{
  "generated": "2026-10-16",
  "schema_version": "1.0",
  "themes": [
    {
      "key": "adult_neurogenesis_memory",
      "title": "Adult-born neurons and memory",
      "pillars": [
        "pillar1",
        "pillar3"
      ],
      "description": "Adult-born neurons in the hippocampal dentate gyrus (and olfactory bulb) and their roles in forming, consolidating and clearing memories, studied with ablation, optogenetic silencing and in vivo calcium imaging in mice.",
      "papers": [
        "sakaguchi-2006-pnas",
        "okano-2007-j-neurochem",
        "frankland-2008-molbrain",
        "akers-2010-jneurosci",
        "sakaguchi-2010-j-neurochem",
        "stone-2011-hippocampus",
        "ikeda-2010-stem-cells",
        "imaizumi-2011-mol-brain",
        "leslie-2011-transl-psychiatry",
        "arruda-carvalho-2011-jneurosci",
        "sakaguchi-2012-dev-neurobiol",
        "hirota-2012-stem-cells",
        "arruda-carvalho-2014-jneurosci",
        "akers-2018-stemcells",
        "koyanagi-2019-neural-regen-res",
        "kumar-2020-neuron",
        "vergara-2020-front-cell-neurosci",
        "carrier-ruiz-2021-star-protocols",
        "vergara-2021-ijms",
        "ohba-2021-neural-regen-res",
        "chavan-2025-neurobiol-learn-mem",
        "srinivasan-2025-nat-commun"
      ]
    },
    {
      "key": "rem_sleep_memory",
      "title": "REM sleep and memory consolidation",
      "pillars": [
        "pillar1"
      ],
      "description": "How REM sleep contributes to memory consolidation, including the reactivation of small neuronal ensembles during REM sleep and its timing relative to the theta rhythm.",
      "papers": [
        "purple-2017-scirep",
        "akers-2018-stemcells",
        "koyanagi-2019-neural-regen-res",
        "maezono-2020-eneuro",
        "kumar-2020-neuron",
        "vergara-2020-front-cell-neurosci",
        "koyanagi-2021-molbrain",
        "carrier-ruiz-2021-star-protocols",
        "tezuka-2021-scirep",
        "ohba-2021-neural-regen-res",
        "chavan-2025-neurobiol-learn-mem",
        "srinivasan-2025-nat-commun",
        "nagai-2026-jove"
      ]
    },
    {
      "key": "fear_memory_ptsd",
      "title": "Fear memory and the biology of PTSD",
      "pillars": [
        "pillar2"
      ],
      "description": "Rodent studies of contextual and cued fear memory — formation, generalization, extinction and reconsolidation — as a basis for understanding trauma-related memory in PTSD.",
      "papers": [
        "sakaguchi-2011-mol-brain",
        "arruda-carvalho-2011-jneurosci",
        "sakaguchi-2012-molbrain",
        "sakaguchi-2015-plos-one",
        "fujinaka-2016-molbrain",
        "purple-2017-scirep",
        "kumar-2020-neuron",
        "koyanagi-2021-molbrain",
        "vergara-2021-ijms",
        "yu-2021-bbrc",
        "ohba-2021-neural-regen-res",
        "sakaguchi-2022-jpn-j-trauma-stress",
        "kawakami-2024-bbrc",
        "li-2024-natcommun",
        "chavan-2025-neurobiol-learn-mem",
        "srinivasan-2025-nat-commun",
        "nagai-2026-jove",
        "ino-2026-medrxiv"
      ]
    },
    {
      "key": "sound_exposure_during_sleep",
      "title": "Sound during sleep (including Sound Exposure during Sleep, SES)",
      "pillars": [
        "pillar2"
      ],
      "description": "Delivery of sounds during sleep to influence memory processing, from rodent experiments with conditioned auditory cues during NREM sleep to Sound Exposure during Sleep (SES) in people with PTSD. Human SES work is exploratory and is not an established treatment.",
      "papers": [
        "sakaguchi-2022-jpn-j-trauma-stress",
        "ino-2026-medrxiv"
      ]
    },
    {
      "key": "sleep_staging_closed_loop_tools",
      "title": "Automatic sleep staging and closed-loop tools",
      "pillars": [
        "pillar1"
