Continuous-Time Identification of SISO Systems using Laguerre Functions

This paper looks at the problem of estimating the coefficients of a continuous-time transfer function given samples of its input and output data. We first prove that any nth-order continuous-time transfer function can be written as a fraction of the form /spl Sigma//sub k=0//sup n/b~/sub k/L/sub k/(s)//spl Sigma//sub k=0//sup n/a~/sub k/L/sub k/(s), where L/sub k/(s) denotes the continuous-time Laguerre basis functions. Based on this model, we derive an asymptotically consistent parameter estimation scheme that consists of the following two steps: (1) filter both the input and output data by L/sub k/(s), and (2) estimate {a~/sub k/, b~/sub k/} and relate them to the coefficients of the transfer function. For practical implementation, we require the discrete-time approximation of L/sub k/(s) since only sampled data is available. We propose a scheme that is based on higher order Pade approximations, and we prove that this scheme produces discrete-time filters that are approximately orthogonal and, consequently, a well-conditioned numerical problem. Some other features of this new algorithm include the possibility to implement it as either an off-line or a quasi-on-line algorithm and the incorporation of constraints on the transfer function coefficients. A simple example is given to illustrate the properties of the proposed algorithm

Real-time wavefront reconstruction from intensity measurements

We propose an efficient approximation to the nonlinear phase diversity method for wavefront reconstruction from intensity measurements. The new method, iterative linear phase diversity (ILPD), assumes that the residual phase aberration is small and makes use of a first order Taylor expansion of the point spread function (PSF) performed for an arbitrary (large) diversity in order to optimize the phase retrieval. For static aberrations, ILPD makes use of two images collected at each iteration of the algorithm. In each step, the residual phase aberrations are estimated by solving a linear least squares problem, followed by the use of a deformable mirror to correct for the aberrations. A further contribution of the paper is the extension of the static ILPD to the case of dynamic wavefront reconstruction for which a computationally efficient H2 controller is presented.Delft Center for Systems and ControlMechanical, Maritime and Materials Engineerin

Structure of the specific combining ability between two species of Eucalyptus. I. RAPD data

International audienceWithin the context of the reciprocal recurrent selection scheme developed in 1989 by CIRAD-Fore t on Eucalyptus, RAPD essays were performed to assess the genetic diversity in the two species E. urophylla and E. grandis. The molecular markers were split into two parts: the speciÞc markers (present with di¤erent fre- quencies in the two species) and the common markers (present with similar frequencies in the two species). The study analyses the structure of genetic diversity within and between the two species of Eucalyptus. Dif- ferent genetic distances are worked out for use in pre- diction equations of the individual tree trunk volume of hybrids at 38 months. Each distance is expressed as the sum of the general genetic distance and the speciÞc genetic distance. The general genetic distance based on the double presence plus the double absence of bands seems to be an interesting co-variate to use in a factor regression model. Through this model the distance calculated between species explains the general com- bining ability (GCA) and the speciÞc combining ability (SCA) of the phenotypic character with a global coe¦c- ient of determination of 81.6

Structure of the specific combining ability between two species of Eucalyptus. II. A clustering approach and a multiplicative model

International audienceThe Eucalyptus breeding program of URPPI (a partnership between CIRAD-Fore t, Centre National de la Recherche Forestie re du Congo, and Unite dÕAforestation Industrielle du Congo) consists of a re- ciprocal recurrent selection scheme developed in the Congo between the two species Eucalyptus urophylla and Eucalyptus grandis. Two approaches are proposed in order to model and predict the speciÞc combining ability (SCA) between these species. The clustering ap- proach uses a simultaneous clustering procedure of the two species based on SCA and reveals heterotic groups coherent with the geographical origins of E. urophylla genotypes. The second approach uses a multiplicative model to partition the SCA into three multiplicative terms explaining 95% of the interactio

Nosocomial infective endocarditis: should the definition be extended to 6 months after discharge

ABSTRACTBecause the microbiology and patient population of infective endocarditis (IE) have evolved, the traditional definition of nosocomial IE may require revision. The question of whether this definition should be extended to 6 months after discharge was explored, and a high rate of episodes with nosocomial pathogens (coagulase-negative staphylococci) and a low rate of episodes with community pathogens (streptococci) in the extended nosocomial group were found. Therefore, modification of the traditional definition is proposed, distinguishing between early (as traditionally described) and late nosocomial IE (IE in association with a significant invasive procedure performed during a hospitalization between 8 weeks and 6 months before the onset of symptoms)

Laboratory study of the impact of repetitive electrical and mechanical stimulation on brown shrimp Crangon crangon

