HIV-1 Informatics

  • Yong Shi
  • Yingjie Tian
  • Gang Kou
  • Yi Peng
  • Jianping Li
Part of the Advanced Information and Knowledge Processing book series (AI&KP)


The ability to identify neuronal damage in the dendritic arbor during HIV-1-associated dementia (HAD) is crucial for designing specific therapies for the treatment of HAD. In this chapter, we utilized a computer based image analysis method to quantitatively assess HIV-1 viral protein gp120 and glutamate mediated individual neuronal damage in cultured cortical neurons. Changes in the number of neurites, arbors, branch nodes, cell body area, and average arbor lengths were determined and a database was formed. We further proposed a two class model of MCLP to classify such HIV-1mediated neuronal dendritic and synaptic damages. Given certain classes, including treatments with brain-derived neurotrophic factor (BDNF), glutamate, gp120 or non-treatment controls from our in vitro experimental systems, we used the two-class MCLP model to determine the data patterns between classes in order to gain insight about neuronal dendritic damages. This knowledge can be applied in principle to the design and study of specific therapies for the prevention or reversal of neuronal damage associated with HAD. Finally, the MCLP method was compared with a well-known artificial neural network algorithm to test for the relative potential of different data mining applications in HAD research.


Brain Derive Neurotrophic Factor Neuronal Damage Mononuclear Phagocyte Dendritic Arbor Branch Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 11.
    Ascoli, G.A., Krichmar, J.L., Nasuto, S.J., Senft, S.L.: Generation, description and storage of dendritic morphology data. Philos. Trans. R. Soc. Lond. B, Biol. Sci. 356, 1131–1145 (2001) CrossRefGoogle Scholar
  2. 27.
    Brenneman, D.E., Westbrook, G.L., Fitzgerald, S.P., et al.: Neuronal cell killing by the envelope protein of HIV and its prevention by vasoactive intestinal peptide. Nature 335, 639–642 (1988) CrossRefGoogle Scholar
  3. 32.
    Cesar, R.M., Costa, L.F.: Neural cell classification by wavelets and multiscale curvature. Biol. Cybern. 79, 347–360 (1998) zbMATHCrossRefGoogle Scholar
  4. 43.
    Coelho, R.C., Costa, L.F.: Realistic neuromorphic models and their application to neural reorganization simulations. Neurocomputing 48, 555–571 (2002) zbMATHCrossRefGoogle Scholar
  5. 47.
    Costa Lda, F., Manoel, E.T.M., Faucereau, F., Chelly, J., van Pelt, J., Ramakers, G.: A shape analysis framework for neuromorphometry. Netw. Comput. Neural Syst. 13, 283–310 (2002) CrossRefGoogle Scholar
  6. 48.
    Costa Lda, F., Velte, T.J.: Automatic characterization and classification of ganglion cells from the salamander retina. J. Comp. Neurol. 404, 33–51 (1999) CrossRefGoogle Scholar
  7. 67.
    Elkabes, S., DiCicco-Bloom, E.M., Black, I.B.: Brain microglia/macrophages express neurotrophins that selectively regulate microglial proliferation and function. J. Neurosci. 16, 2508–2521 (1996) Google Scholar
  8. 68.
    Epstein, L.G., Gelbard, H.A.: HIV-1-induced neuronal injury in the developing brain. J. Leukoc. Biol. 65, 453–457 (1999) Google Scholar
  9. 82.
    Gabuzda, D., Wang, J., Gorry, P.: HIV-1-associated dementia. In: Ransohoff, R.M., Suzuki, K., Proudfoot, A.E.I., Hickey, W.F., Harrison, J.K. (eds.) Chemokines and the Nervous System, pp. 345–360. Elsevier Science, Amsterdam (2002) Google Scholar
  10. 83.
    Garden, G.A., Budd, S.L., Tsai, E., et al.: Caspase cascades in human immunodeficiency virus-associated neurodegeneration. J. Neurosci. 22, 4015–4024 (2002) Google Scholar
  11. 84.
    Gelbard, H.A., Epstein, L.G.: HIV-1 encephalopathy in children. Curr. Opin. Pediatr. 7, 655–662 (1995) Google Scholar
  12. 85.
    Gelbard, H., Nottet, H., Dzenko, K., et al.: Platelet-activating factor: a candidate human immunodeficiency virus type-1 infection neurotoxin. J. Virol. 68, 4628–4635 (1994) Google Scholar
