{"paper_id": "yamauchi-2026-acm-trans-comput-healthc", "finding_no": 1, "doi": "10.1145/3723048", "year": 2026, "journal": "ACM Transactions on Computing for Healthcare", "finding": "Scenario-building time differed across the three conditions (p = 1.7e-7), averaging 1,317 s when humans worked alone, 325 s when humans edited system proposals and 50 s when the system worked alone.", "evidence": "Section 5.5, Fig. 3", "species": "human (clinician raters)", "n": "n = 36 scenarios", "stats": "Kruskal-Wallis p = 1.7e-7; Tukey-HSD A vs B p = 0.015, A vs C p = 7.2e-8, B vs C p = 0.015", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamauchi-2026-acm-trans-comput-healthc.md"}
{"paper_id": "yamauchi-2026-acm-trans-comput-healthc", "finding_no": 2, "doi": "10.1145/3723048", "year": 2026, "journal": "ACM Transactions on Computing for Healthcare", "finding": "Clinician-rated scenario validity was lower for system-only scenarios than for human-only ones (p = 0.0084), whereas human-edited system scenarios did not differ from human-only ones (p = 0.21), suggesting the system works best as a draft that humans adjust.", "evidence": "Section 5.5, Fig. 3", "species": "human (clinician raters)", "n": "n = 108 ratings from three clinicians", "stats": "Friedman p = 0.012; A vs C p = 0.0084; A vs B p = 0.21; B vs C p = 0.40", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamauchi-2026-acm-trans-comput-healthc.md"}
{"paper_id": "yamauchi-2026-acm-trans-comput-healthc", "finding_no": 3, "doi": "10.1145/3723048", "year": 2026, "journal": "ACM Transactions on Computing for Healthcare", "finding": "All three clinicians obtained audio output in all nine trials without problems, making on average 1.7 modifications per trial, mostly to the scenario rather than to sound positions.", "evidence": "Section 7.1, Table 1", "species": "human (clinicians)", "n": "three participants, nine trials", "stats": "descriptive", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamauchi-2026-acm-trans-comput-healthc.md"}
{"paper_id": "yamauchi-2026-acm-trans-comput-healthc", "finding_no": 4, "doi": "10.1145/3723048", "year": 2026, "journal": "ACM Transactions on Computing for Healthcare", "finding": "Clinicians rated spatial grounding at an average of 6.2 and audio clarity at an average of 6.7 on 7-point scales.", "evidence": "Section 7.2, Fig. 8", "species": "human (clinicians)", "n": "three participants", "stats": "descriptive means", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamauchi-2026-acm-trans-comput-healthc.md"}
{"paper_id": "yamauchi-2026-acm-trans-comput-healthc", "finding_no": 5, "doi": "10.1145/3723048", "year": 2026, "journal": "ACM Transactions on Computing for Healthcare", "finding": "The mean SUS score was 72.7, above the benchmark of 68, but individual scores ranged from 55 to 82.5.", "evidence": "Section 7.3", "species": "human (clinicians)", "n": "three participants", "stats": "descriptive", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamauchi-2026-acm-trans-comput-healthc.md"}
{"paper_id": "yamauchi-2026-acm-trans-comput-healthc", "finding_no": 6, "doi": "10.1145/3723048", "year": 2026, "journal": "ACM Transactions on Computing for Healthcare", "finding": "Scenes requiring several closely related sounds to overlap, such as a car accident, were the weakest, with an average consistency score of 4.3, because the system played such sounds sequentially and users rarely noticed timing errors in text proposals.", "evidence": "Sections 7.2 and 8", "species": "human (clinicians)", "n": "three participants", "stats": "descriptive", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamauchi-2026-acm-trans-comput-healthc.md"}
{"paper_id": "ino-2026-medrxiv", "finding_no": 1, "doi": "10.64898/2026.05.02.26352243", "year": 2026, "journal": "medRxiv", "finding": "Of 13 patients who gave written consent, 8 entered the sound-development phase and 6 of those 8 (75%) went on to the overnight session.", "evidence": "Fig. 2", "species": "human", "n": "13 consented; 8 entered sound development; 6 reached Visit 4", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md"}
{"paper_id": "ino-2026-medrxiv", "finding_no": 2, "doi": "10.64898/2026.05.02.26352243", "year": 2026, "journal": "medRxiv", "finding": "All 6 participants who reached the overnight session completed it (completion rate 100%), none asked to stop early, and all attended the follow-up visit.", "evidence": "Results, Primary Outcome", "species": "human", "n": "n = 6", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md"}
{"paper_id": "ino-2026-medrxiv", "finding_no": 3, "doi": "10.64898/2026.05.02.26352243", "year": 2026, "journal": "medRxiv", "finding": "All recorded adverse events were CTCAE grade 1, none were judged attributable to sound delivered during sleep, and no confusion, delirium or suicidal ideation was observed.", "evidence": "Results, Safety and Adverse Events", "species": "human", "n": "n = 6", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md"}
{"paper_id": "ino-2026-medrxiv", "finding_no": 4, "doi": "10.64898/2026.05.02.26352243", "year": 2026, "journal": "medRxiv", "finding": "Device-related events occurred in three participants overnight (an unresponsive tagging button, a recording-PC power shortfall after sound delivery, and a wrong earphone), but none prevented completion of the session.", "evidence": "Results; Methods, Equipment and Data Handling", "species": "human", "n": "3 of 6 participants", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md"}
{"paper_id": "nagai-2026-jove", "finding_no": 1, "doi": "10.3791/69042", "year": 2026, "journal": "Journal of Visualized Experiments", "finding": "Brushing the nose during REM sleep produced arousal with a mean latency of 0.89 ± 0.063 s from stimulus onset, judged by whisker movement.", "evidence": "Protocol step 5.1.1", "species": "mouse", "n": null, "stats": "mean ± SEM", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/nagai-2026-jove.md"}
{"paper_id": "nagai-2026-jove", "finding_no": 2, "doi": "10.3791/69042", "year": 2026, "journal": "Journal of Visualized Experiments", "finding": "In the deprived group over 85% of brushing events fell in REM sleep, whereas in the yoked group more than 90% fell in wakefulness or NREM sleep, confirming REM-targeted delivery.", "evidence": "Fig. 1B", "species": "mouse", "n": "n = 12 REM-deprived mice (6 males and 6 females) and n = 12 yoked mice (6 males and 6 females)", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/nagai-2026-jove.md"}
{"paper_id": "nagai-2026-jove", "finding_no": 3, "doi": "10.3791/69042", "year": 2026, "journal": "Journal of Visualized Experiments", "finding": "Over the 6-hour deprivation period, deprived mice had significantly less total REM sleep, less wake and more NREM sleep than yoked controls, which the authors suggest reflects homeostatic compensation of lost REM by NREM sleep.", "evidence": "Fig. 1C", "species": "mouse", "n": "n = 12 mice in both groups", "stats": "p < 0.01 or p < 0.05, two-tailed unpaired t test with Welch's correction", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/nagai-2026-jove.md"}
{"paper_id": "nagai-2026-jove", "finding_no": 4, "doi": "10.3791/69042", "year": 2026, "journal": "Journal of Visualized Experiments", "finding": "The protocol shortened individual REM episodes but did not change the number of REM episodes or overall sleep-stage transitions.", "evidence": "Fig. 1D–F", "species": "mouse", "n": "n = 12 mice in both groups", "stats": "p < 0.05, two-way ANOVA (sleep stage x group) with post hoc bootstrap and Fisher's LSD test (episode duration)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/nagai-2026-jove.md"}
{"paper_id": "nagai-2026-jove", "finding_no": 5, "doi": "10.3791/69042", "year": 2026, "journal": "Journal of Visualized Experiments", "finding": "The relationship between REM amount and NREM-to-REM transitions differed between groups, with a significantly different regression slope, and some deprived mice showed REM episode counts beyond the mean ± 2 SD range because of increased REM transitions.", "evidence": "Fig. 1C, 1G", "species": "mouse", "n": "n = 12 mice per group", "stats": "p < 0.0001, linear regression slope comparison", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/nagai-2026-jove.md"}
{"paper_id": "nagai-2026-jove", "finding_no": 6, "doi": "10.3791/69042", "year": 2026, "journal": "Journal of Visualized Experiments", "finding": "After comparable conditioning in both groups, 6 h of REM deprivation following trace fear conditioning produced no significant group differences in contextual or sound-cued freezing or in the discrimination index, and REM amount did not correlate significantly with freezing.", "evidence": "Fig. 1H–M", "species": "mouse", "n": "n = 12 mice in both groups", "stats": "not significant; two-tailed unpaired t test with Welch's correction (contextual freezing, discrimination index); Pearson correlation", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/nagai-2026-jove.md"}
{"paper_id": "srinivasan-2025-nat-commun", "finding_no": 1, "doi": "10.1038/s41467-025-62554-8", "year": 2025, "journal": "Nature Communications", "finding": "Activity-dependent tagging labelled only a few young adult-born neurons per mouse, and the authors report that REM sleep reactivation of ensembles of as few as ~3 such neurons is necessary for fear memory consolidation.", "evidence": "Fig. 2b-d; Fig. 3a-b", "species": "mouse", "n": "n = 8 mice", "stats": "mean (standard deviation) of 2.4 (3.2) tagged neurons per mouse", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"}
{"paper_id": "srinivasan-2025-nat-commun", "finding_no": 2, "doi": "10.1038/s41467-025-62554-8", "year": 2025, "journal": "Nature Communications", "finding": "Population activity of adult-born neurons was more stable over time than that of granule neurons and showed stronger correlations between the conditioning context and subsequent REM sleep.", "evidence": "Fig. 1i-k; Supplementary Table 2", "species": "mouse", "n": "GNs, n = 363 neurons in 3 mice; ABNs, n = 136 neurons in 3 mice", "stats": "linear model of population vector correlations", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"}
{"paper_id": "srinivasan-2025-nat-commun", "finding_no": 3, "doi": "10.1038/s41467-025-62554-8", "year": 2025, "journal": "Nature Communications", "finding": "Optogenetically silencing context A-tagged young adult-born neurons only during REM sleep after conditioning reduced later contextual freezing compared with controls, with light delivery in REM sleep reaching a mean sensitivity of 0.83 and precision of 0.82.", "evidence": "Fig. 3a-b; Supplementary Fig. 4d, 5a-b", "species": "mouse", "n": "cfos-, n = 15 mice; cfos+, n = 14", "stats": "p = 0.002, two-tailed unpaired t-test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"}
{"paper_id": "srinivasan-2025-nat-commun", "finding_no": 4, "doi": "10.1038/s41467-025-62554-8", "year": 2025, "journal": "Nature Communications", "finding": "REM sleep silencing had no detectable effect on memory when the tagged ensembles came from a different context (p = 0.69), from 10-week-old adult-born neurons (p = 0.38), or from developmentally born granule neurons (p = 0.77).", "evidence": "Fig. 3c-h", "species": "mouse", "n": "context C: cfos-, n = 10, cfos+, n = 11; 10-week-old ABNs: cfos-, n = 10, cfos+, n = 12; GNs: cfos-, n = 13, cfos+, n = 14 mice", "stats": "p = 0.69, p = 0.38, p = 0.77, two-tailed unpaired t-test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"}
{"paper_id": "srinivasan-2025-nat-commun", "finding_no": 5, "doi": "10.1038/s41467-025-62554-8", "year": 2025, "journal": "Nature Communications", "finding": "Silencing tagged adult-born neurons during memory retrieval tests in wakefulness did not change freezing.", "evidence": "Fig. 2i-l", "species": "mouse", "n": "n = 14 mice; n = 10", "stats": "p = 0.21 and p = 0.056, two-tailed paired t-test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"}
{"paper_id": "srinivasan-2025-nat-commun", "finding_no": 6, "doi": "10.1038/s41467-025-62554-8", "year": 2025, "journal": "Nature Communications", "finding": "Closed-loop silencing of adult-born neurons at Phase 1 of the local theta cycle during REM sleep, but not at the other three phases, reduced freezing in both context and trace fear tests versus yoked controls.", "evidence": "Fig. 4c-e", "species": "mouse", "n": "Yoked control, n = 12 mice; Phase 1, n = 7; Phase 2, n = 9; Phase 3, n = 10; Phase 4, n = 9 mice", "stats": "Context test: p = 0.042; Trace test: p = 0.013; one-way ANOVA with Dunnett's multiple comparisons", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"}
{"paper_id": "chen-2025-embc", "finding_no": 1, "doi": "10.1109/EMBC58623.2025.11253414", "year": 2025, "journal": "2025 47th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "The dataset comprised 549,595 four-second epochs from 610 hours of single-channel mouse EEG, each labelled by experts as REM, NREM, high-theta wake or low-theta wake.", "evidence": "Section III (Dataset)", "species": "mouse", "n": "549,595 epochs from 610 hours of recording", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chen-2025-embc.md"}
{"paper_id": "chen-2025-embc", "finding_no": 2, "doi": "10.1109/EMBC58623.2025.11253414", "year": 2025, "journal": "2025 47th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "With no resampling of either training or validation data, the overall F1 score on the test data was 85.00%, whereas undersampling only the validation data raised it to 86.04%, the highest of the 16 combinations tested.", "evidence": "Table IV; Section VII", "species": "mouse", "n": "16 training/validation combinations; 60% training, 20% validation, 20% test", "stats": "overall F1 85.00% (raw/raw) vs 86.04% (raw train, undersampled validation); class-size-weighted averages", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chen-2025-embc.md"}
{"paper_id": "chen-2025-embc", "finding_no": 3, "doi": "10.1109/EMBC58623.2025.11253414", "year": 2025, "journal": "2025 47th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "The raw-training, undersampled-validation combination also gave the highest per-class F1 for low-theta wake, high-theta wake and NREM, but not for REM, where it was only slightly below the raw/raw combination.", "evidence": "Table IV; Section VII", "species": "mouse", "n": null, "stats": "per-class F1 scores", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chen-2025-embc.md"}
{"paper_id": "chen-2025-embc", "finding_no": 4, "doi": "10.1109/EMBC58623.2025.11253414", "year": 2025, "journal": "2025 47th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "During training, undersampling started with low accuracy but caught up with the other methods after many iterations, while oversampling reached the highest training accuracy; test accuracy fluctuated more but stayed close to training accuracy.", "evidence": "Fig. 5; Fig. 6", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chen-2025-embc.md"}
{"paper_id": "chen-2025-embc", "finding_no": 5, "doi": "10.1109/EMBC58623.2025.11253414", "year": 2025, "journal": "2025 47th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "The authors suggest that adjusting the class distribution of the validation data alone, without preprocessing the training data, can improve overall accuracy and precision.", "evidence": "Section VII", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chen-2025-embc.md"}
{"paper_id": "sekiba-2025-medrxiv", "finding_no": 1, "doi": "10.1101/2025.07.02.25330609", "year": 2025, "journal": "medRxiv", "finding": "People with PTSD had a lower sleep regularity index than controls, while the within-group variation of midsleep time was similar (p = 0.22).", "evidence": "Fig. 2b-c", "species": "human", "n": "Healthy (n = 28) versus PTSD (n = 29)", "stats": "Mann-Whitney test, U = 252, p = 0.014", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"}
{"paper_id": "sekiba-2025-medrxiv", "finding_no": 2, "doi": "10.1101/2025.07.02.25330609", "year": 2025, "journal": "medRxiv", "finding": "Total sleep time did not differ (p = 0.70), but people with PTSD took longer to fall asleep (p = 0.018), had lower sleep efficiency (p = 0.0096) and a higher arousal index (p = 0.020).", "evidence": "Fig. 3a-d", "species": "human", "n": "Healthy (n = 29) versus PTSD (n = 29)", "stats": "Welch's t-test for total sleep time; Mann-Whitney tests for latency, efficiency and arousal index", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"}
{"paper_id": "sekiba-2025-medrxiv", "finding_no": 3, "doi": "10.1101/2025.07.02.25330609", "year": 2025, "journal": "medRxiv", "finding": "People with PTSD had less REM sleep (p = 0.045) and more N2 (p = 0.042), a longer latency to REM sleep (p < 0.001), shorter REM episodes (p = 0.0042) and a higher REM fragmentation index (p = 0.0033), whereas most NREM parameters did not differ.", "evidence": "Fig. 4a-e", "species": "human", "n": "Healthy (n = 29) versus PTSD (n = 29)", "stats": "REM latency: Mann-Whitney test, U = 181, p < 0.001; REM episode duration: t(56) = 3.0, p = 0.0042; fragmentation: U = 234, p = 0.0033", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"}
{"paper_id": "sekiba-2025-medrxiv", "finding_no": 4, "doi": "10.1101/2025.07.02.25330609", "year": 2025, "journal": "medRxiv", "finding": "Across all recorded nights, controls showed a first REM sleep peak around 75 minutes and a second N3 peak around 110 minutes after sleep onset, and both peaks were absent in people with PTSD.", "evidence": "Fig. 5, Fig. S2", "species": "human", "n": "Healthy: 130 nights; PTSD: 149 nights", "stats": "descriptive (group stacked-area probability)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"}
{"paper_id": "sekiba-2025-medrxiv", "finding_no": 5, "doi": "10.1101/2025.07.02.25330609", "year": 2025, "journal": "medRxiv", "finding": "REM sleep latency was more variable in PTSD, and REM rhythmicity was weaker both as deviation of the REM autocorrelation from shuffled data (p < 0.001) and as a wider spread of intervals between REM episodes within nights (p = 0.0019).", "evidence": "Fig. 6b, 6e-f", "species": "human", "n": "Healthy (n = 28) versus PTSD (n = 27) participants; interval analysis Healthy (n = 108) versus PTSD (n = 76) nights", "stats": "latency variability: F(28, 28) = 3.7, p < 0.001; rhythmicity: Mann-Whitney test, U = 180, p < 0.001; interval SD: U = 3006, p = 0.0019", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"}
{"paper_id": "sekiba-2025-medrxiv", "finding_no": 6, "doi": "10.1101/2025.07.02.25330609", "year": 2025, "journal": "medRxiv", "finding": "N3 rhythmicity was also weaker in PTSD (p = 0.011), whereas N2 rhythmicity was similar between groups and neither group showed rhythmic N1 or WASO.", "evidence": "Fig. 7c-d, Fig. S3, Fig. S4", "species": "human", "n": "Healthy (n = 27) versus PTSD (n = 22)", "stats": "Two-tailed unpaired t-test, t(47) = 2.6, p = 0.011", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"}
{"paper_id": "chavan-2025-neurobiol-learn-mem", "finding_no": 1, "doi": "10.1016/j.nlm.2025.108062", "year": 2025, "journal": "Neurobiology of Learning and Memory", "finding": "The review argues that adult-born neurons pass through a transient window of heightened excitability and synaptic plasticity, approximately 4 to 6 weeks after cell division, which suits them to discriminating novel or similar experiences.", "evidence": "Section 1; Abstract", "species": "mouse; rat", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chavan-2025-neurobiol-learn-mem.md"}
{"paper_id": "chavan-2025-neurobiol-learn-mem", "finding_no": 2, "doi": "10.1016/j.nlm.2025.108062", "year": 2025, "journal": "Neurobiology of Learning and Memory", "finding": "The authors emphasize that adult-born neurons reactivated during REM sleep after contextual fear conditioning are needed for memory consolidation, a function they describe as absent in developmentally born granule cells.", "evidence": "Section 2.6; Fig. 5", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chavan-2025-neurobiol-learn-mem.md"}
