Upload extract stage outputs 2025-11-27T17:17:03.861548Z (batch 1/2)

stage1/sample_00000/document.md

@@ -1,45 +1 @@
-21 April 2023 Accepted: 03 June 2023 Published: 07 June 2023  
-
-## Ethics approval and consent to participate  
-
-The study was conducted in accordance with the ethical principles of the Declaration of Helsinki (2013). Ethical approval was obtained from Sakhiya Skin Clinic, Surat, Gujarat, India. (Approval No: 2023/06). Consent forms were signed by patient. He was informed that he had the right to withdraw from the study at any time without any consequences. All pictures reported in this case- report study belong to Sakhiya Skin Clinic, Surat- 395003, Gujarat, India.  
-
-## Consent for publication  
-
-Not applicable  
-
-## Competing interest  
-
-The authors declare that they have no competing interests.  
-
-## Open Access  
-
-This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article unless otherwise stated.  
-
-## Author Details  
-
-1Department of Dermatology, Sakhiya Skin Clinic, Surat, Gujarat, India. 2Department of Medical Writing, Sakhiya Skin Clinic, Surat, Gujarat, India  
-
-## Article Info  
-
-Received: 21 April 2023 Accepted: 03 June 2023 Published: 07 June 2023  
-
-## References  
-
-1. Grando SA. Pemphigus autoimmunity: hypotheses and realities. Autoimmunity. 2012 Feb;45(1):7-35. doi: 10.3109/08916934.2011.606444. 
-2. Lever WF, Schaumburg-Lever G. Immunosuppressants and prednisone in pemphigus vulgaris: therapeutic results obtained in 63 patients between 1961 and 1975. Arch Dermatol. 1977 Sep;113(9):1236-41. doi: 10.1001/archderm.1977.016400900084013. 
-3. Pasricha JS, Gupta R. Pulse therapy with dexamethasonecyclophosphamide in pemphigus. Indian J Dermatol Venereol Leprol. 1984; 50:199-203. 
-4. Bystryn JC, Steinman NM. The adjuvant therapy of pemphigus. An update. Arch Dermatol. 1996 Sep;132(2):203-12.  
-
-5. Heizmann M, Itin P, Wernli M, Borradori L, Bargetzi MJ. Successful treatment of paraneoplastic pemphigus in follicular NHL with rituximab: report of a case and review of treatment for paraneoplastic pemphigus in NHL and CLL. Am J Hematol. Feb 2001;66(2):142-4. doi: 10.1002/1096-8652(200102)66:2<142::AID-AJH1032>3.0.CO;2-0. 
-6. Food and Drug Administration. Rituxan label; 2012 [cited Feb 2, 2021]. Available from: http://www.accessdata.fda.gov/drugsatfda_docs/label/2012 /103705s5373lbl.pdf. 
-7. Belgi AS, Azeze M, Hoyle C, Williams REA. Response of pemphigus vulgaris to anti-CD20 antibody therapy (rituximab) may be delayed. Clin Exp Dermatol. 2006 Jan;31(1):143. doi: 10.1111/j.1365-2230.2005.01941. x. 
-8. Schmidt E, Seitz CS, Benoit S, Bröcker EB, Goebeler M. Rituximab in autoimmune bullous diseases: mixed responses and adverse effects. Br J Dermatol. 2007 Feb;156(2):352-6. doi: 10.1111/j.1365-2133.2006.07646. x. 
-9. Barrera MV, Mendiola MV, Bosch RJ, Herrera E. Prolonged treatment with rituximab in patients with refractory pemphigus vulgaris. J Dermatol Treat. 2007 Jan;18(5):312-4. doi: 10.1080/09546630701323988. 
-10. Faurschou A, Gniadecki R. Two courses of rituximab (anti-CD20 monoclonal antibody) for recalcitrant pemphigus vulgaris. Int J Dermatol. 2008 Mar;47(3):292-4. doi: 10.1111/j.1365-4632.2008.03423. x. 
-11. Craythorne EE, Mufti G, DuVivier AW. Rituximab used as a first-line single agent in the treatment of pemphigus vulgaris. J Am Acad Dermatol. 2011 Nov;65(5):1064-5. doi: 10.1016/j.jaad.2010.06.033. 
-12. Horvath B, Huizinga J, Pas HH, Mulder AB, Jonkman MF. Low-dose rituximab is effective in pemphigus. Br J Dermatol. 2012 Feb;166(2):405-12. doi: 10.1111/j.1365-2133.2011.10663. x. 
-13. Craythorne E, Du Vivier A, Mufti GJ, Warnakulasuriya S. Rituximab for the treatment of corticosteroid—refractory pemphigus vulgaris with oral and skin manifestations. J Oral Pathol Med. 2011 Sep;40(8):616-20. doi: 10.1111/j.1600-0714.2011.01017. x. 
-14. Kim JH, Kim YH, Kim MR, Kim SC. Clinical efficacy of different doses of rituximab in the treatment of pemphigus: a retrospective study of 27 patients. Br J Dermatol. 2011Sep;165(3):646-51. doi: 10.1111/j.1365-2133.2011.10411. x. 
-15. Kasperkiewicz M, Shimanovich I, Ludwig RJ, Rose C, Zillikens D, Schmidt E. Rituximab for treatment-refractory pemphigus and pemphigoid: a case series of 17 patients. J Am Acad Dermatol. 2011 Sep;65(3):552-8. doi: 10.1016/j.jaad.2010.07.032 
-16. Investor update. Basel; June 12, 2019. [cited Feb 5, 2021]. Available from: https://www.roche.com/investors/updates/inv-update-2019-06-12. htm.
+21 (2): 82-84. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012

stage1/sample_00000/raw_response.md

@@ -1,60 +1 @@
-21 April 2023 Accepted: 03 June 2023 Published: 07 June 2023  
-
-<|ref|>sub_title<|/ref|><|det|>[[95, 88, 369, 101]]<|/det|>
-## Ethics approval and consent to participate  
-
-<|ref|>text<|/ref|><|det|>[[94, 100, 482, 203]]<|/det|>
-The study was conducted in accordance with the ethical principles of the Declaration of Helsinki (2013). Ethical approval was obtained from Sakhiya Skin Clinic, Surat, Gujarat, India. (Approval No: 2023/06). Consent forms were signed by patient. He was informed that he had the right to withdraw from the study at any time without any consequences. All pictures reported in this case- report study belong to Sakhiya Skin Clinic, Surat- 395003, Gujarat, India.  
-
-<|ref|>sub_title<|/ref|><|det|>[[94, 216, 247, 228]]<|/det|>
-## Consent for publication  
-
-<|ref|>text<|/ref|><|det|>[[94, 228, 179, 241]]<|/det|>
-Not applicable  
-
-<|ref|>sub_title<|/ref|><|det|>[[94, 255, 218, 267]]<|/det|>
-## Competing interest  
-
-<|ref|>text<|/ref|><|det|>[[94, 268, 444, 280]]<|/det|>
-The authors declare that they have no competing interests.  
-
-<|ref|>sub_title<|/ref|><|det|>[[94, 295, 177, 306]]<|/det|>
-## Open Access  
-
-<|ref|>text<|/ref|><|det|>[[93, 308, 482, 434]]<|/det|>
-This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article unless otherwise stated.  
-
-<|ref|>sub_title<|/ref|><|det|>[[94, 448, 192, 460]]<|/det|>
-## Author Details  
-
-<|ref|>text<|/ref|><|det|>[[93, 460, 461, 513]]<|/det|>
-1Department of Dermatology, Sakhiya Skin Clinic, Surat, Gujarat, India. 2Department of Medical Writing, Sakhiya Skin Clinic, Surat, Gujarat, India  
-
-<|ref|>sub_title<|/ref|><|det|>[[93, 528, 170, 538]]<|/det|>
-## Article Info  
-
-<|ref|>text<|/ref|><|det|>[[93, 541, 244, 578]]<|/det|>
-Received: 21 April 2023 Accepted: 03 June 2023 Published: 07 June 2023  
-
-<|ref|>sub_title<|/ref|><|det|>[[93, 594, 165, 605]]<|/det|>
-## References  
-
-<|ref|>text<|/ref|><|det|>[[93, 607, 482, 784]]<|/det|>
-1. Grando SA. Pemphigus autoimmunity: hypotheses and realities. Autoimmunity. 2012 Feb;45(1):7-35. doi: 10.3109/08916934.2011.606444. 
-2. Lever WF, Schaumburg-Lever G. Immunosuppressants and prednisone in pemphigus vulgaris: therapeutic results obtained in 63 patients between 1961 and 1975. Arch Dermatol. 1977 Sep;113(9):1236-41. doi: 10.1001/archderm.1977.016400900084013. 
-3. Pasricha JS, Gupta R. Pulse therapy with dexamethasonecyclophosphamide in pemphigus. Indian J Dermatol Venereol Leprol. 1984; 50:199-203. 
-4. Bystryn JC, Steinman NM. The adjuvant therapy of pemphigus. An update. Arch Dermatol. 1996 Sep;132(2):203-12.  
-
-<|ref|>text<|/ref|><|det|>[[512, 72, 905, 781]]<|/det|>
-5. Heizmann M, Itin P, Wernli M, Borradori L, Bargetzi MJ. Successful treatment of paraneoplastic pemphigus in follicular NHL with rituximab: report of a case and review of treatment for paraneoplastic pemphigus in NHL and CLL. Am J Hematol. Feb 2001;66(2):142-4. doi: 10.1002/1096-8652(200102)66:2<142::AID-AJH1032>3.0.CO;2-0. 
-6. Food and Drug Administration. Rituxan label; 2012 [cited Feb 2, 2021]. Available from: http://www.accessdata.fda.gov/drugsatfda_docs/label/2012 /103705s5373lbl.pdf. 
-7. Belgi AS, Azeze M, Hoyle C, Williams REA. Response of pemphigus vulgaris to anti-CD20 antibody therapy (rituximab) may be delayed. Clin Exp Dermatol. 2006 Jan;31(1):143. doi: 10.1111/j.1365-2230.2005.01941. x. 
-8. Schmidt E, Seitz CS, Benoit S, Bröcker EB, Goebeler M. Rituximab in autoimmune bullous diseases: mixed responses and adverse effects. Br J Dermatol. 2007 Feb;156(2):352-6. doi: 10.1111/j.1365-2133.2006.07646. x. 
-9. Barrera MV, Mendiola MV, Bosch RJ, Herrera E. Prolonged treatment with rituximab in patients with refractory pemphigus vulgaris. J Dermatol Treat. 2007 Jan;18(5):312-4. doi: 10.1080/09546630701323988. 
-10. Faurschou A, Gniadecki R. Two courses of rituximab (anti-CD20 monoclonal antibody) for recalcitrant pemphigus vulgaris. Int J Dermatol. 2008 Mar;47(3):292-4. doi: 10.1111/j.1365-4632.2008.03423. x. 
-11. Craythorne EE, Mufti G, DuVivier AW. Rituximab used as a first-line single agent in the treatment of pemphigus vulgaris. J Am Acad Dermatol. 2011 Nov;65(5):1064-5. doi: 10.1016/j.jaad.2010.06.033. 
-12. Horvath B, Huizinga J, Pas HH, Mulder AB, Jonkman MF. Low-dose rituximab is effective in pemphigus. Br J Dermatol. 2012 Feb;166(2):405-12. doi: 10.1111/j.1365-2133.2011.10663. x. 
-13. Craythorne E, Du Vivier A, Mufti GJ, Warnakulasuriya S. Rituximab for the treatment of corticosteroid—refractory pemphigus vulgaris with oral and skin manifestations. J Oral Pathol Med. 2011 Sep;40(8):616-20. doi: 10.1111/j.1600-0714.2011.01017. x. 
-14. Kim JH, Kim YH, Kim MR, Kim SC. Clinical efficacy of different doses of rituximab in the treatment of pemphigus: a retrospective study of 27 patients. Br J Dermatol. 2011Sep;165(3):646-51. doi: 10.1111/j.1365-2133.2011.10411. x. 
-15. Kasperkiewicz M, Shimanovich I, Ludwig RJ, Rose C, Zillikens D, Schmidt E. Rituximab for treatment-refractory pemphigus and pemphigoid: a case series of 17 patients. J Am Acad Dermatol. 2011 Sep;65(3):552-8. doi: 10.1016/j.jaad.2010.07.032 
-16. Investor update. Basel; June 12, 2019. [cited Feb 5, 2021]. Available from: https://www.roche.com/investors/updates/inv-update-2019-06-12. htm.
+21 (2): 82-84. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2012. (2012). 2012. 2012. 2012. 2012. 2012. 2012. 2012. 2021. 2012. 2012. 2012. 2012. 2012. 2012

stage1/sample_00001/document.md

@@ -1,52 +1,37 @@
-0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
+0.5mm
 
 For more than a century, Xylem's pump technologies and solutions have satisfied customers all over the world. The e-SH pump continues that tradition, with higher efficiencies and proven performance. Here are just a few of the markets and applications in which we're helping customers solve their water and fluid management challenges. 
 
-·Water intake 
+• Water intake 
 
-·Water transfer and circulation 
+• Water transfer and circulation 
 
-·Pressure boosting 
+• Pressure boosting 
 
-·Process cooling and heating 
+• Process cooling and heating 
 
-·Fluid transfer and transport 
+• Fluid transfer and transport 
 
-·Produced water transfer and boosting 
+• Produced water transfer and boosting 
 
-·Boiler feed booster 
+• Boiler feed booster 
 
 ## PUMPED FLUIDS 
 
-·Groundwater 
+• Groundwater 
 
-·Potable water 
+• Potable water 
 
-·Process water 
+• Process water 
 
-·Gray/used water 
+• Gray/used water 
 
-·Heat transfer fluids 
+• Heat transfer fluids 
 
-·Produced water 
+• Produced water 
 
 ## SPECIFICATIONS 
 
 <table><tr><td>Maximum flow</td><td>1,140 gpm</td></tr><tr><td>Maximum head</td><td>464 ft. TDH</td></tr><tr><td>Maximum working pressure</td><td>230 psi</td></tr><tr><td>Maximum temperature</td><td>250 °F</td></tr><tr><td>Hydraulic performance</td><td>compliant with ANSI/HI 14.6 Grade 2B</td></tr><tr><td>Suction and discharge flanges</td><td>1" - 4" ANSI class 150 flanges</td></tr><tr><td>Motor</td><td>Standard 60 HZ NEMA premium efficient motors</td></tr></table>
 
-## POWER GENERATION 
-
-![Figure sample_00001_fig01](figures/sample_00001_fig01.png)
- 
-
-## OIL AND GAS 
-
-![Figure sample_00001_fig02](figures/sample_00001_fig02.png)
- 
-
-## GENERAL MANUFACTURING 
-
-![Figure sample_00001_fig03](figures/sample_00001_fig03.png)
- 
-
-## COMMERCIAL BUILDING
+![Figure sample_00001_fig01](figures/sample_00001_fig01.png)

stage1/sample_00001/raw_response.md

@@ -1,73 +1,54 @@
-0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
+0.5mm
 
-<|ref|>text<|/ref|><|det|>[[55, 145, 937, 230]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[54, 146, 939, 230]]<|/det|>
 For more than a century, Xylem's pump technologies and solutions have satisfied customers all over the world. The e-SH pump continues that tradition, with higher efficiencies and proven performance. Here are just a few of the markets and applications in which we're helping customers solve their water and fluid management challenges. 
 
-<|ref|>text<|/ref|><|det|>[[56, 279, 164, 291]]<|/det|>
-·Water intake 
+<|ref|>text<|/ref|><|det|>[[57, 277, 165, 291]]<|/det|>
+• Water intake 
 
-<|ref|>text<|/ref|><|det|>[[56, 302, 292, 316]]<|/det|>
-·Water transfer and circulation 
+<|ref|>text<|/ref|><|det|>[[57, 300, 291, 316]]<|/det|>
+• Water transfer and circulation 
 
-<|ref|>text<|/ref|><|det|>[[56, 326, 209, 339]]<|/det|>
-·Pressure boosting 
+<|ref|>text<|/ref|><|det|>[[57, 325, 206, 338]]<|/det|>
+• Pressure boosting 
 
-<|ref|>text<|/ref|><|det|>[[56, 349, 281, 362]]<|/det|>
-·Process cooling and heating 
+<|ref|>text<|/ref|><|det|>[[57, 347, 280, 362]]<|/det|>
+• Process cooling and heating 
 
-<|ref|>text<|/ref|><|det|>[[56, 371, 277, 384]]<|/det|>
-·Fluid transfer and transport 
+<|ref|>text<|/ref|><|det|>[[57, 370, 276, 384]]<|/det|>
+• Fluid transfer and transport 
 
-<|ref|>text<|/ref|><|det|>[[56, 394, 352, 408]]<|/det|>
-·Produced water transfer and boosting 
+<|ref|>text<|/ref|><|det|>[[57, 394, 353, 408]]<|/det|>
+• Produced water transfer and boosting 
 
-<|ref|>text<|/ref|><|det|>[[56, 418, 216, 430]]<|/det|>
-·Boiler feed booster 
+<|ref|>text<|/ref|><|det|>[[57, 417, 218, 431]]<|/det|>
+• Boiler feed booster 
 
-<|ref|>sub_title<|/ref|><|det|>[[56, 493, 288, 511]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[57, 491, 288, 512]]<|/det|>
 ## PUMPED FLUIDS 
 
-<|ref|>text<|/ref|><|det|>[[56, 523, 172, 535]]<|/det|>
-·Groundwater 
+<|ref|>text<|/ref|><|det|>[[57, 523, 172, 536]]<|/det|>
+• Groundwater 
 
-<|ref|>text<|/ref|><|det|>[[56, 546, 174, 559]]<|/det|>
-·Potable water 
+<|ref|>text<|/ref|><|det|>[[57, 546, 172, 560]]<|/det|>
+• Potable water 
 
-<|ref|>text<|/ref|><|det|>[[56, 570, 174, 582]]<|/det|>
-·Process water 
+<|ref|>text<|/ref|><|det|>[[57, 570, 172, 583]]<|/det|>
+• Process water 
 
-<|ref|>text<|/ref|><|det|>[[56, 592, 195, 606]]<|/det|>
-·Gray/used water 
+<|ref|>text<|/ref|><|det|>[[57, 593, 195, 607]]<|/det|>
+• Gray/used water 
 
-<|ref|>text<|/ref|><|det|>[[56, 616, 211, 629]]<|/det|>
-·Heat transfer fluids 
+<|ref|>text<|/ref|><|det|>[[57, 617, 212, 630]]<|/det|>
+• Heat transfer fluids 
 
