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Selected AbstractsDetecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unknownGENETIC EPIDEMIOLOGY, Issue 4 2010Joanna L. Davies Abstract Standard techniques for single marker quantitative trait mapping perform poorly in detecting complex interacting genetic influences. When a genetic marker interacts with other genetic markers and/or environmental factors to influence a quantitative trait, a sample of individuals will show different effects according to their exposure to other interacting factors. This paper presents a Bayesian mixture model, which effectively models heterogeneous genetic effects apparent at a single marker. We compute approximate Bayes factors which provide an efficient strategy for screening genetic markers (genome-wide) for evidence of a heterogeneous effect on a quantitative trait. We present a simulation study which demonstrates that the approximation is good and provide a real data example which identifies a population-specific genetic effect on gene expression in the HapMap CEU and YRI populations. We advocate the use of the model as a strategy for identifying candidate interacting markers without any knowledge of the nature or order of the interaction. The source of heterogeneity can be modeled as an extension. Genet. Epidemiol. 34: 299,308, 2010. © 2009 Wiley-Liss, Inc. [source] Dynamical similarity of explosions at Stromboli volcanoGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 3 2004S. De Martino SUMMARY We analyse Strombolian explosions recorded with broadband seismometers to quantify the degree of similarity among explosions. First, we construct the trajectory space. This reconstruction is analogous to that of phase space but, unlike the phase space which relies on the analysis of a single trajectory of a dynamic system, the trajectory space takes into account many trajectories of the dynamic process to study the overlapping properties. Based on the scaling of distances between each pair of histories, it is possible to evaluate the dimension of the trajectory space. We consider the different explosions as different trajectories and, after normalizing all the records, we find that the scaling region is spread over less than one order of magnitude. This absence of scaling implies that all the trajectories cover the same attractor in the trajectory space, and that the trajectories are generated by the same dynamic system. Accordingly, we conclude that all the events are very similar to each other. This result is confirmed by the energy distribution of these events. Standard techniques of energy estimation are inadequate in this case, and we propose an evaluation method based on a quantity that is proportional to energy. The distribution function of this quantity, calculated on 580 events, displays a log-normal behaviour with very low variability (less than two orders of magnitude in energy). These results provide quantitative support for the observation that there is a great degree of similarity among Strombolian explosions and support the idea that a dynamic model underlying these events can be elaborated through the study of just one event. [source] Bayesian Semiparametric Multiple ShrinkageBIOMETRICS, Issue 2 2010Richard F. MacLehose Summary High-dimensional and highly correlated data leading to non- or weakly identified effects are commonplace. Maximum likelihood will typically fail in such situations and a variety of shrinkage methods have been proposed. Standard techniques, such as ridge regression or the lasso, shrink estimates toward zero, with some approaches allowing coefficients to be selected out of the model by achieving a value of zero. When substantive information is available, estimates can be shrunk to nonnull values; however, such information may not be available. We propose a Bayesian semiparametric approach that allows shrinkage to multiple locations. Coefficients are given a mixture of heavy-tailed double exponential priors, with location and scale parameters assigned Dirichlet process hyperpriors to allow groups of coefficients to be shrunk toward the same, possibly nonzero, mean. Our approach favors sparse, but flexible, structure by shrinking toward a small number of random locations. The methods are illustrated using a study of genetic polymorphisms and Parkinson's disease. [source] Ball-Pen Probe Measurements in L-Mode and H-Mode on ASDEX UpgradeCONTRIBUTIONS TO PLASMA PHYSICS, Issue 9 2010J. Adamek Abstract Experimental investigations of the plasma potential, poloidal electric field and electron temperature during L-mode and ELMy H-mode were performed on ASDEX Upgrade by means of a probe head containing four ball-pen probes and four Langmuir probes. This allows to measure simultaneously the floating and plasma potential at the same time which are related by the electron temperature. Thus a combination of ball-pen probes and Langmuir probes offers the possibility to determine the electron temperature directly with high temporal resolution. This novel temperature measurement method is compared to standard techniques. The influence of the electron temperature on the usual calculation of the poloidal electric field from the gradient of the floating potential is determined by a comparison to the poloidal electric field derived from the plasma potential (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Dense array EEG: Methodology and new hypothesis on epilepsy syndromesEPILEPSIA, Issue 2008Mark D. Holmes Summary Dense array EEG is a method of recording electroencephalography (EEG) with many more electrodes (up to 256) than is utilized with standard techniques that typically employ 19,21 scalp electrodes. The rationale for this approach is to enhance the spatial resolution of scalp EEG. In our research, dense array EEG is used in conjunction with a realistic model of head tissue conductivity and methods of electrographic source analysis to determine cerebral cortical localization of epileptiform discharges. In studies of patients with absence seizures, only localized cortical regions are involved during the attack. Typically, absences are accompanied by "wave,spike" complexes that show, both at the beginning and throughout the ictus, repetitive cycles of stereotyped, localized involvement of mainly mesial and orbital frontal cortex. Dense array EEG can also be used for long-term EEG video monitoring (LTM). We have used dense array EEG LTM to capture seizures in over 40 patients with medically