PMC:7574920 / 30183-32589 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T123","span":{"begin":158,"end":161},"obj":"Body_part"},{"id":"T124","span":{"begin":1681,"end":1685},"obj":"Body_part"},{"id":"T125","span":{"begin":1842,"end":1846},"obj":"Body_part"}],"attributes":[{"id":"A123","pred":"fma_id","subj":"T123","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A124","pred":"fma_id","subj":"T124","obj":"http://purl.org/sig/ont/fma/fma12520"},{"id":"A125","pred":"fma_id","subj":"T125","obj":"http://purl.org/sig/ont/fma/fma12520"}],"text":"Heterogeneity of specimen pH in the swab–to–RT-LAMP assay\nComparison of the results of the direct swab–to–RT-LAMP assay with the RT-LAMP assay using isolated RNA revealed a much broader distribution of the ΔOD measurements in negative samples (Fig. 5A versus Fig. 3A). This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction. This might have affected the interpretability of the measurement at 30 min (ΔOD30min). We investigated how this pH shift influenced the RT-LAMP assay. For three plates, the data acquired for the RT-LAMP assay also included measurements for the 10-min time point (ΔOD10min) (Fig. 6A). We plotted the change of the ΔOD between the 10- and 30-min time points (i.e., the difference ΔOD30min – ΔOD10min, corresponding to the slope of the lines) versus ΔOD30min (Fig. 6B). This removed the variability of the values for samples that did not change their color (negative samples) and permitted a better separation of the positive from the negative samples.\nFig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.\n(A) The colorimetric readouts (ΔOD) for the direct (left) and hot (right) swab–to–RT-LAMP assays were assessed every 10 min. Heterogeneity is notable at the early time points. ΔOD values at the zero time point were not measured for the hot swab–to–RT-LAMP assay. Also, the 40-min time point was not available for one plate. The kink in some lines at 30 min (right) was due to a transient equipment malfunction. (B) Comparison of two scoring schemes. The readout used in Fig. 5 to score the direct (left) and hot (right) swab–to–RT-LAMP assays, namely, ΔOD at 30 min, is shown on the y axis, and compared to an alternative score, namely, the difference between the ΔOD signals at 30 min and at 10 min after the start of incubation, shown on the x axis. The latter shows better separation between positive and negative samples. We noticed that the pH variability depended on the sample volume used for the RT-LAMP assay and the composition of the medium used for the swabs. For swabs in Amies medium (which was used for the clinical samples in this study), an RT-LAMP assay containing 1 μl of sample in a total volume of 20 μl was optimal. Our results obtained using native and heat-treated swab specimens suggested better performance when using heat treatment of swab specimens before running the RT-LAMP assay."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T71","span":{"begin":207,"end":209},"obj":"Disease"},{"id":"T72","span":{"begin":690,"end":692},"obj":"Disease"},{"id":"T73","span":{"begin":1128,"end":1130},"obj":"Disease"},{"id":"T74","span":{"begin":1273,"end":1275},"obj":"Disease"},{"id":"T75","span":{"begin":1649,"end":1651},"obj":"Disease"},{"id":"T76","span":{"begin":1761,"end":1763},"obj":"Disease"}],"attributes":[{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A72","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A73","pred":"mondo_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A74","pred":"mondo_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A75","pred":"mondo_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A76","pred":"mondo_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"}],"text":"Heterogeneity of specimen pH in the swab–to–RT-LAMP assay\nComparison of the results of the direct swab–to–RT-LAMP assay with the RT-LAMP assay using isolated RNA revealed a much broader distribution of the ΔOD measurements in negative samples (Fig. 5A versus Fig. 3A). This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction. This might have affected the interpretability of the measurement at 30 min (ΔOD30min). We investigated how this pH shift influenced the RT-LAMP assay. For three plates, the data acquired for the RT-LAMP assay also included measurements for the 10-min time point (ΔOD10min) (Fig. 6A). We plotted the change of the ΔOD between the 10- and 30-min time points (i.e., the difference ΔOD30min – ΔOD10min, corresponding to the slope of the lines) versus ΔOD30min (Fig. 6B). This removed the variability of the values for samples that did not change their color (negative samples) and permitted a better separation of the positive from the negative samples.\nFig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.