{ "dataset": { "archive": "dandi", "id": "000931", "label": "DANDI:000931" }, "page": "datasets/dandi/000931/", "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": 0, "not_reproduced": 0, "blocked": 37 }, "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": "000931-dehaqani-2024-01", "dataset": { "archive": "dandi", "id": "000931", "version": "0.261011.1559", "doi": "10.48324/dandi.000931/0.261011.1559" }, "key": "dandi:000931", "label": "DANDI:000931", "dataset_version": "0.261011.1559", "paper": "10.1016/j.celrep.2024.114013", "paper_title": "A mechanosensory feedback that uncouples external and self-generated sensory responses in the olfactory cortex", "date": "2026-10-31", "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/41223948341" }, "tier": "agent_verified", "deprecated": "", "deprecated_on": null, "entry": "000931-dehaqani-2024", "entry_title": "Sniffing and odor responses in the olfactory cortex (Dehaqani, Michelon et al. 2024)", "description": "Tests the findings of Dehaqani, Michelon, Patella, Petrucco, Piasini and Iurilli (2024) on dandiset 000931. The dandiset holds one NWB file, the sorted spike times of 1013 units from one mouse, placed in the concentration-series experiment only by a keyword, with no breathing signal, inhalation times, odor trials, airflow pulses, unit waveforms or brain regions. Every claim of the paper needs at least one of these, so all are blocked; the notebook lists what the file holds and checks the unit table against its description and the paper's spike-sorting criteria.", "notebooks": [ { "path": "reproduce_dehaqani_2024.ipynb", "title": "Reproducing Dehaqani, Michelon et al. (2024) from dandiset 000931", "executed": "notebooks/000931-dehaqani-2024/reproduce_dehaqani_2024.html" } ], "outcomes": [ { "claim": "inhalation-sorting", "statement": "Inhalation durations appear bimodal, and a Gaussian-mixture and hierarchical clustering of inhalation waveforms sorts them into slow and fast inhalations; fast inhalations are shorter and have steeper airflow changes than slow ones.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 1; Figure 1C; STAR Methods, Inhalation clustering", "quote": "Since the distribution of inhalation durations appeared bimodal, we developed a semi-unsupervised method that sorted inhalations into slow and fast depending on their airflow rate waveforms ... Fast inhalations had shorter duration and steeper changes in airflow rate than slow inhalations.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, which the criterion needs; it also pools the eight awake mice of the leave-one-mouse-out test, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs1a-phase-decoding", "statement": "PCx population activity encodes the inhalation phase; a cross-validated support vector regression predicts the phase above a shuffle null in individual mice.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 3; Figures 1E and S1A", "quote": "Hence, PCx activity encoded the phase and speed of each inhalation (Figures 1E and 1F; Figures S1A and S1B).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times or the brain area of each unit, which the criterion needs; it also pools the awake mice whose phase decoding the paper reports, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs1b-speed-decoding-single-mice", "statement": "The inhalation speed (fast against slow) can be decoded above chance from the mean firing rate in the first 180 ms of inhalation in individual mice.", "source": "Figure S1B; Results, Sniffing causes unstable odor responses in the PCx, paragraph 3", "quote": "Decoding the inhalation speed (fast versus slow) using the mean firing rate in the early 180 ms of inhalation in individual mice.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs. The paper says its processed data are available on request, and no public source holds them. The criterion asks for every mouse, and the other five mice of Figure 1 are not in the dandiset; even the one mouse in the file cannot be tested, as its inhalations are not in it.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1-odor-responsive-fraction", "statement": "Of 660 PCx neurons in six mice, 31.1% (205) reliably respond to at least one odor concentration.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 3; Figure 1H legend", "quote": "Of the recorded neurons, 31.1% reliably responded to at least one odor concentration (205 of 660 neurons; six mice).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other five of the six mice of Figure 1, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1hi-sniff-changes-responses", "statement": "In 72.2% of odor-responsive neurons (148 of 205) the response amplitude during inhalation depends on how fast the animal inhales, more than expected by chance.