[midterm]ECG poetry from a cancer research paper{Dual Color imaging}

I really wanted to play with the NLTK library and specifically with syllable counts.

Metric feet in poetry are very compelling as a structural approach to writing and generating shapes, but difficult to recreate programmatically.
Specific examples like “aged” show this clearly, since it would be a different syllabic count for man, rather than camembert.
So I wanted to see if there is a cyclical approach that can be taken by varying syllabic and letter count.
I’ve been reading alot of imaging research papers, doing research into cell cycle markers and pathways for my synthetic bio thesis at ITP, and this one while useless for thesis caught my eye for this project.
The final result of my manipulation resulted in a steady ECG pattern, extracted from the cancer research text.
The representation of text as a narrative in it’s structure creates a story about the mouse, which is not an experimental object any longer but a living creature. Rather than a statement this is an interesting aspect of treating text as self referential to the direct object of its content – mus musculus.
Here is the code:

what it is

text:

DOI:10.1158/0008-5472.CAN-05-2958
Dual-Color Imaging of Nuclear-Cytoplasmic Dynamics,
Viability, and Proliferation of Cancer Cells in the Portal Vein Area
Kazuhiko Tsuji, Kensuke Yamauchi, Meng Yang, et al.
Cancer Res 2006;66:303-306. Published online January 5, 2006.
Updated Version Access the most recent version of this article at: doi:10.1158/0008-5472.CAN-05-2958
Cited Articles This article cites 12 articles, 8 of which you can access for free at: http://cancerres.aacrjournals.org/content/66/1/303.full.html#ref-list-1
Citing Articles This article has been cited by 6 HighWire-hosted articles. Access the articles at: http://cancerres.aacrjournals.org/content/66/1/303.full.html#related-urls
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Downloaded from cancerres.aacrjournals.org on February 27, 2012 Copyright © 2006 American Association for Cancer Research
Abstract I
We used dual-color in vivo cellular imaging to visualize trafficking, nuclear-cytoplasmic dynamics, and the viability of cancer cells after their injection into the portal vein of mice. For these studies, we used dual-color fluorescent cancer cells that express green fluorescent protein (GFP) linked to histone H2B in the nucleus and retroviral red fluorescent protein (RFP) in the cytoplasm. Human HCT-116-GFP-RFP colon cancer and mouse mammary tumor (MMT) cells were HCT-116-GFP-RFP in the portal vein of nude mice. The cells were observed intravitally in the liver at the single-cell level using the Olympus OV100 whole-mouse imaging system. Most HCT-116-GFP-RFP cells remained in sinusoids near peripheral portal veins. Only a small fraction of the cancer cells invaded the lobular area. Extensive clasmocytosis (destruction of the cytoplasm) of the HCT-116-GFP-RFP I cells occurred within 6 hours. The number of apoptotic cells rapidly increased within the portal vein within 12 hours of injection. Apoptosis was readily visualized in the dual-color cells by their altered nuclear morphology. The data suggest rapid death of HCT-116-GFP-RFP cells in the portal vein. In contrast, dual-color MMT-GFP-RFP cells injected into the portal vein mostly survived in the liver of nude mice 24 hours after injection. Many surviving MMT-GFP- RFP cells showed invasive figures with cytoplasmic protrusions. The cells grew aggressively and formed colonies in the liver. However, when the host mice were pretreated with cyclophos- phamide, the HCT-116-GFP-RFP cells also survived and formed colonies in the liver after portal vein injection. These results suggest that a cyclophosphamide-sensitive host cellular system attacked the HCT-116-GFP-RFP cells but could not effectively kill the MMT-GFP-RFP cells. (Cancer Res 2006; 66(1): 303-6)
Introduction
The portal vein is a critical route for cancer cell metastasis to the liver. However, the early fate of cancer cells in the portal vein circulation is poorly understood because it has been difficult to visualize the behavior of single cancer cells and micrometastasis. Previously, cancer cells were transfected with the Escherichia coli h-galactosidase (lacZ) gene, which enables detection of micro- metastases in tissue sections. However, lacZ does not allow direct visualization of cancer cells in live animals (1–5). We developed an approach to visualizing cancer cells in vivo through the use of green fluorescent protein (GFP; refs. 1–4).
