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fixes and cleanup for bibchecker #54

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merged 6 commits into from
Nov 8, 2021
Merged

fixes and cleanup for bibchecker #54

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991c82a
fix CoppEtal17
paxtonfitzpatrick Nov 8, 2021
109ec89
fix formatting per bibchecker
paxtonfitzpatrick Nov 8, 2021
92456fd
force checker to accept institution for CartEtal16
paxtonfitzpatrick Nov 8, 2021
e3343fd
add EMBS and BHI to hard-coded caps
paxtonfitzpatrick Nov 8, 2021
402471d
tweak brace placement to please bibchecker (see ContextLab/CDL-biblio…
paxtonfitzpatrick Nov 8, 2021
31ab9bf
[ci skip] remove BibDesk auto heading
paxtonfitzpatrick Nov 8, 2021
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4 changes: 3 additions & 1 deletion bibcheck/caps.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -380,4 +380,6 @@ WAISIII
WAIS
Wechsler
Pyparse
Landauer
Landauer
EMBS
BHI
70 changes: 10 additions & 60 deletions cdl.bib
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,5 @@


@article{FinnBand21,
author = {E S Finn and P A Bandettini},
date-added = {2021-10-27 22:57:39 -0400},
date-modified = {2021-10-27 22:58:15 -0400},
journal = {{NeuroImage}},
pages = {117963},
title = {Movie-watching outperforms rest for functional connectivity-based prediction of behavior},
Expand All @@ -12,8 +8,6 @@ @article{FinnBand21

@article{FinnRose21,
author = {E S Finn and M D Rosenberg},
date-added = {2021-10-27 22:56:53 -0400},
date-modified = {2021-10-27 22:57:32 -0400},
journal = {{NeuroImage}},
pages = {118254},
title = {Beyond fingerprinting: choosing predictive connectomes over reliable connectomes},
Expand All @@ -22,17 +16,13 @@ @article{FinnRose21

@article{Finn21,
author = {E S Finn},
date-added = {2021-10-27 22:55:50 -0400},
date-modified = {2021-10-27 22:56:26 -0400},
journal = {Trends in Cognitive Sciences},
title = {Is it time to put rest to rest?},
volume = {doi.org/10.1016/j.tics.2021.09.005},
year = {2021}}

@article{MurpEtal13,
author = {K Murphy and R M Birn and P A Bandettini},
date-added = {2021-10-27 22:54:48 -0400},
date-modified = {2021-10-27 22:55:24 -0400},
journal = {{NeuroImage}},
pages = {349--359},
title = {Resting-state {fMRI} confounds and cleanup},
Expand All @@ -41,8 +31,6 @@ @article{MurpEtal13

@article{SmitEtal13c,
author = {S M Smith and D Vidaurre and C F Beckmann and M F Glasser and M Jenkinson and K L Miller and T E Nichols and E C Robinson and G Salimi-Khorshidi and M W Woolrich and D M Barch and K U{\u{g}}urbil and D C {Van Essen}},
date-added = {2021-10-27 22:53:31 -0400},
date-modified = {2021-10-27 22:54:43 -0400},
journal = {Trends in Cognitive Sciences},
number = {12},
pages = {666--682},
Expand All @@ -52,9 +40,7 @@ @article{SmitEtal13c

@article{LeeEtal13,
author = {M H Lee and C D Smyser and J S Shimony},
date-added = {2021-10-27 22:52:38 -0400},
date-modified = {2021-10-27 22:53:25 -0400},
journal = {American Journal of Neuroradiology},
journal = {{American} Journal of Neuroradiology},
number = {10},
pages = {1866--1872},
title = {Resting-state {fMRI}: a review of methods and clinical applications},
Expand All @@ -63,8 +49,6 @@ @article{LeeEtal13

@article{SmitEtal13b,
author = {S M Smith and C F Beckmann and J Andersson and E J Auerbach and J Bijsterbosch and G Douaud and E Duff and D A Feinberg and L Griffanti and M P Harms and M Kelly and T Laumann and K L Miller and S Moeller and S Peterson and J Power and G Salimi-Khorshidi and A Z Snyder and A T Vu and M W Woolrich and J Xu and E Yacoub and K U{\u{g}}urbil and D C {Van Essen} and M F Glasser},
date-added = {2021-10-27 22:49:31 -0400},
date-modified = {2021-10-27 22:52:27 -0400},
journal = {{NeuroImage}},
pages = {144--168},
title = {Resting-state {fMRI} in the {Human Connectome Project}},
Expand All @@ -73,17 +57,13 @@ @article{SmitEtal13b

