Hierarchical imputation of systematically and sporadically missing data: An approximate Bayesian approach using chained equations.

PubMed

Jolani, Shahab

2018-03-01

In health and medical sciences, multiple imputation (MI) is now becoming popular to obtain valid inferences in the presence of missing data. However, MI of clustered data such as multicenter studies and individual participant data meta-analysis requires advanced imputation routines that preserve the hierarchical structure of data. In clustered data, a specific challenge is the presence of systematically missing data, when a variable is completely missing in some clusters, and sporadically missing data, when it is partly missing in some clusters. Unfortunately, little is known about how to perform MI when both types of missing data occur simultaneously. We develop a new class of hierarchical imputation approach based on chained equations methodology that simultaneously imputes systematically and sporadically missing data while allowing for arbitrary patterns of missingness among them. Here, we use a random effect imputation model and adopt a simplification over fully Bayesian techniques such as Gibbs sampler to directly obtain draws of parameters within each step of the chained equations. We justify through theoretical arguments and extensive simulation studies that the proposed imputation methodology has good statistical properties in terms of bias and coverage rates of parameter estimates. An illustration is given in a case study with eight individual participant datasets. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Minimum number of clusters and comparison of analysis methods for cross sectional stepped wedge cluster randomised trials with binary outcomes: A simulation study.

PubMed

Barker, Daniel; D'Este, Catherine; Campbell, Michael J; McElduff, Patrick

2017-03-09

Stepped wedge cluster randomised trials frequently involve a relatively small number of clusters. The most common frameworks used to analyse data from these types of trials are generalised estimating equations and generalised linear mixed models. A topic of much research into these methods has been their application to cluster randomised trial data and, in particular, the number of clusters required to make reasonable inferences about the intervention effect. However, for stepped wedge trials, which have been claimed by many researchers to have a statistical power advantage over the parallel cluster randomised trial, the minimum number of clusters required has not been investigated. We conducted a simulation study where we considered the most commonly used methods suggested in the literature to analyse cross-sectional stepped wedge cluster randomised trial data. We compared the per cent bias, the type I error rate and power of these methods in a stepped wedge trial setting with a binary outcome, where there are few clusters available and when the appropriate adjustment for a time trend is made, which by design may be confounding the intervention effect. We found that the generalised linear mixed modelling approach is the most consistent when few clusters are available. We also found that none of the common analysis methods for stepped wedge trials were both unbiased and maintained a 5% type I error rate when there were only three clusters. Of the commonly used analysis approaches, we recommend the generalised linear mixed model for small stepped wedge trials with binary outcomes. We also suggest that in a stepped wedge design with three steps, at least two clusters be randomised at each step, to ensure that the intervention effect estimator maintains the nominal 5% significance level and is also reasonably unbiased.

The Post-polyketide Synthase Steps in iso-Migrastatin Biosynthesis Featuring Tailoring Enzymes with Broad Substrate Specificity

PubMed Central

Ma, Ming; Kwong, Thomas; Lim, Si-Kyu; Ju, Jianhua; Lohman, Jeremy R.; Shen, Ben

2013-01-01

The iso-migrastatin (iso-MGS) biosynthetic gene cluster from Streptomyces platensis NRRL 18993 consists of 11 genes, featuring an acyltransferase (AT)-less type I polyketide synthase (PKS) and three tailoring enzymes MgsIJK. Systematic inactivation of mgsIJK in S. platensis enabled us to (i) identify two nascent products (10 and 13) of the iso-MGS AT-less type I PKS, establishing an unprecedented novel feature for AT-less type I PKSs, and (ii) account for the formation of all known post-PKS biosynthetic intermediates (10-17) generated by the three tailoring enzymes MgsIJK, which possessed significant substrate promiscuities. PMID:23394593

Unbiased methods for removing systematics from galaxy clustering measurements

NASA Astrophysics Data System (ADS)

Elsner, Franz; Leistedt, Boris; Peiris, Hiranya V.

2016-02-01

Measuring the angular clustering of galaxies as a function of redshift is a powerful method for extracting information from the three-dimensional galaxy distribution. The precision of such measurements will dramatically increase with ongoing and future wide-field galaxy surveys. However, these are also increasingly sensitive to observational and astrophysical contaminants. Here, we study the statistical properties of three methods proposed for controlling such systematics - template subtraction, basic mode projection, and extended mode projection - all of which make use of externally supplied template maps, designed to characterize and capture the spatial variations of potential systematic effects. Based on a detailed mathematical analysis, and in agreement with simulations, we find that the template subtraction method in its original formulation returns biased estimates of the galaxy angular clustering. We derive closed-form expressions that should be used to correct results for this shortcoming. Turning to the basic mode projection algorithm, we prove it to be free of any bias, whereas we conclude that results computed with extended mode projection are biased. Within a simplified setup, we derive analytical expressions for the bias and discuss the options for correcting it in more realistic configurations. Common to all three methods is an increased estimator variance induced by the cleaning process, albeit at different levels. These results enable unbiased high-precision clustering measurements in the presence of spatially varying systematics, an essential step towards realizing the full potential of current and planned galaxy surveys.

Bootstrap-based methods for estimating standard errors in Cox's regression analyses of clustered event times.

PubMed

Xiao, Yongling; Abrahamowicz, Michal

2010-03-30

We propose two bootstrap-based methods to correct the standard errors (SEs) from Cox's model for within-cluster correlation of right-censored event times. The cluster-bootstrap method resamples, with replacement, only the clusters, whereas the two-step bootstrap method resamples (i) the clusters, and (ii) individuals within each selected cluster, with replacement. In simulations, we evaluate both methods and compare them with the existing robust variance estimator and the shared gamma frailty model, which are available in statistical software packages. We simulate clustered event time data, with latent cluster-level random effects, which are ignored in the conventional Cox's model. For cluster-level covariates, both proposed bootstrap methods yield accurate SEs, and type I error rates, and acceptable coverage rates, regardless of the true random effects distribution, and avoid serious variance under-estimation by conventional Cox-based standard errors. However, the two-step bootstrap method over-estimates the variance for individual-level covariates. We also apply the proposed bootstrap methods to obtain confidence bands around flexible estimates of time-dependent effects in a real-life analysis of cluster event times.

Two-step entanglement concentration for arbitrary electronic cluster state

NASA Astrophysics Data System (ADS)

Zhao, Sheng-Yang; Liu, Jiong; Zhou, Lan; Sheng, Yu-Bo

2013-12-01

We present an efficient protocol for concentrating an arbitrary four-electron less-entangled cluster state into a maximally entangled cluster state. As a two-step entanglement concentration protocol (ECP), it only needs one pair of less-entangled cluster state, which makes this ECP more economical. With the help of electronic polarization beam splitter (PBS) and the charge detection, the whole concentration process is essentially the quantum nondemolition (QND) measurement. Therefore, the concentrated maximally entangled state can be remained for further application. Moreover, the discarded terms in some traditional ECPs can be reused to obtain a high success probability. It is feasible and useful in current one-way quantum computation.

Unequal cluster sizes in stepped-wedge cluster randomised trials: a systematic review

PubMed Central

Morris, Tom; Gray, Laura

2017-01-01

Objectives To investigate the extent to which cluster sizes vary in stepped-wedge cluster randomised trials (SW-CRT) and whether any variability is accounted for during the sample size calculation and analysis of these trials. Setting Any, not limited to healthcare settings. Participants Any taking part in an SW-CRT published up to March 2016. Primary and secondary outcome measures The primary outcome is the variability in cluster sizes, measured by the coefficient of variation (CV) in cluster size. Secondary outcomes include the difference between the cluster sizes assumed during the sample size calculation and those observed during the trial, any reported variability in cluster sizes and whether the methods of sample size calculation and methods of analysis accounted for any variability in cluster sizes. Results Of the 101 included SW-CRTs, 48% mentioned that the included clusters were known to vary in size, yet only 13% of these accounted for this during the calculation of the sample size. However, 69% of the trials did use a method of analysis appropriate for when clusters vary in size. Full trial reports were available for 53 trials. The CV was calculated for 23 of these: the median CV was 0.41 (IQR: 0.22–0.52). Actual cluster sizes could be compared with those assumed during the sample size calculation for 14 (26%) of the trial reports; the cluster sizes were between 29% and 480% of that which had been assumed. Conclusions Cluster sizes often vary in SW-CRTs. Reporting of SW-CRTs also remains suboptimal. The effect of unequal cluster sizes on the statistical power of SW-CRTs needs further exploration and methods appropriate to studies with unequal cluster sizes need to be employed. PMID:29146637

Clustering of longitudinal data by using an extended baseline: A new method for treatment efficacy clustering in longitudinal data.

PubMed

Schramm, Catherine; Vial, Céline; Bachoud-Lévi, Anne-Catherine; Katsahian, Sandrine

2018-01-01

Heterogeneity in treatment efficacy is a major concern in clinical trials. Clustering may help to identify the treatment responders and the non-responders. In the context of longitudinal cluster analyses, sample size and variability of the times of measurements are the main issues with the current methods. Here, we propose a new two-step method for the Clustering of Longitudinal data by using an Extended Baseline. The first step relies on a piecewise linear mixed model for repeated measurements with a treatment-time interaction. The second step clusters the random predictions and considers several parametric (model-based) and non-parametric (partitioning, ascendant hierarchical clustering) algorithms. A simulation study compares all options of the clustering of longitudinal data by using an extended baseline method with the latent-class mixed model. The clustering of longitudinal data by using an extended baseline method with the two model-based algorithms was the more robust model. The clustering of longitudinal data by using an extended baseline method with all the non-parametric algorithms failed when there were unequal variances of treatment effect between clusters or when the subgroups had unbalanced sample sizes. The latent-class mixed model failed when the between-patients slope variability is high. Two real data sets on neurodegenerative disease and on obesity illustrate the clustering of longitudinal data by using an extended baseline method and show how clustering may help to identify the marker(s) of the treatment response. The application of the clustering of longitudinal data by using an extended baseline method in exploratory analysis as the first stage before setting up stratified designs can provide a better estimation of treatment effect in future clinical trials.

The PULSAR Specialist Care protocol: a stepped-wedge cluster randomized control trial of a training intervention for community mental health teams in recovery-oriented practice.

PubMed

Shawyer, Frances; Enticott, Joanne C; Brophy, Lisa; Bruxner, Annie; Fossey, Ellie; Inder, Brett; Julian, John; Kakuma, Ritsuko; Weller, Penelope; Wilson-Evered, Elisabeth; Edan, Vrinda; Slade, Mike; Meadows, Graham N

2017-05-08

Recovery features strongly in Australian mental health policy; however, evidence is limited for the efficacy of recovery-oriented practice at the service level. This paper describes the Principles Unite Local Services Assisting Recovery (PULSAR) Specialist Care trial protocol for a recovery-oriented practice training intervention delivered to specialist mental health services staff. The primary aim is to evaluate whether adult consumers accessing services where staff have received the intervention report superior recovery outcomes compared to adult consumers accessing services where staff have not yet received the intervention. A qualitative sub-study aims to examine staff and consumer views on implementing recovery-oriented practice. A process evaluation sub-study aims to articulate important explanatory variables affecting the interventions rollout and outcomes. The mixed methods design incorporates a two-step stepped-wedge cluster randomized controlled trial (cRCT) examining cross-sectional data from three phases, and nested qualitative and process evaluation sub-studies. Participating specialist mental health care services in Melbourne, Victoria are divided into 14 clusters with half randomly allocated to receive the staff training in year one and half in year two. Research participants are consumers aged 18-75 years who attended the cluster within a previous three-month period either at baseline, 12 (step 1) or 24 months (step 2). In the two nested sub-studies, participation extends to cluster staff. The primary outcome is the Questionnaire about the Process of Recovery collected from 756 consumers (252 each at baseline, step 1, step 2). Secondary and other outcomes measuring well-being, service satisfaction and health economic impact are collected from a subset of 252 consumers (63 at baseline; 126 at step 1; 63 at step 2) via interviews. Interview-based longitudinal data are also collected 12 months apart from 88 consumers with a psychotic disorder diagnosis (44 at baseline, step 1; 44 at step 1, step 2). cRCT data will be analyzed using multilevel mixed-effects modelling to account for clustering and some repeated measures, supplemented by thematic analysis of qualitative interview data. The process evaluation will draw on qualitative, quantitative and documentary data. Findings will provide an evidence-base for the continued transformation of Australian mental health service frameworks toward recovery. Australian and New Zealand Clinical Trial Registry: ACTRN12614000957695 . Date registered: 8 September 2014.

Multiple imputation by chained equations for systematically and sporadically missing multilevel data.

PubMed

Resche-Rigon, Matthieu; White, Ian R

2018-06-01

In multilevel settings such as individual participant data meta-analysis, a variable is 'systematically missing' if it is wholly missing in some clusters and 'sporadically missing' if it is partly missing in some clusters. Previously proposed methods to impute incomplete multilevel data handle either systematically or sporadically missing data, but frequently both patterns are observed. We describe a new multiple imputation by chained equations (MICE) algorithm for multilevel data with arbitrary patterns of systematically and sporadically missing variables. The algorithm is described for multilevel normal data but can easily be extended for other variable types. We first propose two methods for imputing a single incomplete variable: an extension of an existing method and a new two-stage method which conveniently allows for heteroscedastic data. We then discuss the difficulties of imputing missing values in several variables in multilevel data using MICE, and show that even the simplest joint multilevel model implies conditional models which involve cluster means and heteroscedasticity. However, a simulation study finds that the proposed methods can be successfully combined in a multilevel MICE procedure, even when cluster means are not included in the imputation models.

A Mixed Approach to Similarity Metric Selection in Affinity Propagation-Based WiFi Fingerprinting Indoor Positioning.

PubMed

Caso, Giuseppe; de Nardis, Luca; di Benedetto, Maria-Gabriella

2015-10-30

The weighted k-nearest neighbors (WkNN) algorithm is by far the most popular choice in the design of fingerprinting indoor positioning systems based on WiFi received signal strength (RSS). WkNN estimates the position of a target device by selecting k reference points (RPs) based on the similarity of their fingerprints with the measured RSS values. The position of the target device is then obtained as a weighted sum of the positions of the k RPs. Two-step WkNN positioning algorithms were recently proposed, in which RPs are divided into clusters using the affinity propagation clustering algorithm, and one representative for each cluster is selected. Only cluster representatives are then considered during the position estimation, leading to a significant computational complexity reduction compared to traditional, flat WkNN. Flat and two-step WkNN share the issue of properly selecting the similarity metric so as to guarantee good positioning accuracy: in two-step WkNN, in particular, the metric impacts three different steps in the position estimation, that is cluster formation, cluster selection and RP selection and weighting. So far, however, the only similarity metric considered in the literature was the one proposed in the original formulation of the affinity propagation algorithm. This paper fills this gap by comparing different metrics and, based on this comparison, proposes a novel mixed approach in which different metrics are adopted in the different steps of the position estimation procedure. The analysis is supported by an extensive experimental campaign carried out in a multi-floor 3D indoor positioning testbed. The impact of similarity metrics and their combinations on the structure and size of the resulting clusters, 3D positioning accuracy and computational complexity are investigated. Results show that the adoption of metrics different from the one proposed in the original affinity propagation algorithm and, in particular, the combination of different metrics can significantly improve the positioning accuracy while preserving the efficiency in computational complexity typical of two-step algorithms.

A Mixed Approach to Similarity Metric Selection in Affinity Propagation-Based WiFi Fingerprinting Indoor Positioning

PubMed Central

Caso, Giuseppe; de Nardis, Luca; di Benedetto, Maria-Gabriella

2015-01-01

The weighted k-nearest neighbors (WkNN) algorithm is by far the most popular choice in the design of fingerprinting indoor positioning systems based on WiFi received signal strength (RSS). WkNN estimates the position of a target device by selecting k reference points (RPs) based on the similarity of their fingerprints with the measured RSS values. The position of the target device is then obtained as a weighted sum of the positions of the k RPs. Two-step WkNN positioning algorithms were recently proposed, in which RPs are divided into clusters using the affinity propagation clustering algorithm, and one representative for each cluster is selected. Only cluster representatives are then considered during the position estimation, leading to a significant computational complexity reduction compared to traditional, flat WkNN. Flat and two-step WkNN share the issue of properly selecting the similarity metric so as to guarantee good positioning accuracy: in two-step WkNN, in particular, the metric impacts three different steps in the position estimation, that is cluster formation, cluster selection and RP selection and weighting. So far, however, the only similarity metric considered in the literature was the one proposed in the original formulation of the affinity propagation algorithm. This paper fills this gap by comparing different metrics and, based on this comparison, proposes a novel mixed approach in which different metrics are adopted in the different steps of the position estimation procedure. The analysis is supported by an extensive experimental campaign carried out in a multi-floor 3D indoor positioning testbed. The impact of similarity metrics and their combinations on the structure and size of the resulting clusters, 3D positioning accuracy and computational complexity are investigated. Results show that the adoption of metrics different from the one proposed in the original affinity propagation algorithm and, in particular, the combination of different metrics can significantly improve the positioning accuracy while preserving the efficiency in computational complexity typical of two-step algorithms. PMID:26528984

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

NASA Astrophysics Data System (ADS)

Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F.; Neese, Frank

2016-01-01

Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous implementation.

Weak lensing measurement of the mass–richness relation of SDSS redMaPPer clusters

DOE PAGES

Simet, Melanie; McClintock, Tom; Mandelbaum, Rachel; ...

2016-12-15

Here, we perform a measurement of the mass–richness relation of the redMaPPer galaxy cluster catalogue using weak lensing data from the Sloan Digital Sky Survey. We carefully characterized a broad range of systematic uncertainties, including shear calibration errors, photo-zz biases, dilution by member galaxies, source obscuration, magnification bias, incorrect assumptions about cluster mass profiles, cluster centering, halo triaxiality, and projection effects. We then compare measurements of the lensing signal from two independently-produced shear and photometric redshift catalogues to characterize systematic errors in the lensing signal itself. Using a sample of 5,570 clusters from 0.1 ≤ zz ≤ 0.33, the normalization of our power-law mass vs. λ relation is log 10[M 200m/h -1 M ⊙] = 14.344 ± 0.021 (statistical) ±0.023 (systematic) at a richness λ = 40, a 7 per cent calibration uncertainty, with a power-law index of 1.33+0.09-0.101.33more » $$+0.09\\atop{-0.10}$$ (1σ). Finally, the detailed systematics characterization in this work renders it the definitive weak lensing mass calibration for SDSS redMaPPer clusters at this time.« less

Classification Order of Surface-Confined Intermixing at Epitaxial Interface

NASA Astrophysics Data System (ADS)

Michailov, M.

The self-organization phenomena at epitaxial interface hold special attention in contemporary material science. Being relevant to the fundamental physical problem of competing, long-range and short-range atomic interactions in systems with reduced dimensionality, these phenomena have found exacting academic interest. They are also of great technological importance for their ability to bring spontaneous formation of regular nanoscale surface patterns and superlattices with exotic properties. The basic phenomenon involved in this process is surface diffusion. That is the motivation behind the present study which deals with important details of diffusion scenarios that control the fine atomic structure of epitaxial interface. Consisting surface imperfections (terraces, steps, kinks, and vacancies), the interface offers variety of barriers for surface diffusion. Therefore, the adatoms and clusters need a certain critical energy to overcome the corresponding diffusion barriers. In the most general case the critical energies can be attained by variation of the system temperature. Hence, their values define temperature limits of system energy gaps associated with different diffusion scenarios. This systematization imply classification order of surface alloying: blocked, incomplete, and complete. On that background, two diffusion problems, related to the atomic-scale surface morphology, will be discussed. The first problem deals with diffusion of atomic clusters on atomically smooth interface. On flat domains, far from terraces and steps, we analyzed the impact of size, shape, and cluster/substrate lattice misfit on the diffusion behavior of atomic clusters (islands). We found that the lattice constant of small clusters depends on the number N of building atoms at 1 < N ≤ 10. In heteroepitaxy, this effect of variable lattice constant originates from the enhanced charge transfer and the strong influence of the surface potential on cluster atomic arrangement. At constant temperature, the variation of the lattice constant leads to variable misfit which affects the island migration. The cluster/substrate commensurability influences the oscillation behavior of the diffusion coefficient caused by variation in the cluster shape. We discuss the results in a physical model that implies cluster diffusion with size-dependent cluster/substrate misfit. The second problem is devoted to diffusion phenomena in the vicinity of atomic terraces on stepped or vicinal surfaces. Here, we develop a computational model that refines important details of diffusion behavior of adatoms accounting for the energy barriers at specific atomic sites (smooth domains, terraces, and steps) located on the crystal surface. The dynamic competition between energy gained by mixing and substrate strain energy results in diffusion scenario where adatoms form alloyed islands and alloyed stripes in the vicinity of terrace edges. Being in agreement with recent experimental findings, the observed effect of stripe and island alloy formation opens up a way regular surface patterns to be configured at different atomic levels on the crystal surface. The complete surface alloying of the entire interface layer is also briefly discussed with critical analysis and classification of experimental findings and simulation data.

User Activity Recognition in Smart Homes Using Pattern Clustering Applied to Temporal ANN Algorithm.

PubMed

Bourobou, Serge Thomas Mickala; Yoo, Younghwan

2015-05-21

This paper discusses the possibility of recognizing and predicting user activities in the IoT (Internet of Things) based smart environment. The activity recognition is usually done through two steps: activity pattern clustering and activity type decision. Although many related works have been suggested, they had some limited performance because they focused only on one part between the two steps. This paper tries to find the best combination of a pattern clustering method and an activity decision algorithm among various existing works. For the first step, in order to classify so varied and complex user activities, we use a relevant and efficient unsupervised learning method called the K-pattern clustering algorithm. In the second step, the training of smart environment for recognizing and predicting user activities inside his/her personal space is done by utilizing the artificial neural network based on the Allen's temporal relations. The experimental results show that our combined method provides the higher recognition accuracy for various activities, as compared with other data mining classification algorithms. Furthermore, it is more appropriate for a dynamic environment like an IoT based smart home.

Coarse Point Cloud Registration by Egi Matching of Voxel Clusters

NASA Astrophysics Data System (ADS)

Wang, Jinhu; Lindenbergh, Roderik; Shen, Yueqian; Menenti, Massimo

2016-06-01

Laser scanning samples the surface geometry of objects efficiently and records versatile information as point clouds. However, often more scans are required to fully cover a scene. Therefore, a registration step is required that transforms the different scans into a common coordinate system. The registration of point clouds is usually conducted in two steps, i.e. coarse registration followed by fine registration. In this study an automatic marker-free coarse registration method for pair-wise scans is presented. First the two input point clouds are re-sampled as voxels and dimensionality features of the voxels are determined by principal component analysis (PCA). Then voxel cells with the same dimensionality are clustered. Next, the Extended Gaussian Image (EGI) descriptor of those voxel clusters are constructed using significant eigenvectors of each voxel in the cluster. Correspondences between clusters in source and target data are obtained according to the similarity between their EGI descriptors. The random sampling consensus (RANSAC) algorithm is employed to remove outlying correspondences until a coarse alignment is obtained. If necessary, a fine registration is performed in a final step. This new method is illustrated on scan data sampling two indoor scenarios. The results of the tests are evaluated by computing the point to point distance between the two input point clouds. The presented two tests resulted in mean distances of 7.6 mm and 9.5 mm respectively, which are adequate for fine registration.

High-order harmonic generation from a two-dimensional band structure

NASA Astrophysics Data System (ADS)

Jin, Jian-Zhao; Xiao, Xiang-Ru; Liang, Hao; Wang, Mu-Xue; Chen, Si-Ge; Gong, Qihuang; Peng, Liang-You

2018-04-01

In the past few years, harmonic generation in solids has attracted tremendous attention. Recently, some experiments of two-dimensional (2D) monolayer or few-layer materials have been carried out. These studies demonstrated that harmonic generation in the 2D case shows a strong dependence on the laser's orientation and ellipticity, which calls for a quantitative theoretical interpretation. In this work, we carry out a systematic study on the harmonic generation from a 2D band structure based on a numerical solution to the time-dependent Schrödinger equation. By comparing with the 1D case, we find that the generation dynamics can have a significant difference due to the existence of many crossing points in the 2D band structure. In particular, the higher conduction bands can be excited step by step via these crossing points and the total contribution of the harmonic is given by the mixing of transitions between different clusters of conduction bands to the valence band. We also present the orientation dependence of the harmonic yield on the laser polarization direction.

[Study of the clinical phenotype of symptomatic chronic airways disease by hierarchical cluster analysis and two-step cluster analyses].

PubMed

Ning, P; Guo, Y F; Sun, T Y; Zhang, H S; Chai, D; Li, X M

2016-09-01

To study the distinct clinical phenotype of chronic airway diseases by hierarchical cluster analysis and two-step cluster analysis. A population sample of adult patients in Donghuamen community, Dongcheng district and Qinghe community, Haidian district, Beijing from April 2012 to January 2015, who had wheeze within the last 12 months, underwent detailed investigation, including a clinical questionnaire, pulmonary function tests, total serum IgE levels, blood eosinophil level and a peak flow diary. Nine variables were chosen as evaluating parameters, including pre-salbutamol forced expired volume in one second(FEV1)/forced vital capacity(FVC) ratio, pre-salbutamol FEV1, percentage of post-salbutamol change in FEV1, residual capacity, diffusing capacity of the lung for carbon monoxide/alveolar volume adjusted for haemoglobin level, peak expiratory flow(PEF) variability, serum IgE level, cumulative tobacco cigarette consumption (pack-years) and respiratory symptoms (cough and expectoration). Subjects' different clinical phenotype by hierarchical cluster analysis and two-step cluster analysis was identified. (1) Four clusters were identified by hierarchical cluster analysis. Cluster 1 was chronic bronchitis in smokers with normal pulmonary function. Cluster 2 was chronic bronchitis or mild chronic obstructive pulmonary disease (COPD) patients with mild airflow limitation. Cluster 3 included COPD patients with heavy smoking, poor quality of life and severe airflow limitation. Cluster 4 recognized atopic patients with mild airflow limitation, elevated serum IgE and clinical features of asthma. Significant differences were revealed regarding pre-salbutamol FEV1/FVC%, pre-salbutamol FEV1% pred, post-salbutamol change in FEV1%, maximal mid-expiratory flow curve(MMEF)% pred, carbon monoxide diffusing capacity per liter of alveolar(DLCO)/(VA)% pred, residual volume(RV)% pred, total serum IgE level, smoking history (pack-years), St.George's respiratory questionnaire(SGRQ) score, acute exacerbation in the past one year, PEF variability and allergic dermatitis (P<0.05). (2) Four clusters were also identified by two-step cluster analysis as followings, cluster 1, COPD patients with moderate to severe airflow limitation; cluster 2, asthma and COPD patients with heavy smoking, airflow limitation and increased airways reversibility; cluster 3, patients having less smoking and normal pulmonary function with wheezing but no chronic cough; cluster 4, chronic bronchitis patients with normal pulmonary function and chronic cough. Significant differences were revealed regarding gender distribution, respiratory symptoms, pre-salbutamol FEV1/FVC%, pre-salbutamol FEV1% pred, post-salbutamol change in FEV1%, MMEF% pred, DLCO/VA% pred, RV% pred, PEF variability, total serum IgE level, cumulative tobacco cigarette consumption (pack-years), and SGRQ score (P<0.05). By different cluster analyses, distinct clinical phenotypes of chronic airway diseases are identified. Thus, individualized treatments may guide doctors to provide based on different phenotypes.

Probable alpha and 14C cluster emission from hyper Ac nuclei

NASA Astrophysics Data System (ADS)

Santhosh, K. P.

2013-10-01

A systematic study on the probability for the emission of 4He and 14C cluster from hyper {Λ/207-234}Ac and non-strange normal 207-234Ac nuclei are performed for the first time using our fission model, the Coulomb and proximity potential model (CPPM). The predicted half lives show that hyper {Λ/207-234}Ac nuclei are unstable against 4He emission and 14C emission from hyper {Λ/217-228}Ac are favorable for measurement. Our study also show that hyper {Λ/207-234}Ac are stable against hyper {Λ/4}He and {Λ/14}C emission. The role of neutron shell closure ( N = 126) in hyper {Λ/214}Fr daughter and role of proton/neutron shell closure ( Z ≈ 82, N = 126) in hyper {Λ/210}Bi daughter are also revealed. As hyper-nuclei decays to normal nuclei by mesonic/non-mesonic decay and since most of the predicted half lives for 4He and 14C emission from normal Ac nuclei are favourable for measurement, we presume that alpha and 14C cluster emission from hyper Ac nuclei can be detected in laboratory in a cascade (two-step) process.

Unequal cluster sizes in stepped-wedge cluster randomised trials: a systematic review.

PubMed

Kristunas, Caroline; Morris, Tom; Gray, Laura

2017-11-15

To investigate the extent to which cluster sizes vary in stepped-wedge cluster randomised trials (SW-CRT) and whether any variability is accounted for during the sample size calculation and analysis of these trials. Any, not limited to healthcare settings. Any taking part in an SW-CRT published up to March 2016. The primary outcome is the variability in cluster sizes, measured by the coefficient of variation (CV) in cluster size. Secondary outcomes include the difference between the cluster sizes assumed during the sample size calculation and those observed during the trial, any reported variability in cluster sizes and whether the methods of sample size calculation and methods of analysis accounted for any variability in cluster sizes. Of the 101 included SW-CRTs, 48% mentioned that the included clusters were known to vary in size, yet only 13% of these accounted for this during the calculation of the sample size. However, 69% of the trials did use a method of analysis appropriate for when clusters vary in size. Full trial reports were available for 53 trials. The CV was calculated for 23 of these: the median CV was 0.41 (IQR: 0.22-0.52). Actual cluster sizes could be compared with those assumed during the sample size calculation for 14 (26%) of the trial reports; the cluster sizes were between 29% and 480% of that which had been assumed. Cluster sizes often vary in SW-CRTs. Reporting of SW-CRTs also remains suboptimal. The effect of unequal cluster sizes on the statistical power of SW-CRTs needs further exploration and methods appropriate to studies with unequal cluster sizes need to be employed. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Two-step evolution of endosymbiosis between hydra and algae.

PubMed

Ishikawa, Masakazu; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-10-01

In the Hydra vulgaris group, only 2 of the 25 strains in the collection of the National Institute of Genetics in Japan currently show endosymbiosis with green algae. However, whether the other non-symbiotic strains also have the potential to harbor algae remains unknown. The endosymbiotic potential of non-symbiotic strains that can harbor algae may have been acquired before or during divergence of the strains. With the aim of understanding the evolutionary process of endosymbiosis in the H. vulgaris group, we examined the endosymbiotic potential of non-symbiotic strains of the H. vulgaris group by artificially introducing endosymbiotic algae. We found that 12 of the 23 non-symbiotic strains were able to harbor the algae until reaching the grand-offspring through the asexual reproduction by budding. Moreover, a phylogenetic analysis of mitochondrial genome sequences showed that all the strains with endosymbiotic potential grouped into a single cluster (cluster γ). This cluster contained two strains (J7 and J10) that currently harbor algae; however, these strains were not the closest relatives. These results suggest that evolution of endosymbiosis occurred in two steps; first, endosymbiotic potential was gained once in the ancestor of the cluster γ lineage; second, strains J7 and J10 obtained algae independently after the divergence of the strains. By demonstrating the evolution of the endosymbiotic potential in non-symbiotic H. vulgaris group strains, we have clearly distinguished two evolutionary steps. The step-by-step evolutionary process provides significant insight into the evolution of endosymbiosis in cnidarians. Copyright © 2016 Elsevier Inc. All rights reserved.

Clustering of Variables for Mixed Data

NASA Astrophysics Data System (ADS)

Saracco, J.; Chavent, M.

2016-05-01

This chapter presents clustering of variables which aim is to lump together strongly related variables. The proposed approach works on a mixed data set, i.e. on a data set which contains numerical variables and categorical variables. Two algorithms of clustering of variables are described: a hierarchical clustering and a k-means type clustering. A brief description of PCAmix method (that is a principal component analysis for mixed data) is provided, since the calculus of the synthetic variables summarizing the obtained clusters of variables is based on this multivariate method. Finally, the R packages ClustOfVar and PCAmixdata are illustrated on real mixed data. The PCAmix and ClustOfVar approaches are first used for dimension reduction (step 1) before applying in step 2 a standard clustering method to obtain groups of individuals.

User Activity Recognition in Smart Homes Using Pattern Clustering Applied to Temporal ANN Algorithm

PubMed Central

Bourobou, Serge Thomas Mickala; Yoo, Younghwan

2015-01-01

This paper discusses the possibility of recognizing and predicting user activities in the IoT (Internet of Things) based smart environment. The activity recognition is usually done through two steps: activity pattern clustering and activity type decision. Although many related works have been suggested, they had some limited performance because they focused only on one part between the two steps. This paper tries to find the best combination of a pattern clustering method and an activity decision algorithm among various existing works. For the first step, in order to classify so varied and complex user activities, we use a relevant and efficient unsupervised learning method called the K-pattern clustering algorithm. In the second step, the training of smart environment for recognizing and predicting user activities inside his/her personal space is done by utilizing the artificial neural network based on the Allen’s temporal relations. The experimental results show that our combined method provides the higher recognition accuracy for various activities, as compared with other data mining classification algorithms. Furthermore, it is more appropriate for a dynamic environment like an IoT based smart home. PMID:26007738

Constraining the baryon-dark matter relative velocity with the large-scale three-point correlation function of the SDSS BOSS DR12 CMASS galaxies

NASA Astrophysics Data System (ADS)

Slepian, Zachary; Eisenstein, Daniel J.; Blazek, Jonathan A.; Brownstein, Joel R.; Chuang, Chia-Hsun; Gil-Marín, Héctor; Ho, Shirley; Kitaura, Francisco-Shu; McEwen, Joseph E.; Percival, Will J.; Ross, Ashley J.; Rossi, Graziano; Seo, Hee-Jong; Slosar, Anže; Vargas-Magaña, Mariana

2018-02-01

We search for a galaxy clustering bias due to a modulation of galaxy number with the baryon-dark matter relative velocity resulting from recombination-era physics. We find no detected signal and place the constraint bv < 0.01 on the relative velocity bias for the CMASS galaxies. This bias is an important potential systematic of baryon acoustic oscillation (BAO) method measurements of the cosmic distance scale using the two-point clustering. Our limit on the relative velocity bias indicates a systematic shift of no more than 0.3 per cent rms in the distance scale inferred from the BAO feature in the BOSS two-point clustering, well below the 1 per cent statistical error of this measurement. This constraint is the most stringent currently available and has important implications for the ability of upcoming large-scale structure surveys such as the Dark Energy Spectroscopic Instrument (DESI) to self-protect against the relative velocity as a possible systematic.

Clustering evolving proteins into homologous families.

PubMed

Chan, Cheong Xin; Mahbob, Maisarah; Ragan, Mark A

2013-04-08

Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biologically meaningful families depends strongly on characteristics of the data, including content bias and degree of divergence. New, highly scalable methods have recently been introduced to cluster the very large datasets being generated by next-generation sequencing technologies. However, there has been little systematic investigation of how characteristics of the data impact the performance of these approaches. Using clusters from a manually curated dataset as reference, we examined the performance of a widely used graph-based Markov clustering algorithm (MCL) and a greedy heuristic approach (UCLUST) in delineating protein families coded by three sets of bacterial genomes of different G+C content. Both MCL and UCLUST generated clusters that are comparable to the reference sets at specific parameter settings, although UCLUST tends to under-cluster compositionally biased sequences (G+C content 33% and 66%). Using simulated data, we sought to assess the individual effects of sequence divergence, rate heterogeneity, and underlying G+C content. Performance decreased with increasing sequence divergence, decreasing among-site rate variation, and increasing G+C bias. Two MCL-based methods recovered the simulated families more accurately than did UCLUST. MCL using local alignment distances is more robust across the investigated range of sequence features than are greedy heuristics using distances based on global alignment. Our results demonstrate that sequence divergence, rate heterogeneity and content bias can individually and in combination affect the accuracy with which MCL and UCLUST can recover homologous protein families. For application to data that are more divergent, and exhibit higher among-site rate variation and/or content bias, MCL may often be the better choice, especially if computational resources are not limiting.

Learner Typologies Development Using OIndex and Data Mining Based Clustering Techniques

ERIC Educational Resources Information Center

Luan, Jing

2004-01-01

This explorative data mining project used distance based clustering algorithm to study 3 indicators, called OIndex, of student behavioral data and stabilized at a 6-cluster scenario following an exhaustive explorative study of 4, 5, and 6 cluster scenarios produced by K-Means and TwoStep algorithms. Using principles in data mining, the study…

The effect of billboard design specifications on driving: A pilot study.

PubMed

Marciano, Hadas; Setter, Pe'erly

2017-07-01

Decades of research on the effects of advertising billboards on road accident rates, driver performance, and driver visual scanning behavior, has produced no conclusive findings. We suggest that road safety researchers should shift their focus and attempt to identify the billboard characteristics that are most distracting to drivers. This line of research may produce concrete guidelines for permissible billboards that would be likely to reduce the influence of the billboards on road safety. The current study is a first step towards this end. A pool of 161 photos of real advertising billboards was used as stimuli within a triple task paradigm designed to simulate certain components of driving. Each trial consisted of one ongoing tracking task accompanied by two additional concurrent tasks: (1) billboard observation task; and (2) circle color change identification task. Five clusters of billboards, identified by conducting a cluster analysis of their graphic content, were used as a within variable in one-way ANOVAs conducted on performance level data collected from the multiple tasks. Cluster 5, labeled Loaded Billboards, yielded significantly deteriorated performance on the tracking task. Cluster 4, labeled Graphical Billboards, yielded deteriorated performance primarily on the color change identification task. Cluster 3, labeled Minimal Billboards, had no effect on any of these tasks. We strongly recommend that these clusters be systematically explored in experiments involving additional real driving settings, such as driving simulators and field studies. This will enable validation of the current results and help incorporate them into real driving situations. Copyright © 2017. Published by Elsevier Ltd.

Generalized quantum kinetic expansion: Higher-order corrections to multichromophoric Förster theory

NASA Astrophysics Data System (ADS)

Wu, Jianlan; Gong, Zhihao; Tang, Zhoufei

2015-08-01

For a general two-cluster energy transfer network, a new methodology of the generalized quantum kinetic expansion (GQKE) method is developed, which predicts an exact time-convolution equation for the cluster population evolution under the initial condition of the local cluster equilibrium state. The cluster-to-cluster rate kernel is expanded over the inter-cluster couplings. The lowest second-order GQKE rate recovers the multichromophoric Förster theory (MCFT) rate. The higher-order corrections to the MCFT rate are systematically included using the continued fraction resummation form, resulting in the resummed GQKE method. The reliability of the GQKE methodology is verified in two model systems, revealing the relevance of higher-order corrections.