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 3; Figures 1H and 1I", "quote": "Strikingly, how fast an animal inhaled influenced the response amplitude during inhalation in 72.2% of those neurons (148 of 205 neurons; Figures 1G\u20131I).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other five of the six mice of Figure 1, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1h-direction-of-change", "statement": "A faster inhalation increases 37.3% of odor responses and decreases 19.2% of them.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 3; Figure 1H", "quote": "The impact of a faster inhalation was not uniform across odor responses: 37.3% of the odor responses increased with a rapid inhalation, whereas 19.2% decreased in amplitude.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other five of the six mice of Figure 1, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs1c-early-70ms", "statement": "The sniff-driven variability in odor responses is already significant in the first 70 ms of an inhalation.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 3; Figure S1C", "quote": "This sniffdriven variability in odor responses was already significant during the first 70 ms of an inhalation (Figure S1C).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other five of the six mice of Figure 1, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs1d-rs-fs-similar", "statement": "Regular-spiking (putatively excitatory or feedforward inhibitory) and fast-spiking (putatively feedback inhibitory) neurons show similar effects of inhalation speed on their odor responses.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 3; Figure S1D", "quote": "After sorting neurons into regular spiking (RS; putatively excitatory or feedforward inhibitory) and fast spiking (FS; putatively feedback inhibitory), we observed similar effects of the inhalation speed in both types (Figure S1D).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration, unit waveforms or the brain area of each unit, which the criterion needs; it also pools the other five of the six mice of Figure 1, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1j-sniff-change-larger-than-concentration", "statement": "Across odor-responsive neurons, the absolute response change caused by a slow-to-fast switch in inhalation (at 0.01%) is larger than that caused by a tenfold increase in concentration (0.01 to 0.1%, slow inhalations).", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 4; Figure 1J", "quote": "On average, sniffs caused a response amplitude change bigger than that caused by a 10-fold increase in odor concentration in the odor-responsive neurons (Figure 1J).", "statistics": [ { "test": "Wilcoxon signed-rank test", "p": 0.0001, "p_relation": "<", "n": "477 neuron-odor pairs of odor-responsive neurons" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other five of the six mice of Figure 1, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig1l-cdi-mixed-lower", "statement": "Concentration discriminability (CDI) of single neurons is lower when slow and fast inhalations are mixed than when computed within one inhalation speed.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 4; Figure 1L", "quote": "Combining responses from slow and fast inhalations decreased the CDI compared with responses observed during uniform inhalation speeds (Figure 1L).", "statistics": [ { "test": "Wilcoxon signed-rank test", "p": 0.0001, "p_relation": "<", "n": "477 neuron-odor pairs" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other five of the six mice of Figure 1, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2-glm-variance", "statement": "A regularised Poisson GLM with inhalation speed, concentration and their interaction explains 91.9% of the variance in the mean spike count during the first 180 ms of odor inhalation across neurons.", "source": "Results, PCx neurons randomly mix olfactory and non-olfactory inputs during inhalations, paragraph 2", "quote": "This model explained 91.9% of the variance in the mean number of spikes generated during the first 180 ms of odor inhalation across all neurons.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2c-interaction-small", "statement": "In the GLM, the interaction between inhalation speed and concentration has a small effect on the odor response, while the inhalation-speed (non-olfactory) term has a larger additive or subtractive effect.", "source": "Results, PCx neurons randomly mix olfactory and non-olfactory inputs during inhalations, paragraph 3; Figure 2C", "quote": "The GLM analysis revealed that the interaction between inhalation speed and concentration response had a small effect on the odor response amplitude during an inhalation (Figure 2C). Instead, the non-olfactory input had a more significant additive or subtractive effect (Figure 2C).