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At least 991 records · Page 55Linked to original sources
PubMed2026

Benchmarking computational decontamination of ambient RNA.

Gene expression profiling of single cells using single-cell and single-nucleus RNA sequencing (sxRNA-seq) enables researchers to characterize cellular heterogeneity and unraveling complex biological processes at unprecedented resolution. However, sxRNA-seq faces challenges due to the presence of ambient RNA, extraneous RNA molecules not originating from the cells of interest. Sample preparation is a major source of ambient RNA, where harsh conditions can lead to cell lysis and the release of intracellular RNA. This inescapable inclusion of ambient RNA can cause erroneous results and hinder downstream analyses. To address this issue, various methodologies have been developed to identify, quantify, and remove ambient RNA. Here, we rigorously evaluate 7 state-of-the-art methodologies for ambient RNA removal using simulated datasets, species-mixing experiments of varying complexities, and genotype-mixing experiments. We find that no single method performs the best across all datasets and metrics, but CellBender, DecontX and SoupX generally perform well.

ambient RNA↗
PubMed1978

[Radiolytic decontamination of Di-n-butyl phthalate from water (author's transl)].

Recently, a considerable amount of phthalic acid esters (PAE), the most widely utilized plasticizer, has been released into and polluted the environment. Since their toxicity and teratogenicity, although fairly low, to experimental animals have recently been shown, the removal of them from the environment, especially from the drinking water, is desirable. As an attempt for the removal, the radiolytic degradation of 7-14C-di-n-butyl phthalate (14C-DBP) in water was investigated at several pHs. Approximately 50% of 14C-DBP (1 ppm aqueous solution) was decomposed by 60Co gamma-irradiation to a dose of 3 X 10(4) rad at pH 7 and the main product was mono-n-butyl phthalate (MBP). At pHs 3 and 11 14C-DBP was more easily radiolyzed and converted to ether-soluble compounds other than MBP or phthalic acid (PA). By irradiation to 10(6) rad 14C-DBP as well as 14C-MBP and 14C-PA, at pH value tested, was almost completely decomposed to volatile or water-soluble substances of possibly low molecular weight. These findings suggest that the gamma-irradiation is effective to make the PAE-polluted water clean.

Chemical Phenomena↗
PubMed1979

Fundamental study on decontamination of tritium from gaseous phases by copper oxide.

Some fundamental studies on removal of tritium from gaseous streams by a small column of copper oxide were carried out. An about 10 cm length of column packed with 100 g of copper oxide was examined on the conversion ratios of hydrogen and tritium into water. The experiment with hydrogen of 0.1% in argon showed that the logarithmic plot of remaining ratio of hydrogen by passing through the column is proportional to the reciprocal of gas flow rate and to the length of oxide column. The oxide column was also used for treating tritium-bearing waste gas from an evacuating system of alpha D-T neutron generator. It was observed that at column temperatures lower than 450 degrees C the conversion ratio of tritium in the waste gas into water is considerably smaller than that of hydrogen of 0.1% in argon.

Copper↗
PubMed1998

Use of hot water for beef carcass decontamination.

Hot water treatment of beef carcass surfaces for reduction of Escherichia coli O157:H7, Salmonella typhimurium, and various indicator organisms was studied using a model carcass spray cabinet. Paired hot carcass surface regions with different external fat characteristics (inside round, outside round, brisket, flank, and clod) were removed from carcasses immediately after the slaughter and dressing process. All cuts were inoculated with bovine feces containing 10(6)/g each of rifampicin-resistant E. coli O157:H7 and S. typhimurium, or with uninoculated bovine feces. Surfaces then were exposed to a carcass water wash or a water wash followed by hot water spray (95 degrees C). Counts of rifampicin-resistant Salmonella and E. coli or aerobic plate count (APC) and coliform counts were conducted before and after each treatment. All treatments significantly reduced levels of pathogens from the initial inoculation level of 5.0 log(10) CFU/cm2. Treatments including hot water sprays provided mean reductions of initial counts for E. coli O157:H7 and S. typhimurium of 3.7 and 3.8 log, APC reductions of 2.9 log, and coliform and thermotolerant coliform count reductions of 3.3 log. The efficacy of hot water treatments was affected by the carcass surface region, but not by delaying the treatment (30 min) after contaminating the surface. Verification of efficacy of hot water interventions used as critical control points in a hazard analysis critical control point (HACCP) system may be possible using coliform counts.

Animals↗
PubMed1999

Decontamination of beef carcass surface tissue by steam vacuuming alone and combined with hot water and lactic acid sprays.

Hot beef carcass surface regions (outside round, brisket, and clod) contaminated with feces spread over a 5-cm2 (1-in2) area were cleaned using a steam-vacuum spot-cleaning system alone or combined with subsequent sanitizing treatments of hot water (95 degrees C at the nozzle), or warm (55 degrees C) 2% lactic acid spray, or combinations of these two sanitizing methods. These treatments were compared for effectiveness in reducing aerobic plate counts (APC) and counts of Enterobacteriaceae, total coliforms, thermotolerant coliforms, and Escherichia coli. All treatments significantly reduced the numbers of each group of bacteria on beef carcass surfaces. However, reductions obtained by steam vacuuming were significantly smaller than those obtained by a combination of steam vacuuming with any sanitizing treatment. No differences in bacterial reductions were observed between different carcass surface regions. Steam vacuuming reduced the number of different indicator organisms tested by ca. 3.0 log cycles but also spread the bacterial contamination to areas of the carcass surface adjacent to the contaminated sites. This relocated contamination after steam vacuuming was most effectively reduced by spraying with hot water and then lactic acid. This combined treatment consistently reduced the numbers of Enterobacteriaceae, total and thermotolerant coliforms, and E. coli to undetectable levels (<1.0 log10 CFU/cm2) on areas outside the initial 5-cm2 inoculated areas.

Abattoirs↗