Dark Energy Survey Year 1 results: cross-correlation redshifts - methods and systematics characterization

NASA Astrophysics Data System (ADS)

Gatti, M.; Vielzeuf, P.; Davis, C.; Cawthon, R.; Rau, M. M.; DeRose, J.; De Vicente, J.; Alarcon, A.; Rozo, E.; Gaztanaga, E.; Hoyle, B.; Miquel, R.; Bernstein, G. M.; Bonnett, C.; Carnero Rosell, A.; Castander, F. J.; Chang, C.; da Costa, L. N.; Gruen, D.; Gschwend, J.; Hartley, W. G.; Lin, H.; MacCrann, N.; Maia, M. A. G.; Ogando, R. L. C.; Roodman, A.; Sevilla-Noarbe, I.; Troxel, M. A.; Wechsler, R. H.; Asorey, J.; Davis, T. M.; Glazebrook, K.; Hinton, S. R.; Lewis, G.; Lidman, C.; Macaulay, E.; Möller, A.; O'Neill, C. R.; Sommer, N. E.; Uddin, S. A.; Yuan, F.; Zhang, B.; Abbott, T. M. C.; Allam, S.; Annis, J.; Bechtol, K.; Brooks, D.; Burke, D. L.; Carollo, D.; Carrasco Kind, M.; Carretero, J.; Cunha, C. E.; D'Andrea, C. B.; DePoy, D. L.; Desai, S.; Eifler, T. F.; Evrard, A. E.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Goldstein, D. A.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; Hoormann, J. K.; Jain, B.; James, D. J.; Jarvis, M.; Jeltema, T.; Johnson, M. W. G.; Johnson, M. D.; Krause, E.; Kuehn, K.; Kuhlmann, S.; Kuropatkin, N.; Li, T. S.; Lima, M.; Marshall, J. L.; Melchior, P.; Menanteau, F.; Nichol, R. C.; Nord, B.; Plazas, A. A.; Reil, K.; Rykoff, E. S.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sheldon, E.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Tucker, B. E.; Tucker, D. L.; Vikram, V.; Walker, A. R.; Weller, J.; Wester, W.; Wolf, R. C.

2018-06-01

We use numerical simulations to characterize the performance of a clustering-based method to calibrate photometric redshift biases. In particular, we cross-correlate the weak lensing source galaxies from the Dark Energy Survey Year 1 sample with redMaGiC galaxies (luminous red galaxies with secure photometric redshifts) to estimate the redshift distribution of the former sample. The recovered redshift distributions are used to calibrate the photometric redshift bias of standard photo-z methods applied to the same source galaxy sample. We apply the method to two photo-z codes run in our simulated data: Bayesian Photometric Redshift and Directional Neighbourhood Fitting. We characterize the systematic uncertainties of our calibration procedure, and find that these systematic uncertainties dominate our error budget. The dominant systematics are due to our assumption of unevolving bias and clustering across each redshift bin, and to differences between the shapes of the redshift distributions derived by clustering versus photo-zs. The systematic uncertainty in the mean redshift bias of the source galaxy sample is Δz ≲ 0.02, though the precise value depends on the redshift bin under consideration. We discuss possible ways to mitigate the impact of our dominant systematics in future analyses.

Segmentation and Quantitative Analysis of Apoptosis of Chinese Hamster Ovary Cells from Fluorescence Microscopy Images.

PubMed

Du, Yuncheng; Budman, Hector M; Duever, Thomas A

2017-06-01

Accurate and fast quantitative analysis of living cells from fluorescence microscopy images is useful for evaluating experimental outcomes and cell culture protocols. An algorithm is developed in this work to automatically segment and distinguish apoptotic cells from normal cells. The algorithm involves three steps consisting of two segmentation steps and a classification step. The segmentation steps are: (i) a coarse segmentation, combining a range filter with a marching square method, is used as a prefiltering step to provide the approximate positions of cells within a two-dimensional matrix used to store cells' images and the count of the number of cells for a given image; and (ii) a fine segmentation step using the Active Contours Without Edges method is applied to the boundaries of cells identified in the coarse segmentation step. Although this basic two-step approach provides accurate edges when the cells in a given image are sparsely distributed, the occurrence of clusters of cells in high cell density samples requires further processing. Hence, a novel algorithm for clusters is developed to identify the edges of cells within clusters and to approximate their morphological features. Based on the segmentation results, a support vector machine classifier that uses three morphological features: the mean value of pixel intensities in the cellular regions, the variance of pixel intensities in the vicinity of cell boundaries, and the lengths of the boundaries, is developed for distinguishing apoptotic cells from normal cells. The algorithm is shown to be efficient in terms of computational time, quantitative analysis, and differentiation accuracy, as compared with the use of the active contours method without the proposed preliminary coarse segmentation step.

Clustering on Magnesium Surfaces - Formation and Diffusion Energies.

PubMed

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and [Formula: see text]. In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a [Formula: see text], clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface [Formula: see text] is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich-Schwoebel barriers converge as the step height is three atomic layers or thicker. Adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.

Hierarchical clustering of EMD based interest points for road sign detection

NASA Astrophysics Data System (ADS)

Khan, Jesmin; Bhuiyan, Sharif; Adhami, Reza

2014-04-01

This paper presents an automatic road traffic signs detection and recognition system based on hierarchical clustering of interest points and joint transform correlation. The proposed algorithm consists of the three following stages: interest points detection, clustering of those points and similarity search. At the first stage, good discriminative, rotation and scale invariant interest points are selected from the image edges based on the 1-D empirical mode decomposition (EMD). We propose a two-step unsupervised clustering technique, which is adaptive and based on two criterion. In this context, the detected points are initially clustered based on the stable local features related to the brightness and color, which are extracted using Gabor filter. Then points belonging to each partition are reclustered depending on the dispersion of the points in the initial cluster using position feature. This two-step hierarchical clustering yields the possible candidate road signs or the region of interests (ROIs). Finally, a fringe-adjusted joint transform correlation (JTC) technique is used for matching the unknown signs with the existing known reference road signs stored in the database. The presented framework provides a novel way to detect a road sign from the natural scenes and the results demonstrate the efficacy of the proposed technique, which yields a very low false hit rate.

Pollen morphology and plant taxonomy of red oaks in eastern North America

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solomon, A.M.

Identification of Quercus (oak) pollen taxa could enhance Quaternary palynological interpretations from eastern North America. A first step is to determine a morphological and taxonomic basis for such identifications. Scanning electron microscopy was utilized to examine exine-surface features of 266 specimens representing 21 red oak (subgen. Erythrobalanus) species from eastern North America, and two intermediate oak (subgen. Protobalanus) species from the desert southwest. Twenty pollen morphological characteristics defined previously were tabulated for each of 324 pollen grains. The data were subjected to cluster analyses. Cluster diagrams were compared with traditional oak systematics. Pollen morphology and plant taxonomy compared poorly withmore » respect to series and species relationships among the red oaks, apparently due as much to high intraspecific and low interspecific variability in pollen-morphological characters as to the uncertain taxonomy of red oaks. Pollen morphology, however, does support the hypothesis of subgeneric oak evolution from intermediate oaks to the series Virentes of white oaks, and from more advanced white oaks to the red oak species. 19 references, 25 figures, 1 table.« less

Study of shallow junction formation by boron-containing cluster ion implantation of silicon and two-stage annealing

NASA Astrophysics Data System (ADS)

Lu, Xin-Ming

Shallow junction formation made by low energy ion implantation and rapid thermal annealing is facing a major challenge for ULSI (ultra large scale integration) as the line width decreases down to the sub micrometer region. The issues include low beam current, the channeling effect in low energy ion implantation and TED (transient enhanced diffusion) during annealing after ion implantation. In this work, boron containing small cluster ions, such as GeB, SiB and SiB2, was generated by using the SNICS (source of negative ion by cesium sputtering) ion source to implant into Si substrates to form shallow junctions. The use of boron containing cluster ions effectively reduces the boron energy while keeping the energy of the cluster ion beam at a high level. At the same time, it reduces the channeling effect due to amorphization by co-implanted heavy atoms like Ge and Si. Cluster ions have been used to produce 0.65--2keV boron for low energy ion implantation. Two stage annealing, which is a combination of low temperature (550°C) preannealing and high temperature annealing (1000°C), was carried out to anneal the Si sample implanted by GeB, SiBn clusters. The key concept of two-step annealing, that is, the separation of crystal regrowth, point defects removal with dopant activation from dopant diffusion, is discussed in detail. The advantages of the two stage annealing include better lattice structure, better dopant activation and retarded boron diffusion. The junction depth of the two stage annealed GeB sample was only half that of the one-step annealed sample, indicating that TED was suppressed by two stage annealing. Junction depths as small as 30 nm have been achieved by two stage annealing of sample implanted with 5 x 10-4/cm2 of 5 keV GeB at 1000°C for 1 second. The samples were evaluated by SIMS (secondary ion mass spectrometry) profiling, TEM (transmission electron microscopy) and RBS (Rutherford Backscattering Spectrometry)/channeling. Cluster ion implantation in combination with two-step annealing is effective in fabricating ultra-shallow junctions.

Measuring galaxy cluster masses with CMB lensing using a Maximum Likelihood estimator: statistical and systematic error budgets for future experiments

NASA Astrophysics Data System (ADS)

Raghunathan, Srinivasan; Patil, Sanjaykumar; Baxter, Eric J.; Bianchini, Federico; Bleem, Lindsey E.; Crawford, Thomas M.; Holder, Gilbert P.; Manzotti, Alessandro; Reichardt, Christian L.

2017-08-01

We develop a Maximum Likelihood estimator (MLE) to measure the masses of galaxy clusters through the impact of gravitational lensing on the temperature and polarization anisotropies of the cosmic microwave background (CMB). We show that, at low noise levels in temperature, this optimal estimator outperforms the standard quadratic estimator by a factor of two. For polarization, we show that the Stokes Q/U maps can be used instead of the traditional E- and B-mode maps without losing information. We test and quantify the bias in the recovered lensing mass for a comprehensive list of potential systematic errors. Using realistic simulations, we examine the cluster mass uncertainties from CMB-cluster lensing as a function of an experiment's beam size and noise level. We predict the cluster mass uncertainties will be 3 - 6% for SPT-3G, AdvACT, and Simons Array experiments with 10,000 clusters and less than 1% for the CMB-S4 experiment with a sample containing 100,000 clusters. The mass constraints from CMB polarization are very sensitive to the experimental beam size and map noise level: for a factor of three reduction in either the beam size or noise level, the lensing signal-to-noise improves by roughly a factor of two.

Applying Machine Learning to Star Cluster Classification

NASA Astrophysics Data System (ADS)

Fedorenko, Kristina; Grasha, Kathryn; Calzetti, Daniela; Mahadevan, Sridhar

2016-01-01

Catalogs describing populations of star clusters are essential in investigating a range of important issues, from star formation to galaxy evolution. Star cluster catalogs are typically created in a two-step process: in the first step, a catalog of sources is automatically produced; in the second step, each of the extracted sources is visually inspected by 3-to-5 human classifiers and assigned a category. Classification by humans is labor-intensive and time consuming, thus it creates a bottleneck, and substantially slows down progress in star cluster research.We seek to automate the process of labeling star clusters (the second step) through applying supervised machine learning techniques. This will provide a fast, objective, and reproducible classification. Our data is HST (WFC3 and ACS) images of galaxies in the distance range of 3.5-12 Mpc, with a few thousand star clusters already classified by humans as a part of the LEGUS (Legacy ExtraGalactic UV Survey) project. The classification is based on 4 labels (Class 1 - symmetric, compact cluster; Class 2 - concentrated object with some degree of asymmetry; Class 3 - multiple peak system, diffuse; and Class 4 - spurious detection). We start by looking at basic machine learning methods such as decision trees. We then proceed to evaluate performance of more advanced techniques, focusing on convolutional neural networks and other Deep Learning methods. We analyze the results, and suggest several directions for further improvement.

Simulation modeling for stratified breast cancer screening - a systematic review of cost and quality of life assumptions.

PubMed

Arnold, Matthias

2017-12-02

The economic evaluation of stratified breast cancer screening gains momentum, but produces also very diverse results. Systematic reviews so far focused on modeling techniques and epidemiologic assumptions. However, cost and utility parameters received only little attention. This systematic review assesses simulation models for stratified breast cancer screening based on their cost and utility parameters in each phase of breast cancer screening and care. A literature review was conducted to compare economic evaluations with simulation models of personalized breast cancer screening. Study quality was assessed using reporting guidelines. Cost and utility inputs were extracted, standardized and structured using a care delivery framework. Studies were then clustered according to their study aim and parameters were compared within the clusters. Eighteen studies were identified within three study clusters. Reporting quality was very diverse in all three clusters. Only two studies in cluster 1, four studies in cluster 2 and one study in cluster 3 scored high in the quality appraisal. In addition to the quality appraisal, this review assessed if the simulation models were consistent in integrating all relevant phases of care, if utility parameters were consistent and methodological sound and if cost were compatible and consistent in the actual parameters used for screening, diagnostic work up and treatment. Of 18 studies, only three studies did not show signs of potential bias. This systematic review shows that a closer look into the cost and utility parameter can help to identify potential bias. Future simulation models should focus on integrating all relevant phases of care, using methodologically sound utility parameters and avoiding inconsistent cost parameters.

Sample size determination for GEE analyses of stepped wedge cluster randomized trials.

PubMed

Li, Fan; Turner, Elizabeth L; Preisser, John S

2018-06-19

In stepped wedge cluster randomized trials, intact clusters of individuals switch from control to intervention from a randomly assigned period onwards. Such trials are becoming increasingly popular in health services research. When a closed cohort is recruited from each cluster for longitudinal follow-up, proper sample size calculation should account for three distinct types of intraclass correlations: the within-period, the inter-period, and the within-individual correlations. Setting the latter two correlation parameters to be equal accommodates cross-sectional designs. We propose sample size procedures for continuous and binary responses within the framework of generalized estimating equations that employ a block exchangeable within-cluster correlation structure defined from the distinct correlation types. For continuous responses, we show that the intraclass correlations affect power only through two eigenvalues of the correlation matrix. We demonstrate that analytical power agrees well with simulated power for as few as eight clusters, when data are analyzed using bias-corrected estimating equations for the correlation parameters concurrently with a bias-corrected sandwich variance estimator. © 2018, The International Biometric Society.

ctsGE-clustering subgroups of expression data.

PubMed

Sharabi-Schwager, Michal; Or, Etti; Ophir, Ron

2017-07-01

A pre-requisite to clustering noisy data, such as gene-expression data, is the filtering step. As an alternative to this step, the ctsGE R-package applies a sorting step in which all of the data are divided into small groups. The groups are divided according to how the time points are related to the time-series median. Then clustering is performed separately on each group. Thus, the clustering is done in two steps. First, an expression index (i.e. a sequence of 1, -1 and 0) is defined and genes with the same index are grouped together, and then each group of genes is clustered by k-means to create subgroups. The ctsGE package also provides an interactive tool to visualize and explore the gene-expression patterns and their subclusters. ctsGE proposes a way of organizing and exploring expression data without eliminating valuable information. Freely available as part of the Bioconductor project at https://bioconductor.org/packages/ctsGE/ . ron@agri.gov.il. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Onto-clust--a methodology for combining clustering analysis and ontological methods for identifying groups of comorbidities for developmental disorders.

PubMed

Peleg, Mor; Asbeh, Nuaman; Kuflik, Tsvi; Schertz, Mitchell

2009-02-01

Children with developmental disorders usually exhibit multiple developmental problems (comorbidities). Hence, such diagnosis needs to revolve on developmental disorder groups. Our objective is to systematically identify developmental disorder groups and represent them in an ontology. We developed a methodology that combines two methods (1) a literature-based ontology that we created, which represents developmental disorders and potential developmental disorder groups, and (2) clustering for detecting comorbid developmental disorders in patient data. The ontology is used to interpret and improve clustering results and the clustering results are used to validate the ontology and suggest directions for its development. We evaluated our methodology by applying it to data of 1175 patients from a child development clinic. We demonstrated that the ontology improves clustering results, bringing them closer to an expert generated gold-standard. We have shown that our methodology successfully combines an ontology with a clustering method to support systematic identification and representation of developmental disorder groups.

Do protein crystals nucleate within dense liquid clusters?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maes, Dominique, E-mail: dommaes@vub.ac.be; Vorontsova, Maria A.; Potenza, Marco A. C.

2015-06-27

The evolution of protein-rich clusters and nucleating crystals were characterized by dynamic light scattering (DLS), confocal depolarized dynamic light scattering (cDDLS) and depolarized oblique illumination dark-field microscopy. Newly nucleated crystals within protein-rich clusters were detected directly. These observations indicate that the protein-rich clusters are locations for crystal nucleation. Protein-dense liquid clusters are regions of high protein concentration that have been observed in solutions of several proteins. The typical cluster size varies from several tens to several hundreds of nanometres and their volume fraction remains below 10{sup −3} of the solution. According to the two-step mechanism of nucleation, the protein-rich clustersmore » serve as locations for and precursors to the nucleation of protein crystals. While the two-step mechanism explained several unusual features of protein crystal nucleation kinetics, a direct observation of its validity for protein crystals has been lacking. Here, two independent observations of crystal nucleation with the proteins lysozyme and glucose isomerase are discussed. Firstly, the evolutions of the protein-rich clusters and nucleating crystals were characterized simultaneously by dynamic light scattering (DLS) and confocal depolarized dynamic light scattering (cDDLS), respectively. It is demonstrated that protein crystals appear following a significant delay after cluster formation. The cDDLS correlation functions follow a Gaussian decay, indicative of nondiffusive motion. A possible explanation is that the crystals are contained inside large clusters and are driven by the elasticity of the cluster surface. Secondly, depolarized oblique illumination dark-field microscopy reveals the evolution from liquid clusters without crystals to newly nucleated crystals contained in the clusters to grown crystals freely diffusing in the solution. Collectively, the observations indicate that the protein-rich clusters in lysozyme and glucose isomerase solutions are locations for crystal nucleation.« less

Cluster-based analysis improves predictive validity of spike-triggered receptive field estimates

PubMed Central

Malone, Brian J.

2017-01-01

Spectrotemporal receptive field (STRF) characterization is a central goal of auditory physiology. STRFs are often approximated by the spike-triggered average (STA), which reflects the average stimulus preceding a spike. In many cases, the raw STA is subjected to a threshold defined by gain values expected by chance. However, such correction methods have not been universally adopted, and the consequences of specific gain-thresholding approaches have not been investigated systematically. Here, we evaluate two classes of statistical correction techniques, using the resulting STRF estimates to predict responses to a novel validation stimulus. The first, more traditional technique eliminated STRF pixels (time-frequency bins) with gain values expected by chance. This correction method yielded significant increases in prediction accuracy, including when the threshold setting was optimized for each unit. The second technique was a two-step thresholding procedure wherein clusters of contiguous pixels surviving an initial gain threshold were then subjected to a cluster mass threshold based on summed pixel values. This approach significantly improved upon even the best gain-thresholding techniques. Additional analyses suggested that allowing threshold settings to vary independently for excitatory and inhibitory subfields of the STRF resulted in only marginal additional gains, at best. In summary, augmenting reverse correlation techniques with principled statistical correction choices increased prediction accuracy by over 80% for multi-unit STRFs and by over 40% for single-unit STRFs, furthering the interpretational relevance of the recovered spectrotemporal filters for auditory systems analysis. PMID:28877194

Proposed variations of the stepped-wedge design can be used to accommodate multiple interventions.

PubMed

Lyons, Vivian H; Li, Lingyu; Hughes, James P; Rowhani-Rahbar, Ali

2017-06-01

Stepped-wedge design (SWD) cluster-randomized trials have traditionally been used for evaluating a single intervention. We aimed to explore design variants suitable for evaluating multiple interventions in an SWD trial. We identified four specific variants of the traditional SWD that would allow two interventions to be conducted within a single cluster-randomized trial: concurrent, replacement, supplementation, and factorial SWDs. These variants were chosen to flexibly accommodate study characteristics that limit a one-size-fits-all approach for multiple interventions. In the concurrent SWD, each cluster receives only one intervention, unlike the other variants. The replacement SWD supports two interventions that will not or cannot be used at the same time. The supplementation SWD is appropriate when the second intervention requires the presence of the first intervention, and the factorial SWD supports the evaluation of intervention interactions. The precision for estimating intervention effects varies across the four variants. Selection of the appropriate design variant should be driven by the research question while considering the trade-off between the number of steps, number of clusters, restrictions for concurrent implementation of the interventions, lingering effects of each intervention, and precision of the intervention effect estimates. Copyright © 2017 Elsevier Inc. All rights reserved.

Scoring clustering solutions by their biological relevance.

PubMed

Gat-Viks, I; Sharan, R; Shamir, R

2003-12-12

A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering gene expression data into homogeneous groups was shown to be instrumental in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on clustering algorithms for gene expression analysis, very few works addressed the systematic comparison and evaluation of clustering results. Typically, different clustering algorithms yield different clustering solutions on the same data, and there is no agreed upon guideline for choosing among them. We developed a novel statistically based method for assessing a clustering solution according to prior biological knowledge. Our method can be used to compare different clustering solutions or to optimize the parameters of a clustering algorithm. The method is based on projecting vectors of biological attributes of the clustered elements onto the real line, such that the ratio of between-groups and within-group variance estimators is maximized. The projected data are then scored using a non-parametric analysis of variance test, and the score's confidence is evaluated. We validate our approach using simulated data and show that our scoring method outperforms several extant methods, including the separation to homogeneity ratio and the silhouette measure. We apply our method to evaluate results of several clustering methods on yeast cell-cycle gene expression data. The software is available from the authors upon request.

Stacked Weak Lensing Mass Calibration: Estimators, Systematics, and Impact on Cosmological Parameter Constraints

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rozo, Eduardo; /U. Chicago /Chicago U., KICP; Wu, Hao-Yi

2011-11-04

When extracting the weak lensing shear signal, one may employ either locally normalized or globally normalized shear estimators. The former is the standard approach when estimating cluster masses, while the latter is the more common method among peak finding efforts. While both approaches have identical signal-to-noise in the weak lensing limit, it is possible that higher order corrections or systematic considerations make one estimator preferable over the other. In this paper, we consider the efficacy of both estimators within the context of stacked weak lensing mass estimation in the Dark Energy Survey (DES). We find that the two estimators havemore » nearly identical statistical precision, even after including higher order corrections, but that these corrections must be incorporated into the analysis to avoid observationally relevant biases in the recovered masses. We also demonstrate that finite bin-width effects may be significant if not properly accounted for, and that the two estimators exhibit different systematics, particularly with respect to contamination of the source catalog by foreground galaxies. Thus, the two estimators may be employed as a systematic cross-check of each other. Stacked weak lensing in the DES should allow for the mean mass of galaxy clusters to be calibrated to {approx}2% precision (statistical only), which can improve the figure of merit of the DES cluster abundance experiment by a factor of {approx}3 relative to the self-calibration expectation. A companion paper investigates how the two types of estimators considered here impact weak lensing peak finding efforts.« less

Quantum mean-field approximation for lattice quantum models: Truncating quantum correlations and retaining classical ones

NASA Astrophysics Data System (ADS)

Malpetti, Daniele; Roscilde, Tommaso

2017-02-01

The mean-field approximation is at the heart of our understanding of complex systems, despite its fundamental limitation of completely neglecting correlations between the elementary constituents. In a recent work [Phys. Rev. Lett. 117, 130401 (2016), 10.1103/PhysRevLett.117.130401], we have shown that in quantum many-body systems at finite temperature, two-point correlations can be formally separated into a thermal part and a quantum part and that quantum correlations are generically found to decay exponentially at finite temperature, with a characteristic, temperature-dependent quantum coherence length. The existence of these two different forms of correlation in quantum many-body systems suggests the possibility of formulating an approximation, which affects quantum correlations only, without preventing the correct description of classical fluctuations at all length scales. Focusing on lattice boson and quantum Ising models, we make use of the path-integral formulation of quantum statistical mechanics to introduce such an approximation, which we dub quantum mean-field (QMF) approach, and which can be readily generalized to a cluster form (cluster QMF or cQMF). The cQMF approximation reduces to cluster mean-field theory at T =0 , while at any finite temperature it produces a family of systematically improved, semi-classical approximations to the quantum statistical mechanics of the lattice theory at hand. Contrary to standard MF approximations, the correct nature of thermal critical phenomena is captured by any cluster size. In the two exemplary cases of the two-dimensional quantum Ising model and of two-dimensional quantum rotors, we study systematically the convergence of the cQMF approximation towards the exact result, and show that the convergence is typically linear or sublinear in the boundary-to-bulk ratio of the clusters as T →0 , while it becomes faster than linear as T grows. These results pave the way towards the development of semiclassical numerical approaches based on an approximate, yet systematically improved account of quantum correlations.

A cross-species bi-clustering approach to identifying conserved co-regulated genes.

PubMed

Sun, Jiangwen; Jiang, Zongliang; Tian, Xiuchun; Bi, Jinbo

2016-06-15

A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified from different species to reveal common subgroups. This approach is ineffective to deal with the noise in the expression data introduced by the complicated procedures in quantifying gene expression. Furthermore, due to the sequential nature of the approach, the gene clusters identified in the first step may have little overlap among different species in the second step, thus difficult to detect conserved co-regulated genes. We propose a cross-species bi-clustering approach which first denoises the gene expression data of each species into a data matrix. The rows of the data matrices of different species represent the same set of genes that are characterized by their expression patterns over the developmental stages of each species as columns. A novel bi-clustering method is then developed to cluster genes into subgroups by a joint sparse rank-one factorization of all the data matrices. This method decomposes a data matrix into a product of a column vector and a row vector where the column vector is a consistent indicator across the matrices (species) to identify the same gene cluster and the row vector specifies for each species the developmental stages that the clustered genes co-regulate. Efficient optimization algorithm has been developed with convergence analysis. This approach was first validated on synthetic data and compared to the two-step method and several recent joint clustering methods. We then applied this approach to two real world datasets of gene expression during the pre-implantation embryonic development of the human and mouse. Co-regulated genes consistent between the human and mouse were identified, offering insights into conserved functions, as well as similarities and differences in genome activation timing between the human and mouse embryos. The R package containing the implementation of the proposed method in C ++ is available at: https://github.com/JavonSun/mvbc.git and also at the R platform https://www.r-project.org/ jinbo@engr.uconn.edu. © The Author 2016. Published by Oxford University Press.

Rain volume estimation over areas using satellite and radar data

NASA Technical Reports Server (NTRS)

Doneaud, A. A.; Vonderhaar, T. H.

1985-01-01

The feasibility of rain volume estimation over fixed and floating areas was investigated using rapid scan satellite data following a technique recently developed with radar data, called the Area Time Integral (ATI) technique. The radar and rapid scan GOES satellite data were collected during the Cooperative Convective Precipitation Experiment (CCOPE) and North Dakota Cloud Modification Project (NDCMP). Six multicell clusters and cells were analyzed to the present time. A two-cycle oscillation emphasizing the multicell character of the clusters is demonstrated. Three clusters were selected on each day, 12 June and 2 July. The 12 June clusters occurred during the daytime, while the 2 July clusters during the nighttime. A total of 86 time steps of radar and 79 time steps of satellite images were analyzed. There were approximately 12-min time intervals between radar scans on the average.

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE PAGES

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu, Haijian; Huang, Hanchen; Wang, Jian

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Measuring galaxy cluster masses with CMB lensing using a Maximum Likelihood estimator: statistical and systematic error budgets for future experiments

DOE PAGES

Raghunathan, Srinivasan; Patil, Sanjaykumar; Baxter, Eric J.; ...

2017-08-25

We develop a Maximum Likelihood estimator (MLE) to measure the masses of galaxy clusters through the impact of gravitational lensing on the temperature and polarization anisotropies of the cosmic microwave background (CMB). We show that, at low noise levels in temperature, this optimal estimator outperforms the standard quadratic estimator by a factor of two. For polarization, we show that the Stokes Q/U maps can be used instead of the traditional E- and B-mode maps without losing information. We test and quantify the bias in the recovered lensing mass for a comprehensive list of potential systematic errors. Using realistic simulations, wemore » examine the cluster mass uncertainties from CMB-cluster lensing as a function of an experiment’s beam size and noise level. We predict the cluster mass uncertainties will be 3 - 6% for SPT-3G, AdvACT, and Simons Array experiments with 10,000 clusters and less than 1% for the CMB-S4 experiment with a sample containing 100,000 clusters. The mass constraints from CMB polarization are very sensitive to the experimental beam size and map noise level: for a factor of three reduction in either the beam size or noise level, the lensing signal-to-noise improves by roughly a factor of two.« less

Measuring galaxy cluster masses with CMB lensing using a Maximum Likelihood estimator: statistical and systematic error budgets for future experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raghunathan, Srinivasan; Patil, Sanjaykumar; Baxter, Eric J.

We develop a Maximum Likelihood estimator (MLE) to measure the masses of galaxy clusters through the impact of gravitational lensing on the temperature and polarization anisotropies of the cosmic microwave background (CMB). We show that, at low noise levels in temperature, this optimal estimator outperforms the standard quadratic estimator by a factor of two. For polarization, we show that the Stokes Q/U maps can be used instead of the traditional E- and B-mode maps without losing information. We test and quantify the bias in the recovered lensing mass for a comprehensive list of potential systematic errors. Using realistic simulations, wemore » examine the cluster mass uncertainties from CMB-cluster lensing as a function of an experiment’s beam size and noise level. We predict the cluster mass uncertainties will be 3 - 6% for SPT-3G, AdvACT, and Simons Array experiments with 10,000 clusters and less than 1% for the CMB-S4 experiment with a sample containing 100,000 clusters. The mass constraints from CMB polarization are very sensitive to the experimental beam size and map noise level: for a factor of three reduction in either the beam size or noise level, the lensing signal-to-noise improves by roughly a factor of two.« less

Measuring galaxy cluster masses with CMB lensing using a Maximum Likelihood estimator: statistical and systematic error budgets for future experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raghunathan, Srinivasan; Patil, Sanjaykumar; Bianchini, Federico

We develop a Maximum Likelihood estimator (MLE) to measure the masses of galaxy clusters through the impact of gravitational lensing on the temperature and polarization anisotropies of the cosmic microwave background (CMB). We show that, at low noise levels in temperature, this optimal estimator outperforms the standard quadratic estimator by a factor of two. For polarization, we show that the Stokes Q/U maps can be used instead of the traditional E- and B-mode maps without losing information. We test and quantify the bias in the recovered lensing mass for a comprehensive list of potential systematic errors. Using realistic simulations, wemore » examine the cluster mass uncertainties from CMB-cluster lensing as a function of an experiment's beam size and noise level. We predict the cluster mass uncertainties will be 3 - 6% for SPT-3G, AdvACT, and Simons Array experiments with 10,000 clusters and less than 1% for the CMB-S4 experiment with a sample containing 100,000 clusters. The mass constraints from CMB polarization are very sensitive to the experimental beam size and map noise level: for a factor of three reduction in either the beam size or noise level, the lensing signal-to-noise improves by roughly a factor of two.« less

Fast clustering using adaptive density peak detection.

PubMed

Wang, Xiao-Feng; Xu, Yifan

2017-12-01

Common limitations of clustering methods include the slow algorithm convergence, the instability of the pre-specification on a number of intrinsic parameters, and the lack of robustness to outliers. A recent clustering approach proposed a fast search algorithm of cluster centers based on their local densities. However, the selection of the key intrinsic parameters in the algorithm was not systematically investigated. It is relatively difficult to estimate the "optimal" parameters since the original definition of the local density in the algorithm is based on a truncated counting measure. In this paper, we propose a clustering procedure with adaptive density peak detection, where the local density is estimated through the nonparametric multivariate kernel estimation. The model parameter is then able to be calculated from the equations with statistical theoretical justification. We also develop an automatic cluster centroid selection method through maximizing an average silhouette index. The advantage and flexibility of the proposed method are demonstrated through simulation studies and the analysis of a few benchmark gene expression data sets. The method only needs to perform in one single step without any iteration and thus is fast and has a great potential to apply on big data analysis. A user-friendly R package ADPclust is developed for public use.

Adsorption configurations and scanning voltage determined STM images of small hydrogen clusters on bilayer graphene.

PubMed

Cao, Teng Fei; Huang, Liang Feng; Zheng, Xiao Hong; Zhou, Wang Huai; Zeng, Zhi

2013-11-21

By density functional theory calculations, the scanning tunneling microscopy (STM) images of various hydrogen clusters adsorbed on bilayer-graphene are systematically simulated. The hydrogen configurations of the STM images observed in the experiments have been thoroughly figured out. In particular, two kinds of hydrogen dimers (ortho-dimer, para-dimer) and two kinds of tetramers (tetramer-A, -B) are determined to be the hydrogen configurations corresponding to the ellipsoidal-like STM images with different structures and sizes. One particular hexamer (hexamer-B) is the hydrogen configuration generating the star-like STM images. For each hydrogen cluster, the simulated STM images show unique voltage-dependent features, which provides a feasible way to determine hydrogen adsorption states on graphene or graphite surface in the experiments by varying-voltage measurements. Stability analysis proves that the above determined hydrogen configurations are quite stable on graphene, hence they are likely to be detected in the STM experiments. Consequently, through systematic analysis of the STM images and the stability of hydrogen clusters on bilayer graphene, many experimental observations have been consistently explained.

Enhancing systematic implementation of skills training modules for persons with schizophrenia: three steps forward and two steps back?

PubMed

van Erp, Nicole H J; van Vugt, Maaike; Verhoeven, Dorien; Kroon, Hans

2009-01-01

This brief report addresses the systematic implementation of skills training modules for persons with schizophrenia or related disorders in three Dutch mental health agencies. Information on barriers, strategies and integration into routine daily practice was gathered at 0, 12 and 24 months through interviews with managers, program leaders, trainers, practitioners and clients. Overall implementation of the skills training modules for 74% of the persons with schizophrenia or related disorders was not feasible. Implementation was impeded by an incapable program leader, organizational changes, disappointing referrals and loss of trainers. The agencies made important steps forward to integrate the modules into routine daily practice. A reach percentage of 74% in two years time is too ambitious and needs to be adjusted. Systematic integration of the modules into routine daily practice is feasible, but requires solid program management and continuous effort to involve clients and practitioners.

Systematic review finds major deficiencies in sample size methodology and reporting for stepped-wedge cluster randomised trials

PubMed Central

Martin, James; Taljaard, Monica; Girling, Alan; Hemming, Karla

2016-01-01

Background Stepped-wedge cluster randomised trials (SW-CRT) are increasingly being used in health policy and services research, but unless they are conducted and reported to the highest methodological standards, they are unlikely to be useful to decision-makers. Sample size calculations for these designs require allowance for clustering, time effects and repeated measures. Methods We carried out a methodological review of SW-CRTs up to October 2014. We assessed adherence to reporting each of the 9 sample size calculation items recommended in the 2012 extension of the CONSORT statement to cluster trials. Results We identified 32 completed trials and 28 independent protocols published between 1987 and 2014. Of these, 45 (75%) reported a sample size calculation, with a median of 5.0 (IQR 2.5–6.0) of the 9 CONSORT items reported. Of those that reported a sample size calculation, the majority, 33 (73%), allowed for clustering, but just 15 (33%) allowed for time effects. There was a small increase in the proportions reporting a sample size calculation (from 64% before to 84% after publication of the CONSORT extension, p=0.07). The type of design (cohort or cross-sectional) was not reported clearly in the majority of studies, but cohort designs seemed to be most prevalent. Sample size calculations in cohort designs were particularly poor with only 3 out of 24 (13%) of these studies allowing for repeated measures. Discussion The quality of reporting of sample size items in stepped-wedge trials is suboptimal. There is an urgent need for dissemination of the appropriate guidelines for reporting and methodological development to match the proliferation of the use of this design in practice. Time effects and repeated measures should be considered in all SW-CRT power calculations, and there should be clarity in reporting trials as cohort or cross-sectional designs. PMID:26846897

Clustering of amines and hydrazines in atmospheric nucleation

NASA Astrophysics Data System (ADS)

Li, Siyang; Qu, Kun; Zhao, Hailiang; Ding, Lei; Du, Lin

2016-06-01

It has been proved that the presence of amines in the atmosphere can enhance aerosol formation. Hydrazine (HD) and its substituted derivatives, monomethylhydrazine (MMH) and unsymmetrical dimethylhydrazine (UDMH), which are organic derivatives of amine and ammonia, are common trace atmospheric species that may contribute to the growth of nucleation clusters. The structures of the hydrazine and amine clusters containing one or two common nucleation molecules (ammonia, water, methanol and sulfuric acid) have been optimized using density functional theory (DFT) methods. The clusters growth mechanism has been explored from the thermochemistry by calculating the Gibbs free energies of adding an ammonia, water, methanol or sulfuric acid molecule step by step at room temperature, respectively. The results show that hydrazine and its derivatives could enhance heteromolecular homogeneous nucleation in the earth's atmosphere.

