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At least 19 records

Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis

Background: Investigators using metagenomic sequencing to study microbiomes often trim and decontaminate reads without knowing their effect on downstream analyses. Objective: This study was designed to evaluate the impacts JGI trimming and decontamination procedures have on assembly and binning metrics, placement of MAGs into species trees, and functional profiles of MAGs extracted from complex rhizosphere metagenomes, as well as how more aggressive trimming impacts these binning metrics. Methods: Twenty-three Miscanthus x giganteus rhizosphere metagenomes were subjected to different combinations and thresholds of force, kmer, and quality trimming and decontamination using BBDuk. Reads were assembled and binned in KBase. Phylogenomic and statistical analyses were applied to evaluate the effects of trimming and decontamination on downstream analyses. Results: We found that JGI trimmed and decontaminated reads had significant impacts on assembly and binning metrics compared to raw reads, including significantly higher total contig counts, more contigs greater than 10k bp in length, and larger total lengths of raw assemblies compared to QC assemblies, and 2.0% lower average contamination of QC MAGs compared to raw MAGs. We also found that differences in the placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. Furthermore, aggressive trimming (Q20) was found to significantly reduce MAG counts. Conclusion: Trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing?” However, mild trimming and decontamination of metagenomic reads with high-quality scores are recommended for removing sample processing and sequencing artifacts.

Whitham, Jason M.↗

Designing a Decontamination Solution for the Low-Earth-Orbit, Cryogenic SPHEREx Mission

To address the scientific goals of NASA’s astrophysics division, the JPL and Caltech’s SPHEREx mission conducts the first near-infrared all-sky spectral survey in low-earth-orbit using a passively-cooled, cryogenic telescope. Several unique water contamination issues arise due to the combination of cryogenic operation temperatures and the limited temperature control authority of passive cooling. Because water molecules have adsorption bands within the wavelengths of interest for SPHEREx’s survey, it is imperative that water contamination be controlled and minimized. In this work, a model is developed for the SPHEREx mission to predict the transport and accumulation of outgassed water onto sensitive payload components. The model utilizes the time dependent thermal profiles of the individual payload components, initial water content, and spacecraft geometry to calculate the time dependent water diffusion, transport, and adsorption. This model is subsequently used to predict water contamination risks and design decontamination solutions for each risk. Two major water contamination risks were predicted, water accumulation during cooldown and on cryogenic surfaces during the mission. The first risk occurs during the cooldown of the payload to cryogenic temperatures, predicting water accumulation on optical surfaces in excess of the allowable levels. To mitigate this accumulation, the temperature of the optical surfaces is controlled during cooldown through a combination of heaters and spacecraft pointing. The second risk is that over the course of the mission, is unavoidable water accumulation onto the payload thermal system’s cryogenic surfaces, possibly jeopardizing thermal performance and temperature stability, both of which are required for science success. To decontaminate any water that had collected onto cryogenic thermal system surfaces, a decontamination maneuver was designed. In this decontamination maneuver, cryogenic surfaces of the thermal system are warmed to a temperature where water will desorb by spacecraft pointing while still meeting all avoidance constraints, and thereby avoiding undue risk to the observatory hardware. Through application of the developed analytical model and inclusion of the decontamination maneuver in the mission design, SPHEREx can confidently demonstrate that it is able to decontaminate, at the start of and during the mission as needed to meet its end of life science performance requirements.

Soares, Carolos E.↗

Decontamination of Mixed Paper and Plastic Municipal Solid Waste Increases Low and High Temperature Conversion Yields

