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Mark Anderson, Emily Venanzi, L. Klein, Zhibin Chen, S. Berzins, S. Turley, H. Boehmer, R. Bronson, A. Dierich, C. Benoist, D. Mathis (2002)
Projection of an Immunological Self Shadow Within the Thymus by the Aire ProteinScience, 298
F. Boogerd, F. Bruggeman, J. Hofmeyr, H. Westerhoff (2007)
Systems Biology: Philosophical Foundations
M. Tedre (2014)
Science of the Artificial
J. Bach, L. Chatenoud (2012)
The hygiene hypothesis: an explanation for the increased frequency of insulin-dependent diabetes.Cold Spring Harbor perspectives in medicine, 2 2
J. Ziman (1973)
Bridging the Culture GapNature, 242
E. Fuchs, P. Matzinger (1996)
Is cancer dangerous to the immune system?Seminars in immunology, 8 5
Bart Tambuyzer, P. Ponsaerts, E. Nouwen (2009)
Microglia: gatekeepers of central nervous system immunologyJournal of Leukocyte Biology, 85
J. Salk (2010)
Clonal evolution in cancer
P. Matzinger (2002)
The Danger Model: A Renewed Sense of SelfScience, 296
B. Hrz, Mengchu Zhou (2007)
Modeling and Control of Discrete-event Dynamic Systems: With Petri Nets and Other Tools
P. Yu, Youjin Lee, Wenhua Liu, T. Krausz, A. Chong, H. Schreiber, yang-xin fu (2005)
Intratumor depletion of CD4+ cells unmasks tumor immunogenicity leading to the rejection of late-stage tumorsThe Journal of Experimental Medicine, 201
Jim Williams (1991)
Analog Circuit Design: Art, Science and Personalities
A. Mailloux, M. Young (2010)
Regulatory T-cell trafficking: from thymic development to tumor-induced immune suppression.Critical reviews in immunology, 30 5
S. Juvet, Li Zhang (2012)
Double negative regulatory T cells in transplantation and autoimmunity: recent progress and future directions.Journal of molecular cell biology, 4 1
Paul Thagard (1998)
Explaining Disease: Correlations, Causes, and MechanismsMinds and Machines, 8
A. Soto, C. Sonnenschein (2011)
The tissue organization field theory of cancer: A testable replacement for the somatic mutation theoryBioEssays, 33
A Clark (2008)
Supersizing the mind: embodiment, action, and cognitive extension
K. Wood, A. Bushell, J. Hester (2012)
Regulatory immune cells in transplantationNature Reviews Immunology, 12
J. Uhr, K. Pantel (2011)
Controversies in clinical cancer dormancyProceedings of the National Academy of Sciences, 108
M. Mapara, M. Sykes (2004)
Tolerance and cancer: mechanisms of tumor evasion and strategies for breaking tolerance.Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 22 6
W. Byrne, K. Mills, J. Lederer, G. O'sullivan (2011)
Targeting regulatory T cells in cancer.Cancer research, 71 22
J Gall (1986)
Systemantics: the underground text of systems lore, 2nd edn
J. Folkman, R. Kalluri (2004)
Cancer without diseaseNature, 427
A. Fasano, T. Shea-Donohue (2005)
Mechanisms of Disease: the role of intestinal barrier function in the pathogenesis of gastrointestinal autoimmune diseasesNature Clinical Practice Gastroenterology &Hepatology, 2
A. Dalgleish, B. Haefner (2006)
The link between inflammation and cancer : wounds that do not heal
G. Baronzio, I. Freitas (2008)
Tumor microenvironment genesis and implications on cancer immune response
B. Bredeweg, P. Struss (2004)
Current Topics in Qualitative ReasoningAI Mag., 24
Afonso Almeida, Inês Amado, Joseph Reynolds, Julien Berges, G. Lythe, C. Molina‐París, A. Freitas (2012)
Quorum-Sensing in CD4+ T Cell Homeostasis: A Hypothesis and a ModelFrontiers in Immunology, 3
L. Darden, D. Hull, M. Ruse (2007)
Mechanisms and Models
(1995)
Tumor angiogenesis - basic mechanisms and cancer therapy
P. Matzinger, T. Kamala (2011)
Tissue-based class control: the other side of toleranceNature Reviews Immunology, 11
HA Simon (1996)
The science of the artificial, 3rd edn
Samantha Bailey-bucktrout, J. Bluestone (2011)
Regulatory T cells: stability revisited.Trends in immunology, 32 7
A. Bayonas (2011)
An Evolutionary Explanation for the Perturbation of the Dynamics of Metastatic Tumors Induced by Surgery and Acute InflammationCancers, 3
W. Terry (1975)
BCG in the treatment of human cancerCA: A Cancer Journal for Clinicians, 25
Sharon Ahluwalia (2012)
Peripheral Education of the Immune System by Colonic Commensal Microbiota
G Baronzio, I Freitas (2008)
Atlas effectors of anti-tumor immunity, chap 2
M. French (1994)
Invention and evolution : design in nature and engineering, 2nd ed.
