{ "dataset": { "archive": "dandi", "id": "000489", "label": "DANDI:000489" }, "page": "datasets/dandi/000489/", "generated": "2026-11-05T07:41:23+00:00", "caution": "A failure to reproduce is not a finding that the paper is wrong. It may be a failure of the attempt.", "outcome_counts": { "reproduced": 0, "partially_reproduced": 1, "not_reproduced": 4, "blocked": 17 }, "outcome_counts_with_outside_data": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_elsewhere": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "outcome_counts_links": { "reproduced": 0, "partially_reproduced": 0, "not_reproduced": 0, "blocked": 0 }, "attempts": [ { "id": "000489-kim-2022-01", "dataset": { "archive": "dandi", "id": "000489", "version": "0.230518.1811", "doi": "10.48324/dandi.000489/0.230518.1811" }, "key": "dandi:000489", "label": "DANDI:000489", "dataset_version": "0.230518.1811", "paper": "10.1016/j.bioelechem.2022.108319", "paper_title": "Action spectra and mechanisms of (in) efficiency of bipolar electric pulses at electroporation", "date": "2026-10-30", "kind": "agent", "accountable": "CatalystNeuro", "agent": { "harness": "Claude Code", "model": "claude-opus-5-5", "protocol": "pilot-12" }, "runner": { "platform": "GitHub Actions", "url": "https://github.com/catalystneuro/encore/actions/runs/41081361942" }, "tier": "agent_verified", "deprecated": "", "deprecated_on": null, "entry": "000489-kim-2022", "entry_title": "Bipolar cancellation of electroporation by the second phase amplitude (Kim et al. 2022)", "description": "Tests the findings of Kim, Semenov, Kiester, Keppler, Ibey, Bixler and Pakhomov (2022) on dandiset 000489, which holds stitched MemBrite and YO-PRO-1 images of 17 dishes of endothelial cells exposed to unipolar or bipolar 600 ns pulses with a second phase of 25 to 100% (Fig. 2). It measures YO-PRO-1 uptake along the line between the electrodes against the field of a recomputed electrode model, and tests the rise of uptake with field, its exponential slope and the inhibition by the second phase. The experiments of Figs. 3 to 7 and the thermometry are not in the dandiset.", "notebooks": [ { "path": "reproduce_kim_2022.ipynb", "title": "Reproducing Kim et al. (2022) from dandiset 000489", "executed": "notebooks/000489-kim-2022/reproduce_kim_2022.html" } ], "outcomes": [ { "claim": "fig2a-uptake-rises-with-field", "statement": "For unipolar 600 ns pulses and for bipolar 600+600 ns pulses with every second phase amplitude, a train of 5 pulses at 1 Hz evoked YP uptake that increased with the local electric field strength.", "source": "Results 3.1, paragraph 1; Figure 2A", "quote": "A train of 5 pulses applied at 1 Hz evoked YP uptake proportionally to the local electric field strength ( Fig. 2A ), along with a strong dependence on the 2 nd phase amplitude.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "partially_reproduced", "blocked_by": null, "notebook": "reproduce_kim_2022.ipynb", "notes": "Mean YP rises with field for all five amplitudes (Spearman rho 0.98 to 0.99 over 16 ROI from 5.13 to 15.38 kV/cm). Strongest against weakest ROI, YP is higher with p < 0.05 for 50, 75 and 100% under both readings (paired p 0.011, 0.041, 0.003; unpaired p 0.0008, 0.014, below 0.0001) and not for unipolar (2 dishes; paired p 0.17, unpaired p 0.11) or 25% (3 dishes; paired p 0.19, unpaired p 0.15). Paired and unpaired agree on 3 of 5 amplitudes, so the criterion gives partially reproduced. The unipolar test has 2 dishes because the third, sub-Fig2-0-03, holds another dish's YP image. On the top side, with the scale from the electrodes, with the right footprint and with the field scaled to 15.1 kV/cm at the centre the outcome is the same. On the bottom side of bb' alone, or with YP_0 and MB_0 from the left footprint alone, the paired test passes for 2 amplitudes and the unpaired for 3, which the criterion would call methods_underspecified. With the weakest ROI at 2.0 mm (8.14 kV/cm) the outcome is the same; at 2.4 mm (6.75 kV/cm) the paired test passes for 2 and the unpaired for 3.", "deviations": [ "The ROI positions are not in the dataset or the paper. 200 um ROI are tiled contiguously along bb' from the midpoint of the electrode centres out to 3 mm, and the two ROI at the same distance are averaged per dish (the claims file's reading a). This is assumed as the reading the paper best supports, since Methods 2.3 and Fig. 1C treat bb' as one line through the centre; one side only is shown for each side.", "YP_0 and MB_0 are averaged over discs of 0.5 mm radius in both footprints (Methods 2.5 says \"within the electrodes' footprints\"); each footprint alone is shown as a variant.", "The field per ROI is recomputed from the electrode geometry (Methods 2.3) in closed form for two cylinders in the plane, which gives 15.38 kV/cm at the centre against the 15.1 kV/cm the paper cites. The pixel size, absent from the files, is taken as 0.65 um (6.5 um camera pixel, 10x