@article{GralFinn21,
author = {C Grall and E S Finn},
date-added = {2021-10-27 22:21:50 -0400},
date-modified = {2021-10-27 22:24:22 -0400},
journal = {{PsyArXiv}},
title = {Leveraging the power of media to drive cognition: a media-informed approach to naturalistic neuroscience},
volume = {doi.org/10.31234/osf.io/c8z9t},
year = {2021}}

@article{ChenEtal15b,
author = {J Chen and U Hasson and C J Honey},
date-added = {2021-10-27 10:59:50 -0400},
date-modified = {2021-10-27 11:00:24 -0400},
journal = {Neuron},
number = {2},
pages = {244--246},
Expand All @@ -93,8 +73,6 @@ @article{ChenEtal15b

@article{YeshEtal17,
author = {Y Yeshurun and S Swanson and E Simony and J Chen and C Lazaridi and C J Honey and U Hasson},
date-added = {2021-10-27 10:58:35 -0400},
date-modified = {2021-10-27 10:59:28 -0400},
journal = {Psychological Science},
number = {3},
pages = {307--319},
Expand All @@ -104,8 +82,6 @@ @article{YeshEtal17

@article{HaufEtal18,
author = {S Haufe and P {DeGuzman} and S Henin and M Arcaro and C J Honey and U Hasson and L C Parra},
date-added = {2021-10-27 10:57:11 -0400},
date-modified = {2021-10-27 10:58:21 -0400},
journal = {{NeuroImage}},
number = {1},
pages = {79--91},
Expand All @@ -115,17 +91,13 @@ @article{HaufEtal18

@article{GoldEtal21,
author = {A Goldstein and Z Zada and E Buchnik and M Schain and A Price and B Aubrey and S A Nastase and A Feder and D Emanuel and A Cohen and A Jansen and H Gazula and G Choe and A Rao and C Kim and C Casto and F Lora and A Flinker and S Devore and W Doyle and P Dugan and D Friedman and A Hassidim and M Brenner and Y Matias and K A Norman and O Devinsky and U Hasson},
date-added = {2021-10-27 10:55:03 -0400},
date-modified = {2021-10-27 10:56:55 -0400},
journal = {{bioRxiv}},
pages = {doi.org/10.1101/2020.12.02.403477},
title = {Thinking ahead: prediction in context as a keystone of language in humans and machines},
year = {2021}}

@article{NeelKeef89,
author = {J H Neely and D E Keefe},
date-added = {2021-10-27 10:54:06 -0400},
date-modified = {2021-10-27 10:54:51 -0400},
journal = {Psychology of Learning and Motivation},
pages = {207--248},
title = {Semantic context effects on visual word processing: a hybrid prospective-retrospective processing theory},
Expand All @@ -134,8 +106,6 @@ @article{NeelKeef89

@article{Beck80,
author = {C A Becker},
date-added = {2021-10-27 10:53:27 -0400},
date-modified = {2021-10-27 10:53:58 -0400},
journal = {Memory and Cognition},
pages = {493--512},
title = {Semantic context effects in visual word recognition: an analysis of semantic strategies},
Expand All @@ -144,8 +114,6 @@ @article{Beck80

@article{WoodMcDe18,
author = {K J P Woods and J H {McDermott}},
date-added = {2021-10-27 10:52:04 -0400},
date-modified = {2021-10-27 10:52:48 -0400},
journal = {Proceedings of the National Academy of Sciences, {USA}},
number = {14},
pages = {E3313--E3322},
Expand All @@ -155,19 +123,15 @@ @article{WoodMcDe18

@article{BraiFree97,
author = {D H Brainard and W T Freeman},
date-added = {2021-10-27 10:50:19 -0400},
date-modified = {2021-10-27 10:51:05 -0400},
journal = {Journal of the Optical Society of America A},
journal = {Journal of the Optical Society of America {A}},
number = {7},
pages = {1393--1411},
title = {Bayesian color constancy},
title = {{Bayesian} color constancy},
volume = {14},
year = {1997}}

@article{Fost11,
author = {D H Foster},
date-added = {2021-10-27 10:49:35 -0400},
date-modified = {2021-10-27 10:50:13 -0400},
journal = {Vision Research},
number = {7},
pages = {674--700},
Expand All @@ -177,8 +141,6 @@ @article{Fost11

@article{AlthEtal16,
author = {T Althoff and K Clark and J Leskovec},
date-added = {2021-10-26 21:36:29 -0400},
date-modified = {2021-10-26 21:37:27 -0400},
journal = {Transactions of the Association for Computational Linguistics},
pages = {463--476},
title = {Large-scale analysis of counseling conversations: an application of natural language processing to mental health},
Expand All @@ -187,8 +149,6 @@ @article{AlthEtal16