  13. 86.
    Gendelman, H.E.: The neuropathogenesis of HIV-1-dementia. In: Gendelman, H.E., Lipton, S.A., Epstein, L.G., Swindells, S. (eds.) The Neurology of AIDS, pp. 1–10. Chapman and Hall, New York (1997) Google Scholar
  14. 87.
    Glass, J.D., Wesselingh, S.L., Selnes, O.A., McArthur, J.C.: Clinical neuropathologic correlation in HIV-associated dementia. Neurology 43, 2230–2237 (1993) Google Scholar
  15. 88.
    Glass, J.D., Fedor, H., Wesselingh, S.L., McArthur, J.C.: Immunocytochemical quantitation of human immunodeficiency virus in the brain: correlations with dementia. Ann. Neurol. 38, 755–762 (1995) CrossRefGoogle Scholar
  16. 96.
    Granato, A., Van Pelt, J.: Effects of early ethanol exposure on dendrite growth of cortical pyramidal neurons: inferences from a computational model. Dev. Brain Res. 142, 223–227 (2003) CrossRefGoogle Scholar
  17. 108.
    Heese, K., Hock, C., Otten, U.: Inflammatory signals induce neurotrophin expression in human microglial cells. J. Neurochem. 70, 699–707 (1998) CrossRefGoogle Scholar
  18. 111.
    Hesselgesser, J., Taub, D., Baskar, P., Greenberg, M., Hoxie, J., Kolson, D.L., Horuk, R.: Neuronal apoptosis induced by HIV-1 gp120 and the chemokine SDF-1alpha mediated by the chemokine receptor CXCR4. Curr. Biol. 8, 595–598 (1998) CrossRefGoogle Scholar
  19. 116.
    Jiang, Z., Piggee, C., Heyes, M.P., et al.: Glutamate is a mediator of neurotoxicity in secretions of activated HIV-1-infected macrophages. J. Neuroimmunol. 117, 97–107 (2001) CrossRefGoogle Scholar
  20. 123.
    Kaul, M., Garden, G.A., Lipton, S.A.: Pathways to neuronal injury and apoptosis in HIV-associated dementia. Nature 410, 988–994 (2001) CrossRefGoogle Scholar
  21. 131.
    Krichmar, J.L., Nasuto, S.J., Scorcioni, R., Washington, S.D., Ascoli, G.A.: Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: a simulation study. Brain Res. 941, 11–28 (2002) CrossRefGoogle Scholar
  22. 135.
    Lazarov-Spiegler, O., Solomon, A.S., Schwartz, M.: Peripheral nerve-stimulated macrophages simulate a peripheral nerve-like regenerative response in rat transected optic nerve. GLIA 24, 329–337 (1998) CrossRefGoogle Scholar
  23. 138.
    Lipton, S.A., Gendelman, H.E.: Dementia associated with the acquired immunodeficiency syndrome. N. Engl. J. Med. 16, 934–940 (1995) Google Scholar
  24. 143.
    Masliah, E., DeTeresa, R.M., Mallory, M.E., Hansen, L.A.: Changes in pathological findings at autopsy in AIDS cases for the last 15 years. AIDS 14, 69–74 (2000) CrossRefGoogle Scholar
  25. 144.
    Masliah, E., Heaton, R.K., Marcotte, T.D.: Dendritic injury is a pathological substrate for human immunodeficiency virus-related cognitive disorders. Ann. Neurol. 42, 963–972 (1997) CrossRefGoogle Scholar
  26. 145.
    McArthur, J.C., Sacktor, N., Selnes, O.: Human immunodeficiency virus-associated dementia. Semin. Neurol. 19, 129–150 (1999) CrossRefGoogle Scholar
  27. 151.
    Moses, A.V., Bloom, F.E., Pauza, C.D., Nelson, J.A.: HIV infection of human brain capillary endothelial cells occurs via a CD4 galactosylceramide-independent mechanism. Proc. Natl. Acad. Sci. USA 90, 10474–10478 (1993) CrossRefGoogle Scholar
  28. 153.
    Nath, A., Hartloper, V., Furer, M., Fowke, K.R.: Infection of human fetal astrocytes with HIV-1: viral tropism and the role of cell to cell contact in viral transmission. J. Neuropathol. Exp. Neurol. 54, 320–330 (1995) CrossRefGoogle Scholar
  29. 154.
    Navia, B.A.: Clinical and biologic features of the AIDS dementia complex. Neuroimaging Clin. N. Am. 7, 581–592 (1997) Google Scholar
  30. 155.
    Navia, B.A., Jordan, B.D., Price, R.W.: The AIDS dementia complex: I. Clinical features. Ann. Neurol. 19, 517–524 (1986) CrossRefGoogle Scholar
  31. 167.