Pulse trawling is currently the best available alternative to beam trawling in the brown shrimp Crangon crangon and Sole Solea solea (also known as Solea vulgaris) fisheries. To evaluate the effect of repetitive exposure to electrical fields, brown shrimp were exposed to the commercial electrodes and pulse settings used to catch brown shrimp (shrimp startle pulse) or Sole (Sole cramp pulse) 20 times in 4 d and monitored for up to 14 d after the first exposure. Survival, egg loss, molting, and the degree of intranuclear bacilliform virus (IBV) infection were evaluated and compared with those in stressed but not electrically exposed (procedural control) and nonstressed, nonexposed (control) brown shrimp as well as brown shrimp exposed to mechanical stimuli. The lowest survival at 14 d (57.3%) occurred in the Sole cramp pulse treatment, and this was significantly lower than in the group with the highest survival, the procedural control (70.3%). No effect of electrical stimulation on the severity of IBV infection was found. The lowest percentage of molts occurred in the repetitive mechanical stimulation treatment (14.0%), and this was significantly lower than in the group with the highest percentage of molts, the procedural control (21.7%). Additionally, the mechanically stimulated brown shrimp that died during the experiment had a significantly larger size than the surviving individuals. Finally, no effect of the shrimp startle pulse was found. Therefore, it can be concluded that repetitive exposure to a cramp stimulus and mechanical stimulation may have negative effects on the growth and/or survival of brown shrimp. However, there is no evidence that electrical stimulation during electrotrawls would have a larger negative impact on brown shrimp stocks than mechanical stimulation during conventional beam trawling

Strain-level metagenomic data analysis of enriched in vitro and in silico spiked food samples : paving the way towards a culture-free foodborne outbreak investigation using STEC as a case study

Culture-independent diagnostics, such as metagenomic shotgun sequencing of food samples, could not only reduce the turnaround time of samples in an outbreak investigation, but also allow the detection of multi-species and multi-strain outbreaks. For successful foodborne outbreak investigation using a metagenomic approach, it is, however, necessary to bioinformatically separate the genomes of individual strains, including strains belonging to the same species, present in a microbial community, which has up until now not been demonstrated for this application. The current work shows the feasibility of strain-level metagenomics of enriched food matrix samples making use of data analysis tools that classify reads against a sequence database. It includes a brief comparison of two database-based read classification tools, Sigma and Sparse, using a mock community obtained by in vitro spiking minced meat with a Shiga toxin-producing Escherichia coli (STEC) isolate originating from a described outbreak. The more optimal tool Sigma was further evaluated using in silico simulated metagenomic data to explore the possibilities and limitations of this data analysis approach. The performed analysis allowed us to link the pathogenic strains from food samples to human isolates previously collected during the same outbreak, demonstrating that the metagenomic approach could be applied for the rapid source tracking of foodborne outbreaks. To our knowledge, this is the first study demonstrating a data analysis approach for detailed characterization and phylogenetic placement of multiple bacterial strains of one species from shotgun metagenomic WGS data of an enriched food sample

First detection of a plasmid located carbapenem resistant bla(VIM-1) gene in E. coli isolated from meat products at retail in Belgium in 2015

Carbapenemase-producing Enterobacteriaceae (CPE) confer resistance to antibiotics that are of critical importance to human medicine. There have only been a few reported cases of CPEs in the European food chain. We report the first detection of a carbapenemase-producing Escherichia coli (ST 5869) in the Belgian food chain. Our aim was to characterize the origin of the carbapenem resistance in the E. coli isolate. The isolate was detected during the screening of 178 minced pork samples and was shown to contain the carbapenemase gene bla(VIM-1) by PCR and Sanger sequencing. Whole genome short and long read sequencing (MiSeq and MinION) was performed to characterize the isolate. With a hybrid assembly we reconstructed a 190,205 bp IncA/C2 plasmid containing bla(VIM-1) (S15FP06257_p), in addition to other critically important resistance genes. This plasmid showed only low similarity to plasmids containing bla(VIM-1) previously reported in Germany. Moreover, no sequences existed in the NCBI nucleotide database that completely covered S15FP06257_p. Analysis of the bla(VIM-1) gene cassette demonstrated that it likely originated from an integron of a Klebsiella plasmid reported previously in a clinical isolate in Europe, suggesting that the meat could have been contaminated by human handling in one of the steps of the food chain. This study shows the relevance of fully reconstructing plasmids to characterize their genetic content and to allow source attribution. This is especially important in view of the potential risk of antimicrobial resistance gene transmission through mobile elements as was reported here for the of public health concern bla(VIM-1)

A practical method to implement strain-level metagenomics-based foodborne outbreak investigation and source tracking in routine

The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific real-time polymerase chain reactions (qPCRs) are used in routine. In recent years, the use of whole genome sequencing (WGS) of bacterial isolates has proven its value to collect relevant information for strain characterization as well as tracing the origin of the contamination by linking the food isolate with the patient’s isolate with high resolution. However, the isolation of a bacterial pathogen from food matrices is often time-consuming and not always successful. Therefore, we aimed to improve outbreak investigation by developing a method that can be implemented in reference laboratories to characterize the pathogen in the food vehicle without its prior isolation and link it back to human cases. We tested and validated a shotgun metagenomics approach by spiking food pathogens in specific food matrices using the Shiga toxin-producing Escherichia coli (STEC) as a case study. Different DNA extraction kits and enrichment procedures were investigated to obtain the most practical workflow. We demonstrated the feasibility of shotgun metagenomics to obtain the same information as in ISO/TS 13136:2012 and WGS of the isolate in parallel by inferring the genome of the contaminant and characterizing it in a shorter timeframe. This was achieved in food samples containing different E. coli strains, including a combination of different STEC strains. For the first time, we also managed to link individual strains from a food product to isolates from human cases, demonstrating the power of shotgun metagenomics for rapid outbreak investigation and source tracking