objective, Methods 2.5); a scale set from each dish's electrode distance is a variant.", "Unipolar pulses have 2 dishes, not 3, because sub-Fig2-0-03 is left out (its YP channel is a copy of sub-Fig2-25-04's).", "The ROI with the weakest field is the outermost tiled ROI (3.0 mm, 5.13 kV/cm); the paper does not give how far its ROI extend. This is an assumption (bipolar.py, N_ROI_SIDE), and the notebook shows the test with the weakest ROI at 2.0 and 2.4 mm." ], "assumed": true, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2a-vertical-scales", "statement": "Although the panels of Fig. 2A look similar, their vertical scale goes from 1200 a.u. for unipolar pulses down to only 250 a.u. for bipolar pulses with a 75% second phase.", "source": "Results 3.1, paragraph 1; Figure 2A", "quote": "note the difference in the vertical scale, which is varied from 1200 a.u. for unipolar pulses to only 250 a.u. for 75% bipolar pulses", "statistics": [], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_kim_2022.ipynb", "notes": "The largest unipolar mean YP is 571.1 a.u. (mean plus s.e.m. 785.4), within 1200 and above 250, but the largest 75% mean plus s.e.m. is 283.2 a.u., above the 250 limit (largest mean 239.5). Under every variant of the data the 75% value is 255.2 to 342.8. The ratio of the largest unipolar to the largest 75% mean is 2.38, where the axis limits differ 4.8-fold.", "deviations": [ "The files hold uint16 camera counts with conversion 1.0 and unit n.a.; they are assumed to be the units the paper measured in MetaMorph, as nothing in the files or the paper says they were rescaled. Under that assumption the claim is tested on absolute values.", "ROI placement, footprints, field and the missing third unipolar dish as for fig2a-uptake-rises-with-field." ], "assumed": true, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2b-exponential-same-slope", "statement": "YP uptake increased exponentially with the field strength, and the second phase did not change the slope of the exponential fits on a semi-log scale.", "source": "Results 3.1, paragraph 1; Figure 2B and its legend", "quote": "YP uptake increased exponentially with the electric field, and the presence of the 2nd phase did not change the apparent slope of exponential fits when plotted on a semi-log scale", "statistics": [], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_kim_2022.ipynb", "notes": "The criterion calls the claim reproduced when no bipolar slope differs from the unipolar slope at p < 0.05 and the exponential beats a straight line for at least four of five amplitudes, and not reproduced when a slope differs. None of the 12 readings (cutoff 6, 7 or 8 kV/cm; nonlinear least squares or log-linear fit; per-dish slopes or slopes of the fits to the means) meets both parts. In 10 a bipolar slope differs; in the other 2 (least squares with the per-dish test at 7 kV/cm and with the means test at 8 kV/cm) no slope differs but the exponential beats a straight line for only 3 of 5 amplitudes. The exponential is adequate in 2 of 12 readings. Log-linear fits put every bipolar slope below the unipolar one (ratios 0.50 to 0.75; all four differ at p < 0.01 in the means test); least squares gives ratios 0.68 to 1.04. On the bottom side, with the left footprint and with the scaled field every reading also gives not reproduced; on the top side, with the scale from the electrodes and with the right footprint some readings give reproduced, so the outcome rests on the main reading of the ROI, the footprints and the scale. Which fit Grapher made is a question for the paper's authors (findings).", "deviations": [ "Log-linear fits drop points with YP at or below zero (2 of 14 unipolar means at the 6 kV/cm cutoff); the count is printed.", "A reading in which no slope differs but the exponential is not adequate was labelled partially reproduced in round 1, a category the criterion does not define; it is now not reproduced, as the criterion's reproduced requires both parts.", "ROI placement, footprints, field and the missing third unipolar dish as for fig2a-uptake-rises-with-field." ], "assumed": true, "disagreed": true, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2c-max-inhibition-50-75", "statement": "The strongest inhibition of YP uptake, to about 20% of the uptake after unipolar pulses, was reached with a second phase of 50 to 75% of the first (p < 0.01).", "source": "Results 3.1, paragraph 2; Figure 2C and its legend", "quote": "The maximum inhibition of YP uptake, down to ~20% of the unipolar pulses, was achieved with the 2 nd phase set to 50-75% of the first one (p<0.01, Fig. 2C ).", "statistics": [ { "test": "two-sided Student's t-test", "p": 0.01, "p_relation": "<", "n": "3 to 8 exposures per protocol" } ], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_kim_2022.ipynb", "notes": "Over the ROI from 8.94 to 15.24 kV/cm (nearest 8.7 and 15.1), the 50% second phase inhibits most and the