Tracking pathogen transmission at the human-wildlife interface: banded mongoose and Escherichia coli.

PubMed

Pesapane, R; Ponder, M; Alexander, K A

2013-06-01

A primary challenge to managing emerging infectious disease is identifying pathways that allow pathogen transmission at the human-wildlife interface. Using Escherichia coli as a model organism, we evaluated fecal bacterial transmission between banded mongoose (Mungos mungo) and humans in northern Botswana. Fecal samples were collected from banded mongoose living in protected areas (n = 87, 3 troops) and surrounding villages (n = 92, 3 troops). Human fecal waste was collected from the same environment (n = 46). Isolates were evaluated for susceptibility to 10 antibiotics. Resistant E. coli isolates from mongoose were compared to human isolates using rep-PCR fingerprinting and MLST-PCR. Antimicrobial resistant isolates were identified in 57 % of the mongoose fecal samples tested (range 31-78% among troops). At least one individual mongoose fecal sample demonstrated resistance to each tested antibiotic, and multidrug resistance was highest in the protected areas (40.9%). E. coli isolated from mongoose and human sources in this study demonstrated an extremely high degree of genetic similarity on rep-PCR (AMOVA, F ST = 0.0027, p = 0.18) with a similar pattern identified on MLST-PCR. Human waste may be an important source of microbial exposure to wildlife. Evidence of high levels of antimicrobial resistance even within protected areas identifies an emerging health threat and highlights the need for improved waste management in these systems.

Nonradioactive heteroduplex tracking assay for the detection of minority-variant chloroquine-resistant Plasmodium falciparum in Madagascar

PubMed Central

Juliano, Jonathan J; Randrianarivelojosia, Milijaona; Ramarosandratana, Benjamin; Ariey, Frédéric; Mwapasa, Victor; Meshnick, Steven R

2009-01-01

Background Strains of Plasmodium falciparum genetically resistant to chloroquine (CQ) due to the presence of pfcrt 76T appear to have been recently introduced to the island of Madagascar. The prevalence of such resistant genotypes is reported to be low (< 3%) when evaluated by conventional PCR. However, these methods are insensitive to low levels of mutant parasites present in patients with polyclonal infections. Thus, the current estimates may be an under representation of the prevalence of the CQ-resistant P. falciparum isolates on the island. Previously, minority variant chloroquine resistant parasites were described in Malawian patients using an isotopic heteroduplex tracking assay (HTA), which can detect pfcrt 76T-bearing P. falciparum minority variants in individual patients that were undetectable by conventional PCR. However, as this assay required a radiolabeled probe, it could not be used in many resource-limited settings. Methods This study describes a digoxigenin (DIG)-labeled chemiluminescent heteroduplex tracking assay (DIG-HTA) to detect pfcrt 76T-bearing minority variant P. falciparum. This assay was compared to restriction fragment length polymorphism (RFLP) analysis and to the isotopic HTA for detection of genetically CQ-resistant parasites in clinical samples. Results Thirty one clinical P. falciparum isolates (15 primary isolates and 16 recurrent isolates) from 17 Malagasy children treated with CQ for uncomplicated malaria were genotyped for the pfcrt K76T mutation. Two (11.7%) of 17 patients harboured genetically CQ-resistant P. falciparum strains after therapy as detected by HTA. RFLP analysis failed to detect any pfcrt K76T-bearing isolates. Conclusion These findings indicate that genetically CQ-resistant P. falciparum are more common than previously thought in Madagascar even though the fitness of the minority variant pfcrt 76T parasites remains unclear. In addition, HTAs for malaria drug resistance alleles are promising tools for the surveillance of anti-malarial resistance. The use of a non-radioactive label allows for the use of HTAs in malaria endemic countries. PMID:19291288

Origins and Distribution of Chondritic Olivine Inferred from Wild 2 and Chondrite Matrix

NASA Technical Reports Server (NTRS)

Frank, D. R.; Zolensky, M. E.

2014-01-01

To date, only 180 particle impact tracks from Wild 2 have been extracted from the Stardust aerogel collector and even fewer have been thoroughly characterized. In order to provide a cohesive compositional dataset that can be compared to the meteorite record, we have made both major and minor element analyses (TEM/EDXS) of olivine and low-Ca pyroxene for 39 particles harvested from 26 tracks. However, the dearth of equivalent analyses for these phases in chondrite matrix hinders their comparison to the Wild 2 samples. To properly permit comparison of chondritic olivine and pyroxene to the Wild 2 samples, we have also provided a large, comprehensive EPMA dataset (greater than10(exp 3) analyses) of analogous grains (5-30 micrometers) isolated in L/LL3.0-4, CI, CM, CR, CH, CO, CV, Acfer 094, EH3, EL6, and Kakangari matrix

Optimization of single plate-serial dilution spotting (SP-SDS) with sample anchoring as an assured method for bacterial and yeast cfu enumeration and single colony isolation from diverse samples.

PubMed

Thomas, Pious; Sekhar, Aparna C; Upreti, Reshmi; Mujawar, Mohammad M; Pasha, Sadiq S

2015-12-01

We propose a simple technique for bacterial and yeast cfu estimations from diverse samples with no prior idea of viable counts, designated as single plate-serial dilution spotting (SP-SDS) with the prime recommendation of sample anchoring (10 0 stocks). For pure cultures, serial dilutions were prepared from 0.1 OD (10 0 ) stock and 20 μl aliquots of six dilutions (10 1 -10 6 ) were applied as 10-15 micro-drops in six sectors over agar-gelled medium in 9-cm plates. For liquid samples 10 0 -10 5 dilutions, and for colloidal suspensions and solid samples (10% w/v), 10 1 -10 6 dilutions were used. Following incubation, at least one dilution level yielded 6-60 cfu per sector comparable to the standard method involving 100 μl samples. Tested on diverse bacteria, composite samples and Saccharomyces cerevisiae , SP-SDS offered wider applicability over alternative methods like drop-plating and track-dilution for cfu estimation, single colony isolation and culture purity testing, particularly suiting low resource settings.

Cutting Silica Aerogel for Particle Extraction

NASA Technical Reports Server (NTRS)

Tsou, P.; Brownlee, D. E.; Glesias, R.; Grigoropoulos, C. P.; Weschler, M.

2005-01-01

The detailed laboratory analyses of extraterrestrial particles have revolutionized our knowledge of planetary bodies in the last three decades. This knowledge of chemical composition, morphology, mineralogy, and isotopics of particles cannot be provided by remote sensing. In order to acquire these detail information in the laboratories, the samples need be intact, unmelted. Such intact capture of hypervelocity particles has been developed in 1996. Subsequently silica aerogel was introduced as the preferred medium for intact capturing of hypervelocity particles and later showed it to be particularly suitable for the space environment. STARDUST, the 4th NASA Discovery mission to capture samples from 81P/Wild 2 and contemporary interstellar dust, is the culmination of these new technologies. In early laboratory experiments of launching hypervelocity projectiles into aerogel, there was the need to cut aerogel to isolate or extract captured particles/tracks. This is especially challenging for space captures, since there will be many particles/tracks of wide ranging scales closely located, even collocated. It is critical to isolate and extract one particle without compromising its neighbors since the full significance of a particle is not known until it is extracted and analyzed. To date, three basic techniques have been explored: mechanical cutting, lasers cutting and ion beam milling. We report the current findings.

Localized strain measurements of the intervertebral disc annulus during biaxial tensile testing.

PubMed

Karakolis, Thomas; Callaghan, Jack P

2015-01-01

Both inter-lamellar and intra-lamellar failures of the annulus have been described as potential modes of disc herniation. Attempts to characterize initial lamellar failure of the annulus have involved tensile testing of small tissue samples. The purpose of this study was to evaluate a method of measuring local surface strains through image analysis of a tensile test conducted on an isolated sample of annular tissue in order to enhance future studies of intervertebral disc failure. An annulus tissue sample was biaxial strained to 10%. High-resolution images captured the tissue surface throughout testing. Three test conditions were evaluated: submerged, non-submerged and marker. Surface strains were calculated for the two non-marker conditions based on motion of virtual tracking points. Tracking algorithm parameters (grid resolution and template size) were varied to determine the effect on estimated strains. Accuracy of point tracking was assessed through a comparison of the non-marker conditions to a condition involving markers placed on tissue surface. Grid resolution had a larger effect on local strain than template size. Average local strain error ranged from 3% to 9.25% and 0.1% to 2.0%, for the non-submerged and submerged conditions, respectively. Local strain estimation has a relatively high potential for error. Submerging the tissue provided superior strain estimates.

Environmental manipulations alter age differences in attribution of incentive salience to reward-paired cues

PubMed Central

Anderson, Rachel I.; Bush, Peter C.; Spear, Linda P.

2013-01-01

Cues repeatedly paired with rewards often themselves become imbued with enhanced motivational value, or incentive salience. During Pavlovian conditioned approach procedures, a cue repeatedly preceding reward delivery often elicits conditioned responses at either the reward delivery location (“goal-tracking”) or the cue itself (“sign-tracking”). Sign-tracking behavior is thought to reflect the individual differences in attribution of incentive salience to reward-paired cues that may contribute to addiction vulnerability. Adolescent rats typically demonstrate less sign-tracking behavior than adult rats, a surprising finding given that adolescence is hypothesized to be a time of heightened addiction vulnerability. Given evidence that adult sign-tracking behavior can be influenced by environmental conditions, the present study compared the effects of isolate housing and food deprivation on expression of sign-tacking and goal-tracking behavior in adolescent and adult male rats across eight days of a Pavlovian conditioned approach procedure. Pair-housed adults exhibited more sign-tracking behavior than pair-housed adolescents; however, this age difference was not apparent in isolate-housed subjects. Adolescents often appeared more sensitive than adults to both food restriction- and isolate housing-induced changes in behavior, with food restriction promoting an increase in sign-tracking among isolate-housed adolescents and an increase in goal-tracking among pair-housed adolescents. For adults, food restriction resulted in a modest increase in overall expression of both sign-and goal-tracking behavior. To the extent that sign-tracking behavior reflects attribution of incentive salience to reward-paired cues, results from the present study provide evidence that reactivity to rewards during adolescence is strongly related to the nature of the surrounding environment. PMID:24050888

A Comparative Study of Serum Exosome Isolation Using Differential Ultracentrifugation and Three Commercial Reagents.

PubMed

Helwa, Inas; Cai, Jingwen; Drewry, Michelle D; Zimmerman, Arthur; Dinkins, Michael B; Khaled, Mariam Lotfy; Seremwe, Mutsa; Dismuke, W Michael; Bieberich, Erhard; Stamer, W Daniel; Hamrick, Mark W; Liu, Yutao

2017-01-01

Exosomes play a role in cell-to-cell signaling and serve as possible biomarkers. Isolating exosomes with reliable quality and substantial concentration is a major challenge. Our purpose is to compare the exosomes extracted by three different exosome isolation kits (miRCURY, ExoQuick, and Invitrogen Total Exosome Isolation Reagent) and differential ultracentrifugation (UC) using six different volumes of a non-cancerous human serum (5 ml, 1 ml, 500 μl, 250 μl, 100 μl, and 50 μl) and three different volumes (1 ml, 500 μl and 100 μl) of six individual commercial serum samples collected from human donors. The smaller starting volumes (100 μl and 50 μl) are used to mimic conditions of limited availability of heterogeneous biological samples. The isolated exosomes were characterized based upon size, quantity, zeta potential, CD63 and CD9 protein expression, and exosomal RNA (exRNA) quality and quantity using several complementary methods: nanoparticle tracking analysis (NTA) with ZetaView, western blot, transmission electron microscopy (TEM), the Agilent Bioanalyzer system, and droplet digital PCR (ddPCR). Our NTA results showed that all isolation techniques produced exosomes within the expected size range (40-150 nm). The three kits, though, produced a significantly higher yield (80-300 fold) of exosomes as compared to UC for all serum volumes, except 5 mL. We also found that exosomes isolated by the different techniques and serum volumes had similar zeta potentials to previous studies. Western blot analysis and TEM immunogold labelling confirmed the expression of two common exosomal protein markers, CD63 and CD9, in samples isolated by all techniques. All exosome isolations yielded high quality exRNA, containing mostly small RNA with a peak between 25 and 200 nucleotides in size. ddPCR results indicated that exosomes isolated from similar serum volumes but different isolation techniques rendered similar concentrations of two selected exRNA: hsa-miR-16 and hsa-miR-451. In summary, the three commercial exosome isolation kits are viable alternatives to UC, even when limited amounts of biological samples are available.

Sensor for detecting and differentiating chemical analytes

DOEpatents

Yi, Dechang [Metuchen, NJ; Senesac, Lawrence R [Knoxville, TN; Thundat, Thomas G [Knoxville, TN

2011-07-05

A sensor for detecting and differentiating chemical analytes includes a microscale body having a first end and a second end and a surface between the ends for adsorbing a chemical analyte. The surface includes at least one conductive heating track for heating the chemical analyte and also a conductive response track, which is electrically isolated from the heating track, for producing a thermal response signal from the chemical analyte. The heating track is electrically connected with a voltage source and the response track is electrically connected with a signal recorder. The microscale body is restrained at the first end and the second end and is substantially isolated from its surroundings therebetween, thus having a bridge configuration.

Search for the Associated Production of Charginos and Neutralinos in Proton-Antiproton Collisions at √s=1.96 TeV with the D0 Detector at the Tevatron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mundal, Olav M.

2008-10-01

A search for Supersymmetry is performed via the associated production of charginos and neutralinos in fi states consisting of three charged leptons and missing transverse energy using data collected with the DØ detector at a center-of-mass energy of 1.96 TeV at the Fermilab Tevatron Collider. The data sample corresponds to an integrated luminosity of ~ 2.3 fb -1. This fi state is considered one of the most promising channels in the search for supersymmetric particles because of its low Standard Model background. A dedicated event selection is developed and events with two muons plus an additional isolated track or eventsmore » with two electrons plus an additional isolated track are analyzed. The requirement of an isolated track replaces the third charged lepton in the event. After all selection cuts are applied, in total 7 events are selected in the data with an expected number of background events of 5.24±0.40 (stat)±0.30 (syst). Due to the good agreement of events observed in data with the expectation of the Standard Model backgrounds, no evidence for Supersymmetry is found. The present analyses are considered in combination with three other decay channels and limits on the production cross section times leptonic branching fraction are set. The results are interpreted in a constrained scenario and exclusion regions are derived as a function of m 0 and m 1/2.« less

Assessment of Giardia and Cryptosporidium spp. as a microbial source tracking tool for surface water: application in a mixed-use watershed.

PubMed

Prystajecky, Natalie; Huck, Peter M; Schreier, Hans; Isaac-Renton, Judith L

2014-04-01

Knowledge of host specificity, combined with genomic sequencing of Giardia and Cryptosporidium spp., has demonstrated a microbial source tracking (MST) utility for these common waterborne microbes. To explore the source attribution potential of these pathogens, water samples were collected in a mixed rural-urban watershed in the Township of Langley, in southwestern British Columbia (BC), Canada, over a 2-year period. Cryptosporidium was detected in 63% of surface water samples at concentrations ranging from no positive detection (NPD) to 20,600 oocysts per 100 liters. Giardia was detected in 86% of surface water samples at concentrations ranging from NPD to 3,800 cysts per 100 liters of water. Sequencing at the 18S rRNA locus revealed that 50% of Cryptosporidium samples and 98% of Giardia samples contained species/genotypes (Cryptosporidium) or assemblages (Giardia) that are capable of infecting humans, based on current knowledge of host specificity and taxonomy. Cryptosporidium genotyping data were more promising for source tracking potential, due to the greater number of host-adapted (i.e., narrow-host-range) species/genotypes compared to Giardia, since 98% of Giardia isolates were zoonotic and the potential host could not be predicted. This report highlights the benefits of parasite genomic sequencing to complement Method 1623 (U.S. Environmental Protection Agency) and shows that Cryptosporidium subtyping for MST purposes is superior to the use of Giardia subtyping, based on better detection limits for Cryptosporidium-positive samples than for Giardia-positive samples and on greater host specificity among Cryptosporidium species. These additional tools could be used for risk assessment in public health and watershed management decisions.

Assessment of Giardia and Cryptosporidium spp. as a Microbial Source Tracking Tool for Surface Water: Application in a Mixed-Use Watershed

PubMed Central

Huck, Peter M.; Schreier, Hans; Isaac-Renton, Judith L.

2014-01-01

Knowledge of host specificity, combined with genomic sequencing of Giardia and Cryptosporidium spp., has demonstrated a microbial source tracking (MST) utility for these common waterborne microbes. To explore the source attribution potential of these pathogens, water samples were collected in a mixed rural-urban watershed in the Township of Langley, in southwestern British Columbia (BC), Canada, over a 2-year period. Cryptosporidium was detected in 63% of surface water samples at concentrations ranging from no positive detection (NPD) to 20,600 oocysts per 100 liters. Giardia was detected in 86% of surface water samples at concentrations ranging from NPD to 3,800 cysts per 100 liters of water. Sequencing at the 18S rRNA locus revealed that 50% of Cryptosporidium samples and 98% of Giardia samples contained species/genotypes (Cryptosporidium) or assemblages (Giardia) that are capable of infecting humans, based on current knowledge of host specificity and taxonomy. Cryptosporidium genotyping data were more promising for source tracking potential, due to the greater number of host-adapted (i.e., narrow-host-range) species/genotypes compared to Giardia, since 98% of Giardia isolates were zoonotic and the potential host could not be predicted. This report highlights the benefits of parasite genomic sequencing to complement Method 1623 (U.S. Environmental Protection Agency) and shows that Cryptosporidium subtyping for MST purposes is superior to the use of Giardia subtyping, based on better detection limits for Cryptosporidium-positive samples than for Giardia-positive samples and on greater host specificity among Cryptosporidium species. These additional tools could be used for risk assessment in public health and watershed management decisions. PMID:24463970

Evaluation of antibiotic resistance analysis and ribotyping for identification of faecal pollution sources in an urban watershed.

PubMed

Moore, D F; Harwood, V J; Ferguson, D M; Lukasik, J; Hannah, P; Getrich, M; Brownell, M

2005-01-01

The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sources of faecal bacterial pollution in an urban southern California watershed was determined using blinded proficiency samples. Antibiotic resistance patterns and HindIII ribotypes of Escherichia coli (n = 997), and antibiotic resistance patterns of Enterococcus spp. (n = 3657) were used to construct libraries from sewage samples and from faeces of seagulls, dogs, cats, horses and humans within the watershed. The three libraries were analysed to determine the accuracy of host source prediction. The internal accuracy of the libraries (average rate of correct classification, ARCC) with six source categories was 44% for E. coli ARA, 69% for E. coli ribotyping and 48% for Enterococcus ARA. Each library's predictive ability towards isolates that were not part of the library was determined using a blinded proficiency panel of 97 E. coli and 99 Enterococcus isolates. Twenty-eight per cent (by ARA) and 27% (by ribotyping) of the E. coli proficiency isolates were assigned to the correct source category. Sixteen per cent were assigned to the same source category by both methods, and 6% were assigned to the correct category. Addition of 2480 E. coli isolates to the ARA library did not improve the ARCC or proficiency accuracy. In contrast, 45% of Enterococcus proficiency isolates were correctly identified by ARA. None of the methods performed well enough on the proficiency panel to be judged ready for application to environmental samples. Most microbial source tracking (MST) studies published have demonstrated library accuracy solely by the internal ARCC measurement. Low rates of correct classification for E. coli proficiency isolates compared with the ARCCs of the libraries indicate that testing of bacteria from samples that are not represented in the library, such as blinded proficiency samples, is necessary to accurately measure predictive ability. The library-based MST methods used in this study may not be suited for determination of the source(s) of faecal pollution in large, urban watersheds.

Coordinated Analyses of Diverse Components in Whole Stardust Cometary Tracks

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, Keiko; Keller, Lindsay P.; Messenger, Scott R.; Clemett, Simon J.; Nguyen, Lan-Anh N.; Frank, David

2011-01-01

Analyses of samples returned from Comet 81P/Wild-2 by the Stardust spacecraft have resulted in a number of surprising findings that show the origins of comets are more complex than previously suspected. However, these samples pose new experimental challenges because they are diverse and suffered fragmentation, thermal alteration, and fine scale mixing with aerogel. Questions remain about the nature of Wild-2 materials, such as the abundances of organic matter, crystalline materials, and presolar grains. To overcome these challenges, we have developed new sample preparation and analytical techniques tailored for entire aerogel tracks. We have successfully ultramicrotomed entire "carrot" and "bulbous" type tracks along their axis while preserving their original shapes. This innovation allowed us to examine the distribution of fragments along the track from the entrance hole all the way to the terminal particle (TP). We will present results of our coordinated analysis of the "carrot" type aerogel tracks #112 and #148, and the "bulbous" type aerogel tracks #113, #147 and #168 from the nanometer to the millimeter scale. Scanning TEM (STEM) was used for elemental and detailed mineralogy characterization, NanoSIMS was used for isotopic analyses, and ultrafast two-step laser mass spectrometry (ultra L2MS) was used to investigate the nature and distribution of organic phases. The isotopic measurements were performed following detailed TEM characterization for coordinated mineralogy. This approach also enabled spatially resolving the target sample from fine-scale mixtures of compressed aerogel and melt. Eight of the TPs of track #113 are dominated by coarse-grained enstatite (En90) that is largely orthoenstatite with minor, isolated clinoenstatite lamellae. One TP contains minor forsterite (Fo88) and small inclusions of diopside with % levels of Al, Cr and Fe. Two of the TPs contain angular regions of fine-grained nepheline surrounded by enstatite. Their O isotopic compositions are in the range of meteoritic materials, implying that they originated in the inner Solar System. Complex aromatic hydrocarbons are distributed along aerogel tracks and in TPs. These organics are likely cometary but were affected by shock heating. Three TPs of track #147 and two of track 168 have completely different mineralogy. TP2 of track #147 entirely consists of Fe-Ni alloy (5 at% Ni) and TP3 contains Fa28 with partial olivine-pyroxene intergrowth and minor albite. TP4 contains pentlandite, Fe-olivine, albite and high Ca pyroxene with Na and Cr (kosmochlor component). TP1 of #168 contains Fe-olivine, albite and pentlandite, and the concentric TP2 has a core of olivine grains with co-existing indigenous amorphous SiO2 surrounded by a carbon mantle, which in turn is surrounded by a layer of compressed aerogel. The TP of the carrot track #112 is a (16)O-rich forsteritic olivine grain that likely formed in the inner Solar System. The track also contains submicron-sized diamond grains of likely Solar System origin.

Coordinated Analyses of Diverse Components in Whole Stardust Cometary Tracks

NASA Astrophysics Data System (ADS)

Nakamura-Messenger, K.; Keller, L. P.; Messenger, S. R.; Clemett, S. J.; Nguyen, L. N.; Frank, D.

2011-12-01

Analyses of samples returned from Comet 81P/Wild-2 by the Stardust spacecraft have resulted in a number of surprising findings that show the origins of comets are more complex than previously suspected. However, these samples pose new experimental challenges because they are diverse and suffered fragmentation, thermal alteration, and fine scale mixing with aerogel. Questions remain about the nature of Wild-2 materials, such as the abundances of organic matter, crystalline materials, and presolar grains. To overcome these challenges, we have developed new sample preparation and analytical techniques tailored for entire aerogel tracks [Nakamura-Messenger et al. 2011]. We have successfully ultramicrotomed entire "carrot" and "bulbous" type tracks along their axis while preserving their original shapes. This innovation allowed us to examine the distribution of fragments along the track from the entrance hole all the way to the terminal particle (TP). We will present results of our coordinated analysis of the "carrot" type aerogel tracks #112 and #148, and the "bulbous" type aerogel tracks #113, #147 and #168 from the nanometer to the millimeter scale. Scanning TEM (STEM) was used for elemental and detailed mineralogy characterization, NanoSIMS was used for isotopic analyses, and ultrafast two-step laser mass spectrometry (ultra L2MS) was used to investigate the nature and distribution of organic phases. The isotopic measurements were performed following detailed TEM characterization for coordinated mineralogy. This approach also enabled spatially resolving the target sample from fine-scale mixtures of compressed aerogel and melt. Eight of the TPs of track #113 are dominated by coarse-grained enstatite (En90) that is largely orthoenstatite with minor, isolated clinoenstatite lamellae. One TP contains minor forsterite (Fo88) and small inclusions of diopside with % levels of Al, Cr and Fe. Two of the TPs contain angular regions of fine-grained nepheline surrounded by enstatite. Their O isotopic compositions are in the range of meteoritic materials, implying that they originated in the inner Solar System. Complex aromatic hydrocarbons are distributed along aerogel tracks and in TPs. These organics are likely cometary but were affected by shock heating. Three TPs of track #147 and two of track 168 have completely different mineralogy. TP2 of track #147 entirely consists of Fe-Ni alloy (5 at% Ni) and TP3 contains Fa28 with partial olivine-pyroxene intergrowth and minor albite. TP4 contains pentlandite, Fe-olivine, albite and high Ca pyroxene with Na and Cr (kosmochlor component). TP1 of #168 contains Fe-olivine, albite and pentlandite, and the concentric TP2 has a core of olivine grains with co-existing indigenous amorphous SiO2 surrounded by a carbon mantle, which in turn is surrounded by a layer of compressed aerogel. The TP of the carrot track #112 is a 16O-rich forsteritic olivine grain that likely formed in the inner Solar System. The track also contains submicron-sized diamond grains of likely Solar System origin.

Ocular TRUST: nationwide antimicrobial susceptibility patterns in ocular isolates.

PubMed

Asbell, Penny A; Colby, Kathryn A; Deng, Sophie; McDonnell, Peter; Meisler, David M; Raizman, Michael B; Sheppard, John D; Sahm, Daniel F

2008-06-01

Ocular Tracking Resistance in U.S. Today (TRUST) annually evaluates in vitro antimicrobial susceptibility of Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae to ciprofloxacin, gatifloxacin, levofloxacin, moxifloxacin, penicillin, azithromycin, tobramycin, trimethoprim, and polymyxin B in national samples of ocular isolates. Laboratory investigation. Prospectively collected ocular isolates (197 S. aureus, 49 S. pneumoniae, and 32 H. influenzae) from 35 institutions and archived ocular isolates (760 S. pneumoniae and 356 H. influenzae) from 34 institutions were tested by an independent, central laboratory. Mean minimum inhibitory concentrations that would inhibit growth of 90% of the tested isolates (MIC(90)) were interpreted as susceptible, intermediate, or resistant according to standardized breakpoints for systemic treatment. S. aureus isolates were classified as methicillin susceptible (MSSA) or methicillin resistant (MRSA). MSSA or MRSA susceptibility patterns were virtually identical for the fluoroquinolones, that is, MSSA susceptibility was 79.9% to 81.1% and MRSA susceptibility was 15.2%. Trimethoprim was the only agent tested with high activity against MRSA. All S. pneumoniae isolates were susceptible to gatifloxacin, levofloxacin, and moxifloxacin; 89.8% were susceptible to ciprofloxacin. H. influenzae isolates were 100% susceptible to all tested agents but trimethoprim. Ocular TRUST 1 data were consistent with the eight-year longitudinal sample of archived ocular isolates. The fluoroquinolones were consistently active in MSSA, S. pneumoniae, and H. influenzae. After more than a decade of intensive ciprofloxacin and levofloxacin use as systemic therapy, 100% of ocular S. pneumoniae isolates were susceptible to gatifloxacin, levofloxacin, and moxifloxacin; nonsusceptibility to ciprofloxacin was less than 15%. High-level in vitro MRSA resistance suggests the need to consider alternative therapy to fluoroquinolones when MRSA is a likely pathogen.

Whole-genome sequencing to determine Neisseria gonorrhoeae transmission: an observational study

PubMed Central

Cole, Kevin; Cole, Michelle J; Cresswell, Fiona; Dean, Gillian; Dave, Jayshree; Thomas, Daniel Rh; Foster, Kirsty; Waldram, Alison; Wilson, Daniel J; Didelot, Xavier; Grad, Yonatan H; Crook, Derrick W; Peto, Tim EA; Walker, A Sarah

2016-01-01

Background New approaches are urgently required to address increasing rates of gonorrhoea and the emergence and global spread of antibiotic-resistant Neisseria gonorrhoeae. Whole genome sequencing (WGS) can be applied to study transmission and track resistance. Methods We performed WGS on 1659 isolates from Brighton, UK, and 217 additional isolates from other UK locations. We included WGS data (n=196) from the USA. Estimated mutation rates, plus diversity observed within patients across anatomical sites and probable transmission pairs, were used to fit a coalescent model to determine the number of single nucleotide polymorphisms (SNPs) expected between sequences related by direct/indirect transmission, depending on the time between samples. Findings We detected extensive local transmission. 281/1061(26%) Brighton cases were indistinguishable (0 SNPs) to ≥1 previous case(s), and 786(74%) had evidence of a sampled direct or indirect Brighton source. There was evidence of sustained transmission of some lineages. We observed multiple related samples across geographic locations. Of 1273 infections in Brighton, 225(18%) were linked to another case from elsewhere in the UK, and 115(9%) to a case from the USA. Four lineages initially identified in Brighton could be linked to 70 USA sequences, including 61 from a lineage carrying the mosaic penA XXXIV associated with reduced cefixime susceptibility. Interpretation We present a WGS-based tool for genomic contact tracing of N. gonorrhoeae and demonstrate local, national and international transmission. WGS can be applied across geographical boundaries to investigate gonorrhoea transmission and to track antimicrobial resistance. Funding Oxford NIHR Health Protection Research Unit and Biomedical Research Centre. PMID:27427203

Salmonella prevalence and characterization in a free-range pig processing plant: tracking in trucks, lairage, slaughter line and quartering.

PubMed

Hernández, Manuela; Gómez-Laguna, Jaime; Luque, Inmaculada; Herrera-León, Silvia; Maldonado, Alfonso; Reguillo, Lucía; Astorga, Rafael J

2013-03-01

New consumer tendencies are focused on products derived from systems which allow both a high animal welfare condition and a high food safety level. However, sometimes animal welfare regulations make the adoption of adequate bio-security measures difficult, representing a barrier for animal health and food safety. Thus the aim of this study was to determine the prevalence of Salmonella at different points of the pig slaughtering process (Trucks, Lairage, Slaughter line and Quartering, TLSQ) from pigs reared in free-range systems. From eight samplings a total of 126 Salmonella isolates out of 1160 different samples were recovered (10.86%). The highest percentage of isolates was detected at the points of pre-scalding (29/80, 36.25%), trucks (13/56, 23.21%), cecal contents (17/80, 21.25%), tonsils (14/80, 17.50%), ileocecal lymph nodes (13/80, 16.25%) and lairage (9/64, 14.06%). Furthermore, eighteen isolates were obtained from different environmental samples from slaughter line and quartering plant (knives and surface of tables) (5.63%) and three isolates at the quartering plant samples (ham, shoulder and loin) (3.75%). Fourteen different serotypes were isolated: Bredeney, Rissen, Derby, Typhimurium, Montevideo, Israel, Anatum, Emek, Monophasic Salmonella Typhimurium (mST), Choleraesuis, Durban, Kentucky, London and Sandiego. S. Typhimurium phage types U311, 193, 104b and UT were identified. Moreover, mST strain was phage typed as U311. From TLSQ1, TLSQ2 and TLSQ4, different strains of S. Derby, S. Rissen and S. Bredeney serotypes were isolated from pig and environmental samples, pointing to a potential cross contamination. Molecular typing (Pulsed-Field Gel Electrophoresis, PFGE) of these strains confirmed the cross contamination. In the remaining samplings, different serotypes were obtained in each sampled point of the chain, assuming that the isolated serotypes belonged to different epidemiological origins. Our results show the isolation of different serotypes of Salmonella spp. from both pigs and environmental samples, which constitutes a great risk for the contamination of pork from free-range pigs both prior and post slaughter. These data support the intensification of the cleaning and disinfection in the pre-slaughter environment (i.e. trucks, lairage), especially when a higher workload is present, as well as the inclusion of new strategies to decrease or eliminate the risk of Salmonella spp. infection or recontamination from the environment in pork from organic or eco-friendly systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Presence and Persistence of Viable, Clinically Relevant Legionella pneumophila Bacteria in Garden Soil in the Netherlands

PubMed Central

van Heijnsbergen, E.; van Deursen, A.; Bouwknegt, M.; Bruin, J. P.; Schalk, J. A. C.

2016-01-01

ABSTRACT Garden soils were investigated as reservoirs and potential sources of pathogenic Legionella bacteria. Legionella bacteria were detected in 22 of 177 garden soil samples (12%) by amoebal coculture. Of these 22 Legionella-positive soil samples, seven contained Legionella pneumophila. Several other species were found, including the pathogenic Legionella longbeachae (4 gardens) and Legionella sainthelensi (9 gardens). The L. pneumophila isolates comprised 15 different sequence types (STs), and eight of these STs were previously isolated from patients according to the European Working Group for Legionella Infections (EWGLI) database. Six gardens that were found to be positive for L. pneumophila were resampled after several months, and in three gardens, L. pneumophila was again isolated. One of these gardens was resampled four times throughout the year and was found to be positive for L. pneumophila on all occasions. IMPORTANCE Tracking the source of infection for sporadic cases of Legionnaires' disease (LD) has proven to be hard. L. pneumophila ST47, the sequence type that is most frequently isolated from LD patients in the Netherlands, is rarely found in potential environmental sources. As L. pneumophila ST47 was previously isolated from a garden soil sample during an outbreak investigation, garden soils were investigated as reservoirs and potential sources of pathogenic Legionella bacteria. The detection of viable, clinically relevant Legionella strains indicates that garden soil is a potential source of Legionella bacteria, and future research should assess the public health implication of the presence of L. pneumophila in garden soil. PMID:27316958

Presence and Persistence of Viable, Clinically Relevant Legionella pneumophila Bacteria in Garden Soil in the Netherlands.

PubMed

van Heijnsbergen, E; van Deursen, A; Bouwknegt, M; Bruin, J P; de Roda Husman, A M; Schalk, J A C

2016-09-01

Garden soils were investigated as reservoirs and potential sources of pathogenic Legionella bacteria. Legionella bacteria were detected in 22 of 177 garden soil samples (12%) by amoebal coculture. Of these 22 Legionella-positive soil samples, seven contained Legionella pneumophila Several other species were found, including the pathogenic Legionella longbeachae (4 gardens) and Legionella sainthelensi (9 gardens). The L. pneumophila isolates comprised 15 different sequence types (STs), and eight of these STs were previously isolated from patients according to the European Working Group for Legionella Infections (EWGLI) database. Six gardens that were found to be positive for L. pneumophila were resampled after several months, and in three gardens, L. pneumophila was again isolated. One of these gardens was resampled four times throughout the year and was found to be positive for L. pneumophila on all occasions. Tracking the source of infection for sporadic cases of Legionnaires' disease (LD) has proven to be hard. L. pneumophila ST47, the sequence type that is most frequently isolated from LD patients in the Netherlands, is rarely found in potential environmental sources. As L. pneumophila ST47 was previously isolated from a garden soil sample during an outbreak investigation, garden soils were investigated as reservoirs and potential sources of pathogenic Legionella bacteria. The detection of viable, clinically relevant Legionella strains indicates that garden soil is a potential source of Legionella bacteria, and future research should assess the public health implication of the presence of L. pneumophila in garden soil. Copyright © 2016 van Heijnsbergen et al.

Detection of enterotoxigenic Clostridium perfringens in meat samples by using molecular methods.

PubMed

Kaneko, Ikuko; Miyamoto, Kazuaki; Mimura, Kanako; Yumine, Natsuko; Utsunomiya, Hirotoshi; Akimoto, Shigeru; McClane, Bruce A

2011-11-01

To prevent food-borne bacterial diseases and to trace bacterial contamination events to foods, microbial source tracking (MST) methods provide important epidemiological information. To apply molecular methods to MST, it is necessary not only to amplify bacterial cells to detection limit levels but also to prepare DNA with reduced inhibitory compounds and contamination. Isolates carrying the Clostridium perfringens enterotoxin gene (cpe) on the chromosome or a plasmid rank among the most important food-borne pathogens. Previous surveys indicated that cpe-positive C. perfringens isolates are present in only ∼5% of nonoutbreak food samples and then only at low numbers, usually less than 3 cells/g. In this study, four molecular assays for the detection of cpe-positive C. perfringens isolates, i.e., ordinary PCR, nested PCR, real-time PCR, and loop-mediated isothermal amplification (LAMP), were developed and evaluated for their reliability using purified DNA. For use in the artificial contamination of meat samples, DNA templates were prepared by three different commercial DNA preparation kits. The four molecular assays always detected cpe when >10³ cells/g of cpe-positive C. perfringens were present, using any kit. Of three tested commercial DNA preparation kits, the InstaGene matrix kit appeared to be most suitable for the testing of a large number of samples. By using the InstaGene matrix kit, the four molecular assays efficiently detected cpe using DNA prepared from enrichment culture specimens of meat samples contaminated with low numbers of cpe-positive C. perfringens vegetative cells or spores. Overall, the current study developed molecular assay protocols for MST to detect the contamination of foods with low numbers of cells, and at a low frequency, of cpe-positive C. perfringens isolates.

Pulsed-Field Gel Electrophoresis characterization of Listeria monocytogenes isolates from cheese manufacturing plants in São Paulo, Brazil.

PubMed

Barancelli, Giovana V; Camargo, Tarsila M; Gagliardi, Natália G; Porto, Ernani; Souza, Roberto A; Campioni, Fabio; Falcão, Juliana P; Hofer, Ernesto; Cruz, Adriano G; Oliveira, Carlos A F

2014-03-03

This study aimed to evaluate the occurrence of Listeria monocytogenes in cheese and in the environment of three small-scale dairy plants (A, B, C) located in the Northern region state of São Paulo, Brazil, and to characterize the isolates using conventional serotyping and PFGE. A total of 393 samples were collected and analyzed from October 2008 to September 2009. From these, 136 came from dairy plant A, where only L. seeligeri was isolated. In dairy plant B, 136 samples were analyzed, and L. innocua, L. seeligeri and L. welshimeri were isolated together with L. monocytogenes. In dairy plant C, 121 samples were analyzed, and L. monocytogenes and L. innocua were isolated. Cheese from dairy plants B and C were contaminated with Listeria spp, with L. innocua being found in Minas frescal cheese from both dairy plants, and L. innocua and L. monocytogenes in Prato cheese from dairy plant C. A total of 85 L. monocytogenes isolates were classified in 3 serotypes: 1/2b, 1/2c, and 4b, with predominance of serotype 4b in both dairy plants. The 85 isolates found in the dairy plants were characterized by genomic macrorestriction using ApaI and AscI with Pulsed Field Gel Electrophoresis (PFGE). Macrorestriction yielded 30 different pulsotypes. The presence of indistinguishable profiles repeatedly isolated during a 12-month period indicated the persistence of L. monocytogenes in dairy plants B and C, which were more than 100 km away from each other. Brine used in dairy plant C contained more than one L. monocytogenes lineage. The routes of contamination were identified in plants B and C, and highlighted the importance of using molecular techniques and serotyping to track L. monocytogenes sources of contamination, distribution, and routes of contamination in dairy plants, and to develop improved control strategies for L. monocytogenes in dairy plants and dairy products. Copyright © 2013 Elsevier B.V. All rights reserved.

Ribotype diversity of Listeria monocytogenes isolates from two salmon processing plants in Norway.

PubMed

Klaeboe, Halvdan; Rosef, Olav; Fortes, Esther; Wiedmann, Martin

2006-10-01

The purpose of this study was to use automated ribotyping procedure to track Listeria monocytogenes transmission in the cold smoked fish production chain and to characterize L. monocytogenes subtypes associated with the salmon processing industry. A total of 104 isolates, which had previously been obtained from a raw fish slaughter and processing plant (plant B) and an adjacent, downstream, salmon smoking operation (plant A), were characterized. These isolates had been obtained through a longitudinal study on Listeria presence, which covered a 31-week period, in both plants. Isolates had been obtained from samples taken from different machinery used throughout the production process. In addition, six isolates obtained from products produced in plant A two years after the initial study were included, so that a total of 110 isolates were characterized. Automated ribotyping was performed using both the restriction enzymes EcoRI and PvuII to increase the discriminatory power. The 110 L. monocytogenes isolates could be divided into 11 EcoRI ribotypes; PvuII ribotype data yielded multiple subtypes within 7 EcoRI ribotypes for a total of 21 subtypes based on both EcoRI and PvuII ribotyping. A total of three EcoRI ribotypes (DUP-1023C, DUP-1045B, and DUP-1053E) were isolated at multiple sampling times from both plants. In addition, one subtype (DUP-1053B) was isolated at multiple sampling times in only plant A, the salmon smoking operation. These data not only support that L. monocytogenes can persist throughout the salmon production system, but also showed that L. monocytogenes may be transmitted between slaughter and smoking operations or may be unique to smoking operations. While the majority of subtypes isolated have been rarely or never linked to human listeriosis cases, some subtypes have previously caused human listeriosis outbreaks and cases. Molecular subtyping thus is critical to identify L. monocytogenes transmission and niches in order to allow design and implementation of control strategies at the appropriate stage of production and in order to reduce the prevalence of L. monocytogenes linked to human disease.

Exosome-like vesicles in uterine aspirates: a comparison of ultracentrifugation-based isolation protocols.

PubMed

Campoy, Irene; Lanau, Lucia; Altadill, Tatiana; Sequeiros, Tamara; Cabrera, Silvia; Cubo-Abert, Montserrat; Pérez-Benavente, Assumpción; Garcia, Angel; Borrós, Salvador; Santamaria, Anna; Ponce, Jordi; Matias-Guiu, Xavier; Reventós, Jaume; Gil-Moreno, Antonio; Rigau, Marina; Colas, Eva

2016-06-18

Uterine aspirates are used in the diagnostic process of endometrial disorders, yet further applications could emerge if its complex milieu was simplified. Exosome-like vesicles isolated from uterine aspirates could become an attractive source of biomarkers, but there is a need to standardize isolation protocols. The objective of the study was to determine whether exosome-like vesicles exist in the fluid fraction of uterine aspirates and to compare protocols for their isolation, characterization, and analysis. We collected uterine aspirates from 39 pre-menopausal women suffering from benign gynecological diseases. The fluid fraction of 27 of those aspirates were pooled and split into equal volumes to evaluate three differential centrifugation-based procedures: (1) a standard protocol, (2) a filtration protocol, and (3) a sucrose cushion protocol. Characterization of isolated vesicles was assessed by electron microscopy, nanoparticle tracking analysis and immunoblot. Specifically for RNA material, we evaluate the effect of sonication and RNase A treatment at different steps of the protocol. We finally confirmed the efficiency of the selected methods in non-pooled samples. All protocols were useful to isolate exosome-like vesicles. However, the Standard procedure was the best performing protocol to isolate exosome-like vesicles from uterine aspirates: nanoparticle tracking analysis revealed a higher concentration of vesicles with a mode of 135 ± 5 nm, and immunoblot showed a higher expression of exosome-related markers (CD9, CD63, and CD81) thus verifying an enrichment in this type of vesicles. RNA contained in exosome-like vesicles was successfully extracted with no sonication treatment and exogenous nucleic acids digestion with RNaseA, allowing the analysis of the specific inner cargo by Real-Time qPCR. We confirmed the existence of exosome-like vesicles in the fluid fraction of uterine aspirates. They were successfully isolated by differential centrifugation giving sufficient proteomic and transcriptomic material for further analyses. The Standard protocol was the best performing procedure since the other two tested protocols did not ameliorate neither yield nor purity of exosome-like vesicles. This study contributes to establishing the basis for future comparative studies to foster the field of biomarker research in gynecology.

Multilocus sequence type profiles of Bacillus cereus isolates from infant formula in China.

PubMed

Yang, Yong; Yu, Xiaofeng; Zhan, Li; Chen, Jiancai; Zhang, Yunyi; Zhang, Junyan; Chen, Honghu; Zhang, Zheng; Zhang, Yanjun; Lu, Yiyu; Mei, Lingling

2017-04-01

Bacillus cereus sensu stricto is an opportunistic foodborne pathogen. The multilocus sequence type (MLST) of 74 B. cereus isolated from 513 non-random infant formula in China was analyzed. Of 64 sequence types (STs) detected, 50 STs and 6 alleles were newly found in PubMLST database. All isolates except for one singleton (ST-1049), were classified into 7 clonal complexes (CC) by BURST (n-4), in which CC1 with core ancestral clone ST-26 was the largest group including 86% isolates, and CC2, 3, 9, 10 and 13 were first reported in China. MLST profiles of the isolates from 8 infant formula brands were compared. It was found the brands might be potentially tracked by the variety of STs, such as ST-1049 of singleton and ST-1062 of isolate from goat milk source, though they could not be easily tracked just by clonal complex types of the isolates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept.

PubMed

Nastasijevic, Ivan; Milanov, Dubravka; Velebit, Branko; Djordjevic, Vesna; Swift, Craig; Painset, Anais; Lakicevic, Brankica

2017-09-18

Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and modified atmosphere packaging (MAP). The precondition for such cross contamination is the previous introduction of Listeria into meat processing facilities and subsequent colonization of the production environment, associated with formation of biofilms resilient to common sanitation procedures regularly applied in meat establishments. The use of Whole Genome Sequencing (WGS) can facilitate the understanding of contamination and colonization routes of pathogens within the food production environment and enable efficient pathogen tracking among different departments. This study aimed to: a) provide a proof of concept on practical use of WGS in a meat establishment to define the entry routes and spread pattern of L. monocytogenes, and b) to consider the regular use of WGS in meat processing establishments as a strong support of food safety management system. The results revealed that Listeria spp. was present in slaughter line, chilling chambers, deboning, slicing, MAP, as well as in corridors and dispatch (53 positive samples, out of 240). Eight L. monocytogenes isolates (out of 53) were identified from the slaughterhouse, chilling chambers, deboning, MAP and dispatch. L. monocytogenes isolates were of three different serotypes (1/2a, 1/2c, 4b) and correspondingly of three MLST sequence types. Overall, two pairs of L. monocytogenes isolates were genetically identical, i.e. two serotype 4b isolates (ST1), isolated from water drain at dispatch unit and two isolates obtained from slaughterhouse (floorwall junction at the carcass wash point) and MAP (water drain). These findings indicated that L. monocytogenes isolates identified in meat processing units (MAP, chilling chamber and dispatch) originated from the slaughter line. Further, all eight L. monocytogenes isolates were confirmed to be biofilm producers on glass and stainless steel surfaces. The identification of the main entry routes of L. monocytogenes into meat establishments and tracking the routes for spread of the pathogen are of essential importance to define appropriate risk mitigation strategies for L. monocytogenes in meat production environment. The routine use of WGS for bacterial characterization, as a strong support of food safety management system in meat establishments, will require the cost-effective approach. It may encompass in-house sequencing when sequencing equipment is used for multiple applications (e.g. WGS of pathogens, starter cultures and spoilage organisms). Copyright © 2017 Elsevier B.V. All rights reserved.

High-purity capture and release of circulating exosomes using an exosome-specific dual-patterned immunofiltration (ExoDIF) device.

PubMed

Kang, Yoon-Tae; Kim, Young Jun; Bu, Jiyoon; Cho, Young-Ho; Han, Sae-Won; Moon, Byung-In

2017-09-21

We present a microfluidic device for the capture and release of circulating exosomes from human blood. The exosome-specific dual-patterned immunofiltration (ExoDIF) device is composed of two distinct immuno-patterned layers, and is capable of enhancing the chance of binding between the antibody and exosomes by generating mechanical whirling, thus achieving high-throughput exosome isolation with high specificity. Moreover, follow-up recovery after the immuno-affinity based isolation, via cleavage of a linker, enables further downstream analysis. We verified the performance of the present device using MCF-7 secreted exosomes and found that both the concentration and proportion of exosome-sized vesicles were higher than in the samples obtained from the conventional exosome isolation kit. We then isolated exosomes from the human blood samples with our device to compare the exosome level between cancer patients and healthy donors. Cancer patients show a significantly higher exosome level with higher selectivity when validating the exosome-sized vesicles using both electron microscopy and nanoparticle tracking analysis. The captured exosomes from cancer patients also express abundant cancer-associated antigens, the epithelial cell adhesion molecule (EpCAM) on their surface. Our simple and rapid exosome recovery technique has huge potential to elucidate the function of exosomes in cancer patients and can thus be applied for various exosome-based cancer research studies.

Tracking sources of Staphylococcus aureus hand contamination in food handlers by spa typing.

PubMed

Ho, Jeffery; Boost, Maureen V; O'Donoghue, Margaret M

2015-07-01

We aimed to identify the source of Staphylococcus aureus contaminating hands of food handlers. Nasal samples and direct fingertip imprints were collected on 2 occasions from food handlers and characterized to determine likely sources of hand contamination. Most hand contamination was attributable to nasal isolates of persistently colonized coworkers who had presumably contaminated the environment. Regular handwashing should be supplemented by effective environmental disinfection. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Evaluation of the measurement uncertainty when measuring the resistance of solid isolating materials to tracking

NASA Astrophysics Data System (ADS)

Stare, E.; Beges, G.; Drnovsek, J.

2006-07-01

This paper presents the results of research into the measurement of the resistance of solid isolating materials to tracking. Two types of tracking were investigated: the proof tracking index (PTI) and the comparative tracking index (CTI). Evaluation of the measurement uncertainty in a case study was performed using a test method in accordance with the IEC 60112 standard. In the scope of the tests performed here, this particular test method was used to ensure the safety of electrical appliances. According to the EN ISO/IEC 17025 standard (EN ISO/IEC 17025), in the process of conformity assessment, the evaluation of the measurement uncertainty of the test method should be carried out. In the present article, possible influential parameters that are in accordance with the third and fourth editions of the standard IEC 60112 are discussed. The differences, ambiguities or lack of guidance referring to both editions of the standard are described in the article 'Ambiguities in technical standards—case study IEC 60112—measuring the resistance of solid isolating materials to tracking' (submitted for publication). Several hundred measurements were taken in the present experiments in order to form the basis for the results and conclusions presented. A specific problem of the test (according to the IEC 60112 standard) is the great variety of influential physical parameters (mechanical, electrical, chemical, etc) that can affect the results. At the end of the present article therefore, there is a histogram containing information on the contributions to the measurement uncertainty.

Whole-Genome Sequencing Reveals Laboratory Salmonella Typhimurium Strain 14028s as a Likely Source of Outbreak Isolates from 2009-2010

USDA-ARS?s Scientific Manuscript database

Background: Next-generation sequencing (NGS) of bacterial isolates has emerged as valuable tool for tracking of an outbreak source. Between 2009 and 2011, clinical isolates of Salmonella Typhimurium sharing the JPXX01.0014 (XbaI) PFGE type were isolated across the U.S. The initial isolates were asso...

Effect of distribution of striated laser hardening tracks on dry sliding wear resistance of biomimetic surface

NASA Astrophysics Data System (ADS)

Su, Wei; Zhou, Ti; Zhang, Peng; Zhou, Hong; Li, Hui

2018-01-01

Some biological surfaces were proved to have excellent anti-wear performance. Being inspired, Nd:YAG pulsed laser was used to create striated biomimetic laser hardening tracks on medium carbon steel samples. Dry sliding wear tests biomimetic samples were performed to investigate specific influence of distribution of laser hardening tracks on sliding wear resistance of biomimetic samples. After comparing wear weight loss of biomimetic samples, quenched sample and untreated sample, it can be suggested that the sample covered with dense laser tracks (3.5 mm spacing) has lower wear weight loss than the one covered with sparse laser tracks (4.5 mm spacing); samples distributed with only dense laser tracks or sparse laser tracks (even distribution) were proved to have better wear resistance than samples distributed with both dense and sparse tracks (uneven distribution). Wear mechanisms indicate that laser track and exposed substrate of biomimetic sample can be regarded as hard zone and soft zone respectively. Inconsecutive striated hard regions, on the one hand, can disperse load into small branches, on the other hand, will hinder sliding abrasives during wear. Soft regions with small range are beneficial in consuming mechanical energy and storing lubricative oxides, however, soft zone with large width (>0.5 mm) will be harmful to abrasion resistance of biomimetic sample because damages and material loss are more obvious on surface of soft phase. As for the reason why samples with even distributed bionic laser tracks have better wear resistance, it can be explained by the fact that even distributed laser hardening tracks can inhibit severe worn of local regions, thus sliding process can be more stable and wear extent can be alleviated as well.

Non-invasive surveillance for Plasmodium in reservoir macaque species.

PubMed

Siregar, Josephine E; Faust, Christina L; Murdiyarso, Lydia S; Rosmanah, Lis; Saepuloh, Uus; Dobson, Andrew P; Iskandriati, Diah

2015-10-12

Primates are important reservoirs for human diseases, but their infection status and disease dynamics are difficult to track in the wild. Within the last decade, a macaque malaria, Plasmodium knowlesi, has caused disease in hundreds of humans in Southeast Asia. In order to track cases and understand zoonotic risk, it is imperative to be able to quantify infection status in reservoir macaque species. In this study, protocols for the collection of non-invasive samples and isolation of malaria parasites from naturally infected macaques are optimized. Paired faecal and blood samples from 60 Macaca fascicularis and four Macaca nemestrina were collected. All animals came from Sumatra or Java and were housed in semi-captive breeding colonies around West Java. DNA was extracted from samples using a modified protocol. Nested polymerase chain reactions (PCR) were run to detect Plasmodium using primers targeting mitochondrial DNA. Sensitivity of screening faecal samples for Plasmodium was compared to other studies using Kruskal Wallis tests and logistic regression models. The best primer set was 96.7 % (95 % confidence intervals (CI): 83.3-99.4 %) sensitive for detecting Plasmodium in faecal samples of naturally infected macaques (n = 30). This is the first study to produce definitive estimates of Plasmodium sensitivity and specificity in faecal samples from naturally infected hosts. The sensitivity was significantly higher than some other studies involving wild primates. Faecal samples can be used for detection of malaria infection in field surveys of macaques, even when there are no parasites visible in thin blood smears. Repeating samples from individuals will improve inferences of the epidemiology of malaria in wild primates.

Comparative analysis of EV isolation procedures for miRNAs detection in serum samples.

PubMed

Andreu, Zoraida; Rivas, Eva; Sanguino-Pascual, Aitana; Lamana, Amalia; Marazuela, Mónica; González-Alvaro, Isidoro; Sánchez-Madrid, Francisco; de la Fuente, Hortensia; Yáñez-Mó, María

2016-01-01

Extracellular vesicles (EVs) are emerging as potent non-invasive biomarkers. However, current methodologies are time consuming and difficult to translate to clinical practice. To analyse EV-encapsulated circulating miRNA, we searched for a quick, easy and economic method to enrich frozen human serum samples for EV. We compared the efficiency of several protocols and commercial kits to isolate EVs. Different methods based on precipitation, columns or filter systems were tested and compared with ultracentrifugation, which is the most classical protocol to isolate EVs. EV samples were assessed for purity and quantity by nanoparticle tracking analysis and western blot or cytometry against major EV protein markers. For biomarker validation, levels of a set of miRNAs were determined in EV fractions and compared with their levels in total serum. EVs isolated with precipitation-based methods were enriched for a subgroup of miRNAs that corresponded to miRNAs described to be encapsulated into EVs (miR-126, miR-30c and miR-143), while the detection of miR-21, miR-16-5p and miR-19a was very low compared with total serum. Our results point to precipitation using polyethylene glycol (PEG) as a suitable method for an easy and cheap enrichment of serum EVs for miRNA analyses. The overall performance of PEG was very similar, or better than other commercial precipitating reagents, in both protein and miRNA yield, but in comparison to them PEG is much cheaper. Other methods presented poorer results, mostly when assessing miRNA by qPCR analyses. Using PEG precipitation in a longitudinal study with human samples, we demonstrated that miRNA could be assessed in frozen samples up to 8 years of storage. We report a method based on a cut-off value of mean of fold EV detection versus serum that provides an estimate of the degree of encapsulation of a given miRNA.

Advantages and challenges in automated apatite fission track counting

NASA Astrophysics Data System (ADS)

Enkelmann, E.; Ehlers, T. A.

2012-04-01

Fission track thermochronometer data are often a core element of modern tectonic and denudation studies. Soon after the development of the fission track methods interest emerged for the developed an automated counting procedure to replace the time consuming labor of counting fission tracks under the microscope. Automated track counting became feasible in recent years with increasing improvements in computer software and hardware. One such example used in this study is the commercial automated fission track counting procedure from Autoscan Systems Pty that has been highlighted through several venues. We conducted experiments that are designed to reliably and consistently test the ability of this fully automated counting system to recognize fission tracks in apatite and a muscovite external detector. Fission tracks were analyzed in samples with a step-wise increase in sample complexity. The first set of experiments used a large (mm-size) slice of Durango apatite cut parallel to the prism plane. Second, samples with 80-200 μm large apatite grains of Fish Canyon Tuff were analyzed. This second sample set is characterized by complexities often found in apatites in different rock types. In addition to the automated counting procedure, the same samples were also analyzed using conventional counting procedures. We found for all samples that the fully automated fission track counting procedure using the Autoscan System yields a larger scatter in the fission track densities measured compared to conventional (manual) track counting. This scatter typically resulted from the false identification of tracks due surface and mineralogical defects, regardless of the image filtering procedure used. Large differences between track densities analyzed with the automated counting persisted between different grains analyzed in one sample as well as between different samples. As a result of these differences a manual correction of the fully automated fission track counts is necessary for each individual surface area and grain counted. This manual correction procedure significantly increases (up to four times) the time required to analyze a sample with the automated counting procedure compared to the conventional approach.

Phylogenetics of a fungal invasion: Origins and widespread dispersal of white-nose syndrome

USGS Publications Warehouse

Drees, Kevin P.; Lorch, Jeffrey M.; Puechmaille, Sebastein J.; Parise, Katy L.; Wibbelt, Gudrun; Hoyt, Joseph R.; Sun, Keping; Jargalsaikhan, Ariunbold; Dalannast, Munkhnast; Palmer, Jonathan M.; Linder, Daniel L.; Kilpatrick, Marm; Pearson, Talima; Keim, Paul S.; Blehert, David; Foster, Jeffrey T.

2017-01-01

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans. Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia.

Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

PubMed Central

Drees, Kevin P.; Lorch, Jeffrey M.; Puechmaille, Sebastien J.; Parise, Katy L.; Wibbelt, Gudrun; Hoyt, Joseph R.; Sun, Keping; Jargalsaikhan, Ariunbold; Dalannast, Munkhnast; Lindner, Daniel L.; Marm Kilpatrick, A.; Pearson, Talima; Blehert, David S.

2017-01-01

ABSTRACT Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans. Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia. PMID:29233897

B-spline based image tracking by detection

NASA Astrophysics Data System (ADS)

Balaji, Bhashyam; Sithiravel, Rajiv; Damini, Anthony; Kirubarajan, Thiagalingam; Rajan, Sreeraman

2016-05-01

Visual image tracking involves the estimation of the motion of any desired targets in a surveillance region using a sequence of images. A standard method of isolating moving targets in image tracking uses background subtraction. The standard background subtraction method is often impacted by irrelevant information in the images, which can lead to poor performance in image-based target tracking. In this paper, a B-Spline based image tracking is implemented. The novel method models the background and foreground using the B-Spline method followed by a tracking-by-detection algorithm. The effectiveness of the proposed algorithm is demonstrated.

Serotypes and Pulsotypes diversity of Listeria monocytogenes in a beef-processing environment.

PubMed

Camargo, Anderson Carlos; Dias, Mariane Rezende; Cossi, Marcus Vinícius Coutinho; Lanna, Frederico Germano Piscitelli Alvarenga; Cavicchioli, Valéria Quintana; Vallim, Deyse Christina; Pinto, Paulo Sérgio de Arruda; Hofer, Ernesto; Nero, Luís Augusto

2015-04-01

Utensils and equipment from meat-processing facilities are considered relevant cross-contamination points of Listeria monocytogenes to foods, demanding tracking studies to identify their specific origins, and predict proper control. The present study aimed to detect L. monocytogenes in a beef-processing facility, investigating the diversity of serotypes and pulsotypes in order to identify the possible contamination routes. Surface samples from knives (n=26), tables (n=78), and employees hands (n=74) were collected before and during the procedures from a beef-processing facility, in addition to surface samples of end cuts: round (n=32), loin (n=30), and chuck (n=32). All samples were subjected to L. monocytogenes screening according ISO 11.290-1, and the obtained isolates were subjected to serotyping and pulsed-field gel electrophoresis. Listeria spp. were identified in all processing steps, in 61 samples, and L. monocytogenes was detected in 17 samples, not being found only in knives. Eighty-five isolates were identified as L. monocytogenes, from serotypes 1/2c (n=65), 4b (n=13), and 1/2b (n=7), being grouped in 19 pulsotypes. Considering these results, cross-contamination among hands, tables, and beef cuts could be identified. The obtained data indicated the relevance of cross-contamination in the beef-processing facility, and the occurrence of serotypes 1/2b and 4b in beef cuts distributed for retail sale is a public health concern.

A Measurement of the t anti-t Cross Section in p anti-p Collisions at s**(1/2) = 1.96-TeV using Dilepton Events with a Lepton plus Track Selection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaltonen, T.; /Helsinki Inst. of Phys.; Adelman, Jahred A.

This paper reports a measurement of the cross section for the pair production of top quarks in p{bar p} collisions at {radical}s = 1.96 TeV at the Fermilab Tevatron. The data was collected from the CDF II detector in a set of runs with a total integrated luminosity of 1.1 fb{sup -1}. The cross section is measured in the dilepton channel, the subset of t{bar t} events in which both top quarks decay through t {yields} Wb {yields} {ell}{nu}b, where {ell} = e, {mu}, or {tau}. The lepton pair is reconstructed as one identified electron or muon and one isolatedmore » track. The use of an isolated track to identify the second lepton increases the t{bar t} acceptance, particularly for the case in which one W decays as W {yields} {tau}{nu}. The purity of the sample may be further improved at the cost of a reduction in the number of signal events, by requiring an identified b-jet. They present the results of measurements performed with and without the request of an identified b-jet. the former is the first published CDF result for which a b-jet requirement is added to the dilepton selection. In the CDF data there are 129 pretag lepton + track candidate events, of which 69 are tagged. With the tagging information, the sample is divided into tagged and untagged sub-samples, and a combined cross section is calculated by maximizing a likelihood. The result is {sigma}{sub t{bar t}} = 9.6 {+-} 1.2(stat.){sub -0.5}{sup +0.6}(sys.) {+-} 0.6(lum.) pb, assuming a branching ratio of BR(W {yields} {ell}{nu}) = 10.8% and a top mass of m{sub t} = 175 GeV/c{sup 2}.« less

49 CFR 213.309 - Restoration or renewal of track under traffic conditions.

Code of Federal Regulations, 2014 CFR

2014-10-01

....g., as in joint bar replacement or rail replacement; (2) Any work that adversely affects the lateral or vertical stability of the track with the exception of spot tamping an isolated condition where not...

49 CFR 213.309 - Restoration or renewal of track under traffic conditions.

Code of Federal Regulations, 2011 CFR

2011-10-01

....g., as in joint bar replacement or rail replacement; (2) Any work that adversely affects the lateral or vertical stability of the track with the exception of spot tamping an isolated condition where not...

49 CFR 213.309 - Restoration or renewal of track under traffic conditions.

Code of Federal Regulations, 2012 CFR

2012-10-01

....g., as in joint bar replacement or rail replacement; (2) Any work that adversely affects the lateral or vertical stability of the track with the exception of spot tamping an isolated condition where not...

49 CFR 213.309 - Restoration or renewal of track under traffic conditions.

Code of Federal Regulations, 2013 CFR

2013-10-01

....g., as in joint bar replacement or rail replacement; (2) Any work that adversely affects the lateral or vertical stability of the track with the exception of spot tamping an isolated condition where not...

Diversity of Listeria Species in Urban and Natural Environments

PubMed Central

Overdevest, Jon; Fortes, Esther; Windham, Katy; Schukken, Ynte; Lembo, Arthur; Wiedmann, Martin

2012-01-01

A total of 442 Listeria isolates, including 234 Listeria seeligeri, 80 L. monocytogenes, 74 L. welshimeri, 50 L. innocua, and 4 L. marthii isolates, were obtained from 1,805 soil, water, and other environmental samples collected over 2 years from four urban areas and four areas representing natural environments. Listeria spp. showed similar prevalences in samples from natural (23.4%) and urban (22.3%) environments. While L. seeligeri and L. welshimeri were significantly associated with natural environments (P ≤ 0.0001), L. innocua and L. monocytogenes were significantly associated with urban environments (P ≤ 0.0001). Sequencing of sigB for all isolates revealed 67 allelic types with a higher level of allelic diversity among isolates from urban environments. Some Listeria spp. and sigB allelic types showed significant associations with specific urban and natural areas. Nearest-neighbor analyses also showed that certain Listeria spp. and sigB allelic types were spatially clustered within both natural and urban environments, and there was evidence that these species and allelic types persisted over time in specific areas. Our data show that members of the genus Listeria not only are common in urban and natural environments but also show species- and subtype-specific associations with different environments and areas. This indicates that Listeria species and subtypes within these species may show distinct ecological preferences, which suggests (i) that molecular source-tracking approaches can be developed for Listeria and (ii) that detection of some Listeria species may not be a good indicator for L. monocytogenes. PMID:22504820

Human T-lymphotropic virus-1/2 detected in drug abused men who have sex with men in Surakarta Indonesia

NASA Astrophysics Data System (ADS)

Prasetyo, Afiono Agung; Sari, Yulia

2017-02-01

Human T-cell lymphotropic virus types 1 and 2 (HTLV-1/2) are retroviruses that probably among the most neglected blood-borne pathogens. The molecular epidemiology data of HTLV-1/2 in Indonesia is very rare. This study evaluated the prevalence of HTLV-1 and 2 in men who have sex with men with drug abused history in Surakarta Indonesia, to track the presentation of HTLV-1/2 in Indonesia. All blood samples collected from men who have sex with men with drug abused history in Surakarta in 2009-2013 were tested using enzyme linked immunosorbent assays and confirmed by RT-PCR nested addressed the part of HTLV-1 LTR and HTLV-2 LTR region, respectively. The specificity of the molecular assays was confirmed by sequencing the amplicons. The anti HTLV-1/2 positive rate was 4.8% (6/126). All positive serological samples were confirmed by nested RT-PCR. Of these, two was HTLV-1 positive and four was HTLV-2 positive. Molecular analysis of positive PCR products revealed that all HTLV-1 isolate had close relationship with HTLV-1 isolated in Japan while all HTLV-2 isolate with that of isolated in USA. HTLV-1 and HTLV-2 were detected in men who have sex with men with drug abused history in Surakarta indicated that these viruses were circulated in Indonesia, especially in the high risk communities

EPA's Review of DOE's Inventory Tracking for TRU Wastes at Waste Control Specialists

EPA Pesticide Factsheets

On April 9, 2014, EPA's Waste Isolation Pilot Plant (WIPP) waste characterization team visited Waste Control Specialists (WCS) to determine whether DOE was meeting EPA's waste inventory tracking requirements at 40 CFR 194.24(c)(4).

MICROBIAL SOURCE TRACKING: DIFFERENT USES AND APPROACHES

EPA Science Inventory

Microbial Source Tracking (MST) methods are used to determine the origin of fecal pollution impacting natural water systems. Several methods require the isolation of pure cultures in order to develop phenotypic or genotypic fingerprint libraries of both source and water bacterial...

Comparison of seven protocols to identify fecal contamination sources using Escherichia coli

USGS Publications Warehouse

Stoeckel, D.M.; Mathes, M.V.; Hyer, K.E.; Hagedorn, C.; Kator, H.; Lukasik, J.; O'Brien, T. L.; Fenger, T.W.; Samadpour, M.; Strickler, K.M.; Wiggins, B.A.

2004-01-01

Microbial source tracking (MST) uses various approaches to classify fecal-indicator microorganisms to source hosts. Reproducibility, accuracy, and robustness of seven phenotypic and genotypic MST protocols were evaluated by use of Escherichia coli from an eight-host library of known-source isolates and a separate, blinded challenge library. In reproducibility tests, measuring each protocol's ability to reclassify blinded replicates, only one (pulsed-field gel electrophoresis; PFGE) correctly classified all test replicates to host species; three protocols classified 48-62% correctly, and the remaining three classified fewer than 25% correctly. In accuracy tests, measuring each protocol's ability to correctly classify new isolates, ribotyping with EcoRI and PvuII approached 100% correct classification but only 6% of isolates were classified; four of the other six protocols (antibiotic resistance analysis, PFGE, and two repetitive-element PCR protocols) achieved better than random accuracy rates when 30-100% of challenge isolates were classified. In robustness tests, measuring each protocol's ability to recognize isolates from nonlibrary hosts, three protocols correctly classified 33-100% of isolates as "unknown origin," whereas four protocols classified all isolates to a source category. A relevance test, summarizing interpretations for a hypothetical water sample containing 30 challenge isolates, indicated that false-positive classifications would hinder interpretations for most protocols. Study results indicate that more representation in known-source libraries and better classification accuracy would be needed before field application. Thorough reliability assessment of classification results is crucial before and during application of MST protocols.

Two-axis tracking solar collector mechanism

DOEpatents

Johnson, Kenneth C.

1992-01-01

This invention is a novel solar tracking mechanism incorporating a number of practical features that give it superior environmental resilience and exceptional tracking accuracy. The mechanism comprises a lightweight space-frame assembly supporting an array of point-focus Fresnel lenses in a two-axis tracking structure. The system is enclosed under a glass cover which isolates it from environmental exposure and enhances tracking accuracy by eliminating wind loading. Tracking accuracy is also enhanced by the system's broad-based tracking support. The system's primary intended application would be to focus highly concentrated sunlight into optical fibers for transmission to core building illumination zones, and the system may also have potential for photovoltaic or photothermal solar energy conversion.

Two-axis tracking solar collector mechanism

DOEpatents

Johnson, Kenneth C.

1990-01-01

This invention is a novel solar tracking mechanism incorporating a number of practical features that give it superior environmental resilience and exceptional tracking accuracy. The mechanism comprises a lightweight space-frame assembly supporting an array of point-focus Fresnel lenses in a two-axis tracking structure. The system is enclosed under a glass cover which isolates it from environmental exposure and enhances tracking accuracy by eliminating wind loading. Tracking accuracy is also enhanced by the system's broad-based tracking support. The system's primary intended application would be to focus highly concentrated sunlight into optical fibers for transmission to core building illumination zones, and the system may also have potential for photovoltaic or photothermal solar energy conversion.

Two-axis tracking solar collector mechanism

DOEpatents

Johnson, K.C.

1992-12-08

This invention is a novel solar tracking mechanism incorporating a number of practical features that give it superior environmental resilience and exceptional tracking accuracy. The mechanism comprises a lightweight space-frame assembly supporting an array of point-focus Fresnel lenses in a two-axis tracking structure. The system is enclosed under a glass cover which isolates it from environmental exposure and enhances tracking accuracy by eliminating wind loading. Tracking accuracy is also enhanced by the system's broad-based tracking support. The system's primary intended application would be to focus highly concentrated sunlight into optical fibers for transmission to core building illumination zones, and the system may also have potential for photovoltaic or photothermal solar energy conversion. 16 figs.

Prevalence and Antimicrobial Resistance of Enterococci Isolated from Retail Meats in the United States, 2002 to 2014.

PubMed

Tyson, Gregory H; Nyirabahizi, Epiphanie; Crarey, Emily; Kabera, Claudine; Lam, Claudia; Rice-Trujillo, Crystal; McDermott, Patrick F; Tate, Heather

2018-01-01

Bacteria of the genus Enterococcus are important human pathogens that are frequently resistant to a number of clinically important antibiotics. They are also used as markers of animal fecal contamination of human foods and are employed as sentinel organisms for tracking trends in resistance to antimicrobials with Gram-positive activity. As part of the National Antimicrobial Resistance Monitoring System (NARMS), we evaluated several retail meat commodities for the presence of enterococci from 2002 to 2014, and we found 92.0% to be contaminated. The majority of isolates were either Enterococcus faecalis (64.0%) or Enterococcus faecium (28.6%), and the antimicrobial resistance of each isolate was assessed by broth microdilution. The resistance prevalences for several drugs, including erythromycin and gentamicin, were significantly higher among poultry isolates, compared to retail beef or pork isolates. None of the isolates was resistant to the clinically important human drug vancomycin, only 1 isolate was resistant to linezolid, and resistance to tigecycline was below 1%. In contrast, a majority of both E. faecalis (67.5%) and E. faecium (53.7%) isolates were resistant to tetracycline. Overall, the robust NARMS testing system employed consistent sampling practices and methods throughout the testing period, with the only significant trend in resistance prevalence being decreased E. faecium resistance to penicillin. These data provide excellent baseline levels of resistance that can be used to measure future changes in resistance prevalence that may result from alterations in the use of antimicrobials in food animal production. IMPORTANCE Enterococci, including E. faecalis and E. faecium , are present in the guts of food-producing animals and are used as a measure of fecal contamination of meat. We used the large consistent sampling methods of NARMS to assess the prevalence of Enterococcus strains isolated from retail meats, and we found over 90% of meats to be contaminated with enterococci. We also assessed the resistance of the Enterococcus strains, commonly used as a measure of resistance to agents with Gram-positive activity, in foods. Resistance prevalence was over 25% for some antimicrobials and sample sources but was less than 1% for several of the most important therapeutic agents used in human medicine. This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

Persistence of F-Specific RNA Coliphages in Surface Waters from a Produce Production Region along the Central Coast of California.

PubMed

Ravva, Subbarao V; Sarreal, Chester Z

2016-01-01

F+ RNA coliphages (FRNA) are used to source-track fecal contamination and as surrogates for enteric pathogen persistence in the environment. However, the environmental persistence of FRNA is not clearly understood and necessitates the evaluation of the survival of prototype and environmental isolates of FRNA representing all four genogroups in surface waters from the central coast of California. Water temperature played a significant role in persistence-all prototype and environmental strains survived significantly longer at 10 °C compared to 25 °C. Similarly, the availability of host bacterium was found to be critical in FRNA survival. In the absence of E. coli F(amp), all prototypes of FRNA disappeared rapidly with a D-value (days for one log reduction) of <1.2 d from water samples incubated at 25 °C; the longest surviving prototype was SP. However, in the presence of the host, the order of persistence at 25 °C was QB>MS2>SP>GA and at 10 °C it was QB = MS2>GA>SP. Significant differences in survival were observed between prototypes and environmental isolates of FRNA. While most environmental isolates disappeared rapidly at 25 °C and in the absence of the host, members of genogroups GIII and GI persisted longer with the host compared to members of GII and GIV. Consequentially, FRNA based source tracking methods can be used to detect phages from recent fecal contamination along with those that persist longer in the environment as a result of cooler temperatures and increased host presence.

Persistence of F-Specific RNA Coliphages in Surface Waters from a Produce Production Region along the Central Coast of California

PubMed Central

Ravva, Subbarao V.; Sarreal, Chester Z.

2016-01-01

F+ RNA coliphages (FRNA) are used to source-track fecal contamination and as surrogates for enteric pathogen persistence in the environment. However, the environmental persistence of FRNA is not clearly understood and necessitates the evaluation of the survival of prototype and environmental isolates of FRNA representing all four genogroups in surface waters from the central coast of California. Water temperature played a significant role in persistence–all prototype and environmental strains survived significantly longer at 10°C compared to 25°C. Similarly, the availability of host bacterium was found to be critical in FRNA survival. In the absence of E. coli Famp, all prototypes of FRNA disappeared rapidly with a D-value (days for one log reduction) of <1.2 d from water samples incubated at 25°C; the longest surviving prototype was SP. However, in the presence of the host, the order of persistence at 25°C was QB>MS2>SP>GA and at 10°C it was QB = MS2>GA>SP. Significant differences in survival were observed between prototypes and environmental isolates of FRNA. While most environmental isolates disappeared rapidly at 25°C and in the absence of the host, members of genogroups GIII and GI persisted longer with the host compared to members of GII and GIV. Consequentially, FRNA based source tracking methods can be used to detect phages from recent fecal contamination along with those that persist longer in the environment as a result of cooler temperatures and increased host presence. PMID:26784030

Reports on work in support of NASA's tracking and communication division

NASA Technical Reports Server (NTRS)

Feagin, Terry; Lekkos, Anthony

1991-01-01

This is a report on the research conducted during the period October 1, 1991 through December 31, 1991. The research is divided into two primary areas: (1) generalization of the Fault Isolation using Bit Strings (FIBS) technique to permit fuzzy information to be used to isolate faults in the tracking and communications system of the Space Station; and (2) a study of the activity that should occur in the on board systems in order to attempt to recover from failures that are external to the Space Station.

