Archive MaleCNS research sources, provenance, bibliography and immutable data inventory

2026-09-29 03:38:32 +08:00
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+# 论文与引用数据
+
+本目录保留可引用书目和官方入口，不擅自再分发受版权约束的论文全文。
+
+- `papers.json`：核心及历史 DOI 去重后的出版元数据、作者、年份、官方链接、获取状态和用途。
+- `papers.bib`：可导入 Zotero/JabRef/LaTeX 的 BibTeX。
+- `papers.md`：可读索引。
+- `crossref/`：Crossref 出版商登记元数据原始 JSON；生成工具逐项记录失败，不虚构信息。
+- `evidence-map.md`：各类证据能说明什么、不能说明什么。
+- `../registry/catalog-20260929/source-citations.json`：历史文件中的 URL/DOI 原位引用链。
+- `../registry/catalog-20260929/external-resources.lock.json`：实际使用的外部数据/代码版本和许可证证据。
+
+论文、preprint、数据版本和代码 commit 分开；正式论文不是当前本地数据每个字段的替代品。
+Crossref 来源为 `https://api.crossref.org/works/{doi}`；论文阅读以对应 DOI/出版社/作者提供全文为准。
+元数据中的年份保留出版商记录，在线发表与卷期年份可能不同。
+自动抽取的 DOI 尾部标点清理有记录；无法解析的项保留 error，不为了“文献齐全”补假引用。
+
+如果后续需要离线全文，应逐篇确认允许归档的版本和许可证，另建 PDF/补充材料索引、下载日期和 SHA-256；本次未宣称已经拥有全部全文。
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+# 文献证据与建模边界
+
+| 主题 | 主来源（DOI） | 用途与局限 |
+|---|---|---|
+| 正式 MaleCNS | 10.1016/j.cell.2026.08.015 | 166,700 neurons / 11,710 types 的论文口径；不覆盖本地 schema 差异 |
+| 官方视觉通路 | 10.1016/j.cell.2026.08.014 | pathway/retinotopy 的作者资源；不能补造缺失坐标 |
+| Shiu-like LIF | 10.1038/s41586-024-07763-9 | 全脑计算模型参考；数据集、transmitter inventory 与本项目不同 |
+| FlyVis | 10.1038/s41586-024-07939-3 | 独立视觉模型/engineering front-end，不共享 MaleCNS body ID |
+| DoOR | 10.1038/srep21841 | 气味响应/受体通道来源，不是 MaleCNS 每个 neuron 的实测响应 |
+| NT 自动识别 | 10.1016/j.cell.2024.03.016 | EM transmitter 分类与局限；不能把其他数据集误分类直接当本地 sign 真值 |
+| DPM physiology | 10.7554/eLife.03868 | 支持研究 GABA/5HT 与慢调制；不自动给所有目标统一 sign |
+| APL 局部抑制 | 10.7554/eLife.56954；10.7554/eLife.74172 | 局部、PN bouton/KC dendrite 等机制；不提供本项目整细胞负电流系数 |
+| MB→AL feedback | 10.1073/pnas.0914912107 | 反馈存在的生理研究；项目具体路径仍须真实边和事件支持 |
+| AL 兴奋回路 | 10.1016/j.cell.2006.12.034；10.1016/j.neuron.2010.08.025 | 不能因模型爆发就随意改变真实 ACh 分类 |
+| 时序塑性 | 10.1016/j.cell.2019.05.040；10.1016/j.cell.2015.11.019 | compartment/timing-dependent，不把 positive reward 等同全体 PAM 增强 |
+| KC→MBON efficacy | 10.7554/eLife.76712；10.1523/ENEURO.0275-23.2023；10.7554/eLife.80445 | presynaptic/postsynaptic 不同位置和条件，不能编造统一 MaleCNS 数值 |
+| 身体物理与 Google DeepMind | 10.1038/s41586-025-09029-4 | FlyBody 是独立运动/物理研究，不证明冻结 MaleCNS 已具备自主关联学习 |
+
+区分四层：原始数据事实、论文观察、工程模型假设、当前实验结论。所有引用都不能替代本项目的 held-out、control、确定性与因果验证。
+更多阶段-specific 文献评估保留在 catalog 的 literature-audit 及原模型源码中，不因本次总览而覆盖旧解释。
@@ -0,0 +1,225 @@
+@article{malecns_ref_001,
+  title = {Excitatory Local Circuits and Their Implications for Olfactory Processing in the Fly Antennal Lobe},
+  author = {Shang, Yuhua and Claridge-Chang, Adam and Sjulson, Lucas and Pypaert, Marc and Miesenböck, Gero},
+  year = {2007},
+  journal = {Cell},
+  doi = {10.1016/j.cell.2006.12.034},
+  url = {https://doi.org/10.1016/j.cell.2006.12.034},
+  volume = {128},
+  pages = {601-612},
+}
+
+@article{malecns_ref_002,
+  title = {Coordinated and Compartmentalized Neuromodulation Shapes Sensory Processing in Drosophila},
+  author = {Cohn, Raphael and Morantte, Ianessa and Ruta, Vanessa},
+  year = {2015},
+  journal = {Cell},
+  doi = {10.1016/j.cell.2015.11.019},
+  url = {https://doi.org/10.1016/j.cell.2015.11.019},
+  volume = {163},
+  pages = {1742-1755},
+}
