Feature/joss paper

.github/workflows/draft-pdf.yml

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+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: Paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: Paper/paper.pdf

Paper/bibliography.bib

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+@article{Simmonds:2006,
+        year = {2006},
+        title = {{Surgical resection of hepatic metastases from colorectal cancer: A systematic review of published studies}},
+        author = {Simmonds, P C and Primrose, J N and Colquitt, J L and Garden, O J and Poston, G J and Rees, M},
+        journal = {British Journal of Cancer},
+        issn = {0007-0920},
+        doi = {10.1038/sj.bjc.6603033},
+        pmid = {16538219},
+        pmcid = {PMC2361241},
+        pages = {982--999},
+        number = {7},
+        volume = {94}
+}
+
+@article{Hansen:2014,
+        year = {2014},
+        title = {{Impact of model-based risk analysis for liver surgery planning}},
+        author = {Hansen, C. and Zidowitz, S. and Preim, B. and Stavrou, G. and Oldhafer, K. J. and Hahn, H. K.},
+        journal = {International Journal of Computer Assisted Radiology and Surgery},
+        issn = {1861-6410},
+        doi = {10.1007/s11548-013-0937-0},
+        pmid = {24122443},
+        pages = {473--480},
+        number = {3},
+        volume = {9}
+}
+
+@article{Lamata:2010,
+       year = {2010},
+       title = {{Use of the Resection Map system as guidance during hepatectomy}},
+       author = {Lamata, Pablo and Lamata, Félix and Sojar, Valentin and Makowski, Piotr and Massoptier, Laurent and Casciaro, Sergio and Ali, Wajid and Stüdeli, Thomas and Declerck, Jérôme and Elle, Ole Jakob and Elle, Ole Jackov and Edwin, Bjørn and Edwin, Björn},
+       journal = {Surgical Endoscopy},
+       issn = {0930-2794},
+       doi = {10.1007/s00464-010-0915-3},
+       pmid = {20177937},
+       pmcid = {PMC2939346},
+       pages = {2327--2337},
+       number = {9},
+       volume = {24}
+}
+
+@article{Palomar:2017,
+       year = {2017},
+       rating = {0},
+       title = {{A novel method for planning liver resections using deformable Bézier surfaces and distance maps}},
+       author = {Palomar, Rafael and Cheikh, Faouzi A and Edwin, Bjørn and Fretland, Åsmund and Beghdadi, Azeddine and Elle, Ole J},
+       journal = {Computer Methods and Programs in Biomedicine},
+       doi = {10.1016/j.cmpb.2017.03.019},
+       pmid = {28494998},
+       url = {http://dx.doi.org/10.1016/j.cmpb.2017.03.019},
+       abstract = {{Computer Methods and Programs in Biomedicine, 144 (2017) 135-145. doi:10.1016/j.cmpb.2017.03.019}},
+       pages = {135 -- 145},
+       volume = {144},
+       language = {English},
+       month = {06}
+}
+
+@book{Preim:2013,
+  title={Visual computing for medicine: theory, algorithms, and applications},
+  author={Preim, Bernhard and Botha, Charl P},
+  year={2013},
+  publisher={Newnes}
+}
+@article{Warmann:2016,
+  title={Computer-assisted surgery planning in children with complex liver tumors identifies variability of the classical Couinaud classification},
+  author={Warmann, Steven W and Schenk, Andrea and Schaefer, Juergen F and Ebinger, Martin and Blumenstock, Gunnar and Tsiflikas, Ilias and Fuchs, Joerg},
+  journal={Journal of Pediatric Surgery},
+  volume={51},
+  number={11},
+  pages={1801--1806},
+  year={2016},
+  publisher={Elsevier}
+}
+@article{Bismuth:2013,
+  title={Revisiting liver anatomy and terminology of hepatectomies},
+  author={Bismuth, Henri},
+  journal={Annals of surgery},
+  volume={257},
+  number={3},
+  pages={383--386},
+  year={2013},
+  publisher={LWW}
+}
+@incollection{Kikinis:2013,
+  title={3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support},
+  author={Kikinis, Ron and Pieper, Steve D and Vosburgh, Kirby G},
+  booktitle={Intraoperative imaging and image-guided therapy},
+  pages={277--289},
+  year={2013},
+  publisher={Springer}
+}
+
+@book{d'Albenzio:2023, type={preprint},
+  title={Patient-Specific Functional Liver Segments based on Centerline Classification of the Hepatic and Portal Veins},
+  url={https://www.researchsquare.com/article/rs-3574517/v1},
+  DOI={10.21203/rs.3.rs-3574517/v1},