\n(A) The colorimetric readouts (ΔOD) for the direct (left) and hot (right) swab–to–RT-LAMP assays were assessed every 10 min. Heterogeneity is notable at the early time points. ΔOD values at the zero time point were not measured for the hot swab–to–RT-LAMP assay. Also, the 40-min time point was not available for one plate. The kink in some lines at 30 min (right) was due to a transient equipment malfunction. (B) Comparison of two scoring schemes. The readout used in Fig. 5 to score the direct (left) and hot (right) swab–to–RT-LAMP assays, namely, ΔOD at 30 min, is shown on the y axis, and compared to an alternative score, namely, the difference between the ΔOD signals at 30 min and at 10 min after the start of incubation, shown on the x axis. The latter shows better separation between positive and negative samples. We noticed that the pH variability depended on the sample volume used for the RT-LAMP assay and the composition of the medium used for the swabs. For swabs in Amies medium (which was used for the clinical samples in this study), an RT-LAMP assay containing 1 μl of sample in a total volume of 20 μl was optimal. Our results obtained using native and heat-treated swab specimens suggested better performance when using heat treatment of swab specimens before running the RT-LAMP assay."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T272","span":{"begin":171,"end":172},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T273","span":{"begin":292,"end":293},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T274","span":{"begin":963,"end":964},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T275","span":{"begin":1097,"end":1098},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T276","span":{"begin":1472,"end":1473},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T277","span":{"begin":1508,"end":1509},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T278","span":{"begin":1764,"end":1771},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T279","span":{"begin":2197,"end":2198},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Heterogeneity of specimen pH in the swab–to–RT-LAMP assay\nComparison of the results of the direct swab–to–RT-LAMP assay with the RT-LAMP assay using isolated RNA revealed a much broader distribution of the ΔOD measurements in negative samples (Fig. 5A versus Fig. 3A). This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction. This might have affected the interpretability of the measurement at 30 min (ΔOD30min). We investigated how this pH shift influenced the RT-LAMP assay. For three plates, the data acquired for the RT-LAMP assay also included measurements for the 10-min time point (ΔOD10min) (Fig. 6A). We plotted the change of the ΔOD between the 10- and 30-min time points (i.e., the difference ΔOD30min – ΔOD10min, corresponding to the slope of the lines) versus ΔOD30min (Fig. 6B). This removed the variability of the values for samples that did not change their color (negative samples) and permitted a better separation of the positive from the negative samples.\nFig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.\n(A) The colorimetric readouts (ΔOD) for the direct (left) and hot (right) swab–to–RT-LAMP assays were assessed every 10 min. Heterogeneity is notable at the early time points. ΔOD values at the zero time point were not measured for the hot swab–to–RT-LAMP assay. Also, the 40-min time point was not available for one plate. The kink in some lines at 30 min (right) was due to a transient equipment malfunction. (B) Comparison of two scoring schemes. The readout used in Fig. 5 to score the direct (left) and hot (right) swab–to–RT-LAMP assays, namely, ΔOD at 30 min, is shown on the y axis, and compared to an alternative score, namely, the difference between the ΔOD signals at 30 min and at 10 min after the start of incubation, shown on the x axis. The latter shows better separation between positive and negative samples. We noticed that the pH variability depended on the sample volume used for the RT-LAMP assay and the composition of the medium used for the swabs. For swabs in Amies medium (which was used for the clinical samples in this study), an RT-LAMP assay containing 1 μl of sample in a total volume of 20 μl was optimal. Our results obtained using native and heat-treated swab specimens suggested better performance when using heat treatment of swab specimens before running the RT-LAMP assay."}

