Search results for "Computation"
showing 10 items of 7362 documents
Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
2022
6 p.-2 fig.-2 tab.
The Chaperonopathies: Classification, Mechanisms, Structural Features
2013
The classification of chaperonopathies is presented in this chapter. Like many other diseases, chaperonopathies can be genetic or acquired, primary or secondary, structural and/or functional, and qualitative and/or quantitative. In addition, considering pathogenic mechanism, chaperonopathies can be by defect, excess, or mistake. In the latter, a chaperone is normal but favors disease, a situation that occurs, for instance, in various types of cancers. Structural chaperonopathies are characterized by a change in the molecule of a chaperone due to mutation (genetic chaperonopathy) or due to aberrant post-translational modification (acquired chaperonopathy). In both cases, the impact of the st…
Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing
2018
The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant. Despite the poor quality of the starting DNA, BRAF mutation was su…
High-accuracy extrapolated ab initio thermochemistry. II. Minor improvements to the protocol and a vital simplification
2006
The recently developed high-accuracy extrapolated ab initio thermochemistry method for theoretical thermochemistry, which is intimately related to other high-precision protocols such as the Weizmann-3 and focal-point approaches, is revisited. Some minor improvements in theoretical rigor are introduced which do not lead to any significant additional computational overhead, but are shown to have a negligible overall effect on the accuracy. In addition, the method is extended to completely treat electron correlation effects up to pentuple excitations. The use of an approximate treatment of quadruple and pentuple excitations is suggested; the former as a pragmatic approximation for standard cas…
Harmonization of Immune Biomarker Assays for Clinical Studies
2011
Assays that measure a patient's immune response play an increasingly important role in the development of immunotherapies. The inherent complexity of these assays and independent protocol development between laboratories result in high data variability and poor reproducibility. Quality control through harmonization--based on integration of laboratory-specific protocols with standard operating procedures and assay performance benchmarks--is one way to overcome these limitations. Harmonization guidelines can be widely implemented to address assay performance variables. This process enables objective interpretation and comparison of data across clinical trial sites and also facilitates the ide…
Prelogical Test: An Alternative Tool for Early Detection of Learning Difficulties
2014
Abstract Difficulties during the preschool age commonly lead to children who cannot solve problems, organize information and create meaning. It is necessary to predict factors that may affect their future learning. The aim is to develop an evaluation tool, to be applied in groups and that can easily evaluate results, to detect future learning problems in children of 3-6 years old. Computational intelligence techniques could contribute greatly to analyze results and to detect patterns that otherwise would not be apparent. Two protocols were implemented: an Indirect Variables Protocol (IVP) which captures children's personal data, and a Direct Variables Protocol (DVP) that assesses the graphi…
Development of multiparametric cell-based protocol to assess and classify hepatotoxicity potential of drugs
2010
Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism
2013
Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine–cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contrib…
Density functional theory (DFT) prediction of structural and spectroscopic parameters of cytosine using harmonic and anharmonic approximations
2015
The applicability of popular and efficient B3LYP hybrid density functional and medium-size Pople-type basis set in combination with computationally expensive anharmonic model to obtain more accurate theoretical structure, vibrational frequencies and GIAO NMR parameters of cytosine was tested. We report on prediction of cytosine equilibrium (R e ) and rovibrationally averaged (R v ) structures and vibrational frequencies in the gas phase and DMSO solution using density functional theory combined with 6-311++G** basis set. The harmonic and anharmonic vibrational frequencies (using second-order vibrational perturbation theory, VPT2) were critically discussed. In comparison with initial harmoni…
Influence of structure on the polarizability of hydrated methane sulfonic acid clusters
2015
Abstract: The relationship between polarizability and structure is investigated in methane sulfonic acid (MSA) and in 36 hydrated MSA clusters. The polarizabilities are calculated at B3LYP and MP2 level and further partitioned into molecular contributions using classic and iterative Hirshfeld methods. The differences in the two approaches for partitioning of polarizabilities are thoroughly analyzed. The polarizabilities of the molecules are found to be influenced in a systematic way by the hydrogen bond network in the clusters, proton transfer between MSA and water molecules, and weak interactions between water molecules and the methyl group of MSA.