Gulls identified as major source of fecal pollution in coastal waters: a microbial source tracking study.

PubMed

Araújo, Susana; Henriques, Isabel S; Leandro, Sérgio Miguel; Alves, Artur; Pereira, Anabela; Correia, António

2014-02-01

Gulls were reported as sources of fecal pollution in coastal environments and potential vectors of human infections. Microbial source tracking (MST) methods were rarely tested to identify this pollution origin. This study was conducted to ascertain the source of water fecal contamination in the Berlenga Island, Portugal. A total of 169 Escherichia coli isolates from human sewage, 423 isolates from gull feces and 334 water isolates were analyzed by BOX-PCR. An average correct classification of 79.3% was achieved. When an 85% similarity cutoff was applied 24% of water isolates were present in gull feces against 2.7% detected in sewage. Jackknifing resulted in 29.3% of water isolates classified as gull, and 10.8% classified as human. Results indicate that gulls constitute a major source of water contamination in the Berlenga Island. This study validated a methodology to differentiate human and gull fecal pollution sources in a real case of a contaminated beach. © 2013.

A microfluidic chip integrated with a high-density PDMS-based microfiltration membrane for rapid isolation and detection of circulating tumor cells.

PubMed

Fan, Xiaoyun; Jia, Chunping; Yang, Jun; Li, Gang; Mao, Hongju; Jin, Qinghui; Zhao, Jianlong

2015-09-15

Isolation of circulating tumor cells (CTCs) by size exclusion is a widely researched technique that offers the advantage of capturing tumor cells without reliance on cell surface expression markers. In this work, we report the development of a novel polydimethylsiloxane (PDMS) membrane filter-based microdevice for rapid and highly efficient isolation of CTCs from peripheral blood. A precise and highly porous PDMS microfilter was fabricated and integrated into the microfiltration chip by combining a sacrificial transferring film with a sandwich molding method. We achieved >90% recovery when isolating lung cancer cells from spiked blood samples, with a relatively high processing throughput of 10 mL/h. In contrast to existing CTC filtration systems, which rely on low-porosity track-etch filters or expensive lithography-based filters, our microfiltration chip does not require complex e-beam lithography or the reactive ion etching process, therefore it offers a low-cost alternative tool for highly efficient CTC enrichment and in situ analysis. Thus, this new microdevice has the potential for use in routine monitoring of cancer development and cancer therapy in a clinical setting. Copyright © 2015 Elsevier B.V. All rights reserved.

Sampling Analysis of Aerosol Retrievals by Single-track Spaceborne Instrument for Climate Research

NASA Astrophysics Data System (ADS)

Geogdzhayev, I. V.; Cairns, B.; Alexandrov, M. D.; Mishchenko, M. I.

2012-12-01

We examine to what extent the reduced sampling of along-track instruments such as Cloud-Aerosol LIdar with Orthogonal Polarisation (CALIOP) and Aerosol Polarimetry Sensor (APS) affects the statistical accuracy of a satellite climatology of retrieved aerosol optical thickness (AOT) by sub-sampling the retrievals from a wide-swath imaging instrument (MODerate resolution Imaging Spectroradiometer (MODIS)). Owing to its global coverage, longevity, and extensive characterization versus ground based data, the MODIS level-2 aerosol product is an instructive testbed for assessing sampling effects on climatic means derived from along-track instrument data. The advantage of using daily pixel-level aerosol retrievals from MODIS is that limitations caused by the presence of clouds are implicit in the sample, so that their seasonal and regional variations are captured coherently. However, imager data can exhibit cross-track variability of monthly global mean AOTs caused by a scattering-angle dependence. We found that single along-track values can deviate from the imager mean by 15% over land and by more than 20% over ocean. This makes it difficult to separate natural variability from viewing-geometry artifacts complicating direct comparisons of an along-track sub-sample with the full imager data. To work around this problem, we introduce "flipped-track" sampling which, by design, is statistically equivalent to along-track sampling and while closely approximating the imager in terms of angular artifacts. We show that the flipped-track variability of global monthly mean AOT is much smaller than the cross-track one for the 7-year period considered. Over the ocean flipped-track standard error is 85% less than the cross-track one (absolute values 0.0012 versus 0.0079), and over land it is about one third of the cross-track value (0.0054 versus 0.0188) on average. This allows us to attribute the difference between the two errors to the viewing-geometry artifacts and obtain an upper limit on AOT errors caused by along-track sampling. Our results show that using along-track subsets of MODIS aerosol data directly to analyze the sampling adequacy of single-track instruments can lead to false conclusions owing to the apparent enhancement of natural aerosol variability by the track-to-track artifacts. The analysis based on the statistics of the flipped-track means yields better estimates because it allows for better separation of the viewing-geometry artifacts and true natural variability. Published assessments estimate that a global AOT change of 0.01 would yield a climatically important flux change of 0.25 W/m2. Since the standard error estimates that we have obtained are comfortably below 0.01, we conclude that along-track instruments flown on a sun-synchronous orbiting platform have sufficient spatial sampling for estimating aerosol effects on climate. Since AOT is believed to be the most variable characteristic of tropospheric aerosols, our results imply that pixel-wide along-track coverage also provides adequate statistical representation of the global distribution of aerosol microphysical parameters.

Human bony labyrinth is an indicator of population history and dispersal from Africa

PubMed Central

Ponce de León, Marcia S.; Koesbardiati, Toetik; Weissmann, John David; Milella, Marco; Reyna-Blanco, Carlos S.; Suwa, Gen; Kondo, Osamu; Malaspinas, Anna-Sapfo; White, Tim D.; Zollikofer, Christoph P. E.

2018-01-01

The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations. Phenetic skeletal data, such as cranial and pelvic morphologies, also exhibit a dispersal-from-Africa signal, which, however, tends to be blurred by the effects of local adaptation and in vivo phenotypic plasticity, and that is often deteriorated by postmortem damage to skeletal remains. These complexities raise the question of which skeletal structures most effectively track neutral population history. The cavity system of the inner ear (the so-called bony labyrinth) is a good candidate structure for such analyses. It is already fully formed by birth, which minimizes postnatal phenotypic plasticity, and it is generally well preserved in archaeological samples. Here we use morphometric data of the bony labyrinth to show that it is a surprisingly good marker of the global dispersal of modern humans from Africa. Labyrinthine morphology tracks genetic distances and geography in accordance with an isolation-by-distance model with dispersal from Africa. Our data further indicate that the neutral-like pattern of variation is compatible with stabilizing selection on labyrinth morphology. Given the increasingly important role of the petrous bone for ancient DNA recovery from archaeological specimens, we encourage researchers to acquire 3D morphological data of the inner ear structures before any invasive sampling. Such data will constitute an important archive of phenotypic variation in present and past populations, and will permit individual-based genotype–phenotype comparisons. PMID:29610337

A rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for single-plasmid tracking in an outbreak of carbapenem-resistant Enterobacteriaceae.

PubMed

Lau, Anna F; Wang, Honghui; Weingarten, Rebecca A; Drake, Steven K; Suffredini, Anthony F; Garfield, Mark K; Chen, Yong; Gucek, Marjan; Youn, Jung-Ho; Stock, Frida; Tso, Hanna; DeLeo, Jim; Cimino, James J; Frank, Karen M; Dekker, John P

2014-08-01

Carbapenem-resistant Enterobacteriaceae (CRE) have spread globally and represent a serious and growing threat to public health. Rapid methods for tracking plasmids carrying carbapenemase genes could greatly benefit infection control efforts. Here, we demonstrate that real-time, direct tracking of a single plasmid in a bacterial strain responsible for an outbreak is possible using a commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system. In this case, we retrospectively tracked the bla(KPC) carbapenemase gene-bearing pKpQIL plasmid responsible for a CRE outbreak that occurred at the NIH Clinical Center in 2011. An ∼ 11,109-Da MS peak corresponding to a gene product of the bla(KPC) pKpQIL plasmid was identified and characterized using a combination of proteomics and molecular techniques. This plasmid peak was present in spectra from retrospectively analyzed K. pneumoniae outbreak isolates, concordant with results from whole-genome sequencing, and absent from a diverse control set of bla(KPC)-negative clinical Enterobacteriaceae isolates. Notably, the gene characterized here is located adjacent to the bla(KPC) Tn4401 transposon on the pKpQIL plasmid. Sequence analysis demonstrates the presence of this gene in other bla(KPC) Tn4401-containing plasmids and suggests that this signature MS peak may be useful in tracking other plasmids conferring carbapenem resistance. Plasmid identification using this MALDI-TOF MS method was accomplished in as little as 10 min from isolated colonies and 30 min from positive (spiked) blood cultures, demonstrating the potential clinical utility for real-time plasmid tracking in an outbreak. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

A Rapid Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Method for Single-Plasmid Tracking in an Outbreak of Carbapenem-Resistant Enterobacteriaceae

PubMed Central

Lau, Anna F.; Wang, Honghui; Weingarten, Rebecca A.; Drake, Steven K.; Suffredini, Anthony F.; Garfield, Mark K.; Chen, Yong; Gucek, Marjan; Youn, Jung-Ho; Stock, Frida; Tso, Hanna; DeLeo, Jim; Cimino, James J.; Frank, Karen M.

2014-01-01

Carbapenem-resistant Enterobacteriaceae (CRE) have spread globally and represent a serious and growing threat to public health. Rapid methods for tracking plasmids carrying carbapenemase genes could greatly benefit infection control efforts. Here, we demonstrate that real-time, direct tracking of a single plasmid in a bacterial strain responsible for an outbreak is possible using a commercial matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system. In this case, we retrospectively tracked the blaKPC carbapenemase gene-bearing pKpQIL plasmid responsible for a CRE outbreak that occurred at the NIH Clinical Center in 2011. An ∼11,109-Da MS peak corresponding to a gene product of the blaKPC pKpQIL plasmid was identified and characterized using a combination of proteomics and molecular techniques. This plasmid peak was present in spectra from retrospectively analyzed K. pneumoniae outbreak isolates, concordant with results from whole-genome sequencing, and absent from a diverse control set of blaKPC-negative clinical Enterobacteriaceae isolates. Notably, the gene characterized here is located adjacent to the blaKPC Tn4401 transposon on the pKpQIL plasmid. Sequence analysis demonstrates the presence of this gene in other blaKPC Tn4401-containing plasmids and suggests that this signature MS peak may be useful in tracking other plasmids conferring carbapenem resistance. Plasmid identification using this MALDI-TOF MS method was accomplished in as little as 10 min from isolated colonies and 30 min from positive (spiked) blood cultures, demonstrating the potential clinical utility for real-time plasmid tracking in an outbreak. PMID:24850353

Tracking Listeria monocytogenes contamination and virulence-associated characteristics in the ready-to-eat meat-based food products industry according to the hygiene level.

PubMed

Henriques, A R; Gama, L T; Fraqueza, M J

2017-02-02

Listeria monocytogenes isolates collected from final products and food contact surfaces of 10 ready-to-eat meat-based food products (RTEMP) producing industries were analyzed to relate their virulence-associated characteristics and genetic profiles with the hygiene assessment of those industries. Together with sample collection, an audit was performed to evaluate the implemented food safety management system and to investigate the specific audit requisites more associated to the occurrence of those L. monocytogenes serogroups frequently related with human disease. L. monocytogenes was present in 18% of the samples. The isolates (n=62) were serogrouped and detection of virulence-associated genes inlA, inlB, inlC and inlJ, and also plcA, hlyA, actA and iap was done by multiplex PCR. After this initial characterization, selected isolates (n=31) were submitted to antibiotic resistance testing by the disk diffusion method for the currently most used human and veterinary antibiotics and resistance was low. These isolates were also subtyped by pulsed-field gel electrophoresis. Genotyping and serogrouping of L. monocytogenes isolates revealed a genetically diverse population. Our data indicate that contamination of final products does not seem to be uniquely related to the sampled food surfaces. The occurrence of those L. monocytogenes serogroups more commonly associated with human disease in industries with a high hygienic audit classification could be the result of a previous identification of the pathogen, with an enforcement of the hygiene program without recognizing the real source of contamination. This reinforces the importance of a conjoined diagnosis using audit data and microbiological testing. Food safety management systems of those industries need improvement, particularly in cleaning and sanitizing operations, analytical control, preventive maintenance, personal hygiene and root cause analysis. Copyright © 2016. Published by Elsevier B.V.

Application of Template Matching for Improving Classification of Urban Railroad Point Clouds

PubMed Central

Arastounia, Mostafa; Oude Elberink, Sander

2016-01-01

This study develops an integrated data-driven and model-driven approach (template matching) that clusters the urban railroad point clouds into three classes of rail track, contact cable, and catenary cable. The employed dataset covers 630 m of the Dutch urban railroad corridors in which there are four rail tracks, two contact cables, and two catenary cables. The dataset includes only geometrical information (three dimensional (3D) coordinates of the points) with no intensity data and no RGB data. The obtained results indicate that all objects of interest are successfully classified at the object level with no false positives and no false negatives. The results also show that an average 97.3% precision and an average 97.7% accuracy at the point cloud level are achieved. The high precision and high accuracy of the rail track classification (both greater than 96%) at the point cloud level stems from the great impact of the employed template matching method on excluding the false positives. The cables also achieve quite high average precision (96.8%) and accuracy (98.4%) due to their high sampling and isolated position in the railroad corridor. PMID:27973452

Bacteriophages infecting Bacteroides as a marker for microbial source tracking.

PubMed

Jofre, Joan; Blanch, Anicet R; Lucena, Francisco; Muniesa, Maite

2014-05-15

Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Multi-Scale Modeling of the Gamma Radiolysis of Nitrate Solutions.

PubMed

Horne, Gregory P; Donoclift, Thomas A; Sims, Howard E; Orr, Robin M; Pimblott, Simon M

2016-11-17

A multiscale modeling approach has been developed for the extended time scale long-term radiolysis of aqueous systems. The approach uses a combination of stochastic track structure and track chemistry as well as deterministic homogeneous chemistry techniques and involves four key stages: radiation track structure simulation, the subsequent physicochemical processes, nonhomogeneous diffusion-reaction kinetic evolution, and homogeneous bulk chemistry modeling. The first three components model the physical and chemical evolution of an isolated radiation chemical track and provide radiolysis yields, within the extremely low dose isolated track paradigm, as the input parameters for a bulk deterministic chemistry model. This approach to radiation chemical modeling has been tested by comparison with the experimentally observed yield of nitrite from the gamma radiolysis of sodium nitrate solutions. This is a complex radiation chemical system which is strongly dependent on secondary reaction processes. The concentration of nitrite is not just dependent upon the evolution of radiation track chemistry and the scavenging of the hydrated electron and its precursors but also on the subsequent reactions of the products of these scavenging reactions with other water radiolysis products. Without the inclusion of intratrack chemistry, the deterministic component of the multiscale model is unable to correctly predict experimental data, highlighting the importance of intratrack radiation chemistry in the chemical evolution of the irradiated system.

State Recognition of High Voltage Isolation Switch Based on Background Difference and Iterative Search

NASA Astrophysics Data System (ADS)

Xu, Jiayuan; Yu, Chengtao; Bo, Bin; Xue, Yu; Xu, Changfu; Chaminda, P. R. Dushantha; Hu, Chengbo; Peng, Kai

2018-03-01

The automatic recognition of the high voltage isolation switch by remote video monitoring is an effective means to ensure the safety of the personnel and the equipment. The existing methods mainly include two ways: improving monitoring accuracy and adopting target detection technology through equipment transformation. Such a method is often applied to specific scenarios, with limited application scope and high cost. To solve this problem, a high voltage isolation switch state recognition method based on background difference and iterative search is proposed in this paper. The initial position of the switch is detected in real time through the background difference method. When the switch starts to open and close, the target tracking algorithm is used to track the motion trajectory of the switch. The opening and closing state of the switch is determined according to the angle variation of the switch tracking point and the center line. The effectiveness of the method is verified by experiments on different switched video frames of switching states. Compared with the traditional methods, this method is more robust and effective.

Genetic analysis of hepatitis A virus variants circulating among children presenting with acute diarrhea in Cameroon.

PubMed

Forbi, Joseph C; Agwale, Simon M; Ndip, Lucy M; Esona, Mathew D

2012-05-01

Molecular investigation was undertaken of circulating hepatitis A virus (HAV) associated with cases of acute diarrhea among children under 5 years of age in Kumba-Cameroon. Reverse transcription PCR, sequencing, and phylogenetic analysis of a 371 bp segment of the VP1/P2A junction of six isolates obtained from stool samples showed the exclusive emergence of genetically related HAV subgenotype IA. All the isolates clustered within a unique lineage exhibiting a 99.5% nucleotide identity suggesting infection from a common source. The Cameroonian HAV isolates did not intermix or cluster with those from other regions of Africa and the rest of the world. Tajima's neutralization tests using the six sequences suggested HAV/IA population expansion (D = -1.37; P = 0.016). This is the first description of indigenous HAV genotypes circulating in Cameroon revealing a community-wide spread and predominance of HAV/1A infection in the Kumba area. These findings stress the need for routine molecular tracking of HAV infection as a contributory cause of acute diarrhea in Cameroonian children. Copyright © 2012 Wiley Periodicals, Inc.

Tracking Foodborne Pathogenic Bacteria in Raw and Ready-to-Eat Food Illegally Sold at the Eastern EU Border.

PubMed

Ciolacu, Luminita; Stessl, Beatrix; Bolocan, Andrei Sorin; Oniciuc, Elena Alexandra; Wagner, Martin; Rychli, Kathrin; Nicolau, Anca Ioana

2016-03-01

Food illegally brought into the European Union, mainly in the personal luggage of travelers, represents a potential threat to consumers' health. The aim of this study was to investigate the presence of five pathogens in food brought into the European Union by Moldavian citizens as personal goods and illegally sold in Romania in the vicinity of the border. The occurrence of Staphylococcus aureus and Listeria monocytogenes was 7.5% and 8%, while Campylobacter spp., Escherichia coli O157:H7, and Salmonella spp. were absent in all samples. L. monocytogenes sequence type 2, 9, 121, and 155, highly prevalent among foodstuffs worldwide, was also present among isolates from ready-to-eat food illegally sold in Romania, even at the same date of sampling, indicating cross-contamination during food handling. S. aureus spa types t449, t304, and t524 were most often isolated from raw-milk cheeses contaminated with 10(3)-10(5) colony-forming units per gram, evidencing a contamination at herd level or unhygienic conditions during processing. S. aureus t011 and t3625, both included in the livestock-associated CC398, were isolated from pork lard and poultry meat. This study shows that cross-border trade from nonmember states represents a neglected route of transmission of foodborne pathogens into the European Union that could lead to sporadic or family-associated cases of disease.

A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination.

PubMed

Ankarklev, Johan; Lebbad, Marianne; Einarsson, Elin; Franzén, Oscar; Ahola, Harri; Troell, Karin; Svärd, Staffan G

2018-06-01

Molecular epidemiology and genotyping studies of the parasitic protozoan Giardia intestinalis have proven difficult due to multiple factors, such as low discriminatory power in the commonly used genotyping loci, which has hampered molecular analyses of outbreak sources, zoonotic transmission and virulence types. Here we have focused on assemblage A Giardia and developed a high-resolution assemblage-specific multilocus sequence typing (MLST) method. Analyses of sequenced G. intestinalis assemblage A genomes from different sub-assemblages identified a set of six genetic loci with high genetic variability. DNA samples from both humans (n = 44) and animals (n = 18) that harbored Giardia assemblage A infections, were PCR amplified (557-700 bp products) and sequenced at the six novel genetic loci. Bioinformatic analyses showed five to ten-fold higher levels of polymorphic sites than what was previously found among assemblage A samples using the classic genotyping loci. Phylogenetically, a division of two major clusters in assemblage A became apparent, separating samples of human and animal origin. A subset of human samples (n = 9) from a documented Giardia outbreak in a Swedish day-care center, showed full complementarity at nine genetic loci (the six new and the standard BG, TPI and GDH loci), strongly suggesting one source of infection. Furthermore, three samples of human origin displayed MLST profiles that were phylogenetically more closely related to MLST profiles from animal derived samples, suggesting zoonotic transmission. These new genotyping loci enabled us to detect events of recombination between different assemblage A isolates but also between assemblage A and E isolates. In summary, we present a novel and expanded MLST strategy with significantly improved sensitivity for molecular analyses of virulence types, zoonotic potential and source tracking for assemblage A Giardia. Copyright © 2018. Published by Elsevier B.V.

Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants

PubMed Central

Zhi, Shuai; Banting, Graham; Li, Qiaozhi; Edge, Thomas A.; Topp, Edward; Sokurenko, Mykola; Scott, Candis; Braithwaite, Shannon; Ruecker, Norma J.; Yasui, Yutaka; McAllister, Tim; Chui, Linda

2016-01-01

ABSTRACT Escherichia coli has been proposed to have two habitats—the intestines of mammals/birds and the nonhost environment. Our goal was to assess whether certain strains of E. coli have evolved toward adaptation and survival in wastewater. Raw sewage samples from different treatment plants were subjected to chlorine stress, and ∼59% of the surviving E. coli strains were found to contain a genetic insertion element (IS30) located within the uspC-flhDC intergenic region. The positional location of the IS30 element was not observed across a library of 845 E. coli isolates collected from various animal hosts or within GenBank or whole-genome reference databases for human and animal E. coli isolates (n = 1,177). Phylogenetics clustered the IS30 element-containing wastewater E. coli isolates into a distinct clade, and biomarker analysis revealed that these wastewater isolates contained a single nucleotide polymorphism (SNP) biomarker pattern that was specific for wastewater. These isolates belonged to phylogroup A, possessed generalized stress response (RpoS) activity, and carried the locus of heat resistance, features likely relevant to nonhost environmental survival. Isolates were screened for 28 virulence genes but carried only the fimH marker. Our data suggest that wastewater contains a naturalized resident population of E. coli. We developed an endpoint PCR targeting the IS30 element within the uspC-flhDC intergenic region, and all raw sewage samples (n = 21) were positive for this marker. Conversely, the prevalence of this marker in E. coli-positive surface and groundwater samples was low (≤5%). This simple PCR assay may represent a convenient microbial source-tracking tool for identification of water samples affected by municipal wastewater. IMPORTANCE The results of this study demonstrate that some strains of E. coli appear to have evolved to become naturalized populations in the wastewater environment and possess a number of stress-related genetic elements likely important for survival in this nonhost environment. The presence of non-host-adapted strains in wastewater challenges our understanding of using E. coli as a microbial indicator of wastewater treatment performance, suggesting that the E. coli strains present in human and animal feces may be very different from those found in treated wastewater. PMID:27371583

Isolating the Incentive Salience of Reward-Associated Stimuli: Value, Choice, and Persistence

ERIC Educational Resources Information Center

Beckmann, Joshua S.; Chow, Jonathan J.

2015-01-01

Sign- and goal-tracking are differentially associated with drug abuse-related behavior. Recently, it has been hypothesized that sign- and goal-tracking behavior are mediated by different neurobehavioral valuation systems, including differential incentive salience attribution. Herein, we used different conditioned stimuli to preferentially elicit…

Topography as a contextual variable in infectious disease transmission.

PubMed

Montoya, Isaac D

2004-01-01

This paper examines whether or not topography is a contextual variable that indirectly influences the transmission of infectious diseases. Age, gender, race/ethnicity, education level, economic status, injection drug use, and high-risk sexual behavior are known to influence infectious diseases transmission, but the effects of topography are often overlooked. A sample of 395 drug users were chosen from census tracts based upon a target profile of drug use behavior and demographics for the city of Houston. HIV was chosen as the infectious disease used to test this hypothesis. Residents of 16 census tracts in Houston, Texas participated in this study. The findings revealed that census tracts that were 'isolated' by topographic barriers, such as bayous, parks, railroad tracks, railway yards, major thoroughfares, freeways, and unique street grids had fewer cases of HIV than census tracks that were more accessible to thru-traffic. The research findings suggest that future research studies should consider topography as being contextually related to infectious disease transmission.

Surveillance systems to track progress toward global polio eradication - worldwide, 2012-2013.

PubMed

Levitt, Alexandra; Diop, Ousmane M; Tangermann, Rudolf H; Paladin, Fem; Kamgang, Jean Baptiste; Burns, Cara C; Chenoweth, Paul J; Goel, Ajay; Wassilak, Steven G F

2014-04-25

In 2012, the World Health Assembly of the World Health Organization (WHO) declared completion of polio eradication a programmatic emergency. Polio cases are detected through surveillance of acute flaccid paralysis (AFP) cases and subsequent testing of stool specimens for polioviruses (PVs) at WHO-accredited laboratories within the Global Polio Laboratory Network (GPLN). AFP surveillance is supplemented by environmental surveillance, testing sewage samples from selected sites for PVs. Virologic surveillance, including genomic sequencing to identify isolates by genotype and measure divergence between isolates, guides Global Polio Eradication Initiative (GPEI) activities by confirming the presence of PV, tracking chains of PV transmission, and highlighting gaps in AFP surveillance quality. This report provides AFP surveillance quality indicators at national and subnational levels during 2012-2013 for countries that experienced PV cases during 2009-2013 in the WHO African Region (AFR) and Eastern Mediterranean Region (EMR), the remaining polio-endemic regions. It also summarizes the results of environmental surveillance and reviews indicators assessing the timeliness of reporting of PV isolation and of virus strain characterization globally. Regional-level performance indicators for timely reporting of PV isolation were met in five of six WHO regions in 2012 and 2013. Of 30 AFR and EMR countries that experienced cases of PV (wild poliovirus [WPV], circulating vaccine-derived poliovirus [cVDPV], or both) during 2009-2013, national performance indicator targets for AFP surveillance and collection of adequate specimens were met in 27 (90%) countries in 2012 and 22 (73%) in 2013. In 17 (57%) countries, ≥80% of the population lived in subnational areas meeting both AFP performance indicators in 2012, decreasing to 13 (43%) in 2013. To achieve polio eradication and certify interruption of PV transmission, intensive efforts to strengthen and maintain AFP surveillance are needed at subnational levels, including in field investigation and prompt collection of specimens, particularly in countries with current or recent active PV transmission.

Tracking the establishment of local endemic populations of an emergent enteric pathogen

PubMed Central

Holt, Kathryn E.; Thieu Nga, Tran Vu; Thanh, Duy Pham; Vinh, Ha; Kim, Dong Wook; Vu Tra, My Phan; Campbell, James I.; Hoang, Nguyen Van Minh; Vinh, Nguyen Thanh; Minh, Pham Van; Thuy, Cao Thu; Nga, Tran Thi Thu; Thompson, Corinne; Dung, Tran Thi Ngoc; Nhu, Nguyen Thi Khanh; Vinh, Phat Voong; Tuyet, Pham Thi Ngoc; Phuc, Hoang Le; Lien, Nguyen Thi Nam; Phu, Bui Duc; Ai, Nguyen Thi Thuy; Tien, Nguyen Manh; Dong, Nguyen; Parry, Christopher M.; Hien, Tran Tinh; Farrar, Jeremy J.; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R.; Baker, Stephen

2013-01-01

Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population. PMID:24082120

Self-paced model learning for robust visual tracking

NASA Astrophysics Data System (ADS)

Huang, Wenhui; Gu, Jason; Ma, Xin; Li, Yibin

2017-01-01

In visual tracking, learning a robust and efficient appearance model is a challenging task. Model learning determines both the strategy and the frequency of model updating, which contains many details that could affect the tracking results. Self-paced learning (SPL) has recently been attracting considerable interest in the fields of machine learning and computer vision. SPL is inspired by the learning principle underlying the cognitive process of humans, whose learning process is generally from easier samples to more complex aspects of a task. We propose a tracking method that integrates the learning paradigm of SPL into visual tracking, so reliable samples can be automatically selected for model learning. In contrast to many existing model learning strategies in visual tracking, we discover the missing link between sample selection and model learning, which are combined into a single objective function in our approach. Sample weights and model parameters can be learned by minimizing this single objective function. Additionally, to solve the real-valued learning weight of samples, an error-tolerant self-paced function that considers the characteristics of visual tracking is proposed. We demonstrate the robustness and efficiency of our tracker on a recent tracking benchmark data set with 50 video sequences.

Different exosome cargo from plasma/bronchoalveolar lavage in non-small-cell lung cancer.

PubMed

Rodríguez, Marta; Silva, Javier; López-Alfonso, Ana; López-Muñiz, María Belen; Peña, Cristina; Domínguez, Gemma; García, Jose Miguel; López-Gónzalez, Ana; Méndez, Miriam; Provencio, Mariano; García, Vanesa; Bonilla, Félix

2014-09-01

Tumor-derived exosomes mediate tumorigenesis by facilitating tumor growth, metastasis, development of drug resistance, and immunosuppression. However, little is known about the exosomes isolated from bronchoalveolar lavage (BAL) in patients with lung neoplasm. Exosomes isolated in plasma and BAL from 30 and 75 patients with tumor and nontumor pathology were quantified by acetylcholinesterase activity and characterized by Western Blot, Electron Microscopy, and Nanoparticle Tracking Analysis. Differences in exosome cargo were analyzed by miRNA quantitative PCR in pooled samples and validated in a second series of patients. More exosomes were detected in plasma than in BAL in both groups (P < 0.001). The most miRNAs evaluated by PCR array were detected in tumor plasma, tumor BAL, and nontumor BAL pools, but only 56% were detected in the nontumor plasma pool. Comparing the top miRNAs with the highest levels detected in each pool, we found close homology only between the BAL samples of the two pathologies. In tumor plasma, we found a higher percentage of miRNAs with increased levels than in tumor BAL or in nontumor plasma. The data reveal differences between BAL and plasma exosome amount and miRNA content. © 2014 Wiley Periodicals, Inc.

NASA satellite to track North Pole expedition

NASA Technical Reports Server (NTRS)

1978-01-01

The proposed expedition of a lone explorer and the use of Nimbus 6 (NASA meteorological research satellite) to track his journey is reported. The journey is scheduled to start March 4, 1978, and will cover a distance of 6.000 Km (3,728 miles) from northern Canada to the North Pole and return, traveling the length of Greenland's isolated interior. The mode of transportation for the explorer will be by dog sled. Instrumentation and tracking techniques are discussed.

Population Genetics of Plasmodium vivax in Four High Malaria Endemic Areas in Thailand.

PubMed

Congpuong, Kanungnit; Ubalee, Ratawan

2017-10-01

Recent trends of malaria in Thailand illustrate an increasing proportion of Plasmodium vivax, indicating the importance of P. vivax as a major causative agent of malaria. P. vivax malaria is usually considered a benign disease so the knowledge of this parasite has been limited, especially the genetic diversity and genetic structure of isolates from different endemic areas. The aim of this study was to examine the population genetics and structure of P. vivax isolates from 4 provinces with different malaria endemic settings in Thailand using 6 microsatellite markers. Total 234 blood samples from P. vivax mono-infected patients were collected. Strong genetic diversity was observed across all study sites; the expected heterozygosity values ranged from 0.5871 to 0.9033. Genetic variability in this study divided P. vivax population into 3 clusters; first was P. vivax isolates from Mae Hong Son and Kanchanaburi Provinces located on the western part of Thailand; second, Yala isolates from the south; and third, Chanthaburi isolates from the east. P. vivax isolates from patients having parasite clearance time (PCT) longer than 24 hr after the first dose of chloroquine treatment had higher diversity when compared with those having PCT within 24 hr. This study revealed a clear evidence of different population structure of P. vivax from different malaria endemic areas of Thailand. The findings provide beneficial information to malaria control programme as it is a useful tool to track the source of infections and current malaria control efforts.

Human bony labyrinth is an indicator of population history and dispersal from Africa.

PubMed

Ponce de León, Marcia S; Koesbardiati, Toetik; Weissmann, John David; Milella, Marco; Reyna-Blanco, Carlos S; Suwa, Gen; Kondo, Osamu; Malaspinas, Anna-Sapfo; White, Tim D; Zollikofer, Christoph P E

2018-04-17

The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations. Phenetic skeletal data, such as cranial and pelvic morphologies, also exhibit a dispersal-from-Africa signal, which, however, tends to be blurred by the effects of local adaptation and in vivo phenotypic plasticity, and that is often deteriorated by postmortem damage to skeletal remains. These complexities raise the question of which skeletal structures most effectively track neutral population history. The cavity system of the inner ear (the so-called bony labyrinth) is a good candidate structure for such analyses. It is already fully formed by birth, which minimizes postnatal phenotypic plasticity, and it is generally well preserved in archaeological samples. Here we use morphometric data of the bony labyrinth to show that it is a surprisingly good marker of the global dispersal of modern humans from Africa. Labyrinthine morphology tracks genetic distances and geography in accordance with an isolation-by-distance model with dispersal from Africa. Our data further indicate that the neutral-like pattern of variation is compatible with stabilizing selection on labyrinth morphology. Given the increasingly important role of the petrous bone for ancient DNA recovery from archaeological specimens, we encourage researchers to acquire 3D morphological data of the inner ear structures before any invasive sampling. Such data will constitute an important archive of phenotypic variation in present and past populations, and will permit individual-based genotype-phenotype comparisons. Copyright © 2018 the Author(s). Published by PNAS.

A VIEW TO THE SOUTHWEST TOWARD MT. SAN ANTONIO FROM ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

A VIEW TO THE SOUTHWEST TOWARD MT. SAN ANTONIO FROM THE UNION PACIFIC RAILROAD TRACK NEAR CAJON PASS. VISIBLE FROM LEFT TO RIGHT ARE THE SANDSTONE OUTCROPS AT SULLIVAN’S CURVE IN THE FAR LEFT DISTANCE; BNSF RAILROAD MAIN TRACK 2 CURVING THROUGH THE HILLS IN THE LEFT DISTANCE; HILL 58.2 AT CENTER, MARKED BY AN ISOLATED STAND OF TREES; BNSF RAILROAD MAIN TRACK 1, RUNNING STRAIGHT THROUGH THE CENTER OF THE PHOTOGRAPH; AND THE UNION PACIFIC TRACK AT THE FAR RIGHT. 123 - Burlington Northern Santa Fe Railroad, Cajon Subdivision, Between Cajon Summit and Keenbrook, Devore, San Bernardino County, CA

Communications and tracking expert systems study

NASA Technical Reports Server (NTRS)

Leibfried, T. F.; Feagin, Terry; Overland, David

1987-01-01

The original objectives of the study consisted of five broad areas of investigation: criteria and issues for explanation of communication and tracking system anomaly detection, isolation, and recovery; data storage simplification issues for fault detection expert systems; data selection procedures for decision tree pruning and optimization to enhance the abstraction of pertinent information for clear explanation; criteria for establishing levels of explanation suited to needs; and analysis of expert system interaction and modularization. Progress was made in all areas, but to a lesser extent in the criteria for establishing levels of explanation suited to needs. Among the types of expert systems studied were those related to anomaly or fault detection, isolation, and recovery.

Robust online tracking via adaptive samples selection with saliency detection

NASA Astrophysics Data System (ADS)

Yan, Jia; Chen, Xi; Zhu, QiuPing

2013-12-01

Online tracking has shown to be successful in tracking of previously unknown objects. However, there are two important factors which lead to drift problem of online tracking, the one is how to select the exact labeled samples even when the target locations are inaccurate, and the other is how to handle the confusors which have similar features with the target. In this article, we propose a robust online tracking algorithm with adaptive samples selection based on saliency detection to overcome the drift problem. To deal with the problem of degrading the classifiers using mis-aligned samples, we introduce the saliency detection method to our tracking problem. Saliency maps and the strong classifiers are combined to extract the most correct positive samples. Our approach employs a simple yet saliency detection algorithm based on image spectral residual analysis. Furthermore, instead of using the random patches as the negative samples, we propose a reasonable selection criterion, in which both the saliency confidence and similarity are considered with the benefits that confusors in the surrounding background are incorporated into the classifiers update process before the drift occurs. The tracking task is formulated as a binary classification via online boosting framework. Experiment results in several challenging video sequences demonstrate the accuracy and stability of our tracker.

Molecular Tracking, through Processing, of Campylobacter Strains Colonizing Broiler Flocks▿

PubMed Central

Elvers, Karen T.; Morris, Victoria K.; Newell, Diane G.; Allen, Vivien M.

2011-01-01

Many of the poultry flocks produced in the United Kingdom are colonized with Campylobacter, and the intensive nature of poultry processing usually results in contaminated carcasses. In this study, a previously reported molecular oligonucleotide probe method was used to track a specific flock-colonizing strain(s) on broiler carcasses during processing in two United Kingdom commercial poultry processing plants. Five Campylobacter-positive flocks were sampled at four points along the processing line, postbleed, postpluck, prechill, and postchill, and two Campylobacter-negative flocks processed immediately after positive flocks were sampled prechill. flaA was sequenced from Campylobacter strains isolated from these flocks, and strain-specific probes were synthesized. Skin and cecal samples were plated onto selective agar to give individual colonies, which were transferred onto membranes. These were then hybridized with the strain- and genus-specific probes. For all the 5 positive flocks, there was a significant reduction in campylobacters postbleed compared to postpluck but no subsequent fall on sampling pre- and postchill, and the strain(s) predominating on the carcasses throughout processing came from the flock being processed. This indicates that strains from the abattoir environment were not a significant cause of carcass contamination in flocks with well-established campylobacter colonization. However, negative flocks that were preceded by positive flocks were contaminated by strains that did not generally originate from the predominating strains recovered from the ceca of the previous positive flocks. This suggests that the abattoir environment has a significant role in the contamination of carcasses from negative but not fully colonized flocks. PMID:21705532

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR TRACKING SYSTEM (UA-D-28.0)

EPA Science Inventory

The Arizona Border Study used a system that tracks what occurs to a sample and provides the status of that sample at any given time. In essence, the tracking system provides an electronic chain of custody record for each sample as it moves through the project. This is achieved ...

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR TRACKING SYSTEM (UA-D-28.0)

EPA Science Inventory

The NHEXAS Arizona project designed a system that tracks what occurs to a sample and provides the status of that sample at any given time. In essence, the tracking system provides an electronic chain of custody record for each sample as it moves through the project. This is ach...

Analytical and experimental study of sleeper SAT S 312 in slab track Sateba system

NASA Astrophysics Data System (ADS)

Guigou-Carter, C.; Villot, M.; Guillerme, B.; Petit, C.

2006-06-01

In this paper, a simple prediction tool based on a two-dimensional model is developed for a slab track system composed of two rails with rail pads, sleepers with sleeper pads, and a concrete base slab. The track and the slab are considered as infinite beams with bending stiffness, loss factor and mass per unit length. The track system is represented by its impedance per unit length of track and the ground by its line input impedance calculated using a two-dimensional elastic half-space ground model based on the wave approach. Damping of each track component is modelled as hysteretic damping and is taken into account by using a complex stiffness. The unsprung mass of the vehicle is considered as a concentrated mass at the excitation point on the rail head. The effect of the dynamic stiffness of the sleeper pads on the vibration isolation is studied in detail, the vibration isolation provided by the track system being quantified by an insertion gain in dB per one-third octave band. The second part of this paper presents an experimental test rig used to measure the dynamic stiffness of the sleeper pads on a full width section of the track (two rails). The experimental set-up is submitted to vertical as well as horizontal static loads (via hydraulic jacks) and an electrodynamic shaker is used for dynamic excitation of the system. The determination of the dynamic stiffness of the sleeper pads is based on the approach called the "direct method". The limitations of the experimental set-up are discussed. The measurement results for one type of sleeper pad are presented.

Comparative persistence of human sewage-specific enterococcal bacteriophages in freshwater and seawater.

PubMed

Booncharoen, Namfon; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

2018-07-01

Enterococcus faecalis bacteria have been recently reported for their ability to host bacteriophages that are specifically from human sewage, suggesting their application to track human fecal contamination in water resources. However, little is known about the survivability of sewage-specific enterococcal bacteriophages in various water matrices under ambient and storage conditions. In this study, bacteriophages that were derived from the Thailand-isolated E. faecalis strains AIM06 and SR14 exhibited morphologies consistent with the Siphoviridae, Podoviridae, and Myoviridae families. Four representative bacteriophages were separately spiked into environmental water samples (n = 7) comprising freshwater and seawater with low- and high-pollution (LF, HF, LS, and HS, respectively) levels, defined according to Thailand Water Quality Standards. All bacteriophages decayed fastest in HS or HF samples at 30 °C, reaching a 5-log 10 reduction in 2.2 to 9.8 days, and slowest in LS samples, requiring 8.8 to 23.5 days. The decay rates were 5 to 53 times lower at a storage temperature of 5 °C. HF samples could be stored for as little as 2.5 days to prevent the decay of 50% of the phages. Myoviridae phages decayed faster than Siphoviridae phages and Podoviridae phages in most water matrices at 30 °C. Moreover, the decay rates were 1.8 to 92 times slower in filtered samples, emphasizing a strong role for water constituents, i.e., suspended solids and natural microorganisms, in phage persistence. This study emphasized that differential enterococcal bacteriophage persistence should be considered when planning the monitoring and interpreting of fecal sources by microbial source tracking.

Canadian integrated program for antimicrobial resistance surveillance: Retail food highlights, 2003–2012

PubMed Central

Avery, BP; Parmley, EJ; Reid-Smith, RJ; Daignault, D; Finley, RL; Irwin, RJ

2014-01-01

Background The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) is a collaborative, integrated program designed to track antimicrobial resistance (AMR) among enteric bacteria isolated from various livestock commodities along the food-producing continuum (“farm to fork”) and in humans. Objective To provide a summary of the prevalence and trends in AMR among select bacteria isolated from raw, fresh chicken, pork, and beef in 2012 at the retail food level and to link these data with other findings from CIPARS. Methods Meat samples were collected from randomly selected geographic areas across Canada weighted by population for subsequent isolation of bacteria and interpretation of the associated AMR profiles. Salmonella, Campylobacter and generic Escherichia coli (E. coli) were tested in chicken, and E. coli was tested in beef and pork. Data were analyzed for 2012 and temporal and regional trends were examined between 2003 and 2012 by province/region. Results Overall, resistance levels to Salmonella in retail chicken varied widely by region and year. For example, ceftiofur resistance to Salmonella in retail chicken was significantly lower in 2012 than in 2004 in Ontario and in Québec; however, among all regions sampled, resistance was significantly higher in 2012 compared to 2006. Across all regions sampled, resistance to Campylobacter in retail chicken was relatively low in 2012 (<16%) with the exception of tetracycline resistance. In 2012, ciprofloxacin resistance to Campylobacter in chicken declined in British Columbia but significantly increased in Ontario, compared to 2011. In 2012, β-lactam resistance to E. coli in retail beef remained low (≤1%) and was also relatively low comparable to previous years in pork. Conclusion In Canada, as is the case worldwide, there is evidence of resistance to medically important antimicrobials among bacteria from retail meats. Resistance among organisms isolated from poultry, beef, and pork at the retail food level is characterized by wide variation over time and across different regions.

Canadian integrated program for antimicrobial resistance surveillance: Retail food highlights, 2003-2012.

PubMed

Avery, B P; Parmley, E J; Reid-Smith, R J; Daignault, D; Finley, R L; Irwin, R J

2014-11-07

The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) is a collaborative, integrated program designed to track antimicrobial resistance (AMR) among enteric bacteria isolated from various livestock commodities along the food-producing continuum ("farm to fork") and in humans. To provide a summary of the prevalence and trends in AMR among select bacteria isolated from raw, fresh chicken, pork, and beef in 2012 at the retail food level and to link these data with other findings from CIPARS. Meat samples were collected from randomly selected geographic areas across Canada weighted by population for subsequent isolation of bacteria and interpretation of the associated AMR profiles. Salmonella, Campylobacter and generic Escherichia coli ( E. coli ) were tested in chicken, and E. coli was tested in beef and pork. Data were analyzed for 2012 and temporal and regional trends were examined between 2003 and 2012 by province/region. Overall, resistance levels to Salmonella in retail chicken varied widely by region and year. For example, ceftiofur resistance to Salmonella in retail chicken was significantly lower in 2012 than in 2004 in Ontario and in Québec; however, among all regions sampled, resistance was significantly higher in 2012 compared to 2006. Across all regions sampled, resistance to Campylobacter in retail chicken was relatively low in 2012 (<16%) with the exception of tetracycline resistance. In 2012, ciprofloxacin resistance to Campylobacter in chicken declined in British Columbia but significantly increased in Ontario, compared to 2011. In 2012, β-lactam resistance to E. coli in retail beef remained low (≤1%) and was also relatively low comparable to previous years in pork. In Canada, as is the case worldwide, there is evidence of resistance to medically important antimicrobials among bacteria from retail meats. Resistance among organisms isolated from poultry, beef, and pork at the retail food level is characterized by wide variation over time and across different regions.

Image analysis used to count and measure etched tracks from ionizing radiation

NASA Technical Reports Server (NTRS)

Blanford, George E.; Schulz, Cindy K.

1995-01-01

We have developed techniques to use digitized scanning electron micrographs and computer image analysis programs to measure track densities in lunar soil grains and plastic dosimeters. Tracks in lunar samples are formed by highly ionizing solar energetic particles and cosmic rays during near surface exposure on the Moon. The track densities are related to the exposure conditions (depth and time). Distributions of the number of grains as a function of their track densities can reveal the modality of soil maturation. We worked on two samples identified for a consortium study of lunar weathering effects, 61221 and 67701. They were prepared by the lunar curator's staff as polished grain mounts that were etched in boiling 1 N NaOH for 6 h to reveal tracks. We determined that backscattered electron images taken at 10 percent contrast and approximately 50 percent brightness produced suitable high contrast images for analysis. We used the NIH Image program to cut out areas that were unsuitable for measurement such as edges, cracks, etc. We ascertained a gray-scale threshold of 25 to separate tracks from background. We used the computer to count everything that was two pixels or greater in size and to measure the area to obtain track densities. We found an excellent correlation with manual measurements for track densities below 1 x 10(exp 8) cm(exp -2). For track densities between 1 x 10(exp 8) cm(exp -2) to 1 x 10(exp 9) cm(exp -2) we found that a regression formula using the percentage area covered by tracks gave good agreement with manual measurements. We determined the track density distributions for 61221 and 67701. Sample 61221 is an immature sample, but not pristine. Sample 67701 is a submature sample that is very close to being fully mature. Because only 10 percent of the grains have track densities less than 10(exp 9) cm(exp -2), it is difficulty to determine whether the sample matured in situ or is a mixture of a mature and a submature soil. Although our analysis of plastic dosimeters is at an early stage of development, results are encouraging. The dosimeter was etched in 6.25 N NaOH at 70 deg C for 16 h. We took 200x secondary electron images of the sample and used the NIH Image software to count and measure major and minor diameters of the etched tracks. We calculated the relative track etch rate from a formula that relates it to the major and minor diameters. We made a histogram of the number of tracks versus their relative etch rate. The relative track etching rate is proportional to the linear energy transfer of the particle. With appropriate calibration experiments, the histogram could be used to calculate the radiation dose.

Image analysis used to count and measure etched tracks from ionizing radiation

NASA Astrophysics Data System (ADS)

Blanford, George E.; Schulz, Cindy K.

1995-07-01

We have developed techniques to use digitized scanning electron micrographs and computer image analysis programs to measure track densities in lunar soil grains and plastic dosimeters. Tracks in lunar samples are formed by highly ionizing solar energetic particles and cosmic rays during near surface exposure on the Moon. The track densities are related to the exposure conditions (depth and time). Distributions of the number of grains as a function of their track densities can reveal the modality of soil maturation. We worked on two samples identified for a consortium study of lunar weathering effects, 61221 and 67701. They were prepared by the lunar curator's staff as polished grain mounts that were etched in boiling 1 N NaOH for 6 h to reveal tracks. We determined that backscattered electron images taken at 10 percent contrast and approximately 50 percent brightness produced suitable high contrast images for analysis. We used the NIH Image program to cut out areas that were unsuitable for measurement such as edges, cracks, etc. We ascertained a gray-scale threshold of 25 to separate tracks from background. We used the computer to count everything that was two pixels or greater in size and to measure the area to obtain track densities. We found an excellent correlation with manual measurements for track densities below 1 x 10(exp 8) cm(exp -2). For track densities between 1 x 10(exp 8) cm(exp -2) to 1 x 10(exp 9) cm(exp -2) we found that a regression formula using the percentage area covered by tracks gave good agreement with manual measurements. We determined the track density distributions for 61221 and 67701. Sample 61221 is an immature sample, but not pristine. Sample 67701 is a submature sample that is very close to being fully mature. Because only 10 percent of the grains have track densities less than 10(exp 9) cm(exp -2), it is difficulty to determine whether the sample matured in situ or is a mixture of a mature and a submature soil. Although our analysis of plastic dosimeters is at an early stage of development, results are encouraging. The dosimeter was etched in 6.25 N NaOH at 70 deg C for 16 h.

Incidence and tracking of Clostridium perfringens through an integrated broiler chicken operation

USDA-ARS?s Scientific Manuscript database

Clostridium perfringens has been shown to be widespread in the broiler chicken hatchery, grow-out, and processing operations. In a previous study, ribotypes of certain strains of C. perfringens isolated from processed chicken carcasses were shown to match ribotypes isolated from paper pad lining tra...

NM-Scale Anatomy of an Entire Stardust Carrot Track

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Keller, L. P.; Clemett, S. J.; Messenger, S.

2009-01-01

Comet Wild-2 samples collected by NASA s Stardust mission are extremely complex, heterogeneous, and have experienced wide ranges of alteration during the capture process. There are two major types of track morphologies: "carrot" and "bulbous," that reflect different structural/compositional properties of the impactors. Carrot type tracks are typically produced by compact or single mineral grains which survive essentially intact as a single large terminal particle. Bulbous tracks are likely produced by fine-grained or organic-rich impactors [1]. Owing to their challenging nature and especially high value of Stardust samples, we have invested considerable effort in developing both sample preparation and analytical techniques tailored for Stardust sample analyses. Our report focuses on our systematic disassembly and coordinated analysis of Stardust carrot track #112 from the mm to nm-scale.

Computer image analysis of etched tracks from ionizing radiation

NASA Technical Reports Server (NTRS)

Blanford, George E.

1994-01-01

I proposed to continue a cooperative research project with Dr. David S. McKay concerning image analysis of tracks. Last summer we showed that we could measure track densities using the Oxford Instruments eXL computer and software that is attached to an ISI scanning electron microscope (SEM) located in building 31 at JSC. To reduce the dependence on JSC equipment, we proposed to transfer the SEM images to UHCL for analysis. Last summer we developed techniques to use digitized scanning electron micrographs and computer image analysis programs to measure track densities in lunar soil grains. Tracks were formed by highly ionizing solar energetic particles and cosmic rays during near surface exposure on the Moon. The track densities are related to the exposure conditions (depth and time). Distributions of the number of grains as a function of their track densities can reveal the modality of soil maturation. As part of a consortium effort to better understand the maturation of lunar soil and its relation to its infrared reflectance properties, we worked on lunar samples 67701,205 and 61221,134. These samples were etched for a shorter time (6 hours) than last summer's sample and this difference has presented problems for establishing the correct analysis conditions. We used computer counting and measurement of area to obtain preliminary track densities and a track density distribution that we could interpret for sample 67701,205. This sample is a submature soil consisting of approximately 85 percent mature soil mixed with approximately 15 percent immature, but not pristine, soil.

Partnership for a Drug-Free America: Partnership Attitude Tracking Study. Teens: Ethnic and Racial Trends, Spring 2002.

ERIC Educational Resources Information Center

Delaney, Barbara

The annual Partnership Attitude Tracking Study (PATS) tracks consumers' attitudes about illegal drugs. PATS consists of two nationally projectable samples: a teen sample for students in grades 7-12 and a parent sample. The 2002 PATS, conducted in homes and schools, collected data using self-report surveys. Results indicate that after a decade of…

Performance of the all-digital data-transition tracking loop in the advanced receiver

NASA Astrophysics Data System (ADS)

Cheng, U.; Hinedi, S.

1989-11-01

The performance of the all-digital data-transition tracking loop (DTTL) with coherent or noncoherent sampling is described. The effects of few samples per symbol and of noncommensurate sampling rates and symbol rates are addressed and analyzed. Their impacts on the loop phase-error variance and the mean time to lose lock (MTLL) are quantified through computer simulations. The analysis and preliminary simulations indicate that with three to four samples per symbol, the DTTL can track with negligible jitter because of the presence of earth Doppler rate. Furthermore, the MTLL is also expected to be large engough to maintain lock over a Deep Space Network track.

Estimation of dynamic rotor loads for the rotor systems research aircraft: Methodology development and validation

NASA Technical Reports Server (NTRS)

Duval, R. W.; Bahrami, M.

1985-01-01

The Rotor Systems Research Aircraft uses load cells to isolate the rotor/transmission systm from the fuselage. A mathematical model relating applied rotor loads and inertial loads of the rotor/transmission system to the load cell response is required to allow the load cells to be used to estimate rotor loads from flight data. Such a model is derived analytically by applying a force and moment balance to the isolated rotor/transmission system. The model is tested by comparing its estimated values of applied rotor loads with measured values obtained from a ground based shake test. Discrepancies in the comparison are used to isolate sources of unmodeled external loads. Once the structure of the mathematical model has been validated by comparison with experimental data, the parameters must be identified. Since the parameters may vary with flight condition it is desirable to identify the parameters directly from the flight data. A Maximum Likelihood identification algorithm is derived for this purpose and tested using a computer simulation of load cell data. The identification is found to converge within 10 samples. The rapid convergence facilitates tracking of time varying parameters of the load cell model in flight.

Gene Scanning of an Internalin B Gene Fragment Using High-Resolution Melting Curve Analysis as a Tool for Rapid Typing of Listeria monocytogenes

PubMed Central

Pietzka, Ariane T.; Stöger, Anna; Huhulescu, Steliana; Allerberger, Franz; Ruppitsch, Werner

2011-01-01

The ability to accurately track Listeria monocytogenes strains involved in outbreaks is essential for control and prevention of listeriosis. Because current typing techniques are time-consuming, cost-intensive, technically demanding, and difficult to standardize, we developed a rapid and cost-effective method for typing of L. monocytogenes. In all, 172 clinical L. monocytogenes isolates and 20 isolates from culture collections were typed by high-resolution melting (HRM) curve analysis of a specific locus of the internalin B gene (inlB). All obtained HRM curve profiles were verified by sequence analysis. The 192 tested L. monocytogenes isolates yielded 15 specific HRM curve profiles. Sequence analysis revealed that these 15 HRM curve profiles correspond to 18 distinct inlB sequence types. The HRM curve profiles obtained correlated with the five phylogenetic groups I.1, I.2, II.1, II.2, and III. Thus, HRM curve analysis constitutes an inexpensive assay and represents an improvement in typing relative to classical serotyping or multiplex PCR typing protocols. This method provides a rapid and powerful screening tool for simultaneous preliminary typing of up to 384 samples in approximately 2 hours. PMID:21227395

Summary of the ISEV workshop on extracellular vesicles as disease biomarkers, held in Birmingham, UK, during December 2017

PubMed Central

Carter, David R. F.; Cheng, Lesley; Compton, Carolyn; Daaboul, George; Devitt, Andrew; Falcon-Perez, Juan Manuel; Gardiner, Chris; Helmbrecht, Clemens; Hendrix, An; Hoffman, Andrew; Kalluri, Raghu; Kang, Ji Yoon; Lässer, Cecilia; Lawson, Charlotte; Lenassi, Metka; Levin, Carina; Llorente, Alicia; Martens-Uzunova, Elena S.; Möller, Andreas; Ochiya, Takahiro; Pink, Ryan C; Tahara, Hidetoshi; Wauben, Marca H. M.; Webber, Jason P.; Yin, Hang; Nieuwland, Rienk

2018-01-01

ABSTRACT This report summarises the presentations and activities of the ISEV Workshop on extracellular vesicle biomarkers held in Birmingham, UK during December 2017. Among the key messages was broad agreement about the importance of biospecimen science. Much greater attention needs to be paid towards the provenance of collected samples. The workshop also highlighted clear gaps in our knowledge about pre-analytical factors that alter extracellular vesicles (EVs). The future utility of certified standards for credentialing of instruments and software, to analyse EV and for tracking the influence of isolation steps on the structure and content of EVs were also discussed. Several example studies were presented, demonstrating the potential utility for EVs in disease diagnosis, prognosis, longitudinal serial testing and stratification of patients. The conclusion of the workshop was that more effort focused on pre-analytical issues and benchmarking of isolation methods is needed to strengthen collaborations and advance more effective biomarkers.

Description and performance of track and primary-vertex reconstruction with the CMS tracker

DOE PAGES

Chatrchyan, Serguei

2014-10-16

A description is provided of the software algorithms developed for the CMS tracker both for reconstructing charged-particle trajectories in proton-proton interactions and for using the resulting tracks to estimate the positions of the LHC luminous region and individual primary-interaction vertices. Despite the very hostile environment at the LHC, the performance obtained with these algorithms is found to be excellent. For tbar t events under typical 2011 pileup conditions, the average track-reconstruction efficiency for promptly-produced charged particles with transverse momenta of p T > 0.9GeV is 94% for pseudorapidities of |η| < 0.9 and 85% for 0.9 < |η| < 2.5.more » The inefficiency is caused mainly by hadrons that undergo nuclear interactions in the tracker material. For isolated muons, the corresponding efficiencies are essentially 100%. For isolated muons of p T = 100GeV emitted at |η| < 1.4, the resolutions are approximately 2.8% in p T, and respectively, 10μm and 30μm in the transverse and longitudinal impact parameters. The position resolution achieved for reconstructed primary vertices that correspond to interesting pp collisions is 10–12μm in each of the three spatial dimensions. The tracking and vertexing software is fast and flexible, and easily adaptable to other functions, such as fast tracking for the trigger, or dedicated tracking for electrons that takes into account bremsstrahlung.« less

Assessment of statistical methods used in library-based approaches to microbial source tracking.

PubMed

Ritter, Kerry J; Carruthers, Ethan; Carson, C Andrew; Ellender, R D; Harwood, Valerie J; Kingsley, Kyle; Nakatsu, Cindy; Sadowsky, Michael; Shear, Brian; West, Brian; Whitlock, John E; Wiggins, Bruce A; Wilbur, Jayson D

2003-12-01

Several commonly used statistical methods for fingerprint identification in microbial source tracking (MST) were examined to assess the effectiveness of pattern-matching algorithms to correctly identify sources. Although numerous statistical methods have been employed for source identification, no widespread consensus exists as to which is most appropriate. A large-scale comparison of several MST methods, using identical fecal sources, presented a unique opportunity to assess the utility of several popular statistical methods. These included discriminant analysis, nearest neighbour analysis, maximum similarity and average similarity, along with several measures of distance or similarity. Threshold criteria for excluding uncertain or poorly matched isolates from final analysis were also examined for their ability to reduce false positives and increase prediction success. Six independent libraries used in the study were constructed from indicator bacteria isolated from fecal materials of humans, seagulls, cows and dogs. Three of these libraries were constructed using the rep-PCR technique and three relied on antibiotic resistance analysis (ARA). Five of the libraries were constructed using Escherichia coli and one using Enterococcus spp. (ARA). Overall, the outcome of this study suggests a high degree of variability across statistical methods. Despite large differences in correct classification rates among the statistical methods, no single statistical approach emerged as superior. Thresholds failed to consistently increase rates of correct classification and improvement was often associated with substantial effective sample size reduction. Recommendations are provided to aid in selecting appropriate analyses for these types of data.

Genetic source tracking of an anthrax outbreak in Shaanxi province, China.

PubMed

Liu, Dong-Li; Wei, Jian-Chun; Chen, Qiu-Lan; Guo, Xue-Jun; Zhang, En-Min; He, Li; Liang, Xu-Dong; Ma, Guo-Zhu; Zhou, Ti-Cao; Yin, Wen-Wu; Liu, Wei; Liu, Kai; Shi, Yi; Ji, Jian-Jun; Zhang, Hui-Juan; Ma, Lin; Zhang, Fa-Xin; Zhang, Zhi-Kai; Zhou, Hang; Yu, Hong-Jie; Kan, Biao; Xu, Jian-Guo; Liu, Feng; Li, Wei

2017-01-17

Anthrax is an acute zoonotic infectious disease caused by the bacterium known as Bacillus anthracis. From 26 July to 8 August 2015, an outbreak with 20 suspected cutaneous anthrax cases was reported in Ganquan County, Shaanxi province in China. The genetic source tracking analysis of the anthrax outbreak was performed by molecular epidemiological methods in this study. Three molecular typing methods, namely canonical single nucleotide polymorphisms (canSNP), multiple-locus variable-number tandem repeat analysis (MLVA), and single nucleotide repeat (SNR) analysis, were used to investigate the possible source of transmission and identify the genetic relationship among the strains isolated from human cases and diseased animals during the outbreak. Five strains isolated from diseased mules were clustered together with patients' isolates using canSNP typing and MLVA. The causative B. anthracis lineages in this outbreak belonged to the A.Br.001/002 canSNP subgroup and the MLVA15-31 genotype (the 31 genotype in MLVA15 scheme). Because nine isolates from another four provinces in China were clustered together with outbreak-related strains by the canSNP (A.Br.001/002 subgroup) and MLVA15 method (MLVA15-31 genotype), still another SNR analysis (CL10, CL12, CL33, and CL35) was used to source track the outbreak, and the results suggesting that these patients in the anthrax outbreak were probably infected by the same pathogen clone. It was deduced that the anthrax outbreak occurred in Shaanxi province, China in 2015 was a local occurrence.

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

NASA Technical Reports Server (NTRS)

Castro, V.A.; Ott, C.M.; Garcia, V.M.; John, J.; Buttner, M.P.; Cruz, P.; Pierson, D.L.

2009-01-01

The determination of risk from infectious disease during long-duration missions is composed of several factors including the concentration and the characteristics of the infectious agent. Thus, a thorough knowledge of the microorganisms aboard spacecraft is essential in mitigating infectious disease risk to the crew. While stringent steps are taken to minimize the transfer of potential pathogens to spacecraft, several medically significant organisms have been isolated from both the Mir and International Space Station (ISS). Historically, the method for isolation and identification of microorganisms from spacecraft environmental samples depended upon their growth on culture media. Unfortunately, only a fraction of the organisms may grow on a culture medium, potentially omitting those microorganisms whose nutritional and physical requirements for growth are not met. Thus, several pathogens may not have been detected, such as Legionella pneumophila, the etiological agent of Legionnaire s disease. We hypothesize that environmental analysis using non-culture-based technologies will reveal microorganisms, allergens, and microbial toxins not previously reported in spacecraft, allowing for a more complete health assessment. The development of techniques for this flight experiment, operationally named SWAB, has already provided advances in NASA laboratory processes and beneficial information toward human health risk assessment. The translation of 16S ribosomal DNA sequencing for the identification of bacteria from the SWAB experiment to nominal operations has increased bacterial speciation of environmental isolates from previous flights three fold compared to previous conventional methodology. The incorporation of molecular-based DNA fingerprinting using repetitive sequence-based polymerase chain reaction (rep-PCR) into the capabilities of the laboratory has provided a methodology to track microorganisms between crewmembers and their environment. Both 16S ribosomal DNA identification and bacterial fingerprinting have improved NASA s capability to better understand spacecraft environments and determine the source of contamination events. Preflight sampling has been completed for air, surface, and water samples. In-flight sample collection has been completed for a total of 8 air and surface sample collection sessions. In-flight hardware has performed well and the surface sampling device received positive feedback from the crew for its ease of use. While processing and analysis continue for these samples, early results have begun to provide information on the spacecraft environment. Using a method called Denaturing Gradient Gel Electrophoresis (DGGE), several air and samples were evaluated to determine the types of organisms that were present. Using only molecular techniques, DGGE does not depend on any microbial growth on culture media, allowing a more comprehensive assessment of the spacecraft interior. Preliminary results have identified several microorganisms that would not have been isolated using current technology, though none of these organisms would be considered medically significant. Interestingly, the isolation of Gram negative organisms is greater using DGGE than conventional media based isolation. The cause of this finding is unclear, though it may be the result of the technique s ability to isolate both viable and non-viable bacteria. The next phase of the SWAB sample analysis is the use of quantitative polymerase chain reaction (QPCR) to look for specific medically significant organisms. While not as broad as DGGE, QPCR is much more sensitive and may reveal findings that were not seen during the initial evaluation. Together, this information will lead toward an accurate microbial risk assessment to help set flight requirements to protect the safety, health, and performance of the crew.

Rats track odour trails accurately using a multi-layered strategy with near-optimal sampling.

PubMed

Khan, Adil Ghani; Sarangi, Manaswini; Bhalla, Upinder Singh

2012-02-28

Tracking odour trails is a crucial behaviour for many animals, often leading to food, mates or away from danger. It is an excellent example of active sampling, where the animal itself controls how to sense the environment. Here we show that rats can track odour trails accurately with near-optimal sampling. We trained rats to follow odour trails drawn on paper spooled through a treadmill. By recording local field potentials (LFPs) from the olfactory bulb, and sniffing rates, we find that sniffing but not LFPs differ between tracking and non-tracking conditions. Rats can track odours within ~1 cm, and this accuracy is degraded when one nostril is closed. Moreover, they show path prediction on encountering a fork, wide 'casting' sweeps on encountering a gap and detection of reappearance of the trail in 1-2 sniffs. We suggest that rats use a multi-layered strategy, and achieve efficient sampling and high accuracy in this complex task.

Dinosaur tracks from the Cedar Mountain Formation (Lower Cretaceous), Arches National Park, Utah

USGS Publications Warehouse

Lockley, Martin G.; White, Diane K.; Kirkland, James I.; Santucci, Vincent L.

2004-01-01

The seventh and largest known dinosaur tracksite from the Cedar Mountain Formation is reported from two important stratigraphic levels in the Ruby Ranch Member within the boundaries of Arches National Park. Previous reports of sites with a few isolated tracks are of limited utility in indicating the fauna represented by track makers. The Arches site reveals evidence of several theropod morphotypes, including a possible match for the coelurosaur Nedcolbertia and an apparently didactyl Utahraptor-like dromeosaurid. Sauropod tracks indicate a wide-gauge morphotype (cf. Brontopodus). Ornithischian tracks suggest the presence of an iguandontid-like ornithopod and a large ankylosaur. Dinosaur track diversity is high in comparison with other early Cretaceous vertebrate ichnofaunas, and it correlates well with faunal lists derived from skeletal remains, thus providing a convincing census of the known fauna.

Dynamic changes in the rice blast population in the USA over six decades

USDA-ARS?s Scientific Manuscript database

Rice blast disease caused by Magnaporthe oryzae is one of the most destructive diseases of rice. Field isolates of M. oryzae rapidly adapt to the hosts and climate. Tracking the genetic and pathogenic variability of the field isolates is essential to understand how M. oryzae interacts with hosts an...

Bacterial succession within an ephemeral hypereutrophic Mojave Desert playa Lake.

PubMed

Navarro, Jason B; Moser, Duane P; Flores, Andrea; Ross, Christian; Rosen, Michael R; Dong, Hailiang; Zhang, Gengxin; Hedlund, Brian P

2009-02-01

Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by approximately 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of approximately 1x10(6) cells ml(-1) of culturable heterotrophs was replaced by a dense population of more than 1x10(9) cells ml(-1), which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria.

Bacterial succession within an ephemeral hypereutrophic mojave desert playa lake

USGS Publications Warehouse

Navarro, J.B.; Moser, D.P.; Flores, A.; Ross, C.; Rosen, Michael R.; Dong, H.; Zhang, G.; Hedlund, B.P.

2009-01-01

Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of 1 ?????106 cells ml-1 of culturable heterotrophs was replaced by a dense population of more than 1????????109 cells ml-1, which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria. ?? 2008 Springer Science+Business Media, LLC.

Molecular Characterization of Plasmids Encoding CTX-M β-Lactamases and their Associated Addiction Systems Circulating Among Escherichia coli from Retail Chickens, Chicken Farms, and Slaughterhouses in Korea.

PubMed

Jo, Su-Jin; Woo, Gun-Jo

2016-02-01

Extended-spectrum β-lactamases (ESBLs), particularly those of the CTX-M types, are the predominant resistance determinants of Escherichia coli that are rapidly spreading worldwide. To determine CTX-M types, E. coli isolates were collected from retail chickens (n = 390) and environmental samples from chicken farms (n = 32) and slaughterhouses (n = 67) in Korea. Fifteen strains harboring blaCTX-M genes were isolated from 358 E. coli isolates. The most common CTX-M type was eight of CTX-M-15, followed by six of CTX-M-1 and one of CTX-M- 14. The blaCTX-M genes were identified in the isolates from retail chickens (n = 9), followed by feces, water pipes, floors, and walls. Conjugations confirmed the transferability of the plasmids carrying blaCTX-M genes to the recipient E. coli J53 strain. Furthermore, eight addiction systems carried by the replicons in CTX-M types were confirmed. The dominant system was identified as ccdAB, vagCD, and pndAC in donor strains and transconjugants. The clonal relationship between the two strains carrying blaCTX-M genes indicates that E. coli may transmit from the farm to retail chickens, suggesting a possible public health risk. Our findings demonstrate that the detection of CTX-M types in E. coli isolates is important for tracking ESBL production in animals, and suggest linkage of multiple addiction systems in plasmids bearing blaCTX-M genes.

Study on rejection characteristic of current loop to the base disturbance of optical communication system

NASA Astrophysics Data System (ADS)

Mao, Yao; Deng, Chao; Liu, Qiong; Cao, Zheng

2016-10-01

As laser has narrow transmitting beam and small divergence angle, the LOS (Line of Sight) stabilization of optical communication system is a primary precondition of laser communication links. Compound axis control is usually adopted in LOS stabilization of optical communication system, in which coarse tracking and fine tracking are included. Rejection against high frequency disturbance mainly depends on fine tracking LOS stabilization platform. Limited by different factors such as mechanical characteristic of the stabilization platform and bandwidth/noise of the sensor, the control bandwidth of LOS stabilization platform is restricted so that effective rejection of high frequency disturbance cannot be achieved as it mainly depends on the isolation characteristic of the platform itself. It is proposed by this paper that current loop may reject the effect of back-EMF. By adopting the method of electric control, high frequency isolation characteristic of the platform can be improved. The improvement effect is similar to increasing passive vibration reduction devices. Adopting the double closed loop control structure of velocity and current with the combining of the rejection effect of back-EMF caused by current loop is equivalent to reducing back-EMF coefficient, which can enhance the isolation ability of the LOS stabilization platform to high frequency disturbance.

A single dynamic observer-based module for design of simultaneous fault detection, isolation and tracking control scheme

NASA Astrophysics Data System (ADS)

Davoodi, M.; Meskin, N.; Khorasani, K.

2018-03-01

The problem of simultaneous fault detection, isolation and tracking (SFDIT) control design for linear systems subject to both bounded energy and bounded peak disturbances is considered in this work. A dynamic observer is proposed and implemented by using the H∞/H-/L1 formulation of the SFDIT problem. A single dynamic observer module is designed that generates the residuals as well as the control signals. The objective of the SFDIT module is to ensure that simultaneously the effects of disturbances and control signals on the residual signals are minimised (in order to accomplish the fault detection goal) subject to the constraint that the transfer matrix from the faults to the residuals is equal to a pre-assigned diagonal transfer matrix (in order to accomplish the fault isolation goal), while the effects of disturbances, reference inputs and faults on the specified control outputs are minimised (in order to accomplish the fault-tolerant and tracking control goals). A set of linear matrix inequality (LMI) feasibility conditions are derived to ensure solvability of the problem. In order to illustrate and demonstrate the effectiveness of our proposed design methodology, the developed and proposed schemes are applied to an autonomous unmanned underwater vehicle (AUV).

Combining Particle Filters and Consistency-Based Approaches for Monitoring and Diagnosis of Stochastic Hybrid Systems

NASA Technical Reports Server (NTRS)

Narasimhan, Sriram; Dearden, Richard; Benazera, Emmanuel

2004-01-01

Fault detection and isolation are critical tasks to ensure correct operation of systems. When we consider stochastic hybrid systems, diagnosis algorithms need to track both the discrete mode and the continuous state of the system in the presence of noise. Deterministic techniques like Livingstone cannot deal with the stochasticity in the system and models. Conversely Bayesian belief update techniques such as particle filters may require many computational resources to get a good approximation of the true belief state. In this paper we propose a fault detection and isolation architecture for stochastic hybrid systems that combines look-ahead Rao-Blackwellized Particle Filters (RBPF) with the Livingstone 3 (L3) diagnosis engine. In this approach RBPF is used to track the nominal behavior, a novel n-step prediction scheme is used for fault detection and L3 is used to generate a set of candidates that are consistent with the discrepant observations which then continue to be tracked by the RBPF scheme.

Tracking sources of Clostridium botulinum type E contamination in seal meat.

PubMed

Leclair, Daniel; Farber, Jeffrey M; Pagotto, Franco; Suppa, Sandy; Doidge, Bill; Austin, John W

2017-01-01

Botulism in Nunavik, Quebec is associated with the consumption of aged marine mammal meat and fat. The objective was to identify meat handling practices presenting a risk of contamination of seal meat with C. botulinum. Potential sources of contamination were assessed through interviews with igunaq producers from five communities of Nunavik. These sources were verified by detection and isolation of C. botulinum from igunaq prepared in the field from seal carcasses. Interviews indicated practices presenting a risk for contamination included: placing meat or fat on coastal rocks, using seawater for rinsing, and ageing meat in inverted seal skin pouches. Although the presence of C. botulinum type E spores was detected in only two of 32 (6.3%) meat or fat samples collected during the butchering process, two of four igunaq preparations from these samples contained type E botulinum toxin. Analysis of C. botulinum type E isolates recovered from these preparations indicated that shoreline soil may be a source of contamination. Seal meat and fat may be contaminated with C. botulinum type E during the butchering process. Measures can be adopted to reduce the risks of contamination in the field and possibly decrease the incidence of type E botulism in Nunavik.

Statistical and sampling issues when using multiple particle tracking

NASA Astrophysics Data System (ADS)

Savin, Thierry; Doyle, Patrick S.

2007-08-01

Video microscopy can be used to simultaneously track several microparticles embedded in a complex material. The trajectories are used to extract a sample of displacements at random locations in the material. From this sample, averaged quantities characterizing the dynamics of the probes are calculated to evaluate structural and/or mechanical properties of the assessed material. However, the sampling of measured displacements in heterogeneous systems is singular because the volume of observation with video microscopy is finite. By carefully characterizing the sampling design in the experimental output of the multiple particle tracking technique, we derive estimators for the mean and variance of the probes’ dynamics that are independent of the peculiar statistical characteristics. We expose stringent tests of these estimators using simulated and experimental complex systems with a known heterogeneous structure. Up to a certain fundamental limitation, which we characterize through a material degree of sampling by the embedded probe tracking, these estimators can be applied to quantify the heterogeneity of a material, providing an original and intelligible kind of information on complex fluid properties. More generally, we show that the precise assessment of the statistics in the multiple particle tracking output sample of observations is essential in order to provide accurate unbiased measurements.

Molecular epidemiology biomarkers-Sample collection and processing considerations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holland, Nina T.; Pfleger, Laura; Berger, Eileen

2005-08-07

Biomarker studies require processing and storage of numerous biological samples with the goals of obtaining a large amount of information and minimizing future research costs. An efficient study design includes provisions for processing of the original samples, such as cryopreservation, DNA isolation, and preparation of specimens for exposure assessment. Use of standard, two-dimensional and nanobarcodes and customized electronic databases assure efficient management of large sample collections and tracking results of data analyses. Standard operating procedures and quality control plans help to protect sample quality and to assure validity of the biomarker data. Specific state, federal and international regulations are inmore » place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples. Appropriate informed consent must be obtained from the study subjects prior to sample collection and confidentiality of results maintained. Finally, examples of three biorepositories of different scale (European Cancer Study, National Cancer Institute and School of Public Health Biorepository, University of California, Berkeley) are used to illustrate challenges faced by investigators and the ways to overcome them. New software and biorepository technologies are being developed by many companies that will help to bring biological banking to a new level required by molecular epidemiology of the 21st century.« less

A molecular tool for detection and tracking of a potential indigenous Beauveria bassiana strain for managing emerald ash borer populations in Canada.

