Cogprints: No conditions. Results ordered -Date, Title. 2018-01-17T14:26:06ZEPrintshttp://cogprints.org/images/sitelogo.gifhttp://cogprints.org/2011-12-16T00:58:48Z2011-12-16T00:58:48Zhttp://cogprints.org/id/eprint/7739This item is in the repository with the URL: http://cogprints.org/id/eprint/77392011-12-16T00:58:48ZNonlinear Models of Neural and Genetic Network Dynamics:
Natural Transformations of Łukasiewicz Logic LM-Algebras in a Łukasiewicz-Topos as Representations of Neural Network Development and Neoplastic Transformations
A categorical and Łukasiewicz-Topos framework for Algebraic Logic models of nonlinear dynamics in complex functional systems such as Neural Networks, Cell Genome and Interactome Networks is introduced. Łukasiewicz Algebraic Logic models of both neural and genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable next-state/transfer functions is extended to a Łukasiewicz Topos with an N-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.
Professor I.C. Baianuibaianu@illinois.edu2011-12-16T00:04:40Z2011-12-16T00:04:40Zhttp://cogprints.org/id/eprint/7754This item is in the repository with the URL: http://cogprints.org/id/eprint/77542011-12-16T00:04:40ZCategorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.
KEYWORDS: Emergence of Life and Human Consciousness;
Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments.
Prof. Dr. I.C. Baianuibaianu@illinois.eduProf. Dr. James F. Glazebrookjfglazebrook@eiu.edu2011-12-16T00:58:12Z2011-12-16T00:58:12Zhttp://cogprints.org/id/eprint/7751This item is in the repository with the URL: http://cogprints.org/id/eprint/77512011-12-16T00:58:12ZŁukasiewicz-Moisil Many-Valued Logic Algebra of Highly-Complex SystemsA novel approach to self-organizing, highly-complex systems (HCS), such as living organisms and artificial intelligent systems (AIs), is presented which is relevant to Cognition, Medical Bioinformatics and Computational Neuroscience. Quantum Automata (QAs) were defined in our previous work as generalized, probabilistic automata with quantum state spaces (Baianu, 1971). Their next-state functions operate through transitions between quantum states defined by the quantum equations of motion in the Schroedinger representation, with both initial and boundary conditions in space-time. Such quantum automata operate with a quantum logic, or Q-logic, significantly different from either Boolean or Łukasiewicz many-valued logic. A new theorem is proposed which states that the category of quantum automata and automata--homomorphisms has both limits and colimits. Therefore, both categories of quantum automata and classical automata (sequential machines) are bicomplete. A second new theorem establishes that the standard automata category is a subcategory of the quantum automata category. The quantum automata category has a faithful representation in the category of Generalized (M,R)--Systems which are open, dynamic biosystem networks with defined biological relations that represent physiological functions of primordial organisms, single cells and higher organisms.Professor I.C. Baianuibaianu@illinois.eduProfessor George Georgescugeorgescu@funinf.cs.unibuc.roProfessor James F. Glazebrookjfglazebrook@eiu.edu2011-12-16T00:59:06Z2011-12-16T00:59:06Zhttp://cogprints.org/id/eprint/7756This item is in the repository with the URL: http://cogprints.org/id/eprint/77562011-12-16T00:59:06ZOncogenomics and Cancer InteractomicsAn overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general, ‘personalized medicine’. Several cancer detection techniques are currently under development both in the direction of improved detection sensitivity and increased time resolution of cellular events, with the limits of single molecule detection and picosecond time resolution already reached. The urgency for the complete mapping of a human cancer