TOPS-MODE

Another form of array is called a microchannel plate detector. A time-of-flight (TOP) mass spectrometer collects ions sequentially in time and can use a point detector, but increasingly, the TOP instrument uses a microchannel plate, most particularly in an orthogonal TOP mode. Because the arrays and microchannel plates are both essentially arrays or assemblies of small electron multipliers, there may be confusion over their roles. This chapter illustrates the differences between the two arrays. 

Cabrera MA, Bermejo M, Perez M and Ramos R. TOPS-MODE approach for the prediction of blood-brain barrier permeation. J Pharm Sci 2004 93 1701-17. 

There can be many different cycle configurations for the hybrid fuel cell/turbine plant. In the topping mode described above, the fuel cell serves as the combustor for the gas turbine, while the gas turbine is the balance of plant for the fuel cell, with some generation. In the bottoming mode, the fuel cell uses the gas turbine exhaust as air supply, while the gas turbine is the balance of plant. In indirect systems, high-temperature heat exchangers are used. 

Cabrera et al. [50] modeled a set of 163 drugs using TOPS-MODE descriptors with a linear discriminant model to predict p-glycoprotein efflux. Model accuracy was 81% for the training set and 77.5% for a validation set of 40 molecules. A "combinatorial QSAR" approach was used by de Lima et al. [51] to test multiple model types (kNN, decision tree, binary QSAR, SVM) with multiple descriptor sets from various software packages (MolconnZ, Atom Pair, VoSurf, MOE) for the prediction of p-glycoprotein substrates for a dataset of 192 molecules. Best overall performance on a test set of 51 molecules was achieved with an SVM and AP or VolSurf descriptors (81% accuracy each). 

A variety of other QSAR-type models for the prediction of plasma protein binding have also been published recently, including neural networks/support vector machines [64], 4-D fingerprints [65], and TOPS-MODE descriptors [66]. 

There can be many different cycle configurations for the hybrid fuel cell/ turbine plant. In the topping mode described above, the fuel cell serves as the combustor for the gas turbine while the... 

FIGURE 3.13 The three normal vibrational modes of water. For the top mode (the symmetric stretch) both O-H bonds are extended or compressed at the same time. For the middle mode (the antisymmetric stretch) one O-H bond is extended when the other is compressed. The bottom mode is called the bend. In every case the hydrogen atoms move more than the oxygen, because the center of mass has to stay in the same position (otherwise the molecule would be translating). For a classical molecule (built out of balls and perfect springs) these three modes are independent. Thus, for example, energy in the symmetric stretch will never leak into the antisymmetric stretch or bend modes. 

Helguera-Morales et al. [83] used a topological sub-structural molecular design (TOPS-MODE) approach to predict the carcinogenicity of 48 nitro-aromatic compounds in female rodents. Topological descriptors are derived mainly from knowledge of the connectivity between atoms within a molecule, and are based to some extent on information on atom types and their electronic environment. The model was able to describe 79.1% of the experimental data. It was found that the carcinogenic activity of the compounds analyzed increases in the presence of a primary... 

Helguera AM, Gonzalez MP, Briones JR. TOPS-MODE approach to predict mutagenicity in dental monomers. Polymer 2004 45(6) 2045-50. 

Cabrera Perez et al., European Journal of Medicinal Chemistry, 2004 A topological sub-structural approach for predicting human intestinal absorption of drugs 209 LDA 93% TOPS-MODE (nfinai = 3)... 

Cabrera et al. pursued a topological substructural approach for the prediction of P-gp substrates. A linear discriminant model classified 163 compounds with an accuracy of 81% based on standard bond distance, polarizability, and the Casteiger-Marsilli atomic charge [35]. Furthermore, the predictive potential ofthis TOPS-MODE approach was demonstrated for a set of 6-fluoroquinolones not included in the training set. 

A graph-theoretical approach called TOPological Substructural MOlecular DEsign (TOPS-MODE), previously called TOpological SubStructural MOlecular DEsign (TOSS-MODE), was... 

Applications of the TOPS-MODE approach reported in literature are [Estrada, Gutierrez et al,... 

TOPS-MODE = TOPological Substructural Molecular DEsign edge adjacency matrix... 

Estrada, E. and Gonzalez, H. (2003) What are the limits of applicability for graph theoretic descriptors in QSPR/QSAR Modeling dipole moments of aromatic compormds with TOPS-MODE descriptors. /. Chem. Inf. Comput. Sci., 43, 75-84. 

TOPS-MODE. 2. Neurotoxicity of a noncongeneric series of solvents. SAR ej QSAR Environ. Res., 12, 445-459. 

Basketter, D. and Larhey, S. (2003) Computer-aided knowledge generation for understanding skin sensitization mechanisms the TOPS-MODE approach. Chem. Res. Toxicol, 16, 1226-1235. 

Estrada, E Quincoces, J. and Patlewicz, G. (2004) Creating molecular diversity from antioxidants in Brazilian propolis. Combination of TOPS-MODE QSAR and virtual structure generation. Mol Div, 8, 21-33. 

Estrada, E., Uriarte, E., Gutierrez, Y. and Gonzalez, H. (2003) Quantitative structure-toxicity relationships using TOPS-MODE. 3. Structural factors influencing the permeability of commercial solvents through living human skin. SAR el QSAR Environ. Res., 14, 145-163. 

Estrada, E., Vilar, S., Uriarte, E. and Gutierrez, Y. (2002) In silico studies toward the discovery of new anti-HIV nucleoside compounds with the use of TOPS-MODE and 2D/3D connectivity indices. 1. 

Perez Gonzalez, M., Gonzalez, H., Molina Ruiz, R., Cabrera, M.A. and Ramos de Armas, R. (2003) TOPS-MODE based QSARs derived from heterogeneous series of compounds. Applications to the design of new herbicides. J. Chem. Inf. Comput. Scl, 43, 1192-1199. 

Perez Gonzalez, M., Helguera Morales, A. and Diaz, H.G. (2004) A TOPS-MODE approach to predict permeability coefficients. Polymer, 45, 2073-2079. 

Perez Gonzalez, M. and Helguera, A.M. (2003) TOPS-MODE versus DRAGON descriptors to predict permeability coefficients through low-density polyethylene. J. Comput. Aid. Mol. Des., 17, 665-672. 

Perez Gonzalez, M., Helguera, A.M. and Rodriguez, Y.M. (2004) TOPS-MODE and DRAGON descriptors in QSAR. 1. Skin permeation. Internet Electron.]. Mol. Des., 3, 750-758. 

---