Proposed variations of the stepped-wedge design can be used to accommodate multiple interventions

PubMed Central

Lyons, Vivian H; Li, Lingyu; Hughes, James P; Rowhani-Rahbar, Ali

2018-01-01

Objective Stepped wedge design (SWD) cluster randomized trials have traditionally been used for evaluating a single intervention. We aimed to explore design variants suitable for evaluating multiple interventions in a SWD trial. Study Design and Setting We identified four specific variants of the traditional SWD that would allow two interventions to be conducted within a single cluster randomized trial: Concurrent, Replacement, Supplementation and Factorial SWDs. These variants were chosen to flexibly accommodate study characteristics that limit a one-size-fits-all approach for multiple interventions. Results In the Concurrent SWD, each cluster receives only one intervention, unlike the other variants. The Replacement SWD supports two interventions that will not or cannot be employed at the same time. The Supplementation SWD is appropriate when the second intervention requires the presence of the first intervention, and the Factorial SWD supports the evaluation of intervention interactions. The precision for estimating intervention effects varies across the four variants. Conclusion Selection of the appropriate design variant should be driven by the research question while considering the trade-off between the number of steps, number of clusters, restrictions for concurrent implementation of the interventions, lingering effects of each intervention, and precision of the intervention effect estimates. PMID:28412466

Effectiveness of electronic guideline-based implementation systems in ambulatory care settings - a systematic review

PubMed Central

2009-01-01

Background Electronic guideline-based decision support systems have been suggested to successfully deliver the knowledge embedded in clinical practice guidelines. A number of studies have already shown positive findings for decision support systems such as drug-dosing systems and computer-generated reminder systems for preventive care services. Methods A systematic literature search (1990 to December 2008) of the English literature indexed in the Medline database, Embase, the Cochrane Central Register of Controlled Trials, and CRD (DARE, HTA and NHS EED databases) was conducted to identify evaluation studies of electronic multi-step guideline implementation systems in ambulatory care settings. Important inclusion criterions were the multidimensionality of the guideline (the guideline needed to consist of several aspects or steps) and real-time interaction with the system during consultation. Clinical decision support systems such as one-time reminders for preventive care for which positive findings were shown in earlier reviews were excluded. Two comparisons were considered: electronic multidimensional guidelines versus usual care (comparison one) and electronic multidimensional guidelines versus other guideline implementation methods (comparison two). Results Twenty-seven publications were selected for analysis in this systematic review. Most designs were cluster randomized controlled trials investigating process outcomes more than patient outcomes. With success defined as at least 50% of the outcome variables being significant, none of the studies were successful in improving patient outcomes. Only seven of seventeen studies that investigated process outcomes showed improvements in process of care variables compared with the usual care group (comparison one). No incremental effect of the electronic implementation over the distribution of paper versions of the guideline was found, neither for the patient outcomes nor for the process outcomes (comparison two). Conclusions There is little evidence at the moment for the effectiveness of an increasingly used and commercialised instrument such as electronic multidimensional guidelines. After more than a decade of development of numerous electronic systems, research on the most effective implementation strategy for this kind of guideline-based decision support systems is still lacking. This conclusion implies a considerable risk towards inappropriate investments in ineffective implementation interventions and in suboptimal care. PMID:20042070

Sample size calculation for stepped wedge and other longitudinal cluster randomised trials.

PubMed

Hooper, Richard; Teerenstra, Steven; de Hoop, Esther; Eldridge, Sandra

2016-11-20

The sample size required for a cluster randomised trial is inflated compared with an individually randomised trial because outcomes of participants from the same cluster are correlated. Sample size calculations for longitudinal cluster randomised trials (including stepped wedge trials) need to take account of at least two levels of clustering: the clusters themselves and times within clusters. We derive formulae for sample size for repeated cross-section and closed cohort cluster randomised trials with normally distributed outcome measures, under a multilevel model allowing for variation between clusters and between times within clusters. Our formulae agree with those previously described for special cases such as crossover and analysis of covariance designs, although simulation suggests that the formulae could underestimate required sample size when the number of clusters is small. Whether using a formula or simulation, a sample size calculation requires estimates of nuisance parameters, which in our model include the intracluster correlation, cluster autocorrelation, and individual autocorrelation. A cluster autocorrelation less than 1 reflects a situation where individuals sampled from the same cluster at different times have less correlated outcomes than individuals sampled from the same cluster at the same time. Nuisance parameters could be estimated from time series obtained in similarly clustered settings with the same outcome measure, using analysis of variance to estimate variance components. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Deciphering the sugar biosynthetic pathway and tailoring steps of nucleoside antibiotic A201A unveils a GDP-l-galactose mutase

PubMed Central

Zhu, Qinghua; Chen, Qi; Song, Yongxiang; Huang, Hongbo; Li, Jun; Ma, Junying; Li, Qinglian; Ju, Jianhua

2017-01-01

Galactose, a monosaccharide capable of assuming two possible configurational isomers (d-/l-), can exist as a six-membered ring, galactopyranose (Galp), or as a five-membered ring, galactofuranose (Galf). UDP-galactopyranose mutase (UGM) mediates the conversion of pyranose to furanose thereby providing a precursor for d-Galf. Moreover, UGM is critical to the virulence of numerous eukaryotic and prokaryotic human pathogens and thus represents an excellent antimicrobial drug target. However, the biosynthetic mechanism and relevant enzymes that drive l-Galf production have not yet been characterized. Herein we report that efforts to decipher the sugar biosynthetic pathway and tailoring steps en route to nucleoside antibiotic A201A led to the discovery of a GDP-l-galactose mutase, MtdL. Systematic inactivation of 18 of the 33 biosynthetic genes in the A201A cluster and elucidation of 10 congeners, coupled with feeding and in vitro biochemical experiments, enabled us to: (i) decipher the unique enzyme, GDP-l-galactose mutase associated with production of two unique d-mannose-derived sugars, and (ii) assign two glycosyltransferases, four methyltransferases, and one desaturase that regiospecifically tailor the A201A scaffold and display relaxed substrate specificities. Taken together, these data provide important insight into the origin of l-Galf-containing natural product biosynthetic pathways with likely ramifications in other organisms and possible antimicrobial drug targeting strategies. PMID:28438999

Automated modal parameter estimation using correlation analysis and bootstrap sampling

NASA Astrophysics Data System (ADS)

Yaghoubi, Vahid; Vakilzadeh, Majid K.; Abrahamsson, Thomas J. S.

2018-02-01

The estimation of modal parameters from a set of noisy measured data is a highly judgmental task, with user expertise playing a significant role in distinguishing between estimated physical and noise modes of a test-piece. Various methods have been developed to automate this procedure. The common approach is to identify models with different orders and cluster similar modes together. However, most proposed methods based on this approach suffer from high-dimensional optimization problems in either the estimation or clustering step. To overcome this problem, this study presents an algorithm for autonomous modal parameter estimation in which the only required optimization is performed in a three-dimensional space. To this end, a subspace-based identification method is employed for the estimation and a non-iterative correlation-based method is used for the clustering. This clustering is at the heart of the paper. The keys to success are correlation metrics that are able to treat the problems of spatial eigenvector aliasing and nonunique eigenvectors of coalescent modes simultaneously. The algorithm commences by the identification of an excessively high-order model from frequency response function test data. The high number of modes of this model provides bases for two subspaces: one for likely physical modes of the tested system and one for its complement dubbed the subspace of noise modes. By employing the bootstrap resampling technique, several subsets are generated from the same basic dataset and for each of them a model is identified to form a set of models. Then, by correlation analysis with the two aforementioned subspaces, highly correlated modes of these models which appear repeatedly are clustered together and the noise modes are collected in a so-called Trashbox cluster. Stray noise modes attracted to the mode clusters are trimmed away in a second step by correlation analysis. The final step of the algorithm is a fuzzy c-means clustering procedure applied to a three-dimensional feature space to assign a degree of physicalness to each cluster. The proposed algorithm is applied to two case studies: one with synthetic data and one with real test data obtained from a hammer impact test. The results indicate that the algorithm successfully clusters similar modes and gives a reasonable quantification of the extent to which each cluster is physical.

Systematic procedure for designing processes with multiple environmental objectives.

PubMed

Kim, Ki-Joo; Smith, Raymond L

2005-04-01

Evaluation of multiple objectives is very important in designing environmentally benign processes. It requires a systematic procedure for solving multiobjective decision-making problems due to the complex nature of the problems, the need for complex assessments, and the complicated analysis of multidimensional results. In this paper, a novel systematic procedure is presented for designing processes with multiple environmental objectives. This procedure has four steps: initialization, screening, evaluation, and visualization. The first two steps are used for systematic problem formulation based on mass and energy estimation and order of magnitude analysis. In the third step, an efficient parallel multiobjective steady-state genetic algorithm is applied to design environmentally benign and economically viable processes and to provide more accurate and uniform Pareto optimal solutions. In the last step a new visualization technique for illustrating multiple objectives and their design parameters on the same diagram is developed. Through these integrated steps the decision-maker can easily determine design alternatives with respect to his or her preferences. Most importantly, this technique is independent of the number of objectives and design parameters. As a case study, acetic acid recovery from aqueous waste mixtures is investigated by minimizing eight potential environmental impacts and maximizing total profit. After applying the systematic procedure, the most preferred design alternatives and their design parameters are easily identified.

Cosmological constraints from Chandra observations of galaxy clusters.

PubMed

Allen, Steven W

2002-09-15

Chandra observations of rich, relaxed galaxy clusters allow the properties of the X-ray gas and the total gravitating mass to be determined precisely. Here, we present results for a sample of the most X-ray luminous, dynamically relaxed clusters known. We show that the Chandra data and independent gravitational lensing studies provide consistent answers on the mass distributions in the clusters. The mass profiles exhibit a form in good agreement with the predictions from numerical simulations. Combining Chandra results on the X-ray gas mass fractions in the clusters with independent measurements of the Hubble constant and the mean baryonic matter density in the Universe, we obtain a tight constraint on the mean total matter density of the Universe, Omega(m), and an interesting constraint on the cosmological constant, Omega(Lambda). We also describe the 'virial relations' linking the masses, X-ray temperatures and luminosities of galaxy clusters. These relations provide a key step in linking the observed number density and spatial distribution of clusters to the predictions from cosmological models. The Chandra data confirm the presence of a systematic offset of ca. 40% between the normalization of the observed mass-temperature relation and the predictions from standard simulations. This finding leads to a significant revision of the best-fit value of sigma(8) inferred from the observed temperature and luminosity functions of clusters.

Dynamical evolution of globular-cluster systems in clusters of galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muzzio, J.C.

1987-04-01

The dynamical processes that affect globular-cluster systems in clusters of galaxies are analyzed. Two-body and impulsive approximations are utilized to study dynamical friction, drag force, tidal stripping, tidal radii, globular-cluster swapping, tidal accretion, and galactic cannibalism. The evolution of galaxies and the collision of galaxies are simulated numerically; the steps involved in the simulation are described. The simulated data are compared with observations. Consideration is given to the number of galaxies, halo extension, location of the galaxies, distribution of the missing mass, nonequilibrium initial conditions, mass dependence, massive central galaxies, globular-cluster distribution, and lost globular clusters. 116 references.

A two-step approach for mining patient treatment pathways in administrative healthcare databases.

PubMed

Najjar, Ahmed; Reinharz, Daniel; Girouard, Catherine; Gagné, Christian

2018-05-01

Clustering electronic medical records allows the discovery of information on healthcare practices. Entries in such medical records are usually composed of a succession of diagnostics or therapeutic steps. The corresponding processes are complex and heterogeneous since they depend on medical knowledge integrating clinical guidelines, the physician's individual experience, and patient data and conditions. To analyze such data, we are first proposing to cluster medical visits, consultations, and hospital stays into homogeneous groups, and then to construct higher-level patient treatment pathways over these different groups. These pathways are then also clustered to distill typical pathways, enabling interpretation of clusters by experts. This approach is evaluated on a real-world administrative database of elderly people in Québec suffering from heart failures. Copyright © 2018 Elsevier B.V. All rights reserved.

Apparatus for simultaneously disreefing a centrally reefed clustered parachute system

DOEpatents

Johnson, Donald W.

1988-01-01

A single multi-line cutter is connected to each of a cluster of parachutes by a separate short tether line that holds the parachutes, initially reefed by closed loop reefing lines, close to one another. The closed loop reefing lines and tether lines, one from each parachute, are disposed within the cutter to be simultaneously cut by its actuation when a central line attached between the payload and the cutter is stretched upon deployment of the cluster. A pyrotechnic or electronic time delay may be included in the cutter to delay the actual simultaneous cutting of all lines until the clustered parachutes attain a measure of stability prior to being disreefed. A second set of reefing lines and second tether lines may be provided for each parachute, to enable a two-stage, separately timed, step-by-step disreefing.

Apparatus for simultaneously disreefing a centrally reefed clustered parachute system

DOEpatents

Johnson, D.W.

1988-06-21

A single multi-line cutter is connected to each of a cluster of parachutes by a separate short tether line that holds the parachutes, initially reefed by closed loop reefing lines, close to one another. The closed loop reefing lines and tether lines, one from each parachute, are disposed within the cutter to be simultaneously cut by its actuation when a central line attached between the payload and the cutter is stretched upon deployment of the cluster. A pyrotechnic or electronic time delay may be included in the cutter to delay the actual simultaneous cutting of all lines until the clustered parachutes attain a measure of stability prior to being disreefed. A second set of reefing lines and second tether lines may be provided for each parachute, to enable a two-stage, separately timed, step-by-step disreefing. 13 figs.

Accounting for measurement error in biomarker data and misclassification of subtypes in the analysis of tumor data.

PubMed

Nevo, Daniel; Zucker, David M; Tamimi, Rulla M; Wang, Molin

2016-12-30

A common paradigm in dealing with heterogeneity across tumors in cancer analysis is to cluster the tumors into subtypes using marker data on the tumor, and then to analyze each of the clusters separately. A more specific target is to investigate the association between risk factors and specific subtypes and to use the results for personalized preventive treatment. This task is usually carried out in two steps-clustering and risk factor assessment. However, two sources of measurement error arise in these problems. The first is the measurement error in the biomarker values. The second is the misclassification error when assigning observations to clusters. We consider the case with a specified set of relevant markers and propose a unified single-likelihood approach for normally distributed biomarkers. As an alternative, we consider a two-step procedure with the tumor type misclassification error taken into account in the second-step risk factor analysis. We describe our method for binary data and also for survival analysis data using a modified version of the Cox model. We present asymptotic theory for the proposed estimators. Simulation results indicate that our methods significantly lower the bias with a small price being paid in terms of variance. We present an analysis of breast cancer data from the Nurses' Health Study to demonstrate the utility of our method. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Triadic split-merge sampler

NASA Astrophysics Data System (ADS)

van Rossum, Anne C.; Lin, Hai Xiang; Dubbeldam, Johan; van der Herik, H. Jaap

2018-04-01

In machine vision typical heuristic methods to extract parameterized objects out of raw data points are the Hough transform and RANSAC. Bayesian models carry the promise to optimally extract such parameterized objects given a correct definition of the model and the type of noise at hand. A category of solvers for Bayesian models are Markov chain Monte Carlo methods. Naive implementations of MCMC methods suffer from slow convergence in machine vision due to the complexity of the parameter space. Towards this blocked Gibbs and split-merge samplers have been developed that assign multiple data points to clusters at once. In this paper we introduce a new split-merge sampler, the triadic split-merge sampler, that perform steps between two and three randomly chosen clusters. This has two advantages. First, it reduces the asymmetry between the split and merge steps. Second, it is able to propose a new cluster that is composed out of data points from two different clusters. Both advantages speed up convergence which we demonstrate on a line extraction problem. We show that the triadic split-merge sampler outperforms the conventional split-merge sampler. Although this new MCMC sampler is demonstrated in this machine vision context, its application extend to the very general domain of statistical inference.

Hubble Frontier Fields: systematic errors in strong lensing models of galaxy clusters - implications for cosmography

NASA Astrophysics Data System (ADS)

Acebron, Ana; Jullo, Eric; Limousin, Marceau; Tilquin, André; Giocoli, Carlo; Jauzac, Mathilde; Mahler, Guillaume; Richard, Johan

2017-09-01

Strong gravitational lensing by galaxy clusters is a fundamental tool to study dark matter and constrain the geometry of the Universe. Recently, the Hubble Space Telescope Frontier Fields programme has allowed a significant improvement of mass and magnification measurements but lensing models still have a residual root mean square between 0.2 arcsec and few arcseconds, not yet completely understood. Systematic errors have to be better understood and treated in order to use strong lensing clusters as reliable cosmological probes. We have analysed two simulated Hubble-Frontier-Fields-like clusters from the Hubble Frontier Fields Comparison Challenge, Ares and Hera. We use several estimators (relative bias on magnification, density profiles, ellipticity and orientation) to quantify the goodness of our reconstructions by comparing our multiple models, optimized with the parametric software lenstool, with the input models. We have quantified the impact of systematic errors arising, first, from the choice of different density profiles and configurations and, secondly, from the availability of constraints (spectroscopic or photometric redshifts, redshift ranges of the background sources) in the parametric modelling of strong lensing galaxy clusters and therefore on the retrieval of cosmological parameters. We find that substructures in the outskirts have a significant impact on the position of the multiple images, yielding tighter cosmological contours. The need for wide-field imaging around massive clusters is thus reinforced. We show that competitive cosmological constraints can be obtained also with complex multimodal clusters and that photometric redshifts improve the constraints on cosmological parameters when considering a narrow range of (spectroscopic) redshifts for the sources.

An improved K-means clustering method for cDNA microarray image segmentation.

PubMed

Wang, T N; Li, T J; Shao, G F; Wu, S X

2015-07-14

Microarray technology is a powerful tool for human genetic research and other biomedical applications. Numerous improvements to the standard K-means algorithm have been carried out to complete the image segmentation step. However, most of the previous studies classify the image into two clusters. In this paper, we propose a novel K-means algorithm, which first classifies the image into three clusters, and then one of the three clusters is divided as the background region and the other two clusters, as the foreground region. The proposed method was evaluated on six different data sets. The analyses of accuracy, efficiency, expression values, special gene spots, and noise images demonstrate the effectiveness of our method in improving the segmentation quality.

Systematics in lensing reconstruction: dark matter rings in the sky?

NASA Astrophysics Data System (ADS)

Ponente, P. P.; Diego, J. M.

2011-11-01

Context. Non-parametric lensing methods are a useful way of reconstructing the lensing mass of a cluster without making assumptions about the way the mass is distributed in the cluster. These methods are particularly powerful in the case of galaxy clusters with a large number of constraints. The advantage of not assuming implicitly that the luminous matter follows the dark matter is particularly interesting in those cases where the cluster is in a non-relaxed dynamical state. On the other hand, non-parametric methods have several limitations that should be taken into account carefully. Aims: We explore some of these limitations and focus on their implications for the possible ring of dark matter around the galaxy cluster CL0024+17. Methods: We project three background galaxies through a mock cluster of known radial profile density and obtain a map for the arcs (θ map). We also calculate the shear field associated with the mock cluster across the whole field of view (3.3 arcmin). Combining the positions of the arcs and the two-direction shear, we perform an inversion of the lens equation using two separate methods, the biconjugate gradient, and the quadratic programming (QADP) to reconstruct the convergence map of the mock cluster. Results: We explore the space of the solutions of the convergence map and compare the radial density profiles to the density profile of the mock cluster. When the inversion matrix algorithms are forced to find the exact solution, we encounter systematic effects resembling ring structures, that clearly depart from the original convergence map. Conclusions: Overfitting lensing data with a non-parametric method can produce ring-like structures similar to the alleged one in CL0024.

Tics in TACs: A Step into an Avalanche? Systematic Literature Review and Conclusions.

PubMed

Wöber, Christian

2017-11-01

Trigeminal autonomic cephalalgias (TACs) comprise cluster headache, paroxysmal hemicrania, short-lasting unilateral neuralgiform headache attacks, and hemicrania continua. In some cases, trigeminal neuralgia (TN, "tic douloureux") or TN-like pain may co-occur with TACs. This article will review the co-occurrence and overlap of TACs and tics in order to contribute to a better understanding of the issue and an improved management of the patients. For performing a systematic literature review Pubmed was searched using a total of ten terms. The articles identified were screened for further articles of relevance. TACs are related to tics in various ways. TN or TN-like paroxysms may co-occur with CH, PH, and HC, labeled as cluster-tic syndrome, PH-tic syndrome, and HC-tic syndrome. Such co-occurrence was not only found in the primary TACs but also in secondary headaches resembling TACs. The initial onset of TAC and tic may be simultaneous or separated by months or years. In acute attacks, tic and TAC may occur concurrently or much more often independently of each other. The term "cluster-tic syndrome" was also used in patients with a single type of pain in a twilight zone between TACs and TN fulfilling none of the relevant diagnostic criteria. Short-lasting neuralgiform headache attacks overlap with TN in terms of clinical features, imaging findings, and therapy. © 2017 American Headache Society.

Exploiting the spatial locality of electron correlation within the parametric two-electron reduced-density-matrix method

NASA Astrophysics Data System (ADS)

DePrince, A. Eugene; Mazziotti, David A.

2010-01-01

The parametric variational two-electron reduced-density-matrix (2-RDM) method is applied to computing electronic correlation energies of medium-to-large molecular systems by exploiting the spatial locality of electron correlation within the framework of the cluster-in-molecule (CIM) approximation [S. Li et al., J. Comput. Chem. 23, 238 (2002); J. Chem. Phys. 125, 074109 (2006)]. The 2-RDMs of individual molecular fragments within a molecule are determined, and selected portions of these 2-RDMs are recombined to yield an accurate approximation to the correlation energy of the entire molecule. In addition to extending CIM to the parametric 2-RDM method, we (i) suggest a more systematic selection of atomic-orbital domains than that presented in previous CIM studies and (ii) generalize the CIM method for open-shell quantum systems. The resulting method is tested with a series of polyacetylene molecules, water clusters, and diazobenzene derivatives in minimal and nonminimal basis sets. Calculations show that the computational cost of the method scales linearly with system size. We also compute hydrogen-abstraction energies for a series of hydroxyurea derivatives. Abstraction of hydrogen from hydroxyurea is thought to be a key step in its treatment of sickle cell anemia; the design of hydroxyurea derivatives that oxidize more rapidly is one approach to devising more effective treatments.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Efficient One-Step Generation of Cluster State with Charge Qubits in Circuit QED

NASA Astrophysics Data System (ADS)

Wang, Yi-Min; Li, Cheng-Zu

2010-01-01

We propose theoretical schemes to generate highly entangled cluster state with superconducting qubits in a circuit QED architecture. Charge qubits are located inside a superconducting transmission line, which serves as a quantum data bus. We show that large clusters state can be efficiently generated in just one step with the long-range Ising-like unitary operators. The quantum operations which are generally realized by two coupling mechanisms: either voltage coupling or current coupling, depend only on global geometric features and are insensitive not only to the thermal state of the transmission line but also to certain random operation errors. Thus high-fidelity one-way quantum computation can be achieved.

Cluster structures influenced by interaction with a surface.

PubMed

Witt, Christopher; Dieterich, Johannes M; Hartke, Bernd

2018-05-30

Clusters on surfaces are vitally important for nanotechnological applications. Clearly, cluster-surface interactions heavily influence the preferred cluster structures, compared to clusters in vacuum. Nevertheless, systematic explorations and an in-depth understanding of these interactions and how they determine the cluster structures are still lacking. Here we present an extension of our well-established non-deterministic global optimization package OGOLEM from isolated clusters to clusters on surfaces. Applying this approach to intentionally simple Lennard-Jones test systems, we produce a first systematic exploration that relates changes in cluster-surface interactions to resulting changes in adsorbed cluster structures.

Studies of carbon incorporation on the diamond [100] surface during chemical vapor deposition using density functional theory.

PubMed

Cheesman, Andrew; Harvey, Jeremy N; Ashfold, Michael N R

2008-11-13

Accurate potential energy surface calculations are presented for many of the key steps involved in diamond chemical vapor deposition on the [100] surface (in its 2 x 1 reconstructed and hydrogenated form). The growing diamond surface was described by using a large (approximately 1500 atoms) cluster model, with the key atoms involved in chemical steps being described by using a quantum mechanical (QM, density functional theory, DFT) method and the bulk of the atoms being described by molecular mechanics (MM). The resulting hybrid QM/MM calculations are more systematic and/or at a higher level of theory than previous work on this growth process. The dominant process for carbon addition, in the form of methyl radicals, is predicted to be addition to a surface radical site, opening of the adjacent C-C dimer bond, insertion, and ultimate ring closure. Other steps such as insertion across the trough between rows of dimer bonds or addition to a neighboring dimer leading to formation of a reconstruction on the next layer may also contribute. Etching of carbon can also occur; the most likely mechanism involves loss of a two-carbon moiety in the form of ethene. The present higher-level calculations confirm that migration of inserted carbon along both dimer rows and chains should be relatively facile, with barriers of approximately 150 kJ mol (-1) when starting from suitable diradical species, and that this step should play an important role in establishing growth of smooth surfaces.

Which modifiable health risk behaviours are related? A systematic review of the clustering of Smoking, Nutrition, Alcohol and Physical activity ('SNAP') health risk factors.

PubMed

Noble, Natasha; Paul, Christine; Turon, Heidi; Oldmeadow, Christopher

2015-12-01

There is a growing body of literature examining the clustering of health risk behaviours, but little consensus about which risk factors can be expected to cluster for which sub groups of people. This systematic review aimed to examine the international literature on the clustering of smoking, poor nutrition, excess alcohol and physical inactivity (SNAP) health behaviours among adults, including associated socio-demographic variables. A literature search was conducted in May 2014. Studies examining at least two SNAP risk factors, and using a cluster or factor analysis technique, or comparing observed to expected prevalence of risk factor combinations, were included. Fifty-six relevant studies were identified. A majority of studies (81%) reported a 'healthy' cluster characterised by the absence of any SNAP risk factors. More than half of the studies reported a clustering of alcohol with smoking, and half reported clustering of all four SNAP risk factors. The methodological quality of included studies was generally weak to moderate. Males and those with greater social disadvantage showed riskier patterns of behaviours; younger age was less clearly associated with riskier behaviours. Clustering patterns reported here reinforce the need for health promotion interventions to target multiple behaviours, and for such efforts to be specifically designed and accessible for males and those who are socially disadvantaged. Copyright © 2015 Elsevier Inc. All rights reserved.

Determination of the structures of small gold clusters on stepped magnesia by density functional calculations.

PubMed

Damianos, Konstantina; Ferrando, Riccardo

2012-02-21

The structural modifications of small supported gold clusters caused by realistic surface defects (steps) in the MgO(001) support are investigated by computational methods. The most stable gold cluster structures on a stepped MgO(001) surface are searched for in the size range up to 24 Au atoms, and locally optimized by density-functional calculations. Several structural motifs are found within energy differences of 1 eV: inclined leaflets, arched leaflets, pyramidal hollow cages and compact structures. We show that the interaction with the step clearly modifies the structures with respect to adsorption on the flat defect-free surface. We find that leaflet structures clearly dominate for smaller sizes. These leaflets are either inclined and quasi-horizontal, or arched, at variance with the case of the flat surface in which vertical leaflets prevail. With increasing cluster size pyramidal hollow cages begin to compete against leaflet structures. Cage structures become more and more favourable as size increases. The only exception is size 20, at which the tetrahedron is found as the most stable isomer. This tetrahedron is however quite distorted. The comparison of two different exchange-correlation functionals (Perdew-Burke-Ernzerhof and local density approximation) show the same qualitative trends. This journal is © The Royal Society of Chemistry 2012

A VTVH MCD and EPR Spectroscopic Study of the Maturation of the "Second" Nitrogenase P-Cluster.

PubMed

Rupnik, Kresimir; Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W; Hales, Brian J

2018-04-16

The P-cluster of the nitrogenase MoFe protein is a [ Fe 8 S 7 ] cluster that mediates efficient transfer of electrons to the active site for substrate reduction. Arguably the most complex homometallic FeS cluster found in nature, the biosynthetic mechanism of the P-cluster is of considerable theoretical and synthetic interest to chemists and biochemists alike. Previous studies have revealed a biphasic assembly mechanism of the two P-clusters in the MoFe protein upon incubation with Fe protein and ATP, in which the first P-cluster is formed through fast fusion of a pair of [ Fe 4 S 4 ] + clusters within 5 min and the second P-cluster is formed through slow fusion of the second pair of [ Fe 4 S 4 ] + clusters in a period of 2 h. Here we report a VTVH MCD and EPR spectroscopic study of the biosynthesis of the slow-forming, second P-cluster within the MoFe protein. Our results show that the first major step in the formation of the second P-cluster is the conversion of one of the precursor [ Fe 4 S 4 ] + clusters into the integer spin cluster [ Fe 4 S 3-4 ] α , a process aided by the assembly protein NifZ, whereas the second major biosynthetic step appears to be the formation of a diamagnetic cluster with a possible structure of [ Fe 8 S 7-8 ] β , which is eventually converted into the P-cluster.

An aggregation-volume-bias Monte Carlo investigation on the condensation of a Lennard-Jones vapor below the triple point and crystal nucleation in cluster systems: an in-depth evaluation of the classical nucleation theory.

PubMed

Chen, Bin; Kim, Hyunmi; Keasler, Samuel J; Nellas, Ricky B

2008-04-03

The aggregation-volume-bias Monte Carlo based simulation technique, which has led to our recent success in vapor-liquid nucleation research, was extended to the study of crystal nucleation processes. In contrast to conventional bulk-phase techniques, this method deals with crystal nucleation events in cluster systems. This approach was applied to the crystal nucleation of Lennard-Jonesium under a wide range of undercooling conditions from 35% to 13% below the triple point. It was found that crystal nucleation in these model clusters proceeds initially via a vapor-liquid like aggregation followed by the formation of crystals inside the aggregates. The separation of these two stages of nucleation is distinct except at deeper undercooling conditions where the crystal nucleation barrier was found to diminish. The simulation results obtained for these two nucleation steps are separately compared to the classical nucleation theory (CNT). For the vapor-liquid nucleation step, the CNT was shown to provide a reasonable description of the critical cluster size but overestimate the barrier heights, consistent with previous simulation studies. On the contrary, for the crystal nucleation step, nearly perfect agreement with the barrier heights was found between the simulations and the CNT. For the critical cluster size, the comparison is more difficult as the simulation data were found to be sensitive to the definition of the solid cluster, but a stringent criterion and lower undercooling conditions generally lead to results closer with the CNT. Additional simulations at undercooling conditions of 40% or above indicate a nearly barrierless transition from the liquid to crystalline-like structure for sufficiently large clusters, which leads to further departure of the barrier height predicted by the CNT from the simulation data for the aggregation step. This is consistent with the latest experimental results on argon that show an unusually large underestimation of the nucleation rate by the CNT toward deep undercooling conditions.

[Alcohol consumption and positive alcohol expectancies in young adults: a typological approach using TwoStep cluster].

PubMed

Vautier, S; Jmel, S; Fourio, C; Moncany, D

2007-09-01

The present study investigates the heterogeneity of the population of young adult drinkers with respect to alcohol consumption and Positive Alcohol Expectancies (PAEs). Based on the positive relationship between both kinds of variables, PAE is commonly viewed as a potential motivational factor of alcoholic addiction. Empirical analyses based on the regression of alcohol consumption on PAEs suppose that the observations are statistically homogeneous with respect to the level of alcohol consumption, however. We explored the existence of moderate drinkers with a high PAE profile, and abusive drinkers with a low PAE profile. 1,017 young adult drinkers, mean age=23 +/- 2.84, with various educational levels, comprising 506 males and 511 females, were recruited as voluntary participants in a survey by undergraduate psychology students from the University of Toulouse Le Mirail. They completed a French version of the Alcohol Use Disorders Identifiction Test (AUDIT) and a French adaptation of the Alcohol Expectancy Questionnaire (AEQ). Three levels of alcohol consumption were defined using the AUDIT score, and six composite scores were obtained by averaging the relevant item-scores from the AEQ. The AEQ scores were interpreted as measurement of six kinds of PAEs, namely Global positive change, Sexual enhancement, Social and physical pleasure, Social assertiveness, Relaxation, and Arousal/Power. The TwoStep cluster methodology was used to explore the data. This methodology is convenient to deal with a mix of quantitative and qualitative variables, and it provides a classification model which is optimized through the use of an information criterion as Schwarz's Bayesian Information Criterion (BIC). The automatic clustering suggested five clusters, whose stability was ascertained until 75% of the sample size. Low drinkers (n=527) were split into one cluster of low PAEs (I1) and, interestingly, one cluster of high PAEs (I3, 46%). High drinkers (n=344) were split into one cluster of intermediate PAEs (II4) and one cluster of high PAEs (II5, 52%). Interestingly again, abusive drinkers (n=146) remained a single group (III2), exhibiting high PAEs. Clusters I3 and III3 comprised a significant proportion of males. Constraining the algorithm to find 6 clusters did not affect class III2, but split low drinkers into three clusters. Although the present results should be considered cautiously because of the novelty of TwoStep cluster methodology, they suggest a group of moderate drinkers with high PAEs. Also, abusive drinkers express high PAEs (except for 2 cases). Statistical homogeneity of moderate drinkers with respect to PAE variables appears as a dubious assumption.

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations.

PubMed

Peng, Bo; Kowalski, Karol

2017-09-12

The representation and storage of two-electron integral tensors are vital in large-scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this work, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition of the two-electron integral tensor in our implementation. For the size of the atomic basis set, N b , ranging from ∼100 up to ∼2,000, the observed numerical scaling of our implementation shows [Formula: see text] versus [Formula: see text] cost of performing single CD on the two-electron integral tensor in most of the other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic orbital (AO) two-electron integral tensor from [Formula: see text] to [Formula: see text] with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled cluster formalism employing single and double excitations (CCSD) on several benchmark systems including the C 60 molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10 -4 to 10 -3 to give acceptable compromise between efficiency and accuracy.

Room-temperature current blockade in atomically defined single-cluster junctions

NASA Astrophysics Data System (ADS)

Lovat, Giacomo; Choi, Bonnie; Paley, Daniel W.; Steigerwald, Michael L.; Venkataraman, Latha; Roy, Xavier

2017-11-01

Fabricating nanoscopic devices capable of manipulating and processing single units of charge is an essential step towards creating functional devices where quantum effects dominate transport characteristics. The archetypal single-electron transistor comprises a small conducting or semiconducting island separated from two metallic reservoirs by insulating barriers. By enabling the transfer of a well-defined number of charge carriers between the island and the reservoirs, such a device may enable discrete single-electron operations. Here, we describe a single-molecule junction comprising a redox-active, atomically precise cobalt chalcogenide cluster wired between two nanoscopic electrodes. We observe current blockade at room temperature in thousands of single-cluster junctions. Below a threshold voltage, charge transfer across the junction is suppressed. The device is turned on when the temporary occupation of the core states by a transiting carrier is energetically enabled, resulting in a sequential tunnelling process and an increase in current by a factor of ∼600. We perform in situ and ex situ cyclic voltammetry as well as density functional theory calculations to unveil a two-step process mediated by an orbital localized on the core of the cluster in which charge carriers reside before tunnelling to the collector reservoir. As the bias window of the junction is opened wide enough to include one of the cluster frontier orbitals, the current blockade is lifted and charge carriers can tunnel sequentially across the junction.

Metabolic network visualization eliminating node redundance and preserving metabolic pathways

PubMed Central

Bourqui, Romain; Cottret, Ludovic; Lacroix, Vincent; Auber, David; Mary, Patrick; Sagot, Marie-France; Jourdan, Fabien

2007-01-01

Background The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult. Results We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster. Conclusion The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism. PMID:17608928

Surfactant-controlled polymerization of semiconductor clusters to quantum dots through competing step-growth and living chain-growth mechanisms.

PubMed

Evans, Christopher M; Love, Alyssa M; Weiss, Emily A

2012-10-17

This article reports control of the competition between step-growth and living chain-growth polymerization mechanisms in the formation of cadmium chalcogenide colloidal quantum dots (QDs) from CdSe(S) clusters by varying the concentration of anionic surfactant in the synthetic reaction mixture. The growth of the particles proceeds by step-addition from initially nucleated clusters in the absence of excess phosphinic or carboxylic acids, which adsorb as their anionic conjugate bases, and proceeds indirectly by dissolution of clusters, and subsequent chain-addition of monomers to stable clusters (Ostwald ripening) in the presence of excess phosphinic or carboxylic acid. Fusion of clusters by step-growth polymerization is an explanation for the consistent observation of so-called "magic-sized" clusters in QD growth reactions. Living chain-addition (chain addition with no explicit termination step) produces QDs over a larger range of sizes with better size dispersity than step-addition. Tuning the molar ratio of surfactant to Se(2-)(S(2-)), the limiting ionic reagent, within the living chain-addition polymerization allows for stoichiometric control of QD radius without relying on reaction time.

Statistical detection of geographic clusters of resistant Escherichia coli in a regional network with WHONET and SaTScan.

PubMed

Park, Rachel; O'Brien, Thomas F; Huang, Susan S; Baker, Meghan A; Yokoe, Deborah S; Kulldorff, Martin; Barrett, Craig; Swift, Jamie; Stelling, John

2016-11-01

While antimicrobial resistance threatens the prevention, treatment, and control of infectious diseases, systematic analysis of routine microbiology laboratory test results worldwide can alert new threats and promote timely response. This study explores statistical algorithms for recognizing geographic clustering of multi-resistant microbes within a healthcare network and monitoring the dissemination of new strains over time. Escherichia coli antimicrobial susceptibility data from a three-year period stored in WHONET were analyzed across ten facilities in a healthcare network utilizing SaTScan's spatial multinomial model with two models for defining geographic proximity. We explored geographic clustering of multi-resistance phenotypes within the network and changes in clustering over time. Geographic clustering identified from both latitude/longitude and non-parametric facility groupings geographic models were similar, while the latter was offers greater flexibility and generalizability. Iterative application of the clustering algorithms suggested the possible recognition of the initial appearance of invasive E. coli ST131 in the clinical database of a single hospital and subsequent dissemination to others. Systematic analysis of routine antimicrobial resistance susceptibility test results supports the recognition of geographic clustering of microbial phenotypic subpopulations with WHONET and SaTScan, and iterative application of these algorithms can detect the initial appearance in and dissemination across a region prompting early investigation, response, and containment measures.

Suicide Contagion: A Systematic Review of Definitions and Research Utility

PubMed Central

Cheng, Qijin; Li, Hong; Silenzio, Vincent; Caine, Eric D.

2014-01-01

Objectives Despite the common use of contagion to analogize the spread of suicide, there is a lack of rigorous assessment of the underlying concept or theory supporting the use of this term. The present study aims to examine the varied definitions and potential utility of the term contagion in suicide-related research. Methods 100 initial records and 240 reference records in English were identified as relevant with our research objectives, through systematic literature screening. We then conducted narrative syntheses of various definitions and assessed their potential value for generating new research. Results 20.3% of the 340 records used contagion as equivalent to clustering (contagion-as-cluster); 68.5% used it to refer to various, often related mechanisms underlying the clustering phenomenon (contagion-as-mechanism); and 11.2% without clear definition. Under the category of contagion-as-mechanism, four mechanisms have been proposed to explain how suicide clusters occurred: transmission (contagion-as-transmission), imitation (contagion-as-imitation), contextual influence (contagion-as-context), and affiliation (contagion-as-affiliation). Contagion-as-cluster both confounds and constrains inquiry into suicide clustering by blending proposed mechanism with the phenomenon to be studied. Contagion-as-transmission is, in essence, a double or internally redundant metaphor. Contagion-as-affiliation and contagion-as-context involve mechanisms that are common mechanisms that often occur independently of apparent contagion, or may serve as a facilitating background. When used indiscriminately, these terms may create research blind spots. Contagion-as-imitation combines perspectives from psychology, sociology, and public health research and provides the greatest heuristic utility for examining whether and how suicide and suicidal behaviors may spread among persons at both individual and population levels. Conclusion Clarifying the concept of “suicide contagion” is an essential step for more thoroughly investigating its mechanisms. Developing a clearer understanding of the apparent spread of suicide-promoting influences can, in turn, offer insights necessary to build the scientific foundation for prevention and intervention strategies that can be applied at both individual and community levels. PMID:25259604

Student Motivational Profiles in an Introductory MIS Course: An Exploratory Cluster Analysis

ERIC Educational Resources Information Center

Nelson, Klara

2014-01-01

This study profiles students in an introductory MIS course according to a variety of variables associated with choice of academic major. The data were collected through a survey administered to 12 sections of the course. A two-step cluster analysis was performed with gender as a categorical variable and students' perceptions of task value…

Galaxy Clustering, Photometric Redshifts and Diagnosis of Systematics in the DES Science Verification Data

DOE PAGES

Crocce, M.

