DANDI:000059

Reproducing Petersen & Buzsaki (2020) from dandiset 000059 37

Notebook reproduce_petersen_2020.ipynb

• ✕Not reproducedResults, MS cooling decreases hippocampal theta frequency and power, paragraph 2; Figure 2H

  Theta power also decreased with MS temperature, less tightly than frequency (R = 0.54, P = 1.2e-16).

  this relationship was more consistent across animals than the effect on theta power (R = 0.54

  Results, MS cooling decreases hippocampal theta frequency and power, paragraph 2; Figure 2H

  What the paper reports

  • R = 0.54, p = 1.2 × 10⁻¹⁶

  Theta power does not follow temperature, R = -0.056 (P = 0.44) over TEMP sessions and R = 0.123 (P = 0.085) with the MS10 curves; over single trials pooled R = 0.107. Power is the spectrogram magnitude of the band-passed LFP as in calcInstantaneousTheta.m, minus each session's mean, at frames above 30 cm/s, and the 10 cm/s variant gives R = 0.135. Per rat the power R ranges from -0.346 to 0.376.

  How the test differed from the paper’s method

  • The theta electrode is the one flagged theta_reference in the files, which may differ from the paper's; power depends on the electrode more than frequency does. The LFP column read is that row in every session (checked through the LFP electrodes region).
  • Power is taken from the spectrogram of the 4 to 10 Hz band-passed LFP, as in the paper's code (calcInstantaneousTheta.m); the band-pass weights frequencies within the band unequally.
• ✕Not reproducedResults, MS cooling increases behavioral errors, paragraph 1; Figure 6I and 6J

  The incidence of errors did not correlate with the running speed of the rat (R about 0.1, P > 0.05 for all animals).

  The incidence of errors negatively and significantly correlated with ... and not with the running speed of the rat (R ~ 0.1; P > 0.05 for all animals

  Results, MS cooling increases behavioral errors, paragraph 1; Figure 6I and 6J

  What the paper reports

  • R ~ 0.1, p > 0.05 (n = all animals)

  Three of five rats have P < 0.05, MS13 (R = -0.493, P = 8e-11), MS21 (R = 0.216, P = 0.0034) and MS22 (R = 0.247, P = 0.001); MS10 and MS12 do not (P = 0.32 and 0.49). Over all sessions together R = 0.093 (P = 0.19). The correlations are over about 150 to 190 aligned positions, so small R values reach significance.

• ✕Not reproducedResults, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 2verifier disagreed at first

  Mean running speed was 87.3 +- 8.0 cm/s in control trials and 86.2 +- 9.9 cm/s during MS cooling.

  we combined trials before and after cooling into a single control group (mean running speed = 87.3±8.0). During MS cooling (mean running speed = 86.2±9.9)

  Results, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 2

  Over 15 sessions, reading (a) gives control 78.9 and cooling 74.9 cm/s, both outside; reading (b) gives control 79.6, within 87.3 +- 8.0, and cooling 76.0, 0.3 cm/s below 86.2 +- 9.9. The criterion needs both values within tolerance under one reading, and neither reading gives both. Speed is lower during cooling than in control (P = 0.035 to 0.041).

  How the test differed from the paper’s method

  • 15 of the code's 18 Figure 5 sessions; the paper does not define its speed measure.
• ✕Not reproducedResults, MS cooling decreases hippocampal theta frequency and power, paragraph 3 (Supplementary Figure 1G)

  The waveforms of hippocampal action potentials were not affected by MS cooling.

  Finally, the waveforms of action potentials in the hippocampus ... were not affected by MS cooling (Suppl. Fig. 1g).

  Results, MS cooling decreases hippocampal theta frequency and power, paragraph 3 (Supplementary Figure 1G)

  Over 646 units, trough-to-peak differs (P = 4.9e-10, median change 0 as most units do not move by a whole 0.05 ms sample) and amplitude rises by a median 0.8% (P = 0.00057). The windows start 7.1 to 31.8 minutes apart (5.1 to 29.8 minutes from the end of the pre window), so drift cannot be separated from cooling; for interneurons alone neither differs (P = 0.066 and 0.2). Fewer spikes are averaged in the cooling window (median 200 against 247.5), but in the 208 units whose two means both use the 300-spike cap the changes remain (amplitude 0.7%, P = 0.032; trough-to-peak P = 2.2e-05), so the spike count does not explain them. The effect is small, and the outcome follows the paper's test as written; it does not show that cooling changes the waveforms.