-<|ref|>text<|/ref|><|det|>[[56, 639, 192, 652]]<|/det|>
-·Produced water 
+<|ref|>text<|/ref|><|det|>[[57, 640, 192, 653]]<|/det|>
+• Produced water 
 
-<|ref|>sub_title<|/ref|><|det|>[[512, 278, 648, 291]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[512, 277, 648, 290]]<|/det|>
 ## SPECIFICATIONS 
 
-<|ref|>table<|/ref|><|det|>[[510, 302, 940, 618]]<|/det|>
+<|ref|>table<|/ref|><|det|>[[511, 300, 942, 618]]<|/det|>
 <table><tr><td>Maximum flow</td><td>1,140 gpm</td></tr><tr><td>Maximum head</td><td>464 ft. TDH</td></tr><tr><td>Maximum working pressure</td><td>230 psi</td></tr><tr><td>Maximum temperature</td><td>250 °F</td></tr><tr><td>Hydraulic performance</td><td>compliant with ANSI/HI 14.6 Grade 2B</td></tr><tr><td>Suction and discharge flanges</td><td>1" - 4" ANSI class 150 flanges</td></tr><tr><td>Motor</td><td>Standard 60 HZ NEMA premium efficient motors</td></tr></table>
 
-<|ref|>sub_title<|/ref|><|det|>[[34, 727, 214, 740]]<|/det|>
-## POWER GENERATION 
-
-<|ref|>image<|/ref|><|det|>[[0, 752, 997, 952]]<|/det|>
- 
-
-<|ref|>sub_title<|/ref|><|det|>[[317, 727, 431, 740]]<|/det|>
-## OIL AND GAS 
-
-<|ref|>image<|/ref|><|det|>[[0, 752, 299, 952]]<|/det|>
- 
-
-<|ref|>sub_title<|/ref|><|det|>[[508, 727, 738, 740]]<|/det|>
-## GENERAL MANUFACTURING 
-
-<|ref|>image<|/ref|><|det|>[[508, 752, 997, 952]]<|/det|>
- 
-
-<|ref|>sub_title<|/ref|><|det|>[[774, 727, 975, 740]]<|/det|>
-## COMMERCIAL BUILDING
+<|ref|>image<|/ref|><|det|>[[0, 746, 999, 956]]<|/det|>

stage1/sample_00002/document.md

@@ -1,17 +1 @@
-0.5mm, 0.5mm, and 0.5mm. The results are shown in Figure 1a-i.  
-
-## Case presentation  
-
-A 39- year- old male patient who lives in Surat, Gujarat, was referred with a 3- month history of painful ulcerated lesions in the oral cavity. On enquiring about the patient's history, we came to know that initially, the patient had difficulty chewing food and the severity increased gradually. The ulcerations caused considerable discomfort, affecting his normal oral functions. Subsequently, fluid- filled lesions developed involving the scalp, trunk, limbs, and axilla. Lesions were increasing in size and number and had little tendency to heal. Blisters were flaccid and burst on their own to form erosions within 2- 3 days. Medical and family history was non- contributory. No history of fever, joint pain, malaise, and photosensitivity. He had weak oral hygiene due to the bad habit of taking betel quid with tobacco five times a day and smoking seven bids per day for the past 12 years. Further, he consumes two- quarters of alcohol on an alternative day for the last 12 years. History of any drug intake before the appearance of lesions was also absent. Intraoral examination revealed that approximately \(1.0 \times 1.5\) dimensions ulceration lesions were present on the buccal mucosa. Dermatological examination revealed multiple vesicular lesions ranging from \(0.3 \times 0.3\) to \(1.5 \times 1.5\) involving the face, trunk, upper limbs, and dorsum of the penis (Figure 1a- i).  
-
-![Figure sample_00002_fig01](figures/sample_00002_fig01.png)
-
-<center>Figure 1: Showing (a) ulcerative lesions present on the buccal mucosa (b) multiple vesicular lesions present on the face (c) multiple vesicular lesions with erosion present on the lower neck (d) multiple vesicular lesions present on the umbilicus (e) multiple vesicular lesions with erosion present on the upper limb (f) multiple vesicular lesions with erosion present on the back (g) multiple vesicular lesions with erosion on the axilla (h) flaccid blister lesions on the scalp (i) multiple vesicular lesions present on the dorsum of the penis. </center>  
-
-There was a positive Nikolsky sign and a bulla spread sign. The clinical manifestations of oral ulcers, flaccid bullae, and positive Nikolsky sign hinted at the provisional diagnosis of PV. Mucous membrane pemphigoid, bullous lichen planus, paraneoplastic pemphigus, chronic ulcerative stomatitis, recurrent herpes lesions in immunocompromised patients, and erythema multiforme were the potential differential diagnosis of this condition. Regarding this, a biopsy was performed from a new vesicle to confirm the diagnosis. Histopathological examination revealed an intraepidermal supraslab acantholytic blister. Several acantholytic cells and neutrophils could be seen in the blister. The floor of the blister showed a tombstone pattern with occasional acantholytic cells. A moderately dense superficial perivascular mixed infiltrate was present in the dermis. Mild spongiosis with neutrophils was present at the periphery of the blister (Figure 2).   
-
-![Figure sample_00002_fig02](figures/sample_00002_fig02.png)
-
-<center>Figure 2: Photomicrograph showing acantholysis of the keratinocytes, tombstone appearance, epithelium exhibiting spongiosis, and superficial perivascular mixed infiltrate (H & E stain, \(\times 5\) ). </center>  
-
-The hematological test had all findings within standard limits and, routine urine examination was unremarkable. In accordance with these findings, the definite diagnosis of PV was made and the treatment with oral cefuroxime (500mg twice a day) and oral prednisolone (20mg twice a day) with azathioprine (50mg twice a day) was started. Topical antibiotics and triamcinolone gel are advised for local application in the oral cavity. The dose of oral prednisolone was gradually tapered to 20mg, 10mg, 5mg, and 2.5mg (twice a day) every 30 days. The patient was maintained on the same dose of azathioprine (50mg twice a day) for one year. With the given therapy, complete remission was not achieved. Also, azathioprine was discontinued due to an elevated level of liver enzymes. Hence, the patient was shifted to rituximab therapy. The patient was initially given three doses of rituximab 1 gm each on days 1, 15, and 45. As premedication, ceftriaxone 1gm intravenously, hydrocortisone 100mg intravenously, paracetamol 650mg stat orally, and pheniramine maleate 2cc stat intravenously were given, sequentially on the day of infusion. After 30 minutes of these premedications rituximab (1gm) intravenously in 500ml of normal saline was given slowly over six to eight hours. The last dosage of rituximab was given after 3 months. A administration of rituximab lead to decrease Dsg 3 antibody levels which in turn resulted in the complete remission of the skin lesions within the next year (Figure 3a- g).
+3. 3. 1. 1. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 3. 3. 3. 3. 3. 3. 3. 3. 3. 3. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 5. 5. 5. 5. 5. 5. 5. 5. 5. 5. 6. 6. 6. 6. 6. 6. 6. 6. 6. 6. 7. 7. 7. 7. 7. 7. 7. 7. 7. 8. 8. 8. 8. 8. 8. 8. 8. 8. 8. 9. 9. 9. 9. 9. 9. 9. 9. 9. 9. 10. 10. 10. 10. 10. 10. 10. 10. 11. 11. 11. 11. 11. 11. 11. 11. 11. 12. 12. 12. 12. 12. 12. 12. 12. 12. 13. 13. 13. 13. 13. 13. 13. 13. 14. 14. 14. 14. 14. 14. 14. 14. 15. 15. 15. 15. 15. 15. 15. 15. 15. 16. 16. 16. 16. 16. 16. 16. 16. 16. 17. 17. 17. 17. 17. 17. 17. 17. 17. 18. 18. 18. 18. 18. 18. 18. 18. 18. 19. 19. 19. 19. 19. 19. 19. 19. 19. 20. 20. 20. 20. 20. 20. 20. 20. 21. 21. 21. 21. 21. 21. 21. 21. 22. 22. 22. 22. 22. 22. 22. 22. 23. 23. 23. 23. 23. 23. 23. 23. 24. 24. 24. 24. 24. 24. 24. 24. 25. 25. 25. 25. 25. 25. 25. 25. 26. 26. 26. 26. 26. 26. 26. 26. 27. 27. 27. 27. 27. 27. 27. 27. 28. 28. 28. 28. 28. 28. 28. 28. 29. 29. 29. 29. 29. 29. 29. 29. 29. 30. 30. 30. 30. 30. 30. 30. 30. 31. 31. 31. 31. 31. 31. 31. 31. 32. 32. 32. 32. 32. 32. 32. 32. 33. 33. 33. 33. 33. 33. 33. 33. 33. 34. 34. 34. 34. 34. 34. 34. 34. 35. 35. 35. 35. 35. 35. 35. 35. 36. 36. 36. 36. 36. 36. 36. 36. 37. 37. 37. 37. 37. 37. 37. 37. 38. 38. 38. 38. 38. 38. 38. 38. 39. 39. 39. 39. 39. 39. 39. 39. 40. 40. 40. 40. 40. 40. 40. 40. 41. 41. 41. 41. 41. 41. 41. 41. 42. 42. 42. 42. 42. 42. 42. 42. 43. 43. 43. 43. 43. 43. 43. 43. 44. 44. 44. 44. 44. 44. 44. 44. 45. 45. 45. 45. 45. 45. 45. 45. 46. 46. 46. 46. 46. 46. 46. 46. 47. 47. 47. 47. 47. 47. 47. 47. 48. 48. 48. 48. 48. 48. 48. 48. 49. 49. 49. 49. 49. 49. 49. 49. 50. 50. 50. 50. 50. 50. 50. 50. 51. 51. 51. 51. 51. 51. 51. 51. 52. 52. 52. 52. 52. 52. 52. 52. 53. 53. 53. 53. 53. 53. 53. 53. 54. 54. 54. 54. 54. 54. 54. 54. 55. 55. 55. 55. 55. 55. 55. 55. 56. 56. 56. 56. 56. 56. 56. 56. 57. 57. 57. 57. 57. 57. 57. 57. 58. 58. 58. 58. 58. 58. 58. 58. 59. 59. 59. 59. 59. 59. 59. 59. 60. 60. 60. 60. 60. 60. 60. 60. 61. 61. 61. 61. 61. 61. 61. 61. 62. 62. 62. 62. 62. 62. 62. 62. 63. 63. 63. 63. 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94. 94. 95. 95. 95. 95. 95. 95. 95. 95. 96. 96. 96. 96. 96. 96. 96. 96. 97. 97. 97. 97. 97. 97. 97. 97. 98. 98. 98. 98. 98. 98. 98. 98. 99. 99. 99. 99. 99. 99. 99. 99. 100. 100. 100. 100. 100. 100. 100. 100. 101. 101. 101. 101. 101. 101. 101. 102. 102. 102. 102. 102. 102. 102. 102. 103. 103. 103. 103. 103. 103. 103. 103. 104. 104. 104. 104. 104. 104. 104. 104. 105. 105. 105. 105. 105. 105. 105. 105. 106. 106. 106. 106. 106. 106. 106. 107. 107. 107. 107. 107. 107. 107. 107. 108. 108. 108. 108. 108. 108. 108. 109. 109. 109. 109. 109. 109. 109. 109. 110. 110. 110. 110. 110. 110. 110. 110. 111. 111. 111. 111. 111. 111. 111. 111. 112. 112. 112. 112. 112. 112. 112. 112. 113. 113. 113. 113. 113. 113. 113. 113. 114. 114. 114. 114. 114. 114. 114. 115. 115. 115. 115. 115. 115. 115. 115. 116. 116. 116. 116. 116. 116. 116. 116. 117. 117. 117. 117. 117. 117. 117. 117. 118. 118. 118. 118. 118. 118. 118. 118. 119. 119. 119. 119. 119. 119. 119. 119. 120. 120. 120. 120. 120. 120. 120. 120. 121. 121. 121. 121. 121. 121. 121. 121. 122. 122. 122. 122. 122. 122. 122. 122. 123. 123. 123. 123. 123. 123. 123. 123. 124. 124. 124. 124. 124. 124. 124. 124. 125. 125. 125. 125. 125. 125. 125. 125. 126. 126. 126. 126. 126. 126. 126. 126. 127. 127. 127. 127. 127. 127. 127. 127. 128. 128. 128. 128. 128. 128. 128. 129. 129. 129. 129. 129. 129. 129. 129. 130. 130. 130. 130. 130. 130. 130. 130. 131. 131. 131. 131. 131. 131. 131. 131. 132. 132. 132. 132. 132. 132. 132. 132. 133. 133. 133. 133. 133. 133. 133. 133. 134. 134. 134. 134. 134. 134. 134. 134. 135. 135. 135. 135. 135. 135. 135. 135. 136. 136. 136. 136. 136. 136. 136. 136. 137. 137. 137. 137. 137. 137. 137. 137. 138. 138. 138. 138. 138. 138. 138. 138. 139. 139. 139. 139. 139. 139. 139. 139. 140. 140. 140. 140. 140. 140. 140. 140. 141. 141. 141. 141. 141. 141. 141. 141. 142. 142. 142. 142. 142. 142. 142. 142. 143. 143. 143. 143. 143. 143. 143. 143. 144. 144. 144. 144. 144. 144. 144. 144. 145. 145. 145. 145. 145. 145. 145. 145. 146. 146. 146. 146. 146. 146. 146. 146. 147. 147. 147. 147. 147. 147. 147. 147. 148. 148. 148. 148. 148. 148. 148. 148. 149. 149. 149. 149. 149. 149. 149. 149. 150. 150. 150. 150. 150. 150. 150. 150. 151. 151. 151. 151. 151. 151. 151. 151. 152. 152. 152. 152. 152. 152. 152. 152. 153. 153. 153. 153. 153. 153. 153. 153. 154. 154. 154. 154. 154. 154. 154. 154. 155. 155. 155. 155. 155. 155. 155. 155. 156. 156. 156. 156. 156. 156. 156. 156. 157. 157. 157. 157. 157. 157. 157. 157. 158. 158. 158. 158. 158. 158. 158. 158. 159. 159. 159. 159. 159. 159. 159. 159. 160. 160. 160. 160. 160. 160. 160. 160. 161. 161. 161. 161. 161. 161. 161. 161. 162. 162. 162. 162. 162. 162. 162. 162. 163. 163. 163. 163. 163. 163. 163. 163. 164. 164. 164. 164. 164. 164. 164. 164. 165. 165. 165. 165. 165. 165. 165. 165. 166. 166. 166. 166. 166. 166. 166. 166. 167. 167. 167. 167. 167. 167. 167. 167. 168. 168. 168. 168. 168. 168. 168. 168. 169. 169. 169. 169. 169. 169. 169