2015-12-09

We study the clustering of galaxies detected at i < 22.5 in the Science Verification observations of the Dark Energy Survey (DES). Two-point correlation functions are measured using 2.3 × 106 galaxies over a contiguous 116 deg 2 region in five bins of photometric redshift width Δz = 0.2 in the range 0.2 < z < 1.2. The impact of photometric redshift errors is assessed by comparing results using a template-based photo-zalgorithm (BPZ) to a machine-learning algorithm (TPZ). A companion paper presents maps of several observational variables (e.g. seeing, sky brightness) which could modulate the galaxy density. Here we characterizemore » and mitigate systematic errors on the measured clustering which arise from these observational variables, in addition to others such as Galactic dust and stellar contamination. After correcting for systematic effects, we then measure galaxy bias over a broad range of linear scales relative to mass clustering predicted from the Planck Λ cold dark matter model, finding agreement with the Canada-France-Hawaii Telescope Legacy Survey (CFHTLS) measurements with χ 2 of 4.0 (8.7) with 5 degrees of freedom for the TPZ (BPZ) redshifts. Furthermore, we test a ‘linear bias’ model, in which the galaxy clustering is a fixed multiple of the predicted non-linear dark matter clustering. The precision of the data allows us to determine that the linear bias model describes the observed galaxy clustering to 2.5 percent accuracy down to scales at least 4–10 times smaller than those on which linear theory is expected to be sufficient.« less

Galaxy Clustering, Photometric Redshifts and Diagnosis of Systematics in the DES Science Verification Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crocce, M.

We study the clustering of galaxies detected at i < 22.5 in the Science Verification observations of the Dark Energy Survey (DES). Two-point correlation functions are measured using 2.3 × 106 galaxies over a contiguous 116 deg 2 region in five bins of photometric redshift width Δz = 0.2 in the range 0.2 < z < 1.2. The impact of photometric redshift errors is assessed by comparing results using a template-based photo-zalgorithm (BPZ) to a machine-learning algorithm (TPZ). A companion paper presents maps of several observational variables (e.g. seeing, sky brightness) which could modulate the galaxy density. Here we characterizemore » and mitigate systematic errors on the measured clustering which arise from these observational variables, in addition to others such as Galactic dust and stellar contamination. After correcting for systematic effects, we then measure galaxy bias over a broad range of linear scales relative to mass clustering predicted from the Planck Λ cold dark matter model, finding agreement with the Canada-France-Hawaii Telescope Legacy Survey (CFHTLS) measurements with χ 2 of 4.0 (8.7) with 5 degrees of freedom for the TPZ (BPZ) redshifts. Furthermore, we test a ‘linear bias’ model, in which the galaxy clustering is a fixed multiple of the predicted non-linear dark matter clustering. The precision of the data allows us to determine that the linear bias model describes the observed galaxy clustering to 2.5 percent accuracy down to scales at least 4–10 times smaller than those on which linear theory is expected to be sufficient.« less

LoCuSS: comparison of observed X-ray and lensing galaxy cluster scaling relations with simulations

NASA Astrophysics Data System (ADS)

Zhang, Y.-Y.; Finoguenov, A.; Böhringer, H.; Kneib, J.-P.; Smith, G. P.; Kneissl, R.; Okabe, N.; Dahle, H.

2008-05-01

The Local Cluster Substructure Survey (LoCuSS, Smith et al.) is a systematic multi-wavelength survey of more than 100 X-ray luminous galaxy clusters in the redshift range 0.14-0.3 selected from the ROSAT All Sky Survey. We used data on 37 LoCuSS clusters from the XMM-Newton archive to investigate the global scaling relations of galaxy clusters. The scaling relations based solely on the X-ray data (S-T, S-Y_X, P-Y_X, M-T, M-Y_X, M-M_gas, M_gas-T, L-T, L-Y_X, and L-M) obey empirical self-similarity and reveal no additional evolution beyond the large-scale structure growth. They also reveal up to 17 per cent segregation between all 37 clusters and non-cool core clusters. Weak lensing mass measurements are also available in the literature for 19 of the clusters with XMM-Newton data. The average of the weak lensing mass to X-ray based mass ratio is 1.09± 0.08, setting the limit of the non-thermal pressure support to 9 ± 8 per cent. The mean of the weak lensing mass to X-ray based mass ratio of these clusters is ~1, indicating good agreement between X-ray and weak lensing masses for most clusters, although with 31-51 per cent scatter. The scatter in the mass-observable relations (M-Y_X, M-M_gas, and M-T) is smaller using X-ray based masses than using weak lensing masses by a factor of 2. With the scaled radius defined by the YX profile - r500 Y_X,X, r500YX,wl, and r500Y_X,si, we obtain lower scatter in the weak lensing mass based mass-observable relations, which means the origin of the scatter is M^wl and MX instead of Y_X. The normalization of the M-YX relation using X-ray mass estimates is lower than the one from simulations by up to 18-24 per cent at 3σ significance. This agrees with the M-YX relation based on weak lensing masses, the normalization of the latter being ~20 per cent lower than the one from simulations at ~2σ significance. This difference between observations and simulations is also indicated in the M-M_gas and M-T relations. Despite the large scatter in the comparison of X-ray to lensing, the agreement between these two completely independent observational methods is an important step towards controlling astrophysical and measurement systematics in cosmological scaling relations. This work is based on observations made with the XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA member states and the USA (NASA). Appendices A-C are only available in electronic form at http://www.aanda.org

Systematic Serendipity: A Method to Discover the Anomalous

NASA Astrophysics Data System (ADS)

Giles, Daniel; Walkowicz, Lucianne

2018-01-01

One of the challenges in the era of big data astronomical surveys is identifying anomalous data, data that exhibits as-of-yet unobserved behavior. These data may result from systematic errors, extreme (or rare) forms of known phenomena, or, most interestingly, truly novel phenomena that has historically required a trained eye and often fortuitous circumstance to identify. We describe a method that uses machine clustering techniques to discover anomalous data in Kepler lightcurves, as a step towards systematizing the detection of novel phenomena in the era of LSST. As a proof of concept, we apply our anomaly detection method to Kepler data including Boyajian's Star (KIC 8462852). We examine quarters 4, 8, 11, and 16 of the Kepler data which contain Boyajian’s Star acting normally (quarters 4 and 11) and anomalously (quarters 8 and 16). We demonstrate that our method is capable of identifying Boyajian’s Star’s anomalous behavior in quarters of interest, and we further identify other anomalous light curves that exhibit a range of interesting variability.

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Bo; Kowalski, Karol

The representation and storage of two-electron integral tensors are vital in large- scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this paper, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition ofmore » the two-electron integral tensor in our implementation. For the size of atomic basis set N_b ranging from ~ 100 up to ~ 2, 000, the observed numerical scaling of our implementation shows O(N_b^{2.5~3}) versus O(N_b^{3~4}) of single CD in most of other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic-orbital (AO) two-electron integral tensor from O(N_b^4) to O(N_b^2 log_{10}(N_b)) with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled- cluster formalism employing single and double excitations (CCSD) on several bench- mark systems including the C_{60} molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10^{-4} to 10^{-3} to give acceptable compromise between efficiency and accuracy.« less

Understanding Gas Phase Modifier Interactions in Rapid Analysis by Differential Mobility-Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kafle, Amol; Coy, Stephen L.; Wong, Bryan M.; Fornace, Albert J.; Glick, James J.; Vouros, Paul

2014-07-01

A systematic study involving the use and optimization of gas-phase modifiers in quantitative differential mobility-mass spectrometry (DMS-MS) analysis is presented using nucleoside-adduct biomarkers of DNA damage as an important reference point for analysis in complex matrices. Commonly used polar protic and polar aprotic modifiers have been screened for use against two deoxyguanosine adducts of DNA: N-(deoxyguanosin-8-yl)-4-aminobiphenyl (dG-C8-4-ABP) and N-(deoxyguanosin-8-y1)-2-amino-l-methyl-6-phenylimidazo[4,5-b]pyridine (dG-C8-PhIP). Particular attention was paid to compensation voltage (CoV) shifts, peak shapes, and product ion signal intensities while optimizing the DMS-MS conditions. The optimized parameters were then applied to rapid quantitation of the DNA adducts in calf thymus DNA. After a protein precipitation step, adduct levels corresponding to less than one modification in 106 normal DNA bases were detected using the DMS-MS platform. Based on DMS fundamentals and ab initio thermochemical results, we interpret the complexity of DMS modifier responses in terms of thermal activation and the development of solvent shells. At very high bulk gas temperature, modifier dipole moment may be the most important factor in cluster formation and cluster geometry, but at lower temperatures, multi-neutral clusters are important and less predictable. This work provides a useful protocol for targeted DNA adduct quantitation and a basis for future work on DMS modifier effects.

Understanding gas phase modifier interactions in rapid analysis by Differential Mobility-Tandem Mass Spectrometry

PubMed Central

Kafle, Amol; Coy, Stephen L.; Wong, Bryan M.; Fornace, Albert J.; Glick, James J.; Vouros, Paul

2014-01-01

A systematic study involving the use and optimization of gas phase modifiers in quantitative differential mobility- mass spectrometry (DMS-MS) analysis is presented using mucleoside-adduct biomarkers of DNA damage as an important reference point for analysis in complex matrices. Commonly used polar protic and polar aprotic modifiers have been screened for use against two deoxyguanosine adducts of DNA: N-(deoxyguanosin-8-yl)-4-aminobiphenyl (dG-C8-4-ABP) and N-(deoxyguanosin-8-y1)-2-amino-l-methyl-6-phenylimidazo[4,5-b]pyridine (dG-C8-PhIP). Particular attention was paid to compensation voltage (CoV) shifts, peak shapes and product ion signal intensities while optimizing the DMS-MS conditions. The optimized parameters were then applied to rapid quantitation of the DNA adducts in calf thymus DNA. After a protein precipitation step, adduct levels corresponding to less than one modification in 106 normal DNA bases were detected using the DMS-MS platform. Based on DMS fundamentals and ab-initio thermochemical results we interpret the complexity of DMS modifier responses in terms of thermal activation and the development of solvent shells. At very high bulk gas temperature, modifier dipole moment may be the most important factor in cluster formation and cluster geometry in mobility differences, but at lower temperatures multi-neutral clusters are important and less predictable. This work provides a useful protocol for targeted DNA adduct quantitation and a basis for future work on DMS modifier effects. PMID:24452298

Focusing cosmic telescopes: systematics of strong lens modeling

NASA Astrophysics Data System (ADS)

Johnson, Traci Lin; Sharon, Keren q.

2018-01-01

The use of strong gravitational lensing by galaxy clusters has become a popular method for studying the high redshift universe. While diverse in computational methods, lens modeling techniques have grasped the means for determining statistical errors on cluster masses and magnifications. However, the systematic errors have yet to be quantified, arising from the number of constraints, availablity of spectroscopic redshifts, and various types of image configurations. I will be presenting my dissertation work on quantifying systematic errors in parametric strong lensing techniques. I have participated in the Hubble Frontier Fields lens model comparison project, using simulated clusters to compare the accuracy of various modeling techniques. I have extended this project to understanding how changing the quantity of constraints affects the mass and magnification. I will also present my recent work extending these studies to clusters in the Outer Rim Simulation. These clusters are typical of the clusters found in wide-field surveys, in mass and lensing cross-section. These clusters have fewer constraints than the HFF clusters and thus, are more susceptible to systematic errors. With the wealth of strong lensing clusters discovered in surveys such as SDSS, SPT, DES, and in the future, LSST, this work will be influential in guiding the lens modeling efforts and follow-up spectroscopic campaigns.

Deciphering the sugar biosynthetic pathway and tailoring steps of nucleoside antibiotic A201A unveils a GDP-l-galactose mutase.

PubMed

Zhu, Qinghua; Chen, Qi; Song, Yongxiang; Huang, Hongbo; Li, Jun; Ma, Junying; Li, Qinglian; Ju, Jianhua

2017-05-09

Galactose, a monosaccharide capable of assuming two possible configurational isomers (d-/l-), can exist as a six-membered ring, galactopyranose (Gal p ), or as a five-membered ring, galactofuranose (Gal f ). UDP-galactopyranose mutase (UGM) mediates the conversion of pyranose to furanose thereby providing a precursor for d-Gal f Moreover, UGM is critical to the virulence of numerous eukaryotic and prokaryotic human pathogens and thus represents an excellent antimicrobial drug target. However, the biosynthetic mechanism and relevant enzymes that drive l-Gal f production have not yet been characterized. Herein we report that efforts to decipher the sugar biosynthetic pathway and tailoring steps en route to nucleoside antibiotic A201A led to the discovery of a GDP-l-galactose mutase, MtdL. Systematic inactivation of 18 of the 33 biosynthetic genes in the A201A cluster and elucidation of 10 congeners, coupled with feeding and in vitro biochemical experiments, enabled us to: ( i ) decipher the unique enzyme, GDP-l-galactose mutase associated with production of two unique d-mannose-derived sugars, and ( ii ) assign two glycosyltransferases, four methyltransferases, and one desaturase that regiospecifically tailor the A201A scaffold and display relaxed substrate specificities. Taken together, these data provide important insight into the origin of l-Gal f -containing natural product biosynthetic pathways with likely ramifications in other organisms and possible antimicrobial drug targeting strategies.

A comparison of regional flood frequency analysis approaches in a simulation framework

NASA Astrophysics Data System (ADS)

Ganora, D.; Laio, F.

2016-07-01

Regional frequency analysis (RFA) is a well-established methodology to provide an estimate of the flood frequency curve at ungauged (or scarcely gauged) sites. Different RFA approaches exist, depending on the way the information is transferred to the site of interest, but it is not clear in the literature if a specific method systematically outperforms the others. The aim of this study is to provide a framework wherein carrying out the intercomparison by building up a virtual environment based on synthetically generated data. The considered regional approaches include: (i) a unique regional curve for the whole region; (ii) a multiple-region model where homogeneous subregions are determined through cluster analysis; (iii) a Region-of-Influence model which defines a homogeneous subregion for each site; (iv) a spatially smooth estimation procedure where the parameters of the regional model vary continuously along the space. Virtual environments are generated considering different patterns of heterogeneity, including step change and smooth variations. If the region is heterogeneous, with the parent distribution changing continuously within the region, the spatially smooth regional approach outperforms the others, with overall errors 10-50% lower than the other methods. In the case of a step-change, the spatially smooth and clustering procedures perform similarly if the heterogeneity is moderate, while clustering procedures work better when the step-change is severe. To extend our findings, an extensive sensitivity analysis has been performed to investigate the effect of sample length, number of virtual stations, return period of the predicted quantile, variability of the scale parameter of the parent distribution, number of predictor variables and different parent distribution. Overall, the spatially smooth approach appears as the most robust approach as its performances are more stable across different patterns of heterogeneity, especially when short records are considered.

A holistic image segmentation framework for cloud detection and extraction

NASA Astrophysics Data System (ADS)

Shen, Dan; Xu, Haotian; Blasch, Erik; Horvath, Gregory; Pham, Khanh; Zheng, Yufeng; Ling, Haibin; Chen, Genshe

2013-05-01

Atmospheric clouds are commonly encountered phenomena affecting visual tracking from air-borne or space-borne sensors. Generally clouds are difficult to detect and extract because they are complex in shape and interact with sunlight in a complex fashion. In this paper, we propose a clustering game theoretic image segmentation based approach to identify, extract, and patch clouds. In our framework, the first step is to decompose a given image containing clouds. The problem of image segmentation is considered as a "clustering game". Within this context, the notion of a cluster is equivalent to a classical equilibrium concept from game theory, as the game equilibrium reflects both the internal and external (e.g., two-player) cluster conditions. To obtain the evolutionary stable strategies, we explore three evolutionary dynamics: fictitious play, replicator dynamics, and infection and immunization dynamics (InImDyn). Secondly, we use the boundary and shape features to refine the cloud segments. This step can lower the false alarm rate. In the third step, we remove the detected clouds and patch the empty spots by performing background recovery. We demonstrate our cloud detection framework on a video clip provides supportive results.

Chapter 7. Cloning and analysis of natural product pathways.

PubMed

Gust, Bertolt

2009-01-01

The identification of gene clusters of natural products has lead to an enormous wealth of information about their biosynthesis and its regulation, and about self-resistance mechanisms. Well-established routine techniques are now available for the cloning and sequencing of gene clusters. The subsequent functional analysis of the complex biosynthetic machinery requires efficient genetic tools for manipulation. Until recently, techniques for the introduction of defined changes into Streptomyces chromosomes were very time-consuming. In particular, manipulation of large DNA fragments has been challenging due to the absence of suitable restriction sites for restriction- and ligation-based techniques. The homologous recombination approach called recombineering (referred to as Red/ET-mediated recombination in this chapter) has greatly facilitated targeted genetic modifications of complex biosynthetic pathways from actinomycetes by eliminating many of the time-consuming and labor-intensive steps. This chapter describes techniques for the cloning and identification of biosynthetic gene clusters, for the generation of gene replacements within such clusters, for the construction of integrative library clones and their expression in heterologous hosts, and for the assembly of entire biosynthetic gene clusters from the inserts of individual library clones. A systematic approach toward insertional mutation of a complete Streptomyces genome is shown by the use of an in vitro transposon mutagenesis procedure.

The implementation of hybrid clustering using fuzzy c-means and divisive algorithm for analyzing DNA human Papillomavirus cause of cervical cancer

NASA Astrophysics Data System (ADS)

Andryani, Diyah Septi; Bustamam, Alhadi; Lestari, Dian

2017-03-01

Clustering aims to classify the different patterns into groups called clusters. In this clustering method, we use n-mers frequency to calculate the distance matrix which is considered more accurate than using the DNA alignment. The clustering results could be used to discover biologically important sub-sections and groups of genes. Many clustering methods have been developed, while hard clustering methods considered less accurate than fuzzy clustering methods, especially if it is used for outliers data. Among fuzzy clustering methods, fuzzy c-means is one the best known for its accuracy and simplicity. Fuzzy c-means clustering uses membership function variable, which refers to how likely the data could be members into a cluster. Fuzzy c-means clustering works using the principle of minimizing the objective function. Parameters of membership function in fuzzy are used as a weighting factor which is also called the fuzzier. In this study we implement hybrid clustering using fuzzy c-means and divisive algorithm which could improve the accuracy of cluster membership compare to traditional partitional approach only. In this study fuzzy c-means is used in the first step to find partition results. Furthermore divisive algorithms will run on the second step to find sub-clusters and dendogram of phylogenetic tree. To find the best number of clusters is determined using the minimum value of Davies Bouldin Index (DBI) of the cluster results. In this research, the results show that the methods introduced in this paper is better than other partitioning methods. Finally, we found 3 clusters with DBI value of 1.126628 at first step of clustering. Moreover, DBI values after implementing the second step of clustering are always producing smaller IDB values compare to the results of using first step clustering only. This condition indicates that the hybrid approach in this study produce better performance of the cluster results, in term its DBI values.

The use of feasibility studies for stepped-wedge cluster randomised trials: protocol for a review of impact and scope

PubMed Central

Kristunas, Caroline A; Hemming, Karla; Eborall, Helen C; Gray, Laura J

2017-01-01

Introduction The stepped-wedge cluster randomised trial (SW-CRT) is a complex design, for which many decisions about key design parameters must be made during the planning. These include the number of steps and the duration of time needed to embed the intervention. Feasibility studies are likely to be useful for informing these decisions and increasing the likelihood of the main trial's success. However, the number of feasibility studies being conducted for SW-CRTs is currently unknown. This review aims to establish the number of feasibility studies being conducted for SW-CRTs and determine which feasibility issues are commonly investigated. Methods and analysis Fully published feasibility studies for SW-CRTs will be identified, according to predefined inclusion criteria, from searches conducted in Ovid MEDLINE, Scopus, Embase and PsycINFO. To also identify and gain information on unpublished feasibility studies the following will be contacted: authors of published SW-CRTs (identified from the most recent systematic reviews); contacts for registered SW-CRTs (identified from clinical trials registries); lead statisticians of UK registered clinical trials units and researchers known to work in the area of SW-CRTs. Data extraction will be conducted independently by two reviewers. For the fully published feasibility studies, data will be extracted on the study characteristics, the rationale for the study, the process for determining progression to a main trial, how the study informed the main trial and whether the main trial went ahead. The researchers involved in the unpublished feasibility studies will be contacted to elicit the same information. A narrative synthesis will be conducted and provided alongside a descriptive analysis of the study characteristics. Ethics and dissemination This review does not require ethical approval, as no individual patient data will be used. The results of this review will be published in an open-access peer-reviewed journal. PMID:28765139

The use of feasibility studies for stepped-wedge cluster randomised trials: protocol for a review of impact and scope.

PubMed

Kristunas, Caroline A; Hemming, Karla; Eborall, Helen C; Gray, Laura J

2017-08-01

The stepped-wedge cluster randomised trial (SW-CRT) is a complex design, for which many decisions about key design parameters must be made during the planning. These include the number of steps and the duration of time needed to embed the intervention. Feasibility studies are likely to be useful for informing these decisions and increasing the likelihood of the main trial's success. However, the number of feasibility studies being conducted for SW-CRTs is currently unknown. This review aims to establish the number of feasibility studies being conducted for SW-CRTs and determine which feasibility issues are commonly investigated. Fully published feasibility studies for SW-CRTs will be identified, according to predefined inclusion criteria, from searches conducted in Ovid MEDLINE, Scopus, Embase and PsycINFO. To also identify and gain information on unpublished feasibility studies the following will be contacted: authors of published SW-CRTs (identified from the most recent systematic reviews); contacts for registered SW-CRTs (identified from clinical trials registries); lead statisticians of UK registered clinical trials units and researchers known to work in the area of SW-CRTs.Data extraction will be conducted independently by two reviewers. For the fully published feasibility studies, data will be extracted on the study characteristics, the rationale for the study, the process for determining progression to a main trial, how the study informed the main trial and whether the main trial went ahead. The researchers involved in the unpublished feasibility studies will be contacted to elicit the same information.A narrative synthesis will be conducted and provided alongside a descriptive analysis of the study characteristics. This review does not require ethical approval, as no individual patient data will be used. The results of this review will be published in an open-access peer-reviewed journal. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

An imbalance in cluster sizes does not lead to notable loss of power in cross-sectional, stepped-wedge cluster randomised trials with a continuous outcome.

PubMed

Kristunas, Caroline A; Smith, Karen L; Gray, Laura J

2017-03-07

The current methodology for sample size calculations for stepped-wedge cluster randomised trials (SW-CRTs) is based on the assumption of equal cluster sizes. However, as is often the case in cluster randomised trials (CRTs), the clusters in SW-CRTs are likely to vary in size, which in other designs of CRT leads to a reduction in power. The effect of an imbalance in cluster size on the power of SW-CRTs has not previously been reported, nor what an appropriate adjustment to the sample size calculation should be to allow for any imbalance. We aimed to assess the impact of an imbalance in cluster size on the power of a cross-sectional SW-CRT and recommend a method for calculating the sample size of a SW-CRT when there is an imbalance in cluster size. The effect of varying degrees of imbalance in cluster size on the power of SW-CRTs was investigated using simulations. The sample size was calculated using both the standard method and two proposed adjusted design effects (DEs), based on those suggested for CRTs with unequal cluster sizes. The data were analysed using generalised estimating equations with an exchangeable correlation matrix and robust standard errors. An imbalance in cluster size was not found to have a notable effect on the power of SW-CRTs. The two proposed adjusted DEs resulted in trials that were generally considerably over-powered. We recommend that the standard method of sample size calculation for SW-CRTs be used, provided that the assumptions of the method hold. However, it would be beneficial to investigate, through simulation, what effect the maximum likely amount of inequality in cluster sizes would be on the power of the trial and whether any inflation of the sample size would be required.

Density-Aware Clustering Based on Aggregated Heat Kernel and Its Transformation

DOE PAGES

Huang, Hao; Yoo, Shinjae; Yu, Dantong; ...

2015-06-01

Current spectral clustering algorithms suffer from the sensitivity to existing noise, and parameter scaling, and may not be aware of different density distributions across clusters. If these problems are left untreated, the consequent clustering results cannot accurately represent true data patterns, in particular, for complex real world datasets with heterogeneous densities. This paper aims to solve these problems by proposing a diffusion-based Aggregated Heat Kernel (AHK) to improve the clustering stability, and a Local Density Affinity Transformation (LDAT) to correct the bias originating from different cluster densities. AHK statistically\\ models the heat diffusion traces along the entire time scale, somore » it ensures robustness during clustering process, while LDAT probabilistically reveals local density of each instance and suppresses the local density bias in the affinity matrix. Our proposed framework integrates these two techniques systematically. As a result, not only does it provide an advanced noise-resisting and density-aware spectral mapping to the original dataset, but also demonstrates the stability during the processing of tuning the scaling parameter (which usually controls the range of neighborhood). Furthermore, our framework works well with the majority of similarity kernels, which ensures its applicability to many types of data and problem domains. The systematic experiments on different applications show that our proposed algorithms outperform state-of-the-art clustering algorithms for the data with heterogeneous density distributions, and achieve robust clustering performance with respect to tuning the scaling parameter and handling various levels and types of noise.« less

Fe-S Cluster Hsp70 Chaperones: The ATPase Cycle and Protein Interactions.

PubMed

Dutkiewicz, Rafal; Nowak, Malgorzata; Craig, Elizabeth A; Marszalek, Jaroslaw

2017-01-01

Hsp70 chaperones and their obligatory J-protein cochaperones function together in many cellular processes. Via cycles of binding to short stretches of exposed amino acids on substrate proteins, Hsp70/J-protein chaperones not only facilitate protein folding but also drive intracellular protein transport, biogenesis of cellular structures, and disassembly of protein complexes. The biogenesis of iron-sulfur (Fe-S) clusters is one of the critical cellular processes that require Hsp70/J-protein action. Fe-S clusters are ubiquitous cofactors critical for activity of proteins performing diverse functions in, for example, metabolism, RNA/DNA transactions, and environmental sensing. This biogenesis process can be divided into two sequential steps: first, the assembly of an Fe-S cluster on a conserved scaffold protein, and second, the transfer of the cluster from the scaffold to a recipient protein. The second step involves Hsp70/J-protein chaperones. Via binding to the scaffold, chaperones enable cluster transfer to recipient proteins. In eukaryotic cells mitochondria have a key role in Fe-S cluster biogenesis. In this review, we focus on methods that enabled us to dissect protein interactions critical for the function of Hsp70/J-protein chaperones in the mitochondrial process of Fe-S cluster biogenesis in the yeast Saccharomyces cerevisiae. © 2017 Elsevier Inc. All rights reserved.

Biocatalyst including porous enzyme cluster composite immobilized by two-step crosslinking and its utilization as enzymatic biofuel cell

NASA Astrophysics Data System (ADS)

Chung, Yongjin; Christwardana, Marcelinus; Tannia, Daniel Chris; Kim, Ki Jae; Kwon, Yongchai

2017-08-01

An enzyme cluster composite (TPA/GOx) formed from glucose oxidase (GOx) and terephthalaldehyde (TPA) that is coated onto polyethyleneimine (PEI) and carbon nanotubes (CNTs) is suggested as a new catalyst ([(TPA/GOx)/PEI]/CNT). In this catalyst, TPA promotes inter-GOx links by crosslinking to form a large and porous structure, and the TPA/GOx composite is again crosslinked with PEI/CNT to increase the amount of immobilized GOx. Such a two-step crosslinking (i) increases electron transfer because of electron delocalization by π conjugation and (ii) reduces GOx denaturation because of the formation of strong chemical bonds while its porosity facilitates mass transfer. With these features, an enzymatic biofuel cell (EBC) employing the new catalyst is fabricated and induces an excellent maximum power density (1.62 ± 0.08 mW cm-2), while the catalytic activity of the [(TPA/GOx)/PEI]/CNT catalyst is outstanding. This is clear evidence that the two-step crosslinking and porous structure caused by adoption of the TPA/GOx composite affect the performance enhancement of EBC.

Cluster observations of ion dispersion discontinuities in the polar cusp

NASA Astrophysics Data System (ADS)

Escoubet, C. P.; Berchem, J.; Pitout, F.; Richard, R. L.; Trattner, K. J.; Grison, B.; Taylor, M. G.; Masson, A.; Dunlop, M. W.; Dandouras, I. S.; Reme, H.; Fazakerley, A. N.

2009-12-01

The reconnection between the interplanetary magnetic field (IMF) and the Earth’s magnetic field is taking place at the magnetopause on magnetic field lines threading through the polar cusp. When the IMF is southward, reconnection occurs near the subsolar point, which is magnetically connected to the equatorward boundary of the polar cusp. Subsequently the ions injected through the reconnection point precipitate in the cusp and are dispersed poleward. If reconnection is continuous and operates at constant rate, the ion dispersion is smooth and continuous. On the other hand if the reconnection rate varies, we expect interruption in the dispersion forming energy steps or staircase. Similarly, multiple entries near the magnetopause could also produce steps at low or mid-altitude when a spacecraft is crossing subsequently the field lines originating from these multiple sources. In addition, motion of the magnetopause induced by solar wind pressure changes or erosion due to reconnection can also induce a motion of the polar cusp and a disruption of the ions dispersion observed by a spacecraft. Cluster with four spacecraft following each other in the mid-altitude cusp can be used to distinguish between these “temporal” and “spatial” effects. We will present a cusp crossing with two spacecraft, separated by around two minutes. The two spacecraft observed a very similar dispersion with a step in energy in its centre and two other dispersions poleward. We will show that the steps could be temporal (assuming that the time between two reconnection bursts corresponds to the time delay between the two spacecraft) but it would be a fortuitous coincidence. On the other hand the steps and the two poleward dispersions could be explained by spatial effects if we take into account the motion of the open-closed boundary between the two spacecraft crossings.

A complete, multi-level conformational clustering of antibody complementarity-determining regions

PubMed Central

Nikoloudis, Dimitris; Pitts, Jim E.

2014-01-01

Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation. PMID:25071986

Interplay between atomic disorder, lattice swelling and defect energy in ion-irradiation-induced amorphization of SiC

DOE PAGES

Debelle, Aurelien; Boulle, Alexandre; Chartier, Alain; ...

2014-11-25

We present a combination of experimental and computational evaluations of disorder level and lattice swelling in ion-irradiated materials. Information obtained from X-ray diffraction experiments is compared to X-ray diffraction data generated using atomic-scale simulations. The proposed methodology, which can be applied to a wide range of crystalline materials, is used to study the amorphization process in irradiated SiC. Results show that this process can be divided into two steps. In the first step, point defects and small defect clusters are produced and generate both large lattice swelling and high elastic energy. In the second step, enhanced coalescence of defects andmore » defect clusters occurs to limit this increase in energy, which rapidly leads to complete amorphization.« less

Hebbian self-organizing integrate-and-fire networks for data clustering.

PubMed

Landis, Florian; Ott, Thomas; Stoop, Ruedi

2010-01-01

We propose a Hebbian learning-based data clustering algorithm using spiking neurons. The algorithm is capable of distinguishing between clusters and noisy background data and finds an arbitrary number of clusters of arbitrary shape. These properties render the approach particularly useful for visual scene segmentation into arbitrarily shaped homogeneous regions. We present several application examples, and in order to highlight the advantages and the weaknesses of our method, we systematically compare the results with those from standard methods such as the k-means and Ward's linkage clustering. The analysis demonstrates that not only the clustering ability of the proposed algorithm is more powerful than those of the two concurrent methods, the time complexity of the method is also more modest than that of its generally used strongest competitor.

Border preserving skin lesion segmentation

NASA Astrophysics Data System (ADS)

Kamali, Mostafa; Samei, Golnoosh

2008-03-01

Melanoma is a fatal cancer with a growing incident rate. However it could be cured if diagnosed in early stages. The first step in detecting melanoma is the separation of skin lesion from healthy skin. There are particular features associated with a malignant lesion whose successful detection relies upon accurately extracted borders. We propose a two step approach. First, we apply K-means clustering method (to 3D RGB space) that extracts relatively accurate borders. In the second step we perform an extra refining step for detecting the fading area around some lesions as accurately as possible. Our method has a number of novelties. Firstly as the clustering method is directly applied to the 3D color space, we do not overlook the dependencies between different color channels. In addition, it is capable of extracting fine lesion borders up to pixel level in spite of the difficulties associated with fading areas around the lesion. Performing clustering in different color spaces reveals that 3D RGB color space is preferred. The application of the proposed algorithm to an extensive data-base of skin lesions shows that its performance is superior to that of existing methods both in terms of accuracy and computational complexity.

Photon-Induced Thermal Desorption of CO from Small Metal-Carbonyl Clusters

NASA Astrophysics Data System (ADS)

Lüttgens, G.; Pontius, N.; Bechthold, P. S.; Neeb, M.; Eberhardt, W.

2002-02-01

Thermal CO desorption from photoexcited free metal-carbonyl clusters has been resolved in real time using two-color pump-probe photoelectron spectroscopy. Sequential energy dissipation steps between the initial photoexcitation and the final desorption event, e.g., electron relaxation and thermalization, have been resolved for Au2(CO)- and Pt2(CO)-5. The desorption rates for the two clusters differ considerably due to the different numbers of vibrational degrees of freedom. The unimolecular CO-desorption thresholds of Au2(CO)- and Pt2(CO)-5 have been approximated by means of a statistical Rice-Ramsperger-Kassel calculation using the experimentally derived desorption rate constants.

Weighing the Giants - I. Weak-lensing masses for 51 massive galaxy clusters: project overview, data analysis methods and cluster images

NASA Astrophysics Data System (ADS)

von der Linden, Anja; Allen, Mark T.; Applegate, Douglas E.; Kelly, Patrick L.; Allen, Steven W.; Ebeling, Harald; Burchat, Patricia R.; Burke, David L.; Donovan, David; Morris, R. Glenn; Blandford, Roger; Erben, Thomas; Mantz, Adam

2014-03-01

This is the first in a series of papers in which we measure accurate weak-lensing masses for 51 of the most X-ray luminous galaxy clusters known at redshifts 0.15 ≲ zCl ≲ 0.7, in order to calibrate X-ray and other mass proxies for cosmological cluster experiments. The primary aim is to improve the absolute mass calibration of cluster observables, currently the dominant systematic uncertainty for cluster count experiments. Key elements of this work are the rigorous quantification of systematic uncertainties, high-quality data reduction and photometric calibration, and the `blind' nature of the analysis to avoid confirmation bias. Our target clusters are drawn from X-ray catalogues based on the ROSAT All-Sky Survey, and provide a versatile calibration sample for many aspects of cluster cosmology. We have acquired wide-field, high-quality imaging using the Subaru Telescope and Canada-France-Hawaii Telescope for all 51 clusters, in at least three bands per cluster. For a subset of 27 clusters, we have data in at least five bands, allowing accurate photometric redshift estimates of lensed galaxies. In this paper, we describe the cluster sample and observations, and detail the processing of the SuprimeCam data to yield high-quality images suitable for robust weak-lensing shape measurements and precision photometry. For each cluster, we present wide-field three-colour optical images and maps of the weak-lensing mass distribution, the optical light distribution and the X-ray emission. These provide insights into the large-scale structure in which the clusters are embedded. We measure the offsets between X-ray flux centroids and the brightest cluster galaxies in the clusters, finding these to be small in general, with a median of 20 kpc. For offsets ≲100 kpc, weak-lensing mass measurements centred on the brightest cluster galaxies agree well with values determined relative to the X-ray centroids; miscentring is therefore not a significant source of systematic uncertainty for our weak-lensing mass measurements. In accompanying papers, we discuss the key aspects of our photometric calibration and photometric redshift measurements (Kelly et al.), and measure cluster masses using two methods, including a novel Bayesian weak-lensing approach that makes full use of the photometric redshift probability distributions for individual background galaxies (Applegate et al.). In subsequent papers, we will incorporate these weak-lensing mass measurements into a self-consistent framework to simultaneously determine cluster scaling relations and cosmological parameters.

Statistical detection of geographic clusters of resistant Escherichia coli in a regional network with WHONET and SaTScan

PubMed Central

Park, Rachel; O'Brien, Thomas F.; Huang, Susan S.; Baker, Meghan A.; Yokoe, Deborah S.; Kulldorff, Martin; Barrett, Craig; Swift, Jamie; Stelling, John

2016-01-01

Objectives While antimicrobial resistance threatens the prevention, treatment, and control of infectious diseases, systematic analysis of routine microbiology laboratory test results worldwide can alert new threats and promote timely response. This study explores statistical algorithms for recognizing geographic clustering of multi-resistant microbes within a healthcare network and monitoring the dissemination of new strains over time. Methods Escherichia coli antimicrobial susceptibility data from a three-year period stored in WHONET were analyzed across ten facilities in a healthcare network utilizing SaTScan's spatial multinomial model with two models for defining geographic proximity. We explored geographic clustering of multi-resistance phenotypes within the network and changes in clustering over time. Results Geographic clustering identified from both latitude/longitude and non-parametric facility groupings geographic models were similar, while the latter was offers greater flexibility and generalizability. Iterative application of the clustering algorithms suggested the possible recognition of the initial appearance of invasive E. coli ST131 in the clinical database of a single hospital and subsequent dissemination to others. Conclusion Systematic analysis of routine antimicrobial resistance susceptibility test results supports the recognition of geographic clustering of microbial phenotypic subpopulations with WHONET and SaTScan, and iterative application of these algorithms can detect the initial appearance in and dissemination across a region prompting early investigation, response, and containment measures. PMID:27530311

Role of protein-glutathione contacts in defining glutaredoxin-3 [2Fe-2S] cluster chirality, ligand exchange and transfer chemistry.