    Pyle, D.: Normalizing and Redistributing of Variables in Data Preparation for Data Mining. Morgan Kaufmann, San Francisco (1999) Google Scholar
  32. 171.
    Rapalino, O., Lazarov-Spiegler, O., Agranov, E., et al.: Implantation of stimulated homologous macrophages results in partial recovery of paraplegic rats. Nat. Med. 4, 814–821 (1998) CrossRefGoogle Scholar
  33. 173.
    Ryan, L.A., Peng, H., Erichsen, D.A., et al.: TNF-related apoptosis-inducing ligand mediates human neuronal apoptosis: links to HIV-1 associated dementia. J. Neuroimmunol. 148, 127–139 (2004) CrossRefGoogle Scholar
  34. 176.
    Scorcioni, R., Ascoli, G.: Algorithmic extraction of morphological statistics from electronic archives of neuroanatomy. In: Lecture Notes Comp. Sci., vol. 2084, pp. 30–37 (2001) Google Scholar
  35. 182.
    Shi, Y., Peng, Y., Xu, W., Tang, X.: Data mining via multiple criteria linear programming: applications in credit card portfolio management. Int. J. Inf. Technol. Decis. Mak. 1, 131–151 (2002) CrossRefGoogle Scholar
  36. 183.
    Shi, Y., Wise, M., Luo, M., Lin, Y.: Data mining in credit card portfolio management: a multiple criteria decision making approach. In: Koksalan, M., Zionts, S. (eds.) Multiple Criteria Decision Making in the New Millennium, pp. 427–436. Springer, Berlin (2001) Google Scholar
  37. 185.
    Shibata, A., Zelivyanskaya, M., Limoges, J., et al.: Peripheral nerve induces macrophage neurotrophic activities: regulation of neuronal process outgrowth, intracellular signaling and synaptic function. J. Neuroimmunol. 142, 112–129 (2003) CrossRefGoogle Scholar
  38. 190.
    Sterratt, D.C., van Ooyen, A.: Does morphology influence temporal plasticity. In: Dorronsoro, J.R. (ed.) Artificial Neural Networks—ICANN 2002, International Conference, Madrid, Spain. Lecture Notes in Computer Science, vol. 2415, pp. 186–191. Springer, Berlin (2002) Google Scholar
  39. 205.
    van Ooyen, A., Willshaw, D., Ramakers, G.: Influence of dendritic morphology on axonal competition. Neurocomputing 32, 255–260 (2000) CrossRefGoogle Scholar
  40. 233.
    Zeev-Brann, A.B., Lazarov-Spiegler, O., Brenner, T., Schwartz, M.: Differential effects of central and peripheral nerves on macrophages and microglia. GLIA 23, 181–190 (1998) CrossRefGoogle Scholar
  41. 242.
    Zhao, J., Lopez, A.L., Erichsen, D., Herek, S., Cotter, R.L., Curthoys, N.P., Zheng, J.: Mitochondrial glutaminase enhances extracellular glutamate production in HIV-1-infected macrophages: linkage to HIV-1 associated dementia. J. Neurochem. 88, 169–180 (2004) CrossRefGoogle Scholar
  42. 246.
    Zheng, J., Thylin, M., Ghorpade, A., et al.: Intracellular CXCR4 signaling, neuronal apoptosis and neuropathogenic mechanisms of HIV-1-associated dementia. J. Neuroimmunol. 98, 185–200 (1999) CrossRefGoogle Scholar
  43. 247.
    Zheng, J., Thylin, M.R., Cotter, R.L., et al.: HIV-1 infected and immune competent mononuclear phagocytes induce quantitative alterations in neuronal dendritic arbor: relevance for HIV-1-associated dementia. Neurotox. Res. 3, 443–459 (2001) CrossRefGoogle Scholar
  44. 248.
    Zheng, J., Thylin, M.R., Persidsky, Y., et al.: HIV-1 infected immune competent mononuclear phagocytes influence the pathways to neuronal demise. Neurotox. Res. 3, 461–484 (2001) CrossRefGoogle Scholar

Copyright information

© Springer-Verlag London Limited 2011

Authors and Affiliations

  • Yong Shi
    • 1
    • 2
  • Yingjie Tian
    • 1
  • Gang Kou
    • 3
  • Yi Peng
    • 3
  • Jianping Li
    • 4
  1. 1.Research Center on Fictitious Economy and Data ScienceChinese Academy of SciencesBeijingChina
  2. 2.College of Information Science & TechnologyUniversity of Nebraska at OmahaOmahaUSA
  3. 3.School of Management and EconomicsUniversity of Electronic Science and Technology of ChinaChengduChina
  4. 4.Institute of Policy and ManagementChinese Academy of SciencesBeijingChina

Personalised recommendations