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig2d-mixed-sensitivities", "statement": "The signs of the inhalation-speed and concentration weights can differ within a neuron, so that a fast inhalation can raise or lower a response regardless of how the neuron responds to a higher concentration; the combination is heterogeneous across neurons.", "source": "Results, PCx neurons randomly mix olfactory and non-olfactory inputs during inhalations, paragraph 3; Figure 2D", "quote": "Importantly, the sign of the weight for the non-olfactory input and the odor concentration factors could differ in the same neuron (Figure 2D). The non-olfactory input caused by a fast inhalation could increase or decrease the odor response amplitude regardless of how the neuron responded to a higher concentration of that odor.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs2ab-rs-fs-heterogeneous", "statement": "RS and FS neurons both show a heterogeneous distribution of inhalation-speed and concentration sensitivities.", "source": "Results, PCx neurons randomly mix olfactory and non-olfactory inputs during inhalations, paragraph 3; Figures S2A and S2B", "quote": "We similarly found a heterogeneous distribution of non-olfactory sensitivities in RS and FS neurons (Figures S2A and S2B).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration, unit waveforms or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs2c-waveform-no-prediction", "statement": "Spike waveform features (asymmetry and trough-to-peak delay) cannot predict a neuron's inhalation-speed weight, concentration weight, or both, with any of three models.", "source": "Results, PCx neurons randomly mix olfactory and non-olfactory inputs during inhalations, paragraph 3; Figure S2C; STAR Methods, Prediction of encoding properties from waveforms", "quote": "In none of the 9 cases, the predictive model could extract a significant relationship (as measured by the cross-validated R2 of the regression) between the spike waveform and the encoding parameters.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration, unit waveforms or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs2d-70ms-similar", "statement": "Restricting the GLM analysis to the first 70 ms of inhalation gives similar results.", "source": "Results, PCx neurons randomly mix olfactory and non-olfactory inputs during inhalations, paragraph 3; Figure S2D", "quote": "Finally, restricting the analysis to the early 70 ms of inhalation also gave similar results (Figure S2D).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig3c-airflow-tuning-anesthetized", "statement": "In tracheostomized anesthetized mice, 57.1% of PCx neurons (144 of 252) encode the rate of artificial nasal airflow, 117 with positive and 27 with negative slopes.", "source": "Results, A mechanosensory input signals the nasal airflow rate to the PCx, paragraph 2; Figure 3C", "quote": "We found that 57.1% of neurons displayed mechanosensory responses, meaning that they encoded the airflow rate.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the times and rates of the artificial suction pulses or the brain area of each unit, which the criterion needs; it also pools the three tracheostomized anesthetized mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig3b-latency-shortens", "statement": "Faster artificial airflow shortens response latency without significantly changing the order in which neurons are activated.", "source": "Results, A mechanosensory input signals the nasal airflow rate to the PCx, paragraph 2; Figures 3B and S3B", "quote": "Faster airflow also decreased the response latency without significantly changing the sequential activation order across neurons (Figure 3B; Figure S3B).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the times and rates of the artificial suction pulses or the brain area of each unit, which the criterion needs; it also pools the three tracheostomized anesthetized mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig3f-airflow-tuning-awake", "statement": "In awake, normally breathing mice without odor, 78.3% of PCx neurons (748 of 955, 10 mice) and 77.2% of odor-responsive neurons encode the peak inhalation airflow with a monotonic change; 36.7% increase and 41.7% decrease their response with faster inhalation.", "source": "Results, A mechanosensory input signals the nasal airflow rate to the PCx, paragraph 3; Figures 3E and 3F", "quote": "This analysis revealed that 78.3% of the PCx neurons (77.2% of the odorresponsive neurons) encoded the peak inhalation airflow rate with a monotonic change in spiking activity after the inhalation (Figure 3E) ... 