(1969)
What you should know about trailer brakes
O. Rajka (1963)
[TUMOR IMMUNOLOGY].Orvosi hetilap, 104
A Foote, W. Blakemore (2005)
Inflammation stimulates remyelination in areas of chronic demyelination.Brain : a journal of neurology, 128 Pt 3
E. Gilboa (2004)
The promise of cancer vaccinesNature Reviews Cancer, 4
P. Sorger (2005)
A reductionist’s systems biology
CF McKhann, MA Yarlott (1975)
Tumor immunologyCA Cancer J Clin, 25
B. Rouse, S. Suvas (2004)
Regulatory Cells and Infectious Agents: Détentes Cordiale and ContraireThe Journal of Immunology, 173
R. Medzhitov, C. Janeway (2002)
Decoding the Patterns of Self and Nonself by the Innate Immune SystemScience, 296
J. Couper (2001)
Environmental triggers of type 1 diabetesJournal of Paediatrics and Child Health, 37
Gang Zhou, Zhi-Chun Ding, Jie Fu, H. Levitsky (2011)
Presentation of Acquired Peptide-MHC Class II Ligands by CD4+ Regulatory T Cells or Helper Cells Differentially Regulates Antigen-Specific CD4+ T Cell ResponseThe Journal of Immunology, 186
Y. Belkaid (2007)
Regulatory T cells and infection: a dangerous necessityNature Reviews Immunology, 7
M. Retsky, R. Demicheli, W. Hrushesky, M. Baum, I. Gukas (2008)
Dormancy and surgery‐driven escape from dormancy help explain some clinical features of breast cancerAPMIS, 116
C. Kurts, B. Robinson, P. Knolle (2010)
Cross-priming in health and diseaseNature Reviews Immunology, 10
D. Smithers (1962)
CANCER AN ATTACK ON CYTOLOGISMThe Lancet, 279
W. Mcd
An AutobiographyNature, 70
M. French (1988)
Invention and Evolution:Design in Nature and Engineering
Suzy Eldershaw, David Sansom, Partheepan Narendran (2011)
Expression and function of the autoimmune regulator (Aire) gene in non‐thymic tissueClinical & Experimental Immunology, 163
U. Christen, M. Herrath (2005)
Infections and Autoimmunity—Good or Bad?1The Journal of Immunology, 174
(2012)
Cellular and molecular immunology, 7th edn
W. Gibbs (2001)
Cybernetic cells.Scientific American, 285 2
R. Schreiber, L. Old, M. Smyth (2011)
Cancer Immunoediting: Integrating Immunity’s Roles in Cancer Suppression and PromotionScience, 331
S. Sakaguchi, Tomoyuki Yamaguchi, T. Nomura, M. Ono (2008)
Regulatory T Cells and Immune ToleranceCell, 133
M. Schäfer, S. Werner (2008)
Cancer as an overhealing wound: an old hypothesis revisitedNature Reviews Molecular Cell Biology, 9
Raffaele Simone (1987)
Languages as Méthodes Analytiques in Condillac
Bikul Das, S. Kashino, Ista Pulu, D. Kalita, V. Swami, H. Yeger, D. Felsher, A. Campos-Neto (2013)
CD271+ Bone Marrow Mesenchymal Stem Cells May Provide a Niche for Dormant Mycobacterium tuberculosisScience Translational Medicine, 5
Andrew Moore (2012)
Have we produced enough results yet, sir?BioEssays, 34
S. Sozzani, M. Rusnati, E. Riboldi, S. Mitola, M. Presta (2007)
Dendritic cell-endothelial cell cross-talk in angiogenesis.Trends in immunology, 28 9
Lenny Moss, D. Nicholson (2012)
On nature and normativity: Normativity, teleology, and mechanism in biological explanation.Studies in history and philosophy of biological and biomedical sciences, 43 1
Ridgway Pf (2002)
Tumours : wounds that do not heal.
