Merge branch '2024' into Gagnon_Kebe_Tahiri

papers/Alireza_Vaezi/myst.yml

@@ -1,50 +1,51 @@
 version: 1
+extends: ../proceedings.yml
 project:
+  doi: 10.25080/HXCJ6205
   # Update this to match `scipy-2024-<folder>` the folder should be `<firstname_surname>`
   id: scipy-2024-alireza-vaezi
   # Ensure your title is the same as in your `main.md`
   title: Training a Supervised Cilia Segmentation Model from Self-Supervision
-  subtitle: University Of Georgia
+  description: Understanding cilia behavior is essential in diagnosing and treating such diseases, but, the tasks of automatically analyzing cilia are often a labor and time-intensive. In this work we overcome this bottleneck by developing a robust, self-supervised framework exploiting the visual similarity of normal and dysfunctional cilia.
   # Authors should have affiliations, emails and ORCIDs if available
   authors:
-  - name: Seyed Alireza Vaezi
-    email: sv22900@uga.edu
-    orcid: 0009-0000-2089-8362
-    affiliations:
-    - University of Georgia
-    corresponding: true
-  - name: Shannon Quinn
-    email: spq@uga.edu
-    affiliations:
-    - University of Georgia
+    - name: Seyed Alireza Vaezi
+      email: sv22900@uga.edu
+      orcid: 0009-0000-2089-8362
+      affiliations:
+        - name: University of Georgia
+          ror: https://ror.org/00te3t702
+      corresponding: true
+    - name: Shannon Quinn
+      email: spq@uga.edu
+      affiliations:
+        - name: University of Georgia
+          ror: https://ror.org/00te3t702
   keywords:
-  - Cilia
-  - Unsupervised biomedical Image Segmentation
-  - Optical Flow
-  - Autoregressive
-  - Deep Learning
+    - Cilia
+    - Unsupervised biomedical Image Segmentation
+    - Optical Flow
+    - Autoregressive
+    - Deep Learning
   # Add the abbreviations that you use in your paper here
   abbreviations:
-    MyST: Markedly Structured Text
+    OF: optical flow
+    PCD: primary ciliary dyskinesia
+    ZCA: Zero-phase PCA Sphering
+    SAE: Sparse Autoencoders
+    AR: autoregressive
+    FPN: Feature Pyramid Network
   # It is possible to explicitly ignore the `doi-exists` check for certain citation keys
   error_rules:
-  - rule: doi-exists
-    severity: ignore
-    keys:
-    - Atr03
-    - terradesert
-    - jupyter
-    - sklearn1
-    - sklearn2
-    - Iakubovskii:2019
-    - settles2009active
-  # A banner will be generated for you on publication, this is a placeholder
-  banner: banner.jpg
-  # The rest of the information shouldn't be modified
-  subject: Research Article
-  open_access: true
-  license: CC-BY-4.0
-  venue: Scipy 2024
-  date: 2024-07-10
+    - rule: doi-exists
+      severity: ignore
+      keys:
+        - Atr03
+        - terradesert
+        - jupyter
+        - sklearn1
+        - sklearn2
+        - Iakubovskii:2019
+        - settles2009active
 site:
   template: article-theme

papers/Arushi_Nath/mybib.bib

@@ -1,130 +1,93 @@
-# Feel free to delete these first few references, which are specific to the template:
-
-@book{hume48,
-  author    = "David Hume",
-  year      = "1748",
-  title     = "An enquiry concerning human understanding",
-  address   = "Indianapolis, IN",
-  publisher = "Hackett",
-  doi       = {https://doi.org/10.1017/CBO9780511808432},
+@misc{CNEOS_Totals,
+  author       = {{Center for Near-Earth Object Studies}},
+  title        = {Total number of asteroids discovered monthly},
+  howpublished = {\url{https://cneos.jpl.nasa.gov/stats/totals.html}},
+  note         = {Accessed: October 1, 2024}
 }
 