PubMed

Sen, Sambuddha; Cowan, J A

2017-10-01

Monothiol glutaredoxins (Grx) serve as intermediate cluster carriers in iron-sulfur cluster trafficking. The [2Fe-2S]-bound holo forms of Grx proteins display cysteinyl coordination from exogenous glutathione (GSH), in addition to contact from protein-derived Cys. Herein, we report mechanistic studies that investigate the role of exogenous glutathione in defining cluster chirality, ligand exchange, and the cluster transfer chemistry of Saccharomyces cerevisiae Grx3. Systematic perturbations were introduced to the glutathione-binding site by substitution of conserved charged amino acids that form crucial electrostatic contacts with the glutathione molecule. Native Grx3 could also be reconstituted in the absence of glutathione, with either DTT, BME or free L-cysteine as the source of the exogenous Fe-S ligand contact, while retaining full functional reactivity. The delivery of the [2Fe-2S] cluster to Grx3 from cluster donor proteins such as Isa, Nfu, and a [2Fe-2S](GS) 4 complex, revealed that electrostatic contacts are of key importance for positioning the exogenous glutathione that in turn influences the chiral environment of the cluster. All Grx3 derivatives were reconstituted by standard chemical reconstitution protocols and found to transfer cluster to apo ferredoxin 1 (Fdx1) at rates comparable to native protein, even when using DTT, BME or free L-cysteine as a thiol source in place of GSH during reconstitution. Kinetic analysis of cluster transfer from holo derivatives to apo Fdx1 has led to a mechanistic model for cluster transfer chemistry of native holo Grx3, and identification of the likely rate-limiting step for the reaction.

A Survey on Clustering Routing Protocols in Wireless Sensor Networks

PubMed Central

Liu, Xuxun

2012-01-01

The past few years have witnessed increased interest in the potential use of wireless sensor networks (WSNs) in a wide range of applications and it has become a hot research area. Based on network structure, routing protocols in WSNs can be divided into two categories: flat routing and hierarchical or clustering routing. Owing to a variety of advantages, clustering is becoming an active branch of routing technology in WSNs. In this paper, we present a comprehensive and fine grained survey on clustering routing protocols proposed in the literature for WSNs. We outline the advantages and objectives of clustering for WSNs, and develop a novel taxonomy of WSN clustering routing methods based on complete and detailed clustering attributes. In particular, we systematically analyze a few prominent WSN clustering routing protocols and compare these different approaches according to our taxonomy and several significant metrics. Finally, we summarize and conclude the paper with some future directions. PMID:23112649

A survey on clustering routing protocols in wireless sensor networks.

PubMed

Liu, Xuxun

2012-01-01

The past few years have witnessed increased interest in the potential use of wireless sensor networks (WSNs) in a wide range of applications and it has become a hot research area. Based on network structure, routing protocols in WSNs can be divided into two categories: flat routing and hierarchical or clustering routing. Owing to a variety of advantages, clustering is becoming an active branch of routing technology in WSNs. In this paper, we present a comprehensive and fine grained survey on clustering routing protocols proposed in the literature for WSNs. We outline the advantages and objectives of clustering for WSNs, and develop a novel taxonomy of WSN clustering routing methods based on complete and detailed clustering attributes. In particular, we systematically analyze a few prominent WSN clustering routing protocols and compare these different approaches according to our taxonomy and several significant metrics. Finally, we summarize and conclude the paper with some future directions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xiang; Zhang, Shuai; Jiao, Fang

Two-step nucleation pathways in which disordered, amorphous, or dense liquid states precede appearance of crystalline phases have been reported for a wide range of materials, but the dynamics of such pathways are poorly understood. Moreover, whether these pathways are general features of crystallizing systems or a consequence of system-specific structural details that select for direct vs two-step processes is unknown. Using atomic force microscopy to directly observe crystallization of sequence-defined polymers, we show that crystallization pathways are indeed sequence dependent. When a short hydrophobic region is added to a sequence that directly forms crystalline particles, crystallization instead follows a two-stepmore » pathway that begins with creation of disordered clusters of 10-20 molecules and is characterized by highly non-linear crystallization kinetics in which clusters transform into ordered structures that then enter the growth phase. The results shed new light on non-classical crystallization mechanisms and have implications for design of self-assembling polymer systems.« less

The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs.

PubMed

Thompson, Jennifer A; Fielding, Katherine; Hargreaves, James; Copas, Andrew

2017-12-01

Background/Aims We sought to optimise the design of stepped wedge trials with an equal allocation of clusters to sequences and explored sample size comparisons with alternative trial designs. Methods We developed a new expression for the design effect for a stepped wedge trial, assuming that observations are equally correlated within clusters and an equal number of observations in each period between sequences switching to the intervention. We minimised the design effect with respect to (1) the fraction of observations before the first and after the final sequence switches (the periods with all clusters in the control or intervention condition, respectively) and (2) the number of sequences. We compared the design effect of this optimised stepped wedge trial to the design effects of a parallel cluster-randomised trial, a cluster-randomised trial with baseline observations, and a hybrid trial design (a mixture of cluster-randomised trial and stepped wedge trial) with the same total cluster size for all designs. Results We found that a stepped wedge trial with an equal allocation to sequences is optimised by obtaining all observations after the first sequence switches and before the final sequence switches to the intervention; this means that the first sequence remains in the control condition and the last sequence remains in the intervention condition for the duration of the trial. With this design, the optimal number of sequences is [Formula: see text], where [Formula: see text] is the cluster-mean correlation, [Formula: see text] is the intracluster correlation coefficient, and m is the total cluster size. The optimal number of sequences is small when the intracluster correlation coefficient and cluster size are small and large when the intracluster correlation coefficient or cluster size is large. A cluster-randomised trial remains more efficient than the optimised stepped wedge trial when the intracluster correlation coefficient or cluster size is small. A cluster-randomised trial with baseline observations always requires a larger sample size than the optimised stepped wedge trial. The hybrid design can always give an equally or more efficient design, but will be at most 5% more efficient. We provide a strategy for selecting a design if the optimal number of sequences is unfeasible. For a non-optimal number of sequences, the sample size may be reduced by allowing a proportion of observations before the first or after the final sequence has switched. Conclusion The standard stepped wedge trial is inefficient. To reduce sample sizes when a hybrid design is unfeasible, stepped wedge trial designs should have no observations before the first sequence switches or after the final sequence switches.

Finite-sample corrected generalized estimating equation of population average treatment effects in stepped wedge cluster randomized trials.

PubMed

Scott, JoAnna M; deCamp, Allan; Juraska, Michal; Fay, Michael P; Gilbert, Peter B

2017-04-01

Stepped wedge designs are increasingly commonplace and advantageous for cluster randomized trials when it is both unethical to assign placebo, and it is logistically difficult to allocate an intervention simultaneously to many clusters. We study marginal mean models fit with generalized estimating equations for assessing treatment effectiveness in stepped wedge cluster randomized trials. This approach has advantages over the more commonly used mixed models that (1) the population-average parameters have an important interpretation for public health applications and (2) they avoid untestable assumptions on latent variable distributions and avoid parametric assumptions about error distributions, therefore, providing more robust evidence on treatment effects. However, cluster randomized trials typically have a small number of clusters, rendering the standard generalized estimating equation sandwich variance estimator biased and highly variable and hence yielding incorrect inferences. We study the usual asymptotic generalized estimating equation inferences (i.e., using sandwich variance estimators and asymptotic normality) and four small-sample corrections to generalized estimating equation for stepped wedge cluster randomized trials and for parallel cluster randomized trials as a comparison. We show by simulation that the small-sample corrections provide improvement, with one correction appearing to provide at least nominal coverage even with only 10 clusters per group. These results demonstrate the viability of the marginal mean approach for both stepped wedge and parallel cluster randomized trials. We also study the comparative performance of the corrected methods for stepped wedge and parallel designs, and describe how the methods can accommodate interval censoring of individual failure times and incorporate semiparametric efficient estimators.

Group sequential designs for stepped-wedge cluster randomised trials

PubMed Central

Grayling, Michael J; Wason, James MS; Mander, Adrian P

2017-01-01

Background/Aims: The stepped-wedge cluster randomised trial design has received substantial attention in recent years. Although various extensions to the original design have been proposed, no guidance is available on the design of stepped-wedge cluster randomised trials with interim analyses. In an individually randomised trial setting, group sequential methods can provide notable efficiency gains and ethical benefits. We address this by discussing how established group sequential methodology can be adapted for stepped-wedge designs. Methods: Utilising the error spending approach to group sequential trial design, we detail the assumptions required for the determination of stepped-wedge cluster randomised trials with interim analyses. We consider early stopping for efficacy, futility, or efficacy and futility. We describe first how this can be done for any specified linear mixed model for data analysis. We then focus on one particular commonly utilised model and, using a recently completed stepped-wedge cluster randomised trial, compare the performance of several designs with interim analyses to the classical stepped-wedge design. Finally, the performance of a quantile substitution procedure for dealing with the case of unknown variance is explored. Results: We demonstrate that the incorporation of early stopping in stepped-wedge cluster randomised trial designs could reduce the expected sample size under the null and alternative hypotheses by up to 31% and 22%, respectively, with no cost to the trial’s type-I and type-II error rates. The use of restricted error maximum likelihood estimation was found to be more important than quantile substitution for controlling the type-I error rate. Conclusion: The addition of interim analyses into stepped-wedge cluster randomised trials could help guard against time-consuming trials conducted on poor performing treatments and also help expedite the implementation of efficacious treatments. In future, trialists should consider incorporating early stopping of some kind into stepped-wedge cluster randomised trials according to the needs of the particular trial. PMID:28653550

Group sequential designs for stepped-wedge cluster randomised trials.

PubMed

Grayling, Michael J; Wason, James Ms; Mander, Adrian P

2017-10-01

The stepped-wedge cluster randomised trial design has received substantial attention in recent years. Although various extensions to the original design have been proposed, no guidance is available on the design of stepped-wedge cluster randomised trials with interim analyses. In an individually randomised trial setting, group sequential methods can provide notable efficiency gains and ethical benefits. We address this by discussing how established group sequential methodology can be adapted for stepped-wedge designs. Utilising the error spending approach to group sequential trial design, we detail the assumptions required for the determination of stepped-wedge cluster randomised trials with interim analyses. We consider early stopping for efficacy, futility, or efficacy and futility. We describe first how this can be done for any specified linear mixed model for data analysis. We then focus on one particular commonly utilised model and, using a recently completed stepped-wedge cluster randomised trial, compare the performance of several designs with interim analyses to the classical stepped-wedge design. Finally, the performance of a quantile substitution procedure for dealing with the case of unknown variance is explored. We demonstrate that the incorporation of early stopping in stepped-wedge cluster randomised trial designs could reduce the expected sample size under the null and alternative hypotheses by up to 31% and 22%, respectively, with no cost to the trial's type-I and type-II error rates. The use of restricted error maximum likelihood estimation was found to be more important than quantile substitution for controlling the type-I error rate. The addition of interim analyses into stepped-wedge cluster randomised trials could help guard against time-consuming trials conducted on poor performing treatments and also help expedite the implementation of efficacious treatments. In future, trialists should consider incorporating early stopping of some kind into stepped-wedge cluster randomised trials according to the needs of the particular trial.

A superior edge preserving filter with a systematic analysis

NASA Technical Reports Server (NTRS)

Holladay, Kenneth W.; Rickman, Doug

1991-01-01

A new, adaptive, edge preserving filter for use in image processing is presented. It had superior performance when compared to other filters. Termed the contiguous K-average, it aggregates pixels by examining all pixels contiguous to an existing cluster and adding the pixel closest to the mean of the existing cluster. The process is iterated until K pixels were accumulated. Rather than simply compare the visual results of processing with this operator to other filters, some approaches were developed which allow quantitative evaluation of how well and filter performs. Particular attention is given to the standard deviation of noise within a feature and the stability of imagery under iterative processing. Demonstrations illustrate the performance of several filters to discriminate against noise and retain edges, the effect of filtering as a preprocessing step, and the utility of the contiguous K-average filter when used with remote sensing data.

[Autism Spectrum Disorder and DSM-5: Spectrum or Cluster?].

PubMed

Kienle, Xaver; Freiberger, Verena; Greulich, Heide; Blank, Rainer

2015-01-01

Within the new DSM-5, the currently differentiated subgroups of "Autistic Disorder" (299.0), "Asperger's Disorder" (299.80) and "Pervasive Developmental Disorder" (299.80) are replaced by the more general "Autism Spectrum Disorder". With regard to a patient-oriented and expedient advising therapy planning, however, the issue of an empirically reproducible and clinically feasible differentiation into subgroups must still be raised. Based on two Autism-rating-scales (ASDS and FSK), an exploratory two-step cluster analysis was conducted with N=103 children (age: 5-18) seen in our social-pediatric health care centre to examine potentially autistic symptoms. In the two-cluster solution of both rating scales, mainly the problems in social communication grouped the children into a cluster "with communication problems" (51 % and 41 %), and a cluster "without communication problems". Within the three-cluster solution of the ASDS, sensory hypersensitivity, cleaving to routines and social-communicative problems generated an "autistic" subgroup (22%). The children of the second cluster ("communication problems", 35%) were only described by social-communicative problems, and the third group did not show any problems (38%). In the three-cluster solution of the FSK, the "autistic cluster" of the two-cluster solution differentiated in a subgroup with mainly social-communicative problems (cluster 1) and a second subgroup described by restrictive, repetitive behavior. The different cluster solutions will be discussed with a view to the new DSM-5 diagnostic criteria, for following studies a further specification of some of the ASDS and FSK items could be helpful.

Extracting Galaxy Cluster Gas Inhomogeneity from X-Ray Surface Brightness: A Statistical Approach and Application to Abell 3667

NASA Astrophysics Data System (ADS)

Kawahara, Hajime; Reese, Erik D.; Kitayama, Tetsu; Sasaki, Shin; Suto, Yasushi

2008-11-01

Our previous analysis indicates that small-scale fluctuations in the intracluster medium (ICM) from cosmological hydrodynamic simulations follow the lognormal probability density function. In order to test the lognormal nature of the ICM directly against X-ray observations of galaxy clusters, we develop a method of extracting statistical information about the three-dimensional properties of the fluctuations from the two-dimensional X-ray surface brightness. We first create a set of synthetic clusters with lognormal fluctuations around their mean profile given by spherical isothermal β-models, later considering polytropic temperature profiles as well. Performing mock observations of these synthetic clusters, we find that the resulting X-ray surface brightness fluctuations also follow the lognormal distribution fairly well. Systematic analysis of the synthetic clusters provides an empirical relation between the three-dimensional density fluctuations and the two-dimensional X-ray surface brightness. We analyze Chandra observations of the galaxy cluster Abell 3667, and find that its X-ray surface brightness fluctuations follow the lognormal distribution. While the lognormal model was originally motivated by cosmological hydrodynamic simulations, this is the first observational confirmation of the lognormal signature in a real cluster. Finally we check the synthetic cluster results against clusters from cosmological hydrodynamic simulations. As a result of the complex structure exhibited by simulated clusters, the empirical relation between the two- and three-dimensional fluctuation properties calibrated with synthetic clusters when applied to simulated clusters shows large scatter. Nevertheless we are able to reproduce the true value of the fluctuation amplitude of simulated clusters within a factor of 2 from their two-dimensional X-ray surface brightness alone. Our current methodology combined with existing observational data is useful in describing and inferring the statistical properties of the three-dimensional inhomogeneity in galaxy clusters.

Systematic Approaches for Identifying and Organizing Content for Training Programs.

ERIC Educational Resources Information Center

Ammerman, Harry L.

This paper concentrates on two aspects in the development of curriculums for technical training: the identification of curriculum content for specific courses of study; and the organization of such content in training programs. Seven steps in the HumRRO procedure for systematic curriculum engineering are identified: determining the performance…

A Dimensionality Reduction-Based Multi-Step Clustering Method for Robust Vessel Trajectory Analysis

PubMed Central

Liu, Jingxian; Wu, Kefeng

2017-01-01

The Shipboard Automatic Identification System (AIS) is crucial for navigation safety and maritime surveillance, data mining and pattern analysis of AIS information have attracted considerable attention in terms of both basic research and practical applications. Clustering of spatio-temporal AIS trajectories can be used to identify abnormal patterns and mine customary route data for transportation safety. Thus, the capacities of navigation safety and maritime traffic monitoring could be enhanced correspondingly. However, trajectory clustering is often sensitive to undesirable outliers and is essentially more complex compared with traditional point clustering. To overcome this limitation, a multi-step trajectory clustering method is proposed in this paper for robust AIS trajectory clustering. In particular, the Dynamic Time Warping (DTW), a similarity measurement method, is introduced in the first step to measure the distances between different trajectories. The calculated distances, inversely proportional to the similarities, constitute a distance matrix in the second step. Furthermore, as a widely-used dimensional reduction method, Principal Component Analysis (PCA) is exploited to decompose the obtained distance matrix. In particular, the top k principal components with above 95% accumulative contribution rate are extracted by PCA, and the number of the centers k is chosen. The k centers are found by the improved center automatically selection algorithm. In the last step, the improved center clustering algorithm with k clusters is implemented on the distance matrix to achieve the final AIS trajectory clustering results. In order to improve the accuracy of the proposed multi-step clustering algorithm, an automatic algorithm for choosing the k clusters is developed according to the similarity distance. Numerous experiments on realistic AIS trajectory datasets in the bridge area waterway and Mississippi River have been implemented to compare our proposed method with traditional spectral clustering and fast affinity propagation clustering. Experimental results have illustrated its superior performance in terms of quantitative and qualitative evaluations. PMID:28777353

Systematic Perturbation of the Trinuclear Copper Cluster in the Multicopper Oxidases: The Role of Active Site Asymmetry in its Reduction of O2 to H2O

PubMed Central

Augustine, Anthony J.; Kjaergaard, Christian; Qayyum, Munzarin; Ziegler, Lynn; Kosman, Daniel J.; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

2010-01-01

The multicopper oxidase Fet3p catalyzes the four-electron reduction of dioxygen to water, coupled to the one-electron oxidation of four equivalents of substrate. To carry out this process the enzyme utilizes four Cu atoms: a type 1, a type 2, and a coupled binuclear, type 3 site. Substrates are oxidized at the T1 Cu, which rapidly transfers electrons, 13 Å away, to a trinuclear copper cluster composed of the T2 and T3 sites where dioxygen is reduced to water in two sequential 2e− steps. This study focuses on two variants of Fet3p, H126Q and H483Q, that perturb the two T3 Cu's, T3α and T3β, respectively. The variants have been isolated in both holo and type 1 depleted (T1D) forms, T1DT3αQ and T1DT3βQ, and their trinuclear copper clusters have been characterized in their oxidized and reduced states. While the variants are only mildly perturbed relative to T1D in the resting oxidized state, in contrast to T1D they are both found to have lost a ligand in their reduced states. Importantly, T1DT3αQ reacts with O2 but T1DT3βQ does not. Thus loss of a ligand at T3β, but not at T3α, turns off O2 reactivity, indicating that T3β and T2 are required for the 2e− reduction of O2 to form the peroxide intermediate (PI), whereas T3α remains reduced. This is supported by the spectroscopic features of PI in T1DT3αQ, which are identical to T1D PI. This selective redox activity of one edge of the trinuclear cluster demonstrates its asymmetry in O2 reactivity. The structural origin of this asymmetry between the T3α and T3β is discussed as is its contribution to reactivity. PMID:20377263

Subtypes of female juvenile offenders: a cluster analysis of the Millon Adolescent Clinical Inventory.

PubMed

Stefurak, Tres; Calhoun, Georgia B

2007-01-01

The current study sought to explore subtypes of adolescents within a sample of female juvenile offenders. Using the Millon Adolescent Clinical Inventory with 101 female juvenile offenders, a two-step cluster analysis was performed beginning with a Ward's method hierarchical cluster analysis followed by a K-Means iterative partitioning cluster analysis. The results suggest an optimal three-cluster solution, with cluster profiles leading to the following group labels: Externalizing Problems, Depressed/Interpersonally Ambivalent, and Anxious Prosocial. Analysis along the factors of age, race, offense typology and offense chronicity were conducted to further understand the nature of found clusters. Only the effect for race was significant with the Anxious Prosocial and Depressed Intepersonally Ambivalent clusters appearing disproportionately comprised of African American girls. To establish external validity, clusters were compared across scales of the Behavioral Assessment System for Children - Self Report of Personality, and corroborative distinctions between clusters were found here.

Post-genome research on the biosynthesis of ergot alkaloids.

PubMed

Li, Shu-Ming; Unsöld, Inge A

2006-10-01

Genome sequencing provides new opportunities and challenges for identifying genes for the biosynthesis of secondary metabolites. A putative biosynthetic gene cluster of fumigaclavine C, an ergot alkaloid of the clavine type, was identified in the genome sequence of ASPERGILLUS FUMIGATUS by a bioinformatic approach. This cluster spans 22 kb of genomic DNA and comprises at least 11 open reading frames (ORFs). Seven of them are orthologous to genes from the biosynthetic gene cluster of ergot alkaloids in CLAVICEPS PURPUREA. Experimental evidence of the identified cluster was provided by heterologous expression and biochemical characterization of two ORFs, FgaPT1 and FgaPT2, in the cluster of A. FUMIGATUS, which show remarkable similarities to dimethylallyltryptophan synthase from C. PURPUREA and function as prenyltransferases. FgaPT2 converts L-tryptophan to dimethylallyltryptophan and thereby catalyzes the first step of ergot alkaloid biosynthesis, whilst FgaPT1 catalyzes the last step of the fumigaclavine C biosynthesis, i. e., the prenylation of fumigaclavine A at C-2 position of the indole nucleus. In addition to information obtained from the gene cluster of ergot alkaloids from C. PURPUREA, the identification of the biosynthetic gene cluster of fumigaclavine C in A. FUMIGATUS opens an alternative way to study the biosynthesis of ergot alkaloids in fungi.

Two Ti13-oxo-clusters showing non-compact structures, film electrode preparation and photocurrent properties.

PubMed

Hou, Jin-Le; Luo, Wen; Wu, Yin-Yin; Su, Hu-Chao; Zhang, Guang-Lin; Zhu, Qin-Yu; Dai, Jie

2015-12-14

Two benzene dicarboxylate (BDC) and salicylate (SAL) substituted titanium-oxo-clusters, Ti13O10(o-BDC)4(SAL)4(O(i)Pr)16 (1) and Ti13O10(o-BDC)4(SAL-Cl)4(O(i)Pr)16 (2), are prepared by one step in situ solvothermal synthesis. Single crystal analysis shows that the two Ti13 clusters take a paddle arrangement with an S4 symmetry. The non-compact (non-sphere) structure is stabilized by the coordination of BDC and SAL. Film photoelectrodes are prepared by the wet coating process using the solution of the clusters and the photocurrent response properties of the electrodes are studied. It is found that the photocurrent density and photoresponsiveness of the electrodes are related to the number of coating layers and the annealing temperature. Using ligand coordinated titanium-oxo-clusters as the molecular precursors of TiO2 anatase films is found to be effective due to their high solubility, appropriate stability in solution and hence the easy controllability.

A Bridging [4Fe-4S] Cluster and Nucleotide Binding Are Essential for Function of the Cfd1-Nbp35 Complex as a Scaffold in Iron-Sulfur Protein Maturation*

PubMed Central

Netz, Daili J. A.; Pierik, Antonio J.; Stümpfig, Martin; Bill, Eckhard; Sharma, Anil K.; Pallesen, Leif J.; Walden, William E.; Lill, Roland

2012-01-01

The essential P-loop NTPases Cfd1 and Nbp35 of the cytosolic iron-sulfur (Fe-S) protein assembly machinery perform a scaffold function for Fe-S cluster synthesis. Both proteins contain a nucleotide binding motif of unknown function and a C-terminal motif with four conserved cysteine residues. The latter motif defines the Mrp/Nbp35 subclass of P-loop NTPases and is suspected to be involved in transient Fe-S cluster binding. To elucidate the function of these two motifs, we first created cysteine mutant proteins of Cfd1 and Nbp35 and investigated the consequences of these mutations by genetic, cell biological, biochemical, and spectroscopic approaches. The two central cysteine residues (CPXC) of the C-terminal motif were found to be crucial for cell viability, protein function, coordination of a labile [4Fe-4S] cluster, and Cfd1-Nbp35 hetero-tetramer formation. Surprisingly, the two proximal cysteine residues were dispensable for all these functions, despite their strict evolutionary conservation. Several lines of evidence suggest that the C-terminal CPXC motifs of Cfd1-Nbp35 coordinate a bridging [4Fe-4S] cluster. Upon mutation of the nucleotide binding motifs Fe-S clusters could no longer be assembled on these proteins unless wild-type copies of Cfd1 and Nbp35 were present in trans. This result indicated that Fe-S cluster loading on these scaffold proteins is a nucleotide-dependent step. We propose that the bridging coordination of the C-terminal Fe-S cluster may be ideal for its facile assembly, labile binding, and efficient transfer to target Fe-S apoproteins, a step facilitated by the cytosolic iron-sulfur (Fe-S) protein assembly proteins Nar1 and Cia1 in vivo. PMID:22362766

Supporting family caregivers to identify their own needs in end-of-life care: Qualitative findings from a stepped wedge cluster trial.

PubMed

Aoun, Samar; Deas, Kathleen; Toye, Chris; Ewing, Gail; Grande, Gunn; Stajduhar, Kelli

2015-06-01

The Carer Support Needs Assessment Tool encompasses the physical, psychological, social, practical, financial, and spiritual support needs that government policies in many countries emphasize should be assessed and addressed for family caregivers during end-of-life care. To describe the experience of family caregivers of terminally ill people of the Carer Support Needs Assessment Tool intervention in home-based palliative care. This study was conducted during 2012-2014 in Silver Chain Hospice Care Service in Western Australia. This article reports on one part of a three-part evaluation of a stepped wedge cluster trial. All 233 family caregivers receiving the Carer Support Needs Assessment Tool intervention provided feedback on their experiences via brief end-of-trial semi-structured telephone interviews. Data were subjected to a thematic analysis. The overwhelming majority reported finding the Carer Support Needs Assessment Tool assessment process straightforward and easy. Four key themes were identified: (1) the practicality and usefulness of the systematic assessment; (2) emotional responses to caregiver reflection; (3) validation, reassurance, and empowerment; and (4) accessing support and how this was experienced. Family caregivers appreciated the value of the Carer Support Needs Assessment Tool intervention in engaging them in conversations about their needs, priorities, and solutions. The Carer Support Needs Assessment Tool presented a simple, yet potentially effective intervention to help palliative care providers systematically assess and address family caregivers' needs. The Carer Support Needs Assessment Tool provided a formal structure to facilitate discussions with family caregivers to enable needs to be addressed. Such discussions can also inform an evidence base for the ongoing development of services for family caregivers, ensuring that new or improved services are designed to meet the explicit needs of family caregivers. © The Author(s) 2015.

Accounting for measurement error in biomarker data and misclassification of subtypes in the analysis of tumor data

PubMed Central

Nevo, Daniel; Zucker, David M.; Tamimi, Rulla M.; Wang, Molin

2017-01-01

A common paradigm in dealing with heterogeneity across tumors in cancer analysis is to cluster the tumors into subtypes using marker data on the tumor, and then to analyze each of the clusters separately. A more specific target is to investigate the association between risk factors and specific subtypes and to use the results for personalized preventive treatment. This task is usually carried out in two steps–clustering and risk factor assessment. However, two sources of measurement error arise in these problems. The first is the measurement error in the biomarker values. The second is the misclassification error when assigning observations to clusters. We consider the case with a specified set of relevant markers and propose a unified single-likelihood approach for normally distributed biomarkers. As an alternative, we consider a two-step procedure with the tumor type misclassification error taken into account in the second-step risk factor analysis. We describe our method for binary data and also for survival analysis data using a modified version of the Cox model. We present asymptotic theory for the proposed estimators. Simulation results indicate that our methods significantly lower the bias with a small price being paid in terms of variance. We present an analysis of breast cancer data from the Nurses’ Health Study to demonstrate the utility of our method. PMID:27558651

Diagnostics of models and observations in the contexts of exoplanets, brown dwarfs, and very low-mass stars.

NASA Astrophysics Data System (ADS)

Kopytova, Taisiya

2016-01-01

When studying isolated brown dwarfs and directly imaged exoplanets with insignificant orbital motion,we have to rely on theoretical models to determine basic parameters such as mass, age, effective temperature, and surface gravity.While stellar and atmospheric models are rapidly evolving, we need a powerful tool to test and calibrate them.In my thesis, I focussed on comparing interior and atmospheric models with observational data, in the effort of taking into account various systematic effects that can significantly influence the data analysis.As a first step, about 460 candidate member os the Hyades were screened for companions using diffraction limited imaging observation (both our own data and archival data). As a result I could establish the single star sequence for the Hyades comprising about 250 stars (Kopytova et al. 2015, accepted to A&A). Open clusters contain many coeval objects of the same chemical composition and age, and spanning a range of masses. We compare the obtained sequence with a set of theoretical isochrones identifying systematic offsets and revealing probable issues in the models.However, there are many cases when it is impossible to test models before comparing them with observations.As a second step, we apply atmospheric models for constraining parameters of WISE 0855-07, the coolest known Y dwarf(Kopytova et al. 2014, ApJ 797, 3). We demonstrate the limits of constraining effective temperature and the presence/absence of water clouds.As a third step, we introduce a novel method to take into account the above-mentioned systematics. We construct a "systematics vector" that allows us to reveal problematic wavelength ranges when fitting atmospheric models to observed near-infrared spectraof brown dwarfs and exoplanets (Kopytova et al., in prep.). This approach plays a crucial role when retrieving abundances for these objects, in particularly, a C/O ratio. The latter parameter is an important key to formation scenarios of brown dwarf and exoplanets. We show the way to constrain a C/O ratio while eliminating systematics effects, which significantly improves the reliability of a final result and our conclusions about formation history of certain exoplanets and brown dwarfs.

Integrating K-means Clustering with Kernel Density Estimation for the Development of a Conditional Weather Generation Downscaling Model

NASA Astrophysics Data System (ADS)

Chen, Y.; Ho, C.; Chang, L.

2011-12-01

In previous decades, the climate change caused by global warming increases the occurrence frequency of extreme hydrological events. Water supply shortages caused by extreme events create great challenges for water resource management. To evaluate future climate variations, general circulation models (GCMs) are the most wildly known tools which shows possible weather conditions under pre-defined CO2 emission scenarios announced by IPCC. Because the study area of GCMs is the entire earth, the grid sizes of GCMs are much larger than the basin scale. To overcome the gap, a statistic downscaling technique can transform the regional scale weather factors into basin scale precipitations. The statistic downscaling technique can be divided into three categories include transfer function, weather generator and weather type. The first two categories describe the relationships between the weather factors and precipitations respectively based on deterministic algorithms, such as linear or nonlinear regression and ANN, and stochastic approaches, such as Markov chain theory and statistical distributions. In the weather type, the method has ability to cluster weather factors, which are high dimensional and continuous variables, into weather types, which are limited number of discrete states. In this study, the proposed downscaling model integrates the weather type, using the K-means clustering algorithm, and the weather generator, using the kernel density estimation. The study area is Shihmen basin in northern of Taiwan. In this study, the research process contains two steps, a calibration step and a synthesis step. Three sub-steps were used in the calibration step. First, weather factors, such as pressures, humidities and wind speeds, obtained from NCEP and the precipitations observed from rainfall stations were collected for downscaling. Second, the K-means clustering grouped the weather factors into four weather types. Third, the Markov chain transition matrixes and the conditional probability density function (PDF) of precipitations approximated by the kernel density estimation are calculated respectively for each weather types. In the synthesis step, 100 patterns of synthesis data are generated. First, the weather type of the n-th day are determined by the results of K-means clustering. The associated transition matrix and PDF of the weather type were also determined for the usage of the next sub-step in the synthesis process. Second, the precipitation condition, dry or wet, can be synthesized basing on the transition matrix. If the synthesized condition is dry, the quantity of precipitation is zero; otherwise, the quantity should be further determined in the third sub-step. Third, the quantity of the synthesized precipitation is assigned as the random variable of the PDF defined above. The synthesis efficiency compares the gap of the monthly mean curves and monthly standard deviation curves between the historical precipitation data and the 100 patterns of synthesis data.

Step 6: Does Not Routinely Employ Practices, Procedures Unsupported by Scientific Evidence

PubMed Central

Goer, Henci; Sagady Leslie, Mayri; Romano, Amy

2007-01-01

Step 6 of the Ten Steps of Mother-Friendly Care addresses two issues: 1) the routine use of interventions (shaving, enemas, intravenous drips, withholding food and fluids, early rupture of membranes, and continuous electronic fetal monitoring; and 2) the optimal rates of induction, episiotomy, cesareans, and vaginal births after cesarean. Rationales for compliance and systematic reviews are presented. PMID:18523680

Ligand Rearrangements at Fe/S Cofactors: Slow Isomerization of a Biomimetic [2Fe-2S] Cluster.

PubMed

Bergner, Marie; Roy, Lisa; Dechert, Sebastian; Neese, Frank; Ye, Shengfa; Meyer, Franc

2017-04-18

Ligand exchange plays an important role in the biogenesis of Fe/S clusters, most prominently during cluster transfer from a scaffold protein to its target protein. Although in vivo and in vitro studies have provided some insight into this process, the microscopic details of the ligand exchange steps are mostly unknown. In this work, the kinetics of the ligand rearrangement in a biomimetic [2Fe-2S] cluster with mixed S/N capping ligands have been studied. Two geometrical isomers of the cluster are present in solution, and mechanistic insight into the isomerization process was obtained by variable-temperature 1 H NMR spectroscopy. Combined experimental and computational results reveal that this is an associative process that involves the coordination of a solvent molecule to one of the ferric ions. The cluster isomerizes at least two orders of magnitude faster in its protonated and mixed-valent states. These findings may contribute to a deeper understanding of cluster transfer and sensing processes occurring in Fe/S cluster biogenesis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing.

PubMed

Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

2016-01-01

Flax ( Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5-8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs.

Body typing of children and adolescents using 3D-body scanning

PubMed Central

Vogel, Mandy; Kirsten, Toralf; Glock, Fabian; Poulain, Tanja; Körner, Antje; Loeffler, Markus; Kiess, Wieland; Binder, Hans

2017-01-01

Three-dimensional (3D-) body scanning of children and adolescents allows the detailed study of physiological development in terms of anthropometrical alterations which potentially provide early onset markers for obesity. Here, we present a systematic analysis of body scanning data of 2,700 urban children and adolescents in the age range between 5 and 18 years with the special aim to stratify the participants into distinct body shape types and to describe their change upon development. In a first step, we extracted a set of eight representative meta-measures from the data. Each of them collects a related group of anthropometrical features and changes specifically upon aging. In a second step we defined seven body types by clustering the meta-measures of all participants. These body types describe the body shapes in terms of three weight (lower, normal and overweight) and three age (young, medium and older) categories. For younger children (age of 5–10 years) we found a common ‘early childhood body shape’ which splits into three weight-dependent types for older children, with one or two years delay for boys. Our study shows that the concept of body types provides a reliable option for the anthropometric characterization of developing and aging populations. PMID:29053732

An extended affinity propagation clustering method based on different data density types.

PubMed

Zhao, XiuLi; Xu, WeiXiang

2015-01-01

Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself.

Uncertainties in the cluster-cluster correlation function

NASA Astrophysics Data System (ADS)

Ling, E. N.; Frenk, C. S.; Barrow, J. D.

1986-12-01

The bootstrap resampling technique is applied to estimate sampling errors and significance levels of the two-point correlation functions determined for a subset of the CfA redshift survey of galaxies and a redshift sample of 104 Abell clusters. The angular correlation function for a sample of 1664 Abell clusters is also calculated. The standard errors in xi(r) for the Abell data are found to be considerably larger than quoted 'Poisson errors'. The best estimate for the ratio of the correlation length of Abell clusters (richness class R greater than or equal to 1, distance class D less than or equal to 4) to that of CfA galaxies is 4.2 + 1.4 or - 1.0 (68 percentile error). The enhancement of cluster clustering over galaxy clustering is statistically significant in the presence of resampling errors. The uncertainties found do not include the effects of possible systematic biases in the galaxy and cluster catalogs and could be regarded as lower bounds on the true uncertainty range.

Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at

Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy ismore » constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.« less

Critical behavior of a two-step contagion model with multiple seeds

NASA Astrophysics Data System (ADS)

Choi, Wonjun; Lee, Deokjae; Kahng, B.

2017-06-01

A two-step contagion model with a single seed serves as a cornerstone for understanding the critical behaviors and underlying mechanism of discontinuous percolation transitions induced by cascade dynamics. When the contagion spreads from a single seed, a cluster of infected and recovered nodes grows without any cluster merging process. However, when the contagion starts from multiple seeds of O (N ) where N is the system size, a node weakened by a seed can be infected more easily when it is in contact with another node infected by a different pathogen seed. This contagion process can be viewed as a cluster merging process in a percolation model. Here we show analytically and numerically that when the density of infectious seeds is relatively small but O (1 ) , the epidemic transition is hybrid, exhibiting both continuous and discontinuous behavior, whereas when it is sufficiently large and reaches a critical point, the transition becomes continuous. We determine the full set of critical exponents describing the hybrid and the continuous transitions. Their critical behaviors differ from those in the single-seed case.

Automated Comparative Metabolite Profiling of Large LC-ESIMS Data Sets in an ACD/MS Workbook Suite Add-in, and Data Clustering on a New Open-Source Web Platform FreeClust.

PubMed

Božičević, Alen; Dobrzyński, Maciej; De Bie, Hans; Gafner, Frank; Garo, Eliane; Hamburger, Matthias

2017-12-05

The technological development of LC-MS instrumentation has led to significant improvements of performance and sensitivity, enabling high-throughput analysis of complex samples, such as plant extracts. Most software suites allow preprocessing of LC-MS chromatograms to obtain comprehensive information on single constituents. However, more advanced processing needs, such as the systematic and unbiased comparative metabolite profiling of large numbers of complex LC-MS chromatograms remains a challenge. Currently, users have to rely on different tools to perform such data analyses. We developed a two-step protocol comprising a comparative metabolite profiling tool integrated in ACD/MS Workbook Suite, and a web platform developed in R language designed for clustering and visualization of chromatographic data. Initially, all relevant chromatographic and spectroscopic data (retention time, molecular ions with the respective ion abundance, and sample names) are automatically extracted and assembled in an Excel spreadsheet. The file is then loaded into an online web application that includes various statistical algorithms and provides the user with tools to compare and visualize the results in intuitive 2D heatmaps. We applied this workflow to LC-ESIMS profiles obtained from 69 honey samples. Within few hours of calculation with a standard PC, honey samples were preprocessed and organized in clusters based on their metabolite profile similarities, thereby highlighting the common metabolite patterns and distributions among samples. Implementation in the ACD/Laboratories software package enables ulterior integration of other analytical data, and in silico prediction tools for modern drug discovery.