refractory localization-related epilepsy, including both temporal and extra temporal cases, where standard LTM failed to reveal reliable ictal localization. One research goal is to test the validity of dense array LTM findings by comparison with invasive LTM and surgical outcome. Collection of a prospective series of surgical candidates who undergo both procedures is currently underway. Analysis of subjects with either generalized or localization-related seizures suggest that all seizures, including those traditionally classified as "generalized," propagate through discrete cortical networks. Furthermore, based on initial review of propagation patterns, we hypothesize that all epileptic seizures may be fundamentally corticothalamic or corticolimbic in nature. Dense array EEG may prove useful in noninvasive ictal localization, when standard methods fail. Future research will determine if the method will reduce the need for invasive EEG recordings, or assist in the appropriate placement of novel treatment devices. [source] Synthesis, Characterisation and Optical Properties of Silica Nanoparticles Coated with Anthracene Fluorophore and Thiourea Hydrogen-Bonding SubunitsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 36 2008Pilar Calero Abstract Bifunctionalised hybrid silica nanoparticles have been synthesised and characterised, and their optical emission properties in the presence of certain anions in acetonitrile solutions have been studied. The alkoxysilane derivatives N -butyl- N, -[3-(trimethoxysilyl)propyl]thiourea (1), N -phenyl- N, -[3-(trimethoxysilyl)propyl]thiourea (2) and 3-[(anthracen-10-yl)methylthio]propyltriethoxysilane (3) were prepared and used to functionalise uncoated LUDOX silica nanoparticles with a mean diameter of 18,±,2 nm. The functionalisation of the nanoparticle surfaces was carried out by two different approaches. The first approach relies on the consecutive grafting of the two subunits. In this protocol, the nanoparticles were first functionalised with anthracene derivative 3 (solid NA), and then treated with the corresponding binding sites 1 or 2 to result in the NA-Pt3 and NA-Bt3 solids. The second approach deals with the simultaneous grafting of 1 or 2 and the signalling subunit 3 in different ratios. This method was used for the preparation of the NA1Pt1, NA1Bt1, NA1Pt3 and NA1Bt3 nanoparticles. The bifunctionalised silica nanoparticles were characterised by using standard techniques. Acetonitrile suspensions of NA nanoparticles (5 mg in 20 mL) showed anthracene bands centred at ca. 350, 370 and 390 nm. Upon excitation at 365 nm, a typical emission band with fine structure in the 390,450 nm range was observed. Similar absorption and emission spectra were found for the bifunctionalised nanoparticles. The work is completed with a prospective study of the fluorescence of the prepared nanoparticles in the presence of organic (acetate, benzoate) and inorganic (F,, Cl,, Br,, CN,, HSO4, and H2PO4,) anions. The apparent binding constants (adsorption constants) for the interaction of NA-Pt3 with anions in acetonitrile were determined by performing a Langmuir-type analysis of fluorescence titration data.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Pentadentate Ligands for the 1:1 Coordination of Lanthanide(III) Salts,EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 20 2007Markus Albrecht Abstract Three hydrazone type ligands, namely 2 -H, 3, and 4, which were designed to form 1:1 complexes with lanthanoid(III) ions, are presented. Although the tetradentate ligand 2, leads to an interesting complex [(2)(2 -H)YCl2] with yttrium(III), a more general principle for the coordination of the metal ions by hydrazone-type ligands can be found with ligand 3, where 1:1 complexes are obtained with an effective coordination of the metal salts by the ligand. The stabledimer [{(3)Nd(CF3SO3)}2(,-CF3SO3)3]CF3SO3 was characterized by X-ray structure determination. Depending on the size of the metal ion, additional co-ligands can also be bound to the metal centers. This is observed in the molecular structures of [(3)Pr(NO3)2(MeOH)2](NO3), [(3)NdCl2(MeOH)(EtOH)]Cl, [(3)ErCl2(MeOH)]Cl, and [(3)LuCl2]Cl. The solid-state molecular structures of 4 and 4·HCl show the helicating ability of this ligand upon metal coordination. The corresponding lanthanide complexes of 4 are characterized by standard techniques such as NMR and CD spectroscopy and mass spectrometry.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Levels of pre-kallikrein in resting and stimulated human parotid and submandibular salivaEUROPEAN JOURNAL OF ORAL SCIENCES, Issue 5 2001Carol A. Francis Salivary tissue kallikrein is stored in an active form in human salivary glands. Pre-kallikrein has been demonstrated in mixed saliva, but it is not clear if the various salivary glands contribute equally. This study set out to determine if pre-kallikrein is present in human parotid and submandibular salivas at rest, whether levels change during stimulation, and to compare the pattern of pre-kallikrein and kallikrein secretion with that of total protein. Resting and citric acid-stimulated parotid and submandibular, and gum-stimulated parotid saliva samples were collected from 6 healthy subjects. Salivary flows were determined gravimetrically. Total protein concentration and kallikrein enzymic activity were assayed using standard techniques. Pre-kallikrein was assayed following trypsinisation of duplicate samples. Pre-kallikrein was present in parotid and submandibular ductal saliva. Proportions of pre-kallikrein and active kallikrein were similar in salivas secreted at rest and during stimulation, and both outputs mirrored protein output in both major glands. Gum-stimulated parotid saliva showed lower activity than resting, and no differences were seen between resting and stimulated submandibular samples. [source] The design of an optimal filter for monthly GRACE gravity modelsGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 2 2008R. Klees SUMMARY Most applications of the publicly released Gravity Recovery and Climate Experiment monthly gravity field models require the application of a spatial filter to help suppressing noise and other systematic errors present in the data. The most common approach makes use of a simple Gaussian averaging process, which is often combined with a ,destriping' technique in which coefficient correlations within a given degree are removed. As brute force methods, neither of these techniques takes into