecular ([M+H]+) ions. The fragmentations observed were characteristic of the ligands, and were interpreted based on the chemistry of these compounds.

The role of a minor party : a comparative study of the British Liberal Party and the Australian Country Party since 1918

and the Australian Country Party since 1918. 2. The thesis examines the proposition that the role of a minor party is determined, not by its total strength expressed as a percentage of the national vote, but by how its strength is concentrated. Australia and Britain were chosen for the comparison because of the many similarities in political culture and in the extent of class voting. Each country has a party - the Country Party in Australia and the Liberal Party in Britain - which has had a distinct impact on the political scene in their respective countries. In the period from 1918 to the present day neither party, at the national level, has ever held the largest number of seats in parliament let alone a majority of seats, and it is in this sense that they are herein defined as minor parties. In the thesis the constitutional background of and differences between Australia and Britain are reviewed, followed by a brief historical picture of each of the two parties being studied. The sources of supporc of the two parties are analysed and it is here that real differences emerge. The Country Party in Australia is a deliberately sectional party with a narrow rural base, whereas the British Liberal Party is more broadly based than either the Labour or Conservative Parties in Britain. 3. Party leadership and organisation are then discussed. Both parties have had outstanding leaders, Earle Page and McEwen for the Country Party; Asquith, Lloyd George and Grimond for the Liberal Party. Both parties have had relatively fewer leaders than their major party opponents. However, whereas the Country Party has been free of serious splits the Liberal Party was shattered on the leadership struggles of Asquith and Lloyd George. Both parties have been identified with decentralisation of state power, the Country Party through its support, albeit sometimes lukewarm of the New States Movement; the Liberal Party through its espousal of a federal system for Britain with separate Welsh, Scottish and regional assemblies. Unfortunately for the British Liberal Party the beneficiaries of their policies in this area have been relatively new nationalist parties in both Wales arid Scotland. The major part of the thesis is devoted to a study of how the electoral systems in the two countries have, in practice, worked to the advantage or disadvantage of the Country Party and the British Liberal Party. The Country Party has been as consistently over-represented in the House of Representatives as the Liberal Party has been under-represented in the British House of Commons. With the even distribution of its support the introduction of the single transferable vote, in itself, would bring little benefit to the British Liberal Party in terms of seats. Multimember urban constituencies combined with some type of list system are the only way the Liberals are likely to obtain House of Commons seats in proportion to their votes. 4. Finally, the relations of the two minor parties with their respective major parties are considered. In the conclusion the future of the two parties is reviewed. In general terms it appears that the Country Party is faced with a slow decline. Although the British Liberal Party made a major breakthrough, in terms of votes, in the February 1974 election, they were unable to maintain this momentum in the October election, even though they lost very little ground. In the long term they must make an inroad into Labour held seats if they are to progress further.

A crisis of social democracy : organized labour and the NDP in an era of neoliberalism

The NDP was founded out of the ashes of the Co-Operative Commonwealth Federation to cooperate with the Canadian Labour Congress to become the 'political arm of organized labour' in Canada. The NDP has long claimed they are the party which represents the policy goals of organized labour in Canada: that the NDP alone will fight for trade union rights, and will fight for Canadian workers. Divergent Paths is an examination of the links between the labour movement and the ND P in an era ofneo-liberalism. Provincial NDP governments have become increasingly neoliberal in their ideological orientation, and have often proved to be no friend to the labour movement when they hold office. The Federal party has never held power, nor have they ever formed the Official Opposition. This thesis charts the progress of the federal NDP as they become more neoliberal from 1988 to 2006, and shows how this trend effects the links between the NDP and labour. Divergent Paths studies each federal election from 1988 to 2006, looking at the interactions between Labour and the NDP during these elections. Elections provide critical junctions to study discourse - party platforms, speeches, and other official documents can be used to examine discourse. Extensive newspaper searches were used to follow campaign events and policy speeches. Studying the party's discourse can be used to determine the ideological orientation of the party itself: the fact that the party's discourse has become neoliberal is a sure sign that the party itself is neoliberal. The NDP continues to drive towards the centre of the political spectrum in an attempt to gain multi-class support. The NDP seems more interested in gaining seats at any cost, rather then promoting the agenda of Labour. As the party attempts to open up to more multi-class support, Labour becomes increasingly marginalised in the party. A rift which arguably started well before the 1988 election was exacerbated during that election; labour encouraged the NDP to campaign solely on the issue of Free Trade, and the NDP did not. The 1993 election saw the rift between the two grow even further as the Federal NDP suffered major blowbacks from the actions of the Ontario NDP. The 1997 and 2000 elections saw the NDP make a deliberate move to the centre of the political spectrum which increasingly marginalised labour. In the 2004 election, Jack Layton made no attempt to move the party back to the left; and in 2006 the link between labour and the NDP was perhaps irreparably damaged when the CAW endorsed the Liberal party in a strategic voting strategy, and the CLC did not endorse the NDP. The NDP is no longer a reliable ally of organized labour. The Canadian labour movement must decide wether the NDP can be 'salvaged' or if the labour movement should end their alliance with the NDP and engage in a new political project.