  How the test differed from the paper’s method

  • Waveforms from 120 s windows of the wide-band data at 20 kHz, high-passed at 300 Hz, on the channel of largest amplitude; the paper's measure is in its supplement, which could not be read.
• ✕Not reproducedResults, Effects of MS cooling on single neuron properties, paragraph 2; Discussion, Theta phase organization of hippocampal cell assemblies, paragraph 3

  During MS cooling fp and fLFP decreased in parallel, so the difference fp - fLFP remained constant.

  during MS cooling fp and fLFP decreased proportionally (i.e., fp–fLFP difference remained constant)

  Results, Effects of MS cooling on single neuron properties, paragraph 2; Discussion, Theta phase organization of hippocampal cell assemblies, paragraph 3

  fp - fLFP falls from 2.009 to 1.806 Hz (median change -0.128 Hz, P = 0.000132, 361 fields) and stays at 1.790 Hz after cooling; the ratio fp/fLFP is preserved (1.237 and 1.232, P = 0.84). By rat the mean change is -1.03 Hz (MS12), 0.01 (MS13), -0.19 (MS21) and 0.10 (MS22).

  How the test differed from the paper’s method

  • The paper names no test; its default paired test was used.
• ✕Not reproducedFigure 3F; Results, Effect of MS cooling on place field features, paragraph 2

  The information content of place cell spikes was not altered by MS cooling (P > 0.26).

  Information content of place cell spikes was also left unaltered by MS cooling (P > 0.26; Fig. 3f).

  Figure 3F; Results, Effect of MS cooling on place field features, paragraph 2

  What the paper reports

  • p > 0.26

  Over 374 place cells information is lower during cooling than before (median change -0.029 against a median of 1.253 bits/spike, P = 0.014) and lower after than before (P = 0.0064); cooling and post do not differ (P = 0.31). The changes are small. Bits per spike rise when fewer spikes are used, and the pre state has the fewest trials, but with each state's spikes subsampled to the same count (360 cells) pre against cooling gives P = 0.0073 and pre against post P = 0.0092, so the decrease does not come from the spike counts.

  How the test differed from the paper’s method

  • The paper names its comparisons but not its test; its default paired test was used.
• ✕Not reproducedFigure 5C and 5G; Results, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 2

  Distance-time compression of place cell pairs (0.54 cm/ms before cooling) decreased during MS cooling (P = 0.02), while distance-phase compression was unchanged (P = 0.92).

  Compression index, c (cm/ms; i.e., the slope in c), significantly decreased during MS cooling (* P = 0.02) but the distance/phase lag compression (cm/radian) remained unaffected (P = 0.92).

  Figure 5C and 5G; Results, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 2

  What the paper reports

  • distance-time compression, cooling against control: p = 0.02
  • distance-phase compression, cooling against control: p = 0.92

  Pooled pre compression 0.273 cm/ms against 0.54. Per session it is lower during cooling in 8 of 9 sessions without significance (0.298 against 0.191, P = 0.0547); phase compression does not change (P = 0.426). Lag and distance correlate weakly (R = 0.195), so the slope depends on the fit (inverse regression over pooled pre pairs 7.175 cm/ms). The 70 ms window can hold more than one candidate peak; in 10.5% of pre pairs the lag changes when the window is narrowed to half the theta period, which gives 0.156 cm/ms. The compression magnitude cannot be judged from this method. The direction of the change agrees with the paper under the criterion's fit; the inverse slope goes the other way (control 9.085, cooling 10.420 cm/ms, lower in 1 of 9).

  How the test differed from the paper’s method

  • Lags from each pair's correlogram peak and compression from a regression, where the paper fits a surface to the density of all pairs; pairs without a peak within 70 ms are dropped.
• ✕Not reproducedResults, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 3; Figure 5I

  Theta phase lags between place cell pairs were not affected by MS cooling (P > 0.24 between all conditions).

  In contrast, phase lags between spikes of place cell pairs were not affected by MS cooling (Fig. 5i; P > 0.24 between all conditions).

  Results, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 3; Figure 5I

  What the paper reports

  • Wilcoxon signed rank test, p > 0.24

  Phase lags are slightly larger during cooling than before (1.367 against 1.304 rad, mean difference 0.051 rad, P = 0.0015) and after (P = 0.0043); pre and post do not differ (P = 0.51). Per session medians, cooling against pre P = 0.062. The +-pi window spans about 1.15 periods of the phase correlogram (1.74 pi). With the lag picked within +-pi/2 (a variant), 43.3% of pre pairs get another lag or none, and cooling is still above pre (mean difference 0.025 rad, P = 0.0196) but not above post (P = 0.162); pre and post do not differ (P = 0.178). Part of the increase may come from how the lag is picked.

