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At least 271 records · Page 15

ContScout: sensitive detection and removal of contamination from annotated genomes

Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.

59 BASIC BIOLOGICAL SCIENCES↗

Modeled sensitivity of multi-MA accelerator performance to electrode contaminant inventory

Significant particle-in-cell code development has enabled simulations of power flow in multi-MA accelerators to include the desorption of surface contaminants, their ionization into surface plasmas, and the impact of these plasmas on efficiency. The simulations base desorption on an Arrhenius equation, whose most significant unknown is the surface contaminant inventory. The sensitivity of power-flow simulations to this inventory is studied here using Sandia National Laboratories' Z accelerator with a 7-nH MagLIF load [Phys. Plasmas 17, 056303 (2010)]. Simulations are conducted in 3D cylindrical coordinates for the current-adder, or “convolute,” region of Z and in 2D for the final feed only. Simulated contaminant inventories are varied from 1 to 32 monolayers (MLs) in 2D, and 2 to 4 ML in 3D. The results reveal sensitivities to the local ratio of E/B⁠. The high B-field, low E-field region near the short-circuit load is insensitive to the contaminant inventory, where assumed values of 4–32 ML change the load current by ≤ 2%, and agree with experiment to within 2% at peak current. A 1-ML value is the outlier, increasing the load current by 5%, but still within measurement uncertainty. In contrast, the relatively higher E-field, lower B-field convolute region has slower contaminant desorption and higher-magnitude E-field penetration of the surface plasmas. The current loss in the convolute region does increase with contaminant inventory. The loss assuming 4 ML is 12% larger than for 2 ML, with 4 ML being the better match to experiment.

Arrhenius equation↗

Dark Energy Survey Year 1 results: validation of weak lensing cluster member contamination estimates from P(z) decomposition

Weak lensing source galaxy catalogues used in estimating the masses of galaxy clusters can be heavily contaminated by cluster members, prohibiting accurate mass calibration. In this study, we test the performance of an estimator for the extent of cluster member contamination based on decomposing the photometric redshift P(z) of source galaxies into contaminating and background components. We perform a full scale mock analysis on a simulated sky survey approximately mirroring the observational properties of the Dark Energy Survey Year One observations (DES Y1), and find excellent agreement between the true number profile of contaminating cluster member galaxies in the simulation and the estimated one. We further apply the method to estimate the cluster member contamination for the DES Y1 redMaPPer cluster mass calibration analysis, and compare the results to an alternative approach based on the angular correlation of weak lensing source galaxies. We find indications that the correlation based estimates are biased by the selection of the weak lensing sources in the cluster vicinity, which does not strongly impact the P(z) decomposition method. Collectively, these benchmarks demonstrate the strength of the P(z) decomposition method in alleviating membership contamination and enabling highly accurate cluster weak lensing studies without broad exclusion of source galaxies, thereby improving the total constraining power of cluster mass calibration via weak lensing.

79 ASTRONOMY AND ASTROPHYSICS↗

Measurable radiation levels around individuals externally contaminated by nuclear fallout

During the early response to large-scale radioactive contamination events, people who are potentially affected need to be screened for radioactive contamination and public health staff need to triage individuals who may need immediate decontamination. This is typically done by screening individuals for external contamination using ionising radiation detection equipment. In this study, spatially and temporally dependent isotopic compositions from a simulated nuclear detonation and Monte Carlo methods were used to relate contamination activity levels to the measurable radiation levels at select distances away from an individual with whole-body contamination. Radionuclide-specific air kerma rate coefficients and Geiger–Mueller instrument response coefficients at five select distances from contaminated individuals are presented for 662 radionuclides. Temporally and spatially dependent incident-specific coefficients are presented for a hypothetical surface detonation of a 235 U-fueled device.

61 RADIATION PROTECTION AND DOSIMETRY↗

Microbial contamination and good manufacturing practices in school kitchen

Abstract This study evaluated microbial contamination and good manufacturing practices (GMP) in school kitchens. Thus, the kitchen of four municipal schools have been assessed through microbiological analysis performed in their cutting boards ( n = 12), kitchen sinks ( n = 12), dish cloths ( n = 12), hands of food handlers ( n = 22), kitchen sponges ( n = 12), milk ( n = 10), and water ( n = 10). A questionnaire was also applied to food handlers in order to access their profiles and get to know their daily practices inside school kitchens. The results this study showed that all samples (surfaces, cutting boards, kitchen sponges, milk, and water) were contaminated with heterotrophic bacteria. Staphylococcus aureus was found on the surface of sinks, dish cloths, cutting boards, and on the hands of food handlers. Fecal coliforms were found on sinks, water, and milk. Results from the survey reveal that food handlers know about GMP, but they do not perform these activities in school kitchens. Practical applications The presented study shows that the schools there are failures in good manufacturing practices (GMP), which increase the risks of food contamination. In addition, we also showed microbial contamination on surface, cutting boards, kitchen sponges, and in food (milk and water) on schools which it make a risk for the development of foodborne diseases, since children have a relatively lower immunity than adults, additional safety measures are needed to protect them from foodborne pathogens and high microbial contamination in school. The microbial contamination in schools show that although the food handlers know about GMP, but there is a necessity for correct surface cleaning in food preparation to avoid foodborne illnesses proliferation in schools