+
+@article{malecns_ref_003,
+  title = {Distinct Dopamine Receptor Pathways Underlie the Temporal Sensitivity of Associative Learning},
+  author = {Handler, Annie and Graham, Thomas G.W. and Cohn, Raphael and Morantte, Ianessa and Siliciano, Andrew F. and Zeng, Jianzhi and Li, Yulong and Ruta, Vanessa},
+  year = {2019},
+  journal = {Cell},
+  doi = {10.1016/j.cell.2019.05.040},
+  url = {https://doi.org/10.1016/j.cell.2019.05.040},
+  volume = {178},
+  pages = {60-75.e19},
+}
+
+@article{malecns_ref_004,
+  title = {Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster},
+  author = {Eckstein, Nils and Bates, Alexander Shakeel and Champion, Andrew and Du, Michelle and Yin, Yijie and Schlegel, Philipp and Lu, Alicia Kun-Yang and Rymer, Thomson and Finley-May, Samantha and Paterson, Tyler and Parekh, Ruchi and Dorkenwald, Sven and Matsliah, Arie and Yu, Szi-Chieh and McKellar, Claire and Sterling, Amy and Eichler, Katharina and Costa, Marta and Seung, Sebastian and Murthy, Mala and Hartenstein, Volker and Jefferis, Gregory S.X.E. and Funke, Jan},
+  year = {2024},
+  journal = {Cell},
+  doi = {10.1016/j.cell.2024.03.016},
+  url = {https://doi.org/10.1016/j.cell.2024.03.016},
+  volume = {187},
+  pages = {2574-2594.e23},
+}
+
+@article{malecns_ref_005,
+  title = {The organization of visual pathways in the Drosophila brain},
+  author = {Hoeller, Judith and Zhao, Arthur and Nern, Aljoscha and Rogers, Edward M. and Romani, Sandro and Reiser, Michael B.},
+  year = {2026},
+  journal = {Cell},
+  doi = {10.1016/j.cell.2026.08.014},
+  url = {https://doi.org/10.1016/j.cell.2026.08.014},
+  volume = {189},
+  pages = {5552-5570.e10},
+}
+
+@article{malecns_ref_006,
+  title = {Sexual dimorphism in the complete Drosophila male central nervous system connectome},
+  author = {Berg, Stuart and Beckett, Isabella R. and Costa, Marta and Schlegel, Philipp and Januszewski, Michał and Marin, Elizabeth C. and Nern, Aljoscha and Preibisch, Stephan and Qiu, Wei and Takemura, Shin-ya and Fragniere, Alexandra M.C. and Champion, Andrew S. and Adjavon, Diane-Yayra and Cook, Michael and Gkantia, Marina and Hayworth, Kenneth J. and Huang, Gary B. and Katz, William T. and Kämpf, Florian and Lu, Zhiyuan and Ordish, Christopher and Paterson, Tyler and Stürner, Tomke and Trautman, Eric T. and Whittle, Catherine R. and Burnett, Laura E. and Hoeller, Judith and Li, Feng and Loesche, Frank and Morris, Billy J. and Pietzsch, Tobias and Pleijzier, Markus W. and Silva, Valeria and Yin, Yijie and Ali, Iris and Badalamente, Griffin and Bates, Alexander Shakeel and Beresford, Rory J. and Bogovic, John and Brooks, Paul and Cachero, Sebastian and Canino, Brandon S. and Chaisrisawatsuk, Bhumpanya and Clements, Jody and Crowe, Arthur and de Haan Vicente, Inês and Dempsey, Georgia and Donà, Erika and Dos Santos, Márcia and Dreher, Marisa and Dunne, Christopher R. and Eichler, Katharina and Finley-May, Samantha and Flynn, Miriam A. and Hameed, Imran and Hopkins, Gary Patrick and Hubbard, Philip M. and Kiassat, Ladann and Kovalyak, Julie and Lauchie, Shirley A. and Leonard, Meghan and Lohff, Alanna and Longden, Kit D. and Maldonado, Charli A. and Moitra, Ilina and Moon, Sung Soo and Mooney, Caroline