Sequential Importance Sampling for Online Bayesian Changepoint Detection

Online detection of abrupt changes in the parameters of a generative model for a time series is useful when modelling data in areas of application such as finance, robotics, and biometrics. We present an algorithm based on Sequential Importance Sampling which allows this problem to be solved in an online setting without relying on conjugate priors. Our results are exact and unbiased as we avoid using posterior approximations, and only rely on Monte Carlo integration when computing predictive probabilities. We apply the proposed algorithm to three example data sets. In two of the examples we compare our results to previously published analyses which used conjugate priors. In the third example we demonstrate an application where conjugate priors are not available. Avoiding conjugate priors allows a wider range of models to be considered with Bayesian changepoint detection, and additionally allows the use of arbitrary informative priors to quantify the uncertainty more flexibly

Greece at the Paris Universal Exhibition in 1878

Peer Reviewe

Complete genome sequence of the dairy isolate Streptococcus macedonicus ACA-DC 198

Within the Streptococcus genus, only Streptococcus thermophilus is considered to be non-pathogenic due to its adaptation to the milk environment. Streptococcus macedonicus is also an intriguing streptococcal species since its most frequent source of isolation to date is fermented foods, mainly of dairy origin. Sequencing of S. macedonicus ACA-DC 198 genome was performed using a combination of 454 GS FLX pyrosequencing and HiSeq 2000 Illumina sequencing. The hybrid assembly between 454 and HiSeq2000 data (>200x coverage) resulted in one continuous genomic scaffold of 2,130,034 bp and a plasmid of 12,728 bp. The genome assembly was validated against a NheI optical map of the S. macedonicus genome. Sequences were annotated with the BaSys and the RAST pipelines and manually curated using Kodon. Final corrections were made based on the quality assessment of the annotation using GenePRIMP. We found 2,192 protein-coding genes on the chromosome, 192 of which were identified as potential pseudogenes, indicating an ongoing genome decay process. This hypothesis is also supported by the approximately 220 kb-smaller genome size of S. macedonicus compared to the S. gallolyticus genomes, despite the high level of gene synteny between the two species. Such a reductive evolutionary process is common for lactic acid bacteria domesticated to the food environment, which in the case of S. thermophilus was also accompanied by the loss of pathogenicity traits. With our in silico analysis we attempt to investigate whether S. macedonicus shows traits that would support its adaptation to the dairy environment at the genomic level

Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex

Background: Within the genus Streptococcus, only Streptococcus thermophilus is used as a starter culture in food fermentations. Streptococcus macedonicus though, which belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC), is also frequently isolated from fermented foods mainly of dairy origin. Members of the SBSEC have been implicated in human endocarditis and colon cancer. Here we compare the genome sequence of the dairy isolate S. macedonicus ACA-DC 198 to the other SBSEC genomes in order to assess in silico its potential adaptation to milk and its pathogenicity status. Results: Despite the fact that the SBSEC species were found tightly related based on whole genome phylogeny of streptococci, two distinct patterns of evolution were identified among them. Streptococcus macedonicus, Streptococcus infantarius CJ18 and Streptococcus pasteurianus ATCC 43144 seem to have undergone reductive evolution resulting in significantly diminished genome sizes and increased percentages of potential pseudogenes when compared to Streptococcus gallolyticus subsp. gallolyticus. In addition, the three species seem to have lost genes for catabolizing complex plant carbohydrates and for detoxifying toxic substances previously linked to the ability of S. gallolyticus to survive in the rumen. Analysis of the S. macedonicus genome revealed features that could support adaptation to milk, including an extra gene cluster for lactose and galactose metabolism, a proteolytic system for casein hydrolysis, auxotrophy for several vitamins, an increased ability to resist bacteriophages and horizontal gene transfer events with the dairy Lactococcus lactis and S. thermophilus as potential donors. In addition, S. macedonicus lacks several pathogenicity-related genes found in S. gallolyticus. For example, S. macedonicus has retained only one (i.e. the pil3) of the three pilus gene clusters which may mediate the binding of S. gallolyticus to the extracellular matrix. Unexpectedly, similar findings were obtained not only for the dairy S. infantarius CJ18, but also for the blood isolate S. pasteurianus ATCC 43144. Conclusions: Our whole genome analyses suggest traits of adaptation of S. macedonicus to the nutrient-rich dairy environment. During this process the bacterium gained genes presumably important for this new ecological niche. Finally, S. macedonicus carries a reduced number of putative SBSEC virulence factors, which suggests a diminished pathogenic potential

