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Search Results: 1 - 10 of 1683 matches for " Arno Lukas "
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DATA ANNOTATION AND RELATIONS MODELING FOR INTEGRATED OMICS IN CLINICAL RESEARCH
Arno Lukas,Bernd Mayer
The IIOAB Journal , 2010,
Abstract: Omics has massively permeated translational clinical research with numerous diseases being covered by Omics studies from the genome to the metabolome level. Integrating these disease specific Omics tracks appears a logical next step for building the fundament of Systems Biology and Systems Medicine. Here, coherence of individual Omics tracks regarding clinical hypothesis, samples and clinical descriptors, and finally data handling and integration become pivotal. We present a data integration, annotation and relations modeling concept for heterogeneous Omics data and workflows. With molecular features at the center of all Omics we link the result profiles from different Omics tracks characterizing a specific disease phenotype to a common human molecular reference network for allowing a seamless integration and subsequent support in interpretation of Omics screening results. Our concept rests on data structures for representing objects specified by metadata and content. For handling diverse Omics tracks a flexible structure for content is proposed allowing data representation at different levels of granularity as demanded by the type of Omics and specific type of data. Content on the molecular level includes deep annotation of molecular features on gene and protein level. Based on this annotation pair-wise relations between molecular objects are built, traversing the molecular annotation into a network of relations (molecular feature graph). Such a relation network is also built on the Omics data level, combining explicit relations derived from study setup and implicit relations generated by mining metadata and content (Omics data graph). Finally both graphs are merged utilizing the molecular feature level as common denominator, enabling a persistent integration and subsequently interpretation of Omics profiling results in the realm of a given clinical hypothesis. We present a case study on integrating transcriptomics and proteomics data on chronic kidney disease for demonstrating the feasibility of this concept.
Characterization of protein-interaction networks in tumors
Alexander Platzer, Paul Perco, Arno Lukas, Bernd Mayer
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-224
Abstract: This paper outlines features of PINs derived from 29 studies on differential gene expression in cancer. For each study the number of differentially regulated genes was determined and used as a basis for PIN construction utilizing the Online Predicted Human Interaction Database.Graph measures calculated for the largest subgraph of a PIN for a given differential-gene-expression data set comprised properties reflecting the size, distribution, biological relevance, density, modularity, and cycles. The values of a distinct set of graph measures, namely Closeness Centrality, Graph Diameter, Index of Aggregation, Assortative Mixing Coefficient, Connectivity, Sum of the Wiener Number, modified Vertex Distance Number, and Eigenvalues differed clearly between PINs derived on the basis of differential gene expression data sets characterizing malignant tissue and PINs derived on the basis of randomly selected protein lists.Cancer PINs representing differentially regulated genes are larger than those of randomly selected protein lists, indicating functional dependencies among protein lists that can be identified on the basis of transcriptomics experiments. However, the prevalence of hub proteins was not increased in the presence of cancer. Interpretation of such graphs in the context of robustness may yield novel therapies based on synthetic lethality that are more effective than focusing on single-action drugs for cancer treatment.The "omics" revolution has dramatically increased the amount of data available for characterizing intracellular events at the cellular level. The main experimental methodologies responsible for this development have included differential gene expression analysis for recording mRNA concentration profiles, and proteomics for providing data on protein abundance [1,2]. Each technique generates data related to a defined intracellular aspect, such as differential-gene-expression profiles at the transcriptional level, and currently the main focus is on inter
From molecular signatures to predictive biomarkers: modeling disease pathophysiology and drug mechanism of action
Andreas Heinzel,Gert Mayer,Rainer Oberbauer,Arno Lukas,Bernd Mayer
Frontiers in Cell and Developmental Biology , 2014, DOI: 10.3389/fcell.2014.00037
Abstract: Omics profiling significantly expanded the molecular landscape describing clinical phenotypes. Association analysis resulted in first diagnostic and prognostic biomarker signatures entering clinical utility. However, utilizing Omics for deepening our understanding of disease pathophysiology, and further including specific interference with drug mechanism of action on a molecular process level still sees limited added value in the clinical setting. We exemplify a computational workflow for expanding from statistics-based association analysis toward deriving molecular pathway and process models for characterizing phenotypes and drug mechanism of action. Interference analysis on the molecular model level allows identification of predictive biomarker candidates for testing drug response. We discuss this strategy on diabetic nephropathy (DN), a complex clinical phenotype triggered by diabetes and presenting with renal as well as cardiovascular endpoints. A molecular pathway map indicates involvement of multiple molecular mechanisms, and selected biomarker candidates reported as associated with disease progression are identified for specific molecular processes. Selective interference of drug mechanism of action and disease-associated processes is identified for drug classes in clinical use, in turn providing precision medicine hypotheses utilizing predictive biomarkers.
