Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

We present a general approach to forming structure-activity relationships (SARs). This approach is based on representing chemical structure by atoms and their bond connectivities in combination with the inductive logic programming (ILP) algorithm PROGOL. Existing SAR methods describe chemical structure by using attributes which are general properties of an object. It is not possible to map chemical structure directly to attribute-based descriptions, as such descriptions have no internal organization. A more natural and general way to describe chemical structure is to use a relational description, where the internal construction of the description maps that of the object described. Our atom and bond connectivities representation is a relational description. ILP algorithms can form SARs with relational descriptions. We have tested the relational approach by investigating the SARs of 230 aromatic and heteroaromatic nitro compounds. These compounds had been split previously into two subsets, 188 compounds that were amenable to regression and 42 that were not. For the 188 compounds, a SAR was found that was as accurate as the best statistical or neural network-generated SARs. The PROGOL SAR has the advantages that it did not need the use of any indicator variables handcrafted by an expert, and the generated rules were easily comprehensible. For the 42 compounds, PROGOL formed a SAR that was significantly (P < 0.025) more accurate than linear regression, quadratic regression, and back-propagation. This SAR is based on an automatically generated structural alert for mutagenicity.

Intermolecular and Intramolecular Charge Transfer in Functional Molecular Materials

This thesis is devoted to the investigation of inter and intramolecular charge transfer (CT) in molecular functional materials and specifically organic dyes and CT crystals. An integrated approach encompassing quantum-chemical calculations, semiempirical tools, theoretical models and spectroscopic measurements is applied to understand structure-property relationships governing the low-energy physics of these materials. Four main topics were addressed: 1) Spectral properties of organic dyes. Charge-transfer dyes are constituted by electron donor (D) and electron acceptor (A) units linked through bridge(s) to form molecules with different symmetry and dimensionality. Their low-energy physics is governed by the charge resonance between D and A groups and is effectively described by a family of parametric Hamiltonians known as essential-state models. These models account for few electronic states, corresponding to the main resonance structures of the relevant dye, leading to a simple picture that is completed introducing the coupling of the electronic system to molecular vibrations, treated in a non-adiabatic way, and an effective classical coordinate, describing polar solvation. In this work a specific essential-state model was proposed and parametrized for the dye Brilliant Green. The central issue in this work has been the definition of the diabatic states, a not trivial task for a multi-branched chromophore. In a second effort, we have used essential-state models for the description of the early-stage dynamics of excited states after ultrafast excitation. Crucial to this work is the fully non-adiabatic treatment of the coupled electronic and vibrational motion, allowing for a reliable description of the dynamics of systems showing a multistable, broken-symmetry excited state. 2) Mixed-stack CT salts. Mixed-stack (MS) CT crystals are an interesting class of multifunctional molecular materials, where D and A molecules arrange themselves to form stacks, leading to delocalized electrons in one dimension. The interplay between the intermolecular CT, electrostatic interactions, lattice phonons and molecular vibrations leads to intriguing physical properties that include (photoinduced) phase transitions, multistability, antiferromagnetism, ferroelectricity and potential multiferroicity. The standard microscopic model to describe this family of materials is the Modified Hubbard model accounting for electron-phonon coupling (Peierls coupling), electron-molecular vibrations coupling (Holstein coupling) and electrostatic interactions. We adopt and validate a method, based on DFT calculations on dimeric DA structures, to extract relevant model parameters. The approach offers a powerful tool to shed light on the complex physics of MS-CT salts. 3) Charge transfer in organic radical dipolar dyes. In collaboration with the group of Prof. Jaume Veciana (ICMAB- Barcellona), we have studied spectral properties of a special class of CT dyes with D-bridge-A structure where the acceptor group is a stable radical (of the perchlorotriphenylmethyl, PTM, family), leading to an open-shell CT dyes. These materials are of interest since they associate the electronic and optical properties of CT dyes with magnetic properties from the unpaired electron. The first effort was devoted to the parametrization of the relevant essential-state model. Two strategies were adopted, one based on the calculation of the low-energy spectral properties, the other based on the variation of ground state properties with an applied electric field. 4) The spectral properties of organic nanoparticles based on radical species are investigated in collaboration with Dr. I. Ratera (ICMAB- Barcellona). Intriguing spectroscopic behavior was observed pointing to the presence of excimer states. In an attempt to rationalize these findings, extensive calculations (TD-DFT and ZINDO) were performed. The results for the isolated dyes are validated against experimental spectra in solution. To address intermolecular interactions we studied dimeric structures in the gas phase, but the preliminary results obtained do not support excimer formation.

Fermi-edge singularities in linear and nonlinear ultrafast spectroscopy

We discuss Fermi-edge singularity effects on the linear and nonlinear transient response of an electron gas in a doped semiconductor. We use a bosonization scheme to describe the low-energy excitations, which allows us to compute the time and temperature dependence of the response functions. Coherent control of the energy absorption at resonance is analyzed in the linear regime. It is shown that a phase shift appears in the coherent control oscillations, which is not present in the excitonic case. The nonlinear response is calculated analytically and used to predict that four wave-mixing experiments would present a Fermi-edge singularity when the exciting energy is varied. A new dephasing mechanism is predicted in doped samples that depends linearly on temperature and is produced by the low-energy bosonic excitations in the conduction band.