Requests for reprints: Robert M. Hoffman, AntiCancer, Inc., 7917 Ostrow Street, San Diego, CA 92111. Phone: 858-654-2555; Fax: 858-268-4175; E-mail: all@ anticancer.com.
Two processes have been proposed to explain the high incidence of colon cancer metastasis in liver. One explanation is based on the seed-and-soil theory of Paget, in which preferential growth of colon cancer cells to the liver forms the basis. Other studies have shown that cancer cells remain in the liver because they are arrested physically in the too-narrow sinusoids of the liver.
Mook et al. (6) used intravital videomicroscopy to visualize early events after injection of GFP-expressing colon cancer cells in the portal vein. Initial arrest of the colon cancer cells in sinusoids of the liver was due to size restriction. Adhesion of cancer cells to endothelial cells was never found. Instead, endothelial cells retracted rapidly and interactions were observed only between cancer cells and hepatocytes. Tumor cells divided exclusively intravascularly during the first 4 days.
Wang et al. (7) also visualized the trafficking of GFP-expressing metastatic cancer cells targeting the liver via the portal vein. Within 72 hours after transplantation of tumor cells on the ascending colon in nude mice, metastasis was visualized ex vivo on a single-cell basis around the portal vein by GFP imaging. At this early time point, a few cells were visualized trafficking to the liver via the portal vein. By post-implantation day 5, the caudate lobe of the liver was involved with trafficking metastatic cells, which subsequently formed colonies.
Real-time intravital videomicroscopy analysis of liver metastases after intraportal injection of GFP-expressing cells via a mesenteric vein revealed that both metastatic LM-EGFP and nonmetastatic E2-EGFP rat tongue tumor cells arrested similarly in sinusoidal vessels near terminal portal venules (8). The nonmetastatic E2- EGFP cells were completely eliminated from the liver sinusoids within 3 days, with no solitary dormant cells. However, a subs- tantial number of LM-EGFP cells remained in the liver, possibly due to stable attachment to the sinusoidal wall. The LM-EGFP cells began to grow 3 to 4 days after inoculation (8).
In the current study, we visualized the early trafficking of dual- colored cancer cells, labeled with GFP in the nucleus and red fluorescent protein (RFP) in the cytoplasm (9), injected into the portal vein of nude mice. We report here the fate of different cancer cell types in the portal circulation. We also report the effect of cyclophosphamide pretreatment of the host mouse on the fate of the cancer cells in the portal circulation.
Materials and Methods
Production of RFP retroviral vector. For RFP retrovirus production, the HindIII/NotI fragment from pDsRed2 (Clontech Laboratories, Inc., Palo Alto, CA), containing the full-length RFP cDNA, was inserted into the Hind III/Not I site of pLNCX2 (Clontech Laboratories) containing the neomycin resistance gene (4). PT67, an NIH3T3-derived packaging cell line (Clontech Laboratories) expressing the 10 Al viral envelope, was cultured in DMEM (Irvine Scientific, Santa Ana, CA) supplemented with 10%
DOI:10.1158/0008-5472.CAN-05-2958
Dual-Color Imaging of Nuclear-Cytoplasmic Dynamics, Viability, and Proliferation of Cancer Cells in the Portal Vein Area
Kazuhiko Tsuji,1,2,3 Kensuke Yamauchi,1 Meng Yang,1 Ping Jiang,1 Michael Bouvet,2 Hitoshi Endo,3 Yoshikatsu Kanai,3 Koji Yamashita,1 Abdool R. Moossa,2 and Robert M. Hoffman1,2
1AntiCancer, Inc.; 2Department of Surgery, University of California, San Diego, California; and 3Department of Pharmacology and Toxicology, Kyorin University, Tokyo, Japan
Research Article
I2006 American Association for Cancer Research.
doi:10.1158/0008-5472.CAN-05-2958 heat-inactivated fetal bovine serum (Gemini Bio-Products, Calabasas, CA).
www.aacrjournals.org 303 Cancer Res 2006; 66: (1). January 1, 2006
Downloaded from cancerres.aacrjournals.org on February 27, 2012 Copyright © 2006 American Association for Cancer Research
DOI:10.1158/0008-5472.CAN-05-2958
Cancer Research
Figure1. A-F,fateofHCT-116-GFP-RFPhumancoloncancercellsafterportal vein injection. A laparotomy was done on nude mice under ketamine anesthesia
Figure2. FateofMMTGFP-RFPmousemammarytumorcellsafterportalvein injection. A, MMT GFP-RFP mouse mammary tumor cells (0.25