• ✕Not reproducedResults, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 4; Figure 5J

  The fraction of place cells active in a theta cycle was not significantly affected by MS cooling (P = 0.2).

  we found that the fraction of place cells active in a given theta cycle was not significantly affected by MS cooling (Fig. 5j; P = 0.2).

  Results, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 4; Figure 5J

  What the paper reports

  • p = 0.2

  The fraction active is higher during cooling (0.2405 against 0.226, rank-sum P = 1.5e-22 over 9037 and 10152 cycles). Per session the cooling mean is lower than pre in 5 of 9 sessions (P = 0.734); cooling against post gives P = 0.074 and pre against post P = 0.004. Session means range from 0.159 to 0.315 and sessions contribute different numbers of cycles in each state, so the pooled test reflects the make-up of the pool as much as an effect. Cycles are longer during cooling (131.1 ms against 117.8 and 117.2 ms).

  How the test differed from the paper’s method

  • The paper does not name its test; the default rank-sum test over cycles was fixed before the analysis.
• ✕Not reproducedResults, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 4; Figure 5K

  The number of spikes emitted by all neurons per theta cycle was preserved during MS cooling (P > 0.058 between all conditions).

  The number of spikes emitted by all neurons per theta cycle was also preserved after MS cooling (Fig. 5k)

  Results, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 4; Figure 5K

  What the paper reports

  • p > 0.058

  Pre and cooling do not differ (45.68 and 44.98 spikes, P = 0.0758), but post (51.68) differs from both (P below 1e-50). Per session, cooling differs from neither pre (P = 0.57) nor post (P = 0.129), and post differs from pre (P = 0.02). Session means range from 17.66 to 91.37 spikes, so the pooled tests depend on how many cycles each session contributes.

  How the test differed from the paper’s method

  • Spikes of all good and good2 units; the paper's 'all neurons' may include other units.
• ◐Partially reproducedSTAR Methods, Electrophysiological Recordings

  MS cooling peaked about 60 s after its onset and lasted about 10 to 12 minutes.

  The cooling typically peaked after about 60 sec after the cooling onset (suppl. fig. 1G) and lasted for about 10–12 minutes

  STAR Methods, Electrophysiological Recordings

  Over 37 sessions with a recorded temperature the minimum comes a median 121 s after the onset (IQR 89 to 138 s; 119 to 122 s for onset thresholds of 0.5 to 2 C), against 60 s. The duration holds under reading (b), 12.16 minutes until the temperature is within 1 C of baseline; under reading (a) the temperature is below 32 C for 8.77 minutes. The median minimum is 21.2 C. The drop is fast and the temperature then stays near its minimum, so the time to the minimum overstates the time to the peak effect. 90% of each session's drop is reached a median 53 s after onset (IQR 44 to 63 s), and the onset-aligned mean trace is within 0.5 C of its minimum from 70 to 152 s. Without the five sessions whose baseline has artefacts above 38 C or whose onset is detected early, the values are 121.5 s and 12.22 minutes.

  How the test differed from the paper’s method

  • The onset is taken from the temperature trace (1 C below the pre-cooling median), as the files have no time of dry-ice placement; the Methods do not define the onset.
• ◐Partially reproducedFigure 2I; Results, MS cooling decreases hippocampal theta frequency and power, paragraph 2

  Theta frequency and power were lower during MS cooling than before and after it.

  MS cooling induced fast and reversible change in the frequency and power of hippocampal theta oscillations (Figure 2d, e, f, i).

  Figure 2I; Results, MS cooling decreases hippocampal theta frequency and power, paragraph 2

  Frequency is lower during cooling than before (44 of 45 sessions, P = 1.4e-12) and after (45 of 45, P = 5.7e-14). Power is lower than before at P = 0.048 (26 of 45) but not lower than after (19 of 45, P = 0.94); during cooling it is 0.972 of the session mean of the three states.

  How the test differed from the paper’s method

  • State means over trials, from the dandiset's labels, with 'Cooling off' trials left out.
• ◐Partially reproducedDiscussion, Theta phase organization of hippocampal cell assemblies, paragraph 5

  During MS cooling LFP theta frequency decreased by 12%.

  During MS cooling, LFP theta frequency decreased by 12 %

  Discussion, Theta phase organization of hippocampal cell assemblies, paragraph 5

  The decrease is 8.88% (a), 9.18% (b) and 9.23% (c), none within 12 +- 1.2%. The slowest cooling trial of a session is a mean 16.93% below pre. Per rat 4.76% (MS12) to 10.74% (MS21). The paper's within-field values (8.4 and 7.7 Hz) are reproduced in fig4b-fp-flfp-decrease.

