Optimization of Drinking Water and Sewer Hydraulic Management: Coupling of a Genetic Algorithm and Two Network Hydraulic Tools

AbstractVeolia has developed an optimization platform for the operation of sewer networks (POSTEVENT) and drinking water networks (OPTIM’HYDRO). This platform couples a genetic algorithm NSGA-II with hydraulic network simulation tools (INFOWORKS CS and EPANET). The challenge is to optimize the design and operation of networks according to given objectives and constraints, by changing asset control parameters. This article deals with optimization challenges raised and developed off-line support tools. It ends with a case study on a French drinking water network consisting in upscale set points for pumping stations to optimize the procurement management of water and reduce the energy costs

A first generation BAC-based physical map of the channel catfish genome

BACKGROUND: Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL) and the effective positional cloning of genes. RESULTS: A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF) of 46,548 Bacterial Artificial Chromosomes (BAC) clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1) anchoring 19 of the largest contigs to the microsatellite linkage map 2) comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP) patterns seen in Southern blots, and 3) contig sequencing. CONCLUSION: This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits

Usability improvements of the Thermipig model for precision pig farming

Pig livestock farming systems encounter several economic and environmental challenges, connected with meat price decrease, sanitary norms, emissions etc. To deal with these issues, methods and models to assess the performance of a pig production system have been developed. For instance, Thermipig model represents the pig fattening room and simulates performances of pigs at the batch level, taking into account interactions between the individual variability of pigs, farmer's practices, room characteristics and outdoor climate conditions. The model requires some static basic inputs fulfilled in several spreadsheets (such as rooms, pigs, and dietary characteristics) but also data files for voluminous variable inputs (such as outdoor temperature or climate control box parameters) for further modelling and outcome producing. This leads to challenges in data providing by the farmers and have to be improved. This paper deals with the implementation of the separate modules of the developed data warehouse system for usability improvements of the Thermipig model. The idea is to substitute input from the data files with online data input and automated variable processing by the model using the python script for connection to the remote data warehouse. The data warehouse system is extended with ‘Property Sets’ section dealing with all the operations that can be performed to a set of input variables. This approach demonstrates the ability of the data warehouse to act as data supplier for the remote model. As well the outcome of the model is also transferable back to the data warehouse for evaluation. This work is done within the Era-Net SuSan PigSys project - Improving pig system performance through a whole system approach

Reconnaissance d'événements structurés temporellement dans un signal par raisonnement temporel

- Une nouvelle approche basée sur le raisonnement temporel est proposée pour la reconnaissance automatique d'arythmies. Les arythmies sont représentées par un ensemble de modèles de chroniques. Chaque modèle est composé d'un ensemble d'événements liés par des contraintes temporelles qui limite le délai de leurs occurrences. Un raisonneur temporel appelé, système de reconnaissance de chronique, instancie à partir du flot d'événements en entrée les modèles représentant différentes arythmies. Les résultats démontrent que l'approche proposée est appropriée à la reconnaissance d'arythmies complexes

Image resonance in the many-body density of states at a metal surface

The electronic properties of a semi-infinite metal surface without a bulk gap are studied by a formalism that is able to account for the continuous spectrum of the system. The density of states at the surface is calculated within the GW approximation of many-body perturbation theory. We demonstrate the presence of an unoccupied surface resonance peaked at the position of the first image state. The resonance encompasses the whole Rydberg series of image states and cannot be resolved into individual peaks. Its origin is the shift in spectral weight when many-body correlation effects are taken into account

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter

Deep Lenses of Circumpolar Water in the Argentine Basin

Three deep anticyclonic eddies of a species only reported once before [ Gordon and Greengrove, 1986 ] were intersected by hydrographic lines of the World Ocean Circulation Experiment (WOCE) and South Atlantic Ventilation Experiment (SAVE) programs in the Argentine Basin. The vortices are centered near 3500 m depth at the interface between North Atlantic Deep Water and Bottom Water. They have ∼1500-m-thick cores containing Lower Circumpolar Deep Water and a dynamic influence that may span up to two thirds of the water column. As one eddy was observed just downstream of the western termination of the Falkland Escarpment, a destabilization of the deep boundary current by the sudden slope relaxation is suggested as a potential cause of eddy formation. Besides isopycnal interleaving at the eddy perimeters, strongly eroded core properties in the upper parts of the lenses, associated with low density ratios, hint at double diffusion at the top of the structures as another major decay mechanism. The presence of an eddy in the northern Argentine Basin shows the possibility for a northward drift of the vortices, in this basin at least. Deep events in recent current measurements from the Vema Channel are presented that raise the question of further equatorward motion to the Brazil Basin

A pilot study for channel catfish whole genome sequencing and de novo assembly

<p>Abstract</p> <p>Background</p> <p>Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for <it>de novo </it>sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs.</p> <p>Results</p> <p>A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp.</p> <p>Conclusions</p> <p>A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.</p

A novel family of diversified immunoregulatory receptors in teleosts is homologous to both mammalian Fc receptors and molecules encoded within the leukocyte receptor complex

Three novel and closely related leukocyte immune-type receptors (IpLITR) have been identified in channel catfish (Ictalurus punctatus). These receptors belong to a large polymorphic and polygenic subset of the Ig superfamily with members located on at least three independently segregating loci. Like mammalian and avian innate immune regulatory receptors, IpLITRs have both putative inhibitory and stimulatory forms, with multiple types coexpressed in various lymphoid tissues and clonal leukocyte cell lines. IpLITRs have an unusual and novel relationship to mammalian and avian innate immune receptors: the membrane distal Ig domains of an individual IpLITR are related to fragment crystallizable receptors (FcRs) and FcR-like proteins, whereas the membrane proximal Ig domains are related to several leukocyte receptor complex encoded receptors. This unique composition of Ig domains within individual receptors supports the hypothesis that functionally and genomically distinct immune receptor families found in tetrapods may have evolved from such ancestral genes by duplication and recombination events. Furthermore, the discovery of a large heterogeneous family of immunoregulatory receptors in teleosts, reminiscent of amphibian, avian, and mammalian Ig-like receptors, suggests that complex innate immune receptor networks have been conserved during vertebrate evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at http://dx.doi.org/10.1007/s00251-006-0134-1 and is accessible for authorized users