With the implementation of China’s Green Fence Policy and the following National Sword Policy, there is a need to divert previously accepted waste materials away from the landfill. Mixed plastic and paper wastes that are too contaminated to be economically recycled can be used for conversion into fuels and products. The effect of common contaminants present in waste streams must be determined to make municipal solid waste (MSW) a viable alternative to agricultural feedstocks for conversion. In this study, MSW was sourced from a dual stream materials recovery facility (MRF) in Emmet County, Michigan and characterized via mass balance. The most common contaminants in mixed paper and plastic were quantified and targeted for decontamination when mixed paper was explored for low temperature conversion pathways and plastics for high temperature conversion pathways. Ink, stickies, and plastic contamination were sorted out of the mixed paper stream and did not have an impact on sugar yields during enzymatic hydrolysis (EH). Although no improvement in yield was found, it was noted that copy paper within the mixed paper stream had an elevated pH and higher concentration of fermentation inhibitors, suggesting that intrinsic properties of some paper types may not be ideal for EH and fermentation conversion. Dilute alkaline pretreatment and mechanical refining of mixed paper increased the EH yield of mixed paper, suggesting this previously established process could be used as a decontamination method. “Dirt” and particulates were washed from mixed plastic using either an aqueous detergent or a non-aqueous chemical washing method. Liquid oil yields were increased during microwave assisted fast pyrolysis. All decontamination techniques met the cost target of less than $30/dry ton with plastic decontamination ranging from $18.16 to $24.81/dry ton. Because dilute alkaline pre-treatment and mechanical refining is considered part of the conversion process, the decontamination cost during feedstock preprocessing was considered $0/dry ton.

09 BIOMASS FUELS↗

Decontamination Strategies to Increase Fuel and Product Conversion Yields of Municipal Solid Waste

Since the implementation of China’s Green Fence and National Sword policies, many areas lost a market for heavily contaminated municipal solid waste (MSW). Approximately 17.2 million tons of paper and 26.9 million tons of plastic were landfilled in the United States in 2018. This non-recyclable waste that would normally be landfilled can be converted into fuels and chemicals, but common contaminants that are present in non-recyclable waste can negatively affect low and high-temperature conversion yields. In addition, MSW is a heterogeneous feedstock whose composition can vary widely across geographical areas and socio-economic statuses. This presents a unique challenge for providing a consistent feedstock to biorefineries around the world. Techniques that are commonly used in other industries, in addition to pre-processing methods used for traditional biomass, can be used to increase conversion yields. Drawing on established techniques, as well as experimental decontamination strategies, non-recyclable MSW could represent a viable alternative to agricultural residues for biofuel production. Although many of the techniques explored in this chapter have been used extensively in other industries, the feedstock composition needs to be carefully considered when choosing prospective decontamination methods. It is likely that there is not a “one-size-fits-all” decontamination method for MSW. In conclusion, a pre-processing and decontamination plan will rely heavily on the composition of the individual waste stream.

09 BIOMASS FUELS↗

Using radioactive material to evaluate decontamination of contaminated electronics

Electronic materials are used everywhere and can get easily contaminated by their use in the field/laboratory. The goal of this project was to use radioactive material to track the effectiveness of a cleaning procedure using an off-the-shelf cleaning gel. Radioactive potassium bromide (KBr) was used as a model contaminant in four contamination scenarios to gauge the effectiveness of a cleaning gel in the decontamination of contaminated raspberry pi’s. Finally, the investigated decontamination technique was found to be 75–97% effective in removing contamination from the tested electronic devices. 95% of the contaminated electronic devices retained their functionality post-decontamination.

38 - RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCL↗

Lipid Decontamination Procedures for Life Detection Missions

Molecular biosignatures are key targets for current, proposed, and future life detection missions. With the high accuracy and low limit of detection (LOD) that new and future instruments will require, decontamination of life detection hardware is necessary to prevent false positives. Lipids are a molecular biosignature of interest, as they are ubiquitous to all life as we know it, can survive unaltered in the geologic record for longer than any other biomolecule (i.e. billions of years), and form through both biotic and abiotic processes. Lipids display origin-diagnostic molecular patterns that can reveal biotic or abiotic synthesis, so finding them and ascertaining their molecular features is important for potentially detecting evidence of life elsewhere. Traditional methods of decontamination, or contamination control (CC), primarily clean hardware through fabrication in sterile (cleanroom) environments, killing microbes, and removing/flushing contaminants off instrument and spacecraft components. However, research suggests that some standard cleaning methods are either unlikely to remove lipid contaminants or are incompatible with life detection instrument materials. To solve this problem, I propose to find, test, and verify a decontamination method that thoroughly cleans instruments by destroying lipid molecules, but is simultaneously compatible with major materials used in these instruments. I will study the effects of traditional CC methods (including Dry Heat Microbial Reduction and Vapor phase Hydrogen Peroxide) and experimental CC methods (Electron Beam Irradiation) on lipid molecules for application to life detection instrumentation. I will then develop a CC plan for a novel lipid detector (ExCALiBR, Extractor for Chemical Analysis of Lipid Biomarkers in Regolith) searching for lipids in either soil or icy world scenarios. This plan will uphold planetary protection regulation requirements and validate experimental analyses of in-situ life detection tests.