F. Gzil (2008)
Introduction à l'étude de la médecine expérimentale
P. Bousso (2008)
T-cell activation by dendritic cells in the lymph node: lessons from the moviesNature Reviews Immunology, 8
A. Aranda-Anzaldo (2001)
Cancer Development and Progression: A Non-Adaptive Process Driven by Genetic DriftActa Biotheoretica, 49
P. Kitcher (2007)
Philosophy of Biology
P Thagard (2000)
Explanation and cognition, chap 10.
D. Davis (2007)
Intercellular transfer of cell-surface proteins is common and can affect many stages of an immune responseNature Reviews Immunology, 7
PK Coyle (2011)
Clinical neuroimmunology: multiple sclerosis and related disorders, chap 3
B Gilbert (1991)
Analog circuit design: art, science, and personalities, chap 19.
Wenhao Chen, M. Ford, K. Young, Li Zhang (2004)
The role and mechanisms of double negative regulatory T cells in the suppression of immune responses.Cellular & molecular immunology, 1 5
RW Hamming (1962)
Numerical methods for scientists and engineers
R Simone (1987)
Speculative grammar, universal grammar, and philosophical analysis of language, vol 42
(2004)
metastatic tumors induced by surgery and acute inflammation. Cancers
RG Collingwood (2002)
An essay on metaphysics, 3rd edn
S. Sakaguchi (2005)
Naturally arising Foxp3-expressing CD25+CD4+ regulatory T cells in immunological tolerance to self and non-selfNature Immunology, 6
C. Nathan (2002)
Points of control in inflammationNature, 420
N. Nersessian (2008)
Creating Scientific Concepts
S Sakaguchi (2011)
Regulatory T cells: methods and protocols, vol 707, chap 1
Y. Lazebnik (2004)
Can a biologist fix a radio? — or, what I learned while studying apoptosisBiochemistry (Moscow), 69
L. Russo (2004)
The forgotten revolution
J. Diez, Yongsoo Park, M. Zeller, Douglas Brown, D. Garza, C. Ricordi, J. Hutton, G. Eisenbarth, A. Pugliese (2001)
Differential splicing of the IA-2 mRNA in pancreas and lymphoid organs as a permissive genetic mechanism for autoimmunity against the IA-2 type 1 diabetes autoantigen.Diabetes, 50 4
C. Starnes (1992)
Coley's toxins in perspectiveNature, 357
Shalom Madar, I. Goldstein, V. Rotter (2009)
Did experimental biology die? Lessons from 30 years of p53 research.Cancer research, 69 16
L. Zhang, F. Gu, J. Chan, Andrew Wang, R. Langer, O. Farokhzad (2008)
Nanoparticles in Medicine: Therapeutic Applications and DevelopmentsClinical Pharmacology & Therapeutics, 83
J. Knight (2002)
Physics meets biology: Bridging the culture gapNature, 419
S. Gallucci, P. Matzinger (2001)
Danger signals: SOS to the immune system.Current opinion in immunology, 13 1
Lauren Merlo, J. Pepper, B. Reid, C. Maley (2006)
Cancer as an evolutionary and ecological processNature Reviews Cancer, 6
G. Coukos, F. Benencia (2009)
Dendritic Cells: From Inducers of Specific T-Cell Responses to Promoters of Angiogenesis
Scott Valastyan, R. Weinberg (2011)
Tumor Metastasis: Molecular Insights and Evolving ParadigmsCell, 147
F. Dyson (2004)
A meeting with Enrico FermiNature, 427
P. Coyle (2011)
MS: Pathology and Immunology
(1986)
2 type 1 diabetes autoantigen. Diabetes
Ende Zhao, Huanbin Xu, Lin Wang, Ilona Kryczek, Ke Wu, Yu Hu, Guobin Wang, W. Zou (2011)
Bone marrow and the control of immunityCellular and Molecular Immunology, 9
A. Embry (2004)
The Multiple Factors of Multiple Sclerosis: A Darwinian PerspectiveJournal of Nutritional & Environmental Medicine, 14
G Coukos, F Benencia (2009)
Dendritic cells in cancer chap 16.