{"paper_id": "chavan-2025-neurobiol-learn-mem", "finding_no": 3, "doi": "10.1016/j.nlm.2025.108062", "year": 2025, "journal": "Neurobiology of Learning and Memory", "finding": "Although human adult neurogenesis is still debated, the review cites a survey in which 84% of 57 studies supported the presence of newborn neurons in the adult human hippocampus.", "evidence": "Introduction; Section 5", "species": "human", "n": "57 studies", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chavan-2025-neurobiol-learn-mem.md"}
{"paper_id": "chavan-2025-neurobiol-learn-mem", "finding_no": 4, "doi": "10.1016/j.nlm.2025.108062", "year": 2025, "journal": "Neurobiology of Learning and Memory", "finding": "The review proposes that raising neurogenesis, for example with memantine, which promotes forgetting of conditioned fear in rodents, is a direction worth testing for PTSD, while stressing that human data so far lack placebo-controlled trials.", "evidence": "Sections 2.8 and 3", "species": "mouse; human", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chavan-2025-neurobiol-learn-mem.md"}
{"paper_id": "arai-2025-jneurosci", "finding_no": 1, "doi": "10.1523/JNEUROSCI.2365-24.2025", "year": 2025, "journal": "The Journal of Neuroscience", "finding": "Of 58 opto-tagged Crhbp-positive neurons recorded from eight mice, the largest group was REM sleep-active (41.4%, n = 24) and the next largest was wake-active (22.4%, n = 13).", "evidence": "Fig. 1H,I", "species": "mouse", "n": "n = 58 neurons from eight mice", "stats": "proportions did not differ between narrow- and broad-waveform neurons (Fisher's exact test; p = 0.725)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arai-2025-jneurosci.md"}
{"paper_id": "arai-2025-jneurosci", "finding_no": 2, "doi": "10.1523/JNEUROSCI.2365-24.2025", "year": 2025, "journal": "The Journal of Neuroscience", "finding": "Among Crhbp-positive neurons projecting to the medulla, three of four recorded cells (75%) were REM sleep-active and one (25%) was wake-active.", "evidence": "Fig. 6C-E", "species": "mouse", "n": "n = 4 neurons from 3 mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arai-2025-jneurosci.md"}
{"paper_id": "arai-2025-jneurosci", "finding_no": 3, "doi": "10.1523/JNEUROSCI.2365-24.2025", "year": 2025, "journal": "The Journal of Neuroscience", "finding": "K-means clustering split the 24 REM sleep-active neurons into four subtypes (9, 7, 3 and 5 neurons) that differed in firing rate across states, with low-rate Cluster 1 cells mostly having broad spike waveforms.", "evidence": "Fig. 2C-I", "species": "mouse", "n": "n = 24 REM sleep-active neurons", "stats": "optimal K chosen by BIC calculated 100 times", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arai-2025-jneurosci.md"}
{"paper_id": "arai-2025-jneurosci", "finding_no": 4, "doi": "10.1523/JNEUROSCI.2365-24.2025", "year": 2025, "journal": "The Journal of Neuroscience", "finding": "Eight of 27 REM sleep-active Crhbp-positive neurons (25.9%) met the classical REM-on criteria of continuous firing in REM sleep and increased firing before REM onset, suggesting partial overlap between the two populations.", "evidence": "Fig. 6O", "species": "mouse", "n": "N = 8 neurons; n = 8 transitions", "stats": "Dunnett's test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arai-2025-jneurosci.md"}
{"paper_id": "arai-2025-jneurosci", "finding_no": 5, "doi": "10.1523/JNEUROSCI.2365-24.2025", "year": 2025, "journal": "The Journal of Neuroscience", "finding": "During REM sleep, the firing of 20 of 62 Crhbp-positive neurons (32.3%) correlated significantly with EEG theta power and 10 (16.1%) with EEG gamma power.", "evidence": "Fig. 7", "species": "mouse", "n": "n = 62 neurons", "stats": "Pearson's correlation test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arai-2025-jneurosci.md"}
{"paper_id": "arai-2025-jneurosci", "finding_no": 6, "doi": "10.1523/JNEUROSCI.2365-24.2025", "year": 2025, "journal": "The Journal of Neuroscience", "finding": "During REM sleep, 14 of 62 Crhbp-positive neurons (22.6%) showed firing correlated with EMG, mostly negatively (10 neurons, 71.4%), which the authors take as further support for a role in REM sleep muscle atonia.", "evidence": "Fig. 9A-C", "species": "mouse", "n": "n = 62 neurons", "stats": "Pearson's correlation test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arai-2025-jneurosci.md"}
{"paper_id": "vergara-2025-natcommun", "finding_no": 1, "doi": "10.1038/s41467-025-58817-z", "year": 2025, "journal": "Nature Communications", "finding": "Across seven dentate gyrus imaging sessions spanning 99 days, the blood-vessel-plus-neuron alignment gave higher spatial correlation and crispness of aligned neuron projections than registration methods from existing calcium imaging packages.", "evidence": "Fig. 2d-f", "species": "mouse", "n": "n = 7 sessions", "stats": "repeated measures one-way ANOVA with Geisser-Greenhouse correction and Dunnett's multiple comparison test; p < 0.05 to p < 0.001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"}
{"paper_id": "vergara-2025-natcommun", "finding_no": 2, "doi": "10.1038/s41467-025-58817-z", "year": 2025, "journal": "Nature Communications", "finding": "Tracking performance stayed stable when a blood-vessel similarity score was above a threshold of 2.7 and dropped sharply below it; in dentate gyrus recordings the score stayed above this threshold for over 90 days with an adjusted focal plane and over 40 days with a fixed focal plane.", "evidence": "Fig. 3a, d", "species": "mouse", "n": "n = 46 session pairs (constant focal plane); n = 15 session pairs (adjusted focal plane)", "stats": "", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"}
{"paper_id": "vergara-2025-natcommun", "finding_no": 3, "doi": "10.1038/s41467-025-58817-z", "year": 2025, "journal": "Nature Communications", "finding": "In dual-color recordings where a stable tdTomato label defined the true neuron identities, the new alignment reduced the distance between matched neurons significantly more than the other algorithms tested.", "evidence": "Fig. 4d-e", "species": "mouse", "n": "20,708 neuron pairs", "stats": "two-sided two-sample Kolmogorov-Smirnov test with correction for multiple comparisons; p < 0.001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"}
{"paper_id": "vergara-2025-natcommun", "finding_no": 4, "doi": "10.1038/s41467-025-58817-z", "year": 2025, "journal": "Nature Communications", "finding": "On published CA1 place cell data, concatenated processing did not change within-session spatial information, but it tracked more neurons and gave lower cross-session position decoding errors than CellReg or SCOUT.", "evidence": "Fig. 6b, g, k-m", "species": "mouse", "n": "n = 12 session pairs/3 mice", "stats": "spatial information F(1, 6432) = 0.109; decoding error repeated measures one-way ANOVA F(2, 70) = 18.72", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"}
{"paper_id": "vergara-2025-natcommun", "finding_no": 5, "doi": "10.1038/s41467-025-58817-z", "year": 2025, "journal": "Nature Communications", "finding": "In dentate gyrus opto-tagging experiments over 4 weeks, only a minority (32.4%) of extracted components responded to light, and neurons tracked with the new suite showed a higher percentage of opto-consistent responses across sessions than other methods.", "evidence": "Fig. 7f-h", "species": "mouse", "n": "n = 6 session pairs", "stats": "repeated measures one-way ANOVA with Dunnett's multiple comparisons, F(1.4, 7.0) = 16.5", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"}
{"paper_id": "vergara-2025-natcommun", "finding_no": 6, "doi": "10.1038/s41467-025-58817-z", "year": 2025, "journal": "Nature Communications", "finding": "Dentate gyrus neurons tracked for 99 days had lower population vector distances across sessions than with other methods and showed a linear rather than exponential drift over time, which the authors suggest reflects gradual, continuous drift in neuronal representations.", "evidence": "Fig. 8b-c; Supplementary Fig. 15", "species": "mouse", "n": "n = 21 session pairs", "stats": "repeated measures one-way ANOVA with Dunnett's multiple comparisons, F(2.4, 48.3) = 106.6", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"}
{"paper_id": "wang-2024-biorxiv", "finding_no": 1, "doi": "10.1101/2024.10.07.616920", "year": 2024, "journal": "bioRxiv", "finding": "Replacing the LED with a laser input port, mirror, diffusers and a new dichroic raised the device weight to about 4 g, with no noticeable behavioral change after a 1-week habituation with a dummy scope.", "evidence": "Fig. 1a; Results", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/wang-2024-biorxiv.md"}
{"paper_id": "wang-2024-biorxiv", "finding_no": 2, "doi": "10.1101/2024.10.07.616920", "year": 2024, "journal": "bioRxiv", "finding": "The tagging protocol used 10 trials, each a 29-s baseline followed by 1-s stimulation with a 589-nm laser, while a 445-nm laser imaged GCaMP6s continuously.", "evidence": "Methods; Results", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/wang-2024-biorxiv.md"}
{"paper_id": "wang-2024-biorxiv", "finding_no": 3, "doi": "10.1101/2024.10.07.616920", "year": 2024, "journal": "bioRxiv", "finding": "In the mouse co-expressing GCaMP6s and ChrimsonR, a subset of dentate gyrus neurons showed prominent calcium events time-locked to each orange-light pulse, which were absent in the GCaMP6s-only control mouse.", "evidence": "Fig. 1d-g", "species": "mouse", "n": "one co-expressing mouse and one control mouse", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/wang-2024-biorxiv.md"}
{"paper_id": "wang-2024-biorxiv", "finding_no": 4, "doi": "10.1101/2024.10.07.616920", "year": 2024, "journal": "bioRxiv", "finding": "The distribution of average stimulus-evoked responses differed between control neurons (n = 23) and co-expressing neurons (n = 126; P = 0.0010), whereas control neurons did not differ from circularly shifted surrogate data (P = 0.18).", "evidence": "Fig. 1h", "species": "mouse", "n": "GC (n = 23) neurons; GC-Chr (n = 126) neurons", "stats": "Kolmogorov-Smirnov test with Bonferroni correction; P = 0.0010 and P = 0.18", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/wang-2024-biorxiv.md"}
{"paper_id": "kashiwagi-2024-cell", "finding_no": 1, "doi": "10.1016/j.cell.2024.08.046", "year": 2024, "journal": "Cell", "finding": "Ablating Crhbp+ neurons in the SubLDT and adjacent areas reduced both REM and NREM sleep, increased wakefulness and raised muscle tone during REM sleep.", "evidence": "Fig. 1I-1K", "species": "mouse", "n": "n = 8 mice in WT group, n = 7 mice in Crhbp-Cre group", "stats": "unpaired t test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"}
{"paper_id": "kashiwagi-2024-cell", "finding_no": 2, "doi": "10.1016/j.cell.2024.08.046", "year": 2024, "journal": "Cell", "finding": "Chemogenetic activation of Crhbp+ SubLDT neurons projecting to the gigantocellular nucleus (CNO 1.5 mg/kg at ZT5) increased REM sleep at the expense of wakefulness and deepened REM atonia, whereas the separate basal forebrain-projecting subset increased NREM sleep.", "evidence": "Fig. 3C-3D, Fig. 4C-4D, Fig. S2G", "species": "mouse", "n": "n = 8 mice/group (Gi-projecting); n = 5 mice/group (BF-projecting)", "stats": "two-way repeated-measures ANOVA followed by Bonferroni's test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"}
{"paper_id": "kashiwagi-2024-cell", "finding_no": 3, "doi": "10.1016/j.cell.2024.08.046", "year": 2024, "journal": "Cell", "finding": "Population calcium activity of the Gi-projecting Crhbp+ SubLDT neurons, measured by fiber photometry, was highest during REM sleep.", "evidence": "Fig. 3G-3I", "species": "mouse", "n": "n = 6 mice", "stats": "one-way ANOVA followed by Tukey's test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"}
{"paper_id": "kashiwagi-2024-cell", "finding_no": 4, "doi": "10.1016/j.cell.2024.08.046", "year": 2024, "journal": "Cell", "finding": "Activating Nos1+ neurons in the dorsal paragigantocellular/prepositus region of the medulla, which project back to the SubLDT and to thalamus and medial septum, strongly increased REM sleep and caused direct transitions from wakefulness to REM sleep.", "evidence": "Fig. 6C-6J, Fig. 6K-6M", "species": "mouse", "n": "n = 8 mice", "stats": "two-way repeated-measures ANOVA followed by Bonferroni's test; paired Student's t test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"}
{"paper_id": "kashiwagi-2024-cell", "finding_no": 5, "doi": "10.1016/j.cell.2024.08.046", "year": 2024, "journal": "Cell", "finding": "In post-mortem brains, CRHBP-immunoreactive neurons in the presumed human SubLDT were reduced in Parkinson's disease patients with REM sleep behavior disorder compared with controls, cholinergic neurons were not significantly reduced, and CRHBP-immunoreactive neurons contained phosphorylated S129 alpha-synuclein.", "evidence": "Fig. 7A-7E", "species": "human (post-mortem tissue)", "n": "control patients without neurodegenerative diseases, n = 4; PD patients with RBD symptoms, n = 4", "stats": "p < 0.01 (bootstrap)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"}
{"paper_id": "kashiwagi-2024-cell", "finding_no": 6, "doi": "10.1016/j.cell.2024.08.046", "year": 2024, "journal": "Cell", "finding": "In BAC-SNCA A53T mice tested at 5 months, REM and NREM sleep were reduced, and chemogenetic activation of the Gi-projecting Crhbp+ SubLDT neurons brought these sleep measures back to control levels; the authors suggest these neurons might be a target in Parkinson's disease.", "evidence": "Fig. S7A-S7D", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"}
{"paper_id": "li-2024-natcommun", "finding_no": 1, "doi": "10.1038/s41467-024-52466-4", "year": 2024, "journal": "Nature Communications", "finding": "Largely separate subpopulations of vCA1 pyramidal neurons responded to anxiety (37.7%) and to the fear-predicting tone (39.7%).", "evidence": "Fig. 1g, p, t", "species": "mouse", "n": "n = 77 neurons, 5 mice (anxiety); n = 81 neurons, 5 mice (fear)", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md"}
{"paper_id": "li-2024-natcommun", "finding_no": 2, "doi": "10.1038/s41467-024-52466-4", "year": 2024, "journal": "Nature Communications", "finding": "Optogenetic activation of Sst interneurons during trace fear conditioning reduced fear learning and dropped the fraction of CS+-responsive pyramidal neurons at the memory test from 48.4% to 23.1%.", "evidence": "Fig. 2p-t", "species": "mouse", "n": "tdTomato n = 9 mice; ChrimsonR n = 8 mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md"}
{"paper_id": "li-2024-natcommun", "finding_no": 3, "doi": "10.1038/s41467-024-52466-4", "year": 2024, "journal": "Nature Communications", "finding": "Sst interneurons were mostly inhibited by the fear cue (68.4% at the cued fear test), and rabies tracing showed nearly 9% of their local presynaptic inputs came from VIP interneurons versus 3.2% from PV interneurons.", "evidence": "Fig. 2k-o; Fig. 3a, b", "species": "mouse", "n": "n = 39 neurons, 5 mice; n = 1068 tdTomato+ cells from 5 mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md"}
{"paper_id": "li-2024-natcommun", "finding_no": 4, "doi": "10.1038/s41467-024-52466-4", "year": 2024, "journal": "Nature Communications", "finding": "VIP interneurons were recruited by the fear cue (41.9% during conditioning, 57.6% at retrieval) but rarely by anxiety (9% in the FAST), and their optogenetic inhibition during CS+-US pairing reduced trace fear learning and impaired next-day retrieval.", "evidence": "Fig. 3c-v", "species": "mouse", "n": "tdTomato n = 8 mice; eNpHR3.0 n = 8 mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md"}
{"paper_id": "li-2024-natcommun", "finding_no": 5, "doi": "10.1038/s41467-024-52466-4", "year": 2024, "journal": "Nature Communications", "finding": "PV interneurons were activated in anxiogenic compartments, and silencing them disinhibited pyramidal neurons and increased anxiety-like behavior without affecting trace fear learning or retrieval.", "evidence": "Fig. 4", "species": "mouse", "n": "tdTomato n = 6 mice; eNpHR3.0 n = 6 mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md"}
{"paper_id": "he-2024-embc", "finding_no": 1, "doi": "10.1109/EMBC53108.2024.10782461", "year": 2024, "journal": "2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "On semi-synthetic data built from three significant real spike sequences, the factorization most often selected 3 factors, matching the embedded motifs, and AICc was lowest at a motif length of 11 bins.", "evidence": "Fig. 9; Fig. 10a-b; Fig. 11", "species": "mouse (semi-synthetic data derived from recordings)", "n": "70 neurons; 20 fittings", "stats": "lambda0 = 0.019; AICc minimum at L = 11", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/he-2024-embc.md"}
{"paper_id": "he-2024-embc", "finding_no": 2, "doi": "10.1109/EMBC53108.2024.10782461", "year": 2024, "journal": "2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "With a 10-bin detection window and an Hfit threshold of 0.936 chosen by maximizing F1 in training, online detection on a laptop processor averaged 11.2 ms per iteration, with each bin covering 167 milliseconds.", "evidence": "Section V", "species": "mouse (semi-synthetic data derived from recordings)", "n": null, "stats": "average detection time 11.2 ms per iteration", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/he-2024-embc.md"}
{"paper_id": "he-2024-embc", "finding_no": 3, "doi": "10.1109/EMBC53108.2024.10782461", "year": 2024, "journal": "2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "In noise-robustness tests for one motif with 36 replay events in 10,000 bins, detection was best without noise, the F1 curve fluctuated most under Type II firing noise, and performance was sensitive to increasing jitter.", "evidence": "Fig. 12", "species": "mouse (semi-synthetic data derived from recordings)", "n": "36 replay events in 10,000 bins", "stats": "F1 score across noise probabilities", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/he-2024-embc.md"}
{"paper_id": "he-2024-embc", "finding_no": 4, "doi": "10.1109/EMBC53108.2024.10782461", "year": 2024, "journal": "2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "On a 2500-bin test segment with mixed noise containing seven replay events, five were detected, with two incorrect detections, and detections occurred well before the end of each event.", "evidence": "Fig. 14", "species": "mouse (semi-synthetic data derived from recordings)", "n": "seven replay events in 2500 test bins", "stats": "five of seven detected; two incorrect detections", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/he-2024-embc.md"}
{"paper_id": "he-2024-embc", "finding_no": 5, "doi": "10.1109/EMBC53108.2024.10782461", "year": 2024, "journal": "2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)", "finding": "The method performed well for large motifs of 10 neurons or more but less well for smaller motifs.", "evidence": "Section VI", "species": "mouse (semi-synthetic data derived from recordings)", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/he-2024-embc.md"}
{"paper_id": "kawakami-2024-bbrc", "finding_no": 1, "doi": "10.1016/j.bbrc.2024.150071", "year": 2024, "journal": "Biochemical and Biophysical Research Communications", "finding": "Mice responded similarly to the first extinction tone regardless of presentation pattern or shock intensity (interaction F = 0.18, p = 0.89; group effect F = 2.45, p = 0.13).", "evidence": "Fig. 1d", "species": "mouse", "n": "n = 5 mice in the 0.5 mA continuous group, n = 6 mice in all other groups", "stats": "two-way ANOVA; interaction F = 0.18, p = 0.89; group main effect F = 2.45, p = 0.13", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kawakami-2024-bbrc.md"}
