Select-divide-and-conquer method for large-scale configuration interaction

A select-divide-and-conquer variational method to approximate configuration interaction (CI) is presented. Given an orthonormal set made up of occupied orbitals (Hartree-Fock or similar) and suitable correlation orbitals (natural or localized orbitals), a large N-electron target space S is split into subspaces S0,S1,S2,...,SR. S0, of dimension d0, contains all configurations K with attributes (energy contributions, etc.) above thresholds T0={T0egy, T0etc.}; the CI coefficients in S0 remain always free to vary. S1 accommodates KS with attributes above T1≤T0. An eigenproblem of dimension d0+d1 for S0+S 1 is solved first, after which the last d1 rows and columns are contracted into a single row and column, thus freezing the last d1 CI coefficients hereinafter. The process is repeated with successive Sj(j≥2) chosen so that corresponding CI matrices fit random access memory (RAM). Davidson's eigensolver is used R times. The final energy eigenvalue (lowest or excited one) is always above the corresponding exact eigenvalue in S. Threshold values {Tj;j=0, 1, 2,...,R} regulate accuracy; for large-dimensional S, high accuracy requires S 0+S1 to be solved outside RAM. From there on, however, usually a few Davidson iterations in RAM are needed for each step, so that Hamiltonian matrix-element evaluation becomes rate determining. One μhartree accuracy is achieved for an eigenproblem of order 24 × 106, involving 1.2 × 1012 nonzero matrix elements, and 8.4×109 Slater determinants

Simple finite field nuclear relaxation method for calculating vibrational contribution to degenerate four-wave mixing

A simple extended finite field nuclear relaxation procedure for calculating vibrational contributions to degenerate four-wave mixing (also known as the intensity-dependent refractive index) is presented. As a by-product one also obtains the static vibrationally averaged linear polarizability, as well as the first and second hyperpolarizability. The methodology is validated by illustrative calculations on the water molecule. Further possible extensions are suggested

Simple finite field method for calculation of static and dynamic vibrational hyperpolarizabilities: curvature contributions

In the static field limit, the vibrational hyperpolarizability consists of two contributions due to: (1) the shift in the equilibrium geometry (known as nuclear relaxation), and (2) the change in the shape of the potential energy surface (known as curvature). Simple finite field methods have previously been developed for evaluating these static field contributions and also for determining the effect of nuclear relaxation on dynamic vibrational hyperpolarizabilities in the infinite frequency approximation. In this paper the finite field approach is extended to include, within the infinite frequency approximation, the effect of curvature on the major dynamic nonlinear optical processes

A new efficient approach to the direct restricted active space self-consistent field method

An implicitly parallel method for integral-block driven restricted active space self-consistent field (RASSCF) algorithms is presented. The approach is based on a model space representation of the RAS active orbitals with an efficient expansion of the model subspaces. The applicability of the method is demonstrated with a RASSCF investigation of the first two excited states of indole

Using a Bayesian method to assign individuals to karyotypic taxa in shrew hybrid zones.

Individuals sampled in hybrid zones are usually analysed according to their sampling locality, morphology, behaviour or karyotype. But the increasing availability of genetic information more and more favours its use for individual sorting purposes and numerous assignment methods based on the genetic composition of individuals have been developed. The shrews of the Sorex araneus group offer good opportunities to test the genetic assignment on individuals identified by their karyotype. Here we explored the potential and efficiency of a Bayesian assignment method combined or not with a reference dataset to study admixture and individual assignment in the difficult context of two hybrid zones between karyotypic species of the Sorex araneus group. As a whole, we assigned more than 80% of the individuals to their respective karyotypic categories (i.e. 'pure' species or hybrids). This assignment level is comparable to what was obtained for the same species away from hybrid zones. Additionally, we showed that the assignment result for several individuals was strongly affected by the inclusion or not of a reference dataset. This highlights the importance of such comparisons when analysing hybrid zones. Finally, differences between the admixture levels detected in both hybrid zones support the hypothesis of an impact of chromosomal rearrangements on gene flow.