lower of 50 and 75% is below 25 and 100% at every ROI, so the ordering holds. The percent of the unipolar mean is 54.5% averaged over the range (reading a, given as measured) and 31.6% at its lowest, at 14.24 kV/cm (reading b), both outside 18 to 22%, so the claim is at most partially reproduced. Where the p < 0.01 test is made is not given; four readings are run. At every ROI of the range it fails for both amplitudes (largest p for 50%, 0.79 against unipolar and 0.072 against 25 and 100%; for 75%, 0.996 and 0.249); on dish means over the range it fails (smallest p 0.011, 50% against 25 and 100%, normalised values); at both named fields it fails (50% against unipolar, p 0.79 at 8.94 and 0.0018 at 15.24 kV/cm). At one ROI or more it holds, 50% against unipolar at 15.24 kV/cm (p 0.0018), the only one of 36 tests (2 amplitudes, 2 comparisons, 9 ROI) below 0.01; that reading would give partially reproduced. At the ROI of strongest inhibition (14.24 kV/cm) p is 0.027 against unipolar and 0.019 against 25 and 100%. With the right footprint alone the pooled test reaches p < 0.01 (partially reproduced); every other variant gives not reproduced under the first three readings. The 100% dishes show more uptake than the unipolar dishes at most ROI (89.6 to 229.9% of unipolar), which the paper does not report.", "deviations": [ "Where the p < 0.01 test is made is not given (claims file, criterion; Results 3.1 cites only \"Fig. 2C\"). It is run at every ROI of the range, on each dish's mean over the range, at both named fields, and at one ROI or more. The outcome assumes the paper's p < 0.01 applies over the range of fields where it reports the inhibition (the first three readings, which agree), not to one ROI chosen from 36 tests; the per-ROI p values are printed.", "The range from 8.7 to 15.1 kV/cm is read as the ROI nearest each named field and those between (claims file, opening comment), j 1 to 9; the central ROI (15.38 kV/cm) is above 15.1 in the recomputed field. With the field scaled so that the centre is at 15.1 kV/cm the range starts at the centre ROI, and the mean percent is 52.9%.", "ROI placement, footprints, field and the missing third unipolar dish as for fig2a-uptake-rises-with-field." ], "assumed": true, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2c-inhibition-flat-above-8-7", "statement": "Between 8.7 and 15.1 kV/cm the degree of inhibition by the second phase did not depend on the field strength.", "source": "Results 3.1, paragraph 2; Figure 2C", "quote": "The degree of inhibition showed no dependence on the electric field strength between 8.7 and 15.1 kV/cm.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "not_reproduced", "blocked_by": null, "notebook": "reproduce_kim_2022.ipynb", "notes": "The percent of the unipolar mean rises from the ROI at 15.24 to the ROI at 8.94 kV/cm for every amplitude (25%, 76.8 to 199.0; 50%, 34.8 to 113.2; 75%, 42.0 to 155.7; 100%, 133.4 to 229.9). It differs for 50% and 75% under both the paired (p 0.012, 0.049) and the unpaired test (p 0.0016, 0.018), so the criterion gives not reproduced. Of the 36 pairs of ROI in the range, 23 (paired) and 18 (unpaired) differ for 50%. Every variant of the data gives the same outcome. The rise comes from the unipolar mean falling faster with field than the bipolar means in these 2 unipolar dishes (570.4 to 47.7 a.u. over the range).", "deviations": [ "ROI placement, footprints, field and the missing third unipolar dish as for fig2a-uptake-rises-with-field." ], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2c-weaker-at-6-7", "statement": "Inhibition was weaker at 6.7 kV/cm than at the higher field strengths, with p < 0.01 for the 50% bipolar pulses and p < 0.05 for the 100% bipolar pulses.", "source": "Results 3.1, paragraph 2; Figure 2C", "quote": "However, inhibition was weaker at 6.7 kV/cm (p<0.01 compared to the higher electric field strengths for 50% bipolar pulses, and p<0.05 for 100% bipolar pulses).", "statistics": [ { "about": "50% bipolar, 6.7 kV/cm against higher field strengths", "test": "two-sided Student's t-test", "p": 0.01, "p_relation": "<" }, { "about": "100% bipolar, 6.7 kV/cm against higher field strengths", "test": "two-sided Student's t-test", "p": 0.05, "p_relation": "<" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": "reproduce_kim_2022.ipynb", "notes": "The criterion divides each bipolar dish by the unipolar mean at the same ROI. At the ROI nearest 6.7 kV/cm (6.75 kV/cm) the unipolar mean YP is -8.6 a.u. with an s.e.m. of 19.6 (the two unipolar dishes give 11.0 and -28.2), not above background, so the percent there (-399% for 50%, -579% for 100%) is a ratio to background and does not measure inhibition. The claim cannot be tested on these two unipolar dishes under the main reading. The unipolar mean is also at background on the top side, with the right footprint, with the scale from the electrodes and with the scaled field. On the