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15 changes: 15 additions & 0 deletions discovery/fulltext.py
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,21 @@ def fetch_and_save_bibtex(yaml_path):
if not bibtex or "@" not in bibtex:
return None

# Normalize month names to the lowercase 3-letter abbreviations that
# bibtexparser's `common_strings=True` recognizes. CrossRef sometimes
# emits `month=July` (capitalized full name) or `month=Sept` (the
# non-standard 4-letter abbreviation), either of which would raise
# UndefinedString during parsing.
_MONTH_VARIANTS = {
"January": "jan", "February": "feb", "March": "mar", "April": "apr",
"May": "may", "June": "jun", "July": "jul", "August": "aug",
"September": "sep", "October": "oct", "November": "nov",
"December": "dec",
"Sept": "sep", # non-standard CrossRef abbreviation
}
for _variant, _abbr in _MONTH_VARIANTS.items():
bibtex = re.sub(rf"(month\s*=\s*){_variant}\b", rf"\g<1>{_abbr}", bibtex, flags=re.IGNORECASE)

# Save companion .bib file
bib_path = yaml_path.with_suffix(".bib")
bib_path.write_text(bibtex, encoding="utf-8")
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12 changes: 10 additions & 2 deletions pipeline/approved/2024_integration.yaml
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Expand Up @@ -26,8 +26,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Erofeev_2024, title={Integration of Single-Photon Miniature
Fluorescence Microscopy and Electrophysiological Recording Methods for in vivo
Studying Hippocampal Neuronal Activity}, volume={60}, ISSN={1608-3202}, url={http://dx.doi.org/10.1134/s0022093024040264},
DOI={10.1134/s0022093024040264}, number={4}, journal={Journal of Evolutionary Biochemistry
and Physiology}, publisher={Pleiades Publishing Ltd}, author={Erofeev, A. I. and
Vinokurov, E. K. and Antifeev, I. E. and Vlasova, O. L. and Bezprozvanny, I. B.},
year={2024}, month=jul, pages={1586–1606} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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12 changes: 10 additions & 2 deletions pipeline/approved/2024_optimizing.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Erofeev_2024, title={On Optimizing Miniscope Data Analysis
with Simulated Data: A Study of Parameter Optimization in the Minian Analysis Pipeline},
volume={54}, ISSN={1573-899X}, url={http://dx.doi.org/10.1007/s11055-024-01593-y},
DOI={10.1007/s11055-024-01593-y}, number={2}, journal={Neuroscience and Behavioral
Physiology}, publisher={Springer Science and Business Media LLC}, author={Erofeev,
A. I. and Petrushan, M. V. and Lysenko, L. V. and Vinokurov, E. K. and Vlasova,
O. L. and Bezprozvanny, I. B.}, year={2024}, month=Feb, pages={251–262} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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11 changes: 9 additions & 2 deletions pipeline/approved/aseyev_2024_cadence.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Aseyev_2024, title={CADENCE — Neuroinformatics Tool for Supervised
Calcium Events Detection}, volume={22}, ISSN={1559-0089}, url={http://dx.doi.org/10.1007/s12021-024-09677-3},
DOI={10.1007/s12021-024-09677-3}, number={3}, journal={Neuroinformatics}, publisher={Springer
Science and Business Media LLC}, author={Aseyev, Nikolay and Borodinova, Anastasia
and Pavlova, Svetlana and Roshchina, Marina and Roshchin, Matvey and Nikitin, Evgeny
and Balaban, Pavel}, year={2024}, month=jul, pages={379–387} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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12 changes: 10 additions & 2 deletions pipeline/approved/barry_2022_dissociable.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Barry_2022, title={Dissociable effects of oxycodone on behavior,
calcium transient activity, and excitability of dorsolateral striatal neurons},
volume={16}, ISSN={1662-5110}, url={http://dx.doi.org/10.3389/fncir.2022.983323},
DOI={10.3389/fncir.2022.983323}, journal={Frontiers in Neural Circuits}, publisher={Frontiers
Media SA}, author={Barry, Joshua and Oikonomou, Katerina D. and Peng, Allison and
Yu, Daniel and Yang, Chenyi and Golshani, Peyman and Evans, Christopher J. and Levine,
Michael S. and Cepeda, Carlos}, year={2022}, month=Oct }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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11 changes: 9 additions & 2 deletions pipeline/approved/berigan_2023_imaging.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Berigan_2023, title={Imaging neuro-urodynamics of mouse major
pelvic ganglion with a micro-endoscopic approach}, volume={129}, ISSN={1522-1598},
url={http://dx.doi.org/10.1152/jn.00450.2022}, DOI={10.1152/jn.00450.2022}, number={2},
journal={Journal of Neurophysiology}, publisher={American Physiological Society},
author={Berigan, Benton R. and Wang, Jing and Schulz, David J. and Ozden, Ilker},
year={2023}, month=Feb, pages={479–493} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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13 changes: 11 additions & 2 deletions pipeline/approved/borkar_2024_topdown.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,17 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Borkar_2024, title={Top-down control of flight by a non-canonical
cortico-amygdala pathway}, volume={625}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-023-06912-w},
DOI={10.1038/s41586-023-06912-w}, number={7996}, journal={Nature}, publisher={Springer
Science and Business Media LLC}, author={Borkar, Chandrashekhar D. and Stelly, Claire
E. and Fu, Xin and Dorofeikova, Maria and Le, Quan-Son Eric and Vutukuri, Rithvik
and Vo, Catherine and Walker, Alice Breaux and Basavanhalli, Samhita and Duong,
Anh and Bean, Erin and Resendez, Alexis and Parker, Jones G. and Tasker, Jeffrey
G. and Fadok, Jonathan P.}, year={2024}, month=Jan, pages={743–749} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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11 changes: 9 additions & 2 deletions pipeline/approved/bowles_2021_vagus.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Bowles_2021, title={Vagus nerve stimulation accelerates motor
learning through cholinergic modulation}, url={http://dx.doi.org/10.1101/2021.10.28.466306},
DOI={10.1101/2021.10.28.466306}, publisher={openRxiv}, author={Bowles, Spencer and
Hickman, Jordan and Peng, Xiaoyu and Williamson, W. Ryan and Huang, Rongchen and
Washington, Kayden and Donegan, Dane and Welle, Cristin G}, year={2021}, month=Oct
}