Decontamination↗

Removable coatings: Thermal stability and decontamination of steel surfaces from 241 Am

This study presents a comparative analysis of several strippable materials for decontamination of steel surfaces from 241 Am. The strippable coatings were chosen to have a history of application, to be commercially available, easily handled and have different composition and formulation. Carbon steel and stainless steel surfaces (coupons) were utilized as the most representative industrial materials, and the experimental series were expanded to include the rusting treatment of these surfaces as it is common for decommissioned old nuclear facilities. The experiments followed the path of pre-screening of the strippable materials (easiness of application, peeling etc.), their characterization with Fourier-transform infrared (FTIR) spectroscopy and thermogravimetric analysis (TGA), decontamination factors (DF) or removal efficiencies for different types of steel surfaces, and enhancement of the removal efficiencies of the select strippable coatings via amendment with EDTA. As a result, DF and removal efficiencies for stainless steel (both pristine and with rusting treatment) are higher than for pristine carbon steel, and decontamination factors and removal efficiencies are higher for pristine than for rusted carbon steel across all the coatings. It is also shown that EDTA amendment can improve DF and removal efficiency for a strippable coating (i.e., CC Strip), however other factors should also be considered. Thus, the coating CC Strip exhibited easiness in handling and high DF (up to 97% when EDTA-amended), but its drying period was the longest among the rest of the materials and its thermal decomposition indicates on a risk of intense release of heat in case of a fire event.

36 MATERIALS SCIENCE↗

RCT: Module 2.14 Personnel Decontamination [Slides]

In our work environment, one of the major concerns of radiological control is the prevention of personnel contamination. When personnel contamination has been identified, it is the responsibility of the RCTs to perform or oversee the decontamination of the individual using the best methods available. n this course we will address the methods used to detect personnel contamination, the factors that determine decontamination actions, the responsibilities of the RCTs, and the approved methods for decontamination of personnel. This course will prepare the student with the skills necessary for RCT qualification.

61 RADIATION PROTECTION AND DOSIMETRY↗

An Organic Decontamination Method for Sampling Devices used in Life-detection Studies

Organic decontamination of sampling and storage devices are crucial steps for life-detection, habitability, and ecological investigations of extremophiles living in the most inhospitable niches of Earth, Mars and elsewhere. However, one of the main stumbling blocks for Mars-analogue life-detection studies in terrestrial remote field-sites is the capability to clean instruments and sampling devices to organic levels consistent with null values. Here we present a new seven-step, multi-reagent cleaning and decontamination protocol that was adapted and tested on a glacial ice-coring device and on a rover-guided scoop used for sediment sampling both deployed multiple times during two field seasons of the Arctic Mars Analog Svalbard Expedition AMASE). The effectiveness of the protocols for both devices was tested by (1)in situ metabolic measurements via APT, (2)in situ lipopolysacchride (LPS) quantifications via low-level endotoxin assays, and(3) laboratory-based molecular detection via gas chromatography-mass spectrometry. Our results show that the combination and step-wise application of disinfectants with oxidative and solvation properties for sterilization are effective at removing cellular remnants and other organic traces to levels necessary for molecular organic- and life-detection studies. The validation of this seven-step protocol - specifically for ice sampling - allows us to proceed with confidence in kmskia4 analogue investigations of icy environments. However, results from a rover scoop test showed that this protocol is also suitable for null-level decontamination of sample acquisition devices. Thus, this protocol may be applicable to a variety of sampling devices and analytical instrumentation used for future astrobiology missions to Enceladus, and Europa, as well as for sample-return missions.