  How the test differed from the paper’s method

  • The paper does not say how the 12% is computed; three readings were tested.
• ◐Partially reproducedResults, MS cooling increases behavioral errors, paragraph 1; Figure 6D and 6E

  MS cooling increased choice errors about 3-fold, within each rat (P < 0.05 for all animals) and across all animals (P = 1e-6).

  Overall, the number of memory errors increased approximately 3-fold, assessed either within rats (P < 0.05 for all animals) or across all animals

  Results, MS cooling increases behavioral errors, paragraph 1; Figure 6D and 6E

  What the paper reports

  • within each rat: p < 0.05
  • across all animals: p = 10⁻⁶

  Errors are 6.67% before and 15.23% during cooling (40 of 45 sessions higher, P = 3e-07), ratios 2.28 (a), 2.31 (b) and 2.53 (c), all below 2.7. Per rat, P = 0.0078 (MS10), 0.039 (MS12), 0.027 (MS21) and 0.064 (MS22, 10 of 12 higher); MS13 has 5 sessions, all higher (P = 0.0625, the smallest possible). Counting 'Cooling off' trials as cooling gives a ratio of 1.98; TEMP sessions alone 1.96.

  How the test differed from the paper’s method

  • States from the dandiset's trial labels; the code counts errors by time windows from the cooling onsets and offsets, which are not in the files.
  • 45 of 53 sessions; MS13 has 5 sessions here, too few for an exact signed-rank test to reach 0.05.
• ◐Partially reproducedResults, MS cooling increases behavioral errors, paragraph 1; Figure 6F

  The incidence of errors correlated negatively with MS temperature (R = -0.35, P < 0.01).

  The incidence of errors negatively and significantly correlated with temperature change (R = − 0.35; P < 0.01; all animals)

  Results, MS cooling increases behavioral errors, paragraph 1; Figure 6F

  What the paper reports

  • R = − 0.35, p < 0.01

  Negative and stronger than reported, R = -0.838 (a, P = 5.9e-41), -0.789 (b) and -0.868 (c), none within -0.35 +- 0.035. Over single trials pooled R = -0.127 (P = 5.5e-20); per rat -0.298 to -0.860. The paper's value may come from a different unit of analysis, which its text does not give.

  How the test differed from the paper’s method

  • 37 sessions with a recorded temperature.
• ◐Partially reproducedResults, MS cooling increases behavioral errors, paragraph 1; Figure 6G

  The incidence of errors correlated negatively with theta frequency (R = -0.35, P < 0.01).

  The incidence of errors negatively and significantly correlated with ... theta frequency (R = − 0.35; P < 0.01; all animals)

  Results, MS cooling increases behavioral errors, paragraph 1; Figure 6G

  What the paper reports

  • R = − 0.35, p < 0.01

  R = -0.868 (a, P = 3.9e-47) and -0.733 (b), stronger than -0.35; per rat -0.341 to -0.829.

• ◐Partially reproducedResults, MS cooling increases behavioral errors, paragraph 1; Figure 6H and 6J

  The incidence of errors correlated less with theta power; only 2 of 5 animals had a significant correlation (R beyond -0.3, P < 0.01).

  The incidence of errors negatively and significantly correlated with ... and less so with theta power (only 2 of 5 animals had significant R > − 0.3; P < 0.01)

  Results, MS cooling increases behavioral errors, paragraph 1; Figure 6H and 6J

  One rat counts (MS10, R = -0.425, P = 1.1e-09). MS21 is significant with R = -0.202 (P = 0.0063), and MS22 with the opposite sign (R = 0.325, P = 1.2e-05).

• ◐Partially reproducedResults, Effects of MS cooling on single neuron properties, paragraph 2 (Supplementary Figure 2)

  Within-field and peak firing rates of place cells decreased moderately during MS cooling (11% and 12%; P < 1e-9 and P < 1e-11).

  Both within-field and peak firing rates of place cells decreased moderately during MS cooling (Suppl. Fig. 2; 11% and 12%

  Results, Effects of MS cooling on single neuron properties, paragraph 2 (Supplementary Figure 2)

  What the paper reports

  • within-field firing rate: p < 10⁻⁹
  • peak firing rate: p < 10⁻¹¹

  Over 636 fields both rates fall (P = 0.0024 and 0.0013), by 3.7% and 5.3% as medians (a), 7.7% and 6.7% as ratios of means (b); reading (c) is dominated by fields with near-zero pre rates (-111% and -70%). Fields with at least 50 spikes in each state give 10.8% and 9.9%. The decrease differs between rats (MS12 rises by 10.1%, MS13 falls by 27.8%).