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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12 changes: 10 additions & 2 deletions pipeline/approved/bowles_2022_vagus.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Bowles_2022, title={Vagus nerve stimulation drives selective
circuit modulation through cholinergic reinforcement}, volume={110}, ISSN={0896-6273},
url={http://dx.doi.org/10.1016/j.neuron.2022.06.017}, DOI={10.1016/j.neuron.2022.06.017},
number={17}, journal={Neuron}, publisher={Elsevier BV}, author={Bowles, Spencer
and Hickman, Jordan and Peng, Xiaoyu and Williamson, W. Ryan and Huang, Rongchen
and Washington, Kayden and Donegan, Dane and Welle, Cristin G.}, year={2022}, month=sep,
pages={2867–2885.e7} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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2 changes: 1 addition & 1 deletion pipeline/approved/cai_2016_shared.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ bibtex_raw: ' @article{Cai_2016, title={A shared neural ensemble links distinct
and Veshkini, Michael and La-Vu, Mimi and Lou, Jerry and Flores, Sergio E. and Kim,
Isaac and Sano, Yoshitake and Zhou, Miou and Baumgaertel, Karsten and Lavi, Ayal
and Kamata, Masakazu and Tuszynski, Mark and Mayford, Mark and Golshani, Peyman
and Silva, Alcino J.}, year={2016}, month=May, pages={115–118} }
and Silva, Alcino J.}, year={2016}, month=may, pages={115–118} }