Construction and engineering of large biochemical pathways via DNA assembler

PubMed Central

Shao, Zengyi; Zhao, Huimin

2015-01-01

Summary DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. Here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing multiple genes using the DNA assembler approach. Methods for construct design, pathway assembly, pathway confirmation, and functional analysis are shown. The protocol for fine genetic modifications such as site-directed mutagenesis for engineering the aureothin gene cluster is also illustrated. PMID:23996442

Communication: Two-step explosion processes of highly charged fullerene cations C{sub 60}{sup q+} (q = 20–60)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamazaki, Kaoru; Nakamura, Takashi; Kanno, Manabu

2014-09-28

To establish the fundamental understanding of the fragmentation dynamics of highly positive charged nano- and bio-materials, we carried out on-the-fly classical trajectory calculations on the fragmentation dynamics of C{sub 60}{sup q+} (q = 20–60). We used the UB3LYP/3-21G level of density functional theory and the self-consistent charge density-functional based tight-binding theory. For q ≥ 20, we found that a two-step explosion mechanism governs the fragmentation dynamics: C{sub 60}{sup q+} first ejects singly and multiply charged fast atomic cations C{sup z+} (z ≥ 1) via Coulomb explosions on a timescale of 10 fs to stabilize the remaining core cluster. Thermal evaporationsmore » of slow atomic and molecular fragments from the core cluster subsequently occur on a timescale of 100 fs to 1 ps. Increasing the charge q makes the fragments smaller. This two-step mechanism governs the fragmentation dynamics in the most likely case that the initial kinetic energy accumulated upon ionization to C{sub 60}{sup q+} by ion impact or X-ray free electron laser is larger than 100 eV.« less

Clustering of color map pixels: an interactive approach

NASA Astrophysics Data System (ADS)

Moon, Yiu Sang; Luk, Franklin T.; Yuen, K. N.; Yeung, Hoi Wo

2003-12-01

The demand for digital maps continues to arise as mobile electronic devices become more popular nowadays. Instead of creating the entire map from void, we may convert a scanned paper map into a digital one. Color clustering is the very first step of the conversion process. Currently, most of the existing clustering algorithms are fully automatic. They are fast and efficient but may not work well in map conversion because of the numerous ambiguous issues associated with printed maps. Here we introduce two interactive approaches for color clustering on the map: color clustering with pre-calculated index colors (PCIC) and color clustering with pre-calculated color ranges (PCCR). We also introduce a memory model that could enhance and integrate different image processing techniques for fine-tuning the clustering results. Problems and examples of the algorithms are discussed in the paper.

Dense module enumeration in biological networks

NASA Astrophysics Data System (ADS)

Tsuda, Koji; Georgii, Elisabeth

2009-12-01

Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

Three-Dimensional Computer-Aided Detection of Microcalcification Clusters in Digital Breast Tomosynthesis.

PubMed

Jeong, Ji-Wook; Chae, Seung-Hoon; Chae, Eun Young; Kim, Hak Hee; Choi, Young-Wook; Lee, Sooyeul

2016-01-01

We propose computer-aided detection (CADe) algorithm for microcalcification (MC) clusters in reconstructed digital breast tomosynthesis (DBT) images. The algorithm consists of prescreening, MC detection, clustering, and false-positive (FP) reduction steps. The DBT images containing the MC-like objects were enhanced by a multiscale Hessian-based three-dimensional (3D) objectness response function and a connected-component segmentation method was applied to extract the cluster seed objects as potential clustering centers of MCs. Secondly, a signal-to-noise ratio (SNR) enhanced image was also generated to detect the individual MC candidates and prescreen the MC-like objects. Each cluster seed candidate was prescreened by counting neighboring individual MC candidates nearby the cluster seed object according to several microcalcification clustering criteria. As a second step, we introduced bounding boxes for the accepted seed candidate, clustered all the overlapping cubes, and examined. After the FP reduction step, the average number of FPs per case was estimated to be 2.47 per DBT volume with a sensitivity of 83.3%.

Ab initio calculations of optical properties of silver clusters: cross-over from molecular to nanoscale behavior

NASA Astrophysics Data System (ADS)

Titantah, John T.; Karttunen, Mikko

2016-05-01

Electronic and optical properties of silver clusters were calculated using two different ab initio approaches: (1) based on all-electron full-potential linearized-augmented plane-wave method and (2) local basis function pseudopotential approach. Agreement is found between the two methods for small and intermediate sized clusters for which the former method is limited due to its all-electron formulation. The latter, due to non-periodic boundary conditions, is the more natural approach to simulate small clusters. The effect of cluster size is then explored using the local basis function approach. We find that as the cluster size increases, the electronic structure undergoes a transition from molecular behavior to nanoparticle behavior at a cluster size of 140 atoms (diameter ~1.7 nm). Above this cluster size the step-like electronic structure, evident as several features in the imaginary part of the polarizability of all clusters smaller than Ag147, gives way to a dominant plasmon peak localized at wavelengths 350 nm ≤ λ ≤ 600 nm. It is, thus, at this length-scale that the conduction electrons' collective oscillations that are responsible for plasmonic resonances begin to dominate the opto-electronic properties of silver nanoclusters.

A Primer on Systematic Reviews and Meta-Analyses.

PubMed

Nguyen, Nghia H; Singh, Siddharth

2018-05-01

With the rapid growth of biomedical literature, there is increasing need to make meaningful inferences from a comprehensive and complex body of evidence. Systematic reviews with or without meta-analyses offer an objective and summative approach to synthesize knowledge and critically appraise evidence to inform clinical practice. Systematic reviews also help identify key knowledge gaps for future investigation. In this review, the authors provide a step-by-step approach to conducting a systematic review. These include: (1) formulating a focused and clinically-relevant question; (2) designing a detailed review protocol with explicit inclusion and exclusion criteria; (3) performing a systematic literature search of multiple databases and unpublished data, in consultation with a medical librarian, to identify relevant studies; (4) meticulous data abstraction by at least two sets of investigators independently; (5) assessing risk of bias in individual studies; (6) quantitative synthesis with meta-analysis; and (7) critically and transparently ascertaining quality of evidence. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Segmentation of dermatoscopic images by frequency domain filtering and k-means clustering algorithms.

PubMed

Rajab, Maher I

2011-11-01

Since the introduction of epiluminescence microscopy (ELM), image analysis tools have been extended to the field of dermatology, in an attempt to algorithmically reproduce clinical evaluation. Accurate image segmentation of skin lesions is one of the key steps for useful, early and non-invasive diagnosis of coetaneous melanomas. This paper proposes two image segmentation algorithms based on frequency domain processing and k-means clustering/fuzzy k-means clustering. The two methods are capable of segmenting and extracting the true border that reveals the global structure irregularity (indentations and protrusions), which may suggest excessive cell growth or regression of a melanoma. As a pre-processing step, Fourier low-pass filtering is applied to reduce the surrounding noise in a skin lesion image. A quantitative comparison of the techniques is enabled by the use of synthetic skin lesion images that model lesions covered with hair to which Gaussian noise is added. The proposed techniques are also compared with an established optimal-based thresholding skin-segmentation method. It is demonstrated that for lesions with a range of different border irregularity properties, the k-means clustering and fuzzy k-means clustering segmentation methods provide the best performance over a range of signal to noise ratios. The proposed segmentation techniques are also demonstrated to have similar performance when tested on real skin lesions representing high-resolution ELM images. This study suggests that the segmentation results obtained using a combination of low-pass frequency filtering and k-means or fuzzy k-means clustering are superior to the result that would be obtained by using k-means or fuzzy k-means clustering segmentation methods alone. © 2011 John Wiley & Sons A/S.

Systematic Braiding of Two Evidence-Based Parent Training Programs: Qualitative Results from the Pilot Phase

PubMed Central

Guastaferro, Kate; Miller, Katy; Shanley Chatham, Jenelle R.; Whitaker, Daniel J.; McGilly, Kate; Lutzker, John R.

2017-01-01

An effective approach in early intervention for children and families, including child maltreatment prevention, is home-based services. Though several evidence-based programs exist, they are often grouped together, despite having different foci. This paper describes an ongoing cluster randomized trial systematically braiding two evidence-based home-based models, SafeCare® and Parents as Teachers (PAT)®, to better meet the needs of families at-risk. We describe the methodology for braiding model implementation and curriculum, specifically focusing on how structured qualitative feedback from pilot families and providers was used to create the braided curriculum and implementation. Systematic braiding of two models at the implementation and curriculum levels is a mechanism that has the potential to meet the more comprehensive needs of families at-risk for maltreatment. PMID:27870760

The study of structures and properties of PdnHm(n=1-10, m=1,2) clusters by density functional theory

NASA Astrophysics Data System (ADS)

Wen, Jun-Qing; Chen, Guo-Xiang; Zhang, Jian-Min; Wu, Hua

2018-04-01

The geometrical evolution, local relative stability, magnetism and charge transfer characteristics of PdnHm(n = 1-10, m = 1,2) have been systematically calculated by using density functional theory. The studied results show that the most stable geometries of PdnH and PdnH2 (n = 1-10) can be got by doping one or two H atoms on the sides of Pdn clusters except Pd6H and Pd6H2. It is found that doping one or two H atoms on Pdn clusters cannot change the basic framework of Pdn. The analysis of stability shows that Pd2H, Pd4H, Pd7H, Pd2H2, Pd4H2 and Pd7H2 clusters have higher local relative stability than neighboring clusters. The analysis of magnetic properties demonstrates that absorption of hydrogen atoms decreases the average atomic magnetic moments compared with pure Pdn clusters. More charges transfer from H atoms to Pd atoms for Pd6H and Pd6H2 clusters, demonstrating the adsorption of hydrogen atoms change from side adsorption to surface adsorption.

[Achene morphology cluster analysis of Taraxacum F. H. Wigg. from northeast China and molecule systematics evidence determined by SRAP].

PubMed

Li, Hai-juan; Zhao, Xin; Jia, Qing-fei; Li, Tian-lai; Ning, Wei

2012-08-01

The achenes morphological and micro-morphological characteristics of six species of genus Taraxacum from northeastern China as well as SRAP cluster analysis were observed for their classification evidences. The achenes were observed by microscope and EPMA. Cluster analysis was given on the basis of the size, shape, cone proportion, color and surface sculpture of achenes. The Taraxacum inter-species achene shape characteristic difference is obvious, particularly spinulose distribution and size, achene color and achene size; with the Taraxacum plant achene shape the cluster method T. antungense Kitag. and the T. urbanum Kitag. should combine for the identical kind; the achene morphology cluster analysis and the SRAP tagged molecule systematics's cluster result retrieves in the table with "the Chinese flora". The class group to divide the result is consistent. Taraxacum plant achene shape characteristic stable conservative, may carry on the inter-species division and the sibship analysis according to the achene shape characteristic combination difference; the achene morphology cluster analysis as well as the SRAP tagged molecule systematics confirmation support dandelion classification result of "the Chinese flora".

Dynamic Trajectory Extraction from Stereo Vision Using Fuzzy Clustering

NASA Astrophysics Data System (ADS)

Onishi, Masaki; Yoda, Ikushi

In recent years, many human tracking researches have been proposed in order to analyze human dynamic trajectory. These researches are general technology applicable to various fields, such as customer purchase analysis in a shopping environment and safety control in a (railroad) crossing. In this paper, we present a new approach for tracking human positions by stereo image. We use the framework of two-stepped clustering with k-means method and fuzzy clustering to detect human regions. In the initial clustering, k-means method makes middle clusters from objective features extracted by stereo vision at high speed. In the last clustering, c-means fuzzy method cluster middle clusters based on attributes into human regions. Our proposed method can be correctly clustered by expressing ambiguity using fuzzy clustering, even when many people are close to each other. The validity of our technique was evaluated with the experiment of trajectories extraction of doctors and nurses in an emergency room of a hospital.

Who attends a Children's Hospital Emergency Department for dental reasons? A two-step cluster analysis approach.

PubMed

Marshman, Z; Broomhead, T; Rodd, H D; Jones, K; Burke, D; Baker, S R

2016-09-28

Emergency departments (EDs) have been identified as key providers of dental care although few studies have examined patterns of attendance or clusters of characteristics. The aim was to identify the reasons for visits to an ED, whether these remained stable over time, and characterize clusters of patients by socio-demographic and attendance variables. Pseudonymized data were obtained for children who attended the ED in 2003-2004, 2004-2005 and 2012-2013. Presenting complaint was categorized as attending for dental or nondental reasons. Other variables analysed included patient (age, sex, ethnicity and deprivation) and attendance characteristics (distance travelled, season, nature of complaint, time elapsed since onset of symptoms, day of week and hours of attendance), together with treatment outcome (advice, antibiotics and referral). To assess trends over time, analyses were conducted on patient, attendance and treatment outcome variables. To examine whether patients could be characterized by socio-demographic and attendance variables, a two-step cluster analysis was undertaken on 2003-2004 data set and validated on 2004-2005 and 2012-2013 data sets. In 2003-2004, 550 children attended the ED for dental reasons rising to 687 in 2012-2013. The most important predictors of dental attendance were as follows: nature of complaint, ethnicity, time elapsed, sex and deprivation of the area in which children lived. The analysis showed two clusters: cluster 1 was comprised of children who attended the ED for dental injury, were of White ethnicity and attended within 24 h of onset of symptoms. Children in this cluster were likely to be from the least or less deprived areas (compared to Cluster 2) and were more likely to be males. Cluster 2 comprised of children attending the ED for caries, oral mucosal lesions or other complaints, were likely to be of other (non-White) ethnicities and were likely to attend more than 24 h after symptoms began. Children in this cluster were more likely to come from the most deprived areas and were both males and females. The clusters varied according to treatment outcome; those patients in Cluster 2 were more likely to be prescribed medication, whilst those children in Cluster 1 were more likely to be referred to another specialty. A significant number of visits to the ED were for dental reasons with two clusters of children. The results have identified groups of patients for whom appropriate dental provision is lacking and where targeted services are needed to improve outcomes for children and reduce the burden on EDs. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Galaxy Cluster Mass Reconstruction Project – III. The impact of dynamical substructure on cluster mass estimates

DOE PAGES

Old, L.; Wojtak, R.; Pearce, F. R.; ...

2017-12-20

With the advent of wide-field cosmological surveys, we are approaching samples of hundreds of thousands of galaxy clusters. While such large numbers will help reduce statistical uncertainties, the control of systematics in cluster masses is crucial. Here we examine the effects of an important source of systematic uncertainty in galaxy-based cluster mass estimation techniques: the presence of significant dynamical substructure. Dynamical substructure manifests as dynamically distinct subgroups in phase-space, indicating an ‘unrelaxed’ state. This issue affects around a quarter of clusters in a generally selected sample. We employ a set of mock clusters whose masses have been measured homogeneously withmore » commonly used galaxy-based mass estimation techniques (kinematic, richness, caustic, radial methods). We use these to study how the relation between observationally estimated and true cluster mass depends on the presence of substructure, as identified by various popular diagnostics. We find that the scatter for an ensemble of clusters does not increase dramatically for clusters with dynamical substructure. However, we find a systematic bias for all methods, such that clusters with significant substructure have higher measured masses than their relaxed counterparts. This bias depends on cluster mass: the most massive clusters are largely unaffected by the presence of significant substructure, but masses are significantly overestimated for lower mass clusters, by ~ 10 percent at 10 14 and ≳ 20 percent for ≲ 10 13.5. Finally, the use of cluster samples with different levels of substructure can therefore bias certain cosmological parameters up to a level comparable to the typical uncertainties in current cosmological studies.« less

Galaxy Cluster Mass Reconstruction Project – III. The impact of dynamical substructure on cluster mass estimates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Old, L.; Wojtak, R.; Pearce, F. R.

With the advent of wide-field cosmological surveys, we are approaching samples of hundreds of thousands of galaxy clusters. While such large numbers will help reduce statistical uncertainties, the control of systematics in cluster masses is crucial. Here we examine the effects of an important source of systematic uncertainty in galaxy-based cluster mass estimation techniques: the presence of significant dynamical substructure. Dynamical substructure manifests as dynamically distinct subgroups in phase-space, indicating an ‘unrelaxed’ state. This issue affects around a quarter of clusters in a generally selected sample. We employ a set of mock clusters whose masses have been measured homogeneously withmore » commonly used galaxy-based mass estimation techniques (kinematic, richness, caustic, radial methods). We use these to study how the relation between observationally estimated and true cluster mass depends on the presence of substructure, as identified by various popular diagnostics. We find that the scatter for an ensemble of clusters does not increase dramatically for clusters with dynamical substructure. However, we find a systematic bias for all methods, such that clusters with significant substructure have higher measured masses than their relaxed counterparts. This bias depends on cluster mass: the most massive clusters are largely unaffected by the presence of significant substructure, but masses are significantly overestimated for lower mass clusters, by ~ 10 percent at 10 14 and ≳ 20 percent for ≲ 10 13.5. Finally, the use of cluster samples with different levels of substructure can therefore bias certain cosmological parameters up to a level comparable to the typical uncertainties in current cosmological studies.« less

Clustering of financial time series with application to index and enhanced index tracking portfolio

NASA Astrophysics Data System (ADS)

Dose, Christian; Cincotti, Silvano

2005-09-01

A stochastic-optimization technique based on time series cluster analysis is described for index tracking and enhanced index tracking problems. Our methodology solves the problem in two steps, i.e., by first selecting a subset of stocks and then setting the weight of each stock as a result of an optimization process (asset allocation). Present formulation takes into account constraints on the number of stocks and on the fraction of capital invested in each of them, whilst not including transaction costs. Computational results based on clustering selection are compared to those of random techniques and show the importance of clustering in noise reduction and robust forecasting applications, in particular for enhanced index tracking.

Elderly patients attended in emergency health services in Brazil: a study for victims of falls and traffic accidents.

PubMed

de Freitas, Mariana Gonçalves; Bonolo, Palmira de Fátima; de Moraes, Edgar Nunes; Machado, Carla Jorge

2015-03-01

The article aims to describe the profile of elderly victims of falls and traffic accidents from the data of the Surveillance Survey of Violence and Accidents (VIVA). The VIVA Survey was conducted in the emergency health-services of the Unified Health System in the capitals of Brazil in 2011. The sample of elderly by type of accident was subjected to the two-step cluster procedure. Of the 2463 elderly persons in question, 79.8% suffered falls and 20.2% were the victims of traffic accidents. The 1812 elderly who fell were grouped together into 4 clusters: Cluster 1, in which all had disabilities; Cluster 2, all were non-white and falls took place in the home; Cluster 3, younger and active seniors; and Cluster 4, with a higher proportion of seniors 80 years old or above who were white. Among cases of traffic accidents, 446 seniors were grouped into two clusters: Cluster 1 of younger elderly, drivers or passengers; Cluster 2, with higher age seniors, mostly pedestrians. The main victims of falls were women with low schooling and unemployed; traffic accident victims were mostly younger and male. Complications were similar in victims of falls and traffic accidents. Clusters allow adoption of targeted measures of care, prevention and health promotion.

Modeling solute clustering in the diffusion layer around a growing crystal.

PubMed

Shiau, Lie-Ding; Lu, Yung-Fang

2009-03-07

The mechanism of crystal growth from solution is often thought to consist of a mass transfer diffusion step followed by a surface reaction step. Solute molecules might form clusters in the diffusion step before incorporating into the crystal lattice. A model is proposed in this work to simulate the evolution of the cluster size distribution due to the simultaneous aggregation and breakage of solute molecules in the diffusion layer around a growing crystal in the stirred solution. The crystallization of KAl(SO(4))(2)12H(2)O from aqueous solution is studied to illustrate the effect of supersaturation and diffusion layer thickness on the number-average degree of clustering and the size distribution of solute clusters in the diffusion layer.

Automated Measurement of P- and S-Wave Differential Times for Imaging Spatial Distributions of Vp/Vs Ratio, with Moving-Window Cross-Correlation Technique

NASA Astrophysics Data System (ADS)

Taira, T.; Kato, A.

2013-12-01

A high-resolution Vp/Vs ratio estimate is one of the key parameters to understand spatial variations of composition and physical state within the Earth. Lin and Shearer (2007, BSSA) recently developed a methodology to obtain local Vp/Vs ratios in individual similar earthquake clusters, based on P- and S-wave differential times. A waveform cross-correlation approach is typically employed to measure those differential times for pairs of seismograms from similar earthquakes clusters, at narrow time windows around the direct P and S waves. This approach effectively collects P- and S-wave differential times and however requires the robust P- and S-wave time windows that are extracted based on either manually or automatically picked P- and S-phases. We present another technique to estimate P- and S-wave differential times by exploiting temporal properties of delayed time as a function of elapsed time on the seismograms with a moving-window cross-correlation analysis (e.g., Snieder, 2002, Phys. Rev. E; Niu et al. 2003, Nature). Our approach is based on the principle that the delayed time for the direct S wave differs from that for the direct P wave. Two seismograms aligned by the direct P waves from a pair of similar earthquakes yield that delayed times become zero around the direct P wave. In contrast, delayed times obtained from time windows including the direct S wave have non-zero value. Our approach, in principle, is capable of measuring both P- and S-wave differential times from single-component seismograms. In an ideal case, the temporal evolution of delayed time becomes a step function with its discontinuity at the onset of the direct S wave. The offset in the resulting step function would be the S-wave differential time, relative to the P-wave differential time as the two waveforms are aligned by the direct P wave. We apply our moving-window cross-correlation technique to the two different data sets collected at: 1) the Wakayama district, Japan and 2) the Geysers geothermal field, California. The both target areas are characterized by earthquake swarms that provide a number of similar events clusters. We use the following automated procedure to systematically analyze the two data sets: 1) the identification of the direct P arrivals by using an Akaike Information Criterion based phase picking algorithm introduced by Zhang and Thurber (2003, BSSA), 2) the waveform alignment by the P-wave with a waveform cross-correlation to obtain P-wave differential time, 3) the moving-time window analysis to estimate the S-differential time. Kato et al. (2010, GRL) have estimated the Vp/Vs ratios for a few similar earthquake clusters from the Wakayama data set, by a conventional approach to obtain differential times. We find that the resulting Vp/Vs ratios from our approach for the same earthquake clusters are comparable with those obtained from Kato et al. (2010, GRL). We show that the moving-window cross-correlation technique effectively measures both P- and S-wave differential times for the seismograms in which the clear P and S phases are not observed. We will show spatial distributions in Vp/Vs ratios in our two target areas.

The Rise of Radicals in Bioinorganic Chemistry.

PubMed

Gray, Harry B; Winkler, Jay R

2016-10-01

Prior to 1950, the consensus was that biological transformations occurred in two-electron steps, thereby avoiding the generation of free radicals. Dramatic advances in spectroscopy, biochemistry, and molecular biology have led to the realization that protein-based radicals participate in a vast array of vital biological mechanisms. Redox processes involving high-potential intermediates formed in reactions with O 2 are particularly susceptible to radical formation. Clusters of tyrosine (Tyr) and tryptophan (Trp) residues have been found in many O 2 -reactive enzymes, raising the possibility that they play an antioxidant protective role. In blue copper proteins with plastocyanin-like domains, Tyr/Trp clusters are uncommon in the low-potential single-domain electron-transfer proteins and in the two-domain copper nitrite reductases. The two-domain muticopper oxidases, however, exhibit clusters of Tyr and Trp residues near the trinuclear copper active site where O 2 is reduced. These clusters may play a protective role to ensure that reactive oxygen species are not liberated during O 2 reduction.

Constraining the mass–richness relationship of redMaPPer clusters with angular clustering

DOE PAGES

Baxter, Eric J.; Rozo, Eduardo; Jain, Bhuvnesh; ...

2016-08-04

The potential of using cluster clustering for calibrating the mass–richness relation of galaxy clusters has been recognized theoretically for over a decade. In this paper, we demonstrate the feasibility of this technique to achieve high-precision mass calibration using redMaPPer clusters in the Sloan Digital Sky Survey North Galactic Cap. By including cross-correlations between several richness bins in our analysis, we significantly improve the statistical precision of our mass constraints. The amplitude of the mass–richness relation is constrained to 7 per cent statistical precision by our analysis. However, the error budget is systematics dominated, reaching a 19 per cent total errormore » that is dominated by theoretical uncertainty in the bias–mass relation for dark matter haloes. We confirm the result from Miyatake et al. that the clustering amplitude of redMaPPer clusters depends on galaxy concentration as defined therein, and we provide additional evidence that this dependence cannot be sourced by mass dependences: some other effect must account for the observed variation in clustering amplitude with galaxy concentration. Assuming that the observed dependence of redMaPPer clustering on galaxy concentration is a form of assembly bias, we find that such effects introduce a systematic error on the amplitude of the mass–richness relation that is comparable to the error bar from statistical noise. Finally, the results presented here demonstrate the power of cluster clustering for mass calibration and cosmology provided the current theoretical systematics can be ameliorated.« less

Systematic and Scalable Testing of Concurrent Programs

DTIC Science & Technology

2013-12-16

The evaluation of CHESS [107] checked eight different programs ranging from process management libraries to a distributed execution engine to a research...tool (§3.1) targets systematic testing of scheduling nondeterminism in multi- threaded components of the Omega cluster management system [129], while...tool for systematic testing of multithreaded com- ponents of the Omega cluster management system [129]. In particular, §3.1.1 defines a model for

Feature Selection Using Information Gain for Improved Structural-Based Alert Correlation

PubMed Central

Siraj, Maheyzah Md; Zainal, Anazida; Elshoush, Huwaida Tagelsir; Elhaj, Fatin

2016-01-01

Grouping and clustering alerts for intrusion detection based on the similarity of features is referred to as structurally base alert correlation and can discover a list of attack steps. Previous researchers selected different features and data sources manually based on their knowledge and experience, which lead to the less accurate identification of attack steps and inconsistent performance of clustering accuracy. Furthermore, the existing alert correlation systems deal with a huge amount of data that contains null values, incomplete information, and irrelevant features causing the analysis of the alerts to be tedious, time-consuming and error-prone. Therefore, this paper focuses on selecting accurate and significant features of alerts that are appropriate to represent the attack steps, thus, enhancing the structural-based alert correlation model. A two-tier feature selection method is proposed to obtain the significant features. The first tier aims at ranking the subset of features based on high information gain entropy in decreasing order. The‏ second tier extends additional features with a better discriminative ability than the initially ranked features. Performance analysis results show the significance of the selected features in terms of the clustering accuracy using 2000 DARPA intrusion detection scenario-specific dataset. PMID:27893821

A survey for dwarf galaxy remnants around 14 globular clusters in the outer halo

NASA Astrophysics Data System (ADS)

Sollima, A.; Martínez Delgado, D.; Muñoz, R. R.; Carballo-Bello, J. A.; Valls-Gabaud, D.; Grebel, E. K.; Santana, F. A.; Côté, P.; Djorgovski, S. G.

2018-06-01

We report the results of a systematic photometric survey of the peripheral regions of a sample of 14 globular clusters in the outer halo of the Milky Way at distances dGC > 25 kpc from the Galactic Centre. The survey is aimed at searching for the remnants of the host satellite galaxies where these clusters could originally have been formed before being accreted on to the Galactic halo. The limiting surface brightness varies within our sample, but reaches μV, lim = 30-32 mag arcsec-2. For only two globular clusters (NGC 7492 and Whiting 1; already suggested to be associated with the Sagittarius galaxy), we detect extended stellar populations that cannot be associated with either the clusters themselves or with the surrounding Galactic field population. We show that the lack of substructures around globular clusters at these Galactocentric distances is still compatible with the predictions of cosmological simulations whereby in the outer halo the Galactic globular cluster system is built up through hierarchical accretion at early epochs.

A hierarchical clustering methodology for the estimation of toxicity.

PubMed

Martin, Todd M; Harten, Paul; Venkatapathy, Raghuraman; Das, Shashikala; Young, Douglas M

2008-01-01

ABSTRACT A quantitative structure-activity relationship (QSAR) methodology based on hierarchical clustering was developed to predict toxicological endpoints. This methodology utilizes Ward's method to divide a training set into a series of structurally similar clusters. The structural similarity is defined in terms of 2-D physicochemical descriptors (such as connectivity and E-state indices). A genetic algorithm-based technique is used to generate statistically valid QSAR models for each cluster (using the pool of descriptors described above). The toxicity for a given query compound is estimated using the weighted average of the predictions from the closest cluster from each step in the hierarchical clustering assuming that the compound is within the domain of applicability of the cluster. The hierarchical clustering methodology was tested using a Tetrahymena pyriformis acute toxicity data set containing 644 chemicals in the training set and with two prediction sets containing 339 and 110 chemicals. The results from the hierarchical clustering methodology were compared to the results from several different QSAR methodologies.

An Empirical Typology of Narcissism and Mental Health in Late Adolescence

ERIC Educational Resources Information Center

Lapsley, Daniel K.; Aalsma, Matthew C.

2006-01-01

A two-step cluster analytic strategy was used in two studies to identify an empirically derived typology of narcissism in late adolescence. In Study 1, late adolescents (N=204) responded to the profile of narcissistic dispositions and measures of grandiosity (''superiority'') and idealization (''goal instability'') inspired by Kohut's theory,…

Strong-lensing analysis of A2744 with MUSE and Hubble Frontier Fields images

NASA Astrophysics Data System (ADS)

Mahler, G.; Richard, J.; Clément, B.; Lagattuta, D.; Schmidt, K.; Patrício, V.; Soucail, G.; Bacon, R.; Pello, R.; Bouwens, R.; Maseda, M.; Martinez, J.; Carollo, M.; Inami, H.; Leclercq, F.; Wisotzki, L.

2018-01-01

We present an analysis of Multi Unit Spectroscopic Explorer (MUSE) observations obtained on the massive Frontier Fields (FFs) cluster A2744. This new data set covers the entire multiply imaged region around the cluster core. The combined catalogue consists of 514 spectroscopic redshifts (with 414 new identifications). We use this redshift information to perform a strong-lensing analysis revising multiple images previously found in the deep FF images, and add three new MUSE-detected multiply imaged systems with no obvious Hubble Space Telescope counterpart. The combined strong-lensing constraints include a total of 60 systems producing 188 images altogether, out of which 29 systems and 83 images are spectroscopically confirmed, making A2744 one of the most well-constrained clusters to date. Thanks to the large amount of spectroscopic redshifts, we model the influence of substructures at larger radii, using a parametrization including two cluster-scale components in the cluster core and several group scale in the outskirts. The resulting model accurately reproduces all the spectroscopic multiple systems, reaching an rms of 0.67 arcsec in the image plane. The large number of MUSE spectroscopic redshifts gives us a robust model, which we estimate reduces the systematic uncertainty on the 2D mass distribution by up to ∼2.5 times the statistical uncertainty in the cluster core. In addition, from a combination of the parametrization and the set of constraints, we estimate the relative systematic uncertainty to be up to 9 per cent at 200 kpc.

Antisymmetric vortex interactions in the wake behind a step cylinder

NASA Astrophysics Data System (ADS)

Tian, Cai; Jiang, Fengjian; Pettersen, Bjørnar; Andersson, Helge I.

2017-10-01

Flow around a step cylinder at the Reynolds number 150 was simulated by directly solving the full Navier-Stokes equations. The configuration was adopted from the work of Morton and Yarusevych ["Vortex shedding in the wake of a step cylinder," Phys. Fluids 22, 083602 (2010)], in which the wake dynamics were systematically described. A more detailed investigation of the vortex dislocation process has now been performed. Two kinds of new loop vortex structures were identified. Additionally, antisymmetric vortex interactions in two adjacent vortex dislocation processes were observed and explained. The results in this letter serve as a supplement for a more thorough understanding of the vortex dynamics in the step cylinder wake.

The Sunyaev-Zel'dovich Effect in Abell 370

NASA Technical Reports Server (NTRS)

Grego, Laura; Carlstrom, John E.; Joy, Marshall K.; Reese, Erik D.; Holder, Gilbert P.; Patel, Sandeep; Holzapfel, William L.; Cooray, Asantha K.

1999-01-01

We present interferometric measurements of the Sunyaev-Zel'dovich (SZ) effect towards the galaxy cluster Abell 370. These measurements, which directly probe the pressure of the cluster's gas, show the gas is strongly aspherical, on agreement with the morphology revealed by x-ray and gravitational lensing observations. We calculate the cluster's gas mass fraction by comparing the gas mass derived from the SZ measurements to the lensing-derived gravitational mass near the critical lensing radius. We also calculate the gas mass fraction from the SZ data by deriving the total mass under the assumption that the gas is in hydrostatic equilibrium (HSE). We test the assumptions in the HSE method by comparing the total cluster mass implied by the two methods. The Hubble constant derived for this cluster, when the known systematic uncertainties are included, has a very wide range of values and therefore does not provide additional constraints on the validity of the assumptions. We examine carefully the possible systematic errors in the gas fraction measurement. The gas fraction is a lower limit to the cluster's baryon fraction and so we compare the gas mass fraction, calibrated by numerical simulations to approximately the virial radius, to measurements of the global mass fraction of baryonic matter, OMEGA(sub B)/OMEGA(sub matter). Our lower limit to the cluster baryon fraction is f(sub B) = (0.043 +/- 0.014)/h (sub 100). From this, we derive an upper limit to the universal matter density, OMEGA(sub matter) <= 0.72/h(sub 100), and a likely value of OMEGA(sub matter) <= (0.44(sup 0.15, sub -0.12)/h(sub 100).

CHEERS: The chemical evolution RGS sample

NASA Astrophysics Data System (ADS)

de Plaa, J.; Kaastra, J. S.; Werner, N.; Pinto, C.; Kosec, P.; Zhang, Y.-Y.; Mernier, F.; Lovisari, L.; Akamatsu, H.; Schellenberger, G.; Hofmann, F.; Reiprich, T. H.; Finoguenov, A.; Ahoranta, J.; Sanders, J. S.; Fabian, A. C.; Pols, O.; Simionescu, A.; Vink, J.; Böhringer, H.

2017-11-01

Context. The chemical yields of supernovae and the metal enrichment of the intra-cluster medium (ICM) are not well understood. The hot gas in clusters of galaxies has been enriched with metals originating from billions of supernovae and provides a fair sample of large-scale metal enrichment in the Universe. High-resolution X-ray spectra of clusters of galaxies provide a unique way of measuring abundances in the hot intracluster medium (ICM). The abundance measurements can provide constraints on the supernova explosion mechanism and the initial-mass function of the stellar population. This paper introduces the CHEmical Enrichment RGS Sample (CHEERS), which is a sample of 44 bright local giant ellipticals, groups, and clusters of galaxies observed with XMM-Newton. Aims: The CHEERS project aims to provide the most accurate set of cluster abundances measured in X-rays using this sample. This paper focuses specifically on the abundance measurements of O and Fe using the reflection grating spectrometer (RGS) on board XMM-Newton. We aim to thoroughly discuss the cluster to cluster abundance variations and the robustness of the measurements. Methods: We have selected the CHEERS sample such that the oxygen abundance in each cluster is detected at a level of at least 5σ in the RGS. The dispersive nature of the RGS limits the sample to clusters with sharp surface brightness peaks. The deep exposures and the size of the sample allow us to quantify the intrinsic scatter and the systematic uncertainties in the abundances using spectral modeling techniques. Results: We report the oxygen and iron abundances as measured with RGS in the core regions of all 44 clusters in the sample. We do not find a significant trend of O/Fe as a function of cluster temperature, but we do find an intrinsic scatter in the O and Fe abundances from cluster to cluster. The level of systematic uncertainties in the O/Fe ratio is estimated to be around 20-30%, while the systematic uncertainties in the absolute O and Fe abundances can be as high as 50% in extreme cases. Thanks to the high statistics of the observations, we were able to identify and correct a systematic bias in the oxygen abundance determination that was due to an inaccuracy in the spectral model. Conclusions: The lack of dependence of O/Fe on temperature suggests that the enrichment of the ICM does not depend on cluster mass and that most of the enrichment likely took place before the ICM was formed. We find that the observed scatter in the O/Fe ratio is due to a combination of intrinsic scatter in the source and systematic uncertainties in the spectral fitting, which we are unable to separate. The astrophysical source of intrinsic scatter could be due to differences in active galactic nucleus activity and ongoing star formation in the brightest cluster galaxy. The systematic scatter is due to uncertainties in the spatial line broadening, absorption column, multi-temperature structure, and the thermal plasma models.

An empirical method to cluster objective nebulizer adherence data among adults with cystic fibrosis.

PubMed

Hoo, Zhe H; Campbell, Michael J; Curley, Rachael; Wildman, Martin J

2017-01-01

The purpose of using preventative inhaled treatments in cystic fibrosis is to improve health outcomes. Therefore, understanding the relationship between adherence to treatment and health outcome is crucial. Temporal variability, as well as absolute magnitude of adherence affects health outcomes, and there is likely to be a threshold effect in the relationship between adherence and outcomes. We therefore propose a pragmatic algorithm-based clustering method of objective nebulizer adherence data to better understand this relationship, and potentially, to guide clinical decisions. This clustering method consists of three related steps. The first step is to split adherence data for the previous 12 months into four 3-monthly sections. The second step is to calculate mean adherence for each section and to score the section based on mean adherence. The third step is to aggregate the individual scores to determine the final cluster ("cluster 1" = very low adherence; "cluster 2" = low adherence; "cluster 3" = moderate adherence; "cluster 4" = high adherence), and taking into account adherence trend as represented by sequential individual scores. The individual scores should be displayed along with the final cluster for clinicians to fully understand the adherence data. We present three cases to illustrate the use of the proposed clustering method. This pragmatic clustering method can deal with adherence data of variable duration (ie, can be used even if 12 months' worth of data are unavailable) and can cluster adherence data in real time. Empirical support for some of the clustering parameters is not yet available, but the suggested classifications provide a structure to investigate parameters in future prospective datasets in which there are accurate measurements of nebulizer adherence and health outcomes.

Towards a realistic population of simulated galaxy groups and clusters

NASA Astrophysics Data System (ADS)

Le Brun, Amandine M. C.; McCarthy, Ian G.; Schaye, Joop; Ponman, Trevor J.