{"paper_id": "kawakami-2024-bbrc", "finding_no": 2, "doi": "10.1016/j.bbrc.2024.150071", "year": 2024, "journal": "Biochemical and Biophysical Research Communications", "finding": "With continuous tone presentation, the extinction time course depended on conditioning shock intensity (p = 0.0052).", "evidence": "Fig. 1e", "species": "mouse", "n": null, "stats": "two-way ANOVA, p = 0.0052", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kawakami-2024-bbrc.md"}
{"paper_id": "kawakami-2024-bbrc", "finding_no": 3, "doi": "10.1016/j.bbrc.2024.150071", "year": 2024, "journal": "Biochemical and Biophysical Research Communications", "finding": "Under continuous presentation, mice shocked at 1.0 mA showed greater residual freezing than mice shocked at 0.5 or 0.75 mA, whereas spaced-group mice extinguished similarly across intensities.", "evidence": "Fig. 1f", "species": "mouse", "n": null, "stats": "one-way ANOVA, p < 0.0001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kawakami-2024-bbrc.md"}
{"paper_id": "kawakami-2024-bbrc", "finding_no": 4, "doi": "10.1016/j.bbrc.2024.150071", "year": 2024, "journal": "Biochemical and Biophysical Research Communications", "finding": "After 1.0 mA conditioning, spaced tone presentation produced a steeper extinction slope than continuous presentation (p = 0.0030), despite a shorter total tone duration; no group difference was seen at 0.5 or 0.75 mA.", "evidence": "Fig. 1g", "species": "mouse", "n": null, "stats": "simple linear regression slope comparison, p = 0.0030", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kawakami-2024-bbrc.md"}
{"paper_id": "kawakami-2024-bbrc", "finding_no": 5, "doi": "10.1016/j.bbrc.2024.150071", "year": 2024, "journal": "Biochemical and Biophysical Research Communications", "finding": "Pre-tone freezing in the new context (contextual generalization) did not correlate with the extinction index for either presentation pattern (r = -0.07, p = 0.79 continuous; r = -0.27, p = 0.28 spaced).", "evidence": "Fig. 1h", "species": "mouse", "n": null, "stats": "Pearson correlation; r = -0.07, p = 0.79 (continuous); r = -0.27, p = 0.28 (spaced)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kawakami-2024-bbrc.md"}
{"paper_id": "koyama-2024-fuzzieee", "finding_no": 1, "doi": "10.1109/FUZZ-IEEE60900.2024.10611847", "year": 2024, "journal": "2024 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE)", "finding": "Permutation entropy analysis suggested an embedding dimension of 5 and a time delay of 8 ms for mouse EEG, regardless of sleep stage.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyama-2024-fuzzieee.md"}
{"paper_id": "koyama-2024-fuzzieee", "finding_no": 2, "doi": "10.1109/FUZZ-IEEE60900.2024.10611847", "year": 2024, "journal": "2024 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE)", "finding": "Permutation entropy distinguished REM sleep from wakefulness, whereas a linear power spectrum density approach did not.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyama-2024-fuzzieee.md"}
{"paper_id": "koyama-2024-fuzzieee", "finding_no": 3, "doi": "10.1109/FUZZ-IEEE60900.2024.10611847", "year": 2024, "journal": "2024 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE)", "finding": "The authors argue that conventional correlation integration fails to give correct embedding parameters for EEG because of noise, motivating the permutation-entropy approach.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyama-2024-fuzzieee.md"}
{"paper_id": "vergara-2023-biorxiv", "finding_no": 1, "doi": "10.1101/2023.05.19.540935", "year": 2023, "journal": "bioRxiv", "finding": "In simulated misaligned videos, using blood vessel shapes for registration gave better alignment and smaller maximum displacement errors than neuron shapes or mean-frame projections, with the gain seen when blood vessel spatial correlation between sessions was higher than 0.4.", "evidence": "Fig. 1d-i; Extended Data Figs. 3-5", "species": "simulation", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md"}
{"paper_id": "vergara-2023-biorxiv", "finding_no": 2, "doi": "10.1101/2023.05.19.540935", "year": 2023, "journal": "bioRxiv", "finding": "In mouse recordings, blood vessel correlation stayed at this level for up to 40 days between sessions.", "evidence": "Fig. 1j", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md"}
{"paper_id": "vergara-2023-biorxiv", "finding_no": 3, "doi": "10.1101/2023.05.19.540935", "year": 2023, "journal": "bioRxiv", "finding": "CaliAli tracked neurons better than other methods in simulations with low neuron overlap, high neuron overlap, and remapping of active populations.", "evidence": "Fig. 2d-f; Extended Data Fig. 6b-d", "species": "simulation", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md"}
{"paper_id": "vergara-2023-biorxiv", "finding_no": 4, "doi": "10.1101/2023.05.19.540935", "year": 2023, "journal": "bioRxiv", "finding": "In a dentate gyrus opto-tagging experiment, 49.6% ± 2.8% of neurons were tagged by orange light, and the proportion of optogenetically consistent neurons across sessions was higher with CaliAli than with other methods.", "evidence": "Fig. 2j-m", "species": "mouse", "n": "data from one mouse", "stats": "Permutation test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md"}
{"paper_id": "vergara-2023-biorxiv", "finding_no": 5, "doi": "10.1101/2023.05.19.540935", "year": 2023, "journal": "bioRxiv", "finding": "When a mouse explored two contexts over 4 weeks, CaliAli detected more dentate gyrus neurons active in all sessions, and population vectors from the same context were more highly correlated than with other methods.", "evidence": "Fig. 2n-q", "species": "mouse", "n": null, "stats": "Two-way ANOVA with Sidak's multiple comparisons", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md"}
{"paper_id": "koyanagi-2023-neurosci-res", "finding_no": 1, "doi": "10.1016/j.neures.2022.10.001", "year": 2023, "journal": "Neuroscience Research", "finding": "Driving TTL output during REM sleep, the system achieved about 90 % sensitivity and 86 % precision without prior configuration to each mouse, and REM-targeted pulses resembled those of a human scorer.", "evidence": "Abstract; Tables 2 and 3", "species": "mouse", "n": "Manual, n = 6; UTSN-L2, n = 3; UTSN-L2-DS, n = 4 (mice = recordings)", "stats": "mean (standard deviation)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md"}
{"paper_id": "koyanagi-2023-neurosci-res", "finding_no": 2, "doi": "10.1016/j.neures.2022.10.001", "year": 2023, "journal": "Neuroscience Research", "finding": "Run live on four mice simultaneously, the model's stage classifications matched a blinded human expert in light and dark periods, with REM specificity and accuracy above 97 %, although it scored more and shorter REM episodes.", "evidence": "Figs. 2-3; Table 1", "species": "mouse", "n": "n = 12 recordings from 4 mice", "stats": "two-way ANOVA", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md"}
{"paper_id": "koyanagi-2023-neurosci-res", "finding_no": 3, "doi": "10.1016/j.neures.2022.10.001", "year": 2023, "journal": "Neuroscience Research", "finding": "EEG recorded at 512 Hz and down-sampled online to 128 Hz yielded total amounts of each stage similar to the human expert, with differences only in some episode counts and durations.", "evidence": "Figs. 3B, 4", "species": "mouse", "n": "n = 12 recordings from the same four mice", "stats": "two-way ANOVA", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md"}
{"paper_id": "koyanagi-2023-neurosci-res", "finding_no": 4, "doi": "10.1016/j.neures.2022.10.001", "year": 2023, "journal": "Neuroscience Research", "finding": "A variant classifying stages in 4-s rather than 10-s windows performed similarly to the original model in five-fold cross-validation on 154 recordings, and gave similar results on an independent dataset from a different laboratory.", "evidence": "Table 1; Fig. 5; Figs. S3-S4", "species": "mouse", "n": "154 recordings from 96 mice", "stats": "cross-validation", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md"}
{"paper_id": "koyanagi-2023-neurosci-res", "finding_no": 5, "doi": "10.1016/j.neures.2022.10.001", "year": 2023, "journal": "Neuroscience Research", "finding": "A model that additionally separated high-theta wakefulness did not improve REM classification, because high-theta wakefulness itself was detected with low sensitivity (30.4 %) and precision (70.5 %), mostly confused with low-theta wakefulness.", "evidence": "Table 1; Fig. 5", "species": "mouse", "n": "154 recordings from 96 mice", "stats": "cross-validation", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md"}
{"paper_id": "sakaguchi-2022-jpn-j-trauma-stress", "finding_no": 1, "doi": null, "year": 2022, "journal": "トラウマティック・ストレス（Japanese Journal of Traumatic Stress）", "finding": "The review argues that prolonged exposure works through fear extinction, and that in PTSD the extreme avoidance of trauma reminders keeps normal extinction from taking place.", "evidence": "Sections 'Extinctionと持続エクスポージャー療法' and 'トラウマ記憶と条件付け恐怖記憶'; Fig. 1", "species": "human", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2022-jpn-j-trauma-stress.md"}
{"paper_id": "sakaguchi-2022-jpn-j-trauma-stress", "finding_no": 2, "doi": null, "year": 2022, "journal": "トラウマティック・ストレス（Japanese Journal of Traumatic Stress）", "finding": "The review identifies the cost of prolonged exposure (10 to 15 sessions over about 3 months, distress from deliberately recalling the trauma, the need for skilled therapists, and high dropout) as the motivation for new approaches.", "evidence": "Section '情報処理理論と持続エクスポージャー療法'", "species": "human", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2022-jpn-j-trauma-stress.md"}
{"paper_id": "sakaguchi-2022-jpn-j-trauma-stress", "finding_no": 3, "doi": null, "year": 2022, "journal": "トラウマティック・ストレス（Japanese Journal of Traumatic Stress）", "finding": "Citing the authors' mouse work, the review reports that adult-born dentate gyrus neurons aged 4 to 6 weeks that were active during learning reactivate in later REM sleep, that silencing them during REM sleep impairs fear memory consolidation, and that the activity involved may total 500 events or fewer.", "evidence": "Section '新生ニューロンと睡眠中の恐怖記憶固定化' (ref. 18)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2022-jpn-j-trauma-stress.md"}
{"paper_id": "sakaguchi-2022-jpn-j-trauma-stress", "finding_no": 4, "doi": null, "year": 2022, "journal": "トラウマティック・ストレス（Japanese Journal of Traumatic Stress）", "finding": "The review reports the authors' mouse replication in which only a conditioned sound played during slow-wave sleep, and not during REM sleep, weakened fear responses, and suggests that presenting sounds during sleep merits further study as a new approach.", "evidence": "Section '睡眠中の音刺激を用いた新しいエクスポージャーの開発' (refs. 13, 25)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2022-jpn-j-trauma-stress.md"}
{"paper_id": "soares-2021-cells", "finding_no": 1, "doi": "10.3390/cells10113047", "year": 2021, "journal": "Cells", "finding": "In the healthy mouse brain Galectin-3 is expressed in subventricular zone ependymal cells, stem cells and some progenitors but not neuroblasts, and its loss disrupts neuroblast migration and reduces olfactory bulb neurogenesis.", "evidence": "Section 2", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/soares-2021-cells.md"}
{"paper_id": "soares-2021-cells", "finding_no": 2, "doi": "10.3390/cells10113047", "year": 2021, "journal": "Cells", "finding": "In the postnatal subventricular zone, Galectin-3 regulates gliogenesis rather than neurogenesis, increasing BMP signaling and reducing Wnt signaling, and the authors describe it as a switch for astrocyte generation.", "evidence": "Section 3.1", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/soares-2021-cells.md"}
{"paper_id": "soares-2021-cells", "finding_no": 3, "doi": "10.3390/cells10113047", "year": 2021, "journal": "Cells", "finding": "The review summarizes evidence that Galectin-3 is elevated in Alzheimer's disease and that reducing it in mouse models lowers inflammation and is associated with better cognition.", "evidence": "Section 5.1", "species": "human; mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/soares-2021-cells.md"}
{"paper_id": "soares-2021-cells", "finding_no": 4, "doi": "10.3390/cells10113047", "year": 2021, "journal": "Cells", "finding": "The authors conclude that, despite many binding partners, Galectin-3 has specific context-dependent effects, and its cell-type expression in the subventricular zone stays stable across disease models.", "evidence": "Section 8", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/soares-2021-cells.md"}
{"paper_id": "taniguchi-2021-embc", "finding_no": 1, "doi": "10.1109/embc46164.2021.9629611", "year": 2021, "journal": "2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)", "finding": "Combining temporal-trace and spatial-footprint branches (Conv-LSTM + 2D-CNN) gave accuracy 0.894 and F1 0.920 for false-positive neuron detection, versus 0.878 and 0.910 for the TPOT model, the best existing automated-curation method.", "evidence": "Table I", "species": "mouse (annotated public 1p dataset)", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md"}
{"paper_id": "taniguchi-2021-embc", "finding_no": 2, "doi": "10.1109/embc46164.2021.9629611", "year": 2021, "journal": "2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)", "finding": "Models using only the temporal trace (LSTM: accuracy 0.849, F1 0.888) or only the spatial footprint (2D-CNN: accuracy 0.884, F1 0.909) did not outperform TPOT, indicating both kinds of information contribute.", "evidence": "Table I", "species": "mouse (annotated public 1p dataset)", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md"}
{"paper_id": "taniguchi-2021-embc", "finding_no": 3, "doi": "10.1109/embc46164.2021.9629611", "year": 2021, "journal": "2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)", "finding": "Replacing the spatial branch with large ImageNet-pretrained backbones changed accuracy only slightly (for example WideResNet 50: accuracy 0.903, F1 0.923), which the authors attribute possibly to limited training data or an unsuitable pretraining domain.", "evidence": "Table I; Section IV-A", "species": "mouse (annotated public 1p dataset)", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md"}
{"paper_id": "taniguchi-2021-embc", "finding_no": 4, "doi": "10.1109/embc46164.2021.9629611", "year": 2021, "journal": "2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)", "finding": "In whole-system tests the processing rate was higher with the deep classifier, which the authors explain by fewer neurons being detected rather than faster classification.", "evidence": "Table III; Section IV-B", "species": null, "n": "two public 2p datasets and two in-house 1p videos", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md"}
{"paper_id": "taniguchi-2021-embc", "finding_no": 5, "doi": "10.1109/embc46164.2021.9629611", "year": 2021, "journal": "2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)", "finding": "When applied to 2p data from a different domain, the deep classifiers appeared less robust than TPOT given the 15% false-neuron ratio of the training data, so the authors recommend training on images from the same domain.", "evidence": "Table IV; Section IV-B", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md"}
{"paper_id": "taniguchi-2021-embc", "finding_no": 6, "doi": "10.1109/embc46164.2021.9629611", "year": 2021, "journal": "2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)", "finding": "The system uses the first 500 frames of the stream for initialization and then extracts and filters neuron candidates frame by frame.", "evidence": "Fig. 1; Section III-B", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md"}
{"paper_id": "ohba-2021-neural-regen-res", "finding_no": 1, "doi": "10.4103/1673-5374.317966", "year": 2021, "journal": "Neural Regeneration Research", "finding": "The authors argue, from their prior mouse work, that sparse activity of adult-born neurons during REM sleep after contextual fear learning is necessary for memory consolidation.", "evidence": "Main text (citing Kumar et al., 2020)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2021-neural-regen-res.md"}
{"paper_id": "ohba-2021-neural-regen-res", "finding_no": 2, "doi": "10.4103/1673-5374.317966", "year": 2021, "journal": "Neural Regeneration Research", "finding": "Only adult-born neurons at an age of heightened plasticity matter: silencing 4-week-old cells, but not 2- or 10-week-old cells, during REM sleep impairs consolidation, and random activation of 4-week-old cells also impairs memory.", "evidence": "Main text (citing Kumar et al., 2020)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2021-neural-regen-res.md"}
{"paper_id": "ohba-2021-neural-regen-res", "finding_no": 3, "doi": "10.4103/1673-5374.317966", "year": 2021, "journal": "Neural Regeneration Research", "finding": "The authors hypothesize that theta phase-locked activity stabilizes spines in a sparse subset of adult-born neurons, which then inhibit mature granule cells in a phase-specific way so that connected mature cells fire at the reciprocal theta phase and establish a memory trace.", "evidence": "Fig. 1A-D", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2021-neural-regen-res.md"}
{"paper_id": "ohba-2021-neural-regen-res", "finding_no": 4, "doi": "10.4103/1673-5374.317966", "year": 2021, "journal": "Neural Regeneration Research", "finding": "Testing the hypothesis would require phase-specific closed-loop optogenetic manipulation and methods with higher time resolution than genetically encoded calcium sensors.", "evidence": "Main text", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2021-neural-regen-res.md"}
{"paper_id": "yu-2021-bbrc", "finding_no": 1, "doi": "10.1016/j.bbrc.2021.04.072", "year": 2021, "journal": "Biochemical and Biophysical Research Communications", "finding": "Mice exposed to a neutral context similar to the training context soon after conditioning showed fear generalization 6 h after training, immediately after contextual fear memory consolidation.", "evidence": "Abstract", "species": "mouse", "n": "", "stats": "", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yu-2021-bbrc.md"}
{"paper_id": "yu-2021-bbrc", "finding_no": 2, "doi": "10.1016/j.bbrc.2021.04.072", "year": 2021, "journal": "Biochemical and Biophysical Research Communications", "finding": "Exposure to a clearly different neutral context after training did not produce this early fear generalization.", "evidence": "Abstract", "species": "mouse", "n": "", "stats": "", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yu-2021-bbrc.md"}
{"paper_id": "yu-2021-bbrc", "finding_no": 3, "doi": "10.1016/j.bbrc.2021.04.072", "year": 2021, "journal": "Biochemical and Biophysical Research Communications", "finding": "The generalized fear was expressed as a change in both the total amount and the pattern of freezing between the conditioned and generalized contexts.", "evidence": "Abstract", "species": "mouse", "n": "", "stats": "", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yu-2021-bbrc.md"}
{"paper_id": "tezuka-2021-scirep", "finding_no": 1, "doi": "10.1038/s41598-021-90332-1", "year": 2021, "journal": "Scientific Reports", "finding": "The UTSN-L system reached 90% overall accuracy and 81% multi-class Matthews Correlation Coefficient, with 91% sensitivity and 98% specificity for REM sleep.", "evidence": "Abstract; Table 1", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"}
{"paper_id": "tezuka-2021-scirep", "finding_no": 2, "doi": "10.1038/s41598-021-90332-1", "year": 2021, "journal": "Scientific Reports", "finding": "The classifiers were built from 214 expert-scored recordings of 6 h each, of which 192 were used for training and validation and 22 were held out for testing.", "evidence": "Results, Training, validation, and testing", "species": "mouse", "n": "214 recordings (192 training/validation, 22 testing)", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"}