bottom side alone (14.8 a.u., s.e.m. 3.3) or with the left footprint alone (7.9 a.u., s.e.m. 3.0) it is more than twice its s.e.m. above zero, and the claim is reproduced under both pairings, with a denominator below 3% of the largest unipolar mean of the main reading (571.1 a.u.). The block thus rests on the main reading of the ROI and the footprints (both sides, both footprints). Dandiset 000548 holds the YP image of the third unipolar dish, 0-03, but it is outside this dandiset and could not be measured as the others are (data check).", "deviations": [ "The unipolar mean is taken to be at background when it is not more than twice its s.e.m. above zero (the attempt's rule; in the main reading it is below zero).", "ROI placement (both sides averaged) and footprints (both averaged) are the assumptions of fig2a-uptake-rises-with-field; here they decide whether the claim can be tested, and the readings that give reproduced are shown.", "The field and the missing third unipolar dish as for fig2a-uptake-rises-with-field." ], "assumed": false, "disagreed": true, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig3-uptake-linear-in-pulse-number", "statement": "Uptake rose with field strength and with pulse number for both uni- and bipolar pulses, almost linearly with the number of pulses, so that plots for 5, 10 and 15 pulses look alike when the y-axis is scaled to 800, 1600 and 2400 a.u.", "source": "Results 3.2, paragraph 1; Figure 3A to C", "quote": "Increasing the pulse number increased YP uptake almost linearly [ 15 ]. Therefore, YP uptake plots for 5, 10, and 15 pulses appeared almost identical when plotted with the y-axis scaled proportionally (to 800, 1600, and 2400 a.u., respectively).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The trains of 10 and 15 pulses of Fig. 3 are not in the dandiset, which holds only 5-pulse trains (Fig. 2). The data are in dandiset 000548 (doi:10.48324/dandi.000548/0.230519.1825), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 3 to 5 dishes per arm, except 1 dish of 10-pulse bipolar. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig3d-cancellation-independent-of-number", "statement": "The relative efficiency of 50% bipolar pulses was the same for 5, 10 and 15 pulses and did not depend on the field strength.", "source": "Results 3.2, paragraph 2; Figure 3D and its legend", "quote": "The plots for 5, 10, and 15 pulses nearly overlapped, showing that within the studied limits cancellation of electroporation by adding a 50% opposite polarity phase did not depend on the pulse number or the electric field strength.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The trains of 10 and 15 pulses of Fig. 3 are not in the dandiset, which holds only 5-pulse trains (Fig. 2). The data are in dandiset 000548 (doi:10.48324/dandi.000548/0.230519.1825), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 3 to 5 dishes per arm, except 1 dish of 10-pulse bipolar. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4ac-ns-bipolar-20-25pct", "statement": "Bipolar 300+300 and 600+600 ns pulses with a 50% second phase gave 20 to 25% of the uptake of the respective unipolar pulses, independent of the field strength.", "source": "Results 3.3, paragraph 1; Figure 4A to D", "quote": "Electroporation by 300+300 and 600+600 ns pulses was at 20-25% of the respective unipolar pulses and did not depend on the electric field strength.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The dishes of the pulse duration experiment (Fig. 4) are not in the dandiset; it has no 300 ns pulses. The Fig. 2 dishes with 0 and 50% second phase had the same exposure as the 600 ns pair; on them the claim's measure gives a ratio of the bipolar to the unipolar fit of 34.4 to 64.9% with exponential fits. With polynomial fits the ratio crosses zero above 7 kV/cm (minimum -457.4%) and runs from 34.8 to 1537.4% above 8 kV/cm (notebook, section on the 600 ns exposure). These are other dishes, so this decides no outcome. The data are in dandiset 000549 (doi:10.48324/dandi.000549/0.230519.2043), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds the 300 ns dishes (3 per arm) and no 600 ns files. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4d-1200ns-tenfold", "statement": "Bipolar 1200+1200 ns pulses cancelled more at moderate field strengths, reducing YP uptake to a tenth of unipolar pulses.", "source": "Results 3.3, paragraph 1; Figure 4D", "quote": "However, longer 1200+1200 ns pulses were somewhat more efficient at cancellation at moderate electric field strengths, reducing the YP fluorescence 10-fold ( Fig. 4D ).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The 1200 ns pulses of Fig. 4 are not in the dandiset. The data are in dandiset 000549 (doi:10.48324/dandi.000549/0.230519.2043), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 2 unipolar and 3 bipolar 1200 ns dishes. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4eg-us-bipolar-30-50pct", "statement": "A 50% second phase also reduced uptake by 50, 100 and 500 us pulses, to 30 to 50% of the unipolar effect, a weak but highly significant cancellation (p < 0.01).", "source": "Results 3.3, paragraph 2; Figure 4E to H", "quote": "Cancellation by these longer pulses was relatively weak (to 30-50% of the unipolar pulse effect) but highly significant (p<0.01).", "statistics": [ { "test": "two-sided Student's t-test", "p": 0.01, "p_relation": "<", "n": "3 to 8 exposures per protocol" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The 50, 100 and 500 us pulses of Fig. 4 are not in the dandiset. The data are in dandiset 000549 (doi:10.48324/dandi.000549/0.230519.2043), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 2 or 3 dishes per arm; dish Uni50us-03 is there as two files of the same size. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4h-us-stronger-at-low-field", "statement": "For microsecond pulses, cancellation was stronger at lower field strengths.", "source": "Results 3.3, paragraph 2; Figure 4H", "quote": "The trend for more efficient cancellation at the lower electric field strengths persisted throughout the microsecond range ( Fig. 4H ).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The 50, 100 and 500 us pulses of Fig. 4 are not in the dandiset. The data are in dandiset 000549 (doi:10.48324/dandi.000549/0.230519.2043), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 2 or 3 dishes per arm. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5-ns-symmetric-along-aa", "statement": "Along the line from anode to cathode, YP uptake was nearly symmetrical for 300 and 600 ns pulses.", "source": "Results 3.3, paragraph 4; Figure 5A and B", "quote": "YP uptake data measured along the aa' line was nearly symmetrical for 300- and 600-ns pulses ( Fig. 5A , B ).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "Fig. 5 re-analyses the Fig. 4 dishes, which are not in the dandiset, and the files do not say which electrode was the anode. On the Fig. 2 dishes with the 600 ns exposure, YP on the two sides of aa' differs at p < 0.05 at no distance under both pairings (1 of 6 distances for 50% paired only); these are other dishes, and this dandiset has no 300 ns pulses, so this decides no outcome. The data are in dandiset 000549 (doi:10.48324/dandi.000549/0.230519.2043), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds the Fig. 4 dishes, whose aa' line can be measured; whether the files say which electrode was the anode was not checked. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5-us-anode-stronger", "statement": "For 50 to 500 us pulses, YP uptake was significantly stronger on the anodic side (p < 0.01), and for 1200 ns unipolar pulses marginally stronger there.", "source": "Results 3.3, paragraph 4; Figure 5C to F", "quote": "At 1200 ns, the effect of unipolar pulses appeared marginally stronger at the anodic side ( Fig. 5C ), and still longer 50-500 \u03bcs pulses showed significantly stronger YP uptake (p<0.01) at the anodic site.", "statistics": [ { "about": "anodic against cathodic side, 50 to 500 us pulses", "test": "two-sided Student's t-test", "p": 0.01, "p_relation": "<" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The microsecond and 1200 ns pulses of Figs. 4 and 5 are not in the dandiset, and the files do not say which electrode was the anode. The data are in dandiset 000549 (doi:10.48324/dandi.000549/0.230519.2043), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds the Fig. 4 dishes; whether the files say which electrode was the anode was not checked. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig6ad-unipolar-833khz-enhanced", "statement": "Unipolar 600 ns pulse trains at 10 to 500 kHz were as efficient as at 1 Hz, while at 833 kHz uptake was 2 to 3 times higher across the field range.", "source": "Results 3.4, paragraph 1; Figure 6A and D", "quote": "Unipolar pulses at 10 to 500 kHz showed the same efficiency as at 1 Hz ( Fig. 6A , D ). ... YP uptake after 833 kHz exposure was 2-3 fold higher than at other frequencies throughout the studied range of the electric field strengths.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The trains at 10 to 833 kHz of Fig. 6 are not in the dandiset, which holds only 1 Hz trains. The data are in dandiset 000550 (doi:10.48324/dandi.000550/0.230520.1609), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 10 kHz, 100 kHz and 833 kHz dishes (2 or 3 per arm) and no 500 kHz files. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig6be-bipolar-khz-less-than-1hz", "statement": "Bipolar 600+600 ns pulse trains at all kHz rates were less efficient than at 1 Hz, barely above background, the difference being largest (2.5 times) at the highest field.", "source": "Results 3.4, paragraph 2; Figure 6B and E", "quote": "In contrast, the efficiency of bipolar pulses at all kHz frequencies was less than at 1 Hz, and the electroporative uptake of YP was just marginally above the background level ( Fig. 6B , E ). The difference between 1 Hz and kHz-rate trains was maximum (2.5 times) at the highest electric field strength.