interactome with the help of such novel, high-efficiency / low-cost and ultra-sensitive techniques is also pointed out.Prof. Dr I.C. Baianuibaianu@illinois.edu2010-10-18T11:00:45Z2011-03-11T08:57:45Zhttp://cogprints.org/id/eprint/7048This item is in the repository with the URL: http://cogprints.org/id/eprint/70482010-10-18T11:00:45ZOctologyThe manuscript describes a new sciencific discipline called Octology, which should unify morphogenetic linguistics and neurobiology to investigate the development of the words, cognition and behavior.Dr. Andrej Poleevandrejpoleev@yahoo.com2010-09-13T03:59:01Z2011-03-11T08:57:40Zhttp://cogprints.org/id/eprint/6939This item is in the repository with the URL: http://cogprints.org/id/eprint/69392010-09-13T03:59:01ZUner Tan Syndrome: History, Clinical Evaluations, Genetics, and the
Dynamics of Human QuadrupedalismAbstract: This review includes for the first time a dynamical systems analysis of human quadrupedalism in Uner Tan syndrome, which is characterized by habitual quadrupedalism, impaired intelligence, and rudimentary speech. The first family was discovered in a small village near Iskenderun, and families were later found in Adana and two other small villages near Gaziantep and Canakkale. In all the affected individuals dynamic balance was impaired during upright walking,and they habitually preferred walking on all four extremities. MRI scans showed inferior cerebellovermian hypoplasia with slightly simplified cerebral gyri in three of the families, but appeared normal in the fourth. PET scans showed a decreased glucose metabolic activity in the cerebellum, vermis and, to a lesser extent the cerebral cortex, except for one patient,
whose MRI scan also appeared to be normal. All four families had consanguineous marriages in their pedigrees,
suggesting autosomal recessive transmission. The syndrome was genetically heterogeneous. Since the initial discoveries
more cases have been found, and these exhibit facultative quadrupedal locomotion, and in one case, late childhood onset. It has been suggested that the human quadrupedalism may, at least, be a phenotypic example of reverse evolution. From the viewpoint of dynamic systems theory, it was concluded there may not be a single factor that predetermines human quadrupedalism in Uner Tan syndrome, but that it may involve self-organization, brain plasticity, and rewiring, from the many decentralized and local interactions among neuronal, genetic, and environmental subsystems.Prof. Dr. Uner Tanunertan37@yahoo.com2009-12-19T12:22:18Z2011-09-17T17:47:07Zhttp://cogprints.org/id/eprint/6738This item is in the repository with the URL: http://cogprints.org/id/eprint/67382009-12-19T12:22:18ZCharacterization of Fragile X mental retardation antibodies for use in cross-species immunoblotting, immunohistochemistry, and electron microscopyThis information is provided on Cogprints for colleagues in the Fragile X field who have requested it directly in the past. It is also a companion work to the article “Human Fragile X gene locus P1 artificial chromosome transgenic mice” from our group (manuscript to be made available on Cogprints).Dr. Robert Bauchwitzrpb3@columbia.edu2006-07-23Z2011-03-11T08:56:32Zhttp://cogprints.org/id/eprint/5011This item is in the repository with the URL: http://cogprints.org/id/eprint/50112006-07-23ZEVIDENCE FOR "UNERTAN SYNDROME" AND THE EVOLUTION OF THE HUMAN MINDA new family exhibiting “Unertan Sydnrome” was discovered. The pedigree analysis showed marriages between relatives. This family was similar to the first one (see Tan, 2006a), providing a firm evidence for the new syndrome. The affected children showed habitual quadrupedal walking gait, that is, they walked on wrists and feet with straight legs and arms. Their heads and bodies were mildly flexed; they exhibited mild cerebellar signs, and severe mental retardation. The pedigree demonstrated a typical autosomal-recessive inheritance. The genetic nature of