and Munnelly, Eva J. and Okeoma, Nneoma and Olbris, Donald J. and Pai, Anika and Patel, Birava and Phillips, Emily M. and Plaza, Stephen M. and Richards, Alana and Rivas Salinas, Jennifer and Roberts, Ruairí J.V. and Rogers, Edward M. and Scott, Ashley L. and Scuderi, Louis A. and Seenivasan, Pavithraa and Serratosa Capdevila, Laia and Smith, Claire and Svirskas, Rob and Takemura, Satoko and Tastekin, Ibrahim and Thomson, Alexander and Umayam, Lowell and Walsh, John J. and Whittome, Holly and Xu, C. Shan and Yakal, Emily A. and Yang, Tansy and Zhao, Arthur and George, Reed and Jain, Viren and Jayaraman, Vivek and Korff, Wyatt and Meissner, Geoffrey W. and Romani, Sandro and Funke, Jan and Knecht, Christopher and Saalfeld, Stephan and Scheffer, Louis K. and Waddell, Scott and Card, Gwyneth M. and Ribeiro, Carlos and Reiser, Michael B. and Hess, Harald F. and Rubin, Gerald M. and Jefferis, Gregory S.X.E.},
+  year = {2026},
+  journal = {Cell},
+  doi = {10.1016/j.cell.2026.08.015},
+  url = {https://doi.org/10.1016/j.cell.2026.08.015},
+  volume = {189},
+  pages = {5504-5526.e15},
+}
+
+@article{malecns_ref_007,
+  title = {Functional Connectivity and Selective Odor Responses of Excitatory Local Interneurons in Drosophila Antennal Lobe},
+  author = {Huang, Ju and Zhang, Wei and Qiao, Wenhui and Hu, Aiqun and Wang, Zuoren},
+  year = {2010},
+  journal = {Neuron},
+  doi = {10.1016/j.neuron.2010.08.025},
+  url = {https://doi.org/10.1016/j.neuron.2010.08.025},
+  volume = {67},
+  pages = {1021-1033},
+}
+
+@article{malecns_ref_008,
+  title = {Transient photocurrents in a subthreshold evidence accumulator accelerate perceptual decisions},
+  author = {Wong, Timothy L. H. and Talbot, Clifford B. and Miesenböck, Gero},
+  year = {2023},
+  journal = {Nature Communications},
+  doi = {10.1038/s41467-023-38487-5},
+  url = {https://doi.org/10.1038/s41467-023-38487-5},
+  volume = {14},
+}
+
+@article{malecns_ref_009,
+  title = {A Drosophila computational brain model reveals sensorimotor processing},
+  author = {Shiu, Philip K. and Sterne, Gabriella R. and Spiller, Nico and Franconville, Romain and Sandoval, Andrea and Zhou, Joie and Simha, Neha and Kang, Chan Hyuk and Yu, Seongbong and Kim, Jinseop S. and Dorkenwald, Sven and Matsliah, Arie and Schlegel, Philipp and Yu, Szi-chieh and McKellar, Claire E. and Sterling, Amy and Costa, Marta and Eichler, Katharina and Bates, Alexander Shakeel and Eckstein, Nils and Funke, Jan and Jefferis, Gregory S. X. E. and Murthy, Mala and Bidaye, Salil S. and Hampel, Stefanie and Seeds, Andrew M. and Scott, Kristin},
+  year = {2024},
+  journal = {Nature},
+  doi = {10.1038/s41586-024-07763-9},
+  url = {https://doi.org/10.1038/s41586-024-07763-9},
+  volume = {634},
+  pages = {210-219},
+}
+
+@article{malecns_ref_010,
+  title = {Connectome-constrained networks predict neural activity across the fly visual system},
+  author = {Lappalainen, Janne K. and Tschopp, Fabian D. and Prakhya, Sridhama and McGill, Mason and Nern, Aljoscha and Shinomiya, Kazunori and Takemura, Shin-ya and Gruntman, Eyal and Macke, Jakob H. and Turaga, Srinivas C.},
+  year = {2024},
+  journal = {Nature},
+  doi = {10.1038/s41586-024-07939-3},
