Population structure and genetic diversity of Streptococcus suis isolates obtained from the United States

Diseases caused by the zoonotic pathogen Streptococcus suis are an extensive economic problem as well as an animal welfare concern for the global swine industry. Previous studies have evaluated the genomic diversity and population structure of S. suis isolates, however, the majority of these studies utilized isolates obtained from countries other than the U.S. This study applied whole genome sequencing and cgMLST-based typing to evaluate the population structure and genetic relatedness among S. suis isolates obtained within the U.S. The established high-resolution phylogenomic framework revealed extensive genomic variation and diversity among the sampled S. suis isolates, with isolates from the U.S. and from countries outside the U.S. found interspersed in the phylogeny. S. suis isolates obtained within the U.S. did not cluster by state or geographic location, however, isolates with similar serotypes, both obtained from within and outside the U.S., generally clustered together. Average nucleotide identity (ANI) values determined for the S. suis genomes were extensively broad, approaching the recommended species demarcation value, and correlated with the phylogenetic group distribution of the cgMLST-based tree. Numerous antimicrobial resistance (AMR) elements were identified among both U.S. and non-U.S. isolates with ble, tetO, and ermB genes identified as the most prevalent. The epf, mrp, and sly genes, historically used as markers for virulence potential, were also observed in the genomes of isolates that grouped together forming a subclade of clonal complex 1 (CC1) isolates. Collectively, the data in this report provides critical information needed to address potential biosurveillance needs and insights into the genetic diversity and population structure of S. suis isolates obtained within the U.S

Performance of Coupled Product Development Activities with a Deadline

This paper explores the performance of coupled development tasks subject to a deadline constraint by proposing a performance generation model (PGM). The goal of the PGM is to develop insights about optimal strategies (i.e. sequential, concurrent, or overlapped) to manage coupled design tasks that share fixed amount of engineering resources subject to performance and deadline constraints. Model analysis characterizes the solution space for the coupled development problem. The solution space is used to explore the generation of product performance and the associated dynamic forces affecting concurrent development practices. We use these forces to explain conditions under which concurrency is a desirable strategy

Responsible design : recognising the impact of how we design

We live in a period during which human activity is the dominant influence on climate and the environment. Schoolchildren across the world take to the streets calling on all of us –individuals, businesses, and governments – to act responsibly for the future of humanity. University students demand education on doing well by doing good. Member states of the United Nations have committed to the 2030 Agenda for Sustainable Development. Realising sustainable futures inclusive of a good information society certainly sounds attractive to students, business, and governments alike, and we certainly notice heightened awareness and a sense of urgency to tackle large-scale and interconnected challenges such as clean energy, global health, and well-being. Yet, the focus on complex, global challenges has perhaps made it more difficult for individual designers, engineers, and entrepreneurs to feel that their own actions can have a direct impact. Having said this, we also notice that many individuals, businesses, and governments are beginning to ask how might we foresee the impact of the physical and digital products, services, experiences and systems solutions we create. The term "responsible design" is now gaining traction. Still, we can all think of examples of 'successful design' that is harmful to people, damaging to the environment, or bad for our society. We need to recognise our responsibility to change this trajectory, learn from examples of responsible design, and accept the responsibility to make the necessary changes in our own design practice, to achieve system-level change, creating solutions that are regenerative in nature. Many of us are familiar with the 3-point design challenge — desirability, feasibility, and viability. These terms conveniently map to three critical disciplines closely associated with successful design — market, technical, and business. We believe that responsible design is now critical for successful design and thus needs to be part of our community’s discussion, curriculum, and practice. To achieve this goal, we must articulate what responsible design might mean and how we can act accordingly. We offer a definition of responsible design that focuses on responsible behaviour, environmental responsibility, and social responsibility. We illustrate these principles using examples drawn from energy, health care, food, automobile, consumer electronics, and other domains. We propose responsible design as a collective journey that requires the actions of individual designers and design teams. This transition will also affect the nature of innovation processes and the structure of organisations where they take place. The practice of responsible design offers the possibility to engage generations of designers, engineers, entrepreneurs, business, and policy makers to make a difference in our own society through our future products, services, and system solutions. Finally, based on a survey conducted in the lead-up to the conference, in this keynote, we provide a glimpse into how members of the worldwide Design Society are working with the Sustainable Development Goals in research, teaching, and societal outreach

Coordination Implications of Software Coupling in Open Source Projects

The effect of software coupling on the quality of software has been studied quite widely since the seminal paper on software modularity by Parnas [1]. However, the effect of the increase in software coupling on the coordination of the developers has not been researched as much. In commercial software development environments there normally are coordination mechanisms in place to manage the coordination requirements due to software dependencies. But, in the case of Open Source software such coordination mechanisms are harder to implement, as the developers tend to rely solely on electronic means of communication. Hence, an understanding of the changing coordination requirements is essential to the management of an Open Source project. In this paper we study the effect of changes in software coupling on the coordination requirements in a case study of a popular Open Source project called JBoss

Monitoring of lung edema by microwave reflectometry during lung ischemia-reperfusion injury in vivo