  How the test differed from the paper’s method

  • Place fields by the automatic criteria of the Methods for Figure 5; the paper defined the fields of this analysis by hand.
  • Putative pyramidal cells typed here from waveforms and rates; the files have no cell types.
• ◐Partially reproducedDiscussion, Theta phase organization of hippocampal cell assemblies, paragraph 5; Results, Effects of MS cooling on single neuron properties, paragraph 2

  Firing rates of interneurons decreased during MS cooling by about 14%.

  During MS cooling, LFP theta frequency decreased by 12 % and within-field firing rates of place cells decreased by a similar proportion (12%; interneurons 14%).

  Discussion, Theta phase organization of hippocampal cell assemblies, paragraph 5; Results, Effects of MS cooling on single neuron properties, paragraph 2

  127 putative interneurons, lower in 75 (P = 0.0017), by 6.5% (a) or 9.1% (b); thresholds of 0.35 and 0.5 ms, and narrow units alone, give 9.4% to 9.9%.

  How the test differed from the paper’s method

  • Putative interneurons typed here (trough-to-peak at most 0.425 ms, or above 10 Hz).
• ◐Partially reproducedFigure 4C

  fp and fLFP were correlated across place fields before, during and after cooling (R = 0.61, 0.59 and 0.36; P < 1e-6 each).

  Correlation between LFP theta frequency (fLFP) and place cell oscillation frequency (fp; Rpre = 0.61; Rcooling = 0.59; Rpost = 036

  Figure 4C

  What the paper reports

  • before cooling: Rpre = 0.61, p < 10⁻⁶
  • during cooling: Rcooling = 0.59, p < 10⁻⁶
  • after cooling: Rpost = 036, p < 10⁻⁶

  All positive (P = 1.5e-05, 6.7e-19 and 0.0029) and weaker than 0.61, 0.59 and 0.36; within rats R ranges from -0.05 to 0.64.

• ◐Partially reproducedResults, Effects of MS cooling on single neuron properties, paragraph 1; Figure 4A

  fLFP and fp measured within place fields decreased linearly with MS temperature (fLFP R = 0.66, slope 0.071 Hz per C; fp R = 0.38, slope 0.09 Hz per C).

  The theta oscillation frequency of pyramidal neurons decreased linearly and paralleled the downward frequency shift of LFP theta oscillation (Fig. 4a; fLFP: R = 0.66, Slope = 0.071. fp: R = 0.38, slope = 0.09).

  Results, Effects of MS cooling on single neuron properties, paragraph 1; Figure 4A

  Over 52474 windows from 563 fields, fLFP R = 0.678 and slope 0.0716 Hz per C, fp slope 0.0859, within tolerance; fp R = 0.338, just below 0.342. The windows overlap (stepped by one trial), so the P values over windows overstate the evidence; the paper's code does the same.

  How the test differed from the paper’s method

  • Windows of 20 trials stepped by one trial, as calc_trial_averages.m; the paper's figure does not say which windows it plots.
• ◐Partially reproducedFigure 3D

  Place field size and fp were negatively correlated before, during and after cooling (R = -0.49, -0.40, -0.40; P < 1e-9).

  Place field size continues to be inversely correlated with fp after MS cooling (Rpre = − 0.49; Rcooling = − 0.40; Rpost = − 0.40

  Figure 3D

  What the paper reports

  • before cooling: Rpre = − 0.49, p < 10⁻⁹
  • during cooling: Rcooling = − 0.40, p < 10⁻⁹
  • after cooling: Rpost = − 0.40, p < 10⁻⁹

  All negative with P below 3e-09, weaker than -0.49 and -0.40.

• ◐Partially reproducedResults, Effect of MS cooling on place field features, paragraph 2; Figure 3E

  Measured place field size correlated with the size predicted by SPF = v / (fp - fLFP) before (R = 0.55) and during (R = 0.54) cooling, and weakly after (R = 0.11).

  We found a reliable and similar relationships between measured place field sizes and model-predicted sizes for trials before (R = 0.55), during (R = 0.54) and after (R = 0.11) MS cooling (Fig. 3e).

  Results, Effect of MS cooling on place field features, paragraph 2; Figure 3E

  Pre and cooling positive (P = 4.7e-06 and 4.9e-11) and weaker than 0.55 and 0.54; post 0.325 against 0.11. Predicted sizes (median 47 to 48 cm) are smaller than measured (65 cm).

