Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori

BACKGROUND: Population structures are normally determined using genes under minimal functional selection. In this study we have assessed genes that are not always essential, show differences in alleles between strains, and are involved in the directly host-selectable phenotype of LPS biosynthesis. RESULTS: Eight complete LPS biosynthesis genes, seven of which are associated with phase variation in some or all strains of Helicobacter pylori, have been sequenced and their divergence analyzed. The differences observed indicate that recombination within these genes largely reflects exchange between strains within the population lineages previously determined on the basis of MLST using housekeeping genes. This indicates that the differences that are used for MLST are likely to broadly associate with genes under functional selection, and differences in strain behaviour. However, instances of exchange between the subpopulations were identified, including the hpAfrica2 subpopulation. Further, there were other differences in gene complements and the chromosomal location of genes indicative of greater diversity within the population than is revealed by the available genome sequences and comparative genome hybridization studies. CONCLUSION: These results indicate that the described population structure based upon MLST is broadly a good basis for studying the biology of H. pylori, but that individual alleles may not follow these associations. As a consequence, when working in unsequenced strains, it is necessary to carefully check the presence, sequence, and distribution of any individual gene of interest

Analysis and Verification of Service Interaction Protocols - A Brief Survey

Modeling and analysis of interactions among services is a crucial issue in Service-Oriented Computing. Composing Web services is a complicated task which requires techniques and tools to verify that the new system will behave correctly. In this paper, we first overview some formal models proposed in the literature to describe services. Second, we give a brief survey of verification techniques that can be used to analyse services and their interaction. Last, we focus on the realizability and conformance of choreographies.Comment: In Proceedings TAV-WEB 2010, arXiv:1009.330

Tau Be or not Tau Be? - A Perspective on Service Compatibility and Substitutability

One of the main open research issues in Service Oriented Computing is to propose automated techniques to analyse service interfaces. A first problem, called compatibility, aims at determining whether a set of services (two in this paper) can be composed together and interact with each other as expected. Another related problem is to check the substitutability of one service with another. These problems are especially difficult when behavioural descriptions (i.e., message calls and their ordering) are taken into account in service interfaces. Interfaces should capture as faithfully as possible the service behaviour to make their automated analysis possible while not exhibiting implementation details. In this position paper, we choose Labelled Transition Systems to specify the behavioural part of service interfaces. In particular, we show that internal behaviours (tau transitions) are necessary in these transition systems in order to detect subtle errors that may occur when composing a set of services together. We also show that tau transitions should be handled differently in the compatibility and substitutability problem: the former problem requires to check if the compatibility is preserved every time a tau transition is traversed in one interface, whereas the latter requires a precise analysis of tau branchings in order to make the substitution preserve the properties (e.g., a compatibility notion) which were ensured before replacement.Comment: In Proceedings WCSI 2010, arXiv:1010.233

Efficient Gradient Estimation via Adaptive Sampling and Importance Sampling

Machine learning problems rely heavily on stochastic gradient descent (SGD) for optimization. The effectiveness of SGD is contingent upon accurately estimating gradients from a mini-batch of data samples. Instead of the commonly used uniform sampling, adaptive or importance sampling reduces noise in gradient estimation by forming mini-batches that prioritize crucial data points. Previous research has suggested that data points should be selected with probabilities proportional to their gradient norm. Nevertheless, existing algorithms have struggled to efficiently integrate importance sampling into machine learning frameworks. In this work, we make two contributions. First, we present an algorithm that can incorporate existing importance functions into our framework. Second, we propose a simplified importance function that relies solely on the loss gradient of the output layer. By leveraging our proposed gradient estimation techniques, we observe improved convergence in classification and regression tasks with minimal computational overhead. We validate the effectiveness of our adaptive and importance-sampling approach on image and point-cloud datasets.Comment: 15 pages, 10 figure