Influence of Elevation on Carbonate Contents in Stratified Soils, Northern Great Basin and Adjacent Mountains, U.S.A  [PDF]
Arno Kleber
Open Journal of Soil Science (OJSS) , 2011, DOI: 10.4236/ojss.2011.12009
Abstract: Many soils in the western U.S.A. contain one or several carbonate-enriched zones (CEZ). Their carbonate admixture is often attributed to steady eolian influx, with intermittent leaching episodes of variable intensity leading to pedogenic enrichment at various depths. This hypothesis would require carbonate contents to decrease and depths to those horizons to increase with elevation. Here I compute correlations for the upper three CEZ of the surface soil and of up to two buried soils between elevation, carbonate content, depth to horizon, and particle-size distribution to test for elevation- dependent trends. Actually, carbonate-content decreases with elevation indicate such trends exist and can be determined with this approach. However, some significant relationship of elevation and depth to CEZ is not supported by the data. Furthermore, influence of local carbonate on CEZ in the surface soils calls for lateral translocation. Gravelly, now-buried sediments collected eolian carbonate better than finer ones, which finding implies these sediments were at the surface once and fossilized later. Altogether, the data indicate cyclical evolution: Several cycles of the formation of colluvial slope deposits with admixed carbonate-bearing loess particles were each followed by pedogenic translocation of the carbonate just to the depth of the next parent-material disconformity. Thus, disconformities are major triggers of soil-carbonate accumulation.
Linking the ovarian cancer transcriptome and immunome
Ronald Rapberger, Paul Perco, Cornelia Sax, Thomas Pangerl, Christian Siehs, Dietmar Pils, Andreas Bernthaler, Arno Lukas, Bernd Mayer, Michael Krainer
BMC Systems Biology , 2008, DOI: 10.1186/1752-0509-2-2
Abstract: This paper analyzes the proposed link between increased abundance of a protein in cancerous tissue and the increased potential of the protein for induction of a humoral immune response, using ovarian cancer as an example. Public domain data sources on differential gene expression and on autoantigens associated with this malignancy were extracted and compared, using bioinformatics analysis, on the levels of individual genes and proteins, transcriptional coregulation, joint functional pathways, and shared protein-protein interaction networks. Finally, a selected list of ovarian cancer-associated, differentially regulated proteins was tested experimentally for reactivity with antibodies prevalent in sera of ovarian cancer patients.Genes reported as showing differential expression in ovarian cancer exhibited only minor overlap with the public domain list of ovarian cancer autoantigens. However, experimental screening for antibodies directed against antigenic determinants from ovarian cancer-associated proteins yielded clear reactions with sera.A link between tumor protein abundance and the likelihood of induction of a humoral immune response in ovarian cancer appears evident.An intriguing interplay between cancer cells and the body's immune system has been reported, and includes both humoral and cellular pathways [1-3]. Research into links between cancer and the immune system has aimed to acquire further understanding of the mechanisms involved [4], but also addresses applications in diagnostics, disease surveillance, and therapeutic approaches [5-9].The antibody profile triggered in the course of tumor development (i.e., the spectrum of antibodies directed against tumor-associated components) may be an immunologic fingerprint of the malignant tissue, in turn providing information on disease-associated proteins. Experimental technologies for identification of such autoantigens include display methods such as phage display, serological expression cloning analysis (SEREX)
Existence and Uniqueness of Global Smooth Solutions for Vlasov Maxwell Equations  [PDF]
Lukas Degu Petros
Advances in Pure Mathematics (APM) , 2018, DOI: 10.4236/apm.2018.81005
Abstract: Global existence of classical solutions to the relativistic Vlasov-Maxwell system, given sufficiently regular initial data, is a long-standing open problem. The aim of this project is to present in details the results of a paper published in 1986 by Robert Glassey and Walter Strauss. In that paper, a sufficient condition for the global existence of a smooth solution to the relativistic Vlasov-Maxwell system is derived. In the following, the resulting theorem is proved by taking initial data \"\", \"\". A small data global existence result is presented as well.