@article{LowEtal20,
author = {D M Low and L Rumker and T Talkar and J Torous and G Cecchi and S S Chosh},
date-added = {2021-10-26 21:35:09 -0400},
date-modified = {2021-10-26 21:36:24 -0400},
journal = {Journal of Medical Internet Research},
number = {10},
pages = {e22635},
Expand All @@ -198,27 +158,22 @@ @article{LowEtal20

@article{StewVelu21,
author = {R Stewart and S Velupillai},
date-added = {2021-10-26 21:34:07 -0400},
date-modified = {2021-10-26 21:38:24 -0400},
journal = {Neuropsychopharmacology},
pages = {252--253},
title = {Applied natural language processing in mental health big data},
volume = {46},
year = {2021}}

@article{CoppEtal17,
@inproceedings{CoppEtal17,
author = {G Coppersmith and C Hilland and O Frieder and R Leary},
date-added = {2021-10-26 21:32:51 -0400},
date-modified = {2021-10-26 21:34:02 -0400},
journal = {{IEEE} {Xplore}},
pages = {doi.org/10.1109/BHI.2017.7897288},
booktitle = {2017 {IEEE} {EMBS} International Conference on Biomedical \& Health Informatics {(BHI})},
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is the {(BHI}) part correct?

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it's "correct" in that it passses the checker -- I opened #53 about this.

I agree that I'd expect it to be ({BHI}) instead, and the checker should probably be fixed to accept this, but since the difference shouldn't actually affect the output, I went ahead and formatted as the checker wanted for now.

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👍

organization = {IEEE},
pages = {393--396},
title = {Scalable mental health analysis in the clinical whitespace via natural language processing},
year = {2017}}

@article{CookEtal16,
author = {B J Cook and A M Progovac and P Chen and B Mullin and S Hou and E Baca-Garcia},
date-added = {2021-10-26 21:30:46 -0400},
date-modified = {2021-10-26 21:32:36 -0400},
journal = {Computational and Mathematical Methods in Medicine},
number = {8708434},
pages = {1--9},
Expand All @@ -228,7 +183,6 @@ @article{CookEtal16

@article{OnoEtal16,
author = {M Ono and G J Devilly and D H K Shum},
date-modified = {2021-10-26 21:13:23 -0400},
journal = {Psychological Trauma: Theory, Research, Practice, and Policy},
number = {2},
pages = {157--164},
Expand Down Expand Up @@ -361,14 +315,13 @@ @article{DalgWatt90

@techreport{CartEtal16,
author = {C Carter and N Cohen and J {DeVylder} and D Dickinson and D Fair and M Kutas and S Park and L Uddin},
date-modified = {2021-10-26 21:14:23 -0400},
institution = {National Institutes of Mental Health},
title = {Behavioral assessment methods for {RDoC} constructs: cognitive systems final report},
year = {2016}}
year = {2016},
force = {True}}

@article{MannEtal21,
author = {J R Manning and G M Notaro and E Chen and P C Fitzpatrick},
date-modified = {2021-10-27 22:27:03 -0400},
journal = {{bioRxiv}},
title = {Fitness tracking reveals task-specific associations between memory, mental health, and exercise},
volume = {doi.org/10.1101/2021.10.22.465441},
Expand Down Expand Up @@ -1712,8 +1665,7 @@ @article{AdacEtal12
year = {2012}}

@article{GoniEtal14,
author = {J Go{\~ n}i and M P van den Heuvel and A Avena-Koenigsberger and N V de Mendizabal and R F Betzel and A Griffa and P Hagmann and B Corominas-Murtra and J-P Thiran and O Sporns},
date-modified = {2021-10-27 22:28:35 -0400},
author = {J Go{\~n}i and M P van den Heuvel and A Avena-Koenigsberger and N V de Mendizabal and R F Betzel and A Griffa and P Hagmann and B Corominas-Murtra and J-P Thiran and O Sporns},
journal = {Proceedings of the National Academy of Sciences, {USA}},
number = {2},
pages = {833--838},
Expand Down Expand Up @@ -6177,7 +6129,6 @@ @article{Scho66
@incollection{ChenEtal15a,
author = {P-H Chen and J Chen and Y Yeshurun and U Hasson and J Haxby and P J Ramadge},
booktitle = {Advances in Neural Information Processing Systems},
date-modified = {2021-10-27 10:59:48 -0400},
editor = {C Cortes and N D Lawrence and D D Lee and M Sugiyama and R Garnett},
pages = {460--468},
publisher = {Curran Associates, Incorporated},
Expand Down Expand Up @@ -43763,7 +43714,6 @@ @article{HiggJohn09

@article{SmitEtal13a,
author = {T A Smith and A E Hasinksi and P B Sederberg},
date-modified = {2021-10-27 22:50:24 -0400},
journal = {Journal of Experimental Psychology: General},
title = {The context repetition effect: predicted events are remembered better, even when they don't happen},
volume = {In press},
Expand Down