Greece at the Paris Universal Exhibition in 1878

Peer Reviewe

Milk adaptation and pathogenic potential among members of the Streptococcus bovis/Streptococcus equinus complex

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) consists of species commonly found in the gastrointestinal tract (GIT) of herbivores. Certain members of the complex like Streptococcus macedonicus and Streptococcus infantarius are frequently isolated from traditional fermented foods, mostly of dairy origin. However, some species of this complex, like Streptococcus gallolyticus and Streptococcus pasteurianus are known pathogens of humans involved in a range of diseases including endocarditis, menengitis, bacteremia, colon cancer etc. Analysis of the genome of S. macedonicus strain ACA-DC 198 isolated from traditional Greek Kasseri cheese revealed important traits of adaptation to the dairy environment. The strain contains a significant percentage of potential pseudogenes indicating that it may have evolved through genome decay processes. Streptococcus macedonicus has an extra gene cluster for lactose and galactose metabolism unique among the SBSEC members and a typical proteolytic system required for casein hydrolysis. Furthermore, we found evidence in the genome of S. macedonicus suggesting HGT (horizontal gene transfer) events with potential donors Lactococcus lactis and Streptococcus thermophilus. Perhaps the most pronounced among these HGT events is the presence in S. macedonicus of pSMA198 which belongs to the lactococcal pCI305/pWV02 family of plasmids. Our analysis suggests that pSMA198 may have been acquired by S. macedonicus from L. lactis. Analogous traits have been reported for S. infantarius suggesting that at least these two strains present adaptations to the dairy environment among SBSEC. Finally, we were able to identify a number of potential virulence factors (VFs) within the SBSEC members whose presence varied among species of the complex. Streptococcus macedonicus and S. infantarius miss some of the VFs present in S. gallolyticus suggesting a diminished pathogenic potential for the two species

Bayesian optimal experimental design for the study of natural phenomena

Modern science has been progressively moving towards the study of increasingly complex structures, investigating not only their individual components but also their interactions, dependencies and co-existence as a whole. This thesis is concerned with optimal experimental design methodology for the study of such phenomena. A decision-theoretic framework for optimal experimental design is adopted in this thesis. The employed methods operate based on an optimality criterion, quantifying the benefit incurred from each alternative experimental design - commonly known as the expected utility. An analytical expression is, in most studies of interest, not available for this quantity and so estimation techniques are typically required for its evaluation. Currently, existing estimation methods fail to adequately address issues arising in optimal design problems within a modern scientific framework. This is predominantly attributed to the considerable computational cost incurred by consideration of mathematical models sophisticated enough to adequately capture the complexity of the studied structures. In face of this restriction, researchers often resort to consideration of rather simplistic models, hindering the progress towards a more realistic representation and better understanding of such systems. Efficient methodology for evaluation of the expected utility constitutes the first main contribution of this thesis. The presented approach adopts a flexible, non-parametric framework combined with variational approximation techniques that translate the initial evaluation problem to an alternative, more tractable problem, solution of which is achieved through more efficient and computationally inexpensive procedures. A problem shift is thus achieved under which, estimation of the expected utility is accomplished through its corresponding dual problem. This alternative representation is shown to incur considerable computational gains compared to traditionally adopted approaches without compromising the quality of the produced estimates. The proposed estimator paves the way to an autonomous, comprehensive framework for the optimal study of complex phenomena within a realistic time frame, currently posing an ongoing challenge. Establishment of such a setup composes the second main contribution of this thesis. The proposed framework attempts to emulate a typical research scheme of closed-loop data collection, knowledge update and optimal decision making which, combined with instrument control software, facilitates modern scientific studies under minimal human input. The class of Bayesian optimisation algorithms is finally considered, allowing for truly optimal decision making during the established procedure. This class of algorithms, although particularly well-suited to optimal experimental design problems, has been given little consideration in the relevant literature. Their integration to the proposed framework, thus, constitutes an additional contribution of this thesis. Application of the adopted experimental design framework is examined in three increasingly challenging case studies, addressing a broad range of issues typically encountered in optimal design problems. The first study explores the optimal experimental design for a model discrimination problem adopting a set of simpler, polynomial models. An initial assessment of the proposed estimator and a comparison with the currently adopted methodology is performed, under a setup where application of the latter is not hindered by the incurred computational complexity. The subsequent two cases represent real-life problems of optimal experimental design for model inference in Systems Biology and Spectroscopy, employing models under which, traditionally adopted methods can become from highly inefficient to intractable and thus alternative approaches are needed for the study of such phenomena

Reviewing the benefits and clinical outcomes of oral fibroblasts over mesenchymal stem cells for repairing periodontal defects during or after orthodontic tooth movement.