It is still unclear whether lung edema can be monitored by microwave reflectometry and whether the measured changes in lung dry matter content (DMC) are accompanied by changes in PaO(2) and in pro-to anti-inflammatory cytokine expression (IFN-gamma and IL-10). Right rat lung hili were cross-clamped at 37 degrees C for 0, 60, 90 or 120 min ischemia followed by 120 min reperfusion. After 90 min (DMC: 15.9 +/- 1.4%; PaO(2): 76.7 +/- 18 mm Hg) and 120 min ischemia (DMC: 12.8 +/- 0.6%; PaO(2): 43 +/- 7 mm Hg), a significant decrease in DMC and PaO(2) throughout reperfusion compared to 0 min ischemia (DMC: 19.5 +/- 1.11%; PaO(2): 247 +/- 33 mm Hg; p < 0.05) was observed. DMC and PaO(2) decreased after 60 min ischemia but recovered during reperfusion (DMC: 18.5 +/- 2.4%; PaO(2) : 173 +/- 30 mm Hg). DMC values reflected changes on the physiological and molecular level. In conclusion, lung edema monitoring by microwave reflectometry might become a tool for the thoracic surgeon. Copyright (c) 2006 S. Karger AG, Basel

Extension of internationalisation models: drivers and processes for the globalisation of product development – a comparison of Danish and Chinese engineering firms

This paper develops an extension to established production- and supply chain management focused internationalisation models. It applies explorative case studies in Danish and Chinese engineering firms to discover how the globalisation process of product development differs from Danish and Chinese perspectives. The paper uses internationalisation and global product development theory to explain similarities and differences in the approaches. Grounded in case study results, a new model for internationalisation is proposed. The new model expands the internationalisation process model to include steps of product development and collaborative distributed development beyond sourcing, sales and production elements. The paper then provides propositions for how to further develop the suggested model, and how western companies can learn from the Chinese approaches, and globalise their product development activities from the front end of the value chain rather than from the back-end

The Complete Genome Sequence of Yersinia pseudotuberculosis IP31758, the Causative Agent of Far East Scarlet-Like Fever

The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation, exanthema, hyperhemic tongue, and a toxic shock syndrome. The term FESLF was coined for the infection because it shares clinical presentations with scarlet fever caused by group A streptococci. The causative agent was later identified as Yersinia pseudotuberculosis, although the range of morbidities was vastly different from classical pseudotuberculosis symptoms. To understand the origin and emergence of the peculiar clinical features of FESLF, we have sequenced the genome of the FESLF-causing strain Y. pseudotuberculosis IP31758 and compared it with that of another Y. pseudotuberculosis strain, IP32953, which causes classical gastrointestinal symptoms. The unique gene pool of Y pseudotuberculosis IP31758 accounts for more than 260 strain-specific genes and introduces individual physiological capabilities and virulence determinants, with a significant proportion horizontally acquired that likely originated from Enterobacteriaceae and other soil-dwelling bacteria that persist in the same ecological niche. The mobile genome pool includes two novel plasmids phylogenetically unrelated to all currently reported Yersinia plasmids. An icm/dot type IVB secretion system, shared only with the intracellular persisting pathogens of the order Legionellales, was found on the larger plasmid and could contribute to scarlatinoid fever symptoms in patients due to the introduction of immunomodulatory and immunosuppressive capabilities. We determined the common and unique traits resulting from genome evolution and speciation within the genus Yersinia and drew a more accurate species border between Y. pseudotuberculosis and Y. pestis. In contrast to the lack of genetic diversity observed in the evolutionary young descending Y. pestis lineage, the population genetics of Y. pseudotuberculosis is more heterogenous. Both Y. pseudotuberculosis strains IP31758 and the previously sequenced Y. pseudotuberculosis strain IP32953 have evolved by the acquisition of specific plasmids and by the horizontal acquisition and incorporation of different genetic information into the chromosome, which all together or independently seems to potentially impact the phenotypic adaptation of these two strains

Novel Plasmids and Resistance Phenotypes in Yersinia pestis: Unique Plasmid Inventory of Strain Java 9 Mediates High Levels of Arsenic Resistance

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium

Identifying component modules

A computer-based system for modelling component dependencies and identifying component modules is presented. A variation of the Dependency Structure Matrix (DSM) representation was used to model component dependencies. The system utilises a two-stage approach towards facilitating the identification of a hierarchical modular structure. The first stage calculates a value for a clustering criterion that may be used to group component dependencies together. A Genetic Algorithm is described to optimise the order of the components within the DSM with the focus of minimising the value of the clustering criterion to identify the most significant component groupings (modules) within the product structure. The second stage utilises a 'Module Strength Indicator' (MSI) function to determine a value representative of the degree of modularity of the component groupings. The application of this function to the DSM produces a 'Module Structure Matrix' (MSM) depicting the relative modularity of available component groupings within it. The approach enabled the identification of hierarchical modularity in the product structure without the requirement for any additional domain specific knowledge within the system. The system supports design by providing mechanisms to explicitly represent and utilise component and dependency knowledge to facilitate the nontrivial task of determining near-optimal component modules and representing product modularity