stage1/sample_00002/raw_response.md

@@ -1,21 +1 @@
-0.5mm, 0.5mm, and 0.5mm. The results are shown in Figure 1a-i.  
-
-<|ref|>sub_title<|/ref|><|det|>[[92, 156, 236, 170]]<|/det|>
-## Case presentation  
-
-<|ref|>text<|/ref|><|det|>[[92, 172, 484, 497]]<|/det|>
-A 39- year- old male patient who lives in Surat, Gujarat, was referred with a 3- month history of painful ulcerated lesions in the oral cavity. On enquiring about the patient's history, we came to know that initially, the patient had difficulty chewing food and the severity increased gradually. The ulcerations caused considerable discomfort, affecting his normal oral functions. Subsequently, fluid- filled lesions developed involving the scalp, trunk, limbs, and axilla. Lesions were increasing in size and number and had little tendency to heal. Blisters were flaccid and burst on their own to form erosions within 2- 3 days. Medical and family history was non- contributory. No history of fever, joint pain, malaise, and photosensitivity. He had weak oral hygiene due to the bad habit of taking betel quid with tobacco five times a day and smoking seven bids per day for the past 12 years. Further, he consumes two- quarters of alcohol on an alternative day for the last 12 years. History of any drug intake before the appearance of lesions was also absent. Intraoral examination revealed that approximately \(1.0 \times 1.5\) dimensions ulceration lesions were present on the buccal mucosa. Dermatological examination revealed multiple vesicular lesions ranging from \(0.3 \times 0.3\) to \(1.5 \times 1.5\) involving the face, trunk, upper limbs, and dorsum of the penis (Figure 1a- i).  
-
-<|ref|>image<|/ref|><|det|>[[93, 510, 484, 796]]<|/det|>
-<|ref|>image_caption<|/ref|><|det|>[[92, 798, 484, 865]]<|/det|>
-<center>Figure 1: Showing (a) ulcerative lesions present on the buccal mucosa (b) multiple vesicular lesions present on the face (c) multiple vesicular lesions with erosion present on the lower neck (d) multiple vesicular lesions present on the umbilicus (e) multiple vesicular lesions with erosion present on the upper limb (f) multiple vesicular lesions with erosion present on the back (g) multiple vesicular lesions with erosion on the axilla (h) flaccid blister lesions on the scalp (i) multiple vesicular lesions present on the dorsum of the penis. </center>  
-
-<|ref|>text<|/ref|><|det|>[[92, 877, 484, 919], [513, 72, 903, 254]]<|/det|>
-There was a positive Nikolsky sign and a bulla spread sign. The clinical manifestations of oral ulcers, flaccid bullae, and positive Nikolsky sign hinted at the provisional diagnosis of PV. Mucous membrane pemphigoid, bullous lichen planus, paraneoplastic pemphigus, chronic ulcerative stomatitis, recurrent herpes lesions in immunocompromised patients, and erythema multiforme were the potential differential diagnosis of this condition. Regarding this, a biopsy was performed from a new vesicle to confirm the diagnosis. Histopathological examination revealed an intraepidermal supraslab acantholytic blister. Several acantholytic cells and neutrophils could be seen in the blister. The floor of the blister showed a tombstone pattern with occasional acantholytic cells. A moderately dense superficial perivascular mixed infiltrate was present in the dermis. Mild spongiosis with neutrophils was present at the periphery of the blister (Figure 2).   
-
-<|ref|>image<|/ref|><|det|>[[514, 267, 904, 507]]<|/det|>
-<|ref|>image_caption<|/ref|><|det|>[[512, 512, 903, 552]]<|/det|>
-<center>Figure 2: Photomicrograph showing acantholysis of the keratinocytes, tombstone appearance, epithelium exhibiting spongiosis, and superficial perivascular mixed infiltrate (H & E stain, \(\times 5\) ). </center>  
-
-<|ref|>text<|/ref|><|det|>[[512, 567, 903, 924]]<|/det|>
-The hematological test had all findings within standard limits and, routine urine examination was unremarkable. In accordance with these findings, the definite diagnosis of PV was made and the treatment with oral cefuroxime (500mg twice a day) and oral prednisolone (20mg twice a day) with azathioprine (50mg twice a day) was started. Topical antibiotics and triamcinolone gel are advised for local application in the oral cavity. The dose of oral prednisolone was gradually tapered to 20mg, 10mg, 5mg, and 2.5mg (twice a day) every 30 days. The patient was maintained on the same dose of azathioprine (50mg twice a day) for one year. With the given therapy, complete remission was not achieved. Also, azathioprine was discontinued due to an elevated level of liver enzymes. Hence, the patient was shifted to rituximab therapy. The patient was initially given three doses of rituximab 1 gm each on days 1, 15, and 45. As premedication, ceftriaxone 1gm intravenously, hydrocortisone 100mg intravenously, paracetamol 650mg stat orally, and pheniramine maleate 2cc stat intravenously were given, sequentially on the day of infusion. After 30 minutes of these premedications rituximab (1gm) intravenously in 500ml of normal saline was given slowly over six to eight hours. The last dosage of rituximab was given after 3 months. A administration of rituximab lead to decrease Dsg 3 antibody levels which in turn resulted in the complete remission of the skin lesions within the next year (Figure 3a- g).
+3. 3. 1. 1. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 3. 3. 3. 3. 3. 3. 3. 3. 3. 3. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 5. 5. 5. 5. 5. 5. 5. 5. 5. 5. 6. 6. 6. 6. 6. 6. 6. 6. 6. 6. 7. 7. 7. 7. 7. 7. 7. 7. 7. 8. 8. 8. 8. 8. 8. 8. 8. 8. 8. 9. 9. 9. 9. 9. 9. 9. 9. 9. 9. 10. 10. 10. 10. 10. 10. 10. 10. 11. 11. 11. 11. 11. 11. 11. 11. 11. 12. 12. 12. 12. 12. 12. 12. 12. 12. 13. 13. 13. 13. 13. 13. 13. 13. 14. 14. 14. 14. 14. 14. 14. 14. 15. 15. 15. 15. 15. 15. 15. 15. 15. 16. 16. 16. 16. 16. 16. 16. 16. 16. 17. 17. 17. 17. 17. 17. 17. 17. 17. 18. 18. 18. 18. 18. 18. 18. 18. 18. 19. 19. 19. 19. 19. 19. 19. 19. 19. 20. 20. 20. 20. 20. 20. 20. 20. 21. 21. 21. 21. 21. 21. 21. 21. 22. 22. 22. 22. 22. 22. 22. 22. 23. 23. 23. 23. 23. 23. 23. 23. 24. 24. 24. 24. 24. 24. 24. 24. 25. 25. 25. 25. 25. 25. 25. 25. 26. 26. 26. 26. 26. 26. 26. 26. 27. 27. 27. 27. 27. 27. 27. 27. 28. 28. 28. 28. 28. 28. 28. 28. 29. 29. 29. 29. 29. 29. 29. 29. 29. 30. 30. 30. 30. 30. 30. 30. 30. 31. 31. 31. 31. 31. 31. 31. 31. 32. 32. 32. 32. 32. 32. 32. 32. 33. 33. 33. 33. 33. 33. 33. 33. 33. 34. 34. 34. 34. 34. 34. 34. 34. 35. 35. 35. 35. 35. 35. 35. 35. 36. 36. 36. 36. 36. 36. 36. 36. 37. 37. 37. 37. 37. 37. 37. 37. 38. 38. 38. 38. 38. 38. 38. 38. 39. 39. 39. 39. 39. 39. 39. 39. 40. 40. 40. 40. 40. 40. 40. 40. 41. 41. 41. 41. 41. 41. 41. 41. 42. 42. 42. 42. 42. 42. 42. 42. 43. 43. 43. 43. 43. 43. 43. 43. 44. 44. 44. 44. 44. 44. 44. 44. 45. 45. 45. 45. 45. 45. 45. 45. 46. 46. 46. 46. 46. 46. 46. 46. 47. 47. 47. 47. 47. 47. 47. 47. 48. 48. 48. 48. 48. 48. 48. 48. 49. 49. 49. 49. 49. 49. 49. 49. 50. 50. 50. 50. 50. 50. 50. 50. 51. 51. 51. 51. 51. 51. 51. 51. 52. 52. 52. 52. 52. 52. 52. 52. 53. 53. 53. 53. 53. 53. 53. 53. 54. 54. 54. 54. 54. 54. 54. 54. 55. 55. 55. 55. 55. 55. 55. 55. 56. 56. 56. 56. 56. 56. 56. 56. 57. 57. 57. 57. 57. 57. 57. 57. 58. 58. 58. 58. 58. 58. 58. 58. 59. 59. 59. 59. 59. 59. 59. 59. 60. 60. 60. 60. 60. 60. 60. 60. 61. 61. 61. 61. 61. 61. 61. 61. 62. 62. 62. 62. 62. 62. 62. 62. 63. 63. 63. 63. 63. 63. 63. 63. 64. 64. 64. 64. 64. 64. 64. 64. 65. 65. 65. 65. 65. 65. 65. 65. 66. 66. 66. 66. 66. 66. 66. 66. 67. 67. 67. 67. 67. 67. 67. 67. 68. 68. 68. 68. 68. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 74. 74. 74. 74. 74. 74. 74. 74. 75. 75. 75. 75. 75. 75. 75. 75. 76. 76. 76. 76. 76. 76. 76. 76. 77. 77. 77. 77. 77. 77. 77. 77. 78. 78. 78. 78. 78. 78. 78. 78. 79. 79. 79. 79. 79. 79. 79. 79. 80. 80. 80. 80. 80. 80. 80. 80. 81. 81. 81. 81. 81. 81. 81. 81. 82. 82. 82. 82. 82. 82. 82. 82. 83. 83. 83. 83. 83. 83. 83. 83. 84. 84. 84. 84. 84. 84. 84. 84. 85. 85. 85. 85. 85. 85. 85. 85. 86. 86. 86. 86. 86. 86. 86. 86. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 89. 89. 89. 89. 89. 89. 89. 89. 90. 90. 90. 90. 90. 90. 90. 90. 91. 91. 91. 91. 91. 91. 91. 91. 92. 92. 92. 92. 92. 92. 92. 92. 93. 93. 93. 93. 93. 93. 93. 93. 94. 94. 94. 94. 94. 94. 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121. 121. 121. 121. 121. 121. 122. 122. 122. 122. 122. 122. 122. 122. 123. 123. 123. 123. 123. 123. 123. 123. 124. 124. 124. 124. 124. 124. 124. 124. 125. 125. 125. 125. 125. 125. 125. 125. 126. 126. 126. 126. 126. 126. 126. 126. 127. 127. 127. 127. 127. 127. 127. 127. 128. 128. 128. 128. 128. 128. 128. 129. 129. 129. 129. 129. 129. 129. 129. 130. 130. 130. 130. 130. 130. 130. 130. 131. 131. 131. 131. 131. 131. 131. 131. 132. 132. 132. 132. 132. 132. 132. 132. 133. 133. 133. 133. 133. 133. 133. 133. 134. 134. 134. 134. 134. 134. 134. 134. 135. 135. 135. 135. 135. 135. 135. 135. 136. 136. 136. 136. 136. 136. 136. 136. 137. 137. 137. 137. 137. 137. 137. 137. 138. 138. 138. 138. 138. 138. 138. 138. 139. 139. 139. 139. 139. 139. 139. 139. 140. 140. 140. 140. 140. 140. 140. 140. 141. 141. 141. 141. 141. 141. 141. 141. 142. 142. 142. 142. 142. 142. 142. 142. 143. 143. 143. 143. 143. 143. 143. 143. 144. 144. 144. 144. 144. 144. 144. 144. 145. 145. 145. 145. 145. 145. 145. 145. 146. 146. 146. 146. 146. 146. 146. 146. 147. 147. 147. 147. 147. 147. 147. 147. 148. 148. 148. 148. 148. 148. 148. 148. 149. 149. 149. 149. 149. 149. 149. 149. 150. 150. 150. 150. 150. 150. 150. 150. 151. 151. 151. 151. 151. 151. 151. 151. 152. 152. 152. 152. 152. 152. 152. 152. 153. 153. 153. 153. 153. 153. 153. 153. 154. 154. 154. 154. 154. 154. 154. 154. 155. 155. 155. 155. 155. 155. 155. 155. 156. 156. 156. 156. 156. 156. 156. 156. 157. 157. 157. 157. 157. 157. 157. 157. 158. 158. 158. 158. 158. 158. 158. 158. 159. 159. 159. 159. 159. 159. 159. 159. 160. 160. 160. 160. 160. 160. 160. 160. 161. 161. 161. 161. 161. 161. 161. 161. 162. 162. 162. 162. 162. 162. 162. 162. 163. 163. 163. 163. 163. 163. 163. 163. 164. 164. 164. 164. 164. 164. 164. 164. 165. 165. 165. 165. 165. 165. 165. 165. 166. 166. 166. 166. 166. 166. 166. 166. 167. 167. 167. 167. 167. 167. 167. 167. 168. 168. 168. 168. 168. 168. 168. 168. 169. 169. 169. 169. 169. 169. 169

stage1/sample_00003/document.md

@@ -1,13 +1,27 @@
-0 to 70% (vs. fixed speed) while reducing installation time.  
+0 to 70% (vs. fixed speed) while reducing installation time.
 
-![Figure sample_00003_fig01](figures/sample_00003_fig01.png)  
+# AQUAVAR® IPC VARIABLE SPEED CONTROLLER 
 
-SPECIFICATIONS   
+## SPECIFICATIONS 
 
-<table><tr><td>Indoor enclosures</td><td>IP20 Open, TYPE 1, TYPE 12</td></tr><tr><td>Outdoor enclosures</td><td>TYPE 3R, TYPE 4X</td></tr><tr><td>Input supply</td><td>1.5 - 600 hp (frame A - D) wall or base mounted</td></tr><tr><td>Ambient temperature</td><td>14°F - 113°F (-10°C - 45°C)</td></tr><tr><td>Communication</td><td>Higher temperatures can be achieved by derating the output amperage of the drive 10% for up to 122°F (50°C)</td></tr><tr><td>Altitudes</td><td>Modbus® RTU, Metasys N2, FLN, and BACnet standard<br>Others available with option cards</td></tr><tr><td>Relative humidity</td><td>At altitudes from 0 to 1,000 meters (0 to 3,300 ft)<br>Nameplate rated current is available<br>Derate for altitudes above 1,000 (3,300 ft) with a maximum operating altitude of 3,000 m (9,900 ft)<br>Consult factory for applications above 3,000 m (9,900 ft)</td></tr><tr><td>Electrical input power</td><td>Lower than 95% without condensation</td></tr><tr><td>Electrical output power</td><td>3 phase 380 V to 480 V ±10%<br>1 phase 200 V to 240 V ±10%<br>3 phase 200 V to 240 V ±10%<br>3 phase 525 V to 600 V ±10%<br>Frequency 50 or 60 Hz, ±2 Hz</td></tr><tr><td>Electrical input power</td><td>3 phase from 0 to V supply</td></tr></table>  
+<table><tr><td>Indoor enclosures</td><td>IP20 Open, TYPE 1, TYPE 12</td></tr><tr><td>Outdoor enclosures</td><td>TYPE 3R, TYPE 4X</td></tr><tr><td>Input supply</td><td>1.5 - 600 hp (frame A - D) wall or base mounted</td></tr><tr><td>Ambient temperature</td><td>14°F - 113°F (-10°C - 45°C)</td></tr><tr><td>Communication</td><td>Higher temperatures can be achieved by derating the output amperage of the drive 10% for up to 122° F (50°C)</td></tr><tr><td>Atitudes</td><td>Modbus® RTU, Metasys N2, FLN, and BACnet standard<br/>Others available with option cards</td></tr><tr><td>Relative humidity</td><td>At altitudes from 0 to 1,000 meters (0 to 3,300 ft)<br/>Nameplate rated current is available<br/>Derate for altitudes above 1,000 (3,300 ft) with a maximum operating altitude of 3,000 m (9,900 ft)<br/>Consult factory for applications above 3,000 m (9,900 ft)</td></tr><tr><td>Electrical input power</td><td>Lower than 95% without condensation</td></tr><tr><td>Electrical - output power</td><td>3 phase 380 V to 480 V ±10%<br/>1 phase 200 V to 240 V ±10%<br/>3 phase 200 V to 240 V ±10%<br/>3 phase 525 V to 600 V ±10%<br/>Frequency 50 or 60 Hz, ±2 Hz</td></tr><tr><td>Electrical - output power</td><td>3 phase from 0 to V supply</td></tr></table>
 
-## AQUAVAR® IPC VARIABLE SPEED CONTROLLER  
+## FEATURES 
 
-## FEATURES  
-
-- EASIER start-up and programming with Start-Up Genie- Wide range of standard and permanent magnet motors with power up to 600 hp- Multi-pump configuration for up to four (4) pumps - no need for programmable logic controller (PLC)- Remote commissioning and monitoring with USB connectivity and software- Two wire multi-pump connection for faster installation- Hand on, off, and auto-on buttons available for easy pump operation at the keypad. No toggling between local and remote operation- System redundancy with multi-master control in case of drive failure- BACnet and Modbus as a standard for seamless BMS integration- Submersible and above ground applications- Wide range of voltage and enclosure options- True 208 V coverage- Dedicated single phase input- Remote commissioning and monitoring with USB connectivity and software- In-panel or handheld keypad with backlit display- Alarm Log for last 5 alarms and maintenance events- EMC/RFI filters and dual DC-link reactors to reduce drive noise emissions and interference- I/O expansion cards, factory installed or field configured
+- Easier start-up and programming with Start-Up Genie
+- Wide range of standard and permanent magnet motors with power up to 600 hp
+- Multi-pump configuration for up to four (4) pumps - no need for programmable logic controller (PLC)
+- Remote commissioning and monitoring with USB connectivity and software
+- Two wire multi-pump connection for faster installation
+- Hand on, off, and auto-on buttons available for easy pump operation at the keypad. No toggling between local and remote operation
+- System redundancy with multi-master control in case of drive failure
+- BACnet and Modbus as a standard for seamless BMS integration
+- Submersible and above ground applications
+- Wide range of voltage and enclosure options
+- True 208 V coverage
+- Dedicated single phase input
+- Remote commissioning and monitoring with USB connectivity and software
+- In-panel or handheld keypad with backlit display
+- Alarm Log for last 5 alarms and maintenance events
+- EMC/RFI filters and dual DC-link reactors to reduce drive noise emissions and interference
+- I/O expansion cards, factory installed or field configured

stage1/sample_00003/raw_response.md

@@ -1,18 +1,32 @@
-0 to 70% (vs. fixed speed) while reducing installation time.  
+0 to 70% (vs. fixed speed) while reducing installation time.
 
-<|ref|>image<|/ref|><|det|>[[53, 240, 403, 516]]<|/det|>  
+<|ref|>title<|/ref|><|det|>[[512, 309, 750, 385]]<|/det|>
+# AQUAVAR® IPC VARIABLE SPEED CONTROLLER 
 
-<|ref|>table<|/ref|><|det|>[[55, 544, 483, 951]]<|/det|>
-<|ref|>table_caption<|/ref|><|det|>[[55, 526, 195, 540]]<|/det|>
-SPECIFICATIONS   
+<|ref|>sub_title<|/ref|><|det|>[[55, 528, 198, 542]]<|/det|>
+## SPECIFICATIONS 
 
-<table><tr><td>Indoor enclosures</td><td>IP20 Open, TYPE 1, TYPE 12</td></tr><tr><td>Outdoor enclosures</td><td>TYPE 3R, TYPE 4X</td></tr><tr><td>Input supply</td><td>1.5 - 600 hp (frame A - D) wall or base mounted</td></tr><tr><td>Ambient temperature</td><td>14°F - 113°F (-10°C - 45°C)</td></tr><tr><td>Communication</td><td>Higher temperatures can be achieved by derating the output amperage of the drive 10% for up to 122°F (50°C)</td></tr><tr><td>Altitudes</td><td>Modbus® RTU, Metasys N2, FLN, and BACnet standard<br>Others available with option cards</td></tr><tr><td>Relative humidity</td><td>At altitudes from 0 to 1,000 meters (0 to 3,300 ft)<br>Nameplate rated current is available<br>Derate for altitudes above 1,000 (3,300 ft) with a maximum operating altitude of 3,000 m (9,900 ft)<br>Consult factory for applications above 3,000 m (9,900 ft)</td></tr><tr><td>Electrical input power</td><td>Lower than 95% without condensation</td></tr><tr><td>Electrical output power</td><td>3 phase 380 V to 480 V ±10%<br>1 phase 200 V to 240 V ±10%<br>3 phase 200 V to 240 V ±10%<br>3 phase 525 V to 600 V ±10%<br>Frequency 50 or 60 Hz, ±2 Hz</td></tr><tr><td>Electrical input power</td><td>3 phase from 0 to V supply</td></tr></table>  
+<|ref|>table<|/ref|><|det|>[[56, 547, 486, 950]]<|/det|>
+<table><tr><td>Indoor enclosures</td><td>IP20 Open, TYPE 1, TYPE 12</td></tr><tr><td>Outdoor enclosures</td><td>TYPE 3R, TYPE 4X</td></tr><tr><td>Input supply</td><td>1.5 - 600 hp (frame A - D) wall or base mounted</td></tr><tr><td>Ambient temperature</td><td>14°F - 113°F (-10°C - 45°C)</td></tr><tr><td>Communication</td><td>Higher temperatures can be achieved by derating the output amperage of the drive 10% for up to 122° F (50°C)</td></tr><tr><td>Atitudes</td><td>Modbus® RTU, Metasys N2, FLN, and BACnet standard<br/>Others available with option cards</td></tr><tr><td>Relative humidity</td><td>At altitudes from 0 to 1,000 meters (0 to 3,300 ft)<br/>Nameplate rated current is available<br/>Derate for altitudes above 1,000 (3,300 ft) with a maximum operating altitude of 3,000 m (9,900 ft)<br/>Consult factory for applications above 3,000 m (9,900 ft)</td></tr><tr><td>Electrical input power</td><td>Lower than 95% without condensation</td></tr><tr><td>Electrical - output power</td><td>3 phase 380 V to 480 V ±10%<br/>1 phase 200 V to 240 V ±10%<br/>3 phase 200 V to 240 V ±10%<br/>3 phase 525 V to 600 V ±10%<br/>Frequency 50 or 60 Hz, ±2 Hz</td></tr><tr><td>Electrical - output power</td><td>3 phase from 0 to V supply</td></tr></table>
 