PubMed

Johny, Shajahan; Kyei-Poku, George

2014-10-01

Emerald ash borer is an invasive species from Asia. Beauveria bassiana strain L49-1AA is being tested for the control of emerald ash borer in Canada, using an autocontamination trapping system. We have developed a simplified allele discrimination polymerase chain reaction (PCR) assay to screen B. bassiana strain, L49-1AA from other Beauveria species by targeting the inter-strain genetic differences in 5' end of EF1-α gene of the genus Beauveria. A single nucleotide polymorphism (SNP) site, T→C was identified only in L49-1AA and was used to develop a simplified allele discrimination polymerase chain reaction (PCR) assay based on a modified allelic inhibition of displacement activity (AIDA) approach for distinguishing B. bassiana L49-1AA from all background Beauveria isolates. The SNP site was employed to design inner primers but with a deliberate mismatch introduced at the 3' antepenultimate from the mutation site in order to maximize specificity and detection efficiency. Amplification was specific to L49-1AA without cross-reaction with DNA from other Beauveria strains. In addition, the designed primers were also tested against environmental samples in L49-1AA released plots and observed to be highly efficient in detecting and discriminating the target strain, L49-1AA from both pure and crude DNA samples. This new method can potentially allow for more discriminatory tracking and monitoring of released L49-1AA in our autocontamination and dissemination projects for managing EAB populations. Additionally, the modified-AIDA format has potential as a tool for simultaneously identifying and differentiating closely related Beauveria species, strains/isolates as well as general classification of other pathogens or organisms. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

Multiple player tracking in sports video: a dual-mode two-way bayesian inference approach with progressive observation modeling.

PubMed

Xing, Junliang; Ai, Haizhou; Liu, Liwei; Lao, Shihong

2011-06-01

Multiple object tracking (MOT) is a very challenging task yet of fundamental importance for many practical applications. In this paper, we focus on the problem of tracking multiple players in sports video which is even more difficult due to the abrupt movements of players and their complex interactions. To handle the difficulties in this problem, we present a new MOT algorithm which contributes both in the observation modeling level and in the tracking strategy level. For the observation modeling, we develop a progressive observation modeling process that is able to provide strong tracking observations and greatly facilitate the tracking task. For the tracking strategy, we propose a dual-mode two-way Bayesian inference approach which dynamically switches between an offline general model and an online dedicated model to deal with single isolated object tracking and multiple occluded object tracking integrally by forward filtering and backward smoothing. Extensive experiments on different kinds of sports videos, including football, basketball, as well as hockey, demonstrate the effectiveness and efficiency of the proposed method.

Returning ex-patriot Chinese to Guangdong, China, increase the risk for local transmission of Zika virus.

PubMed

Sun, Jiufeng; Wu, De; Zhong, Haojie; Guan, Dawei; Zhang, Huan; Tan, Qiqi; Zhou, Huiqiong; Zhang, Meng; Ning, Dan; Zhang, Baohuan; Ke, Changwen; Song, Tie; Lin, Jinyan; Zhang, Yonghui; Koopmans, Marion; Gao, George F

2017-10-01

Fast expansion and linkage to microcephaly and Guillain Barre syndrome have made Zika virus (ZIKV) track attention of global health authority concerns. The epidemiology, virological characteristics and genetic evolution of introduced ZIKV to Guangdong, China, were investigated. Analyses of the epidemiological characteristics and genetic diversity of ZIKV isolates were performed. A total of twenty-eight confirmed ZIKV infection cases were imported into China in 2016, of which 19 were imported into Guangdong, China from Venezuela (16), the Samoa Islands (1), Suriname (1) and Guatemala (1). Serial sampling studies of the cases indicated longer shedding times of ZIKV particles from urine and saliva samples than from serum and conjunctiva swab samples. Seven ZIKV strains were successfully isolated from serum, urine and conjunctiva swab samples using cell culture and neonatal mouse injection methods. Genomic analysis indicated that all viruses belonged to the Asian lineage but had different evolutionary transmission routes with different geographic origins. The molecular clock phylogenetic analysis of the ZIKV genomes indicated independent local transmission that appeared to have been previously established in Venezuela and Samoa. Additionally, we found 7 unique non-synonymous mutations in the genomes of ZIKV that were imported to China. The mutations may indicate that ZIKV has undergone independent evolutionary history not caused by sudden adaptation to Chinese hosts. The increasing number of ex-patriot Chinese returning from ZIKV hyper-endemic areas to Guangdong combined with the presence of a variety of Aedes species indicate the potential for autochthonous transmission of ZIKV in Guangdong. Copyright © 2017 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Scientific Journals as Fossil Traces of Sweeping Change in the Structure and Practice of Modern Geology

ERIC Educational Resources Information Center

Fratesi, Sarah E.; Vacher, H. L.

2008-01-01

In our attempts to track changes in geological practice over time and to isolate the source of these changes, we have found that they are largely connected with the germination of new geologic subdisciplines. We use keyword and title data from articles in 68 geology journals to track the changes in influence of each subdiscipline on geology over…

Complete Genome Sequence of Escherichia coli Strain M8, Isolated from ob/ob Mice

PubMed Central

Siddharth, Jay; Membrez, Mathieu; Chakrabarti, Anirikh; Betrisey, Bertrand; Chou, Chieh Jason

2017-01-01

ABSTRACT Escherichia coli is one of the common inhabitants of the mammalian gastrointestinal track. We isolated a strain from an ob/ob mouse and performed whole-genome sequencing, which yielded a chromosome of ~5.1 Mb and three plasmids of ~160 kb, ~6 kb, and ~4 kb. PMID:28572322

Tracking an Unusual Carbapenemase-producing Organism from Drains to Patient Using Whole Genome Sequencing

PubMed Central

Ramsburg, Amanda M; Weingarten, Rebecca A; Conlan, Sean P; Dekker, John P; Michelin, Angela V; Odom, Robin T; Bordner, MaryAnn; Zellmer, Caroline J; Henderson, David K; Segre, Julia A; Frank, Karen M; Palmore, Tara N

2017-01-01

Abstract Background The NIH Clinical Center conducts patient and environmental surveillance for carbapenemase-producing organisms (CPO). Previous investigation revealed that sink drains can become colonized with CPO. Subsequent surveillance targets included potential aqueous reservoirs, such as floor drains of environmental services (EVS) closets. Methods Premoistened swabs were used to culture sink drains, floor drains, and equipment for CPO. Perirectal swabs were ordered monthly for all patients in non-behavioral health wards. Specimens were plated to CRE- and ESBL-selective media, and colonies identified by MALDI-TOF. The presence of the blaKPC gene was confirmed by PCR. When environmental CPO isolates were detected, EVS procedures and practices were reviewed. Results In June 2016, blaKPC+ Leclercia adecarboxylata was isolated from an EVS closet floor drain, and in August 2016, from drains in four additional closets. In the previous 10 years, Leclercia sp. was isolated just once from a clinical culture. In September 2016, routine surveillance revealed new-onset blaKPC+ L. adecarboxylata colonization in a stem cell transplant recipient. Investigation included 33 cultures collected from sink and floor drains, EVS equipment, and other items. EVS equipment, especially mop buckets, were identified as a likely point source due to their use in patient care areas and closets with contaminated floor drains. Among seven mop buckets sampled, one grew blaKPC+ L. adecarboxylata. Whole genome sequencing demonstrated genetic relatedness of the Leclercia isolates. Floor cleaner was changed to a disinfectant solution. Extensive decontamination of 67 EVS closets and equipment was performed urgently. No further patient or environmental cultures have grown blaKPC+ L. adecarboxylata. Conclusion The recovery of a highly unusual organism, rarely found in clinical specimens, that was also carrying a blaKPC+ plasmid, allowed us to detect environmental spread of this organism in the hospital. The ability to track this organism using genome sequencing provided strong evidence of the mode of spread, leading to effective remediation. No evidence-based methods exist for remediating drain contamination, which can serve as a potential reservoir for transmission. Disclosures All authors: No reported disclosures.

Whole-rock uranium analysis by fission track activation

NASA Technical Reports Server (NTRS)

Weiss, J. R.; Haines, E. L.

1974-01-01

We report a whole-rock uranium method in which the polished sample and track detector are separated in a vacuum chamber. Irradiation with thermal neutrons induces uranium fission in the sample, and the detector records the integrated fission track density. Detection efficiency and geometric factors are calculated and compared with calibration experiments.

Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host

PubMed Central

Lê Van, Amandine; Gladieux, Pierre; Lemaire, Christophe; Cornille, Amandine; Giraud, Tatiana; Durel, Charles-Eric; Caffier, Valérie; Le Cam, Bruno

2012-01-01

Understanding how pathogens emerge is essential to bring disease-causing agents under durable human control. Here, we used cross-pathogenicity tests to investigate the changes in life-history traits of the fungal pathogen Venturia inaequalis associated with host-tracking during the domestication of apple and subsequent host-range expansion on the wild European crabapple (Malus sylvestris). Pathogenicity of 40 isolates collected in wild and domesticated ecosystems was assessed on the domesticated apple, its Central Asian main progenitor (M. sieversii) and M. sylvestris. Isolates from wild habitats in the centre of origin of the crop were not pathogenic on the domesticated apple and less aggressive than other isolates on their host of origin. Isolates from the agro-ecosystem in Central Asia infected a higher proportion of plants with higher aggressiveness, on both the domesticated host and its progenitor. Isolates from the European crabapple were still able to cause disease on other species but were less aggressive and less frequently virulent on these hosts than their endemic populations. Our results suggest that the domestication of apple was associated with the acquisition of virulence in the pathogen following host-tracking. The spread of the disease in the agro-ecosystem would also have been accompanied by an increase in overall pathogenicity. PMID:23144656

Automated Proton Track Identification in MicroBooNE Using Gradient Boosted Decision Trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woodruff, Katherine

MicroBooNE is a liquid argon time projection chamber (LArTPC) neutrino experiment that is currently running in the Booster Neutrino Beam at Fermilab. LArTPC technology allows for high-resolution, three-dimensional representations of neutrino interactions. A wide variety of software tools for automated reconstruction and selection of particle tracks in LArTPCs are actively being developed. Short, isolated proton tracks, the signal for low- momentum-transfer neutral current (NC) elastic events, are easily hidden in a large cosmic background. Detecting these low-energy tracks will allow us to probe interesting regions of the proton's spin structure. An effective method for selecting NC elastic events is tomore » combine a highly efficient track reconstruction algorithm to find all candidate tracks with highly accurate particle identification using a machine learning algorithm. We present our work on particle track classification using gradient tree boosting software (XGBoost) and the performance on simulated neutrino data.« less

Investigations of lunar materials

NASA Technical Reports Server (NTRS)

Comstock, G. M.; Fvwaraye, A. O.; Fleischer, R. L.; Hart, H. R., Jr.

1972-01-01

The investigations were directed at determining the radiation history and surface chronology of lunar materials using the etched particle track technique. The major lunar materials studied are the igneous rocks and double core from Apollo 12, the breccia and soil samples from Apollo 14, and the core samples from Luna 16. In the course of this work two new and potentially important observations were made: (1) Cosmic ray-induced spallation-recoil tracks were identified. The density of such tracks, when compared with the density of tracks induced by a known flux of accelerator protons, yields the time of exposure of a sample within the top meter or two of moon's surface. (2) Natural, fine scale plastic deformation was found to have fragmented pre-existing charged particle tracks, allowing the dating of the mechanical event causing the deformation.

Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome.

PubMed

Drees, Kevin P; Lorch, Jeffrey M; Puechmaille, Sebastien J; Parise, Katy L; Wibbelt, Gudrun; Hoyt, Joseph R; Sun, Keping; Jargalsaikhan, Ariunbold; Dalannast, Munkhnast; Palmer, Jonathan M; Lindner, Daniel L; Marm Kilpatrick, A; Pearson, Talima; Keim, Paul S; Blehert, David S; Foster, Jeffrey T

2017-12-12

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans , a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia. IMPORTANCE This phylogenetic study of the bat white-nose syndrome agent, P. destructans , uses genomics to elucidate evolutionary relationships among populations of the fungal pathogen to understand the epizoology of this biological invasion. We analyze hypervariable and abundant genetic characters (microsatellites and genomic SNPs, respectively) to reveal previously uncharacterized diversity among populations of the pathogen from North America and Eurasia. We present new evidence supporting recent introduction of the fungus to North America from a diverse Eurasian population, with limited increase in genetic variation in North America since that introduction. Copyright © 2017 Drees et al.

Surveying drainage culvert use by carnivores: sampling design and cost-benefit analyzes of track-pads vs. video-surveillance methods.

PubMed

Mateus, Ana Rita A; Grilo, Clara; Santos-Reis, Margarida

2011-10-01

Environmental assessment studies often evaluate the effectiveness of drainage culverts as habitat linkages for species, however, the efficiency of the sampling designs and the survey methods are not known. Our main goal was to estimate the most cost-effective monitoring method for sampling carnivore culvert using track-pads and video-surveillance. We estimated the most efficient (lower costs and high detection success) interval between visits (days) when using track-pads and also determined the advantages of using each method. In 2006, we selected two highways in southern Portugal and sampled 15 culverts over two 10-day sampling periods (spring and summer). Using the track-pad method, 90% of the animal tracks were detected using a 2-day interval between visits. We recorded a higher number of crossings for most species using video-surveillance (n = 129) when compared with the track-pad technique (n = 102); however, the detection ability using the video-surveillance method varied with type of structure and species. More crossings were detected in circular culverts (1 m and 1.5 m diameter) than in box culverts (2 m to 4 m width), likely because video cameras had a reduced vision coverage area. On the other hand, carnivore species with small feet such as the common genet Genetta genetta were detected less often using the track-pad surveying method. The cost-benefit analyzes shows that the track-pad technique is the most appropriate technique, but video-surveillance allows year-round surveys as well as the behavior response analyzes of species using crossing structures.

Molecular characterization of Vibrio cholerae isolates from Iran 2012 and 2013 outbreaks.

PubMed

Bakhshi, B

2016-06-01

The aim of this study was to assess the genetic diversity of Vibrio cholerae isolated from 2012 and 2013 outbreaks in Iran, with regard to their virulence properties. A total of 20 V. cholerae strains were collected from Sistan-Baluchestan province of Iran during 2012 and 2013 outbreaks. Hybridization assays showed the presence of ctx, zot, ace and rstC genes related to CTX and RS1 phages in all of the isolates. PCR assay indicated the concomitant presence of ORFs within RTX (1448, 1451) and TLC (1465, 1469) elements within the genome of the isolates. ERIC-PCR analysis showed four homogeneous profiles among which strains from 2013 outbreak and 72·7% of 2012 outbreak uniformly showed a common ERIC-PCR fingerprint. Ribotyping assay showed a single dominant profile (ribotype A) among 77·7 and 72·7% of isolates recovered from 2013 and 2012 outbreaks respectively. In conclusion, this study reports high degree of homogeneity among isolates from 2012 and 2013 outbreaks in Iran and emphasizes on the primary application of ERIC-PCR to generate fingerprints and differentiate between V. cholerae isolates of clinical origin in a timely manner for epidemiological investigations and source tracking purposes, although ribotyping method was proved to be more discriminatory. The clonality of Vibrio cholerae isolates recovered from patients with Afghan nationality during 2012 and 2013 outbreaks in Iran emphasizes on the need for monitoring Iran boundaries. This highlights the demand for a simple, reproducible and time-saving typing method for rapid and reliable assessment of clonal correlation of isolates in outbreaks. In this regard, ERIC-PCR produced results comparable with those obtained by PFGE and ribotyping which is of great significance in public health and source tracking purposes. © 2016 The Society for Applied Microbiology.

Enterococcus phages as potential tool for identifying sewage inputs in the Great Lakes region

USGS Publications Warehouse

Vijayavel, K.; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Ebdon, J.; Taylor, H.; Kashian, D.R.

2014-01-01

Bacteriophages are viruses living in bacteria that can be used as a tool to detect fecal contamination in surface waters around the world. However, the lack of a universal host strain makes them unsuitable for tracking fecal sources. We evaluated the suitability of two newly isolated Enterococcus host strains (ENT-49 and ENT-55) capable for identifying sewage contamination in impacted waters by targeting phages specific to these hosts. Both host strains were isolated from wastewater samples and identified as E. faecium by 16S rRNA gene sequencing. Occurrence of Enterococcus phages was evaluated in sewage samples (n = 15) from five wastewater treatment plants and in fecal samples from twenty-two species of wild and domesticated animals (individual samples; n = 22). Levels of Enterococcus phages, F + coliphages, Escherichia coli and enterococci were examined from four rivers, four beaches, and three harbors. Enterococcus phages enumeration was at similar levels (Mean = 6.72 Log PFU/100 mL) to F + coliphages in all wastewater samples, but were absent from all non-human fecal sources tested. The phages infecting Enterococcus spp. and F + coliphages were not detected in the river samples (detection threshold < 10 PFU/100 mL), but were present in the beach and harbor samples (range = 1.83 to 2.86 Log PFU/100 mL). Slightly higher concentrations (range = 3.22 to 3.69 Log MPN/100 mL) of E. coli and enterococci when compared to F + coliphages and Enterococcus phages, were observed in the river, beach and harbor samples. Our findings suggest that the bacteriophages associated with these particular Enterococcus host strains offer potentially sensitive and human-source specific indicators of enteric pathogen risk.

Identification of subsurface microorganisms at Yucca Mountain; Third quarterly report, January 1, 1994--March 31, 1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stetzenbach, L.D.

1994-05-01

Bacteria isolated from ground water samples taken from 31 springs during 1993 were collected and processed according to procedures described in earlier reports. These procedures required aseptic collection of surface water samples in sterile screw-capped containers, transportation to the HRC microbiology laboratory, and culture by spread plating onto R2A medium. The isolates were further processed for identification using a gas chromatographic analysis of fatty acid methyl esters (FAME) extracted from cell membranes. This work generated a presumptive identification of 113 bacterial species distributed among 45 genera using a database obtained from Microbial ID, Inc., Newark, Delaware (MIDI). A preliminary examinationmore » of the FAME data was accomplished using cluster analysis and principal component analysis software obtained from MIDI. Typically, bacterial strains that cluster at less than 10 Euclidian distance units have fatty acid patterns consistent among members of the same species. Thus an organism obtained from one source can be recognized if it is isolated again from the same or any other source. This makes it possible to track the distribution of organisms and monitor environmental conditions or fluid transport mechanisms. Microorganisms are seldom found as monocultures in natural environments. They are more likely to be closely associated with other genera with complementary metabolic requirements. An understanding of the indigenous microorganism population is useful in understanding subtle changes in the environment. However, classification of environmental organisms using traditional methods is not ideal because differentiation of species with small variations or genera with very similar taxonomic characteristics is beyond the capabilities of traditional microbiological methods.« less

A sub-GeV charged-current quasi-elastic $$\

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walding, Joseph James

2009-12-01

Neutrino-nucleus charged-current quasi-elastic scattering is the signal interaction used by many neutrino oscillation experiments. For muon disappearance studies the signal mode is ν μn → μp. Modern oscillation experiments, such as T2K, produce neutrino beams with peak beam energies of order a few-GeV. It is therefore vitally important to have accurate measurements of the charged-current quasi-elastic crosssection for future neutrino oscillation experiments. Neutrino-nucleus cross-sections in the few-GeV region are not well understood, with the main uncertainties coming from understanding of the neutrino beam flux and the final state interactions within nuclei. SciBooNE is a sub-GeV neutrino-nucleus cross-section experiment based atmore » Fermilab, Batavia, USA, with the goal to measure neutrino cross-sections with precision of order 5%. SciBooNE took data from June 2007 until August 2008, in total 0.99×10 20 and 1.53×10 20 protons on target were collected in neutrino and anti-neutrino mode, respectively. In this thesis a ν μ charged-current quasi-elastic (CCQE) cross-section contained within the SciBar sub-detector is presented. A method to tag muons in SciBar was developed and three samples were isolated. An excess in backwards tracks in the one-track sample is observed. A Poisson maximum likelihood is used to extract the CCQE cross-section. The fit was applied using a basic fit parameter model, successfully used to obtain the cross-section in the SciBar-MRD matched CCQE analysis. This method was found to be insufficient in describing the data for the SciBarcontained CCQE analysis. By adding two migration parameters the cross-section was calculated to be 1.004 ± 0.031 (stat) +0.101 -0.150(sys) × 10 -38 cm 2/neutron, excluding backwards tracks with a χ 2 = 203.8/76 d.o.f. and 1.083 ± 0.030(stat) +0.115 -0.177(sys) × 10 -38 cm 2/neutron, including backwards tracks with a χ 2 = 659.8/133 d.o.f. Only neutrino beam and detector systematics have been considered. Further study of the SciBar-contained sample is suggested, introducing additional fit parameters and considering the remaining systematics. The end goal is to extract a SciBooNE CCQE cross-section using the SciBar-contained and SciBar-MRD matched samples.« less

A GPU-accelerated 3D Coupled Sub-sample Estimation Algorithm for Volumetric Breast Strain Elastography

PubMed Central

Peng, Bo; Wang, Yuqi; Hall, Timothy J; Jiang, Jingfeng

2017-01-01

Our primary objective of this work was to extend a previously published 2D coupled sub-sample tracking algorithm for 3D speckle tracking in the framework of ultrasound breast strain elastography. In order to overcome heavy computational cost, we investigated the use of a graphic processing unit (GPU) to accelerate the 3D coupled sub-sample speckle tracking method. The performance of the proposed GPU implementation was tested using a tissue-mimicking (TM) phantom and in vivo breast ultrasound data. The performance of this 3D sub-sample tracking algorithm was compared with the conventional 3D quadratic sub-sample estimation algorithm. On the basis of these evaluations, we concluded that the GPU implementation of this 3D sub-sample estimation algorithm can provide high-quality strain data (i.e. high correlation between the pre- and the motion-compensated post-deformation RF echo data and high contrast-to-noise ratio strain images), as compared to the conventional 3D quadratic sub-sample algorithm. Using the GPU implementation of the 3D speckle tracking algorithm, volumetric strain data can be achieved relatively fast (approximately 20 seconds per volume [2.5 cm × 2.5 cm × 2.5 cm]). PMID:28166493

An Improved Wake Vortex Tracking Algorithm for Multiple Aircraft

NASA Technical Reports Server (NTRS)

Switzer, George F.; Proctor, Fred H.; Ahmad, Nashat N.; LimonDuparcmeur, Fanny M.

2010-01-01

The accurate tracking of vortex evolution from Large Eddy Simulation (LES) data is a complex and computationally intensive problem. The vortex tracking requires the analysis of very large three-dimensional and time-varying datasets. The complexity of the problem is further compounded by the fact that these vortices are embedded in a background turbulence field, and they may interact with the ground surface. Another level of complication can arise, if vortices from multiple aircrafts are simulated. This paper presents a new technique for post-processing LES data to obtain wake vortex tracks and wake intensities. The new approach isolates vortices by defining "regions of interest" (ROI) around each vortex and has the ability to identify vortex pairs from multiple aircraft. The paper describes the new methodology for tracking wake vortices and presents application of the technique for single and multiple aircraft.

A new servo method using servo layer and transverse MR head for submicron track servo on hard computer disks

NASA Astrophysics Data System (ADS)

Tan, Baolin; Mapps, Desmond J.; Pan, Genhua; Robinson, Paul

1996-03-01

A disk with a data, servo and isolation layer has been fabricated with the data layer magnetized along the circumferential direction. The servo layer was recorded with servo pattern magnetized along the radial direction. A continuous servo signal is obtained and the servo does not occupy any data area. In this new method, the servo and data bits can share media surface area on the disk without interference. Track following on 0.7 μm tracks has been demonstrated using the new servo method on longitudinal rigid disks.

Juvenile habitat partitioning and relative productivity in allochronically isolated sockeye salmon (Oncorhynchus nerka).

PubMed

Miller, Ek Fillatre; Bradbury, Ir; Heath, Dd

2011-12-01

Allochronic divergence, like spatial isolation, may contribute to population diversity and adaptation, however the challenges for tracking habitat utilization in shared environments are far greater. Adult Klukshu River (Yukon, Canada) sockeye salmon, Oncorhynchus nerka, return as genetically distinct "early" and "late" runs. Early and late adult spawning populations (1999 and 2000) and their subsequent fry (sampled at 7 sites in 2000 and at 8 sites in 2001 throughout Klukshu Lake and River) were genotyped at eight microsatellite loci. Bayesian assignment was used to determine the spatial distribution of early versus late fry; although intermixed, the distribution of fry significantly differed in Klukshu Lake and in the Klukshu River in 2001, based on crosstab analyses. Late-run fry predominated in Klukshu Lake at all sites, while early-run fry were most common in the north and south of Klukshu Lake and in Klukshu River. Early-run spawners had significantly higher relative productivity (early life survival) than late-run fish (2.9 times more fry produced per early-run adult in 2000, and 9.2 times more in 2001). This study demonstrates spatial habitat partitioning and differences in the contribution of allochronically isolated populations to fry abundance, and highlights annual variability that likely contributes to recruitment variation.

Juvenile habitat partitioning and relative productivity in allochronically isolated sockeye salmon (Oncorhynchus nerka)

PubMed Central

Miller, EK Fillatre; Bradbury, IR; Heath, DD

2011-01-01

Allochronic divergence, like spatial isolation, may contribute to population diversity and adaptation, however the challenges for tracking habitat utilization in shared environments are far greater. Adult Klukshu River (Yukon, Canada) sockeye salmon, Oncorhynchus nerka, return as genetically distinct “early” and “late” runs. Early and late adult spawning populations (1999 and 2000) and their subsequent fry (sampled at 7 sites in 2000 and at 8 sites in 2001 throughout Klukshu Lake and River) were genotyped at eight microsatellite loci. Bayesian assignment was used to determine the spatial distribution of early versus late fry; although intermixed, the distribution of fry significantly differed in Klukshu Lake and in the Klukshu River in 2001, based on crosstab analyses. Late-run fry predominated in Klukshu Lake at all sites, while early-run fry were most common in the north and south of Klukshu Lake and in Klukshu River. Early-run spawners had significantly higher relative productivity (early life survival) than late-run fish (2.9 times more fry produced per early-run adult in 2000, and 9.2 times more in 2001). This study demonstrates spatial habitat partitioning and differences in the contribution of allochronically isolated populations to fry abundance, and highlights annual variability that likely contributes to recruitment variation. PMID:22393527

Lunar sample contracts

NASA Technical Reports Server (NTRS)

Walker, R. M.

1974-01-01

The major scientific accomplishments through 1971 are reported for the particle track studies of lunar samples. Results are discussed of nuclear track measurements by optical and electron microscopy, thermoluminescence, X-ray diffraction, and differential thermal analysis.

Towards Automated Three-Dimensional Tracking of Nephrons through Stacked Histological Image Sets

PubMed Central

Bhikha, Charita; Andreasen, Arne; Christensen, Erik I.; Letts, Robyn F. R.; Pantanowitz, Adam; Rubin, David M.; Thomsen, Jesper S.; Zhai, Xiao-Yue

2015-01-01

An automated approach for tracking individual nephrons through three-dimensional histological image sets of mouse and rat kidneys is presented. In a previous study, the available images were tracked manually through the image sets in order to explore renal microarchitecture. The purpose of the current research is to reduce the time and effort required to manually trace nephrons by creating an automated, intelligent system as a standard tool for such datasets. The algorithm is robust enough to isolate closely packed nephrons and track their convoluted paths despite a number of nonideal, interfering conditions such as local image distortions, artefacts, and interstitial tissue interference. The system comprises image preprocessing, feature extraction, and a custom graph-based tracking algorithm, which is validated by a rule base and a machine learning algorithm. A study of a selection of automatically tracked nephrons, when compared with manual tracking, yields a 95% tracking accuracy for structures in the cortex, while those in the medulla have lower accuracy due to narrower diameter and higher density. Limited manual intervention is introduced to improve tracking, enabling full nephron paths to be obtained with an average of 17 manual corrections per mouse nephron and 58 manual corrections per rat nephron. PMID:26170896

Towards Automated Three-Dimensional Tracking of Nephrons through Stacked Histological Image Sets.

PubMed

Bhikha, Charita; Andreasen, Arne; Christensen, Erik I; Letts, Robyn F R; Pantanowitz, Adam; Rubin, David M; Thomsen, Jesper S; Zhai, Xiao-Yue

2015-01-01

An automated approach for tracking individual nephrons through three-dimensional histological image sets of mouse and rat kidneys is presented. In a previous study, the available images were tracked manually through the image sets in order to explore renal microarchitecture. The purpose of the current research is to reduce the time and effort required to manually trace nephrons by creating an automated, intelligent system as a standard tool for such datasets. The algorithm is robust enough to isolate closely packed nephrons and track their convoluted paths despite a number of nonideal, interfering conditions such as local image distortions, artefacts, and interstitial tissue interference. The system comprises image preprocessing, feature extraction, and a custom graph-based tracking algorithm, which is validated by a rule base and a machine learning algorithm. A study of a selection of automatically tracked nephrons, when compared with manual tracking, yields a 95% tracking accuracy for structures in the cortex, while those in the medulla have lower accuracy due to narrower diameter and higher density. Limited manual intervention is introduced to improve tracking, enabling full nephron paths to be obtained with an average of 17 manual corrections per mouse nephron and 58 manual corrections per rat nephron.

Fast Track Extubation In Adult Patients On Pump Open Heart Surgery At A Tertiary Care Hospital.

PubMed

Akhtar, Mohammad Irfan; Sharif, Hasanat; Hamid, Mohammad; Samad, Khalid; Khan, Fazal Hameed

2016-01-01

Fast-track cardiac surgery programs have been established as the standard of cardiac surgical care. Studies have shown that early extubation in elective cardiac surgery patients, including coronary and non-coronary open-heart surgery patients does not increase perioperative morbidity and mortality. The objective of this observational study was to determine the success and failure profile of fast track extubation (FTE) practice in adult open-heart surgical patients. The study was conducted at cardiac operating room and Cardiac Intensive Care Unit (CICU) of a tertiary care hospital for a period of nine months, i.e., from Oct 2014 to June-2015. All on pump elective adult cardiac surgery patients including isolated CABG, isolated Valve replacements, combined procedures and aortic root replacements were enrolled in the study. Standardized anesthetic technique was adopted. Surgical and bypass techniques were tailored according to the procedure. Success of Fast track extubation was defined as extubation within 6 hours of arrival in CICU. A total of 290 patients were recruited. The average age of the patients was 56.3±10.5 years. There were 77.6% male and 22.4% female patients. Overall success rate was 51.9% and failure rate was 48.1%. The peri-operative renal insufficiency, cross clamp time and CICU stay (hours) were significantly lower in success group. Re-intubation rate was 0.74%. The perioperative parameters were significantly better in success group and the safety was also demonstrated in the patients who were fast tracked successfully. To implement the practice in its full capacity and benefit, a fast track protocol needs to be devised to standardize the current practices and to disseminate the strategy among junior anaesthesiologists, perfusionists and nursing staff.

Antibiotic resistance and biofilm formation of some bacteria isolated from sediment, water and fish farms in Malaysia

NASA Astrophysics Data System (ADS)

Faja, Orooba Meteab; Usup, Gires; Ahmad, Asmat

2018-04-01

A total of 90 isolates of bacteria were isolated, from sediment (10) samples, water (10) samples and fish (12) samples (Sea bass, Snapper, Grouper and Tilapia). These include 22 isolates of bacteria from sediment, 28 isolates from water and 40 isolates from fish. All the isolates were tested for sensitivity to 13 antibiotics using disc diffusion method. The isolates showed high resistance to some antibiotics based on samples source. Isolates from sediment showed highest resistance toward novobiocin, kanamycin, ampicillin and streptomycin while isolates from water showed highest resistance against vancomycin, penicillin, streptomycin and tetracycline, in contrast, in fish sample showed highest resistance toward vancomycin, ampicillin, streptomycin and tetracycline. Most of the isolates showed biofilm formation ability with different degrees. Out of 22 bacteria isolates from water, two isolates were weak biofilm formers, six isolates moderate biofilm formers and fourteen isolates strong biofilm formers. While, out of 28 bacteria isolates from water one isolate was weak biofilm former, five isolates moderate biofilm formers and 22 strong biofilm formers Fish isolate showed three isolates (8%) moderate biofilm formers and 27 isolates strong biofilm formers. Biofilm formation was one of the factors that lead to antibiotic resistance of the bacterial isolates from these samples.

Consistently Sampled Correlation Filters with Space Anisotropic Regularization for Visual Tracking

PubMed Central

Shi, Guokai; Xu, Tingfa; Luo, Jiqiang; Li, Yuankun

2017-01-01

Most existing correlation filter-based tracking algorithms, which use fixed patches and cyclic shifts as training and detection measures, assume that the training samples are reliable and ignore the inconsistencies between training samples and detection samples. We propose to construct and study a consistently sampled correlation filter with space anisotropic regularization (CSSAR) to solve these two problems simultaneously. Our approach constructs a spatiotemporally consistent sample strategy to alleviate the redundancies in training samples caused by the cyclical shifts, eliminate the inconsistencies between training samples and detection samples, and introduce space anisotropic regularization to constrain the correlation filter for alleviating drift caused by occlusion. Moreover, an optimization strategy based on the Gauss-Seidel method was developed for obtaining robust and efficient online learning. Both qualitative and quantitative evaluations demonstrate that our tracker outperforms state-of-the-art trackers in object tracking benchmarks (OTBs). PMID:29231876

Molecular typing of Legionella pneumophila from air-conditioning cooling waters using mip gene, SBT, and FAFLP methods.

PubMed

Gong, Xiangli; Li, Juntao; Zhang, Ying; Hou, Shuiping; Qu, Pinghua; Yang, Zhicong; Chen, Shouyi

2017-08-01

Legionella spp. are important waterborne pathogens. Molecular typing has become an important method for outbreaks investigations and source tracking of Legionnaires. In a survey program conducted by the Guangzhou Center for Disease Control and Prevention, multiple serotypes Legionella pneumophila (L. pneumophila) were isolated from waters in air-conditioning cooling towers in urban Guangzhou region, China between 2008 and 2011. Three genotyping methods, mip (macrophage infectivity potentiator) genotyping, SBT (sequence-based typing), and FAFLP (fluorescent amplified fragment length polymorphism analysis) were used to type these waterborne L. pneumophila isolates. The three methods were capable of typing all the 134 isolates and a reference strain of L. pneumophila (ATCC33153), with discriminatory indices of 0.7034, 0.9218, and 0.9376, for the mip, SBT, and FAFLP methods respectively. Among the 9 serotypes of the 134 isolates, 10, 50, and 34 molecular types were detected by the mip, SBT, and FAFLP methods respectively. The mip genotyping and SBT typing are more feasible for inter-laboratory results sharing and comparison of different types of L. pneumophila. The SBT and FAFLP typing methods were rapid with higher discriminatory abilities. Combinations of two or more of the typing methods enables more accurate typing of Legionella isolates for outbreak investigations and source tracking of Legionnaires. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence.

PubMed

Kumar, Nitin; Miyajima, Fabio; He, Miao; Roberts, Paul; Swale, Andrew; Ellison, Louise; Pickard, Derek; Smith, Godfrey; Molyneux, Rebecca; Dougan, Gordon; Parkhill, Julian; Wren, Brendan W; Parry, Christopher M; Pirmohamed, Munir; Lawley, Trevor D

2016-03-15

Accurate tracking of Clostridium difficile transmission within healthcare settings is key to its containment but is hindered by the lack of discriminatory power of standard genotyping methods. We describe a whole-genome phylogenetic-based method to track the transmission of individual clones in infected hospital patients from the epidemic C. difficile 027/ST1 lineage, and to distinguish between the 2 causes of recurrent disease, relapse (same strain), or reinfection (different strain). We monitored patients with C. difficile infection in a UK hospital over a 2-year period. We performed whole-genome sequencing and phylogenetic analysis of 108 strains isolated from symptomatic patients. High-resolution phylogeny was integrated with in-hospital transfers and contact data to create an infection network linking individual patients and specific hospital wards. Epidemic C. difficile 027/ST1 caused the majority of infections during our sampling period. Integration of whole-genome single nucleotide polymorphism (SNP) phylogenetic analysis, which accurately discriminated between 27 distinct SNP genotypes, with patient movement and contact data identified 32 plausible transmission events, including ward-based contamination (66%) or direct donor-recipient contact (34%). Highly contagious donors were identified who contributed to the persistence of clones within distinct hospital wards and the spread of clones between wards, especially in areas of intense turnover. Recurrent cases were identified between 4 and 26 weeks, highlighting the limitation of the standard <8-week cutoff used for patient diagnosis and management. Genome-based infection tracking to monitor the persistence and spread of C. difficile within healthcare facilities could inform infection control and patient management. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

Diversity and antibiotic resistance of Aeromonas spp. in drinking and waste water treatment plants.

PubMed

Figueira, Vânia; Vaz-Moreira, Ivone; Silva, Márcia; Manaia, Célia M

2011-11-01

The taxonomic diversity and antibiotic resistance phenotypes of aeromonads were examined in samples from drinking and waste water treatment plants (surface, ground and disinfected water in a drinking water treatment plant, and raw and treated waste water) and tap water. Bacteria identification and intra-species variation were determined based on the analysis of the 16S rRNA, gyrB and cpn60 gene sequences. Resistance phenotypes were determined using the disc diffusion method. Aeromonas veronii prevailed in raw surface water, Aeromonas hydrophyla in ozonated water, and Aeromonas media and Aeromonas puntacta in waste water. No aeromonads were detected in ground water, after the chlorination tank or in tap water. Resistance to ceftazidime or meropenem was detected in isolates from the drinking water treatment plant and waste water isolates were intrinsically resistant to nalidixic acid. Most of the times, quinolone resistance was associated with the gyrA mutation in serine 83. The gene qnrS, but not the genes qnrA, B, C, D or qepA, was detected in both surface and waste water isolates. The gene aac(6')-ib-cr was detected in different waste water strains isolated in the presence of ciprofloxacin. Both quinolone resistance genes were detected only in the species A. media. This is the first study tracking antimicrobial resistance in aeromonads in drinking, tap and waste water and the importance of these bacteria as vectors of resistance in aquatic environments is discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Characterization of Escherichia coli populations from gulls, landfill trash, and wastewater using ribotyping.

PubMed

Nelson, M; Jones, S H; Edwards, C; Ellis, J C

2008-08-19

Due to their opportunistic and gregarious nature, gulls may be important reservoirs and vectors for anthropogenically derived fecal pathogens in coastal areas. We used ribotyping, a genotypic bacterial source tracking method, to compare populations of Escherichia coli among herring gulls Larus argentatus, great black-backed gulls L. marinus, wastewater, and landfill trash in New Hampshire and Maine, USA. Concentrations of E. coli in gull feces varied widely among individuals, but were generally high (6.0 x 10(1) to 2.5 x 10(9) g(-1) wet weight). Of 39 E. coli isolates from L. argentatus, 67% had banding patterns that were > or = 90% similar to those from wastewater and trash, whereas only 39% of 36 L. marinus isolates exhibited > or = 90% similarity to these sources. Strains of E. coli from gulls matched (> or = 90% similarity) more strains from wastewater (39% matching) than from trash (15% matching). E. coli isolates from L. marinus feces exhibited a greater diversity of banding patterns than did isolates from L. argentatus. There were more unique E. coli banding patterns in trash samples than in wastewater, and higher diversity indices in the former compared to the latter. These findings suggest that both species of gulls, especially L. argentatus, obtain fecal bacteria from wastewater and landfill trash, which they may transport to recreational beaches and waters. Our results also indicate that E. coli populations may vary widely between gull species, and between the anthropogenic habitats that they frequent, i.e. landfills and wastewater treatment facilities.

Experimental evidence regarding the pressure dependence of fission track annealing in apatite

NASA Astrophysics Data System (ADS)

Schmidt, J. S.; Lelarge, M. L. M. V.; Conceicao, R. V.; Balzaretti, N. M.

2014-03-01

The main purposes of fission track thermochronology are unravelling the thermal histories of sedimentary basins, determining uplift and denudation rates, identifying the structural evolution of orogenic belts, determining sedimentary provenance, and dating volcanic rocks. The effect of temperature on fission tracks is well known and is used to determine the thermal history; however, the effect of pressure on the stability of tracks is still under debate. The present work aims to understand the role of pressure on the annealing kinetics of apatite fission tracks. The samples of Durango apatite used in our experiments were chosen for their international recognition as a calibration standard for geological dating. Neutron irradiation of the samples, after total annealing of their spontaneous tracks, produced induced tracks with homogeneous densities and lengths. The effect of pressure associated with temperature on fission track annealing was verified by experimental procedures using a hydraulic press of 1000 t with a toroidal chamber profile. The experiments consisted of a combination of applying 2 and 4 GPa with 20,150,190,235, and 290 °C for 1 and 10 h. The annealing rate was analysed by measuring the lengths of the fission tracks after each experiment using optical microscopy. The results demonstrate that the annealing of apatite fission tracks has a pressure dependence for samples subjected to 2 and 4 GPa. However, when extrapolated to pressures of ⩽150 MPa, compatible with the normal geological context in which apatite fission track methodology is broadly used, this dependence becomes insignificant compared to the temperature effect.

Size-exclusion chromatography-based enrichment of extracellular vesicles from urine samples

PubMed Central

Lozano-Ramos, Inés; Bancu, Ioana; Oliveira-Tercero, Anna; Armengol, María Pilar; Menezes-Neto, Armando; Del Portillo, Hernando A.; Lauzurica-Valdemoros, Ricardo; Borràs, Francesc E.

2015-01-01

Renal biopsy is the gold-standard procedure to diagnose most of renal pathologies. However, this invasive method is of limited repeatability and often describes an irreversible renal damage. Urine is an easily accessible fluid and urinary extracellular vesicles (EVs) may be ideal to describe new biomarkers associated with renal pathologies. Several methods to enrich EVs have been described. Most of them contain a mixture of proteins, lipoproteins and cell debris that may be masking relevant biomarkers. Here, we evaluated size-exclusion chromatography (SEC) as a suitable method to isolate urinary EVs. Following a conventional centrifugation to eliminate cell debris and apoptotic bodies, urine samples were concentrated using ultrafiltration and loaded on a SEC column. Collected fractions were analysed by protein content and flow cytometry to determine the presence of tetraspanin markers (CD63 and CD9). The highest tetraspanin content was routinely detected in fractions well before the bulk of proteins eluted. These tetraspanin-peak fractions were analysed by cryo-electron microscopy (cryo-EM) and nanoparticle tracking analysis revealing the presence of EVs. When analysed by sodium dodecyl sulphate–polyacrylamide gel electrophoresis, tetraspanin-peak fractions from urine concentrated samples contained multiple bands but the main urine proteins (such as Tamm–Horsfall protein) were absent. Furthermore, a preliminary proteomic study of these fractions revealed the presence of EV-related proteins, suggesting their enrichment in concentrated samples. In addition, RNA profiling also showed the presence of vesicular small RNA species. To summarize, our results demonstrated that concentrated urine followed by SEC is a suitable option to isolate EVs with low presence of soluble contaminants. This methodology could permit more accurate analyses of EV-related biomarkers when further characterized by -omics technologies compared with other approaches. PMID:26025625

Reproducibility of apatite fission-track length data and thermal history reconstruction

NASA Astrophysics Data System (ADS)

Ketcham, Richard A.; Donelick, Raymond A.; Balestrieri, Maria Laura; Zattin, Massimiliano

2009-07-01

The ability to derive detailed thermal history information from apatite fission-track analysis is predicated on the reliability of track length measurements. However, insufficient attention has been given to whether and how these measurements should be standardized. In conjunction with a fission-track workshop we conducted an experiment in which 11 volunteers measured ~ 50 track lengths on one or two samples. One mount contained Durango apatite with unannealed induced tracks, and one contained apatite from a crystalline rock containing spontaneous tracks with a broad length distribution caused by partial resetting. Results for both mounts showed scatter indicative of differences in measurement technique among the individual analysts. The effects of this variability on thermal history inversion were tested using the HeFTy computer program to model the spontaneous track measurements. A cooling-only scenario and a reheating scenario more consistent with the sample's geological history were posed. When a uniform initial length value from the literature was used, results among analysts were very inconsistent in both scenarios, although normalizing for track angle by projecting all lengths to a c-axis parallel crystallographic orientation improved some aspects of congruency. When the induced track measurement was used as the basis for thermal history inversion congruency among analysts, and agreement with inversions based on data previously collected, was significantly improved. Further improvement was obtained by using c-axis projection. Differences among inversions that persisted could be traced to differential sampling of long- and short-track populations among analysts. The results of this study, while demonstrating the robustness of apatite fission-track thermal history inversion, nevertheless point to the necessity for a standardized length calibration schema that accounts for analyst variation.

Effect of α-damage on fission-track annealing in zircon

USGS Publications Warehouse

Kasuya, Masao; Naeser, Charles W.

1988-01-01

The thermal stability of confined fission-track lengths in four zircon samples having different spontaneous track densities (i.e., different amounts of ??-damage) has been studied by one-hour isochronal annealing experiments. The thermal stability of spontaneous track lengths is independent of initial spontaneous track density. The thermal stability of induced track lengths in pre-annealed zircon, however, is significantly higher than that of spontaneous track lengths. The results indicate that the presence of ??-damage lowers the thermal stability of fission-tracks in zircon.

Isolation, Culture, and Motility Measurements of Epidermal Melanocytes from GFP-Expressing Reporter Mice.

PubMed

Dagnino, Lina; Crawford, Melissa

2018-03-27

In this article, we provide a method to isolate primary epidermal melanocytes from reporter mice, which also allow targeted gene inactivation. The mice from which these cells are isolated are bred into a Rosa26 mT/mG reporter background, which results in GFP expression in the targeted melanocytic cell population. These cells are isolated and cultured to >95% purity. The cells can be used for gene expression studies, clonogenic experiments, and biological assays, such as capacity for migration. Melanocytes are slow moving cells, and we also provide a method to measure motility using individual cell tracking and data analysis.

Research Associate | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) at the Frederick National Laboratory for Cancer Research (FNLCR) pursues independent, multidisciplinary research programs in basic or applied molecular biology, immunology, retrovirology, cancer biology or human genetics. As part of the BSP, the Microbiome and Genetics Core (the Core) characterizes microbiomes by next-generation sequencing to determine their composition and variation, as influenced by immune, genetic, and host health factors. The Core provides support across a spectrum of processes, from nucleic acid isolation through bioinformatics and statistical analysis. KEY ROLES/RESPONSIBILITIES The Research Associate II will provide support in the areas of automated isolation, preparation, PCR and sequencing of DNA on next generation platforms (Illumina MiSeq and NextSeq). An opportunity exists to join the Core’s team of highly trained experimentalists and bioinformaticians working to characterize microbiome samples. The following represent requirements of the position: A minimum of five (5) years related of biomedical experience. Experience with high-throughput nucleic acid (DNA/RNA) extraction. Experience in performing PCR amplification (including quantitative real-time PCR). Experience or familiarity with robotic liquid handling protocols (especially on the Eppendorf epMotion 5073 or 5075 platforms). Experience in operating and maintaining benchtop Illumina sequencers (MiSeq and NextSeq). Ability to evaluate experimental quality and to troubleshoot molecular biology protocols. Experience with sample tracking, inventory management and biobanking. Ability to operate and communicate effectively in a team-oriented work environment.

Efficient Sample Tracking With OpenLabFramework

PubMed Central

List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-01-01

The advance of new technologies in biomedical research has led to a dramatic growth in experimental throughput. Projects therefore steadily grow in size and involve a larger number of researchers. Spreadsheets traditionally used are thus no longer suitable for keeping track of the vast amounts of samples created and need to be replaced with state-of-the-art laboratory information management systems. Such systems have been developed in large numbers, but they are often limited to specific research domains and types of data. One domain so far neglected is the management of libraries of vector clones and genetically engineered cell lines. OpenLabFramework is a newly developed web-application for sample tracking, particularly laid out to fill this gap, but with an open architecture allowing it to be extended for other biological materials and functional data. Its sample tracking mechanism is fully customizable and aids productivity further through support for mobile devices and barcoded labels. PMID:24589879

Fast emulation of track reconstruction in the CMS simulation

NASA Astrophysics Data System (ADS)

Komm, Matthias; CMS Collaboration

2017-10-01

Simulated samples of various physics processes are a key ingredient within analyses to unlock the physics behind LHC collision data. Samples with more and more statistics are required to keep up with the increasing amounts of recorded data. During sample generation, significant computing time is spent on the reconstruction of charged particle tracks from energy deposits which additionally scales with the pileup conditions. In CMS, the FastSimulation package is developed for providing a fast alternative to the standard simulation and reconstruction workflow. It employs various techniques to emulate track reconstruction effects in particle collision events. Several analysis groups in CMS are utilizing the package, in particular those requiring many samples to scan the parameter space of physics models (e.g. SUSY) or for the purpose of estimating systematic uncertainties. The strategies for and recent developments in this emulation are presented, including a novel, flexible implementation of tracking emulation while retaining a sufficient, tuneable accuracy.

New color-based tracking algorithm for joints of the upper extremities

NASA Astrophysics Data System (ADS)

Wu, Xiangping; Chow, Daniel H. K.; Zheng, Xiaoxiang

2007-11-01

To track the joints of the upper limb of stroke sufferers for rehabilitation assessment, a new tracking algorithm which utilizes a developed color-based particle filter and a novel strategy for handling occlusions is proposed in this paper. Objects are represented by their color histogram models and particle filter is introduced to track the objects within a probability framework. Kalman filter, as a local optimizer, is integrated into the sampling stage of the particle filter that steers samples to a region with high likelihood and therefore fewer samples is required. A color clustering method and anatomic constraints are used in dealing with occlusion problem. Compared with the general basic particle filtering method, the experimental results show that the new algorithm has reduced the number of samples and hence the computational consumption, and has achieved better abilities of handling complete occlusion over a few frames.

Observing rotation and deformation of sea ice with synthetic aperture radar

NASA Technical Reports Server (NTRS)

Vesecky, J. F.; Samadani, R.; Daida, J. M.; Smith, M. P.; Bracewell, R. N.

1987-01-01

The ESA's ERS-1 satellite will carry SARs over the polar regions; an important component in the use of these data is an automated scheme for the extraction of sea ice velocity fields from a sequence of SAR images of the same geographical region. The image pyramid area-correlation hierarchical method is noted to be vulnerable to uncertainties for sea ice rotations greater than 10-15 deg between SAR observations. Rotation-invariant methods can successfully track isolated floes in the marginal ice zone. Hu's (1962) invariant moments are also worth considering as a possible basis for rotation-invariant tracking methods. Feature tracking is inherently robust for tracking rotating sea ice, but is limited when features are floe-lead boundaries. A variety of techniques appears neccessary.

Nanometer-scale anatomy of entire Stardust tracks

NASA Astrophysics Data System (ADS)

Nakamura-Messenger, Keiko; Keller, Lindsay P.; Clemett, Simon J.; Messenger, Scott; Ito, Motoo

2011-07-01

We have developed new sample preparation and analytical techniques tailored for entire aerogel tracks of Wild 2 sample analyses both on "carrot" and "bulbous" tracks. We have successfully ultramicrotomed an entire track along its axis while preserving its original shape. This innovation allowed us to examine the distribution of fragments along the entire track from the entrance hole all the way to the terminal particle. The crystalline silicates we measured have Mg-rich compositions and O isotopic compositions in the range of meteoritic materials, implying that they originated in the inner solar system. The terminal particle of the carrot track is a 16O-rich forsteritic grain that may have formed in a similar environment as Ca-, Al-rich inclusions and amoeboid olivine aggregates in primitive carbonaceous chondrites. The track also contains submicron-sized diamond grains likely formed in the solar system. Complex aromatic hydrocarbons distributed along aerogel tracks and in terminal particles. These organics are likely cometary but affected by shock heating.

Vapor etching of nuclear tracks in dielectric materials

DOEpatents

Musket, Ronald G.; Porter, John D.; Yoshiyama, James M.; Contolini, Robert J.

2000-01-01

A process involving vapor etching of nuclear tracks in dielectric materials for creating high aspect ratio (i.e., length much greater than diameter), isolated cylindrical holes in dielectric materials that have been exposed to high-energy atomic particles. The process includes cleaning the surface of the tracked material and exposing the cleaned surface to a vapor of a suitable etchant. Independent control of the temperatures of the vapor and the tracked materials provide the means to vary separately the etch rates for the latent track region and the non-tracked material. As a rule, the tracked regions etch at a greater rate than the non-tracked regions. In addition, the vapor-etched holes can be enlarged and smoothed by subsequent dipping in a liquid etchant. The 20-1000 nm diameter holes resulting from the vapor etching process can be useful as molds for electroplating nanometer-sized filaments, etching gate cavities for deposition of nano-cones, developing high-aspect ratio holes in trackable resists, and as filters for a variety of molecular-sized particles in virtually any liquid or gas by selecting the dielectric material that is compatible with the liquid or gas of interest.

Experimental set up for the irradiation of biological samples and nuclear track detectors with UV C

PubMed Central

Portu, Agustina Mariana; Rossini, Andrés Eugenio; Gadan, Mario Alberto; Bernaola, Omar Alberto; Thorp, Silvia Inés; Curotto, Paula; Pozzi, Emiliano César Cayetano; Cabrini, Rómulo Luis; Martin, Gisela Saint

2016-01-01

Aim In this work we present a methodology to produce an “imprint” of cells cultivated on a polycarbonate detector by exposure of the detector to UV C radiation. Background The distribution and concentration of 10B atoms in tissue samples coming from BNCT (Boron Neutron Capture Therapy) protocols can be determined through the quantification and analysis of the tracks forming its autoradiography image on a nuclear track detector. The location of boron atoms in the cell structure could be known more accurately by the simultaneous observation of the nuclear tracks and the sample image on the detector. Materials and Methods A UV C irradiator was constructed. The irradiance was measured along the lamp direction and at different distances. Melanoma cells were cultured on polycarbonate foils, incubated with borophenylalanine, irradiated with thermal neutrons and exposed to UV C radiation. The samples were chemically attacked with a KOH solution. Results A uniform irradiation field was established to expose the detector foils to UV C light. Cells could be seeded on the polycarbonate surface. Both imprints from cells and nuclear tracks were obtained after chemical etching. Conclusions It is possible to yield cellular imprints in polycarbonate. The nuclear tracks were mostly present inside the cells, indicating a preferential boron uptake. PMID:26933396

The AlSi10Mg samples produced by selective laser melting: single track, densification, microstructure and mechanical behavior

NASA Astrophysics Data System (ADS)

Wei, Pei; Wei, Zhengying; Chen, Zhen; Du, Jun; He, Yuyang; Li, Junfeng; Zhou, Yatong

2017-06-01

This densification behavior and attendant microstructural characteristics of the selective laser melting (SLM) processed AlSi10Mg alloy affected by the processing parameters were systematically investigated. The samples with a single track were produced by SLM to study the influences of laser power and scanning speed on the surface morphologies of scan tracks. Additionally, the bulk samples were produced to investigate the influence of the laser power, scanning speed, and hatch spacing on the densification level and the resultant microstructure. The experimental results showed that the level of porosity of the SLM-processed samples was significantly governed by energy density of laser beam and the hatch spacing. The tensile properties of SLM-processed samples and the attendant fracture surface can be enhanced by decreasing the level of porosity. The microstructure of SLM-processed samples consists of supersaturated Al-rich cellular structure along with eutectic Al/Si situated at the cellular boundaries. The Si content in the cellular boundaries increases with increasing the laser power and decreasing the scanning speed. The hardness of SLM-processed samples was significantly improved by this fine microstructure compared with the cast samples. Moreover, the hardness of SLM-processed samples at overlaps was lower than the hardness observed at track cores.

Forensic Spoorology: Seeing and Understanding Human Behavior through Observation, Classification and Interpretation of Spoor Evidence

DTIC Science & Technology

2011-06-10

SASA Stride and Step Analysis SCS Spoor-Chain Signature SID Self -Imposed Distortion SMS Steadfast-Mind State SSA Secondary Spoor Area TEC Track...because there was no self -regulating body of professional trackers whom by education, training, and experience had come together to establish an...registered in soft ground or in snow by isolated tracks. This visibility gap in knowledge leaves an examiner‘s eyes outside the realm of linearity

Using location tracking data to assess efficiency in established clinical workflows.

PubMed

Meyer, Mark; Fairbrother, Pamela; Egan, Marie; Chueh, Henry; Sandberg, Warren S

2006-01-01

Location tracking systems are becoming more prevalent in clinical settings yet applications still are not common. We have designed a system to aid in the assessment of clinical workflow efficiency. Location data is captured from active RFID tags and processed into usable data. These data are stored and presented visually with trending capability over time. The system allows quick assessments of the impact of process changes on workflow, and isolates areas for improvement.

A fast-initializing digital equalizer with on-line tracking for data communications

NASA Technical Reports Server (NTRS)

Houts, R. C.; Barksdale, W. J.

1974-01-01

A theory is developed for a digital equalizer for use in reducing intersymbol interference (ISI) on high speed data communications channels. The equalizer is initialized with a single isolated transmitter pulse, provided the signal-to-noise ratio (SNR) is not unusually low, then switches to a decision directed, on-line mode of operation that allows tracking of channel variations. Conditions for optimal tap-gain settings are obtained first for a transversal equalizer structure by using a mean squared error (MSE) criterion, a first order gradient algorithm to determine the adjustable equalizer tap-gains, and a sequence of isolated initializing pulses. Since the rate of tap-gain convergence depends on the eigenvalues of a channel output correlation matrix, convergence can be improved by making a linear transformation on to obtain a new correlation matrix.

Automated blood-sample handling in the clinical laboratory.

PubMed

Godolphin, W; Bodtker, K; Uyeno, D; Goh, L O

1990-09-01

The only significant advances in blood-taking in 25 years have been the disposable needle and evacuated blood-drawing tube. With the exception of a few isolated barcode experiments, most sample-tracking is performed through handwritten or computer-printed labels. Attempts to reduce the hazards of centrifugation have resulted in air-tight lids or chambers, the use of which is time-consuming and cumbersome. Most commonly used clinical analyzers require serum or plasma, distributed into specialized containers, unique to that analyzer. Aliquots for different tests are prepared by handpouring or pipetting. Moderate to large clinical laboratories perform so many different tests that even multi-analyzers performing multiple analyses on a single sample may account for only a portion of all tests ordered for a patient. Thus several aliquots of each specimen are usually required. We have developed a proprietary serial centrifuge and blood-collection tube suitable for incorporation into an automated or robotic sample-handling system. The system we propose is (a) safe--avoids or prevents biological danger to the many "handlers" of blood; (b) small--minimizes the amount of sample taken and space required to adapt to the needs of satellite and mobile testing, and direct interfacing with analyzers; (c) serial--permits each sample to be treated according to its own "merits," optimizes throughput, and facilitates flexible automation; and (d) smart--ensures quality results through monitoring and intelligent control of patient identification, sample characteristics, and separation process.

Intraoperative visualization and assessment of electromagnetic tracking error

NASA Astrophysics Data System (ADS)

Harish, Vinyas; Ungi, Tamas; Lasso, Andras; MacDonald, Andrew; Nanji, Sulaiman; Fichtinger, Gabor

2015-03-01

Electromagnetic tracking allows for increased flexibility in designing image-guided interventions, however it is well understood that electromagnetic tracking is prone to error. Visualization and assessment of the tracking error should take place in the operating room with minimal interference with the clinical procedure. The goal was to achieve this ideal in an open-source software implementation in a plug and play manner, without requiring programming from the user. We use optical tracking as a ground truth. An electromagnetic sensor and optical markers are mounted onto a stylus device, pivot calibrated for both trackers. Electromagnetic tracking error is defined as difference of tool tip position between electromagnetic and optical readings. Multiple measurements are interpolated into the thin-plate B-spline transform visualized in real time using 3D Slicer. All tracked devices are used in a plug and play manner through the open-source SlicerIGT and PLUS extensions of the 3D Slicer platform. Tracking error was measured multiple times to assess reproducibility of the method, both with and without placing ferromagnetic objects in the workspace. Results from exhaustive grid sampling and freehand sampling were similar, indicating that a quick freehand sampling is sufficient to detect unexpected or excessive field distortion in the operating room. The software is available as a plug-in for the 3D Slicer platforms. Results demonstrate potential for visualizing electromagnetic tracking error in real time for intraoperative environments in feasibility clinical trials in image-guided interventions.

Correlated microanalysis of cometary organic grains returned by Stardust

NASA Astrophysics Data System (ADS)

de Gregorio, Bradley T.; Stroud, Rhonda M.; Cody, George D.; Nittler, Larry R.; David Kilcoyne, A. L.; Wirick, Sue

2011-09-01

Abstract- Carbonaceous matter in Stardust samples returned from comet 81P/Wild 2 is observed to contain a wide variety of organic functional chemistry. However, some of this chemical variety may be due to contamination or alteration during particle capture in aerogel. We investigated six carbonaceous Stardust samples that had been previously analyzed and six new samples from Stardust Track 80 using correlated transmission electron microscopy (TEM), X-ray absorption near-edge structure spectroscopy (XANES), and secondary ion mass spectroscopy (SIMS). TEM revealed that samples from Track 35 containing abundant aliphatic XANES signatures were predominantly composed of cometary organic matter infilling densified silica aerogel. Aliphatic organic matter from Track 16 was also observed to be soluble in the epoxy embedding medium. The nitrogen-rich samples in this study (from Track 22 and Track 80) both contained metal oxide nanoparticles, and are likely contaminants. Only two types of cometary organic matter appear to be relatively unaltered during particle capture. These are (1) polyaromatic carbonyl-containing organic matter, similar to that observed in insoluble organic matter (IOM) from primitive meteorites, interplanetary dust particles (IDPs), and in other carbonaceous Stardust samples, and (2) highly aromatic refractory organic matter, which primarily constitutes nanoglobule-like features. Anomalous isotopic compositions in some of these samples also confirm their cometary heritage. There also appears to be a significant labile aliphatic component of Wild 2 organic matter, but this material could not be clearly distinguished from carbonaceous contaminants known to be present in the Stardust aerogel collector.

Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution.

PubMed

Johnson, LeeAnn K; Brown, Mary B; Carruthers, Ethan A; Ferguson, John A; Dombek, Priscilla E; Sadowsky, Michael J

2004-08-01

A horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique (HFERP) was developed and evaluated as a means to differentiate human from animal sources of Escherichia coli. Box A1R primers and PCR were used to generate 2,466 rep-PCR and 1,531 HFERP DNA fingerprints from E. coli strains isolated from fecal material from known human and 12 animal sources: dogs, cats, horses, deer, geese, ducks, chickens, turkeys, cows, pigs, goats, and sheep. HFERP DNA fingerprinting reduced within-gel grouping of DNA fingerprints and improved alignment of DNA fingerprints between gels, relative to that achieved using rep-PCR DNA fingerprinting. Jackknife analysis of the complete rep-PCR DNA fingerprint library, done using Pearson's product-moment correlation coefficient, indicated that animal and human isolates were assigned to the correct source groups with an 82.2% average rate of correct classification. However, when only unique isolates were examined, isolates from a single animal having a unique DNA fingerprint, Jackknife analysis showed that isolates were assigned to the correct source groups with a 60.5% average rate of correct classification. The percentages of correctly classified isolates were about 15 and 17% greater for rep-PCR and HFERP, respectively, when analyses were done using the curve-based Pearson's product-moment correlation coefficient, rather than the band-based Jaccard algorithm. Rarefaction analysis indicated that, despite the relatively large size of the known-source database, genetic diversity in E. coli was very great and is most likely accounting for our inability to correctly classify many environmental E. coli isolates. Our data indicate that removal of duplicate genotypes within DNA fingerprint libraries, increased database size, proper methods of statistical analysis, and correct alignment of band data within and between gels improve the accuracy of microbial source tracking methods.

Investigation into the prevalence, persistence and antibiotic resistance profiles of staphylococci isolated from euro currency.

PubMed

Gabriel, E M; Coffey, A; O'Mahony, J M

2013-08-01

The study set out to sample € 10 banknotes for the presence of coagulase-positive staphylococci (CPS) such as Staphylococcus aureus (S. aureus) and coagulase-negative staphylococci (CoNS) in Southern Ireland, to assess the levels of antibiotic resistance among those isolated, and determine the persistence of S. aureus on € 10 banknotes and € 2 coins. We report that 97% of € 10 banknotes screened (n = 155) harboured multiple species of staphylococci. From the generated bank of strains, a total of 150 representative staphylococci isolates were used for further study, 71 were CPS and 79 were CoNS. Of these, we found that 62% of the staphylococci demonstrated resistance to at least one of the first-line antibiotics (52.11% of CPS isolates and 76.71% of the CoNS isolates). Resistance to multiple antibiotics was seen in 31.18% of the resistant isolates. In relation to persistence studies, S. aureus was shown to remain viable on euro banknotes and coins for significant periods (on average, 19.33 days on € 10 banknotes and 16.67 days on € 2 coins) as determined using bioluminescence. We advocate the expansion of antibiotic surveillance programs, with a view to tracking/monitoring antibiotic resistance dissemination among environmental contaminants. Additionally, we propose that 'cashless transactions' should be encouraged in high-risk environments such as hospitals and healthcare settings, as well as stricter infection controls. Although it is accepted that circulating currency has the potential to harbour disease-causing pathogens, studies investigating prevalence and persistence of such pathogens on euro currency are virtually nonexistent. In an attempt to rectify this, we examined the prevalence of staphylococci on € 10 banknotes in Ireland and reported relatively high levels of antibiotic resistance among the isolates. Furthermore, we have established the persistence of S. aureus on euro currency for the first time. © 2013 The Society for Applied Microbiology.

Molecular epidemiology and antimicrobial resistance of Salmonella Typhimurium DT104 on Ontario swine farms

PubMed Central

Farzan, Abdolvahab; Friendship, Robert M.; Poppe, Cornelis; Martin, Laura; Dewey, Catherine E.; Funk, Julie

2008-01-01

This study was conducted to examine antimicrobial resistances, plasmid profiles, and pulsed-field gel electrophoresis patterns of 80 Salmonella Typhimurium (including var. Copenhagen) DT104 strains (including DT104a and DT104b) recovered from pig and environmental fecal samples on 17 swine farms in Ontario. No resistance was observed to amoxicillin/clavulanic acid, apramycin, carbadox, cephalothin, ceftriaxone, ceftiofur, cefoxitin, ciprofloxacin, nalidixic acid, trimethoprim, and tobramycin. However, the isolates exhibited resistance against 4 to 10 antimicrobials with the most frequent resistance being to sulfonamides (Su), ampicillin (A), streptomycin (S), spectinomycin (Sp), chloramphenicol (C), tetracycline (T), and florfenicol (F). Thirteen distinct resistance patterns were determined but 88% of isolates shared the typical resistance pattern “ACSpSSuT.” Twelve different plasmid profiles were observed; the 62 MDa virulence-associated plasmid was detected in 95% of the isolates. The 2.1 MDa plasmid was the second most frequent one, which was harbored by 65% isolates. The isolates were classified into 23 distinct genotypes by PFGE-SpeI + BlnI when difference in at least one fragment was defined as a distinct genotype. In total, 39 distinct “types” were observed when defining a “type” based on the combination of antimicrobial resistance, plasmid pattern, and PFGE-SpeI + BlnI for each isolate. The highest diversity was 0.96 (95% CI: 0.92, 0.96) for the “type” described above followed by 0.92 (95% CI: 0.88, 0.93) for PFGE-SpeI + BlnI. The diversity of DT104 isolates indicates there might be multiple sources for this microorganism on swine farms. This knowledge might be used to track these sources, as well as to study the extent of human salmonellosis attributed to pork compared to food products derived from other food-producing animals. PMID:18505209

The Contours of Tracking in North Carolina

ERIC Educational Resources Information Center

Kelly, Sean

2007-01-01

In this analysis of North Carolina high schools the author examines school tracking policies using an amended version of Sorensen's (1970) conceptualization of the organizational dimensions of tracking. Data from curriculum guides in a stratified sample of 92 high schools reveal both consistency and variation in how tracking is implemented at the…

The effect of α-damage on fission-track annealing in zircon

USGS Publications Warehouse

Kasuya, M.; Naeser, C.W.

1988-01-01

The thermal stability of confined fission-track lengths in four zircon samples having different spontaneous track densities (i.e. different amounts of ??-damage) has been studied by one hour isochronal annealing experiments. The thermal stability of spontaneous track lengths is independent of initial spontaneous track density. The thermal stability of induced track lengths in pre-annealed zircon, however, is significantly higher than that of spontaneous track lengths. The results indicate that the presence of ??-damage lowers the thermal stability of fission-tracks in zircon. ?? 1988.

Isolating the incentive salience of reward-associated stimuli: value, choice, and persistence

PubMed Central

Chow, Jonathan J.

2015-01-01

Sign- and goal-tracking are differentially associated with drug abuse-related behavior. Recently, it has been hypothesized that sign- and goal-tracking behavior are mediated by different neurobehavioral valuation systems, including differential incentive salience attribution. Herein, we used different conditioned stimuli to preferentially elicit different response types to study the different incentive valuation characteristics of stimuli associated with sign- and goal-tracking within individuals. The results demonstrate that all stimuli used were equally effective conditioned stimuli; however, only a lever stimulus associated with sign-tracking behavior served as a robust conditioned reinforcer and was preferred over a tone associated with goal-tracking. Moreover, the incentive value attributed to the lever stimulus was capable of promoting suboptimal choice, leading to a significant reduction in reinforcers (food) earned. Furthermore, sign-tracking to a lever was more persistent than goal-tracking to a tone under omission and extinction contingencies. Finally, a conditional discrimination procedure demonstrated that sign-tracking to a lever and goal-tracking to a tone were dependent on learned stimulus–reinforcer relations. Collectively, these results suggest that the different neurobehavioral valuation processes proposed to govern sign- and goal-tracking behavior are independent but parallel processes within individuals. Examining these systems within individuals will provide a better understanding of how one system comes to dominate stimulus–reward learning, thus leading to the differential role these systems play in abuse-related behavior. PMID:25593298

Inverted Apatite (U-Th)/He and Fission-track Dates from the Rae craton, Baffin Island, Canada and Implications for Apatite Radiation Damage-He Diffusivity Models

NASA Astrophysics Data System (ADS)

Ault, A. K.; Reiners, P. W.; Thomson, S. N.; Miller, G. H.

2015-12-01

Coupled apatite (U-Th)/He and fission-track (AFT) thermochronology data from the same sample can be used to decipher complex low temperature thermal histories and evaluate compatibility between these two methods. Existing apatite He damage-diffusivity models parameterize radiation damage annealing as fission-track annealing and yield inverted apatite He and AFT dates for samples with prolonged residence in the He partial retention zone. Apatite chemistry also impacts radiation damage and fission-track annealing, temperature sensitivity, and dates in both systems. We present inverted apatite He and AFT dates from the Rae craton, Baffin Island, Canada, that cannot be explained by apatite chemistry or existing damage-diffusivity and fission track models. Apatite He dates from 34 individual analyses from 6 samples range from 237 ± 44 Ma to 511 ± 25 Ma and collectively define a positive date-eU relationship. AFT dates from these same samples are 238 ± 15 Ma to 350 ± 20 Ma. These dates and associated track length data are inversely correlated and define the left segment of a boomerang diagram. Three of the six samples with 20-90 ppm eU apatite grains yield apatite He and AFT dates inverted by 300 million years. These samples have average apatite Cl chemistry of ≤0.02 wt.%, with no correlation between Cl content and Dpar. Thermal history simulations using geologic constraints, an apatite He radiation damage accumulation and annealing model, apatite He dates with the range of eU values, and AFT date and track length data, do not yield any viable time-temperature paths. Apatite He and AFT data modeled separately predict thermal histories with Paleozoic-Mesozoic peaks reheating temperatures differing by ≥15 °C. By modifying the parameter controlling damage annealing (Rmr0) from the canonical 0.83 to 0.5-0.6, forward models reproduce the apatite He date-eU correlation and AFT dates with a common thermal history. Results imply apatite radiation damage anneals at higher temperatures than fission-track damage and the impact on coupled apatite He and AFT dates is magnified for protracted cooling histories. Further experimental and field-based tests are important for refining radiation damage and fission-track annealing parameters for accurate interpretation of apatite He- and AFT-derived thermal histories.

Development of the U.S. Army Railroad Track Maintenance Management System (RAILER).

DTIC Science & Technology

1986-05-01

availability is both feasible and desirable. Section 5 of this study discusses measurement and analysis equipment. .5 *- Sample Deduct Value Calculations... Sample of Five Groups of 50 Ties From Same Mile on Track 72 C2 Bad Tie Count Adjustment Factors 80 C3 Adjusted Badtie Count Factors Under Conservative...economic analysis developed as part of the PAVER system 3 can be used for RAILER; however, guidelines for providing track information inputs to the

Isolation of animal viruses from farm livestock waste, soil and water.

PubMed Central

Derbyshire, J. B.; Brown, E. G.

1978-01-01

Ten porcine enteroviruses, 2 porcine adenoviruses and 1 coronavirus were isolated directly from 32 samples of slurry collected from a pig fattening house. Concentration of the same samples by adsorption with the polyelectrolyte PE-60 yielded 24 porcine enteroviruses and 3 porcine adenoviruses. A porcine enterovirus was isolated, following PE-60 concentration, from 1 to 6 slurry samples from a sow farrowing house. No virus was isolated from 12 samples of slurry from dairy cows nor from 6 slurry samples from a calf-rearing unit. A porcine enterovirus was isolated from soil samples, after concentration with PE-60, collected 1, 2 and 8 days after pig slurry was spread on hay stubble. Two porcine enteroviruses were isolated by membrane filtration from 26 samples of surface run-off from land on which pig slurry was routinely spread, and 2 bovine enteroviruses were isolated from cattle feedlot run-off after adsorption to layers of talc and celite followed by hydroextraction. A porcine enterovirus was also isolated from 1 of 33 samples of surface water collected on farms on which pig slurry was routinely spread on the land, but no virus was isolated from 36 samples of ground water from the same farms. The surface water and ground water samples were concentrated by talc-celite adsorption and hydroextraction. PMID:100551

Population Genetic Structure of Apple Scab (Venturia inaequalis (Cooke) G. Winter) in Iran

PubMed Central

Ebrahimi, Leila; Fotuhifar, Khalil-Berdi; Javan Nikkhah, Mohammad; Naghavi, Mohammad-Reza; Baisakh, Niranjan

2016-01-01

The population genetic structure of 278 Venturia inaequalis isolates, collected from different apple cultivars of eighteen different provinces in Iran, was investigated using 22 polymorphic microsatellite markers. Analysis of molecular variation, Bayesian clustering and Nei's genetic distance analyses based on 88 microsatellite alleles indicated substantial levels of gene flow among the collection sites. Ninety three percent of the variation was observed among the individuals within the populations and only 7% variation was observed among the populations. Structure analysis grouped the isolates into two populations. Maximum number of pathogen genotypes (44) was observed in the North of Iran that grows various different apple cultivars. Investigation on the variation of the pathogen on different cultivars in the North of Iran suggested a significant differentiation of the pathogen populations between wild apple and commercial cultivars. During sampling, varying ranges of scab infection were observed on various apple cultivars in forests, monoculture and mix orchards. Wild type apple (Malus orientalis) along the Caspian Sea Coast had the most infection in comparison with the Iranian endemic and commercial cultivars. Based on the genetic analysis and host tracking scenario of the pathogen, it was presumed that Iran could potentially be the center of origin of V. inaequalis, which requires further detailed studies with isolates collected from different parts of central Asia and world for confirmation. PMID:27631622

Active Narrow-Band Vibration Isolation of Large Engineering Structures

NASA Technical Reports Server (NTRS)

Rahman, Zahidul; Spanos, John

1994-01-01

We present a narrow-band tracking control method using a variant of the Least Mean Squares (LMS) algorithm to isolate slowly changing periodic disturbances from engineering structures. The advantage of the algorithm is that it has a simple architecture and is relatively easy to implement while it can isolate disturbances on the order of 40-50 dB over decades of frequency band. We also present the results of an experiment conducted on a flexible truss structure. The average disturbance rejection achieved is over 40 dB over the frequency band of 5 Hz to 50 Hz.

Solar Flare Track Exposure Ages in Regolith Particles: A Calibration for Transmission Electron Microscope Measurements

NASA Technical Reports Server (NTRS)

Berger, Eve L.; Keller, Lindsay P.