consideration the statistical information from the gravity solution itself and, while they perform well overall, they can often end up removing more signal than necessary. Other optimal filters have been proposed in the literature; however, none have attempted to make full use of all information available from the monthly solutions. By examining the underlying principles of filter design, a filter has been developed that incorporates the noise and full signal variance,covariance matrix to tailor the filter to the error characteristics of a particular monthly solution. The filter is both anisotropic and non-symmetric, meaning it can accommodate noise of an arbitrary shape, such as the characteristic stripes. The filter minimizes the mean-square error and, in this sense, can be considered as the most optimal filter possible. Through both simulated and real data scenarios, this improved filter will be shown to preserve the highest amount of gravity signal when compared to other standard techniques, while simultaneously minimizing leakage effects and producing smooth solutions in areas of low signal. [source] Artificial neural network inversion of magnetotelluric data in terms of three-dimensional earth macroparametersGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 1 2000Vjacheslav Spichak The possibility of solving the three-dimensional (3-D) inverse problem of geoelectrics using the artificial neural network (ANN) approach is investigated. The properties of a supervised ANN based on the back-propagation scheme with three layers of neurons are studied, and the ANN architecture is adjusted. A model class consisting of a dipping dyke in the basement of a two-layer earth with the dyke in contact with the overburden is used for numerical experiments. Six macroparameters of the 3-D model, namely the thickness of the top layer, which coincides with the depth of the dyke (D), the conductivity ratio between the first and second layers (C1,/C2,), the conductivity contrast of the dyke (C/C2,), and the width (W ), length (L ) and dip angle of the dyke (A), are used. Various groups of magnetotelluric field components and their transformations are studied in order to estimate the effect of the data type used on the ANN recognition ability. It is found that use of only the xy - and yx -components of impedance phases results in reasonable recognition errors for all unknown parameters (D: 0.02 per cent, C1/C2: 8.4 per cent, C/C2: 26.8 per cent, W : 0.02 per cent, L : 0.02 per cent, A: 0.24 per cent). The influence of the size and shape of the training data pool (including the ,gaps in education' and ,no target' effects) on the recognition properties is studied. Results from numerous ANN tests demonstrate that the ANN possesses good enough interpolation and extrapolation abilities if the training data pool contains a sufficient number of representative data sets. The effect of noise is estimated by means of mixing the synthetic data with 30, 50 and 100 per cent Gaussian noise. The unusual behaviour of the recognition errors for some of the model parameters when the data become more noisy (in particular, the fact that an increase in error is followed by a decrease) indicates that the use of standard techniques of noise reduction may give an opposite result, so the development of a special noise treatment methodology is required. Thus, it is shown that ANN-based recognition can be successfully used for inversion if the data correspond to the model class familiar to the ANN. No initial guess regarding the parameters of the 3-D target or 1-D layering is required. The ability of the ANN to teach itself using real geophysical (not only electromagnetic) data measured at a given location over a sufficiently long period means that there is the potential to use this approach for interpreting monitoring data. [source] Towards an integrated computational tool for spatial analysis in macroecology and biogeographyGLOBAL ECOLOGY, Issue 4 2006Thiago Fernando L. V. B. Rangel ABSTRACT Because most macroecological and biodiversity data are spatially autocorrelated, special tools for describing spatial structures and dealing with hypothesis testing are usually required. Unfortunately, most of these methods have not been available in a single statistical package. Consequently, using these tools is still a challenge for most ecologists and biogeographers. In this paper, we present sam (Spatial Analysis in Macroecology), a new, easy-to-use, freeware package for spatial analysis in macroecology and biogeography. Through an intuitive, fully graphical interface, this package allows the user to describe spatial patterns in variables and provides an explicit spatial framework for standard techniques of regression and correlation. Moran's I autocorrelation coefficient can be calculated based on a range of matrices describing spatial relationships, for original variables as well as for residuals of regression models, which can also include filtering components (obtained by standard trend surface analysis or by principal coordinates of neighbour matrices). sam also offers tools for correcting the number of degrees of freedom when calculating the significance of correlation coefficients. Explicit spatial modelling using several forms of autoregression and generalized least-squares models are also available. We believe this new tool will provide researchers with the basic statistical tools to resolve autocorrelation problems and, simultaneously, to explore spatial components in macroecological and biogeographical data. Although the program was designed primarily for the applications in macroecology and biogeography, most of sam's statistical tools will be useful for all kinds of surface pattern spatial analysis. The program is freely available at http://www.ecoevol.ufg.br/sam (permanent URL at http://purl.oclc.org/sam/). [source] Sliding,window neural state estimation in a power plant heater lineINTERNATIONAL JOURNAL OF ADAPTIVE CONTROL AND SIGNAL PROCESSING, Issue 8 2001A. Alessandri Abstract The state estimation problem for a section of a real power plant is addressed by means of a recently proposed sliding-window neural state estimator. The complexity and the nonlinearity of the considered application prevent us from successfully using standard techniques as Kalman filtering. The statistics of the distribution of the initial state and of noises are assumed to be unknown and the estimator is designed by minimizing a given generalized least-squares cost function. The