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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.↗

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↗

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↗

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↗

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↗

Decontamination of MSW Improves Conversion Efficiency

Municipal solid waste (MSW) offers a significant opportunity for energy conversion pathways. Paper and plastic waste can be converted and upgraded to fuels through low- and high-temperature conversion, respectively. The objective of this study is to develop MSW paper and plastic decontamination methods to increase conversion efficiencies.

09 BIOMASS FUELS↗

Decontamination and Sterilization of Surfaces using Low Cost Ionic Liquids (CRADA Final Report)

The current study made a comprehensive literature review of the structure activity relationship (SAR) for microcidal and virucidal influence of ionic liquids. It summarized the key structure parameters that have close correlation to the antimicrobial and antiviral properties of the ILs. It proposed an experimental plan on developing and testing an effective ionic liquid from renewable lignocellulosic biomass. The goal is to understand the structure activity relationship (SAR) for virucidal influence of ionic liquids through comprehensive literature search and data analysis. A full experimental plan will be drafted based on the literature summary. Perform a comprehensive literature search to aid the development of an effective and easily deployable method to inactivate SARS-CoV-2 and decontaminate surfaces based on low-cost functional ionic liquids. These designer solvents have the potential to be a compelling and environmentally friendly alternative to common chemical disinfectants. Literature summary report including reported ionic liquid structures, synthesis and testing methods, and the structure activity relationship. Experimental plan on developing a low cost effective antiviral ionic liquid.

59 BASIC BIOLOGICAL SCIENCES↗

Results for the October 2023 Semiannual Salt Waste Processing Facility Decontaminated Salt Solution Sample

In this Technical Report, the chemical and radionuclide contaminant results from the October 2023 Semiannual sample of the Salt Waste Processing Facility (SWPF) Decontaminated Salt Solution (DSS) salt solution are presented in tabulated form. The information from this characterization will be used by Savannah River Mission Completion (SRMC) for the transfer of aqueous waste from SWPF to the Saltstone Production Facility (SPF) where the waste will be treated and disposed in the Saltstone Disposal Facility. This Technical Report compares results, where applicable, to SPF Waste Acceptance Criteria (WAC) LIMITS and TARGETS that were established at the time the SWPF DSS sample was obtained. The October 2023 Semiannual sample of the SWPF DSS is a composite from the six months of SWPF processing during the Third Quarter Fiscal Year 2023 (3QFY2023) and the Fourth Quarter Fiscal Year 2023 (4QFY2023).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Gamma-Ray Emitting Radionuclides Concentrations and Decontamination Factors of ATR Loop Liquid Samples Cycle 171B

This report contains the gamma-ray emitting radionuclides concentration and decontamination factor results from gamma-ray spectrometry measurements of ATR loop liquid samples by the Radiation Measurements Laboratory (RML) for ATR Cycle 171B Jun. 20, 2023, to Sep. 27, 2023. This report consists of five subsections, one for each loop. Each subsection contains the results for each sampling of the loop along with the date and time of sampling, spectral data identifications, sample type, and reactor power (MW). The results are reported in units of disintegrations per minute per milliliter of sample. The results are obtained with the gamma-ray spectral data analysis routines of the RML computer. Some of this report is also generated by RML data storage and handling routines.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Gamma-Ray Emitting Radionuclides Concentrations and Decontamination Factors of ATR Loop Liquid Samples: Cycle 172A

This report contains the gamma-ray emitting radionuclides concentration and decontamination factor results from gamma-ray spectrometry measurements of ATR loop liquid samples by the Radiation Measurements Laboratory (RML) for ATR Cycle 172A running March 2, 2024, to March 16, 2024. This report consists of five subsections, one for each loop. Each subsection contains the results for each sampling of the loop along with the date and time of sampling, spectral data identifications, sample type, and reactor power (MW). The results are reported in units of disintegrations per minute per milliliter of sample. The results are obtained with the gamma-ray spectral data analysis routines of the RML computer. Some of this report is also generated by RML data storage and handling routines.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Results for the April 2024 Semiannual Salt Waste Processing Facility Decontaminated Salt Solution Sample

In this Technical Report, the chemical and radionuclide contaminant results from the April 2024 Semiannual sample of the Salt Waste Processing Facility (SWPF) Decontaminated Salt Solution (DSS) salt solution are presented in tabulated form. The information from this characterization will be used by Savannah River Mission Completion (SRMC) for the transfer of aqueous waste from SWPF to the Saltstone Production Facility (SPF) where the waste will be treated and disposed in the Saltstone Disposal Facility. This Technical Report compares results, where applicable, to SPF Waste Acceptance Criteria (WAC) LIMITS and TARGETS that were established at the time the SWPF DSS sample was obtained.1 The April 2024 Semiannual sample of the SWPF DSS is a composite from the six months of SWPF processing during the First Quarter Fiscal Year 2024 (1QFY2024) and the Second Quarter Fiscal Year 2024 (2QFY2024). The following facts pertaining to the WAC are drawn from the analytical results provided in this report. WAC TARGETS and LIMITS were met for all analyzed chemical and radioactive contaminants for which the detection limits are below the WAC TARGETS and LIMITS. Nitrosamines were not detected in the SWPF DSS salt solution sample above the instrument detection limits of <1 mg/L. The minimum detection limit (<3.33E-01 pCi/mL) is reported for 94 Nb as determined from the minimum detectable activity associated with the radiochemical method used for this radionuclide. The reported detection limit is above the requested SRMC target minimum detection limit concentration. However, the minimum detection limit reported for the April 2024 semiannual SWPF DSS sample for 94 Nb is lower than the estimated detection limit of 4.38E-01 pCi/mL initially established by SRNL in 2009. Thus, per guidance from SRMC, 2 SRNL continues to achieve as low as practical detection limits for this radionuclide.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