Eigenbrode, Jennifer↗

Ares I Reaction Control System Propellant Feedline Decontamination Modeling

The objective of the work presented here is to quantify the effects of purge gas temperature, pressure, and mass flow rate on Hydrazine (Hz) decontamination rates of the Ares I Roll Control System and Reaction Control System. A survey of experts in this field revealed the absence of any decontamination rate prediction models. Three basic decontamination methods were identified for analysis and modeling. These include low pressure eduction, high flow rate purge, and pulse purge. For each method, an approach to predict the Hz mass transfer rate, as a function of system pressure, temperature, and purge gas mass flow rate, is developed based on the applicable physics. The models show that low pressure eduction is two orders of magnitude more effective than the high velocity purge, which in turn is two orders of magnitude more effective than the pure diffusion component of pulse purging of deadheads. Eduction subjects the system to low pressure conditions that promote the extraction of Hz vapors. At 120 F, Hz is saturated at approximately 1 psia. At lower pressures and 120 F, Hz will boil, which is an extremely efficient means to remove liquid Hz. The Hz boiling rate is predicted by equating the rate at which energy is added to the saturated liquid Hz through heaters at the tube outer wall with the energy removed from the liquid through evaporation. Boil-off fluxes were predicted by iterating through the range of local pressures with limits set by the minimum allowed pressure of 0.2 psia and maximum allowed wall temperature of 120 F established by the heaters, which gives a saturation pressure of approximately 1.0 psia. Figure 1 shows the resulting boil-off fluxes as a function of local eduction pressure. As depicted in figure 1, the flux is a strong inverse function of eduction pressure, and that minimizing the eduction pressure maximizes the boil-off flux. Also, higher outer wall temperatures lead to higher boil-off fluxes and allow for boil-off over a greater range of eduction pressures.

Pasch, James J.↗

MSW Decontamination: Methods to Improve Biofuel Yields

MSW is usually contaminated with a variety of undesirable materials (food, chemicals, glass, metal) that can impact downstream applications such as conversion to biofuels. This presentation will showcase two decontamination methods using either a detergent wash or an organic solvent extraction to demonstrate up to 30% increase in biofuel precursor yields for plastic and paper MSW. The economics of the two decontamination methods will also be presented.

09 BIOMASS FUELS↗

Performance and electret charge of N95 respirators after decontamination [Slides]

Filtration, pressure drop and quantitative fit of N95 respirators were robust to several decontamination methods including vaporous hydrogen peroxide, wet heat, bleach, and ultraviolet light. Bleach may not have penetrated the hydrophobic outer layers of the N95 respirator. Isopropyl alcohol and detergent both severely degraded the electrostatic charge of the electret filtration layer. First data in N95 respirators that the loss of filtration efficiency was directly correlated with loss of surface potential on the filtration layer. The pressure drop was unchanged, so loss of filtration efficacy would not be apparent during a user seal check. Mechanical straps degrade with repeated mechanical cycling during extended use. Decontamination did not appear to degrade the elastic straps. Significant loss of strap elasticity would be apparent during a user negative pressure seal check.

36 MATERIALS SCIENCE↗

Phased Construction Completion Report for Decontamination Laundry Demolition at the Oak Ridge National Laboratory

This Phased Construction Completion Report (PCCR) documents completion of demolition, waste disposition, and slab stabilization activities of Building 2523 (Decontamination Laundry) for the Oak Ridge National Laboratory (ORNL). The Decontamination Laundry is located directly north of the intersection of White Oak Avenue and the 2519 Access Road. This demolition scope included the removal of the above-grade structures and facility components associated with Building 2523. This scope included the removal of Building 2523 (and all remaining contents inside), Trailer 2523A (and all remaining contents inside), an above-grade wastewater tank, and a wooden access porch connecting Buildings 2523 and Trailer 2523A. On the north side of Building 2523, above-grade portions of selected remaining foundations/stairs were removed from former Building 2517 to make room to stage waste containers. Building 2621 is west of the Laundry Building and Buildings 2547 and 2649 are to the east, while Building 2525 is to the north. Building 2523 is located within Bethel Valley Exposure Unit (EU) 3. The total area of the EU is approximately 39 acres. The area within EU 3 is bounded by First Street on the west, Central Avenue on the north, Third Street on the east and south. The slab of Building 2523 has been stabilized with a cap of flowable fill concrete and asphalt to contain residual radiological contamination and to provide surface suitable for vehicle parking. No below-grade demolition actions were performed during this task.