36.7% of the neurons increased the amplitude of their responses when the inhalation speed increased, and another 41.7% decreased their responses", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the ten control mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs3-aen-neurectomy", "statement": "Cutting the anterior ethmoidal nerve leaves PCx responses to inhalation intact; airflow tuning curves after neurectomy (551 of 752 neurons tuned, 5 mice) are similar to those of control mice.", "source": "Results, A mechanosensory input signals the nasal airflow rate to the PCx, paragraph 4; Figures S3D and S3E", "quote": "Severing the AEN left intact the responses of PCx neurons to inhalations. The tuning curves for the airflow rate after the neurectomy remained similar to those of control mice (Figures S3D and S3E).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times or the brain area of each unit, which the criterion needs; it also pools the five neurectomized mice and the ten control mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs4-bulbectomy-no-odor-no-phase", "statement": "After bulbectomy, PCx neurons do not respond to odors and the population does not encode the inhalation phase.", "source": "Results, A top-down input may supply behavioral state information during a sniff, paragraph 2; Figures S4A and S4B", "quote": "In bulbectomized mice, PCx neurons were unresponsive to odors (Figure S4A). Moreover, the population activity did not encode the inhalation phase (Figure 4B; Figure S4B).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the four bulbectomized mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4-sniff-preferring-fraction", "statement": "After bulbectomy, 15.7% of PCx neurons still fire more during fast sniffs than normal inhalations, against 29.7% in control mice.", "source": "Results, A top-down input may supply behavioral state information during a sniff, paragraph 2; Figure 4D", "quote": "Nonetheless, 15.7% of PCx neurons exhibited increased spiking activity during fast sniffs compared with normal inhalations (see example neuron in Figure 4C). For comparison, this proportion was 29.7% in control mice.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the four bulbectomized and ten control mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4e-sniff-response-smaller", "statement": "In bulbectomized mice the sniff-induced response of sniff-preferring PCx neurons is smaller in amplitude than in control mice.", "source": "Results, A top-down input may supply behavioral state information during a sniff, paragraph 2; Figure 4E", "quote": "However, the sniff-induced activity in bulbectomized mice was smaller in amplitude and more variable across sniffs than in control mice (Figures 4D\u20134F).", "statistics": [ { "test": "two-tailed t test with unequal variances", "p": 0.0002, "n": "284 control and 23 bulbectomized sniff-preferring neurons" }, { "about": "PCx control, PCx bulbectomized and MCx control (Figure S4D)", "test": "1-way ANOVA, Tukey-Kramer post hoc", "p": 0.0001, "p_relation": "<" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the four bulbectomized and ten control mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4f-sniff-response-more-variable", "statement": "The coefficient of variation of the response across first sniffs is larger in bulbectomized than in control mice.", "source": "Figure 4F; Results, A top-down input may supply behavioral state information during a sniff, paragraph 2", "quote": "Coefficient of variation of the response amplitude across first sniffs in control and bulbectomized mice (p < 0.0001; two-tailed t test).", "statistics": [ { "test": "two-tailed t test", "p": 0.0001, "p_relation": "<", "n": "sniff-preferring neurons, 284 control and 23 bulbectomized" }, { "about": "PCx control, PCx bulbectomized and MCx control (Figure S4E)", "test": "1-way ANOVA, Tukey-Kramer post hoc", "p": 0.0001, "p_relation": "<" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the four bulbectomized and ten control mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4g-sniff-decoding-reduced", "statement": "A linear classifier distinguishes sniffs from regular inhalations from PCx activity in both control and bulbectomized mice, but with clearly lower accuracy after bulbectomy.", "source": "Results, A top-down input may supply behavioral state information during a sniff, paragraph 2; Figure 4G", "quote": "Correspondingly, while a linear classifier could differentiate a sniff from a regular inhalation based on PCx activity in both groups, its accuracy was notably reduced post-bulbectomy (Figure 4G).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the four bulbectomized and ten control mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig4d-pre-sniff-rise", "statement": "In bulbectomized mice the sniff-induced activity starts rising several tens of milliseconds before the nominal sniff onset.", "source": "Results, A top-down input may supply behavioral state information during a sniff, paragraph 2; Figure 4D", "quote": "Remarkably, the sniff-induced activity observed in the bulbectomized mice seemed to start rising several tens of milliseconds before the nominal onset of the sniff.