-<|ref|>sub_title<|/ref|><|det|>[[510, 306, 751, 384]]<|/det|>
-## AQUAVAR® IPC VARIABLE SPEED CONTROLLER  
+<|ref|>sub_title<|/ref|><|det|>[[512, 433, 597, 448]]<|/det|>
+## FEATURES 
 
-<|ref|>sub_title<|/ref|><|det|>[[511, 431, 596, 445]]<|/det|>
-## FEATURES  
-
-<|ref|>text<|/ref|><|det|>[[510, 451, 933, 951]]<|/det|>
-- EASIER start-up and programming with Start-Up Genie- Wide range of standard and permanent magnet motors with power up to 600 hp- Multi-pump configuration for up to four (4) pumps - no need for programmable logic controller (PLC)- Remote commissioning and monitoring with USB connectivity and software- Two wire multi-pump connection for faster installation- Hand on, off, and auto-on buttons available for easy pump operation at the keypad. No toggling between local and remote operation- System redundancy with multi-master control in case of drive failure- BACnet and Modbus as a standard for seamless BMS integration- Submersible and above ground applications- Wide range of voltage and enclosure options- True 208 V coverage- Dedicated single phase input- Remote commissioning and monitoring with USB connectivity and software- In-panel or handheld keypad with backlit display- Alarm Log for last 5 alarms and maintenance events- EMC/RFI filters and dual DC-link reactors to reduce drive noise emissions and interference- I/O expansion cards, factory installed or field configured
+<|ref|>text<|/ref|><|det|>[[512, 456, 932, 951]]<|/det|>
+- Easier start-up and programming with Start-Up Genie
+- Wide range of standard and permanent magnet motors with power up to 600 hp
+- Multi-pump configuration for up to four (4) pumps - no need for programmable logic controller (PLC)
+- Remote commissioning and monitoring with USB connectivity and software
+- Two wire multi-pump connection for faster installation
+- Hand on, off, and auto-on buttons available for easy pump operation at the keypad. No toggling between local and remote operation
+- System redundancy with multi-master control in case of drive failure
+- BACnet and Modbus as a standard for seamless BMS integration
+- Submersible and above ground applications
+- Wide range of voltage and enclosure options
+- True 208 V coverage
+- Dedicated single phase input
+- Remote commissioning and monitoring with USB connectivity and software
+- In-panel or handheld keypad with backlit display
+- Alarm Log for last 5 alarms and maintenance events
+- EMC/RFI filters and dual DC-link reactors to reduce drive noise emissions and interference
+- I/O expansion cards, factory installed or field configured

stage1/sample_00004/document.md

@@ -1,8 +1,8 @@
-2645-9248 Journal homepage: www.jidhealth.com Open A ccess  
+2645-9248 Journal homepage: www.jidhealth.com Open Acess Original Article  
 
 # A case report on generalized pemphigus vulgaris treated with rituximaba  
 
-J agdish J adavbhai Sakhiya \(^{1\ast}\) , Dhruv J agdish Sakhiya \(^{1}\) , J ashmine Mukeshbhai Gandhi \(^{1}\) , F eral Ravi Daruwala \(^{2}\)  
+J agdish J adavbhai Sakhiya \(^{1\ast}\) , Dhruv J agdish Sakhiya \(^{1}\) , J ashmine Mukeshbhai Gandhi \(^{1}\) , Feral Ravi Daruwala \(^{2}\)  
 
 ## Abstract  
 
@@ -16,6 +16,4 @@ Keywords: Autoantibodies; Pemphigus, Rituximab, Oral Hygiene, Ulceration, Tobacc
 
 ## Background  
 
-The term pemphigus implies a group of autoimmune, mucocutaneous blistering diseases, in which the keratinocyte antigens are the target of the autoantibodies, prompting acantholysis and the formation of blisters. Main variants of pemphigus include pemphigus vulgaris (PV) and pemphigus folicaceus (PF). PV is the most common subtype and represents well over \(80\%\) of cases. As being a serious and potentially lifethreatening condition, early treatment is of utmost importance [1]. The advent of corticosteroids in the amelioration of pemphigus has dramatically changed the outlook of this perpetually disastrous disease; thus, corticosteroids have become the cornerstone of pemphigus therapy. One case reported favorable outcomes with combined therapy of highdose corticosteroids and other immunosuppressants. However, such a high dose of corticosteroids can cause serious adverse events such as several metabolic problems, global reduction of  
-
-immune system efficacy, antecedent risk of serious infections, and mortality [2]. To overcome these long- term events, Pasricha and Gupta introduced dexamethasone cyclophosphamide pulse (DCP) therapy in 1984 [3]. Later on, DCP and oral corticosteroids with or without adjuvant immunosuppressants (azathioprine, cyclophosphamide, mycophenolate mofetil, and cyclosporine) have emerged as the backbone of pemphigus treatment, however, they are associated with the high death rate in pemphigus [4]. With these conventional treatments, some patients fail to improve or some have contraindications for their usage, or some encounter relapse. Hence, advanced research has continuously been going on for finding newer molecules in pemphigus. In 2001, Heizmann et al. [5] first used rituximab for the therapy of autoimmune bullous diseases. He reported a case of paraneoplastic pemphigus favorably managed with rituximab, since then there was a drastic development in the pemphigus treatment era. Rituximab chimeric monoclonal antibody selectively acts on the CD20 expressing B cells, which are known to secrete auto- antibodies targeting the epidermal desmogleins (DSG). It has been used nearly in one million patients for treating lymphoma worldwide. Recently, rituximab has been approved for rheumatoid arthritis that is unresponsive
+The term pemphigus implies a group of autoimmune, mucocutaneous blistering diseases, in which the keratinocyte antigens are the target of the autoantibodies, prompting acantholysis and the formation of blisters. Main variants of pemphigus include pemphigus vulgaris (PV) and pemphigus foliaceus (PF). PV is the most common subtype and represents well over \(80\%\) of cases. As being a serious and potentially lifethreatening condition, early treatment is of utmost importance [1]. The advent of corticosteroids in the amelioration of pemphigus has dramatically changed the outlook of this perpetually disastrous disease; thus, corticosteroids have become the cornerstone of pemphigus therapy. One case reported favorable outcomes with combined therapy of highdose corticosteroids and other immunosuppressants. However, such a high dose of corticosteroids can cause serious adverse events such as several metabolic problems, global reduction of immune system efficacy, antecedent risk of serious infections, and mortality [2]. To overcome these long- term events, Psaricha and Gupta introduced dexamethasone cyclophosphamide pulse (DCP) therapy in 1984 [3]. Later on, DCP and oral corticosteroids with or without adjuvant immunosuppressants (azathioprine, cyclophosphamide, mycophenolate mofetil, and cyclosporine) have emerged as the backbone of pemphigus treatment, however, they are associated with the high death rate in pemphigus [4]. With these conventional treatments, some patients fail to improve or some have contraindications for their usage, or some encounter relapse. Hence, advanced research has continuously been going on for finding newer molecules in pemphigus. In 2001, Heizmann et al. [5] first used rituximab for the therapy of autoimmune bullous diseases. He reported a case of paraneoplastic pemphigus favorably managed with rituximab, since then there was a drastic development in the pemphigus treatment era. Rituximab chimeric monoclonal antibody selectively acts on the CD20 expressing B cells, which are known to secrete auto- antibodies targeting the epidermal desmogleins (DSG). It has been used nearly in one million patients for treating lymphoma worldwide. Recently, rituximab has been approved for rheumatoid arthritis that is unresponsive

stage1/sample_00004/raw_response.md

@@ -1,31 +1,28 @@
-2645-9248 Journal homepage: www.jidhealth.com Open A ccess  
+2645-9248 Journal homepage: www.jidhealth.com Open Acess Original Article  
 
-<|ref|>title<|/ref|><|det|>[[88, 217, 794, 266]]<|/det|>
+<|ref|>title<|/ref|><|det|>[[88, 215, 797, 266]]<|/det|>
 # A case report on generalized pemphigus vulgaris treated with rituximaba  
 
-<|ref|>text<|/ref|><|det|>[[87, 291, 896, 328]]<|/det|>
-J agdish J adavbhai Sakhiya \(^{1\ast}\) , Dhruv J agdish Sakhiya \(^{1}\) , J ashmine Mukeshbhai Gandhi \(^{1}\) , F eral Ravi Daruwala \(^{2}\)  
+<|ref|>text<|/ref|><|det|>[[89, 290, 897, 327]]<|/det|>
+J agdish J adavbhai Sakhiya \(^{1\ast}\) , Dhruv J agdish Sakhiya \(^{1}\) , J ashmine Mukeshbhai Gandhi \(^{1}\) , Feral Ravi Daruwala \(^{2}\)  
 
-<|ref|>sub_title<|/ref|><|det|>[[102, 351, 175, 365]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[102, 351, 175, 364]]<|/det|>
 ## Abstract  
 
-<|ref|>text<|/ref|><|det|>[[101, 367, 877, 406]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[100, 366, 876, 406]]<|/det|>
 Background: Pemphigus vulgaris has an obscure etiology; the presence of autoantibodies is coherent with an autoimmune disease. Rituximab a monoclonal antibody that specifically targets the CD20 antigen of B lymphocytes, has arisen as a novel treatment approach for pemphigus vulgaris.  
 
-<|ref|>text<|/ref|><|det|>[[101, 413, 888, 476]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[100, 412, 890, 477]]<|/det|>
 Case presentation: A 39- year- old male patient presented with a three- month history of mouth ulcers, poor oral hygiene accompanied with heavy tobacco smoking and alcohol consumption. He was diagnosed with pemphigus vulgaris. The disease gradually progressed to involve other body parts. The patient had shown partial improvement after conventional therapy (oral cefuroxime, oral prednisolone with azathioprine) and was later on successfully treated with rituximab. After 90 days of follow- up, no future recurrence was observed.  
 
-<|ref|>text<|/ref|><|det|>[[100, 486, 892, 514]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[100, 486, 890, 514]]<|/det|>
 Conclusion: With this case, the authors would like to aware other clinicians of the potential use of rituximab in treating pemphigus vulgaris, especially when the conventional therapy fails.  
 
-<|ref|>text<|/ref|><|det|>[[101, 524, 814, 559]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[100, 523, 814, 558]]<|/det|>
 Keywords: Autoantibodies; Pemphigus, Rituximab, Oral Hygiene, Ulceration, Tobacco Smoking, Alcohol consumption, India  
 
-<|ref|>sub_title<|/ref|><|det|>[[90, 595, 192, 609]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[90, 595, 193, 610]]<|/det|>
 ## Background  
 
-<|ref|>text<|/ref|><|det|>[[90, 609, 484, 835]]<|/det|>
-The term pemphigus implies a group of autoimmune, mucocutaneous blistering diseases, in which the keratinocyte antigens are the target of the autoantibodies, prompting acantholysis and the formation of blisters. Main variants of pemphigus include pemphigus vulgaris (PV) and pemphigus folicaceus (PF). PV is the most common subtype and represents well over \(80\%\) of cases. As being a serious and potentially lifethreatening condition, early treatment is of utmost importance [1]. The advent of corticosteroids in the amelioration of pemphigus has dramatically changed the outlook of this perpetually disastrous disease; thus, corticosteroids have become the cornerstone of pemphigus therapy. One case reported favorable outcomes with combined therapy of highdose corticosteroids and other immunosuppressants. However, such a high dose of corticosteroids can cause serious adverse events such as several metabolic problems, global reduction of  
-
-<|ref|>text<|/ref|><|det|>[[512, 593, 905, 904]]<|/det|>
-immune system efficacy, antecedent risk of serious infections, and mortality [2]. To overcome these long- term events, Pasricha and Gupta introduced dexamethasone cyclophosphamide pulse (DCP) therapy in 1984 [3]. Later on, DCP and oral corticosteroids with or without adjuvant immunosuppressants (azathioprine, cyclophosphamide, mycophenolate mofetil, and cyclosporine) have emerged as the backbone of pemphigus treatment, however, they are associated with the high death rate in pemphigus [4]. With these conventional treatments, some patients fail to improve or some have contraindications for their usage, or some encounter relapse. Hence, advanced research has continuously been going on for finding newer molecules in pemphigus. In 2001, Heizmann et al. [5] first used rituximab for the therapy of autoimmune bullous diseases. He reported a case of paraneoplastic pemphigus favorably managed with rituximab, since then there was a drastic development in the pemphigus treatment era. Rituximab chimeric monoclonal antibody selectively acts on the CD20 expressing B cells, which are known to secrete auto- antibodies targeting the epidermal desmogleins (DSG). It has been used nearly in one million patients for treating lymphoma worldwide. Recently, rituximab has been approved for rheumatoid arthritis that is unresponsive
+<|ref|>text<|/ref|><|det|>[[91, 611, 483, 834], [512, 595, 905, 902]]<|/det|>
+The term pemphigus implies a group of autoimmune, mucocutaneous blistering diseases, in which the keratinocyte antigens are the target of the autoantibodies, prompting acantholysis and the formation of blisters. Main variants of pemphigus include pemphigus vulgaris (PV) and pemphigus foliaceus (PF). PV is the most common subtype and represents well over \(80\%\) of cases. As being a serious and potentially lifethreatening condition, early treatment is of utmost importance [1]. The advent of corticosteroids in the amelioration of pemphigus has dramatically changed the outlook of this perpetually disastrous disease; thus, corticosteroids have become the cornerstone of pemphigus therapy. One case reported favorable outcomes with combined therapy of highdose corticosteroids and other immunosuppressants. However, such a high dose of corticosteroids can cause serious adverse events such as several metabolic problems, global reduction of immune system efficacy, antecedent risk of serious infections, and mortality [2]. To overcome these long- term events, Psaricha and Gupta introduced dexamethasone cyclophosphamide pulse (DCP) therapy in 1984 [3]. Later on, DCP and oral corticosteroids with or without adjuvant immunosuppressants (azathioprine, cyclophosphamide, mycophenolate mofetil, and cyclosporine) have emerged as the backbone of pemphigus treatment, however, they are associated with the high death rate in pemphigus [4]. With these conventional treatments, some patients fail to improve or some have contraindications for their usage, or some encounter relapse. Hence, advanced research has continuously been going on for finding newer molecules in pemphigus. In 2001, Heizmann et al. [5] first used rituximab for the therapy of autoimmune bullous diseases. He reported a case of paraneoplastic pemphigus favorably managed with rituximab, since then there was a drastic development in the pemphigus treatment era. Rituximab chimeric monoclonal antibody selectively acts on the CD20 expressing B cells, which are known to secrete auto- antibodies targeting the epidermal desmogleins (DSG). It has been used nearly in one million patients for treating lymphoma worldwide. Recently, rituximab has been approved for rheumatoid arthritis that is unresponsive

stage1/sample_00005/document.md

@@ -2,24 +2,24 @@
 
 Information Pertinent to Performance of the Procedure  
 
-- Patient history with particular focus on previous surgery and/or radiation therapy as well as current and past neurological or psychiatric status.- History of diabetes, fasting state.- Information regarding recent morphological imaging studies (CT, MRI).- Current medication and when last taken, especially psychotropic pharmaceuticals. These may influence regional metabolic rate of glucose (rCMRGI).- Patient's ability to lie still for 20-40 min for PET to \(\sim 1\) h for SPECT.  
+- Patient history with particular focus on previous surgery and/or radiation therapy as well as current and past neurological or psychiatric status.- History of diabetes, fasting state.- Information regarding recent morphological imaging studies (CT, MRI).- Current medication and when last taken, especially psychotropic pharmaceuticals. These may influence regional metabolic rate of glucose (rCMRGI).  
 
-## Precautions and Conscious Sedation  
+Precautions and Conscious Sedation  
 
 - Continuous supervision of the patients during the whole scanning procedure is necessary. This is especially important for patients with tumor associated seizures.- In uncooperative patients, it may be worthwhile to apply conscious sedation (e.g., by a short acting benzodiazepine such as i.v., midazolam). For FDG, administration should take place at least 20 min after tracer injection, preferably starting only a few minutes before data acquisition.- Appropriate monitoring (pulse-oximetry) should be performed to recognize the possibility of cardiopulmonary depression and appropriate antidote/emergency backup should be foreseen. Doses of sedation should be reduced in elderly patients.  
 
-## Radiopharmaceutical  
+Radiopharmaceutical  
 
-## Radiopharmaceutical  
+Radiopharmaceutical  
 
 - [18F]Fluoro-2-deoxyglucose (FDG).  
-- 3-[123I]Iodo-α-methyl-L-tyrosine (IMT).  
-- [Methyl-11C]-L-methionine (MET).  
-- \(O-(2-[18F]\mathrm{Fluoroethyl}) - \mathrm{L}\) -tyrosine (FET).  
+- 3-\[^{123}\mathrm{I}\]Iodo-α-methyl-L-tyrosine (IMT).  
+- \[ \mathrm{Methyl-}^{11}\mathrm{C} \]-L-methionine (MET).  
+- \(O-(2-[^{18}\mathrm{F}]\mathrm{Fluoroethyl})-L\)-tyrosine (FET).  
 
 ## Recommended Dosage  
 
-The dose recommendations for FDG, MET, and FET mentioned here are valid for full ring dedicated PET- cameras with BGO- crystals in 3D- mode.  
+The dose recommendations for FDG, MET, and FET mentioned here are valid for full ring dedicated PET-cameras with BGO- crystals in 3D- mode.  
 
 - FDG: in adults, 125-250 MBq (typically 150 MBq) in 3D-mode. In children, 2-4 MBq/kg in 3D-mode with a minimum of 10 MBq in newborn infants.  
 - IMT: 100-400 MBq (typically 185 MBq).  
@@ -30,6 +30,6 @@ The administered dose may increase using 2D- mode and vary for other systems acc
 
 ## Radiation Dosimetry (Table 2.1)  
 
-## Radiation Dosimetry of Brain Transmission Scans  
+Radiation Dosimetry of Brain Transmission Scans  
 
-Based on transmission scans of 10 min and CT- based scans of 5- 10 s, the effective doses per scan are: 20- 30 μSv for Germanium- based transmission, \(\sim 20 \mu \mathrm{Sv}\) for low- dose high- speed CT, and between 220 and 450 μSv for high- quality CT.
+Based on transmission scans of 10 min and CT- based scans of 5- 10 s, the effective doses per scan are: 20- 30 μSv for Germanium- based transmission, \(\sim 20\) μSv for low- dose high- speed CT, and between 220 and 450 μSv for high- quality CT.

stage1/sample_00005/raw_response.md

@@ -1,49 +1,49 @@
 1,000 mg given at least 30 min prior to injection) to prevent possible thyroid uptake of free radioactive iodine.  
 
