In-Between-Patient Decontamination of CT Rooms and Equipment Following COVID-19 Exposure Using Pulsed Plasma Activated Fog
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Background Investigators using metagenomic sequencing to study their microbiomes are often provided data that has been trimmed and decontaminated or do it themselves without knowing the effect these procedures can have on their downstream analyses. Here we evaluated the impact that JGI trimming and decontamination procedures had on assembly and binning metrics, placement of metagenome assembled genomes into species trees, and functional profiles of metagenome-assembled genomes (MAGs) extracted from twenty three complex rhizosphere metagenomes. We also investigated how more aggressive trimming impacts these binning metrics. Results We found that JGI trimmed and decontamination of input reads had some significant impacts in assembly and binning metrics compared to raw reads, and that differences in placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. More aggressive trimming beyond those used by JGI were found to reduce MAG counts. Conclusions Mild 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 is recommended for those who elect to do so.
Growing interest in sustainable food and biofuel research has necessitated high quality axenic oleaginous microalgal strains. Unfortunately, most strains available in culture banks contain commensal microbes such as bacteria and the default decontamination method involves antibiotic treatment which has begun to exacerbate the emergence of antibiotic resistance. To overcome this problem, anoxic photosensitisation was investigated as an alternate approach. Four oleaginous microalgal species (Tetradesmus obliquus, Desmodesmus armatus, Chlorella vulgaris and Nannochloropsis limnetica) were incubated in varying concentrations of Rose Bengal (0 μM, 1 μM, 3 μM or 9 μM) either in normal (oxic) or anoxic conditions, for 72 h under light (8.85 ± 0.4 W/m 2 ) in a specially designed heterotrophic growth complex (HGC) medium, followed by 72 h in standard Bold's Basal Medium (BBM). Commonly used antibiotics-based protocol was used as the control method. Post treatment, cell numbers and percentage populations were counted with Flow Cytometry, and viability was tested using standard plating methods using BBM and LB. Additionally, the contaminating microbes in the cultures were profiled using 16Ss rRNA sequencing. Anoxic conditions were able to significantly decrease bacterial content, albeit with an equally detrimental effect on the microalgal population. Although the responses differed between the microalgae, anoxic incubation along with Rose Bengal at 3 μM was able to completely decontaminate N. limnetica and C. vulgaris, while D. armatus and T. obliquus could be decontaminated with an additional streak-plating step. None of the cultures could be decontaminated using antibiotics treatment. These results suggest that axenisation of microalgal cultures was largely due to anoxy, that was synergistically enhanced by Rose Bengal at a concentration of ≥3 μM.
In times of crisis, including the current COVID-19 pandemic, the supply chain of filtering facepiece respirators, such as N95 respirators, are disrupted. To combat shortages of N95 respirators, many institutions were forced to decontaminate and reuse respirators. While several reports have evaluated the impact on filtration as a measurement of preservation of respirator function after decontamination, the equally important fact of maintaining proper fit to the users’ face has been understudied. In the current study, we demonstrate the complete inactivation of SARS-CoV-2 and preservation of fit test performance of N95 respirators following treatment with dry heat. We apply scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDS), X-ray diffraction (XRD) measurements, Raman spectroscopy, and contact angle measurements to analyze filter material changes as a consequence of different decontamination treatments. We further compared the integrity of the respirator after autoclaving versus dry heat treatment via quantitative fit testing and found that autoclaving, but not dry heat, causes the fit of the respirator onto the users face to fail, thereby rendering the decontaminated respirator unusable. Our findings highlight the importance to account for both efficacy of disinfection and mask fit when reprocessing respirators to for clinical redeployment.
Recovery of Zr from nuclear fuel is of high interest because the Zr cladding material comprises up to 50% of the high-level radioactive waste (HLW) that requires disposition. An ideal Zr-recovery process would not only recover the bulk Zr from the fuel or cladding but would also provide decontamination from the components that give rise to the HLW designation. A simplified decontamination pathway providing recovered Zr in compliance with low-level radioactive waste acceptance criteria could significantly reduce the burden of HLW requiring geologic disposition. A newly developed advanced low-temperature chlorination process presents an opportunity to recover a ZrCl4 product that is effectively decontaminated from the elements of concern. This advanced low-temperature chlorination process uses a mixture of the sulfur-containing chlorination compounds sulfur monochloride (S 2 Cl 2 ) and thionyl chloride (SOCl 2 ).