Os indígenas do Brasil entre a raz?o de Estado e o Direito Natural: as contribui??es de André Thévet e Jean de Léry
Wehling, Arno;
História (S?o Paulo) , 2012, DOI: 10.1590/S0101-90742012000200003
Abstract: analysis of perception, in andré thévet and jean de léry, of the issues of the state of nature, natural law and natural goodness in brazilian indigenous who the chroniclers of antarctic france had contact. here, we inquire if the authors have already the clear awareness of those issues, or if it has been deducted by aftermost authors, who have an a priori conception on the subject. reference is made to the trajectory of the natural law from maquiavel to locke with the emergence of a new jusracionalismo and the information of the two authors is contemplated. it concludes with an evaluation of the reception of the chroniclers, the meaning assigned by them to the issues and the role of natural law in their speech. the texts are shown as empirical element in a long process of establishment of the new natural law, the "rational law" in bobbio's classification, a process which conflicts with other emerging doctrine in the sixteenth century - the reason of state.
A teoria das duas consciências: comentários
Engelmann, Arno;
Paidéia (Ribeir?o Preto) , 2002, DOI: 10.1590/S0103-863X2002000100012
Abstract: lívia sim?o referred to the similarities between her constructivist-semiotic-cultural psychological approach and engelmann's two consciousness proposal. nelson coelho jr. comments the similarities between husserl and merleau-ponty approach and engelmann's studies of consciousness. nevertheless, despite the origin of the knowledge in himself, coelho jr. accept the reality of other people and the reality of the world. arno engelmann answered the arguments of the two commentators. in answering to coelho jr., he declared that he is faithful to a skeptic thesis. the reality of other people and of the world is an hypothesis, although a very high probability hypothesis.
A teoria das duas consciências
Engelmann, Arno;
Paidéia (Ribeir?o Preto) , 2002, DOI: 10.1590/S0103-863X2002000100009
Abstract: based on tolman's "consciousness" partition, engelmann call the two by the same noun qualified by different adjectives: the individual and present immediate-consciousness, and the remaining mediate-consciousness. according to engelmann, this remaining consciousness can be parted again in an individual but past observer's-mediate-consciousness and an other's-mediate-consciousness. three more related theories are presented by engelmann: the eight basic hypotheses theory, name given to the first hypotheses that conduct someone to leave immediate-consciousness and arrive at the other's-mediate-consciousness; the consciousness indicators theory, a name that comprehends the verbal report; and the five percept echelon's theory, name given to conscious perception attitude in human beings.
Dois Tipos de Consciência: a Busca da Autenticidade
Engelmann, Arno;
Psicologia USP , 1997, DOI: 10.1590/S0103-65641997000200003
Abstract: two authentic occurences should be recognized by contemporary scientists: (1) the rapid development of empirical knowledge, today, and (2) immediate and momentary consciousness. the latter is called immediate consciousness. empirical, or natural, knowledge is acquired by being passed from an individual and momentary observation towards a collective and temporal universe. this is a change from absolute truth to probabilistic knowledge. seven basic hypotheses are presented to permit knowledge of the probabilistic universe. i have chosen an emergentist explanation for this universe, with an evolutionary explanation in terms of increasing levels. i observe presently different levels and i move simultaneously between these levels with causal interaction. therefore, there is only one universe. in most animals there is a level called organism, a level which encompasses the whole animal. in human beings and in some nonhuman animals, there is a small part which knows itself. this part is called mediate consciousness. mediate consciousness is the observer's own past consciousness (observer's mediate consciousness) or part of the organism of other persons or nonhuman animals (other's mediate consciousness). research on others' mediate consciousness is similar to research on any other part of animals. in this case, others' mediate consciousness is a part of an authentic universal occurence.
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