Formalizing Adaptation On-the-Fly

AbstractParadigm models specify coordination of collaborating components via constraint control. Component McPal allows for later addition of new constraints and new control in view of unforeseen adaptation. After addition McPal starts coordinating migration accordingly, adapting the system towards to-be collaboration. Once done, McPal removes obsolete control and constraints. All coordination remains ongoing while migrating on-the-fly, being deflected without any quiescence. Through translation into process algebra, supporting formal analysis is arranged carefully, showing that as-is and to-be processes are proper abstractions of the migrating process. A canonical critical section problem illustrates the approach

On Negotiation as Concurrency Primitive

We introduce negotiations, a model of concurrency close to Petri nets, with multiparty negotiation as primitive. We study the problems of soundness of negotiations and of, given a negotiation with possibly many steps, computing a summary, i.e., an equivalent one-step negotiation. We provide a complete set of reduction rules for sound, acyclic, weakly deterministic negotiations and show that, for deterministic negotiations, the rules compute the summary in polynomial time

Toward a better understanding of tool wear effect through a comparison between experiments and SPH numerical modelling of machining hard materials

The aim of this study is to improve the general understanding of tungsten carbide (WC–Co) tool wear under dry machining of the hard-to-cut titanium alloy Ti6Al4V. The chosen approach includes experimental and numerical tests. The experimental part is designed to identify wear mechanisms using cutting force measurements, scanning electron microscope observations and optical profilometer analysis. Machining tests were conducted in the orthogonal cutting framework and showed a strong evolution of the cutting forces and the chip profiles with tool wear. Then, a numerical method has been used in order to model the machining process with both new and worn tools. The use of smoothed particle hydrodynamics model (SPH model) as a numerical tool for a better understanding of the chip formation with worn tools is a key aspect of this work. The redicted chip morphology and the cutting force evolution with respect to the tool wear are qualitatively compared with experimental trends. The chip formation mechanisms during dry cutting process are shown to be quite dependent from the worn tool geometry. These mechanisms explain the high variation of the experimental and numerical feed force between new and worn tools

Ab initio investigation of lattice dynamics of fluoride scheelite LiYF4

We report on the phonon dynamics of LiYF4 obtained by direct method using first principle calculations. The agreement between experimental and calculated modes is satisfactory. An inversion between two Raman active modes is noticed compared to inelastic neutron scattering and Raman measurements. The atomic displacements corresponding to these modes are discussed. Multiple inversions between Raman and infrared active groups are present above 360 cm-1. The total and partial phonon density of state is also calculated and analyzed

Plant extract enhances the viability of Lactobacillus delbrueckii subsp. bulgaricus and Lactobacillus acidophilus in probiotic nonfat yogurt

Citation: Michael, M., Phebus, R. K., & Schmidt, K. A. (2015). Plant extract enhances the viability of Lactobacillus delbrueckii subsp. bulgaricus and Lactobacillus acidophilus in probiotic nonfat yogurt. Food Science & Nutrition, 3(1), 48-55. doi:10.1002/fsn3.189A commercial plant extract (prepared from olive, garlic, onion and citrus extracts with sodium acetate (SA) as a carrier) was evaluated to extend the viability of yogurt starter and probiotic bacteria as a means to enhance the shelf life of live and active culture, probiotic nonfat yogurt. Yogurts prepared from three different formulas (0.5% plant extract, 0.25% SA, or no supplement) and cultures (yogurt starter plus Bifidobacterium animalis, Lactobacillus acidophilus, or both probiotics) were assessed weekly during 29 days of storage at 5 degrees C. Supplemented yogurt mixes had greater buffering capacities than non-supplemented yogurt mixes. At the end of storage, Lactobacillus bulgaricus and L. acidophilus counts in supplemented yogurts were greater compared with non-supplemented yogurts. Supplementation did not affect Streptococcus thermophilus and B. animalis counts. Hence the greater buffering capacity of yogurt containing plant extract could enhance the longevity of the probiotics, L. bulgaricus and L. acidophilus, during storage