-@article{Atr03,
-  author  = "P Atreides",
-  year    = "2003",
-  title   = "How to catch a sandworm",
-  journal = "Transactions on Terraforming",
-  volume  = 21,
-  issue   = 3,
-  pages   = {261-300}
+@misc{NASA_DART2022,
+  author       = {{NASA/Johns Hopkins University Applied Physics Laboratory}},
+  title        = {NASA's first planetary defense technology demonstration to collide with asteroid in 2022},
+  month        = {March},
+  year         = {2022},
+  howpublished = {\url{https://www.nasa.gov/feature/nasa-s-first-planetary-defense-technology-demonstration-to-collide-with-asteroid-in-2022}},
+  note         = {Accessed: October 1, 2024}
 }
 
-@misc{terradesert,
-  author  = {{TerraDesert Team}},
-  title   = {Code for terraforming a desert},
-  year    = {2000},
-  url     = {https://terradesert.com/code/},
-  note    = {Accessed 1 Jan. 2000}
+@article{Shevchenko2019,
+  author  = {Shevchenko, V. G. and Tedesco, E. F. and Kovalchuk, L. O. and Fiacconi, A. M. and Zubarev, V. A.},
+  title   = {Phase integral of asteroids},
+  journal = {Astronomy \& Astrophysics},
+  volume  = {626},
+  pages   = {A87},
+  year    = {2019},
+  doi     = {10.1051/0004-6361/201935588}
 }
 
-# These references may be helpful:
-
-@inproceedings{jupyter,
-  abstract  = {It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.},
-  author    = {Kluyver, Thomas and Ragan-Kelley, Benjamin and Pérez, Fernando and Granger, Brian and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica and Grout, Jason and Corlay, Sylvain and Ivanov, Paul and Avila, Damián and Abdalla, Safia and Willing, Carol and {Jupyter development team}},
-  editor    = {Loizides, Fernando and Scmidt, Birgit},
-  location  = {Netherlands},
-  publisher = {IOS Press},
-  url       = {https://eprints.soton.ac.uk/403913/},
-  booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
-  year      = {2016},
-  pages     = {87--90},
-  title     = {Jupyter Notebooks - a publishing format for reproducible computational workflows},
+@misc{Talbert2022,
+  author       = {Talbert, Tricia},
+  title        = {NASA DART imagery shows changed orbit of target asteroid},
+  howpublished = {NASA},
+  month        = {October},
+  day          = {11},
+  year         = {2022},
+  url          = {https://www.nasa.gov/solar-system/nasa-dart-imagery-shows-changed-orbit-of-target-asteroid/},
+  note         = {Accessed: October 1, 2024}
 }
 
-@article{matplotlib,
-  abstract     = {Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.},
-  author       = {Hunter, J. D.},
-  publisher    = {IEEE COMPUTER SOC},
-  year         = {2007},
-	doi          = {https://doi.org/10.1109/MCSE.2007.55},
-  journal      = {Computing in Science \& Engineering},
-  number       = {3},
-  pages        = {90--95},
-  title        = {Matplotlib: A 2D graphics environment},
-  volume       = {9},
+@misc{JPL_SBDB,
+  author       = {{Jet Propulsion Laboratory}},
+  title        = {Small-Body Database Lookup},
+  howpublished = {\url{https://ssd.jpl.nasa.gov/tools/sbdb_lookup.html\#/?sstr=65803}},
+  note         = {Accessed: October 1, 2024}
 }
 
-@article{numpy,
-  author       = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, Stéfan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and del Río, Jaime Fernández and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
-  publisher    = {Springer Science and Business Media {LLC}},
-  doi          = {https://doi.org/10.1038/s41586-020-2649-2},
-  date         = {2020-09},
-  year         = {2020},
-  journal      = {Nature},
-  number       = {7825},
-  pages        = {357--362},
-  title        = {Array programming with {NumPy}},
-  volume       = {585},
+@misc{FinkBroker,
+  author       = {{Fink Broker}},
+  title        = {ZTF Minor Planet Photometric Data Release},
+  howpublished = {\url{https://fink-portal.org/}},
+  note         = {Accessed: October 1, 2024}
 }
 