A Finite Element Numerical Algorithm for Modelling and Data Fitting in Complex Systems

Numerical modelling methodologies are important by their application to engineering and scientific problems, because there are processes where analytical mathematical expressions cannot be obtained to model them. When the only available information is a set of experimental values for the variables that determine the state of the system, the modelling problem is equivalent to determining the hyper-surface that best fits the data. This paper presents a methodology based on the Galerkin formulation of the finite elements method to obtain representations of relationships that are defined a priori, between a set of variables: y = z(x1, x2,...., xd). These representations are generated from the values of the variables in the experimental data. The approximation, piecewise, is an element of a Sobolev space and has derivatives defined in a general sense into this space. The using of this approach results in the need of inverting a linear system with a structure that allows a fast solver algorithm. The algorithm can be used in a variety of fields, being a multidisciplinary tool. The validity of the methodology is studied considering two real applications: a problem in hydrodynamics and a problem of engineering related to fluids, heat and transport in an energy generation plant. Also a test of the predictive capacity of the methodology is performed using a cross-validation method.

The energy and environmental consequences of increased vehicle size and weight - volume I - final report.

Transportation Department, Research and Special Programs Administration, Washington, D.C.

Soil and plant relationships of fission products /

"Prepared for Presentation at the Hearings on Fallout Before the Joint Committee on Atomic Energy, May 5-8, 1959."

Free-piston Stirling engine/linear alternator 1000-hour endurance test /

Mode of access: Internet.

A pulsed bending magnet for the beam switchyard area of the Stanford two-mile linear electron accelerator /

"AEC Contract AT(04-3)-400."

A linear scanner for human radioisotope research /

"Contract No. AT(40-1)-Gen-33."

The linear scanner in clinical studies /

"August 1960."

Food-chain relationships of iodine-131 in Nevada following the Sedan Test of July 1962 /

Prepared for the U.S Atomic Energy Commission.

Food-chain relationships of radiostrontium in the Sedan fallout field /

"Nuclear explosions - Peaceful Applications (TID-4500, 42nd ed.)."

Effect of nuclear radiation on organic materials, specifically magnet insulations in high-energy accelerators /

"March 1965."

Relationships of Efficiency to Reproductive Disorders in Danish Milk Production: A Stochastic Frontier Analysis

Relationships of various reproductive disorders and milk production performance of Danish dairy farms were investigated. A stochastic frontier production function was estimated using data collected in 1998 from 514 Danish dairy farms. Measures of farm-level milk production efficiency relative to this production frontier were obtained, and relationships between milk production efficiency and the incidence risk of reproductive disorders were examined. There were moderate positive relationships between milk production efficiency and retained placenta, induction of estrus, uterine infections, ovarian cysts, and induction of birth. Inclusion of reproductive management variables showed that these moderate relationships disappeared, but directions of coefficients for almost all those variables remained the same. Dystocia showed a weak negative correlation with milk production efficiency. Farms that were mainly managed by young farmers had the highest average efficiency scores. The estimated milk losses due to inefficiency averaged 1142, 488, and 256 kg of energy-corrected milk per cow, respectively, for low-, medium-, and high-efficiency herds. It is concluded that the availability of younger cows, which enabled farmers to replace cows with reproductive disorders, contributed to high cow productivity in efficient farms. Thus, a high replacement rate more than compensates for the possible negative effect of reproductive disorders. The use of frontier production and efficiency/ inefficiency functions to analyze herd data may enable dairy advisors to identify inefficient herds and to simulate the effect of alternative management procedures on the individual herd's efficiency.

Personality disorders in the community: Results from the Australian National Survey of Mental Health and Well-Being Part III - Relationships between specific type of personality disorder, Axis 1 mental disorders and physical conditions with disability and health consultations

Background The aims of this study were threefold. First, to ascertain whether personality disorder (PD) was a significant predictor of disability (as measured in a variety of ways) over and above that contributed by Axis I mental disorders and physical conditions. Second, whether the number of PD diagnoses given to an individual resulted in increasing severity of disability, and third, whether PD was a significant predictor of health and mental health consultations with GPs, psychiatrists, and psychologists, respectively, over the last 12 months. Method Data were obtained from the National Survey of Mental Health and Wellbeing, conducted between May and August 1997. A stratified random sample of households was generated, from which all those aged 18 and over were considered potential interviewees. There were 10 641 respondents to the survey, and this represented a response rate of 78%. Each interviewee was asked questions indexing specific ICD-10 PD criteria. Results Five measures of disability were examined. It was found that PD was a significant predictor of disability once Axis I and physical conditions were taken into account for four of the five disability measures. For three of the dichotomously-scored disability measures, odds ratios ranged from 1.88 to 6.32 for PD, whilst for the dimensionally-scored Mental Summary Subscale of the SF-12, a beta weight of -0.17 was recorded for PD. As regards number of PDs having a quasi-linear relationship to disability, there was some indication of this on the SF-12 Mental Summary Subscale and the two role functioning measures, and less so on the other two measures. As regards mental consultations, PD was a predictor of visits to GPs, psychiatrists and psychologists, over and above Axis I disorders and physical conditions. Conclusion The study reports findings from a nationwide survey conducted within Australia and as such the data are less influenced by the selection and setting bias inherent in other germane studies. However, it does support previous findings that PD is a significant predictor of disability and mental health consultations independent of Axis I disorders and physical conditions.