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The trains at 10 to 833 kHz of Fig. 6 are not in the dandiset, which holds only 1 Hz trains. The data are in dandiset 000550 (doi:10.48324/dandi.000550/0.230520.1609), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 10 kHz, 100 kHz and 833 kHz dishes (3 bipolar each) and no 500 kHz files. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig6cf-833khz-thirtyfold", "statement": "At 833 kHz and 12 to 15 kV/cm, bipolar pulses had only 3 to 4% of the effect of unipolar pulses, about a 30-fold reduction, the strongest cancellation in the study.", "source": "Results 3.4, paragraph 3; Figure 6C and F", "quote": "At 12-15 kV/cm, the effect of bipolar pulses at 833 kHz was only 3-4% of the effect of unipolar pulses (~30-fold reduction).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The trains at 833 kHz of Fig. 6 are not in the dandiset. The data are in dandiset 000550 (doi:10.48324/dandi.000550/0.230520.1609), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 2 unipolar and 3 bipolar 833 kHz dishes. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig6cf-cancellation-stronger-at-high-field", "statement": "For high-frequency bursts of nsEP, a stronger electric field enhanced bipolar cancellation.", "source": "Discussion, paragraph 1; Figure 6C and F", "quote": "For high-frequency nsEP bursts, stronger electric field enhanced cancellation ( Fig. 6C , F ).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The trains at 10 to 833 kHz of Fig. 6 are not in the dandiset. The data are in dandiset 000550 (doi:10.48324/dandi.000550/0.230520.1609), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 10 kHz, 100 kHz and 833 kHz dishes and no 500 kHz files. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig7-charging-time-constant", "statement": "Fitting the cathodic pole response to the first unipolar pulse gave a charging time constant of 200 ns and a maximum polarization of 31% emission change (425 points, r = 0.93, p < 0.0001), and the discharge after it a time constant of 520 ns from 31.5% (425 points, r = 0.85, p < 0.0001).", "source": "Results 3.5, paragraph 2; Figure 7 (dotted lines, top panel)", "quote": "The best fit for membrane charging with an exponential function (using the first pulse in the unipolar pulse train) yielded the time constant of 200 ns and the maximum membrane polarization at 31% emission change (425 datapoints, correlation coefficient 0.93, p<0.0001). The best fit for the discharging portion of the curve yielded the same initial polarization (31.5% emission change) but, unexpectedly, a 2.5 times larger time constant of 520 ns", "statistics": [ { "about": "charging fit", "test": "exponential fit, correlation coefficient", "statistic": "r = 0.93", "p": 0.0001, "p_relation": "<", "n": "425 datapoints" }, { "about": "discharging fit", "test": "exponential fit, correlation coefficient", "statistic": "r = 0.85", "p": 0.0001, "p_relation": "<", "n": "425 datapoints" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The strobe imaging of CHO cells with FluoVolt (Fig. 7) is not in the dandiset. The data are in dandiset 000448 (doi:10.48324/dandi.000448/0.230421.1844), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 9 cells (5 unipolar, 4 bipolar by the session descriptions), each recorded forward and reverse, against the paper's 18 unipolar and 17 bipolar. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig7-bipolar-overshoot", "statement": "Bipolar pulses caused the same initial polarization as unipolar ones during the first phase, followed by a faster discharge and an overshoot into the opposite polarity.", "source": "Results 3.5, paragraph 1; Figure 7", "quote": "Bipolar nsEP caused the same initial polarization during the first phase of the pulse, followed by a faster discharge and an overshoot into the opposite polarity.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The strobe imaging of CHO cells with FluoVolt (Fig. 7) is not in the dandiset. The data are in dandiset 000448 (doi:10.48324/dandi.000448/0.230421.1844), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 9 cells (5 unipolar, 4 bipolar by the session descriptions), each recorded forward and reverse, against the paper's 18 unipolar and 17 bipolar. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig7-summation-without-buildup", "statement": "With 600 ns unipolar pulses at 833 kHz, each pulse charged the membrane to the same peak, with no stepwise build-up; the pulses merged into a continuous sawtooth polarization.", "source": "Results 3.5, paragraph 3; Figure 7", "quote": "Although charging by the subsequent pulses in unipolar pulse trains started with the partially charged membrane, it reached the same peak potential. A stepwise build-up of the peak membrane potential ... did not occur in our experiments with 833-kHz, 600-ns unipolar pulses.