{"paper_id": "tezuka-2021-scirep", "finding_no": 3, "doi": "10.1038/s41598-021-90332-1", "year": 2021, "journal": "Scientific Reports", "finding": "Adding the LSTM memory of past epochs improved classification: UTSN-L performed better overall than UTSN, which tended to call more and shorter sleep episodes than the expert scoring.", "evidence": "Table 1; Fig. 3A-D", "species": "mouse", "n": "n=22 recordings", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"}
{"paper_id": "tezuka-2021-scirep", "finding_no": 4, "doi": "10.1038/s41598-021-90332-1", "year": 2021, "journal": "Scientific Reports", "finding": "On held-out test recordings, results were consistent with validation, total sleep amounts were almost identical to expert scoring, and power spectra of classified epochs were almost identical to ground truth.", "evidence": "Table 2; Suppl. Table 1; Figs. 3B, 4", "species": "mouse", "n": "n=22 recordings", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"}
{"paper_id": "tezuka-2021-scirep", "finding_no": 5, "doi": "10.1038/s41598-021-90332-1", "year": 2021, "journal": "Scientific Reports", "finding": "A graphical interface runs the classifier on a personal computer, can output decisions to an Arduino device for closed-loop control with a 10 s delay set by the epoch window, and the code is open source.", "evidence": "Fig. 5; VIDEO S1", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"}
{"paper_id": "vergara-2021-ijms", "finding_no": 1, "doi": "10.3390/ijms22062874", "year": 2021, "journal": "International Journal of Molecular Sciences", "finding": "Exposure to the novel conditioning context increased adult-born neuron activity, with ~28% of cells increasing activity in the preshock period and ~10% decreasing activity after the shock.", "evidence": "Fig. 1D-F", "species": "mouse", "n": "n = 94 neurons from 4 mice", "stats": "bootstrap, p < 0.05; moving block bootstrap for individual neurons", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md"}
{"paper_id": "vergara-2021-ijms", "finding_no": 2, "doi": "10.3390/ijms22062874", "year": 2021, "journal": "International Journal of Molecular Sciences", "finding": "Similarity clustering of population activity vectors showed that a similar population was active before and after the shock, whereas a different population was active during the retrieval test, so learning and retrieval populations did not overlap.", "evidence": "Fig. 2B-C", "species": "mouse", "n": "n = 94 neurons from 4 mice", "stats": "hierarchical clustering on cosine similarity, significant clusters p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md"}
{"paper_id": "vergara-2021-ijms", "finding_no": 3, "doi": "10.3390/ijms22062874", "year": 2021, "journal": "International Journal of Molecular Sciences", "finding": "Across 15 min bins of the consolidation period, a remapping index declined steadily with time (all data r = -0.97, p < 0.0001), and this drift was seen in both sleep (r = -0.98) and wake (r = -0.93, p = 0.008).", "evidence": "Fig. 3A-B", "species": "mouse", "n": "n = 94 neurons from 4 mice", "stats": "r = -0.97 p < 0.0001 (all); r = -0.98 p < 0.0001 (sleep); r = -0.93 p = 0.008 (wake)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md"}
{"paper_id": "vergara-2021-ijms", "finding_no": 4, "doi": "10.3390/ijms22062874", "year": 2021, "journal": "International Journal of Molecular Sciences", "finding": "Remapping was carried by subsets of neurons whose activity changed with time (15 decreasing, 9 increasing, 70 unchanged); decreasing cells were mainly active during learning and increasing cells mainly at the test, and significant clusters appeared only among remapping cells.", "evidence": "Fig. 3C-F", "species": "mouse", "n": "decreasing n = 15; increasing n = 9; non-remapping n = 70", "stats": "Pearson's correlation p < 0.05, FDR q < 0.05; bootstrap p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md"}
{"paper_id": "vergara-2021-ijms", "finding_no": 5, "doi": "10.3390/ijms22062874", "year": 2021, "journal": "International Journal of Molecular Sciences", "finding": "Adult-born neurons previously shown to be reactivated during REM sleep overlapped with the cells that decreased their activity during consolidation, which the authors suggest may link REM reactivation and remapping, without demonstrating causality.", "evidence": "Fig. S1C", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md"}
{"paper_id": "carrier-ruiz-2021-star-protocols", "finding_no": 1, "doi": "10.1016/j.xpro.2020.100238", "year": 2021, "journal": "STAR Protocols", "finding": "Adult-born neurons are scarce and sparsely active in the imaging field, which makes their activity hard to detect by eye.", "evidence": "Quantification and statistical analysis, step notes", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"}
{"paper_id": "carrier-ruiz-2021-star-protocols", "finding_no": 2, "doi": "10.1016/j.xpro.2020.100238", "year": 2021, "journal": "STAR Protocols", "finding": "The authors report that about 50% of preparations succeed, since GCaMP3 signal from the few labeled neurons may be undetectable before post-processing.", "evidence": "Step-by-step method details, note on baseplate attachment", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"}
{"paper_id": "carrier-ruiz-2021-star-protocols", "finding_no": 3, "doi": "10.1016/j.xpro.2020.100238", "year": 2021, "journal": "STAR Protocols", "finding": "Compared with overlapping-batch analysis, an estimated 34% of components extracted by conventional whole-video CNMF-E were classified as false positives based on low circularity.", "evidence": "Figure 11E", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"}
{"paper_id": "carrier-ruiz-2021-star-protocols", "finding_no": 4, "doi": "10.1016/j.xpro.2020.100238", "year": 2021, "journal": "STAR Protocols", "finding": "On average, 61% of neurons found by the overlapping-batch method were missed when only an individual batch was analyzed, because their peak-to-noise ratio fell below the detection threshold.", "evidence": "Figure 11H", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"}
{"paper_id": "carrier-ruiz-2021-star-protocols", "finding_no": 5, "doi": "10.1016/j.xpro.2020.100238", "year": 2021, "journal": "STAR Protocols", "finding": "Components from the overlapping-batch method were spatially and temporally closer to those from individual-batch analysis, which the authors interpret as fewer false positives without loss of true detections.", "evidence": "Figure 11G", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"}
{"paper_id": "carrier-ruiz-2021-star-protocols", "finding_no": 6, "doi": "10.1016/j.xpro.2020.100238", "year": 2021, "journal": "STAR Protocols", "finding": "Newer GCaMP6 reporter lines crossed with Nestin-CreERT2 mice did not produce indicator expression in adult-born neurons in the authors' hands, so the GCaMP3 line Ai38 is recommended.", "evidence": "Before you begin, notes", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"}
{"paper_id": "koyanagi-2021-molbrain", "finding_no": 1, "doi": "10.1186/s13041-021-00733-6", "year": 2021, "journal": "Molecular Brain", "finding": "More than 200 metabolites were consistently detected in the dentate gyrus, and PLS-DA separated REM and NREM sleep from wakefulness (Q2 value 0.52).", "evidence": "Fig. 1d", "species": "mouse", "n": "REM, n=10 mice; NREM, n=10 mice; Wake, n=11 mice", "stats": "permutation test, REM vs. Wake, p<0.05; NREM vs. Wake, p<0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md"}
{"paper_id": "koyanagi-2021-molbrain", "finding_no": 2, "doi": "10.1186/s13041-021-00733-6", "year": 2021, "journal": "Molecular Brain", "finding": "Pairwise comparisons identified 86 metabolites (with some overlap) changed between sleep-wake states, including decreased GSSG and increased GSH, allantoin and cysteine during sleep, which the authors suggest reflects an antioxidative environment.", "evidence": "Fig. 1g-k", "species": "mouse", "n": null, "stats": "p<0.05, fold change>|1.5|", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md"}
{"paper_id": "koyanagi-2021-molbrain", "finding_no": 3, "doi": "10.1186/s13041-021-00733-6", "year": 2021, "journal": "Molecular Brain", "finding": "Fear conditioning produced less distinct metabolite phenotypes than sleep-wake transitions, but purine metabolism changed both across sleep-wake states and with fear memory consolidation.", "evidence": "Figs. 2, 3", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md"}
{"paper_id": "koyanagi-2021-molbrain", "finding_no": 4, "doi": "10.1186/s13041-021-00733-6", "year": 2021, "journal": "Molecular Brain", "finding": "One week of oral hypoxanthine, xanthine, allantoin or urea did not change sleep architecture except shorter REM sleep episodes with urea, and did not change mean freezing in context or tone tests.", "evidence": "Figs. 4, 5b-f", "species": "mouse", "n": "control, n=16; hypoxanthine, n=12; xanthine, n=13; allantoin, n=19; urea, n=16 (behavior)", "stats": "context test group effect F(4, 71)=0.90, p=0.47", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md"}
{"paper_id": "koyanagi-2021-molbrain", "finding_no": 5, "doi": "10.1186/s13041-021-00733-6", "year": 2021, "journal": "Molecular Brain", "finding": "Post-shock freezing correlated with freezing in the context test in control mice (r=0.58) but not in hypoxanthine (r=0.22, p=0.48) or urea (r=0.27, p=0.32) groups.", "evidence": "Fig. 5g-k", "species": "mouse", "n": "control n=16; hypoxanthine n=12; urea n=16", "stats": "two-tailed Pearson's correlation, control r=0.58, p<0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md"}
{"paper_id": "koyanagi-2021-molbrain", "finding_no": 6, "doi": "10.1186/s13041-021-00733-6", "year": 2021, "journal": "Molecular Brain", "finding": "Freezing during the third conditioning tone correlated with tone-test freezing in controls (r=0.54) but not in purine-supplemented groups, suggesting purine supplementation alters relationships between conditioned responses across consolidation.", "evidence": "Fig. 5q-u", "species": "mouse", "n": "control n=14", "stats": "two-tailed Pearson's correlation, r=0.54, p<0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md"}
{"paper_id": "vergara-2020-front-cell-neurosci", "finding_no": 1, "doi": "10.3389/fncel.2020.594401", "year": 2020, "journal": "Frontiers in Cellular Neuroscience", "finding": "The authors restate their prior evidence that adult-born neurons active during learning reactivate in subsequent REM sleep and that disrupting their activity in REM sleep, by either optogenetic activation or silencing, impairs memory consolidation.", "evidence": "Figure 1; Introduction", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2020-front-cell-neurosci.md"}
{"paper_id": "vergara-2020-front-cell-neurosci", "finding_no": 2, "doi": "10.3389/fncel.2020.594401", "year": 2020, "journal": "Frontiers in Cellular Neuroscience", "finding": "The review proposes that weaker inhibition and higher excitability let adult-born neurons fire before granule neurons within a theta cycle, which may prime a subset of CA3 neurons or drive CA3 inhibitory circuits that support pattern separation.", "evidence": "Figure 2C", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2020-front-cell-neurosci.md"}
{"paper_id": "vergara-2020-front-cell-neurosci", "finding_no": 3, "doi": "10.3389/fncel.2020.594401", "year": 2020, "journal": "Frontiers in Cellular Neuroscience", "finding": "The authors hypothesize that learning accelerates integration of a subset of adult-born neurons into inhibitory circuits, so that REM sleep may maintain synapses of oscillation-coupled cells, consistent with their observation that silencing these neurons in REM sleep lengthens spine necks.", "evidence": "Figure 2D-E; section on REM sleep and synaptic plasticity", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2020-front-cell-neurosci.md"}
{"paper_id": "vergara-2020-front-cell-neurosci", "finding_no": 4, "doi": "10.3389/fncel.2020.594401", "year": 2020, "journal": "Frontiers in Cellular Neuroscience", "finding": "Because little overlap was found between adult-born neurons active during fear learning and during retrieval, the review suggests these neurons may not fit the conventional engram definition and may transiently encode information before an engram forms downstream during REM sleep.", "evidence": "Section 'Are ABNs engram cells?'", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2020-front-cell-neurosci.md"}
{"paper_id": "kumar-2020-neuron", "finding_no": 1, "doi": "10.1016/j.neuron.2020.05.008", "year": 2020, "journal": "Neuron", "finding": "After contextual fear conditioning (delayed shock), the calcium event frequency of young adult-born neurons in REM sleep was further reduced, which did not occur in immediate-shock controls or in fully mature granule neurons.", "evidence": "Fig. 1G-H; Fig. S5A-C", "species": "mouse", "n": "n = 88, 47, 113, and 137 neurons in IS-BL, IS-AS, DS-BL, and DS-AS groups", "stats": "p < 0.05, bootstrap", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"}
{"paper_id": "kumar-2020-neuron", "finding_no": 2, "doi": "10.1016/j.neuron.2020.05.008", "year": 2020, "journal": "Neuron", "finding": "About 37.9% of recorded young adult-born neurons were active at least once in post-learning REM sleep, and neurons active right after the shock were more likely to be active in subsequent REM sleep, whereas activity during the retrieval test did not predict REM activity.", "evidence": "Fig. 1I-K", "species": "mouse", "n": "n = 59 and 36 neurons in REM- and REM+ groups from 7 mice", "stats": "p < 0.05, p < 0.01, bootstrap", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"}
{"paper_id": "kumar-2020-neuron", "finding_no": 3, "doi": "10.1016/j.neuron.2020.05.008", "year": 2020, "journal": "Neuron", "finding": "Silencing young adult-born neurons during REM sleep in the 6 h after conditioning did not change sleep architecture, EEG power spectra, or dentate gyrus theta autocorrelation (p = 0.72).", "evidence": "Fig. 3D-L", "species": "mouse", "n": "n = 11-13 mice/genotype; 434 and 468 LFP epochs", "stats": "p = 0.72, Mann-Whitney test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"}
{"paper_id": "kumar-2020-neuron", "finding_no": 4, "doi": "10.1016/j.neuron.2020.05.008", "year": 2020, "journal": "Neuron", "finding": "REM-sleep silencing of young adult-born neurons reduced dentate gyrus expression of immediate early genes such as Zif268, Npas4, and Fos, all decreased genes carried SRF binding motifs, and dendritic spine necks of these neurons became longer.", "evidence": "Fig. 4H-L; Fig. 5C-E", "species": "mouse", "n": "n = 4 mice each (RNA-seq); n = 30-40 dendrites/group (spines)", "stats": "SRF motif enrichment p < 0.0001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"}
{"paper_id": "kumar-2020-neuron", "finding_no": 5, "doi": "10.1016/j.neuron.2020.05.008", "year": 2020, "journal": "Neuron", "finding": "Silencing young adult-born neurons only during REM sleep within the consolidation window reduced contextual freezing the next day, while silencing outside the window (p = 0.98), during NREM sleep or wakefulness, or of 2-week-old or 10-week-old neurons did not significantly impair memory.", "evidence": "Fig. 6A-Q", "species": "mouse", "n": "n = 12-13/genotype (within window); n = 9/genotype (outside window)", "stats": "p < 0.05, two-tailed unpaired t test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"}
{"paper_id": "kumar-2020-neuron", "finding_no": 6, "doi": "10.1016/j.neuron.2020.05.008", "year": 2020, "journal": "Neuron", "finding": "Random 20-Hz optogenetic activation of young adult-born neurons during REM sleep also reduced contextual freezing, suggesting that finely tuned rather than simply more activity is needed for consolidation.", "evidence": "Fig. 6T-V", "species": "mouse", "n": "n = 10-12/genotype", "stats": "p < 0.05, two-tailed paired t test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"}
{"paper_id": "maezono-2020-eneuro", "finding_no": 1, "doi": "10.1523/eneuro.0093-20.2020", "year": 2020, "journal": "eNeuro", "finding": "Homozygous AppNL-G-F mice showed less total REM sleep and a lower REMS/total sleep ratio at six months, mainly during the light phase, with a further REM reduction plus reduced NREM sleep and more wake at 12 months.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": "Games-Howell multiple comparison test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/maezono-2020-eneuro.md"}
{"paper_id": "maezono-2020-eneuro", "finding_no": 2, "doi": "10.1523/eneuro.0093-20.2020", "year": 2020, "journal": "eNeuro", "finding": "Heterozygous mice had sleep architecture broadly similar to age-matched wild-type mice at both six and 12 months.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/maezono-2020-eneuro.md"}
{"paper_id": "maezono-2020-eneuro", "finding_no": 3, "doi": "10.1523/eneuro.0093-20.2020", "year": 2020, "journal": "eNeuro", "finding": "During REM sleep, homozygous mice showed a lower gamma-to-delta power ratio from six months, resembling the EEG slowing reported in early-stage patients; by 12 months delta rose and theta and gamma fell in both sleep stages.", "evidence": "Fig. 3", "species": "mouse", "n": null, "stats": "Games-Howell multiple comparison test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/maezono-2020-eneuro.md"}
{"paper_id": "maezono-2020-eneuro", "finding_no": 4, "doi": "10.1523/eneuro.0093-20.2020", "year": 2020, "journal": "eNeuro", "finding": "In trace fear conditioning, homozygous mice froze less at retrieval at seven months, and at 13 months homozygous (and to a lesser extent heterozygous) mice showed impaired learning during training.", "evidence": "Fig. 5", "species": "mouse", "n": null, "stats": "mixed ANOVA; Games-Howell multiple comparison test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/maezono-2020-eneuro.md"}
{"paper_id": "maezono-2020-eneuro", "finding_no": 5, "doi": "10.1523/eneuro.0093-20.2020", "year": 2020, "journal": "eNeuro", "finding": "In 13-month-old homozygous mice, freezing during the third conditioned stimulus on day 1 correlated strongly and positively with total REM sleep, whereas no significant correlation with sleep parameters was found at seven months.", "evidence": "Fig. 6", "species": "mouse", "n": null, "stats": "Pearson's correlation", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/maezono-2020-eneuro.md"}
{"paper_id": "maezono-2020-eneuro", "finding_no": 6, "doi": "10.1523/eneuro.0093-20.2020", "year": 2020, "journal": "eNeuro", "finding": "Amyloid-β in the pontine tegmental area and ventral medulla rose markedly from seven to 13 months in homozygous mice but was barely detectable in heterozygous mice, a pattern that somewhat resembled the progression of REM sleep loss.", "evidence": "Fig. 7", "species": "mouse", "n": null, "stats": "Welch's t test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/maezono-2020-eneuro.md"}
{"paper_id": "srinivasan-2019-bbrc", "finding_no": 1, "doi": "10.1016/j.bbrc.2019.07.082", "year": 2019, "journal": "Biochemical and Biophysical Research Communications", "finding": "Replacing the LED with a ferrule light input port and internal mirror did not increase miniscope weight (about 1.9 g) and preserved the original imaging capability.", "evidence": "Fig. 1; Results", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md"}
{"paper_id": "srinivasan-2019-bbrc", "finding_no": 2, "doi": "10.1016/j.bbrc.2019.07.082", "year": 2019, "journal": "Biochemical and Biophysical Research Communications", "finding": "Blue laser light delivered through the miniscope revealed CA1 calcium events at a rate matching earlier reports (~0.02 events/s).", "evidence": "Fig. 2B-C", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md"}