2015-01-01

Mineral grains in lunar and asteroidal regolith samples provide a unique record of their interaction with the space environment. Space weathering effects result from multiple processes including: exposure to the solar wind, which results in ion damage and implantation effects that are preserved in the rims of grains (typically the outermost 100 nm); cosmic ray and solar flare activity, which result in track formation; and impact processes that result in the accumulation of vapor-deposited elements, impact melts and adhering grains on particle surfaces. Determining the rate at which these effects accumulate in the grains during their space exposure is critical to studies of the surface evolution of airless bodies. Solar flare energetic particles (mainly Fe-group nuclei) have a penetration depth of a few millimeters and leave a trail of ionization damage in insulating materials that is readily observable by transmission electron microscope (TEM) imaging. The density of solar flare particle tracks is used to infer the length of time an object was at or near the regolith surface (i.e., its exposure age). Track measurements by TEM methods are routine, yet track production rate calibrations have only been determined using chemical etching techniques [e.g., 1, and references therein]. We used focused ion beam-scanning electron microscope (FIB-SEM) sample preparation techniques combined with TEM imaging to determine the track density/exposure age relations for lunar rock 64455. The 64455 sample was used earlier by [2] to determine a track production rate by chemical etching of tracks in anorthite. Here, we show that combined FIB/TEM techniques provide a more accurate determination of a track production rate and also allow us to extend the calibration to solar flare tracks in olivine.

A complete system for head tracking using motion-based particle filter and randomly perturbed active contour

NASA Astrophysics Data System (ADS)

Bouaynaya, N.; Schonfeld, Dan

2005-03-01

Many real world applications in computer and multimedia such as augmented reality and environmental imaging require an elastic accurate contour around a tracked object. In the first part of the paper we introduce a novel tracking algorithm that combines a motion estimation technique with the Bayesian Importance Sampling framework. We use Adaptive Block Matching (ABM) as the motion estimation technique. We construct the proposal density from the estimated motion vector. The resulting algorithm requires a small number of particles for efficient tracking. The tracking is adaptive to different categories of motion even with a poor a priori knowledge of the system dynamics. Particulary off-line learning is not needed. A parametric representation of the object is used for tracking purposes. In the second part of the paper, we refine the tracking output from a parametric sample to an elastic contour around the object. We use a 1D active contour model based on a dynamic programming scheme to refine the output of the tracker. To improve the convergence of the active contour, we perform the optimization over a set of randomly perturbed initial conditions. Our experiments are applied to head tracking. We report promising tracking results in complex environments.

Numbers of fecal streptococci and Escherichia coli in fresh and dry cattle, horse, and sheep manure.

PubMed

Weaver, R W; Entry, J A; Graves, Alexandria

2005-10-01

Livestock are known contributors to stream pollution. Numbers of fecal streptococci and Escherichia coli in manure naturally deposited by livestock in the field are needed for activities related to bacterial source tracking and determining maximum daily bacterial loading of streams. We measured populations of fecal streptococci and E. coli in fresh and dry manure from cattle (Bos taurus L.), horses (Equus caballus L.), and sheep (Ovis aires L.) on farms in southern Idaho. Populations of indicator bacteria in dry manure were often as high as that in fresh manure from horse and sheep. There was a 2 log10 drop in the population of fecal coliform numbers in dry cattle manure from cattle in pastures but not from cattle in pens. Bacterial isolates used in source tracking should include isolates from both fresh and dry manure to better represent the bacterial source loading of streams.

Performance and brain electrical activity during prolonged confinement.

PubMed

Lorenz, B; Lorenz, J; Manzey, D

1996-01-01

A subset of the AGARD-STRES battery including memory search, unstable tracking, and a combination of both tasks (dual-task), was applied repeatedly to the four chamber crew members before, during, and after the 60-day isolation period of EXEMSI. Five ground control group members served as a control group. A subjective state questionnaire was also included. The results were subjected to a quantitative single-subject analysis. Electroencephalograms (EEG) were recorded to permit correlation of changes in task performance with changes in the physiological state. Evaluation of the EEG focused on spectral parameters of spontaneous EEG waves. No physiological data were collected from the control group. Significant decrements in tracking ability were observed in the chamber crew. The time course of these effects followed a triphasic pattern with initial deterioration, intermediate recovery to pre-isolation baseline scores after the first half of the isolation period, and a second deterioration towards the end. None of the control group subjects displayed such an effect. Memory search (speed and accuracy) was only occasionally impaired during isolation, but the control group displayed a similar pattern of changes. It is suggested that a state of decreased alertness causes tracking deterioration, which leads to a reduced efficiency of sustained cue utilization. The assumption of low alertness was further substantiated by higher fatigue ratings by the chamber crew compared to those of the control group. Analysis of the continuous EEG recordings revealed that only two subjects produced reliable alpha wave activity (8-12 Hz) over Pz and, to a much smaller extent, Fz-theta wave activity (5-7 Hz) during task performance. In both subjects Pz-alpha power decreased consistently under task conditions involving single-task and dual-task tracking. Fz-theta activity was increased more by single-task and dual-task memory search than by single-task tracking. The alpha attenuation appears to be associated with an increasing demand on perceptual cue utilization required by the tracking performance. In one subject marked attenuation of alpha power occurred during the first half of the confinement period, where he also scored the highest fatigue ratings. A striking increase in fronto-central theta activity was observed in the same subject after six weeks of isolation. The change was associated with an efficient rather than a degraded task performance, and a high rating of the item "concentrated" and a low rating of the item "fatigued." This finding supports the hypothesis that the activation state associated with increased fronto-central theta activity accompanies efficient performance of demanding mental tasks. The usefulness of standardized laboratory tasks as monitoring instruments is demonstrated by the direct comparability with results of studies obtained from other relevant research applications using the same tasks. The feasibility of a self-administered integrated psychophysiological assessment of the individual state was illustrated by the nearly complete collection of data. The large number of individual data collected over the entire period permitted application of quantitative single-subject analysis, allowing reliable determination of changes in the individual state in the course of time. It thus appears that this assessment technique can be adapted for in-flight monitoring of astronauts during prolonged spaceflights. Parallel EEG recording can provide relevant supplementary information for diagnosing the individual activation state associated with task performance. The existence of large individual differences in the generation of task-sensitive EEG rhythms forms an important issue for further studies.

CMOS imager for pointing and tracking applications

NASA Technical Reports Server (NTRS)

Sun, Chao (Inventor); Pain, Bedabrata (Inventor); Yang, Guang (Inventor); Heynssens, Julie B. (Inventor)

2006-01-01

Systems and techniques to realize pointing and tracking applications with CMOS imaging devices. In general, in one implementation, the technique includes: sampling multiple rows and multiple columns of an active pixel sensor array into a memory array (e.g., an on-chip memory array), and reading out the multiple rows and multiple columns sampled in the memory array to provide image data with reduced motion artifact. Various operation modes may be provided, including TDS, CDS, CQS, a tracking mode to read out multiple windows, and/or a mode employing a sample-first-read-later readout scheme. The tracking mode can take advantage of a diagonal switch array. The diagonal switch array, the active pixel sensor array and the memory array can be integrated onto a single imager chip with a controller. This imager device can be part of a larger imaging system for both space-based applications and terrestrial applications.

A microfluidics assay to study invasion of human placental trophoblast cells.

PubMed

Abbas, Yassen; Oefner, Carolin Melati; Polacheck, William J; Gardner, Lucy; Farrell, Lydia; Sharkey, Andrew; Kamm, Roger; Moffett, Ashley; Oyen, Michelle L

2017-05-01

Pre-eclampsia, fetal growth restriction and stillbirth are major pregnancy disorders throughout the world. The underlying pathogenesis of these diseases is defective placentation characterized by inadequate invasion of extravillous placental trophoblast cells into the uterine arteries. How trophoblast invasion is controlled remains an unanswered question but is influenced by maternal uterine immune cells called decidual natural killer cells. Here, we describe an in vitro microfluidic invasion assay to study the migration of primary human trophoblast cells. Each experiment can be performed with a small number of cells making it possible to conduct research on human samples despite the challenges of isolating primary trophoblast cells. Cells are exposed to a chemical gradient and tracked in a three-dimensional microenvironment using real-time high-resolution imaging, so that dynamic readouts on cell migration such as directionality, motility and velocity are obtained. The microfluidic system was validated using isolated trophoblast and a gradient of granulocyte-macrophage colony-stimulating factor, a cytokine produced by activated decidual natural killer cells. This microfluidic model provides detailed analysis of the dynamics of trophoblast migration compared to previous assays and can be modified in future to study in vitro how human trophoblast behaves during placentation. © 2017 The Authors.

Multiple-locus variable number of tandem repeat analysis as a tool for molecular epidemiology of botulism: The Italian experience.

PubMed

Anniballi, Fabrizio; Fillo, Silvia; Giordani, Francesco; Auricchio, Bruna; Tehran, Domenico Azarnia; di Stefano, Enrica; Mandarino, Giuseppina; De Medici, Dario; Lista, Florigio

2016-12-01

Clostridium botulinum is the bacterial agent of botulism, a rare but severe neuro-paralytic disease. Because of its high impact, in Italy botulism is monitored by an ad hoc surveillance system. The National Reference Centre for Botulism, as part of this system, collects and analyzes all demographic, epidemiologic, microbiological, and molecular data recovered during cases and/or outbreaks occurred in Italy. A panel of 312 C. botulinum strains belonging to group I were submitted to MLVA sub-typing. Strains, isolated from clinical specimens, food and environmental samples collected during the surveillance activities, were representative of all forms of botulism from all Italian regions. Through clustering analysis isolates were grouped into 12 main clusters. No regional or temporal clustering was detected, demonstrating the high heterogeneity of strains circulating in Italy. This study confirmed that MLVA is capable of sub-typing C. botulinum strains. Moreover, MLVA is effective at tracing and tracking the source of contamination and is helpful for the surveillance system in terms of planning and upgrading of procedures, activities and data collection forms. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial Characterization During the Early Habitation of the International Space Station

NASA Technical Reports Server (NTRS)

Castro, V. A.; Thrasher, A. N.; Healy, M.; Ott, C. M.; Pierson, D. L.

2004-01-01

An evaluation of the microbiota from air, water, and surface samples provided a baseline of microbial characterization onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. Using 16S genetic sequencing and rep-PCR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. Of the bacterial strains that were isolated and fingerprinted, 19 displayed similarity to each other. The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants. Strains of Bradyrhizobium and Sphingomonas unable to be identified using sequencing were identified by comparison of rep-PCR DNA fingerprints. Distinct DNA fingerprints for several strains of Methylobacterium provided a clear indication of the source of an ISS water supply contaminant. Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk. Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and will require continued surveillance. Copyright 2004 Springer-Verlag.

Microbial Diversity Aboard Spacecraft: Evaluation of the International Space Station

NASA Technical Reports Server (NTRS)

Castro, Victoria A.; Thrasher, Adrianna N.; Healy, Mimi; Ott, C. Mark; Pierson, Duane L.

2003-01-01

An evaluation of the microbial flora from air, water, and surface samples provided a baseline of microbial diversity onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. Using 16S genetic sequencing and rep-PeR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants. Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk. Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and require continued surveillance.

Spacecraft Doppler tracking with a VLBI antenna

NASA Technical Reports Server (NTRS)

Comoretto, G.; Iess, L.; Bertotti, B.; Brenkle, J. P.; Horton, T.

1990-01-01

Preliminary results are reported from Doppler-shift measurements to the Voyager-2 spacecraft at a distance of 26 AU, obtained using the 32-m VLBI antenna at Medicina (Italy) during July and August 1988. The apparatus comprises the el-az antenna, an S-X-band receiver, a hydrogen maser to generate the reference signal, a Mark III VLBI terminal, and a digital tone extractor capable of isolating a tone of known frequency from a noisy signal and giving its phase and amplitude. A signal transmitted in S-band from the NASA Deep Space Network (DSN) station in Australia and retransmitted coherently in X-band by Voyager, was received 7 h 6 min later at Medicina and at the DSN station in Madrid. Sample data are presented graphically and shown to be of generally high quality; further in-depth analysis is under way.

Sampling strategies for radio-tracking coyotes

USGS Publications Warehouse

Smith, G.J.; Cary, J.R.; Rongstad, O.J.

1981-01-01

Ten coyotes radio-tracked for 24 h periods were most active at night and moved little during daylight hours. Home-range size determined from radio-locations of 3 adult coyotes increased with the number of locations until an asymptote was reached at about 35-40 independent day locations or 3 6 nights of hourly radio-locations. Activity of the coyote did not affect the asymptotic nature of the home-range calculations, but home-range sizes determined from more than 3 nights of hourly locations were considerably larger than home-range sizes determined from daylight locations. Coyote home-range sizes were calculated from daylight locations, full-night tracking periods, and half-night tracking periods. Full- and half-lnight sampling strategies involved obtaining hourly radio-locations during 12 and 6 h periods, respectively. The half-night sampling strategy was the best compromise for our needs, as it adequately indexed the home-range size, reduced time and energy spent, and standardized the area calculation without requiring the researcher to become completely nocturnal. Sight tracking also provided information about coyote activity and sociability.

Metabolic primers for detection of (Per)chlorate-reducing bacteria in the environment and phylogenetic analysis of cld gene sequences.

PubMed

Bender, Kelly S; Rice, Melissa R; Fugate, William H; Coates, John D; Achenbach, Laurie A

2004-09-01

Natural attenuation of the environmental contaminant perchlorate is a cost-effective alternative to current removal methods. The success of natural perchlorate remediation is dependent on the presence and activity of dissimilatory (per)chlorate-reducing bacteria (DPRB) within a target site. To detect DPRB in the environment, two degenerate primer sets targeting the chlorite dismutase (cld) gene were developed and optimized. A nested PCR approach was used in conjunction with these primer sets to increase the sensitivity of the molecular detection method. Screening of environmental samples indicated that all products amplified by this method were cld gene sequences. These sequences were obtained from pristine sites as well as contaminated sites from which DPRB were isolated. More than one cld phylotype was also identified from some samples, indicating the presence of more than one DPRB strain at those sites. The use of these primer sets represents a direct and sensitive molecular method for the qualitative detection of (per)chlorate-reducing bacteria in the environment, thus offering another tool for monitoring natural attenuation. Sequences of cld genes isolated in the course of this project were also generated from various DPRB and provided the first opportunity for a phylogenetic treatment of this metabolic gene. Comparisons of the cld and 16S ribosomal DNA (rDNA) gene trees indicated that the cld gene does not track 16S rDNA phylogeny, further implicating the possible role of horizontal transfer in the evolution of (per)chlorate respiration.

Social networks and incident stroke among women with suspected myocardial ischemia.

PubMed

Rutledge, Thomas; Linke, Sarah E; Olson, Marian B; Francis, Jennifer; Johnson, B Delia; Bittner, Vera; York, Kaki; McClure, Candace; Kelsey, Sheryl F; Reis, Steven E; Cornell, Carol E; Vaccarino, Viola; Sheps, David S; Shaw, Leslee J; Krantz, David S; Parashar, Susmita; Merz, C Noel Bairey

2008-04-01

To describe the prospective relationship between social networks and nonfatal stroke events in a sample of women with suspected myocardial ischemia. Social networks are an independent predictor of all-cause and cardiovascular mortality, but their relationship with stroke events in at-risk populations is largely unknown. A total of 629 women (mean age = 59.6 +/- 11.6 years) were evaluated at baseline for cardiovascular disease risk factors as part of a protocol including coronary angiography; the subjects were followed over a median 5.9 years to track the incidence of cardiovascular events including stroke. Participants also completed the Social Network Index (SNI), measuring the presence/absence of 12 types of common social relationships. Stroke events occurred among 5.1% of the sample over follow-up. More isolated women were older and less educated, with higher rates of smoking and hypertension, and increased use of cardiovascular medications. Women with smaller social networks were also more likely to show elevations (scores of > or =10) on the Beck Depression Inventory (54% versus 41%, respectively; p = .003). Relative to women with higher SNI scores, Cox regression results indicated that more isolated women experienced strokes at greater than twice the rate of those with more social relationships after adjusting for covariates (hazard ratio = 2.7; 95% Confidence Interval = 1.1-6.7). Smaller social networks are a robust predictor of stroke in at-risk women, and the magnitude of the association rivals that of conventional risk factors.

Tracking radar studies of bird migration

NASA Technical Reports Server (NTRS)

Williams, T. C.; Williams, J. M.; Teal, J. M.; Kanwisher, J. W.

1972-01-01

The application of tracking radar for determining the flight paths of migratory birds is discussed. The effects produced by various meteorological parameters are described. Samples of radar scope presentations obtained during tracking studies are presented. The characteristics of the radars and their limitations are examined.

Novel calibration for LA-ICP-MS-based fission-track thermochronology

NASA Astrophysics Data System (ADS)

Soares, C. J.; Guedes, S.; Hadler, J. C.; Mertz-Kraus, R.; Zack, T.; Iunes, P. J.

2014-01-01

We present a novel age-equation calibration for fission-track age determinations by laser ablation inductively coupled plasma mass spectrometry. This new calibration incorporates the efficiency factor of an internal surface, [ ηq]is, which is obtained by measuring the projected fission-track length, allowing the determination of FT ages directly using the recommended spontaneous fission decay constant. Also, the uranium concentrations in apatite samples are determined using a Durango (Dur-2, 7.44 μg/g U) crystal and a Mud Tank (MT-7, 6.88 μg/g U) crystal as uranium reference materials. The use of matrix-matched reference materials allows a reduction in the uncertainty of the uranium measurements to those related to counting statistics, which are ca. 1 % taking into account that no extra source of uncertainty has to be considered. The equations as well as the matrix-matched reference materials are evaluated using well-dated samples from Durango, Fish Canyon Tuff, and Limberg as unknown samples. The results compare well with their respective published ages determined through other dating methods. Additionally, the results agree with traditional fission-track ages using both the zeta approach and the absolute approach, suggesting that the calibration presented in this work can be robustly applied in geological context. Furthermore, considering that fission-track ages can be determined without an age standard sample, the fission-track thermochronology approach presented here is assumed to be a valuable dating tool.

Genotype and enterotoxigenicity of Staphylococcus epidermidis isolate from ready to eat meat products

PubMed Central

Podkowik, Magdalena; Seo, Keun Seok; Schubert, Justyna; Tolo, Isaiah; Robinson, D. Ashley; Bania, Jacek; Bystroń, Jarosław

2016-01-01

We have previously shown that potentially pathogenic isolates of Staphylococcus epidermidis occur at high incidence in ready-to-eat food. Now, within 164 samples of ready-to-eat meat products we identified 32 S. epidermidis isolates. In 8 isolates we detected the genes encoding for staphylococcal enterotoxins, but in 7 S. epidermidis isolates these genes were not stable over passages. One isolate designated 4S was shown to stably harbour sec and sel genes.In the genome sequence of S. epidermidis 4S we identified 21,426-bp region flanked by direct-repeats, encompassing sec and sel genes, corresponding to the previously described composite staphylococcal pathogenicity island (SePI) in S. epidermidis FRI909. Alignment of S. epidermidis 4S and S. epidermidis FRI909 SePIs revealed 6 nucleotide mismatches located in 5 of the total of 29 ORFs. Genomic location of S. epidermidis 4S SePI was the same as in FRI909. S. epidermidis 4S is a single locus variant of ST561, being genetically different from FRI909. SECepi was secreted by S. epidermidis 4S to BHI broth ranging from 14 to almost 36 μg/mL, to milk ranging from 6-9 ng/mL, to beef meat juice from 2-3 μg/mL and to pork meat juice from 1-2 μg/mL after 24 and 48 hours of cultivation, respectively. We provide the first evidence that S. epidermidis occurring in food bears an element encoding an orthologue to S. aureus SEC, and that SECepi can be produced in microbial broth, milk and meat juices. Regarding that only enterotoxins produced by S. aureus are officially tracked in food in EU, the ability to produce enterotoxin by S. epidermidis pose real risk for food safety. PMID:27105039

Genotype and enterotoxigenicity of Staphylococcus epidermidis isolate from ready to eat meat products.

PubMed

Podkowik, Magdalena; Seo, Keun Seok; Schubert, Justyna; Tolo, Isaiah; Robinson, D Ashley; Bania, Jacek; Bystroń, Jarosław

2016-07-16

We have previously shown that potentially pathogenic isolates of Staphylococcus epidermidis occur at high incidence in ready-to-eat food. Now, within 164 samples of ready-to-eat meat products we identified 32 S. epidermidis isolates. In 8 isolates we detected the genes encoding for staphylococcal enterotoxins, but in 7 S. epidermidis isolates these genes were not stable over passages. One isolate designated 4S was shown to stably harbour sec and sel genes. In the genome sequence of S. epidermidis 4S we identified 21,426-bp region flanked by direct-repeats, encompassing sec and sel genes, corresponding to the previously described composite staphylococcal pathogenicity island (SePI) in S. epidermidis FRI909. Alignment of S. epidermidis 4S and S. epidermidis FRI909 SePIs revealed 6 nucleotide mismatches located in 5 of the total of 29 ORFs. Genomic location of S. epidermidis 4S SePI was the same as in FRI909. S. epidermidis 4S is a single locus variant of ST561, being genetically different from FRI909. SECepi was secreted by S. epidermidis 4S to BHI broth ranging from 14 to almost 36μg/mL, to milk ranging from 6 to 9ng/mL, to beef meat juice from 2 to 3μg/mL and to pork meat juice from 1 to 2μg/mL after 24 and 48h of cultivation, respectively. We provide the first evidence that S. epidermidis occurring in food bears an element encoding an orthologue to Staphylococcus aureus SEC, and that SECepi can be produced in microbial broth, milk and meat juices. Regarding that only enterotoxins produced by S. aureus are officially tracked in food in EU, the ability to produce enterotoxin by S. epidermidis pose real risk for food safety. Copyright © 2016 Elsevier B.V. All rights reserved.

Artemisinin resistance without pfkelch13 mutations in Plasmodium falciparum isolates from Cambodia.

PubMed

Mukherjee, Angana; Bopp, Selina; Magistrado, Pamela; Wong, Wesley; Daniels, Rachel; Demas, Allison; Schaffner, Stephen; Amaratunga, Chanaki; Lim, Pharath; Dhorda, Mehul; Miotto, Olivo; Woodrow, Charles; Ashley, Elizabeth A; Dondorp, Arjen M; White, Nicholas J; Wirth, Dyann; Fairhurst, Rick; Volkman, Sarah K

2017-05-12

Artemisinin resistance is associated with delayed parasite clearance half-life in vivo and correlates with ring-stage survival under dihydroartemisinin in vitro. Both phenotypes are associated with mutations in the PF3D7_1343700 pfkelch13 gene. Recent spread of artemisinin resistance and emerging piperaquine resistance in Southeast Asia show that artemisinin combination therapy, such as dihydroartemisinin-piperaquine, are losing clinical effectiveness, prompting investigation of drug resistance mechanisms and development of strategies to surmount emerging anti-malarial resistance. Sixty-eight parasites isolates with in vivo clearance data were obtained from two Tracking Resistance to Artemisinin Collaboration study sites in Cambodia, culture-adapted, and genotyped for pfkelch13 and other mutations including pfmdr1 copy number; and the RSA 0-3h survival rates and response to antimalarial drugs in vitro were measured for 36 of these isolates. Among these 36 parasites one isolate demonstrated increased ring-stage survival for a PfKelch13 mutation (D584V, RSA 0-3h  = 8%), previously associated with slow clearance but not yet tested in vitro. Several parasites exhibited increased ring-stage survival, yet lack pfkelch13 mutations, and one isolate showed evidence for piperaquine resistance. This study of 68 culture-adapted Plasmodium falciparum clinical isolates from Cambodia with known clearance values, associated the D584V PfKelch13 mutation with increased ring-stage survival and identified parasites that lack pfkelch13 mutations yet exhibit increased ring-stage survival. These data suggest mutations other than those found in pfkelch13 may be involved in conferring artemisinin resistance in P. falciparum. Piperaquine resistance was also detected among the same Cambodian samples, consistent with reports of emerging piperaquine resistance in the field. These culture-adapted parasites permit further investigation of mechanisms of both artemisinin and piperaquine resistance and development of strategies to prevent or overcome anti-malarial resistance.

DNA analysis of hair and scat collected along snow tracks to document the presence of Canada Lynx.

Treesearch

Kevin S. McKelvey; Jeffrey von Kienast; Keith B. Aubry; Gary M. Koehler; Bejamin T. Maletzke; John R. Squires; Edward L. Lindquist; Steve Loch; Michael K. Schwartz

2006-01-01

Snow tracking is often used to inventory carnivore communities, but species identification using this method can produce ambiguous and misleading results. DNA can be extracted from hair and scat samples collected from tracks made in snow. Using DNA analysis could allow positive track identification across a broad range of snow conditions, thus increasing survey...

Quasi-metagenomics and realtime sequencing aided detection and subtyping of Salmonella enterica from food samples.

PubMed

Hyeon, Ji-Yeon; Li, Shaoting; Mann, David A; Zhang, Shaokang; Li, Zhen; Chen, Yi; Deng, Xiangyu

2017-12-01

Metagenomics analysis of food samples promises isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. Selective concentration of Salmonella genomic DNA through immunomagnetic separation (IMS) and multiple displacement amplification (MDA) were shown to shorten culture enrichment of Salmonella -spiked raw chicken breast samples by over 12 hours while permitting serotyping and high-fidelity single nucleotide polymorphisms (SNP) typing of the pathogen using short shotgun sequencing reads. The herein termed quasi-metagenomics approach was evaluated on Salmonella -spiked lettuce and black peppercorn samples as well as retail chicken parts naturally contaminated with different serotypes of Salmonella. Between 8 and 24 h culture enrichment was required for detecting and subtyping naturally occurring Salmonella from unspiked chicken parts compared with 4 to 12 h culture enrichment when Salmonella -spiked food samples were analyzed, indicating the likely need for longer culture enrichment to revive low levels of stressed or injured Salmonella cells in food. Further acceleration of the workflow was achieved by real-time nanopore sequencing. After 1.5 hours of analysis on a potable sequencer, sufficient data were generated from sequencing IMS-MDA product of a cultured-enriched lettuce sample to allow serotyping and robust phylogenetic placement of the inoculated isolate. Importance Both culture enrichment and next-generation sequencing remain to be time-consuming processes for food testing where rapid methods for pathogen detection are widely available. Our study demonstrated substantial acceleration of the respective process through IMS-MDA and real-time nanopore sequencing. In one example, the combined use of the two methods delivered a less than 24 h turnaround time from a Salmonella -contaminated lettuce sample to phylogenetic identification of the pathogen. Improved efficiency like this is important for further expanding the use of whole genome and metagenomics sequencing in microbial analysis of food. Our results suggest the potential of the quasi-metagenomics approach in areas where rapid detection and subtyping of foodborne pathogens is important, such as foodborne outbreak response and precision tracking and monitoring of foodborne pathogens in production environments and supply chains. Copyright © 2017 American Society for Microbiology.

Evaluation of Kapton pyrolysis, arc tracking, and flashover on SiO(x)-coated polyimide insulated samples of flat flexible current carriers for Space Station Freedom

NASA Technical Reports Server (NTRS)

Stueber, Thomas J.; Mundson, Chris

1993-01-01

Kapton polyimide wiring insulation was found to be vulnerable to pyrolization, arc tracking, and flashover when momentary short-circuit arcs have occurred on aircraft power systems. Short-circuit arcs between wire pairs can pyrolize the polyimide resulting in a conductive char between conductors that may sustain the arc (arc tracking). Furthermore, the arc tracking may spread (flashover) to other wire pairs within a wire bundle. Polyimide Kapton will also be used as the insulating material for the flexible current carrier (FCC) of Space Station Freedom (SSF). The FCC, with conductors in a planar type geometric layout as opposed to bundles, is known to sustain arc tracking at proposed SSF power levels. Tests were conducted in a vacuum bell jar that was designed to conduct polyimide pyrolysis, arc tracking, and flashover studies on samples of SSF's FCC. Test results will be reported concerning the minimal power level needed to sustain arc tracking and the FCC susceptibility to flashover. Results of the FCC arc tracking tests indicate that only 22 volt amps were necessary to sustain arc tracking (proposed SSF power level is 400 watts). FCC flashover studies indicate that the flashover event is highly unlikely.

Worldwide Abundance and Distribution of Bacillus thuringiensis Isolates

PubMed Central

Martin, Phyllis A. W.; Travers, Russell S.

1989-01-01

We found the insect control agent Bacillus thuringiensis to be a ubiquitous soil microorganism. Using acetate selection to screen soil samples, we isolated B. thuringiensis in 785 of 1,115 soil samples. These samples were obtained in the United States and 29 other countries. A total of 48% of the B. thuringiensis isolates (8,916 isolates) fit the biochemical description of known varieties, while 52% represented undescribed B. thuringiensis types. Over 60% (1,052 isolates) of the isolates tested for toxicity were toxic to insects in the orders Lepidoptera or Diptera. Soil samples were collected from various habitats, including those habitats with different numbers of insects. The current presence of insects did not predict the presence of B. thuringiensis in a particular soil sample. B. thuringiensis was most abundant in samples from Asia. PMID:16348022

Composition dependent thermal annealing behaviour of ion tracks in apatite

NASA Astrophysics Data System (ADS)

Nadzri, A.; Schauries, D.; Mota-Santiago, P.; Muradoglu, S.; Trautmann, C.; Gleadow, A. J. W.; Hawley, A.; Kluth, P.

2016-07-01

Natural apatite samples with different F/Cl content from a variety of geological locations (Durango, Mexico; Mud Tank, Australia; and Snarum, Norway) were irradiated with swift heavy ions to simulate fission tracks. The annealing kinetics of the resulting ion tracks was investigated using synchrotron-based small-angle X-ray scattering (SAXS) combined with ex situ annealing. The activation energies for track recrystallization were extracted and consistent with previous studies using track-etching, tracks in the chlorine-rich Snarum apatite are more resistant to annealing than in the other compositions.

A Customized DNA Microarray for Microbial Source Tracking ...

EPA Pesticide Factsheets

It is estimated that more than 160, 000 miles of rivers and streams in the United States are impaired due to the presence of waterborne pathogens. These pathogens typically originate from human and other animal fecal pollution sources; therefore, a rapid microbial source tracking (MST) method is needed to facilitate water quality assessment and impaired water remediation. We report a novel qualitative DNA microarray technology consisting of 453 probes for the detection of general fecal and host-associated bacteria, viruses, antibiotic resistance, and other environmentally relevant genetic indicators. A novel data normalization and reduction approach is also presented to help alleviate false positives often associated with high-density microarray applications. To evaluate the performance of the approach, DNA and cDNA was isolated from swine, cattle, duck, goose and gull fecal reference samples, as well as soiled poultry liter and raw municipal sewage. Based on nonmetric multidimensional scaling analysis of results, findings suggest that the novel microarray approach may be useful for pathogen detection and identification of fecal contamination in recreational waters. The ability to simultaneously detect a large collection of environmentally important genetic indicators in a single test has the potential to provide water quality managers with a wide range of information in a short period of time. Future research is warranted to measure microarray performance i

Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers

EPA Science Inventory

In this study, we examined the potential for detecting fecal bacteria and microbial source tracking markers in samples discarded during the concentration of Cryptosporidium and Giardia using USEPA Method 1623. Recovery rates for different fecal bacteria were determined using sp...

A DATABASE FOR TRACKING TOXICOGENOMIC SAMPLES AND PROCEDURES WITH GENOMIC, PROTEOMIC AND METABONOMIC COMPONENTS

EPA Science Inventory

A Database for Tracking Toxicogenomic Samples and Procedures with Genomic, Proteomic and Metabonomic Components
Wenjun Bao1, Jennifer Fostel2, Michael D. Waters2, B. Alex Merrick2, Drew Ekman3, Mitchell Kostich4, Judith Schmid1, David Dix1
Office of Research and Developmen...

77 FR 53941 - Emerging Global Advisors, LLC, et al.;

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-04

... sampling strategy to track its Underlying Index. A Fund using a replication strategy will invest in the.... A Fund using a representative sampling strategy will hold some, but not necessarily all, of the... strategy, a Fund is not expected to track the performance of its Underlying Index with the same degree of...

Measuring microbial fitness in a field reciprocal transplant experiment.

PubMed

Boynton, Primrose J; Stelkens, Rike; Kowallik, Vienna; Greig, Duncan

2017-05-01

Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Resolving occlusion and segmentation errors in multiple video object tracking

NASA Astrophysics Data System (ADS)

Cheng, Hsu-Yung; Hwang, Jenq-Neng

2009-02-01

In this work, we propose a method to integrate the Kalman filter and adaptive particle sampling for multiple video object tracking. The proposed framework is able to detect occlusion and segmentation error cases and perform adaptive particle sampling for accurate measurement selection. Compared with traditional particle filter based tracking methods, the proposed method generates particles only when necessary. With the concept of adaptive particle sampling, we can avoid degeneracy problem because the sampling position and range are dynamically determined by parameters that are updated by Kalman filters. There is no need to spend time on processing particles with very small weights. The adaptive appearance for the occluded object refers to the prediction results of Kalman filters to determine the region that should be updated and avoids the problem of using inadequate information to update the appearance under occlusion cases. The experimental results have shown that a small number of particles are sufficient to achieve high positioning and scaling accuracy. Also, the employment of adaptive appearance substantially improves the positioning and scaling accuracy on the tracking results.

Clutter isolation and cardiac monitoring using harmonic doppler radar with heterodyne receiver and passive RF tags.

PubMed

Singh, Aditya; Lubecke, Victor

2010-01-01

A harmonic radar employing the use of harmonic passive RF tags can be successfully used to isolate the human respiration from environmental clutter. This paper describes the successful use of heterodyne receiver architecture with Doppler radar to track the heart-rate of a human being using passive body-worn harmonic tags in presence of a controlled noise generator at distances up to 120 cm. The heterodyne system results have been compared with those of a conventional Doppler radar for cardiopulmonary monitoring that fails to isolate the noise from heart-rate in presence of a noise source.

Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria.

PubMed

Edrington, Tom S; Fox, William E; Callaway, Todd R; Anderson, Robin C; Hoffman, Dennis W; Nisbet, David J

2009-03-01

Composting manure, if done properly, should kill pathogenic bacteria such as Salmonella and Escherichia coli O157:H7, providing for an environmentally safe product. Over a 3-year period, samples of composted dairy manure, representing 11 composting operations (two to six samples per producer; 100 total samples), were screened for Salmonella and E. coli O157:H7 and were all culture negative. Nonpathogenic bacteria were cultured from these compost samples that could theoretically facilitate the spread of antimicrobial resistance from the dairy to compost application sites. Therefore, we collected soil samples (three samples per plot; 10 plots/treatment; 90 total samples) from rangeland that received either composted dairy manure (CP), commercial fertilizer (F), or no treatment (control, CON). Two collections were made appoximately 2 and 7 months following treatment application. Soil samples were cultured for Pseudomonas and Enterobacter and confirmed isolates subjected to antimicrobial susceptibility testing. Three species of Enterobacter (cloacae, 27 isolates; aeroginosa, two isolates; sakazakii, one isolate) and two species of Pseudomonas (aeruginosa, 11 isolates; putida, seven isolates) were identified. Five Enterobacter isolates were resistant to ampicillin and one isolate was resistant to spectinomycin. All Pseudomonas isolates were resistant to ampicillin, ceftiofur, florfenicol, sulphachloropyridazine, sulphadimethoxine, and trimethoprim/sulfamethoxazole and most isolates were resistant to chlortetracycline and spectinomycin. Pseudomonas isolates were resistant to an average of 8.6, 7.9, and 8 antibiotics for CON, CP, and F treatments, respectively. No treatment differences were observed in antimicrobial resistance patterns in any of the soil isolates examined. Results reported herein support the use of composted dairy manure as an environmentally friendly soil amendment.

Evidence against a speed limit in multiple-object tracking.

PubMed

Franconeri, S L; Lin, J Y; Pylyshyn, Z W; Fisher, B; Enns, J T

2008-08-01

Everyday tasks often require us to keep track of multiple objects in dynamic scenes. Past studies show that tracking becomes more difficult as objects move faster. In the present study, we show that this trade-off may not be due to increased speed itself but may, instead, be due to the increased crowding that usually accompanies increases in speed. Here, we isolate changes in speed from variations in crowding, by projecting a tracking display either onto a small area at the center of a hemispheric projection dome or onto the entire dome. Use of the larger display increased retinal image size and object speed by a factor of 4 but did not increase interobject crowding. Results showed that tracking accuracy was equally good in the large-display condition, even when the objects traveled far into the visual periphery. Accuracy was also not reduced when we tested object speeds that limited performance in the small-display condition. These results, along with a reinterpretation of past studies, suggest that we might be able to track multiple moving objects as fast as we can a single moving object, once the effect of object crowding is eliminated.

Modelling of Rail Vehicles and Track for Calculation of Ground-Vibration Transmission Into Buildings

NASA Astrophysics Data System (ADS)

Hunt, H. E. M.

1996-05-01

A methodology for the calculation of vibration transmission from railways into buildings is presented. The method permits existing models of railway vehicles and track to be incorporated and it has application to any model of vibration transmission through the ground. Special attention is paid to the relative phasing between adjacent axle-force inputs to the rail, so that vibration transmission may be calculated as a random process. The vehicle-track model is used in conjunction with a building model of infinite length. The tracking and building are infinite and parallel to each other and forces applied are statistically stationary in space so that vibration levels at any two points along the building are the same. The methodology is two-dimensional for the purpose of application of random process theory, but fully three-dimensional for calculation of vibration transmission from the track and through the ground into the foundations of the building. The computational efficiency of the method will interest engineers faced with the task of reducing vibration levels in buildings. It is possible to assess the relative merits of using rail pads, under-sleeper pads, ballast mats, floating-slab track or base isolation for particular applications.

Study of nuclear multifragmentation induced by ultrarelativistic μ-mesons in nuclear track emulsion

NASA Astrophysics Data System (ADS)

Artemenkov, D. A.; Bradnova, V.; Firu, E.; Kornegrutsa, N. K.; Haiduc, M.; Mamatkulov, K. Z.; Kattabekov, R. R.; Neagu, A.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.

2016-02-01

Exposures of test samples of nuclear track emulsion were analyzed. The formation of high-multiplicity nuclear stars was observed upon irradiating nuclear track emulsions with ultrarelativistic muons. Kinematical features studied in this exposure of nuclear track emulsions for events of the muon-induced splitting of carbon nuclei to three α-particles are indicative of the nuclear-diffraction interaction mechanism.

Fast Compressive Tracking.

PubMed

Zhang, Kaihua; Zhang, Lei; Yang, Ming-Hsuan

2014-10-01

It is a challenging task to develop effective and efficient appearance models for robust object tracking due to factors such as pose variation, illumination change, occlusion, and motion blur. Existing online tracking algorithms often update models with samples from observations in recent frames. Despite much success has been demonstrated, numerous issues remain to be addressed. First, while these adaptive appearance models are data-dependent, there does not exist sufficient amount of data for online algorithms to learn at the outset. Second, online tracking algorithms often encounter the drift problems. As a result of self-taught learning, misaligned samples are likely to be added and degrade the appearance models. In this paper, we propose a simple yet effective and efficient tracking algorithm with an appearance model based on features extracted from a multiscale image feature space with data-independent basis. The proposed appearance model employs non-adaptive random projections that preserve the structure of the image feature space of objects. A very sparse measurement matrix is constructed to efficiently extract the features for the appearance model. We compress sample images of the foreground target and the background using the same sparse measurement matrix. The tracking task is formulated as a binary classification via a naive Bayes classifier with online update in the compressed domain. A coarse-to-fine search strategy is adopted to further reduce the computational complexity in the detection procedure. The proposed compressive tracking algorithm runs in real-time and performs favorably against state-of-the-art methods on challenging sequences in terms of efficiency, accuracy and robustness.

Automatic detection of recoil-proton tracks and background rejection criteria in liquid scintillator-micro-capillary-array fast neutron spectrometer

NASA Astrophysics Data System (ADS)

Mor, Ilan; Vartsky, David; Dangendorf, Volker; Tittelmeier, Kai.; Weierganz, Mathias; Goldberg, Mark Benjamin; Bar, Doron; Brandis, Michal

2018-06-01

We describe an analysis procedure for automatic unambiguous detection of fast-neutron-induced recoil proton tracks in a micro-capillary array filled with organic liquid scintillator. The detector is viewed by an intensified CCD camera. This imaging neutron detector possesses the capability to perform high position-resolution (few tens of μm), energy-dispersive transmission-imaging using ns-pulsed beams. However, when operated with CW or DC beams, it also features medium-quality spectroscopic capabilities for incident neutrons in the energy range 2-20 MeV. In addition to the recoil proton events which display a continuous extended track structure, the raw images exhibit complex ion-tracks from nuclear interactions of fast-neutrons in the scintillator, capillaries quartz-matrix and CCD. Moreover, as expected, one also observes a multitude of isolated scintillation spots of varying intensity (henceforth denoted "blobs") that originate from several different sources, such as: fragmented proton tracks, gamma-rays, heavy-ion reactions as well as events and noise that occur in the image-intensifier and CCD. In order to identify the continuous-track recoil proton events and distinguish them from all these background events, a rapid, computerized and automatic track-recognition-procedure was developed. Based on an appropriately weighted analysis of track parameters such as: length, width, area and overall light intensity, the method is capable of distinguishing a single continuous-track recoil proton from typically surrounding several thousands of background events that are found in each CCD frame.

Adaptive quaternion tracking with nonlinear extended state observer

NASA Astrophysics Data System (ADS)

Bai, Yu-liang; Wang, Xiao-gang; Xu, Jiang-tao; Cui, Nai-gang

2017-10-01

This paper addresses the problem of attitude tracking for spacecraft in the presence of uncertainties in moments of inertia and environmental disturbances. An adaptive quaternion tracking control is combined with a nonlinear extended state observer and the disturbances compensated for in each sampling period. The tracking controller is proved to asymptotically track a prescribed motion in the presence of these uncertainties. Simulations of a nano-spacecraft demonstrate a significant improvement in pointing accuracy and tracking error when compared to a conventional attitude controller. The proposed tracking control is completely deterministic, simple to implement, does not require knowledge of the uncertainties and does not suffer from chattering.

Optical Mapping of Membrane Potential and Epicardial Deformation in Beating Hearts.

PubMed

Zhang, Hanyu; Iijima, Kenichi; Huang, Jian; Walcott, Gregory P; Rogers, Jack M

2016-07-26

Cardiac optical mapping uses potentiometric fluorescent dyes to image membrane potential (Vm). An important limitation of conventional optical mapping is that contraction is usually arrested pharmacologically to prevent motion artifacts from obscuring Vm signals. However, these agents may alter electrophysiology, and by abolishing contraction, also prevent optical mapping from being used to study coupling between electrical and mechanical function. Here, we present a method to simultaneously map Vm and epicardial contraction in the beating heart. Isolated perfused swine hearts were stained with di-4-ANEPPS and fiducial markers were glued to the epicardium for motion tracking. The heart was imaged at 750 Hz with a video camera. Fluorescence was excited with cyan or blue LEDs on alternating camera frames, thus providing a 375-Hz effective sampling rate. Marker tracking enabled the pixel(s) imaging any epicardial site within the marked region to be identified in each camera frame. Cyan- and blue-elicited fluorescence have different sensitivities to Vm, but other signal features, primarily motion artifacts, are common. Thus, taking the ratio of fluorescence emitted by a motion-tracked epicardial site in adjacent frames removes artifacts, leaving Vm (excitation ratiometry). Reconstructed Vm signals were validated by comparison to monophasic action potentials and to conventional optical mapping signals. Binocular imaging with additional video cameras enabled marker motion to be tracked in three dimensions. From these data, epicardial deformation during the cardiac cycle was quantified by computing finite strain fields. We show that the method can simultaneously map Vm and strain in a left-sided working heart preparation and can image changes in both electrical and mechanical function 5 min after the induction of regional ischemia. By allowing high-resolution optical mapping in the absence of electromechanical uncoupling agents, the method relieves a long-standing limitation of optical mapping and has potential to enhance new studies in coupled cardiac electromechanics. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Results of the IRIS UV Burst Survey, Part I: Active Regions Tracked Limb to Limb

NASA Astrophysics Data System (ADS)

Madsen, C. A.; DeLuca, E.

2017-12-01

We present results from the first phase of an effort to thoroughly characterize UV bursts within the Interface Region Imaging Spectrograph (IRIS) data catalogue. The observational signatures of these phenomena include dramatically intensified and broadened NUV/FUV emission line profiles with absorption features from cool metallic ions. These properties suggest that UV bursts originate from plasma at transition region temperatures (≥ 80,000 K) which is deeply embedded in the cool lower chromosphere ( 5,000 K). Rigorously characterizing the energetic and dynamical properties of UV bursts is crucial since they have considerable potential to heat active region chromospheres and could provide critical constraints for models of magnetic reconnection in these regions. The survey first focuses on IRIS observations of active regions tracked from limb to limb. All observations consist of large field-of-view raster scans of 320 or 400 steps each, which allow for widespread detection of many burst profiles at the expense of having limited short-term time evolution information. We detect bursts efficiently by applying a semi-automated single-Gaussian fitting technique to Si IV 1393.8 Å emission profiles that isolates the distinct burst population in a 4-D parameter space. The robust sample of NUV/FUV burst spectra allows for precise constraints of properties critical for modeling reconnection in the chromosphere, including outflow kinetic energy, density estimates from intensity ratios of Si IV 1402.8 Å and O IV 1401.2 Å emission lines, and coincident measures of emission in other wavelengths. We also track burst properties throughout the lifetimes of their host active regions, noting changes in detection rate and preferential location as the active regions evolve. Finally, the tracked active region observations provide a unique opportunity to investigate line-of-sight effects on observed UV burst spectral properties, particularly the strength of Ni II 1393.3 Å absorption, a feature that may be important in identifying the upward conduction of burst thermal energy through the chromosphere.

Textual and shape-based feature extraction and neuro-fuzzy classifier for nuclear track recognition

NASA Astrophysics Data System (ADS)

Khayat, Omid; Afarideh, Hossein

2013-04-01

Track counting algorithms as one of the fundamental principles of nuclear science have been emphasized in the recent years. Accurate measurement of nuclear tracks on solid-state nuclear track detectors is the aim of track counting systems. Commonly track counting systems comprise a hardware system for the task of imaging and software for analysing the track images. In this paper, a track recognition algorithm based on 12 defined textual and shape-based features and a neuro-fuzzy classifier is proposed. Features are defined so as to discern the tracks from the background and small objects. Then, according to the defined features, tracks are detected using a trained neuro-fuzzy system. Features and the classifier are finally validated via 100 Alpha track images and 40 training samples. It is shown that principle textual and shape-based features concomitantly yield a high rate of track detection compared with the single-feature based methods.

Two-Photon-Absorption Scheme for Optical Beam Tracking

NASA Technical Reports Server (NTRS)

Ortiz, Gerardo G.; Farr, William H.

2011-01-01

A new optical beam tracking approach for free-space optical communication links using two-photon absorption (TPA) in a high-bandgap detector material was demonstrated. This tracking scheme is part of the canonical architecture described in the preceding article. TPA is used to track a long-wavelength transmit laser while direct absorption on the same sensor simultaneously tracks a shorter-wavelength beacon. The TPA responsivity was measured for silicon using a PIN photodiode at a laser beacon wavelength of 1,550 nm. As expected, the responsivity shows a linear dependence with incident power level. The responsivity slope is 4.5 x 10(exp -7) A/W2. Also, optical beam spots from the 1,550-nm laser beacon were characterized on commercial charge coupled device (CCD) and complementary metal-oxide semiconductor (CMOS) imagers with as little as 13.7 microWatts of optical power (see figure). This new tracker technology offers an innovative solution to reduce system complexity, improve transmit/receive isolation, improve optical efficiency, improve signal-to-noise ratio (SNR), and reduce cost for free-space optical communications transceivers.

Fission track length distributions in multi-system thermochronology (Invited)

NASA Astrophysics Data System (ADS)

Gleadow, A. J.; Seiler, C.

2013-12-01

Fission track length distributions contain a unique record of past temperature variations and therefore play a key role in low-temperature thermochronology, for which there is no exact equivalent in any other method. Confined track lengths closely approximate the true etchable ranges of latent fission tracks [1] and are therefore favoured for fission track studies, but they still have a number of practical limitations. These include small numbers of suitable tracks, especially when only horizontal confined tracks are measured. Using only track-in-track events for measurement further limits the sample size. These restrictions become acute for low track-density samples, where length measurements may be impossible. Irradiating the surface with 252Cf tracks [2] can substantially increase the number of confined tracks, but many researchers do not have access to a Cf source. An even more significant issue has emerged from inter-laboratory comparison experiments that demonstrate a disturbingly poor reproducibility of length measurements between observers [3], a problem compounded by a lack of standardisation in measurement techniques. As a result, individual observers may measure different positions for the end of a track, contributing significantly to variability, and consequently blurring the thermal histories obtained. New digital microscopes open up important opportunities for improved track length measurements by reducing restrictions on sample size, and eliminating some sources of inter-observer bias. We have developed a track length measurement system that enables precise determination of vertical as well as horizontal track dimensions, allowing 3D lengths to be obtained. Lengths are measured on captured image stacks that can be analysed easily and may also be shared, for greater standardisation between laboratories. Length measurements are highly reproducible between different observers using this system, suggesting that at least one source of variability can be eliminated. The selection of lengths for imaging, however, still remains a source of potential bias between observers. The new measurement system also enables measurement of 3D lengths of surface-intersecting ';semi-tracks', the distributions of which have been well understood theoretically [1,4], but have not been used in practice because of difficulties of measuring vertical dimensions on older microscopes. Semi-track lengths are, of course, a degraded measure compared to confined tracks because they are randomly truncated. However, this is more than compensated by their very much greater abundance, by a factor of >60, compared to confined tracks. They are also more amenable to semi- or fully-automated measurement techniques than confined tracks. Moreover the distribution characteristics of semi-track lengths relative to confined track lengths are well understood so that in principle the two types could be used together in modelling thermal histories. The implementation of these new approaches for track length measurement should significantly improve the precision and standardisation of track length measurements at every stage of their utilisation, from annealing studies to thermal history modelling of unknowns. [1] Galbraith (2003) Statistics for FT Analysis, Chapman & Hall [2] Donelick et al. (2005) Rev Min Geochem 58, 49-94 [3] Ketcham et al. (2009) Ear Planet Sci Lett 284, 504-515 [4] Jonckheere & Van den haute (1999) Rad Meas 30, 155-179

NHEXAS PHASE I MARYLAND STUDY--STANDARD OPERATING PROCEDURE FOR CHAIN-OF-CUSTODY AND SAMPLE TRACKING (G04)

EPA Science Inventory

The purpose of the SOP is to establish the normal procedures for ensuring data chain-of-custody and data tracking. The chain-of-custody form included in this SOP is the standard form to be used for all data collected in the field. Keywords: samples; custody; records.

The Nat...

Modeling of human operator dynamics in simple manual control utilizing time series analysis. [tracking (position)

NASA Technical Reports Server (NTRS)

Agarwal, G. C.; Osafo-Charles, F.; Oneill, W. D.; Gottlieb, G. L.

1982-01-01

Time series analysis is applied to model human operator dynamics in pursuit and compensatory tracking modes. The normalized residual criterion is used as a one-step analytical tool to encompass the processes of identification, estimation, and diagnostic checking. A parameter constraining technique is introduced to develop more reliable models of human operator dynamics. The human operator is adequately modeled by a second order dynamic system both in pursuit and compensatory tracking modes. In comparing the data sampling rates, 100 msec between samples is adequate and is shown to provide better results than 200 msec sampling. The residual power spectrum and eigenvalue analysis show that the human operator is not a generator of periodic characteristics.

Reconnaissance of Surface-Water Quality and Possible Sources of Nutrients and Bacteria in the Turkey Creek Watershed, Northwest Oklahoma, 2002-2003

USGS Publications Warehouse

Becker, Carol J.

2004-01-01

The U.S. Geological Survey in cooperation with the Oklahoma Department of Environmental Quality and the U.S. Environmental Protection Agency investigated the distribution of surface-water quality and possible sources of nutrients and Escherichia coli bacteria to surface water in Turkey Creek, which flows about 70 miles through mostly rural agricultural areas in northwest Oklahoma. Results show that discharge on the main stem of Turkey Creek increased during low-flow conditions from an average of 5.4 cubic feet per second at the upper most site to 39 cubic feet per second at the lower most site in the watershed, indicating that Turkey Creek gains water from ground-water discharge. A portion of the increase in stream discharge may be from discharges of treated effluent from city sewage lagoons. However, the volume and frequency of discharges are unknown. Surface-water-quality samples show that specific conductance ranged from 1,180 to 1,740 microsiemens per centimeter at 25 degrees Celsius during low-flow conditions and in general, decreased downstream with site 1 or site 2 having the largest measurement and site 5 having the lowest. The pH values were slightly alkaline and ranged from 6.8 to 8.5 with a median of 8.2. Dissolved oxygen ranged from 9.3 to 15.9 milligrams per liter in samples collected in the months of November, February, and March and ranged from 5.3 to 13.9 milligrams per liter in samples collected in the months of June, July, and August. Surface-water-quality samples show that the median concentrations of nitrite plus nitrate as nitrogen (1.16 milligrams per liter) and total phosphorus (0.275 milligram per liter) are larger than the average median concentrations of 0.35 and 0.083 milligram per liter, respectively, calculated from water-quality sites in Oklahoma and part of Arkansas (excluding sites in the Ozark Highland and the Ouachita Mountains ecoregions) having similar stream orders and stream slopes. Concentrations of nitrite plus nitrate as nitrogen increased slightly in the winter months and decreased in the summer months, whereas, concentrations of total phosphorus and orthophosphate as phosphorus tended to increase during the summer months and decrease in the winter months. During high-flow conditions total phosphorus increased 7.7 times above the average concentration of 0.261 milligram per liter in low-flow samples. Orthophosphate concentrations increased 3.5 to 4 times during high-flow conditions. Almost all low-flow samples showed 15N values between 4 and 10 parts per thousand, above the range for atmospheric nitrogen and synthetic fertilizer and below the range for animal waste. These samples may represent a mixture of nitrate from these two sources and other sources enriched with 15N, such as soils and plants. Results of the bacterial source tracking indicated that the two source groups having the greatest number of ribopattern matches with surface-water isolates were the cattle group, 53 isolates or 23.5 percent, and the human group, 41 isolates or 18.2 percent. Fewer surface-water isolates matched the deer and horse groups, 8.0 percent and 3.5 percent, respectively. About 43 percent or 96 surface-water isolates were not matched to any source group.

Methicillin-resistant Staphylococcus aureus nasal colonization in a level III neonatal intensive care unit: Incidence and risk factors.

PubMed

Giuffrè, Mario; Amodio, Emanuele; Bonura, Celestino; Geraci, Daniela M; Saporito, Laura; Ortolano, Rita; Corsello, Giovanni; Mammina, Caterina

2015-05-01

To describe epidemiologic features and identify risk factors for methicillin-resistant Staphylococcus aureus (MRSA) acquisition in a level III neonatal intensive care unit (NICU). A prospective, cohort study in a university-affiliated NICU with an infection control program including weekly nasal cultures of all neonates. Demographic, clinical, and microbiologic data were prospectively collected between June 2009 and June 2013. Molecular characterization of MRSA isolates was done by multilocus variable number tandem repeat fingerprinting, staphylococcal cassette chromosome mec typing, and on representative isolates by multilocus sequence typing and spa typing. Of 949 neonates, 217 (22.87%) had a culture growing MRSA, including 117 neonates testing positive at their first sampling. Of these latter infants, 96 (82.05%) were inborn and 59 (50.43%) had been transferred from the nursery. Length of stay and colonization pressure were strong independent predictors of MRSA acquisition. Among MRSA isolates, 7 sequence types were identified, with ST22-IVa, spa type t223, being the predominant strain. In an endemic area, early MRSA acquisition and high colonization pressure, likely related to an influx of colonized infants from a well-infant nursery, can support persistence of MRSA in NICUs. Surveillance, molecular tracking of strains, and reinforcement of infection control practices, involving well-infant nurseries in a comprehensive infection control program, could be helpful in containing MRSA transmission. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Results of interlaboratory comparison of fission-track age standards: Fission-track workshop-1984

USGS Publications Warehouse

Miller, D.S.; Duddy, I.R.; Green, P.F.; Hurford, A.J.; Naeser, C.W.

1985-01-01

Five samples were made available as standards for the 1984 Fission Track Workshop held in the summer of 1984 (Rensselaer Polytechnic Institute, Troy, New York). Two zircons, two apatites and a sphene were distributed prior to the meeting to 40 different laboratories. To date, 24 different analysts have reported results. The isotopic ages of the standards ranged from 16.8 to 98.7 Myr. Only the statement that the age of each sample was less than 200 Myr was provided with the set of standards distributed. Consequently, each laboratory was required to use their laboratory's accepted treatment (irradiation level, etching conditions, counting conditions, etc.) for these samples. The results show that some workers have serious problems in achieving accurate age determinations. This emphasizes the need to calibrate experimental techniques and counting procedures against age standards before unknown ages are determined. Any fission-track age determination published or submitted for publication can only be considered reliable if it is supported by evidence of consistent determinations on age standards. Only this can provide the scientific community with the background to build up confidence concerning the validity of the fission-track method. ?? 1985.

Two-phase Neogene extension in the northwestern basin and range recorded in a single thermochronology sample

USGS Publications Warehouse

Colgan, J.P.; Shuster, D.L.; Reiners, P.W.

2008-01-01

We use a combination of apatite 4He/3He, (U-Th)/ He, and fission-track thermochronology to date slip on the Surprise Valley fault in northeastern California by analyzing a single sample from the Warner Range in the footwall of the fault. This sample, a granitic clast from a conglomerate, yielded a fission-track age of 11.6 ?? 2.8 Ma and a (U-Th)/He age of 3.02 ?? 0.52 Ma. Geologic relationships indicate that this sample was buried to a depth of ???3.3 km prior to exhumation during slip on the Surprise Valley fault. Fission-track age and length data indicate that the sample was fully reset (>120 ??C) prior to exhumation, which began sometime after 14 Ma. A single aliquot of nine apatite grains was step-heated for 4He/3He analysis; modeling of the resulting 4He distribution indicates that cooling from <80 ??C to ???20 ??C occurred between 3 and 1 Ma. Interconsistent time-temperature (t-T) solutions to the combined 4He/3He, (U-Th)/He, and fission-track data require two distinct periods of cooling, consistent with non-continuous slip on the Surprise Valley fault. Early cooling and fault slip took place between 14 and 8 Ma, followed by more recent fault slip ca. 3 Ma. This timing is consistent with both local geologic relationships and with the regional timing of faulting along the western margin of the Basin and Range Province. These data demonstrate the resolving power of combined fission-track, (U-Th)/He, and 4He/3He thermochronometric data to extract low-temperature t-T information from a single sample close to Earth's surface. ?? 2008 The Geological Society of America.

A novel storage system for cryoEM samples.

PubMed

Scapin, Giovanna; Prosise, Winifred W; Wismer, Michael K; Strickland, Corey

2017-07-01

We present here a new CryoEM grid boxes storage system designed to simplify sample labeling, tracking and retrieval. The system is based on the crystal pucks widely used by the X-ray crystallographic community for storage and shipping of crystals. This system is suitable for any cryoEM laboratory, but especially for large facilities that will need accurate tracking of large numbers of samples coming from different sources. Copyright © 2017. Published by Elsevier Inc.

Novel diesel-oil-degrading bacteria and fungi from the Ecuadorian Amazon rainforest.

PubMed

Maddela, N R; Masabanda, M; Leiva-Mora, M

2015-01-01

Isolating new diesel-oil-degrading microorganisms from crude-oil contaminated sites and evaluating their degradation capacities are vitally important in the remediation of oil-polluted environments and crude-oil exploitation. In this research, new hydrocarbon-degrading bacteria and fungi were isolated from the crude-oil contaminated soil of the oil-fields in the Amazon rainforest of north-east Ecuador by using a soil enrichment technique. Degradation analysis was tracked by gas chromatography and a flame ionization detector. Under laboratory conditions, maximum degradability of the total n-alkanes reached up to 77.34 and 62.62 removal ratios after 30 days of incubation for the evaporated diesel oil by fungi (isolate-1) and bacteria (isolate-1), respectively. The 16S/18S rDNA sequence analysis indicated that the microorganisms were most closely (99-100%) related to Bacillus cereus (isolate-1), Bacillus thuringiensis (isolate-2), Geomyces pannorum (isolate-1), and Geomyces sp. (isolate-2). Therefore, these strains enable the degradation of hydrocarbons as the sole carbon source, and these findings will benefit these strains in the remediation of oil-polluted environments and oil exploitation.

Position Affects Performance in Multiple-Object Tracking in Rugby Union Players

PubMed Central

Martín, Andrés; Sfer, Ana M.; D'Urso Villar, Marcela A.; Barraza, José F.

2017-01-01

We report an experiment that examines the performance of rugby union players and a control group composed of graduate student with no sport experience, in a multiple-object tracking task. It compares the ability of 86 high level rugby union players grouped as Backs and Forwards and the control group, to track a subset of randomly moving targets amongst the same number of distractors. Several difficulties were included in the experimental design in order to evaluate possible interactions between the relevant variables. Results show that the performance of the Backs is better than that of the other groups, but the occurrence of interactions precludes an isolated groups analysis. We interpret the results within the framework of visual attention and discuss both, the implications of our results and the practical consequences. PMID:28951725

Object Tracking Using Adaptive Covariance Descriptor and Clustering-Based Model Updating for Visual Surveillance

PubMed Central

Qin, Lei; Snoussi, Hichem; Abdallah, Fahed

2014-01-01

We propose a novel approach for tracking an arbitrary object in video sequences for visual surveillance. The first contribution of this work is an automatic feature extraction method that is able to extract compact discriminative features from a feature pool before computing the region covariance descriptor. As the feature extraction method is adaptive to a specific object of interest, we refer to the region covariance descriptor computed using the extracted features as the adaptive covariance descriptor. The second contribution is to propose a weakly supervised method for updating the object appearance model during tracking. The method performs a mean-shift clustering procedure among the tracking result samples accumulated during a period of time and selects a group of reliable samples for updating the object appearance model. As such, the object appearance model is kept up-to-date and is prevented from contamination even in case of tracking mistakes. We conducted comparing experiments on real-world video sequences, which confirmed the effectiveness of the proposed approaches. The tracking system that integrates the adaptive covariance descriptor and the clustering-based model updating method accomplished stable object tracking on challenging video sequences. PMID:24865883

Canine scent detection and microbial source tracking of human waste contamination in storm drains.

PubMed

Van De Werfhorst, Laurie C; Murray, Jill L S; Reynolds, Scott; Reynolds, Karen; Holden, Patricia A

2014-06-01

Human fecal contamination of surface waters and drains is difficult to diagnose. DNA-based and chemical analyses of water samples can be used to specifically quantify human waste contamination, but their expense precludes routine use. We evaluated canine scent tracking, using two dogs trained to respond to the scent of municipal wastewater, as a field approach for surveying human fecal contamination. Fecal indicator bacteria, as well as DNA-based and chemical markers of human waste, were analyzed in waters sampled from canine scent-evaluated sites (urban storm drains and creeks). In the field, the dogs responded positively (70% and 100%) at sites for which sampled waters were then confirmed as contaminated with human waste. When both dogs indicated a negative response, human waste markers were absent. Overall, canine scent tracking appears useful for prioritizing sampling sites for which DNA-based and similarly expensive assays can confirm and quantify human waste contamination.

Neon and Helium in the Surface of Stardust Cell C2028

NASA Technical Reports Server (NTRS)

Palma, R. L.; Pepin, R. O.; Schlutter, D. J.; Frank, D. R.; Bastien, R.; Rodriguez, M.

2015-01-01

Previous studies of light noble gases in Stardust aerogel samples detected a variety of isotopically non-terrestrial He and Ne compositions. However, with one exception, in none of these samples was there visible evidence for the presence of particles that could have hosted the gases. The exception is materials keystoned from track 41, cell C2044, which contained observable fragments of the impacting Wild 2 comet coma grain. Here we report noble gas data from a second aerogel sample in which grains are observed, cut from the surface of a cell (C2028) riddled with tiny tracks and particles that are thought to be secondary in origin, ejected toward the cell when a parent grain collided with the spacecraft structure and fragmented. Interestingly, measured 20Ne/22Ne ratios in the track 41 and C2028 samples are similar, and within error of the meteoritic "Q-phase" Ne composition.

A new method for evaluating radon and thoron alpha-activities per unit volume inside and outside various natural material samples by calculating SSNTD detection efficiencies for the emitted alpha-particles and measuring the resulting track densities.

PubMed

Misdaq, M A; Aitnouh, F; Khajmi, H; Ezzahery, H; Berrazzouk, S

2001-08-01

A Monte Carlo computer code for determining detection efficiencies of the CR-39 and LR-115 II solid-state nuclear track detectors (SSNTD) for alpha-particles emitted by the uranium and thorium series inside different natural material samples was developed. The influence of the alpha-particle initial energy on the SSNTD detection efficiencies was investigated. Radon (222Rn) and thoron (220Rn) alpha-activities per unit volume were evaluated inside and outside the natural material samples by exploiting data obtained for the detection efficiencies of the SSNTD utilized for the emitted alpha-particles, and measuring the resulting track densities. Results obtained were compared to those obtained by other methods. Radon emanation coefficients have been determined for some of the considered material samples.

Genetic Characterization of Atypical Enteropathogenic Escherichia coli Isolates from Ewes' Milk, Sheep Farm Environments, and Humans by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis

PubMed Central

Otero, Verónica; Rodríguez-Calleja, José-María; Otero, Andrés; García-López, María-Luisa

2013-01-01

A collection of 81 isolates of enteropathogenic Escherichia coli (EPEC) was obtained from samples of bulk tank sheep milk (62 isolates), ovine feces (4 isolates), sheep farm environment (water, 4 isolates; air, 1 isolate), and human stool samples (9 isolates). The strains were considered atypical EPEC organisms, carrying the eae gene without harboring the pEAF plasmid. Multilocus sequence typing (MLST) was carried out with seven housekeeping genes and 19 sequence types (ST) were detected, with none of them having been previously reported for atypical EPEC. The most frequent ST included 41 strains isolated from milk and human stool samples. Genetic typing by pulsed-field gel electrophoresis (PFGE) resulted in 57 patterns which grouped in 24 clusters. Comparison of strains isolated from the different samples showed phylogenetic relationships between milk and human isolates and also between milk and water isolates. The results obtained show a possible risk for humans due to the presence of atypical EPEC in ewes' milk and suggest a transmission route for this emerging pathogen through contaminated water. PMID:23872571

A comparative study of sensor fault diagnosis methods based on observer for ECAS system

NASA Astrophysics Data System (ADS)

Xu, Xing; Wang, Wei; Zou, Nannan; Chen, Long; Cui, Xiaoli

2017-03-01

The performance and practicality of electronically controlled air suspension (ECAS) system are highly dependent on the state information supplied by kinds of sensors, but faults of sensors occur frequently. Based on a non-linearized 3-DOF 1/4 vehicle model, different methods of fault detection and isolation (FDI) are used to diagnose the sensor faults for ECAS system. The considered approaches include an extended Kalman filter (EKF) with concise algorithm, a strong tracking filter (STF) with robust tracking ability, and the cubature Kalman filter (CKF) with numerical precision. We propose three filters of EKF, STF, and CKF to design a state observer of ECAS system under typical sensor faults and noise. Results show that three approaches can successfully detect and isolate faults respectively despite of the existence of environmental noise, FDI time delay and fault sensitivity of different algorithms are different, meanwhile, compared with EKF and STF, CKF method has best performing FDI of sensor faults for ECAS system.

Genotypic Characterization of Enterococci Collected from a Coastal Area Using PFGE

NASA Astrophysics Data System (ADS)

Furukawa, Takashi; Yoshida, Terutoyo; Suzuki, Yoshihiro

Development of microbial source tracking (MST) is crucial to ensure public health and bacteriological safety in coastal areas. In this study, pulsed-field gel electrophoresis (PFGE) , utilized for pollution source tracking of hospital infections, was applied to the aquatic environment as a MST method. Enterococcus faecium and Entecococcus faecalis, fecal indicator bacterias, were isolated and identified from a port area, and the genotype was analyzed by PFGE. A total of 230 enterococcal strains were isolated by PFGE, and forty strains were identified as E. faecium using both PCR and the Api 20 Strep test. Dendrogram analysis of the PFGE types revealed that all the 40 E. faecium strains can be classified separately into 7 different groups at a 0.7 similarity level. The genotypic characterization of E. faecium from the coastal port area revealed diverse types. It is suggested that PFGE can be used to differentiate and characterize fecal pollution indicating bacteria by applying it to the aquatic environment, as well as provide detailed information to specify the pollution source.

The effect of sampling rate on observed statistics in a correlated random walk

PubMed Central

Rosser, G.; Fletcher, A. G.; Maini, P. K.; Baker, R. E.

2013-01-01

Tracking the movement of individual cells or animals can provide important information about their motile behaviour, with key examples including migrating birds, foraging mammals and bacterial chemotaxis. In many experimental protocols, observations are recorded with a fixed sampling interval and the continuous underlying motion is approximated as a series of discrete steps. The size of the sampling interval significantly affects the tracking measurements, the statistics computed from observed trajectories, and the inferences drawn. Despite the widespread use of tracking data to investigate motile behaviour, many open questions remain about these effects. We use a correlated random walk model to study the variation with sampling interval of two key quantities of interest: apparent speed and angle change. Two variants of the model are considered, in which reorientations occur instantaneously and with a stationary pause, respectively. We employ stochastic simulations to study the effect of sampling on the distributions of apparent speeds and angle changes, and present novel mathematical analysis in the case of rapid sampling. Our investigation elucidates the complex nature of sampling effects for sampling intervals ranging over many orders of magnitude. Results show that inclusion of a stationary phase significantly alters the observed distributions of both quantities. PMID:23740484

Prevalence of Fusarium species of the Liseola section on Zimbabwean corn and their ability to produce the mycotoxins zearalenone, moniliformin and fumonisin B1.

PubMed

Mubatanhema, W; Moss, M O; Frank, M J; Wilson, D M

1999-12-01

Maize samples were collected from nine Grain Marketing Board (G.M.B) centers in Zimbabwe during the 1991 harvest season. A further 47 samples collected directly from farmers and from the G.M.B., centers in Chinhoyi and Kwekwe during the 1992 harvest season. These samples were analyzed mycologically and the predominant flora was Fusarium although Penicillium, Nigrospora, Aspergillus and Chaetomium could be isolated from some samples. From the first nine samples studied, F. verticillioides and F. subglutinans were isolated in almost equal proportions on samples from the central and the south of the country whereas only F. verticillioides was isolated on the samples from the north. The subsequent study demonstrated that there was a greater fungal diversity in samples from North (Mashonaland West) than samples from the South (Midlands area) with species of Nigrospora, Chaetomium, Acremonium and Diplodia occurring in significant numbers. From a total of 2821 fungal isolates obtained from all the maize samples analyzed, 1485 (53%) were found to belong to the liseola section of Fusarium. The ability of these isolates to produce the mycotoxins zearalenone, moniliformin and fumonisin B1 was tested using a simplified TLC Agar plate method. Out of the 886 isolates tested, only one produced all the three mycotoxins simultaneously whilst most produced fumonisin B1 and/or moniliformin. Only nine isolates produced zearalenone.

Search for a Very Light CP-Odd Higgs Boson in Top Quark Decays from pp-bar; Collisions at √s = 1.96 TeV

DOE PAGES

Aaltonen, T.

2011-07-11

We present the results of a search for a very light CP-odd Higgs boson a 1 0 originating from top quark decays t→H ±b → W ±(*)a 1 0b, and subsequently decaying into τ +τ -. Using a data sample corresponding to an integrated luminosity of 2.7 fb -1 collected by the CDF II detector in pp-bar collisions at 1.96 TeV, we perform a search for events containing a lepton, three or more jets, and an additional isolated track with transverse momentum in the range 3 to 20 GeV/c. Observed events are consistent with background sources, and 95% C.L. limitsmore » are set on the branching ratio of t→H ±b for various masses of H ± and a 1 0.« less

Narrative accounts of tracking the rural domestic violence survivors' journey: a feminist approach.

PubMed

Davis, K; Taylor, B; Furniss, D

2001-06-01

This research represents the first stage of a project to determine the level of use and effectiveness of informal support networks utilised by Australian rural women. We used a feminist narrative approach with semistructured interviews and a convenience sample of 26 rural women. Only 9 out of 12 women's stories are presented. We found that poverty and geographical, social, and emotional isolation resulted in the privatisation of abuse. Women were triggered to leave the family home when their children, friends, or family became victims of the abuse. They planned their escape by telephone with support of friends and family. Although they used these informal supports, the participants paradoxically expected a high level of expertise in domestic violence knowledge and skills. We recommend an integrated multilevel model of support for rural women in violent intimate relationships and their informal supporters.

Cellular Level Brain Imaging in Behaving Mammals: An Engineering Approach

PubMed Central

Hamel, Elizabeth J.O.; Grewe, Benjamin F.; Parker, Jones G.; Schnitzer, Mark J.

2017-01-01

Fluorescence imaging offers expanding capabilities for recording neural dynamics in behaving mammals, including the means to monitor hundreds of cells targeted by genetic type or connectivity, track cells over weeks, densely sample neurons within local microcircuits, study cells too inactive to isolate in extracellular electrical recordings, and visualize activity in dendrites, axons, or dendritic spines. We discuss recent progress and future directions for imaging in behaving mammals from a systems engineering perspective, which seeks holistic consideration of fluorescent indicators, optical instrumentation, and computational analyses. Today, genetically encoded indicators of neural Ca2+ dynamics are widely used, and those of trans-membrane voltage are rapidly improving. Two complementary imaging paradigms involve conventional microscopes for studying head-restrained animals and head-mounted miniature microscopes for imaging in freely behaving animals. Overall, the field has attained sufficient sophistication that increased cooperation between those designing new indicators, light sources, microscopes, and computational analyses would greatly benefit future progress. PMID:25856491

The DNA isolation method has effect on allele drop-out and on the results of fluorescent PCR and DNA fragment analysis.

PubMed

Nagy, Bálint; Bán, Zoltán; Papp, Zoltán

2005-10-01

The quality and the quantity of isolated DNA have an effect on PCR amplifications. The authors studied three DNA isolation protocols (resin binding method using fresh and frozen amniotic fluid samples, and silica adsorption method using fresh samples) on the quantity and on the quality of the isolated DNA. Amniotic fluid samples were obtained from 20 pregnant women. The isolated DNA concentrations were determined by real-time fluorimeter using SYBRGreen I method. Each sample was studied for the presence of 8 STR markers. The authors compared the number of the detected alleles, electrophoretograms and peak areas. There was a significant difference between the concentration of the obtained DNA and in the peak areas between the three isolation protocols. The numbers of detected alleles were different, we observed the most allele drop outs in the resin type DNA isolation protocol from the fresh sample (detected allele numbers 182), followed by resin binding protocol from the frozen samples (detected allele number 243) and by the silica adsorption method (detected allele number 264). The authors demonstrated that the DNA isolation method has an effect on the quantity and quality of the isolated DNA, and on further PCR amplifications.

The efficacy of obtaining genetic-based identifications from putative wolverine snow tracks

Treesearch

Todd J. Ulizio; John R. Squires; Daniel H. Pletscher; Michael K. Schwartz; James J. Claar; Leonard F. Ruggiero

2006-01-01

Snow-track surveys to detect rare carnivores require unequivocal species identification because of management and political ramifications associated with the presence of such species. Collecting noninvasive genetic samples from putative wolverine (Gulo gulo) snow tracks is an effective method for providing definitive species identification for use in presence-...

Track analysis of laser-illuminated etched track detectors using an opto-digital imaging system

NASA Astrophysics Data System (ADS)

Eghan, Moses J.; Buah-Bassuah, Paul K.; Oppon, Osborne C.

2007-11-01

An opto-digital imaging system for counting and analysing tracks on a LR-115 detector is described. One batch of LR-115 track detectors was irradiated with Am-241 for a determined period and distance for linearity test and another batch was exposed to radon gas. The laser-illuminated etched track detector area was imaged, digitized and analysed by the system. The tracks that were counted on the opto-digital system with the aid of media cybernetics software as well as spark gap counter showed comparable track density results ranging between 1500 and 2750 tracks cm-2 and 65 tracks cm-2 in the two different batch detector samples with 0.5% and 1% track counts, respectively. Track sizes of the incident alpha particles from the radon gas on the LR-115 detector demonstrating different track energies are statistically and graphically represented. The opto-digital imaging system counts and measures other track parameters at an average process time of 3-5 s.