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the four bulbectomized mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs4-motor-cortex-sniff", "statement": "A similar peri-sniff increase occurs in motor cortex, where a slow inhalation modulates 5.8% of neurons but 17.1% show a significant peri-sniff increase.", "source": "Results, A top-down input may supply behavioral state information during a sniff, paragraph 3; Figure S4C", "quote": "Here, a slow inhalation modulated the activity of 5.8% of neurons (see STAR Methods). In contrast, 17.1% of MCx neurons showed a significant peri-sniff increase in spiking activity", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the mice with motor cortex units, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5b-pc1-speed-pc23-concentration", "statement": "Inhalation speed is decoded with high accuracy from the first PC of the population odor response but concentration is not; concentration (and odor identity) are decoded from the second and third PCs, from which speed is not.", "source": "Results, Odor information and inhalation information are independent, paragraphs 2 and 3; Figures 5B, S5C and S5E", "quote": "Linear decoders\u2014namely, linear support vector machine (lSVM) classifiers\u2014could discriminate the inhalation speed with high accuracy using the projection of neural activity onto the first PC. In contrast, decoders could not classify an odor concentration using only the activity explained by the first PC.", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice and the four odor-identity mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5c-encoding-angles", "statement": "The population directions that separate concentrations during slow and during fast inhalation differ but are more similar to each other than to the direction that separates inhalation speeds.", "source": "Results, Odor information and inhalation information are independent, paragraph 4; Figure 5C", "quote": "We found that, even though these two directions were different (as expected, given the high dimensionality of the population response), they were more similar than the directions that tell how fast a mouse breathes in apart from how concentrated the odor is (Figure 5C).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5d-sniff-invariant-decoding", "statement": "Concentration decoders trained on one inhalation speed generalize to the other (trans-decoding) with performance similar to cis-decoding, both on PCs 2 and 3 and on the full population, so the PCx representation of concentration is sniff invariant.", "source": "Results, The distributed representation of odor concentration is sniff invariant, paragraph 1; Figures 5D and S5F", "quote": "A decoder using PCx response projections on the second and third PCs exhibited similar cis- and trans-decoding performances, suggesting that PCx has sniffinvariant representations of odor concentration (Figure 5D; Figures S5F and S5G).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs5gh-other-windows-and-codes", "statement": "Cis- and trans-decoding results are similar with spike counts over 70 ms or 180 ms windows and with population vectors of 10 ms bins or phase bins over a respiratory cycle.", "source": "Results, The distributed representation of odor concentration is sniff invariant, paragraph 1; Figures S5G and S5H", "quote": "We observed similar results when the decoders used spike counts summed over 70 or 180 ms windows and spike counts for concatenated 10 ms or 10", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5ef-correlated-subpopulations", "statement": "Trans-decoding of concentration falls to chance with sub-populations whose inhalation and concentration sensitivities are correlated (positively or negatively), but stays above chance with an uncorrelated sub-population.", "source": "Results, The distributed representation of odor concentration is sniff invariant, paragraph 2; Figures 5E and 5F", "quote": "Thus, a trans-decoder performed at the chancelevel if it could use only the activity of a neural population with correlated sensitivity for non-olfactory and olfactory inputs (Figure 5F).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5gh-mechanosensitive-as-good", "statement": "A population of mechanosensitive neurons carries at least as much sniff-invariant concentration information as a population of sniff-insensitive neurons.", "source": "Results, The distributed representation of odor concentration is sniff invariant, paragraph 3; Figures 5G and 5H", "quote": "This analysis revealed that a population of mechanosensitive neurons carries at least as much sniff-invariant information as a population of only sniff-insensitive neurons (Figure 5H).