{"paper_id": "srinivasan-2019-bbrc", "finding_no": 3, "doi": "10.1016/j.bbrc.2019.07.082", "year": 2019, "journal": "Biochemical and Biophysical Research Communications", "finding": "In neurons expressing only jGCaMP7c, orange laser light did not change calcium fluorescence signals.", "evidence": "Fig. 2E", "species": "mouse", "n": "7 neurons", "stats": "one-way repeated measures ANOVA with Geisser-Greenhouse correction, F(1.3, 9.1) = 0.41, p = 0.59", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md"}
{"paper_id": "srinivasan-2019-bbrc", "finding_no": 4, "doi": "10.1016/j.bbrc.2019.07.082", "year": 2019, "journal": "Biochemical and Biophysical Research Communications", "finding": "In neurons co-expressing Jaws and jGCaMP7c, orange light significantly decreased calcium fluorescence during light-on periods, and activity rose again after light offset.", "evidence": "Fig. 3B-E", "species": "mouse", "n": "7 neurons", "stats": "one-way repeated measures ANOVA with Geisser-Greenhouse correction, F(1.3, 78) = 40.0, p = 0.0002; Tukey's multiple comparisons, p < 0.002", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md"}
{"paper_id": "srinivasan-2019-bbrc", "finding_no": 5, "doi": "10.1016/j.bbrc.2019.07.082", "year": 2019, "journal": "Biochemical and Biophysical Research Communications", "finding": "Orange light did not excite jGCaMP7 even at light onset, indicating no biological crosstalk between Jaws and the calcium sensor.", "evidence": "Fig. 3C-D", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md"}
{"paper_id": "koyanagi-2019-neural-regen-res", "finding_no": 1, "doi": "10.4103/1673-5374.243695", "year": 2019, "journal": "Neural Regeneration Research", "finding": "Adult-born dentate gyrus neurons appear to be recruited into memory circuits during a narrow developmental window: silencing 4-week-old adult-born neurons impairs memory retrieval, whereas silencing 2- or 8-week-old neurons does not.", "evidence": "Section 'Mnemonic Function of the DG and Its Adult-Generated Neurons'; Fig. 1", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2019-neural-regen-res.md"}
{"paper_id": "koyanagi-2019-neural-regen-res", "finding_no": 2, "doi": "10.4103/1673-5374.243695", "year": 2019, "journal": "Neural Regeneration Research", "finding": "The authors propose that integration of adult-born neurons may act as a memory time-stamp that helps separate similar events according to when they occurred.", "evidence": "Section 'Mnemonic Function of the DG and Its Adult-Generated Neurons'", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2019-neural-regen-res.md"}
{"paper_id": "koyanagi-2019-neural-regen-res", "finding_no": 3, "doi": "10.4103/1673-5374.243695", "year": 2019, "journal": "Neural Regeneration Research", "finding": "Rodent studies report a dose-dependent reduction of adult dentate gyrus neurogenesis with sleep deprivation, but the stress induced by deprivation makes it hard to attribute these effects to sleep loss itself.", "evidence": "Section 'Sleep and Adult DG Neurogenesis'", "species": "rodent", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2019-neural-regen-res.md"}
{"paper_id": "koyanagi-2019-neural-regen-res", "finding_no": 4, "doi": "10.4103/1673-5374.243695", "year": 2019, "journal": "Neural Regeneration Research", "finding": "The review argues that future studies should optogenetically manipulate adult-born neurons during specific sleep stages without altering overall sleep architecture to test their special role in sleep-dependent consolidation.", "evidence": "Section 'Sleep and Adult DG Neurogenesis'; Fig. 2", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2019-neural-regen-res.md"}
{"paper_id": "akers-2018-stemcells", "finding_no": 1, "doi": "10.1002/stem.2815", "year": 2018, "journal": "Stem Cells", "finding": "The authors propose that sleep regulates adult dentate gyrus neurogenesis by inducing, or being affected by, epigenetic modifications of gene expression.", "evidence": "Role of sleep in epigenetic regulation section; Fig. 3", "species": "rodents and humans (literature)", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2018-stemcells.md"}
{"paper_id": "akers-2018-stemcells", "finding_no": 2, "doi": "10.1002/stem.2815", "year": 2018, "journal": "Stem Cells", "finding": "Cited work indicates sleep deprivation reduces adult hippocampal neurogenesis partly independently of stress hormones; in rats, 96 hours of sleep deprivation reduced dentate gyrus cell proliferation even after adrenalectomy with low-dose corticosterone.", "evidence": "Sleep Deprivation section", "species": "rat", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2018-stemcells.md"}
{"paper_id": "akers-2018-stemcells", "finding_no": 3, "doi": "10.1002/stem.2815", "year": 2018, "journal": "Stem Cells", "finding": "The review suggests that sleep loss may act on neurogenesis through epigenetic routes, citing reduced hippocampal CBP expression and Bdnf-promoter histone acetylation after 3 days of sleep deprivation in mice.", "evidence": "Sleep Deprivation section", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2018-stemcells.md"}
{"paper_id": "akers-2018-stemcells", "finding_no": 4, "doi": "10.1002/stem.2815", "year": 2018, "journal": "Stem Cells", "finding": "The authors raise the possibility that targeted reactivation of memories during sleep induces epigenetic changes in adult-born dentate gyrus neurons that support further memory consolidation, and suggest combining sleep interventions with epigenetic drugs as a research direction.", "evidence": "Memory Replay During Sleep section; Conclusion", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2018-stemcells.md"}
{"paper_id": "purple-2017-scirep", "finding_no": 1, "doi": "10.1038/srep46247", "year": 2017, "journal": "Scientific Reports", "finding": "Mice cued with the tone during NREM sleep froze significantly less to the tone in a novel context than REM-cued mice, on average 15.2% less than REM-cued and 20.6% less than control mice.", "evidence": "Fig. 5b; Table 2", "species": "mouse", "n": "NREM-cued n=10, REM-cued n=10, control n=9", "stats": "ANOVA F= 4.32, p = 0.024; post-hoc t-tests with Bonferroni correction", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/purple-2017-scirep.md"}
{"paper_id": "purple-2017-scirep", "finding_no": 2, "doi": "10.1038/srep46247", "year": 2017, "journal": "Scientific Reports", "finding": "Contextual fear memory was not affected: freezing on return to the training context without the tone did not differ between groups.", "evidence": "Fig. 5c; Table 2", "species": "mouse", "n": "29 mice in three groups", "stats": "ANOVA F= 1.25, p = 0.302", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/purple-2017-scirep.md"}
{"paper_id": "purple-2017-scirep", "finding_no": 3, "doi": "10.1038/srep46247", "year": 2017, "journal": "Scientific Reports", "finding": "Initial learning was comparable across groups, as reactivity to the first foot shock during training did not differ.", "evidence": "Fig. 4a", "species": "mouse", "n": "29 mice in three groups", "stats": "ANOVA, F= 2.14, p = 0.14", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/purple-2017-scirep.md"}
{"paper_id": "purple-2017-scirep", "finding_no": 4, "doi": "10.1038/srep46247", "year": 2017, "journal": "Scientific Reports", "finding": "Cueing changed sleep architecture only slightly: total NREM, REM and wake time did not differ significantly, but REM-cued mice showed more REM-to-NREM transitions than controls.", "evidence": "Table 1; Fig. 2", "species": "mouse", "n": "NREM-cued n=10, REM-cued n=10, control n=9", "stats": "t-tests with post-hoc Bonferroni correction", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/purple-2017-scirep.md"}
{"paper_id": "purple-2017-scirep", "finding_no": 5, "doi": "10.1038/srep46247", "year": 2017, "journal": "Scientific Reports", "finding": "Both cued groups showed reduced EEG power in the slow-wave range, at 3.5 Hz during NREM sleep and at 1.5, 2 and 3 Hz during REM sleep, which the authors suggest reflects some lightening of sleep.", "evidence": "Fig. 3", "species": "mouse", "n": "NREM-cued n=10, REM-cued n=10, control n=9", "stats": "multivariate general linear models with post-hoc Bonferroni correction", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/purple-2017-scirep.md"}
{"paper_id": "fujinaka-2016-molbrain", "finding_no": 1, "doi": "10.1186/s13041-015-0184-0", "year": 2016, "journal": "Molecular Brain", "finding": "Mice tested in contexts A and B 24 h after training froze more in the shock context A than in context B, indicating no generalization.", "evidence": "Fig. 1a-c", "species": "mouse", "n": "n = 15", "stats": "t(14) = 7.5, p < 0.001, paired t-test (day 1)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/fujinaka-2016-molbrain.md"}
{"paper_id": "fujinaka-2016-molbrain", "finding_no": 2, "doi": "10.1186/s13041-015-0184-0", "year": 2016, "journal": "Molecular Brain", "finding": "When contexts were first presented 6 h after training, mice froze similarly in A and B on day 1, and their freezing pattern differed from the 24 h group.", "evidence": "Fig. 1d-f", "species": "mouse", "n": "n = 30", "stats": "group x context interaction F(1,43) = 4.1, p < 0.05; day 1 A vs B t(29) = 2.0, p > 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/fujinaka-2016-molbrain.md"}
{"paper_id": "fujinaka-2016-molbrain", "finding_no": 3, "doi": "10.1186/s13041-015-0184-0", "year": 2016, "journal": "Molecular Brain", "finding": "Exposure to the familiar unconditioned context B alone 3 h after training was enough to produce comparable freezing in A and B the next day.", "evidence": "Fig. 2a-c", "species": "mouse", "n": "n = 12", "stats": "t(11) = 0.70, p > 0.05, paired t-test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/fujinaka-2016-molbrain.md"}
{"paper_id": "fujinaka-2016-molbrain", "finding_no": 4, "doi": "10.1186/s13041-015-0184-0", "year": 2016, "journal": "Molecular Brain", "finding": "Without prior habituation to the contexts, mice still discriminated A from B on day 1, so familiarity was required for generalization.", "evidence": "Additional file 1: Figure S2", "species": "mouse", "n": "n = 10", "stats": "group x context interaction F(1,38) = 7.0, p < 0.05; day 1 A > B t(9) = 3.3, p < 0.01", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/fujinaka-2016-molbrain.md"}
{"paper_id": "fujinaka-2016-molbrain", "finding_no": 5, "doi": "10.1186/s13041-015-0184-0", "year": 2016, "journal": "Molecular Brain", "finding": "Exposure to a novel, highly dissimilar context C 3 h after training did not produce generalization; these mice froze more in A than B on day 1, unlike the familiar-context group.", "evidence": "Fig. 2j-l", "species": "mouse", "n": "n = 10", "stats": "t(9) = 3.4, p < 0.005; group x context interaction F(1,20) = 5.6, p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/fujinaka-2016-molbrain.md"}
{"paper_id": "fujinaka-2016-molbrain", "finding_no": 6, "doi": "10.1186/s13041-015-0184-0", "year": 2016, "journal": "Molecular Brain", "finding": "Discrimination indices were high only in the 24 h group and the novel dissimilar context group; all other groups showed lower indices than the 24 h group.", "evidence": "Additional file 1: Figure S8", "species": "mouse", "n": null, "stats": "main effect of group F(6,96) = 4.0, p < 0.01", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/fujinaka-2016-molbrain.md"}
{"paper_id": "sakaguchi-2015-plos-one", "finding_no": 1, "doi": "10.1371/journal.pone.0130163", "year": 2015, "journal": "PLOS ONE", "finding": "In the double-transgenic mice, transgene mRNA was found across the forebrain and was strong in CA1 pyramidal and subicular neurons but notably weaker in CA3 and the dentate gyrus, restricted to the pyramidal layer in CA1.", "evidence": "Fig 1A-1F; Fig 2", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md"}
{"paper_id": "sakaguchi-2015-plos-one", "finding_no": 2, "doi": "10.1371/journal.pone.0130163", "year": 2015, "journal": "PLOS ONE", "finding": "Of 41 putative CA1 pyramidal units recorded during 1 min of light delivery, 25 decreased their firing, 8 increased it and 8 showed no apparent change.", "evidence": "Fig 3B and 3C", "species": "mouse", "n": "41 units", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md"}
{"paper_id": "sakaguchi-2015-plos-one", "finding_no": 3, "doi": "10.1371/journal.pone.0130163", "year": 2015, "journal": "PLOS ONE", "finding": "In the suppressed units, the drop in firing was time-locked to the light, with an average suppression of 89%.", "evidence": "Fig 3D", "species": "mouse", "n": "25 units", "stats": "F(2,48) = 11, p < 0.0001, repeated measures one-way ANOVA", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md"}
{"paper_id": "sakaguchi-2015-plos-one", "finding_no": 4, "doi": "10.1371/journal.pone.0130163", "year": 2015, "journal": "PLOS ONE", "finding": "Units whose firing rose during light showed an average increase of 120%, which the authors suggest may reflect homeostatic changes or loss of interneuron-mediated inhibition.", "evidence": "Fig 3E", "species": "mouse", "n": "8 units", "stats": "F(2,14) = 3.9, p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md"}
{"paper_id": "sakaguchi-2015-plos-one", "finding_no": 5, "doi": "10.1371/journal.pone.0130163", "year": 2015, "journal": "PLOS ONE", "finding": "Mice given bilateral green light to CA1 during the first contextual fear test froze little, but froze more in the second test without light, suggesting a transient recall deficit rather than memory loss.", "evidence": "Fig 4D", "species": "mouse", "n": "n = 10", "stats": "paired t-test, t(9) = 3.5, p < 0.005", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md"}
{"paper_id": "arruda-carvalho-2014-jneurosci", "finding_no": 1, "doi": "10.1523/JNEUROSCI.2336-13.2014", "year": 2014, "journal": "The Journal of Neuroscience", "finding": "Tamoxifen tagging labeled about 141,337 cells in the olfactory bulb of adult mice, roughly 10% of all olfactory granule cells.", "evidence": "Fig. 2h", "species": "mouse", "n": null, "stats": "141,337 ± 4106 LacZ+ cells", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2014-jneurosci.md"}
{"paper_id": "arruda-carvalho-2014-jneurosci", "finding_no": 2, "doi": "10.1523/JNEUROSCI.2336-13.2014", "year": 2014, "journal": "The Journal of Neuroscience", "finding": "After posttraining ablation, adult-tagged 2×Tg mice no longer preferred the reinforced odor, whereas controls retained the preference.", "evidence": "Fig. 4b–d", "species": "mouse", "n": "CTR (n = 16) and 2×Tg (n = 26) mice", "stats": "genotype × test time interaction F(1,40) = 4.55, p < 0.05; 2×Tg post-DT t(25) = 0.97, p = 0.34", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2014-jneurosci.md"}
{"paper_id": "arruda-carvalho-2014-jneurosci", "finding_no": 3, "doi": "10.1523/JNEUROSCI.2336-13.2014", "year": 2014, "journal": "The Journal of Neuroscience", "finding": "When training occurred only 10 d after tagging, posttraining ablation did not impair the memory, implicating cells older than 10 d at training.", "evidence": "Fig. 4e–h", "species": "mouse", "n": "CTR (n = 8) and 2×Tg (n = 10) mice", "stats": "genotype × test time ANOVA, no main effects or interactions, all F values <1", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2014-jneurosci.md"}
{"paper_id": "arruda-carvalho-2014-jneurosci", "finding_no": 4, "doi": "10.1523/JNEUROSCI.2336-13.2014", "year": 2014, "journal": "The Journal of Neuroscience", "finding": "Ablating the same cell population before training did not prevent formation or 28 d persistence of the odor–reward memory in adult mice.", "evidence": "Fig. 5", "species": "mouse", "n": "CTR (n = 10) and 2×Tg (n = 11) mice", "stats": "2×Tg: t(10) = 3.66, p < 0.005 at 1 d; t(10) = 3.28, p < 0.01 at 28 d", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2014-jneurosci.md"}
{"paper_id": "arruda-carvalho-2014-jneurosci", "finding_no": 5, "doi": "10.1523/JNEUROSCI.2336-13.2014", "year": 2014, "journal": "The Journal of Neuroscience", "finding": "Posttraining ablation of juvenile-generated granule cells similarly reduced odor preference, although the genotype × test time interaction only approached significance.", "evidence": "Fig. 6", "species": "mouse", "n": "CTR (n = 18) and 2×Tg (n = 19) mice", "stats": "2×Tg pre vs post t(18) = 4.19, p < 0.001; post-DT 2×Tg vs CTR t(35) = 2.70, p = 0.011; interaction F(1,35) = 3.02, p = 0.09", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2014-jneurosci.md"}
{"paper_id": "arruda-carvalho-2014-jneurosci", "finding_no": 6, "doi": "10.1523/JNEUROSCI.2336-13.2014", "year": 2014, "journal": "The Journal of Neuroscience", "finding": "Ablation started about 4 weeks after training did not affect memory expression, suggesting a time-limited role for adult-born granule cells.", "evidence": "Fig. 8", "species": "mouse", "n": "CTR (n = 16) and 2×Tg (n = 8) mice", "stats": "2×Tg post-DT t(7) = 3.28, p < 0.05; genotype × test time ANOVA all F values < 1", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2014-jneurosci.md"}
{"paper_id": "sakaguchi-2012-molbrain", "finding_no": 1, "doi": "10.1186/1756-6606-5-32", "year": 2012, "journal": "Molecular Brain", "finding": "The authors argue that tagging neurons via immediate-early-gene promoters such as c-fos lets researchers reactivate a learning-activated ensemble, and that light reactivation of such dentate gyrus neurons was reported sufficient to retrieve a fear memory.", "evidence": "Figures 3-4", "species": "mouse; rat", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-molbrain.md"}
{"paper_id": "sakaguchi-2012-molbrain", "finding_no": 2, "doi": "10.1186/1756-6606-5-32", "year": 2012, "journal": "Molecular Brain", "finding": "The review highlights that neurons with raised CREB levels are preferentially recruited into a fear memory trace, and that removing or silencing these neurons disrupted the memory, suggesting increased excitability as one underlying mechanism.", "evidence": "Figure 5", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-molbrain.md"}
{"paper_id": "sakaguchi-2012-molbrain", "finding_no": 3, "doi": "10.1186/1756-6606-5-32", "year": 2012, "journal": "Molecular Brain", "finding": "The authors emphasize that optogenetic inhibition, with its finer timing, showed the hippocampus remains engaged in fear memory retrieval even at remote time points, contrasting with conventional lesion results.", "evidence": "Optogenetics section", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-molbrain.md"}
{"paper_id": "sakaguchi-2012-molbrain", "finding_no": 4, "doi": "10.1186/1756-6606-5-32", "year": 2012, "journal": "Molecular Brain", "finding": "At the synaptic level, the review discusses evidence that potentiated synapses may cluster on dendrites and share signaling molecules with neighbors, supporting a clustered rather than dispersed plasticity model.", "evidence": "Figure 6", "species": "rodent", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-molbrain.md"}
{"paper_id": "hirota-2012-stem-cells", "finding_no": 1, "doi": "10.1002/stem.1137", "year": 2012, "journal": "STEM CELLS", "finding": "Interfering with Dishevelled2 or Van Gogh like-2 in subventricular zone precursors changed the distribution of newborn neurons in the olfactory bulb.", "evidence": "abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2012-stem-cells.md"}
{"paper_id": "hirota-2012-stem-cells", "finding_no": 2, "doi": "10.1002/stem.1137", "year": 2012, "journal": "STEM CELLS", "finding": "The same manipulations also altered dendrite formation of the newborn olfactory bulb neurons.", "evidence": "abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2012-stem-cells.md"}
{"paper_id": "hirota-2012-stem-cells", "finding_no": 3, "doi": "10.1002/stem.1137", "year": 2012, "journal": "STEM CELLS", "finding": "The authors conclude that planar cell polarity signaling likely contributes to regulating the maturation of new olfactory bulb neurons.", "evidence": "abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2012-stem-cells.md"}