-<|ref|>text<|/ref|><|det|>[[116, 180, 450, 215]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[115, 181, 448, 217]]<|/det|>
 Information Pertinent to Performance of the Procedure  
 
-<|ref|>text<|/ref|><|det|>[[115, 224, 493, 475]]<|/det|>
-- Patient history with particular focus on previous surgery and/or radiation therapy as well as current and past neurological or psychiatric status.- History of diabetes, fasting state.- Information regarding recent morphological imaging studies (CT, MRI).- Current medication and when last taken, especially psychotropic pharmaceuticals. These may influence regional metabolic rate of glucose (rCMRGI).- Patient's ability to lie still for 20-40 min for PET to \(\sim 1\) h for SPECT.  
+<|ref|>text<|/ref|><|det|>[[113, 227, 492, 473]]<|/det|>
+- Patient history with particular focus on previous surgery and/or radiation therapy as well as current and past neurological or psychiatric status.- History of diabetes, fasting state.- Information regarding recent morphological imaging studies (CT, MRI).- Current medication and when last taken, especially psychotropic pharmaceuticals. These may influence regional metabolic rate of glucose (rCMRGI).  
 
-<|ref|>sub_title<|/ref|><|det|>[[116, 498, 439, 515]]<|/det|>
-## Precautions and Conscious Sedation  
+<|ref|>text<|/ref|><|det|>[[115, 483, 438, 499]]<|/det|>
+Precautions and Conscious Sedation  
 
-<|ref|>text<|/ref|><|det|>[[115, 527, 492, 897]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[113, 528, 492, 899]]<|/det|>
 - Continuous supervision of the patients during the whole scanning procedure is necessary. This is especially important for patients with tumor associated seizures.- In uncooperative patients, it may be worthwhile to apply conscious sedation (e.g., by a short acting benzodiazepine such as i.v., midazolam). For FDG, administration should take place at least 20 min after tracer injection, preferably starting only a few minutes before data acquisition.- Appropriate monitoring (pulse-oximetry) should be performed to recognize the possibility of cardiopulmonary depression and appropriate antidote/emergency backup should be foreseen. Doses of sedation should be reduced in elderly patients.  
 
-<|ref|>sub_title<|/ref|><|det|>[[510, 82, 699, 100]]<|/det|>
-## Radiopharmaceutical  
+<|ref|>text<|/ref|><|det|>[[511, 82, 701, 99]]<|/det|>
+Radiopharmaceutical  
 
-<|ref|>sub_title<|/ref|><|det|>[[510, 111, 688, 127]]<|/det|>
-## Radiopharmaceutical  
+<|ref|>text<|/ref|><|det|>[[511, 111, 689, 126]]<|/det|>
+Radiopharmaceutical  
 
-<|ref|>text<|/ref|><|det|>[[510, 138, 885, 229]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[511, 137, 886, 227]]<|/det|>
 - [18F]Fluoro-2-deoxyglucose (FDG).  
-- 3-[123I]Iodo-α-methyl-L-tyrosine (IMT).  
-- [Methyl-11C]-L-methionine (MET).  
-- \(O-(2-[18F]\mathrm{Fluoroethyl}) - \mathrm{L}\) -tyrosine (FET).  
+- 3-\[^{123}\mathrm{I}\]Iodo-α-methyl-L-tyrosine (IMT).  
+- \[ \mathrm{Methyl-}^{11}\mathrm{C} \]-L-methionine (MET).  
+- \(O-(2-[^{18}\mathrm{F}]\mathrm{Fluoroethyl})-L\)-tyrosine (FET).  
 
-<|ref|>sub_title<|/ref|><|det|>[[510, 259, 696, 276]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[511, 259, 696, 276]]<|/det|>
 ## Recommended Dosage  
 
-<|ref|>text<|/ref|><|det|>[[509, 286, 886, 361]]<|/det|>
-The dose recommendations for FDG, MET, and FET mentioned here are valid for full ring dedicated PET- cameras with BGO- crystals in 3D- mode.  
+<|ref|>text<|/ref|><|det|>[[510, 286, 886, 362]]<|/det|>
+The dose recommendations for FDG, MET, and FET mentioned here are valid for full ring dedicated PET-cameras with BGO- crystals in 3D- mode.  
 
-<|ref|>text<|/ref|><|det|>[[509, 364, 886, 507]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[510, 364, 886, 507]]<|/det|>
 - FDG: in adults, 125-250 MBq (typically 150 MBq) in 3D-mode. In children, 2-4 MBq/kg in 3D-mode with a minimum of 10 MBq in newborn infants.  
 - IMT: 100-400 MBq (typically 185 MBq).  
 - MET: 200-250 MBq.  
 - FET: 200-250 MBq.  
 
-<|ref|>text<|/ref|><|det|>[[509, 520, 886, 692]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[510, 521, 886, 691]]<|/det|>
 The administered dose may increase using 2D- mode and vary for other systems according to differences in sensitivity. For the radiolabeled amino acids, the activity to be administered to children should be a fraction of the adult activity calculated from body weight according to the factors given by the EANM Pediatric Task Group.  
 
-<|ref|>sub_title<|/ref|><|det|>[[510, 721, 775, 738]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[511, 722, 775, 739]]<|/det|>
 ## Radiation Dosimetry (Table 2.1)  
 
-<|ref|>sub_title<|/ref|><|det|>[[510, 748, 866, 783]]<|/det|>
-## Radiation Dosimetry of Brain Transmission Scans  
+<|ref|>text<|/ref|><|det|>[[510, 749, 866, 783]]<|/det|>
+Radiation Dosimetry of Brain Transmission Scans  
 
-<|ref|>text<|/ref|><|det|>[[509, 793, 885, 902]]<|/det|>
-Based on transmission scans of 10 min and CT- based scans of 5- 10 s, the effective doses per scan are: 20- 30 μSv for Germanium- based transmission, \(\sim 20 \mu \mathrm{Sv}\) for low- dose high- speed CT, and between 220 and 450 μSv for high- quality CT.
+<|ref|>text<|/ref|><|det|>[[510, 793, 886, 903]]<|/det|>
+Based on transmission scans of 10 min and CT- based scans of 5- 10 s, the effective doses per scan are: 20- 30 μSv for Germanium- based transmission, \(\sim 20\) μSv for low- dose high- speed CT, and between 220 and 450 μSv for high- quality CT.

stage1/sample_00006/document.md

@@ -1,49 +1 @@
-1? (X) 1? (X) 1? (X) 1? (X) 1? (X) 1? (X)  
-
-Entry for the Engineers Ireland Biomedical Research Medal? (X)  
-
-Post- Doctoral Researcher/Senior Researcher/PI  
-
-## LOAD INDUCED CHANGES IN COLLAGEN FIBRE ARCHITECTURE IN ARTERIES CHARACTERISED BY SMALL ANGLE LIGHT SCATTERING  
-
-Gaul, R.1,2, Lally, C.1,2 1Trinity Centre for Bioengineering, Trinity College Dublin, Dublin, Ireland. 2School of Engineering, Trinity College Dublin, Dublin, Ireland. email: rgau@tcd.ie  
-
-## INTRODUCTION  
-
-The structural strength of arteries is governed by reinforcing collagen fibres present in the vessel wall. Although healthy vessels are capable of fibre remodelling, unhealthy fibre remodelling patterns may be associated with disease [1]. A greater understanding of the remodelling of these fibres may provide greater insight into arteries at risk of disease and how arterial repair may be induced.  
-
-Small angle light scattering (SALS) is a technique which has previously been used to determine the structure of thin, highly organised tissue structures, such as bovine pericardium and porcine aortic valve tissue [2].  
-
-The aim of the present study is to design and develop a fully automated SALS system capable of determining the changes in arterial fibre architecture in response to strain.  
-
-## MATERIALS AND METHODS  
-
-An in- house SALS system has been developed making use of an unpolarised 5mW HeNe laser \((\lambda = 632.8 \text{nm})\) and two focusing lenses in order to pass light through a tissue sample held in an automated sample positioner. The sample positioner incorporates two stepper motors controlled by LabVIEW to allow movement of the sample in the x and y plane with a resolution of \(5 \mu \text{m}\) . The sample is interrogated sequentially in \(250 \times 250 \mu \text{m}\) regions. The resulting scattered light pattern is recorded by a CMOS camera and analysed through a custom Matlab code to determine predominant collagen fibre directions.  
-
-To validate the system, testing was conducted on test plates with known printed configurations. Once validated, SALS testing was carried out on flat porcine carotid artery wall sections fixed at different stretch ratios. Carotid artery samples were fixed and processed using a standard histological tissue sectioning protocol. Validation of the results was achieved through histological staining of the sections.  
-
-## RESULTS  
-
-Figure 1a displays the collagen fibre directions in an unstretched carotid artery section, as predicted by SALS, overlaid on picrosirius red stained histological images. Figure 1b shows the reorganisation of the constituent collagen fibres under circumferential stretch \((\lambda = 1.25)\) .  
-
-Collagen fibre patterns in the artery were also obtained through the thickness of the artery wall using SALS, for both strained and unstrained configurations.  
-
-![Figure sample_00006_fig01](figures/sample_00006_fig01.png)
-
-<center>Figure 1 Fibre orientation as determined by SALS overlaid on histological carotid wall images. a) unstretched \((\lambda = 1)\) and b) stretched circumferentially \((\lambda = 1.25)\) </center>  
-
-## DISCUSSION  
-
-Results shown in Figure 1 highlight the dependence of fibre orientation on the levels of stretch experienced by the artery wall. A clear realignment of collagen fibres in the direction of loading is visible from Figure 1a and 1b. Although these results are widely known and shown in literature, this is the first time they have been resolved through SALS.  
-
-Although SALS is limited to thin samples, time consuming staining protocols are not required for fibre characterisation. The speed, accuracy and ease of use of this system make it a powerful system for providing insights into the response of arterial tissue to load.  
-
-Future work aims to fully identify load induced tissue changes in healthy and diseased arterial tissue using SALS.  
-
-## REFERENCES  
-
-[1] C. Creane et al., Biomech Model Mechanobiol., 10: 831- 843, 2011[2] Billiar, K., and Sacks, M., J. Biomech. 30: 753- 7 56, 1997  
-
-## ACKNOWLEDGEMENTS  
-
-This research was part funded by Science Foundation Ireland (SFI/13/ERC/B2775) and the Irish Research Council (GOIPG/2014/515).
+1) (X) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 2) 1) 1) 1) 1) 1) 1) 1) 1) 1) 3) 1) 1) 1) 1) 1) 1) 1) 1) 1) 4) 1) 1) 1) 1) 1) 1) 1) 1) 1) 5) 1) 1) 1) 1) 1) 1) 1) 1) 6) 1) 1) 1) 1) 1) 1) 1) 1) 1) 7) 1) 1) 1) 1) 1) 1) 1) 1) 1) 8) 1) 1) 1) 1) 1) 1) 1) 1) 1) 9) 1) 1) 1) 1) 1) 1) 1) 1) 1) 10) 1) 1) 1) 1) 1) 1) 1) 1) 1) 11) 1) 1) 1) 1) 1) 1) 1) 1) 1) 12) 1) 1) 1) 1) 1) 1) 1) 1) 1) 13) 1) 1) 1) 1) 1) 1) 1) 1) 1) 14) 1) 1) 1) 1) 1) 1) 1) 1) 1) 15) 1) 1) 1) 1) 1) 1) 1) 1) 1) 16) 1) 1) 1) 1) 1) 1) 1) 1) 1) 17) 1) 1) 1) 1) 1) 1) 1) 1) 1) 18) 1) 1) 1) 1) 1) 1) 1) 1) 1) 19) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 20) 1) 1) 1) 1) 1) 1) 1) 1) 1) 21) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 22) 1) 1) 1) 1) 1) 1) 1) 1) 1) 23) 1) 1) 1) 1) 1) 1) 1) 1) 1) 24) 1) 1) 1) 1) 1) 1) 1) 1) 1) 25) 1) 1) 1) 1) 1) 1) 1) 1) 1) 26) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 27) 1) 1) 1) 1) 1) 1) 1) 1) 1) 28) 1) 1) 1) 1) 1) 1) 1) 1) 1) 29) 1) 1) 1) 1) 1) 1) 1) 1) 30) 1) 1) 1) 1) 1) 1) 1) 1) 1) 31) 1) 1) 1) 1) 1) 1) 1) 1) 1) 32) 1) 1) 1) 1) 1) 1) 1) 1) 1) 33) 1) 1) 1) 1) 1) 1) 1) 1) 1) 34) 1) 1) 1) 1) 1) 1) 1) 1) 1) 35) 1) 1) 1) 1) 1) 1) 1) 1) 1) 36) 1) 1) 1) 1) 1) 1) 1) 1) 1) 37) 1) 1) 1) 1) 1) 1) 1) 1) 1) 38) 1) 1) 1) 1) 1) 1) 1) 1) 1) 39) 1) 1) 1) 1) 1) 1) 1) 1) 1) 40) 1) 1) 1) 1) 1) 1) 1) 1) 1) 41) 1) 1) 1) 1) 1) 1) 1) 1) 1) 42) 1) 1) 1) 1) 1) 1) 1) 1) 1) 43) 1) 1) 1) 1) 1) 1) 1) 1) 1) 44) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 45) 1) 1) 1) 1) 1) 1) 1) 1) 1) 46) 1) 1) 1) 1) 1) 1) 1) 1) 1) 47) 1) 1) 1) 1) 1) 1) 1) 1) 1) 48) 1) 1) 1) 1) 1) 1) 1) 1) 1) 49) 1) 1) 1) 1) 1) 1) 1) 1) 1) 50) 1) 1) 1) 1) 1) 1) 1) 1) 1) 51) 1) 1) 1) 1) 1) 1) 1) 1) 1) 52) 1) 1) 1) 1) 1) 1) 1) 1) 1) 53) 1) 1) 1) 1) 1) 1) 1) 1) 1) 54) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 55) 1) 1) 1) 1) 1) 1) 1) 1) 1) 56) 1) 1) 1) 1) 1) 1) 1) 1) 1) 57) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 58) 1) 1) 1) 1) 1) 1) 1) 1) 1) 59) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 60) 1) 1) 1) 1) 1) 1) 1) 1) 1) 61) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 62) 1) 1) 1) 1) 1) 1) 1) 1) 1) 63) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 64) 1) 1) 1) 1) 1) 1) 1) 1) 1) 65) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 66) 1) 1) 1) 1) 1) 1) 1) 1) 1) 67) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 68) 1) 1) 1) 1) 1) 1) 1) 1) 1) 69) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 70) 1) 1) 1) 1) 1) 1) 1) 1) 1) 71) 1) 1) 1) 1) 1) 1) 1) 1) 1) 72) 1) 1) 1) 1) 1) 1) 1) 1) 1) 73) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 74) 1) 1) 1) 1) 1) 1) 1) 1) 1) 75) 1) 1) 1) 1) 1) 1) 1) 1) 1) 76) 1) 1) 1) 1) 1) 1) 1) 1) 1) 77) 1) 1) 1) 1) 1) 1) 1) 1) 1) 78) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 79) 1) 1) 1) 1) 1) 1) 1) 1) 1) 80) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 81) 1) 1) 1) 1) 1) 1) 1) 1) 1) 82) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 83) 1) 1) 1) 1) 1) 1) 1) 1) 1) 84) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 85) 1) 1) 1) 1) 1) 1) 1) 1) 1) 86) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 87) 1) 1) 1) 1) 1) 1) 1) 1) 1) 88) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 89) 1) 1) 1) 1) 1) 1) 1) 1) 1) 90) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 91) 1) 1) 1) 1) 1) 1) 1) 1) 92) 1) 1) 1) 1) 1) 1) 1) 1) 1) 93) 1) 1) 1) 1) 1) 1) 1) 1) 1) 94) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 95) 1) 1) 1) 1) 1) 1) 1) 1) 1) 96) 1) 1) 1) 1) 1) 1) 1) 1) 1) 97) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 98) 1) 1) 1) 1) 1) 1) 1) 1) 1) 99) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 100) 1) 1) 1) 1) 1) 1) 1) 1) 1) 101) 1) 1) 1) 1) 1) 1) 1) 1) 1) 102) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 103) 1) 1) 1) 1) 1) 1) 1) 1) 1) 104) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 105) 1) 1) 1) 1) 1) 1) 1) 1) 1) 106) 1) 1) 1) 1) 1) 1) 1) 1) 1) 107) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 108) 1) 1) 1) 1) 1) 1) 1) 1) 1) 109) 1) 1) 1) 1) 1) 1) 1) 1) 1) 110) 1) 1) 1) 1) 1) 1) 1) 1) 1) 111) 1) 1) 1) 1) 1) 1) 1) 1) 1) 112) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 113) 1) 1) 1) 1) 1) 1) 1) 1) 1) 114) 1) 1) 1) 1) 1) 1) 1) 1) 115) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 116) 1) 1) 1) 1) 1) 1) 1) 1) 1) 117) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 118) 1) 1) 1) 1) 1) 1) 1) 1) 1) 119) 1) 1) 1) 1) 1) 1) 1) 1) 120) 1) 1) 1) 1) 1) 1) 1) 1) 1) 121) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 122) 1) 1) 1) 1) 1) 1) 1) 1) 1) 123) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 124) 1) 1) 1) 1) 1) 1) 1) 1) 1) 125) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 126) 1) 1) 1) 1) 1) 1) 1) 1) 1) 127) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 128) 1) 1) 1) 1) 1) 1) 1) 1) 1) 129) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 130) 1) 1) 1) 1) 1) 1) 1) 1) 1) 131) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 132) 1) 1) 1) 1) 1) 1) 1) 1) 1) 133) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 134) 1) 1