following approximations are enforced: (i) the state estimator is a finite-memory one, (ii) the estimation functions are given fixed structures in which a certain number of parameters have to be optimized (multilayer feedforward neural networks are chosen from among various possible nonlinear approximators), (iii) the algorithms for optimizing the parameters (i.e., the network weights) rely on a stochastic approximation. Extensive simulation results on a complex model of a part of a real power plant are reported to compare the behaviour of the proposed estimator with the extended Kalman filter. Copyright © 2001 John Wiley & Sons, Ltd. [source] A clonal cutaneous CD30+ lymphoproliferative eruption in a patient with evidence of past exposure to hepatitis EINTERNATIONAL JOURNAL OF DERMATOLOGY, Issue 7 2000Freddye M. Lemons-Estes CDR, MC USN The patient was a 52-year-old white man who had worked in remote areas of the world during the past 2 years, including an extended period in rural areas of Central Africa and in Central and South America. He had no acute illnesses during the 2-year period except for rare, mild, upper respiratory tract infections. For approximately 1 year, however, he had developed recurrent, papular-vesicular, slightly painful lesions on the fingers and palms, that spontaneously healed over weeks to months ( Fig. 1). The patient had no other concurrent illnesses and no abnormal laboratory findings, except for positive enzyme-linked immunoabsorbent assay (ELISA) for immunoglobulin G (IgG) antibodies for hepatitis E virus (HEV) using a recombinant expressed HEV antigen (Genelabs Technologies, Inc., San Antonio). Prolonged treatment with minocycline did not appear to moderate the lesions. At approximately 2.5 years after the development of his first cutaneous lesion, however, the patient reported that he had had no new lesions for over 3 months. Figure 1. Vesicular ,lesion on the finger which regressed over a period of weeks A biopsy specimen showed an intraepidermal vesicle with prominent epidermal necrosis and reticular degeneration ( Fig. 2). Within the epidermis, there was a dense infiltrate of lymphoid cells. The majority of these cells were pleomorphic with prominent nucleoli and frequent mitotic figures ( Fig. 3). Sheets of atypical cells were found in the subjacent dermis. The infiltrate extended down into the reticular dermis. With extension into the dermis, the infiltrate became more polymorphous with more small lymphoid cells, large numbers of eosinophils, and some plasma cells located more deeply. Figure 2. Intraepidermal ,blister showing reticular degeneration and marked epidermotrophism of large atypical cells with extension into the dermis with a mixed infiltrate containing eosinophils and plasma cells (30×) Figure 3. Intraepidermal ,infiltrate of large atypical cells with extension into the dermis with a mixed infiltrate containing eosinophils and plasma cells (400×) Immunohistochemical stains for CD3 (DAKO), CD4 (Becton Dickinson), CD8 (Becton Dickinson), CD15 (LeuM1, Becton Dickinson), CD20 (L-26, DAKO), CD30 (Ber-H2, DAKO), CD45RO (UCHL1, DAKO), S-100 protein (DAKO), T-cell intracellular antigen (TIA) (Coulter), epithelial membrane antigen (EMA) (DAKO), KP-1 (CD68, DAKO), MAC-387 (DAKO), Epstein,Barr virus (EBV) latent membrane antigen-1 (LMP-1, DAKO), and EBV-encoded nuclear antigen 2 (EBNA2, DAKO) were performed on formalin-fixed tissue using the ABC method with DABA as the chromagen. CD3 showed diffuse membrane staining of the large atypical lymphoid cells, as well as the majority of the small lymphoid cells ( Fig. 4). CD4 showed positive membrane staining of the large atypical lymphoid cells and the majority of the small lymphoid cells. CD8 showed only scattered light membrane staining of small lymphoid cells. CD15 was negative, and CD20 showed foci of groups of small lymphoid cells mainly within the reticular dermis. CD30 showed positive membrane and paranuclear staining of the large atypical cells, most abundant within the epidermis and papillary dermis ( Fig. 5). CD45RO showed positive membrane staining of the large atypical cells and the majority of the small lymphoid cells. S-100 protein showed increased dendritic cells within the surrounding viable epidermis and the subjacent papillary dermis ( Fig. 6). TIA showed granular staining in the large atypical lymphoid cells and only rare staining in small lymphoid cells ( Fig. 7). EMA staining was essentially negative. KP-1 showed only scattered positive cells mainly in the lower papillary and the reticular dermis. MAC-387 showed membrane staining in the viable epidermis ( Fig. 8). LMP-1 and EBNA2 for EBV were negative within the lymphoid cells as well as within the overlying epidermis. Figure 4. Immunohistochemical ,staining for CD3 showing diffuse staining of lymphoid cells within the epidermis and dermis (150×) Figure 5. Immunohistochemical ,staining for CD30 showing membrane and paranuclear staining of large atypical lymphoid cells within the epidermis and papillary dermis (a, 150× b, 400×) Figure 6. Immunohistochemical ,staining for S-100 protein within the epidermis and in the papillary dermis (a, 150× b, 300×) Figure 7. Immunohistochemical ,granular staining of large atypical lymphoid cells for TIA (200×) Figure 8. Immunohistochemical ,staining for MAC-387 showing epidermal staining (100×) Gene rearrangement studies showed a ,-T-cell receptor gene rearrangement. The monoclonal band was detected with VJ1, VJ2, and D1J2 primer sets. The T-cell receptor , rearrangement assay has a sensitivity of 61% and a specificity of 94% for the detection of a monoclonal rearrangement in T-cell lymphomas for which amplifiable DNA can be recovered. Electron microscopy was performed on formalin-fixed material, positive-fixed with 2.5% phosphate-buffered glutaraldehyde and further with 1% osmium tetroxide by standard techniques. Intracellular, 50,60-nm, cytoplasmic, spherical, viral-like particles were identified ( Fig. 9). Figure 9. Electron ,microscopy showing 50,60-nm diameter, intracellular, viral-like particles (arrows) (70,000×) [source] Provenance of Coals Recovered from the Wreck of HMAV BountyINTERNATIONAL JOURNAL OF NAUTICAL ARCHAEOLOGY, Issue 1 2008Nigel Erskine Coal samples from HMAV Bounty were analysed using standard techniques to shed light on their provenance. Petrographic analysis indicated they were Carboniferous, with high vitrinite and liptinite content and a mean random reflectance of vitrinite of 0.99%. Palynological