For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information ...remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.
Over a five year period (2004–08), 1171 surface water samples were collected from up to 24 sampling locations representing a wide range of stream orders, in a river basin in eastern Ontario, Canada. ...Water was analyzed for
Cryptosporidium oocysts and
Giardia cyst densities, the presence of
Salmonella enterica subspecies
enterica,
Campylobacter spp.,
Listeria monocytogenes, and
Escherichia coli O157:H7. The study objective was to explore associations among pathogen densities/occurrence and objectively defined land use, weather, hydrologic, and water quality variables using CART (Classification and Regression Tree) and binary logistical regression techniques.
E. coli O157:H7 detections were infrequent, but detections were related to upstream livestock pasture density; 20% of the detections were located where cattle have access to the watercourses. The ratio of detections:non-detections for
Campylobacter spp. was relatively higher (>1) when mean air temperatures were 6% below mean study period temperature values (relatively cooler periods). Cooler water temperatures, which can promote bacteria survival and represent times when land applications of manure typically occur (spring and fall), may have promoted increased frequency of
Campylobacter spp. Fifty-nine percent of all
Salmonella spp. detections occurred when river discharge on a branch of the river system of Shreve stream order = 9550 was >83 percentile. Hydrological events that promote off farm/off field/in stream transport must manifest themselves in order for detection of
Salmonella spp. to occur in surface water in this region. Fifty seven percent of
L. monocytogenes detections occurred in spring, relative to other seasons. It was speculated that a combination of winter livestock housing, silage feeding during winter, and spring application of manure that accrued during winter, contributed to elevated occurrences of this pathogen in spring.
Cryptosporidium and
Giardia oocyst and cyst densities were, overall, positively associated with surface water discharge, and negatively associated with air/water temperature during spring-summer-fall. Yet, some of the highest
Cryptosporidium oocyst densities were associated with low discharge conditions on smaller order streams, suggesting wildlife as a contributing fecal source. Fifty six percent of all detections of ≥2 bacteria pathogens (including
Campylobacter spp.,
Salmonella spp., and
E. coli O157:H7) in water was associated with lower water temperatures (<∼14 °C; primarily spring and fall) and when total rainfall the week prior to sampling was >∼27 mm (62 percentile). During higher water temperatures (>∼14 °C), a higher amount of weekly rainfall was necessary to promote detection of ≥2 pathogens (primarily summer; weekly rainfall ∼>42 mm (>77 percentile); 15% of all ≥2 detections). Less rainfall may have been necessary to mobilize pathogens from adjacent land, and/or in stream sediments, during cooler water conditions; as these are times when manures are applied to fields in the area, and soil water contents and water table depths are relatively higher. Season, stream order, turbidity, mean daily temperature, surface water discharge, cropland coverage, and nearest upstream distance to a barn and pasture were variables that were relatively strong and recurrent with regard to discriminating pathogen presence and absence, and parasite densities in surface water in the region.
► Pathogens were examined at multiple tributaries in an agricultural river basin. ► Data mining uncovered land use, meteorological, hydrology, & seasonal associations. ► Season, stream order, turbidity, temp., discharge, & land use were recurrent predictors. ► Higher occurrence was during cooler temps in spring-fall during higher discharge. ► Land use was not a strong predictor but densities were higher nearer dairy operations.
During the austral summer of 2016–2017, the third-generation camera, SPT-3G, was installed on the South Pole Telescope, increasing the detector count in the focal plane by an order of magnitude ...relative to the previous generation. Designed to map the polarization of the cosmic microwave background, SPT-3G contains ten 6
′
′
-hexagonal modules of detectors, each with 269 trichroic and dual-polarization pixels, read out using 68
×
frequency-domain multiplexing. Here we discuss design, assembly, and layout of the modules, as well as early performance characterization of the first-year array, including yield and detector properties.
In this work, we have measured the properties of membrane-suspended bolometer thermal links and microstrip transmission lines in the transition-edge sensor arrays for the third-generation camera for ...South Pole Telescope (SPT-3G). A promising technique for controlling the end point of the release etch that defines the thermal link has been developed. We have also evaluated the microstrip loss in our detectors by measuring the optical efficiency of detectors with different lengths of microstrip line. The loss tangent is sufficiently low for the use in multi-chronic pixels for cosmic microwave background instruments like SPT-3G.
In this work, we have measured the properties of membrane-suspended bolometer thermal links and microstrip transmission lines in the transition-edge sensor arrays for the third-generation camera for ...South Pole Telescope (SPT-3G). A promising technique for controlling the end point of the release etch that defines the thermal link has been developed. We have also evaluated the microstrip loss in our detectors by measuring the optical efficiency of detectors with different lengths of microstrip line. The loss tangent is sufficiently low for the use in multi-chronic pixels for cosmic microwave background instruments like SPT-3G.