this syndrome suggests a backward stage in human evolution (devolution), which would be consistent with theories of punctuated evolution. The results reflected a
new theory on the evolution of human beings. That is, the evolution of humans would in fact be the evolution of the extensor motor system, responsible for upright posture, against the gravitational forces. This would be coupled with the emergence of the human mind, which can be considered a reflexion of the human motor system, in accord with the psychomotor theory (see Tan, 2005a). The
most important characteristic of the newly emerged human mind was the resistance against gravitational forces. This was the resistive mind, the origins of human creativity.Prof. Dr. Uner Tan2004-11-29Z2011-03-11T08:55:42Zhttp://cogprints.org/id/eprint/3879This item is in the repository with the URL: http://cogprints.org/id/eprint/38792004-11-29ZProtocadherinX/Y, a Candidate Gene-Pair for Schizophrenia and Schizoaffective Disorder: A DHPLC Investigation of Gonomic SequenceProtocadherin X and Protocadherin Y (PCDHX and PCDHY) are cell-surface adhesion molecules expressed predominantly in the brain. The PCDHX/Y gene-pair was generated by an X-Y translocation approximately 3 million years ago (MYA) that gave rise to the Homo sapiens-specific region of Xq21.3 and Yp11.2 homology. Genes within this region are expected to code for sexually dimorphic human characteristics, including, for example, cerebral asymmetry a dimension of variation that has been suggested is relevant to psychosis. We examined differences in patients with schizophrenic or schizoaffective psychosis in the genomic sequence of PCDHX and PCDHY in coding and adjacent intronic sequences using denaturing high performance liquid chromatography (DHPLC). Three coding variants were detected in PCDHX and two in PCDHY. However, neither the coding variants nor the intronic polymorphisms could be related to psychosis within families. Low sequence variation suggests selective pressure against sequence change in modern humans in contrast to the structural chromosomal and sequence changes including fixed X-Y differences that occurred in this region earlier in hominid evolution. Our findings exclude sequence variation in PCDHX/Y as relevant to the aetiology of psychosis. However, we note the unusual status of this region with respect to X-inactivation. Further investigation of the epigenetic control of PCDHX/Y in relation to psychosis is warrantMs M GiouzeliDr NA WilliamsDr LJ LonieProf LE DeLisiProf TJ Crow2004-12-04Z2011-03-11T08:55:42Zhttp://cogprints.org/id/eprint/3871This item is in the repository with the URL: http://cogprints.org/id/eprint/38712004-12-04ZSize of hippocampal pyramidal neurons in schizophreniaBackground Meta-analyses of
hippocampal size have indicated thatthis
structure is smaller in schizophrenia.This
could reflect a reductioninthe size of
constituent neurons or a reduced number
of neurons.
Aims To measure the size of
hippocampalpyramidalneuronsinthe hippocampalpyramidalneurons inthe
brains of peoplewith andwithout
schizophrenia.
Method Pyramidalneuron size in
hippocampal subfieldswas estimated
stereologically fromsections taken at
5mmintervals throughoutthewhole
length of right and left hippocampi from
andleft the brains of13 peoplewith schizophrenia
and16 controls.Resultswere assessed
using repeated-measures analysis of
covariance looking for amain effectof
diagnosis and gender, andinteractions of
and interactions thesewith side.
Results Wewere unable to detect
significantdifferences related to diagnosis,
gender or side for any hippocampal
subfield for this series of cases.
Conclusions For this series of brains,
hippocampal cell size is unchangedin
schizophrenia.