Expanding the research horizon in higher education : master's students' perceptions of research assistantships

This study explores how effectively current research assistantships impart research methods, skills, and attitudes; and how well those experiences prepare the next generation of researchers to meet the evolving needs of an ever-expanding, knowledge- based economy and society. Through personal interviews, 7 graduate student research assistants expressed their perceptions regarding their research assistantships. The open- ended interview questions emphasized (a) what research knowledge and skills the graduate students acquired; (b) what other lessons they took away from the experience; and (c) how the research assistantships influenced their graduate studies and future academic plans. After participants were interviewed, the data were transcribed, memberchecked, and then analyzed using a grounded theory research design. The findings show that research assistantships are valuable educational venues that can not only promote research learning but also benefit research assistants' master's studies and stimulate reflection regarding their future educational and research plans. Although data are limited to the responses of 7 students, findings can contribute to the enhancement of research assistantship opportunities as a means of developing skilled future researchers that in tum will benefit Canada as an emerging leader in research and development. The study is meant to serve as an informative source for (a) experienced researchers who have worked with research assistants; (b) researchers who are planning to hire research assistants; and (c) experienced and novice research assistants. Further, the study has the potential to inform future research training initiatives as well as related policies and practices.

The light and dark sides of perfectionism : implications for health and well-being

The present work presents two studies that examined the association of perfectionism, operationally defined by Hewi t t and Fl e t t ' s (1991) multidimensional mode l of perfectionism, with health and subjective well-being (SWB). The underlying question of this research was whether perfectionism could be beneficial as well as detrimental to health and well-being, as this is one of the mos t highly debated questions in the current literature. In samples of relatively healthy university students (n = 538) and community adults suffering from various chronic illnesses (n = 772), results from Study One indicated that socially prescribed perfectionism (SPP) is directly associated wi th poor e r he a l th and well-being. Results further showed f rom a personcentered perspective that there is a l a rge group of individuals wi th high levels of SPP and that i t is indeed these individuals who reported the poorest health and lowe s t levels of well-being. Other-oriented perfectionism was found to be unrelated to health and SWB. Findings revealed that when perfectionism is self-imposed (i.e., self-oriented perfectionism; SOP), i t is neither healthy nor unhealthy in an absolute sense. From the variable-centered perspective, this conclusion was supported by the f a c t tha t SOP was associated wi th both positive (e.g., be t t e r mental health and highe r levels of SWB in the student sample), and nega t ive correlates (e.g., higher levels of negative affect, stress, and neuroticism in both samples). Evidence f rom the chronically-ill sample further substantiated this conclusion by showing that there may be an optimal level of SOP, because mode r a t e levels of SOP we r e found to be associated with be t t e r health and highe r levels of SWB, whereas levels tha t we r e too low or too high we r e found to be associated with poor e r health and lowe r levels of SWB. Findings f rom the person-centered approach we r e particularly informative, in that they not only demonstrated tha t unique profiles of

Public Notices - Niagara Region collection

This is a collection of public notices posted by various villages, towns and townships in the Niagara Region. The notices alert residents to various civic events and initiatives.

The Informational Value of Corporate Credit Ratings

This thesis examines the quality of credit ratings issued by the three major credit rating agencies - Moody’s, Standard and Poor’s and Fitch. If credit ratings are informative, then prices of underlying credit instruments such as fixed-income securities and credit default insurance should change to reflect the new credit risk information. Using data on 246 different major fixed income securities issuers and spanning January 2000 to December 2011, we find that credit default swaps (CDS) spreads do not react to changes in credit ratings. Hence credit ratings for all three agencies are not price informative. CDS prices are mostly determined by historical CDS prices while ratings are mostly determined by historical ratings. We find that credit ratings are marginally more sensitive to CDS than CDS are sensitive to ratings.

Canadian Federation of University Women--St. Catharines fonds, 1921-2013

The University Women’s Club of St. Catharines was founded in 1921, two years after the formation of its national affiliate, the Canadian Federation of University Women. Membership was limited to women with university degrees. In early 2000 the constitution was expanded to include professions that now require university or college degrees. Associate members (non-voting) and student members were also accepted in 2007 by our local club. The purposes of the club are to assist in maintaining high standards of education in Canada, to stimulate members’ interest and participation in public affairs, to provide an opportunity for collective action, and to facilitate intellectual and social pursuits among members. The club takes an active interest in the status of women, provides scholarships at the university and high school levels, encourages reading in the formative years, makes charitable donations to support women and children’s services. In 1988 our club changed its name to Canadian Federation of University Women – St. Catharines at the direction of the National Office of CFUW.