analysis indicated the samples were derived from the Middle Coal Measures, Westphalian B. Combining coal rank (vitrinite reflectance), age, knowledge of seam distributions and coalfield history indicates the most like source to be the Durham Coalfield, possibly the Hutton or Low Main Seams. These coals were mined along the valley of the Weir in the latter part of the 18th century. © 2007 The Authors [source] Prolactin and macroprolactin in patients with systemic lupus erythematosusINTERNATIONAL JOURNAL OF RHEUMATIC DISEASES, Issue 3 2008Mohammadhassan JOKAR Abstract Aim: The aim of this study was to evaluate plasma levels of prolactin and macroprolactin in a group of systemic lupus erythematosus (SLE) patients and to determine if prolactin and macroprolactin concentrations were related to disease activity, clinical features or serological abnormalities. Methods: Ninety consecutive Iranian patients with SLE were tested for serum prolactin and macroprolactin levels. Total prolactin was measured directly in serum samples by radioimmunoassay. Free prolactin was extracted from the serum using polyethylene glycol. Clinical manifestation and SLE disease activity index (SLEDAI) were recorded. Auto antibodies were determined by standard techniques. Results: There were 90 patients (7 male, 83 female) with a mean age of 27.6 ± 9.1 (range 14,52). The mean disease duration was 27.6 ± 9.1 months. The frequency of high prolactin and macroprolactin, respectively, was 10% (9/90) and 5.6% (5/90) in patients with SLE. Macroprolactinemia was found in 55.55% (5/9) of hyperprolactinemic patients. Lupus activity was present in 63.3% (57/90) of patients without a significant difference in the frequency of high serum prolactin and macroprolactin levels when compared to inactive lupus. There were no statistically significant differences regarding demographic, clinical and laboratory characteristics between the group of patients with macroprolactinemia and the group without macroprolactinemia. Conclusion: Our results suggest that a subgroup of SLE patients have hyperprolactinemia and macroprolactinemia but they do not seem to have positive or negative correlation to clinical and laboratory features and disease activity. [source] Patterns of species richness on very small islands: the plants of the Aegean archipelagoJOURNAL OF BIOGEOGRAPHY, Issue 7 2006Maria Panitsa Abstract Aim, To investigate the species,area relationship (SAR) of plants on very small islands, to examine the effect of other factors on species richness, and to check for a possible Small Island Effect (SIE). Location, The study used data on the floral composition of 86 very small islands (all < 0.050 km2) of the Aegean archipelago (Greece). Methods, We used standard techniques for linear and nonlinear regression in order to check several models of the SAR, and stepwise multiple regression to check for the effects of factors other than area on species richness (,habitat diversity', elevation, and distance from nearest large island), as well as the performance of the Choros model. We also checked for the SAR of certain taxonomic and ecological plant groups that are of special importance in eastern Mediterranean islands, such as halophytes, therophytes, Leguminosae and Gramineae. We used one-way anova to check for differences in richness between grazed and non-grazed islands, and we explored possible effects of nesting seabirds on the islands' flora. Results, Area explained a small percentage of total species richness variance in all cases. The linearized power model of the SAR provided the best fit for the total species list and several subgroups of species, while the semi-log model provided better fits for grazed islands, grasses and therophytes. None of the nonlinear models explained more variance. The slope of the SAR was very high, mainly due to the contribution of non-grazed islands. No significant SIE could be detected. The Choros model explained more variance than all SARs, although a large amount of variance of species richness still remained unexplained. Elevation was found to be the only important factor, other than area, to influence species richness. Habitat diversity did not seem important, although there were serious methodological problems in properly defining it, especially for plants. Grazing was an important factor influencing the flora of small islands. Grazed islands were richer than non-grazed, but the response of their species richness to area was particularly low, indicating decreased floral heterogeneity among islands. We did not detect any important effects of the presence of nesting seabird colonies. Main conclusions, Species richness on small islands may behave idiosyncratically, but this does not always lead to a typical SIE. Plants of Aegean islets conform to the classical Arrhenius model of the SAR, a result mainly due to the contribution of non-grazed islands. At the same time, the factors examined explain a small portion of total variance in species richness, indicating the possible contribution of other, non-standard factors, or even of stochastic effects. The proper definition of habitat diversity as pertaining to the taxon examined in each case is a recurrent problem in such studies. Nevertheless, the combined effect of area and a proxy for environmental heterogeneity is once again superior to area alone in explaining species richness. [source] On-line monitoring of wastewater quality: a reviewJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 4 2001Wilfrid Bourgeois Abstract Real-time monitoring of wastewater quality remains an unresolved problem to the wastewater treatment industry. In order to comply with increasingly stringent environmental regulations, plant operators as well as instrument manufacturers have expressed the need for new standards and improved comparability and reliability of existing techniques. A review of currently available methods for monitoring global organic parameters (BOD, COD, TOC) is given. The study reviews both existing standard techniques and new innovative technologies with the focus on the sensors' potential for on-line and real-time monitoring and control. Current developments of biosensors, optical sensors and sensor arrays as well as virtual sensors for the monitoring of wastewater organic load are presented and the interests and limitations of these techniques with respect to their application to the wastewater monitoring are discussed. © 2001 Society of Chemical Industry [source] Hyperlink