-@misc{pandas1,
-  author    = {{The Pandas Development Team}},
-  title     = {pandas-dev/pandas: Pandas},
-  month     = feb,
-  year      = {2020},
-  publisher = {Zenodo},
-  version   = {latest},
-  url       = {https://doi.org/10.5281/zenodo.3509134},
+@misc{ESA_Gaia_DR3,
+  author       = {{European Space Agency}},
+  title        = {Gaia Data Release 3},
+  howpublished = {\url{https://www.cosmos.esa.int/web/gaia/dr3}},
+  note         = {Accessed: October 1, 2024}
 }
 
-@inproceedings{pandas2,
-  author    = {Wes McKinney},
-  title     = {{D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython},
-  booktitle = {{P}roceedings of the 9th {P}ython in {S}cience {C}onference},
-  pages     = {56 - 61},
-  year      = {2010},
-  editor    = {{S}t\'efan van der {W}alt and {J}arrod {M}illman},
-	doi       = {https://doi.org/10.25080/Majora-92bf1922-00a},
+@misc{ALCDEF,
+  author       = {{ALCDEF}},
+  title        = {Asteroid Lightcurve Photometry Database},
+  howpublished = {\url{https://alcdef.org/}},
+  note         = {Accessed: October 1, 2024}
 }
 
-@article{scipy,
-  author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
-            Haberland, Matt and Reddy, Tyler and Cournapeau, David and
-            Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
-            Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
-            Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
-            Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
-            Kern, Robert and Larson, Eric and Carey, C J and
-            Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
-            {VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
-            Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
-            Harris, Charles R. and Archibald, Anne M. and
-            Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and
-            {van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
-  title   = {{{SciPy} 1.0: Fundamental Algorithms for Scientific
-            Computing in Python}},
-  journal = {Nature Methods},
-  year    = {2020},
-  volume  = {17},
-  pages   = {261--272},
-  adsurl  = {https://rdcu.be/b08Wh},
-	doi     = {https://doi.org/10.1038/s41592-019-0686-2},
+@misc{PSI_APC,
+  author       = {{Planetary Science Institute}},
+  title        = {Asteroid Photometric Catalog (APC) "Third Update"},
+  howpublished = {\url{https://sbn.psi.edu/pds/resource/apc.html}},
+  note         = {Accessed: October 1, 2024}
 }
 
-@article{sklearn1,
-  author       = {Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
-  year         = {2011},
-  journal      = {Journal of Machine Learning Research},
-  pages        = {2825--2830},
-  title        = {Scikit-learn: Machine Learning in {P}ython},
-  volume       = {12},
+@article{Pravec2000,
+  author  = {Pravec, P. and Harris, A. W.},
+  title   = {Fast and Slow Rotation of Asteroids},
+  journal = {Icarus},
+  volume  = {148},
+  number  = {1},
+  pages   = {12--20},
+  year    = {2000},
+  doi     = {10.1006/icar.2000.6482}
 }
 
-@inproceedings{sklearn2,
-  author    = {Buitinck, Lars and Louppe, Gilles and Blondel, Mathieu and Pedregosa, Fabian and Mueller, Andreas and Grisel, Olivier and Niculae, Vlad and Prettenhofer, Peter and Gramfort, Alexandre and Grobler, Jaques and Layton, Robert and VanderPlas, Jake and Joly, Arnaud and Holt, Brian and Varoquaux, Gaël},
-  booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
-  year      = {2013},
-  pages     = {108--122},
-  title     = {{API} design for machine learning software: experiences from the scikit-learn project},
+@article{DeMeo2014,
+  author  = {DeMeo, F. E. and Carry, B.},
+  title   = {Solar System evolution from compositional mapping of the asteroid belt},
+  journal = {Nature},
+  volume  = {505},
+  number  = {7485},
+  pages   = {629--634},
+  year    = {2014},
+  doi     = {10.1038/nature12908}
 }