• ◐Partially reproducedResults, Effects of MS cooling on single neuron properties, paragraph 2; Figure 4D

  The phase precession slope decreased slightly but significantly during MS cooling (P < 0.007 and P < 0.0003).

  The slope of the relationship between travel distance across the place field and phase advancement of spikes ... decreased slightly, but nevertheless significantly, during MS cooling (Fig. 4d).

  Results, Effects of MS cooling on single neuron properties, paragraph 2; Figure 4D

  What the paper reports

  • comparison marked ** in Figure 4D: p < 0.007
  • comparison marked *** in Figure 4D: p < 3 × 10⁻⁴

  Under reading (a), the slope magnitude during cooling does not differ from pre (median change 0, P = 0.83) and is smaller than post (P = 0.022); under (b) neither comparison differs (P = 0.32 and 0.15). 87.5% of fields have a negative slope before cooling.

  How the test differed from the paper’s method

  • The direction of 'decreased' is not stated; two readings were tested.
  • Slopes by a grid search of circular-linear regression up to two cycles per field.
• ◐Partially reproducedFigure 5D, 5E and 5F

  The theta-repeated cross-correlograms of place cell pairs had a period of about 85 ms before cooling, which lengthened during MS cooling (P = 0.002), while the period of the phase cross-correlograms was unaffected (P = 0.32).

  Duration of the theta-repeated spike cross-correlograms (as in d), calculated for each session, significantly increased during MS cooling ... whereas the spike phase-lag correlations remained unaffected (n.s., P = 0.32).

  Figure 5D, 5E and 5F

  What the paper reports

  • period of the time cross-correlograms, cooling against control: two-sided signed rank test, p = 0.002
  • period of the phase cross-correlograms, cooling against control: p = 0.32

  Over 9 sessions the period lengthens from 109.2 to 114.0 ms (8 of 9, P = 0.0195) and the phase period does not change (1.740 and 1.760 pi rad, P = 0.59); the control period is not 85 +- 8.5 ms. The criterion's estimator takes the largest neighbouring peak 60 to 200 ms from the main peak, and in 47.7% of pre pairs that peak is more than 1.25 times as far as the nearest one, so it often picks the second neighbour and the 109.2 ms is biased upward. With the nearest neighbouring peak (a variant) the control period is 91.0 ms, within tolerance, and it lengthens to 95.5 ms (7 of 9, P = 0.031); pairs with |Ltr| below 10 cm give 91.0 ms. Under that variant the phase period, also from the nearest peak, does not change (1.285 pi rad in both, P = 0.367), so all three parts of the criterion hold; but that estimator is biased downward, as 211 of 3499 pre pairs give 60 to 70 ms, at the floor of the search window and below any plausible theta period, so its 91.0 ms is not a clean test of 85 ms either. The outcome follows the criterion's estimator. Both control periods are shorter than the LFP theta period (115.7 ms).

  How the test differed from the paper’s method

  • The period is measured per pair and summarised per session; the paper reads it from the sum over pairs. The criterion was changed to this before the analysis across sessions, after a pilot session showed that the summed correlogram's spectrum follows its envelope; the summed correlogram is shown as a variant (99 to 200 ms).
  • 9 sessions in 4 rats, against 18 in 5.
  • The criterion's period estimator often takes the second neighbouring peak; the nearest-peak estimator is shown as a variant.
• ✓ReproducedResults, MS cooling decreases hippocampal theta frequency and power, paragraph 2; STAR Methods, Electrophysiological Recordings

  A session holds about 40 control trials, 20 to 60 cooling trials and 20 to 80 recovery trials, 80 to 200 trials in all with a mean of 150.

  After a block of control trials (~ 40 trials) ... about 20 to 60 ‘cooling’ trials), followed by recovery trials (20 to 80) ... a total number of trials ranging from 80 to 200 (mean: 150 trials).

  Results, MS cooling decreases hippocampal theta frequency and power, paragraph 2; STAR Methods, Electrophysiological Recordings

  Over 45 BEH sessions the mean is 143.8 trials (80 to 204); medians of 39 pre-cooling, 47 cooling and 44 post-cooling trials. 12 sessions have two cooling blocks, which the paper does not mention; in each the second block follows post-cooling trials, and the onset-aligned series stops before it. 'Cooling off' trials (median 14 per session) are counted in no state.

  How the test differed from the paper’s method

  • 45 of the paper's 53 sessions.
• ✓ReproducedResults, MS cooling decreases hippocampal theta frequency and power, paragraph 2; Figure 2G

  Theta frequency decreased linearly with MS temperature (R = 0.81, P = 5.4e-48).