stage1/sample_00006/raw_response.md

@@ -1,71 +1 @@
-1? (X) 1? (X) 1? (X) 1? (X) 1? (X) 1? (X)  
-
-<|ref|>text<|/ref|><|det|>[[155, 75, 361, 98]]<|/det|>
-Entry for the Engineers Ireland Biomedical Research Medal? (X)  
-
-<|ref|>text<|/ref|><|det|>[[492, 75, 768, 89]]<|/det|>
-Post- Doctoral Researcher/Senior Researcher/PI  
-
-<|ref|>sub_title<|/ref|><|det|>[[217, 112, 795, 146]]<|/det|>
-## LOAD INDUCED CHANGES IN COLLAGEN FIBRE ARCHITECTURE IN ARTERIES CHARACTERISED BY SMALL ANGLE LIGHT SCATTERING  
-
-<|ref|>text<|/ref|><|det|>[[241, 168, 768, 231]]<|/det|>
-Gaul, R.1,2, Lally, C.1,2 1Trinity Centre for Bioengineering, Trinity College Dublin, Dublin, Ireland. 2School of Engineering, Trinity College Dublin, Dublin, Ireland. email: rgau@tcd.ie  
-
-<|ref|>sub_title<|/ref|><|det|>[[145, 237, 272, 251]]<|/det|>
-## INTRODUCTION  
-
-<|ref|>text<|/ref|><|det|>[[145, 259, 470, 362]]<|/det|>
-The structural strength of arteries is governed by reinforcing collagen fibres present in the vessel wall. Although healthy vessels are capable of fibre remodelling, unhealthy fibre remodelling patterns may be associated with disease [1]. A greater understanding of the remodelling of these fibres may provide greater insight into arteries at risk of disease and how arterial repair may be induced.  
-
-<|ref|>text<|/ref|><|det|>[[145, 365, 470, 432]]<|/det|>
-Small angle light scattering (SALS) is a technique which has previously been used to determine the structure of thin, highly organised tissue structures, such as bovine pericardium and porcine aortic valve tissue [2].  
-
-<|ref|>text<|/ref|><|det|>[[145, 435, 470, 489]]<|/det|>
-The aim of the present study is to design and develop a fully automated SALS system capable of determining the changes in arterial fibre architecture in response to strain.  
-
-<|ref|>sub_title<|/ref|><|det|>[[145, 502, 367, 516]]<|/det|>
-## MATERIALS AND METHODS  
-
-<|ref|>text<|/ref|><|det|>[[145, 524, 470, 681]]<|/det|>
-An in- house SALS system has been developed making use of an unpolarised 5mW HeNe laser \((\lambda = 632.8 \text{nm})\) and two focusing lenses in order to pass light through a tissue sample held in an automated sample positioner. The sample positioner incorporates two stepper motors controlled by LabVIEW to allow movement of the sample in the x and y plane with a resolution of \(5 \mu \text{m}\) . The sample is interrogated sequentially in \(250 \times 250 \mu \text{m}\) regions. The resulting scattered light pattern is recorded by a CMOS camera and analysed through a custom Matlab code to determine predominant collagen fibre directions.  
-
-<|ref|>text<|/ref|><|det|>[[145, 684, 470, 788]]<|/det|>
-To validate the system, testing was conducted on test plates with known printed configurations. Once validated, SALS testing was carried out on flat porcine carotid artery wall sections fixed at different stretch ratios. Carotid artery samples were fixed and processed using a standard histological tissue sectioning protocol. Validation of the results was achieved through histological staining of the sections.  
-
-<|ref|>sub_title<|/ref|><|det|>[[145, 801, 223, 814]]<|/det|>
-## RESULTS  
-
-<|ref|>text<|/ref|><|det|>[[145, 823, 470, 901]]<|/det|>
-Figure 1a displays the collagen fibre directions in an unstretched carotid artery section, as predicted by SALS, overlaid on picrosirius red stained histological images. Figure 1b shows the reorganisation of the constituent collagen fibres under circumferential stretch \((\lambda = 1.25)\) .  
-
-<|ref|>text<|/ref|><|det|>[[528, 237, 853, 277]]<|/det|>
-Collagen fibre patterns in the artery were also obtained through the thickness of the artery wall using SALS, for both strained and unstrained configurations.  
-
-<|ref|>image<|/ref|><|det|>[[526, 288, 837, 415]]<|/det|>
-<|ref|>image_caption<|/ref|><|det|>[[527, 416, 853, 453]]<|/det|>
-<center>Figure 1 Fibre orientation as determined by SALS overlaid on histological carotid wall images. a) unstretched \((\lambda = 1)\) and b) stretched circumferentially \((\lambda = 1.25)\) </center>  
-
-<|ref|>sub_title<|/ref|><|det|>[[528, 465, 630, 479]]<|/det|>
-## DISCUSSION  
-
-<|ref|>text<|/ref|><|det|>[[528, 488, 852, 577]]<|/det|>
-Results shown in Figure 1 highlight the dependence of fibre orientation on the levels of stretch experienced by the artery wall. A clear realignment of collagen fibres in the direction of loading is visible from Figure 1a and 1b. Although these results are widely known and shown in literature, this is the first time they have been resolved through SALS.  
-
-<|ref|>text<|/ref|><|det|>[[528, 581, 852, 649]]<|/det|>
-Although SALS is limited to thin samples, time consuming staining protocols are not required for fibre characterisation. The speed, accuracy and ease of use of this system make it a powerful system for providing insights into the response of arterial tissue to load.  
-
-<|ref|>text<|/ref|><|det|>[[528, 652, 852, 692]]<|/det|>
-Future work aims to fully identify load induced tissue changes in healthy and diseased arterial tissue using SALS.  
-
-<|ref|>sub_title<|/ref|><|det|>[[528, 706, 640, 720]]<|/det|>
-## REFERENCES  
-
-<|ref|>text<|/ref|><|det|>[[527, 728, 852, 782]]<|/det|>
-[1] C. Creane et al., Biomech Model Mechanobiol., 10: 831- 843, 2011[2] Billiar, K., and Sacks, M., J. Biomech. 30: 753- 7 56, 1997  
-
-<|ref|>sub_title<|/ref|><|det|>[[528, 794, 715, 807]]<|/det|>
-## ACKNOWLEDGEMENTS  
-
-<|ref|>text<|/ref|><|det|>[[527, 814, 852, 855]]<|/det|>
-This research was part funded by Science Foundation Ireland (SFI/13/ERC/B2775) and the Irish Research Council (GOIPG/2014/515).
+1) (X) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 2) 1) 1) 1) 1) 1) 1) 1) 1) 1) 3) 1) 1) 1) 1) 1) 1) 1) 1) 1) 4) 1) 1) 1) 1) 1) 1) 1) 1) 1) 5) 1) 1) 1) 1) 1) 1) 1) 1) 6) 1) 1) 1) 1) 1) 1) 1) 1) 1) 7) 1) 1) 1) 1) 1) 1) 1) 1) 1) 8) 1) 1) 1) 1) 1) 1) 1) 1) 1) 9) 1) 1) 1) 1) 1) 1) 1) 1) 1) 10) 1) 1) 1) 1) 1) 1) 1) 1) 1) 11) 1) 1) 1) 1) 1) 1) 1) 1) 1) 12) 1) 1) 1) 1) 1) 1) 1) 1) 1) 13) 1) 1) 1) 1) 1) 1) 1) 1) 1) 14) 1) 1) 1) 1) 1) 1) 1) 1) 1) 15) 1) 1) 1) 1) 1) 1) 1) 1) 1) 16) 1) 1) 1) 1) 1) 1) 1) 1) 1) 17) 1) 1) 1) 1) 1) 1) 1) 1) 1) 18) 1) 1) 1) 1) 1) 1) 1) 1) 1) 19) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 20) 1) 1) 1) 1) 1) 1) 1) 1) 1) 21) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 22) 1) 1) 1) 1) 1) 1) 1) 1) 1) 23) 1) 1) 1) 1) 1) 1) 1) 1) 1) 24) 1) 1) 1) 1) 1) 1) 1) 1) 1) 25) 1) 1) 1) 1) 1) 1) 1) 1) 1) 26) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 27) 1) 1) 1) 1) 1) 1) 1) 1) 1) 28) 1) 1) 1) 1) 1) 1) 1) 1) 1) 29) 1) 1) 1) 1) 1) 1) 1) 1) 30) 1) 1) 1) 1) 1) 1) 1) 1) 1) 31) 1) 1) 1) 1) 1) 1) 1) 1) 1) 32) 1) 1) 1) 1) 1) 1) 1) 1) 1) 33) 1) 1) 1) 1) 1) 1) 1) 1) 1) 34) 1) 1) 1) 1) 1) 1) 1) 1) 1) 35) 1) 1) 1) 1) 1) 1) 1) 1) 1) 36) 1) 1) 1) 1) 1) 1) 1) 1) 1) 37) 1) 1) 1) 1) 1) 1) 1) 1) 1) 38) 1) 1) 1) 1) 1) 1) 1) 1) 1) 39) 1) 1) 1) 1) 1) 1) 1) 1) 1) 40) 1) 1) 1) 1) 1) 1) 1) 1) 1) 41) 1) 1) 1) 1) 1) 1) 1) 1) 1) 42) 1) 1) 1) 1) 1) 1) 1) 1) 1) 43) 1) 1) 1) 1) 1) 1) 1) 1) 1) 44) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 45) 1) 1) 1) 1) 1) 1) 1) 1) 1) 46) 1) 1) 1) 1) 1) 1) 1) 1) 1) 47) 1) 1) 1) 1) 1) 1) 1) 1) 1) 48) 1) 1) 1) 1) 1) 1) 1) 1) 1) 49) 1) 1) 1) 1) 1) 1) 1) 1) 1) 50) 1) 1) 1) 1) 1) 1) 1) 1) 1) 51) 1) 1) 1) 1) 1) 1) 1) 1) 1) 52) 1) 1) 1) 1) 1) 1) 1) 1) 1) 53) 1) 1) 1) 1) 1) 1) 1) 1) 1) 54) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 55) 1) 1) 1) 1) 1) 1) 1) 1) 1) 56) 1) 1) 1) 1) 1) 1) 1) 1) 1) 57) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 58) 1) 1) 1) 1) 1) 1) 1) 1) 1) 59) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 60) 1) 1) 1) 1) 1) 1) 1) 1) 1) 61) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 62) 1) 1) 1) 1) 1) 1) 1) 1) 1) 63) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 64) 1) 1) 1) 1) 1) 1) 1) 1) 1) 65) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 66) 1) 1) 1) 1) 1) 1) 1) 1) 1) 67) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 68) 1) 1) 1) 1) 1) 1) 1) 1) 1) 69) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 70) 1) 1) 1) 1) 1) 1) 1) 1) 1) 71) 1) 1) 1) 1) 1) 1) 1) 1) 1) 72) 1) 1) 1) 1) 1) 1) 1) 1) 1) 73) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 74) 1) 1) 1) 1) 1) 1) 1) 1) 1) 75) 1) 1) 1) 1) 1) 1) 1) 1) 1) 76) 1) 1) 1) 1) 1) 1) 1) 1) 1) 77) 1) 1) 1) 1) 1) 1) 1) 1) 1) 78) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 79) 1) 1) 1) 1) 1) 1) 1) 1) 1) 80) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 81) 1) 1) 1) 1) 1) 1) 1) 1) 1) 82) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 83) 1) 1) 1) 1) 1) 1) 1) 1) 1) 84) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 85) 1) 1) 1) 1) 1) 1) 1) 1) 1) 86) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 87) 1) 1) 1) 1) 1) 1) 1) 1) 1) 88) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 89) 1) 1) 1) 1) 1) 1) 1) 1) 1) 90) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 91) 1) 1) 1) 1) 1) 1) 1) 1) 92) 1) 1) 1) 1) 1) 1) 1) 1) 1) 93) 1) 1) 1) 1) 1) 1) 1) 1) 1) 94) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 95) 1) 1) 1) 1) 1) 1) 1) 1) 1) 96) 1) 1) 1) 1) 1) 1) 1) 1) 1) 97) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 98) 1) 1) 1) 1) 1) 1) 1) 1) 1) 99) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 100) 1) 1) 1) 1) 1) 1) 1) 1) 1) 101) 1) 1) 1) 1) 1) 1) 1) 1) 1) 102) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 103) 1) 1) 1) 1) 1) 1) 1) 1) 1) 104) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 105) 1) 1) 1) 1) 1) 1) 1) 1) 1) 106) 1) 1) 1) 1) 1) 1) 1) 1) 1) 107) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 108) 1) 1) 1) 1) 1) 1) 1) 1) 1) 109) 1) 1) 1) 1) 1) 1) 1) 1) 1) 110) 1) 1) 1) 1) 1) 1) 1) 1) 1) 111) 1) 1) 1) 1) 1) 1) 1) 1) 1) 112) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 113) 1) 1) 1) 1) 1) 1) 1) 1) 1) 114) 1) 1) 1) 1) 1) 1) 1) 1) 115) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 116) 1) 1) 1) 1) 1) 1) 1) 1) 1) 117) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 118) 1) 1) 1) 1) 1) 1) 1) 1) 1) 119) 1) 1) 1) 1) 1) 1) 1) 1) 120) 1) 1) 1) 1) 1) 1) 1) 1) 1) 121) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 122) 1) 1) 1) 1) 1) 1) 1) 1) 1) 123) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 124) 1) 1) 1) 1) 1) 1) 1) 1) 1) 125) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 126) 1) 1) 1) 1) 1) 1) 1) 1) 1) 127) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 128) 1) 1) 1) 1) 1) 1) 1) 1) 1) 129) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 130) 1) 1) 1) 1) 1) 1) 1) 1) 1) 131) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 132) 1) 1) 1) 1) 1) 1) 1) 1) 1) 133) 1) 1) 1) 1) 1) 1) 1) 1) 1) 1) 134) 1) 1

stage1/sample_00007/document.md

@@ -1 +1 @@
-2011, XLVI, 394 p., Hardcover ISBN: 978-90-481-8664-8
+2011, XLVI, 394 p., HardcoverISBN: 978-90-481-8664-8

stage1/sample_00007/raw_response.md

@@ -1 +1 @@
-2011, XLVI, 394 p., Hardcover ISBN: 978-90-481-8664-8
+2011, XLVI, 394 p., HardcoverISBN: 978-90-481-8664-8

stage1/sample_00008/raw_response.md

@@ -1,26 +1,26 @@
-<|ref|>text<|/ref|><|det|>[[89, 80, 862, 109]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[89, 80, 860, 107]]<|/det|>
 The parametric equations for a projectile with constant gravity g: 
 
-<|ref|>equation<|/ref|><|det|>[[152, 109, 423, 145]]<|/det|>
+<|ref|>equation<|/ref|><|det|>[[153, 108, 426, 140]]<|/det|>
 \[x = v_0 t \cos \theta + x_0\]
 
-<|ref|>equation<|/ref|><|det|>[[152, 156, 567, 227]]<|/det|>
+<|ref|>equation<|/ref|><|det|>[[153, 154, 566, 227]]<|/det|>
 \[y = -\frac{1}{2} gt^2 + v_0 t \sin \theta + y_0\]
 
-<|ref|>text<|/ref|><|det|>[[89, 255, 866, 307]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[89, 257, 868, 308]]<|/det|>
 ex. A shell is fired from ground level with an initial speed of 768 ft/sec. at an angle of 30°. Find: 
 
-<|ref|>text<|/ref|><|det|>[[92, 310, 183, 352]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[92, 307, 183, 349]]<|/det|>
 1. \(\vec{r}(t)\) 
 
-<|ref|>text<|/ref|><|det|>[[91, 357, 485, 381]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[91, 357, 483, 381]]<|/det|>
 2. the maximum altitude attained 
 
-<|ref|>text<|/ref|><|det|>[[91, 383, 374, 408]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[91, 383, 372, 407]]<|/det|>
 3. the range of the shell 
 
-<|ref|>text<|/ref|><|det|>[[91, 410, 363, 434]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[91, 410, 361, 433]]<|/det|>
 4. the speed on impact 
 
-<|ref|>text<|/ref|><|det|>[[91, 437, 608, 462]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[91, 436, 607, 461]]<|/det|>
 5. the horizontal distance when \(y = 2240\) ft.

stage1/sample_00009/document.md

@@ -1,4 +1,4 @@
-4) purpose of attenuation correction. The scanning parameters may vary according to the type of CT scanner. Usually the tube voltage is set at 140 kV, which permits the conversion of the Hounsfield units into attenuation coefficients at 511 keV. The CT scan can be performed after the injection of FDG and has the advantage to significantly reduce the total scan time (usual duration is \(< 10\) s). However, the dose of the CT scan to the patient can be reduced by lowering the tube current (see radiation dosimetry above) if anatomical information is not needed. When performing PET-CT of the brain it is recommended to check for movements between the CT and the PET sessions, which might produce artefacts in the attenuation correction.
+purpose of attenuation correction. The scanning parameters may vary according to the type of CT scanner. Usually the tube voltage is set at 140 kV, which permits the conversion of the Hounsfield units into attenuation coefficients at 511 keV. The CT scan can be performed after the injection of FDG and has the advantage to significantly reduce the total scan time (usual duration is <10 s). However, the dose of the CT scan to the patient can be reduced by lowering the tube current (see radiation dosimetry above) if anatomical information is not needed. When performing PET-CT of the brain it is recommended to check for movements between the CT and the PET sessions, which might produce artefacts in the attenuation correction. 
 
 - Emission scan. As semiquantitative estimates of tumor-to-background uptake ratios are typically used, it is recommended to use a standardized acquisition protocol with a fixed time for start of acquisition to make the data of different patients or repeated scans comparable. If data are acquired in 3-D mode, appropriate scatter correction is mandatory. The duration of emission image acquisition should be related to the minimum required number of counts. For FDG, typically data are acquired over 15–30 min aiming to collect 50–200 million counts. Even though shorter acquisition times can still be used for diagnostic pattern evaluation (Chen et al. 2005), a minimum of 15 min in 3D mode is advocated. For MET and FET typically data are acquired for 20 min (20–40 min p.i.), often supplemented by dynamic data starting directly with tracer injection. 
 
@@ -6,13 +6,13 @@
 
 - Multiple detectors (triple or dual head) or other dedicated SPECT cameras for brain imaging should be used for acquisition. Single detector units cannot generally be recommended. They may only be used if scan time is prolonged appropriately, a dose in the upper suggested range is applied, and meticulous care is taken to produce high-quality images. 
 
-- LEHR or LEUHR parallel-hole collimators are the mostly available collimator sets for brain imaging. All purpose collimators are not suitable. The use of medium energy collimators could be advantageous; however, usually they are hampered by a low sensitivity. They may only be used if acceptable count rates are obtained. If available, collimator sets specifically adapted to the characteristics of \(^{123}\)I may be used. Fanbeam collimators may be generally preferred over parallel-hole collimators due to the advantageous trade-off between resolution and count rate capability. The acquisition parameters are summarized in Table 2.2. 
+- LEHR or LEUHR parallel-hole collimators are the mostly available collimator sets for brain imaging. All purpose collimators are not suitable. The use of medium energy collimators could be advantageous; however, usually they are hampered by a low sensitivity. They may only be used if acceptable count rates are obtained. If available, collimator sets specifically adapted to the characteristics of \(^{123}\mathrm{I}\) may be used. Fanbeam collimators may be generally preferred over parallel-hole collimators due to the advantageous trade-off between resolution and count rate capability. The acquisition parameters are summarized in Table 2.2. 
 