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "other", "notebook": null, "notes": "The strobe imaging of CHO cells with FluoVolt (Fig. 7) is not in the dandiset. The data are in dandiset 000448 (doi:10.48324/dandi.000448/0.230421.1844), which names this paper (IsPublishedIn) and is a separate target of the registry. The claims file does not name it as a source for 000489, so it is not used here, and the claim is blocked for this dataset, not for the archive. It holds 9 cells (5 unipolar, 4 bipolar by the session descriptions), each recorded forward and reverse, against the paper's 18 unipolar and 17 bipolar. The paper itself names no deposit (it has no data statement).", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1e-heating", "statement": "In the worst case tested, trains of 5 bipolar pulses (second phase 50%) at 1 Hz heated the sample to no more than 30 degrees C; at 833 kHz heating exceeded 30 degrees C but never reached 44 degrees C, and stayed close to 30 degrees C along the bb' line.", "source": "Methods 2.4, paragraph 2; Figure 1E", "quote": "Pulses applied at 1 Hz (the repetition rate used in all but one sets of experiments) caused only modest heating, not exceeding 30 \u00b0C. At a high repetition rate of 833 kHz, heating exceeded 30 \u00b0C but never reached the next transition point of 44 \u00b0C and remained close to 30 \u00b0C (green to blue transition) along the bb' line", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": null, "notes": "The thermochromic liquid crystal photographs (Methods 2.4, Fig. 1E) are not in the dandiset, nor in the four other dandisets that name the paper (000548, 000549, 000550, 000448, listed in the data check). The paper names no deposit of its data (it has no data statement or supplement), and the verifier's search of the archive found none.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds only the Fig. 2 experiment (17 dishes, 5 pulses at 1 Hz with a second phase of 0 to 100%) and a sample image named for Fig. 1F. The experiments on pulse number (Fig. 3), pulse duration (Figs. 4 and 5), repetition rate (Fig. 6), the strobe imaging of membrane charging (Fig. 7) and the thermometry (Fig. 1E) are not in it, so 16 of the 22 claims cannot be tested on it. Those of Figs. 3 to 7 are in dandisets 000548, 000549, 000550 and 000448, which name the same paper, but nothing in 000489's metadata or files points to them.", "found": null, "status": null }, { "kind": "other", "statement": "The YP channel of sub-Fig2-0-03 (unipolar) is identical, pixel for pixel in the overview, to the YP channel of sub-Fig2-25-04 (25% bipolar), while their MemBrite channels differ. The YP channel of sub-Fig2-25-04 registers with its own MemBrite channel (phase-correlation peak 0.454) and that of sub-Fig2-0-03 does not (0.028, the level of two unrelated dishes, 0.007 to 0.031). The YP image of unipolar dish 0-03 is missing and replaced by that of dish 25-04, leaving 2 unipolar dishes. Dandiset 000548 holds dish 0-03 as sub-Fig3-Uni5-03, with the same MemBrite channel and a YP channel that registers with it (peak 0.301), so the correct image exists in another dandiset.", "found": null, "status": null }, { "kind": "metadata_error", "statement": "The file sub-Fig1F holds the same image in both channels, although its series is described as two channels (MemBrite and YO-PRO-1).", "found": null, "status": null }, { "kind": "format_error", "statement": "Each stitched two-channel image is stored as an ImageSeries with data of shape (22323, 22323, 2) and a starting_time rate of 2 Hz. As an ImageSeries the first axis is time, so the file reads as 22323 frames of 22323 x 2 pixels; an Images container with two GrayscaleImage objects, or a series of shape (1, 22323, 22323) per channel, would describe it. The unit is n.a. and the three 25% files share the acquisition name Fig2_25.", "found": null, "status": null }, { "kind": "metadata_insufficient", "statement": "The files give no pixel size, electrode positions, ROI, field per ROI, footprint values (YP_0, MB_0) or pulse voltage, and identify the channels only in free text. Everything the paper plots has to be remeasured from the images, and the field recomputed from the paper's geometry. The data are consistent with 0.65 um per pixel (electrode centres 4.54 mm apart, footprints 1.49 mm across, against 4.5 and 1.5 mm in the paper).", "found": null, "status": null }, { "kind": "metadata_error", "statement": "The series description says the image was stitched from 144 images (12 x 12) of \"a whole well from a six-well plate\"; the paper says 216 images of cells in 35 mm glass-bottom dishes (Methods 2.1 and 2.5). The images show a 12 x 12 tile grid over a round glass bottom about 14.5 mm across.", "found": null, "status": null }, { "kind": "selection_undocumented", "statement": "Dish