{"project":"LitCovid-PubTator","denotations":[{"id":"223","span":{"begin":26,"end":28},"obj":"Gene"},{"id":"225","span":{"begin":351,"end":353},"obj":"Gene"},{"id":"228","span":{"begin":1942,"end":1944},"obj":"Gene"},{"id":"229","span":{"begin":2081,"end":2093},"obj":"Chemical"}],"attributes":[{"id":"A223","pred":"tao:has_database_id","subj":"223","obj":"Gene:5053"},{"id":"A225","pred":"tao:has_database_id","subj":"225","obj":"Gene:5053"},{"id":"A228","pred":"tao:has_database_id","subj":"228","obj":"Gene:5053"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Heterogeneity of specimen pH in the swab–to–RT-LAMP assay\nComparison of the results of the direct swab–to–RT-LAMP assay with the RT-LAMP assay using isolated RNA revealed a much broader distribution of the ΔOD measurements in negative samples (Fig. 5A versus Fig. 3A). This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction. This might have affected the interpretability of the measurement at 30 min (ΔOD30min). We investigated how this pH shift influenced the RT-LAMP assay. For three plates, the data acquired for the RT-LAMP assay also included measurements for the 10-min time point (ΔOD10min) (Fig. 6A). We plotted the change of the ΔOD between the 10- and 30-min time points (i.e., the difference ΔOD30min – ΔOD10min, corresponding to the slope of the lines) versus ΔOD30min (Fig. 6B). This removed the variability of the values for samples that did not change their color (negative samples) and permitted a better separation of the positive from the negative samples.\nFig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.\n(A) The colorimetric readouts (ΔOD) for the direct (left) and hot (right) swab–to–RT-LAMP assays were assessed every 10 min. Heterogeneity is notable at the early time points. ΔOD values at the zero time point were not measured for the hot swab–to–RT-LAMP assay. Also, the 40-min time point was not available for one plate. The kink in some lines at 30 min (right) was due to a transient equipment malfunction. (B) Comparison of two scoring schemes. The readout used in Fig. 5 to score the direct (left) and hot (right) swab–to–RT-LAMP assays, namely, ΔOD at 30 min, is shown on the y axis, and compared to an alternative score, namely, the difference between the ΔOD signals at 30 min and at 10 min after the start of incubation, shown on the x axis. The latter shows better separation between positive and negative samples. We noticed that the pH variability depended on the sample volume used for the RT-LAMP assay and the composition of the medium used for the swabs. For swabs in Amies medium (which was used for the clinical samples in this study), an RT-LAMP assay containing 1 μl of sample in a total volume of 20 μl was optimal. Our results obtained using native and heat-treated swab specimens suggested better performance when using heat treatment of swab specimens before running the RT-LAMP assay."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T184","span":{"begin":44,"end":46},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T185","span":{"begin":106,"end":108},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T186","span":{"begin":129,"end":131},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T187","span":{"begin":512,"end":514},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T188","span":{"begin":571,"end":573},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T189","span":{"begin":1071,"end":1073},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T190","span":{"begin":1178,"end":1180},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T191","span":{"begin":1344,"end":1346},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T192","span":{"begin":1624,"end":1626},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T193","span":{"begin":2000,"end":2002},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T194","span":{"begin":2154,"end":2156},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T195","span":{"begin":2392,"end":2394},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"Heterogeneity of specimen pH in the swab–to–RT-LAMP assay\nComparison of the results of the direct swab–to–RT-LAMP assay with the RT-LAMP assay using isolated RNA revealed a much broader distribution of the ΔOD measurements in negative samples (Fig. 5A versus Fig. 3A). This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction. This might have affected the interpretability of the measurement at 30 min (ΔOD30min). We investigated how this pH shift influenced the RT-LAMP assay. For three plates, the data acquired for the RT-LAMP assay also included measurements for the 10-min time point (ΔOD10min) (Fig. 6A). We plotted the change of the ΔOD between the 10- and 30-min time points (i.e., the difference ΔOD30min – ΔOD10min, corresponding to the slope of the lines) versus ΔOD30min (Fig. 6B). This removed the variability of the values for samples that did not change their color (negative samples) and permitted a better separation of the positive from the negative samples.\nFig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.