Rossi, Eliandra Mirlei↗

Microscale Investigations of Soil Heterogeneity: Impacts on Zinc Retention and Uptake in Zinc-Contaminated Soils

Here, metal contaminants in soils can persist for millennia, causing lasting negative impacts on local ecosystems. Long-term contaminant bioavailability is related to soil pH and to the strength and stability of solid-phase associations. We combined physical density separation with synchrotron-based microspectroscopy to reduce solid-phase complexity and to study Zn speciation in field-contaminated soils. We also investigated Zn uptake in two Zn-hyperaccumulating ecotypes of Noccaea caerulescens (Ganges and Prayon). Soils were either moderately contaminated (500–800 mg Zn kg –1 via contaminated biosolids application) or grossly enriched (26,000 mg Zn kg –1 via geogenic enrichment). Soils were separated using sodium polytungstate into three fractions: light fraction (LF) (<1.6 g cm –3 ), medium fraction (MF) (1.6–2.8 g cm –3 ), and heavy fraction (HF) (>2.8 g cm –3 ). Approximately 45% of the total Zn was associated with MF in biosolids-contaminated soils. From these data, we infer redistribution to the MF after biosolids application because Zn in biosolids is principally associated with HF and LF. Our results suggest that increasing proportions of HF-associated Zn in soils may be related to greater relative Zn removal by Zn hyperaccumulating plants. Using density fractions enabled assessment of Zn speciation on a microscale despite incomplete fractionation. Analyzing both density fractions and whole soils revealed certain phases (e.g., ZnS, Zn coprecipitated with Fe oxides) that were not obvious in all analyses, indicating multiple views of the same soils enable a more complete understanding of Zn speciation.

36 MATERIALS SCIENCE↗

Results of Temporary Shutdown Testing and Groundwater Pump-Testing at Agra, Kansas, February-September 2016 and march 2017, and Assessment of Groundwater and Contaminant Migration

In 2005, the Commodity Credit Corporation/U.S. Department of Agriculture (CCC/USDA) conducted a comprehensive investigation of potential contaminant source areas on, and in the vicinity of, the former CCC/USDA grain storage facility in Agra, Kansas (Argonne 2006). The data collected during this investigation identified three primary source areas for carbon tetrachloride contamination. One source is located on the former CCC/USDA property, and the other two (western and eastern) sources are located on adjacent property owned by Pro-Ag Marketing. The soil source located at the western end of the Pro-Ag property has been identified as the sole source of carbon tetrachloride contamination to the groundwater in this portion of the Agra site, and is not associated with any grain storage activities on the former CCC/USDA property. In 2008-2009, to address the carbon tetrachloride contamination detected on its former property, the CCC/USDA initiated source area cleanup as an interim measure (IM). The cleanup employs five large-diameter boreholes (LDBs) that were excavated by auger drilling. The purposes of these borings were to (1) physically remove soils impacted by carbon tetrachloride from the most contaminated area for treatment by onsite land farming and (2) provide locations for the installation of coupled soil vapor extraction (SVE) and air sparging (AS) wells to facilitate in-situ treatment of the carbon tetrachloride in the soils and underlying groundwater. With the approval of the KDHE, operation of the SVE/AS systems began in May 2009, and has generally continued with minimal interruption since that time. Land farming operations to treat contaminated soil excavated from the LDBs were successfully completed in October 2010.

54 ENVIRONMENTAL SCIENCES↗

Flue-Gas Desulfurization Effluent Management using an Innovative Low-Energy Biosorpotion Treatment System to Remove Key Contaminants