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig5i-time-course-similar", "statement": "Over 20 consecutive 10 ms bins of an inhalation, concentration decoding within and across inhalation speeds is similar for mechanosensitive and sniff-insensitive neurons.", "source": "Results, The distributed representation of odor concentration is sniff invariant, paragraph 4; Figure 5I", "quote": "Linear decoders using only mechanosensitive or sniff-insensitive neurons performed similarly throughout this inhalation window (Figure 5I).", "statistics": [ { "test": "two-way ANOVA", "p": 0.05, "p_relation": ">", "n": "143 neurons per sub-population" } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs5i-coefficients-similar", "statement": "Mechanosensitive and sniff-invariant neurons have similar distributions of concentration coefficients.", "source": "Results, The distributed representation of odor concentration is sniff invariant, paragraph 3; Figure S5I", "quote": "Cumulative distribution of concentration regressor coefficients for mechano-sensitive and sniff-invariant neurons (Kolmogorov-Smirnov test, P-value = 0.4793).", "statistics": [ { "test": "Kolmogorov-Smirnov test", "p": 0.4793 } ], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "fig6-simulation-mechanosensory-rescues", "statement": "In a population simulated from the fitted coefficients, an inhalation-driven concentration change makes concentration decoding across inhalation speeds worse than within speed as the change grows, and adding the mechanosensory input restores decoding of the true concentration for any change.", "source": "Results, Airflow information affords tolerance to flow-dependent concentration fluctuations, paragraph 1; Figures 6B and 6C; STAR Methods, Simulation of sniff-induced concentration changes", "quote": "Consistently, decoders trained on the responses during slow and fast inhalations classified the odor concentration worse than decoders trained using only one inhalation speed as the simulated influence of the airflow on the concentration increased (Figure 6C). However, supplementing this population with mechanosensory responses was sufficient to reduce ambiguity and retrieve the actual concentration for any DIC (Figures 6B and 6C).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of the nasal airflow signal or inhalation times, the odor trial times with odor and concentration or the brain area of each unit, which the criterion needs; it also pools the other three concentration-series mice, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null }, { "claim": "figs6h-waveforms-homogeneous", "statement": "Classifiers cannot decode the experimental condition from the spike waveform features of the recorded units, suggesting homogeneous sampling of cell types across conditions.", "source": "Results, Sniffing causes unstable odor responses in the PCx, paragraph 2; Figures S6G and S6H", "quote": "The distributions of the waveform features were comparable across experiments, and neither crossvalidated linear nor non-linear classifiers could discriminate an experimental condition based on the spike waveforms of the units recorded (see STAR Methods).", "statistics": [], "kind": "finding", "inferred": "", "outcome": "blocked", "blocked_by": "data_missing", "notebook": "reproduce_dehaqani_2024.ipynb", "notes": "The dandiset's one file holds spike times of one mouse and none of unit waveforms, which the criterion needs; it also pools the recordings of the other experimental conditions, which are not in the dandiset. The paper says its processed data are available on request, and no public source holds them.", "deviations": [], "assumed": false, "disagreed": false, "data": "dataset", "where": null, "proposed": null } ], "findings": [ { "kind": "data_missing", "statement": "The dandiset holds one NWB file from one of the paper's 22 mice, with the spike times of 1013 sorted units and their labels. The four signals the Methods say were recorded besides the spikes (the nasal airflow, the odor signal of the photo-ionization detector, the odor-trial TTL and the inhalation-onset TTL), the artificial airflow pulses, the unit waveforms and the brain area of each unit are not in it, and neither are the other 21 mice. All 37 claims need some of these, so none can be tested. The paper says its processed data are available from the lead contact on request, and its code deposit (Zenodo 10.5281/zenodo.10381293) loads preprocessed files it does not hold.", "found": null, "status": null }, { "kind": "metadata_insufficient", "statement": "The file gives no brain area for its units and has no electrodes table. Phy-good units lie along the whole probe (depth 80 to 3840 for the 359 good units, with 97, 127, 53 and 82 of them in the four 1000-um bands), so they include structures above the piriform cortex, and the paper's selection of PCx layer 2 and 3 units cannot be repeated. The experiment the mouse belongs to is given only by the keyword \"Concentration Series\", and the odors given are not stated.", "found": null, "status": null }, { "kind": "metadata_error", "statement": "KSLabel is \"good\" for all 1013 units and ContamPct is 100 for all of them. Kilosort labels a cluster good when its estimated contamination is low, so the two columns contradict each other and say nothing about the units. The Phy curation (quality) is good for 359 units, mua for 10 and missing for 644.", "found": null, "status": null }, { "kind": "metadata_insufficient", "statement": "Of the unit table's columns only quality, spike_times and unit_name have a description. The others (KSLabel, sh, ch, depth, Amplitude, amp, ContamPct, fr, n_spikes, original_cluster_id) say \"No description.