+  url = {https://doi.org/10.1038/s41586-024-07939-3},
+  volume = {634},
+  pages = {1132-1140},
+}
+
+@article{malecns_ref_011,
+  title = {Whole-body physics simulation of fruit fly locomotion},
+  author = {Vaxenburg, Roman and Siwanowicz, Igor and Merel, Josh and Robie, Alice A. and Morrow, Carmen and Novati, Guido and Stefanidi, Zinovia and Both, Gert-Jan and Card, Gwyneth M. and Reiser, Michael B. and Botvinick, Matthew M. and Branson, Kristin M. and Tassa, Yuval and Turaga, Srinivas C.},
+  year = {2025},
+  journal = {Nature},
+  doi = {10.1038/s41586-025-09029-4},
+  url = {https://doi.org/10.1038/s41586-025-09029-4},
+  volume = {643},
+  pages = {1312-1320},
+}
+
+@article{malecns_ref_012,
+  title = {DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses},
+  author = {Münch, Daniel and Galizia, C. Giovanni},
+  year = {2016},
+  journal = {Scientific Reports},
+  doi = {10.1038/srep21841},
+  url = {https://doi.org/10.1038/srep21841},
+  volume = {6},
+}
+
+@article{malecns_ref_013,
+  title = {Functional feedback from mushroom bodies to antennal lobes in the
+                    <i>Drosophila</i>
+                    olfactory pathway},
+  author = {Hu, Aiqun and Zhang, Wei and Wang, Zuoren},
+  year = {2010},
+  journal = {Proceedings of the National Academy of Sciences},
+  doi = {10.1073/pnas.0914912107},
+  url = {https://doi.org/10.1073/pnas.0914912107},
+  volume = {107},
+  pages = {10262-10267},
+}
+
+@article{malecns_ref_014,
+  title = {Dopamine-Dependent Plasticity Is Heterogeneously Expressed by Presynaptic Calcium Activity across Individual Boutons of the<i>Drosophila</i>Mushroom Body},
+  author = {Davidson, Andrew M. and Kaushik, Shivam and Hige, Toshihide},
+  year = {2023},
+  journal = {eneuro},
+  doi = {10.1523/ENEURO.0275-23.2023},
+  url = {https://doi.org/10.1523/eneuro.0275-23.2023},
+  volume = {10},
+  pages = {ENEURO.0275-23.2023},
+}
+
+@article{malecns_ref_015,
+  title = {Aversive Training Induces Both Presynaptic and Postsynaptic Suppression in<i>Drosophila</i>},
+  author = {Zhang, Xiaofan and Noyes, Nathaniel C. and Zeng, Jianzhi and Li, Yulong and Davis, Ronald L.},
+  year = {2019},
+  journal = {The Journal of Neuroscience},
+  doi = {10.1523/JNEUROSCI.1420-19.2019},
+  url = {https://doi.org/10.1523/jneurosci.1420-19.2019},
+  volume = {39},
+  pages = {9164-9172},
+}
+
+@article{malecns_ref_016,
+  title = {Trace Conditioning in Drosophila Induces Associative Plasticity in Mushroom Body Kenyon Cells and Dopaminergic Neurons},
+  author = {Dylla, Kristina V. and Raiser, Georg and Galizia, C. Giovanni and Szyszka, Paul},
+  year = {2017},
+  journal = {Frontiers in Neural Circuits},
+  doi = {10.3389/fncir.2017.00042},
+  url = {https://doi.org/10.3389/fncir.2017.00042},
+  volume = {11},
+}
+
+@article{malecns_ref_017,
+  title = {A single pair of neurons links sleep to memory consolidation in Drosophila melanogaster},
+  author = {Haynes, Paula R and Christmann, Bethany L and Griffith, Leslie C},
+  year = {2015},
+  journal = {eLife},
+  doi = {10.7554/eLife.03868},
+  url = {https://doi.org/10.7554/elife.03868},
+  volume = {4},
+}
+
+@article{malecns_ref_018,
+  title = {Localized inhibition in the Drosophila mushroom body},