'
bibtex_source: crossref
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9 changes: 7 additions & 2 deletions pipeline/approved/carrasco_2024_monthslong.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,13 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Carrasco_2024, title={Months-long stability of the head-direction
system}, url={http://dx.doi.org/10.1101/2024.06.13.598909}, DOI={10.1101/2024.06.13.598909},
publisher={openRxiv}, author={Carrasco, Sofia Skromne and Viejo, Guillaume and Peyrache,
Adrien}, year={2024}, month=jun }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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10 changes: 8 additions & 2 deletions pipeline/approved/carrasco_2026_monthslong.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Skromne_Carrasco_2026, title={Months-long stability of the
head-direction system}, volume={652}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-025-10096-w},
DOI={10.1038/s41586-025-10096-w}, number={8108}, journal={Nature}, publisher={Springer
Science and Business Media LLC}, author={Skromne Carrasco, Sofia and Viejo, Guillaume
and Peyrache, Adrien}, year={2026}, month=Feb, pages={167–173} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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10 changes: 8 additions & 2 deletions pipeline/approved/chen_2021_fast.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,14 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @inproceedings{Chen_2021, title={Fast Calcium Trace Extraction for Large-Field-of-View
Miniscope}, url={http://dx.doi.org/10.1109/biocas49922.2021.9644936}, DOI={10.1109/biocas49922.2021.9644936},
booktitle={2021 IEEE Biomedical Circuits and Systems Conference (BioCAS)}, publisher={IEEE},
author={Chen, Zhe and Blair, Garrett J. and Blair, Hugh T. and Cong, Jason}, year={2021},
month=Oct, pages={1–5} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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13 changes: 11 additions & 2 deletions pipeline/approved/chen_2022_circuit.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,17 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Chen_2022, title={A circuit from lateral septum neurotensin
neurons to tuberal nucleus controls hedonic feeding}, volume={27}, ISSN={1476-5578},
url={http://dx.doi.org/10.1038/s41380-022-01742-0}, DOI={10.1038/s41380-022-01742-0},
number={12}, journal={Molecular Psychiatry}, publisher={Springer Science and Business
Media LLC}, author={Chen, Zijun and Chen, Gaowei and Zhong, Jiafeng and Jiang, Shaolei
and Lai, Shishi and Xu, Hua and Deng, Xiaofei and Li, Fengling and Lu, Shanshan
and Zhou, Kuikui and Li, Changlin and Liu, Zhongdong and Zhang, Xu and Zhu, Yingjie},
year={2022}, month=Aug, pages={4843–4860} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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11 changes: 9 additions & 2 deletions pipeline/approved/chen_2022_ubiquitous.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Chen_2022, title={Ubiquitous proximity to a critical state
for collective neural activity in the CA1 region of freely moving mice}, volume={77},
ISSN={0577-9073}, url={http://dx.doi.org/10.1016/j.cjph.2021.12.010}, DOI={10.1016/j.cjph.2021.12.010},
journal={Chinese Journal of Physics}, publisher={Elsevier BV}, author={Chen, Yi-Ling
and Chen, Chun-Chung and Mei, Yu-Ying and Zhou, Ning and Wu, Dongchuan and Lee,
Ting-Kuo}, year={2022}, month=jun, pages={497–510} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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11 changes: 9 additions & 2 deletions pipeline/approved/chung_2021_cognitive.yaml
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Expand Up @@ -29,8 +29,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Chung_2021, title={Cognitive control persistently enhances
hippocampal information processing}, volume={600}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/s41586-021-04070-5},
DOI={10.1038/s41586-021-04070-5}, number={7889}, journal={Nature}, publisher={Springer
Science and Business Media LLC}, author={Chung, Ain and Jou, Claudia and Grau-Perales,
Alejandro and Levy, Eliott R. J. and Dvorak, Dino and Hussain, Nida and Fenton,
André A.}, year={2021}, month=Nov, pages={484–488} }

'
bibtex_source: crossref
fulltext:
source: null
pdf_local_path: null
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2 changes: 1 addition & 1 deletion pipeline/approved/dong_2025_simultaneous.yaml
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Expand Up @@ -55,7 +55,7 @@ bibtex_raw: ' @article{Dong_2025, title={Simultaneous two-color imaging with a d
Yu and Diego, Keziah and Baggetta, Austin M. and Sweis, Brian M. and Pennington,
Zachary T. and Lamsifer, Sophia I. and Zaki, Yosif and Sangiuliano, Federico and
Philipsberg, Paul A. and Morales-Rodriguez, Denisse and Kircher, Daniel and Slesinger,
Paul and Shuman, Tristan and Aharoni, Daniel and Cai, Denise J.}, year={2025}, month=July
Paul and Shuman, Tristan and Aharoni, Daniel and Cai, Denise J.}, year={2025}, month=jul
}

'
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11 changes: 9 additions & 2 deletions pipeline/approved/etter_2023_optogenetic.yaml
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Expand Up @@ -24,8 +24,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Etter_2023, title={Optogenetic frequency scrambling of hippocampal
theta oscillations dissociates working memory retrieval from hippocampal spatiotemporal
codes}, volume={14}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-023-35825-5},
DOI={10.1038/s41467-023-35825-5}, number={1}, journal={Nature Communications}, publisher={Springer
Science and Business Media LLC}, author={Etter, Guillaume and van der Veldt, Suzanne
and Choi, Jisoo and Williams, Sylvain}, year={2023}, month=Jan }