{"paper_id": "sakaguchi-2012-dev-neurobiol", "finding_no": 1, "doi": "10.1002/dneu.22023", "year": 2012, "journal": "Developmental Neurobiology", "finding": "In the adult mouse dentate gyrus, most Galectin-1-positive cells are type 2a progenitors and 7% match type 1 cells; knockout on a C57BL/6J background increased proliferation of these early progenitors, which the review takes to suggest Galectin-1 down-regulates them.", "evidence": "Section 'Function of Galectin-1 in Adult DG Neurogenesis' (Imaizumi et al., 2011)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-dev-neurobiol.md"}
{"paper_id": "sakaguchi-2012-dev-neurobiol", "finding_no": 2, "doi": "10.1002/dneu.22023", "year": 2012, "journal": "Developmental Neurobiology", "finding": "In the adult subventricular zone, infusion of oxidation-resistant recombinant Galectin-1 (but not the oxidized form) promoted neural stem cell proliferation, while a neutralizing antibody or knockout reduced stem cell numbers; the review argues Galectin-1 acts through its lectin activity, upstream of beta1 integrin signaling.", "evidence": "Sections 'Function of Galectin-1 in Adult SVZ NSCs' and 'Mechanisms of Galectin-1 Function in Adult SVZ NSCs' (Sakaguchi et al., 2006, 2010)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-dev-neurobiol.md"}
{"paper_id": "sakaguchi-2012-dev-neurobiol", "finding_no": 3, "doi": "10.1002/dneu.22023", "year": 2012, "journal": "Developmental Neurobiology", "finding": "Galectin-1 knockout mice on a C57BL/6J background, which have more adult-born dentate neurons, were impaired in contextual fear conditioning and the Morris water maze; the review notes it is unresolved whether this reflects increased neurogenesis or loss of Galectin-1 in other hippocampal cells.", "evidence": "Section 'Function of Galectin-1 in Hippocampal-Dependent Memory' (Sakaguchi et al., 2011)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-dev-neurobiol.md"}
{"paper_id": "sakaguchi-2012-dev-neurobiol", "finding_no": 4, "doi": "10.1002/dneu.22023", "year": 2012, "journal": "Developmental Neurobiology", "finding": "In animal injury models, infusion of oxidation-resistant Galectin-1 after brain ischemia improved motor and sensory function, and transplanted human neural stem cells engineered to express Galectin-1 gave better recovery than unmodified cells after ischemia and in a marmoset spinal cord injury model.", "evidence": "Sections 'Galectin-1 in Brain Ischemia' and 'Galectin-1 in Spinal Cord Injury' (Ishibashi et al., 2007; Yamane et al., 2010, 2011)", "species": "rodent; common marmoset", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2012-dev-neurobiol.md"}
{"paper_id": "arruda-carvalho-2011-jneurosci", "finding_no": 1, "doi": "10.1523/JNEUROSCI.3432-11.2011", "year": 2011, "journal": "The Journal of Neuroscience", "finding": "The tagged population was mostly mature neurons and made up about 6% of all dentate gyrus neurons, and diphtheria toxin virtually abolished the receptor-expressing cells.", "evidence": "Fig. 3, Fig. 4a, Table 2", "species": "mouse", "n": "DT n = 4, PBS n = 6 (ablation check)", "stats": "100% reduction; t(8) = 1.93, p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2011-jneurosci.md"}
{"paper_id": "arruda-carvalho-2011-jneurosci", "finding_no": 2, "doi": "10.1523/JNEUROSCI.3432-11.2011", "year": 2011, "journal": "The Journal of Neuroscience", "finding": "Ablating adult-generated neurons after contextual fear training abolished discrimination between the trained context and a similar context, while tone fear memory was spared.", "evidence": "Fig. 7d-g", "species": "mouse", "n": "CTR n = 12, 2xTg n = 11", "stats": "Genotype x Context interaction F(1,21) = 17.66, p < 0.005; discrimination t(21) = 4.27, p < 0.001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2011-jneurosci.md"}
{"paper_id": "arruda-carvalho-2011-jneurosci", "finding_no": 3, "doi": "10.1523/JNEUROSCI.3432-11.2011", "year": 2011, "journal": "The Journal of Neuroscience", "finding": "Ablating the same population before training did not prevent formation of a new contextual fear memory, and both groups still discriminated the contexts.", "evidence": "Fig. 8", "species": "mouse", "n": "CTR n = 13, 2xTg n = 14", "stats": "effect of Context only, F(1,25) = 9.41, p < 0.005", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2011-jneurosci.md"}
{"paper_id": "arruda-carvalho-2011-jneurosci", "finding_no": 4, "doi": "10.1523/JNEUROSCI.3432-11.2011", "year": 2011, "journal": "The Journal of Neuroscience", "finding": "Posttraining ablation made mice search less selectively for the hidden platform in the water maze probe test, whereas pretraining ablation did not impair new spatial learning.", "evidence": "Fig. 9a-c, 9g-i", "species": "mouse", "n": "CTR n = 12, 2xTg n = 12 (posttraining)", "stats": "Genotype x Zone interaction F(1,22) = 5.67, p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2011-jneurosci.md"}
{"paper_id": "arruda-carvalho-2011-jneurosci", "finding_no": 5, "doi": "10.1523/JNEUROSCI.3432-11.2011", "year": 2011, "journal": "The Journal of Neuroscience", "finding": "Ablation delivered one month after water maze training also reduced time in the target zone, suggesting an enduring role of these neurons; the interaction term itself was only a trend.", "evidence": "Fig. 9j-l", "species": "mouse", "n": "CTR n = 14, 2xTg n = 12", "stats": "Genotype x Zone interaction F(1,24) = 3.53, p = 0.07; planned comparisons p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2011-jneurosci.md"}
{"paper_id": "arruda-carvalho-2011-jneurosci", "finding_no": 6, "doi": "10.1523/JNEUROSCI.3432-11.2011", "year": 2011, "journal": "The Journal of Neuroscience", "finding": "Posttraining ablation abolished discrimination between reinforced and nonreinforced visual cues in the water maze, a milder deficit than hippocampal lesions, consistent with degradation rather than erasure of the memory.", "evidence": "Fig. 10e-h", "species": "mouse", "n": "CTR n = 12, 2xTg n = 11", "stats": "CTR paired t(11) = 3.02, p < 0.01; 2xTg p > 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/arruda-carvalho-2011-jneurosci.md"}
{"paper_id": "yamane-2011-molbrain", "finding_no": 1, "doi": "10.1186/1756-6606-4-35", "year": 2011, "journal": "Molecular Brain", "finding": "After ischemia, Gal1 was induced in and around the lesion, mostly in GFAP-positive astrocytes (many of them BrdU-positive and proliferating), with no more than 1% of Gal1-expressing cells being NeuN-positive neurons, and expression declined at later time points.", "evidence": "Fig. 1; Additional file 3, Fig. S3", "species": "Mongolian gerbil", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2011-molbrain.md"}
{"paper_id": "yamane-2011-molbrain", "finding_no": 2, "doi": "10.1186/1756-6606-4-35", "year": 2011, "journal": "Molecular Brain", "finding": "Thirty days after transplantation, ischemic volume was significantly smaller in the hGal1-hNSPCs group than in the hNSPCs group (t(9) = 3, p = 0.01).", "evidence": "Fig. 2C, D; Additional file 5, Fig. S5", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "planned comparison t(9) = 3, p = 0.01", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2011-molbrain.md"}
{"paper_id": "yamane-2011-molbrain", "finding_no": 3, "doi": "10.1186/1756-6606-4-35", "year": 2011, "journal": "Molecular Brain", "finding": "On the elevated body swing test of motor asymmetry, the hGal1-hNSPCs group recovered better than the hNSPCs group, with a day-30 planned comparison of t(11) = 4, p = 0.002.", "evidence": "Fig. 3C", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "time x group ANOVA interaction F(4, 44) = 6.4, p = 0.05; planned comparison on day 30 t(11) = 4, p = 0.002", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2011-molbrain.md"}
{"paper_id": "yamane-2011-molbrain", "finding_no": 4, "doi": "10.1186/1756-6606-4-35", "year": 2011, "journal": "Molecular Brain", "finding": "On the bilateral asymmetry (sensory) test both groups recovered, with only a trend favoring the hGal1-hNSPCs group on day 30 (t(11) = 2, p = 0.06).", "evidence": "Fig. 3B", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "interaction F(4, 44) = 1.3, p = 0.3; planned comparison t(11) = 2, p = 0.06", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2011-molbrain.md"}
{"paper_id": "yamane-2011-molbrain", "finding_no": 5, "doi": "10.1186/1756-6606-4-35", "year": 2011, "journal": "Molecular Brain", "finding": "On the T-maze spontaneous alternation test of cognition, both groups recovered over time with no group difference (interaction F(4, 44) = 0.52, p = 0.7).", "evidence": "Fig. 3A", "species": "Mongolian gerbil", "n": "hGal1-hNSPCs n = 7, hNSPCs n = 6", "stats": "interaction F(4, 44) = 0.52, p = 0.7", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2011-molbrain.md"}
{"paper_id": "sakaguchi-2011-mol-brain", "finding_no": 1, "doi": "10.1186/1756-6606-4-33", "year": 2011, "journal": "Molecular Brain", "finding": "In the adult hippocampus, galectin-1 in the dentate granule cell layer was confined to GFAP-positive cells (astrocytes or putative neural stem cells), whereas in CA3 it was found in NeuN-positive mature neurons.", "evidence": "Fig. 1", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2011-mol-brain.md"}
{"paper_id": "sakaguchi-2011-mol-brain", "finding_no": 2, "doi": "10.1186/1756-6606-4-33", "year": 2011, "journal": "Molecular Brain", "finding": "After a single tone-shock pairing, galectin-1 null mice froze less than wild-type littermates when returned to the training context 24 hours later.", "evidence": "Fig. 2C", "species": "mouse", "n": "WT n = 11, gal-1-/- n = 15", "stats": "t(24) = 1.75, P < 0.05, unpaired t-test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2011-mol-brain.md"}
{"paper_id": "sakaguchi-2011-mol-brain", "finding_no": 3, "doi": "10.1186/1756-6606-4-33", "year": 2011, "journal": "Molecular Brain", "finding": "Tone-cued fear memory tested in an altered context did not differ between genotypes, suggesting the deficit is specific to hippocampus-dependent memory.", "evidence": "Fig. 2D", "species": "mouse", "n": "WT n = 11, gal-1-/- n = 15", "stats": "no main effect of genotype, F(1, 21) = 0.16, P = 0.69", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2011-mol-brain.md"}
{"paper_id": "sakaguchi-2011-mol-brain", "finding_no": 4, "doi": "10.1186/1756-6606-4-33", "year": 2011, "journal": "Molecular Brain", "finding": "With more intensive training (3 tone-shock pairings), galectin-1 null mice froze as much as wild-type mice in the context test, so the contextual deficit could be overcome.", "evidence": "Fig. 3", "species": "mouse", "n": "WT n = 10, gal-1-/- n = 12", "stats": "t(20) = 0.49, P = 0.32, unpaired t-test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2011-mol-brain.md"}
{"paper_id": "sakaguchi-2011-mol-brain", "finding_no": 5, "doi": "10.1186/1756-6606-4-33", "year": 2011, "journal": "Molecular Brain", "finding": "In the hidden-platform water maze, mutants tended to have longer escape latencies and, although both genotypes searched the target zone selectively in the probe test, wild-type mice were more selective, indicating a less precise spatial memory in mutants.", "evidence": "Fig. 4", "species": "mouse", "n": "WT n = 14, gal-1-/- n = 15", "stats": "latency genotype effect F(1, 27) = 4.05, P = 0.054; probe target-zone time WT > mutant, t(27) = 2.06, P < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2011-mol-brain.md"}
{"paper_id": "sakaguchi-2011-mol-brain", "finding_no": 6, "doi": "10.1186/1756-6606-4-33", "year": 2011, "journal": "Molecular Brain", "finding": "Control tests did not reveal non-memory deficits: visible-platform performance, startle and prepulse inhibition were normal, and although mutants were more active in the open field, their spatial distribution of activity was similar to wild-type mice.", "evidence": "Fig. 5", "species": "mouse", "n": "open field WT n = 12, gal-1-/- n = 17; startle/PPI WT n = 13, gal-1-/- n = 8; visible maze n = 3 per genotype", "stats": "open field activity genotype effect P < 0.01; PPI no main effect of genotype F(1, 19) = 0.02, P = 0.90", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2011-mol-brain.md"}
{"paper_id": "leslie-2011-transl-psychiatry", "finding_no": 1, "doi": "10.1038/tp.2011.38", "year": 2011, "journal": "Translational Psychiatry", "finding": "Maternal separation did not change the number of proliferating cells in the adult dentate gyrus 1 day after BrdU injection.", "evidence": "Fig. 1a", "species": "mouse", "n": "separated n = 15, control n = 15", "stats": "no significant group effect", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/leslie-2011-transl-psychiatry.md"}
{"paper_id": "leslie-2011-transl-psychiatry", "finding_no": 2, "doi": "10.1038/tp.2011.38", "year": 2011, "journal": "Translational Psychiatry", "finding": "Four weeks after BrdU labelling, maternally separated mice had fewer surviving new cells.", "evidence": "Fig. 1b", "species": "mouse", "n": "separated n = 16, control n = 18", "stats": "F1,32 = 7.88, P = 0.008", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/leslie-2011-transl-psychiatry.md"}
{"paper_id": "leslie-2011-transl-psychiatry", "finding_no": 3, "doi": "10.1038/tp.2011.38", "year": 2011, "journal": "Translational Psychiatry", "finding": "A smaller proportion of surviving cells expressed the mature neuronal marker NeuN in maternally separated mice.", "evidence": "Fig. 1c", "species": "mouse", "n": "separated n = 16, control n = 18", "stats": "F1,32 = 6.90, P = 0.013", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/leslie-2011-transl-psychiatry.md"}
{"paper_id": "leslie-2011-transl-psychiatry", "finding_no": 4, "doi": "10.1038/tp.2011.38", "year": 2011, "journal": "Translational Psychiatry", "finding": "Adult-born granule neurons in maternally separated mice had fewer dendritic intersections and shorter total dendritic length 4 weeks after retroviral labelling.", "evidence": "Fig. 2c-d", "species": "mouse", "n": "separated n = 5, control n = 5 mice", "stats": "intersections F1,8 = 9.09, P = 0.017; length F1,8 = 7.50, P = 0.026", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/leslie-2011-transl-psychiatry.md"}
{"paper_id": "leslie-2011-transl-psychiatry", "finding_no": 5, "doi": "10.1038/tp.2011.38", "year": 2011, "journal": "Translational Psychiatry", "finding": "Spine density was unchanged (5.54±0.60 vs 5.93±0.24 spines per 10 µm), but total spines per neuron were reduced, which the authors suggest means fewer synapses with incoming fibres.", "evidence": "Fig. 2e", "species": "mouse", "n": "separated n = 5, control n = 5 mice", "stats": "total spines F1,8 = 5.59, P = 0.046", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/leslie-2011-transl-psychiatry.md"}
{"paper_id": "imaizumi-2011-mol-brain", "finding_no": 1, "doi": "10.1186/1756-6606-4-7", "year": 2011, "journal": "Molecular Brain", "finding": "Galectin-1 was found in a subset of type 1 cells: 33.1% of DG cells with type-1 morphology expressed it, and 7.3% of Galectin-1+ cells had type-1 morphology, with most others resembling type 2 cells.", "evidence": "Fig. 2", "species": "mouse", "n": "n = 5 mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/imaizumi-2011-mol-brain.md"}
{"paper_id": "imaizumi-2011-mol-brain", "finding_no": 2, "doi": "10.1186/1756-6606-4-7", "year": 2011, "journal": "Molecular Brain", "finding": "Galectin-1 did not co-label with DCX+, Calretinin+, SGZ NeuN+ or PE-CAM1+ endothelial cells, placing its expression in early-stage progenitors.", "evidence": "Fig. 2 G-J", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/imaizumi-2011-mol-brain.md"}
{"paper_id": "imaizumi-2011-mol-brain", "finding_no": 3, "doi": "10.1186/1756-6606-4-7", "year": 2011, "journal": "Molecular Brain", "finding": "After short-term BrdU labeling, knockout mice had more BrdU+ cells, more FABP7+/BrdU+ cells and more BrdU+ type 1 cells in the SGZ than controls.", "evidence": "Fig. 3 A-F", "species": "mouse", "n": "n = 5 mice each", "stats": "P < 0.05 (BrdU+, FABP7+/BrdU+); P < 0.01 (BrdU+ type 1 cells, main text)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/imaizumi-2011-mol-brain.md"}
{"paper_id": "imaizumi-2011-mol-brain", "finding_no": 4, "doi": "10.1186/1756-6606-4-7", "year": 2011, "journal": "Molecular Brain", "finding": "After 7 days of BrdU in drinking water and a 10-day chase, knockout mice had more BrdU+, DCX+/BrdU+ and NeuN+/BrdU+ cells, indicating increased production of new neurons.", "evidence": "Fig. 3 G-J", "species": "mouse", "n": "n > 5 mice each", "stats": "P < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/imaizumi-2011-mol-brain.md"}
{"paper_id": "imaizumi-2011-mol-brain", "finding_no": 5, "doi": "10.1186/1756-6606-4-7", "year": 2011, "journal": "Molecular Brain", "finding": "Total Ki67+ cells did not differ, but proliferating FABP7+/DCX- (type 1/2a) cells increased in knockouts while proliferating FABP7+/DCX+ (type 2b) cells did not differ.", "evidence": "Fig. 4 A-C", "species": "mouse", "n": "n > 5 mice each", "stats": "P = 0.25 (total Ki67+); P < 0.05 (type 1/2a); P = 0.08 (type 2b)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/imaizumi-2011-mol-brain.md"}
{"paper_id": "imaizumi-2011-mol-brain", "finding_no": 6, "doi": "10.1186/1756-6606-4-7", "year": 2011, "journal": "Molecular Brain", "finding": "Apoptosis measured by cleaved-Caspase-3 was comparable between genotypes, both overall and in FABP7/DCX/cv-Casp3 triple-positive cells, so the increase is attributed to proliferation rather than reduced cell death.", "evidence": "Fig. 4 D-F", "species": "mouse", "n": "n > 22 mice each", "stats": "P = 0.18 (total); P = 0.44 (triple-positive)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/imaizumi-2011-mol-brain.md"}
{"paper_id": "ikeda-2010-stem-cells", "finding_no": 1, "doi": "10.1002/stem.516", "year": 2010, "journal": "Stem Cells", "finding": "Diversin is expressed in neuroblasts and mature neurons in the subventricular zone and hippocampus of neonatal and adult mice.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ikeda-2010-stem-cells.md"}
{"paper_id": "ikeda-2010-stem-cells", "finding_no": 2, "doi": "10.1002/stem.516", "year": 2010, "journal": "Stem Cells", "finding": "Overexpressing Diversin increased neuroblast proliferation and the number of neuroblasts that reached the olfactory bulb.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ikeda-2010-stem-cells.md"}
{"paper_id": "ikeda-2010-stem-cells", "finding_no": 3, "doi": "10.1002/stem.516", "year": 2010, "journal": "Stem Cells", "finding": "Knocking down Diversin reduced neuroblast proliferation.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ikeda-2010-stem-cells.md"}
{"paper_id": "hirota-2010-development", "finding_no": 1, "doi": "10.1242/dev.050120", "year": 2010, "journal": "Development", "finding": "The share of ependymal cells whose ciliated-area centroid lay in the anterior quadrant rose during postnatal development, being significantly higher at P9 than at P7, indicating that translational polarity is acquired between P5 and P9.", "evidence": "Fig. 1E-H", "species": "mouse", "n": "P5, 105 cells; P7, 91 cells; P9, 109 cells; adult, 137 cells; from three mice in each case", "stats": "P=0.0486 (P9 vs P7)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2010-development.md"}
{"paper_id": "hirota-2010-development", "finding_no": 2, "doi": "10.1242/dev.050120", "year": 2010, "journal": "Development", "finding": "Time-lapse imaging of Centrin 2-GFP basal bodies over 10 hours showed dispersed basal bodies in a single cell migrating simultaneously to accumulate at the anterior apical membrane.", "evidence": "Fig. 2; Movie 1", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2010-development.md"}