Production of decontaminated water from contaminated water using a vessel, an inlet to the vessel wherein the contaminated water is introduced into the vessel, an outlet to the vessel wherein the decontaminated water is removed from the vessel, a plasmonic-photocatalyst membrane connected to the vessel, plasmonic nanoparticles or nanostructures connected to the plasmonic-photocatalyst membrane, and a source of ultraviolet light that directs ultraviolet light onto the vessel, the plasmonic-photocatalyst membrane, the plasmonic nanoparticles or nanostructures, and the contaminated water to produce the decontaminated water from the contaminated water.
During washing of radiologically impacted building surfaces, penetration of radionuclide ions into complex solids associated with these surfaces may occur. This study investigates the penetration of Cs-137, Sr-85, and Eu-152 solutions into numerous common building materials and radionuclide behavior when these materials were exposed to a static bath or low-pressure flow of tap water, 0.1 M potassium chloride (KCl), and 0.5 M KCl. The decontamination efficacy and the depth profile for residual contamination were measured to determine the conditions under which applying a wash solution has benefit compared to physically removing the surface material. On asphalt, 70-80% of the radionuclides were found to be within 0.02 mm of the surface. Concrete is more porous than asphalt, and 80% of the radionuclides were within 0.2 mm of the surface for Cs-137 and Eu-152 and 50-80% for Sr-85. Water effectively removed all contaminants from hard nonporous surfaces. Finally, this paper illustrates that a wash penalty factor concept-defined as ratio of the depth at which 50% of the radioactivity is found in the washed sample divided by the depth at which 50% of radioactivity is found in the control-can serve as a way to quantify whether the wash method increases the depth at which contamination penetrates into the material and thus the material becomes more difficult to decontaminate.
The simultaneous removal of radionuclides technetium-99 and iodine-129 from an actual decontaminated Hanford tank waste sample (a mixture of decontaminated waste from tanks 241-AP-105 and 241-AP-107) was demonstrated for the first time in this work. A series of commercially available ion exchange resins were evaluated in batch contact tests in the tank waste, and all showed removal of both Tc and I. The highest Tc removal was observed for Purolite A530e while the highest iodine removal was observed for ResinTech SIR-110-MP. Batch tests in simulated tank waste with these two resins showed that the SIR-110-HP-MP had consistently higher K d for both pertechnetate and iodide and much higher K d than previous works on Tc removal from Hanford waste. As such, the SIR-110-MP was evaluated in a dual -column (lead/lag) test processing 5.2L of the tank waste mixture showing 60% breakthrough of Tc on the lead column and no significant breakthrough on the lag after 625 bed volumes (BV, 6 mL size) while significant iodine breakthrough (>50%) occurred after 28 BV. The limited iodine uptake was attributed to the column conditions generating mass transfer limitations. A fraction of the Tc and I was not captured by the resin (<10%) in either the batch tests or column tests. The iodine fraction was identified to be an iodide, likely organo-iodide. The fraction of the Tc was identified as a non-pertechnetate species, which is the first time non-pertechnetate has been identified in AP-105 and AP-107 tanks, although the exact species is still unknown.
To mitigate the effects following a large-scale nuclear or radiological material release in an urban environment and to expedite recovery, the Integrated Wash-Aid Treatment Emergency Reuse System (IWATERS) was developed. IWATERS consists of three operations: washing contaminated surfaces with an ionic wash solution, collecting, and treating the contaminated wash solution on-site to remove contaminants, and reusing the treated solution throughout operations to preserve the clean water resource. This study develops a framework to simulate the logistics of IWATERS deployment, thereby gaining an understanding of the timeline for decontamination operations. For this purpose, the Analysis of Mobility Platform and GoldSim were leveraged for a hypothetical contamination scenario covering 65,200 m 2 of an urban center. The framework reveals that remediation progress is limited by several resources, notably the availability of vermiculite, a reactive clay that is required to treat the contaminated wash solution. Further, this study also presents how the simulation approach can be used to characterize alternatives to reduce the influence of limited resources on operational progress. Overall, this work lays the foundation for evaluating different decontamination methods through detailed logistics simulation, i.e., by refining simulation assumptions and expanding the range of scenarios the simulation can depict.