'
bibtex_source: crossref
fulltext:
source: null
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9 changes: 7 additions & 2 deletions pipeline/approved/farrell_2021_midbrain.yaml
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Expand Up @@ -21,8 +21,13 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Farrell_2021, title={Midbrain dopamine neurons provide teaching
signals for goal-directed navigation}, url={http://dx.doi.org/10.1101/2021.02.17.431585},
DOI={10.1101/2021.02.17.431585}, publisher={openRxiv}, author={Farrell, Karolina
and Lak, Armin and Saleem, Aman B}, year={2021}, month=Feb }

'
bibtex_source: crossref
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source: null
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13 changes: 11 additions & 2 deletions pipeline/approved/gabriel_2022_behaviordepot.yaml
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Expand Up @@ -44,8 +44,17 @@ source: openalex_cites
seed_paper_doi: 10.1038/s41593-019-0559-0
discovered_date: '2026-04-10'
batch_id: backlog_2026-04-10
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Gabriel_2022, title={BehaviorDEPOT is a simple, flexible tool
for automated behavioral detection based on markerless pose tracking}, volume={11},
ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.74314}, DOI={10.7554/elife.74314},
journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Gabriel,
Christopher J and Zeidler, Zachary and Jin, Benita and Guo, Changliang and Goodpaster,
Caitlin M and Kashay, Adrienne Q and Wu, Anna and Delaney, Molly and Cheung, Jovian
and DiFazio, Lauren E and Sharpe, Melissa J and Aharoni, Daniel and Wilke, Scott
A and DeNardo, Laura A}, year={2022}, month=Aug }

'
bibtex_source: crossref
fulltext:
source: unpaywall
pdf_local_path: null
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2 changes: 1 addition & 1 deletion pipeline/approved/gagliardi_2024_distinct.yaml
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Expand Up @@ -38,7 +38,7 @@ bibtex_raw: ' @article{Gagliardi_2024, title={Distinct neural mechanisms for hea
DOI={10.1038/s41467-024-50112-7}, number={1}, journal={Nature Communications}, publisher={Springer
Science and Business Media LLC}, author={Gagliardi, Celia M. and Normandin, Marc
E. and Keinath, Alexandra T. and Julian, Joshua B. and Lopez, Matthew R. and Ramos-Alvarez,
Manuel-Miguel and Epstein, Russell A. and Muzzio, Isabel A.}, year={2024}, month=July
Manuel-Miguel and Epstein, Russell A. and Muzzio, Isabel A.}, year={2024}, month=jul
}

'
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11 changes: 9 additions & 2 deletions pipeline/approved/gao_2020_novel.yaml
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Expand Up @@ -27,8 +27,15 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @inproceedings{Gao_2020, title={Novel Virtual Reality System for Auditory
Tasks in Head-fixed Mice}, url={http://dx.doi.org/10.1109/embc44109.2020.9176536},
DOI={10.1109/embc44109.2020.9176536}, booktitle={2020 42nd Annual International
Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)}, publisher={IEEE},
author={Gao, Sibo and Webb, James and Mridha, Zakir and Banta, Anton and Kemere,
Caleb and McGinley, Matthew}, year={2020}, month=jul, pages={2925–2928} }

'
bibtex_source: crossref
fulltext:
source: null
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12 changes: 10 additions & 2 deletions pipeline/approved/hart_2020_chemogenetic.yaml
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Expand Up @@ -26,8 +26,16 @@ source: trusted_bib
seed_paper_doi: trusted_bib:Publications Using Our Tools.bib
discovered_date: '2026-05-13'
batch_id: trusted_bib_ingest_2026-05-13
bibtex_raw: null
bibtex_source: null
bibtex_raw: ' @article{Hart_2020, title={Chemogenetic Modulation and Single-Photon
Calcium Imaging in Anterior Cingulate Cortex Reveal a Mechanism for Effort-Based
Decisions}, volume={40}, ISSN={1529-2401}, url={http://dx.doi.org/10.1523/jneurosci.2548-19.2020},
DOI={10.1523/jneurosci.2548-19.2020}, number={29}, journal={The Journal of Neuroscience},
publisher={Society for Neuroscience}, author={Hart, Evan E. and Blair, Garrett J.
and O’Dell, Thomas J. and Blair, Hugh T. and Izquierdo, Alicia}, year={2020}, month=jun,
pages={5628–5643} }

'
bibtex_source: crossref
fulltext:
source: null
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