      ],
      "description": "Software and devices that classify sleep stages automatically and in real time from EEG/EMG, and that trigger stage-specific interventions (closed loop) during sleep.",
      "papers": [
        "tezuka-2021-scirep",
        "koyanagi-2023-neurosci-res",
        "koyama-2024-fuzzieee",
        "chen-2025-embc",
        "nagai-2026-jove"
      ]
    },
    {
      "key": "imaging_tools",
      "title": "Miniature microscopes and calcium-imaging analysis",
      "pillars": [
        "pillar1"
      ],
      "description": "Head-mounted miniature fluorescence microscopes and analysis software for recording and tracking the activity of the same neurons across sessions in freely moving animals.",
      "papers": [
        "sakaguchi-2005-inflamm-regen",
        "srinivasan-2019-bbrc",
        "kumar-2020-neuron",
        "carrier-ruiz-2021-star-protocols",
        "vergara-2021-ijms",
        "taniguchi-2021-embc",
        "vergara-2023-biorxiv",
        "he-2024-embc",
        "li-2024-natcommun",
        "wang-2024-biorxiv",
        "vergara-2025-natcommun"
      ]
    },
    {
      "key": "sleep_circuits",
      "title": "Neural circuits of sleep",
      "pillars": [
        "pillar1"
      ],
      "description": "Neural circuits in the brainstem and hippocampus that generate or regulate sleep states and sleep-related network activity.",
      "papers": [
        "kashiwagi-2024-cell",
        "arai-2025-jneurosci"
      ]
    },
    {
      "key": "neural_stem_cells_galectin",
      "title": "Neural stem cells and Galectin-1",
      "pillars": [
        "pillar3"
      ],
      "description": "Biology of adult neural stem and progenitor cells, including the identification of Galectin-1 as a factor that promotes their proliferation and the signaling pathways that regulate them.",
      "papers": [
        "ohba-2004-neurosci-lett",
        "sakaguchi-2005-inflamm-regen",
        "okano-2006-tissue-stem-cells",
        "sakaguchi-2006-pnas",
        "sakaguchi-2007-cell-mol-life-sci",
        "okano-2007-j-neurochem",
        "adachi-2007-stem-cells",
        "ishibashi-2007-expneurol",
        "yamane-2010-j-neurosci-res",
        "sakaguchi-2010-j-neurochem",
        "imaizumi-2011-mol-brain",
        "sakaguchi-2011-mol-brain",
        "yamane-2011-molbrain",
        "sakaguchi-2012-dev-neurobiol",
        "soares-2021-cells"
      ]
    },
    {
      "key": "neural_regeneration_transplantation",
      "title": "Transplantation and neural regeneration",
      "pillars": [
        "pillar3"
      ],
      "description": "Transplantation of neural stem/progenitor cells and other cells into injured or diseased central nervous system, aimed at regeneration.",
      "papers": [
        "mikami-2004-j-neurosci-res",
        "ishibashi-2004-j-neurosci-res",
        "yamashita-2006-jneurosci",
        "okano-2007-j-neurochem",
        "ishibashi-2007-expneurol",
        "yamane-2010-j-neurosci-res",
        "yamane-2011-molbrain",
        "sakaguchi-2012-dev-neurobiol"
      ]
    },
    {
      "key": "human_sleep_clinical",
      "title": "Human sleep and clinical observation",
      "pillars": [
        "pillar2"
      ],
      "description": "Observational studies of human sleep, including sleep-rhythm signatures in people with PTSD.",
      "papers": [
        "sekiba-2025-medrxiv",
        "ino-2026-medrxiv"
      ]
    },
    {
      "key": "other",
      "title": "Other studies",
      "pillars": [],
      "description": "Other studies by the PI and collaborators that do not fall under the main themes.",
      "papers": [
        "frankland-2008-molbrain",
        "hirota-2010-development",
        "sakaguchi-2012-molbrain",
        "maezono-2020-eneuro",
        "yamauchi-2026-acm-trans-comput-healthc"
      ]
    }
  ]
}