Molecular epidemiology of nontuberculous mycobacteria isolates from clinical and environmental sources of a metropolitan city.

PubMed

Velayati, Ali Akbar; Farnia, Parissa; Mozafari, Mohadese; Malekshahian, Donya; Seif, Shima; Rahideh, Snaz; Mirsaeidi, Mehdi

2014-01-01

While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran. A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations. Out of 4014 samples, mycobacteria were isolated from 862 (21.4%) specimens; 536 (62.1%) belonged to slow growing mycobacteria (SGM) and 326 (37.8%) were rapid growing mycobacteria (RGM). The five most frequent NTM were M. farcinogens (105/862; 12.1%), M. fortuitum (72/862; 8.3%), M. senegalense (58/862; 6.7%), M. kansasii (54/862; 6.2%), and M. simiae (46/862; 5.3%). In total, 62.5% (539/862) of mycobacterial positive samples were isolated from water and only 37.4% (323/862) of them were isolated from soil samples (P<0.05). Out of 5314 positive clinical samples for mycobacteria, 175 (3.2%) isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078) in 2004 to 3.8% (39 out of 1005) in 2014 (P = 0.0001). The major clinical isolates were M. simiae (51; 29.1%), M. kansasii (26; 14.8%), M. chelonae (28; 16%), and M. fortuitum (13; 7.4%). Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.

High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert.

PubMed

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R; Vincent, Warwick F

2013-01-01

In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.

Penicillin-Binding Protein Transpeptidase Signatures for Tracking and Predicting β-Lactam Resistance Levels in Streptococcus pneumoniae

PubMed Central

Metcalf, Benjamin J.; Chochua, Sopio; Li, Zhongya; Gertz, Robert E.; Walker, Hollis; Hawkins, Paulina A.; Tran, Theresa; Whitney, Cynthia G.; McGee, Lesley; Beall, Bernard W.

2016-01-01

ABSTRACT β-Lactam antibiotics are the drugs of choice to treat pneumococcal infections. The spread of β-lactam-resistant pneumococci is a major concern in choosing an effective therapy for patients. Systematically tracking β-lactam resistance could benefit disease surveillance. Here we developed a classification system in which a pneumococcal isolate is assigned to a “PBP type” based on sequence signatures in the transpeptidase domains (TPDs) of the three critical penicillin-binding proteins (PBPs), PBP1a, PBP2b, and PBP2x. We identified 307 unique PBP types from 2,528 invasive pneumococcal isolates, which had known MICs to six β-lactams based on broth microdilution. We found that increased β-lactam MICs strongly correlated with PBP types containing divergent TPD sequences. The PBP type explained 94 to 99% of variation in MICs both before and after accounting for genomic backgrounds defined by multilocus sequence typing, indicating that genomic backgrounds made little independent contribution to β-lactam MICs at the population level. We further developed and evaluated predictive models of MICs based on PBP type. Compared to microdilution MICs, MICs predicted by PBP type showed essential agreement (MICs agree within 1 dilution) of >98%, category agreement (interpretive results agree) of >94%, a major discrepancy (sensitive isolate predicted as resistant) rate of <3%, and a very major discrepancy (resistant isolate predicted as sensitive) rate of <2% for all six β-lactams. Thus, the PBP transpeptidase signatures are robust indicators of MICs to different β-lactam antibiotics in clinical pneumococcal isolates and serve as an accurate alternative to phenotypic susceptibility testing. PMID:27302760

Contour Tracking with a Spatio-Temporal Intensity Moment.

PubMed

Demi, Marcello

2016-06-01

Standard edge detection operators such as the Laplacian of Gaussian and the gradient of Gaussian can be used to track contours in image sequences. When using edge operators, a contour, which is determined on a frame of the sequence, is simply used as a starting contour to locate the nearest contour on the subsequent frame. However, the strategy used to look for the nearest edge points may not work when tracking contours of non isolated gray level discontinuities. In these cases, strategies derived from the optical flow equation, which look for similar gray level distributions, appear to be more appropriate since these can work with a lower frame rate than that needed for strategies based on pure edge detection operators. However, an optical flow strategy tends to propagate the localization errors through the sequence and an additional edge detection procedure is essential to compensate for such a drawback. In this paper a spatio-temporal intensity moment is proposed which integrates the two basic functions of edge detection and tracking.

Diversity, Frequency, and Persistence of Escherichia coli O157 Strains from Range Cattle Environments†

PubMed Central

Renter, David G.; Sargeant, Jan M.; Oberst, Richard D.; Samadpour, Mansour

2003-01-01

Genetic diversity, isolation frequency, and persistence were determined for Escherichia coli O157 strains from range cattle production environments. Over the 11-month study, analysis of 9,122 cattle fecal samples, 4,083 water source samples, and 521 wildlife fecal samples resulted in 263 isolates from 107 samples presumptively considered E. coli O157 as determined by culture and latex agglutination. Most isolates (90.1%) were confirmed to be E. coli O157 by PCR detection of intimin and Shiga toxin genes. Pulsed-field gel electrophoresis (PFGE) of XbaI-digested preparations revealed 79 unique patterns (XbaI-PFGE subtypes) from 235 typeable isolates confirmed to be E. coli O157. By analyzing up to three isolates per positive sample, we detected an average of 1.80 XbaI-PFGE subtypes per sample. Most XbaI-PFGE subtypes (54 subtypes) were identified only once, yet the seven most frequently isolated subtypes represented over one-half of the E. coli O157 isolates (124 of 235 isolates). Recurring XbaI-PFGE subtypes were recovered from samples on up to 10 sampling occasions and up to 10 months apart. Seven XbaI-PFGE subtypes were isolated from both cattle feces and water sources, and one of these also was isolated from the feces of a wild opossum (Didelphis sp.). The number of XbaI-PFGE subtypes, the variable frequency and persistence of subtypes, and the presence of identical subtypes in cattle feces, free-flowing water sources, and wildlife feces indicate that the complex molecular epidemiology of E. coli O157 previously described for confined cattle operations is also evident in extensively managed range cattle environments. PMID:12514039

Quantifying Antimicrobial Resistance at Veal Calf Farms

PubMed Central

Bosman, Angela B.; Wagenaar, Jaap; Stegeman, Arjan; Vernooij, Hans; Mevius, Dik

2012-01-01

This study was performed to determine a sampling strategy to quantify the prevalence of antimicrobial resistance on veal calf farms, based on the variation in antimicrobial resistance within and between calves on five farms. Faecal samples from 50 healthy calves (10 calves/farm) were collected. From each individual sample and one pooled faecal sample per farm, 90 selected Escherichia coli isolates were tested for their resistance against 25 mg/L amoxicillin, 25 mg/L tetracycline, 0.5 mg/L cefotaxime, 0.125 mg/L ciprofloxacin and 8/152 mg/L trimethoprim/sulfamethoxazole (tmp/s) by replica plating. From each faecal sample another 10 selected E. coli isolates were tested for their resistance by broth microdilution as a reference. Logistic regression analysis was performed to compare the odds of testing an isolate resistant between both test methods (replica plating vs. broth microdilution) and to evaluate the effect of pooling faecal samples. Bootstrap analysis was used to investigate the precision of the estimated prevalence of resistance to each antimicrobial obtained by several simulated sampling strategies. Replica plating showed similar odds of E. coli isolates tested resistant compared to broth microdilution, except for ciprofloxacin (OR 0.29, p≤0.05). Pooled samples showed in general lower odds of an isolate being resistant compared to individual samples, although these differences were not significant. Bootstrap analysis showed that within each antimicrobial the various compositions of a pooled sample provided consistent estimates for the mean proportion of resistant isolates. Sampling strategies should be based on the variation in resistance among isolates within faecal samples and between faecal samples, which may vary by antimicrobial. In our study, the optimal sampling strategy from the perspective of precision of the estimated levels of resistance and practicality consists of a pooled faecal sample from 20 individual animals, of which 90 isolates are tested for their susceptibility by replica plating. PMID:22970313

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

PubMed Central

Dugan, Vivien G.; Emrich, Scott J.; Giraldo-Calderón, Gloria I.; Harb, Omar S.; Newman, Ruchi M.; Pickett, Brett E.; Schriml, Lynn M.; Stockwell, Timothy B.; Stoeckert, Christian J.; Sullivan, Dan E.; Singh, Indresh; Ward, Doyle V.; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M.; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H.; Cuomo, Christina A.; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W. Florian; Giovanni, Maria; Henn, Matthew R.; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C.; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F.; Murphy, Cheryl I.; Myers, Garry; Neafsey, Daniel E.; Nelson, Karen E.; Nierman, William C.; Puzak, Julia; Rasko, David; Roos, David S.; Sadzewicz, Lisa; Silva, Joana C.; Sobral, Bruno; Squires, R. Burke; Stevens, Rick L.; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H.

2014-01-01

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant. PMID:24936976

Standardized metadata for human pathogen/vector genomic sequences.

PubMed

Dugan, Vivien G; Emrich, Scott J; Giraldo-Calderón, Gloria I; Harb, Omar S; Newman, Ruchi M; Pickett, Brett E; Schriml, Lynn M; Stockwell, Timothy B; Stoeckert, Christian J; Sullivan, Dan E; Singh, Indresh; Ward, Doyle V; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H; Cuomo, Christina A; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W Florian; Giovanni, Maria; Henn, Matthew R; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F; Murphy, Cheryl I; Myers, Garry; Neafsey, Daniel E; Nelson, Karen E; Nierman, William C; Puzak, Julia; Rasko, David; Roos, David S; Sadzewicz, Lisa; Silva, Joana C; Sobral, Bruno; Squires, R Burke; Stevens, Rick L; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H

2014-01-01

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

Assertiveness of Lactobacillus sakei and Lactobacillus curvatus in a fermented sausage model.

PubMed

Janßen, Dorothee; Eisenbach, Lara; Ehrmann, Matthias A; Vogel, Rudi F

2018-04-20

Fresh meat harbors autochthonous microbiota with unknown risk potential, which is introduced in raw fermented sausages. Their growth can be limited by the use of safe, competitive starter strains. In the lack of time and cost-effective methods to track those starters at strain level, their assertiveness upon meat fermentation is widely unknown. Lactobacillus (L.) sakei and L. curvatus, which can be isolated from a variety of habitats, are frequently used as starter cultures. We monitored the assertiveness of 9 L. sakei and 9 L. curvatus strains in a model fermentation using MALDI-TOF-MS. An "in-house" MALDI-TOF-MS database with sub-proteome spectra of L. sakei and L. curvatus strains, as well as members of the autochthonous, spontaneously growing meat microbiota was established, validated and recognition rates were determined for each L. curvatus and L. sakei strain used. Competition studies were performed with standardized sausage batter, which was inoculated with a total of 10 6 cells of sets of 4-5 strains each of L. sakei and L. curvatus and 10 6 Staphylococcus carnosus ssp. carnosus cells. The pH and redox potential were monitored continuously. On days 0, 2 and 5 samples were taken to determine the CfU/g and a total of 96 isolates per sample were identified via MALDI-TOF-MS. MALDI-TOF-MS generally proved suitable for identification of isolates on strain level within the starter sets employed, but the recognition rate varied depending on the strain. Competition studies revealed dominance or co-dominance of strains within each set. However, their assertiveness significantly depended on the composition of the strain sets. Still, co-dominance or cooperation appeared effective to outgrow other members of the autochthonous meat microbiota, rather than dominance of single strains. For the latter, the ability to produce bacteriocins suggested itself for a crucial role in the assertiveness of starter strains. Copyright © 2018 Elsevier B.V. All rights reserved.

Characterization of polymorphic microsatellites for Tripterygium (Celastraceae), a monospecific genus of medicinal importance.

PubMed

Novy, Ari; Jones, Kenneth C

2011-10-01

Microsatellite markers were developed for the medicinal plant Tripterygium (Celastraceae) to assess its population structure and to facilitate source tracking of plant materials used for medicinal extracts. Ten microsatellite markers were isolated and characterized in T. wilfordii using an enriched genomic library. The number of alleles per locus ranged from five to 12. Observed and expected heterozygosity ranged from 0.166 to 0.630 and 0.392 to 0.562, respectively. These markers will be useful for a variety of applications including source tracking of plant materials, resolution of taxonomic issues, and population genetics studies.

Mercury Stable Isotopic Composition of Monomethylmercury in Estuarine Sediments and Pure Cultures of Mercury Methylating Bacteria

NASA Astrophysics Data System (ADS)

Janssen, S.; Johnson, M. W.; Barkay, T.; Blum, J. D.; Reinfelder, J. R.

2014-12-01

Tracking monomethylmercury (MeHg) from its source in soils and sediments through various environmental compartments and transformations is critical to understanding its accumulation in aquatic and terrestrial food webs. Advances in the field of mercury (Hg) stable isotopes have allowed for the tracking of discrete Hg sources and the examination of photochemical and bacterial transformations. Despite analytical advances, measuring the Hg stable isotopic signature of MeHg in environmental samples or laboratory experiments remains challenging due to difficulties in the quantitative separation of MeHg from complex matrices with high concentrations of inorganic Hg. To address these challenges, we have developed a MeHg isolation method for sediments and bacterial cultures which involves separation by gas chromatography. The MeHg eluting from the GC is passed through a pyrolysis column and purged onto a gold amalgam trap which is then desorbed into a final oxidizing solution. A MeHg reference standard carried through our separation process retained its isotopic composition within 0.02 ‰ for δ202Hg, and for native estuarine sediments, MeHg recoveries were 80% to 100%. For sediment samples from the Hackensack and Passaic Rivers (New Jersey, USA), δ202Hg values for MeHg varied from -1.2 to +0.58 ‰ (relative to SRM 3133) and for individual samples were significantly different from that of total Hg (-0.38 ± 0.06 ‰). No mass independent fractionation was observed in MeHg or total Hg from these sediments. Pure cultures of Geobacter sulfurreducens, grown under fermentative conditions showed preferential enrichment of lighter isotopes (lower δ202Hg) during Hg methylation. The Hg stable isotope signatures of MeHg in sediments and laboratory methylation experiments will be discussed in the context of the formation and degradation of MeHg in the environment and the bioaccumulation of MeHg in estuarine food webs.

Effects of low sampling rate in the digital data-transition tracking loop

NASA Technical Reports Server (NTRS)

Mileant, A.; Million, S.; Hinedi, S.

1994-01-01

This article describes the performance of the all-digital data-transition tracking loop (DTTL) with coherent and noncoherent sampling using nonlinear theory. The effects of few samples per symbol and of noncommensurate sampling and symbol rates are addressed and analyzed. Their impact on the probability density and variance of the phase error are quantified through computer simulations. It is shown that the performance of the all-digital DTTL approaches its analog counterpart when the sampling and symbol rates are noncommensurate (i.e., the number of samples per symbol is an irrational number). The loop signal-to-noise ratio (SNR) (inverse of phase error variance) degrades when the number of samples per symbol is an odd integer but degrades even further for even integers.

Improving Lab Sample Management - POS/MCEARD

EPA Science Inventory

"Scientists face increasing challenges in managing their laboratory samples, including long-term storage of legacy samples, tracking multiple aliquots of samples for many experiments, and linking metadata to these samples. Other factors complicating sample management include the...

Detection of Salmonella spp. from chevon, mutton and its environment in retail meat shops in Anand city (Gujarat), India

PubMed Central

Makwana, P. P.; Nayak, J. B.; Brahmbhatt, M. N.; Chaudhary, J. H.

2015-01-01

Aim: The aim of this study was (i) To attempt isolation and identification of Salmonella species from samples. (ii) Serotyping of Salmonella isolates. (iii) Detection of virulence factor associated genes by polymerase chain reaction (PCR). Materials and Methods: A total of 284 samples comprised of chevon and mutton (112 samples each) as well as 60 samples (20 each of retail meat shops environment samples viz. Butchers’ hands, knives and log swabs) were collected from the retail meat shops in and around Anand City under aseptic precautions. Rappaport-vassiliadis soy bean meal broth and tetrathionate broth was used for the enrichment of all the samples and inoculation was done on brilliant green agar and xylose lysine deoxycholate agar. This was followed by the confirmation of isolates using biochemical tests. For the serotyping, isolates were sent to the National Salmonella and Escherichia Centre, Central Research Institute, Kasauli, Himachal Pradesh. Detection of virulence genes was performed by PCR technique using previously reported primer. Result: Of 284 meats and retail meat shops environment samples, 13 (4.58%) samples were found positive for Salmonella. It was interesting to know that incidence of Salmonella was more in mutton (6.25%) than chevon (3.57%). In case of meat shop environmental samples 1 (5.00%) sample observed positive for Salmonella separately among the butchers’ hands and knives swabs (Each of 20 samples) examined. Out of 13, eleven isolates detected as Salmonella Typhimurium, whereas only two isolates were detected as Salmonella Enteritidis. All Salmonella isolates possess invA and stn genes, whereas nine isolates had a presence of spvR gene while only five of the isolates revealed the presence of spvC gene as shown by in vitro detection of virulence genes by PCR. Conclusion: Therefore, might be suggested that the good hygiene practices and effective control measures should be taken to encourage clean meat production with prolonged shelf-life. PMID:27047102

Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis

PubMed Central

Techaruvichit, Punnida; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

2015-01-01

Campylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation of C. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring of C. jejuni and investigation of epidemics caused by C. jejuni. PMID:26025899

Micro-organisms isolated from cadaveric samples of allograft musculoskeletal tissue.

PubMed

Varettas, Kerry

2013-12-01

Allograft musculoskeletal tissue is commonly used in orthopaedic surgical procedures. Cadaveric donors of musculoskeletal tissue supply multiple allografts such as tendons, ligaments and bone. The microbiology laboratory of the South Eastern Area Laboratory Services (SEALS, Australia) has cultured cadaveric allograft musculoskeletal tissue samples for bacterial and fungal isolates since 2006. This study will retrospectively review the micro-organisms isolated over a 6-year period, 2006-2011. Swab and tissue samples were received for bioburden testing and were inoculated onto agar and/or broth culture media. Growth was obtained from 25.1 % of cadaveric allograft musculoskeletal tissue samples received. The predominant organisms isolated were coagulase-negative staphylococci and coliforms, with the heaviest bioburden recovered from the hemipelvis. The rate of bacterial and fungal isolates from cadaveric allograft musculoskeletal tissue samples is higher than that from living donors. The type of organism isolated may influence the suitability of the allograft for transplant.

LIDAR-based characterization and conservation of the first theropod dinosaur trackways from Arkansas, USA.

PubMed

Platt, Brian F; Suarez, Celina A; Boss, Stephen K; Williamson, Malcolm; Cothren, Jackson; Kvamme, Jo Ann C

2018-01-01

LIDAR-based analyses of the first theropod dinosaur trackways known from the state of Arkansas, USA are reported. The trackways were found on a limestone bedding plane in the Albian De Queen Formation in an active gypsum quarry. Because limited access precluded thorough field study, fieldwork focused on preserving the entire site digitally with ground-based LIDAR, and detailed measurements were later taken digitally from point cloud data. The site contains eight tridactyl trackways associated with sauropod trackways and numerous isolated tracks. Although there appear to be two different tridactyl morphotypes, we show that the tracks are all likely from a single species of trackmaker. We apply a simple method of estimating substrate consistency by comparing the differences between true track dimensions and apparent track dimensions. The tridactyl tracks at the southern end of the site are preserved with significantly greater differences in true vs. apparent dimensions and are shallower than the rest of the tridactyl tracks at the site, which we interpret as the result of outward expansion of the soft tissues of the foot upon contact with a firm substrate. We interpret the firm substrate as having high bulk density and high shear strength, which also explain associated manus-only sauropod tracks. We show that the tridactyl tracks are likely from theropod trackmakers and that footprint lengths, trackway paces, stride lengths, and pace angulations of the De Queen trackways are statistically indistinguishable from equivalent measurements of theropod trackways in the Glen Rose Formation. The Glen Rose tracks are attributed to the large-bodied theropod, Acrocanthosaurus and we likewise attribute the De Queen tracks to Acrocanthosaurus, which is known from skeletal remains in temporally equivalent units and from the mine itself.

A User Guide for Smoothing Air Traffic Radar Data

NASA Technical Reports Server (NTRS)

Bach, Ralph E.; Paielli, Russell A.

2014-01-01

Matlab software was written to provide smoothing of radar tracking data to simulate ADS-B (Automatic Dependent Surveillance-Broadcast) data in order to test a tactical conflict probe. The probe, called TSAFE (Tactical Separation-Assured Flight Environment), is designed to handle air-traffic conflicts left undetected or unresolved when loss-of-separation is predicted to occur within approximately two minutes. The data stream that is down-linked from an aircraft equipped with an ADS-B system would include accurate GPS-derived position and velocity information at sample rates of 1 Hz. Nation-wide ADS-B equipage (mandated by 2020) should improve surveillance accuracy and TSAFE performance. Currently, position data are provided by Center radar (nominal 12-sec samples) and Terminal radar (nominal 4.8-sec samples). Aircraft ground speed and ground track are estimated using real-time filtering, causing lags up to 60 sec, compromising performance of a tactical resolution tool. Offline smoothing of radar data reduces wild-point errors, provides a sample rate as high as 1 Hz, and yields more accurate and lag-free estimates of ground speed, ground track, and climb rate. Until full ADS-B implementation is available, smoothed radar data should provide reasonable track estimates for testing TSAFE in an ADS-B-like environment. An example illustrates the smoothing of radar data and shows a comparison of smoothed-radar and ADS-B tracking. This document is intended to serve as a guide for using the smoothing software.

Adolescent Student Burnout Inventory in Mainland China: Measurement Invariance across Gender and Educational Track

ERIC Educational Resources Information Center

Li, Bi; Wu, Yan; Wen, Zhonglin; Wang, Mengcheng

2014-01-01

This article assessed the measurement in variance of the Adolescent Student Burnout Inventory (ASBI) across gender and educational track, and investigated the main and interaction effects of gender and educational track on the facets of student burnout with a sample consisting of 2,216 adolescent students from China. Multigroup confirmatory factor…

The software peculiarities of pattern recognition in track detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starkov, N.

The different kinds of nuclear track recognition algorithms are represented. Several complicated samples of use them in physical experiments are considered. The some processing methods of complicated images are described.

Phase fluctuation spectra: New radio science information to become available in the DSN tracking system Mark III-77

NASA Technical Reports Server (NTRS)

Berman, A. L.

1977-01-01

An algorithm was developed for the continuous and automatic computation of Doppler noise concurrently at four sample rate intervals, evenly spanning three orders of magnitude. Average temporal Doppler phase fluctuation spectra will be routinely available in the DSN tracking system Mark III-77 and require little additional processing. The basic (noise) data will be extracted from the archival tracking data file (ATDF) of the tracking data management system.

Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics.

PubMed

Reischer, G H; Haider, J M; Sommer, R; Stadler, H; Keiblinger, K M; Hornek, R; Zerobin, W; Mach, R L; Farnleitner, A H

2008-10-01

The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.

Qualitative Event-Based Diagnosis: Case Study on the Second International Diagnostic Competition

NASA Technical Reports Server (NTRS)

Daigle, Matthew; Roychoudhury, Indranil

2010-01-01

We describe a diagnosis algorithm entered into the Second International Diagnostic Competition. We focus on the first diagnostic problem of the industrial track of the competition in which a diagnosis algorithm must detect, isolate, and identify faults in an electrical power distribution testbed and provide corresponding recovery recommendations. The diagnosis algorithm embodies a model-based approach, centered around qualitative event-based fault isolation. Faults produce deviations in measured values from model-predicted values. The sequence of these deviations is matched to those predicted by the model in order to isolate faults. We augment this approach with model-based fault identification, which determines fault parameters and helps to further isolate faults. We describe the diagnosis approach, provide diagnosis results from running the algorithm on provided example scenarios, and discuss the issues faced, and lessons learned, from implementing the approach

A sialic acid assay in isolation and purification of bovine k-casein glycomacropeptide: a review.

PubMed

Nakano, Takuo; Ozimek, Lech

2014-01-01

Sialic acid is a carbohydrate moiety of k-casein glycomacropeptide (GMP), which is a 64 amino acid residue C-terminal sialylated phosphorylated glycopeptide released from k-casein by the action of chymosin during cheese making. GMP lacks aromatic amino acids including phenylalanine, tyrosine, and tryptophan. Because of its unique amino acid composition and various biological activities, GMP is thought to be a potential ingredient for dietetic foods (e.g., a food for PKU patients) and pharmaceuticals. Thus, increased attention has been given to the development of techniques to purify GMP. In this review, techniques of GMP purification described in patents and scientific research papers were introduced. A sialic acid assay is the important method to track GMP isolation and purification processes, for which the thiobarbituric acid reaction with 1-propanol as a chromophore extracting solvent is an inexpensive, practical and specific technique. Sephacryl S-200 gel filtration chromatography, cellulose acetate electrophoresis, and sodium dodecyl sulfate polyacrylamide gel electrophoresis are the major techniques to identify sialic acid specific to GMP. Sephacryl S-200 chromatography and cellulose acetate electrophoresis are also used to detect GMP sialic acid in whey pearmeate and whey added commercial margarine samples. Future research includes development of an economical industrial scale method to produce high purity GMP.

General Aspects

NASA Astrophysics Data System (ADS)

Höfle, Gerhard

Epothilone is a microbial product, and thus its history may be traced back to the discovery of the respective microbe, Sorangium cellulosum, a bacterium belonging to the taxonomic group of myxobacteria, which originally has been described by Roland Thaxter in 1892 (1). Today this group of organisms comprises around 40 species, one of which is Sorangium cellulosum. For a long time, myxobacteria were only known for their gliding motility and sophisticated life cycle, although it had been occasionally speculated that they might produce secondary metabolites like actinomycetes or bacilli (2). In 1975 Hans Reichenbach and his group at the German Centre for Biotechnology (GBF; now called the Helmholtz Centre for Infection Research) set out to isolate strains of myxobacteria from soil samples collected all over the world, and to examine their secondary metabolism. In 1978, while work was already ongoing, I joined them and took over the chemistry part. In the same year the first structure of a myxobacterial metabolite, ambruticin, was published by a group from Warner-Lambert (3) making us very confident of being on the right track. Ambruticin had been isolated from a Sorangium cellulosum strain, and was identified as a unique cyclopropane polyketide structure exhibiting potentially useful antifungal properties. Ambruticin and its derivatives had been developed for medical application for some time, and recently gained new interest (4).

Heterotrophic monitoring at a drinking water treatment plant by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry after different drinking water treatments.

PubMed

Sala-Comorera, Laura; Blanch, Anicet R; Vilaró, Carles; Galofré, Belén; García-Aljaro, Cristina

2017-10-01

The aim of this work was to assess the suitability of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for routine heterotrophic monitoring in a drinking water treatment plant. Water samples were collected from raw surface water and after different treatments during two campaigns over a 1-year period. Heterotrophic bacteria were studied and isolates were identified by MALDI-TOF MS. Moreover, the diversity index and the coefficient of population similarity were also calculated using biochemical fingerprinting of the populations studied. MALDI-TOF MS enabled us to characterize and detect changes in the bacterial community composition throughout the water treatment plant. Raw water showed a large and diverse population which was slightly modified after initial treatment steps (sand filtration and ultrafiltration). Reverse osmosis had a significant impact on the microbial diversity, while the final chlorination step produced a shift in the composition of the bacterial community. Although MALDI-TOF MS could not identify all the isolates since the available MALDI-TOF MS database does not cover all the bacterial diversity in water, this technique could be used to monitor bacterial changes in drinking water treatment plants by creating a specific protein profile database for tracking purposes.

Optimisation of Substrate Angles for Multi-material and Multi-functional Inkjet Printing.

PubMed

Vaithilingam, Jayasheelan; Saleh, Ehab; Wildman, Ricky D; Hague, Richard J M; Tuck, Christopher J

2018-06-13

Three dimensional inkjet printing of multiple materials for electronics applications are challenging due to the limited material availability, inconsistencies in layer thickness between dissimilar materials and the need to expose the printed tracks of metal nanoparticles to temperature above 100 °C for sintering. It is envisaged that instead of printing a dielectric and a conductive material on the same plane, by printing conductive tracks on an angled dielectric surface, the required number of silver layers and consequently, the exposure of the polymer to high temperature and the build time of the component can be significantly reduced. Conductive tracks printed with a fixed print height (FH) showed significantly better resolution for all angles than the fixed slope (FS) sample where the print height varied to maintain the slope length. The electrical resistance of the tracks remained under 10Ω up to 60° for FH; whereas for the FS samples, the resistance remained under 10Ω for samples up to 45°. Thus by fixing the print height to 4 mm, precise tracks with low resistance can be printed at substrate angles up to 60°. By adopting this approach, the build height "Z" can be quickly attained with less exposure of the polymer to high temperature.

Direct investigation of collective phenomena in patterned Ising-like arrays using high-resolution Kerr microscopy

NASA Astrophysics Data System (ADS)

Fraleigh, Robert Douglas

Magnetic systems with interacting ferromagnetic single-domain elements are a useful landscape to explore a wide range of fundamental and technological phenomena. In this dissertation, we consider a system of interacting ferromagnetic islands with perpendicular anisotropy. Islands are lithographically-defined to be single-domain and are arranged into large arrays with geometries that are geometrically frustrated and unfrustrated. We explore field-driven local and global magnetic switching behavior using a home-built diffraction-limited magneto-optical Kerr microscope wherein individual islands in each array are isolated, indexed, and tracked in the presence of an applied external field. Global and local switching behavior is directly accessed through analysis island switching fields in the presence of magnetic hysteresis loops. We first explore the considerations regarding lithographic definition of disconnected islands and deposition of Co/Pt multilayers with strong perpendicular anisotropy. The thickness and number of stacked Co/Pt bilayers as well as deposition method significantly affect the strength of perpendicular anisotropy. We find sputter deposition of a 8-stack bilayer of Co0.3 nm=Pt 1 nm optimizes strong perpendicular anisotropy with square hysteresis loops. Our experimental sample contains several sets of ordered arrays with varying geometry and inter-island spacing. Each island is single-domain with length scales amenable to Kerr imaging such that magnetic degrees of freedom are optically accessible. We next discuss the development, calibration, and operation of a home-built magneto-optical Kerr microscope. The Kerr microscope uses a xenon stabilized white light source, Glan-Thompson polarizers, and a 100x oil objective lens to illuminate a sample with linear polarized light. A cooled CCD camera receives the re ected light and transmits it to the computer in a sequence timed with the application of an external magnetic field. We use LabVIEW software to isolate, index, track, and extract intensity information and corresponding switching fields associated with individual islands in each array as a function of a magnetic field. We find the switching field distribution width is well-fit by a simple model comprising the sum of an array-independent contribution (interpreted as disorder-induced), and a term proportional to the maximum field the entire rest of the array could exert on a single island, i.e., in a fully polarized state. This supports the claim that disorder in these arrays is primarily a single-island property.

Enrichment of Multilocus Sequence Typing Clade 1 with Oral Candida albicans Isolates in Patients with Untreated Periodontitis

PubMed Central

McManus, Brenda A.; Maguire, Rory; Cashin, Phillipa J.; Claffey, Noel; Flint, Stephen; Abdulrahim, Mohammed H.

2012-01-01

This study investigated the prevalence and cell density of Candida species in periodontal pockets, healthy subgingival sites, and oral rinse samples of patients with untreated periodontitis. Twenty-one periodontitis patients underwent sampling at two periodontitis sites, and 19/21 of these patients underwent sampling at one periodontally healthy site. Both paper point and curette sampling techniques were employed. The periodontitis patients and 50 healthy subjects were also sampled by oral rinse. Candida isolates were recovered on CHROMagar Candida medium, and representative isolates were identified. Candida spp. were recovered from 10/21 (46.7%) periodontitis patients and from 16/50 (32%) healthy subjects. C. albicans predominated in both groups and was recovered from all Candida-positive subjects. Candida-positive periodontitis patients yielded Candida from periodontal pockets with average densities of 3,528 and 3,910 CFU/sample from curette and paper point samples, respectively, and 1,536 CFU/ml from oral rinse samples. The majority (18/19) of the healthy sites sampled from periodontitis patients were Candida negative. The 16 Candida-positive healthy subjects yielded an average of 279 CFU/ml from oral rinse samples. C. albicans isolates were investigated by multilocus sequence typing (MLST) to determine if specific clonal groups were associated with periodontitis. MLST analysis of 31 C. albicans isolates from periodontitis patients yielded 19 sequence types (STs), 13 of which were novel. Eleven STs belonged to MLST clade 1. In contrast, 16 C. albicans isolates from separate healthy subjects belonged to 16 STs, with 4 isolates belonging to clade 1. The distributions of STs between both groups were significantly different (P = 0.04) and indicated an enrichment of C. albicans isolates in periodontal pockets, which warrants a larger study. PMID:22875886

Antimicrobial Susceptibility Test with Plasmonic Imaging and Tracking of Single Bacterial Motions on Nanometer Scale.

PubMed

Syal, Karan; Iriya, Rafael; Yang, Yunze; Yu, Hui; Wang, Shaopeng; Haydel, Shelley E; Chen, Hong-Yuan; Tao, Nongjian

2016-01-26

Antimicrobial susceptibility tests (ASTs) are important for confirming susceptibility to empirical antibiotics and detecting resistance in bacterial isolates. Currently, most ASTs performed in clinical microbiology laboratories are based on bacterial culturing, which take days to complete for slowly growing microorganisms. A faster AST will reduce morbidity and mortality rates and help healthcare providers administer narrow spectrum antibiotics at the earliest possible treatment stage. We report the development of a nonculture-based AST using a plasmonic imaging and tracking (PIT) technology. We track the motion of individual bacterial cells tethered to a surface with nanometer (nm) precision and correlate the phenotypic motion with bacterial metabolism and antibiotic action. We show that antibiotic action significantly slows down bacterial motion, which can be quantified for development of a rapid phenotypic-based AST.

Advanced Navigation Strategies For Asteroid Sample Return Missions

NASA Technical Reports Server (NTRS)

Getzandanner, K.; Bauman, J.; Williams, B.; Carpenter, J.

2010-01-01

Flyby and rendezvous missions to asteroids have been accomplished using navigation techniques derived from experience gained in planetary exploration. This paper presents analysis of advanced navigation techniques required to meet unique challenges for precision navigation to acquire a sample from an asteroid and return it to Earth. These techniques rely on tracking data types such as spacecraft-based laser ranging and optical landmark tracking in addition to the traditional Earth-based Deep Space Network radio metric tracking. A systematic study of navigation strategy, including the navigation event timeline and reduction in spacecraft-asteroid relative errors, has been performed using simulation and covariance analysis on a representative mission.

Tracking and data relay satellite fault isolation and correction using PACES: Power and attitude control expert system

NASA Technical Reports Server (NTRS)

Erikson, Carol-Lee; Hooker, Peggy

1989-01-01

The Power and Attitude Control Expert System (PACES) is an object oriented and rule based expert system which provides spacecraft engineers with assistance in isolating and correcting problems within the Power and Attitude Control Subsystems of the Tracking and Data Relay Satellites (TDRS). PACES is designed to act in a consultant role. It will not interface to telemetry data, thus preserving full operator control over spacecraft operations. The spacecraft engineer will input requested information. This information will include telemetry data, action being performed, problem characteristics, spectral characteristics, and judgments of spacecraft functioning. Questions are answered either by clicking on appropriate responses (for text), or entering numeric values. A context sensitive help facility allows access to additional information when the user has difficulty understanding a question or deciding on an answer. The major functionality of PACES is to act as a knowledge rich system which includes block diagrams, text, and graphics, linked using hypermedia techniques. This allows easy movement among pieces of the knowledge. Considerable documentation of the spacecraft Power and Attitude Control Subsystems is embedded within PACES. The development phase of TDRSS expert system technology is intended to provide NASA with the necessary expertise and capability to define requirements, evaluate proposals, and monitor the development progress of a highly competent expert system for NASA's Tracking and Data Relay Satellite Program.

Quantifying the degree of persistence in random amoeboid motion based on the Hurst exponent of fractional Brownian motion.

PubMed

Makarava, Natallia; Menz, Stephan; Theves, Matthias; Huisinga, Wilhelm; Beta, Carsten; Holschneider, Matthias

2014-10-01

Amoebae explore their environment in a random way, unless external cues like, e.g., nutrients, bias their motion. Even in the absence of cues, however, experimental cell tracks show some degree of persistence. In this paper, we analyzed individual cell tracks in the framework of a linear mixed effects model, where each track is modeled by a fractional Brownian motion, i.e., a Gaussian process exhibiting a long-term correlation structure superposed on a linear trend. The degree of persistence was quantified by the Hurst exponent of fractional Brownian motion. Our analysis of experimental cell tracks of the amoeba Dictyostelium discoideum showed a persistent movement for the majority of tracks. Employing a sliding window approach, we estimated the variations of the Hurst exponent over time, which allowed us to identify points in time, where the correlation structure was distorted ("outliers"). Coarse graining of track data via down-sampling allowed us to identify the dependence of persistence on the spatial scale. While one would expect the (mode of the) Hurst exponent to be constant on different temporal scales due to the self-similarity property of fractional Brownian motion, we observed a trend towards stronger persistence for the down-sampled cell tracks indicating stronger persistence on larger time scales.

Genomic sequences of two novel Levivirus single-stranded RNA coliphages (family Leviviridae): Evidence for recombination in environmental strains

EPA Science Inventory

Bacteriophages are likely the most abundant entities in the aquatic environment, yet knowledge of their ecology is limited. During a fecal source-tracking study, two genetically novel Leviviridae strains were discovered. Although the novel strains were isolated from coastal wat...

Mycobacterium bovis in Panama, 2013

PubMed Central

Acosta, Fermín; Chernyaeva, Ekatherina; Mendoza, Libardo; Sambrano, Dilcia; Correa, Ricardo; Rotkevich, Mikhail; Tarté, Miroslava; Hernández, Humberto; Velazco, Bredio; de Escobar, Cecilia; de Waard, Jacobus H.

2015-01-01

Panama remains free of zoonotic tuberculosis caused by Mycobacterium bovis. However, DNA fingerprinting of 7 M. bovis isolates from a 2013 bovine tuberculosis outbreak indicated minimal homology with strains previously circulating in Panama. M. bovis dispersion into Panama highlights the need for enhanced genotype testing to track zoonotic infections. PMID:25988479

Measuring zebrafish turning rate.

PubMed

Mwaffo, Violet; Butail, Sachit; di Bernardo, Mario; Porfiri, Maurizio

2015-06-01

Zebrafish is becoming a popular animal model in preclinical research, and zebrafish turning rate has been proposed for the analysis of activity in several domains. The turning rate is often estimated from the trajectory of the fish centroid that is output by commercial or custom-made target tracking software run on overhead videos of fish swimming. However, the accuracy of such indirect methods with respect to the turning rate associated with changes in heading during zebrafish locomotion is largely untested. Here, we compare two indirect methods for the turning rate estimation using the centroid velocity or position data, with full shape tracking for three different video sampling rates. We use tracking data from the overhead video recorded at 60, 30, and 15 frames per second of zebrafish swimming in a shallow water tank. Statistical comparisons of absolute turning rate across methods and sampling rates indicate that, while indirect methods are indistinguishable from full shape tracking, the video sampling rate significantly influences the turning rate measurement. The results of this study can aid in the selection of the video capture frame rate, an experimental design parameter in zebrafish behavioral experiments where activity is an important measure.

Comparison of CHROMagar Salmonella Medium and Hektoen Enteric Agar for Isolation of Salmonellae from Stool Samples

PubMed Central

Gaillot, Olivier; Di Camillo, Patrick; Berche, Patrick; Courcol, René; Savage, Colette

1999-01-01

CHROMagar Salmonella (CAS), a new chromogenic medium, was retrospectively compared to Hektoen enteric agar (HEA) with 501 Salmonella stock isolates and was then prospectively compared to HEA for the detection and presumptive identification of Salmonella spp. with 508 stool samples before and after enrichment. All stock cultures (100%), including cultures of H2S-negative isolates, yielded typical mauve colonies on CAS, while 497 (99%) isolates produced typical lactose-negative, black-centered colonies on HEA. Following overnight incubation at 37°C, a total of 20 Salmonella strains were isolated from the 508 clinical samples. Sensitivities for primary plating and after enrichment were 95% (19 isolates) and 100% (20 isolates), respectively, for CAS and 80% (16 isolates) and 100% (20 isolates), respectively, for HEA. The specificity of CAS (88.9%) was significantly higher than that of HEA (78.5%; P < 0.0001). On the basis of its good sensitivity and specificity, CAS medium can be recommended for use for primary plating when human stool samples are screened for Salmonella spp. PMID:9986847

High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

DOE PAGES

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; ...

2013-08-13

In this paper we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relativemore » abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Finally, taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.« less

High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

PubMed Central

Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; Vincent, Warwick F.

2013-01-01

In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost. PMID:23967218

Clinical Validation of the Glenoid Track Concept in Anterior Glenohumeral Instability.

PubMed

Shaha, James S; Cook, Jay B; Rowles, Douglas J; Bottoni, Craig R; Shaha, Steven H; Tokish, John M

2016-11-16

Glenoid and humeral bone loss are well-described risk factors for failure of arthroscopic shoulder stabilization. Recently, consideration of the interactions of these types of bone loss (bipolar bone loss) has been used to determine if a lesion is "on-track" or "off-track." The purpose of this study was to study the relationship of the glenoid track to the outcomes of arthroscopic Bankart reconstructions. Over a 2-year period, 57 shoulders that were treated with an isolated, primary arthroscopic Bankart reconstruction performed at a single facility were included in this study. The mean patient age was 25.5 years (range, 20 to 42 years) at the time of the surgical procedure, and the mean follow-up was 48.3 months (range, 23 to 58 months). Preoperative magnetic resonance imaging was used to determine glenoid bone loss and Hill-Sachs lesion size and location and to measure the glenoid track to classify the shoulders as on-track or off-track. Outcomes were assessed according to shoulder stability on examination and subjective outcome. There were 10 recurrences (18%). Of the 49 on-track patients, 4 (8%) had treatment that failed compared with 6 (75%) of 8 off-track patients (p = 0.0001). Six (60%) of 10 patients with recurrence of instability were off-track compared with 2 (4%) of 47 patients in the stable group (p = 0.0001). The positive predictive value of an off-track measurement was 75% compared with 44% for the predictive value of glenoid bone loss of >20%. The application of the glenoid track concept to our cohort was superior to using glenoid bone loss alone with regard to predicting postoperative stability. This method of assessment is encouraged as a routine part of the preoperative evaluation of all patients under consideration for arthroscopic anterior stabilization. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence. Copyright © 2016 by The Journal of Bone and Joint Surgery, Incorporated.

Tracking the emerging human pathogen Pseudallescheria boydii by using highly specific monoclonal antibodies.

PubMed

Thornton, Christopher R

2009-05-01

Pseudallescheria boydii has long been known to cause white grain mycetoma in immunocompetent humans, but it has recently emerged as an opportunistic pathogen of humans, causing potentially fatal invasive infections in immunocompromised individuals and evacuees of natural disasters, such as tsunamis and hurricanes. The diagnosis of P. boydii is problematic since it exhibits morphological characteristics similar to those of other hyaline fungi that cause infectious diseases, such as Aspergillus fumigatus and Scedosporium prolificans. This paper describes the development of immunoglobulin M (IgM) and IgG1 kappa-light chain monoclonal antibodies (MAbs) specific to P. boydii and certain closely related fungi. The MAbs bind to an immunodominant carbohydrate epitope on an extracellular 120-kDa antigen present in the spore and hyphal cell walls of P. boydii and Scedosporium apiospermum. The MAbs do not react with S. prolificans, Scedosporium dehoogii, or a large number of clinically relevant fungi, including A. fumigatus, Candida albicans, Cryptococcus neoformans, Fusarium solani, and Rhizopus oryzae. The MAbs were used in immunofluorescence and double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISAs) to accurately differentiate P. boydii from other infectious fungi and to track the pathogen in environmental samples. Specificity of the DAS-ELISA was confirmed by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2 rRNA-encoding regions of environmental isolates.

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.

PubMed

Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed M Vargas; Parker, Brian J; Rasmussen, Morten; Lindgreen, Stinus; Lilje, Berit; Tobin, Desmond J; Kelly, Theresa K; Vang, Søren; Andersson, Robin; Jones, Peter A; Hoover, Cindi A; Tikhonov, Alexei; Prokhortchouk, Egor; Rubin, Edward M; Sandelin, Albin; Gilbert, M Thomas P; Krogh, Anders; Willerslev, Eske; Orlando, Ludovic

2014-03-01

Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics.

Integrated Multivariate Analysis with Nondetects for the Development of Human Sewage Source-Tracking Tools Using Bacteriophages of Enterococcus faecalis.

PubMed

Wangkahad, Bencharong; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

2017-02-21

We developed sewage-specific microbial source tracking (MST) tools using enterococci bacteriophages and evaluated their performance with univariate and multivariate analyses involving data below detection limits. Newly isolated Enterococci faecalis bacterial strains AIM06 (DSM100702) and SR14 (DSM100701) demonstrated 100% specificity and 90% sensitivity to human sewage without detecting 68 animal manure pooled samples of cats, chickens, cows, dogs, ducks, pigs, and pigeons. AIM06 and SR14 bacteriophages were present in human sewage at 2-4 orders of magnitude. A principal component analysis confirmed the importance of both phages as main water quality parameters. The phages presented only in the polluted water, as classified by a cluster analysis, and at median concentrations of 1.71 × 10 2 and 4.27 × 10 2 PFU/100 mL, respectively, higher than nonhost specific RYC2056 phages and sewage-specific KS148 phages (p < 0.05). Interestingly, AIM06 and SR14 phages exhibited significant correlations with each other and with total coliforms, E. coli, enterococci, and biochemical oxygen demand (Kendall's tau = 0.348 to 0.605, p < 0.05), a result supporting their roles as water quality indicators. This research demonstrates the multiregional applicability of enterococci hosts in MST application and highlights the significance of multivariate analysis with nondetects in evaluating the performance of new MST host strains.

Migratory Whooper Swans Cygnus cygnus Transmit H5N1 Virus between China and Mongolia: Combination Evidence from Satellite Tracking and Phylogenetics Analysis.

PubMed

Li, Shuhong; Meng, Weiyue; Liu, Dongping; Yang, Qiqi; Chen, Lixia; Dai, Qiang; Ma, Tian; Gao, Ruyi; Ru, Wendong; Li, Yunfeng; Yu, Pengbo; Lu, Jun; Zhang, Guogang; Tian, Huaiyu; Chai, Hongliang; Li, Yanbing

2018-05-04

In late 2014, a highly pathogenic avian influenza (hereafter HPAI) H5N1 outbreak infected whooper swans Cygnus cygnus wintering at the Sanmenxia Reservoir area, China, and raised concerns about migratory linkages between wintering and breeding grounds of whooper swans. In this study, 61 swans were satellite tracked from 2013 to 2016 to determine the spatial association of their migration routes and H5N1 outbreaks, and 3596 fecal samples were collected along the migration routes for virology testing. Swans departed the wintering grounds and migrated along the Yellow River, and flew over the Yin Mountains in China. The Brownian bridge movement model showed there was a high degree of spatiotemporal overlap between the core use area along the spring migration pathway and historical H5N1 events in China and Mongolia from 2005 to 2015. The H5N1 strain was isolated and phylogenetic analyses confirmed that the HA gene sequence generated is genetically similar to that of the epidemic strain at a previous wintering site (the Sanmenxia Reservoir area) along its flyway. Our results identified a previously unknown migratory link of whooper swans in central China with Mongolia and confirmed that the swans could carry the HPAI H5N1 virus during migration, resulting in long-distance transmission.

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

PubMed Central

Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed M. Vargas; Parker, Brian J.; Rasmussen, Morten; Lindgreen, Stinus; Lilje, Berit; Tobin, Desmond J.; Kelly, Theresa K.; Vang, Søren; Andersson, Robin; Jones, Peter A.; Hoover, Cindi A.; Tikhonov, Alexei; Prokhortchouk, Egor; Rubin, Edward M.; Sandelin, Albin; Gilbert, M. Thomas P.; Krogh, Anders; Willerslev, Eske; Orlando, Ludovic

2014-01-01

Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics. PMID:24299735

Evaluation of a chromogenic culture medium for isolation of Clostridium difficile within 24 hours.

PubMed

Perry, John D; Asir, Kerry; Halimi, Diane; Orenga, Sylvain; Dale, Joanne; Payne, Michelle; Carlton, Ruth; Evans, Jim; Gould, F Kate

2010-11-01

Rapid and effective methods for the isolation of Clostridium difficile from stool samples are desirable to obtain isolates for typing or to facilitate accurate diagnosis of C. difficile-associated diarrhea. We report on the evaluation of a prototype chromogenic medium (ID C. difficile prototype [IDCd]) for isolation of C. difficile. The chromogenic medium was compared using (i) 368 untreated stool samples that were also inoculated onto CLO medium, (ii) 339 stool samples that were subjected to alcohol shock and also inoculated onto five distinct selective agars, and (iii) standardized suspensions of 10 C. difficile ribotypes (untreated and alcohol treated) that were also inoculated onto five distinct selective agars. Two hundred thirty-six isolates of C. difficile were recovered from 368 untreated stool samples, and all but 1 of these strains (99.6%) were recovered on IDCd within 24 h, whereas 74.6% of isolates were recovered on CLO medium after 48 h. Of 339 alcohol-treated stool samples cultured onto IDCd and five other selective agars, C. difficile was recovered from 218 samples using a combination of all media. The use of IDCd allowed recovery of 96.3% of isolates within 24 h, whereas 51 to 83% of isolates were recovered within 24 h using the five other media. Finally, when they were challenged with pure cultures, all 10 ribotypes of C. difficile generated higher colony counts on IDCd irrespective of alcohol pretreatment or duration of incubation. We conclude that IDCd is an effective medium for isolation of C. difficile from stool samples within 24 h.

Evaluation of a Chromogenic Culture Medium for Isolation of Clostridium difficile within 24 Hours ▿

PubMed Central

Perry, John D.; Asir, Kerry; Halimi, Diane; Orenga, Sylvain; Dale, Joanne; Payne, Michelle; Carlton, Ruth; Evans, Jim; Gould, F. Kate

2010-01-01

Rapid and effective methods for the isolation of Clostridium difficile from stool samples are desirable to obtain isolates for typing or to facilitate accurate diagnosis of C. difficile-associated diarrhea. We report on the evaluation of a prototype chromogenic medium (ID C. difficile prototype [IDCd]) for isolation of C. difficile. The chromogenic medium was compared using (i) 368 untreated stool samples that were also inoculated onto CLO medium, (ii) 339 stool samples that were subjected to alcohol shock and also inoculated onto five distinct selective agars, and (iii) standardized suspensions of 10 C. difficile ribotypes (untreated and alcohol treated) that were also inoculated onto five distinct selective agars. Two hundred thirty-six isolates of C. difficile were recovered from 368 untreated stool samples, and all but 1 of these strains (99.6%) were recovered on IDCd within 24 h, whereas 74.6% of isolates were recovered on CLO medium after 48 h. Of 339 alcohol-treated stool samples cultured onto IDCd and five other selective agars, C. difficile was recovered from 218 samples using a combination of all media. The use of IDCd allowed recovery of 96.3% of isolates within 24 h, whereas 51 to 83% of isolates were recovered within 24 h using the five other media. Finally, when they were challenged with pure cultures, all 10 ribotypes of C. difficile generated higher colony counts on IDCd irrespective of alcohol pretreatment or duration of incubation. We conclude that IDCd is an effective medium for isolation of C. difficile from stool samples within 24 h. PMID:20739493

The shape of ion tracks in natural apatite

NASA Astrophysics Data System (ADS)

Schauries, D.; Afra, B.; Bierschenk, T.; Lang, M.; Rodriguez, M. D.; Trautmann, C.; Li, W.; Ewing, R. C.; Kluth, P.

2014-05-01

Small angle X-ray scattering measurements were performed on natural apatite of different thickness irradiated with 2.2 GeV Au swift heavy ions. The evolution of the track radius along the full ion track length was estimated by considering the electronic energy loss and the velocity of the ions. The shape of the track is nearly cylindrical, slightly widening with a maximum diameter approximately 30 μm before the ions come to rest, followed by a rapid narrowing towards the end within a cigar-like contour. Measurements of average ion track radii in samples of different thicknesses, i.e. containing different sections of the tracks are in good agreement with the shape estimate.

Assessing Developmental Education through Student Tracking. AIR 1995 Annual Forum Paper.

ERIC Educational Resources Information Center

Weissman, Julie; And Others

The effectiveness of developmental education policies at a comprehensive community college was investigated using a new student tracking system. A sample of 1,644 students were tracked from fall 1992 until the end of the fall 1994 semester, 1,226 of whom evidenced basic skills and were eligible for college-level courses, and 418 of whom were…

Semi-Supervised Tensor-Based Graph Embedding Learning and Its Application to Visual Discriminant Tracking.

PubMed

Hu, Weiming; Gao, Jin; Xing, Junliang; Zhang, Chao; Maybank, Stephen

2017-01-01

An appearance model adaptable to changes in object appearance is critical in visual object tracking. In this paper, we treat an image patch as a two-order tensor which preserves the original image structure. We design two graphs for characterizing the intrinsic local geometrical structure of the tensor samples of the object and the background. Graph embedding is used to reduce the dimensions of the tensors while preserving the structure of the graphs. Then, a discriminant embedding space is constructed. We prove two propositions for finding the transformation matrices which are used to map the original tensor samples to the tensor-based graph embedding space. In order to encode more discriminant information in the embedding space, we propose a transfer-learning- based semi-supervised strategy to iteratively adjust the embedding space into which discriminative information obtained from earlier times is transferred. We apply the proposed semi-supervised tensor-based graph embedding learning algorithm to visual tracking. The new tracking algorithm captures an object's appearance characteristics during tracking and uses a particle filter to estimate the optimal object state. Experimental results on the CVPR 2013 benchmark dataset demonstrate the effectiveness of the proposed tracking algorithm.

Application of neutron capture autoradiography to Boron Delivery seeking techniques for selective accumulation of boron compounds to tumor with intra-arterial administration of boron entrapped water-in-oil-in-water emulsion

NASA Astrophysics Data System (ADS)

Mikado, S.; Yanagie, H.; Yasuda, N.; Higashi, S.; Ikushima, I.; Mizumachi, R.; Murata, Y.; Morishita, Y.; Nishimura, R.; Shinohara, A.; Ogura, K.; Sugiyama, H.; Iikura, H.; Ando, H.; Ishimoto, M.; Takamoto, S.; Eriguchi, M.; Takahashi, H.; Kimura, M.

2009-06-01

It is necessary to accumulate the 10B atoms selectively to the tumor cells for effective Boron Neutron Capture Therapy (BNCT). In order to achieve an accurate measurement of 10B accumulations in the biological samples, we employed a technique of neutron capture autoradiography (NCAR) of sliced samples of tumor tissues using CR-39 plastic track detectors. The CR-39 track detectors attached with the biological samples were exposed to thermal neutrons in the thermal column of the JRR3 of Japan Atomic Energy Agency (JAEA). We obtained quantitative NCAR images of the samples for VX-2 tumor in rabbit liver after injection of 10BSH entrapped water-in-oil-in-water (WOW) emulsion by intra-arterial injection via proper hepatic artery. The 10B accumulations and distributions in VX-2 tumor and normal liver of rabbit were investigated by means of alpha-track density measurements. In this study, we showed the selective accumulation of 10B atoms in the VX-2 tumor by intra-arterial injection of 10B entrapped WOW emulsion until 3 days after injection by using digitized NCAR images (i.e. alpha-track mapping).

Fungi Isolated from Flue-cured Tobacco at Time of Sale and After Storage.

PubMed

Welty, R E; Lucas, G B

1969-03-01

The fungi isolated from 100 samples of flue-cured tobacco from 12 markets in 2 tobacco belts comprised 11 genera, including 10 species of Aspergillus. The mean percentage per sample isolated from 62 samples of tobacco from Middle Belt markets was Alternaria, 40.6%; Aspergillus niger, 47.8%; Aspergillus repens, 38.0%; and Penicillium, 25.8%. The mean percentage per sample isolated from 38 samples of tobacco from Old Belt markets was Alternaria, 74.0%; Penicillium, 52.5%; Aspergillus repens, 38.0%; and Aspergillus ruber, 36.2%. Damaged (74 samples) and nondamaged (26 samples) stored tobacco yielded species of six genera of fungi, including eight species of Aspergillus. Species of Aspergillus and Penicillium were commonly isolated from both damaged and nondamaged tobacco, whereas species of Alternaria, Cladosporium, Fusarium, and Rhizopus were isoalted more frequently from nondamaged tobacco. The fungi that occurred in the highest population in damaged tobacco were Aspergillus repens, A. niger, A. ruber, and Penicillium species.

Fungi Isolated from Flue-cured Tobacco at Time of Sale and After Storage1

PubMed Central

Welty, R. E.; Lucas, G. B.

1969-01-01

The fungi isolated from 100 samples of flue-cured tobacco from 12 markets in 2 tobacco belts comprised 11 genera, including 10 species of Aspergillus. The mean percentage per sample isolated from 62 samples of tobacco from Middle Belt markets was Alternaria, 40.6%; Aspergillus niger, 47.8%; Aspergillus repens, 38.0%; and Penicillium, 25.8%. The mean percentage per sample isolated from 38 samples of tobacco from Old Belt markets was Alternaria, 74.0%; Penicillium, 52.5%; Aspergillus repens, 38.0%; and Aspergillus ruber, 36.2%. Damaged (74 samples) and nondamaged (26 samples) stored tobacco yielded species of six genera of fungi, including eight species of Aspergillus. Species of Aspergillus and Penicillium were commonly isolated from both damaged and nondamaged tobacco, whereas species of Alternaria, Cladosporium, Fusarium, and Rhizopus were isoalted more frequently from nondamaged tobacco. The fungi that occurred in the highest population in damaged tobacco were Aspergillus repens, A. niger, A. ruber, and Penicillium species. PMID:16349841

Patterns of Antimicrobial Resistance Observed in Escherichia coli Isolates Obtained from Domestic- and Wild-Animal Fecal Samples, Human Septage, and Surface Water

PubMed Central

Sayah, Raida S.; Kaneene, John B.; Johnson, Yvette; Miller, RoseAnn

2005-01-01

A repeated cross-sectional study was conducted to determine the patterns of antimicrobial resistance in 1,286 Escherichia coli strains isolated from human septage, wildlife, domestic animals, farm environments, and surface water in the Red Cedar watershed in Michigan. Isolation and identification of E. coli were done by using enrichment media, selective media, and biochemical tests. Antimicrobial susceptibility testing by the disk diffusion method was conducted for neomycin, gentamicin, streptomycin, chloramphenicol, ofloxacin, trimethoprim-sulfamethoxazole, tetracycline, ampicillin, nalidixic acid, nitrofurantoin, cephalothin, and sulfisoxazole. Resistance to at least one antimicrobial agent was demonstrated in isolates from livestock, companion animals, human septage, wildlife, and surface water. In general, E. coli isolates from domestic species showed resistance to the largest number of antimicrobial agents compared to isolates from human septage, wildlife, and surface water. The agents to which resistance was demonstrated most frequently were tetracycline, cephalothin, sulfisoxazole, and streptomycin. There were similarities in the patterns of resistance in fecal samples and farm environment samples by animal, and the levels of cephalothin-resistant isolates were higher in farm environment samples than in fecal samples. Multidrug resistance was seen in a variety of sources, and the highest levels of multidrug-resistant E. coli were observed for swine fecal samples. The fact that water sample isolates were resistant only to cephalothin may suggest that the resistance patterns for farm environment samples may be more representative of the risk of contamination of surface waters with antimicrobial agent-resistant bacteria. PMID:15746342

Characterization of Candida species isolated from cases of lower respiratory tract infection.

PubMed

Jha, B J; Dey, S; Tamang, M D; Joshy, M E; Shivananda, P G; Brahmadatan, K N

2006-01-01

(1) To identify and characterize the Candida species isolates from lower respiratory tract infection. (2) to determine the rate of isolation of Candida species from sputum samples. This study was carried out in the Department of Microbiology, Manipal Teaching Hospital, Pokhara, Nepal from June 2002 to January 2003. A total of 462 sputum samples were collected from patients suspected lower respiratory tract infection. The samples were processed as Gram staining to find out the suitability of the specimen, cultured on Sabouraud's Dextrose Agar (SDA) and also on blood agar and chocolate agar to identify the potential lower respiratory tract pathogens. For the identification of Candida, sputum samples were processed for Gram stain, culture, germ tube test, production of chlamydospore, sugar fermentation and assimilation test. For the identification of bacteria, Gram stain, culture, and biochemical tests were performed by standardized procedure. Out of 462 samples, 246 (53.24%) samples grew potential pathogens of lower respiratory tract. Among them Haemophilus influenzae 61(24.79%) and Streptococcus pneumoniae 57 (23.17%) were the predominant bacterial pathogens. Candida species were isolated from 30 samples (12.2%). The majority of Candida species amongst the Candida isolates were Candida albicans 21(70%) followed by Candida tropicalis 4(13.33%). Candida krusei 3(10%), Candida parapsilosis 1(3.33%) and Candida stellatoidea 1(3.33%). The highest rate of isolation of Candida was between the age of 71 and 80. Candida isolation from sputum samples is important as found in the present study in which Candida species were the third most common pathogen isolated from patients with lower respiratory tract infection.

Visuo‐manual tracking: does intermittent control with aperiodic sampling explain linear power and non‐linear remnant without sensorimotor noise?

PubMed Central

Gawthrop, Peter J.; Lakie, Martin; Loram, Ian D.

2017-01-01

Key points A human controlling an external system is described most easily and conventionally as linearly and continuously translating sensory input to motor output, with the inevitable output remnant, non‐linearly related to the input, attributed to sensorimotor noise.Recent experiments show sustained manual tracking involves repeated refractoriness (insensitivity to sensory information for a certain duration), with the temporary 200–500 ms periods of irresponsiveness to sensory input making the control process intrinsically non‐linear.This evidence calls for re‐examination of the extent to which random sensorimotor noise is required to explain the non‐linear remnant.This investigation of manual tracking shows how the full motor output (linear component and remnant) can be explained mechanistically by aperiodic sampling triggered by prediction error thresholds.Whereas broadband physiological noise is general to all processes, aperiodic sampling is associated with sensorimotor decision making within specific frontal, striatal and parietal networks; we conclude that manual tracking utilises such slow serial decision making pathways up to several times per second. Abstract The human operator is described adequately by linear translation of sensory input to motor output. Motor output also always includes a non‐linear remnant resulting from random sensorimotor noise from multiple sources, and non‐linear input transformations, for example thresholds or refractory periods. Recent evidence showed that manual tracking incurs substantial, serial, refractoriness (insensitivity to sensory information of 350 and 550 ms for 1st and 2nd order systems respectively). Our two questions are: (i) What are the comparative merits of explaining the non‐linear remnant using noise or non‐linear transformations? (ii) Can non‐linear transformations represent serial motor decision making within the sensorimotor feedback loop intrinsic to tracking? Twelve participants (instructed to act in three prescribed ways) manually controlled two systems (1st and 2nd order) subject to a periodic multi‐sine disturbance. Joystick power was analysed using three models, continuous‐linear‐control (CC), continuous‐linear‐control with calculated noise spectrum (CCN), and intermittent control with aperiodic sampling triggered by prediction error thresholds (IC). Unlike the linear mechanism, the intermittent control mechanism explained the majority of total power (linear and remnant) (77–87% vs. 8–48%, IC vs. CC). Between conditions, IC used thresholds and distributions of open loop intervals consistent with, respectively, instructions and previous measured, model independent values; whereas CCN required changes in noise spectrum deviating from broadband, signal dependent noise. We conclude that manual tracking uses open loop predictive control with aperiodic sampling. Because aperiodic sampling is inherent to serial decision making within previously identified, specific frontal, striatal and parietal networks we suggest that these structures are intimately involved in visuo‐manual tracking. PMID:28833126

The first external quality assessment of isolation and identification of influenza viruses in cell culture in the Asia Pacific region, 2016.

PubMed

Reading, Patrick C; Leung, Vivian K; Buettner, Iwona; Gillespie, Leah; Deng, Yi-Mo; Shaw, Robert; Spirason, Natalie; Todd, Angela; Shah, Aparna Singh; Konings, Frank; Barr, Ian G

2017-12-01

The isolation and propagation of influenza viruses from clinical specimens are essential tools for comprehensive virologic surveillance. Influenza viruses must be amplified in cell culture for detailed antigenic analysis and for phenotypic assays assessing susceptibility to antiviral drugs or for other assays. To conduct an external quality assessment (EQA) of proficiency for isolation and identification of influenza viruses using cell culture techniques among National Influenza Centres (NICs) in the World Health Organisation (WHO) South East Asia and Western Pacific Regions. Twenty-one NICs performed routine influenza virus isolation and identification techniques on a proficiency testing panel comprising 16 samples, containing influenza A or B viruses and negative control samples. One sample was used exclusively to determine their capacity to measure hemagglutination titer and the other 15 samples were used for virus isolation and identification. All NICs performed influenza virus isolation using Madin Darby canine kidney (MDCK) or MDCK-SIAT-1 cells. If virus growth was detected, the type, subtype and/or lineage of virus present in isolates was determined using immunofluorescence, RT-PCR and/or hemagglutination inhibition (HI) assays. Most participating laboratories could detect influenza virus growth and could identify virus amplified from EQA samples. However, some laboratories failed to isolate and identify viruses from EQA samples that contained lower titres of virus, highlighting issues regarding the sensitivity of influenza virus isolation methods between laboratories. This first round of EQA was successfully conducted by NICs in the Asia Pacific Region, revealing good proficiency in influenza virus isolation and identification. Copyright © 2017 Elsevier B.V. All rights reserved.

Sheehan Suicidality Tracking Scale (Sheehan-STS)

PubMed Central

2009-01-01

Objective: Accurate and prospective assessments of treatment-emergent suicidal thoughts and behaviors are essential to both clinical care and randomized clinical trials. The Sheehan Suicidality Tracking Scale is a prospective, patient self-report or clinician-administered rating scale that tracks both treatment-emergent suicidal ideation and behaviors. The Sheehan Suicidality Tracking Scale was incorporated into a multicenter, randomized, double-blind, placebo-controlled, and active comparator study examining the efficacy of an experimental corticotropin-releasing factor antagonist (BMS-562086) for the treatment of generalized anxiety disorder. Method: The Sheehan Suicidality Tracking Scale was administered to subjects at baseline, Week 2, Week 4, and Week 8 or early termination. Subjects completed theSheehan Suicidality Tracking Scale by self report. The Sheehan Suicidality Tracking Scale was designated as an exploratory outcome measure in the study protocol, and post-hoc analyses were performed to examine the performance of the Sheehan Suicidality Tracking Scale. Results: A total of 82 subjects completed the Sheehan Suicidality Tracking Scale during the course of the study. Altogether, these subjects provided 297 completed Sheehan Suicidality Tracking Scale ratings across the study time points. Sixty-one subjects (n=25 placebo, n=24 BMS-562086, and n=12 escitalopram) had a baseline and at least one post-baseline Sheehan Suicidality Tracking Scale measurement. The mean change from baseline at Week 8 in the Sheehan Suicidality Tracking Scale total score was -0.10, -0.02, and -0.06 for escitalopram, placebo, and BMS-562086 groups, respectively. The sensitivity of the Sheehan Suicidality Tracking Scale and HAM-D Item #3 (suicide) for identifying subjects with suicidal thoughts or behaviors was 100 percent and 63 percent, respectively. Conclusions: The Sheehan Suicidality Tracking Scale may be a sensitive psychometric tool to prospectively assess for treatment-emergent suicidal thoughts and behaviors. Despite the small sample size and low occurrence of suicidal ideation during the course of this clinical trial, the self-reported Sheehan Suicidality Tracking Scale demonstrated increased sensitivity over the rater administered HAM-D Item #3 in identifying suicide related ideations and behaviors. Further research in larger study samples as well as in other psychiatric disorders are needed. PMID:19724740

High-throughput microfluidic device for rare cell isolation

NASA Astrophysics Data System (ADS)

Yang, Daniel; Leong, Serena; Lei, Andy; Sohn, Lydia L.

2015-06-01

Enumerating and analyzing circulating tumor cells (CTCs)—cells that have been shed from primary solid tumors—can potentially be used to determine patient prognosis and track the progression of disease. There is a great challenge to create an effective platform that can isolate these cells, as they are extremely rare: only 1-10 CTCs are present in a 7.5mL of a cancer patient's peripheral blood. We have developed a novel microfluidic system that can isolate CTC populations label free. Our system consists of a multistage separator that employs inertial migration to sort cells based on size. We demonstrate the feasibility of our device by sorting colloids that are comparable in size to red blood cells (RBCs) and CTCs.

High-Throughput Microfluidic Device for Rare Cell Isolation.

PubMed

Yang, Daniel; Leong, Serena; Lei, Andy; Sohn, Lydia L

2015-05-04

Enumerating and analyzing circulating tumor cells (CTCs)-cells that have been shed from primary solid tumors-can potentially be used to determine patient prognosis and track the progression of disease. There is a great challenge to create an effective platform that can isolate these cells, as they are extremely rare: only 1-10 CTCs are present in a 7.5mL of a cancer patient's peripheral blood. We have developed a novel microfluidic system that can isolate CTC populations label free. Our system consists of a multistage separator that employs inertial migration to sort cells based on size. We demonstrate the feasibility of our device by sorting colloids that are comparable in size to red blood cells (RBCs) and CTCs.

Ubiquitous giants: a plethora of giant viruses found in Brazil and Antarctica.

PubMed

Andrade, Ana Cláudia Dos S P; Arantes, Thalita S; Rodrigues, Rodrigo A L; Machado, Talita B; Dornas, Fábio P; Landell, Melissa F; Furst, Cinthia; Borges, Luiz G A; Dutra, Lara A L; Almeida, Gabriel; Trindade, Giliane de S; Bergier, Ivan; Abrahão, Walter; Borges, Iara A; Cortines, Juliana R; de Oliveira, Danilo B; Kroon, Erna G; Abrahão, Jônatas S

2018-01-24

Since the discovery of giant viruses infecting amoebae in 2003, many dogmas of virology have been revised and the search for these viruses has been intensified. Over the last few years, several new groups of these viruses have been discovered in various types of samples and environments.In this work, we describe the isolation of 68 giant viruses of amoeba obtained from environmental samples from Brazil and Antarctica. Isolated viruses were identified by hemacolor staining, PCR assays and electron microscopy (scanning and/or transmission). A total of 64 viruses belonging to the Mimiviridae family were isolated (26 from lineage A, 13 from lineage B, 2 from lineage C and 23 from unidentified lineages) from different types of samples, including marine water from Antarctica, thus being the first mimiviruses isolated in this extreme environment to date. Furthermore, a marseillevirus was isolated from sewage samples along with two pandoraviruses and a cedratvirus (the third to be isolated in the world so far). Considering the different type of samples, we found a higher number of viral groups in sewage samples. Our results reinforce the importance of prospective studies in different environmental samples, therefore improving our comprehension about the circulation anddiversity of these viruses in nature.

Stardust Interstellar Preliminary Examination V: XRF Analyses of Interstellar Dust Candidates at ESRF ID13

NASA Technical Reports Server (NTRS)

Brenker, Frank E.; Westphal, Andrew J.; Simionovici, Alexandre S.; Flynn, George J.; Gainsforth, Zack; Allen, Carlton C.; Sanford, Scott; Zolensky, Michael E.; Bastien, Ron K.; Frank, David R.

2014-01-01

Here, we report analyses by synchrotron X-ray fluorescence microscopy of the elemental composition of eight candidate impact features extracted from the Stardust Interstellar Dust Collector (SIDC). Six of the features were unambiguous tracks, and two were crater-like features. Five of the tracks are so-called midnight tracks that is, they had trajectories consistent with an origin either in the interstellar dust stream or as secondaries from impacts on the Sample Return Capsule (SRC). In a companion paper reporting synchrotron X-ray diffraction analyses of ISPE candidates, we show that two of these particles contain natural crystalline materials: the terminal particle of track 30contains olivine and spinel, and the terminal particle of track 34 contains olivine. Here, we show that the terminal particle of track 30, Orion, shows elemental abundances, normalized to Fe, that are close to CI values, and a complex, fine-grained structure. The terminal particle of track 34, Hylabrook, shows abundances that deviate strongly from CI, but shows little fine structure and is nearly homogenous. The terminal particles of other midnight tracks, 29 and 37, had heavy element abundances below detection threshold. A third, track28, showed a composition inconsistent with an extraterrestrial origin, but also inconsistent with known spacecraft materials. A sixth track, with a trajectory consistent with secondary ejecta from an impact on one of the spacecraft solar panels, contains abundant Ce and Zn. This is consistent with the known composition of the glass covering the solar panel. Neither crater-like feature is likely to be associated with extraterrestrial materials. We also analyzed blank aerogel samples to characterize background and variability between aerogel tiles. We found significant differences in contamination levels and compositions, emphasizing the need for local background subtraction for accurate quantification.

Toward isolating the role of dopamine in the acquisition of incentive salience attribution.

PubMed

Chow, Jonathan J; Nickell, Justin R; Darna, Mahesh; Beckmann, Joshua S

2016-10-01

Stimulus-reward learning has been heavily linked to the reward-prediction error learning hypothesis and dopaminergic function. However, some evidence suggests dopaminergic function may not strictly underlie reward-prediction error learning, but may be specific to incentive salience attribution. Utilizing a Pavlovian conditioned approach procedure consisting of two stimuli that were equally reward-predictive (both undergoing reward-prediction error learning) but functionally distinct in regard to incentive salience (levers that elicited sign-tracking and tones that elicited goal-tracking), we tested the differential role of D1 and D2 dopamine receptors and nucleus accumbens dopamine in the acquisition of sign- and goal-tracking behavior and their associated conditioned reinforcing value within individuals. Overall, the results revealed that both D1 and D2 inhibition disrupted performance of sign- and goal-tracking. However, D1 inhibition specifically prevented the acquisition of sign-tracking to a lever, instead promoting goal-tracking and decreasing its conditioned reinforcing value, while neither D1 nor D2 signaling was required for goal-tracking in response to a tone. Likewise, nucleus accumbens dopaminergic lesions disrupted acquisition of sign-tracking to a lever, while leaving goal-tracking in response to a tone unaffected. Collectively, these results are the first evidence of an intraindividual dissociation of dopaminergic function in incentive salience attribution from reward-prediction error learning, indicating that incentive salience, reward-prediction error, and their associated dopaminergic signaling exist within individuals and are stimulus-specific. Thus, individual differences in incentive salience attribution may be reflective of a differential balance in dopaminergic function that may bias toward the attribution of incentive salience, relative to reward-prediction error learning only. Copyright © 2016 Elsevier Ltd. All rights reserved.