{"paper_id": "hirota-2010-development", "finding_no": 3, "doi": "10.1242/dev.050120", "year": 2010, "journal": "Development", "finding": "Cells with anteriorly localized basal bodies showed anteriorly directed coordinated ciliary beating, longer cilia and higher beat frequency than cells with dispersed basal bodies, so translational and rotational polarity arise at around the same stage.", "evidence": "Fig. 3G-I", "species": "mouse", "n": "dispersed, 43 cells; localized, 28 cells; both from four mice", "stats": "P<0.001 for beating direction, cilia length and beat frequency", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2010-development.md"}
{"paper_id": "hirota-2010-development", "finding_no": 4, "doi": "10.1242/dev.050120", "year": 2010, "journal": "Development", "finding": "Dominant-negative Dvl2 disturbed ciliary orientation in vivo (circular SD 55.1±9.3° vs 21.3±5.6° in controls) but did not change the number of cells with anteriorly located basal bodies, suggesting PCP signaling regulates rotational but not translational polarity.", "evidence": "Fig. 4K-R", "species": "mouse", "n": "CSD: four control cells from two mice, five Dvl2ΔPDZ cells from three mice; translational: control, 21 cells from three mice; Dvl2ΔPDZ, 29 cells from five mice", "stats": "anterior-quadrant comparison P=0.8782", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2010-development.md"}
{"paper_id": "hirota-2010-development", "finding_no": 5, "doi": "10.1242/dev.050120", "year": 2010, "journal": "Development", "finding": "Intraventricular blebbistatin or ML-9 reduced anterior basal body localization in a dose-dependent manner, whereas the ROCK inhibitor Y27632 did not; blebbistatin left ciliary beat frequency unchanged (19.1±0.87 Hz vs 19.0±1.05 Hz).", "evidence": "Fig. 6A-I; Movies 10, 11", "species": "mouse", "n": "control for blebbistatin and ML-9, 172 cells from five mice; 22 and 25 cilia from three mice each for beat frequency", "stats": "one-way ANOVA with Tukey's test; beat frequency P=0.9254", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2010-development.md"}
{"paper_id": "hirota-2010-development", "finding_no": 6, "doi": "10.1242/dev.050120", "year": 2010, "journal": "Development", "finding": "Electroporation-based knockdown of Myh9, Myh10 and Myh14 dispersed basal bodies and reduced the number of cells with anterior basal bodies without preventing basal body docking or cilia extension, suggesting cell-autonomous regulation by non-muscle myosin II.", "evidence": "Fig. 6J-P", "species": "mouse", "n": "control, 29 cells from five mice; NMII knockdown, 32 cells from three mice", "stats": "P=0.0316", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/hirota-2010-development.md"}
{"paper_id": "stone-2011-hippocampus", "finding_no": 1, "doi": "10.1002/hipo.20845", "year": 2010, "journal": "Hippocampus", "finding": "Fos was validated as an activity marker in dentate granule cells: spatial memory recall induced Fos in about 1% of granule cells, above home cage levels and well below PTZ seizure levels, and Fos and Arc were almost completely colocalized.", "evidence": "Fig. 1A-D", "species": "mouse", "n": "n = 3 per group (home cage, recall, PTZ)", "stats": "F2,6 = 43.3, P < 0.001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/stone-2011-hippocampus.md"}
{"paper_id": "stone-2011-hippocampus", "finding_no": 2, "doi": "10.1002/hipo.20845", "year": 2010, "journal": "Hippocampus", "finding": "The probability that adult-born cells expressed Fos after water maze testing rose with the delay between BrdU labeling and training, with the largest change between 1 and 5 weeks and no difference across the 5-10 week groups.", "evidence": "Fig. 2F", "species": "mouse", "n": "n = 8 (1 week), n = 18 each (5, 7.5 and 10 weeks)", "stats": "F3,58 = 3.39, P < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/stone-2011-hippocampus.md"}
{"paper_id": "stone-2011-hippocampus", "finding_no": 3, "doi": "10.1002/hipo.20845", "year": 2010, "journal": "Hippocampus", "finding": "Cells labeled one week before training and tested four weeks later (so the same age at testing as the five-week group) showed lower Fos overlap than the five-week group and no different from the one-week group, indicating week-old cells are too immature to be incorporated.", "evidence": "Fig. 2A, 2F", "species": "mouse", "n": "n = 10", "stats": "P < 0.05 vs five-week group; P = 0.39 vs one-week group", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/stone-2011-hippocampus.md"}
{"paper_id": "stone-2011-hippocampus", "finding_no": 4, "doi": "10.1002/hipo.20845", "year": 2010, "journal": "Hippocampus", "finding": "When cells born at E18, P7 or P60 were all 7.5 weeks old at training, the likelihood of Fos expression after the water maze probe test did not differ between groups, although labeled cell numbers did.", "evidence": "Fig. 3C-E", "species": "mouse", "n": "n = 6 (E18), n = 6 (P7), n = 18 (P60)", "stats": "Fos in labeled cells: F2,27 = 0.20, P = 0.82; labeled cell number: F2,27 = 181.0, P < 0.001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/stone-2011-hippocampus.md"}
{"paper_id": "stone-2011-hippocampus", "finding_no": 5, "doi": "10.1002/hipo.20845", "year": 2010, "journal": "Hippocampus", "finding": "In a within-animal comparison using CldU and IdU, embryonically or postnatally generated cells and adult-generated cells in the same mice were equally likely to express Fos after water maze testing, arguing against preferential recruitment of adult-born neurons.", "evidence": "Fig. 5E, 5H", "species": "mouse", "n": "n = 12 (E18/P60 group), n = 14 (P7/P60 group)", "stats": "paired t-test E18/P60: t11 = 0.39, P = 0.70; P7/P60: t13 = 1.03, P = 0.32", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/stone-2011-hippocampus.md"}
{"paper_id": "stone-2011-hippocampus", "finding_no": 6, "doi": "10.1002/hipo.20845", "year": 2010, "journal": "Hippocampus", "finding": "In contextual fear conditioning, adult-born cells trained six weeks after labeling were more likely to express Fos than those trained after one week, while postnatally (P7) and adult (P60) generated cells were recruited at similar rates.", "evidence": "Fig. 6E, Fig. 7F", "species": "mouse", "n": "n = 10 (one week), n = 18 (six weeks); n = 6 (P7), n = 27 (P60)", "stats": "six vs one week: t26 = 2.12, P < 0.05; P7 vs P60: t31 = 0.55, P = 0.58", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/stone-2011-hippocampus.md"}
{"paper_id": "sakaguchi-2010-j-neurochem", "finding_no": 1, "doi": "10.1111/j.1471-4159.2010.06712.x", "year": 2010, "journal": "Journal of Neurochemistry", "finding": "Beta1 Integrin was isolated from adult SEZ tissue as a Galectin-1-binding molecule, appearing at around 130 kDa in the lactose-eluted fraction but not in the mannose wash fraction.", "evidence": "Fig. 1", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2010-j-neurochem.md"}
{"paper_id": "sakaguchi-2010-j-neurochem", "finding_no": 2, "doi": "10.1111/j.1471-4159.2010.06712.x", "year": 2010, "journal": "Journal of Neurochemistry", "finding": "Galectin-1 bound SEZ cells including astrocytes, neuroblasts and ependymal cells, and this binding was reduced by excess lactose, indicating dependence on its carbohydrate-binding activity.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2010-j-neurochem.md"}
{"paper_id": "sakaguchi-2010-j-neurochem", "finding_no": 3, "doi": "10.1111/j.1471-4159.2010.06712.x", "year": 2010, "journal": "Journal of Neurochemistry", "finding": "Most beta1 Integrin-expressing cells in the adult SEZ showed affinity for Galectin-1.", "evidence": "Fig. 3c", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2010-j-neurochem.md"}
{"paper_id": "sakaguchi-2010-j-neurochem", "finding_no": 4, "doi": "10.1111/j.1471-4159.2010.06712.x", "year": 2010, "journal": "Journal of Neurochemistry", "finding": "Infusing a beta1 Integrin-neutralizing antibody into the lateral ventricle reduced BrdU long-labeled cells and blocked the increase in these cells produced by Galectin-1 infusion.", "evidence": "Fig. 3d-f", "species": "mouse", "n": null, "stats": "ANOVA, p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2010-j-neurochem.md"}
{"paper_id": "sakaguchi-2010-j-neurochem", "finding_no": 5, "doi": "10.1111/j.1471-4159.2010.06712.x", "year": 2010, "journal": "Journal of Neurochemistry", "finding": "In culture, Galectin-1 increased progenitor adhesion, a Galectin-1-neutralizing antibody inhibited adhesion to Laminin-coated dishes, and a beta1 Integrin-neutralizing antibody dose-dependently inhibited adhesion in a way that added Galectin-1 could not overcome.", "evidence": "Fig. 4", "species": "mouse", "n": null, "stats": "ANOVA, p < 0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2010-j-neurochem.md"}
{"paper_id": "akers-2010-jneurosci", "finding_no": 1, "doi": "10.1523/JNEUROSCI.0443-10.2010", "year": 2010, "journal": "The Journal of Neuroscience", "finding": "In the reviewed study, antimitotic AraC infusion cut doublecortin-expressing olfactory bulb cells by 75% and lowered the peak gamma oscillation frequency from about 45 Hz to about 39 Hz.", "evidence": "Main text (discussion of Breton-Provencher et al., 2009)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2010-jneurosci.md"}
{"paper_id": "akers-2010-jneurosci", "finding_no": 2, "doi": "10.1523/JNEUROSCI.0443-10.2010", "year": 2010, "journal": "The Journal of Neuroscience", "finding": "Mice with reduced adult neurogenesis discriminated odors normally but failed to habituate when the interval between odor presentations was lengthened from 30 to 60 min, while still retaining an odor-food association for at least 7 d.", "evidence": "Main text", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2010-jneurosci.md"}
{"paper_id": "akers-2010-jneurosci", "finding_no": 3, "doi": "10.1523/JNEUROSCI.0443-10.2010", "year": 2010, "journal": "The Journal of Neuroscience", "finding": "The authors argue that conflicting reports may reflect odor similarity, developmental versus adult-only disruption of neurogenesis, and the maturational stage of the affected neurons, with discrimination deficits appearing mainly after genetic manipulations acting throughout development.", "evidence": "Main text; Table 1", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/akers-2010-jneurosci.md"}
{"paper_id": "yamane-2010-j-neurosci-res", "finding_no": 1, "doi": "10.1002/jnr.22322", "year": 2010, "journal": "Journal of Neuroscience Research", "finding": "Lentiviral transduction did not change NS/PC proliferation (doubling time approximately 150 hr) or the proportions of neurons and astrocytes in vitro, while neurons from galectin-1-expressing NS/PCs had neurites about 1.5 times as long as those from reporter-only NS/PCs.", "evidence": "Fig. 1C-G", "species": "human (cultured fetal NS/PCs)", "n": null, "stats": "P < 0.05 for neurite length", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2010-j-neurosci-res.md"}
{"paper_id": "yamane-2010-j-neurosci-res", "finding_no": 2, "doi": "10.1002/jnr.22322", "year": 2010, "journal": "Journal of Neuroscience Research", "finding": "Grafted human NS/PCs survived mainly around the lesion cavity, with some found up to 10 mm rostral and caudal, differentiated into oligodendrocytes, neurons and astrocytes, and showed no tumor formation 13 weeks after transplantation.", "evidence": "Fig. 4", "species": "common marmoset", "n": "Gal-NS/PCs or GFP-NS/PCs, n = 7", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2010-j-neurosci-res.md"}
{"paper_id": "yamane-2010-j-neurosci-res", "finding_no": 3, "doi": "10.1002/jnr.22322", "year": 2010, "journal": "Journal of Neuroscience Research", "finding": "Contusion reduced myelin and corticospinal fiber areas at the epicenter to approximately 20% of laminectomy values; both graft groups had more myelin, corticospinal and serotonergic fiber area than vehicle controls, with the galectin-1 group highest.", "evidence": "Fig. 3", "species": "common marmoset", "n": null, "stats": "one-way ANOVA with Tukey-Kramer test; *P < 0.05, **P < 0.01", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2010-j-neurosci-res.md"}
{"paper_id": "yamane-2010-j-neurosci-res", "finding_no": 4, "doi": "10.1002/jnr.22322", "year": 2010, "journal": "Journal of Neuroscience Research", "finding": "Spontaneous motor activity at 13 weeks after injury had returned to approximately 80%, 50% and 40% of preinjury levels in the galectin-1 graft, reporter-only graft and vehicle groups, with significant group differences 4–7 weeks after injury.", "evidence": "Fig. 5A", "species": "common marmoset", "n": null, "stats": "one-way ANOVA with multiple comparisons", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2010-j-neurosci-res.md"}
{"paper_id": "yamane-2010-j-neurosci-res", "finding_no": 5, "doi": "10.1002/jnr.22322", "year": 2010, "journal": "Journal of Neuroscience Research", "finding": "Grip strength fell to approximately 5% of preinjury values and plateaued at approximately 70%, 60% and 40% in the three groups, differing significantly from 9 weeks after injury onward.", "evidence": "Fig. 5B", "species": "common marmoset", "n": null, "stats": "significant group differences 9 weeks after injury and thereafter", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2010-j-neurosci-res.md"}
{"paper_id": "yamane-2010-j-neurosci-res", "finding_no": 6, "doi": "10.1002/jnr.22322", "year": 2010, "journal": "Journal of Neuroscience Research", "finding": "On the treadmill, maximum walking speed reached approximately 90% of preinjury velocity in the galectin-1 graft group versus a plateau of approximately 50% in the reporter-only group, differing significantly at 10 weeks and later; vehicle animals were excluded because some could not walk on the treadmill.", "evidence": "Fig. 5C", "species": "common marmoset", "n": null, "stats": "significant differences between graft groups at 10 weeks after SCI and thereafter", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamane-2010-j-neurosci-res.md"}
{"paper_id": "frankland-2008-molbrain", "finding_no": 1, "doi": "10.1186/1756-6606-1-5", "year": 2008, "journal": "Molecular Brain", "finding": "Of 7 mouse lines carrying mutations related to calcineurin signaling that were screened, alpha-CaMKII heterozygous mice showed the most striking behavioral phenotype.", "evidence": "Editorial text (discussing Miyakawa et al., Molecular Brain 2008, 1:6)", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/frankland-2008-molbrain.md"}
{"paper_id": "frankland-2008-molbrain", "finding_no": 2, "doi": "10.1186/1756-6606-1-5", "year": 2008, "journal": "Molecular Brain", "finding": "The alpha-CaMKII heterozygous mice showed severe working memory deficits, unusual aggression, reduced anxiety and strongly disrupted daily activity patterns, a cluster of schizophrenia-related endophenotypes.", "evidence": "Editorial text", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/frankland-2008-molbrain.md"}
{"paper_id": "frankland-2008-molbrain", "finding_no": 3, "doi": "10.1186/1756-6606-1-5", "year": 2008, "journal": "Molecular Brain", "finding": "In the dentate gyrus of these mice, proliferation was increased by about 50% but new neurons did not appear to mature normally, leading to the proposal of an immature dentate gyrus.", "evidence": "Editorial text", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/frankland-2008-molbrain.md"}
{"paper_id": "frankland-2008-molbrain", "finding_no": 4, "doi": "10.1186/1756-6606-1-5", "year": 2008, "journal": "Molecular Brain", "finding": "The authors suggest that abnormal adult hippocampal neurogenesis may contribute to psychiatric disorders such as schizophrenia, so genes regulating neuronal development or adult neurogenesis deserve special attention as susceptibility candidates.", "evidence": "Editorial text", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/frankland-2008-molbrain.md"}
{"paper_id": "ishibashi-2007-expneurol", "finding_no": 1, "doi": "10.1016/j.expneurol.2007.06.024", "year": 2007, "journal": "Experimental Neurology", "finding": "Galectin-1-positive cells were confined to the subventricular zone in sham animals; after ischemia they increased in the ipsilateral striatum, peaking at 2 weeks and still elevated at 16 weeks, and in the ipsilateral subventricular zone, peaking at 2 weeks before returning to control levels, a pattern similar to BrdU-labeled proliferating cells there.", "evidence": "Figs. 2F–N, 3A–C", "species": "gerbil", "n": "group 1: n = 25 ischemic and n = 5 sham-operated gerbils across time points (per-time-point n not stated)", "stats": "P < 0.01 and P < 0.001 versus sham-operated controls, one-way ANOVA with Bonferroni post hoc test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2007-expneurol.md"}
{"paper_id": "ishibashi-2007-expneurol", "finding_no": 2, "doi": "10.1016/j.expneurol.2007.06.024", "year": 2007, "journal": "Experimental Neurology", "finding": "Most galectin-1-positive cells co-expressed GFAP, both in the subventricular zone and in the zone of selective neuronal death around the striatal infarct, where they had the enlarged morphology of reactive astrocytes.", "evidence": "Fig. 4A–B", "species": "gerbil", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2007-expneurol.md"}
{"paper_id": "ishibashi-2007-expneurol", "finding_no": 3, "doi": "10.1016/j.expneurol.2007.06.024", "year": 2007, "journal": "Experimental Neurology", "finding": "Infusion of the carbohydrate-binding galectin-1 variant increased BrdU-labeled cells in the ipsilateral subventricular zone and the numbers of new neuroblasts and neurons in the subventricular zone, striatum and olfactory bulb, whereas the neutralizing antibody decreased them and the oxidized form, which cannot bind carbohydrate, did not change BrdU-labeled cell numbers relative to IgG controls.", "evidence": "Figs. 5A–L, 6A–D", "species": "gerbil", "n": "group 2: n = 40 ischemic gerbils split across four infusion conditions and two survival times (per-group n for histology not stated)", "stats": "P < 0.05 and P < 0.01 versus rabbit IgG controls, one-way ANOVA with Bonferroni post hoc test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2007-expneurol.md"}
{"paper_id": "ishibashi-2007-expneurol", "finding_no": 4, "doi": "10.1016/j.expneurol.2007.06.024", "year": 2007, "journal": "Experimental Neurology", "finding": "Total infarct volume at 14 and 28 days did not differ significantly among the four infusion groups (for example 24.5% ± 4.3% and 22.5% ± 2.5% with the carbohydrate-binding variant versus 25.1% ± 5.3% and 22.2% ± 8.7% with control IgG), so the authors saw no neuroprotective action.", "evidence": "Results, infarct volume section", "species": "gerbil", "n": null, "stats": "not significant", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2007-expneurol.md"}
{"paper_id": "ishibashi-2007-expneurol", "finding_no": 5, "doi": "10.1016/j.expneurol.2007.06.024", "year": 2007, "journal": "Experimental Neurology", "finding": "Over 28 days of behavioral testing, animals given the carbohydrate-binding variant showed less biased body swing from 3 weeks and faster removal of an adhesive stimulus from the affected forelimb at 4 weeks than IgG controls, the antibody group was slower, and T-maze spontaneous alternation did not differ among groups.", "evidence": "Fig. 7A–D", "species": "gerbil", "n": "n = 5 per group", "stats": "repeated-measures ANOVA: significant group factor for body swing (P < 0.01), removal time (P < 0.01) and body weight (P < 0.001), not for spontaneous alternation; Bonferroni post hoc versus rabbit IgG", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2007-expneurol.md"}
{"paper_id": "adachi-2007-stem-cells", "finding_no": 1, "doi": "10.1634/stemcells.2007-0177", "year": 2007, "journal": "Stem Cells", "finding": "A beta-catenin-dependent destabilized GFP reporter was active in progenitor cells of the adult SVZ.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/adachi-2007-stem-cells.md"}