Understanding mechanisms of decontamination of chemical warfare agents (CWA) is an area of intense research aimed at developing new filtration materials to protect soldiers and civilians in case of state-sponsored or terrorist attack. In this study, we employed complementary structural, chemical, and dynamic probes and in situ data collection, to elucidate the complex chemistry, capture, and decomposition of the CWA simulant, dimethyl chlorophosphonate (DMCP). Our work reveals key details of the reactive adsorption of DMCP and demonstrates the versatility of zeolitic imidazolate framework (ZIF-8) as a plausible material for CWA capture and decomposition. Here, the in situ synchrotron-based powder X-ray diffraction (PXRD) and pair distribution function (PDF) studies, combined with Fourier transform infrared (FT-IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), zinc K-edge X-ray absorption near edge structure (XANES), and Raman spectroscopies, showed that the unique structure, chemical state, and topology of ZIF-8 enable accessibility, adsorption, and hydrolysis of DMCP into the pores and revealed the importance of linker chemistry and Zn 2+ sites for nerve agent decomposition. DMCP decontamination and decomposition product(s) formation were observed by thermogravimetric analysis, FT-IR spectroscopy, and phosphorus (P) K-edge XANES studies. Differential PDF analysis indicated that the average structure of ZIF-8 (at the 30 Å scale) remains unchanged after DMCP dosing and provided information on the dynamics of interactions of DMCP with the ZIF-8 framework. Using in situ PXRD and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), we showed that nearly 90% regeneration of the ZIF-8 structure and complete liberation of DMCP and decomposition products occur upon heating.
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ABSTRACT In this work, we present the galaxy clustering measurements of the two DES lens galaxy samples: a magnitude-limited sample optimized for the measurement of cosmological parameters, maglim, and a sample of luminous red galaxies selected with the redmagic algorithm. maglim/redmagic sample contains over 10 million/2.5 million galaxies and is divided into six/five photometric redshift bins spanning the range z ∈ [0.20, 1.05]/z ∈ [0.15, 0.90]. Both samples cover 4143 $\deg ^2$ over which we perform our analysis blind, measuring the angular correlation function with an S/N ∼ 63 for both samples. In a companion paper, these measurements of galaxy clustering are combined with the correlation functions of cosmic shear and galaxy–galaxy lensing of each sample to place cosmological constraints with a 3 × 2pt analysis. We conduct a thorough study of the mitigation of systematic effects caused by the spatially varying survey properties and we correct the measurements to remove artificial clustering signals. We employ several decontamination methods with different configurations to ensure the robustness of our corrections and to determine the systematic uncertainty that needs to be considered for the final cosmology analyses. We validate our fiducial methodology using lognormal mocks, showing that our decontamination procedure induces biases no greater than 0.5σ in the (Ωm, b) plane, where b is the galaxy bias.
Accurate and efficient mapping and localization of both ionizing and non-ionizing radiation sources are important across many different fields. As such, a versatile mapping and navigational path generation algorithm, which can be applied to any point source measurements that follow an inverse-square characteristic, was developed using non-linear least squares methods. Forty thousand simulations were performed on the algorithm, which located sources successfully in a 10 m × 10 m × 10 m three-dimensional space with a success rate of over 80% across different noise functions, given a proportional constant of 10 to 1,000. The algorithm was also verified experimentally with small-scale radioactive decontamination of a 70 cm × 70 cm surface and localization of a lost Wi-Fi router in a 70 m × 70 m open field. One hundred twenty-one measurements were taken from each experiment, which were then fed into the algorithm for navigation. For the radioactive 137Cs source, the estimated locations were within 7 cm × 7 cm of the answer in 79.3% of the scenarios, while the Wi-Fi router was located to within 7 m × 7 m in 57.9% of the tests. In general, the method requires much less information and data than a geographically comprehensive survey and thus shows a lot of potential for practical applications, such as lost source retrieval with unmanned aerial vehicles, small-scale decontamination, mapping undocumented Wi-Fi routers or radio towers, and radiation simulation with radio signals. Here, the different failure modes, desirable features, and potential improvements were also identified but remain as future work.
Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size—currently exceeding 10 12 nucleotides—and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.