Endospores of halophilic bacteria of the family Bacillaceae isolated from non-saline Japanese soil may be transported by Kosa event (Asian dust storm)

PubMed Central

Echigo, Akinobu; Hino, Miki; Fukushima, Tadamasa; Mizuki, Toru; Kamekura, Masahiro; Usami, Ron

2005-01-01

Background Generally, extremophiles have been deemed to survive in the extreme environments to which they had adapted to grow. Recently many extremophiles have been isolated from places where they are not expected to grow. Alkaliphilic microorganisms have been isolated from acidic soil samples with pH 4.0, and thermophiles have been isolated from samples of low temperature. Numerous moderately halophilic microorganisms, defined as those that grow optimally in media containing 0.5–2.5 Molar (3–15%) NaCl, and halotolerant microorganisms that are able to grow in media without added NaCl and in the presence of high NaCl have been isolated from saline environments such as salterns, salt lakes and sea sands. It has tacitly been believed that habitats of halophiles able to grow in media containing more than 20% (3.4 M) are restricted to saline environments, and no reports have been published on the isolation of halophiles from ordinary garden soil samples. Results We demonstrated that many halophilic bacteria that are able to grow in the presence of 20% NaCl are inhabiting in non-saline environments such as ordinary garden soils, yards, fields and roadways in an area surrounding Tokyo, Japan. Analyses of partial 16S rRNA gene sequences of 176 isolates suggested that they were halophiles belonging to genera of the family Bacillaceae, Bacillus (11 isolates), Filobacillus (19 isolates), Gracilibacillus (6 isolates), Halobacillus (102 isolates), Lentibacillus (1 isolate), Paraliobacillus (5 isolates) and Virgibacillus (17 isolates). Sequences of 15 isolates showed similarities less than 92%, suggesting that they may represent novel taxa within the family Bacillaceae. Conclusion The numbers of total bacteria of inland soil samples were in a range from 1.4 × 107/g to 1.1 × 106/g. One tenth of the total bacteria was occupied by endospore-forming bacteria. Only very few of the endospore-forming bacteria, roughly 1 out of 20,000, are halophilic bacteria. Most of the halophilic bacteria were surviving as endospores in the soil samples, in a range of less than 1 to about 500/g soil. Samples collected from seashore in a city confronting Tokyo Bay gave the total numbers of bacteria and endospores roughly 1000 time smaller than those of inland soil samples. Numbers of halophilic bacteria per gram, however, were almost the same as those of inland soil samples. A possible source of the halophilic endospore originating from Asian dust storms is discussed. PMID:16242015

Star Formation Intensities Of Non-Isolated Galaxies With The Califa Survey

NASA Astrophysics Data System (ADS)

Morales Vargas, Abdías; Torres-Papaqui, Juan Pablo; Rosales-Ortega, Fernando Fabián; Sánchez, Sebastián F.; Chow-Martínez, Marcel; Ortega-Minakata, René Alberto; Romero-Cruz, Fernando J.; Trejo-Alonso, Josué de Jesús; Neri-Larios, Daniel Marcos; Robleto-Orús Aitor, Carlos

2017-08-01

Poster presented at the conference Galaxy Evolution Across Time, 12-16 June, Paris, France. The influence of interactions on the star formation (SF) is investigated by studying a sample of 34 CALIFA survey non-isolated galaxies. We use the instantaneous star formation rate intensity (SFRI) obtained from the Halpha recombination line emission normalized by a unit of projected area. We explore the SFRI, stellar mass and stellar age annulus structures (split by morphology group), also for a control population of star-forming isolated galaxies observed with the CALIFA survey likewise. By morphology groups, the SF efficiency of early type spirals (ETSs) results magnified likely because of angular momentum loss. The SFRI of the non-isolated sample is then compared with that one of the isolated sample. It is found statistically and moderately enhanced in the non-isolated sample by a factor of at most 2. We also find the SFRI as to be a function of the degree of tidal perturbation what might consequently suggest interactions as to facilitate the gas transport to central regions. Contrasting behaviors of the SFRI structures, a gradual quench with clear outer presence of SF (isolated sample) while a steeper decrease from the center with poor SFRIs outwards (non-isolated one) are found. Similitudes in a variety of stellar population properties support the closeness of companions as to be the cause of the SFRI differences between samples.

Demonstrating the efficacy of the FoneAstra pasteurization monitor for human milk pasteurization in resource-limited settings.

PubMed

Naicker, Mageshree; Coutsoudis, Anna; Israel-Ballard, Kiersten; Chaudhri, Rohit; Perin, Noah; Mlisana, Koleka

2015-03-01

Human milk provides crucial nutrition and immunologic protection for infants. When a mother's own milk is unavailable, donated human milk, pasteurized to destroy bacteria and viruses, is a lifesaving replacement. Flash-heat pasteurization is a simple, low-cost, and commonly used method to make milk safe, but currently there is no system to monitor milk temperature, which challenges quality control. FoneAstra, a smartphone-based mobile pasteurization monitor, removes this barrier by guiding users through pasteurization and documenting consistent and safe practice. This study evaluated FoneAstra's efficacy as a quality control system, particularly in resource-limited settings, by comparing bacterial growth in donor milk flash-heated with and without the device at a neonatal intensive care unit in Durban, South Africa. For 100 samples of donor milk, one aliquot each of prepasteurized milk, milk flash-heated without FoneAstra, and milk pasteurized with FoneAstra was cultured on routine agar for bacterial growth. Isolated bacteria were identified and enumerated. In total, 300 samples (three from each donor sample) were analyzed. Bacterial growth was found in 86 of the 100 samples before any pasteurization and one of the 100 postpasteurized samples without FoneAstra. None of the samples pasteurized using FoneAstra showed bacterial growth. Both pasteurization methods were safe and effective. FoneAstra, however, provides the additional benefits of user-guided temperature monitoring and data tracking. By improving quality assurance and standardizing the pasteurization process, FoneAstra can support wide-scale implementation of human milk banks in resource-limited settings, increasing access and saving lives.

Infrared and Raman spectroscopic methods for characterization of Taxus baccata L.--Improved taxane isolation by accelerated quality control and process surveillance.

PubMed

Gudi, Gennadi; Krähmer, Andrea; Koudous, Iraj; Strube, Jochen; Schulz, Hartwig

2015-10-01

Different yew species contain poisonous taxane alkaloids which serve as resources for semi-synthesis of anticancer drugs. The highly variable amounts of taxanes demand new methods for fast characterization of the raw plant material and the isolation of the target structures during phyto extraction. For that purpose, applicability of different vibrational spectroscopy methods in goods receipt of raw plant material and in process control was investigated and demonstrated in online tracking isolation and purification of the target taxane 10-deacetylbaccatin III (10-DAB) during solvent extraction. Applying near (NIRS) and mid infrared spectroscopy (IRS) the amount of botanical impurities in mixed samples of two different yew species (R(2)=0.993), the leave-to-wood ratio for Taxus baccata material (R(2)=0.94) and moisture in dried yew needles (R(2)=0.997) can be quantified. By partial least square analysis (PCA) needles of different Coniferales species were successfully discriminated by Attenuated Total Reflectance-Fourier-Transform Infrared Spectroscopy (ATR-FT-IR). The analytical potential of ATR-FT-IR and Fourier Transform-Raman Spectroscopy (FT-RS) in process control of extraction and purification of taxanes is demonstrated for determination of the water content in methanolic yew extracts (R(2)=0.999) and for quantification of 10-DAB (R(2)=0.98) on a highly sophisticated level. The decrease of 10-DAB in the plant tissue during extraction was successfully visualized by FT-IR imaging of thin cross sections providing new perspectives for process control and design. Copyright © 2015 Elsevier B.V. All rights reserved.

Potential of Lactobacillus plantarum IBB3036 and Lactobacillus salivarius IBB3154 to persistence in chicken after in ovo delivery.

PubMed

Aleksandrzak-Piekarczyk, Tamara; Puzia, Weronika; Żylińska, Joanna; Cieśla, Jarosław; Gulewicz, Krzysztof A; Bardowski, Jacek K; Górecki, Roman K

2018-03-25

The aim of this study was to characterize and compare selected Lactobacillus strains originating from different environments (cow milk and hen feces) with respect to their applicative potential to colonize gastrointestinal track of chickens before hatching from an egg. In vitro phenotypic characterization of lactobacilli strains included the investigation of the important prerequisites for persistence in gastrointestinal tract, such as a capability to survive in the presence of bile salts and at low pH, enzymatic and sugar metabolic profiles, adhesion abilities, and resistance to osmolytes, temperature, and antibiotics. Regarding the resistance of lactobacilli to most of the various stress factors tested, the milk isolate Lactobacillus plantarum IBB3036 showed better abilities than the chicken feces isolate Lactobacillus salivarius IBB3154. However, regarding the acidification tolerance and adherence ability, L. salivarius IBB3154 revealed better characteristics. Use of these two selected lactobacilli isolates together with proper prebiotics resulted in the preparation of two S1 and S2 bioformulations, which were injected in ovo into hen Cobb500 FF fertilized eggs. Furthermore, in vivo tests assessing the persistence of L. plantarum IBB3036 and L. salivarius IBB3154 in the chicken gastrointestinal tract was monitored by PCR-based classical and quantitative techniques and revealed the presence of both strains in fecal samples collected 3 days after hatching. Subsequently, the number of L. salivarius IBB3154 increased significantly in the chicken intestine, whereas the presence of L. plantarum IBB3036 was gradually decreased. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Identification of fecal input sites in spring water by selection and genotyping of multiresistant Escherichia coli.

PubMed

Wicki, Melanie; Karabulut, Fatma; Auckenthaler, Adrian; Felleisen, Richard; Tanner, Marcel; Baumgartner, Andreas

2011-12-01

The localization of fecal input sites is important for water quality management. For this purpose, we have developed a new approach based on a three-step procedure, including a preparatory phase, the screening of multiresistant bacteria using selective agar plates, and a typing phase where selected Escherichia coli isolates are characterized by antibiotic resistance profiles and molecular fingerprinting techniques (pulsed-field gel electrophoresis [PFGE]). These two well-known source tracking methods were combined in order to reduce cost and effort. This approach was successfully applied under field conditions in a study area located in the north-western part of Switzerland. E. coli isolates from spring water and surface water samples collected in this area were screened with selective agar plates. In this way, 21 different groups, each consisting of strains with the same pattern of antibiotic resistance, were found. Of these, four groups were further analyzed using PFGE. Strains with identical PFGE profiles were detected repeatedly, demonstrating the suitability of this method for the localization of fecal input sites over an extended period of time. Identical PFGE patterns of strains detected in water from two different springs were also found in the stream flowing through the study area. These results demonstrated the applicability of the new approach for the examination of incidents of fecal contamination in drinking water. The advantages of the described approach over genotyping methods currently being used to identify sources of fecal contaminants are a reduction in time, costs, and the effort required. Identical isolates could be identified without the construction of large libraries.

Fission-track ages of apatites from the Precambrian of Rwanda and Burundi - Relationship to East African rift tectonics

NASA Astrophysics Data System (ADS)

van den Haute, P.

1984-11-01

Fission-track method dating of 27 apatite samples recovered from Precambrian intrusive rocks has yielded ages in the 75-423 million year range, which is noted to be younger than the ages of emplacement or metamorphism for these rocks according to other radiometric methods. On the basis of the regional geology and the length ratios of spontaneous-to-induced tracks for 18 of the 27 samples, it can be inferred that the fission-track ages are not mixed ages due to a recent thermal event, but rather that they date the last cooling history of the studied massifs. This last cooling is interpreted as primarily the result of a slow, epirogenetic uplift which affected the area during the major part of the Phanerozoic. In this way, the large age variations can be ascribed to differential cooling caused by regional epirogenetic uplift rate differences.

Dealing with the time-varying parameter problem of robot manipulators performing path tracking tasks

NASA Technical Reports Server (NTRS)

Song, Y. D.; Middleton, R. H.

1992-01-01

Many robotic applications involve time-varying payloads during the operation of the robot. It is therefore of interest to consider control schemes that deal with time-varying parameters. Using the properties of the element by element (or Hadarmad) product of matrices, we obtain the robot dynamics in parameter-isolated form, from which a new control scheme is developed. The controller proposed yields zero asymptotic tracking errors when applied to robotic systems with time-varying parameters by using a switching type control law. The results obtained are global in the initial state of the robot, and can be applied to rapidly varying systems.

Real-time monitoring and visualization of the multi-dimensional motion of an anisotropic nanoparticle

NASA Astrophysics Data System (ADS)

Go, Gi-Hyun; Heo, Seungjin; Cho, Jong-Hoi; Yoo, Yang-Seok; Kim, Minkwan; Park, Chung-Hyun; Cho, Yong-Hoon

2017-03-01

As interest in anisotropic particles has increased in various research fields, methods of tracking such particles have become increasingly desirable. Here, we present a new and intuitive method to monitor the Brownian motion of a nanowire, which can construct and visualize multi-dimensional motion of a nanowire confined in an optical trap, using a dual particle tracking system. We measured the isolated angular fluctuations and translational motion of the nanowire in the optical trap, and determined its physical properties, such as stiffness and torque constants, depending on laser power and polarization direction. This has wide implications in nanoscience and nanotechnology with levitated anisotropic nanoparticles.

Improved semi-supervised online boosting for object tracking

NASA Astrophysics Data System (ADS)

Li, Yicui; Qi, Lin; Tan, Shukun

2016-10-01

The advantage of an online semi-supervised boosting method which takes object tracking problem as a classification problem, is training a binary classifier from labeled and unlabeled examples. Appropriate object features are selected based on real time changes in the object. However, the online semi-supervised boosting method faces one key problem: The traditional self-training using the classification results to update the classifier itself, often leads to drifting or tracking failure, due to the accumulated error during each update of the tracker. To overcome the disadvantages of semi-supervised online boosting based on object tracking methods, the contribution of this paper is an improved online semi-supervised boosting method, in which the learning process is guided by positive (P) and negative (N) constraints, termed P-N constraints, which restrict the labeling of the unlabeled samples. First, we train the classification by an online semi-supervised boosting. Then, this classification is used to process the next frame. Finally, the classification is analyzed by the P-N constraints, which are used to verify if the labels of unlabeled data assigned by the classifier are in line with the assumptions made about positive and negative samples. The proposed algorithm can effectively improve the discriminative ability of the classifier and significantly alleviate the drifting problem in tracking applications. In the experiments, we demonstrate real-time tracking of our tracker on several challenging test sequences where our tracker outperforms other related on-line tracking methods and achieves promising tracking performance.

Real-time catheter tracking for high-dose-rate prostate brachytherapy using an electromagnetic 3D-guidance device: A preliminary performance study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou Jun; Sebastian, Evelyn; Mangona, Victor

2013-02-15

Purpose: In order to increase the accuracy and speed of catheter reconstruction in a high-dose-rate (HDR) prostate implant procedure, an automatic tracking system has been developed using an electromagnetic (EM) device (trakSTAR, Ascension Technology, VT). The performance of the system, including the accuracy and noise level with various tracking parameters and conditions, were investigated. Methods: A direct current (dc) EM transmitter (midrange model) and a sensor with diameter of 1.3 mm (Model 130) were used in the trakSTAR system for tracking catheter position during HDR prostate brachytherapy. Localization accuracy was assessed under both static and dynamic analyses conditions. For themore » static analysis, a calibration phantom was used to investigate error dependency on operating room (OR) table height (bottom vs midposition vs top), sensor position (distal tip of catheter vs connector end of catheter), direction [left-right (LR) vs anterior-posterior (AP) vs superior-inferior (SI)], sampling frequency (40 vs 80 vs 120 Hz), and interference from OR equipment (present vs absent). The mean and standard deviation of the localization offset in each direction and the corresponding error vectors were calculated. For dynamic analysis, the paths of five straight catheters were tracked to study the effects of directions, sampling frequency, and interference of EM field. Statistical analysis was conducted to compare the results in different configurations. Results: When interference was present in the static analysis, the error vectors were significantly higher at the top table position (3.3 {+-} 1.3 vs 1.8 {+-} 0.9 mm at bottom and 1.7 {+-} 1.0 mm at middle, p < 0.001), at catheter end position (3.1 {+-} 1.1 vs 1.4 {+-} 0.7 mm at the tip position, p < 0.001), and at 40 Hz sampling frequency (2.6 {+-} 1.1 vs 2.4 {+-} 1.5 mm at 80 Hz and 1.8 {+-} 1.1 at 160 Hz, p < 0.001). So did the mean offset errors in the LR direction (-1.7 {+-} 1.4 vs 0.4 {+-} 0.5 mm in AP and 0.8 {+-} 0.8 mm in SI directions, p < 0.001). The error vectors were significantly higher with surrounding interference (2.2 {+-} 1.3 mm) vs without interference (1.0 {+-} 0.7 mm, p < 0.001). An accuracy of 1.6 {+-} 0.2 mm can be reached when using optimum configuration (160 Hz at middle table position). When interference was present in the dynamic tracking, the mean tracking errors in LR direction (1.4 {+-} 0.5 mm) was significantly higher than that in AP direction (0.3 {+-} 0.2 mm, p < 0.001). So did the mean vector errors at 40 Hz (2.1 {+-} 0.2 mm vs 1.3 {+-} 0.2 mm at 80 Hz and 0.9 {+-} 0.2 mm at 160 Hz, p < 0.05). However, when interference was absent, they were comparable in the both directions and at all sampling frequencies. An accuracy of 0.9 {+-} 0.2 mm was obtained for the dynamic tracking when using optimum configuration. Conclusions: The performance of an EM tracking system depends highly on the system configuration and surrounding environment. The accuracy of EM tracking for catheter reconstruction in a prostate HDR brachytherapy procedure can be improved by reducing interference from surrounding equipment, decreasing distance from transmitter to tracking area, and choosing appropriated sampling frequency. A calibration scheme is needed to further reduce the tracking error when the interference is high.« less

Novel particle tracking algorithm based on the Random Sample Consensus Model for the Active Target Time Projection Chamber (AT-TPC)

NASA Astrophysics Data System (ADS)

Ayyad, Yassid; Mittig, Wolfgang; Bazin, Daniel; Beceiro-Novo, Saul; Cortesi, Marco

2018-02-01

The three-dimensional reconstruction of particle tracks in a time projection chamber is a challenging task that requires advanced classification and fitting algorithms. In this work, we have developed and implemented a novel algorithm based on the Random Sample Consensus Model (RANSAC). The RANSAC is used to classify tracks including pile-up, to remove uncorrelated noise hits, as well as to reconstruct the vertex of the reaction. The algorithm, developed within the Active Target Time Projection Chamber (AT-TPC) framework, was tested and validated by analyzing the 4He+4He reaction. Results, performance and quality of the proposed algorithm are presented and discussed in detail.

Correlation of cerium anomalies with indicators of paleoenvironment

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacLeod, K.G.; Irving, A.J.

1996-09-01

Among 21 whole-rock samples of the Upper Cretaceous Niobrara Formation from Colorado, the abundance of cerium relative to other rate earth elements (Ce anomaly), the weight percent organic carbon (%C{sub org}), and the intensity of bioturbation all covary. This covariation is provocative because %C{sub org} and intensity of bioturbation track changes in the concentration of oxygen in the local water column at the time of deposition (Savrda and Bottjer 1989). Ce anomalies in apatite-rich fractions of the Maastrichtian Zumaya-Algorta Formation from France and Spain and the Miocene Monterey Formation from California show changes that also may coincide with changes inmore » ancient oxygen levels. Results for the Niobrara samples are the closest correspondence demonstrated between paleo-redox conditions and Ce anomalies, but the authors cannot yet determine whether the correspondence reflects a cause-and-effect relationship. Variation in Ce anomalies is influenced by a number of factors, including terrigenous input, depositional environment, and diagenetic conditions. Potential interplay of these factors prevents a unique interpretation of the whole-rock data; dissecting whole-rock Ce anomalies through analysis of isolated sedimentary components, though, is a promising avenue of research.« less

Middle-Upper Triassic and Middle Jurassic tetrapod track assemblages of southern Tunisia, Sahara Platform

NASA Astrophysics Data System (ADS)

Niedźwiedzki, Grzegorz; Soussi, Mohamed; Boukhalfa, Kamel; Gierliński, Gerard D.

2017-05-01

Three tetrapod track assemblages from the early-middle Mesozoic of southern Tunisia are reported. The strata exposed at the Tejra 2 clay-pit near the Medenine and Rehach site, located in the vicinity of Kirchaou, contain the first tetrapod tracks found in the Triassic of Tunisia. The Middle Jurassic (early Aalenian) dinosaur tracks are reported from the Mestaoua plain near Tataouine. In the Middle Triassic outcrop of the Tejra 2 clay-pit, tridactyl tracks of small and medium-sized dinosauromorphs, were discovered. These tracks represent the oldest evidence of dinosaur-lineage elements in the Triassic deposits of Tunisia. Similar tracks have been described from the Middle Triassic of Argentina, France and Morocco. An isolated set of the manus and pes of a quadrupedal tetrapod discovered in Late Triassic Rehach tracksite is referred to a therapsid tracemaker. The Middle Jurassic deposits of the Mestaoua plain reveal small and large tridactyl theropod dinosaur tracks (Theropoda track indet. A-C). Based on comparison with the abundant record of Triassic tetrapod ichnofossils from Europe and North America, the ichnofauna described here indicates the presence of a therapsid-dinosauromorph ichnoassociation (without typical Chirotheriidae tracks) in the Middle and Late Triassic, which sheds light on the dispersal of the Middle-Upper Triassic tetrapod ichnofaunas in this part of Gondwana. The reported Middle Jurassic ichnofauna show close similarities to dinosaur track assemblages from the Lower and Middle Jurassic of northwestern Africa, North America, Europe and also southeastern Asia. Sedimentological and lithostratigraphic data of each new tracksite have been defined on published data and new observations. Taken together, these discoveries present a tantalizing window into the evolutionary history of tetrapods from the Triassic and Jurassic of southern Tunisia. Given the limited early Mesozoic tetrapod record from the region, these discoveries are of both temporal and geographic significance.

Characterization of Factors Affecting Nanoparticle Tracking Analysis Results With Synthetic and Protein Nanoparticles.

PubMed

Krueger, Aaron B; Carnell, Pauline; Carpenter, John F

2016-04-01

In many manufacturing and research areas, the ability to accurately monitor and characterize nanoparticles is becoming increasingly important. Nanoparticle tracking analysis is rapidly becoming a standard method for this characterization, yet several key factors in data acquisition and analysis may affect results. Nanoparticle tracking analysis is prone to user input and bias on account of a high number of parameters available, contains a limited analysis volume, and individual sample characteristics such as polydispersity or complex protein solutions may affect analysis results. This study systematically addressed these key issues. The integrated syringe pump was used to increase the sample volume analyzed. It was observed that measurements recorded under flow caused a reduction in total particle counts for both polystyrene and protein particles compared to those collected under static conditions. In addition, data for polydisperse samples tended to lose peak resolution at higher flow rates, masking distinct particle populations. Furthermore, in a bimodal particle population, a bias was seen toward the larger species within the sample. The impacts of filtration on an agitated intravenous immunoglobulin sample and operating parameters including "MINexps" and "blur" were investigated to optimize the method. Taken together, this study provides recommendations on instrument settings and sample preparations to properly characterize complex samples. Copyright © 2016. Published by Elsevier Inc.

Characterization of microbial contamination in United States Air Force aviation fuel tanks.

PubMed

Rauch, Michelle E; Graef, Harold W; Rozenzhak, Sophie M; Jones, Sharon E; Bleckmann, Charles A; Kruger, Randell L; Naik, Rajesh R; Stone, Morley O

2006-01-01

Bacteria and fungi, isolated from United States Air Force (USAF) aviation fuel samples, were identified by gas chromatograph fatty acid methyl ester (GC-FAME) profiling and 16S or 18S rRNA gene sequencing. Thirty-six samples from 11 geographically separated USAF bases were collected. At each base, an above-ground storage tank, a refueling truck, and an aircraft wing tank were sampled at the lowest sample point, or sump, to investigate microbial diversity and dispersion within the fuel distribution chain. Twelve genera, including four Bacillus species and two Staphylococcus species, were isolated and identified. Bacillus licheniformis, the most prevalent organism isolated, was found at seven of the 11 bases. Of the organisms identified, Bacillus sp., Micrococcus luteus, Sphinogmonas sp., Staphylococcus sp., and the fungus Aureobasidium pullulans have previously been isolated from aviation fuel samples. The bacteria Pantoea ananatis, Arthrobacter sp., Alcaligenes sp., Kocuria rhizophilia, Leucobacter komagatae, Dietza sp., and the fungus Discophaerina fagi have not been previously reported in USAF aviation fuel. Only at two bases were the same organisms isolated from all three sample points in the fuel supply distribution chain. Isolation of previously undocumented organisms suggests either, changes in aviation fuel microbial community in response to changes in aviation fuel composition, additives and biocide use, or simply, improvements in isolation and identification techniques.

WaterlooClarke: TREC 2015 Microblog Track

DTIC Science & Technology

2015-11-20

interests [1]. In this track, the representative social media is Twitter , and relevant posts are tweets with respect to a user’s interest. A user’s...every day. II. TASKS EVALUATION The developed systems listen to the Twitter sample stream2 for a period of 10 days and report the relevant tweets. All...manner as qi, but using a corpus of previously collected tweets. Our corpus was collected over approximately seven days from the Twitter sample stream

A new 3D tracking method for cell mechanics investigation exploiting the capabilities of digital holography in microscopy

NASA Astrophysics Data System (ADS)

Miccio, L.; Memmolo, P.; Merola, F.; Fusco, S.; Netti, P. A.; Ferraro, P.

2014-03-01

A method for 3D tracking has been developed exploiting Digital Holography features in Microscopy (DHM). In the framework of self-consistent platform for manipulation and measurement of biological specimen we use DHM for quantitative and completely label free analysis of samples with low amplitude contrast. Tracking capability extend the potentiality of DHM allowing to monitor the motion of appropriate probes and correlate it with sample properties. Complete 3D tracking has been obtained for the probes avoiding the amplitude refocusing in traditional tracking processes. Moreover, in biology and biomedical research fields one of the main topic is the understanding of morphology and mechanics of cells and microorganisms. Biological samples present low amplitude contrast that limits the information that can be retrieved through optical bright-field microscope measurements. The main effect on light propagating in such objects is in phase. This is known as phase-retardation or phase-shift. DHM is an innovative and alternative approach in microscopy, it's a good candidate for no-invasive and complete specimen analysis because its main characteristic is the possibility to discern between intensity and phase information performing quantitative mapping of the Optical Path Length. In this paper, the flexibility of DH is employed to analyze cell mechanics of unstained cells subjected to appropriate stimuli. DHM is used to measure all the parameters useful to understand the deformations induced by external and controlled stresses on in-vitro cells. Our configuration allows 3D tracking of micro-particles and, simultaneously, furnish quantitative phase-contrast maps. Experimental results are presented and discussed for in vitro cells.

High variability in strain estimation errors when using a commercial ultrasound speckle tracking algorithm on tendon tissue.

PubMed

Fröberg, Åsa; Mårtensson, Mattias; Larsson, Matilda; Janerot-Sjöberg, Birgitta; D'Hooge, Jan; Arndt, Anton

2016-10-01

Ultrasound speckle tracking offers a non-invasive way of studying strain in the free Achilles tendon where no anatomical landmarks are available for tracking. This provides new possibilities for studying injury mechanisms during sport activity and the effects of shoes, orthotic devices, and rehabilitation protocols on tendon biomechanics. To investigate the feasibility of using a commercial ultrasound speckle tracking algorithm for assessing strain in tendon tissue. A polyvinyl alcohol (PVA) phantom, three porcine tendons, and a human Achilles tendon were mounted in a materials testing machine and loaded to 4% peak strain. Ultrasound long-axis cine-loops of the samples were recorded. Speckle tracking analysis of axial strain was performed using a commercial speckle tracking software. Estimated strain was then compared to reference strain known from the materials testing machine. Two frame rates and two region of interest (ROI) sizes were evaluated. Best agreement between estimated strain and reference strain was found in the PVA phantom (absolute error in peak strain: 0.21 ± 0.08%). The absolute error in peak strain varied between 0.72 ± 0.65% and 10.64 ± 3.40% in the different tendon samples. Strain determined with a frame rate of 39.4 Hz had lower errors than 78.6 Hz as was the case with a 22 mm compared to an 11 mm ROI. Errors in peak strain estimation showed high variability between tendon samples and were large in relation to strain levels previously described in the Achilles tendon. © The Foundation Acta Radiologica 2016.

Tracking by flow cytometry antigen-specific follicular helper T cells in wild-type animals after protein vaccination.

PubMed

Chakarov, Svetoslav; Fazilleau, Nicolas

2015-01-01

Flow cytometry is a valuable technology used in immunology to characterize and enumerate the different cell subpopulations specific for a nonself-antigen in the context of an ongoing immune response. Among them, follicular helper T cells are the cognate regulators of B cells in secondary lymphoid tissues. Thus, tracking them is of high interest especially in the context of protein vaccination. For this purpose, transgenic antigen-receptor mouse models have been largely used. It is now clear that transgenic models are not always the best means to study the dynamics of the immune response since they can modify the response. In this chapter, we describe how to track endogenous antigen-specific follicular helper T cells by flow cytometry after protein vaccination in nonmodified wild-type animals, which ultimately provides a comprehensive way to enumerate, characterize, and isolate these particular cells in vivo.

Antibiotic Susceptibility, Genetic Diversity, and the Presence of Toxin Producing Genes in Campylobacter Isolates from Poultry.

PubMed

Lee, Jeeyeon; Jeong, Jiyeon; Lee, Heeyoung; Ha, Jimyeong; Kim, Sejeong; Choi, Yukyung; Oh, Hyemin; Seo, Kunho; Yoon, Yohan; Lee, Soomin

2017-11-17

This study examined antibiotic susceptibility, genetic diversity, and characteristics of virulence genes in Campylobacter isolates from poultry. Chicken ( n = 152) and duck ( n = 154) samples were collected from 18 wet markets in Korea. Campylobacter spp. isolated from the carcasses were identified by PCR. The isolated colonies were analyzed for antibiotic susceptibility to chloramphenicol, amikacin, erythromycin, tetracycline, ciprofloxacin, nalidixic acid, and enrofloxacin. The isolates were also used to analyze genetic diversity using the DiversiLab TM system and were tested for the presence of cytolethal distending toxin ( cdt ) genes. Campylobacter spp. were isolated from 45 poultry samples out of 306 poultry samples (14.7%) and the average levels of Campylobacter contamination were 22.0 CFU/g and 366.1 CFU/g in chicken and duck samples, respectively. Moreover, more than 90% of the isolates showed resistance to nalidixic acid and ciprofloxacin. Genetic correlation analysis showed greater than 95% similarity between 84.4% of the isolates, and three cdt genes ( cdtA , cdtB , and cdtC ) were present in 71.1% of Campylobacter isolates. These results indicate that Campylobacter contamination should be decreased to prevent and treat Campylobacter foodborne illness.

Degradation and depolymerization of plastic waste by local bacterial isolates and bubble column reactor

NASA Astrophysics Data System (ADS)

Hussein, Amal A.; Alzuhairi, Mohammed; Aljanabi, Noor H.

2018-05-01

Accumulation of plastics, especially Polyethylene terephthalate (PET), is an ever increasing ecological threat due to its excessive usage in everyday human life. Nowadays, there are many methods to get rid of plastic wastes including burning, recycling and burying. However, these methods are not very active since their long period, anaerobic conditions that increase the rate of toxic materials released into the environment. This work aims to study the biological degradation of PET microorganism isolated from soil sample. Thirty eight (38) bacterial isolates were isolated from ten soil and plastic waste sample collected from four different waste disposal sites in Baghdad city during different periods between December 2016 and March 2017. Isolation was performed using enrichment culture method (flasks method) by culturing the soil samples in flasks with MSM medium where there is no carbon source only PET. Results showed that Al-Za'farania sample gave a higher number of isolates (13 isolates), while other samples gave less number of isolates. Screening was performed depending on their ability to grow in liquid MSM which contains PET powder and pieces and change the color of the PET-emulsified liquid medium as well as their ability to form the clear zone on PET-MSM agar. The results showed that NH-D-1 isolate has the higher ability to degrade DPET and PET pieces. According to morphological, biochemical characterization and Vitek-2 technique, the most active isolate was identified as Acinetobacter baumannii.

The Challenges of Creating a Real-Time Data Management System for TRU-Mixed Waste at the Advanced Mixed Waste Treatment Plant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paff, S. W; Doody, S.

2003-02-25

This paper discusses the challenges associated with creating a data management system for waste tracking at the Advanced Mixed Waste Treatment Plant (AMWTP) at the Idaho National Engineering Lab (INEEL). The waste tracking system combines data from plant automation systems and decision points. The primary purpose of the system is to provide information to enable the plant operators and engineers to assess the risks associated with each container and determine the best method of treating it. It is also used to track the transuranic (TRU) waste containers as they move throughout the various processes at the plant. And finally, themore » goal of the system is to support paperless shipments of the waste to the Waste Isolation Pilot Plant (WIPP). This paper describes the approach, methodologies, the underlying design of the database, and the challenges of creating the Data Management System (DMS) prior to completion of design and construction of a major plant. The system was built utilizing an Oracle database platform, and Oracle Forms 6i in client-server mode. The underlying data architecture is container-centric, with separate tables and objects for each type of analysis used to characterize the waste, including real-time radiography (RTR), non-destructive assay (NDA), head-space gas sampling and analysis (HSGS), visual examination (VE) and coring. The use of separate tables facilitated the construction of automatic interfaces with the analysis instruments that enabled direct data capture. Movements are tracked using a location system describing each waste container's current location and a history table tracking the container's movement history. The movement system is designed to interface both with radio-frequency bar-code devices and the plant's integrated control system (ICS). Collections of containers or information, such as batches, were created across the various types of analyses, which enabled a single, cohesive approach to be developed for verification and validation activities. The DMS includes general system functions, including task lists, electronic signature, non-conformance reports and message systems, that cut vertically across the remaining subsystems. Oracle's security features were utilized to ensure that only authorized users were allowed to log in, and to restrict access to system functionality according to user role.« less

Methicillin-resistant staphylococcus aureus isolates in a hospital of shanghai.

PubMed

Wang, Xiaoguang; Ouyang, Lin; Luo, Lingfei; Liu, Jiqian; Song, Chiping; Li, Cuizhen; Yan, Hongjing; Wang, Ping

2017-01-24

Methicillin-resistant Staphylococcus aureus (MRSA) strains are now common both in the health care setting and in the community. Active surveillance is critical for MRSA control and prevention. Specimens of patients (200 patients with 1119 specimens) as well as medical staff and hospital setting (1000 specimens) were randomly sampled in a level 2 hospital in Shanghai from September 2011 to August 2012. Isolation, cultivation and identification of S. aureus were performed. Totally, 67 S. aureus strains were isolated. 32 S. aureus strains were isolated from patient samples; 13 (13/32, 40.6%) of the 32 S. aureus isolates were MRSA; sputum sample and patients in the department of general internal medicine were the most frequent specimen and patient group for S. aureus strains isolation. Remaining 35 S. aureus strains were isolated from the medical staff and hospital setting; 20 (20/35, 57.1%) of the 35 S. aureus isolates were MRSA; specimens sampled from doctors and nurses' hands and nose and hospital facilities were the most frequent samples to isolate S. aureus. Resistant and virulent genes detection showed that, all 33 MRSA strains were mecA positive which accounts for 49.3% of the 67 S. aureus strains; 38 isolates were Panton-Valentine leukocidin (PVL) gene positive which accounts for 56.7% of the 67 S. aureus strains; and 17 (17/67, 25.4%) isolates are mecA and PVL genes dual positive. Multidrug-resistant strains of MRSA and PVL positive S. aureus are common in patients, medical staff and hospital setting, the potential health threat is worthy of our attention.

BACTERIAL PROFILE OF NECROTIC PULPS IN CHEETAH (ACINONYX JUBATUS) CANINE TEETH.

PubMed

Almansa Ruiz, José C; Bosman, Anna-Mari; Steenkamp, Gerhard

2016-03-01

The role of microbes and their antimicrobial susceptibilities in both acute and chronic infections of the dental pulp in humans has been well studied. Presently, no data are available on endodontic pathogens in cheetahs (Acinonyx jubatus). The aim of this study was to isolate and identify the bacteria found in the canine teeth of cheetahs, where the pulp was necrotic and exposed due to a complicated crown fracture. Thirty-six microbiologic samples were taken from root canals (RCs) of the canine teeth of 19 cheetahs: one pulp sample was taken from 10 cheetahs, four samples from 2 cheetahs, two samples from 3 cheetahs, and three samples from 4 cheetahs. Exposed pulps were cultured for aerobic and anaerobic bacteria; an additional screening with a 16S rRNA-specific polymerase chain reaction (PCR) was used for the last six samples. Antimicrobial susceptibility of isolates was determined by use of the Kirby-Bauer diffusion test. In total, 59 cultivable isolates belonging to 19 microbial species and 13 genera were recovered from the 36 RCs sampled. Only two samples yielded no cultivable bacteria. Thirty-two (54.49%) of the cultivable isolates were Gram positive and 27 (45.71%) were Gram negative. The maximum number of isolates cultivated from an individual RC was six. Facultative anaerobes (62.72%) were the most common bacteria of the RCs that yielded cultivable bacteria. Of the isolates, 28.81% were aerobic and 8.47% were strict anaerobes. The antimicrobials that showed the greatest efficacy in vitro against the different bacteria isolates were amikacin and gentamicin. The more common bacterial species isolated by PCR were anaerobes (60.8%), facultative anaerobes (30.2%), and aerobes (8.6%).

Why Are Associate Professors so Unhappy?

ERIC Educational Resources Information Center

Wilson, Robin

2012-01-01

Life as an associate professor with tenure can be even more isolating and overwhelming than being an assistant professor on the tenure track. The path to achieving what amounts to higher education's golden ring is well marked and includes guidance from more-experienced peers. But once a professor earns tenure, that guidance disappears, the amount…

Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates

USDA-ARS?s Scientific Manuscript database

Methods based on sequence data analysis facilitate the tracking of disease outbreaks, allow relationships between strains to be reconstructed and virulence factors to be identified. However, these methods are used postfactum after an outbreak has happened. Here, we show that support vector machine a...

Reading Polymorphemic Dutch Compounds: Toward a Multiple Route Model of Lexical Processing

ERIC Educational Resources Information Center

Kuperman, Victor; Schreuder, Robert; Bertram, Raymond; Baayen, R. Harald

2009-01-01

This article reports an eye-tracking experiment with 2,500 polymorphemic Dutch compounds presented in isolation for visual lexical decision while readers' eye movements were registered. The authors found evidence that both full forms of compounds ("dishwasher") and their constituent morphemes (e.g., "dish," "washer," "er") and morphological…

Fluorescent probe based subcellular distribution of Cu(II) ions in living electrotrophs isolated from Cu(II)-reduced biocathodes of microbial fuel cells.

PubMed

Tao, Ye; Xue, Hua; Huang, Liping; Zhou, Peng; Yang, Wei; Quan, Xie; Yuan, Jinxiu

2017-02-01

Based on the four indigenous electrotrophs (Stenotrophomonas maltophilia JY1, Citrobacter sp. JY3, Pseudomonas aeruginosa JY5 and Stenotrophomonas sp. JY6) isolated from well adapted Cu(II)-reduced biocathodes of microbial fuel cells (MFCs), a rhodamine based Cu(II) fluorescent probe was used to imaginably and quantitatively track subcellular Cu(II) ions in these electrotrophs. Cathodic electrons led to more Cu(II) ions (14.3-30.1%) in the intracellular sites at operation time of 2-3h with Cu(II) removal rates of 2.90-3.64mg/Lh whereas the absence of cathodic electrons prolonged the appearance of more Cu(II) ions (16.6-22.5%) to 5h with Cu(II) removal rates of 1.96-2.28mg/Lh. This study illustrates that cathodic electrons directed more Cu(II) ions for quicker entrance into the electrotrophic cytoplasm, and gives an alternative approach for developing imaging and functionally tracking Cu(II) ions in the electrotrophs of MFCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Understanding Collective Activities of People from Videos.

PubMed

Wongun Choi; Savarese, Silvio

2014-06-01

This paper presents a principled framework for analyzing collective activities at different levels of semantic granularity from videos. Our framework is capable of jointly tracking multiple individuals, recognizing activities performed by individuals in isolation (i.e., atomic activities such as walking or standing), recognizing the interactions between pairs of individuals (i.e., interaction activities) as well as understanding the activities of group of individuals (i.e., collective activities). A key property of our work is that it can coherently combine bottom-up information stemming from detections or fragments of tracks (or tracklets) with top-down evidence. Top-down evidence is provided by a newly proposed descriptor that captures the coherent behavior of groups of individuals in a spatial-temporal neighborhood of the sequence. Top-down evidence provides contextual information for establishing accurate associations between detections or tracklets across frames and, thus, for obtaining more robust tracking results. Bottom-up evidence percolates upwards so as to automatically infer collective activity labels. Experimental results on two challenging data sets demonstrate our theoretical claims and indicate that our model achieves enhances tracking results and the best collective classification results to date.

Isolation of new Brazilian giant viruses from environmental samples using a panel of protozoa.

PubMed

Dornas, Fábio P; Khalil, Jacques Y B; Pagnier, Isabelle; Raoult, Didier; Abrahão, Jônatas; La Scola, Bernard

2015-01-01

The Megavirales are a newly described order capable of infecting different types of eukaryotic hosts. For the most part, the natural host is unknown. Several methods have been used to detect these viruses, with large discrepancies between molecular methods and co-cultures. To isolate giant viruses, we propose the use of different species of amoeba as a cellular support. The aim of this work was to isolate new Brazilian giant viruses by comparing the protozoa Acanthamoeba castellanii, A. polyphaga, A. griffini, and Vermamoeba vermiformis (VV) as a platform for cellular isolation using environmental samples. One hundred samples were collected from 3 different areas in September 2014 in the Pampulha lagoon of Belo Horizonte city, Minas Gerais, Brazil. PCR was used to identify the isolated viruses, along with hemacolor staining, labelling fluorescence and electron microscopy. A total of 69 viruses were isolated. The highest ratio of isolation was found in A. polyphaga (46.38%) and the lowest in VV (0%). Mimiviruses were the most frequently isolated. One Marseillevirus and one Pandoravirus were also isolated. With Brazilian environmental samples, we demonstrated the high rate of lineage A mimiviruses. This work demonstrates how these viruses survive and circulate in nature as well the differences between protozoa as a platform for cellular isolation.

Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain).

PubMed

Coscollá, Mireia; Gosalbes, María José; Catalán, Vicente; González-Candelas, Fernando

2006-06-01

Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substantial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The analysis of isolates sampled in different years revealed a clear differentiation, with samples from 2001 being significantly distinct from those obtained in 2002 and 2003. Furthermore, although linkage disequilibrium measures indicate a clonal nature for population structure in this sample, the presence of some recombination events cannot be ruled out.

First isolation and molecular characterization of Ehrlichia canis in Costa Rica, Central America.

PubMed

Romero, L E; Meneses, A I; Salazar, L; Jiménez, M; Romero, J J; Aguiar, D M; Labruna, M B; Dolz, G

2011-08-01

The present study investigated Ehrlichia species in blood samples from dogs suspected of clinical ehrlichiosis, using molecular and isolation techniques in cell culture. From a total of 310 canine blood samples analyzed by 16S rRNA nested PCR, 148 (47.7%) were positive for Ehrlichia canis. DNA from Ehrlichia chaffeensis or Ehrlichia ewingii was not detected in any sample using species-specific primers in separated reactions. Leukocytes from five PCR-positive dogs were inoculated into DH82 cells; successful isolation of E. canis was obtained in four samples. Partial sequence of the dsb gene of eight canine blood samples (including the five samples for in vitro isolation) was obtained by PCR and their analyses through BLAST showed 100% of identity with the corresponding sequence of E. canis in GenBank. This study represents the first molecular diagnosis, isolation, and molecular characterization of E. canis in dogs from Costa Rica. Copyright © 2010 Elsevier Ltd. All rights reserved.

[Isolation of pathogenic bacteria in pasteurized type C milk sold in Recife City, Pernambuco, Brazil].

PubMed

Padilha , M R; Fernandes , Z F; Leal, T C; Leal, N C; Almeida, A M

2001-01-01

In order to improve information about the microbiological quality of the milk commercially available in the city of Recife, 250 samples of pasteurized type-C milk and 50 samples of raw milk were analyzed for Yersinia enterocolitica and Listeria monocytogenes and verify the possible occurrence of Yersinia enterocolitica and Listeria monocytogenes. These bacteria can develop in refrigeration temperatures and are responsible for food-born diseases. Neither Y. enterocolitica nor L. monocytogenes were found in the samples analyzed. However, the presence of Y. intermedia and Y. frederiksenii was detected, these environmental species behave as opportunist pathogens. Through the methodology used for Listeria isolation, one isolate of Salmonella Montevideo was obtained from a sample of pasteurized milk and another isolated from one sample of raw milk. Besides these, several other bacteria species were found. It is likely that the large microbiota present in the samples and the procedures employed to destroy it could have hindered the isolation of Y. enterocolitica and L. monocytogenes.

Microbial source tracking markers at three inland recreational lakes in Ohio, 2011

USGS Publications Warehouse

Francy, Donna S.; Stelzer, Erin A.

2012-01-01

During the 2011 recreational season, samples were collected for E. coli and microbial source tracking (MST) marker concentrations to begin to understand potential sources of fecal contamination at three inland recreational lakes in Ohio - Buckeye, Atwood, and Tappan Lakes. The results from 32 regular samples, 4 field blanks, and 7 field replicates collected at 5 sites are presented in this report. At the three lakes, the ruminant-associated marker was found most often (57-73 percent of samples) but at estimated quantities, followed by the dog-associated marker (30-43 percent of samples). The human-associated marker was found in 14 and 50 percent of samples from Atwood and Tappan Lakes, respectively, but was not found in any samples from the two Buckeye Lake sites. The gull-associated marker was detected in only two samples, both from Tappan Lake.

Isolation and clinical sample typing of human leptospirosis cases in Argentina.

PubMed

Chiani, Yosena; Jacob, Paulina; Varni, Vanina; Landolt, Noelia; Schmeling, María Fernanda; Pujato, Nazarena; Caimi, Karina; Vanasco, Bibiana

2016-01-01

Leptospira typing is carried out using isolated strains. Because of difficulties in obtaining them, direct identification of infective Leptospira in clinical samples is a high priority. Multilocus sequence typing (MLST) proved highly discriminatory for seven pathogenic species of Leptospira, allowing isolate characterization and robust assignment to species, in addition to phylogenetic evidence for the relatedness between species. In this study we characterized Leptospira strains circulating in Argentina, using typing methods applied to human clinical samples and isolates. Phylogenetic studies based on 16S ribosomal RNA gene sequences enabled typing of 8 isolates (6 Leptospira interrogans, one Leptospira wolffii and one Leptospira broomii) and 58 out of 85 (68.2%) clinical samples (55 L. interrogans, 2 Leptospira meyeri, and one Leptospira kirschneri). MLST results for the L. interrogans isolates indicated that five were probably Canicola serogroup (ST37) and one was probably Icterohaemorrhagiae serogroup (ST17). Eleven clinical samples (21.6%), provided MLST interpretable data: five were probably Pyrogenes serogroup (ST13), four Sejroe (ST20), one Autumnalis (ST22) and one Canicola (ST37). To the best of our knowledge this study is the first report of the use of an MLST typing scheme with seven loci to identify Leptospira directly from clinical samples in Argentina. The use of clinical samples presents the advantage of the possibility of knowing the infecting strain without resorting to isolates. This study also allowed, for the first time, the characterization of isolates of intermediate pathogenicity species (L. wolffii and L. broomii) from symptomatic patients. Copyright © 2015 Elsevier B.V. All rights reserved.

[Community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan salt lake on Qinghai-Tibet Plateau].

PubMed

Shen, Shuo

2017-04-04

I studied the community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan Salt Lake. I isolated and cultured the moderate halophilic bacteria on different selective media. After the 16S rRNA gene sequences was amplified and measured, I constructed the phylogenic tree, analyzed the community structure and calculated the diversity indexes according to the 16S rRNA gene information. A total of 421 moderate halophilic bacteria were isolated from water and mud samples in Qrhan Salt Lake. The 16S rRNA gene information showed that 4 potential novel species belonged to the family Bacillaceae. Eighty-three model strains belonged to 3 phylurms 6 families 16 genus. Among them, Bacillus sp., Oceanobacillus sp. and Halomonas sp. were dominant species. Diversity analysis showed that the diversity of strains isolated from water sample was higher than that from mud sample, but the dominance degree of strains isolated from mud sample was higher than that from water sample. The genetic diversity of moderate halophilic bacteria isolated from Qrhan Salt Lake was abundant. Also, there were dominant and novel species of culturable moderate halophilic bacteria in this lake.

Detection of Salmonella spp. in Retail Raw Food Samples from Vietnam and Characterization of Their Antibiotic Resistance▿

PubMed Central

Van, Thi Thu Hao; Moutafis, George; Istivan, Taghrid; Tran, Linh Thuoc; Coloe, Peter J.

2007-01-01

A study was conducted to examine the levels of Salmonella spp. contamination in raw food samples, including chicken, beef, pork, and shellfish, from Vietnam and to determine their antibiotic resistance characteristics. A total of 180 samples were collected and examined for the presence of Salmonella spp., yielding 91 Salmonella isolates. Sixty-one percent of meat and 18% of shellfish samples were contaminated with Salmonella spp. Susceptibility of all isolates to a variety of antimicrobial agents was tested, and resistance to tetracycline, ampicillin/amoxicillin, nalidixic acid, sulfafurazole, and streptomycin was found in 40.7%, 22.0%, 18.7%, 16.5%, and 14.3% of the isolates, respectively. Resistance to enrofloxacin, trimethoprim, chloramphenicol, kanamycin, and gentamicin was also detected (8.8 to 2.2%). About half (50.5%) of the isolates were resistant to at least one antibiotic, and multiresistant Salmonella isolates, resistant to at least three different classes of antibiotics, were isolated from all food types. One isolate from chicken (serovar Albany) contained a variant of the Salmonella genomic island 1 antibiotic resistance gene cluster. The results show that antibiotic resistance in Salmonella spp. in raw food samples from Vietnam is significant. PMID:17766455

Irradiation of nuclear track emulsions with thermal neutrons, heavy ions, and muons

NASA Astrophysics Data System (ADS)

Artemenkov, D. A.; Bradnova, V.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.; Kattabekov, R. R.; Mamatkulov, K. Z.; Rusakova, V. V.

2015-07-01

Exposures of test samples of nuclear track emulsion were analyzed. Angular and energy correlations of products originating from the thermal-neutron-induced reaction n th +10 B → 7 Li + (γ)+ α were studied in nuclear track emulsions enriched in boron. Nuclear track emulsions were also irradiated with 86Kr+17 and 124Xe+26 ions of energy about 1.2 MeV per nucleon. Measurements of ranges of heavy ions in nuclear track emulsionsmade it possible to determine their energies on the basis of the SRIM model. The formation of high-multiplicity nuclear stars was observed upon irradiating nuclear track emulsions with ultrarelativistic muons. Kinematical features studied in this exposure of nuclear track emulsions for events of the muon-induced splitting of carbon nuclei to three alpha particles are indicative of the nucleardiffraction interaction mechanism.

Antibiotic Resistance Patterns of Pseudomonas spp. Isolated from the River Danube

PubMed Central

Kittinger, Clemens; Lipp, Michaela; Baumert, Rita; Folli, Bettina; Koraimann, Günther; Toplitsch, Daniela; Liebmann, Astrid; Grisold, Andrea J.; Farnleitner, Andreas H.; Kirschner, Alexander; Zarfel, Gernot

2016-01-01

Spread and persistence of antibiotic resistance pose a severe threat to human health, yet there is still lack of knowledge about reservoirs of antibiotic resistant bacteria in the environment. We took the opportunity of the Joint Danube Survey 3 (JDS3), the world's biggest river research expedition of its kind in 2013, to analyse samples originating from different sampling points along the whole length of the river. Due to its high clinical relevance, we concentrated on the characterization of Pseudomonas spp. and evaluated the resistance profiles of Pseudomonas spp. which were isolated from eight sampling points. In total, 520 Pseudomonas isolates were found, 344 (66.0%) isolates were identified as Pseudomonas putida, and 141 (27.1%) as Pseudomonas fluorescens, all other Pseudomonas species were represented by less than five isolates, among those two P. aeruginosa isolates. Thirty seven percent (37%) of all isolated Pseudomonas species showed resistance to at least one out of 10 tested antibiotics. The most common resistance was against meropenem (30.4%/158 isolates) piperacillin/tazobactam (10.6%/55 isolates) and ceftazidime (4.2%/22 isolates). 16 isolates (3.1%/16 isolates) were multi-resistant. For each tested antibiotic at least one resistant isolate could be detected. Sampling points from the upper stretch of the River Danube showed more resistant isolates than downriver. Our results suggest that antibiotic resistance can be acquired by and persists even in Pseudomonas species that are normally not in direct contact with humans. A possible scenario is that these bacteria provide a reservoir of antibiotic resistance genes that can spread to related human pathogens by horizontal gene transfer. PMID:27199920

Microphysical, microchemical, and adhesive properties of lunar material. III - Gas interaction with lunar material.

NASA Technical Reports Server (NTRS)

Grossman, J. J.; Mukherjee, N. R.; Ryan, J. A.

1972-01-01

Gas adsorption measurements on an Apollo 12 ultrahigh vacuum-stored sample and Apollo 14 and 15 N2-stored samples, show that the cosmic ray track and solar wind damaged surface of lunar soil is very reactive. Room temperature monolayer adsorption of N2 by the Apollo 12 sample at 0.0001 atm was observed. Gas evolution of Apollo 14 lunar soil at liquid nitrogen temperature during adsorption/desorption cycling is probably due to cosmic ray track stored energy release accompanied by solar gas release from depths of 100-200 nm.

Long-term survival of Cryptococcus neoformans and Cryptococcus gattii in stored environmental samples from Colombia.

PubMed

Escandón, Patricia; Castañeda, Elizabeth

2015-01-01

Both Cryptococcus neoformans and Cryptococcus gattii have been isolated from a variety of environmental sources in Colombia. To determine the viability of C. neoformans/C. gattii isolates in stored soil samples, filtrates and bird droppings from which these yeasts were previously recovered. A total of 964 samples collected between 2003 and 2009, and kept at room temperature were processed. From them, 653 samples were from trees decaying wood, 274 from soil filtrates and 37 from bird droppings. When C. neoformans or C. gattii were recovered, the molecular type of each isolate was established by PCR fingerprinting using the single primer (GTG)5. Among the processed samples, 161 isolates were recovered. From those, 81 (50.3%) corresponded to C. gattii recovered from decaying wood of Eucalyptus spp., Corymbia ficifolia, Terminalia catappa and Ficus spp. trees, and 80 (49.7%) corresponded to C. neoformans recovered from Ficus spp. and eucalyptus trees, as well as from bird droppings. The most prevalent molecular type among the C. gattii and C. neoformans isolates was VGII and VNI, respectively. The re-isolation of C. neoformans/C. gattii from 10-year stored samples suggests that these yeasts are able to keep viable in naturally colonized samples. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Cultured bacterial diversity and human impact on alpine glacier cryoconite.

PubMed

Lee, Yung Mi; Kim, So-Yeon; Jung, Jia; Kim, Eun Hye; Cho, Kyeung Hee; Schinner, Franz; Margesin, Rosa; Hong, Soon Gyu; Lee, Hong Kum

2011-06-01

The anthropogenic effect on the microbial communities in alpine glacier cryoconites was investigated by cultivation and physiological characterization of bacteria from six cryoconite samples taken at sites with different amounts of human impact. Two hundred and forty seven bacterial isolates were included in Actinobacteria (9%, particularly Arthrobacter), Bacteroidetes (14%, particularly Olleya), Firmicutes (0.8%), Alphaproteobacteria (2%), Betaproteobacteria (16%, particularly Janthinobacterium), and Gammaproteobacteria (59%, particularly Pseudomonas). Among them, isolates of Arthrobacter were detected only in samples from sites with no human impact, while isolates affiliated with Enterobacteriaceae were detected only in samples from sites with strong human impact. Bacterial isolates included in Actinobacteria and Bacteroidetes were frequently isolated from pristine sites and showed low maximum growth temperature and enzyme secretion. Bacterial isolates included in Gammaproteobacteria were more frequently isolated from sites with stronger human impact and showed high maximum growth temperature and enzyme secretion. Ecotypic differences were not evident among isolates of Janthinobacterium lividum, Pseudomonas fluorescens, and Pseudomonas veronii, which were frequently isolated from sites with different degrees of anthropogenic effect.

Prevalence of Naegleria fowleri in Environmental Samples from Northern Part of India.

PubMed

Panda, Ashutosh; Khalil, Shehla; Mirdha, Bijay Ranjan; Singh, Yogita; Kaushik, Samander

2015-01-01

Naegleria fowleri the causative agent of Primary Amoebic Meningoencephalitis, is ubiquitously distributed worldwide in various warm aquatic environments and soil habitats. The present study reports on the presence of Naegleria spp. in various water bodies present in Rohtak and Jhajjar district, of state Haryana, India. A total of 107 water reservoirs were screened from summer till autumn (2012 and 2013). In order to isolate Naegleria spp. from the collected water samples, the water samples were filtered and the trapped debris after processing were transferred to non-nutrient agar plates already seeded with lawn culture of Escherichia coli. Out of total 107 water samples, 43 (40%) samples were positive by culture for free living amoeba after incubation for 14 days at 37°C. To identify the isolates, the ITS1, 5.8SrDNA and ITS2 regions were targeted for PCR assay. Out of total 43 positive samples, 37 isolates were positive for Naegleria spp. using genus specific primers and the most frequently isolated species was Naegleria australiensis. Out of 37 Naegleria spp. positive isolates, 1 isolate was positive for Naegleria fowleri. The sequence analysis revealed that the Naegleria fowleri strain belonged to Type 2.

Prevalence of Naegleria fowleri in Environmental Samples from Northern Part of India

PubMed Central

Panda, Ashutosh; Khalil, Shehla; Mirdha, Bijay Ranjan; Singh, Yogita; Kaushik, Samander

2015-01-01

Naegleria fowleri the causative agent of Primary Amoebic Meningoencephalitis, is ubiquitously distributed worldwide in various warm aquatic environments and soil habitats. The present study reports on the presence of Naegleria spp. in various water bodies present in Rohtak and Jhajjar district, of state Haryana, India. A total of 107 water reservoirs were screened from summer till autumn (2012 and 2013). In order to isolate Naegleria spp. from the collected water samples, the water samples were filtered and the trapped debris after processing were transferred to non-nutrient agar plates already seeded with lawn culture of Escherichia coli. Out of total 107 water samples, 43 (40%) samples were positive by culture for free living amoeba after incubation for 14 days at 37°C. To identify the isolates, the ITS1, 5.8SrDNA and ITS2 regions were targeted for PCR assay. Out of total 43 positive samples, 37 isolates were positive for Naegleria spp. using genus specific primers and the most frequently isolated species was Naegleria australiensis. Out of 37 Naegleria spp. positive isolates, 1 isolate was positive for Naegleria fowleri. The sequence analysis revealed that the Naegleria fowleri strain belonged to Type 2. PMID:26484533

[Incidence of Campylobacter spp. and Salmonella spp. in raw and roasted chicken in Guadalajara, Mexico].

PubMed

Castillo-Ayala, A; Salas-Ubiarco, M G; Márquez-Padilla, M L; Osorio-Hernández, M D

1993-01-01

The presence of Campylobacter spp. and Salmonella was studied in 70 samples of fresh retail chicken pieces and in 40 samples of roast chicken. Total plate count was performed in every sample as well. Most of the samples of fresh chicken yielded total plate counts > 10(8)/piece (thigh), while in roast chicken these counts ranged from 10(3) to 10(5)/piece (leg and thigh). Campylobacter was isolated from 33% of fresh chicken and from no sample of roast chicken. Salmonella was isolated from 69% of fresh chicken and 2.5% of roast chicken. There was no relationship between total plate counts in fresh chicken and isolation of either Campylobacter or Salmonella. Sixty percent of the Salmonella isolates belonged to serotype S. anatum, and about 50% of the isolates of Campylobacter were identified as being C. coli. The only Salmonella-positive sample of roast chicken yielded three serotypes: S. give, S. muenster, and S. manhattan. Presence of Campylobacter and Salmonella in chicken is of concern, due to the risk of spreading from the raw food to other cooked foods. The isolation of pathogens from roast chicken indicates mishandling during processing and/or storage of the product.

Star formation rates in isolated galaxies selected from the Two-Micron All-Sky Survey

NASA Astrophysics Data System (ADS)

Melnyk, O.; Karachentseva, V.; Karachentsev, I.

2015-08-01

We have considered the star formation properties of 1616 isolated galaxies from the 2MASS XSC (Extended Source Catalog) selected sample (2MIG) with the far-ultraviolet GALEX magnitudes. This sample was then compared with corresponding properties of isolated galaxies from the Local Orphan Galaxies (LOG) catalogue and paired galaxies. We found that different selection algorithms define different populations of isolated galaxies. The population of the LOG catalogue, selected from non-clustered galaxies in the Local Supercluster volume, mostly consists of low-mass spiral and late-type galaxies. The specific star formation rate (SSFR) upper limit in isolated and paired galaxies does not exceed the value of ˜dex(-9.4). This is probably common for galaxies of differing activity and environment (at least at z < 0.06). The fractions of quenched galaxies are nearly twice as high in the paired galaxy sample as in the 2MIG isolated galaxy sample. From the behaviour of (S)SFR versus M* relations we deduced that the characteristic value influencing evolutionary processes is the galaxy mass. However, the environmental influence is notable: paired massive galaxies with logM* > 11.5 have higher (S)SFR than isolated galaxies. Our results suggest that the environment helps to trigger the star formation in the highest mass galaxies. We found that the fraction of AGN in the paired sample is only a little higher than in our isolated galaxy sample. We assume that AGN phenomenon is probably defined by secular galaxy evolution.

Visual Tracking Based on Extreme Learning Machine and Sparse Representation

PubMed Central

Wang, Baoxian; Tang, Linbo; Yang, Jinglin; Zhao, Baojun; Wang, Shuigen

2015-01-01

The existing sparse representation-based visual trackers mostly suffer from both being time consuming and having poor robustness problems. To address these issues, a novel tracking method is presented via combining sparse representation and an emerging learning technique, namely extreme learning machine (ELM). Specifically, visual tracking can be divided into two consecutive processes. Firstly, ELM is utilized to find the optimal separate hyperplane between the target observations and background ones. Thus, the trained ELM classification function is able to remove most of the candidate samples related to background contents efficiently, thereby reducing the total computational cost of the following sparse representation. Secondly, to further combine ELM and sparse representation, the resultant confidence values (i.e., probabilities to be a target) of samples on the ELM classification function are used to construct a new manifold learning constraint term of the sparse representation framework, which tends to achieve robuster results. Moreover, the accelerated proximal gradient method is used for deriving the optimal solution (in matrix form) of the constrained sparse tracking model. Additionally, the matrix form solution allows the candidate samples to be calculated in parallel, thereby leading to a higher efficiency. Experiments demonstrate the effectiveness of the proposed tracker. PMID:26506359

WE-D-BRF-01: FEATURED PRESENTATION - Investigating Particle Track Structures Using Fluorescent Nuclear Track Detectors and Monte Carlo Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dowdell, S; Paganetti, H; Schuemann, J

Purpose: To report on the efforts funded by the AAPM seed funding grant to develop the basis for fluorescent nuclear track detector (FNTD) based radiobiological experiments in combination with dedicated Monte Carlo simulations (MCS) on the nanometer scale. Methods: Two confocal microscopes were utilized in this study. Two FNTD samples were used to find the optimal microscope settings, one FNTD irradiated with 11.1 MeV/u Gold ions and one irradiated with 428.77 MeV/u Carbon ions. The first sample provided a brightly luminescent central track while the latter is used to test the capabilities to observe secondary electrons. MCS were performed usingmore » TOPAS beta9 version, layered on top of Geant4.9.6p02. Two sets of simulations were performed, one with the Geant4-DNA physics list and approximating the FNTDs by water, a second set using the Penelope physics list in a water-approximated FNTD and a aluminum-oxide FNTD. Results: Within the first half of the funding period, we have successfully established readout capabilities of FNTDs at our institute. Due to technical limitations, our microscope setup is significantly different from the approach implemented at the DKFZ, Germany. However, we can clearly reconstruct Carbon tracks in 3D with electron track resolution of 200 nm. A second microscope with superior readout capabilities will be tested in the second half of the funding period, we expect an improvement in signal to background ratio with the same the resolution.We have successfully simulated tracks in FNTDs. The more accurate Geant4-DNA track simulations can be used to reconstruct the track energy from the size and brightness of the observed tracks. Conclusion: We have achieved the goals set in the seed funding proposal: the setup of FNTD readout and simulation capabilities. We will work on improving the readout resolution to validate our MCS track structures down to the nanometer scales.« less

Joint Sensing/Sampling Optimization for Surface Drifting Mine Detection with High-Resolution Drift Model

DTIC Science & Technology

2012-09-01

as potential tools for large area detection coverage while being moderately inexpensive (Wettergren, Performance of Search via Track - Before - Detect for...via Track - Before - Detect for Distribute 34 Sensor Networks, 2008). These statements highlight three specific needs to further sensor network research...Bay hydrography. Journal of Marine Systems, 12, 221–236. Wettergren, T. A. (2008). Performance of search via track - before - detect for distributed

Application of F⁺RNA Coliphages as Source Tracking Enteric Viruses on Parsley and Leek Using RT-PCR.

PubMed

Shahrampour, Dina; Yavarmanesh, Masoud; Najafi, Mohammad Bagher Habibi; Mohebbi, Mohebbat

2015-12-01

The objective of this study was to identify sources of fecal contamination in leek and parsley, by using four different F(+)RNA coliphage genogroups (IV, I indicate animal fecal contamination and II, III indicate human fecal contamination). Three different concentrations (10(2), 10(4), 10(6) pfu/ml) of MS2 coliphage were inoculated on the surface of parsley and leek samples for detection of phage recovery efficiency among two methods of elution concentration (PEG-precipitation and Ultracentrifugation) by performing double agar layer (DAL) assay in three replications. Highest recovery of MS2 was observed in PEG method and in 10(6) inoculation concentration. Accordingly, the PEG method was used for washing and isolation of potentially contaminated phages of 30 collected samples (15 samples from the market and 15 samples from the farm). The final solutions of PEG method were tested for the enumeration of plaques by DAL assay. Total RNA was then extracted from recovered phages, and RT-PCR was performed by using four primer sets I, II, III, and IV. Incidence of F(+)RNA coliphages was observed in 12/15 (80 %) and 10/15 (66/6 %) of samples were obtained from farm and market, respectively, using both DAL and RT-PCR test methods. Different genotypes (I, II, and IV) of F(+)RNA coliphages were found in farm samples, while only genotype I was detected in market samples by using the primer sets. Due to the higher frequency of genotype I and IV, the absence of genotype III, and also the low frequency of genotype II, it is concluded that the contamination of vegetable (parsley and leek) in Neyshabour, Iran is most likely originated from animal sources.

An improved multi-domain convolution tracking algorithm

NASA Astrophysics Data System (ADS)

Sun, Xin; Wang, Haiying; Zeng, Yingsen

2018-04-01

Along with the wide application of the Deep Learning in the field of Computer vision, Deep learning has become a mainstream direction in the field of object tracking. The tracking algorithm in this paper is based on the improved multidomain convolution neural network, and the VOT video set is pre-trained on the network by multi-domain training strategy. In the process of online tracking, the network evaluates candidate targets sampled from vicinity of the prediction target in the previous with Gaussian distribution, and the candidate target with the highest score is recognized as the prediction target of this frame. The Bounding Box Regression model is introduced to make the prediction target closer to the ground-truths target box of the test set. Grouping-update strategy is involved to extract and select useful update samples in each frame, which can effectively prevent over fitting. And adapt to changes in both target and environment. To improve the speed of the algorithm while maintaining the performance, the number of candidate target succeed in adjusting dynamically with the help of Self-adaption parameter Strategy. Finally, the algorithm is tested by OTB set, compared with other high-performance tracking algorithms, and the plot of success rate and the accuracy are drawn. which illustrates outstanding performance of the tracking algorithm in this paper.

Optimised cord blood sample selection for small‑scale CD34+ cell immunomagnetic isolation.

PubMed

Perdomo-Arciniegas, Ana-María; Vernot, Jean-Paul

2012-03-01

Haematopoietic stem cells (HSCs) are defined as multipotential cells, capable of self-renewal and reconstituting in vivo the haematopoietic compartment. The CD34 antigen is considered an important HSCs marker in humans. Immunomagnetic isolation, by targeting CD34 antigen, is widely used for human HSC separation. This method allows the enrichment of human HSCs that are present at low frequencies in umbilical cord blood (CB). Immunomagnetic CD34+-cell isolation reproducibility, regarding cell yield and purity, is affected by the CD34+ cell frequency and total cell numbers present in a given sample; CB HSC purification may thus yield variable results, which also depend on the volume and density fractionation-derived cell loss of a CB sample. The uncertainty of such an outcome and associated technical costs call for a cost-effective sample screening strategy. A correlation analysis using clinical and laboratory data from 59 CB samples was performed to establish predictive variables for CD34+-immunomagnetic HSCs isolation. This study described the positive association of CD34+-cell isolation with white and red cell numbers present after cell fractionation. Furthermore, purity has been correlated with lymphocyte percentages. Predictive variable cut-off values, which are particularly useful in situations involving low CB volumes being collected (such as prevalent late umbilical cord clamping clinical practice), were proposed for HSC isolation sampling. Using the simple and cost-effective CB sample screening criteria described here would lead to avoiding costly inefficient sample purification, thereby ensuring that pure CD34+ cells are obtained in the desired numbers following CD34 immunomagnetic isolation.

Genital mycoplasmas in semen samples of males attending a tertiary care hospital in Nigeria: any role in sperm count reduction?

PubMed

Agbakoba, N R; Adetosoye, A I; Ikechebelu, J I

2007-06-01

Semen samples from 54 married men attending the outpatient clinics for problems of infertility and routine semen analysis were examined for the presence of genital mycoplasmas. The mean age of the men was 36.1 years with a range of 25 55 years. Majority of the men 57.4% (31 of 54) were in their fourth decade of life (30 39 years). This age group also had the highest percentage 57.2% (8 of 14) of positive isolates of genital mycoplasmas on semen culture. A total of 21 organisms obtained from 14 (26.0%) positive samples were isolated. Mycoplasma and Ureaplasma spp. separately isolated from the samples yielded frequencies of 1 (1.9%) and 6 (11.1%) respectively and the remaining 7 (13.0%) samples were infected with both organisms. A breakdown of the mycoplasma species include 5 (23.8%) M. hominis, 2 (9.5%) M. fermentans and 1 (4.8%) M. penetrans. Apart from one isolate of M. hominis other Mycoplasma species were found in association with Ureaplasma species. Fifteen (71.4%) of the 21 isolates [8 (53.3%) ureaplasmas and 7 (46.7%) mycoplasmas] were isolated from samples with sperm counts less than 20 million/ml while the remaining 6 (21.6%) isolates [5 (83.3%) ureaplasmas and 1 (16.7) mycoplasma] were from samples with counts greater than 20 million/ml. This finding could indicate a possible influence of genital mycoplasmas especially mycoplasmas species on sperm count.

Population Genetics of the Aquatic Fungus Tetracladium marchalianum over Space and Time

PubMed Central

Anderson, Jennifer L.; Shearer, Carol A.

2011-01-01

Aquatic hyphomycete fungi are fundamental mediators of energy flow and nutrient spiraling in rivers. These microscopic fungi are primarily dispersed in river currents, undergo substantial annual fluctuations in abundance, and reproduce either predominantly or exclusively asexually. These aspects of aquatic hyphomycete biology are expected to influence levels and distributions of genetic diversity over both spatial and temporal scales. In this study, we investigated the spatiotemporal distribution of genotypic diversity in the representative aquatic hyphomycete Tetracladium marchalianum. We sampled populations of this fungus from seven sites, three sites each in two rivers in Illinois, USA, and one site in a Wisconsin river, USA, and repeatedly sampled one population over two years to track population genetic parameters through two seasonal cycles. The resulting fungal isolates (N = 391) were genotyped at eight polymorphic microsatellite loci. In spite of seasonal reductions in the abundance of this species, genotypic diversity was consistently very high and allele frequencies remarkably stable over time. Likewise, genotypic diversity was very high at all sites. Genetic differentiation was only observed between the most distant rivers (∼450 km). Clear evidence that T. marchalianum reproduces sexually in nature was not observed. Additionally, we used phylogenetic analysis of partial β-tubulin gene sequences to confirm that the fungal isolates studied here represent a single species. These results suggest that populations of T. marchalianum may be very large and highly connected at local scales. We speculate that large population sizes and colonization of alternate substrates in both terrestrial and aquatic environments may effectively buffer the aquatic populations from in-stream population fluctuations and facilitate stability in allele frequencies over time. These data also suggest that overland dispersal is more important for structuring populations of T. marchalianum over geographic scales than expected. PMID:21264239

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

NASA Technical Reports Server (NTRS)

Ott, C. M.; John, J.; Castro, V. A.; Cruz, P.; Buttner, L. M.; Pierson, D. L.

2007-01-01

The determination of risk from infectious disease during long-duration missions is composed of several factors including (1) the host#s susceptibility, (2) the host#s exposure to the infectious disease agent, and (3) the concentration of the infectious agent, and (4) the characteristics of the infectious agent. While stringent steps are taken to minimize the transfer of potential pathogens to spacecraft, several medically significant organisms have been isolated from both the Mir and International Space Station (ISS). Historically, the method for isolation and identification of microorganisms from spacecraft environmental samples depended upon their growth on culture media. Unfortunately, only a fraction of the organisms may grow on a culture medium, potentially omitting those microorganisms whose nutritional and physical requirements for growth are not met. Thus, several pathogens may not have been detected, such as Legionella pneumophila, the etiological agent of Legionnaire#s disease. We hypothesize that environmental analysis using non-culture-based technologies will reveal microorganisms, allergens, and microbial toxins not previously reported in spacecraft, allowing for a more complete health assessment. The development of techniques for this flight experiment, operationally named SWAB, has already provided advances in NASA laboratory processes and beneficial information toward human health risk assessment. The first accomplishment of the SWAB experiment was the incorporation of 16S ribosomal DNA sequencing for the identification of bacteria. The use of this molecular technique has increased bacterial speciation of environmental isolates from previous flights three fold compared to conventional methodology. This increased efficiency in bacterial speciation provides a better understanding of the microbial ecology and the potential risk to the crew. Additional SWAB studies focused on the use of molecular-based DNA fingerprinting using repetitive sequencebased polymerase chain reaction (rep-PCR). This technology has allowed contamination tracking of microorganisms between crewmembers and their environment. This study not only demonstrated that ISS has a greater diversity of organisms than originally expected, but also provided insight into possible routes of infection to the crew. Additional ground-based studies used rep-PCR and protein based assays to determine the potential of methicillin resistant Staphylococcus aureus (MRSA) aboard ISS. MRSA has become increasingly common on Earth and pose a treatment problem for infections during flight. While no MRSA have been isolated from ISS to date, the mecA gene product that is responsible for methicillin resistance was isolated in other Staphylococcus species aboard ISS suggesting a potential of MRSA through gene transfer. Using improved sample collection technologies, flight sampling for SWAB was initiated in August 2006 and should continue through spring of 2007. The focus of these flight samples is the collection of DNA for evaluation by Denaturing Gradient Gel Electrophoresis (DGGE). Unlike other techniques, DGGE does not depend on any microbial growth on culture media allowing a more comprehensive assessment of the spacecraft interior. This study should provide insight into the true microbial ecology that is experienced by the crew during flight. This information will lead toward an accurate microbial risk assessment to help set flight requirements to protect the safety, health, and performance of the crew.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

Covered are: analytical laboratory operations (ALO) sample receipt and control, ALO data report/package preparation review and control, single shell tank (PST) project sample tracking system, sample receiving, analytical balances, duties and responsibilities of sample custodian, sample refrigerator temperature monitoring, security, assignment of staff responsibilities, sample storage, data reporting, and general requirements for glassware.

PREVALENCE, BIOCHEMICAL CHARACTERISTICS, AND ANTIBIOTIC SUSCEPTIBILITY OF AEROMONADS, VIBRIOS, AND PLESIOMONADS ISOLATED FROM DIFFERENT SOURCES AT A ZOO.

PubMed

Kim, Kyoo-Tae; Lee, Seung-Hun; Kwak, Dongmi

2015-06-01

Aeromonas spp., Vibrio parahaemolyticus , and Plesiomonas shigelloides are commonly implicated in foodborne and waterborne diarrheal illnesses of humans and other animals. The present study assessed the prevalence, biochemical characteristics, and antibiotic susceptibility of Aeromonas spp., V. parahaemolyticus , and P. shigelloides by analyzing samples from 729 sources at a zoo, including animal feces (n=607), watering facilities (n=104), and pond water samples (n=18). Of the 729 samples collected, 40 (5.5%) contained one of these four species of bacteria: A. hydrophila (n=16; 2.2%), A. sobria (n=12; 1.6%), V. parahaemolyticus (n=10; 1.4%), and P. shigelloides (n=2; 0.3%). The 16 isolates of A. hydrophila came from three fecal samples, eight watering facilities, and five pond water samples. The 12 isolates of A. sobria came from four fecal samples, three watering facilities, and five pond water samples. The 10 isolates of V. parahaemolyticus came from one fecal sample and nine watering facilities. The two isolates of P. shigelloides came from one watering facility and one pond water sample. Of the 40 isolates, 16 (40.0%), 21 (52.5%), and three (7.5%) originated from mammals, birds, and reptiles, respectively. All isolates tested positive for NO3, tryptophan, p-nitrophenyl-β-D-galactopyranoside, glucose assimilation, N-acetyl-glucosamine, maltose, gluconate, malate, and oxidase. Aeromonas spp. and V. parahaemolyticus exhibited similar biochemical characteristics, whereas P. shigelloides exhibited distinct fermentation characteristics. All the isolated strains exhibited hemolytic activity; variable results of DNase, protease, and Congo red uptake tests; and resistance to ampicillin, bacitracin, novobiocin, penicillin, and vancomycin. All the strains were sensitive to amikacin, chloramphenicol, colistin, gentamicin, kanamycin, norfloxacin, and trimethoprim-sulfadimethoxazole. Because of the high proportion of asymptomatic carriers of these potentially pathogenic bacteria and their wide distribution, consistent monitoring of food and water sources is necessary to prevent disease outbreaks.