Dr JR HighleyMs M WalkerDr B McDonaldProf TJ CrowProf MM Esiri2004-12-04Z2011-03-11T08:55:42Zhttp://cogprints.org/id/eprint/3880This item is in the repository with the URL: http://cogprints.org/id/eprint/38802004-12-04ZA Genome-Wide Scan for Linkage to Chromosomal Regions in 382 Sibling Pairs with Schizophrenia or Schizoaffective DisorderOBJECTIVE: Some genome-wide scans and association studies for schizophrenia susceptibility genes have yielded significant positive findings, but there is disagreement between studies on their locations, and no mutation has yet been found in any gene. Since schizophrenia is a complex disorder, a study with sufficient power to detect a locus with a small or moderate gene effect is necessary. METHOD: In a genome-wide scan of 382 sibling pairs with a diagnosis of schizophrenia or schizoaffective disorder, 396 highly polymorphic markers spaced approximately 10 centimorgans apart throughout the genome were genotyped in all individuals. Multipoint nonparametric linkage analysis was performed to evaluate regions of the genome demonstrating increased allele sharing, as measured by a lod score. RESULTS: Two regions with multipoint maximum lod scores suggesting linkage were found. The highest lod scores occurred on chromosome 10p15-p13 (peak lod score of 3.60 at marker D10S189) and the centromeric region of chromosome 2 (peak lod score of 2.99 at marker D2S139). In addition, a maximum lod score of 2.00 was observed with marker D22S283 on chromosome 22q12, which showed evidence of an imprinting effect, whereby an excess sharing of maternal, but not paternal, alleles was present. No evidence of linkage was obtained at several locations identified in previous studies, including chromosomes 1q, 4p, 5p-q, 6p, 8p, 13q, 15p, and 18p. CONCLUSIONS: The findings of this large genome-wide scan emphasize the weakness and fragility of linkage reports on schizophrenia. No linkage appears to be consistently replicable across large studies. Thus, it has to be questioned whether the genetic contribution to this disorder is detectable by these strategies and the possibility raised that it may be epigenetic, i.e., related to gene expression rather than sequence variation. Nevertheless, the positive findings on chromosome 2, 10, and 22 should be pursued further.
Prof LE DeLisiDr SH ShawProf TJ CrowDr G ShieldsMs AB SmithDr VW LarachMr N WellmanDr J LoftusDr B NanthakumarDr K RaziMr J StewartDr M ComazziDr A VitaDr T HeffnerDr R Sherrington2004-10-28Z2011-03-11T08:55:43Zhttp://cogprints.org/id/eprint/3904This item is in the repository with the URL: http://cogprints.org/id/eprint/39042004-10-28ZA continuum of psychosis, one human gene, and not much else - the case for homogeneityThe contention of this paper is that psychoses are not a collection of separate and unrelated diseases, but a set of diverse expressions of a single underlying entity. It will be argued that there is a basic homogeneity of pathogenesis, that there are not multiple predisposing genes but a single gene that is associated with significant diversity. Therefore the problem is a unitary one. The challenge is to identify the nature and function of the gene. It will be argued that the gene is that by which homo sapiens has separated from other primate species, and that the diversity arises from selective pressures which continue to act on this specifically human gene.
Prof TJ Crow2011-12-16T00:58:34Z2011-12-16T00:58:34Zhttp://cogprints.org/id/eprint/7755This item is in the repository with the URL: http://cogprints.org/id/eprint/77552011-12-16T00:58:34ZNatural Transformations of Organismic StructuresThe mathematical structures underlying the theories of organismic sets, (M, R)-systems and molecular sets are shown to be transformed naturally within the theory of categories and functors. Their natural transformations allow the comparison of distinct entities, as well as the modelling of dynamics in “organismic” structures.Prof. Dr. I. C. Baianuibaianu@illinois.edu2011-12-16T00:58:54Z2011-12-16T00:58:54Zhttp://cogprints.org/id/eprint/7743This item is in the repository with the URL: http://cogprints.org/id/eprint/77432011-12-16T00:58:54ZOrganismic Supercategories: III. Qualitative Dynamics of Systems The representation of biological systems by means of organismic supercategories, developed in previous papers, is further discussed. The different approaches to relational biology, developed by Rashevsky, Rosen and by Baianu and Marinescu, are compared with Qualitative Dynamics of Systems which was initiated by Henri Poincaré (1881). On the basis of this comparison some concrete results concerning dynamics of genetic system, development, fertilization, regeneration, analogies, and oncogenesis are derived.Prof. Dr. I.C. Baianuicb