82 research outputs found
Data handling with SAM and art at the NOνA experiment
During operations, NOvA produces between 5,000 and 7,000 raw files per day with peaks in excess of 12,000. These files must be processed in several stages to produce fully calibrated and reconstructed analysis files. In addition, many simulated neutrino interactions must be produced and processed through the same stages as data. To accommodate the large volume of data and Monte Carlo, production must be possible both on the Fermilab grid and on off-site farms, such as the ones accessible through the Open Science Grid. To handle the challenge of cataloging these files and to facilitate their off-line processing, we have adopted the SAM system developed at Fermilab. SAM indexes files according to metadata, keeps track of each file's physical locations, provides dataset management facilities, and facilitates data transfer to off-site grids. To integrate SAM with Fermilab's art software framework and the NOvA production workflow, we have developed methods to embed metadata into our configuration files, art files, and standalone ROOT files. A module in the art framework propagates the embedded information from configuration files into art files, and from input art files to output art files, allowing us to maintain a complete processing history within our files. Embedding metadata in configuration files also allows configuration files indexed in SAM to be used as inputs to Monte Carlo production jobs. Further, SAM keeps track of the input files used to create each output file. Parentage information enables the construction of self-draining datasets which have become the primary production paradigm used at NOvA. In this paper we will present an overview of SAM at NOvA and how it has transformed the file production framework used by the experiment
Signature of a Heliotail Organized by the Solar Magnetic Field and the Role of Nonideal Processes in Modeled IBEX ENA Maps: A Comparison of the BU and Moscow MHD Models
Energetic neutral atom (ENA) models typically require post-processing routines to convert the distributions of plasma and H atoms into ENA maps. Here we investigate how two kinetic-MHD models of the heliosphere (the BU and Moscow models) manifest in modeled ENA maps using the same prescription and how they compare with Interstellar Boundary Explorer (IBEX) observations. Both MHD models treat the solar wind as a single-ion plasma for protons, which include thermal solar wind ions, pick-up ions (PUIs), and electrons. Our ENA prescription partitions the plasma into three distinct ion populations (thermal solar wind, PUIs transmitted and ones energized at the termination shock) and models the populations with Maxwellian distributions. Both kinetic-MHD heliospheric models produce a heliotail with heliosheath plasma that is organized by the solar magnetic field into two distinct north and south columns that become lobes of high mass flux flowing down the heliotail; however, in the BU model, the ISM flows between the two lobes at distances in the heliotail larger than 300 au. While our prescription produces similar ENA maps for the two different plasma and H atom solutions at the IBEX-Hi energy range (0.5–6 keV), the modeled ENA maps require a scaling factor of ∼2 to be in agreement with the data. This problem is present in other ENA models with the Maxwellian approximation of multiple ion species and indicates that either a higher neutral density or some acceleration of PUIs in the heliosheath is required
Uses of continuum radiation in the AXAF calibration
X-ray calibration of the Advanced X-ray Astrophysics Facility (AXAF) observatory at the MSFC X-Ray Calibration Facility (XRCF) made novel use of the x-ray continuum from a conventional electron-impact source. Taking advantage of the good spectral resolution of solid-state detectors, continuum measurements proved advantageous in calibrating the effective area of AXAF's High-Resolution Mirror Assembly (HRMA) and in verifying its alignment to the XRCF's optical axis
Antimicrobial resistance of Campylobacter isolates from small scale and backyard chicken in Kenya
Background Thermophilic Campylobacter species are a major cause of bacterial
foodborne diarrhoea in humans worldwide. Poultry and their products are the
predominant source for human campylobacteriosis. Resistance of Campylobacter
to antibiotics is increasing worldwide, but little is known about the
antibiotic resistance in Campylobacter isolated from chicken in Kenya. In this
study, 35 suspected Campylobacter strains isolated from faeces and cloacal
swabs of chicken were tested for their susceptibility to seven antibiotics
using a broth microdilution assay and molecular biological investigations.
Results Overall, DNA of thermophilic Campylobacter was identified in 53
samples by PCR (34 C. jejuni, 18 C. coli and one mix of both species) but only
35 Campylobacter isolates (31 C. jejuni and 4 C. coli) could be re-cultivated
after transportation to Germany. Isolates were tested for their susceptibility
to antibiotics using a broth microdilution assay. Additionally, molecular
biological detection of antibiotic resistance genes was carried out. C. jejuni
isolates showed a high rate of resistance to nalidixic acid, tetracycline and
ciprofloxacin of 77.4, 71.0 and 71.0 %, respectively. Low resistance (25.8 %)
was detected for gentamicin and chloramphenicol. Multidrug resistance in C.
jejuni could be detected in 19 (61.3 %) isolates. Resistance pattern of C.
coli isolates was comparable. Resistance to ciprofloxacin was confirmed by
MAMA–PCR and PCR–RFLP in all phenotypically resistant isolates. The tet(O)
gene was detected only in 54.5 % of tetracycline resistant C. jejuni isolates.