99 GENERAL AND MISCELLANEOUS↗

Proceedings of Meeting on Problems and Techniques Associated with the Decontamination and Sterilization of Spacecraft

The United States is about to embark on an ambitious program of Lunar and Space Exploration. This program will not only serve the needs of the national and international scientific community but will also enhance the prestige of the United States in the eyes of the peoples of the world.There are many problems associated with such pioneering investigations, among which is included the effecting of adequate safe- guards against biological contamination of celestial bodies with ter- restrial microorganisms. In the not too distant future, the reverse problem of preventing contamination of our terrestrial body with extraterrestrial microorganisms must be considered. In order to determine the current status of decontamination and sterilization procedures and to arrive at areas of research required in order to increase the knowledge in this field, the NASA sponsored a meeting at which time this problem was discussed. Invitations to attend this meeting were extended to agencies actively concerned with the development of spacecraft and launch vehicles as well as those groups involved in the investigation and development of decontamination and sterilization techniques. The meeting was held in Washington, D, C. on June 29, 1960. The recorded minutes of this meeting, which have been edited, are included in this paper, as well as a listing of recommendations resulting from the deliberations.

Posner, Jack↗

Method of decontaminating a contaminated fluid by using photocatalytic particles

A system for decontaminating the contaminated fluid by using photocatalytic particles. The system includes a reactor tank for holding the contaminated fluid and the photocatalytic particles suspended in the contaminated fluid to form a slurry. Light irradiates the surface of the slurry, thereby activating the photocatalytic properties of the particles. The system also includes stirring blades for continuously agitating the irradiated fluid surface and for maintaining the particles in a suspended state within the fluid. The system also includes a cross flow filter for segregating the fluid (after decomposition) from the semiconductor powder. The cross flow filter is occasionally back flushed to remove any semiconductor powder that might have caked on the filter. The semiconductor powder may be recirculated back to the tank for reuse, or may be stored for future use. A series of such systems may be used to gradually decompose a chemical in the fluid. Preferably, the fluid is pretreated to remove certain metal ions which interfere with the photocatalytic process. Such pretreatment may be accomplished by dispersing semiconductor particles within the fluid, which adsorb ions or photodeposit the metal as the free metal or its insoluble oxide or hydroxide, and then removing the semiconductor particles together with the adsorbed metal ions/oxides/hydroxide/free metal from the fluid. A method of decontaminating a contaminated fluid is also disclosed.

Cooper, Gerald↗

Integrated electrochemical nuclear decontamination system

An electrochemical cell that oxidizes a solution provides a continuous and stable supply of an oxidizing ion solution to a fixture or vessel used for the purposes of decontaminating metal and metal alloys. The electrochemical cell includes an anode compartment that oxidizes the solution in nitric acid or methane sulfonic acid at a rate equal to or greater than a rate of reduction, or generates the oxidizing ions prior to use in a batch. The electrochemical cell is part of a larger system that facilitates online measurement system which measures the oxidizing ion solution and the dissolved PuO 2 , UO 2 , AmO 2 , other radionuclides, or other contaminates in real-time. Solution decontamination system removes the dissolved PuO 2 /UO 2 /AmO 2 , other radionuclides, or other contaminates from the oxidizing ion solution, real time acoustic monitoring of the thickness of the surface being contaminated, and automation of a delivery system facilitates flow between surface and electrochemical cell.

Karmiol, Benjamin↗

Evaluation of sustainable waste management: An analysis of techno-economic and life cycle assessments of municipal solid waste sorting and decontamination

This study evaluates the economic and environmental feasibility of Municipal Solid Waste (MSW) sorting and decontamination technologies across urban, suburban, and rural areas. Using Techno-Economic Analysis (TEA) and Life Cycle Assessment (LCA), the research assesses cost-effectiveness and environmental impacts, with a focus on cost variability analyzed through Monte Carlo simulations. Findings indicate significant cost differences based on population density: rural areas incur high costs up to $$764/ton due to low waste volumes and limited infrastructure, whereas suburban and urban areas have more feasible costs ranging from $36.3 to $142.5/ton. Environmental impacts also vary, with greenhouse gas emissions at 171 kg CO 2 eq/ton for copy paper and 118.6 kg CO 2 eq/ton for plastics. PM2.5 levels are 9.1 g/ton for copy paper and 6.3 g/ton for plastics, with sorting lines being the main contributors. Monte Carlo simulations reveal a 50% probability of costs being below $$102.26/ton for copy paper and $115.8/ton for plastics in suburban settings. Further, the study underscores the importance of customized waste management strategies to improve economic viability and sustainability based on local conditions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