\n(A) The colorimetric readouts (ΔOD) for the direct (left) and hot (right) swab–to–RT-LAMP assays were assessed every 10 min. Heterogeneity is notable at the early time points. ΔOD values at the zero time point were not measured for the hot swab–to–RT-LAMP assay. Also, the 40-min time point was not available for one plate. The kink in some lines at 30 min (right) was due to a transient equipment malfunction. (B) Comparison of two scoring schemes. The readout used in Fig. 5 to score the direct (left) and hot (right) swab–to–RT-LAMP assays, namely, ΔOD at 30 min, is shown on the y axis, and compared to an alternative score, namely, the difference between the ΔOD signals at 30 min and at 10 min after the start of incubation, shown on the x axis. The latter shows better separation between positive and negative samples. We noticed that the pH variability depended on the sample volume used for the RT-LAMP assay and the composition of the medium used for the swabs. For swabs in Amies medium (which was used for the clinical samples in this study), an RT-LAMP assay containing 1 μl of sample in a total volume of 20 μl was optimal. Our results obtained using native and heat-treated swab specimens suggested better performance when using heat treatment of swab specimens before running the RT-LAMP assay."}

{"project":"LitCovid-sentences","denotations":[{"id":"T231","span":{"begin":0,"end":57},"obj":"Sentence"},{"id":"T232","span":{"begin":58,"end":268},"obj":"Sentence"},{"id":"T233","span":{"begin":269,"end":375},"obj":"Sentence"},{"id":"T234","span":{"begin":376,"end":462},"obj":"Sentence"},{"id":"T235","span":{"begin":463,"end":526},"obj":"Sentence"},{"id":"T236","span":{"begin":527,"end":659},"obj":"Sentence"},{"id":"T237","span":{"begin":660,"end":842},"obj":"Sentence"},{"id":"T238","span":{"begin":843,"end":1025},"obj":"Sentence"},{"id":"T239","span":{"begin":1026,"end":1095},"obj":"Sentence"},{"id":"T240","span":{"begin":1096,"end":1220},"obj":"Sentence"},{"id":"T241","span":{"begin":1221,"end":1358},"obj":"Sentence"},{"id":"T242","span":{"begin":1359,"end":1419},"obj":"Sentence"},{"id":"T243","span":{"begin":1420,"end":1545},"obj":"Sentence"},{"id":"T244","span":{"begin":1546,"end":1847},"obj":"Sentence"},{"id":"T245","span":{"begin":1848,"end":1921},"obj":"Sentence"},{"id":"T246","span":{"begin":1922,"end":2067},"obj":"Sentence"},{"id":"T247","span":{"begin":2068,"end":2233},"obj":"Sentence"},{"id":"T248","span":{"begin":2234,"end":2406},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Heterogeneity of specimen pH in the swab–to–RT-LAMP assay\nComparison of the results of the direct swab–to–RT-LAMP assay with the RT-LAMP assay using isolated RNA revealed a much broader distribution of the ΔOD measurements in negative samples (Fig. 5A versus Fig. 3A). This was likely due to a sample-specific variability that influenced the starting pH in the LAMP reaction. This might have affected the interpretability of the measurement at 30 min (ΔOD30min). We investigated how this pH shift influenced the RT-LAMP assay. For three plates, the data acquired for the RT-LAMP assay also included measurements for the 10-min time point (ΔOD10min) (Fig. 6A). We plotted the change of the ΔOD between the 10- and 30-min time points (i.e., the difference ΔOD30min – ΔOD10min, corresponding to the slope of the lines) versus ΔOD30min (Fig. 6B). This removed the variability of the values for samples that did not change their color (negative samples) and permitted a better separation of the positive from the negative samples.\nFig. 6 Colorimetric readouts of the swab–to–RT-LAMP assay over time.\n(A) The colorimetric readouts (ΔOD) for the direct (left) and hot (right) swab–to–RT-LAMP assays were assessed every 10 min. Heterogeneity is notable at the early time points. ΔOD values at the zero time point were not measured for the hot swab–to–RT-LAMP assay. Also, the 40-min time point was not available for one plate. The kink in some lines at 30 min (right) was due to a transient equipment malfunction. (B) Comparison of two scoring schemes. The readout used in Fig. 5 to score the direct (left) and hot (right) swab–to–RT-LAMP assays, namely, ΔOD at 30 min, is shown on the y axis, and compared to an alternative score, namely, the difference between the ΔOD signals at 30 min and at 10 min after the start of incubation, shown on the x axis. The latter shows better separation between positive and negative samples. We noticed that the pH variability depended on the sample volume used for the RT-LAMP assay and the composition of the medium used for the swabs. For swabs in Amies medium (which was used for the clinical samples in this study), an RT-LAMP assay containing 1 μl of sample in a total volume of 20 μl was optimal. Our results obtained using native and heat-treated swab specimens suggested better performance when using heat treatment of swab specimens before running the RT-LAMP assay."}