Satellite accelerometer measurements of neutral density and winds during geomagnetic storms

NASA Technical Reports Server (NTRS)

Marcos, F. A.; Forbes, J. M.

1986-01-01

A new thermospheric wind measurement technique is reported which is based on a Satellite Electrostatic Triaxial Accelerometer (SETA) system capable of accurately measuring accelerations in the satellite's in-track, cross-track and radial directions. Data obtained during two time periods are presented. The first data set describes cross-track winds measured between 170 and 210 km during a 5-day period (25 to 29 March 1979) of mostly high geomagnetic activity. In the second data set, cross-track winds and neutral densities from SETA and exospheric temperatures from the Millstone Hill incoherent scatter radar are examined during an isolated magnetic substorm occurring on 21 March 1979. A polar thermospheric wind circulation consisting of a two cell horizontal convection pattern is reflected in both sets of cross-track acceleration measurements. The density response is highly asymmetric with respect to its day/night behavior. Latitude structures of the density response at successive times following the substorm peak suggest the equatorward propagation of a disturbance with a phase speed between 300 and 600 m/s. A deep depression in the density at high latitudes (less than 70 deg) is evident in conjunction with this phenomenon. The more efficient propagation of the disturbance to lower latitudes during the night is probably due to the midnight surge effect.

Demographics of Isolated Galaxies along the Hubble Sequence

NASA Astrophysics Data System (ADS)

Khim, Hong-geun; Park, Jongwon; Seo, Seong-Woo; Lee, Jaehyun; Smith, Rory; Yi, Sukyoung K.

2015-09-01

Isolated galaxies in low-density regions are significant in the sense that they are least affected by the hierarchical pattern of galaxy growth and interactions with perturbers, at least for the last few gigayears. To form a comprehensive picture of the star-formation history of isolated galaxies, we constructed a catalog of isolated galaxies and their comparison sample in relatively denser environments. The galaxies are drawn from the Sloan Digital Sky Survey Data Release 7 in the redshift range of 0.025\\lt z\\lt 0.044. We performed a visual inspection and classified their morphology following the Hubble classification scheme. For the spectroscopic study, we make use of the catalog provided by Oh et al. in 2011. We confirm most of the earlier understanding on isolated galaxies. The most remarkable additional results are as follows. Isolated galaxies are dominantly late type with the morphology distribution (E:S0:S:Irr) = (9.9:11.3:77.6:1.2)%. The frequency of elliptical galaxies among isolated galaxies is only a third of that of the comparison sample. Most of the photometric and spectroscopic properties are surprisingly similar between the isolated and comparison samples. However, early-type isolated galaxies are less massive by 50% and younger (by Hβ) by 20% than their counterparts in the comparison sample. This can be explained as a result of different merger and star-formation histories for differing environments in the hierarchical merger paradigm. We provide an online catalog for the list and properties of our sample galaxies.

First genetic characterisation of Giardia in human isolates from Jordan.

PubMed

Hijjawi, Nawal; Yang, Rongchang; Mukbel, Rami; Yassin, Yasmeen; Mharib, Taghrid; Ryan, Una

2016-10-01

Little is known about the epidemiology of Giardia in Jordan and to date, no genotyping studies have been conducted on Giardia isolates from Jordanians. In the present study, a total of 49 microscopy-positive faecal samples from Jordanian patients suffering from giardiasis were analysed at two loci: the triose phosphate isomerase (tpi) gene and the glutamate dehydrogenase (gdh) gene. At the tpi locus, a total of 28 samples amplified and assemblage A was identified in 46.4 % (13/28) samples, while assemblage B was identified in 50 % (14/28) samples and a mixed assemblage A and B was identified in one sample (3.6 %) (Table 1). At the gdh locus 48 isolates amplified and of these assemblages A was identified in 43.7 % (21/48) of isolates and assemblage B in 56.3 % (27/48) of isolates. No mixed infections were detected at the gdh locus. Subtyping at the gdh locus identified sub-assemblage AII in 43.7 % (21/48) of isolates and sub-assemblages BIII and BIV in 25 % (12/48) and 31.2 % (15/48) of isolates, respectively, with more genetic diversity in AII isolates than BIII or BIV isolates. Novel sub-types within each sub-assemblage were identified suggesting unique endemicity and anthroponotic transmission of Giardia in Jordanian patients suffering from giardiasis. Further studies are required to better understand the epidemiology and transmission of Giardia in Jordan.

Comparative performance of fetal goat tongue cell line ZZ-R 127 and fetal porcine kidney cell line LFBK-αvβ6 for Foot-and-mouth disease virus isolation.

PubMed

Fukai, Katsuhiko; Morioka, Kazuki; Yamada, Manabu; Nishi, Tatsuya; Yoshida, Kazuo; Kitano, Rie; Yamazoe, Reiko; Kanno, Toru

2015-07-01

The fetal goat tongue cell line ZZ-R 127 and the fetal porcine kidney cell line LFBK-α(v)β(6) have been reported to have high sensitivity to various Foot-and-mouth disease virus (FMDV) strains. The suitability of ZZ-R 127 cells for FMDV isolation not only from epithelial suspensions but also from other clinical samples has already been confirmed in a previous study. However, to our knowledge, the suitability of LFBK-α(v)β(6) cells has not been evaluated using clinical samples other than epithelial materials. In addition, both cell lines have never been compared, in terms of use for FMDV isolation, under the same conditions. Therefore, in the current study, the virus isolation rates of both cell lines were compared using clinical samples collected from animals infected experimentally with FMDV. Viruses were successfully isolated from clinical samples other than epithelial suspensions for both cell lines. The virus isolation rates for the 2 cell lines were not significantly different. The Cohen kappa coefficients between the virus isolation results for both cell lines were significantly high. Taken together, these results confirmed the suitability of LFBK-α(v)β(6) cells for FMDV isolation from clinical samples other than epithelial suspensions. The levels of susceptibility of both cell lines to FMDV isolation were also confirmed to be almost the same. © 2015 The Author(s).

Visuo-manual tracking: does intermittent control with aperiodic sampling explain linear power and non-linear remnant without sensorimotor noise?

PubMed

Gollee, Henrik; Gawthrop, Peter J; Lakie, Martin; Loram, Ian D

2017-11-01

A human controlling an external system is described most easily and conventionally as linearly and continuously translating sensory input to motor output, with the inevitable output remnant, non-linearly related to the input, attributed to sensorimotor noise. Recent experiments show sustained manual tracking involves repeated refractoriness (insensitivity to sensory information for a certain duration), with the temporary 200-500 ms periods of irresponsiveness to sensory input making the control process intrinsically non-linear. This evidence calls for re-examination of the extent to which random sensorimotor noise is required to explain the non-linear remnant. This investigation of manual tracking shows how the full motor output (linear component and remnant) can be explained mechanistically by aperiodic sampling triggered by prediction error thresholds. Whereas broadband physiological noise is general to all processes, aperiodic sampling is associated with sensorimotor decision making within specific frontal, striatal and parietal networks; we conclude that manual tracking utilises such slow serial decision making pathways up to several times per second. The human operator is described adequately by linear translation of sensory input to motor output. Motor output also always includes a non-linear remnant resulting from random sensorimotor noise from multiple sources, and non-linear input transformations, for example thresholds or refractory periods. Recent evidence showed that manual tracking incurs substantial, serial, refractoriness (insensitivity to sensory information of 350 and 550 ms for 1st and 2nd order systems respectively). Our two questions are: (i) What are the comparative merits of explaining the non-linear remnant using noise or non-linear transformations? (ii) Can non-linear transformations represent serial motor decision making within the sensorimotor feedback loop intrinsic to tracking? Twelve participants (instructed to act in three prescribed ways) manually controlled two systems (1st and 2nd order) subject to a periodic multi-sine disturbance. Joystick power was analysed using three models, continuous-linear-control (CC), continuous-linear-control with calculated noise spectrum (CCN), and intermittent control with aperiodic sampling triggered by prediction error thresholds (IC). Unlike the linear mechanism, the intermittent control mechanism explained the majority of total power (linear and remnant) (77-87% vs. 8-48%, IC vs. CC). Between conditions, IC used thresholds and distributions of open loop intervals consistent with, respectively, instructions and previous measured, model independent values; whereas CCN required changes in noise spectrum deviating from broadband, signal dependent noise. We conclude that manual tracking uses open loop predictive control with aperiodic sampling. Because aperiodic sampling is inherent to serial decision making within previously identified, specific frontal, striatal and parietal networks we suggest that these structures are intimately involved in visuo-manual tracking. © 2017 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.

Annealing behaviour of ion tracks in olivine, apatite and britholite

NASA Astrophysics Data System (ADS)

Afra, B.; Lang, M.; Bierschenk, T.; Rodriguez, M. D.; Weber, W. J.; Trautmann, C.; Ewing, R. C.; Kirby, N.; Kluth, P.

2014-05-01

Ion tracks were created in olivine from San Carlos, Arizona (95% Mg2SiO4), apatite (Ca5(PO4)3(F,Cl,O)) from Durango, Mexico, and synthetic silicates with the apatite structure: Nd8Sr2(SiO4)6O2 and Nd8Ca2(SiO4)6O2 using 1.6 and 2.2 GeV Au ions. The morphology and annealing behaviour of the tracks were investigated by means of synchrotron based small angle X-ray scattering in combination with ex situ annealing. Tracks in olivine annealed above ∼400 °C undergo a significant change in track radius due to recrystallisation of the damage tracks. At temperatures higher than 620 °C, the scattering images indicate fragmentation of the track cylinders into smaller subsections. Ion tracks were annealed at elevated temperatures up to 400 °C in the Durango and Ca-britholite, and up to 560 °C in Sr-britholite. While there was a significant change in the track radii in the Durango apatite, tracks in the two synthetic samples remained almost unchanged.

Sex and Adolescent Ethanol Exposure Influence Pavlovian Conditioned Approach

PubMed Central

Madayag, Aric C.; Stringfield, Sierra J.; Reissner, Kathryn J.; Boettiger, Charlotte A.; Robinson, Donita L.

2017-01-01

BACKGROUND Alcohol use among adolescents is widespread and a growing concern due to long-term behavioral deficits, including altered Pavlovian behavior, that potentially contribute to addiction vulnerability. We tested the hypothesis that adolescent intermittent ethanol (AIE) exposure alters Pavlovian behavior in males and females as measured by a shift from goal-tracking to sign-tracking. Additionally, we investigated GLT-1, an astrocytic glutamate transporter, as a potential contributor to a sign-tracking phenotype. METHODS Male and female Sprague-Dawley rats were exposed to AIE (5g/Kg, intragastric) or water intermittently 2 days on, 2 days off from postnatal day (P) 25 to 54. Around P70, animals began 20 daily sessions of Pavlovian conditioned approach, where they learned that a cue predicted non-contingent reward delivery. Lever pressing indicated interaction with the cue, or sign-tracking, and receptacle entries indicated approach to the reward delivery location, or goal-tracking. To test for effects of AIE on nucleus accumbens excitatory signaling, we isolated membrane subfractions and measured protein levels of the glutamate transporter GLT-1 after animals completed behavior as a measure of glutamate homeostasis. RESULTS Females exhibited elevated sign-tracking compared to males with significantly more lever presses, faster latency to first lever press, and greater probability to lever press in a trial. AIE significantly increased lever pressing while blunting goal tracking, as indicated by fewer cue-evoked receptacle entries, slower latency to receptacle entry, and lower probability to enter the receptacle in a trial. No significant Sex-by-Exposure interactions were observed in sign- or goal-tracking metrics. Moreover, we found no significant effects of Sex or Exposure on membrane GLT-1 expression in the nucleus accumbens. CONCLUSIONS Females exhibited enhanced sign-tracking compared to males, while AIE decreased goal-tracking compared to control exposure. Our findings support the hypothesis that adolescent binge ethanol can shift conditioned behavior from goal- to cue-directed in Pavlovian conditioned approach, especially in females. PMID:28196273

Sex and Adolescent Ethanol Exposure Influence Pavlovian Conditioned Approach.

PubMed

Madayag, Aric C; Stringfield, Sierra J; Reissner, Kathryn J; Boettiger, Charlotte A; Robinson, Donita L

2017-04-01

Alcohol use among adolescents is widespread and a growing concern due to long-term behavioral deficits, including altered Pavlovian behavior, that potentially contribute to addiction vulnerability. We tested the hypothesis that adolescent intermittent ethanol (AIE) exposure alters Pavlovian behavior in males and females as measured by a shift from goal-tracking to sign-tracking. Additionally, we investigated GLT-1, an astrocytic glutamate transporter, as a potential contributor to a sign-tracking phenotype. Male and female Sprague-Dawley rats were exposed to AIE (5 g/kg, intragastric) or water intermittently 2 days on and 2 days off from postnatal day (P) 25 to 54. Around P70, animals began 20 daily sessions of Pavlovian conditioned approach (PCA), where they learned that a cue predicted noncontingent reward delivery. Lever pressing indicated interaction with the cue, or sign-tracking, and receptacle entries indicated approach to the reward delivery location, or goal-tracking. To test for effects of AIE on nucleus accumbens (NAcc) excitatory signaling, we isolated membrane subfractions and measured protein levels of the glutamate transporter GLT-1 after animals completed behavior as a measure of glutamate homeostasis. Females exhibited elevated sign-tracking compared to males with significantly more lever presses, faster latency to first lever press, and greater probability to lever press in a trial. AIE significantly increased lever pressing while blunting goal-tracking, as indicated by fewer cue-evoked receptacle entries, slower latency to receptacle entry, and lower probability to enter the receptacle in a trial. No significant sex-by-exposure interactions were observed in sign- or goal-tracking metrics. Moreover, we found no significant effects of sex or exposure on membrane GLT-1 expression in the NAcc. Females exhibited enhanced sign-tracking compared to males, while AIE decreased goal-tracking compared to control exposure. Our findings support the hypothesis that adolescent binge ethanol can shift conditioned behavior from goal- to cue-directed in PCA, especially in females. Copyright © 2017 by the Research Society on Alcoholism.

Characterization of Escherichia coli isolates from different fecal sources by means of classification tree analysis of fatty acid methyl ester (FAME) profiles.

PubMed

Seurinck, Sylvie; Deschepper, Ellen; Deboch, Bishaw; Verstraete, Willy; Siciliano, Steven

2006-03-01

Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.

Are Isolated Indigenous Populations Headed toward Extinction?

PubMed

Walker, Robert S; Kesler, Dylan C; Hill, Kim R

2016-01-01

At least 50 indigenous groups spread across lowland South America remain isolated and have only intermittent and mostly hostile interactions with the outside world. Except in emergency situations, the current policy of governments in Brazil, Colombia, and Peru towards isolated tribes is a "leave them alone" strategy, in which isolated groups are left uncontacted. However, these no-contact policies are based on the assumption that isolated populations are healthy and capable of persisting in the face of mounting external threats, and that they can maintain population viability in the long-term. Here, we test this assumption by tracking the sizes and movements of cleared horticultural areas made by 8 isolated groups over the last 10-14 years. We used deforestation data derived from remote sensing Landsat satellite sensors to identify clearings, and those were then validated and assessed with high-resolution imagery. We found only a single example of a relatively large and growing population (c. 50 cleared ha and 400 people), whereas all of the other 7 groups exhibited much smaller villages and gardens with no sizable growth through time. These results indicated that the smaller groups are critically endangered, and it prompts an urgent re-thinking of policies toward isolated populations, including plans for well-organized contacts that may help save lives and rescue isolated indigenous populations from imminent extinction.

Hawaiian lavas: a window into mantle dynamics

NASA Astrophysics Data System (ADS)

Jones, Tim; Davies, Rhodri; Campbell, Ian

2017-04-01

The emergence of double track volcanism at Hawaii has traditionally posed two problems: (i) the physical emergence of two parallel chains of volcanoes at around 3 Ma, named the Loa and Kea tracks after the largest volcanoes in their sequence, and (ii) the systematic geochemical differences between the erupted lavas along each track. In this study, we dissolve this distinction by providing a geodynamical explanation for the physical emergence of double track volcanism at 3 Ma and use numerical models of the Hawaiian plume to illustrate how this process naturally leads to each volcanic track sampling distinct mantle compositions, which accounts for much of the geochemical characteristics of the Loa and Kea trends.

[Anaerobic bacteria isolated from patients with suspected anaerobic infections].

PubMed

Ercis, Serpil; Tunçkanat, Ferda; Hasçelik, Gülşen

2005-10-01

The study involved 394 clinical samples sent to the Clinical Microbiology Laboratory of Hacettepe University Adult Hospital between January 1997 and May 2004 for anaerobic cultivation. Since multiple cultures from the same clinical samples of the same patient were excluded, the study was carried on 367 samples. The anaerobic cultures were performed in anaerobic jar using AnaeroGen kits (Oxoid, Basingstoke, U.K.) or GENbox (bioMérieux, Lyon, France). The isolates were identified by both classical methods and "BBL Crystal System" (Becton Dickinson, U.S.A.). While no growth was detected in 120 (32.7%) of the clinical samples studied, in 144 samples (39.2%) only aerobes, in 28 (7.6%) only anaerobes and in 75 (20.5%) of the samples both aerobes and anaerobes were isolated. The number of the anaerobic isolates was 217 from 103 samples with anaerobic growth. Of these 103 samples 15 showed single bacterial growth whereas in 88 samples multiple bacterial isolates were detected. Anaerobic isolates consisted of 92 Gram negative bacilli (Bacteroides spp. 50, Prevotella spp. 14, Porphyromonas spp. 10, Fusobacterium spp. 7, Tisierella spp. 2, unidentified 9), 57 Gram positive bacilli (Clostridium spp.17, Propionibacterium spp. 16, Lactobacillus spp. 8, Actinomyces spp. 5, Eubacterium spp. 2, Bifidobacterium adolescentis 1, Mobiluncus mulieris 1, unidentified nonspore forming rods 7), 61 Gram positive cocci (anaerobic cocci 44, microaerophilic cocci 17), and 7 Gram negative cocci (Veillonella spp.). In conclusion, in the samples studied with prediagnosis of anaerobic infection, Bacteroides spp. (23%) were the most common bacteria followed by anaerobic Gram positive cocci (20.3%) and Clostridium spp (7.8%).

Revealing hidden clonal complexity in Mycobacterium tuberculosis infection by qualitative and quantitative improvement of sampling.

PubMed

Pérez-Lago, L; Palacios, J J; Herranz, M; Ruiz Serrano, M J; Bouza, E; García-de-Viedma, D

2015-02-01

The analysis of microevolution events, its functional relevance and impact on molecular epidemiology strategies, constitutes one of the most challenging aspects of the study of clonal complexity in infection by Mycobacterium tuberculosis. In this study, we retrospectively evaluated whether two improved sampling schemes could provide access to the clonal complexity that is undetected by the current standards (analysis of one isolate from one sputum). We evaluated in 48 patients the analysis by mycobacterial interspersed repetitive unit-variable number tandem repeat of M. tuberculosis isolates cultured from bronchial aspirate (BAS) or bronchoalveolar lavage (BAL) and, in another 16 cases, the analysis of a higher number of isolates from independent sputum samples. Analysis of the isolates from BAS/BAL specimens revealed clonal complexity in a very high proportion of cases (5/48); in most of these cases, complexity was not detected when the isolates from sputum samples were analysed. Systematic analysis of isolates from multiple sputum samples also improved the detection of clonal complexity. We found coexisting clonal variants in two of 16 cases that would have gone undetected in the analysis of the isolate from a single sputum specimen. Our results suggest that analysis of isolates from BAS/BAL specimens is highly efficient for recording the true clonal composition of M. tuberculosis in the lungs. When these samples are not available, we recommend increasing the number of isolates from independent sputum specimens, because they might not harbour the same pool of bacteria. Our data suggest that the degree of clonal complexity in tuberculosis has been underestimated because of the deficiencies inherent in a simplified procedure. Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Multilocus Sequence Typing of Cronobacter Strains Isolated from Retail Foods and Environmental Samples.

PubMed

Killer, Jiří; Skřivanová, Eva; Hochel, Igor; Marounek, Milan

2015-06-01

Cronobacter spp. are bacterial pathogens that affect children and immunocompromised adults. In this study, we used multilocus sequence typing (MLST) to determine sequence types (STs) in 11 Cronobacter spp. strains isolated from retail foods, 29 strains from dust samples obtained from vacuum cleaners, and 4 clinical isolates. Using biochemical tests, species-specific polymerase chain reaction, and MLST analysis, 36 strains were identified as Cronobacter sakazakii, and 6 were identified as Cronobacter malonaticus. In addition, one strain that originated from retail food and one from a dust sample from a vacuum cleaner were identified on the basis of MLST analysis as Cronobacter dublinensis and Cronobacter turicensis, respectively. Cronobacter spp. strains isolated from the retail foods were assigned to eight different MLST sequence types, seven of which were newly identified. The strains isolated from the dust samples were assigned to 7 known STs and 14 unknown STs. Three clinical isolates and one household dust isolate were assigned to ST4, which is the predominant ST associated with neonatal meningitis. One clinical isolate was classified based on MLST analysis as Cronobacter malonaticus and belonged to an as-yet-unknown ST. Three strains isolated from the household dust samples were assigned to ST1, which is another clinically significant ST. It can be concluded that Cronobacter spp. strains of different origin are genetically quite variable. The recovery of C. sakazakii strains belonging to ST1 and ST4 from the dust samples suggests the possibility that contamination could occur during food preparation. All of the novel STs and alleles for C. sakazakii, C. malonaticus, C. dublinensis, and C. turicensis determined in this study were deposited in the Cronobacter MLST database available online ( http://pubmlst.org/cronobacter/).

Influence of the amyloid dye Congo red on curli, cellulose, and the extracellular matrix in E. coli during growth and matrix purification.

PubMed

Reichhardt, Courtney; McCrate, Oscar A; Zhou, Xiaoxue; Lee, Jessica; Thongsomboon, Wiriya; Cegelski, Lynette

2016-11-01

Microbial biofilms are communities of cells characterized by a hallmark extracellular matrix (ECM) that confers functional attributes to the community, including enhanced cohesion, adherence to surfaces, and resistance to external stresses. Understanding the composition and properties of the biofilm ECM is crucial to understanding how it functions and protects cells. New methods to isolate and characterize ECM are emerging for different biofilm systems. Solid-state nuclear magnetic resonance was used to quantitatively track the isolation of the insoluble ECM from the uropathogenic Escherichia coli strain UTI89 and understand the role of Congo red in purification protocols. UTI89 assembles amyloid-integrated biofilms when grown on YESCA nutrient agar. The ECM contains curli amyloid fibers and a modified form of cellulose. Biofilms formed by UTI89 and other E. coli and Salmonella strains are often grown in the presence of Congo red to visually emphasize wrinkled agar morphologies and to score the production of ECM. Congo red is a hallmark amyloid-binding dye and binds to curli, yet also binds to cellulose. We found that growth in Congo red enabled more facile extraction of the ECM from UTI89 biofilms and facilitates isolation of cellulose from the curli mutant, UTI89ΔcsgA. Yet, Congo red has no influence on the isolation of curli from curli-producing cells that do not produce cellulose. Sodium dodecyl sulfate can remove Congo red from curli, but not from cellulose. Thus, Congo red binds strongly to cellulose and possibly weakens cellulose interactions with the cell surface, enabling more complete removal of the ECM. The use of Congo red as an extracellular matrix purification aid may be applied broadly to other organisms that assemble extracellular amyloid or cellulosic materials. Graphical abstract Solid-state NMR was used to quantitatively track the isolation of the insoluble amyloid-associated ECM from uropathogenic E. coli and understand the role of Congo red in purification protocols.

Dynamic behaviour of river colloidal and dissolved organic matter through cross-flow ultrafiltration system.

PubMed

Wilding, Andrew; Liu, Ruixia; Zhou, John L

2005-07-01

Through cross-flow filtration (CFF) with a 1-kDa regenerated cellulose Pellicon 2 module, the ultrafiltration characteristics of river organic matter from Longford Stream, UK, were investigated. The concentration of organic carbon (OC) in the retentate in the Longford Stream samples increased substantially with the concentration factor (cf), reaching approximately 40 mg/L at cf 15. The results of dissolved organic carbon (DOC) and colloidal organic carbon (COC) analysis, tracking the isolation of colloids from river waters, show that 2 mg/L of COC was present in those samples and good OC mass balance (77-101%) was achieved. Fluorescence measurements were carried out for the investigation of retentate and permeate behaviour of coloured dissolved organic materials (CDOM). The concentrations of CDOM in both the retentate and permeate increased with increasing cf, although CDOM were significantly more concentrated in the retentate. The permeation model expressing the correlation between log[CDOM] in the permeate and logcf was able to describe the permeation behaviour of CDOM in the river water with regression coefficients (r(2)) of 0.94 and 0.98. Dry weight analysis indicated that the levels of organic colloidal particles were from 49 to 71%, and between 29 and 51% of colloidal particles present were inorganic. COC as a percentage of DOC was found to be 10-16% for Longford Stream samples.

Flux focusing eddy current probe

NASA Technical Reports Server (NTRS)

Simpson, John W. (Inventor); Clendenin, C. Gerald (Inventor); Fulton, James P. (Inventor); Wincheski, Russell A. (Inventor); Todhunter, Ronald G. (Inventor); Namkung, Min (Inventor); Nath, Shridhar C. (Inventor)

1997-01-01

A flux-focusing electromagnetic sensor which uses a ferromagnetic flux-focusing lens simplifies inspections and increases detectability of fatigue cracks and material loss in high conductivity material. The unique feature of the device is the ferrous shield isolating a high-turn pick-up coil from an excitation coil. The use of the magnetic shield is shown to produce a null voltage output across the receiving coil in the presence of an unflawed sample. A redistribution of the current flow in the sample caused by the presence of flaws, however, eliminates the shielding condition and a large output voltage is produced, yielding a clear unambiguous flaw signal. The maximum sensor output is obtained when positioned symmetrically above the crack. Hence, by obtaining the position of the maximum sensor output, it is possible to track the fault and locate the area surrounding its tip. The accuracy of tip location is enhanced by two unique features of the sensor; a very high signal-to-noise ratio of the probe's output which results in an extremely smooth signal peak across the fault, and a rapidly decaying sensor output outside a small area surrounding the crack tip which enables the region for searching to be clearly defined. Under low frequency operation, material thinning due to corrosion damage causes an incomplete shielding of the pick-up coil. The low frequency output voltage of the probe is therefore a direct indicator of the thickness of the test sample.

Isolation of antimicrobial producing Actinobacteria from soil samples.

PubMed

Elbendary, Afaf Ahmed; Hessain, Ashgan Mohamed; El-Hariri, Mahmoud Darderi; Seida, Ahmed Adel; Moussa, Ihab Mohamed; Mubarak, Ayman Salem; Kabli, Saleh A; Hemeg, Hassan A; El Jakee, Jakeen Kamal

2018-01-01

Emergence of multidrug resistant bacteria has made the search for novel bioactive compounds from natural and unexplored habitats a necessity. Actinobacteria have important bioactive substances. The present study investigated antimicrobial activity of Actinobacteria isolated from soil samples of Egypt. One hundred samples were collected from agricultural farming soil of different governorates. Twelve isolates have produced activity against the tested microorganisms ( S. aureus , Bacillus cereus , E. coli , K. pneumoniae , P. aeruginosa , S. Typhi, C. albicans , A. niger and A. flavus ). By VITEK 2 system version: 07.01 the 12 isolates were identified as Kocuria kristinae , Kocuria rosea , Streptomyces griseus , Streptomyces flaveolus and Actinobacteria . Using ethyl acetate extraction method the isolates culture's supernatants were tested by diffusion method against indicator microorganisms. These results indicate that Actinobacteria isolated from Egypt farms could be sources of antimicrobial bioactive substances.

Tracking Matrix Effects in the Analysis of DNA Adducts of Polycyclic Aromatic Hydrocarbons

PubMed Central

Klaene, Joshua J.; Flarakos, Caroline; Glick, James; Barret, Jennifer T.; Zarbl, Helmut; Vouros, Paul

2015-01-01

LC-MS using electrospray ionization is currently the method of choice in bio-organic analysis covering a wide range of applications in a broad spectrum of biological media. The technique is noted for its high sensitivity but one major limitation which hinders achievement of its optimal sensitivity is the signal suppression due to matrix inferences introduced by the presence of co-extracted compounds during the sample preparation procedure. The analysis of DNA adducts of common environmental carcinogens is particularly sensitive to such matrix effects as sample preparation is a multistep process which involves “contamination” of the sample due to the addition of enzymes and other reagents for digestion of the DNA in order to isolate the analyte(s). This problem is further exacerbated by the need to reach low levels of quantitation (LOQ in the ppb level) while also working with limited (2-5 μg) quantities of sample. We report here on the systematic investigation of ion signal suppression contributed by each individual step involved in the sample preparation associated with the analysis of DNA adducts of polycyclic aromatic hydrocarbon (PAH) using as model analyte dG-BaP, the deoxyguanosine adduct of benzo[a]pyrene (BaP). The individual matrix contribution of each one of these sources to analyte signal was systematically addressed as were any interactive effects. The information was used to develop a validated analytical protocol for the target biomarker at levels typically encountered in vivo using as little as 2 μg of DNA and applied to a dose response study using a metabolically competent cell line. PMID:26607319

Measurement of the bottom hadron lifetime at the Z 0 resonancce

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujino, Donald Hideo

1992-06-01

We have measured the bottom hadron lifetime from bmore » $$\\bar{b}$$ events produced at the Z 0 resonance. Using the precision vertex detectors of the Mark II detector at the Stanford Linear Collider, we developed an impact parameter tag to identify bottom hadrons. The vertex tracking system resolved impact parameters to 30 μm for high momentum tracks, and 70 μm for tracks with a momentum of 1 GeV. We selected B hadrons with an efficiency of 40% and a sample purity of 80%, by requiring there be at least two tracks in a single jet that significantly miss the Z 0 decay vertex. From a total of 208 hadronic Z 0 events collected by the Mark II detector in 1990, we tagged 53 jets, of which 22 came from 11 double-tagged events. The jets opposite the tagged ones, referred as the ``untagged`` sample, are rich in B hadrons and unbiased in B decay times. The variable Σδ is the sum of impact parameters from tracks in the jet, and contains vital information on the B decay time. We measured the B lifetime from a one-parameter likelihood fit to the untagged Σδ distribution, obtaining τ b = 1.53 $$+0.55\\atop{-0.45}$$ ± 0.16 ps which agrees with the current world average. The first error is statistical and the second is systematic. The systematic error was dominated by uncertainties in the track resolution function. As a check, we also obtained consistent results using the Σδ distribution from the tagged jets and from the entire hadronic sample without any bottom enrichment.« less

Measurement of the bottom hadron lifetime at the Z sup 0 resonancce

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujino, D.H.

1992-06-01

We have measured the bottom hadron lifetime from b{bar b} events produced at the Z{sup 0} resonance. Using the precision vertex detectors of the Mark II detector at the Stanford Linear Collider, we developed an impact parameter tag to identify bottom hadrons. The vertex tracking system resolved impact parameters to 30 {mu}m for high momentum tracks, and 70 {mu}m for tracks with a momentum of 1 GeV. We selected B hadrons with an efficiency of 40% and a sample purity of 80%, by requiring there be at least two tracks in a single jet that significantly miss the Z{sup 0}more » decay vertex. From a total of 208 hadronic Z{sup 0} events collected by the Mark II detector in 1990, we tagged 53 jets, of which 22 came from 11 double-tagged events. The jets opposite the tagged ones, referred as the untagged'' sample, are rich in B hadrons and unbiased in B decay times. The variable {Sigma}{delta} is the sum of impact parameters from tracks in the jet, and contains vital information on the B decay time. We measured the B lifetime from a one-parameter likelihood fit to the untagged {Sigma}{delta} distribution, obtaining {tau}{sub b} = 1.53{sub {minus}0.45}{sup +0.55}{plus minus}0.16 ps which agrees with the current world average. The first error is statistical and the second is systematic. The systematic error was dominated by uncertainties in the track resolution function. As a check, we also obtained consistent results using the {Sigma}{delta} distribution from the tagged jets and from the entire hadronic sample without any bottom enrichment.« less

Irradiation of nuclear track emulsions with thermal neutrons, heavy ions, and muons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Artemenkov, D. A., E-mail: artemenkov@lhe.jinr.ru; Bradnova, V.; Zaitsev, A. A.

Exposures of test samples of nuclear track emulsion were analyzed. Angular and energy correlations of products originating from the thermal-neutron-induced reaction n{sub th} +{sup 10} B → {sup 7} Li + (γ)+ α were studied in nuclear track emulsions enriched in boron. Nuclear track emulsions were also irradiated with {sup 86}Kr{sup +17} and {sup 124}Xe{sup +26} ions of energy about 1.2 MeV per nucleon. Measurements of ranges of heavy ions in nuclear track emulsionsmade it possible to determine their energies on the basis of the SRIM model. The formation of high-multiplicity nuclear stars was observed upon irradiating nuclear track emulsionsmore » with ultrarelativistic muons. Kinematical features studied in this exposure of nuclear track emulsions for events of the muon-induced splitting of carbon nuclei to three alpha particles are indicative of the nucleardiffraction interaction mechanism.« less

A comparison of surface water natural organic matter in raw filtered water samples, XAD, and reverse osmosis isolates.

PubMed

Maurice, Patricia A; Pullin, Michael J; Cabaniss, Stephen E; Zhou, Qunhui; Namjesnik-Dejanovic, Ksenija; Aiken, George R

2002-05-01

This research compared raw filtered waters (RFWs), XAD resin isolates (XAD-8 and XAD-4), and reverse osmosis (RO) isolates of several surface water samples from McDonalds Branch, a small freshwater fen in the New Jersey Pine Barrens (USA). RO and XAD-8 are two of the most common techniques used to isolate natural organic matter (NOM) for studies of composition and reactivity; therefore, it is important to understand how the isolates differ from bulk (unisolated) samples and from one another. Although, any comparison between the isolation methods needs to consider that XAD-8 is specifically designed to isolate the humic fraction, whereas RO concentrates a broad range of organic matter and is not specific to humics. The comparison included for all samples: weight average molecular weight (Mw), number average molecular weight (Mn), polydispersity (rho), absorbance at 280 nm normalized to moles C (epsilon280) (RFW and isolates); and for isolates only: elemental analysis, % carbon distribution by 13C NMR, and aqueous FTIR spectra. As expected, RO isolation gave higher yield of NOM than XAD-8, but also higher ash content, especially Si and S. Mw decreased in the order: RO > XAD-8 > RFW > XAD-4. The Mw differences of isolates compared with RFW may be due to selective isolation (fractionation), or possibly in the case of RO to condensation or coagulation during isolation. 13C NMR results were roughly similar for the two methods, but the XAD-8 isolate was slightly higher in 'aromatic' C and the RO isolate was slightly higher in heteroaliphatic and carbonyl C. Infrared spectra indicated a higher carboxyl content for the XAD-8 isolates and a higher ester:carboxyl ratio for the RO isolates. The spectroscopic data thus are consistent with selective isolation of more hydrophobic compounds by XAD-8, and also with potential ester hydrolysis during that process, although further study is needed to determine whether ester hydrolysis does indeed occur. Researchers choosing between XAD and RO isolation methods for NOM need to consider first the purpose of the isolation; i.e., whether humic fractionation is desirable. Beyond that, they should consider the C yield and ash content, as well as the potential for alteration of NOM by ester hydrolysis (XAD) or condensation/coagulation (RO). Furthermore, the RO and XAD methods produce different fractions or isolates so that researchers should be careful when comparing the compositions and reactivities of NOM samples isolated by these two different techniques.

A comparison of surface water natural organic matter in raw filtered water samples, XAD, and reverse osmosis isolates

USGS Publications Warehouse

Maurice, P.A.; Pullin, M.J.; Cabaniss, S.E.; Zhou, Q.; Namjesnik-Dejanovic, K.; Aiken, G.R.

2002-01-01

This research compared raw filtered waters (RFWs), XAD resin isolates (XAD-8 and XAD-4), and reverse osmosis (RO) isolates of several surface water samples from McDonalds Branch, a small freshwater fen in the New Jersey Pine Barrens (USA). RO and XAD-8 are two of the most common techniques used to isolate natural organic matter (NOM) for studies of composition and reactivity; therefore, it is important to understand how the isolates differ from bulk (unisolated) samples and from one another. Although, any comparison between the isolation methods needs to consider that XAD-8 is specifically designed to isolate the humic fraction, whereas RO concentrates a broad range of organic matter and is not specific to humics. The comparison included for all samples: weight average molecular weight (Mw), number average molecular weight (Mn), polydispersity (??), absorbance at 280nm normalized to moles C (??280) (RFW and isolates); and for isolates only: elemental analysis, % carbon distribution by 13C NMR, and aqueous FTIR spectra. As expected, RO isolation gave higher yield of NOM than XAD-8, but also higher ash content, especially Si and S. Mw decreased in the order: RO>XAD-8>RFW>XAD-4. The Mw differences of isolates compared with RFW may be due to selective isolation (fractionation), or possibly in the case of RO to condensation or coagulation during isolation. 13C NMR results were roughly similar for the two methods, but the XAD-8 isolate was slightly higher in 'aromatic' C and the RO isolate was slightly higher in heteroaliphatic and carbonyl C. Infrared spectra indicated a higher carboxyl content for the XAD-8 isolates and a higher ester:carboxyl ratio for the RO isolates. The spectroscopic data thus are consistent with selective isolation of more hydrophobic compounds by XAD-8, and also with potential ester hydrolysis during that process, although further study is needed to determine whether ester hydrolysis does indeed occur. Researchers choosing between XAD and RO isolation methods for NOM need to consider first the purpose of the isolation; i.e., whether humic fractionation is desirable. Beyond that, they should consider the C yield and ash content, as well as the potential for alteration of NOM by ester hydrolysis (XAD) or condensation/coagulation (RO). Furthermore, the RO and XAD methods produce different fractions or isolates so that researchers should be careful when comparing the compositions and reactivities of NOM samples isolated by these two different techniques. ?? 2002 Published by Elsevier Science Ltd.

Public School Choice and Racial Sorting: An Examination of Charter Schools in Indianapolis

ERIC Educational Resources Information Center

Stein, Marc L.

2015-01-01

There has been a long-standing concern among education researchers and policy makers that public school choice may lead to increased racial isolation. Improving on aggregate comparisons, I examine the sorting of students into charter schools by tracking individual students from their charter school of enrollment back to the school they were…

Isolating weather effects from seasonal activity patterns of a temperate North American Colubrid

Treesearch

Andrew D. George; Frank R. III Thompson; John Faaborg

2015-01-01

Forecasting the effects of climate change on threatened ecosystems and species will require an understanding of how weather influences processes that drive population dynamics. We have evaluated weather effects on activity patterns of western ratsnakes, a widespread predator of birds and small mammals in eastern North America. From 2010-2013 we radio-tracked 53...

The Educationalising of Early Childhood in Aotearoa New Zealand: Tracking "Free Play" 1940s-2010

ERIC Educational Resources Information Center

Stover, Sue

2016-01-01

Geographically isolated in the south-west Pacific but intellectually and culturally connected to Western Europe, Aotearoa New Zealand's early childhood education sector is a unique mix of influences. The imprint of progressive education is evident in a legacy of "free play" programmes, yet its national curriculum is built on the…

Persistence of F-specific RNA phages in surface waters from a produce production region along the central coast of California

USDA-ARS?s Scientific Manuscript database

F+ RNA coliphages (FRNA) are used to source-track fecal contamination and as surrogates for enteric pathogen persistence in the environment. However, the environmental persistence of FRNA is not clearly understood and thus we evaluated the survival of prototype and environmental isolates of FRNA rep...

Assessing Performance Tradeoffs in Undersea Distributed Sensor Networks

DTIC Science & Technology

2006-09-01

time. We refer to this process as track - before - detect (see [5] for a description), since the final determination of a target presence is not made until...expressions for probability of successful search and probability of false search for modeling the track - before - detect process. We then describe a numerical...random manner (randomly sampled from a uniform distribution). II. SENSOR NETWORK PERFORMANCE MODELS We model the process of track - before - detect by

NPP ATMS Prelaunch Performance Assessment and Sensor Data Record Validation

DTIC Science & Technology

2011-04-29

TMS to sense scattering of cold cosmic background radiance from the tops of preci pitating clouds allows the retrieval of preCipitation intensities...operational and research missions over the last 40 years. The Cross-track Infrared and Microwave Sounding Suite (CrIMSS), consisting of the Cross-track...Infrared Sounder (CrrS) and the flIst space-based, Nyquist-sampled cross-track microwave sounder, the Advanced Technology Microwave Sounder (ATMS), will

Tracking vaginal, anal and oral infection in a mouse papillomavirus infection model.

PubMed

Hu, Jiafen; Budgeon, Lynn R; Cladel, Nancy M; Balogh, Karla; Myers, Roland; Cooper, Timothy K; Christensen, Neil D

2015-12-01

Noninvasive and practical techniques to longitudinally track viral infection are sought after in clinical practice. We report a proof-of-principle study to monitor the viral DNA copy number using a newly established mouse papillomavirus (MmuPV1) mucosal infection model. We hypothesized that viral presence could be identified and quantified by collecting lavage samples from cervicovaginal, anal and oral sites. Nude mice infected at these sites with infectious MmuPV1 were tracked for up to 23 weeks starting at 6 weeks post-infection. Viral DNA copy number was determined by SYBR Green Q-PCR analysis. In addition, we tracked viral DNA load through three complete oestrous cycles to pinpoint whether there was a correlation between the DNA load and the four stages of the oestrous cycle. Our results showed that high viral DNA copy number was reproducibly detected from both anal and cervicovaginal lavage samples. The infection and disease progression were further confirmed by histology, cytology, in situ hybridization, immunohistochemistry and transmission electron microscopy. Interestingly, the viral copy number fluctuated over the oestrous cycle, with the highest level at the oestrus stage, implying that multiple sampling might be necessary to provide a reliable diagnosis. Virus DNA was detected in oral lavage samples at a later time after infection. Lower viral DNA load was found in oral samples when compared with those in anal and vaginal tracts. To our knowledge, our study is the first in vivo study to sequentially monitor papillomavirus infection from mucosal anal, oral and vaginal tracts in a preclinical model.

Insufficiency of the Kanagawa hemolytic test for detecting pathogenic Vibrio parahaemolyticus in Shanghai, China.

PubMed

Hongping, Wang; Jilun, Zhang; Ting, Jiang; Yixi, Bao; Xiaoming, Zhou

2011-01-01

We evaluated the Kanagawa hemolytic test and tdh gene test for accuracy in identifying pathogenic Vibrio parahaemolyticus isolates in Shanghai. One hundred and seventy-two V. parahaemolyticus isolates were collected from diarrhea patients, freshly harvested sea fish, or fresh water samples. Statistical data for the Kanagawa hemolytic test and tdh gene test were compared. There were 83.51% isolates (81/97) from patients and 22.22% isolates (10/45) from sea-fish positive for the tdh gene. However, none of 30 isolates from fresh water samples were tdh-positive. Positive Kanagawa hemolytic tests were obtained in 88.66%, 46.67%, and 76.67% of isolates, which were from patients, sea fish, and fresh water samples, respectively. Positive rates of the Kanagawa hemolytic tests and the tdh gene tests were significantly different in isolates from those 3 sources (P < 0.001). The tdh gene test showed higher specificity than the Kanagawa hemolytic test on identifying pathogenic V. parahaemolyticus isolates in Shanghai, China. Copyright © 2011 Elsevier Inc. All rights reserved.

Testing of male sockeye salmon (Oncorhynchus nerka) and steelhead trout (Salmo gairdneri) for infectious hematopoietic necrosis virus

USGS Publications Warehouse

Mulcahy, D.; Pascho, R.J.; Batts, W.N.

1987-01-01

Infectious hematopoietic necrosis (IHN) virus has been isolated only rarely from whole milt samples of male sockeye salmon (Oncorhynchus nerka). In 3 yr of testing, virus incidences in males ranged from 0 to 13% when milt was sampled but were 60–100% with spleen or kidney. When IHN virus was isolated from sockeye salmon milt at titers less than 3.00 log10 plaque-forming units (pfu)/mL, the level of virus in the kidney or spleen exceeded 7.00 log10 pfu/g. Higher rates of IHN virus isolation from kidney or spleen than from milt were also generally found in steelhead trout (Salmo gairdneri), although the differences were less pronounced than in sockeye salmon. Furthermore, virus was sometimes isolated from steelhead trout milt when the level of virus in kidney or spleen samples was very low, and was recovered from some milt samples when none was isolated from the corresponding spleen sample. When male salmonids are tested for IHN virus, kidney or spleen samples are superior to whole milt, but milt should be included for critical examinations.

Prevalence, bioserotyping and antibiotic resistance of pathogenic Yersinia enterocolitica detected in pigs at slaughter in Sardinia.

PubMed

Fois, Federica; Piras, Francesca; Torpdahl, Mia; Mazza, Roberta; Ladu, Daniela; Consolati, Simonetta G; Spanu, Carlo; Scarano, Christian; De Santis, Enrico P L

2018-06-13

The aims of the present study were to determine Yersinia enterocolitica prevalence in finishing pigs and piglets at slaughter and to characterize the isolates in terms of bioserotype, virulence profile, antimicrobial susceptibility and genetic diversity. During the years 2013-2014, nine pig slaughterhouses placed in Sardinia (Italy) were visited twice, in order to collect animal samples and scalding water. Overall, 609 samples respectively of tonsils (126), colon content (161), mesenteric lymph nodes (161) and carcass surfaces (161) were collected from 126 finishing pigs and 35 piglets. Moreover, 18 scalding water samples were collected. Samples were analyzed for the detection of Y. enterocolitica according to ISO 10273-2003 standard (with some modifications). With regard to finishing pigs, Y. enterocolitica was detected in 11.9% of colon content samples, 3.2% of tonsils and 2.4% of lymph nodes. In piglets, Y. enterocolitica prevalence was 8.6% in colon content and 2.8% lymph nodes samples. Y. enterocolitica was not detected from carcass surface samples of both finishing pigs and piglets and from scalding water samples. Isolates were bio- and serotyped, tested for the presence of four virulence genes by PCR (ail, ystA, ystB and inv) and for antimicrobial resistance by disc-diffusion method. Among 47 confirmed isolates, 33 (70.2%) belonged to bio-serotype 4:O3, 7 (14.9%) to bio-serotype 2/O:5 and 7 (14.9%) to bio-serotype 1A. Bio-serotype 1A was detected only in isolates of piglets' samples. In bio-serotype 4/O:3 isolates the most common virulence genes were ystA (97.0%), ail (84.8%) and inv (78.8%). In bio-serotype 2/O:5, ail, inv and ystA genes were detected in all of the isolates. All bio-serotype 1A isolates were ystB positive (lacking ail, inv and ystA). All isolates were susceptible to cefotaxime, ceftazidime, chloramphenicol, ciprofloxacin, enrofloxacin, gentamicin, nalidixic acid, sulphonamide, tetracycline and trimethoprim-sulphametoxazole. Resistances to ampicillin and cefalothin were the most common (100%), followed by amoxicillin/clavulanic acid (83.0%) and streptomycin (4.3%). Resistance to amoxicillin/clavulanic acid was detected in 57% of bio-serotype 4/O:3 isolates, 71% of bio-serotype 1A and 100% of bio-serotype 2/O:5 isolates. Two bio-serotype 4/O:3 isolates (6%) were resistant to streptomycin. Thirty-two pathogenic Y. enterocolitica isolates were tested by NotI-PFGE, which identified 5 patterns among bio-serotype 4/O:3 isolates and 2 patterns among bio-serotype 2/O:5 isolates. This study provides epidemiological data about human pathogenic Y. enterocolitica and highlight the role of pigs as a potential source of infection for the consumers in Sardinia. Copyright © 2018. Published by Elsevier B.V.

Tracking of multiple targets using online learning for reference model adaptation.

PubMed

Pernkopf, Franz

2008-12-01

Recently, much work has been done in multiple object tracking on the one hand and on reference model adaptation for a single-object tracker on the other side. In this paper, we do both tracking of multiple objects (faces of people) in a meeting scenario and online learning to incrementally update the models of the tracked objects to account for appearance changes during tracking. Additionally, we automatically initialize and terminate tracking of individual objects based on low-level features, i.e., face color, face size, and object movement. Many methods unlike our approach assume that the target region has been initialized by hand in the first frame. For tracking, a particle filter is incorporated to propagate sample distributions over time. We discuss the close relationship between our implemented tracker based on particle filters and genetic algorithms. Numerous experiments on meeting data demonstrate the capabilities of our tracking approach. Additionally, we provide an empirical verification of the reference model learning during tracking of indoor and outdoor scenes which supports a more robust tracking. Therefore, we report the average of the standard deviation of the trajectories over numerous tracking runs depending on the learning rate.

The biofilm-positive Staphylococcus epidermidis isolates in raw materials, foodstuffs and on contact surfaces in processing plants.

PubMed

Schlegelová, J; Babák, V; Holasová, M; Dendis, M

2008-01-01

Isolates from the "farm to fork" samples (182 isolates from 2779 samples) were examined genotypically (icaAB genes) and phenotypically (in vitro biofilm formation, typical growth on Congo red agar; CRA) with the aim to assess the risk of penetration of virulent strains of Staphylococcus epidermidis into the food chain. The contamination of meat and milk products was significantly higher in comparison with raw materials. Contamination of contact surfaces in the meat-processing plants was significantly lower than that of contact surfaces in the dairy plants. The ica genes (which precondition the biofilm formation) were concurrently detected in 20 isolates that also showed a typical growth on CRA. Two ica operon-negative isolates produced biofilm in vitro but perhaps by an ica-independent mechanism. The surfaces in the dairy plants and the milk products were more frequently contaminated with ica operon-positive strains (2.3 and 1.2 % samples) than the other sample types (0-0.6 % samples).

Identification of Prototheca zopfii from Bovine Mastitis

PubMed Central

Zaini, F; Kanani, A; Falahati, M; Fateh, R; Salimi-Asl, M; Saemi, N; Farahyar, Sh; Kheirabad, A Kargar; Nazeri, M

2012-01-01

Background: The aim of this study was identification of the epidemiology of Prototheca zopfii species from the milk samples of dairy cattle in Isfahan, central Iran. Methods: Milk samples were obtained from 230 dairy cattle, 130 with and 100 without mastitis, in Isfahan. The samples were cultured in Prototheca Isolation Medium (PIM) and Sabouraud’s dextrose agar. All P. zopfii isolates were identified by morphological and biochemical methods. Then, as a confirmatory test they were examined by genotype-specific PCR. Results: Four P. zopfii strains (3.07%) were isolated from the 130 samples of dairy cattle with clinical mastitis and there was no isolation from totally 100 samples of healthy bovines without mastitis. Specific PCR product (about 946 bp) was detected in four isolates. Conclusion: It seems that P. zopfii genotype II plays a key role in affecting bovine mastitis that confirmed other previous studies. Our study was the first, which identified the Prototheca species by traditional and molecular methods in Iran and Middle East as well. PMID:23113230

Clinical effectiveness of late maxillary protraction in cleft lip and palate: a methods paper

PubMed Central

Lee, MK; Lane, C; Azeredo, F; Landsberger, M; Kapadia, H; Sheller, B; Yen, SL

2017-01-01

Objectives A prospective parallel cohort trial was conducted to compare outcomes of patients treated with maxillary protraction vs. LeFort 1 maxillary advancement surgery. Setting and Sample Population The primary site for the clinical trial is Children’s Hospital Los Angeles; the satellite test site is Seattle Children’s Hospital. All patients have isolated cleft lip and palate and a skeletal Class III malocclusion. Material & Methods A total of 50 patients, ages 11–14 will be recruited for the maxillary protraction cohort. The maxillary surgery cohort consists of 50 patients, ages 16–21, who will undergo LeFort 1 maxillary advancement surgery. Patients with additional medical or cognitive handicaps were excluded from the study. Results Current recruitment of patients is on track to complete the study within the proposed recruitment period. Conclusion This observational trial is collecting information that will examine dental, skeletal, financial, and quality of life issues from both research cohorts. PMID:28643931

Legionella detection and subgrouping in water air-conditioning cooling tower systems in Kuwait.

PubMed

Al-Matawah, Qadreyah; Al-Zenki, Sameer; Al-Azmi, Ahmad; Al-Waalan, Tahani; Al-Salameen, Fadila; Hejji, Ahmad Ben

2015-07-01

The main aim of the study was to test for the presence of Legionnaires' disease-causing microorganisms in air-conditioned buildings in Kuwait using molecular technologies. For this purpose, 547 samples were collected from 38 cooling towers for the analysis of Legionella pneumophila. These samples included those from water (n = 178), air (n = 231), and swabs (n = 138). Out of the 547 samples, 226 (41%) samples were presumptive positive for L. pneumophila, with L. pneumophila viable counts in the positive water samples ranging from 1 to 88 CFU/ml. Of the Legionella culture-positive samples, 204 isolates were examined by latex agglutination. These isolates were predominately identified as L. pneumophila serogroup (sg) 2-14. Using the Dresden panel of monoclonal antibodies, 74 representatives isolates were further serogrouped. Results showed that 51% of the isolates belonged to serogroup 7 followed by 1 (18%) and 3 (18%). Serogroups 4 (4%) and 10 (7%) were isolated at a lower frequency, and two isolates could not be assigned to a serogroup. These results indicate the wide prevalence of L. pneumophila serogroup 7 as the predominant serogroup at the selected sampling sites. Furthermore, the 74 L. pneumophila (sg1 = 13; sg3 = 13; sg4 = 3; sg7 = 38; sg10 = 5; sgX = 2) isolates were genotyped using the seven gene protocol sequence-based typing (SBT) scheme developed by the European Working Group for Legionella Infections (EWGLI). The results show that Legionella isolates were discriminated into nine distinct sequence typing (ST) profiles, five of which were new to the SBT database of EWGLI. Additionally, all of the ST1 serogroup 1 isolates were of the OLDA/Oxford subgroup. These baseline data will form the basis for the development of a Legionella environmental surveillance program and used for future epidemiological investigations.

Essential tactics of tissue preparation and matrix nano-spotting for successful compound imaging mass spectrometry.

PubMed

Végvári, Akos; Fehniger, Thomas E; Gustavsson, Lena; Nilsson, Anna; Andrén, Per E; Kenne, Kerstin; Nilsson, Johan; Laurell, Thomas; Marko-Varga, György

2010-04-18

The ultimate goal of MALDI-Imaging Mass Spectrometry (MALDI-IMS) is to achieve spatial localization of analytes in tissue sections down to individual tissue compartments or even at the level of a few cells. With compound tissue imaging, it is possible to track the transportation of an unlabelled, inhaled reference compound within lung tissue, through the application of MALDI-IMS. The procedure for isolation and preparation of lung tissues is found to be crucial in order to preserve the anatomy and structure of the pulmonary compartments. To avoid delocalization of analytes within lung tissue compartments we have applied an in-house designed nano-spotter, based on a microdispenser mounted on an XY table, of which movement and spotting functionality were fully computer controlled. We demonstrate the usefulness of this platform in lung tissue sections isolated from rodent in vivo model, applied to compound tissue imaging as exemplified with the determination of the spatial distribution of (1alpha,2beta,4beta,7beta)-7-[(hydroxidi-2-thienylacetyl)oxy]-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0(2,4)]nonane, also known as tiotropium. We provide details on tissue preparation protocols and sample spotting technology for successful identification of drug in mouse lung tissue by using MALDI-Orbitrap instrumentation. Copyright 2010 Elsevier B.V. All rights reserved.

Systematic Examination of Stardust Bulbous Track Wall Materials

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Clemett, S. J.; Nguyen, A. N.; Berger, E. L.; Keller, L. P.; Messenger, S.

2013-01-01

Analyses of Comet Wild-2 samples returned by NASA's Stardust spacecraft have focused primarily on terminal particles (TPs) or well-preserved fine-grained materials along the track walls [1,2]. However much of the collected material was melted and mixed intimately with the aerogel by the hypervelocity impact [3,4]. We are performing systematic examinations of entire Stardust tracks to establish the mineralogy and origins of all comet Wild 2 components [7,8]. This report focuses on coordinated analyses of indigenous crystalline and amorphous/melt cometary materials along the aerogel track walls, their interaction with aerogel during collection and comparisons with their TPs.

Isolation and molecular characterization of Vibrio parahaemolyticus from fresh, low-temperature preserved, dried, and salted seafood products in two coastal areas of eastern China.

PubMed

Yang, Zhen-Quan; Jiao, Xin-An; Zhou, Xiao-Hui; Cao, Guo-Xiang; Fang, Wei-Ming; Gu, Rui-Xia

2008-07-31

A total of 1293 seafood samples from fishing farm, retail markets, restaurants and cooking rooms of hotels in Jiangsu province and Shanghai city of China were collected and analyzed for the prevalence of Vibrio parahaemolyticus during July to October in 2007. Two hundred and fifty one isolates of V. parahaemolyticus were identified, of which 8 isolates were positive for tdh and 2 were positive for trh gene. Three tdh positive isolates were identified from low-temperature preserved seafood samples and 5 isolates from fresh seafood samples, of these tdh positive isolates, 3 were positive in ORF8-PCR test. The genetic diversity among V. parahaemolyticus isolates was assessed using random amplified polymorphic DNA (RAPD)-PCR and the results showed that there were 33 different genetic patterns that were clustered into nine groups (groups A to I) at 82% similarity level. About 31.9% of the isolates belong to type III9d that were widely distributed in fresh, iced, frozen, dried and salted seafood samples. Seven tdh positive isolates belonged to group A and one belonged to group C, 2 trh positive isolates were type I10d belonging to group F, which was identical to that of reference strains isolated from patients. This study demonstrated genetic variability within V. parahaemolyticus isolates from seafood in Chinese markets and confirmed the presence of toxigenic V. parahaemolyticus not only in fresh but also in iced and frozen seafood products indicating that low-temperature preserved seafood might be also a vehicle for transmitting pathogenic V. parahaemolyticus.

Mycobiota and mycotoxins in bee pollen collected from different areas of Slovakia.

PubMed

Kačániová, Miroslava; Juráček, Miroslav; Chlebo, Róbert; Kňazovická, Vladimíra; Kadasi-Horáková, Miriam; Kunová, Simona; Lejková, Jadža; Haščík, Peter; Mareček, Ján; Simko, Milan

2011-01-01

Contamination by microscopic fungi and mycotoxins in different bee pollen samples, which were stored under three different ways of storing as freezing, drying and UV radiation, was investigated. During spring 2009, 45 samples of bee-collected pollen were gathered from beekeepers who placed their bee colonies on monocultures of sunflower, rape and poppy fields within their flying distance. Bee pollen was collected from bees' legs by special devices placed at the entrance to hives. Samples were examined for the concentration and identification of microscopic fungi able to grow on Malt and Czapek-Dox agar and mycotoxins content [deoxynivalenol (DON), T-2 toxin (T-2), zearalenone (ZON) and total aflatoxins (AFL), fumonisins (FUM), ochratoxins (OTA)] by direct competitive enzyme-linked immunosorbent assays (ELISA). The total number of microscopic fungi in this study ranged from 2.98 ± 0.02 in frozen sunflower bee pollen to 4.06 ± 0.10 log cfu.g(-1) in sunflower bee pollen after UV radiation. In this study, 449 isolates belonging to 21 fungal species representing 9 genera were found in 45 samples of bee pollen. The total isolates were detected in frozen poppy pollen 29, rape pollen 40, sunflower pollen 80, in dried poppy pollen 12, rape pollen 36, sunflower 78, in poppy pollen after UV radiation treatment 54, rape 59 and sunflower 58. The most frequent isolates of microscopic fungi found in bee pollen samples of all prevalent species were Mucor mucedo (49 isolates), Alternaria alternata (40 isolates), Mucor hiemalis (40 isolates), Aspergillus fumigatus (33 isolates) and Cladosporium cladosporioides (31 isolates). The most frequently found isolates were detected in sunflower bee pollen frozen (80 isolates) and the lowest number of isolates was observed in poppy bee pollen dried (12 isolates). The most prevalent mycotoxin of poppy bee pollen was ZON (361.55 ± 0.26 μg.kg(-1)), in rape bee pollen T-2 toxin (265.40 ± 0.18 μg.kg(-1)) and in sunflower bee pollen T-2 toxin (364.72 ± 0.13 μg.kg(-1)) in all cases in frozen samples.

Bacterial populations associated with the dirty area of a South African poultry abattoir.

PubMed

Geornaras, I; de Jesus, A E; von Holy, A

1998-06-01

Bacterial populations associated with three sample types from the neck region of poultry carcasses in the dirty area of an abattoir were characterized. Sample types before and after scalding were skin only, feathers only, and a skin and feather combination. The neck skin of carcasses after the defeathering processing stage was also sampled. Bacterial populations associated with water from the scald tank, rubber fingers at the exit of the defeathering machine, and air in the dirty area were also characterized. Bacterial colonies (751) were randomly isolated from yeast extract-supplemented tryptone soya agar plates exhibiting 30 to 300 colonies. Micrococcus spp. were isolated in the highest proportion from pre-and postscalded carcass samples (63.5 to 86.1% of isolates), regardless of the sample type. Conversely, Enterobacteriaceae (40.3%), Acinetobacter (19.4%), and Aeromonas/Vibrio (12.5%) species predominated on neck skin samples taken from mechanically defeathered carcasses. Isolates from the rubber fingers were, however, predominantly Micrococcus spp. (94.4%). Bacterial groups isolated in the highest proportion from scald tank water samples were Micrococcus spp. (38.3%), species of Enterobacteriaceae (29.1%), and lactic acid bacteria (17.0%). Corynebacterium spp., species of Enterobacteriaceae, and Micrococcus spp. were dominant on air settle plates.

Spore populations among bulk tank raw milk and dairy powders are significantly different.

PubMed

Miller, Rachel A; Kent, David J; Watterson, Matthew J; Boor, Kathryn J; Martin, Nicole H; Wiedmann, Martin

2015-12-01

To accommodate stringent spore limits mandated for the export of dairy powders, a more thorough understanding of the spore species present will be necessary to develop prospective strategies to identify and reduce sources (i.e., raw materials or in-plant) of contamination. We characterized 1,523 spore isolates obtained from bulk tank raw milk (n=33 farms) and samples collected from 4 different dairy powder-processing plants producing acid whey, nonfat dry milk, sweet whey, or whey protein concentrate 80. The spores isolated comprised 12 genera, at least 44 species, and 216 rpoB allelic types. Bacillus and Geobacillus represented the most commonly isolated spore genera (approximately 68.9 and 12.1%, respectively, of all spore isolates). Whereas Bacillus licheniformis was isolated from samples collected from all plants and farms, Geobacillus spp. were isolated from samples from 3 out of 4 plants and just 1 out of 33 farms. We found significant differences between the spore population isolated from bulk tank raw milk and those isolated from dairy powder plant samples, except samples from the plant producing acid whey. A comparison of spore species isolated from raw materials and finished powders showed that although certain species, such as B. licheniformis, were found in both raw and finished product samples, other species, such as Geobacillus spp. and Anoxybacillus spp., were more frequently isolated from finished powders. Importantly, we found that 8 out of 12 genera were isolated from at least 2 different spore count methods, suggesting that some spore count methods may provide redundant information if used in parallel. Together, our results suggest that (1) Bacillus and Geobacillus are the predominant spore contaminants in a variety of dairy powders, implying that future research efforts targeted at elucidating approaches to reduce levels of spores in dairy powders should focus on controlling levels of spore isolates from these genera; and (2) the spore populations isolated from bulk tank raw milk and some dairy powder products are significantly different, suggesting that targeting in-plant sources of contamination may be important for achieving low spore counts in the finished product. These data provide important insight regarding the diversity of spore populations isolated from dairy powders and bulk tank raw milk, and demonstrate that several spore genera are detected by multiple spore count methods. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Isolation of Coxiella burnetii from serum of patients with acute Q fever.

PubMed

Vincent, Gemma A; Graves, Stephen R; Robson, Jennifer M; Nguyen, Chelsea; Hussain-Yusuf, Hazizul; Islam, Aminul; Fenwick, Stanley G; Stenos, John

2015-12-01

Worldwide there are few isolate collections of the intracellular bacterium Coxiella burnetii, due to the difficulties associated with working with the organism and the scarcity of suitable samples from which to attempt isolation. Particularly lacking are isolates from acute Q fever patients. The aim of this study was to evaluate whether the serum samples taken from patients with confirmed acute Q fever during the early stage of their disease represented a potential source of viable C. burnetii. Isolation was attempted from 65 of these samples by inoculation of the serum into Vero cell culture and was successful in 36 cases (55%). This high success rate was likely due to extended incubation of up to twelve weeks of the inoculated cultures, allowing the growth of the organism to levels detectable by PCR. Retrospective analysis of the time the sera was stored prior to inoculation into culture demonstrated that C. burnetii remained viable for 224 days in samples stored refrigerated and 371 days in samples stored frozen at -20 °C. These results demonstrate that standard serum samples taken from acute Q fever patients are a valuable source of new isolates of C. burnetii, with no special handling of the specimens required to maintain the organism's viability. Copyright © 2015 Elsevier B.V. All rights reserved.

Nondestructive 3D confocal laser imaging with deconvolution of seven whole stardust tracks with complementary XRF and quantitative analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greenberg, M.; Ebel, D.S.

2009-03-19

We present a nondestructive 3D system for analysis of whole Stardust tracks, using a combination of Laser Confocal Scanning Microscopy and synchrotron XRF. 3D deconvolution is used for optical corrections, and results of quantitative analyses of several tracks are presented. The Stardust mission to comet Wild 2 trapped many cometary and ISM particles in aerogel, leaving behind 'tracks' of melted silica aerogel on both sides of the collector. Collected particles and their tracks range in size from submicron to millimeter scale. Interstellar dust collected on the obverse of the aerogel collector is thought to have an average track length ofmore » {approx}15 {micro}m. It has been our goal to perform a total non-destructive 3D textural and XRF chemical analysis on both types of tracks. To that end, we use a combination of Laser Confocal Scanning Microscopy (LCSM) and X Ray Florescence (XRF) spectrometry. Utilized properly, the combination of 3D optical data and chemical data provides total nondestructive characterization of full tracks, prior to flattening or other destructive analysis methods. Our LCSM techniques allow imaging at 0.075 {micro}m/pixel, without the use of oil-based lenses. A full textural analysis on track No.82 is presented here as well as analysis of 6 additional tracks contained within 3 keystones (No.128, No.129 and No.140). We present a method of removing the axial distortion inherent in LCSM images, by means of a computational 3D Deconvolution algorithm, and present some preliminary experiments with computed point spread functions. The combination of 3D LCSM data and XRF data provides invaluable information, while preserving the integrity of the samples for further analysis. It is imperative that these samples, the first extraterrestrial solids returned since the Apollo era, be fully mapped nondestructively in 3D, to preserve the maximum amount of information prior to other, destructive analysis.« less

ON FARM SAMPLING FOR SALMONELLA: IMPACT OF METHOD AND DESIGN ON RESULTS

USDA-ARS?s Scientific Manuscript database

Current sampling for the National Antimicrobial Resistance Monitoring System (NARMS) is comprised primarily of receipt of Salmonella isolates from the USDA FSIS as part of their regulatory compliance testing. These isolates are received from all commodities and product classes. Isolates are charac...

[Differentiation and characterization of yeasts pathogenic for humans (Candida albicans, Exophiala dermatitidis) and algae pathogenic for animals (Prototheca spp.) using Fourier transform infrared spectroscopy (FTIR) in comparison with conventional methods].

PubMed

Schmalreck, A F; Tränkle, P; Vanca, E; Blaschke-Hellmessen, R

1998-01-01

Due to the Fourier-Transform Infrared Spectroscopy (FT-IR) of strain specific traits demonstrated to be a suitable and efficient method for diagnostic and epidemiological determinations for the yeasts Candida albicans, Exophiala dermatitidis and the chlorophylless algae of the genus Prototheca. FT-IR leads in a rapid and economical way to reproducible results according to the spectral differences of intact cells (IR-fingerprints). Different genera, species and sub-species respectively, different strains can be recognized and grouped into different clusters and subclusters. The FT-IR analysis of Candida albicans isolates (n = 150) of 22 newborns-at-risk of an intensive care unit showed, that 86% of the children were colonised with several (2-4) different strains in the oral cavities and faeces. Stationary cross-infections could definitely be determined. Exophiala dermatitidis isolates (n = 31), mostly isolated repetitively within a period of 3 years from sputa of patients suffering from cystic fibrosis could be characterized and grouped patient-specifically over the total sampling period. Of 6 from 8 patients (75%) their individual strains remain the same and could be tracked over the three years. Cross-infections during the stationary treatment could be clearly identified by FT-IR. The Prototheca isolate (n = 43) from live-stock and farm environment showed clear distinguishable clusters differentiating the species P. wickerhamii, P. zopfii and P. stagnora. In addition, the biotypes of P. zopfii could be distinguished, especially the subclusters of variants II and III. It could be demonstrated, that FT-IR is suitable for the routine identification and differentiation of yeasts and algae. However, in spite of the gain of knowledge by using FT-IR for the characterization of microorganisms, the conventional phenotyping and/or genetic analysis of yeast or algae strains cannot be replaced completely. For a final taxonomic classification a combination of conventional methods on FT-IR together with more sophisticated molecular genetic procedures is necessary.

Uranium determination in natural water by the fissiontrack technique

USGS Publications Warehouse

Reimer, G.M.

1975-01-01

The fission track technique, utilizing the neutron-induced fission of uranium-235, provides a versatile analytical method for the routine analysis of uranium in liquid samples of natural water. A detector is immersed in the sample and both are irradiated. The fission track density observed in the detector is directly proportional to the uranium concentration. The specific advantages of this technique are: (1) only a small quantity of sample, typically 0.1-1 ml, is needed; (2) no sample concentration is necessary; (3) it is capable of providing analyses with a lower reporting limit of 1 ??g per liter; and (4) the actual time spent on an analysis can be only a few minutes. This paper discusses and describes the method. ?? 1975.

Enterohemorrhagic Escherichia coli O157 in milk and dairy products from Libya: Isolation and molecular identification by partial sequencing of 16S rDNA

PubMed Central

Garbaj, Aboubaker M.; Awad, Enas M.; Azwai, Salah M.; Abolghait, Said K.; Naas, Hesham T.; Moawad, Ashraf A.; Gammoudi, Fatim T.; Barbieri, Ilaria; Eldaghayes, Ibrahim M.

2016-01-01

Aim: The aim of this work was to isolate and molecularly identify enterohemorrhagic Escherichia coli (EHEC) O157 in milk and dairy products in Libya, in addition; to clear the accuracy of cultural and biochemical identification as compared with molecular identification by partial sequencing of 16S rDNA for the existing isolates. Materials and Methods: A total of 108 samples of raw milk (cow, she-camel, and goat) and locally made dairy products (fermented cow’s milk, Maasora, Ricotta and ice cream) were collected from some regions (Janzour, Tripoli, Kremiya, Tajoura and Tobruk) in Libya. Samples were subjected to microbiological analysis for isolation of E. coli that was detected by conventional cultural and molecular method using polymerase chain reaction and partial sequencing of 16S rDNA. Results: Out of 108 samples, only 27 isolates were found to be EHEC O157 based on their cultural characteristics (Tellurite-Cefixime-Sorbitol MacConkey) that include 3 isolates from cow’s milk (11%), 3 isolates from she-camel’s milk (11%), two isolates from goat’s milk (7.4%) and 7 isolates from fermented raw milk samples (26%), isolates from fresh locally made soft cheeses (Maasora and Ricotta) were 9 (33%) and 3 (11%), respectively, while none of the ice cream samples revealed any growth. However, out of these 27 isolates, only 11 were confirmed to be E. coli by partial sequencing of 16S rDNA and E. coli O157 Latex agglutination test. Phylogenetic analysis revealed that majority of local E. coli isolates were related to E. coli O157:H7 FRIK944 strain. Conclusion: These results can be used for further studies on EHEC O157 as an emerging foodborne pathogen and its role in human infection in Libya. PMID:27956766

Occurrence and genetic diversity of Arcobacter butzleri in an artisanal dairy plant in Italy.

PubMed

Giacometti, Federica; Lucchi, Alex; Manfreda, Gerardo; Florio, Daniela; Zanoni, Renato Giulio; Serraino, Andrea

2013-11-01

The present study aimed to investigate the presence, distribution, and persistence of Arcobacter spp. in an artisanal dairy plant and to test the isolates to determine their different genotypes in the processing plant and in foods. Samples were collected in an artisanal cheese factory on four occasions between October and December 2012. Food samples (raw milk, ricotta cheese, mozzarella cheese, and conditioning liquid), water samples, and environmental samples were analyzed by the culture method; isolates were identified by multiplex PCR and genotyped by pulsed-field gel electrophoresis (PFGE) analysis. Arcobacter butzleri was isolated from 29 out of 59 samples (46.6%), 22 of which were from environmental samples and 7 of which were from food samples. Cluster analysis divided the strains into 47 PFGE patterns: 14 PFGE clusters and 33 unique types. Our findings indicate that the plant harbored numerous A. butzleri pulsotypes and that the manual cleaning and sanitation in the studied dairy plant do not effectively remove Arcobacter. The recurrent isolation of A. butzleri suggests that the environmental conditions in the dairy plant constitute a good ecological niche for the colonization of this microorganism. In some cases, the presence of indistinguishable strains isolated from the same facilities on different sampling days showed that these strains were persistent in the processing environment.

Detection and molecular characterization of Vibrio parahaemolyticus isolated from seafood harvested along the southwest coast of India.

PubMed

Raghunath, Pendru; Acharya, Sadananda; Bhanumathi, Amarbahadur; Karunasagar, Iddya; Karunasagar, Indrani

2008-09-01

The levels of total and tdh(+)Vibrio parahaemolyticus were estimated in 83 seafood samples from southwest coast of India by colony hybridization. Conventional enrichment and isolation technique was also used to study the prevalence. Polymerase chain reaction (PCR) was performed on bacterial cell lyates for detection of total and pathogenic V. parahaemolyticus by amplification of specific genes. Of 83 samples tested, V. parahaemolyticus could be detected in 74 (89.2%) samples and tdh(+)V. parahaemolyticus in 5 (6.0%) samples by colony hybridization. V. parahaemolyticus was detected in 68 (81.9%) of 83 samples after 18 h of enrichment by PCR, and isolated from 63 (75.9%) of 83 samples by conventional isolation. The virulence genes tdh and trh could be detected in 8.4% and 25.3%, respectively, in the sample enrichment broths by PCR. Use of colony hybridization following enrichment to achieve sensitive detection of tdh(+)V. parahaemolyticus in seafood was evaluated using another set of 58 seafood samples. Thirty pathogenic V. parahaemolyticus strains isolated during the study were screened by PCR for genetic markers to be specific for the detection of the pandemic clone. Results of this study suggest that the GS-PCR may serve as a reliable genetic marker for the pandemic clone of V. parahaemolyticus.

Women in academic general surgery.

PubMed

Schroen, Anneke T; Brownstein, Michelle R; Sheldon, George F

2004-04-01

To portray the professional experiences of men and women in academic general surgery with specific attention to factors associated with differing academic productivity and with leaving academia. A 131-question survey was mailed to all female (1,076) and a random 2:1 sample of male (2,152) members of the American College of Surgeons in three mailings between September 1998 and March 1999. Detailed questions regarding academic rank, career aspirations, publication rate, grant funding, workload, harassment, income, marriage and parenthood were asked. A five-point Likert scale measured influences on career satisfaction. Responses from strictly academic and tenure-track surgeons were analyzed and interpreted by gender, age, and rank. Overall, 317 surgeons in academic practice (168 men, 149 women) responded, of which 150 were in tenure-track positions (86 men, 64 women). Men and women differed in academic rank, tenure status, career aspirations, and income. Women surgeons had published a median of ten articles compared with 25 articles for men (p <.001). Marriage or parenthood did not influence numbers of publications for women. Overall career satisfaction was high, but women reported feeling career advancement opportunities were not equally available to them as to their male colleagues and feeling isolation from surgical peers. Ten percent to 20% of surgeons considered leaving academia, with women assistant professors (29%) contemplating this most commonly. Addressing the differences between men and women academic general surgeons is critical in fostering career development and in recruiting competitive candidates of both sexes to general surgery.