2014-06-01

We present a new suite of large-volume cosmological hydrodynamical simulations called cosmo-OWLS. They form an extension to the OverWhelmingly Large Simulations (OWLS) project, and have been designed to help improve our understanding of cluster astrophysics and non-linear structure formation, which are now the limiting systematic errors when using clusters as cosmological probes. Starting from identical initial conditions in either the Planck or WMAP7 cosmologies, we systematically vary the most important `sub-grid' physics, including feedback from supernovae and active galactic nuclei (AGN). We compare the properties of the simulated galaxy groups and clusters to a wide range of observational data, such as X-ray luminosity and temperature, gas mass fractions, entropy and density profiles, Sunyaev-Zel'dovich flux, I-band mass-to-light ratio, dominance of the brightest cluster galaxy and central massive black hole (BH) masses, by producing synthetic observations and mimicking observational analysis techniques. These comparisons demonstrate that some AGN feedback models can produce a realistic population of galaxy groups and clusters, broadly reproducing both the median trend and, for the first time, the scatter in physical properties over approximately two decades in mass (1013 M⊙ ≲ M500 ≲ 1015 M⊙) and 1.5 decades in radius (0.05 ≲ r/r500 ≲ 1.5). However, in other models, the AGN feedback is too violent (even though they reproduce the observed BH scaling relations), implying that calibration of the models is required. The production of realistic populations of simulated groups and clusters, as well as models that bracket the observations, opens the door to the creation of synthetic surveys for assisting the astrophysical and cosmological interpretation of cluster surveys, as well as quantifying the impact of selection effects.

Excitons in Potassium Bromide: A Study using Embedded Time-dependent Density Functional Theory and Equation-of-Motion Coupled Cluster Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Govind, Niranjan; Sushko, Petr V.; Hess, Wayne P.

2009-03-05

We present a study of the electronic excitations in insulating materials using an embedded- cluster method. The excited states of the embedded cluster are studied systematically using time-dependent density functional theory (TDDFT) and high-level equation-of-motion coupled cluster (EOMCC) methods. In particular, we have used EOMCC models with singles and doubles (EOMCCSD) and two approaches which account for the e®ect of triply excited con¯gurations in non-iterative and iterative fashions. We present calculations of the lowest surface excitations of the well-studied potassium bromide (KBr) system and compare our results with experiment. The bulk-surface exciton shift is also calculated at the TDDFT levelmore » and compared with experiment.« less

Iterative direct inversion: An exact complementary solution for inverting fault-slip data to obtain palaeostresses

NASA Astrophysics Data System (ADS)

Mostafa, Mostafa E.

2005-10-01

The present study shows that reconstructing the reduced stress tensor (RST) from the measurable fault-slip data (FSD) and the immeasurable shear stress magnitudes (SSM) is a typical iteration problem. The result of direct inversion of FSD presented by Angelier [1990. Geophysical Journal International 103, 363-376] is considered as a starting point (zero step iteration) where all SSM are assigned constant value ( λ=√{3}/2). By iteration, the SSM and RST update each other until they converge to fixed values. Angelier [1990. Geophysical Journal International 103, 363-376] designed the function upsilon ( υ) and the two estimators: relative upsilon (RUP) and (ANG) to express the divergence between the measured and calculated shear stresses. Plotting individual faults' RUP at successive iteration steps shows that they tend to zero (simulated data) or to fixed values (real data) at a rate depending on the orientation and homogeneity of the data. FSD of related origin tend to aggregate in clusters. Plots of the estimators ANG versus RUP show that by iteration, labeled data points are disposed in clusters about a straight line. These two new plots form the basis of a technique for separating FSD into homogeneous clusters.

WEIGHING GALAXY CLUSTERS WITH GAS. I. ON THE METHODS OF COMPUTING HYDROSTATIC MASS BIAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lau, Erwin T.; Nagai, Daisuke; Nelson, Kaylea, E-mail: erwin.lau@yale.edu

2013-11-10

Mass estimates of galaxy clusters from X-ray and Sunyeav-Zel'dovich observations assume the intracluster gas is in hydrostatic equilibrium with their gravitational potential. However, since galaxy clusters are dynamically active objects whose dynamical states can deviate significantly from the equilibrium configuration, the departure from the hydrostatic equilibrium assumption is one of the largest sources of systematic uncertainties in cluster cosmology. In the literature there have been two methods for computing the hydrostatic mass bias based on the Euler and the modified Jeans equations, respectively, and there has been some confusion about the validity of these two methods. The word 'Jeans' wasmore » a misnomer, which incorrectly implies that the gas is collisionless. To avoid further confusion, we instead refer these methods as 'summation' and 'averaging' methods respectively. In this work, we show that these two methods for computing the hydrostatic mass bias are equivalent by demonstrating that the equation used in the second method can be derived from taking spatial averages of the Euler equation. Specifically, we identify the correspondences of individual terms in these two methods mathematically and show that these correspondences are valid to within a few percent level using hydrodynamical simulations of galaxy cluster formation. In addition, we compute the mass bias associated with the acceleration of gas and show that its contribution is small in the virialized regions in the interior of galaxy clusters, but becomes non-negligible in the outskirts of massive galaxy clusters. We discuss future prospects of understanding and characterizing biases in the mass estimate of galaxy clusters using both hydrodynamical simulations and observations and their implications for cluster cosmology.« less

Weighing Galaxy Clusters with Gas. I. On the Methods of Computing Hydrostatic Mass Bias

NASA Astrophysics Data System (ADS)

Lau, Erwin T.; Nagai, Daisuke; Nelson, Kaylea

2013-11-01

Mass estimates of galaxy clusters from X-ray and Sunyeav-Zel'dovich observations assume the intracluster gas is in hydrostatic equilibrium with their gravitational potential. However, since galaxy clusters are dynamically active objects whose dynamical states can deviate significantly from the equilibrium configuration, the departure from the hydrostatic equilibrium assumption is one of the largest sources of systematic uncertainties in cluster cosmology. In the literature there have been two methods for computing the hydrostatic mass bias based on the Euler and the modified Jeans equations, respectively, and there has been some confusion about the validity of these two methods. The word "Jeans" was a misnomer, which incorrectly implies that the gas is collisionless. To avoid further confusion, we instead refer these methods as "summation" and "averaging" methods respectively. In this work, we show that these two methods for computing the hydrostatic mass bias are equivalent by demonstrating that the equation used in the second method can be derived from taking spatial averages of the Euler equation. Specifically, we identify the correspondences of individual terms in these two methods mathematically and show that these correspondences are valid to within a few percent level using hydrodynamical simulations of galaxy cluster formation. In addition, we compute the mass bias associated with the acceleration of gas and show that its contribution is small in the virialized regions in the interior of galaxy clusters, but becomes non-negligible in the outskirts of massive galaxy clusters. We discuss future prospects of understanding and characterizing biases in the mass estimate of galaxy clusters using both hydrodynamical simulations and observations and their implications for cluster cosmology.

Bias and inference from misspecified mixed-effect models in stepped wedge trial analysis.

PubMed

Thompson, Jennifer A; Fielding, Katherine L; Davey, Calum; Aiken, Alexander M; Hargreaves, James R; Hayes, Richard J

2017-10-15

Many stepped wedge trials (SWTs) are analysed by using a mixed-effect model with a random intercept and fixed effects for the intervention and time periods (referred to here as the standard model). However, it is not known whether this model is robust to misspecification. We simulated SWTs with three groups of clusters and two time periods; one group received the intervention during the first period and two groups in the second period. We simulated period and intervention effects that were either common-to-all or varied-between clusters. Data were analysed with the standard model or with additional random effects for period effect or intervention effect. In a second simulation study, we explored the weight given to within-cluster comparisons by simulating a larger intervention effect in the group of the trial that experienced both the control and intervention conditions and applying the three analysis models described previously. Across 500 simulations, we computed bias and confidence interval coverage of the estimated intervention effect. We found up to 50% bias in intervention effect estimates when period or intervention effects varied between clusters and were treated as fixed effects in the analysis. All misspecified models showed undercoverage of 95% confidence intervals, particularly the standard model. A large weight was given to within-cluster comparisons in the standard model. In the SWTs simulated here, mixed-effect models were highly sensitive to departures from the model assumptions, which can be explained by the high dependence on within-cluster comparisons. Trialists should consider including a random effect for time period in their SWT analysis model. © 2017 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. © 2017 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd.

Bias and inference from misspecified mixed‐effect models in stepped wedge trial analysis

PubMed Central

Fielding, Katherine L.; Davey, Calum; Aiken, Alexander M.; Hargreaves, James R.; Hayes, Richard J.

2017-01-01

Many stepped wedge trials (SWTs) are analysed by using a mixed‐effect model with a random intercept and fixed effects for the intervention and time periods (referred to here as the standard model). However, it is not known whether this model is robust to misspecification. We simulated SWTs with three groups of clusters and two time periods; one group received the intervention during the first period and two groups in the second period. We simulated period and intervention effects that were either common‐to‐all or varied‐between clusters. Data were analysed with the standard model or with additional random effects for period effect or intervention effect. In a second simulation study, we explored the weight given to within‐cluster comparisons by simulating a larger intervention effect in the group of the trial that experienced both the control and intervention conditions and applying the three analysis models described previously. Across 500 simulations, we computed bias and confidence interval coverage of the estimated intervention effect. We found up to 50% bias in intervention effect estimates when period or intervention effects varied between clusters and were treated as fixed effects in the analysis. All misspecified models showed undercoverage of 95% confidence intervals, particularly the standard model. A large weight was given to within‐cluster comparisons in the standard model. In the SWTs simulated here, mixed‐effect models were highly sensitive to departures from the model assumptions, which can be explained by the high dependence on within‐cluster comparisons. Trialists should consider including a random effect for time period in their SWT analysis model. © 2017 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. PMID:28556355

Reversible cluster formation in concentrated monoclonal antibody solutions

NASA Astrophysics Data System (ADS)

Godfrin, P. Douglas; Porcar, Lionel; Falus, Peter; Zarraga, Isidro; Wagner, Norm; Liu, Yun

2015-03-01

Protein cluster formation in solution is of fundamental interest for both academic research and industrial applications. Recently, industrial scientists are also exploring the effect of reversible cluster formation on biopharmaceutical processing and delivery. However, despite of its importance, the understanding of protein clusters at concentrated solutions remains scientifically very challenging. Using the neutron spin echo technique to study the short time dynamics of proteins in solutions, we have recently systematically studied cluster formation in a few monoclonal antibody (mAb) solutions and their relation with solution viscosity. We show that the existence of anisotropic attraction can cause the formation of finite sized clusters, which increases the solution viscosity. Interestingly, once clusters form at relatively low concentrations, the average size of clusters in solutions remains almost constant over a wide range of concentrations similar to that of micelle formation. For a different mAb we have also investigated, the attraction is mostly induced by hydrophobic patches. As a result, these mAbs form large clusters with loosely linked proteins. In both cases, the formation of clusters all increases the solution viscosity substantially. However, due to different physics origins of cluster formation, solutions viscosities for these two different types of mAbs need to be controlled by different ways.

An enhanced deterministic K-Means clustering algorithm for cancer subtype prediction from gene expression data.

PubMed

Nidheesh, N; Abdul Nazeer, K A; Ameer, P M

2017-12-01

Clustering algorithms with steps involving randomness usually give different results on different executions for the same dataset. This non-deterministic nature of algorithms such as the K-Means clustering algorithm limits their applicability in areas such as cancer subtype prediction using gene expression data. It is hard to sensibly compare the results of such algorithms with those of other algorithms. The non-deterministic nature of K-Means is due to its random selection of data points as initial centroids. We propose an improved, density based version of K-Means, which involves a novel and systematic method for selecting initial centroids. The key idea of the algorithm is to select data points which belong to dense regions and which are adequately separated in feature space as the initial centroids. We compared the proposed algorithm to a set of eleven widely used single clustering algorithms and a prominent ensemble clustering algorithm which is being used for cancer data classification, based on the performances on a set of datasets comprising ten cancer gene expression datasets. The proposed algorithm has shown better overall performance than the others. There is a pressing need in the Biomedical domain for simple, easy-to-use and more accurate Machine Learning tools for cancer subtype prediction. The proposed algorithm is simple, easy-to-use and gives stable results. Moreover, it provides comparatively better predictions of cancer subtypes from gene expression data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Low Temperature Kinetics of the First Steps of Water Cluster Formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bourgalais, J.; Roussel, V.; Capron, M.

2016-03-01

We present a combined experimental and theoretical low temperature kinetic study of water cluster formation. Water cluster growth takes place in low temperature (23-69 K) supersonic flows. The observed kinetics of formation of water clusters are reproduced with a kinetic model based on theoretical predictions for the first steps of clusterization. The temperature-and pressure-dependent association and dissociation rate coefficients are predicted with an ab initio transition state theory based master equation approach over a wide range of temperatures (20-100 K) and pressures (10(-6) - 10 bar).

Novel Anthropometry Based on 3D-Bodyscans Applied to a Large Population Based Cohort.

PubMed

Löffler-Wirth, Henry; Willscher, Edith; Ahnert, Peter; Wirkner, Kerstin; Engel, Christoph; Loeffler, Markus; Binder, Hans

2016-01-01

Three-dimensional (3D) whole body scanners are increasingly used as precise measuring tools for the rapid quantification of anthropometric measures in epidemiological studies. We analyzed 3D whole body scanning data of nearly 10,000 participants of a cohort collected from the adult population of Leipzig, one of the largest cities in Eastern Germany. We present a novel approach for the systematic analysis of this data which aims at identifying distinguishable clusters of body shapes called body types. In the first step, our method aggregates body measures provided by the scanner into meta-measures, each representing one relevant dimension of the body shape. In a next step, we stratified the cohort into body types and assessed their stability and dependence on the size of the underlying cohort. Using self-organizing maps (SOM) we identified thirteen robust meta-measures and fifteen body types comprising between 1 and 18 percent of the total cohort size. Thirteen of them are virtually gender specific (six for women and seven for men) and thus reflect most abundant body shapes of women and men. Two body types include both women and men, and describe androgynous body shapes that lack typical gender specific features. The body types disentangle a large variability of body shapes enabling distinctions which go beyond the traditional indices such as body mass index, the waist-to-height ratio, the waist-to-hip ratio and the mortality-hazard ABSI-index. In a next step, we will link the identified body types with disease predispositions to study how size and shape of the human body impact health and disease.

A Systematic Study of Kelvin-Helmholtz Instability in Galaxy Clusters

NASA Astrophysics Data System (ADS)

Su, Yuanyuan

2017-09-01

Kelvin-Helmholtz instabilities (KHI) were observed at cold fronts in a handful of clusters. KHI are predicted at all cold fronts in hydro simulation of intracluster medium (ICM). Their presence and absence provides a unique probe of transport processes in the hot plasma, which are essential to the dissipation and redistribution of the energy in the ICM. We propose the first systematic study of the prevalence of KHI in galaxy clusters by analyzing the archived Chandra observations of a sample of 50 nearby galaxy clusters. We will associate the occurrence and properties of KHI rolls with various cluster parameters such as their gas temperature and density, and put constraints on effective transport coefficients in the ICM

Dark Energy Survey Year 1 Results: Methodology and Projections for Joint Analysis of Galaxy Clustering, Galaxy Lensing, and CMB Lensing Two-point Functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giannantonio, T.; et al.

Optical imaging surveys measure both the galaxy density and the gravitational lensing-induced shear fields across the sky. Recently, the Dark Energy Survey (DES) collaboration used a joint fit to two-point correlations between these observables to place tight constraints on cosmology (DES Collaboration et al. 2017). In this work, we develop the methodology to extend the DES Collaboration et al. (2017) analysis to include cross-correlations of the optical survey observables with gravitational lensing of the cosmic microwave background (CMB) as measured by the South Pole Telescope (SPT) and Planck. Using simulated analyses, we show how the resulting set of five two-pointmore » functions increases the robustness of the cosmological constraints to systematic errors in galaxy lensing shear calibration. Additionally, we show that contamination of the SPT+Planck CMB lensing map by the thermal Sunyaev-Zel'dovich effect is a potentially large source of systematic error for two-point function analyses, but show that it can be reduced to acceptable levels in our analysis by masking clusters of galaxies and imposing angular scale cuts on the two-point functions. The methodology developed here will be applied to the analysis of data from the DES, the SPT, and Planck in a companion work.« less

Multi-party Measurement-Device-Independent Quantum Key Distribution Based on Cluster States

NASA Astrophysics Data System (ADS)

Liu, Chuanqi; Zhu, Changhua; Ma, Shuquan; Pei, Changxing

2018-03-01

We propose a novel multi-party measurement-device-independent quantum key distribution (MDI-QKD) protocol based on cluster states. A four-photon analyzer which can distinguish all the 16 cluster states serves as the measurement device for four-party MDI-QKD. Any two out of four participants can build secure keys after the analyzers obtains successful outputs and the two participants perform post-processing. We derive a security analysis for the protocol, and analyze the key rates under different values of polarization misalignment. The results show that four-party MDI-QKD is feasible over 280 km in the optical fiber channel when the key rate is about 10- 6 with the polarization misalignment parameter 0.015. Moreover, our work takes an important step toward a quantum communication network.

Statistical analysis and handling of missing data in cluster randomized trials: a systematic review.

PubMed

Fiero, Mallorie H; Huang, Shuang; Oren, Eyal; Bell, Melanie L

2016-02-09

Cluster randomized trials (CRTs) randomize participants in groups, rather than as individuals and are key tools used to assess interventions in health research where treatment contamination is likely or if individual randomization is not feasible. Two potential major pitfalls exist regarding CRTs, namely handling missing data and not accounting for clustering in the primary analysis. The aim of this review was to evaluate approaches for handling missing data and statistical analysis with respect to the primary outcome in CRTs. We systematically searched for CRTs published between August 2013 and July 2014 using PubMed, Web of Science, and PsycINFO. For each trial, two independent reviewers assessed the extent of the missing data and method(s) used for handling missing data in the primary and sensitivity analyses. We evaluated the primary analysis and determined whether it was at the cluster or individual level. Of the 86 included CRTs, 80 (93%) trials reported some missing outcome data. Of those reporting missing data, the median percent of individuals with a missing outcome was 19% (range 0.5 to 90%). The most common way to handle missing data in the primary analysis was complete case analysis (44, 55%), whereas 18 (22%) used mixed models, six (8%) used single imputation, four (5%) used unweighted generalized estimating equations, and two (2%) used multiple imputation. Fourteen (16%) trials reported a sensitivity analysis for missing data, but most assumed the same missing data mechanism as in the primary analysis. Overall, 67 (78%) trials accounted for clustering in the primary analysis. High rates of missing outcome data are present in the majority of CRTs, yet handling missing data in practice remains suboptimal. Researchers and applied statisticians should carry out appropriate missing data methods, which are valid under plausible assumptions in order to increase statistical power in trials and reduce the possibility of bias. Sensitivity analysis should be performed, with weakened assumptions regarding the missing data mechanism to explore the robustness of results reported in the primary analysis.

Response of the Oxygen Sensor NreB to Air In Vivo: Fe-S-Containing NreB and Apo-NreB in Aerobically and Anaerobically Growing Staphylococcus carnosus▿

PubMed Central

Reinhart, F.; Huber, A.; Thiele, R.; Unden, G.

2010-01-01

The sensor kinase NreB from Staphylococcus carnosus contains an O2-sensitive [4Fe-4S]2+ cluster which is converted by O2 to a [2Fe-2S]2+ cluster, followed by complete degradation and formation of Fe-S-less apo-NreB. NreB·[2Fe-2S]2+ and apoNreB are devoid of kinase activity. NreB contains four Cys residues which ligate the Fe-S clusters. The accessibility of the Cys residues to alkylating agents was tested and used to differentiate Fe-S-containing and Fe-S-less NreB. In a two-step labeling procedure, accessible Cys residues in the native protein were first labeled by iodoacetate. In the second step, Cys residues not labeled in the first step were alkylated with the fluorescent monobromobimane (mBBr) after denaturing of the protein. In purified (aerobic) apoNreB, most (96%) of the Cys residues were alkylated in the first step, but in anaerobic (Fe-S-containing) NreB only a small portion (23%) were alkylated. In anaerobic bacteria, a very small portion of the Cys residues of NreB (9%) were accessible to alkylation in the native state, whereas most (89%) of the Cys residues from aerobic bacteria were accessible. The change in accessibility allowed determination of the half-time (6 min) for the conversion of NreB·[4Fe-4S]2+ to apoNreB after the addition of air in vitro. Overall, in anaerobic bacteria most of the NreB exists as NreB·[4Fe-4S]2+, whereas in aerobic bacteria the (Fe-S-less) apoNreB is predominant and represents the physiological form. The number of accessible Cys residues was also determined by iodoacetate alkylation followed by mass spectrometry of Cys-containing peptides. The pattern of mass increases confirmed the results from the two-step labeling experiments. PMID:19854899

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images

PubMed Central

Yang, Zhengfan; Fang, Jia; Chittuluru, Johnathan; Asturias, Francisco J.; Penczek, Pawel A.

2012-01-01

SUMMARY Identification of homogeneous subsets of images in a macromolecular electron microscopy (EM) image data set is a critical step in single-particle analysis. The task is handled by iterative algorithms, whose performance is compromised by the compounded limitations of image alignment and K-means clustering. Here we describe an approach, iterative stable alignment and clustering (ISAC) that, relying on a new clustering method and on the concepts of stability and reproducibility, can extract validated, homogeneous subsets of images. ISAC requires only a small number of simple parameters and, with minimal human intervention, can eliminate bias from two-dimensional image clustering and maximize the quality of group averages that can be used for ab initio three-dimensional structural determination and analysis of macromolecular conformational variability. Repeated testing of the stability and reproducibility of a solution within ISAC eliminates heterogeneous or incorrect classes and introduces critical validation to the process of EM image clustering. PMID:22325773

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Internal and external atomic steps in graphite exhibit dramatically different physical and chemical properties.

PubMed

Lee, Hyunsoo; Lee, Han-Bo-Ram; Kwon, Sangku; Salmeron, Miquel; Park, Jeong Young

2015-04-28

We report on the physical and chemical properties of atomic steps on the surface of highly oriented pyrolytic graphite (HOPG) investigated using atomic force microscopy. Two types of step edges are identified: internal (formed during crystal growth) and external (formed by mechanical cleavage of bulk HOPG). The external steps exhibit higher friction than the internal steps due to the broken bonds of the exposed edge C atoms, while carbon atoms in the internal steps are not exposed. The reactivity of the atomic steps is manifested in a variety of ways, including the preferential attachment of Pt nanoparticles deposited on HOPG when using atomic layer deposition and KOH clusters formed during drop casting from aqueous solutions. These phenomena imply that only external atomic steps can be used for selective electrodeposition for nanoscale electronic devices.

Multi-Spatiotemporal Patterns of Residential Burglary Crimes in Chicago: 2006-2016

NASA Astrophysics Data System (ADS)

Luo, J.

2017-10-01

This research attempts to explore the patterns of burglary crimes at multi-spatiotemporal scales in Chicago between 2006 and 2016. Two spatial scales are investigated that are census block and police beat area. At each spatial scale, three temporal scales are integrated to make spatiotemporal slices: hourly scale with two-hour time step from 12:00am to the end of the day; daily scale with one-day step from Sunday to Saturday within a week; monthly scale with one-month step from January to December. A total of six types of spatiotemporal slices will be created as the base for the analysis. Burglary crimes are spatiotemporally aggregated to spatiotemporal slices based on where and when they occurred. For each type of spatiotemporal slices with burglary occurrences integrated, spatiotemporal neighborhood will be defined and managed in a spatiotemporal matrix. Hot-spot analysis will identify spatiotemporal clusters of each type of spatiotemporal slices. Spatiotemporal trend analysis is conducted to indicate how the clusters shift in space and time. The analysis results will provide helpful information for better target policing and crime prevention policy such as police patrol scheduling regarding times and places covered.

Topic detection using paragraph vectors to support active learning in systematic reviews.

PubMed

Hashimoto, Kazuma; Kontonatsios, Georgios; Miwa, Makoto; Ananiadou, Sophia

2016-08-01

Systematic reviews require expert reviewers to manually screen thousands of citations in order to identify all relevant articles to the review. Active learning text classification is a supervised machine learning approach that has been shown to significantly reduce the manual annotation workload by semi-automating the citation screening process of systematic reviews. In this paper, we present a new topic detection method that induces an informative representation of studies, to improve the performance of the underlying active learner. Our proposed topic detection method uses a neural network-based vector space model to capture semantic similarities between documents. We firstly represent documents within the vector space, and cluster the documents into a predefined number of clusters. The centroids of the clusters are treated as latent topics. We then represent each document as a mixture of latent topics. For evaluation purposes, we employ the active learning strategy using both our novel topic detection method and a baseline topic model (i.e., Latent Dirichlet Allocation). Results obtained demonstrate that our method is able to achieve a high sensitivity of eligible studies and a significantly reduced manual annotation cost when compared to the baseline method. This observation is consistent across two clinical and three public health reviews. The tool introduced in this work is available from https://nactem.ac.uk/pvtopic/. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Electrician Cluster, STEP Training Plan. Skills Training and Education Program.

ERIC Educational Resources Information Center

Alabama State Dept. of Postsecondary Education, Montgomery.

This guide is a training plan for the electrical skills cluster of the Skills Training and Education Program (STEP), an open-entry, open-exit program funded by the Job Training Partnership Act (JTPA). In the STEP training plan, each task has its own lesson plan guide. This manual contains the following information: definitions, instructions for…

Clerical Cluster, STEP Training Plan. Skills Training and Education Program.

ERIC Educational Resources Information Center

Alabama State Dept. of Postsecondary Education, Montgomery.

This guide is a training plan for the clerical skills cluster of the Skills Training and Education Program (STEP), an open-entry, open-exit program funded by the Job Training Partnership Act (JTPA). In the STEP training plan, each task has its own lesson plan guide. This manual contains the following information: definitions, instructions for…

A two step Bayesian approach for genomic prediction of breeding values.

PubMed

Shariati, Mohammad M; Sørensen, Peter; Janss, Luc

2012-05-21

In genomic models that assign an individual variance to each marker, the contribution of one marker to the posterior distribution of the marker variance is only one degree of freedom (df), which introduces many variance parameters with only little information per variance parameter. A better alternative could be to form clusters of markers with similar effects where markers in a cluster have a common variance. Therefore, the influence of each marker group of size p on the posterior distribution of the marker variances will be p df. The simulated data from the 15th QTL-MAS workshop were analyzed such that SNP markers were ranked based on their effects and markers with similar estimated effects were grouped together. In step 1, all markers with minor allele frequency more than 0.01 were included in a SNP-BLUP prediction model. In step 2, markers were ranked based on their estimated variance on the trait in step 1 and each 150 markers were assigned to one group with a common variance. In further analyses, subsets of 1500 and 450 markers with largest effects in step 2 were kept in the prediction model. Grouping markers outperformed SNP-BLUP model in terms of accuracy of predicted breeding values. However, the accuracies of predicted breeding values were lower than Bayesian methods with marker specific variances. Grouping markers is less flexible than allowing each marker to have a specific marker variance but, by grouping, the power to estimate marker variances increases. A prior knowledge of the genetic architecture of the trait is necessary for clustering markers and appropriate prior parameterization.

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters.

PubMed

Parnis, J Mark; Escobar-Cabrera, Eric; Thompson, Matthew G K; Jacula, J Paul; Lafleur, Rick D; Guevara-García, Alfredo; Martínez, Ana; Rayner, David M

2005-08-18

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.

Profiling nurses' job satisfaction, acculturation, work environment, stress, cultural values and coping abilities: A cluster analysis.

PubMed

Goh, Yong-Shian; Lee, Alice; Chan, Sally Wai-Chi; Chan, Moon Fai

2015-08-01

This study aimed to determine whether definable profiles existed in a cohort of nursing staff with regard to demographic characteristics, job satisfaction, acculturation, work environment, stress, cultural values and coping abilities. A survey was conducted in one hospital in Singapore from June to July 2012, and 814 full-time staff nurses completed a self-report questionnaire (89% response rate). Demographic characteristics, job satisfaction, acculturation, work environment, perceived stress, cultural values, ways of coping and intention to leave current workplace were assessed as outcomes. The two-step cluster analysis revealed three clusters. Nurses in cluster 1 (n = 222) had lower acculturation scores than nurses in cluster 3. Cluster 2 (n = 362) was a group of younger nurses who reported higher intention to leave (22.4%), stress level and job dissatisfaction than the other two clusters. Nurses in cluster 3 (n = 230) were mostly Singaporean and reported the lowest intention to leave (13.0%). Resources should be allocated to specifically address the needs of younger nurses and hopefully retain them in the profession. Management should focus their retention strategies on junior nurses and provide a work environment that helps to strengthen their intention to remain in nursing by increasing their job satisfaction. © 2014 Wiley Publishing Asia Pty Ltd.

Light-induced defects in hybrid lead halide perovskite

NASA Astrophysics Data System (ADS)

Sharia, Onise; Schneider, William

One of the main challenges facing organohalide perovskites for solar application is stability. Solar cells must last decades to be economically viable alternatives to traditional energy sources. While some causes of instability can be avoided through engineering, light-induced defects can be fundamentally limiting factor for practical application of the material. Light creates large numbers of electron and hole pairs that can contribute to degradation processes. Using ab initio theoretical methods, we systematically explore first steps of light induced defect formation in methyl ammonium lead iodide, MAPbI3. In particular, we study charged and neutral Frenkel pair formation involving Pb and I atoms. We find that most of the defects, except negatively charged Pb Frenkel pairs, are reversible, and thus most do not lead to degradation. Negative Pb defects create a mid-gap state and localize the conduction band electron. A minimum energy path study shows that, once the first defect is created, Pb atoms migrate relatively fast. The defects have two detrimental effects on the material. First, they create charge traps below the conduction band. Second, they can lead to degradation of the material by forming Pb clusters.

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

PubMed Central

Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

2017-01-01

Flax (Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5–8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs. PMID:28133461

Typology of people with first-episode psychosis.

PubMed

Subramaniam, Mythily; Zheng, Huili; Soh, Pauline; Poon, Lye Yin; Vaingankar, Janhavi A; Chong, Siow Ann; Verma, Swapna

2016-08-01

The aim of the current study was to create a typology of patients with first-episode psychosis based on sociodemographic and clinical characteristics, service use and outcomes using cluster analysis. Data from all respondents who were accepted into the Early Psychosis Intervention Programme (EPIP), Singapore from 2007 to 2011 were analysed. A two-step clustering method was carried out to classify the patients into distinct clusters. Two clusters were identified. Cluster 1 comprised largely of younger people with mean age of 25.5 (6.0) years at treatment contact, who were predominantly male (55.3%), single (98.3%) and living with parents (86.3%). Cluster 1 had a higher proportion of people diagnosed with the schizophrenia spectrum disorder (71.4%) and with a positive family history of psychiatric illness. Patients in cluster 2 were generally older with a mean age of 33.6 (4.7) years and the majority were women (74.2%). Cluster 1 had people with higher Positive and Negative Syndrome Scale (PANSS) scores at baseline as compared with cluster 2. After a 1-year follow up, their scores were still poorer than their counterparts in cluster 2, especially for PANSS negative score. The functioning level of people in cluster 1 showed less improvement than the people in cluster 2 after a year of treatment. There is a compelling need to develop new therapies and intensively treat young people presenting with psychosis as this group tends to have poorer outcomes even after 1 year of treatment. © 2014 Wiley Publishing Asia Pty Ltd.

Terminal-Area Aircraft Intent Inference Approach Based on Online Trajectory Clustering.

PubMed

Yang, Yang; Zhang, Jun; Cai, Kai-quan

2015-01-01

Terminal-area aircraft intent inference (T-AII) is a prerequisite to detect and avoid potential aircraft conflict in the terminal airspace. T-AII challenges the state-of-the-art AII approaches due to the uncertainties of air traffic situation, in particular due to the undefined flight routes and frequent maneuvers. In this paper, a novel T-AII approach is introduced to address the limitations by solving the problem with two steps that are intent modeling and intent inference. In the modeling step, an online trajectory clustering procedure is designed for recognizing the real-time available routes in replacing of the missed plan routes. In the inference step, we then present a probabilistic T-AII approach based on the multiple flight attributes to improve the inference performance in maneuvering scenarios. The proposed approach is validated with real radar trajectory and flight attributes data of 34 days collected from Chengdu terminal area in China. Preliminary results show the efficacy of the presented approach.

Identification of microRNA-mRNA modules using microarray data.

PubMed

Jayaswal, Vivek; Lutherborrow, Mark; Ma, David D F; Yang, Yee H

2011-03-06

MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA expression and are involved in numerous cellular processes. Consequently, miRNAs are an important component of gene regulatory networks and an improved understanding of miRNAs will further our knowledge of these networks. There is a many-to-many relationship between miRNAs and mRNAs because a single miRNA targets multiple mRNAs and a single mRNA is targeted by multiple miRNAs. However, most of the current methods for the identification of regulatory miRNAs and their target mRNAs ignore this biological observation and focus on miRNA-mRNA pairs. We propose a two-step method for the identification of many-to-many relationships between miRNAs and mRNAs. In the first step, we obtain miRNA and mRNA clusters using a combination of miRNA-target mRNA prediction algorithms and microarray expression data. In the second step, we determine the associations between miRNA clusters and mRNA clusters based on changes in miRNA and mRNA expression profiles. We consider the miRNA-mRNA clusters with statistically significant associations to be potentially regulatory and, therefore, of biological interest. Our method reduces the interactions between several hundred miRNAs and several thousand mRNAs to a few miRNA-mRNA groups, thereby facilitating a more meaningful biological analysis and a more targeted experimental validation.

Determining the Number of Clusters in a Data Set Without Graphical Interpretation

NASA Technical Reports Server (NTRS)

Aguirre, Nathan S.; Davies, Misty D.

2011-01-01

Cluster analysis is a data mining technique that is meant ot simplify the process of classifying data points. The basic clustering process requires an input of data points and the number of clusters wanted. The clustering algorithm will then pick starting C points for the clusters, which can be either random spatial points or random data points. It then assigns each data point to the nearest C point where "nearest usually means Euclidean distance, but some algorithms use another criterion. The next step is determining whether the clustering arrangement this found is within a certain tolerance. If it falls within this tolerance, the process ends. Otherwise the C points are adjusted based on how many data points are in each cluster, and the steps repeat until the algorithm converges,

The Problem of Hipparcos Distances to Open Clusters. Report 1; Constraints from Multicolor a Main-Sequence Fitting

NASA Technical Reports Server (NTRS)

Pinsonneault, Marc H.; Stauffer, John; Soderblom, David R.; King, Jeremy R.; Hanson, Robert B.

1998-01-01

Parallax data from the Hipparcos mission allow the direct distance to open clusters to be compared with the distance inferred from main-sequence (MS) fitting. There are surprising differences between the two distance measurements. indicating either the need for changes in the cluster compositions or reddening, underlying problems with the technique of MS fitting, or systematic errors in the Hipparcos parallaxes at the 1 mas level. We examine the different possibilities, focusing on MS fitting in both metallicity-sensitive B-V and metallicity-insensitive V-I for five well-studied systems (the Hyades, Pleiades, alpha Per, Praesepe, and Coma Ber). The Hipparcos distances to the Hyades and alpha Per are within 1 sigma of the MS-fitting distance in B-V and V-I, while the Hipparcos distances to Coma Ber and the Pleiades are in disagreement with the MS-fitting distance at more than the 3 sigma level. There are two Hipparcos measurements of the distance to Praesepe; one is in good agreement with the MS-fitting distance and the other disagrees at the 2 sigma level. The distance estimates from the different colors are in conflict with one another for Coma but in agreement for the Pleiades. Changes in the relative cluster metal abundances, age related effects, helium, and reddening are shown to be unlikely to explain the puzzling behavior of the Pleiades. We present evidence for spatially dependent systematic errors at the 1 mas level in the parallaxes of Pleiades stars. The implications of this result are discussed.

Urea controlled hydrothermal synthesis of ammonium aluminum carbonate hydroxide rods

NASA Astrophysics Data System (ADS)

Wang, Fang; Zhu, Jianfeng; Liu, Hui

2018-03-01

In this study, ammonium aluminum carbonate hydroxide (AACH) rods were controllably prepared using the hydrothermal method by manipulating the amount of urea in the reaction system. The experimental results showed that AACH in rod shape was able to be gradually transformed from γ-AlOOH in cluster shape during the molar ratios of urea to Al in the reactants were ranged from 8 to 10, and the yield of AACH has increased accordingly. When the molar ratio of urea to Al reaches 11, pure AACH rods with a diameter of 500 nm and a length of 10 μm approximately was able to be produced. Due to the slow decomposition of urea during the hydrothermal reaction, the nucleation and growth of AACH crystal proceed step by step. Therefore, the crystal can fully grow on each crystal plane and eventually produce a highly crystalline rod-shaped product. The role of urea in controlling the morphology and yield of AACH was also discussed in this paper systematically.

Impulsivity profiles in pathological slot machine gamblers.

PubMed

Aragay, Núria; Barrios, Maite; Ramirez-Gendrau, Isabel; Garcia-Caballero, Anna; Garrido, Gemma; Ramos-Grille, Irene; Galindo, Yésika; Martin-Dombrowski, Jonatan; Vallès, Vicenç

2018-05-01

In gambling disorder (GD), impulsivity has been related with severity, treatment outcome and a greater dropout rate. The aim of the study is to obtain an empirical classification of GD patients based on their impulsivity and compare the resulting groups in terms of sociodemographic, clinical and gambling behavior variables. 126 patients with slot machine GD attending the Pathological Gambling Unit between 2013 and 2016 were included. The UPPS-P Impulsive Behavior Scale was used to assess impulsivity, and the severity of past-year gambling behavior was established with the Screen for Gambling problems questionnaire (NODS). Depression and anxiety symptoms and executive function were also assessed. A two-step cluster analysis was carried out to determine impulsivity profiles. According to the UPPS-P data, two clusters were generated. Cluster 1 showed the highest scores on all the UPPS-P subscales, whereas patients from cluster 2 exhibited only high scores on two UPPS-P subscales: Negative Urgency and Lack of premeditation. Additionally, patients on cluster 1 were younger and showed significantly higher scores on the Beck Depression Inventory and on the State-Trait Anxiety Inventory questionnaires, worse emotional regulation and executive functioning, and reported more psychiatric comorbidity compared to patients in cluster 2. With regard to gambling behavior, cluster 1 patients had significantly higher NODS scores and a higher percentage presented active gambling behavior at treatment start than in cluster 2. We found two impulsivity subtypes of slot machine gamblers. Patients with high impulsivity showed more severe gambling behavior, more clinical psychopathology and worse emotional regulation and executive functioning than those with lower levels of impulsivity. These two different clinical profiles may require different therapeutic approaches. Copyright © 2018 Elsevier Inc. All rights reserved.