  Theta frequency decreased linearly with MS temperature (Figure 2g; down to 20° C; R = 0.81

  Results, MS cooling decreases hippocampal theta frequency and power, paragraph 2; Figure 2G

  What the paper reports

  • R = 0.81, p = 5.4 × 10⁻⁴⁸

  With the code's aligned series, R = 0.789 (P = 2.8e-43, 198 positions) over 37 TEMP sessions under reading (a), and R = 0.758 (P = 3e-38) with the MS10 temperature curves under reading (b); both are within tolerance. Over single trials pooled R = 0.672, slope 0.065 Hz per C. Per rat R is 0.685 to 0.954.

  How the test differed from the paper’s method

  • 37 sessions with a recorded temperature, where the paper used 53; the MS10 temperature in the dandiset is not a recording.
  • The theta electrode is the one flagged theta_reference in the files; the code's channel numbers could not be mapped to the files' electrodes.
• ✓ReproducedResults, MS cooling decreases hippocampal theta frequency and power, paragraph 2; Figure 2J

  The relationship of theta frequency with MS temperature was more consistent across animals than that of theta power.

  Theta frequency decreased linearly with MS temperature ... and this relationship was more consistent across animals than the effect on theta power

  Results, MS cooling decreases hippocampal theta frequency and power, paragraph 2; Figure 2J

  In each of the four rats with a recorded temperature the frequency R is positive (0.685 to 0.954, every P below 1e-22), a range of 0.269, against a range of 0.722 for power (-0.346 to 0.376). The outcome rests on power varying across rats, since power shows no consistent effect (fig2h-theta-power-temperature).

  How the test differed from the paper’s method

  • Four rats; MS10 has no recorded temperature.
• ✓ReproducedFigure 6E (marked ns)

  The error rate after cooling did not differ from the error rate before it.

  Choice errors shown as boxplots constructed from all sessions. ... ns = nonsignificant.

  Figure 6E (marked ns)

  Post 6.49% against pre 6.67% (median difference -0.13 points, P = 0.837, 45 sessions); cooling against post P = 8e-08.

  How the test differed from the paper’s method

  • The figure's 'ns' was read as pre against post.
• ✓ReproducedResults, MS cooling increases behavioral errors, paragraph 1; Figure 6C

  The worst memory performance occurred between trials 4 and 8 after the onset of cooling, when MS temperature reached its minimum.

  The worst memory performance occurred between trials 4 and 8 after MS cooling, when the MS temperature reached its minimum

  Results, MS cooling increases behavioral errors, paragraph 1; Figure 6C

  The mean smoothed error series over 45 sessions peaks at trial 7 after onset (0.193, against 0.066 over the 40 trials before), the trial of the minimum mean temperature and theta frequency. The peak is narrow and the result fragile. A second rise reaches 0.186 at trial 20, and within single rats the mean peaks later, at trials 14 to 26. All 45 sessions contribute at every trial from 1 to 40.

• ✓ReproducedResults, Effects of MS cooling on single neuron properties, paragraph 3; Figure 4E and 6C

  Running speed decreased relatively monotonically within a session.

  Running speed decreased relatively monotonically within session (Fig. 4e; see also Fig. 5c).

  Results, Effects of MS cooling on single neuron properties, paragraph 3; Figure 4E and 6C

  Speed falls with trial number in 44 of 45 sessions (median rho -0.452, P = 4e-13), in every rat; the aligned mean falls from 86.0 to 73.7 cm/s.

• ✓ReproducedResults, Effects of MS cooling on single neuron properties, paragraph 1 (Supplementary Figure 2D)

  The theta oscillation frequency of putative fast-spiking interneurons decreased during MS cooling, commensurate with the LFP theta.

  Theta frequency oscillation of putative fast spiking interneurons also decelerated (Suppl. Fig. 2d), commensurate with the downward frequency shift of LFP theta oscillation.

  Results, Effects of MS cooling on single neuron properties, paragraph 1 (Supplementary Figure 2D)

  9.55 to 8.66 Hz (lower in 105 of 114, P = 8.7e-16), a 9.4% decrease against 8.8% for the LFP theta of the same sessions; narrow units alone P = 3.1e-11.

  How the test differed from the paper’s method

  • Putative interneurons typed here; the paper's fast-spiking interneurons come from CellExplorer.
• ✓ReproducedResults, Effects of MS cooling on single neuron properties, paragraph 2; Figure 4B

  MS cooling decreased both the oscillation frequency of place cells (fp) and the LFP theta frequency in their fields (fLFP) by about the same degree, and both recovered (fLFP 8.4, 7.7, 8.5 Hz; fp 10.6, 9.5, 10.4 Hz before, during and after; n = 365).