numbers in the subject ids run up to 18 (sub-Fig2-50-18), so more dishes were exposed than deposited, and nothing says which dishes form Fig. 2. All unipolar dishes are from 2021-07-29 and all 75% and 100% dishes from 2021-08-24, a day with no unipolar dish. In these files the 100% dishes show more uptake than the unipolar ones (largest mean 761.0 against 571.1 a.u.), which does not match Fig. 2C, where every second phase inhibits uptake.", "found": null, "status": null }, { "kind": "methods_unavailable", "statement": "Questions for the paper's authors. (1) How were the 200 um ROI placed along bb' (the spacing, how far out, whether both sides of the centre were measured and averaged)? With the two sides averaged, the unipolar mean at 6.7 kV/cm is at background and fig2c-weaker-at-6-7 cannot be tested; with the bottom side alone it is reproduced. (2) Were YP_0 and MB_0 taken from both electrode footprints or one, and over what area? With the left footprint alone fig2c-weaker-at-6-7 is reproduced. (3) Were the exponential fits of Fig. 2B made by nonlinear least squares or on log values, to means or to dish values, and from which field? The slope comparison depends on it. (4) Were the t-tests paired across ROI of the same dish, and for Fig. 2C which groups and which fields does p < 0.01 compare? At one ROI (15.24 kV/cm) 50% differs from unipolar at p < 0.01; over the range it does not. (5) Were the field values of the ROI taken from the Sim4Life model at nominal electrode positions, or adjusted per dish? The recomputed centre field is 15.38 kV/cm against the cited 15.1.", "found": null, "status": null } ], "reconciliation": null, "verifications": [ { "date": "2026-10-30", "kind": "agent", "by": "Independent agent run by CatalystNeuro (verifier-1, run 41096672228; same harness, separate context, did not write the notebook)", "reviewed": "The handover of the author-answers run (commit 3f745fbe5), the executed notebook with the conclusions and summary removed, the helper module and the claims file. The verifier also checked the archive's file lists for the blocked claims and read the paper. It had no attempt record.", "agreed": 20, "of": 22, "disagreements": [ { "claim": "fig2b-exponential-same-slope", "outcome": "not_reproduced", "reason": "10 of 12 readings have a bipolar slope that differs from unipolar at p < 0.05. Slopes for 50% and 75% are 0.68 to 0.72 of unipolar (NLS) or 0.50 to 0.59 (log). The other 2 readings have the exponential beating a straight line for only 3 of 5 amplitudes, so the criterion's reproduced fails there too. The notebook labels \"no slope differs, exponential not adequate\" as partially_reproduced, a category the criterion does not define, and that label is the only source of the disagreement between readings that yields methods_underspecified. Read against the criterion, all 12 readings fail." }, { "claim": "fig2c-weaker-at-6-7", "outcome": "blocked", "reason": "The unipolar mean at 6.75 kV/cm is -8.6 a.u. (dishes at 11 and -28), so the percent of unipolar is -399% (50%) and -579% (100%). That is a ratio to background, not a measure of inhibition. The code divides by a unipolar mean that is at or below background and never flags it; whether the test passes depends on the sign of a near-zero denominator. The outcome flips to reproduced on the bottom side and with the left footprint alone, where this denominator changes. (Blocked, other.)" } ] }, { "date": "2026-10-30", "kind": "agent", "by": "Independent agent run by CatalystNeuro (verifier-2, run 41106506929; same harness, separate context, did not write the notebook)", "reviewed": "The revision of the author-revise-1 run (commit da2f03abf), the full executed notebook with its conclusions and summary, the helper module, the claims file, the README and the attempt record.", "agreed": 22, "of": 22, "disagreements": [] } ] } ], "entries": [ { "name": "000489-kim-2022", "type": "reproduction", "title": "Bipolar cancellation of electroporation by the second phase amplitude (Kim et al. 2022)", "description": "Tests the findings of Kim, Semenov, Kiester, Keppler, Ibey, Bixler and Pakhomov (2022) on dandiset 000489, which holds stitched MemBrite and YO-PRO-1 images of 17 dishes of endothelial cells exposed to unipolar or bipolar 600 ns pulses with a second phase of 25 to 100% (Fig. 2). It measures YO-PRO-1 uptake along the line between the electrodes against the field of a recomputed electrode model, and tests the rise of uptake with field, its exponential slope and the inhibition by the second phase. The experiments of Figs. 3 to 7 and the thermometry are not in the dandiset.", "datasets": [ "dandi:000489" ], "papers": [ "10.1016/j.bioelechem.2022.108319" ], "derived_from": [], "notebooks": [ { "path": "reproduce_kim_2022.ipynb", "title": "Reproducing Kim et al. (2022) from dandiset 000489", "executed": "notebooks/000489-kim-2022/reproduce_kim_2022.html" } ] } ] }