{"paper_id": "adachi-2007-stem-cells", "finding_no": 2, "doi": "10.1634/stemcells.2007-0177", "year": 2007, "journal": "Stem Cells", "finding": "Retroviral expression of stabilized beta-catenin increased proliferation of Mash1-positive cells and blocked their differentiation into neuroblasts, whereas Dkk1 expression reduced their proliferation.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/adachi-2007-stem-cells.md"}
{"paper_id": "adachi-2007-stem-cells", "finding_no": 3, "doi": "10.1634/stemcells.2007-0177", "year": 2007, "journal": "Stem Cells", "finding": "A GSK3 beta inhibitor promoted Mash1-positive cell proliferation and increased new neurons in the olfactory bulb 14 days later.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/adachi-2007-stem-cells.md"}
{"paper_id": "okano-2007-j-neurochem", "finding_no": 1, "doi": "10.1111/j.1471-4159.2007.04674.x", "year": 2007, "journal": "Journal of Neurochemistry", "finding": "The review presents Galectin-1, expressed in slowly dividing GFAP-positive astrocytes of the adult subventricular zone, as an endogenous factor that promotes neural stem cell proliferation through its carbohydrate-binding activity.", "evidence": "Fig. 2; Sakaguchi et al. 2006", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/okano-2007-j-neurochem.md"}
{"paper_id": "okano-2007-j-neurochem", "finding_no": 2, "doi": "10.1111/j.1471-4159.2007.04674.x", "year": 2007, "journal": "Journal of Neurochemistry", "finding": "After stroke, subventricular zone astrocytes are argued to be the main source of neuroblasts that migrate in chains along blood vessels into the injured striatum, yet only a tiny fraction of lost neurons is replaced, so survival and maturation of new neurons need to be improved.", "evidence": "Yamashita et al. 2006; Arvidsson et al. 2002", "species": "rodents", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/okano-2007-j-neurochem.md"}
{"paper_id": "okano-2007-j-neurochem", "finding_no": 3, "doi": "10.1111/j.1471-4159.2007.04674.x", "year": 2007, "journal": "Journal of Neurochemistry", "finding": "Endogenous repair is described as extending beyond neurogenesis: reactive astrocytes, through Stat3-dependent migration, help contract the lesion during the subacute phase of spinal cord injury, and oligodendrocyte progenitors and blood vessels also take part.", "evidence": "Okada et al. 2006; Menn et al. 2006; Palmer et al. 2000", "species": "rodents", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/okano-2007-j-neurochem.md"}
{"paper_id": "okano-2007-j-neurochem", "finding_no": 4, "doi": "10.1111/j.1471-4159.2007.04674.x", "year": 2007, "journal": "Journal of Neurochemistry", "finding": "The authors caution that boosting adult neurogenesis is not uniformly beneficial, as excess neurogenesis can be harmful, for example in epilepsy models, and the in vivo function of new neurons remains incompletely understood.", "evidence": "Conclusion and perspectives", "species": null, "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/okano-2007-j-neurochem.md"}
{"paper_id": "sakaguchi-2007-cell-mol-life-sci", "finding_no": 1, "doi": "10.1007/s00018-007-6476-5", "year": 2007, "journal": "Cellular and Molecular Life Sciences", "finding": "In the adult mouse subventricular zone, galectin-1 was found in GFAP-expressing cells and in a subset of long-term BrdU-retaining cells, which the authors take as evidence that adult neural stem cells express galectin-1.", "evidence": "Fig. 1F-H", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2007-cell-mol-life-sci.md"}
{"paper_id": "sakaguchi-2007-cell-mol-life-sci", "finding_no": 2, "doi": "10.1007/s00018-007-6476-5", "year": 2007, "journal": "Cellular and Molecular Life Sciences", "finding": "Intraventricular infusion of recombinant galectin-1 increased neurosphere formation and long-term BrdU-retaining cells in the subventricular zone without changing apoptotic cell numbers, whereas galectin-1 knockout mice had fewer neural stem cells, supporting a role in promoting stem cell proliferation.", "evidence": "Fig. 2B-D", "species": "mouse", "n": null, "stats": "p<0.05", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2007-cell-mol-life-sci.md"}
{"paper_id": "sakaguchi-2007-cell-mol-life-sci", "finding_no": 3, "doi": "10.1007/s00018-007-6476-5", "year": 2007, "journal": "Cellular and Molecular Life Sciences", "finding": "A cysteine-to-serine mutant that keeps its carbohydrate-binding activity under oxidative conditions increased label-retaining cells, whereas oxidized galectin-1 did not, suggesting that carbohydrate binding is required for the proliferative effect.", "evidence": "text, citing ref. 18", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2007-cell-mol-life-sci.md"}
{"paper_id": "sakaguchi-2007-cell-mol-life-sci", "finding_no": 4, "doi": "10.1007/s00018-007-6476-5", "year": 2007, "journal": "Cellular and Molecular Life Sciences", "finding": "The authors propose that fucosylation of lactosamine to form the LeX antigen on neural stem cells, which lowers galectin-1 affinity, may regulate galectin-1 binding and thus stem cell proliferation, a hypothesis they leave for future studies.", "evidence": "section 'Expression and function of glycan in NSCs'", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2007-cell-mol-life-sci.md"}
{"paper_id": "yamashita-2006-jneurosci", "finding_no": 1, "doi": "10.1523/JNEUROSCI.0149-06.2006", "year": 2006, "journal": "Journal of Neuroscience", "finding": "Stroke transiently increased Dcx-positive neuroblasts in the striatum, peaking above preoperative levels at 18 and 21 days, and 98% of them co-expressed the neuronal marker betaIII-tubulin.", "evidence": "Fig. 1C, 1E", "species": "mouse", "n": "n = 3 at each time point; n = 1108 cells", "stats": "p < 0.01 versus preoperative value (ANOVA, Bonferroni's correction)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamashita-2006-jneurosci.md"}
{"paper_id": "yamashita-2006-jneurosci", "finding_no": 2, "doi": "10.1523/JNEUROSCI.0149-06.2006", "year": 2006, "journal": "Journal of Neuroscience", "finding": "Striatal cells labeled with a Cre adenovirus before stroke did not give rise to neuroblasts: none of the 695 GFP-labeled striatal cells expressed Dcx 18 days after occlusion.", "evidence": "Fig. 2J-K", "species": "mouse", "n": "n = 695 cells in three MCAO mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamashita-2006-jneurosci.md"}
{"paper_id": "yamashita-2006-jneurosci", "finding_no": 3, "doi": "10.1523/JNEUROSCI.0149-06.2006", "year": 2006, "journal": "Journal of Neuroscience", "finding": "After stroke, SVZ cells labeled by intraventricular Cre plasmid appeared in the ipsilateral striatum (82.0 ± 12.1 cells per hemisphere), and 37% of them were Dcx-positive migrating neuroblasts, whereas none reached the striatum in non-ischemic controls.", "evidence": "Fig. 3D-G", "species": "mouse", "n": "control n = 4, MCAO n = 6; n = 45 cells", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamashita-2006-jneurosci.md"}
{"paper_id": "yamashita-2006-jneurosci", "finding_no": 4, "doi": "10.1523/JNEUROSCI.0149-06.2006", "year": 2006, "journal": "Journal of Neuroscience", "finding": "GFAP-expressing SVZ cells infected via the RCAS-TVA system produced Dcx-positive neuroblasts in the peri-infarct striatum in all 3 brains (5 of 13 GFP cells), while striatal infection yielded none (0 of 498).", "evidence": "Fig. 4F-J", "species": "mouse", "n": "n = 3 brains (SVZ); n = 498 cells (striatum)", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamashita-2006-jneurosci.md"}
{"paper_id": "yamashita-2006-jneurosci", "finding_no": 5, "doi": "10.1523/JNEUROSCI.0149-06.2006", "year": 2006, "journal": "Journal of Neuroscience", "finding": "Neuroblast chains in the injured striatum wrapped around blood vessels (all 12 chains) and were mostly oriented mediolaterally toward the lesion (83%), suggesting vessel-associated directed migration.", "evidence": "Fig. 5A-F", "species": "mouse", "n": "n = 12 chains; n = 6 spherical clusters", "stats": "p < 0.05 (χ2 test)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamashita-2006-jneurosci.md"}
{"paper_id": "yamashita-2006-jneurosci", "finding_no": 6, "doi": "10.1523/JNEUROSCI.0149-06.2006", "year": 2006, "journal": "Journal of Neuroscience", "finding": "By 90 days after stroke, 29% of SVZ-derived GFP cells in the striatum expressed NeuN, and labeled axons contained presynaptic vesicles and formed synapses with neighboring cells.", "evidence": "Fig. 6C-F", "species": "mouse", "n": "n = 13 cells (figure legend)", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/yamashita-2006-jneurosci.md"}
{"paper_id": "sakaguchi-2006-pnas", "finding_no": 1, "doi": "10.1073/pnas.0508793103", "year": 2006, "journal": "Proceedings of the National Academy of Sciences", "finding": "OP9 conditioned medium enabled clonal neurosphere formation from 12.4% of single cells, and recombinant Galectin-1 enhanced neurosphere formation in culture.", "evidence": "Fig. 1A-B", "species": "mouse", "n": "n 400 cells (OP9CM)", "stats": "P 0.01, ANOVA (Galectin-1)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2006-pnas.md"}
{"paper_id": "sakaguchi-2006-pnas", "finding_no": 2, "doi": "10.1073/pnas.0508793103", "year": 2006, "journal": "Proceedings of the National Academy of Sciences", "finding": "In the adult subventricular zone, 32.7% of cells were Galectin-1-positive and 71.4% of GFAP-positive cells also expressed Galectin-1, including slowly dividing label-retaining cells.", "evidence": "Fig. 2", "species": "mouse", "n": "n 336 cells from three mice", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2006-pnas.md"}
{"paper_id": "sakaguchi-2006-pnas", "finding_no": 3, "doi": "10.1073/pnas.0508793103", "year": 2006, "journal": "Proceedings of the National Academy of Sciences", "finding": "Intraventricular Galectin-1 infusion increased short-term BrdU-labeled proliferating cells in the subventricular zone without changing apoptosis, and raised proliferating type B and C cell counts by 1.7- and 1.4-fold relative to saline.", "evidence": "Fig. 3D-E; Table 1", "species": "mouse", "n": "n 3 mice each", "stats": "P 0.01; P 0.05, Mann-Whitney U test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2006-pnas.md"}
{"paper_id": "sakaguchi-2006-pnas", "finding_no": 4, "doi": "10.1073/pnas.0508793103", "year": 2006, "journal": "Proceedings of the National Academy of Sciences", "finding": "Galectin-1 infusion increased slowly dividing BrdU-retaining cells at day 17 and day 37, and the reduced carbohydrate-binding form (CS-Galectin-1) did so while the oxidized form did not.", "evidence": "Fig. 3F-H; Fig. 11", "species": "mouse", "n": "n 3 each; n 5 mice each (CS-Galectin-1)", "stats": "day 17, P 0.01; day 37, P 0.001", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2006-pnas.md"}
{"paper_id": "sakaguchi-2006-pnas", "finding_no": 5, "doi": "10.1073/pnas.0508793103", "year": 2006, "journal": "Proceedings of the National Academy of Sciences", "finding": "galectin-1-null mice had fewer PCNA-positive cycling cells, fewer Mash1-positive type C cells, and fewer slowly dividing cells in the subventricular zone than wild-type littermates, and a neutralizing antibody reproduced the loss of slowly dividing cells.", "evidence": "Fig. 4; Fig. 12", "species": "mouse", "n": "n 3 each", "stats": "P 0.01 (PCNA); P 0.05 (Mash1); P 0.01 (slowly dividing)", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2006-pnas.md"}
{"paper_id": "sakaguchi-2005-inflamm-regen", "finding_no": 1, "doi": "10.2492/jsir.25.50", "year": 2005, "journal": "Inflammation and Regeneration", "finding": "The retrovirus transduced neurosphere cells at a low multiplicity of infection, so most GFP-expressing cells were expected to carry only a single copy of the transgene.", "evidence": "Fig. 1; Results", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2005-inflamm-regen.md"}
{"paper_id": "sakaguchi-2005-inflamm-regen", "finding_no": 2, "doi": "10.2492/jsir.25.50", "year": 2005, "journal": "Inflammation and Regeneration", "finding": "FACS staining for CD15 and GFP resolved the dissociated neurosphere cells into double-positive and other fractions, identifying a small CD15+/GFP+ population.", "evidence": "Fig. 2", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2005-inflamm-regen.md"}
{"paper_id": "sakaguchi-2005-inflamm-regen", "finding_no": 3, "doi": "10.2492/jsir.25.50", "year": 2005, "journal": "Inflammation and Regeneration", "finding": "Cells sorted on both GFP and CD15 formed significantly more secondary neurospheres than cells sorted on GFP alone, indicating enrichment for NSCs.", "evidence": "Fig. 3", "species": "mouse", "n": "n > 200, 10 cells/well", "stats": "p < 0.01, one-tail unpaired-T test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2005-inflamm-regen.md"}
{"paper_id": "sakaguchi-2005-inflamm-regen", "finding_no": 4, "doi": "10.2492/jsir.25.50", "year": 2005, "journal": "Inflammation and Regeneration", "finding": "Neurospheres derived from single sorted CD15+ cells remained multipotent, differentiating into neurons, astrocytes and oligodendrocytes.", "evidence": "Fig. 4", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2005-inflamm-regen.md"}
{"paper_id": "sakaguchi-2005-inflamm-regen", "finding_no": 5, "doi": "10.2492/jsir.25.50", "year": 2005, "journal": "Inflammation and Regeneration", "finding": "Transgene expression from the vector persisted long-term without silencing, remaining detectable months after infection.", "evidence": "Results", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2005-inflamm-regen.md"}
{"paper_id": "ishibashi-2004-j-neurosci-res", "finding_no": 1, "doi": "10.1002/jnr.20246", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "Four weeks after grafting, total infarct volume was 22.5% in NSPC-grafted gerbils versus 31.3% in medium-grafted and 29.9% in ischemia-only animals, a significant reduction relative to medium grafts.", "evidence": "Fig. 1A", "species": "Mongolian gerbil", "n": "n = 7 per ischemic group", "stats": "P < 0.05 vs medium-grafted; one-way ANOVA with Bonferroni post-hoc test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2004-j-neurosci-res.md"}
{"paper_id": "ishibashi-2004-j-neurosci-res", "finding_no": 2, "doi": "10.1002/jnr.20246", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "About 8% of the grafted human cells survived, mostly in the injected hemisphere (27,900 cells) with fewer contralaterally (9,300 cells), and they migrated into areas of selective neuronal death rather than the ischemic cavity.", "evidence": "Fig. 1B-C", "species": "Mongolian gerbil", "n": "n = 7 NSPC-grafted animals", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2004-j-neurosci-res.md"}
{"paper_id": "ishibashi-2004-j-neurosci-res", "finding_no": 3, "doi": "10.1002/jnr.20246", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "Surviving donor cells expressed neuronal (NeuN, 36.2%), astrocytic (GFAP, 46.3%) or oligodendrocytic (CNPase, 3.8%) markers, while 10.3% carried none of these and none co-labeled with endothelial or microglial markers.", "evidence": "Fig. 2A-E", "species": "Mongolian gerbil", "n": "n = 7 NSPC-grafted animals", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2004-j-neurosci-res.md"}
{"paper_id": "ishibashi-2004-j-neurosci-res", "finding_no": 4, "doi": "10.1002/jnr.20246", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "Retroviral GFP labeling (transduction efficiency 97.9%) followed by electron microscopy showed donor-derived structures forming synapse-like contacts with host neurons in areas of selective neuronal death.", "evidence": "Fig. 3A-F", "species": "Mongolian gerbil", "n": "n = 4 animals grafted with GFP-labeled cells", "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2004-j-neurosci-res.md"}
{"paper_id": "ishibashi-2004-j-neurosci-res", "finding_no": 5, "doi": "10.1002/jnr.20246", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "Grafted gerbils showed less contralateral body-swing bias than medium-grafted animals, approaching the 50% baseline by 4 weeks, and removed adhesive stimuli from the affected forelimb faster from 2 weeks after grafting.", "evidence": "Fig. 4A-B", "species": "Mongolian gerbil", "n": "n = 7 per ischemic group; n = 8 sham", "stats": "P < 0.001 (body swing) and P < 0.01 (removal time) vs medium-grafted; repeated-measures ANOVA with Bonferroni test", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2004-j-neurosci-res.md"}
{"paper_id": "ishibashi-2004-j-neurosci-res", "finding_no": 6, "doi": "10.1002/jnr.20246", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "Focal ischemia lowered T-maze spontaneous alternation to 23.5% from 75.2% in sham animals, and NSPC-grafted animals recovered this spatial cognitive measure relative to medium-grafted animals.", "evidence": "Fig. 4C-F", "species": "Mongolian gerbil", "n": "n = 7 per ischemic group; n = 8 sham", "stats": "P < 0.01 vs medium-grafted", "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ishibashi-2004-j-neurosci-res.md"}
{"paper_id": "mikami-2004-j-neurosci-res", "finding_no": 1, "doi": "10.1002/jnr.20086", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "Of the immune cell types tested in vitro, dendritic cells most strongly promoted proliferation and survival of neural stem/progenitor cells.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/mikami-2004-j-neurosci-res.md"}
{"paper_id": "mikami-2004-j-neurosci-res", "finding_no": 2, "doi": "10.1002/jnr.20086", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "In injured adult mice receiving dendritic cells, endogenous progenitors in the spinal cord were activated and produced new neurons through cell division.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/mikami-2004-j-neurosci-res.md"}
{"paper_id": "mikami-2004-j-neurosci-res", "finding_no": 3, "doi": "10.1002/jnr.20086", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "The implanted dendritic cells produced neurotrophin-3 and activated resident microglia in the injured cord.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/mikami-2004-j-neurosci-res.md"}
{"paper_id": "mikami-2004-j-neurosci-res", "finding_no": 4, "doi": "10.1002/jnr.20086", "year": 2004, "journal": "Journal of Neuroscience Research", "finding": "Locomotor function recovered significantly more in dendritic cell-implanted mice than in control mice; the authors suggest a trophic mechanism.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/mikami-2004-j-neurosci-res.md"}
{"paper_id": "ohba-2004-neurosci-lett", "finding_no": 1, "doi": "10.1016/j.neulet.2004.01.026", "year": 2004, "journal": "Neuroscience Letters", "finding": "Sox21 is expressed in immature neural stem/progenitor cells of the embryonic ventricular zone but not the cortical plate, and is confined to the subventricular zone in the adult mouse brain.", "evidence": "Abstract", "species": "mouse", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2004-neurosci-lett.md"}
{"paper_id": "ohba-2004-neurosci-lett", "finding_no": 2, "doi": "10.1016/j.neulet.2004.01.026", "year": 2004, "journal": "Neuroscience Letters", "finding": "Endogenous Sox21 is present in undifferentiated PC12 cells but disappears during NGF-induced neuronal differentiation, and overexpressing Sox21 substantially represses NGF-induced neurite outgrowth.", "evidence": "Abstract", "species": "rat (PC12 cell line)", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2004-neurosci-lett.md"}
{"paper_id": "ohba-2004-neurosci-lett", "finding_no": 3, "doi": "10.1016/j.neulet.2004.01.026", "year": 2004, "journal": "Neuroscience Letters", "finding": "Y-box binding protein 1 (YB-1) binds Sox21 and partially restores the NGF-induced neurite outgrowth that Sox21 inhibits, suggesting Sox21 acts as a repressor of neuronal differentiation.", "evidence": "Abstract", "species": "rat (PC12 cell line)", "n": null, "stats": null, "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ohba-2004-neurosci-lett.md"}