+  abstractNote={Couinaud’s liver segment classification has served as the standard basis for liver surgery planning for nearly seven decades. While providing a systematic framework by dividing the liver into eight segments, its reliance on fixed planar boundaries may not always align with individual liver anatomical variations. In this study, we propose a new method for classifying liver functional segments. By integrating patient-specific liver morphology, 3D vascular system, and user-defined landmarks, our approach offers greater flexibility in classifying the liver while respecting individual anatomical variations. We conducted a comprehensive assessment of our method, comparing it with two widely used liver classification techniques: conventional plane-based and portal vein-based classifications. Our results demonstrate that our method’s flexibility extends beyond conventional software. By enabling the inclusion of both hepatic and portal veins, including peripheral branches, our approach deviates from the classical Couinaud classification. Importantly, our findings indicate that our approach not only overcomes the limitations of traditional methods but also provides a more precise and surgery-ready definition of liver segments, particularly in complex cases involving segments 5 and 8. Furthermore, feedback from liver surgery specialists highlights its potential benefits, including improved visualization in complex cases and better assessment of vascular perfusion territories.},
+  institution={In Review},
+  author={d’Albenzio, Gabriella and Meng, Ruoyan and Aghayan, Davit and Pelanis, Egidijus and Sakinis, Tomas and Solberg, Ole Vegard and Tangen, Geir Arne and Kumar, Rahul P. and Elle, Ole Jakob and Edwin, Bjørn and Palomar, Rafael},
+  year={2023},
+  month=nov,
+  language={en} }
+
+@inproceedings {Meng:2023,
+booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine},
+editor = {Hansen, Christian and Procter, James and Renata G. Raidou and Jönsson, Daniel and Höllt, Thomas},
+title = {{Resectograms: Real-Time 2D Visualization of Liver Virtual Resections}},
+author = {Meng, Ruoyan and Aghayan, Davit and Pelanis, Egidijus and Edwin, Bjørn and Cheikh, Faouzi Alaya and Palomar, Rafael},
+year = {2023},
+publisher = {The Eurographics Association},
+ISSN = {2070-5786},
+ISBN = {978-3-03868-216-5},
+DOI = {10.2312/vcbm.20231209}
+}
+
+@article{Aghayan:2023, title={Laparoscopic parenchyma-sparing liver resection for large (≥ 50 mm) colorectal metastases}, volume={37}, ISSN={0930-2794, 1432-2218}, DOI={10.1007/s00464-022-09493-3}, abstractNote={Background  Traditionally, patients with large liver tumors (≥ 50 mm) have been considered for anatomic major hepatectomy. Laparoscopic resection of large liver lesions is technically challenging and often performed by surgeons with extensive experience. The current study aimed to evaluate the surgical and oncologic safety of laparoscopic parenchyma-sparing liver resection in patients with large colorectal metastases.
+Methods  Patients who primarily underwent laparoscopic parenchyma-sparing liver resection (less than 3 consecutive liver segments) for colorectal liver metastases between 1999 and 2019 at Oslo University Hospital were analyzed. In some recent cases, a computer-assisted surgical planning system was used to better visualize and understand the patients’ liver anatomy, as well as a tool to further improve the resection strategy. The surgical and oncologic outcomes of patients with large (≥ 50 mm) and small (< 50 mm) tumors were compared. Multivariable Cox-regression analysis was performed to identify risk factors for survival.
+Results  In total 587 patients met the inclusion criteria (large tumor group, n = 59; and small tumor group, n = 528). Median tumor size was 60 mm (range, 50–110) in the large tumor group and 21 mm (3–48) in the small tumor group (p < 0.001). Patient age and CEA level were higher in the large tumor group (8.4 μg/L vs. 4.6 μg/L, p < 0.001). Operation time and conversion rate were similar, while median blood loss was higher in the large tumor group (500 ml vs. 200 ml, p < 0.001). Patients in the large tumor group had shorter 5 year overall survival (34% vs 49%, p = 0.027). However, in the multivariable Cox-regression analysis tumor size did not impact survival, unlike parameters such as age, ASA score, CEA level, extrahepatic disease at liver surgery, and positive lymph nodes in the primary tumor.