  MS cooling decreased both fp and fLFP, measured within the place fields of neurons, by approximately the same degree ... Both values recovered after cooling.

  Results, Effects of MS cooling on single neuron properties, paragraph 2; Figure 4B

  What the paper reports

  • p < 5.9 × 10⁻⁸

  Over 361 fields (paper 365) all six means are within the paper's spreads; fp falls in 311 (P = 3.5e-44) and fLFP in 352 (P = 1.2e-60), by 9.2% and 9.0%, and both recover. Each rat shows the same pattern and every session the decrease; in MS22-180720-110055 fp does not recover (9.92 Hz after, 10.15 Hz during cooling). Fields with at least 100 or 200 spikes per state give the same means.

  How the test differed from the paper’s method

  • Fields by the automatic criteria of the Methods, from 11 sessions in 4 rats.
• ✓ReproducedResults, Effect of MS cooling on place field features, paragraph 1; Figure 3C

  Place field size was highly correlated before and during MS cooling (R = 0.91).

  Place field size does not change with MS cooling (R = 0.91).

  Results, Effect of MS cooling on place field features, paragraph 1; Figure 3C

  R = 0.8197 over 635 fields, at the edge of the tolerance (0.819). With at least 20 or 50 spikes per state R is 0.8348 and 0.8308, with at least 100 it is 0.8136, outside. Sizes do not differ (62.7 and 64.9 cm, P = 0.084).

  How the test differed from the paper’s method

  • Field size from rate maps of each state (bins above 10% of the peak); the paper does not define it.
• ✓ReproducedResults, Effect of MS cooling on place field features, paragraph 3; Figure 3H and 3I

  The spatial scale of the population vector correlation of pyramidal cells was not affected by MS cooling.

  Population vector correlation of pyramidal cells was not affected by MS cooling (Fig. 3g, h).

  Results, Effect of MS cooling on place field features, paragraph 3; Figure 3H and 3I

  Median change 0.25 cm, P = 0.966 over 11 sessions (paper 21); scales 18.3 to 36.9 cm.

  How the test differed from the paper’s method

  • The decorrelation scale is computed within maze segments at 5 cm bins; 11 sessions.
• ✓ReproducedResults, Effects of MS cooling on single neuron properties, paragraph 3; Figure 4G and 4H

  fp depended on running speed more strongly than fLFP, and fp during cooling was lower at all velocities.

  fp values during cooling were lower at all velocities (Fig. 4g) ... while speed exerted a relatively linear effect on fp, it had no or little effect on the frequency of fLFP

  Results, Effects of MS cooling on single neuron properties, paragraph 3; Figure 4G and 4H

  fp slope 0.0136 Hz per cm/s (P = 3.2e-12), fLFP 0.0061; difference 0.0074 (bootstrap interval 0.0040 to 0.0112). In the three speed bins from 60 to 120 cm/s with at least 10 fields fp is lower during cooling (P below 1e-5 each); below 60 cm/s too few fields had 50 spikes.

  How the test differed from the paper’s method

  • Speed bins of 20 cm/s; the paper's bins are not stated.
• ✓ReproducedResults, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 3; Figure 5H

  During MS cooling the theta time lags between place cell pairs increased compared with before and after cooling (P = 8e-5 and P = 0.00032), and did not differ between before and after (P = 0.79).

  During MS cooling, the time lags increased significantly ... whereas they were not different from each other during precooling and post-cooling sessions (P = 0.79)

  Results, MS temperature effects on theta time/phase compression of place cells sequences, paragraph 3; Figure 5H

  What the paper reports

  • pre against cooling: sign rank test, p = 8 × 10⁻⁵ (n = 10 sessions, 4 rats)
  • post against cooling: sign rank test, p = 3.2 × 10⁻⁴ (n = 10 sessions, 4 rats)
  • pre against post: p = 0.79

  Under reading (a), cooling against pre over 3136 pairs (30.5 against 28.5 ms, P = 1.14e-06) and against post (P = 1.3e-10); pre and post do not differ (P = 0.0967). Reading (b) agrees (P = 0.023, 0.016 and 0.81), and so does the half-period window (P = 3.8e-22 and 2.0e-29).

  How the test differed from the paper’s method

  • The legend's n = 10 sessions cannot give P = 8e-5 with a signed-rank test over sessions, so the test over pairs was taken as the main reading.