Analyses of the World Wide Web: A ReviewJOURNAL OF COMPUTER-MEDIATED COMMUNICATION, Issue 4 2003Han Woo Park We have recently witnessed the growth of hyperlink studies in the field of Internet research. Although investigations have been conducted across many disciplines and topics, their approaches can be largely divided into hyperlink network analysis (HNA) and Webometrics. This article is an extensive review of the two analytical methods, and a reflection on their application. HNA casts hyperlinks between Web sites (or Web pages) as social and communicational ties, applying standard techniques from Social Networks Analysis to this new data source. Webometrics has tended to apply much simpler techniques combined with a more in-depth investigation into the validity of hypotheses about possible interpretations of the results. We conclude that hyperlinks are a highly promising but problematic new source of data that can be mined for previously hidden patterns of information, although much care must be taken in the collection of raw data and in the interpretation of the results. In particular, link creation is an unregulated phenomenon and so it would not be sensible to assume that the meaning of hyperlinks in any given context is evident, without a systematic study of the context of link creation, and of the relationship between link counts, among other measurements. Social Networks Analysis tools and techniques form an excellent resource for hyperlink analysis, but should only be used in conjunction with improved techniques for data collection, validation and interpretation. [source] Beneficial effects of growth hormone on bacterial translocation during the course of acute necrotizing pancreatitis in ratsJOURNAL OF DIGESTIVE DISEASES, Issue 1 2001Wang Xingpeng OBJECTIVE: Because bacterial translocation from the gut is one of the important sources of bacterial infection in acute necrotizing pancreatitis (ANP), and growth hormone (GH) has the ability to promote intestinal epithelial proliferation, we investigated the effects of GH on bacterial translocation in a rat ANP model. METHODS: Acute necrotizing pancreatitis was induced in rats via injection of 5% sodium taurocholate into the biliopancreatic duct. The rats with ANP were treated with either human recombinant GH or a placebo. Laparotomized animals without ANP induction (sham operation) served as controls. Twenty-four hours after the operation, blood was drawn for bacterial culture and determinations of amylase, lipase and endotoxin. Peritoneal fluid and specimens of mesenteric lymph nodes (MLN), liver, pancreas and spleen were taken for bacterial culture by standard techniques. Intestinal mucosal permeability was assessed by measuring the movement of [125I]-labeled albumin from blood to the intestinal lumen. Insulin-like growth factor-1 (IGF-1) mRNA was detected in the liver and ileum by reverse transcription,polymerase chain reaction (RT-PCR). Morphological changes in the pancreas and ileum were also analyzed. RESULTS: Administration of GH significantly decreased the activity of serum amylase and lipase, decreased the plasma endotoxin level and reduced the incidence of bacterial translocation. Moreover, the survival rate of ANP rats was improved. The severity of inflammation in the pancreas and ileum was reduced by GH treatment. Ileal mucosal thickness, villus height and crypt depth in GH-treated rats were obviously increased as compared with those of ANP rats. The intestinal permeability was markedly decreased in the GH group as compared with the ANP group. GH treatment resulted in upregulation of IGF-1 mRNA expression in ileum, but not in liver. CONCLUSIONS: These results suggest that exogenous GH has beneficial effects in maintaining the integrity of the intestinal mucosal barrier and reducing the incidence of bacterial translocation in rats with ANP. One of the mechanisms might be the upregulation of IGF-1 mRNA in the intestine by GH. [source] Long-memory dynamic Tobit modelsJOURNAL OF FORECASTING, Issue 5 2006A. E. Brockwell Abstract We introduce a long-memory dynamic Tobit model, defining it as a censored version of a fractionally integrated Gaussian ARMA model, which may include seasonal components and/or additional regression variables. Parameter estimation for such a model using standard techniques is typically infeasible, since the model is not Markovian, cannot be expressed in a finite-dimensional state-space form, and includes censored observations. Furthermore, the long-memory property renders a standard Gibbs sampling scheme impractical. Therefore we introduce a new Markov chain Monte Carlo sampling scheme, which is orders of magnitude more efficient than the standard Gibbs sampler. The method is inherently capable of handling missing observations. In case studies, the model is fit to two time series: one consisting of volumes of requests to a hard disk over time, and the other consisting of hourly rainfall measurements in Edinburgh over a 2-year period. The resulting posterior distributions for the fractional differencing parameter demonstrate, for these two time series, the importance of the long-memory structure in the models.,,Copyright © 2006 John Wiley & Sons, Ltd. [source] Characterization of dilute species within CVD-grown silicon nanowires doped using trimethylboron: protected lift-out specimen preparation for atom probe tomographyJOURNAL OF MICROSCOPY, Issue 2 2010T. J. PROSA Summary Three-dimensional quantitative compositional analysis of nanowires is a challenge for standard techniques such as secondary ion mass spectrometry because of specimen size and geometry considerations; however, it is precisely the size and geometry of nanowires that makes them attractive candidates for analysis via atom probe tomography. The resulting boron composition of various trimethylboron vapour,liquid,solid grown silicon nanowires were measured both with time-of-flight secondary ion mass spectrometry and pulsed-laser atom probe tomography. Both characterization techniques yielded similar results for relative composition. Specialized specimen preparation for pulsed-laser atom probe tomography was utilized and is described in detail whereby individual silicon nanowires are first protected, then lifted out, trimmed, and finally wet etched to remove the protective layer for subsequent three-dimensional analysis. [source] A quantitative genetic analysis of intermediate asthma phenotypesALLERGY, Issue 3 2009S. F. Thomsen Aim:, To study the relative contribution