papers/Arushi_Nath/myst.yml

@@ -1,5 +1,7 @@
 version: 1
+extends: ../proceedings.yml
 project:
+  doi: 10.25080/TWCF2755
   # Update this to match `scipy-2024-<folder>` the folder should be `<firstname_surname>`
   id: scipy-2024-Arushi_Nath
   # Ensure your title is the same as in your `main.md`
@@ -17,7 +19,18 @@ project:
     - Open Data
     - Citizen Scientists
     - Asteroid Characterization
-
+  abbreviations:
+    ATLAS: Asteroid Terrestrial-impact Last Alert System
+    DART: Double Asteroid Redirection Test
+    ZTF: Zwicky Transient Facility
+    LSST: Legacy Survey of Space and Time
+    ALCDEF: Asteroid Lightcurve Database
+    C-type: carbonaceous
+    S-type: siliceous
+    M-type: metallic
+    PDS: Photometric Data Catalog
+    MPC: Minor Planet Center
+    SNR: Signal-to-Noise Ratio
   # It is possible to explicitly ignore the `doi-exists` check for certain citation keys
   error_rules:
     - rule: doi-exists
@@ -28,13 +41,5 @@ project:
         - jupyter
         - sklearn1
         - sklearn2
-  # A banner will be generated for you on publication, this is a placeholder
-  banner: banner.png
-  # The rest of the information shouldn't be modified
-  subject: Research Article
-  open_access: true
-  license: CC-BY-4.0
-  venue: Scipy 2024
-  date: 2024-07-10
 site:
   template: article-theme

papers/Gagnon_Kebe_Tahiri/main.tex

@@ -388,4 +388,4 @@ \section{Conclusion}\label{conclusion}
 However, it is important to recognize the limitations of our study. In particular, the three missing data points on O\textsubscript{2} concentration (mg/L) and the relatively small sample size ($n=62$) may have induced a bias, which could impact the validity of our interpretations and restrict the generalizability of our results. Moreover, these missing data could provide partial insight into the relationship between O\textsubscript{2} concentration (mg/L) and genetic fluctuation in Cumacea, and our sample size may reduce the statistical power of our results. Future studies should address these gaps by incorporating larger sample sizes and more complete datasets to confirm and expand our conclusions. Additionally, as our research focuses solely on the partial sequence of the mitochondrial 16S rRNA gene, utilizing more elaborate genomic methods, such as whole-gene or even whole-genome sequencing, could help better understand marine species' genetic variety and global acclimatization mechanisms. This would provide more comprehensive genetic databases to improve accuracy and knowledge in identifying existing (and new) marine invertebrate species using DNA barcoding (e.g., mitochondrial DNA cytochrome c oxidase I (COX1)). Finally, multidisciplinary collaborations between ecology, genetics, and oceanography would be essential to enhance knowledge sharing and its application in future research.
 
 \section{Acknowledgments}\label{acknowledgments}
-The authors thank the SciPy conference and reviewers for their valuable comments on this paper as well as Mansour Kebe for his technical support and Carolin Uhlir for her clarifications and advice on her study \citep{uhlir_adding_2021}. This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC), the Fonds de recherche du Québec - Nature et technologies (FRQNT), the Université de Sherbrooke grant, and the Centre de recherche en écologie de l’Université de Sherbrooke (CREUS).
+The authors thank the SciPy conference and reviewers for their valuable comments on this paper as well as Mansour Kebe for his technical support and Carolin Uhlir for her clarifications and advice on her study \citep{uhlir_adding_2021}. This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC), the Fonds de recherche du Québec - Nature et technologies (FRQNT), the Université de Sherbrooke grant, and the Centre de recherche en écologie de l’Université de Sherbrooke (CREUS).

papers/Gagnon_Kebe_Tahiri/myst.yml

@@ -38,4 +38,4 @@ project:
       severity: ignore
       keys:
 site:
-  template: article-theme
+  template: article-theme