The tet(A) gene, which is also responsible for tetracycline resistance, was
found in 90.3 % of C. jejuni and in all C. coli isolates. Thirteen
phenotypically erythromycin-resistant isolates could not be characterised by
using PCR–RFLP and MAMA–PCR. Conclusions To the best of our knowledge, this
study is the first report about resistance to antibiotics in thermophilic
Campylobacter originating from chicken in Kenya. Campylobacter spp. show a
high level of resistance to ciprofloxacin, nalidixic acid and tetracycline but
also a remarkable one to chloramphenicol and gentamicin and they are multidrug
resistant. Resistance to antibiotics is a global public health concern. In
Kenya, resistance surveillance needs further attention in the future. Efforts
to establish at least a National Laboratory with facilities for performing
phenotypic and genotypic characterization of thermophilic Campylobacter is
highly recommended
Molecular and phenotypical investigation of ciprofloxacin resistance among Campylobacter jejuni strains of human origin: high prevalence of resistance in Turkey
Campylobacteriosis is one of the most frequently reported zoonoses worldwide. The well-documented increase in the ciprofloxacin resistance has increased the importance of rapid detection of the resistance. The incidence of ciprofloxacin resistance was investigated using real-time PCR. Identification of one hundred and fifty-eight strains was performed by PCR. Minimum inhibitory concentration (MIC) of ciprofloxacin was determined by Epsilometer test. Following the confirmation of the efficiencies of singleplex real-time PCR methods using two different probes, a cytosine to thymine point mutation at codon 86 was detected by allelic discrimination. Of the 158 strains, 114 (72.2%) were determined to be resistant to ciprofloxacin. The MIC50 and the MIC90 of ciprofloxacin were found to be 8 and >= 32 mg/L, respectively. By real-time PCR, the presence of the mutation was confirmed in all, but one, resistant strains and the absence of the mutation was demonstrated in all, but one, susceptible strains. The rate of resistance is high among C. jejuni strains and ciprofloxacin should not be used in the treatment of such infections in Turkey. A cytosine to thymine mutation is the most frequently detected mechanism for the resistance. Real-time PCR can be used for the quick screening of the resistance
Genotyping and antibiotic resistance of thermophilic Campylobacter isolated from chicken and pig meat in Vietnam
Background Campylobacter species are recognized as the most common cause of
foodborne bacterial gastroenteritis in humans. In this study nine
Campylobacter strains isolated from chicken meat and pork in Hanoi, Vietnam,
were characterized using molecular methods and tested for antibiotic
resistance. Results The nine isolates (eight C. jejuni and one C. coli) were
identified by multiplex PCR, and tested for the presence or absence of 29 gene
loci associated with virulence, lipooligosaccharide (LOS) biosynthesis and
further functions. flaA typing, multilocus sequence typing and microarray
assay investigation showed a high degree of genetic diversity among these
isolates. In all isolates motility genes (flaA, flaB, flhA, fliM),
colonization associated genes (cadF, docB), toxin production genes (cdtA,
cdtB, secD, secF), and the LOS biosynthesis gene pglB were detected. Eight
gene loci (fliY, virB11, Cje1278, Cj1434c, Cj1138, Cj1438c, Cj1440c, Cj1136)
could not be detected by PCR. A differing presence of the gene loci ciaB (22.2
%), Cje1280 (77.8 %), docC (66.7 %), and cgtB (55.6 %) was found. iamA, cdtC,
and the type 6 secretion system were present in all C. jejuni isolates but not
in C. coli. flaA typing resulted in five different genotypes within C. jejuni,
MLST classified the isolates into seven sequence types (ST-5155, ST-6736,
ST-2837, ST-4395, ST-5799, ST-4099 and ST-860). The microarray assay analysis
showed a high genetic diversity within Vietnamese Campylobacter isolates which
resulted in eight different types for C. jejuni. Antibiotic susceptibility
profiles showed that all isolates were sensitive to gentamicin and most
isolates (88.8 %) were sensitive to chloramphenicol, erythromycin and
streptomycin. Resistance rates to nalidixic acid, tetracycline and
ciprofloxacin were 88.9, 77.8 and 66.7 %, respectively. Conclusions To the
best of our knowledge, this study is the first report that shows high genetic
diversity and remarkable antibiotic resistance of Campylobacter strains
isolated from meat in Vietnam which can be considered of high public health
significance. These preliminary data show that large scale screenings are
justified to assess the relevance of Campylobacter infections on human health
in Vietnam
Metabolism-dependent bioaccumulation of uranium by Rhodosporidium toruloides isolated from the flooding water of a former uranium mine
Remediation of former uranium mining sites represents one of the biggest challenges worldwide
that have to be solved in this century. During the last years, the search of alternative
strategies involving environmentally sustainable treatments has started. Bioremediation,
the use of microorganisms to clean up polluted sites in the environment, is considered one
the best alternative. By means of culture-dependent methods, we isolated an indigenous
yeast strain, KS5 (Rhodosporidium toruloides), directly from the flooding water of a former
uranium mining site and investigated its interactions with uranium. Our results highlight
distinct adaptive mechanisms towards high uranium concentrations on the one hand, and
complex interaction mechanisms on the other. The cells of the strain KS5 exhibit high a
uranium tolerance, being able to grow at 6 mM, and also a high ability to accumulate this
radionuclide (350 mg uranium/g dry biomass, 48 h). The removal of uranium by KS5 displays
a temperature- and cell viability-dependent process, indicating that metabolic activity
could be involved. By STEM (scanning transmission electron microscopy) investigations,
we observed that uranium was removed by two mechanisms, active bioaccumulation and
inactive biosorption. This study highlights the potential of KS5 as a representative of indigenous
species within the flooding water of a former uranium mine, which may play a key role
in bioremediation of uranium contaminated sites.This work was supported by the
Bundesministerium für Bildung und Forschung
grand nº 02NUK030F (TransAqua). Further support
took place by the ERDF-co-financed Grants
CGL2012-36505 and 315 CGL2014-59616R,
Ministerio de Ciencia e Innovación, Spain
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