of genetic and environmental factors to the correlation between exhaled nitric oxide (FeNO), airway responsiveness, airway obstruction, and serum total immunoglobulin E (IgE). Methods:, Within a sampling frame of 21 162 twin subjects, 20,49 years of age, from the Danish Twin Registry, a total of 575 subjects (256 intact pairs and 63 single twins) who either themselves and/or their co-twins reported a history of asthma at a nationwide questionnaire survey, were clinically examined. Traits were measured using standard techniques. Latent factor models were fitted to the observed data using maximum likelihood methods. Results:, Additive genetic factors explained 67% of the variation in FeNO, 43% in airway responsiveness, 22% in airway obstruction, and 81% in serum total IgE. In general, traits had genetically and environmentally distinct variance structures. The most substantial genetic similarity was observed between FeNO and serum total IgE, genetic correlation (,A) = 0.37, whereas the strongest environmental resemblance was observed between airway responsiveness and airway obstruction, specific environmental correlation (,E) = ,0.46, and between FeNO and airway responsiveness, ,E = 0.34. Conclusions:, Asthma is a complex disease characterized by a set of etiologically heterogeneous biomarkers, which likely constitute diverse targets of intervention. [source] Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversityMOLECULAR ECOLOGY RESOURCES, Issue 6 2009DOROTA L. PORAZINSKA Abstract Nematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time-consuming, nematode communities are not resolved down to the species level, leaving ecological analysis ambiguous. We assessed the suitability of massively parallel sequencing for analysis of nematode diversity from metagenomic samples. We set up four artificial metagenomic samples involving 41 diverse reference nematodes in known abundances. Two samples came from pooling polymerase chain reaction products amplified from single nematode species. Two additional metagenomic samples consisted of amplified products of DNA extracted from pooled nematode species. Amplified products involved two rapidly evolving ~400-bp sections coding for the small and large subunit of rRNA. The total number of reads ranged from 4159 to 14771 per metagenomic sample. Of these, 82% were > 199 bp in length. Among the reads > 199 bp, 86% matched the referenced species with less than three nucleotide differences from a reference sequence. Although neither rDNA section recovered all nematode species, the use of both loci improved the detection level of nematode species from 90 to 97%. Overall, results support the suitability of massively parallel sequencing for identification of nematodes. In contrast, the frequency of reads representing individual species did not correlate with the number of individuals in the metagenomic samples, suggesting that further methodological work is necessary before it will be justified for inferring the relative abundances of species within a nematode community. [source] Characterization of microsatellite loci in the endangered species of fern Marsilea strigosa Willd. (Marsileaceae, Pteridophyta)MOLECULAR ECOLOGY RESOURCES, Issue 1-2 2001R. Vitalis Abstract Absence of enzymatic polymorphism in the endangered species of fern Marsilea strigosa prompted us to develop microsatellite loci in this species. We used an enriched partial genomic library, from which six polymorphic microsatellite loci were obtained. From a previous attempt to develop microsatellite markers with standard techniques, a single long and polymorphic locus was obtained. This highlights the benefits from using enrichment techniques in those species where microsatellite loci may be rare in the genome. [source] Effects of water storage in the stele on measurements of the hydraulics of young roots of corn and barleyNEW PHYTOLOGIST, Issue 3 2009Ankur Joshi Summary ,,In standard techniques (root pressure probe or high-pressure flowmeter), the hydraulic conductivity of roots is calculated from transients of root pressure using responses following step changes in volume or pressure, which may be affected by a storage of water in the stele. ,,Storage effects were examined using both experimental data of root pressure relaxations and clamps and a physical capacity model. Young roots of corn and barley were treated as a three-compartment system, comprising a serial arrangement of xylem/probe, stele and outside medium/cortex. The hydraulic conductivities of the endodermis and of xylem vessels were derived from experimental data. The lower limit of the storage capacity of stelar tissue was caused by the compressibility of water. This was subsequently increased to account for realistic storage capacities of the stele. ,,When root water storage was varied over up to five orders of magnitude, the results of simulations showed that storage effects could not explain the experimental data, suggesting a major contribution of effects other than water storage. ,,It is concluded that initial water flows may be used to measure root hydraulic conductivity provided that the volumes of water used are much larger than the volumes stored. [source] Multiple imputation for national public-use datasets and its possible application for gestational age in United States Natality filesPAEDIATRIC & PERINATAL EPIDEMIOLOGY, Issue 2007Jennifer D. Parker Summary Multiple imputation (MI) is a technique that can be used for handling missing data in a public-use dataset. With MI, two or more completed versions of the dataset are created, containing possibly different but reasonable replacements for the missing data. Users analyse the completed datasets separately with standard techniques and then combine the results using simple formulae in a way that allows the extra uncertainty due to missing data to be assessed. An advantage of this approach is that the resulting public-use data can be analysed by a variety of users for a variety of purposes, without each user needing to devise a method to deal with the missing data. A recent example for a large public-use dataset is the MI of the family income and personal earnings variables in the National Health Interview Survey. We propose an approach to utilise MI to handle the problems of missing gestational ages and implausible birthweight,gestational age combinations in national vital statistics datasets. This paper describes MI and gives examples of MI for public-use datasets, summarises methods that