J. Goverman (2009)
Autoimmune T cell responses in the central nervous systemNature Reviews Immunology, 9
Anthony Kulis (2009)
Bio-Inspired Artificial Intelligence: Theories, Methods, and TechnologiesScalable Comput. Pract. Exp., 10
U. Krohs, W. Callebaut (2007)
Data without models merging with models without data
W. Wimsatt (2007)
5 On building reliable pictures with unreliable data: 1 An evolutionary and developmental coda for the new systems biology
J. Platt (2007)
Strong Inference
J. Kleer (1984)
How Circuits WorkArtif. Intell., 24
M. Colombo, S. Piconese (2007)
Regulatory T-cell inhibition versus depletion: the right choice in cancer immunotherapyNature Reviews Cancer, 7
S. Sakaguchi (2011)
Regulatory T cells: history and perspective.Methods in molecular biology, 707
D. Hull, M. Ruse (2007)
The Cambridge Companion to the Philosophy of Biology
T. Curiel, G. Coukos, L. Zou, Xavier Alvarez, P. Cheng, P. Mottram, Melina Evdemon-Hogan, J. Conejo-Garcia, Lin Zhang, M. Burow, Yun Zhu, Shuang Wei, Ilona Kryczek, B. Daniel, Alan Gordon, L. Myers, A. Lackner, M. Disis, K. Knutson, Lieping Chen, W. Zou (2004)
Specific recruitment of regulatory T cells in ovarian carcinoma fosters immune privilege and predicts reduced survivalNature Medicine, 10
S. Cann, J. Netten, C. Netten, D. Glover (2002)
Spontaneous regression: a hidden treasure buried in time.Medical hypotheses, 58 2
Si.M Pham, Abdul Rao, Adriana Zeevi, K. McCurry, R. Keenan, J.David Vega, R. Kormos, B. Hattler, J. Fung, T. Starzl, Bartley Griffith (2000)
Effects of donor bone marrow infusion in clinical lung transplantation.The Annals of thoracic surgery, 69 2
C. Klein (2009)
Parallel progression of primary tumours and metastasesNature Reviews Cancer, 9
W. Fridman, F. Pagès, C. Sautès-Fridman, J. Galon (2012)
The immune contexture in human tumours: impact on clinical outcomeNature Reviews Cancer, 12
C. Craver (2007)
Explaining the Brain: Mechanisms and the Mosaic Unity of Neuroscience
DA Norman (1991)
Designing interaction.
P. Tacken, I. Vries, R. Torensma, C. Figdor (2007)
Dendritic-cell immunotherapy: from ex vivo loading to in vivo targetingNature Reviews Immunology, 7
J. Gall, D. Gall, Mark Howell, David Martinez (1986)
Systemantics : the underground text of systems lore : how systems really work and especially how they fail
Y. Yong-ming (2007)
T cells in the suppression of immune responsesInternational Journal of Pathology and Clinical Medicine
C. Mattiussi, D. Marbach, Peter Dürr, D. Floreano (2008)
The Age of Analog NetworksAI Mag., 29
S. Gallucci, M. Lolkema, P. Matzinger (1999)
Natural adjuvants: Endogenous activators of dendritic cellsNature Medicine, 5
A. Wicki, G. Christofori (2008)
The Angiogenic Switch in Tumorigenesis
(1995)
The importance of fixing. In: Williams J (ed) The art and science of analog circuit design
In an instant classic paper (Lazebnik, in Cancer Cell 2(3); 2002: 179–182) biologist Yuri Lazebnik deplores the poor effectiveness of the approach adopted by biologists to understand and “fix” biological systems. Lazebnik suggests that to remedy this state of things biologist should take inspiration from the approach used by engineers to design, understand, and troubleshoot technological systems. In the present paper I substantiate Lazebnik’s analysis by concretely showing how to apply the engineering approach to biological problems. I use an actual example of electronic circuit troubleshooting to ground the thesis that, in engineering, the crucial phases of any non-trivial troubleshooting process are aimed at generating a mechanistic explanation of the functioning of the system, which makes extensive recourse to problem-driven qualitative reasoning possibly based on cognitive artifacts applied to systems that are known to have been designed for function. To show how to translate these findings into biological practice I consider a concrete example of biological model building and “troubleshooting”, aimed at the identification of a “fix” for the human immune system in presence of progressing cancer, autoimmune disease, and transplant rejection. The result is a novel immune system model—the danger model with regulatory cells— and new, original hypotheses concerning the development, prophylaxis, and therapy of these unwanted biological processes. Based on the manifest efficacy of the proposed approach, I suggest a refocusing of the activity of theoretical biologists along the engineering-inspired lines illustrated in the paper.
Acta Biotheoretica – Springer Journals
Published: Mar 3, 2013
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