\", and depth, Amplitude and amp have no unit. The session description is the converter's default.", "found": null, "status": null }, { "kind": "other", "statement": "The file's related_publications names the bioRxiv preprint (10.1101/2023.04.04.535405), not the published paper, and the two 2024 versions of the dandiset (0.240305.0939 and 0.240305.0945) do not name the paper; version 0.261011.1559 and the draft do. All versions hold the same asset.", "found": null, "status": null }, { "kind": "other", "statement": "What could be checked is consistent with the paper. The Phy-good units have ISI violation rates (median 0.0066, Q1 0, Q3 0.029, by the Hill et al. formula at 1.5 ms) and presence ratios (1 in every quartile) in the ranges the Methods report, all fire above the 0.5 Hz threshold, no unit is duplicated, and the summed activity of the good units nearest the probe tip (by the standard Neuropixels 1.0 channel map, which depth follows; the file names no probe) peaks at 2.78 Hz, within the range of mouse breathing; the check of the half frequency leaves that peak at 2.78 Hz.", "found": null, "status": null } ], "reconciliation": null, "verifications": [ { "date": "2026-11-02", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 1. The first executed notebook with the conclusion cells and the summary removed, the helper module and the claims file, with the paper. The verifier queried the archive API and tested helper functions on synthetic inputs. It gave its own outcome for each claim; all 37 agree with the record. Its points that concern no single claim were answered as follows. B3, the claims file path is outside the bundle - the cell now prints the 37 claim ids of mechano.CLAIM_NEEDS and runs the comparison only where the claims file is present. B4, the spectral argmax can report a harmonic - mechano.spectral_peak now moves the peak to its subharmonic when the power there is at least half the peak, shown on synthetic 3 Hz trains (largest power 6.01 Hz, checked peak 2.98 Hz); the 0 to 1000 band stays at 2.78 Hz, and the 2000 to 3000 band moves from 2.93 to 1.51 Hz. The depth convention is now checked against the data - depth lies within 20 of 20 + 20 floor(ch / 2), the standard Neuropixels 1.0 map with channel 0 at the tip, and the notebook says the probe type is assumed, as the file names none.", "agreed": 37, "of": 37, "disagreements": [] }, { "date": "2026-11-02", "kind": "agent", "by": "Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook)", "reviewed": "Round 2. The full executed notebook of the first revision, with its conclusions and summary, the helper module, the claims file, the attempt record and the README, with the paper. The verifier agreed with all 37 outcomes, found that all six round-1 points are resolved, and found no place where the claims file misreads the paper (it checked fig3f, figs3-aen, figs4-motor-cortex and fig5b against the Mice section and the Methods). It listed sentences the outputs do not support or that need a qualifier; none changes an outcome, and each is fixed as given under response. No outcome is proposed for change.", "agreed": 37, "of": 37, "disagreements": [] } ] } ], "entries": [ { "name": "000931-dehaqani-2024", "type": "reproduction", "title": "Sniffing and odor responses in the olfactory cortex (Dehaqani, Michelon et al. 2024)", "description": "Tests the findings of Dehaqani, Michelon, Patella, Petrucco, Piasini and Iurilli (2024) on dandiset 000931. The dandiset holds one NWB file, the sorted spike times of 1013 units from one mouse, placed in the concentration-series experiment only by a keyword, with no breathing signal, inhalation times, odor trials, airflow pulses, unit waveforms or brain regions. Every claim of the paper needs at least one of these, so all are blocked; the notebook lists what the file holds and checks the unit table against its description and the paper's spike-sorting criteria.", "datasets": [ "dandi:000931" ], "papers": [ "10.1016/j.celrep.2024.114013" ], "derived_from": [], "notebooks": [ { "path": "reproduce_dehaqani_2024.ipynb", "title": "Reproducing Dehaqani, Michelon et al. (2024) from dandiset 000931", "executed": "notebooks/000931-dehaqani-2024/reproduce_dehaqani_2024.html" } ] } ] }