Seismic attenuation and velocity dispersion in heterogeneous partially saturated porous rocks

Using a numerical approach, we explore wave-induced fluid flow effects in partially saturated porous rocks in which the gas-water saturation patterns are governed by mesoscopic heterogeneities associated with the dry frame properties. The link between the dry frame properties and the gas saturation is defined by the assumption of capillary pressure equilibrium, which in the presence of heterogeneity implies that neighbouring regions can exhibit different levels of saturation. To determine the equivalent attenuation and phase velocity of the synthetic rock samples considered in this study, we apply a numerical upscaling procedure, which permits to take into account mesoscopic heterogeneities associated with the dry frame properties as well as spatially continuous variations of the pore fluid properties. The multiscale nature of the fluid saturation is taken into account by locally computing the physical properties of an effective fluid, which are then used for the larger-scale simulations. We consider two sets of numerical experiments to analyse such effects in heterogeneous partially saturated porous media, where the saturation field is determined by variations in porosity and clay content, respectively. In both cases we also evaluate the seismic responses of corresponding binary, patchy-type saturation patterns. Our results indicate that significant attenuation and modest velocity dispersion effects take place in this kind of media for both binary patchy-type and spatially continuous gas saturation patterns and in particular in the presence of relatively small amounts of gas. The numerical experiments also show that the nature of the gas distribution patterns is a critical parameter controlling the seismic responses of these environments, since attenuation and velocity dispersion effects are much more significant and occur over a broader saturation range for binary patchy-type gas-water distributions. This analysis therefore suggests that the physical mechanisms governing partial saturation should be accounted for when analysing seismic data in a poroelastic framework. In this context, heterogeneities associated with the dry frame properties, which do not play important roles in wave-induced fluid flow processes per se, should be taken into account since they may determine the kind of gas distribution pattern taking place in the porous rock.

BRAF mutation in 'sarcomas': a possible method to detect de-differentiated melanomas

AIMS: BRAF is mutated in 50-60% of melanomas, but BRAF mutation in sarcomas has not been systematically evaluated. Some melanomas are spindled and may show no immunohistochemical evidence of melanocytic differentiation. Similarly, many sarcomas are undifferentiated, i.e. undifferentiated pleomorphic sarcomas (UPS). Diagnosing melanoma versus sarcoma in an undifferentiated spindle cell malignancy can be challenging. Our aim was to evaluate the prevalence of BRAF mutation in sarcomas and the use of BRAF mutational status in the diagnosis of spindle cell malignancies. METHODS AND RESULTS: BRAF mutational analysis was performed on tissue from 104 patients: 90 with sarcoma only (50 UPS) and 14 with sarcoma and melanoma (seven UPS). In the sarcoma-only group, BRAF mutation was absent. In the sarcoma-melanoma group, three sarcomas showed BRAF mutation; all were UPS, occurred after the melanomas and did not stain for melanocytic markers. One melanoma-sarcoma pair showed identical BRAF V600E mutations. CONCLUSIONS: The presence of BRAF mutation in these tumours raises the possibility that poorly differentiated spindle cell malignancies with BRAF mutation may represent melanomas, and BRAF mutational analysis should be considered in a patient with a spindle cell malignancy and a history of melanoma, as a positive result may indicate de-differentiated melanoma.

"INTERMED": a method to assess health service needs. I. Development and reliability.

The purpose of this paper is to describe the development and to test the reliability of a new method called INTERMED, for health service needs assessment. The INTERMED integrates the biopsychosocial aspects of disease and the relationship between patient and health care system in a comprehensive scheme and reflects an operationalized conceptual approach to case mix or case complexity. The method is developed to enhance interdisciplinary communication between (para-) medical specialists and to provide a method to describe case complexity for clinical, scientific, and educational purposes. First, a feasibility study (N = 21 patients) was conducted which included double scoring and discussion of the results. This led to a version of the instrument on which two interrater reliability studies were performed. In study 1, the INTERMED was double scored for 14 patients admitted to an internal ward by a psychiatrist and an internist on the basis of a joint interview conducted by both. In study 2, on the basis of medical charts, two clinicians separately double scored the INTERMED in 16 patients referred to the outpatient psychiatric consultation service. Averaged over both studies, in 94.2% of all ratings there was no important difference between the raters (more than 1 point difference). As a research interview, it takes about 20 minutes; as part of the whole process of history taking it takes about 15 minutes. In both studies, improvements were suggested by the results. Analyses of study 1 revealed that on most items there was considerable agreement; some items were improved. Also, the reference point for the prognoses was changed so that it reflected both short- and long-term prognoses. Analyses of study 2 showed that in this setting, less agreement between the raters was obtained due to the fact that the raters were less experienced and the scoring procedure was more susceptible to differences. Some improvements--mainly of the anchor points--were specified which may further enhance interrater reliability. The INTERMED proves to be a reliable method for classifying patients' care needs, especially when used by experienced raters scoring by patient interview. It can be a useful tool in assessing patients' care needs, as well as the level of needed adjustment between general and mental health service delivery. The INTERMED is easily applicable in the clinical setting at low time-costs.

