Search results for "TRANSFORMATION"
showing 10 items of 1634 documents
From Requirements to Code in a Model Driven Way
2010
Though there is a lot of support for model driven development the support for complete model driven path from requirements to code is limited. The approach proposed in this paper offers such a path which is fully supported by model transformations. The starting point is semiformal requirements containing behaviour description in a controlled natural language. A chain of models is proposed including analysis, platform independent and platform specific models. A particular architecture style is chosen by means of selecting a set of appropriate design patterns for these models. It is shown how to define informally and then implement in model transformation language MOLA the required transforma…
Efficient computation of root mean square deviations under rigid transformations
2013
The computation of root mean square deviations (RMSD) is an important step in many bioinformatics applications. If approached naively, each RMSD computation takes time linear in the number of atoms. In addition, a careful implementation is required to achieve numerical stability, which further increases runtimes. In practice, the structural variations under consideration are often induced by rigid transformations of the protein, or are at least dominated by a rigid component. In this work, we show how RMSD values resulting from rigid transformations can be computed in constant time from the protein's covariance matrix, which can be precomputed in linear time. As a typical application scenar…
Curcumin Affects HSP60 Folding Activity and Levels in Neuroblastoma Cells.
2020
The fundamental challenge in fighting cancer is the development of protective agents able to interfere with the classical pathways of malignant transformation, such as extracellular matrix remodeling, epithelial−mesenchymal transition and, alteration of protein homeostasis. In the tumors of the brain, proteotoxic stress represents one of the main triggering agents for cell transformation. Curcumin is a natural compound with anti-inflammatory and anti-cancer properties with promising potential for the development of therapeutic drugs for the treatment of cancer as well as neurodegenerative diseases. Among the mediators of cancer development, HSP60 is a key factor for the maintenance of…
Complementation of Saccharomyces cerevisiae mutationsin genes involved in translation and protein folding (EFB1 and SSB1)with Candida albicans cloned…
2000
We have demonstrated that the expression of Candida albicans genes involved in translation and protein folding (EFB1 and SSB1) complements the phenotype of Saccharomyces cerevisiae mutants. The elongation factor 1beta (EF-1beta) is essential for growth and efb1 S. cerevisiae null mutant cells are not viable; however, viable haploid cells, carrying the disrupted chromosomal allele of the S. cerevisiae EFB1 gene and pEFB1, were isolated upon sporulation of a diploid strain which was heterozygous at the EFB1 locus and transformed with pEFB1 (a pEMBLYe23 derivative plasmid containing an 8-kb DNA fragment from the C. albicans genome which contains the EFB1 gene). This indicates that the C. albic…
Theileria parasites secrete a prolyl isomerase to maintain host leukocyte transformation
2015
Infectious agents develop intricate mechanisms to interact with host cell pathways and hijack their genetic and epigenetic machinery to change host cell phenotypic states. Among the Apicomplexa phylum of obligate intracellular parasites, which cause veterinary and human diseases, Theileria is the only genus that transforms its mammalian host cells. Theileria infection of bovine leukocytes induces proliferative and invasive phenotypes associated with activated signalling pathways, notably JNK and AP-1 (ref. 2). The transformed phenotypes are reversed by treatment with the theilericidal drug buparvaquone. We used comparative genomics to identify a homologue of the peptidyl-prolyl isomerase PI…
A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases.
2015
Exploration of chemical reactions in complex explicit environments has become an affordable task with the use of hybrid quantum mechanics/molecular mechanics potentials which allow calculating free energy profiles of chemical reactions under the influence of the surroundings. Tracing these free energy profiles requires the selection of a reaction coordinate, which can be cumbersome for those processes involving more than a single chemical event in a concerted step. We here propose a collective coordinate to be used in the calculation of free energy profiles for complex reactions in condensed phases. This coordinate is based in the definition of the advance along a path introduced by Brandua…
From pseudo-bosons to pseudo-Hermiticity via multiple generalized Bogoliubov transformations
2016
We consider the special type of pseudo-bosonic systems that can be mapped to standard bosons by means of generalized Bogoliubov transformation and demonstrate that a pseudo-Hermitian systems can be obtained from them by means of a second subsequent Bogoliubov transformation. We employ these operators in a simple model and study three different types of scenarios for the constraints on the model parameters giving rise to a Hermitian system, a pseudo-Hermitian system in which the second the Bogoliubov transformations is equivalent to the associated Dyson map and one in which we obtain D-quasi bases.
CD40 ligation protects bronchial epithelium against oxidant-induced caspase-independent cell death.
2006
KEYWORDS CLASSIFICATION: 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide;Antigens,CD40;Apoptosis;Bronchi;cytology;Caspases;Cell Cycle;Cell Death;Cell Line,Transformed;Cell Survival;Cell Transformation,Viral;Cytoprotection;drug effects;Epithelial Cells;Humans;Italy;mechanisms of carcinogenesis;metabolism;Oxidants;pharmacology;physiology;Research;Simian virus 40;toxicity;Transcription Factor AP-1. CD40 and its ligand regulate pleiotropic biological responses, including cell proliferation, differentiation, and apoptosis. In many inflammatory lung diseases, tissue damage by environmental or endogenous oxidants plays a major role in disease pathogenesis. As the epithelial barrier is a major t…
Cystic mucinous adenocarcinoma of the lung: a case report.
2011
Abstract Mucinous cystic tumors of the lung are uncommon, the preoperative pathologic diagnosis is difficult and their biological behavior is still controversial. We report the case of a patient with a clinically benign cystic lesion that post-operatively showed to be consistent with an invasive adenocarcinoma arising in a mucinous cystadenoma of the lung, We underline the difficulty of the clinical pre-operative diagnosis of this cystic neoplasia radiologically mimicking a hydatid cyst, and we report the negative TTF1 immunostaining potentially misleading in the differential diagnosis with metastatic mucinous carcinomas. Finallly, we evidence the presence of a pre-existing mucinous benign …
Metabolism and bioactivation of toxicants in the lung. The in vitro cellular approach.
2005
Lung is a target organ for the toxicity of inhalated compounds. The respiratory tract is frequently exposed to elevated concentrations of these compounds and become the primary target site for toxicity. Occupational, accidental or prolonged exposure to a great variety of chemicals may result in acute or delayed injury to cells of the respiratory tract. Nevertheless, lung has a significant capability of biotransforming such compounds with the aim of reducing its potential toxicity. In some instances, the biotransformation of a given compound can result in the generation of more reactive, and frequently more toxic, metabolites. Indeed, lung tissue is known to activate pro-carcinogens (i.e. po…