-## TABLE 2.2. Acquisition parameters for IMT-SPECT 
+TABLE 2.2. Acquisition parameters for IMT-SPECT 
 
 - Rotational radius: smallest possible with appropriate patient safeguard
 - Matrix: \(128 \times 128\)
-- Angular sampling: \(\leq 3^{\circ}\) (360° rotation)
-- Zoom: acquisition pixel size should be 1/3–1/2 of the expected resolution; therefore it may be necessary to use a hardware zoom to achieve an appropriate pixel size
+- Angular sampling: \(\leq 3^\circ\) (360° rotation)
+- Zoom: acquisition pixel size should be \(1/3-1/2\) of the expected resolution; therefore it may be necessary to use a hardware zoom to achieve an appropriate pixel size
 - Acquisition mode: Step and shoot mode is predominantly used. Continuous mode acquisition may provide shorter total scan time, reduce mechanical wear to the system and improve patient comfort
 - Total scan time: depending on the imaging device, typical scan time for a triple head camera is about 30–50 min (e.g., 120 projections; 40 projections per head; 60 s/projection)

stage1/sample_00009/raw_response.md

@@ -1,24 +1,25 @@
-4) purpose of attenuation correction. The scanning parameters may vary according to the type of CT scanner. Usually the tube voltage is set at 140 kV, which permits the conversion of the Hounsfield units into attenuation coefficients at 511 keV. The CT scan can be performed after the injection of FDG and has the advantage to significantly reduce the total scan time (usual duration is \(< 10\) s). However, the dose of the CT scan to the patient can be reduced by lowering the tube current (see radiation dosimetry above) if anatomical information is not needed. When performing PET-CT of the brain it is recommended to check for movements between the CT and the PET sessions, which might produce artefacts in the attenuation correction.
+<|ref|>text<|/ref|><|det|>[[135, 87, 492, 441]]<|/det|>
+purpose of attenuation correction. The scanning parameters may vary according to the type of CT scanner. Usually the tube voltage is set at 140 kV, which permits the conversion of the Hounsfield units into attenuation coefficients at 511 keV. The CT scan can be performed after the injection of FDG and has the advantage to significantly reduce the total scan time (usual duration is <10 s). However, the dose of the CT scan to the patient can be reduced by lowering the tube current (see radiation dosimetry above) if anatomical information is not needed. When performing PET-CT of the brain it is recommended to check for movements between the CT and the PET sessions, which might produce artefacts in the attenuation correction. 
 
-<|ref|>text<|/ref|><|det|>[[116, 445, 491, 896]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[115, 444, 492, 896]]<|/det|>
 - Emission scan. As semiquantitative estimates of tumor-to-background uptake ratios are typically used, it is recommended to use a standardized acquisition protocol with a fixed time for start of acquisition to make the data of different patients or repeated scans comparable. If data are acquired in 3-D mode, appropriate scatter correction is mandatory. The duration of emission image acquisition should be related to the minimum required number of counts. For FDG, typically data are acquired over 15–30 min aiming to collect 50–200 million counts. Even though shorter acquisition times can still be used for diagnostic pattern evaluation (Chen et al. 2005), a minimum of 15 min in 3D mode is advocated. For MET and FET typically data are acquired for 20 min (20–40 min p.i.), often supplemented by dynamic data starting directly with tracer injection. 
 
-<|ref|>sub_title<|/ref|><|det|>[[512, 81, 825, 97]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[511, 82, 826, 98]]<|/det|>
 ## IMT Single Photon Emission Tomography 
 
-<|ref|>text<|/ref|><|det|>[[512, 107, 886, 296]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[511, 107, 886, 299]]<|/det|>
 - Multiple detectors (triple or dual head) or other dedicated SPECT cameras for brain imaging should be used for acquisition. Single detector units cannot generally be recommended. They may only be used if scan time is prolonged appropriately, a dose in the upper suggested range is applied, and meticulous care is taken to produce high-quality images. 
 
-<|ref|>text<|/ref|><|det|>[[512, 300, 886, 618]]<|/det|>
-- LEHR or LEUHR parallel-hole collimators are the mostly available collimator sets for brain imaging. All purpose collimators are not suitable. The use of medium energy collimators could be advantageous; however, usually they are hampered by a low sensitivity. They may only be used if acceptable count rates are obtained. If available, collimator sets specifically adapted to the characteristics of \(^{123}\)I may be used. Fanbeam collimators may be generally preferred over parallel-hole collimators due to the advantageous trade-off between resolution and count rate capability. The acquisition parameters are summarized in Table 2.2. 
+<|ref|>text<|/ref|><|det|>[[511, 300, 887, 619]]<|/det|>
+- LEHR or LEUHR parallel-hole collimators are the mostly available collimator sets for brain imaging. All purpose collimators are not suitable. The use of medium energy collimators could be advantageous; however, usually they are hampered by a low sensitivity. They may only be used if acceptable count rates are obtained. If available, collimator sets specifically adapted to the characteristics of \(^{123}\mathrm{I}\) may be used. Fanbeam collimators may be generally preferred over parallel-hole collimators due to the advantageous trade-off between resolution and count rate capability. The acquisition parameters are summarized in Table 2.2. 
 
-<|ref|>sub_title<|/ref|><|det|>[[511, 683, 856, 698]]<|/det|>
-## TABLE 2.2. Acquisition parameters for IMT-SPECT 
+<|ref|>table_caption<|/ref|><|det|>[[511, 686, 854, 701]]<|/det|>
+TABLE 2.2. Acquisition parameters for IMT-SPECT 
 
-<|ref|>text<|/ref|><|det|>[[511, 705, 880, 891]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[511, 707, 879, 890]]<|/det|>
 - Rotational radius: smallest possible with appropriate patient safeguard
 - Matrix: \(128 \times 128\)
-- Angular sampling: \(\leq 3^{\circ}\) (360° rotation)
-- Zoom: acquisition pixel size should be 1/3–1/2 of the expected resolution; therefore it may be necessary to use a hardware zoom to achieve an appropriate pixel size
+- Angular sampling: \(\leq 3^\circ\) (360° rotation)
+- Zoom: acquisition pixel size should be \(1/3-1/2\) of the expected resolution; therefore it may be necessary to use a hardware zoom to achieve an appropriate pixel size
 - Acquisition mode: Step and shoot mode is predominantly used. Continuous mode acquisition may provide shorter total scan time, reduce mechanical wear to the system and improve patient comfort
 - Total scan time: depending on the imaging device, typical scan time for a triple head camera is about 30–50 min (e.g., 120 projections; 40 projections per head; 60 s/projection)

stage1/sample_00010/document.md

@@ -1,9 +1,3 @@
-Do: An electron in a TV tube is beamed horizontally at a speed of 5 x \(10^{6}\) m/sec. toward the face of the tube 40 cm away. To determine how far the electron drops before it hits, which equation would be used? 
+Do: An electron in a TV tube is beamed horizontally at a speed of 5 x \(10^{6}\) m/sec. toward the face of the tube 40 cm away. To determine how far the electron drops before it hits, which equation would be used?  
 
-a. \(y = -4.9t^{2}\) 
-
-b. \(y = -4.9t^{2} - 5x10^{6}t\) 
-
-c. \(5x10^{6}t = 4\) 
-
-d. \(5x10^{6}t = 40\)
+a. \(y = -4.9t^2\) b. \(y = -4.9t^2 - 5x10^6t\) c. \(5x10^6t = 4\) d. \(5x10^6t = 40\)

stage1/sample_00010/raw_response.md

@@ -1,14 +1,5 @@
 <|ref|>text<|/ref|><|det|>[[88, 81, 901, 181]]<|/det|>
-Do: An electron in a TV tube is beamed horizontally at a speed of 5 x \(10^{6}\) m/sec. toward the face of the tube 40 cm away. To determine how far the electron drops before it hits, which equation would be used? 
+Do: An electron in a TV tube is beamed horizontally at a speed of 5 x \(10^{6}\) m/sec. toward the face of the tube 40 cm away. To determine how far the electron drops before it hits, which equation would be used?  
 
-<|ref|>text<|/ref|><|det|>[[89, 213, 325, 249]]<|/det|>
-a. \(y = -4.9t^{2}\) 
-
-<|ref|>text<|/ref|><|det|>[[89, 252, 419, 288]]<|/det|>
-b. \(y = -4.9t^{2} - 5x10^{6}t\) 
-
-<|ref|>text<|/ref|><|det|>[[89, 292, 286, 327]]<|/det|>
-c. \(5x10^{6}t = 4\) 
-
-<|ref|>text<|/ref|><|det|>[[89, 330, 306, 363]]<|/det|>
-d. \(5x10^{6}t = 40\)
+<|ref|>text<|/ref|><|det|>[[88, 212, 421, 356]]<|/det|>
+a. \(y = -4.9t^2\) b. \(y = -4.9t^2 - 5x10^6t\) c. \(5x10^6t = 4\) d. \(5x10^6t = 40\)

stage1/sample_00011/document.md

@@ -1,47 +1,45 @@
-0.5cm 0.5cm 0.5cm 0.5cm 0.5cm 0.5cm 0.5cm
+0 
 
 ![Figure sample_00011_fig01](figures/sample_00011_fig01.png)
 
-# Brett Babin
+# Bio 
 
-Postdoctoral Research Fellow, Pathology
+**Bio** 
 
-☉ Curriculum Vitae available Online
+Brett received his B.S. in Chemical Engineering from the University of Massachusetts Amherst in 2009. There he worked in the lab of Dr. Neil Forbes developing microfluidic devices to study the interactions between bacteria and in vitro tumor models. He earned his Ph.D. in Chemical Engineering from the California Institute of Technology in 2016 where he worked with Dr. Dave Tirrell and Dr. Dianne Newman. His thesis focused on the development and application of a method for time- and cell-selective proteomic analysis in bacteria. He used this approach to study protein synthesis by the opportunistic pathogen Pseudomonas aeruginosa under dormancy and biofilm growth conditions. Brett joined the Bogyo lab at Stanford in the fall of 2016. His current focus is on the roles of serine hydrolases in the physiology of pathogenic bacteria. 
 
-# Bio
+# HONORS AND AWARDS 
 
-# BIO
+• A. P. Giannini Postdoctoral Fellowship, A. P. Giannini Foundation (2018) 
 
-Brett received his B.S. in Chemical Engineering from the University of Massachusetts Amherst in 2009. There he worked in the lab of Dr. Neil Forbes developing microfluidic devices to study the interactions between bacteria and in vitro tumor models. He earned his Ph.D. in Chemical Engineering from the California Institute of Technology in 2016 where he worked with Dr. Dave Tirrell and Dr. Dianne Newman. His thesis focused on the development and application of a method for time- and cell-selective proteomic analysis in bacteria. He used this approach to study protein synthesis by the opportunistic pathogen Pseudomonas aeruginosa under dormancy and biofilm growth conditions. Brett joined the Bogyo lab at Stanford in the fall of 2016. His current focus is on the roles of serine hydrolases in the physiology of pathogenic bacteria.
+• Microbiology and Immunology Postdoctoral Fellowship, Stanford School of Medicine (2018) 
 
-# HONORS AND AWARDS
+• Dean's Fellowship, Stanford School of Medicine (2017) 
 
-·A.P. Giannini Postdoctoral Fellowship, A. P. Giannini Foundation (2018)
+# PROFESSIONAL EDUCATION 
 
-·Microbiology and Immunology Postdoctoral Fellowship, Stanford School of Medicine (2018)
+• Bachelor of Science, University of Massachusetts Amherst (2009) 
 
-·Dean's Fellowship, Stanford School of Medicine (2017)
+• Doctor of Philosophy, California Institute of Technology (2016) 
 
-# PROFESSIONAL EDUCATION
+# STANFORD ADVISORS 
 
-·Bachelor of Science, University of Massachusetts Amherst (2009)
+• Matthew Bogyo, Postdoctoral Faculty Sponsor 
 
-·Doctor of Philosophy, California Institute of Technology (2016)
+# Research & Scholarship 
 
-# STANFORD ADVISORS
+**LAB AFFILIATIONS** 
 
-·Matthew Bogyo, Postdoctoral Faculty Sponsor
+• Matthew Bogyo, Bogyo Lab (9/1/2016) 
 
-# Research & Scholarship
+# Publications 
 
-# LAB AFFILIATIONS
+## PUBLICATIONS 
 
-·Matthew Bogyo, Bogyo Lab (9/1/2016)
+• Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Current opinion in chemical biology 
 
-# Publications
+Keller, L. J., Babin, B. M., Lakemeyer, M., Bogyo, M. 
 
-# PUBLICATIONS
+2019; 54: 45-53 
 
-·Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Current opinion in chemical biology Keller, L. J., Babin, B. M., Lakemeyer, M., Bogyo, M. 2019; 54: 45-53
-
-·Leveraging Peptide Substrate Libraries to Design Inhibitors of Bacterial L on Protease ACS CHEMICAL BIOLOGY
+• Leveraging Peptide Substrate Libraries to Design Inhibitors of Bacterial L Proteinase ACS CHEMICAL BIOLOGY

stage1/sample_00011/raw_response.md

@@ -1,69 +1,66 @@
-0.5cm 0.5cm 0.5cm 0.5cm 0.5cm 0.5cm 0.5cm
+0 
 
-<|ref|>image<|/ref|><|det|>[[58, 138, 216, 261]]<|/det|>
+<|ref|>image<|/ref|><|det|>[[57, 138, 217, 260]]<|/det|>
 
-<|ref|>title<|/ref|><|det|>[[233, 136, 465, 174]]<|/det|>
-# Brett Babin
+<|ref|>title<|/ref|><|det|>[[57, 297, 90, 310]]<|/det|>
+# Bio 
 
-<|ref|>text<|/ref|><|det|>[[232, 184, 559, 200]]<|/det|>
-Postdoctoral Research Fellow, Pathology
+<|ref|>text<|/ref|><|det|>[[57, 326, 92, 340]]<|/det|>
+**Bio** 
 
-<|ref|>text<|/ref|><|det|>[[232, 208, 435, 218]]<|/det|>
-☉ Curriculum Vitae available Online
+<|ref|>text<|/ref|><|det|>[[57, 348, 936, 460]]<|/det|>
+Brett received his B.S. in Chemical Engineering from the University of Massachusetts Amherst in 2009. There he worked in the lab of Dr. Neil Forbes developing microfluidic devices to study the interactions between bacteria and in vitro tumor models. He earned his Ph.D. in Chemical Engineering from the California Institute of Technology in 2016 where he worked with Dr. Dave Tirrell and Dr. Dianne Newman. His thesis focused on the development and application of a method for time- and cell-selective proteomic analysis in bacteria. He used this approach to study protein synthesis by the opportunistic pathogen Pseudomonas aeruginosa under dormancy and biofilm growth conditions. Brett joined the Bogyo lab at Stanford in the fall of 2016. His current focus is on the roles of serine hydrolases in the physiology of pathogenic bacteria. 
 
-<|ref|>title<|/ref|><|det|>[[57, 298, 91, 311]]<|/det|>
-# Bio
+<|ref|>title<|/ref|><|det|>[[57, 476, 248, 490]]<|/det|>
+# HONORS AND AWARDS 
 
-<|ref|>title<|/ref|><|det|>[[57, 330, 89, 341]]<|/det|>
-# BIO
+<|ref|>text<|/ref|><|det|>[[57, 495, 519, 509]]<|/det|>
+• A. P. Giannini Postdoctoral Fellowship, A. P. Giannini Foundation (2018) 
 
-<|ref|>text<|/ref|><|det|>[[57, 350, 937, 460]]<|/det|>
-Brett received his B.S. in Chemical Engineering from the University of Massachusetts Amherst in 2009. There he worked in the lab of Dr. Neil Forbes developing microfluidic devices to study the interactions between bacteria and in vitro tumor models. He earned his Ph.D. in Chemical Engineering from the California Institute of Technology in 2016 where he worked with Dr. Dave Tirrell and Dr. Dianne Newman. His thesis focused on the development and application of a method for time- and cell-selective proteomic analysis in bacteria. He used this approach to study protein synthesis by the opportunistic pathogen Pseudomonas aeruginosa under dormancy and biofilm growth conditions. Brett joined the Bogyo lab at Stanford in the fall of 2016. His current focus is on the roles of serine hydrolases in the physiology of pathogenic bacteria.
+<|ref|>text<|/ref|><|det|>[[57, 516, 567, 529]]<|/det|>
+• Microbiology and Immunology Postdoctoral Fellowship, Stanford School of Medicine (2018) 
 
-<|ref|>title<|/ref|><|det|>[[57, 479, 248, 490]]<|/det|>
-# HONORS AND AWARDS
+<|ref|>text<|/ref|><|det|>[[57, 538, 369, 550]]<|/det|>
+• Dean's Fellowship, Stanford School of Medicine (2017) 
 
-<|ref|>text<|/ref|><|det|>[[57, 498, 470, 508]]<|/det|>
-·A.P. Giannini Postdoctoral Fellowship, A. P. Giannini Foundation (2018)
+<|ref|>title<|/ref|><|det|>[[57, 566, 293, 580]]<|/det|>
+# PROFESSIONAL EDUCATION 
 
-<|ref|>text<|/ref|><|det|>[[57, 518, 566, 528]]<|/det|>
-·Microbiology and Immunology Postdoctoral Fellowship, Stanford School of Medicine (2018)
+<|ref|>text<|/ref|><|det|>[[57, 587, 421, 600]]<|/det|>
+• Bachelor of Science, University of Massachusetts Amherst (2009) 
 
-<|ref|>text<|/ref|><|det|>[[57, 540, 368, 549]]<|/det|>
-·Dean's Fellowship, Stanford School of Medicine (2017)
+<|ref|>text<|/ref|><|det|>[[57, 607, 411, 621]]<|/det|>
+• Doctor of Philosophy, California Institute of Technology (2016) 
 
-<|ref|>title<|/ref|><|det|>[[57, 568, 292, 579]]<|/det|>
-# PROFESSIONAL EDUCATION
+<|ref|>title<|/ref|><|det|>[[57, 637, 239, 650]]<|/det|>
+# STANFORD ADVISORS 
 
-<|ref|>text<|/ref|><|det|>[[57, 589, 420, 599]]<|/det|>
-·Bachelor of Science, University of Massachusetts Amherst (2009)
+<|ref|>text<|/ref|><|det|>[[57, 657, 322, 669]]<|/det|>
+• Matthew Bogyo, Postdoctoral Faculty Sponsor 
 
-<|ref|>text<|/ref|><|det|>[[57, 610, 410, 620]]<|/det|>
-·Doctor of Philosophy, California Institute of Technology (2016)
+<|ref|>title<|/ref|><|det|>[[57, 686, 263, 702]]<|/det|>
+# Research & Scholarship 
 
-<|ref|>title<|/ref|><|det|>[[57, 639, 239, 650]]<|/det|>
-# STANFORD ADVISORS
+<|ref|>text<|/ref|><|det|>[[57, 718, 218, 730]]<|/det|>
+**LAB AFFILIATIONS** 
 
-<|ref|>text<|/ref|><|det|>[[57, 659, 320, 669]]<|/det|>
-·Matthew Bogyo, Postdoctoral Faculty Sponsor
+<|ref|>text<|/ref|><|det|>[[57, 737, 284, 750]]<|/det|>
+• Matthew Bogyo, Bogyo Lab (9/1/2016) 
 
-<|ref|>title<|/ref|><|det|>[[57, 688, 262, 702]]<|/det|>
-# Research & Scholarship
+<|ref|>title<|/ref|><|det|>[[57, 767, 164, 781]]<|/det|>
+# Publications 
 
-<|ref|>title<|/ref|><|det|>[[57, 721, 216, 731]]<|/det|>
-# LAB AFFILIATIONS
+<|ref|>sub_title<|/ref|><|det|>[[57, 797, 186, 810]]<|/det|>
+## PUBLICATIONS 
 
-<|ref|>text<|/ref|><|det|>[[57, 740, 283, 750]]<|/det|>
-·Matthew Bogyo, Bogyo Lab (9/1/2016)
+<|ref|>text<|/ref|><|det|>[[57, 820, 927, 844]]<|/det|>
+• Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Current opinion in chemical biology 
 
-<|ref|>title<|/ref|><|det|>[[57, 770, 165, 782]]<|/det|>
-# Publications
+<|ref|>text<|/ref|><|det|>[[69, 847, 360, 858]]<|/det|>
+Keller, L. J., Babin, B. M., Lakemeyer, M., Bogyo, M. 
 