Among the most critical water contaminants of concern affecting wide geographical regions and a number of industries and natural systems is selenium. Selenium found in surface, ground and wastewater in originates from natural sources, as well as industrial sources such as petroleum refineries, electronics manufacturing, pesticides, and coal power plants and mining also contribute to selenium contamination in water in the US. At high concentrations, selenium is toxic to human and wildlife. There are a number of technologies that have been used to treat selenium and other similar contaminants in water. Biological treatment of selenium has been used in the past to reduce soluble SeVI and/or SeIV to insoluble Se0, which is then filtered in the same vessel. The insoluble selenium (Se0) is then backwashed from the system and solids are separated for subsequent disposal, if they meet the leaching and water content criteria. In order to promote biological reduction to insoluble Se0, heating of bioreactor is needed in some applications, and excess food source (electron donor) is added so that all selenium can be filtered. An additional disadvantage of these systems is the significant amount of water lost due to extensive and frequent backwash and rinse cycles. When comparing the advantages and energy requirements of the various treatment technologies, RO membrane filtration immediately stands out due to the excessive energy expenditure needed to pump water across the membrane although RO is an effective way to remove selenium. In addition, RO requires extensive pretreatment, such as MF membrane, and frequent maintenance, rendering it an expensive option that may be out of reach for certain applications. In fact, although the performance was good during the pilot testing by the NSMP Working Group for treatment naturally occurring selenium in the surface water, the high electricity requirements and significant reject water stream made it an infeasible alternative. While conventional ion exchange maybe an effective treatment option, it requires frequent regeneration of the resin when applied to highly contaminated water, which leads to several tons of contaminant-laden, high-salinity brine that needs to be disposed off-site each day. One of the water systems in the west coast currently uses ion exchange for selenium treatment and has been trucking selenium laden hazardous brine waste weekly in the last several years. Pneumatic pumping and rinse water pumping required for ion exchange also increase the energy usage. In comparison, adsorption process is a passive treatment system where contaminated water comes in contact with an adsorption media in a vessel. Typically, there is no mixing, backwash, or recycle pumping required, thus significantly reducing the energy usage. A passive single-use adsorption system does not require backwash, thereby generating small amount of process waste, and producing the highest water yield among the alternatives. The energy and water efficiencies, and applicability for SeVI and SeIV are summarized in Table 1. Despite these benefits though, adsorption typically does not work for the most oxidized form of selenium (SeVI). The innovative biosorption process integrates both process to increase the treatment efficiency while minimizing energy, chemical, and time required to treat both SeVI and SeIV. Additional advantages include simple partial biological reduction with reduced on-site waste generation, which lead to water and electricity savings, and less operational need compared to biological treatment alone. This makes biosorption especially suitable for remote areas, where liquid backwash and brine disposal may be cost prohibitive or infeasible.

20 FOSSIL-FUELED POWER PLANTS↗

Apollo experience reports: Window contamination

The problem of window contamination in the Apollo command module is reviewed. All five command module windows were contaminated while in earth orbit on the first three manned Apollo flights. The contamination sources were identified and eliminated. Preflight testing of lunar module windows showed that no serious contamination should occur, and this conclusion was verified in subsequent manned flights. The command module window designs and materials are described, the window contamination sources are identified, and the inflight and chemical analyses of the contamination are outlined. The corrective actions that were taken are reviewed. For the lunar module, the window design and materials and the preflight and fight evaluations are described. Window design recommendations are made.

Leger, L. J.↗

Organic contamination problems in the Viking molecular analysis experiment

A principal problem in interpreting the results of an organic analysis of an extraterrestrial sample is that of distinguishing contaminating material from indigenous material when unknown types and amounts of contaminants make their way into the sample being analyzed. An approach to control of sample integrity in the Viking molecular analysis experiment has been devised which it is believed, will eliminate such problems. Basically this involves (1) placing an upper limit on the amount of terrestrial contamination that can be tolerated and still allow scientifically meaningful analysis, (2) identifying the potential sources of contamination and analyzing their relative significance, (3) establishing methods to control these sources, and (4) obtaining complete information on the chemical composition of potential contaminants. Previous experience in the Apollo mission has been of great value in developing the Viking program, perhaps the most important carryover being the recognition of the importance of establishing a comprehensive contamination control program in the early stages of mission planning and hardware design.

Flory, D. A.↗

Preliminary results Skylab experiment TO27 optical contamination in space

Current results from the TO27 experiment which was performed on the first two Skylab missions are presented. The purpose of the experiment was to determine the change in optical properties of various transmissive windows, mirrors, and diffraction gratings caused by the deposition of contaminants found about the orbital assembly and to measure the sky brightness background caused by solar illumination of particulate contaminants. The sample array system containing 248 optical surfaces and exposed outside the orbital workshop did not collect any significant contaminants. Only trace amounts of surface deposited contaminants have been seen, in all cases the measurement was near the limiting sensitivity of the instrument. Unfortunate performance compromises and the relative cleanliness of the assembly on the anti-solar side appeared to place the amount of available surface contaminants near the limiting sensitivity of the sample array. Mass spectroscopy on the trace contaminants show the presence of high molecular weight species, up to 773 amu. The data suggests the presence of condensed aromatics.