+  author = {Amin, Hoger and Apostolopoulou, Anthi A and Suárez-Grimalt, Raquel and Vrontou, Eleftheria and Lin, Andrew C},
+  year = {2020},
+  journal = {eLife},
+  doi = {10.7554/eLife.56954},
+  url = {https://doi.org/10.7554/elife.56954},
+  volume = {9},
+}
+
+@article{malecns_ref_019,
+  title = {The anterior paired lateral neuron normalizes odour-evoked activity in the Drosophila mushroom body calyx},
+  author = {Prisco, Luigi and Deimel, Stephan Hubertus and Yeliseyeva, Hanna and Fiala, André and Tavosanis, Gaia},
+  year = {2021},
+  journal = {eLife},
+  doi = {10.7554/eLife.74172},
+  url = {https://doi.org/10.7554/elife.74172},
+  volume = {10},
+}
+
+@article{malecns_ref_020,
+  title = {Associative learning drives longitudinally graded presynaptic plasticity of neurotransmitter release along axonal compartments},
+  author = {Stahl, Aaron and Noyes, Nathaniel C and Boto, Tamara and Botero, Valentina and Broyles, Connor N and Jing, Miao and Zeng, Jianzhi and King, Lanikea B and Li, Yulong and Davis, Ronald L and Tomchik, Seth M},
+  year = {2022},
+  journal = {eLife},
+  doi = {10.7554/eLife.76712},
+  url = {https://doi.org/10.7554/elife.76712},
+  volume = {11},
+}
+
+@article{malecns_ref_021,
+  title = {Postsynaptic plasticity of cholinergic synapses underlies the induction and expression of appetitive and familiarity memories in Drosophila},
+  author = {Pribbenow, Carlotta and Chen, Yi-chun and Heim, M-Marcel and Laber, Desiree and Reubold, Silas and Reynolds, Eric and Balles, Isabella and Fernández-d V Alquicira, Tania and Suárez-Grimalt, Raquel and Scheunemann, Lisa and Rauch, Carolin and Matkovic, Tanja and Rösner, Jörg and Lichtner, Gregor and Jagannathan, Sridhar R and Owald, David},
+  year = {2022},
+  journal = {eLife},
+  doi = {10.7554/eLife.80445},
+  url = {https://doi.org/10.7554/elife.80445},
+  volume = {11},
+}
+
@@ -0,0 +1,27 @@
+# 论文索引
+
+出版元数据由 Crossref 获取；未打包论文全文。许可证据见 JSON，不能默认再分发。
+
+- **2007** [Excitatory Local Circuits and Their Implications for Olfactory Processing in the Fly Antennal Lobe](https://doi.org/10.1016/j.cell.2006.12.034) — Cell。用途：Excitatory antennal-lobe local circuits。
+- **2015** [Coordinated and Compartmentalized Neuromodulation Shapes Sensory Processing in Drosophila](https://doi.org/10.1016/j.cell.2015.11.019) — Cell。用途：Compartment and timing dependence of transmission。
+- **2019** [Distinct Dopamine Receptor Pathways Underlie the Temporal Sensitivity of Associative Learning](https://doi.org/10.1016/j.cell.2019.05.040) — Cell。用途：Timing-dependent dopamine plasticity。
+- **2024** [Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster](https://doi.org/10.1016/j.cell.2024.03.016) — Cell。用途：EM neurotransmitter prediction and limitations。
+- **2026** [The organization of visual pathways in the Drosophila brain](https://doi.org/10.1016/j.cell.2026.08.014) — Cell。用途：Official MaleCNS visual pathways。
+- **2026** [Sexual dimorphism in the complete Drosophila male central nervous system connectome](https://doi.org/10.1016/j.cell.2026.08.015) — Cell。用途：Formal MaleCNS Cell 2026; distinguish release/schema from publication counts。