The Fry method applied to an augen orthogneiss: Problems and results

The application of the Fry method to measure strain in deformed porphyritic granites is discussed. This method requires that the distribution of markers has to satisfy at least two conditions. It has to be homogeneous and isotropic. Statistics on point distribution with the help of a Morishita diagram can easily test homogeneity. Isotropy can be checked with a cumulative histogram of angles between points. Application of these tests to undeformed (Mte Capanne granite, Elba) and to deformed (Randa orthogneiss, Alps of Switzerland) porphyritic granite reveals that their K-feldspars phenocrysts both satisfy these conditions and can be used as strain markers with the Fry method. Other problems are also examined. One is the possible distribution of deformation on discrete shear-bands. Providing several tests are met, we conclude that the Fry method can be used to estimate strain in deformed porphyritic granites. (c) 2006 Elsevier Ltd. All rights reserved.

Estimation of inelastic seismic material properties of a surgical sea-bed from multi-component marine seismic data

To date, state-of-the-art seismic material parameter estimates from multi-component sea-bed seismic data are based on the assumption that the sea-bed consists of a fully elastic half-space. In reality, however, the shallow sea-bed generally consists of soft, unconsolidated sediments that are characterized by strong to very strong seismic attenuation. To explore the potential implications, we apply a state-of-the-art elastic decomposition algorithm to synthetic data for a range of canonical sea-bed models consisting of a viscoelastic half-space of varying attenuation. We find that in the presence of strong seismic attenuation, as quantified by Q-values of 10 or less, significant errors arise in the conventional elastic estimation of seismic properties. Tests on synthetic data indicate that these errors can be largely avoided by accounting for the inherent attenuation of the seafloor when estimating the seismic parameters. This can be achieved by replacing the real-valued expressions for the elastic moduli in the governing equations in the parameter estimation by their complex-valued viscoelastic equivalents. The practical application of our parameter procedure yields realistic estimates of the elastic seismic material properties of the shallow sea-bed, while the corresponding Q-estimates seem to be biased towards too low values, particularly for S-waves. Given that the estimation of inelastic material parameters is notoriously difficult, particularly in the immediate vicinity of the sea-bed, this is expected to be of interest and importance for civil and ocean engineering purposes.

Development of a Method to Determine Pavement Damage Due to Detours, Project 02-105, Apirl 2005

The research presented in this report provides the basis for the development of a new procedure to be used by the Iowa DOT and cities and counties in the state to deal with detours. Even though the project initially focused on investigating new tools to determine condition and compensation, the focus was shifted to traffic and the gas tax method to set the basis for the new procedure. It was concluded that the condition-based approach, even though accurate and consistent condition evaluations can be achieved, is not feasible or cost effective because of the current practices of data collection (two-year cycle) and also the logistics of the procedure (before and after determination). The gas tax method provides for a simple, easy to implement, and consistent approach to dealing with compensation for use of detours. It removes the subjectivity out of the current procedures and provides for a more realistic (traffic based) approach to the compensation determination.

A simplified method of stabilization and hemostasis for minimally invasive coronary artery bypass.

We describe a simple method to achieve both hemostasis and stabilization of the left anterior descending coronary artery during minimally invasive coronary artery bypass grafting. This technique allows the surgeon to perform a precise anastomosis of the left internal mammary artery to the target vessel on a beating heart.

Three-dimensional morphological analysis of intracranial aneurysms: a fully automated method for aneurysm sac isolation and quantification

Morphological descriptors are practical and essential biomarkers for diagnosis andtreatment selection for intracranial aneurysm management according to the current guidelinesin use. Nevertheless, relatively little work has been dedicated to improve the three-dimensionalquanti cation of aneurysmal morphology, automate the analysis, and hence reduce the inherentintra- and inter-observer variability of manual analysis. In this paper we propose a methodologyfor the automated isolation and morphological quanti cation of saccular intracranial aneurysmsbased on a 3D representation of the vascular anatomy.

A method for extracting semantic information from on-line art music discussion forums

In this paper a method for extracting semantic informationfrom online music discussion forums is proposed. The semantic relations are inferred from the co-occurrence of musical concepts in forum posts, using network analysis. The method starts by defining a dictionary of common music terms in an art music tradition. Then, it creates a complex network representation of the online forum by matchingsuch dictionary against the forum posts. Once the complex network is built we can study different network measures, including node relevance, node co-occurrence andterm relations via semantically connecting words. Moreover, we can detect communities of concepts inside the forum posts. The rationale is that some music terms are more related to each other than to other terms. All in all, this methodology allows us to obtain meaningful and relevantinformation from forum discussions.