Prevalence, identification by a DNA microarray-based assay of human and food isolates Listeria spp. from Tunisia.

PubMed

Hmaïed, F; Helel, S; Le Berre, V; François, J-M; Leclercq, A; Lecuit, M; Smaoui, H; Kechrid, A; Boudabous, A; Barkallah, I

2014-02-01

We aimed at evaluating the prevalence of Listeria species isolated from food samples and characterizing food and human cases isolates. Between 2005 and 2007, one hundred food samples collected in the markets of Tunis were analysed in our study. Five strains of Listeria monocytogenes responsible for human listeriosis isolated in hospital of Tunis were included. Multiplex PCR serogrouping and pulsed field gel electrophoresis (PFGE) applying the enzyme AscI and ApaI were used for the characterization of isolates of L. monocytogenes. We have developed a rapid microarray-based assay to a reliable discrimination of species within the Listeria genus. The prevalence of Listeria spp. in food samples was estimated at 14% by using classical biochemical identification. Two samples were assigned to L. monocytogenes and 12 to L. innocua. DNA microarray allowed unambiguous identification of Listeria species. Our results obtained by microarray-based assay were in accordance with the biochemical identification. The two food L. monocytogenes isolates were assigned to the PCR serogroup IIa (serovar 1/2a). Whereas human L. monocytogenes isolates were of PCR serogroup IVb, (serovars 4b). These isolates present a high similarity in PFGE. Food L. monocytogenes isolates were classified into two different pulsotypes. These pulsotypes were different from that of the five strains responsible for the human cases. We confirmed the presence of Listeria spp. in variety of food samples in Tunis. Increased food and clinical surveillance must be taken into consideration in Tunisia to identify putative infections sources. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Comparative study on proximate, functional, mineral, and antinutrient composition of fermented, defatted, and protein isolate of Parkia biglobosa seed.

PubMed

Ogunyinka, Bolajoko I; Oyinloye, Babatunji E; Osunsanmi, Foluso O; Kappo, Abidemi P; Opoku, Andrew R

2017-01-01

The use of plant-derived foods in the prevention, treatment, and management of metabolic diseases especially diabetes has gained prominence; this has been associated with their physicochemical properties. This study was conducted to compare the proximate, functional, mineral, and antinutrient composition of the fermented seeds, the defatted seeds, and the protein isolate from Parkia biglobosa seeds. The results showed that the fermented, defatted, and protein isolate varied in composition within the parameters studied. The proximate analysis revealed that the protein isolate had the highest ash (6.0%) and protein (59.4%) as well as the lowest fat (5.7%) and moisture (5.1%) content when compared to the fermented and defatted samples. In like manner, the functional properties of the protein isolate were relatively better than those of the fermented and defatted samples, with oil absorption capacity of 4.2% and emulsion capacity of 82%. The magnesium and zinc content of the protein isolate were significantly higher when compared with the fermented and defatted samples, while a negligible amount of antinutrient was present in all the samples, with the protein isolate having the lowest quantity. The overall data suggest that the protein isolate had better proximate, mineral, functional, and antinutrient properties when compared to the fermented and defatted samples. Therefore, the synergistic effect of all these components present in the protein isolate from P. biglobosa seed in association with its low carbohydrate and high protein/ash contents could play a vital role in the management of diabetes and its associated complications.

Isolation of Polypeptide Sample and Measurement of Its Concentration.

ERIC Educational Resources Information Center

Beanan, Maureen J.

2000-01-01

Introduces a laboratory experiment that isolates a bacterial polypeptide sample and measures the concentration of polypeptides in the sample. Uses Escherichia coli strain MM294 and performs a bio-rad assay to determine the concentration of polypeptides. (YDS)

Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000

USGS Publications Warehouse

Hyer, Kenneth; Moyer, Douglas

2003-01-01

Surface-water impairment by fecal coliform bacteria is a water-quality issue of national scope and importance. In Virginia, more than 175 stream segments are on the Commonwealth's 1998 303(d) list of impaired waters because of elevated concentrations of fecal coliform bacteria. These fecal coliform-impaired stream segments require the development of total maximum daily load (TMDL) and associated implementation plans, but accurate information on the sources contributing these bacteria usually is lacking. The development of defendable fecal coliform TMDLs and management plans can benefit from reliable information on the bacteria sources that are responsible for the impairment. Bacterial source tracking (BST) recently has emerged as a powerful tool for identifying the sources of fecal coliform bacteria that impair surface waters. In a demonstration of BST technology, three watersheds on Virginia's 1998 303(d) list with diverse land-use practices (and potentially diverse bacteria sources) were studied. Accotink Creek is dominated by urban land uses, Christians Creek by agricultural land uses, and Blacks Run is affected by both urban and agricultural land uses. During the 20-month field study (March 1999?October 2000), water samples were collected from each stream during a range of flow conditions and seasons. For each sample, specific conductance, dissolved oxygen concentration, pH, turbidity, flow, and water temperature were measured. Fecal coliform concentrations of each water sample were determined using the membrane filtration technique. Next, Escherichia coli (E. coli) were isolated from the fecal coliform bacteria and their sources were identified using ribotyping (a method of 'genetic fingerprinting'). Study results provide enhanced understanding of the concentrations and sources of fecal coliform bacteria in these three watersheds. Continuum sampling (sampling along the length of the streams) indicated that elevated concentrations of fecal coliform bacteria (maximum observed concentration of 290,000 colonies/100 milliliters (col/100mL) could occur along the entire length of each stream, and that the samples collected at the downstream monitoring station of each stream were generally representative of the entire upstream reach. Seasonal patterns were observed in the base-flow fecal coliform concentrations of all streams; concentrations were typically highest in the summer and lowest in the winter. Fecal coliform concentrations were lowest during periods of base flow (typically 200?2,000 col/100mL) and increased by 3?4 orders of magnitude during storm events (as high as 700,000 col/100mL). Multiple linear regression models were developed to predict fecal coliform concentrations as a function of streamflow and other water-quality parameters. The source tracking technique provided identification of bacteria contributions from diverse sources that included (but were not limited to) humans, cattle, poultry, horses, dogs, cats, geese, ducks, raccoons, and deer. Seasonal patterns were observed in the contributions of cattle and poultry sources. There were relations between the identified sources of fecal coliform bacteria and the land-use practices within each watershed. There were only minor differences in the distribution of bacteria sources between low-flow periods and high-flow periods. A coupled approach that utilized both a large available source library and a smaller, location-specific source library provided the most success in identifying the unknown E. coli isolates. BST data should provide valuable support and guidance for producing more defendable and scientifically rigorous watershed models. Incorporation of these bacteria-source data into watershed management strategies also should result in the selection of more efficient source-reduction scenarios for improving water quality.

Identification and characterization of the dominant lactic acid bacteria isolated from traditional fermented milk in Mongolia.

PubMed

Sun, Z H; Liu, W J; Zhang, J C; Yu, J; Gao, W; Jiri, M; Menghe, B; Sun, T S; Zhang, H P

2010-05-01

Five samples of Airag and 20 of Tarag (both in Mongolia) were collected from scattered households. One hundred strains of lactic acid bacteria (LAB) were isolated and identified from these samples according to phenotypic characterization and 16S rRNA gene sequence analysis. Eighty-five isolates belonged to the genus Lactobacillus, 15 being classified as coccoid LAB. All isolates belonged to 5 genera and 11 to different species and subspecies. Lactobacillus (Lb.) helveticus was predominant population in Airag samples, Lb. fermentum and Lb. helveticus were the major LAB microflora in Tarag.

Male-specific coliphages for source tracking fecal contamination in surface waters and prevalence of Shiga-toxigenic Escherichia coli in a major produce production region of the Central Coast of California.

PubMed

Ravva, Subbarao V; Sarreal, Chester Z; Cooley, Michael B

2015-07-01

To provide data for traditional trace-back studies from fork to farm, it is necessary to determine the environmental sources for Shiga-toxigenic Escherichia coli. We developed SYBR green based reverse-transcriptase PCR methods to determine the prevalence of F+ RNA coliphages (FRNA) as indicators of fecal contamination. Male-specific coliphages, determined using a single-agar overlay method, were prevalent in all surface waters sampled for 8 months. F+ DNA coliphages (FDNA) were predominant compared to FRNA in water samples from majority of sampling locations. Most (90%) of the FRNA were sourced to humans and originated from human-impacted sites. Members of genogroup III represented 77% of FRNA originated from human sources. Furthermore, 93% of FRNA sourced to animals were also detected in water samples from human-impacted sites. Eighty percent of all FRNA were isolated during the winter months indicating seasonality in prevalence. In contrast, FDNA were more prevalent during summer months. E. coli O157:H7 and Shiga-toxigenic E. coli were detected in water samples from locations predominantly influenced by agriculture. Owing to their scarcity, their numbers could not be correlated with the prevalence of FRNA or FDNA in water samples. Both coliform bacteria and generic E. coli from agricultural or human-impacted sites were similar in numbers and thus could not be used to determine the sources of fecal contamination. Data on the prevalence of male-specific coliphages may be invaluable for predicting the sources of fecal contamination and aid in developing methods to prevent enteric pathogen contamination from likely sources during produce production.

Chemical Constituents in Groundwater from Multiple Zones in the Eastern Snake River Plain Aquifer at the Idaho National Laboratory, Idaho, 2005-08

USGS Publications Warehouse

Bartholomay, Roy C.; Twining, Brian V.

2010-01-01

From 2005 to 2008, the U.S. Geological Survey's Idaho National Laboratory (INL) Project office, in cooperation with the U.S. Department of Energy, collected water-quality samples from multiple water-bearing zones in the eastern Snake River Plain aquifer. Water samples were collected from six monitoring wells completed in about 350-700 feet of the upper part of the aquifer, and the samples were analyzed for major ions, selected trace elements, nutrients, selected radiochemical constituents, and selected stable isotopes. Each well was equipped with a multilevel monitoring system containing four to seven sampling ports that were each isolated by permanent packer systems. The sampling ports were installed in aquifer zones that were highly transmissive and that represented the water chemistry of the top four to five model layers of a steady-state and transient groundwater-flow model. The model's water chemistry and particle-tracking simulations are being used to better define movement of wastewater constituents in the aquifer. The results of the water chemistry analyses indicated that, in each of four separate wells, one zone of water differed markedly from the other zones in the well. In four wells, one zone to as many as five zones contained radiochemical constituents that originated from wastewater disposal at selected laboratory facilities. The multilevel sampling systems are defining the vertical distribution of wastewater constituents in the eastern Snake River Plain aquifer and the concentrations of wastewater constituents in deeper zones in wells Middle 2051, USGS 132, and USGS 103 support the concept of groundwater flow deepening in the southwestern part of the INL.

Demonstrating the Efficacy of the FoneAstra Pasteurization Monitor for Human Milk Pasteurization in Resource-Limited Settings

PubMed Central

Coutsoudis, Anna; Israel-Ballard, Kiersten; Chaudhri, Rohit; Perin, Noah; Mlisana, Koleka

2015-01-01

Abstract Human milk provides crucial nutrition and immunologic protection for infants. When a mother's own milk is unavailable, donated human milk, pasteurized to destroy bacteria and viruses, is a lifesaving replacement. Flash-heat pasteurization is a simple, low-cost, and commonly used method to make milk safe, but currently there is no system to monitor milk temperature, which challenges quality control. FoneAstra, a smartphone-based mobile pasteurization monitor, removes this barrier by guiding users through pasteurization and documenting consistent and safe practice. This study evaluated FoneAstra's efficacy as a quality control system, particularly in resource-limited settings, by comparing bacterial growth in donor milk flash-heated with and without the device at a neonatal intensive care unit in Durban, South Africa. Materials and Methods: For 100 samples of donor milk, one aliquot each of prepasteurized milk, milk flash-heated without FoneAstra, and milk pasteurized with FoneAstra was cultured on routine agar for bacterial growth. Isolated bacteria were identified and enumerated. Results: In total, 300 samples (three from each donor sample) were analyzed. Bacterial growth was found in 86 of the 100 samples before any pasteurization and one of the 100 postpasteurized samples without FoneAstra. None of the samples pasteurized using FoneAstra showed bacterial growth. Conclusions: Both pasteurization methods were safe and effective. FoneAstra, however, provides the additional benefits of user-guided temperature monitoring and data tracking. By improving quality assurance and standardizing the pasteurization process, FoneAstra can support wide-scale implementation of human milk banks in resource-limited settings, increasing access and saving lives. PMID:25668396

User`s and reference guide to the INEL RML/analytical radiochemistry sample tracking database version 1.00

DOE Office of Scientific and Technical Information (OSTI.GOV)

Femec, D.A.

This report discusses the sample tracking database in use at the Idaho National Engineering Laboratory (INEL) by the Radiation Measurements Laboratory (RML) and Analytical Radiochemistry. The database was designed in-house to meet the specific needs of the RML and Analytical Radiochemistry. The report consists of two parts, a user`s guide and a reference guide. The user`s guide presents some of the fundamentals needed by anyone who will be using the database via its user interface. The reference guide describes the design of both the database and the user interface. Briefly mentioned in the reference guide are the code-generating tools, CREATE-SCHEMAmore » and BUILD-SCREEN, written to automatically generate code for the database and its user interface. The appendices contain the input files used by the these tools to create code for the sample tracking database. The output files generated by these tools are also included in the appendices.« less

AquaPathogen X--A template database for tracking field isolates of aquatic pathogens

USGS Publications Warehouse

Emmenegger, Evi; Kurath, Gael

2012-01-01

AquaPathogen X is a template database for recording information on individual isolates of aquatic pathogens and is available for download from the U.S. Geological Survey (USGS) Western Fisheries Research Center (WFRC) website (http://wfrc.usgs.gov). This template database can accommodate the nucleotide sequence data generated in molecular epidemiological studies along with the myriad of abiotic and biotic traits associated with isolates of various pathogens (for example, viruses, parasites, or bacteria) from multiple aquatic animal host species (for example, fish, shellfish, or shrimp). The simultaneous cataloging of isolates from different aquatic pathogens is a unique feature to the AquaPathogen X database, which can be used in surveillance of emerging aquatic animal diseases and clarification of main risk factors associated with pathogen incursions into new water systems. As a template database, the data fields are empty upon download and can be modified to user specifications. For example, an application of the template database that stores the epidemiological profiles of fish virus isolates, called Fish ViroTrak (fig. 1), was also developed (Emmenegger and others, 2011).

Amoeba-Resisting Bacteria and Ventilator-Associated Pneumonia

PubMed Central

La Scola, Bernard; Boyadjiev, Ioanna; Greub, Gilbert; Khamis, Atieh; Martin, Claude

2003-01-01

To evaluate the role of amoeba-associated bacteria as agents of ventilator-associated pneumonia (VAP), we tested the water from an intensive care unit (ICU) every week for 6 months for such bacteria isolates; serum samples and bronchoalveolar lavage samples (BAL) were also obtained from 30 ICU patients. BAL samples were examined for amoeba-associated bacteria DNA by suicide-polymerase chain reaction, and serum samples were tested against ICU amoeba-associated bacteria. A total of 310 amoeba-associated bacteria from10 species were isolated. Twelve of 30 serum samples seroconverted to one amoeba-associated bacterium isolated in the ICU, mainly Legionella anisa and Bosea massiliensis, the most common isolates from water (p=0.021). Amoeba-associated bacteria DNA was detected in BAL samples from two patients whose samples later seroconverted. Seroconversion was significantly associated with VAP and systemic inflammatory response syndrome, especially in patients for whom no etiologic agent was found by usual microbiologic investigations. Amoeba-associated bacteria might be a cause of VAP in ICUs, especially when microbiologic investigations are negative. PMID:12890321

Method for nucleic acid isolation using supercritical fluids

DOEpatents

Nivens, David E.; Applegate, Bruce M.

1999-01-01

A method for detecting the presence of a microorganism in an environmental sample involves contacting the sample with a supercritical fluid to isolate nucleic acid from the microorganism, then detecting the presence of a particular sequence within the isolated nucleic acid. The nucleic acid may optionally be subjected to further purification.

Candidiasis in pediatric patients with cancer interned in a university hospital

PubMed Central

De Carvalho Parahym, Ana Maria Rabelo; De Melo, Luciana Resende Bandeira; De Morais, Vera Lúcia Lins; Neves, Rejane Pereira

2009-01-01

Fungi are common causes of infection in immunocompromised patients. Candida species are frequently involved in these cases. In order to investigate candidiasis in pediatric patients with cancer, clinical samples were collected from one hundred and twenty two patients interned in the Oswaldo Cruz University Hospital in Recife, Brazil. Yeasts were isolated from thirty-four clinical samples. The species isolated were: Candida albicans (fourteen isolates), C. parapsilosis (nine isolates), C. guilliermondii (two isolates) and C. tropicalis (two isolates). We found that candidemia was most frequent in patients with malignant hematology and that C. parapsilosis infections caused the highest mortality. PMID:24031365

Genetic diversity and antimicrobial resistance among isolates of Escherichia coli O157: H7 from feces and hides of super-shedders and low-shedding pen-mates in two commercial beef feedlots

PubMed Central

2012-01-01

Background Cattle shedding at least 104 CFU Escherichia coli O157:H7/g feces are described as super-shedders and have been shown to increase transmission of E. coli O157:H7 to other cattle in feedlots. This study investigated relationships among fecal isolates from super-shedders (n = 162), perineal hide swab isolates (PS) from super-shedders (n = 137) and fecal isolates from low-shedder (< 104 CFU/g feces) pen-mates (n = 496) using pulsed-field gel electrophoresis (PFGE). A subsample of these fecal isolates (n = 474) was tested for antimicrobial resistance. Isolates of E. coli O157:H7 were obtained from cattle in pens (avg. 181 head) at 2 commercial feedlots in southern Alberta with each steer sampled at entry to the feedlot and prior to slaughter. Results Only 1 steer maintained super-shedder status at both samplings, although approximately 30% of super-shedders in sampling 1 had low-shedder status at sampling 2. A total of 85 restriction endonuclease digestion clusters (REPC; 90% or greater similarity) and 86 unique isolates (< 90% similarity) were detected, with the predominant REPC (30% of isolates) being isolated from cattle in all feedlot pens, although it was not associated with shedding status (super- or low-shedder; P = 0.94). Only 2/21 super-shedders had fecal isolates in the same REPC at both samplings. Fecal and PS isolates from individual super-shedders generally belonged to different REPCs, although fecal isolates of E. coli O157:H7 from super- and low-shedders showed greater similarity (P < 0.001) than those from PS. For 77% of super-shedders, PFGE profiles of super-shedder fecal and PS isolates were distinct from all low-shedder fecal isolates collected in the same pen. A low level of antimicrobial resistance (3.7%) was detected and prevalence of antimicrobial resistance did not differ among super- and low-shedder isolates (P = 0.69), although all super-shedder isolates with antimicrobial resistance (n = 3) were resistant to multiple antimicrobials. Conclusions Super-shedders did not have increased antimicrobial resistance compared to low-shedder pen mates. Our data demonstrated that PFGE profiles of individual super-shedders varied over time and that only 1/162 steers remained a super-shedder at 2 samplings. In these two commercial feedlots, PFGE subtypes of E. coli O157:H7 from fecal isolates of super- and low-shedders were frequently different as were subtypes of fecal and perineal hide isolates from super-shedders. PMID:23014060

Development of Polymorphic Microsatellite Loci for Potato Wart from Next-Generation Sequence Data.

PubMed

Gagnon, Marie-Claude; van der Lee, Theo A J; Bonants, Peter J M; Smith, Donna S; Li, Xiang; Lévesque, C André; Bilodeau, Guillaume J

2016-06-01

Synchytrium endobioticum is the fungal agent causing potato wart disease. Because of its severity and persistence, quarantine measures are enforced worldwide to avoid the spread of this disease. Molecular markers exist for species-specific detection of this pathogen, yet markers to study the intraspecific genetic diversity of S. endobioticum were not available. Whole-genome sequence data from Dutch pathotype 1 isolate MB42 of S. endobioticum were mined for perfect microsatellite motifs. Of the 62 selected microsatellites, 21 could be amplified successfully and displayed moderate levels of polymorphism in 22 S. endobioticum isolates from different countries. Nineteen multilocus genotypes were observed, with only three isolates from Canada displaying identical profiles. The majority of isolates from Canada clustered genetically. In contrast, most isolates collected in Europe show no genetic clustering associated with their geographic origin. S. endobioticum isolates with the same pathotype displayed highly variable genotypes and none of the microsatellite markers correlated with a specific pathotype. The markers developed in this study can be used to assess intraspecific genetic diversity of S. endobioticum and allow track and trace of genotypes that will generate a better understanding of the migration and spread of this important fungal pathogen and support management of this disease.

FAST TRACK COMMUNICATION Initial data for the relativistic gravitational N-body problem

NASA Astrophysics Data System (ADS)

Chruściel, Piotr T.; Corvino, Justin; Isenberg, James

2010-11-01

In general relativity, an initial data set for an isolated gravitational system takes the form of a solution of the Einstein constraint equations which is asymptotically Euclidean on a specified end. Given a collection of N such data sets with a subregion of interest (bounded away from the specified end) chosen in each, we show that there exists a family of new initial data sets, each of which contains exact copies of each of the N chosen subregions, positioned in a chosen array in a single asymptotic end. These composite initial data sets model isolated, relativistic gravitational systems containing N chosen bodies in specified initial configurations.

Nonstructural Protein L* Species Specificity Supports a Mouse Origin for Vilyuisk Human Encephalitis Virus.

PubMed

Drappier, Melissa; Opperdoes, Fred R; Michiels, Thomas

2017-07-15

Vilyuisk human encephalitis virus (VHEV) is a picornavirus related to Theiler's murine encephalomyelitis virus (TMEV). VHEV was isolated from human material passaged in mice. Whether this VHEV is of human or mouse origin is therefore unclear. We took advantage of the species-specific activity of the nonstructural L* protein of theiloviruses to track the origin of TMEV isolates. TMEV L* inhibits RNase L, the effector enzyme of the interferon pathway. By using coimmunoprecipitation and functional RNase L assays, the species specificity of RNase L antagonism was tested for L* from mouse (DA) and rat (RTV-1) TMEV strains as well as for VHEV. Coimmunoprecipitation and functional assay data confirmed the species specificity of L* activity and showed that L* from rat strain RTV-1 inhibited rat but not mouse or human RNase L. Next, we showed that the VHEV L* protein was phylogenetically related to L* of mouse viruses and that it failed to inhibit human RNase L but readily antagonized mouse RNase L, unambiguously showing the mouse origin of VHEV. IMPORTANCE Defining the natural host of a virus can be a thorny issue, especially when the virus was isolated only once or when the isolation story is complex. The species Theilovirus includes Theiler's murine encephalomyelitis virus (TMEV), infecting mice and rats, and Saffold virus (SAFV), infecting humans. One TMEV strain, Vilyuisk human encephalitis virus (VHEV), however, was isolated from mice that were inoculated with cerebrospinal fluid of a patient presenting with chronic encephalitis. It is therefore unclear whether VHEV was derived from the human sample or from the inoculated mouse. The L* protein encoded by TMEV inhibits RNase L, a cellular enzyme involved in innate immunity, in a species-specific manner. Using binding and functional assays, we show that this species specificity even allows discrimination between TMEV strains of mouse and of rat origins. The VHEV L* protein clearly inhibited mouse but not human RNase L, indicating that this virus originates from mice. Copyright © 2017 American Society for Microbiology.

Tracking of Cells with a Compact Microscope Imaging System with Intelligent Controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2007-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to autofocus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously

Tracking of cells with a compact microscope imaging system with intelligent controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2007-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to auto-focus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously.

Stardust Interstellar Preliminary Examination II: Curating the Interstellar Dust Collector, Picokeystones, and Sources of Impact Tracks

NASA Technical Reports Server (NTRS)

Frank, David R.; Westphal, Andrew J.; Zolensky, Michael E.; Gainsforth, Zack; Butterworth, Anna L.; Bastien, Ronald K.; Allen, Carlton; Anderson, David; Bechtel, Hans A.; Sandford, Scott A.

2013-01-01

We discuss the inherent difficulties that arise during "ground truth" characterization of the Stardust interstellar dust collector. The challenge of identifying contemporary interstellar dust impact tracks in aerogel is described within the context of background spacecraft secondaries and possible interplanetary dust particles and beta-meteoroids. In addition, the extraction of microscopic dust embedded in aerogel is technically challenging. Specifically, we provide a detailed description of the sample preparation techniques developed to address the unique goals and restrictions of the Interstellar Preliminary Exam. These sample preparation requirements and the scarcity of candidate interstellar impact tracks exacerbate the difficulties. We also illustrate the role of initial optical imaging with critically important examples, and summarize the overall processing of the collection to date.

40 CFR 141.35 - Reporting for unregulated contaminant monitoring results.

Code of Federal Regulations, 2014 CFR

2014-07-01

... up to 30 characters assigned by the laboratory to uniquely identify containers, or groups of containers, containing water samples collected at the same sampling location for the same sampling date. 9... each sample event. This will associate samples with the PWS monitoring plan to allow EPA to track...

40 CFR 141.35 - Reporting for unregulated contaminant monitoring results.

Code of Federal Regulations, 2012 CFR

2012-07-01

... up to 30 characters assigned by the laboratory to uniquely identify containers, or groups of containers, containing water samples collected at the same sampling location for the same sampling date. 9... each sample event. This will associate samples with the PWS monitoring plan to allow EPA to track...

40 CFR 141.35 - Reporting for unregulated contaminant monitoring results.

Code of Federal Regulations, 2013 CFR

2013-07-01

... up to 30 characters assigned by the laboratory to uniquely identify containers, or groups of containers, containing water samples collected at the same sampling location for the same sampling date. 9... each sample event. This will associate samples with the PWS monitoring plan to allow EPA to track...

Tracking progress toward global polio eradication--worldwide, 2009-2010.

PubMed

2011-04-15

Since the Global Polio Eradication Initiative (GPEI) began in 1988, progress has been tracked by 1) surveillance comprised of detection and investigation of cases of acute flaccid paralysis (AFP), coupled with environmental surveillance (sewage testing) in selected areas, and 2) timely testing of fecal specimens in accredited laboratories to identify polioviruses. The sensitivity of AFP case detection and the timeliness of AFP investigations are monitored with performance indicators. Polioviruses are isolated and characterized by the Global Polio Laboratory Network (GPLN). This report assesses the quality of polio surveillance and the timeliness of poliovirus isolation reporting and characterization worldwide during 2009--2010. During that period, 77% of countries affected by wild poliovirus (WPV) met national performance standards for AFP surveillance; underperforming subnational areas were identified in two of four countries with reestablished WPV transmission and in 13 of 22 countries with WPV outbreaks. Targets for timely GPLN reporting of poliovirus isolation results were met in five World Health Organization (WHO) regions in 2009 and in four of six regions in 2010; targets for timely poliovirus characterization were met in four WHO regions in 2009 and in five regions in 2010. Monitoring of surveillance performance indicators at subnational levels continues to be critical to identifying surveillance gaps that might allow WPV circulation to be missed in certain areas or subpopulations. To achieve polio eradication, efforts are needed to further strengthen AFP surveillance, implement targeted environmental surveillance, and ensure that GPLN quality is maintained.

Interfacing with USSTRATCOM and UTTR during Stardust Earth Return

NASA Technical Reports Server (NTRS)

Jefferson, David C.; Baird, Darren T.; Cangahuala, Laureano A.; Lewis, George D.

2006-01-01

The Stardust Sample Return Capsule separated from the main spacecraft four hours prior to atmospheric entry. Between this time and the time at which the SRC touched down at the Utah Test and Training Range, two organizations external to JPL were involved in tracking the Sample Return Capsule. Orbit determination for the Stardust spacecraft during deep space cruise, the encounters of asteroid Annefrank and comet Wild 2, and the final approach to Earth used X-band radio metric Doppler and range data obtained through the Deep Space Network. The SRC lacked the electronics needed for coherently transponded radio metric tracking, so the DSN was not able to track the SRC after it separated from the main spacecraft. Although the expected delivery accuracy at atmospheric entry was well within the capability needed to target the SRC to the desired ground location, it was still desirable to obtain direct knowledge of the SRC trajectory in case of anomalies. For this reason U.S. Strategic Command was engaged to track the SRC between separation and atmospheric entry. Once the SRC entered the atmosphere, ground sensors at UTTR were tasked to acquire the descending SRC and maintain track during the descent in order to determine the landing location, to which the ground recovery team was then directed. This paper discusses organizational interfaces, data products, and delivery schedules, and the actual tracking operations are described.

Deep Space Navigation with Noncoherent Tracking Data

NASA Technical Reports Server (NTRS)

Ellis, J.

1983-01-01

Navigation capabilities of noncoherent tracking data are evaluated for interplanetary cruise phase and planetary (Venus) flyby orbit determination. Results of a formal covariance analysis are presented which show that a combination of one-way Doppler and delta DOR yields orbit accuracies comparable to conventional two-way Doppler tracking. For the interplanetary cruise phase, a tracking cycle consisting of a 3-hour Doppler pass and delta DOR (differential one-way range) from two baselines (one observation per overlap) acquired 3 times a month results in 100-km orbit determination accuracy. For reconstruction of a Venus flyby orbit, 10 days tracking at encounter consisting of continuous one-way Doppler and delta DOR sampled at one observation per overlap is sufficient to satisfy the accuracy requirements.

A Class of Prediction-Correction Methods for Time-Varying Convex Optimization

NASA Astrophysics Data System (ADS)

Simonetto, Andrea; Mokhtari, Aryan; Koppel, Alec; Leus, Geert; Ribeiro, Alejandro

2016-09-01

This paper considers unconstrained convex optimization problems with time-varying objective functions. We propose algorithms with a discrete time-sampling scheme to find and track the solution trajectory based on prediction and correction steps, while sampling the problem data at a constant rate of $1/h$, where $h$ is the length of the sampling interval. The prediction step is derived by analyzing the iso-residual dynamics of the optimality conditions. The correction step adjusts for the distance between the current prediction and the optimizer at each time step, and consists either of one or multiple gradient steps or Newton steps, which respectively correspond to the gradient trajectory tracking (GTT) or Newton trajectory tracking (NTT) algorithms. Under suitable conditions, we establish that the asymptotic error incurred by both proposed methods behaves as $O(h^2)$, and in some cases as $O(h^4)$, which outperforms the state-of-the-art error bound of $O(h)$ for correction-only methods in the gradient-correction step. Moreover, when the characteristics of the objective function variation are not available, we propose approximate gradient and Newton tracking algorithms (AGT and ANT, respectively) that still attain these asymptotical error bounds. Numerical simulations demonstrate the practical utility of the proposed methods and that they improve upon existing techniques by several orders of magnitude.

Performance evaluation of digital phase-locked loops for advanced deep space transponders

NASA Technical Reports Server (NTRS)

Nguyen, T. M.; Hinedi, S. M.; Yeh, H.-G.; Kyriacou, C.

1994-01-01

The performances of the digital phase-locked loops (DPLL's) for the advanced deep-space transponders (ADT's) are investigated. DPLL's considered in this article are derived from the analog phase-locked loop, which is currently employed by the NASA standard deep space transponder, using S-domain to Z-domain mapping techniques. Three mappings are used to develop digital approximations of the standard deep space analog phase-locked loop, namely the bilinear transformation (BT), impulse invariant transformation (IIT), and step invariant transformation (SIT) techniques. The performance in terms of the closed loop phase and magnitude responses, carrier tracking jitter, and response of the loop to the phase offset (the difference between in incoming phase and reference phase) is evaluated for each digital approximation. Theoretical results of the carrier tracking jitter for command-on and command-off cases are then validated by computer simulation. Both theoretical and computer simulation results show that at high sampling frequency, the DPLL's approximated by all three transformations have the same tracking jitter. However, at low sampling frequency, the digital approximation using BT outperforms the others. The minimum sampling frequency for adequate tracking performance is determined for each digital approximation of the analog loop. In addition, computer simulation shows that the DPLL developed by BT provides faster response to the phase offset than IIT and SIT.

The radiation history of material returned by the Soviet automatic stations Luna 16 and Luna 20, according to track studies

NASA Technical Reports Server (NTRS)

Kashkarov, L. L.; Genayeva, L. I.; Lavrukhina, A. K.

1977-01-01

Fission tracks formed by the vH (very heavy) nuclei group of solar and galactic cosmic rays have been studied in silicate minerals of the lunar regolith returned by the Luna 16 and Luna 20 unmanned spacecraft. It is shown that the material in the Luna 16 core sample, from a typical mare region of the lunar surface, has undergone stronger irradiation by cosmic rays than material returned a highland region by Luna 20. A low-irradiation component (about 10 percent of the total number of crystals) has been found in the Luna 20 core sample materials, which can possibly be attributed to material added to the main bulk of the regolith in the formation of the crater Apollonius C. From the track density distribution of crystals, as a function of depth in the regolith core sample, it follows that the process of formation of the upper layer of the regolith, both for the lunar mare and for the highland region, includes sequential layering of finely crushed crystalline matter and subsequent mixing of it by micrometeorite bombardment. A portion of the crystals with a very high track density may be a component added to the lunar surface from outer space.

An automated in vitro model for the evaluation of ultrasound modalities measuring myocardial deformation

PubMed Central

2010-01-01

Background Echocardiography is the method of choice when one wishes to examine myocardial function. Qualitative assessment of the 2D grey scale images obtained is subjective, and objective methods are required. Speckle Tracking Ultrasound is an emerging technology, offering an objective mean of quantifying left ventricular wall motion. However, before a new ultrasound technology can be adopted in the clinic, accuracy and reproducibility needs to be investigated. Aim It was hypothesized that the collection of ultrasound sample data from an in vitro model could be automated. The aim was to optimize an in vitro model to allow for efficient collection of sample data. Material & Methods A tissue-mimicking phantom was made from water, gelatin powder, psyllium fibers and a preservative. Sonomicrometry crystals were molded into the phantom. The solid phantom was mounted in a stable stand and cyclically compressed. Peak strain was then measured by Speckle Tracking Ultrasound and sonomicrometry. Results We succeeded in automating the acquisition and analysis of sample data. Sample data was collected at a rate of 200 measurement pairs in 30 minutes. We found good agreement between Speckle Tracking Ultrasound and sonomicrometry in the in vitro model. Best agreement was 0.83 ± 0.70%. Worst agreement was -1.13 ± 6.46%. Conclusions It has been shown possible to automate a model that can be used for evaluating the in vitro accuracy and precision of ultrasound modalities measuring deformation. Sonomicrometry and Speckle Tracking Ultrasound had acceptable agreement. PMID:20822532

Human Amygdala Tracks a Feature-Based Valence Signal Embedded within the Facial Expression of Surprise.

PubMed

Kim, M Justin; Mattek, Alison M; Bennett, Randi H; Solomon, Kimberly M; Shin, Jin; Whalen, Paul J

2017-09-27

Human amygdala function has been traditionally associated with processing the affective valence (negative vs positive) of an emotionally charged event, especially those that signal fear or threat. However, this account of human amygdala function can be explained by alternative views, which posit that the amygdala might be tuned to either (1) general emotional arousal (activation vs deactivation) or (2) specific emotion categories (fear vs happy). Delineating the pure effects of valence independent of arousal or emotion category is a challenging task, given that these variables naturally covary under many circumstances. To circumvent this issue and test the sensitivity of the human amygdala to valence values specifically, we measured the dimension of valence within the single facial expression category of surprise. Given the inherent valence ambiguity of this category, we show that surprised expression exemplars are attributed valence and arousal values that are uniquely and naturally uncorrelated. We then present fMRI data from both sexes, showing that the amygdala tracks these consensus valence values. Finally, we provide evidence that these valence values are linked to specific visual features of the mouth region, isolating the signal by which the amygdala detects this valence information. SIGNIFICANCE STATEMENT There is an open question as to whether human amygdala function tracks the valence value of cues in the environment, as opposed to either a more general emotional arousal value or a more specific emotion category distinction. Here, we demonstrate the utility of surprised facial expressions because exemplars within this emotion category take on valence values spanning the dimension of bipolar valence (positive to negative) at a consistent level of emotional arousal. Functional neuroimaging data showed that amygdala responses tracked the valence of surprised facial expressions, unconfounded by arousal. Furthermore, a machine learning classifier identified particular visual features of the mouth region that predicted this valence effect, isolating the specific visual signal that might be driving this neural valence response. Copyright © 2017 the authors 0270-6474/17/379510-09$15.00/0.

Isolation, Virulence, and Antimicrobial Resistance of Methicillin-Resistant Staphylococcus aureus (MRSA) and Methicillin Sensitive Staphylococcus aureus (MSSA) Strains from Oklahoma Retail Poultry Meats.

PubMed

Abdalrahman, Lubna S; Stanley, Adriana; Wells, Harrington; Fakhr, Mohamed K

2015-05-29

Staphylococcus aureus is one the top five pathogens causing domestically acquired foodborne illness in the U.S. Only a few studies are available related to the prevalence of S. aureus and MRSA in the U.S. retail poultry industry. The objectives of this study were to determine the prevalence of S. aureus (MSSA and MRSA) in retail chicken and turkey meats sold in Tulsa, Oklahoma and to characterize the recovered strains for their antimicrobial resistance and possession of toxin genes. A total of 167 (114 chicken and 53 turkey) retail poultry samples were used in this study. The chicken samples included 61 organic samples while the rest of the poultry samples were conventional. The overall prevalence of S. aureus was 57/106 (53.8%) in the conventional poultry samples and 25/61 (41%) in the organic ones. Prevalence in the turkey samples (64.2%) was higher than in the chicken ones (42.1%). Prevalence of S. aureus did not vary much between conventional (43.4%) and organic chicken samples (41%). Two chicken samples 2/114 (1.8%) were positive for MRSA. PFGE identified the two MRSA isolates as belonging to PFGE type USA300 (from conventional chicken) and USA 500 (from organic chicken) which are community acquired CA-MRSA suggesting a human based source of contamination. MLST and spa typing also supported this conclusion. A total of 168 Staphylococcus aureus isolates (101 chicken isolates and 67 turkey isolates) were screened for their antimicrobial susceptibility against 16 antimicrobials and their possession of 18 different toxin genes. Multidrug resistance was higher in the turkey isolates compared to the chicken ones and the percentage of resistance to most of the antimicrobials tested was also higher among the turkey isolates. The hemolysin hla and hld genes, enterotoxins seg and sei, and leucocidins lukE-lukD were more prevalent in the chicken isolates. The PVL gene lukS-lukF was detected only in chicken isolates including the MRSA ones. In conclusion, S. aureus is highly prevalent in poultry retail meats sold in Oklahoma with a very low presence of human-originated MRSA. Multidrug resistance is not only prevalent in the MRSA isolates, but also in many MSSA poultry strains, particularly turkey.

Threat of drug resistant Staphylococcus aureus to health in Nepal

PubMed Central

2014-01-01

Background Staphylococcus aureus is the most commonly isolated organism from the different clinical samples in hospital. The emergence and dissemination of methicillin resistant Staphylococcus aureus (MRSA) and growing resistance to non-beta-lactam antibiotics is making treatment of infections due to this organism increasingly difficult. Methods This study was conducted to determine the frequency of Staphylococcus aureus isolated from different clinical samples, rates of MRSA and full antibiotic susceptibility profiles. Clinical samples were cultured and Staphylococcus aureus was identified using standard microbiological methods recommended by the American Society for Microbiology (ASM). Methicillin resistance was confirmed using cefoxitin and oxacillin disks. Inducible clindamycin resistance was identified using D-zone test. Results From the processed samples, 306 isolates of Staphylococcus aureus were recovered. All the isolates were susceptible to vancomycin and teicoplanin. Methicillin resistance was observed in 43.1% of isolates while inducible clindamycin resistance in 12.4% of the isolates. Conclusions The results of our study reveals that rates of resistance to commonly prescribed antibiotics in Staphylococcus aureus clinical isolates is high. In particular, rate of methicillin resistance is alarming, prompting concern on the rational use of antibiotics and vigilant laboratory-based surveillance of resistance rates in Nepal. PMID:24655316

Reconstituting the motility of isolated intracellular cargoes.

PubMed

Hendricks, Adam G; Goldman, Yale E; Holzbaur, Erika L F

2014-01-01

Kinesin, dynein, and myosin transport intracellular cargoes including organelles, membrane-bound vesicles, and mRNA along the cytoskeleton. These motor proteins work collectively in teams to transport cargoes over long distances and navigate around obstacles in the cell. In addition, several types of motors often interact on the same cargo to allow bidirectional transport and switching between the actin and microtubule networks. To examine transport of native cargoes in a simplified in vitro system, techniques have been developed to isolate endogenous cargoes and reconstitute their motility. Isolated cargoes can be tracked and manipulated with high precision using total internal reflection fluorescence microscopy and optical trapping. Through use of native cargoes, we can examine vesicular transport in a minimal system while retaining endogenous motor stoichiometry and the biochemical and mechanical characteristics of both motor and cargo. © 2014 Elsevier Inc. All rights reserved.

Identifying and Tracking Solar Photospheric Bright Points Based on Three-dimensional Segmentation Technology

NASA Astrophysics Data System (ADS)

Xiong, J. P.; Zhang, A. L.; Ji, K. F.; Feng, S.; Deng, H.; Yang, Y. F.

2016-01-01

Photospheric bright points (PBPs) are tiny and short-lived phenomena which can be seen within dark inter-granular lanes. In this paper, we develop a new method to identify and track the PBPs in the three-dimensional data cube. Different from the previous way such as Detection-Before-Tracking, this method is based on the Tracking-While-Detection. Using this method, the whole lifetime of a PBP can be accurately measured while this PBP is possibly separated into several with Laplacian and morphological dilation (LMD) method due to its weak intensity sometimes. With consideration of the G-band PBPs observed by Hinode/SOT (Solar Optical Telescope) for more than two hours, we find that the isolated PBPs have an average lifetime of 3 minutes, and the longest one is up to 27 minutes, which are greater than the values detected by the previous LMD method. Furthermore, we also find that the mean intensity of PBPs is 1.02 times of the mean photospheric intensity, which is less than the values detected by LMD method, and the intensity of PBPs presents a period of oscillation with 2-3 minutes during the whole lifetime.

Environmental Screening for the Scedosporium apiospermum Species Complex in Public Parks in Bangkok, Thailand.

PubMed

Luplertlop, Natthanej; Pumeesat, Potjaman; Muangkaew, Watcharamat; Wongsuk, Thanwa; Alastruey-Izquierdo, Ana

2016-01-01

The Scedosporium apiospermum species complex, comprising filamentous fungal species S. apiospermum sensu stricto, S. boydii, S. aurantiacum, S. dehoogii and S. minutispora, are important pathogens that cause a wide variety of infections. Although some species (S. boydii and S. apiospermum) have been isolated from patients in Thailand, no environmental surveys of these fungi have been performed in Thailand or surrounding countries. In this study, we isolated and identified species of these fungi from 68 soil and 16 water samples randomly collected from 10 parks in Bangkok. After filtration and subsequent inoculation of samples on Scedo-Select III medium, colony morphological examinations and microscopic observations were performed. Scedosporium species were isolated from soil in 8 of the 10 parks, but were only detected in one water sample. Colony morphologies of isolates from 41 of 68 soil samples (60.29%) and 1 of 15 water samples (6.67%) were consistent with that of the S. apiospermum species complex. Each morphological type was selected for species identification based on DNA sequencing and phylogenetic analysis of the β-tubulin gene. Three species of the S. apiospermum species complex were identified: S. apiospermum (71 isolates), S. aurantiacum (6 isolates) and S. dehoogii (5 isolates). In addition, 16 sequences could not be assigned to an exact Scedosporium species. According to our environmental survey, the S. apiospermum species complex is widespread in soil in Bangkok, Thailand.

Environmental Screening for the Scedosporium apiospermum Species Complex in Public Parks in Bangkok, Thailand

PubMed Central

Pumeesat, Potjaman; Muangkaew, Watcharamat; Wongsuk, Thanwa; Alastruey-Izquierdo, Ana

2016-01-01

The Scedosporium apiospermum species complex, comprising filamentous fungal species S. apiospermum sensu stricto, S. boydii, S. aurantiacum, S. dehoogii and S. minutispora, are important pathogens that cause a wide variety of infections. Although some species (S. boydii and S. apiospermum) have been isolated from patients in Thailand, no environmental surveys of these fungi have been performed in Thailand or surrounding countries. In this study, we isolated and identified species of these fungi from 68 soil and 16 water samples randomly collected from 10 parks in Bangkok. After filtration and subsequent inoculation of samples on Scedo-Select III medium, colony morphological examinations and microscopic observations were performed. Scedosporium species were isolated from soil in 8 of the 10 parks, but were only detected in one water sample. Colony morphologies of isolates from 41 of 68 soil samples (60.29%) and 1 of 15 water samples (6.67%) were consistent with that of the S. apiospermum species complex. Each morphological type was selected for species identification based on DNA sequencing and phylogenetic analysis of the β-tubulin gene. Three species of the S. apiospermum species complex were identified: S. apiospermum (71 isolates), S. aurantiacum (6 isolates) and S. dehoogii (5 isolates). In addition, 16 sequences could not be assigned to an exact Scedosporium species. According to our environmental survey, the S. apiospermum species complex is widespread in soil in Bangkok, Thailand. PMID:27467209

High-speed adaptive contact-mode atomic force microscopy imaging with near-minimum-force

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Juan; Zou, Qingze, E-mail: qzzou@rci.rutgers.edu

In this paper, an adaptive contact-mode imaging approach is proposed to replace the traditional contact-mode imaging by addressing the major concerns in both the speed and the force exerted to the sample. The speed of the traditional contact-mode imaging is largely limited by the need to maintain precision tracking of the sample topography over the entire imaged sample surface, while large image distortion and excessive probe-sample interaction force occur during high-speed imaging. In this work, first, the image distortion caused by the topography tracking error is accounted for in the topography quantification. Second, the quantified sample topography is utilized inmore » a gradient-based optimization method to adjust the cantilever deflection set-point for each scanline closely around the minimal level needed for maintaining stable probe-sample contact, and a data-driven iterative feedforward control that utilizes a prediction of the next-line topography is integrated to the topography feeedback loop to enhance the sample topography tracking. The proposed approach is demonstrated and evaluated through imaging a calibration sample of square pitches at both high speeds (e.g., scan rate of 75 Hz and 130 Hz) and large sizes (e.g., scan size of 30 μm and 80 μm). The experimental results show that compared to the traditional constant-force contact-mode imaging, the imaging speed can be increased by over 30 folds (with the scanning speed at 13 mm/s), and the probe-sample interaction force can be reduced by more than 15% while maintaining the same image quality.« less

Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

PubMed

Gavrielides, Mike; Furney, Simon J; Yates, Tim; Miller, Crispin J; Marais, Richard

2014-01-01

Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centres, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments. The current work presents a sample tracking system for oncogenomic studies (Onco-STS) to store these data and make them easily accessible to the researchers who work with the samples. The system is a web application, which includes a database and a front-end web page that allows the remote access, submission and updating of the sample data in the database. The web application development programming framework Grails was used for the development and implementation of the system. The resulting Onco-STS solution is efficient, secure and easy to use and is intended to replace the manual data handling of text records. Onco-STS allows simultaneous remote access to the system making collaboration among researchers more effective. The system stores both information on the samples in oncogenomic studies and details of the analyses conducted on the resulting data. Onco-STS is based on open-source software, is easy to develop and can be modified according to a research group's needs. Hence it is suitable for laboratories that do not require a commercial system.

High-speed adaptive contact-mode atomic force microscopy imaging with near-minimum-force.

PubMed

Ren, Juan; Zou, Qingze

2014-07-01

In this paper, an adaptive contact-mode imaging approach is proposed to replace the traditional contact-mode imaging by addressing the major concerns in both the speed and the force exerted to the sample. The speed of the traditional contact-mode imaging is largely limited by the need to maintain precision tracking of the sample topography over the entire imaged sample surface, while large image distortion and excessive probe-sample interaction force occur during high-speed imaging. In this work, first, the image distortion caused by the topography tracking error is accounted for in the topography quantification. Second, the quantified sample topography is utilized in a gradient-based optimization method to adjust the cantilever deflection set-point for each scanline closely around the minimal level needed for maintaining stable probe-sample contact, and a data-driven iterative feedforward control that utilizes a prediction of the next-line topography is integrated to the topography feeedback loop to enhance the sample topography tracking. The proposed approach is demonstrated and evaluated through imaging a calibration sample of square pitches at both high speeds (e.g., scan rate of 75 Hz and 130 Hz) and large sizes (e.g., scan size of 30 μm and 80 μm). The experimental results show that compared to the traditional constant-force contact-mode imaging, the imaging speed can be increased by over 30 folds (with the scanning speed at 13 mm/s), and the probe-sample interaction force can be reduced by more than 15% while maintaining the same image quality.

Curation and Analysis of Samples from Comet Wild-2 Returned by NASA's Stardust Mission

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, Keiko; Walker, Robert M.

2015-01-01

The NASA Stardust mission returned the first direct samples of a cometary coma from comet 81P/Wild-2 in 2006. Intact capture of samples encountered at 6 km/s was enabled by the use of aerogel, an ultralow dense silica polymer. Approximately 1000 particles were captured, with micron and submicron materials distributed along mm scale length tracks. This sample collection method and the fine scale of the samples posed new challenges to the curation and cosmochemistry communities. Sample curation involved extensive, detailed photo-documentation and delicate micro-surgery to remove particles without loss from the aerogel tracks. This work had to be performed in highly clean facility to minimize the potential of contamination. JSC Curation provided samples ranging from entire tracks to micrometer-sized particles to external investigators. From the analysis perspective, distinguishing cometary materials from aerogel and identifying the potential alteration from the capture process were essential. Here, transmission electron microscopy (TEM) proved to be the key technique that would make this possible. Based on TEM work by ourselves and others, a variety of surprising findings were reported, such as the observation of high temperature phases resembling those found in meteorites, rarely intact presolar grains and scarce organic grains and submicrometer silicates. An important lesson from this experience is that curation and analysis teams must work closely together to understand the requirements and challenges of each task. The Stardust Mission also has laid important foundation to future sample returns including OSIRIS-REx and Hayabusa II and future cometary nucleus sample return missions.

Performance of forty-one microbial source tracking methods: A twenty-seven lab evaluation study

EPA Science Inventory

The last decade has seen development of numerous new microbial source tracking (MST) methodologies, but many of these have been tested in just a few laboratories with a limited number of fecal samples. This method evaluation study examined the specificity and sensitivity of 43 ...

Method for isolating nucleic acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurt, Jr., Richard Ashley; Elias, Dwayne A.

The current disclosure provides methods and kits for isolating nucleic acid from an environmental sample. The current methods and compositions further provide methods for isolating nucleic acids by reducing adsorption of nucleic acids by charged ions and particles within an environmental sample. The methods of the current disclosure provide methods for isolating nucleic acids by releasing adsorbed nucleic acids from charged particles during the nucleic acid isolation process. The current disclosure facilitates the isolation of nucleic acids of sufficient quality and quantity to enable one of ordinary skill in the art to utilize or analyze the isolated nucleic acids formore » a wide variety of applications including, sequencing or species population analysis.« less

Use of Spatial Sampling and Microbial Source-Tracking Tools for Understanding Fecal Contamination at Two Lake Erie Beaches

USGS Publications Warehouse

Francy, Donna S.; Bertke, Erin E.; Finnegan, Dennis P.; Kephart, Christopher M.; Sheets, Rodney A.; Rhoades, John; Stumpe, Lester

2006-01-01

Source-tracking tools were used to identify potential sources of fecal contamination at two Lake Erie bathing beaches: an urban beach (Edgewater in Cleveland, Ohio) and a beach in a small city (Lakeshore in Ashtabula, Ohio). These tools included identifying spatial patterns of Escherichia coli (E. coli) concentrations in each area, determining weather patterns that caused elevated E. coli, and applying microbial source tracking (MST) techniques to specific sites. Three MST methods were used during this study: multiple antibiotic resistance (MAR) indexing of E. coli isolates and the presence of human-specific genetic markers within two types of bacteria, the genus Bacteroides and the species Enterococcus faecium. At Edgewater, sampling for E. coli was done during 2003-05 at bathing-area sites, at nearshore lake sites, and in shallow ground water in foreshore and backshore areas. Spatial sampling at nearshore lake sites showed that fecal contamination was most likely of local origin; E. coli concentrations near the mouths of rivers and outfalls remote to the beach were elevated (greater than 235 colony-forming units per 100 milliliters (CFU/100 mL)) but decreased along transport pathways to the beach. In addition, E. coli concentrations were generally highest in bathing-area samples collected at 1- and 2-foot water depths, midrange at 3-foot depths, and lowest in nearshore lake samples typically collected 150 feet from the shoreline. Elevated E. coli concentrations at bathing-area sites were generally associated with increased wave heights and rainfall, but not always. E. coli concentrations were often elevated in shallow ground-water samples, especially in samples collected less than 10 feet from the edge of water (near foreshore area). The interaction of shallow ground water and waves may be a mechanism of E. coli storage and accumulation in foreshore sands. Infiltration of bird feces through sand with surface water from rainfall and high waves may be concentrating E. coli in shallow ground water in foreshore and backshore sands. At Lakeshore, sampling for E. coli was done at bathing-area, nearshore lake, and parking-lot sites during 2004-05. Low concentrations of E. coli at nearshore lake sites furthest from the shoreline indicated that fecal contamination was most likely of local origin. High concentrations of E. coli in water and bed sediments at several nearshore lake sites showed that contamination was emanating from several points along the shoreline during wet and dry weather, including the boat ramp, an area near the pond drainage, and parking-lot sediments. Physical evidence confirmed that runoff from the parking lot leads to degradation of water quality at the beach. MST samples were collected to help interpret spatial findings and determine whether sources of fecal contamination were from wastewater or bird feces and if a human-specific marker was present. MAR indices were useful in distinguishing between bird feces and wastewater sources because they were about 10 times higher in the latter. The results from MAR indices agreed with results from the two human-specific markers in some but not all of the samples tested. Bacteroides and enterococci human-specific markers were found on one day at Edgewater and two days at Lakeshore. On three days at Edgewater and two days at Lakeshore, the MAR index indicated a mixed source, but neither marker was found in bathing-water samples; this may be because bacterial indicator concentrations were too low to detect a marker. Multiple tools are needed to help identify sources of fecal contamination at coastal beaches. Spatial sampling identified patterns in E. coli concentrations and yielded information on the physical pathways of contamination. MST methods provided information on whether the source was likely of human or nonhuman origin only; however, MST did not provide information on the pathways of contamination.

Occurrence and characterization of Shiga toxin-producing Escherichia coli in raw meat, raw milk, and street vended juices in Bangladesh.

PubMed

Islam, Mohammad A; Mondol, Abdus S; Azmi, Ishrat J; de Boer, Enne; Beumer, Rijkelt R; Zwietering, Marcel H; Heuvelink, Annet E; Talukder, Kaisar A

2010-11-01

The major objective of this study was to investigate the prevalence of Shiga toxin (Stx)-producing Escherichia coli (STEC) in different types of food samples and to compare their genetic relatedness with STEC strains previously isolated from animal sources in Bangladesh. We investigated a total of 213 food samples, including 90 raw meat samples collected from retail butcher shops, 20 raw milk samples from domestic cattle, and 103 fresh juice samples from street vendors in Dhaka city. We found that more than 68% (n = 62) of the raw meat samples were positive for the stx gene(s); 34% (n = 21) of buffalo meats and 66% (n = 41) of beef. Approximately 10% (n = 2) of the raw milk and 8% (n = 8) of the fresh juice samples were positive for stx. We isolated STEC O157 from seven meat samples (7.8%), of which two were from buffalo meats and five from beef; and no other STEC serotypes could be isolated. We could not isolate STEC from any of the stx-positive raw milk and juice samples. The STEC O157 isolates from raw meats were positive for the stx(2), eae, katP, etpD, and enterohemorrhagic E. coli hly virulence genes, and they belonged to three different phage types: 8 (14.3%), 31 (42.8%), and 32 (42.8%). Pulsed-field gel electrophoresis (PFGE) typing revealed six distinct patterns among seven isolates of STEC O157, suggesting a heterogeneous clonal diversity. Of the six PFGE patterns, one was identical and the other two were ≥90% related to PFGE patterns of STEC O157 strains previously isolated from animal feces, indicating that raw meats are readily contaminated with fecal materials. This study represents the first survey of STEC in the food chain in Bangladesh.

A Nonautochthonous U.S. Strain of Vibrio parahaemolyticus Isolated from Chesapeake Bay Oysters Caused the Outbreak in Maryland in 2010

PubMed Central

Haendiges, Julie; Jones, Jessica; Myers, Robert A.; Mitchell, Clifford S.; Butler, Erin

2016-01-01

ABSTRACT In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to the consumption of oysters. Strains isolated from both stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). However, the oysters contained other potentially pathogenic V. parahaemolyticus strains exhibiting different PFGE patterns. In order to assess the identity, genetic makeup, relatedness, and potential pathogenicity of the V. parahaemolyticus strains, we sequenced 11 such strains (2 clinical strains and 9 oyster strains). We analyzed these genomes by in silico multilocus sequence typing (MLST) and determined their phylogeny using a whole-genome MLST (wgMLST) analysis. Our in silico MLST analysis identified six different sequence types (STs) (ST8, ST676, ST810, ST811, ST34, and ST768), with both of the clinical and four of the oyster strains being identified as belonging to ST8. Using wgMLST, we showed that the ST8 strains from clinical and oyster samples were nearly indistinguishable and belonged to the same outbreak, confirming that local oysters were the source of the infections. The remaining oyster strains were genetically diverse, differing in >3,000 loci from the Maryland ST8 strains. eBURST analysis comparing these strains with strains of other STs available at the V. parahaemolyticus MLST website showed that the Maryland ST8 strains belonged to a clonal complex endemic to Asia. This indicates that the ST8 isolates from clinical and oyster sources were likely not endemic to Maryland. Finally, this study demonstrates the utility of whole-genome sequencing (WGS) and associated analyses for source-tracking investigations. IMPORTANCE Vibrio parahaemolyticus is an important foodborne pathogen and the leading cause of bacterial infections in the United States associated with the consumption of seafood. In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to oyster consumption. Strains isolated from stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). The oysters also contained other potentially pathogenic V. parahaemolyticus strains with different PFGE patterns. Since their identity, genetic makeup, relatedness, and potential pathogenicity were unknown, their genomes were determined by using next-generation sequencing. Whole-genome sequencing (WGS) analysis by whole-genome multilocus sequence typing (wgMLST) allowed (i) identification of clinical and oyster strains with matching PFGE profiles as belonging to ST8, (ii) determination of oyster strain diversity, and (iii) identification of the clinical strains as belonging to a clonal complex (CC) described only in Asia. Finally, WGS and associated analyses demonstrated their utility for trace-back investigations. PMID:26994080

A Nonautochthonous U.S. Strain of Vibrio parahaemolyticus Isolated from Chesapeake Bay Oysters Caused the Outbreak in Maryland in 2010.

PubMed

Haendiges, Julie; Jones, Jessica; Myers, Robert A; Mitchell, Clifford S; Butler, Erin; Toro, Magaly; Gonzalez-Escalona, Narjol

2016-06-01

In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to the consumption of oysters. Strains isolated from both stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). However, the oysters contained other potentially pathogenic V. parahaemolyticus strains exhibiting different PFGE patterns. In order to assess the identity, genetic makeup, relatedness, and potential pathogenicity of the V. parahaemolyticus strains, we sequenced 11 such strains (2 clinical strains and 9 oyster strains). We analyzed these genomes by in silico multilocus sequence typing (MLST) and determined their phylogeny using a whole-genome MLST (wgMLST) analysis. Our in silico MLST analysis identified six different sequence types (STs) (ST8, ST676, ST810, ST811, ST34, and ST768), with both of the clinical and four of the oyster strains being identified as belonging to ST8. Using wgMLST, we showed that the ST8 strains from clinical and oyster samples were nearly indistinguishable and belonged to the same outbreak, confirming that local oysters were the source of the infections. The remaining oyster strains were genetically diverse, differing in >3,000 loci from the Maryland ST8 strains. eBURST analysis comparing these strains with strains of other STs available at the V. parahaemolyticus MLST website showed that the Maryland ST8 strains belonged to a clonal complex endemic to Asia. This indicates that the ST8 isolates from clinical and oyster sources were likely not endemic to Maryland. Finally, this study demonstrates the utility of whole-genome sequencing (WGS) and associated analyses for source-tracking investigations. Vibrio parahaemolyticus is an important foodborne pathogen and the leading cause of bacterial infections in the United States associated with the consumption of seafood. In the summer of 2010, Vibrio parahaemolyticus caused an outbreak in Maryland linked to oyster consumption. Strains isolated from stool and oyster samples were indistinguishable by pulsed-field gel electrophoresis (PFGE). The oysters also contained other potentially pathogenic V. parahaemolyticus strains with different PFGE patterns. Since their identity, genetic makeup, relatedness, and potential pathogenicity were unknown, their genomes were determined by using next-generation sequencing. Whole-genome sequencing (WGS) analysis by whole-genome multilocus sequence typing (wgMLST) allowed (i) identification of clinical and oyster strains with matching PFGE profiles as belonging to ST8, (ii) determination of oyster strain diversity, and (iii) identification of the clinical strains as belonging to a clonal complex (CC) described only in Asia. Finally, WGS and associated analyses demonstrated their utility for trace-back investigations. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The prevalence of Escherichia coli O157 and O157:H7 in ground beef and raw meatball by immunomagnetic separation and the detection of virulence genes using multiplex PCR.

PubMed

Cadirci, Ozgür; Siriken, Belgin; Inat, Gökhan; Kevenk, Tahsin Onur

2010-03-01

The present study was conducted to investigate the presence of Escherichia coli O157 and O157:H7 strains and to detect the presence of the stx1, stx2, and eaeA genes in isolates derived from 200 samples (100 samples from fresh ground beef and 100 samples from raw meatball). The samples were purchased from the Samsun Province in Turkey, over a period of 1 year. Enrichment-based immunomagnetic separation and multiplex polymerase chain reaction were applied for these analyses. E. coli O157 was detected in five of the 200 (2.5%) samples tested (one isolated from ground beef and four from meatball samples), whereas E. coli O157: H7 was not detected in any sample. During the analysis, eight strains of E. coli O157 were obtained. The genes stx1, stx2, and eaeA were detected in two E. coli O157 isolates obtained from two meatball samples, whereas only the eaeA and the stx2 genes were detected in four E. coli O157 strains that were isolated from one meatball sample. None of the stx1, stx2, and eaeA was detected in the E. coli O157 isolates obtained from the ground beef and the one meatball samples. Copyright 2009 Elsevier Ltd. All rights reserved.

Zoonotic pathogens isolated from wild animals and environmental samples at two California wildlife hospitals.

PubMed

Siembieda, Jennifer L; Miller, Woutrina A; Byrne, Barbara A; Ziccardi, Michael H; Anderson, Nancy; Chouicha, Nadira; Sandrock, Christian E; Johnson, Christine K

2011-03-15

To determine types and estimate prevalence of potentially zoonotic enteric pathogens shed by wild animals admitted to either of 2 wildlife hospitals and to characterize distribution of these pathogens and of aerobic bacteria in a hospital environment. Cross-sectional study. Fecal samples from 338 animals in 2 wildlife hospitals and environmental samples from 1 wildlife hospital. Fecal samples were collected within 24 hours of hospital admission. Environmental samples were collected from air and surfaces. Samples were tested for zoonotic pathogens via culture techniques and biochemical analyses. Prevalence of pathogen shedding was compared among species groups, ages, sexes, and seasons. Bacterial counts were determined for environmental samples. Campylobacter spp, Vibrio spp, Salmonella spp, Giardia spp, and Cryptosporidium spp (alone or in combination) were detected in 105 of 338 (31%) fecal samples. Campylobacter spp were isolated only from birds. Juvenile passerines were more likely to shed Campylobacter spp than were adults; prevalence increased among juvenile passerines during summer. Non-O1 serotypes of Vibrio cholerae were isolated from birds; during an oil-spill response, 9 of 10 seabirds screened were shedding this pathogen, which was also detected in environmental samples. Salmonella spp and Giardia spp were isolated from birds and mammals; Cryptosporidium spp were isolated from mammals only. Floors of animal rooms had higher bacterial counts than did floors with only human traffic. Potentially zoonotic enteric pathogens were identified in samples from several species admitted to wildlife hospitals, indicating potential for transmission if prevention is not practiced.

Isolation of Canine parvovirus with a view to identify the prevalent serotype on the basis of partial sequence analysis.

PubMed

Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P N; Sharma, N S

2015-01-01

The aim of this study was to isolate Canine parvovirus (CPV) from suspected dogs on madin darby canine kidney (MDCK) cell line and its confirmation by polymerase chain reaction (PCR) and nested PCR (NPCR). Further, VP2 gene of the CPV isolates was amplified and sequenced to determine prevailing antigenic type. A total of 60 rectal swabs were collected from dogs showing signs of gastroenteritis, processed and subjected to isolation in MDCK cell line. The samples showing cytopathic effects (CPE) were confirmed by PCR and NPCR. These samples were subjected to PCR for amplification of VP2 gene of CPV, sequenced and analyzed to study the prevailing antigenic types of CPV. Out of the 60 samples subjected to isolation in MDCK cell line five samples showed CPE in the form of rounding of cells, clumping of cells and finally detachment of the cells. When these samples and the two commercially available vaccines were subjected to PCR for amplification of VP2 gene, a 1710 bp product was amplified. The sequence analysis revealed that the vaccines belonged to the CPV-2 type and the samples were of CPV-2b type. It can be concluded from the present study that out of a total of 60 samples 5 samples exhibited CPE as observed in MDCK cell line. Sequence analysis of the VP2 gene among the samples and vaccine strains revealed that samples belonged to CPV-2b type and vaccines belonging to CPV-2.

C-band radar pulse Doppler error: Its discovery, modeling, and elimination

NASA Technical Reports Server (NTRS)

Krabill, W. B.; Dempsey, D. J.

1978-01-01

The discovery of a C Band radar pulse Doppler error is discussed and use of the GEOS 3 satellite's coherent transponder to isolate the error source is described. An analysis of the pulse Doppler tracking loop is presented and a mathematical model for the error was developed. Error correction techniques were developed and are described including implementation details.

Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).

PubMed

Criscuolo, Alexis; Chesneau, Olivier; Clermont, Dominique; Bizet, Chantal

2018-04-05

Flavobacterium columnare strain PH-97028 (=CIP 109753) is a genomovar III reference strain that was isolated from a diseased Ayu fish in Japan. We report here the analysis of the first available genomovar III sequence of this species to aid in identification, epidemiological tracking, and virulence studies. Copyright © 2018 Criscuolo et al.

Space moving target detection and tracking method in complex background

NASA Astrophysics Data System (ADS)

Lv, Ping-Yue; Sun, Sheng-Li; Lin, Chang-Qing; Liu, Gao-Rui

2018-06-01

The background of the space-borne detectors in real space-based environment is extremely complex and the signal-to-clutter ratio is very low (SCR ≈ 1), which increases the difficulty for detecting space moving targets. In order to solve this problem, an algorithm combining background suppression processing based on two-dimensional least mean square filter (TDLMS) and target enhancement based on neighborhood gray-scale difference (GSD) is proposed in this paper. The latter can filter out most of the residual background clutter processed by the former such as cloud edge. Through this procedure, both global and local SCR have obtained substantial improvement, indicating that the target has been greatly enhanced. After removing the detector's inherent clutter region through connected domain processing, the image only contains the target point and the isolated noise, in which the isolated noise could be filtered out effectively through multi-frame association. The proposed algorithm in this paper has been compared with some state-of-the-art algorithms for moving target detection and tracking tasks. The experimental results show that the performance of this algorithm is the best in terms of SCR gain, background suppression factor (BSF) and detection results.

Navigation for fluoroscopy-guided cryo-balloon ablation procedures of atrial fibrillation

NASA Astrophysics Data System (ADS)

Bourier, Felix; Brost, Alexander; Kleinoeder, Andreas; Kurzendorfer, Tanja; Koch, Martin; Kiraly, Attila; Schneider, Hans-Juergen; Hornegger, Joachim; Strobel, Norbert; Kurzidim, Klaus

2012-02-01

Atrial fibrillation (AFib), the most common arrhythmia, has been identified as a major cause of stroke. The current standard in interventional treatment of AFib is the pulmonary vein isolation (PVI). PVI is guided by fluoroscopy or non-fluoroscopic electro-anatomic mapping systems (EAMS). Either classic point-to-point radio-frequency (RF)- catheter ablation or so-called single-shot-devices like cryo-balloons are used to achieve electrically isolation of the pulmonary veins and the left atrium (LA). Fluoroscopy-based systems render overlay images from pre-operative 3-D data sets which are then merged with fluoroscopic imaging, thereby adding detailed 3-D information to conventional fluoroscopy. EAMS provide tracking and visualization of RF catheters by means of electro-magnetic tracking. Unfortunately, current navigation systems, fluoroscopy-based or EAMS, do not provide tools to localize and visualize single shot devices like cryo-balloon catheters in 3-D. We present a prototype software for fluoroscopy-guided ablation procedures that is capable of superimposing 3-D datasets as well as reconstructing cyro-balloon catheters in 3-D. The 3-D cyro-balloon reconstruction was evaluated on 9 clinical data sets, yielded a reprojected 2-D error of 1.72 mm +/- 1.02 mm.

Method for nucleic acid isolation using supercritical fluids

DOEpatents

Nivens, D.E.; Applegate, B.M.

1999-07-13

A method is disclosed for detecting the presence of a microorganism in an environmental sample involves contacting the sample with a supercritical fluid to isolate nucleic acid from the microorganism, then detecting the presence of a particular sequence within the isolated nucleic acid. The nucleic acid may optionally be subjected to further purification. 4 figs.

Amoebae from antarctic soil and water.

PubMed Central

Brown, T J; Cursons, R T; Keys, E A

1982-01-01

Samples of soil and water were taken from the McMurdo Sound-Dry Valley region of Antarctica. Of the 70 samples cultured, 22 yielded amoebae capable of clonal growth at 30 degrees C. None of the isolates was pathogenic for mice. Acanthamoeba isolates appeared to show better survival potential than Naegleria isolates. PMID:7125658

Toxigenic Aspergillus flavus and other fungi of public health concern in food and organic matter in southwest Nigeria

USDA-ARS?s Scientific Manuscript database

Six Aspergillus flavus isolates out of 17 fungal isolates were sampled from diverse food and organic matter in southwest Nigeria. All the A. flavus samples produced aflatoxin and cyclopiazonic acid. These six isolates constitute a ready mycobank of toxigenic species for analytical research involving...

Availability of a fetal goat tongue cell line ZZ-R 127 for isolation of Foot-and-mouth disease virus (FMDV) from clinical samples collected from animals experimentally infected with FMDV.

PubMed

Fukai, Katsuhiko; Onozato, Hiroyuki; Kitano, Rie; Yamazoe, Reiko; Morioka, Kazuki; Yamada, Manabu; Ohashi, Seiichi; Yoshida, Kazuo; Kanno, Toru

2013-11-01

The availability of the fetal goat tongue cell line ZZ-R 127 for the isolation of Foot-and-mouth disease virus (FMDV) has not been evaluated using clinical samples other than epithelial suspensions. Therefore, in the current study, the availability of ZZ-R 127 cells for the isolation of FMDV was evaluated using clinical samples (e.g., sera, nasal swabs, saliva, feces, and oropharyngeal fluids) collected from animals experimentally infected with an FMDV isolate. Virus isolation rates for the ZZ-R 127 cells were statistically higher than those for the porcine kidney cell line (IB-RS-2) in experimental infections using cattle, goats, and pigs (P < 0.01). Virus titers in the ZZ-R 127 cells were also statistically higher than those in the IB-RS-2 cells. The availability of ZZ-R 127 cells for the isolation of FMDV not only from epithelial suspensions but also from other clinical samples was confirmed in the current study.

Voice over: Audio-visual congruency and content recall in the gallery setting

PubMed Central

Fairhurst, Merle T.; Scott, Minnie; Deroy, Ophelia

2017-01-01

Experimental research has shown that pairs of stimuli which are congruent and assumed to ‘go together’ are recalled more effectively than an item presented in isolation. Will this multisensory memory benefit occur when stimuli are richer and longer, in an ecological setting? In the present study, we focused on an everyday situation of audio-visual learning and manipulated the relationship between audio guide tracks and viewed portraits in the galleries of the Tate Britain. By varying the gender and narrative style of the voice-over, we examined how the perceived congruency and assumed unity of the audio guide track with painted portraits affected subsequent recall. We show that tracks perceived as best matching the viewed portraits led to greater recall of both sensory and linguistic content. We provide the first evidence that manipulating crossmodal congruence and unity assumptions can effectively impact memory in a multisensory ecological setting, even in the absence of precise temporal alignment between sensory cues. PMID:28636667

Rough versus smooth topography along oceanic hotspot tracks: Observations and scaling analysis

NASA Astrophysics Data System (ADS)

Orellana-Rovirosa, Felipe; Richards, Mark

2017-05-01

Some hotspot tracks are topographically smooth and broad (Nazca, Carnegie/Cocos/Galápagos, Walvis, Iceland), while others are rough and discontinuous (Easter/Sala y Gomez, Tristan-Gough, Louisville, St. Helena, Hawaiian-Emperor). Smooth topography occurs when the lithospheric age at emplacement is young, favoring intrusive magmatism, whereas rough topography is due to isolated volcanic edifices constructed on older/thicker lithosphere. The main controls on the balance of intrusive versus extrusive magmatism are expected to be the hotspot swell volume flux Qs, plate hotspot relative speed v, and lithospheric elastic thickness Te, which can be combined as a dimensionless parameter R = (Qs/v)1/2/Te, which represents the ratio of plume heat to the lithospheric heat capacity. Observational constraints show that, except for the Ninetyeast Ridge, R is a good predictor of topographic character: for R < 1.5 hotspot tracks are topographically rough and dominated by volcanic edifices, whereas for R > 3 they are smooth and dominated by intrusion.

Motion control of the rabbit ankle joint with a flat interface nerve electrode.

PubMed

Park, Hyun-Joo; Durand, Dominique M

2015-12-01

A flat interface nerve electrode (FINE) has been shown to improve fascicular and subfascicular selectivity. A recently developed novel control algorithm for FINE was applied to motion control of the rabbit ankle. A 14-contact FINE was placed on the rabbit sciatic nerve (n = 8), and ankle joint motion was controlled for sinusoidal trajectories and filtered random trajectories. To this end, a real-time controller was implemented with a multiple-channel current stimulus isolator. The performance test results showed good tracking performance of rabbit ankle joint motion for filtered random trajectories and sinusoidal trajectories (0.5 Hz and 1.0 Hz) with <10% average root-mean-square (RMS) tracking error, whereas the average range of ankle joint motion was between -20.0 ± 9.3° and 18.1 ± 8.8°. The proposed control algorithm enables the use of a multiple-contact nerve electrode for motion trajectory tracking control of musculoskeletal systems. © 2015 Wiley Periodicals, Inc.

Voice over: Audio-visual congruency and content recall in the gallery setting.

PubMed

Fairhurst, Merle T; Scott, Minnie; Deroy, Ophelia

2017-01-01

Experimental research has shown that pairs of stimuli which are congruent and assumed to 'go together' are recalled more effectively than an item presented in isolation. Will this multisensory memory benefit occur when stimuli are richer and longer, in an ecological setting? In the present study, we focused on an everyday situation of audio-visual learning and manipulated the relationship between audio guide tracks and viewed portraits in the galleries of the Tate Britain. By varying the gender and narrative style of the voice-over, we examined how the perceived congruency and assumed unity of the audio guide track with painted portraits affected subsequent recall. We show that tracks perceived as best matching the viewed portraits led to greater recall of both sensory and linguistic content. We provide the first evidence that manipulating crossmodal congruence and unity assumptions can effectively impact memory in a multisensory ecological setting, even in the absence of precise temporal alignment between sensory cues.