Muscari, J. A.↗

Correlation of an optical system degradation with contamination on a critical surface

The loss of sensitivity of a radiantly cooled radiometer during space operation was investigated. A quartz crystal microbalance (QCM), mounted in the proximity of the instrument filter lens and held at its temperature, measured the contaminant at the location during a vacuum test. The temperature cycling of the lens and the QCM verified the contamination of the lens as the cause of the deterioration. Data on the instrument performance in space and in the chamber allowed estimation of the rate of contaminant accretion on the lens in space service. That rate was used to estimate the contaminant partial pressure. The nature of material was inferred by comparison of the partial pressures and the saturated vapor pressures of materials at the temperature of the contaminated surface. These data, in conjunction with data on fields of view of the lens, are used to identify the sources of contamination.

Scialdone, J. J.↗

Preliminary evaluation of the contaminant induced environment for the space shuttle orbiter

A preliminary evaluation of the on-orbit induced environment from identified major sources of contamination for the STS shuttle orbiter is presented. A contamination computer mathematical model is discussed that was used to develop the description and predictions of the induced environment along with the extent and physical makeup of the molecular induced environment from these sources. The predicted induced molecular environment from each source is evaluated against current Space Shuttle Program on-orbit contamination control criteria. The flash evaporator vents and the VCS 25-lb thrust engines are shown to significantly exceed applicable contamination control criteria and were the subject of extensive evaluation. Preliminary conclusions concerning the contaminant potential of these sources along with recommendations for various measures of contamination control regarding the shuttle orbiter design and operational activities are made.

Bareiss, L. E.↗

Payload/orbiter contamination control requirement study

The Spacelab carrier induced contaminant environment and Spacelab's ability to meet established contamination control criteria for the shuttle program are determined. The primary areas of on-going activity include updating, refining, and improving the Spacelab Contamination Computer Model and contamination analysis methodology; establishing the resulting adjusted induced environment predictions for comparison with the applicable criteria; determining Spacelab design and operational requirements necessary to meet the criteria; conducting mission feasibility analyses of the combined Spacelab/orbiter contaminant environment for specific proposed missions and payload mixes; and establishing a preliminary Spacelab mission support plan and model interface requirements. A summary is given of these activities conducted to date including any modifications in approach or methodology utilized in the contamination assessment of the Spacelab vehicle. The emphasis is placed on the Spacelab modeling efforts.

Bareiss, L. E.↗

Organizational strategies for protection against back contamination

The organizational issues pertaining to the prevention of inbound contamination associated with possible Viking missions to Mars are considered. The completed Apollo missions, which returned samples from the moon, provide a convenient base for analysis of inbound contamination issues. Despite concern over the threat of inbound contamination from the moon and efforts to prevent back contamination, the back contamination efforts in the Apollo missions were considered ineffective had these missions encountered living organisms. Several alternatives for consideration in the design of future programs dealing with back contamination are examined and proposed for special consideration.

Mahoney, T. A.↗

Verification approach for the Shuttle/Payload Contamination Evaluation computer program - Spacelab induced environment

The paper presents a compilation of the results of a systems level Shuttle/payload contamination analysis and related computer modeling activities. The current technical assessment of the contamination problems anticipated during the Spacelab program are discussed and recommendations are presented on contamination abatement designs and operational procedures based on experience gained in the field of contamination analysis and assessment, dating back to the pre-Skylab era. The ultimate test of the Shuttle/Payload Contamination Evaluation program will be through comparison of predictions with measured levels of contamination during actual flight.

Bareiss, L. E.↗

Mechanical impact tests of materials in oxygen effects of contamination

The effect of contaminants on the mechanical impact sensitivity of Teflon, stainless steel, and aluminum in a high-pressure oxygen environment was investigated. Uncontaminated Teflon did not ignite under the test conditions. The liquid contaminants - cutting oil, motor lubricating oil, and toolmaker dye - caused Teflon to ignite. Raising the temperature lowered the impact energy required for ignition. Stainless steel was insensitive to ignition under the test conditions with the contaminants used. Aluminum appeared to react without contaminants under certain test conditions; however, contamination with cutting oil, motor lubricating oil, and toolmakers dye increased the sensitivity of aluminum to mechanical impact. The grit contaminants silicon dioxide and copper powder did not conclusively affect the sensitivity of aluminum.

Ordin, P. M.↗

STS-1 mission contamination evaluation approach

The space transportation system 1 mission will be the first opportunity to assess the induced environment of the orbiter payload bay region. Two tools were developed to aid in this assessment. The shuttle payload contamination evaluation computer program was developed to provide an analytical tool for prediction of the induced molecular contamination environment of the space shuttle orbiter during its onorbit operations. An induced environment contamination monitor was constructed and tested to measure the space shuttle orbiter contamination environment inside the payload bay during ascent and descent and inside and outside the payload bay during the onorbit phase. Measurements are to be performed during the four orbital flight test series. Measurements planned for the first flight are described and predicted environmental data are discussed. The results indicate that the expected data are within the measurement range of the induced environment contamination monitor instruments evaluated, and therefore it is expected that useful contamination environmental data will be available after the first flight.

Jacobs, S.↗