+Conclusion  Laparoscopic parenchyma-sparing resections for large colorectal liver metastases provide satisfactory short and long-term outcomes.}, number={1}, journal={Surgical Endoscopy}, author={Aghayan, Davit L. and d’Albenzio, Gabriella and Fretland, Åsmund A. and Pelanis, Egidijus and Røsok, Bård I. and Yaqub, Sheraz and Palomar, Rafael and Edwin, Bjørn}, year={2023}, month=jan, pages={225–233}, language={en} }
+
+@article{Siegel:2023,
+author = {Siegel, Rebecca L. and Miller, Kimberly D. and Wagle, Nikita Sandeep and Jemal, Ahmedin},
+title = {Cancer statistics, 2023},
+journal = {CA: A Cancer Journal for Clinicians},
+volume = {73},
+number = {1},
+pages = {17-48},
+keywords = {cancer cases, cancer statistics, death rates, incidence, mortality},
+abstract = {Abstract Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths in the United States and compiles the most recent data on population-based cancer occurrence and outcomes using incidence data collected by central cancer registries and mortality data collected by the National Center for Health Statistics. In 2023, 1,958,310 new cancer cases and 609,820 cancer deaths are projected to occur in the United States. Cancer incidence increased for prostate cancer by 3\% annually from 2014 through 2019 after two decades of decline, translating to an additional 99,000 new cases; otherwise, however, incidence trends were more favorable in men compared to women. For example, lung cancer in women decreased at one half the pace of men (1.1\% vs. 2.6\% annually) from 2015 through 2019, and breast and uterine corpus cancers continued to increase, as did liver cancer and melanoma, both of which stabilized in men aged 50 years and older and declined in younger men. However, a 65\% drop in cervical cancer incidence during 2012 through 2019 among women in their early 20s, the first cohort to receive the human papillomavirus vaccine, foreshadows steep reductions in the burden of human papillomavirus-associated cancers, the majority of which occur in women. Despite the pandemic, and in contrast with other leading causes of death, the cancer death rate continued to decline from 2019 to 2020 (by 1.5\%), contributing to a 33\% overall reduction since 1991 and an estimated 3.8 million deaths averted. This progress increasingly reflects advances in treatment, which are particularly evident in the rapid declines in mortality (approximately 2\% annually during 2016 through 2020) for leukemia, melanoma, and kidney cancer, despite stable/increasing incidence, and accelerated declines for lung cancer. In summary, although cancer mortality rates continue to decline, future progress may be attenuated by rising incidence for breast, prostate, and uterine corpus cancers, which also happen to have the largest racial disparities in mortality.},
+year = {2023}
+}
+
+@article{Petrowsky2020,
+  author = {Petrowsky, Henrik and Fritsch, Ralph and Guckenberger, Matthias and De Oliveira, Michelle L. and Dutkowski, Philipp and Clavien, Pierre-Alain},
+  title = {Modern therapeutic approaches for the treatment of malignant liver tumours},
+  journal = {Nature Reviews Gastroenterology \& Hepatology},
+  volume = {17},
+  number = {12},
+  pages = {755--772},
+  year = {2020},
+  doi = {10.1038/s41575-020-0314-8},
+  abstract = {Malignant liver tumours include a wide range of primary and secondary tumours. Although surgery remains the mainstay of curative treatment, modern therapies integrate a variety of neoadjuvant and adjuvant strategies and have achieved dramatic improvements in survival. Extensive tumour loads, which have traditionally been considered unresectable, are now amenable to curative treatment through systemic conversion chemotherapies followed by a variety of interventions such as augmentation of the healthy liver through portal vein occlusion, staged surgeries or ablation modalities. Liver transplantation is established in selected patients with hepatocellular carcinoma but is now emerging as a promising option in many other types of tumour such as perihilar cholangiocarcinomas, neuroendocrine or colorectal liver metastases. In this Review, we summarize the available therapies for the treatment of malignant liver tumours, with an emphasis on surgical and ablative approaches and how they align with other therapies such as modern anticancer drugs or radiotherapy. In addition, we describe three complex case studies of patients with malignant liver tumours. Finally, we discuss the outlook for future treatment, including personalized approaches based on molecular tumour subtyping, response to targeted drugs, novel biomarkers and precision surgery adapted to the specific tumour.},
+  issn = {1759-5053},
+  url = {https://doi.org/10.1038/s41575-020-0314-8}
+}
+
+@misc{3DSlicerExtensionsManager:2024,
+  title={3D Slicer Extension Manager User Guide},
+  url={https://slicer.readthedocs.io/en/latest/user_guide/extensions_manager.html},
+  note={Accessed on April 2, 2024},
+  year={2024}
+}
+
+@article{meng2023resectograms,
+  title={Resectograms: Real-Time 2D Visualization of Liver Virtual Resections},
+  author={Meng, Ruoyan and Aghayan, Davit and Pelanis, Egidijus and Edwin, Bj{\o}rn and Cheikh, Faouzi Alaya and Palomar, Rafael},
+  year={2023}
+}
+
+@article{Bismuth:1982,
+  title={Surgical anatomy and anatomical surgery of the liver},
+  author={Bismuth, Henri},
+  journal={World journal of surgery},
+  volume={6},
+  pages={3--9},
+  year={1982},
+  publisher={Springer},
+  doi = {10.1007/BF01656368},
+  url = {https://doi.org/10.1007/BF01656368}
+}
+