+- **2010** [Functional Connectivity and Selective Odor Responses of Excitatory Local Interneurons in Drosophila Antennal Lobe](https://doi.org/10.1016/j.neuron.2010.08.025) — Neuron。用途：Excitatory local interneuron connectivity。
+- **2023** [Transient photocurrents in a subthreshold evidence accumulator accelerate perceptual decisions](https://doi.org/10.1038/s41467-023-38487-5) — Nature Communications。用途：KC subthreshold response and decision timing。
+- **2024** [A Drosophila computational brain model reveals sensorimotor processing](https://doi.org/10.1038/s41586-024-07763-9) — Nature。用途：Shiu-like LIF reference; not a strict replication claim。
+- **2024** [Connectome-constrained networks predict neural activity across the fly visual system](https://doi.org/10.1038/s41586-024-07939-3) — Nature。用途：FlyVis independent visual model。
+- **2025** [Whole-body physics simulation of fruit fly locomotion](https://doi.org/10.1038/s41586-025-09029-4) — Nature。用途：FlyBody / Google DeepMind; separate physical body/controller research。
+- **2016** [DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses](https://doi.org/10.1038/srep21841) — Scientific Reports。用途：DoOR physiology / odor-receptor-glomerular reference。
+- **2010** [Functional feedback from mushroom bodies to antennal lobes in the
+                    <i>Drosophila</i>
+                    olfactory pathway](https://doi.org/10.1073/pnas.0914912107) — Proceedings of the National Academy of Sciences。用途：MB to antennal-lobe feedback physiology。
+- **2023** [Dopamine-Dependent Plasticity Is Heterogeneously Expressed by Presynaptic Calcium Activity across Individual Boutons of the<i>Drosophila</i>Mushroom Body](https://doi.org/10.1523/eneuro.0275-23.2023) — eneuro。用途：Compartment-specific KC release and bouton heterogeneity。
+- **2019** [Aversive Training Induces Both Presynaptic and Postsynaptic Suppression in<i>Drosophila</i>](https://doi.org/10.1523/jneurosci.1420-19.2019) — The Journal of Neuroscience。用途：Pre/post synaptic odor suppression。
+- **2017** [Trace Conditioning in Drosophila Induces Associative Plasticity in Mushroom Body Kenyon Cells and Dopaminergic Neurons](https://doi.org/10.3389/fncir.2017.00042) — Frontiers in Neural Circuits。用途：Historical citation; consult source file for context。
+- **2015** [A single pair of neurons links sleep to memory consolidation in Drosophila melanogaster](https://doi.org/10.7554/elife.03868) — eLife。用途：DPM physiology; not a universal edge sign assignment。
+- **2020** [Localized inhibition in the Drosophila mushroom body](https://doi.org/10.7554/elife.56954) — eLife。用途：Localized APL inhibition。
+- **2021** [The anterior paired lateral neuron normalizes odour-evoked activity in the Drosophila mushroom body calyx](https://doi.org/10.7554/elife.74172) — eLife。用途：APL / PN-bouton and KC-dendrite normalization。
+- **2022** [Associative learning drives longitudinally graded presynaptic plasticity of neurotransmitter release along axonal compartments](https://doi.org/10.7554/elife.76712) — eLife。用途：KC acetylcholine release plasticity。
+- **2022** [Postsynaptic plasticity of cholinergic synapses underlies the induction and expression of appetitive and familiarity memories in Drosophila](https://doi.org/10.7554/elife.80445) — eLife。用途：Postsynaptic cholinergic memory mechanisms。