-<|ref|>title<|/ref|><|det|>[[57, 801, 185, 812]]<|/det|>
-# PUBLICATIONS
+<|ref|>text<|/ref|><|det|>[[69, 862, 160, 873]]<|/det|>
+2019; 54: 45-53 
 
-<|ref|>text<|/ref|><|det|>[[57, 823, 927, 868]]<|/det|>
-·Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Current opinion in chemical biology Keller, L. J., Babin, B. M., Lakemeyer, M., Bogyo, M. 2019; 54: 45-53
-
-<|ref|>text<|/ref|><|det|>[[57, 890, 710, 900]]<|/det|>
-·Leveraging Peptide Substrate Libraries to Design Inhibitors of Bacterial L on Protease ACS CHEMICAL BIOLOGY
+<|ref|>text<|/ref|><|det|>[[57, 891, 710, 904]]<|/det|>
+• Leveraging Peptide Substrate Libraries to Design Inhibitors of Bacterial L Proteinase ACS CHEMICAL BIOLOGY

stage1/sample_00012/document.md

@@ -1 +1,3 @@
-4.4. Graphical view of the workflow generated by the software. The workflow is a graphical view of the workflow generated by the software. The workflow is a graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. A graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical overview of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical overview of the workflow generated by the software. A graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. A graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is an overview of the workflow generated by the software. The workflow is a graphical overview of the workflow generated by the software. The workflow is a graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical view of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. 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The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview
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+![Figure sample_00012_fig01](figures/sample_00012_fig01.png)

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-4.4. Graphical view of the workflow generated by the software. The workflow is a graphical view of the workflow generated by the software. The workflow is a graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. A graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical overview of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical overview of the workflow generated by the software. A graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is a graphical view. A graphical view of the workflow generated by the software. The workflow is a graphical view. The workflow is a graphical view. The workflow is an overview of the workflow generated by the software. The workflow is a graphical overview of the workflow generated by the software. The workflow is a graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical view of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. 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The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. An overview of the workflow generated. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. A graphical overview of the workflow generated by the software. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview. The workflow is a graphical overview
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+<|ref|>image<|/ref|><|det|>[[361, 205, 760, 844]]<|/det|>

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-2019; 14 (11): 2453-62
+2019; 14 (11): 2453-62  
+
+• The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Molecular microbiology Bergkessel, M., Babin, B. M., VanderVelde, D., Sweredoski, M. J., Moradian, A., Eggleston-Rangel, R., Hess, S., Tirrell, D. A., Artsimovitch, I., Newman, D. K. 2019 
+
+• Covalent Modifiers of Botulinum Neurotoxin Counteract Toxin Persistence ACS CHEMICAL BIOLOGY Garland, M., Babin, B. M., Miyashita, S., Loscher, S., Shen, Y., Dong, M., Bogyo, M. 2019; 14 (1): 76-87 
+
+• Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms. mBio Babin, B. M., Atangcho, L., van Eldijk, M. B., Sweredoski, M. J., Moradian, A., Hess, S., Tolker-Nielsen, T., Newman, D. K., Tirrell, D. A. 2017; 8 (5) 
+
+• SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Babin, B. M., Bergkessel, M., Sweredoski, M. J., Moradian, A., Hess, S., Newman, D. K., Tirrell, D. A. 2016; 113 (5): E597-E605 
+
+• In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry ENVIRONMENTAL MICROBIOLOGY Hatzenpichler, R., Scheller, S., Tavormina, P. L., Babin, B. M., Tirrell, D. A., Orphan, V. J. 2014; 16 (8): 2568-2590 
+
+• State-selective Metabolic Labeling of Cellular Proteins ACS CHEMICAL BIOLOGY Ngo, J. T., Babin, B. M., Champion, J. A., Schuman, E. M., Tirrell, D. A. 2012; 7 (8): 1326-1330 
+
+• Noninvasive characterization of in situ forming implants using diagnostic ultrasound JOURNAL OF CONTROLLED RELEASE Solorio, L., Babin, B. M., Patel, R. B., Mach, J., Azar, N., Exner, A. A. 2010; 143 (2): 183-190 
+
+• A multipurpose microfluidic device designed to mimic microenvironment gradients and develop targeted cancer therapeutics LAB ON A CHIP Walsh, C. L., Babin, B. M., Kasinskas, R. W., Foster, J. A., McGarry, M. J., Forbes, N. S. 2009; 9 (4): 545-554

stage1/sample_00013/raw_response.md

@@ -1 +1,25 @@
-2019; 14 (11): 2453-62
+2019; 14 (11): 2453-62  
+
+<|ref|>text<|/ref|><|det|>[[56, 125, 927, 169]]<|/det|>
+• The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Molecular microbiology Bergkessel, M., Babin, B. M., VanderVelde, D., Sweredoski, M. J., Moradian, A., Eggleston-Rangel, R., Hess, S., Tirrell, D. A., Artsimovitch, I., Newman, D. K. 2019 
+
+<|ref|>text<|/ref|><|det|>[[57, 189, 649, 217]]<|/det|>
+• Covalent Modifiers of Botulinum Neurotoxin Counteract Toxin Persistence ACS CHEMICAL BIOLOGY Garland, M., Babin, B. M., Miyashita, S., Loscher, S., Shen, Y., Dong, M., Bogyo, M. 2019; 14 (1): 76-87 
+
+<|ref|>text<|/ref|><|det|>[[57, 248, 809, 290]]<|/det|>
+• Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms. mBio Babin, B. M., Atangcho, L., van Eldijk, M. B., Sweredoski, M. J., Moradian, A., Hess, S., Tolker-Nielsen, T., Newman, D. K., Tirrell, D. A. 2017; 8 (5) 
+
+<|ref|>text<|/ref|><|det|>[[57, 299, 909, 341]]<|/det|>
+• SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Babin, B. M., Bergkessel, M., Sweredoski, M. J., Moradian, A., Hess, S., Newman, D. K., Tirrell, D. A. 2016; 113 (5): E597-E605 
+
+<|ref|>text<|/ref|><|det|>[[57, 363, 869, 405]]<|/det|>
+• In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry ENVIRONMENTAL MICROBIOLOGY Hatzenpichler, R., Scheller, S., Tavormina, P. L., Babin, B. M., Tirrell, D. A., Orphan, V. J. 2014; 16 (8): 2568-2590 
+
+<|ref|>text<|/ref|><|det|>[[57, 428, 532, 471]]<|/det|>
+• State-selective Metabolic Labeling of Cellular Proteins ACS CHEMICAL BIOLOGY Ngo, J. T., Babin, B. M., Champion, J. A., Schuman, E. M., Tirrell, D. A. 2012; 7 (8): 1326-1330 
+
+<|ref|>text<|/ref|><|det|>[[57, 482, 771, 526]]<|/det|>
+• Noninvasive characterization of in situ forming implants using diagnostic ultrasound JOURNAL OF CONTROLLED RELEASE Solorio, L., Babin, B. M., Patel, R. B., Mach, J., Azar, N., Exner, A. A. 2010; 143 (2): 183-190 
+
+<|ref|>text<|/ref|><|det|>[[57, 535, 865, 579]]<|/det|>
+• A multipurpose microfluidic device designed to mimic microenvironment gradients and develop targeted cancer therapeutics LAB ON A CHIP Walsh, C. L., Babin, B. M., Kasinskas, R. W., Foster, J. A., McGarry, M. J., Forbes, N. S. 2009; 9 (4): 545-554

stage1/sample_00014/document.md

@@ -1,4 +1,4 @@
-4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4.  
+18  
 
 Software functionality: SepINRIA has different functionality which can be loaded from a single main window:  
 
@@ -16,10 +16,10 @@ This section describes concisely dependencies of the software and also its struc
 
 #### 4.2.1 Software dependencies  
 
-SepINRIA is based on several C++ libraries (C.f. Figure 4.2). ITK and MIPS contain both image processing tools. The first one can be downloaded on Internet and is especially used for image conversion. Whereas the second one is inner to the Asclepios team (algorithms presented in chapter 3 can be found in this library).  
+SepINRIA is based on several C++ libraries (C.f. Figure 4.2). ITK \(^2\) and MIPS \(^3\) contain both image processing tools. The first one can be downloaded on Internet and is especially used for image conversion. Whereas the second one is inner to the Asclepios team (algorithms presented in chapter 3 can be found in this library).  
 
 ![Figure sample_00014_fig01](figures/sample_00014_fig01.png)
 
 <center>FIGURE 4.1 - Used libraries and framework in SepINRIA </center>  
 
-The display is supported by the libraries VTK and vtkINRIA3D (C.f. Figure A.1) while the user graphical interface is based on wxWidgets. Finally, the general framework (structure
+The display is supported by the libraries VTK \(^4\) and vtkINRIA3D \(^5\) (C.f. Figure A.1) while the user graphical interface is based on wxWidgets \(^6\) . Finally, the general framework (structure

stage1/sample_00014/raw_response.md

@@ -1,35 +1,35 @@
-4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4.  
+18  
 
-<|ref|>text<|/ref|><|det|>[[106, 129, 866, 163]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[105, 130, 866, 163]]<|/det|>
 Software functionality: SepINRIA has different functionality which can be loaded from a single main window:  
 
-<|ref|>text<|/ref|><|det|>[[132, 177, 867, 219]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[132, 178, 867, 230]]<|/det|>
 - Lesion Segmentation Edition: Manual or semi-automatic segmentation of MS lesions (e.g. a segmentation realized by an expert). Segmentations can be saved and visualized in 2D or 3D. Lesion number and lesion volume can be computed and print.  
 
-<|ref|>text<|/ref|><|det|>[[134, 237, 866, 271]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[133, 240, 866, 273]]<|/det|>
 - Automatic Lesion Segmentation: Automatic segmentation of MS lesions from four MRI sequences (Dual Spin Echo T2-PD, T1, T2-FLAIR).  
 
-<|ref|>text<|/ref|><|det|>[[133, 282, 866, 366]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[133, 283, 867, 367]]<|/det|>
 - Images or Segmentation Comparison: Quantitative comparisons of two images registered to assess evolution and comparison between a segmentation (e.g. automatic segmentation) and a segmentation of reference (segmentation of an expert): by computation of the difference image or by visualizing them in the same window (side to side or image fusion).  
 
-<|ref|>text<|/ref|><|det|>[[133, 376, 867, 444]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[133, 375, 867, 442]]<|/det|>
 - Brain Atrophy Evaluation: Manual and automatic evaluation of the brain atrophy. Linear measurements computation of the brain, lateral ventricle and third ventricle width are available in the manual mode. And evolution of the BPF in function of the exam dates can be perform in the automatic mode.  
 
-<|ref|>sub_title<|/ref|><|det|>[[106, 467, 455, 487]]<|/det|>
+<|ref|>sub_title<|/ref|><|det|>[[105, 465, 456, 485]]<|/det|>
 ### 4.2 Structure based on C++  
 
-<|ref|>text<|/ref|><|det|>[[106, 499, 865, 533]]<|/det|>
+<|ref|>text<|/ref|><|det|>[[105, 498, 865, 532]]<|/det|>
 This section describes concisely dependencies of the software and also its structure by providing a simplify UML scheme of the code architecture.  
 
-<|ref|>title<|/ref|><|det|>[[106, 552, 400, 569]]<|/det|>
+<|ref|>title<|/ref|><|det|>[[106, 551, 399, 568]]<|/det|>
 #### 4.2.1 Software dependencies  
 
-<|ref|>text<|/ref|><|det|>[[106, 577, 866, 647]]<|/det|>
-SepINRIA is based on several C++ libraries (C.f. Figure 4.2). ITK and MIPS contain both image processing tools. The first one can be downloaded on Internet and is especially used for image conversion. Whereas the second one is inner to the Asclepios team (algorithms presented in chapter 3 can be found in this library).  
+<|ref|>text<|/ref|><|det|>[[105, 577, 866, 645]]<|/det|>
+SepINRIA is based on several C++ libraries (C.f. Figure 4.2). ITK \(^2\) and MIPS \(^3\) contain both image processing tools. The first one can be downloaded on Internet and is especially used for image conversion. Whereas the second one is inner to the Asclepios team (algorithms presented in chapter 3 can be found in this library).  
 
-<|ref|>image<|/ref|><|det|>[[193, 672, 783, 717]]<|/det|>
-<|ref|>image_caption<|/ref|><|det|>[[224, 733, 745, 750]]<|/det|>
+<|ref|>image<|/ref|><|det|>[[196, 671, 782, 719]]<|/det|>
+<|ref|>image_caption<|/ref|><|det|>[[225, 734, 746, 750]]<|/det|>
 <center>FIGURE 4.1 - Used libraries and framework in SepINRIA </center>  
 
-<|ref|>text<|/ref|><|det|>[[102, 766, 866, 802]]<|/det|>
-The display is supported by the libraries VTK and vtkINRIA3D (C.f. Figure A.1) while the user graphical interface is based on wxWidgets. Finally, the general framework (structure
+<|ref|>text<|/ref|><|det|>[[105, 766, 867, 801]]<|/det|>
+The display is supported by the libraries VTK \(^4\) and vtkINRIA3D \(^5\) (C.f. Figure A.1) while the user graphical interface is based on wxWidgets \(^6\) . Finally, the general framework (structure

stage1/sample_00015/document.md

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+5. 4 units Term Typically Offered: F,W,SP,SU Prerequisite: Sophomore standing and consent of instructor.  
+
+Full- time work experience in business, industry, government, and other areas of student career interest. Positions are paid and usually require relocation and registration in course for two consecutive quarters. A more fully developed formal report and evaluation by work supervisor required. Credit/No Credit grading only. No major credit allowed; total credit limited to 24 units.  
+
+## CPE 515. Computer Architecture. 4 units  
+
+Term Typically Offered: TBD Prerequisite: CPE 315 and graduate standing, or consent of instructor.  
+
+Comparative study and design of multiprocessor, dataflow, RISC, high level language and other new computer architectures. VLSI processor design techniques. 3 seminars, 1 laboratory. Crosslisted as CPE/CSC 515.  
+
+## CPE 521. Computer Systems. 4 units  
+
+Term Typically Offered: SP Prerequisite: CPE/EE 329 or CPE/EE 336, or equivalent, and graduate standing or consent of instructor.  
+
+Organization of modern general purpose, high speed digital computer systems. Design of arithmetic units, control units, memories and memory subsystems. Cost, power and speed trade- offs in the design of such systems. 3 seminars, 1 laboratory. Crosslisted as CPE/EE 521.  
+
+## CPE 522. Advanced Real-Time Operating Systems Design. 4 units  
+
+Term Typically Offered: W Prerequisite: CPE/EE 439.  
+
+Define and implement a microcontroller- based Real- Time Operating System (RTOS). Advanced real- time concepts, kernel structure, task and time management, various intertask communication constructs including semaphores, queues and mailboxes. Scheduler design, memory management and shared resource management in a resource- constrained microcontroller environment. 3 seminars, 1 laboratory. Crosslisted as CPE/EE 522.  
+
+## CPE 523. Digital Systems Design. 4 units  
+
+Term Typically Offered: F Prerequisite: CPE/EE 329 or CPE/EE 336, and graduate standing.  
+
+Full- custom design and analysis of digital circuits using full CMOS, pass- transistor and dynamic circuit topologies. Transistor sizing for minimizing power consumption, delay and other design criteria. 3 seminars, 1 laboratory. Crosslisted as CPE/EE 523.  
+
+## CPE 564. Computer Networks: Research Topics. 4 units  
+
+Term Typically Offered: TBD Prerequisite: CSC/CPE 464 and graduate standing, or consent of instructor.  
+
+Exploration of advanced topics in emerging computer networking technologies; focus on leading edge computer network research topics. 3 lectures, 1 laboratory. Crosslisted as CPE/CSC 564.  
+
+## CPE 569. Distributed Computing. 4 units  
+
+Term Typically Offered: TBD Prerequisite: CSC 141 or CSC 348; and CPE/CSC 357; or graduate standing and consent of instructor.  
+
+Principles and practices in distributed computing: interprocess communications, group communications, client- server model, distributed objects, message queue system, distributed services, mobile agents, object space, Internet protocols. Distributed algorithms: consensus protocols, global state protocols. Fault tolerance: classification of faults, replication. 3 lectures, 1 laboratory. Crosslisted as CPE/CSC 569.