have been used for identifying implausible gestational age values on birth records, and combines these ideas by setting forth scenarios for identifying and then imputing missing and implausible gestational age values multiple times. Because missing and implausible gestational age values are not missing completely at random, using multiple imputations and, thus, incorporating both the existing relationships among the variables and the uncertainty added from the imputation, may lead to more valid inferences in some analytical studies than simply excluding birth records with inadequate data. [source] Body composition and its components in preterm and term newborns: A cross-sectional, multimodal investigationAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 1 2010Irfan Ahmad A prospective, cross-sectional, observational study in preterm and term infants was performed to compare multimodal measurements of body composition, namely, limb ultrasound, bone quantitative ultrasound, and dual X-ray absorptiometry (DXA). One hundred and two preterm and term infants appropriate for gestational age were enrolled from the newborn nursery and neonatal intensive care unit. Infants were included when they were medically stable, in an open crib, on full enteral feeds and within 1 week of anticipated discharge. Correlations among the various measurements of body composition were performed using standard techniques. A comparison between preterm infant (born at 28,32 weeks) reaching term to term-born infants was performed. Limb ultrasound estimates of cross-sectional areas of lean and fat tissue in a region of tissue (i.e., the leg) were remarkably correlated with regional and whole-body estimates of fat-free mass and fat obtained from DXA suggesting the potential usefulness of muscle ultrasound as an investigative tool for studying aspects of body composition in this fragile population. There was a weak but significant correlation between quantitative ultrasound measurements of bone strength and DXA-derived bone mineral density (BMD). Preterm infants reaching term had significantly lower body weight, length, head circumference, muscle and fat cross-sectional area, bone speed of sound, whole-body and regional lean body mass, fat mass, and BMD compared to term-born infants. Current postnatal care and nutritional support in preterm infants is still unable to match the in-utero environment for optimal growth and bone development. The use of relatively simple bedside, noninvasive body composition measurements may assist in understanding how changes in different components of body composition early in life affect later growth and development. Am. J. Hum. Biol. 2010. © 2009 Wiley-Liss, Inc. [source] In vitro culture of Arabidopsis embryos within their ovulesTHE PLANT JOURNAL, Issue 5 2004Michael Sauer Summary Embryogenesis of flowering plants establishes a basic body plan with apical,basal, radial and bilateral patterns from the single-celled zygote. Arabidopsis embryogenesis exhibits a nearly invariant cell division pattern and therefore is an ideal system for studies of early plant development. However, plant embryos are difficult to access for experimental manipulation, as they develop deeply inside maternal tissues. Here we present a method for the culture of zygotic Arabidopsis embryos in vitro. The technique omits excision of the embryo by culturing the entire ovule, thus greatly facilitating the time and effort involved. It enables external manipulation of embryo development and culture from the earliest developmental stages up to maturity. Administration of various chemical treatments as well as the use of different molecular markers is demonstrated together with standard techniques for visualizing gene expression and protein localization in in vitro cultivated embryos. The presented set of techniques allows for so far unavailable molecular physiology approaches in the study of early plant development. [source] A new, minimally invasive technique for measuring cardiac index: clinical comparison of continuous cardiac dynamic monitoring and pulmonary artery catheter methodsANAESTHESIA, Issue 9 2009J. C. Berridge Summary To assess the utility of a relatively simple bedside method of estimating cardiac index during major surgery or in the intensive care unit, we conducted a prospective study in patients undergoing elective cardiac bypass surgery where a pulmonary artery catheter was inserted as part of routine monitoring. The cardiac index was estimated using standard techniques and compared with estimates from continuous cardiac dynamic monitoring using heartsmart® software. Two hundred and seventy sets of measurements were suitable for comparison. The mean bias (95% limits of agreement), for the pre-bypass cardiac index was ,0.09 (,1.26 to 1.08) l.min,1.m,2, and post-bypass was 0.12 l.min,1.m,2 (,1.32 to 1.56). These results suggest that continuous cardiac dynamic monitoring using heartsmart® is sufficiently accurate for assessment of haemodynamic variables in critically ill patients, facilitating goal-directed therapies. [source] Antibiotic susceptibility of urogenital microbial profile of infertile men in South-eastern NigeriaANDROLOGIA, Issue 4 2010C. J. Uneke Summary Male factors are known to contribute significantly to the infertility problem. The urogenital bacteria profile and semen quality were investigated among 160 men attending infertility clinics in South-eastern Nigeria. Both semen and urine samples were obtained from each subject and analysed according to standard techniques. A total of 16 (10%) had bacterial infection in their semen samples and individuals of older age groups were significantly affected (,2 = 23.18, P < 0.05). Urinary tract infection (UTI) was observed in 30.6% of subjects, with the highest rate occurring among men aged 36,40 years, but the difference was not significant (,2 = 7.62, P > 0.05). A total of 33.8% of the men had semen volume less than 2 ml per ejaculate, 33.8% also recorded total sperm count of <40 × 106 ml,1, while 36.3% recorded sperm motility <50%. Fifty-three individuals (33.1%) had suboptimal sperm morphology (<60%), with the men aged 46,50 years old significantly affected (,2 = 13.03, P < 0.05). All the individuals with bacterial infection in semen also had UTI and suboptimal semen parameters. The commonest bacterial isolates were Proteus species, Staphylococcus aureus and Escherichia coli, which were resistant to most of the antibiotics assessed. [source] | ||||||||||||||||||||||