The Saltstone Production and Disposal Facility is designed and permitted by the state of South Carolina Department of Health and Environmental Control (SCDHEC) to treat and dispose of low-level radioactive and hazardous liquid waste (salt solution) remaining from the processing of radioactive material at the Savannah River Site (SRS). Low-level waste (LEW) aqueous streams from the Effluent Treatment Project (ETP) and decontaminated solutions from the Tank Closure Cesium Removal Unit (TCCR) and the Salt Waste Processing Facility (SWPF) are stored in Tank 50 until the LEW can be transferred to the Saltstone Facility for treatment and disposal. In the past, decontaminated solution from the Modular Caustic Side Solvent Extraction Unit (MCU) was stored in Tank 50 until the LEW could be transferred to the Saltstone Facility for treatment and disposal. MCU is currently in a suspended operations state. LEW that meets the Waste Acceptance Criteria (WAC) can be transferred, stored, and treated in the Saltstone Production Facility (SPF) for subsequent disposal as saltstone grout in the Saltstone Disposal Facility (SDF). Sampling will be conducted as new waste streams are identified for treatment and disposal at the Saltstone Industrial Wastewater Treatment Facility (IWTF) and Z-Area Industrial Solid Waste Landfill (ISWLF), Facility ID# 025500-1603, General Condition B.9 or every six years in accordance with South Carolina (SC) Regulation 61-107.19 Parti C, “Solid Waste Management: Solid Waste Landfills and Structural Fill - General Requirements.”
The interactions between the key processes that control the fate and transport of mercury (Hg) in the sediments, groundwater, and stream water within the Y-12 National Security Complex (Y-12) in Oak Ridge, Tennessee are complex, and many aspects are not well understood. In contaminated environments such as Y-12, conceptual models are frequently developed to aid in visualizing and understanding the dynamic nature of the hydrologic, geochemical, and physical environment. These conceptual models integrate data in an internally consistent manner to understand processes that control the fate and transport of contaminants. Over the past few decades of environmental investigation at Y-12, a number of conceptual models have been developed to identify and define various technical processes at various scales. The main purpose of the activities described in this report is to update the 2011 conceptual model for Upper East Fork Poplar Creek using the most recent Hg concentration and flux data and informed scientific interpretation. Emphasis was placed on improving the previous model by implementing a more detailed spatial and temporal approach to visualize transport pathways in the watershed and trends in flux and concentration over time, and to compare baseflow and stormflow system dynamics. Detailed descriptions of historical and current Hg sources and transport pathways are also provided for the east and west ends of the facility. This conceptual model will allow the US Department of Energy to evaluate past and present remedial activities and provide a strong technical basis for prioritizing and optimizing remedial responses in a cost-effective and efficient manner. Twenty years ago, Hg flux from Outfall (OF) 200 at the headwaters of East Fork Poplar Creek represented approximately 20% of the overall flux leaving Y-12. By the time of the 2011 conceptual model report, that percentage had increased to 70%–80%. Flux estimates compiled for this report using data from 2009 to 2018 show that OF200 accounted for roughly 60% of the flux leaving Y-12. The relative role of the four storm drain conduits to OF200 appeared similar to 2011, with OF163 being the greatest contributor to downstream flux. An increase in Hg concentrations and flux occurred throughout and downstream of west end storm drains in 2011 in response to a storm drain cleanout. Leading up to the 2011 storm drain cleanout, annual baseflow flux was higher at OF200A6 than at Station 17. From 2011 to 2018, the trend reversed with concentrations and flux being higher at Station 17 than at OF200A6. A spike in concentrations occurred in July 2018, potentially due to a one-time influx of Hg that occurred during COLEX decontamination and decommissioning activities at Y-12. This report includes recommendations for improving our conceptual understanding of Hg sources, transport pathways, and flux at Y-12. Important recommendations include further evaluation of transport pathways, concurrent measurement of Hg concentration and flux under baseflow and stormflow conditions at multiple sites, and research to understand the connections among periphyton and methylmercury concentration, bioavailability, and bioaccumulation. Ongoing facility decontamination and decommissioning efforts, site characterization, remedial actions, and research are facilitating the collection of new Hg data at Y-12. The conceptual model update provided herein takes advantage of the extensive recent Hg sampling to provide an updated assessment of Hg mass balance and support a refined understanding of Hg behavior at or near Y-12. This assessment should assist in future environmental management decisions and in mitigating the impacts of Hg on the surrounding environment.