Orthodontic therapy applies forces to teeth, causing an inflammatory reaction in the periodontal ligament. This is repaired by remodeling of the periodontium, allowing tooth displacement. Although orthodontic therapy is mostly initiated during childhood and adolescence, the number of adults seeking this treatment is increasing as our society's esthetic awareness rises. However, adults may already have periodontal tissue abnormalities, rendering orthodontic treatment inefficient because a healthy periodontium is essential for success. Numerous risk factors have been linked to periodontal lesions, with orthodontic tooth movement possibly playing a minimal influence. Although such tissue damages are mostly of esthetic rather than functional concern for patients, restoration frequently requires invasive procedures. Autologous cells for the treatment of periodontal complications have grown in popularity as a less intrusive alternative. The present review analyzed the literature on the use of mesenchymal stem cells and oral tissue-derived fibroblasts for the healing of periodontal defects that may be related to orthodontic tooth movement. Furthermore, the advantages and challenges of the two cell types have been examined. Although the number of clinical studies is currently limited, our study demonstrates that oral fibroblasts have the potential to be the next emergent frontrunners for tissue engineering in the periodontium

Γνώσεις και ενσυναίσθηση των μελλοντικών εκπαιδευτικών για τη Διαταραχή Ελλειμματικής Προσοχής-Υπερκινητικότητα

Η Διαταραχή Ελλειμματικής Προσοχής-Υπερκινητικότητα (ΔΕΠ-Υ) αποτελεί μια νευροβιολογική διαταραχή, η οποία έχει έναρξη από την παιδική ηλικία και διαρκεί δια βίου. Λόγω των δυσκολιών που αντιμετωπίζουν οι μαθητές στο σχολικό περιβάλλον εξαιτίας της διαταραχής, πλήθος ερευνών εστιάζει στην ενημερότητα των εκπαιδευτικών για αυτή. Ωστόσο, την τελευταία δεκαετία ολοένα και αυξανόμενο ερευνητικό ενδιαφέρον αποκτά το επίπεδο γνώσεων των μελλοντικών εκπαιδευτικών αναφορικά με τη διαταραχή. Πρωταρχικό σκοπό της παρούσας εργασίας αποτελεί η διερεύνηση του βαθμού ενημερότητας των φοιτητών για τη ΔΕΠ-Υ, καθώς και η συσχέτιση των γνώσεων τους με την ενσυναίσθηση. Για τις ανάγκες της έρευνας συμμετείχαν 250 φοιτητές από παιδαγωγικές σχολές της Αττικής και της επαρχίας. Για τη συλλογή των δεδομένων χρησιμοποιήθηκε ένα ερωτηματολόγιο που αποτελείται από το Ερωτηματολόγιο Ενσυναίσθησης του Τορόντο (Spreng, McKinnon, Mar, & Levine, 2009), την Κλίμακα Γνώσεων για τη Διαταραχή Ελλειμματικής Προσοχής-Υπερκινητικότητα (Kos, Richdale, & Jackson, 2004), καθώς και από ερωτήσεις δημογραφικών στοιχείων. Τα αποτελέσματα της έρευνας έδειξαν ότι το χαμηλό επίπεδο γνώσεων των φοιτητών συνδέεται με χαμηλού επιπέδου ενσυναίσθησης, ενώ ταυτόχρονα παρατηρήθηκε πως οι προπτυχιακοί φοιτητές δεν έχουν λάβει καμία εκπαίδευση για τη ΔΕΠ-Υ.Attention Deficit Hyperactivity Disorder (ADHD) is a neurological disorder which begins in early childhood and lasts a lifetime with differentiated clinical symptoms during the developmental stages of the person. Students with ADHD face many hardships at school due to the disorder and for this reason many studies try to examine the teachers’ knowledge of ADHD. However, during the recent years many researches focus on the ADHD knowledge of university students. The primary purpose of this study is to examine the level of knowledge that pre-service teachers have for ADHD, as well as their level of empathy for students with ADHD. For the needs of the study, 250 university students, undergraduated and postgraduated who study in the region of Attica as well as in the province, participated in the research. A questionnaire was used in order to collect data, which included the Toronto Empathy Questionnaire (Spreng, McKinnon, Mar, & Levine, 2009), the Knowledge of Attention Deficit Disorder Scale (Kos, Richdale, & Jackson, 2004) and demographic items. The results of survey have shown that university students have little knowledge for ADHD, while there is a correlation between knowledge and empathy. Finally, it is mentioned that undergraduated students have received no formal ADHD education at the university