The South Pole Telescope third-generation (SPT-3G) receiver was installed during the austral summer of 2016–2017. It is designed to measure the cosmic microwave background across three frequency ...bands centered at 95, 150, and 220 GHz. The SPT-3G receiver has ten focal plane modules, each with 269 pixels. Each pixel features a broadband sinuous antenna coupled to a niobium microstrip transmission line. In-line filters define the desired band-passes before the signal is coupled to six bolometers with Ti/Au/Ti/Au transition edge sensors (three bands×two polarizations). In total, the SPT-3G receiver is composed of 16,000 detectors, which are read out using a 68× frequency-domain multiplexing scheme. In this paper, we present the process employed in fabricating the detector arrays.
The third-generation upgrade to the receiver on the South Pole Telescope, SPT-3G, was installed at the South Pole during the 2016–2017 austral summer to measure the polarization of the cosmic ...microwave background. Increasing the number of detectors by a factor of 10 to ~16,000 required the multiplexing factor to increase to 68 and the bandwidth of the frequency-division readout electronics to span 1.6–5.2 MHz. This increase necessitates low-thermal conductance, low-inductance cryogenic wiring. Our cold readout system consists of planar thin-film aluminum inductive–capacitive resonators, wired in series with the detectors, summed together, and connected to 4K SQUIDs by 10-μm -thick niobium–titanium (NbTi) broadside-coupled striplines. Here, we present an overview of the cold readout electronics for SPT-3G, including assembly details and characterization of electrical and thermal properties of the system. We report, for the NbTi striplines, values of R≤10-4Ω , L=21±1 nH , and C=1.47±.02 nF . Additionally, the striplines’ thermal conductivity is described by kA=6.0±0.3 T0.92±0.04 μW mm K-1 . Finally, we provide projections for cross talk induced by parasitic impedances from the stripline and find that the median value of percentage cross talk from leakage current is 0.22 and 0.09% from wiring impedance.
The third-generation South Pole Telescope camera is designed to measure the cosmic microwave background across three frequency bands (centered at 95, 150 and 220 GHz) with ~ 16,000 transition-edge ...sensor (TES) bolometers. Each multichroic array element on a detector wafer has a broadband sinuous antenna that couples power to six TESs, one for each of the three observing bands and both polarizations, via lumped element filters. Ten detector wafers populate the detector array, which is coupled to the sky via a large-aperture optical system. Here we present the frequency band characterization with Fourier transform spectroscopy, measurements of optical time constants, beam properties, and optical and polarization efficiencies of the detector array. The detectors have frequency bands consistent with our simulations and have high average optical efficiency which is 86, 77 and 66% for the 95, 150 and 220 GHz detectors. The time constants of the detectors are mostly between 0.5 and 5 ms. The beam is round with the correct size, and the polarization efficiency is more than 90% for most of the bolometers.
The distribution and prevalence of antibody reactive with Sin Nombre virus were determined in mammals in biotic communities of the southwestern United States. Small mammals (n = 3,069) of 69 species ...were trapped in nine communities from lower Sonoran desert to alpine tundra. Antibody was found in rodents from all communities (overall prevalence = 6.3%); prevalence was lowest at the altitudinal and climatic extremes (0.4% in desert and 2.0% in alpine tundra). Antibody occurred in 11% of 928 deer mice, 20% of 355 brush mice, 23% of 35 western harvest mice, and 12% of 24 Mexican voles. No infected deer mice were found in desert habitat; prevalence varied from 4% in chaparral to 17% in pinyon-juniper. Brush mice were frequently infected in chaparral and montane forest (25%). Seropositivity was higher in males and in heavier animals, suggesting horizontal transmission among adult males. Decreasing prevalence with age among the youngest deer mice suggests that infected dams confer passive immunity to pups.
The CMS tracker readout front end driver Foudas, C.; Bainbridge, R.; Ballard, D. ...
IEEE transactions on nuclear science,
12/2005, Letnik:
52, Številka:
6
Journal Article
Recenzirano
Odprti dostop
The front end driver (FED), is a 9U 400 mm VME64x card designed for reading out the compact muon solenoid (CMS), silicon tracker signals transmitted by the APV25 analogue pipeline application ...specific integrated circuits. The FED receives the signals via 96 optical fibers at a total input rate of 3.4 GB/sec. The signals are digitized and processed by applying algorithms for pedestal and common mode noise subtraction. Algorithms that search for clusters of hits are used to further reduce the input rate. Only the cluster data along with trigger information of the event are transmitted to the CMS data acquisition system using the S-LINK64 protocol at a maximum rate of 400 MB/sec. All data processing algorithms on the FED are executed in large on-board field programmable gate arrays. Results on the design, performance, testing and quality control of the FED are presented and discussed
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