[German translation of Suicidal Patient Observation Chart (SPOC) - an instrument for practice].

PubMed

Löhr, Michael; Schulz, Michael; Hemkendreis, Bruno; Björkdahl, Anna; Nienaber, André

2013-12-01

Nursing of suicidal in-patients is a complex and responsible task. A direct and immediate intensive caring and therapeutic supervision, also known as special observation is still recommended in guidelines (DGPPN, 2012) and maybe one of the most used interventions in the caring of suicidal patients in inpatient settings. It involves many kinds to develop the relationship between the observer and the patient. The original SPOC was developed in Sweden with the aim to increase the quality of a systematically documentation during the supervision of suicidal patients. It is an instrument to ensure systematic documentation of observational behavior or noticeable mood during acute suicidal crisis, for example feelings like "worried, anxious" or other possible influencing factors like "sudden mood variation". By this means the SPOC can ensure the process of systematic documentation of special observation and increase its quality, i. e. who documented what at what time. Furthermore SPOC can facilitate a better communication of the observation process to the multidisciplinary team and to the patient as well. The SPOC includes the 28 items and covers 24 separate observation periods. The aim of this paper is to constitute the translation process from the English to the German SPOC version. The translation process followed a five step model. In the first step the English version was translated from two German native speakers. In the second step, the first two translation results where discussed by the Expert group (authors) and a new version was developed. In the third step the first german version was translated back (two English native Speakers) into English. The fourth step was taken, to review the results by the expert groups (authors) and set up the so called "pre version". The last step includes the proof of content validity by 52 nurses. The proof was able to identify a few misunderstandings and helped to enhance the tool in its final version. With the translation, the German-speaking nursing practice in psychiatry has a tool that can be used by psychiatric nurses regarding their complex interventions to be undertaken in this special group of patients.

LoCuSS: weak-lensing mass calibration of galaxy clusters

NASA Astrophysics Data System (ADS)

Okabe, Nobuhiro; Smith, Graham P.

2016-10-01

We present weak-lensing mass measurements of 50 X-ray luminous galaxy clusters at 0.15 ≤ z ≤ 0.3, based on uniform high-quality observations with Suprime-Cam mounted on the 8.2-m Subaru telescope. We pay close attention to possible systematic biases, aiming to control them at the ≲4 per cent level. The dominant source of systematic bias in weak-lensing measurements of the mass of individual galaxy clusters is contamination of background galaxy catalogues by faint cluster and foreground galaxies. We extend our conservative method for selecting background galaxies with (V - I') colours redder than the red sequence of cluster members to use a colour-cut that depends on cluster-centric radius. This allows us to define background galaxy samples that suffer ≤1 per cent contamination, and comprise 13 galaxies per square arcminute. Thanks to the purity of our background galaxy catalogue, the largest systematic that we identify in our analysis is a shape measurement bias of 3 per cent, that we measure using simulations that probe weak shears up to g = 0.3. Our individual cluster mass and concentration measurements are in excellent agreement with predictions of the mass-concentration relation. Equally, our stacked shear profile is in excellent agreement with the Navarro Frenk and White profile. Our new Local Cluster Substructure Survey mass measurements are consistent with the Canadian Cluster Cosmology Project and Cluster Lensing And Supernova Survey with Hubble surveys, and in tension with the Weighing the Giants at ˜1σ-2σ significance. Overall, the consensus at z ≤ 0.3 that is emerging from these complementary surveys represents important progress for cluster mass calibration, and augurs well for cluster cosmology.

An assessment of fatigue in patients with postural orthostatic tachycardia syndrome.

PubMed

Wise, Shelby; Ross, Amanda; Brown, Abigail; Evans, Meredyth; Jason, Leonard

2017-05-01

Individuals with postural orthostatic tachycardia syndrome share many symptoms with those who have chronic fatigue syndrome; one of which is severe fatigue. Previous literature found that those with chronic fatigue syndrome experience many forms of fatigue. The goal of this study was to investigate whether individuals with postural orthostatic tachycardia syndrome also experience multidimensional fatigue and whether these individuals can be clustered into subgroups based on the types of fatigue they endorse. A convenience sample of 138 participants (aged 14-29) with postural orthostatic tachycardia syndrome completed questionnaires that assessed fatigue, brain fog symptom severity, activities that improve brain fog, and brain fog-related disability. An exploratory factor analysis was conducted on the Fatigue Types Questionnaire, and a three-factor solution was produced. Factor scores were then used to cluster the patients into groups using a TwoStep cluster analysis. This resulted in two clusters, a high severity group and a low severity group. The clusters were then compared on a number of items related to symptom expression. Individuals within the more severe cluster had significantly more brain fog at the beginning and end of the survey when compared to cluster two. Those in the more severe cluster also described more activity impairment as well as more frequent, more severe, and more debilitation from postural orthostatic tachycardia syndrome and brain fog. The findings of the factor analysis suggest that patients with postural orthostatic tachycardia syndrome experience fatigue as a multidimensional construct and they also can be subgrouped based on symptom severity.

Density-functional theory study of the geometries, stabilities, and electronic properties of Au n Rb (n = 1-10) clusters: comparison with pure gold clusters

NASA Astrophysics Data System (ADS)

Hu, Yan-Fei; Jiang, Gang; Meng, Da-Qiao

2012-01-01

The density functional method with the relativistic effective core potential has been employed to investigate systematically the geometric structures, relative stabilities, growth-pattern behavior, and electronic properties of small bimetallic Au n Rb (n = 1-10) and pure gold Au n (n ≤ 11) clusters. For the geometric structures of the Au n Rb (n = 1-10) clusters, the dominant growth pattern is for a Rb-substituted Au n +1 cluster or one Au atom capped on a Au n -1Rb cluster, and the turnover point from a two-dimensional to a three-dimensional structure occurs at n = 4. Moreover, the stability of the ground-state structures of these clusters has been examined via an analysis of the average atomic binding energies, fragmentation energies, and the second-order difference of energies as a function of cluster size. The results exhibit a pronounced even-odd alternation phenomenon. The same pronounced even-odd alternations are found for the HOMO-LUMO gap, VIPs, VEAs, and the chemical hardness. In addition, about one electron charge transfers from the Au n host to the Rb atom in each corresponding Au n Rb cluster.

One step versus two step approach for gestational diabetes screening: systematic review and meta-analysis of the randomized trials.

PubMed

Saccone, Gabriele; Caissutti, Claudia; Khalifeh, Adeeb; Meltzer, Sara; Scifres, Christina; Simhan, Hyagriv N; Kelekci, Sefa; Sevket, Osman; Berghella, Vincenzo

2017-12-03

To compare both the prevalence of gestational diabetes mellitus (GDM) as well as maternal and neonatal outcomes by either the one-step or the two-step approaches. Electronic databases were searched from their inception until June 2017. We included all randomized controlled trials (RCTs) comparing the one-step with the two-step approaches for the screening and diagnosis of GDM. The primary outcome was the incidence of GDM. Three RCTs (n = 2333 participants) were included in the meta-analysis. 910 were randomized to the one step approach (75 g, 2 hrs), and 1423 to the two step approach. No significant difference in the incidence of GDM was found comparing the one step versus the two step approaches (8.4 versus 4.3%; relative risk (RR) 1.64, 95%CI 0.77-3.48). Women screened with the one step approach had a significantly lower risk of preterm birth (PTB) (3.7 versus 7.6%; RR 0.49, 95%CI 0.27-0.88), cesarean delivery (16.3 versus 22.0%; RR 0.74, 95%CI 0.56-0.99), macrosomia (2.9 versus 6.9%; RR 0.43, 95%CI 0.22-0.82), neonatal hypoglycemia (1.7 versus 4.5%; RR 0.38, 95%CI 0.16-0.90), and admission to neonatal intensive care unit (NICU) (4.4 versus 9.0%; RR 0.49, 95%CI 0.29-0.84), compared to those randomized to screening with the two step approach. The one and the two step approaches were not associated with a significant difference in the incidence of GDM. However, the one step approach was associated with better maternal and perinatal outcomes.

From the Superatom Model to a Diverse Array of Super-Elements: A Systematic Study of Dopant Influence on the Electronic Structure of Thiolate-Protected Gold Clusters.

PubMed

Schacht, Julia; Gaston, Nicola

2016-10-18

The electronic properties of doped thiolate-protected gold clusters are often referred to as tunable, but their study to date, conducted at different levels of theory, does not allow a systematic evaluation of this claim. Here, using density functional theory, the applicability of the superatomic model to these clusters is critically evaluated, and related to the degree of structural distortion and electronic inhomogeneity in the differently doped clusters, with dopant atoms Pd, Pt, Cu, and Ag. The effect of electron number is systematically evaluated by varying the charge on the overall cluster, and the nominal number of delocalized electrons, employed in the superatomic model, is compared to the numbers obtained from Bader analysis of individual atomic charges. We find that the superatomic model is highly applicable to all of these clusters, and is able to predict and explain the changing electronic structure as a function of charge. However, significant perturbations of the model arise due to doping, due to distortions of the core structure of the Au 13 [RS(AuSR) 2 ] 6 - cluster. In addition, analysis of the electronic structure indicates that the superatomic character is distributed further across the ligand shell in the case of the doped clusters, which may have implications for the self-assembly of these clusters into materials. The prediction of appropriate clusters for such superatomic solids relies critically on such quantitative analysis of the tunability of the electronic structure. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

RELICS: Strong Lens Models for Five Galaxy Clusters from the Reionization Lensing Cluster Survey

NASA Astrophysics Data System (ADS)

Cerny, Catherine; Sharon, Keren; Andrade-Santos, Felipe; Avila, Roberto J.; Bradač, Maruša; Bradley, Larry D.; Carrasco, Daniela; Coe, Dan; Czakon, Nicole G.; Dawson, William A.; Frye, Brenda L.; Hoag, Austin; Huang, Kuang-Han; Johnson, Traci L.; Jones, Christine; Lam, Daniel; Lovisari, Lorenzo; Mainali, Ramesh; Oesch, Pascal A.; Ogaz, Sara; Past, Matthew; Paterno-Mahler, Rachel; Peterson, Avery; Riess, Adam G.; Rodney, Steven A.; Ryan, Russell E.; Salmon, Brett; Sendra-Server, Irene; Stark, Daniel P.; Strolger, Louis-Gregory; Trenti, Michele; Umetsu, Keiichi; Vulcani, Benedetta; Zitrin, Adi

2018-06-01

Strong gravitational lensing by galaxy clusters magnifies background galaxies, enhancing our ability to discover statistically significant samples of galaxies at {\\boldsymbol{z}}> 6, in order to constrain the high-redshift galaxy luminosity functions. Here, we present the first five lens models out of the Reionization Lensing Cluster Survey (RELICS) Hubble Treasury Program, based on new HST WFC3/IR and ACS imaging of the clusters RXC J0142.9+4438, Abell 2537, Abell 2163, RXC J2211.7–0349, and ACT-CLJ0102–49151. The derived lensing magnification is essential for estimating the intrinsic properties of high-redshift galaxy candidates, and properly accounting for the survey volume. We report on new spectroscopic redshifts of multiply imaged lensed galaxies behind these clusters, which are used as constraints, and detail our strategy to reduce systematic uncertainties due to lack of spectroscopic information. In addition, we quantify the uncertainty on the lensing magnification due to statistical and systematic errors related to the lens modeling process, and find that in all but one cluster, the magnification is constrained to better than 20% in at least 80% of the field of view, including statistical and systematic uncertainties. The five clusters presented in this paper span the range of masses and redshifts of the clusters in the RELICS program. We find that they exhibit similar strong lensing efficiencies to the clusters targeted by the Hubble Frontier Fields within the WFC3/IR field of view. Outputs of the lens models are made available to the community through the Mikulski Archive for Space Telescopes.

An efficient matrix-matrix multiplication based antisymmetric tensor contraction engine for general order coupled cluster.

PubMed

Hanrath, Michael; Engels-Putzka, Anna

2010-08-14

In this paper, we present an efficient implementation of general tensor contractions, which is part of a new coupled-cluster program. The tensor contractions, used to evaluate the residuals in each coupled-cluster iteration are particularly important for the performance of the program. We developed a generic procedure, which carries out contractions of two tensors irrespective of their explicit structure. It can handle coupled-cluster-type expressions of arbitrary excitation level. To make the contraction efficient without loosing flexibility, we use a three-step procedure. First, the data contained in the tensors are rearranged into matrices, then a matrix-matrix multiplication is performed, and finally the result is backtransformed to a tensor. The current implementation is significantly more efficient than previous ones capable of treating arbitrary high excitations.

Unsupervised spike sorting based on discriminative subspace learning.

PubMed

Keshtkaran, Mohammad Reza; Yang, Zhi

2014-01-01

Spike sorting is a fundamental preprocessing step for many neuroscience studies which rely on the analysis of spike trains. In this paper, we present two unsupervised spike sorting algorithms based on discriminative subspace learning. The first algorithm simultaneously learns the discriminative feature subspace and performs clustering. It uses histogram of features in the most discriminative projection to detect the number of neurons. The second algorithm performs hierarchical divisive clustering that learns a discriminative 1-dimensional subspace for clustering in each level of the hierarchy until achieving almost unimodal distribution in the subspace. The algorithms are tested on synthetic and in-vivo data, and are compared against two widely used spike sorting methods. The comparative results demonstrate that our spike sorting methods can achieve substantially higher accuracy in lower dimensional feature space, and they are highly robust to noise. Moreover, they provide significantly better cluster separability in the learned subspace than in the subspace obtained by principal component analysis or wavelet transform.

X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE.

PubMed

Barr, Ian; Stich, Troy A; Gizzi, Anthony S; Grove, Tyler L; Bonanno, Jeffrey B; Latham, John A; Chung, Tyler; Wilmot, Carrie M; Britt, R David; Almo, Steven C; Klinman, Judith P

2018-02-27

The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mössbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mössbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.

Method for exploratory cluster analysis and visualisation of single-trial ERP ensembles.

PubMed

Williams, N J; Nasuto, S J; Saddy, J D

2015-07-30

The validity of ensemble averaging on event-related potential (ERP) data has been questioned, due to its assumption that the ERP is identical across trials. Thus, there is a need for preliminary testing for cluster structure in the data. We propose a complete pipeline for the cluster analysis of ERP data. To increase the signal-to-noise (SNR) ratio of the raw single-trials, we used a denoising method based on Empirical Mode Decomposition (EMD). Next, we used a bootstrap-based method to determine the number of clusters, through a measure called the Stability Index (SI). We then used a clustering algorithm based on a Genetic Algorithm (GA) to define initial cluster centroids for subsequent k-means clustering. Finally, we visualised the clustering results through a scheme based on Principal Component Analysis (PCA). After validating the pipeline on simulated data, we tested it on data from two experiments - a P300 speller paradigm on a single subject and a language processing study on 25 subjects. Results revealed evidence for the existence of 6 clusters in one experimental condition from the language processing study. Further, a two-way chi-square test revealed an influence of subject on cluster membership. Our analysis operates on denoised single-trials, the number of clusters are determined in a principled manner and the results are presented through an intuitive visualisation. Given the cluster structure in some experimental conditions, we suggest application of cluster analysis as a preliminary step before ensemble averaging. Copyright © 2015 Elsevier B.V. All rights reserved.

The two-step assemblies of basic-amino-Acid-rich Peptide with a highly charged polyoxometalate.

PubMed

Zhang, Teng; Li, Hong-Wei; Wu, Yuqing; Wang, Yizhan; Wu, Lixin

2015-06-15

Two-step assembly of a peptide from HPV16 L1 with a highly charged europium-substituted polyoxometalate (POM) cluster, accompanying a great luminescence enhancement of the inorganic polyanions, is reported. The mechanism is discussed in detail by analyzing the thermodynamic parameters from isothermal titration calorimetry (ITC), time-resolved fluorescent and NMR spectra. By comparing the actions of the peptide analogues, a binding process and model are proposed accordingly. The driving forces in each binding step are clarified, and the initial POM aggregation, basic-sequence and hydrophobic C termini of peptide are revealed to contribute essentially to the two-step assembly. The present study demonstrates both a meaningful preparation for bioinorganic materials and a strategy using POMs to modulate the assembly of peptides and even proteins, which could be extended to other proteins and/or viruses by using peptides and POMs with similar properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cosmological Constraints from Galaxy Clustering and the Mass-to-number Ratio of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Tinker, Jeremy L.; Sheldon, Erin S.; Wechsler, Risa H.; Becker, Matthew R.; Rozo, Eduardo; Zu, Ying; Weinberg, David H.; Zehavi, Idit; Blanton, Michael R.; Busha, Michael T.; Koester, Benjamin P.

2012-01-01

We place constraints on the average density (Ω m ) and clustering amplitude (σ8) of matter using a combination of two measurements from the Sloan Digital Sky Survey: the galaxy two-point correlation function, wp (rp ), and the mass-to-galaxy-number ratio within galaxy clusters, M/N, analogous to cluster M/L ratios. Our wp (rp ) measurements are obtained from DR7 while the sample of clusters is the maxBCG sample, with cluster masses derived from weak gravitational lensing. We construct nonlinear galaxy bias models using the Halo Occupation Distribution (HOD) to fit both wp (rp ) and M/N for different cosmological parameters. HOD models that match the same two-point clustering predict different numbers of galaxies in massive halos when Ω m or σ8 is varied, thereby breaking the degeneracy between cosmology and bias. We demonstrate that this technique yields constraints that are consistent and competitive with current results from cluster abundance studies, without the use of abundance information. Using wp (rp ) and M/N alone, we find Ω0.5 m σ8 = 0.465 ± 0.026, with individual constraints of Ω m = 0.29 ± 0.03 and σ8 = 0.85 ± 0.06. Combined with current cosmic microwave background data, these constraints are Ω m = 0.290 ± 0.016 and σ8 = 0.826 ± 0.020. All errors are 1σ. The systematic uncertainties that the M/N technique are most sensitive to are the amplitude of the bias function of dark matter halos and the possibility of redshift evolution between the SDSS Main sample and the maxBCG cluster sample. Our derived constraints are insensitive to the current level of uncertainties in the halo mass function and in the mass-richness relation of clusters and its scatter, making the M/N technique complementary to cluster abundances as a method for constraining cosmology with future galaxy surveys.

Cluster analysis of Southeastern U.S. climate stations

NASA Astrophysics Data System (ADS)

Stooksbury, D. E.; Michaels, P. J.

1991-09-01

A two-step cluster analysis of 449 Southeastern climate stations is used to objectively determine general climate clusters (groups of climate stations) for eight southeastern states. The purpose is objectively to define regions of climatic homogeneity that should perform more robustly in subsequent climatic impact models. This type of analysis has been successfully used in many related climate research problems including the determination of corn/climate districts in Iowa (Ortiz-Valdez, 1985) and the classification of synoptic climate types (Davis, 1988). These general climate clusters may be more appropriate for climate research than the standard climate divisions (CD) groupings of climate stations, which are modifications of the agro-economic United States Department of Agriculture crop reporting districts. Unlike the CD's, these objectively determined climate clusters are not restricted by state borders and thus have reduced multicollinearity which makes them more appropriate for the study of the impact of climate and climatic change.

Systematization of actinides using cluster analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kopyrin, A.A.; Terent`eva, T.N.; Khramov, N.N.

1994-11-01

A representation of the actinides in multidimensional property space is proposed for systematization of these elements using cluster analysis. Literature data for their atomic properties are used. Owing to the wide variation of published ionization potentials, medians are used to estimate them. Vertical dendograms are used for classification on the basis of distances between the actinides in atomic-property space. The properties of actinium and lawrencium are furthest removed from the main group. Thorium and mendelevium exhibit individualized properties. A cluster based on the einsteinium-fermium pair is joined by californium.

Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria

PubMed Central

Cai, Fei; Axen, Seth D.; Kerfeld, Cheryl A.

2013-01-01

Members of the phylum Cyanobacteria inhabit ecologically diverse environments. However, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR associated genes), an extremely adaptable defense system, has not been surveyed in this phylum. We analyzed 126 cyanobacterial genomes and, surprisingly, found CRISPR-Cas in the majority except the marine subclade (Synechococcus and Prochlorococcus), in which cyanophages are a known force shaping their evolution. Multiple observations of CRISPR loci in the absence of cas1/cas2 genes may represent an early stage of losing a CRISPR-Cas locus. Our findings reveal the widespread distribution of their role in the phylum Cyanobacteria and provide a first step to systematically understanding CRISPR-Cas systems in cyanobacteria. PMID:23628889

An algorithm for determining the rotation count of pulsars

NASA Astrophysics Data System (ADS)

Freire, Paulo C. C.; Ridolfi, Alessandro

2018-06-01

We present here a simple, systematic method for determining the correct global rotation count of a radio pulsar; an essential step for the derivation of an accurate phase-coherent ephemeris. We then build on this method by developing a new algorithm for determining the global rotational count for pulsars with sparse timing data sets. This makes it possible to obtain phase-coherent ephemerides for pulsars for which this has been impossible until now. As an example, we do this for PSR J0024-7205aa, an extremely faint Millisecond pulsar (MSP) recently discovered in the globular cluster 47 Tucanae. This algorithm has the potential to significantly reduce the number of observations and the amount of telescope time needed to follow up on new pulsar discoveries.

3D reconstruction from non-uniform point clouds via local hierarchical clustering

NASA Astrophysics Data System (ADS)

Yang, Jiaqi; Li, Ruibo; Xiao, Yang; Cao, Zhiguo

2017-07-01

Raw scanned 3D point clouds are usually irregularly distributed due to the essential shortcomings of laser sensors, which therefore poses a great challenge for high-quality 3D surface reconstruction. This paper tackles this problem by proposing a local hierarchical clustering (LHC) method to improve the consistency of point distribution. Specifically, LHC consists of two steps: 1) adaptive octree-based decomposition of 3D space, and 2) hierarchical clustering. The former aims at reducing the computational complexity and the latter transforms the non-uniform point set into uniform one. Experimental results on real-world scanned point clouds validate the effectiveness of our method from both qualitative and quantitative aspects.

Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

DOEpatents

Alivisatos, A. Paul; Colvin, Vicki L.

1998-01-01

Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed.

An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions.

PubMed

van Haaften, Rachel I M; Luceri, Cristina; van Erk, Arie; Evelo, Chris T A

2009-06-01

Omics technology used for large-scale measurements of gene expression is rapidly evolving. This work pointed out the need of an extensive bioinformatics analyses for array quality assessment before and after gene expression clustering and pathway analysis. A study focused on the effect of red wine polyphenols on rat colon mucosa was used to test the impact of quality control and normalisation steps on the biological conclusions. The integration of data visualization, pathway analysis and clustering revealed an artifact problem that was solved with an adapted normalisation. We propose a possible point to point standard analysis procedure, based on a combination of clustering and data visualization for the analysis of microarray data.

Mapping of terrain by computer clustering techniques using multispectral scanner data and using color aerial film

NASA Technical Reports Server (NTRS)

Smedes, H. W.; Linnerud, H. J.; Woolaver, L. B.; Su, M. Y.; Jayroe, R. R.

1972-01-01

Two clustering techniques were used for terrain mapping by computer of test sites in Yellowstone National Park. One test was made with multispectral scanner data using a composite technique which consists of (1) a strictly sequential statistical clustering which is a sequential variance analysis, and (2) a generalized K-means clustering. In this composite technique, the output of (1) is a first approximation of the cluster centers. This is the input to (2) which consists of steps to improve the determination of cluster centers by iterative procedures. Another test was made using the three emulsion layers of color-infrared aerial film as a three-band spectrometer. Relative film densities were analyzed using a simple clustering technique in three-color space. Important advantages of the clustering technique over conventional supervised computer programs are (1) human intervention, preparation time, and manipulation of data are reduced, (2) the computer map, gives unbiased indication of where best to select the reference ground control data, (3) use of easy to obtain inexpensive film, and (4) the geometric distortions can be easily rectified by simple standard photogrammetric techniques.

Comparison of Cryopreservation Protocols (Single and Two-steps) and Thawing (Fast and Slow) for Canine Sperm.

PubMed

Brito, Maíra M; Lúcio, Cristina F; Angrimani, Daniel S R; Losano, João Diego A; Dalmazzo, Andressa; Nichi, Marcílio; Vannucchi, Camila I

2017-01-02

In addition to the existence of several cryopreservation protocols, no systematic research has been carried out in order to confirm the suitable protocol for canine sperm. This study aims to assess the effect of adding 5% glycerol during cryopreservation at 37°C (one-step) and 5°C (two-steps), in addition of testing two thawing protocols (37°C for 30 seconds, and 70°C for 8 seconds). We used 12 sperm samples divided into four experimental groups: Single-Step - Slow Thawing Group; Two-Step - Slow Thawing Group; Single-Step - Fast Thawing Group; and Two-Step - Fast Thawing Group. Frozen-thawed samples were submitted to automated analysis of sperm motility, evaluation of plasmatic membrane integrity, acrosomal integrity, mitochondrial activity, sperm morphology, sperm susceptibility to oxidative stress, and sperm binding assay to perivitellinic membrane of chicken egg yolk. Considering the comparison between freezing protocols, no statistical differences were verified for any of the response variables. When comparison between thawing protocols was performed, slow thawing protocol presented higher sperm count bound to perivitelline membrane of chicken egg yolk, compared to fast thawing protocol. Regardless of the freezing process, the slow thawing protocol can be recommended for the large scale cryopreservation of canine semen, since it shows a consistent better functional result.

Cluster Observations of Non-Time Continuous Magnetosonic Waves

NASA Technical Reports Server (NTRS)

Walker, Simon N.; Demekhov, Andrei G.; Boardsen, Scott A.; Ganushkina, Natalia Y.; Sibeck, David G.; Balikhin, Michael A.

2016-01-01

Equatorial magnetosonic waves are normally observed as temporally continuous sets of emissions lasting from minutes to hours. Recent observations, however, have shown that this is not always the case. Using Cluster data, this study identifies two distinct forms of these non temporally continuous use missions. The first, referred to as rising tone emissions, are characterized by the systematic onset of wave activity at increasing proton gyroharmonic frequencies. Sets of harmonic emissions (emission elements)are observed to occur periodically in the region +/- 10 off the geomagnetic equator. The sweep rate of these emissions maximizes at the geomagnetic equator. In addition, the ellipticity and propagation direction also change systematically as Cluster crosses the geomagnetic equator. It is shown that the observed frequency sweep rate is unlikely to result from the sideband instability related to nonlinear trapping of suprathermal protons in the wave field. The second form of emissions is characterized by the simultaneous onset of activity across a range of harmonic frequencies. These waves are observed at irregular intervals. Their occurrence correlates with changes in the spacecraft potential, a measurement that is used as a proxy for electron density. Thus, these waves appear to be trapped within regions of localized enhancement of the electron density.

Fourier Decomposition of RR Lyrae light curves and the SX Phe population in the central region of NGC 3201

NASA Astrophysics Data System (ADS)

Arellano Ferro, A.; Ahumada, J. A.; Calderón, J. H.; Kains, N.

2014-10-01

CCD time-series observations of the central region of the globular cluster NGC 3201 were obtained with the aim of performing the Fourier decomposition of the light curves of the RR Lyrae stars present in that field. This procedure gave the mean values, for the metallicity, of [Fe/H] [ZW] = - 1.483±0.006 (statistical) ±0.090 (systematic), and for the distance, 5.000±0.001 kpc (statistical) ±0.220 (systematic). The values found from two RRc stars are consistent with those derived previously. The differential reddening of the cluster was investigated and individual reddenings for the RR Lyrae stars were estimated from their V - I curves. We found an average value of E(B - V) = 0.23±0.02. An investigation of the light curves of stars in the blue straggler region led to the discovery of three new SX Phe stars. The period-luminosity relation of the SX Phe stars was used for an independent determination of the distance to the cluster and of the individual reddenings. We found a distance of 5.0 kpc.

Identification of the coupling step in Na(+)-translocating NADH:quinone oxidoreductase from real-time kinetics of electron transfer.

PubMed

Belevich, Nikolai P; Bertsova, Yulia V; Verkhovskaya, Marina L; Baykov, Alexander A; Bogachev, Alexander V

2016-02-01

Bacterial Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) uses a unique set of prosthetic redox groups-two covalently bound FMN residues, a [2Fe-2S] cluster, FAD, riboflavin and a Cys4[Fe] center-to catalyze electron transfer from NADH to ubiquinone in a reaction coupled with Na(+) translocation across the membrane. Here we used an ultra-fast microfluidic stopped-flow instrument to determine rate constants and the difference spectra for the six consecutive reaction steps of Vibrio harveyi Na(+)-NQR reduction by NADH. The instrument, with a dead time of 0.25 ms and optical path length of 1 cm allowed collection of visible spectra in 50-μs intervals. By comparing the spectra of reaction steps with the spectra of known redox transitions of individual enzyme cofactors, we were able to identify the chemical nature of most intermediates and the sequence of electron transfer events. A previously unknown spectral transition was detected and assigned to the Cys4[Fe] center reduction. Electron transfer from the [2Fe-2S] cluster to the Cys4[Fe] center and all subsequent steps were markedly accelerated when Na(+) concentration was increased from 20 μM to 25 mM, suggesting coupling of the former step with tight Na(+) binding to or occlusion by the enzyme. An alternating access mechanism was proposed to explain electron transfer between subunits NqrF and NqrC. According to the proposed mechanism, the Cys4[Fe] center is alternatively exposed to either side of the membrane, allowing the [2Fe-2S] cluster of NqrF and the FMN residue of NqrC to alternatively approach the Cys4[Fe] center from different sides of the membrane. Copyright © 2015 Elsevier B.V. All rights reserved.

Cluster-randomized Studies in Educational Research: Principles and Methodological Aspects

PubMed Central

Dreyhaupt, Jens; Mayer, Benjamin; Keis, Oliver; Öchsner, Wolfgang; Muche, Rainer

2017-01-01

An increasing number of studies are being performed in educational research to evaluate new teaching methods and approaches. These studies could be performed more efficiently and deliver more convincing results if they more strictly applied and complied with recognized standards of scientific studies. Such an approach could substantially increase the quality in particular of prospective, two-arm (intervention) studies that aim to compare two different teaching methods. A key standard in such studies is randomization, which can minimize systematic bias in study findings; such bias may result if the two study arms are not structurally equivalent. If possible, educational research studies should also achieve this standard, although this is not yet generally the case. Some difficulties and concerns exist, particularly regarding organizational and methodological aspects. An important point to consider in educational research studies is that usually individuals cannot be randomized, because of the teaching situation, and instead whole groups have to be randomized (so-called “cluster randomization”). Compared with studies with individual randomization, studies with cluster randomization normally require (significantly) larger sample sizes and more complex methods for calculating sample size. Furthermore, cluster-randomized studies require more complex methods for statistical analysis. The consequence of the above is that a competent expert with respective special knowledge needs to be involved in all phases of cluster-randomized studies. Studies to evaluate new teaching methods need to make greater use of randomization in order to achieve scientifically convincing results. Therefore, in this article we describe the general principles of cluster randomization and how to implement these principles, and we also outline practical aspects of using cluster randomization in prospective, two-arm comparative educational research studies. PMID:28584874

Cluster-randomized Studies in Educational Research: Principles and Methodological Aspects.

PubMed

Dreyhaupt, Jens; Mayer, Benjamin; Keis, Oliver; Öchsner, Wolfgang; Muche, Rainer

2017-01-01

An increasing number of studies are being performed in educational research to evaluate new teaching methods and approaches. These studies could be performed more efficiently and deliver more convincing results if they more strictly applied and complied with recognized standards of scientific studies. Such an approach could substantially increase the quality in particular of prospective, two-arm (intervention) studies that aim to compare two different teaching methods. A key standard in such studies is randomization, which can minimize systematic bias in study findings; such bias may result if the two study arms are not structurally equivalent. If possible, educational research studies should also achieve this standard, although this is not yet generally the case. Some difficulties and concerns exist, particularly regarding organizational and methodological aspects. An important point to consider in educational research studies is that usually individuals cannot be randomized, because of the teaching situation, and instead whole groups have to be randomized (so-called "cluster randomization"). Compared with studies with individual randomization, studies with cluster randomization normally require (significantly) larger sample sizes and more complex methods for calculating sample size. Furthermore, cluster-randomized studies require more complex methods for statistical analysis. The consequence of the above is that a competent expert with respective special knowledge needs to be involved in all phases of cluster-randomized studies. Studies to evaluate new teaching methods need to make greater use of randomization in order to achieve scientifically convincing results. Therefore, in this article we describe the general principles of cluster randomization and how to implement these principles, and we also outline practical aspects of using cluster randomization in prospective, two-arm comparative educational research studies.

Variable number of tandem repeats and pulsed-field gel electrophoresis cluster analysis of enterohemorrhagic Escherichia coli serovar O157 strains.

PubMed

Yokoyama, Eiji; Uchimura, Masako

2007-11-01

Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.

Cluster Masses Derived from X-ray and Sunyaev-Zeldovich Effect Measurements

NASA Technical Reports Server (NTRS)

Laroque, S.; Joy, Marshall; Bonamente, M.; Carlstrom, J.; Dawson, K.

2003-01-01

We infer the gas mass and total gravitational mass of 11 clusters using two different methods; analysis of X-ray data from the Chandra X-ray Observatory and analysis of centimeter-wave Sunyaev-Zel'dovich Effect (SZE) data from the BIMA and OVRO interferometers. This flux-limited sample of clusters from the BCS cluster catalogue was chosen so as to be well above the surface brightness limit of the ROSAT All Sky Survey; this is therefore an orientation unbiased sample. The gas mass fraction, f_g, is calculated for each cluster using both X-ray and SZE data, and the results are compared at a fiducial radius of r_500. Comparison of the X-ray and SZE results for this orientation unbiased sample allows us to constrain cluster systematics, such as clumping of the intracluster medium. We derive an upper limit on Omega_M assuming that the mass composition of clusters within r_500 reflects the universal mass composition Omega_M h_100 is greater than Omega _B / f-g. We also demonstrate how the mean f_g derived from the sample can be used to estimate the masses of clusters discovered by upcoming deep SZE surveys.

Methods in Computational Cosmology

NASA Astrophysics Data System (ADS)

Vakili, Mohammadjavad

State of the inhomogeneous universe and its geometry throughout cosmic history can be studied by measuring the clustering of galaxies and the gravitational lensing of distant faint galaxies. Lensing and clustering measurements from large datasets provided by modern galaxy surveys will forever shape our understanding of the how the universe expands and how the structures grow. Interpretation of these rich datasets requires careful characterization of uncertainties at different stages of data analysis: estimation of the signal, estimation of the signal uncertainties, model predictions, and connecting the model to the signal through probabilistic means. In this thesis, we attempt to address some aspects of these challenges. The first step in cosmological weak lensing analyses is accurate estimation of the distortion of the light profiles of galaxies by large scale structure. These small distortions, known as the cosmic shear signal, are dominated by extra distortions due to telescope optics and atmosphere (in the case of ground-based imaging). This effect is captured by a kernel known as the Point Spread Function (PSF) that needs to be fully estimated and corrected for. We address two challenges a head of accurate PSF modeling for weak lensing studies. The first challenge is finding the centers of point sources that are used for empirical estimation of the PSF. We show that the approximate methods for centroiding stars in wide surveys are able to optimally saturate the information content that is retrievable from astronomical images in the presence of noise. The fist step in weak lensing studies is estimating the shear signal by accurately measuring the shapes of galaxies. Galaxy shape measurement involves modeling the light profile of galaxies convolved with the light profile of the PSF. Detectors of many space-based telescopes such as the Hubble Space Telescope (HST) sample the PSF with low resolution. Reliable weak lensing analysis of galaxies observed by the HST camera requires knowledge of the PSF at a resolution higher than the pixel resolution of HST. This PSF is called the super-resolution PSF. In particular, we present a forward model of the point sources imaged through filters of the HST WFC3 IR channel. We show that this forward model can accurately estimate the super-resolution PSF. We also introduce a noise model that permits us to robustly analyze the HST WFC3 IR observations of the crowded fields. Then we try to address one of the theoretical uncertainties in modeling of galaxy clustering on small scales. Study of small scale clustering requires assuming a halo model. Clustering of halos has been shown to depend on halo properties beyond mass such as halo concentration, a phenomenon referred to as assembly bias. Standard large-scale structure studies with halo occupation distribution (HOD) assume that halo mass alone is sufficient to characterize the connection between galaxies and halos. However, assembly bias could cause the modeling of galaxy clustering to face systematic effects if the expected number of galaxies in halos is correlated with other halo properties. Using high resolution N-body simulations and the clustering measurements of Sloan Digital Sky Survey (SDSS) DR7 main galaxy sample, we show that modeling of galaxy clustering can slightly improve if we allow the HOD model to depend on halo properties beyond mass. One of the key ingredients in precise parameter inference using galaxy clustering is accurate estimation of the error covariance matrix of clustering measurements. This requires generation of many independent galaxy mock catalogs that accurately describe the statistical distribution of galaxies in a wide range of physical scales. We present a fast and accurate method based on low-resolution N-body simulations and an empirical bias model for generating mock catalogs. We use fast particle mesh gravity solvers for generation of dark matter density field and we use Markov Chain Monti Carlo (MCMC) to estimate the bias model that connects dark matter to galaxies. We show that this approach enables the fast generation of mock catalogs that recover clustering at a percent-level accuracy down to quasi-nonlinear scales. Cosmological datasets are interpreted by specifying likelihood functions that are often assumed to be multivariate Gaussian. Likelihood free approaches such as Approximate Bayesian Computation (ABC) can bypass this assumption by introducing a generative forward model of the data and a distance metric for quantifying the closeness of the data and the model. We present the first application of ABC in large scale structure for constraining the connections between galaxies and dark matter halos. We present an implementation of ABC equipped with Population Monte Carlo and a generative forward model of the data that incorporates sample variance and systematic uncertainties. (Abstract shortened by ProQuest.).

Novel Anthropometry Based on 3D-Bodyscans Applied to a Large Population Based Cohort

PubMed Central

Löffler-Wirth, Henry; Willscher, Edith; Ahnert, Peter; Wirkner, Kerstin; Engel, Christoph; Loeffler, Markus; Binder, Hans

2016-01-01

Three-dimensional (3D) whole body scanners are increasingly used as precise measuring tools for the rapid quantification of anthropometric measures in epidemiological studies. We analyzed 3D whole body scanning data of nearly 10,000 participants of a cohort collected from the adult population of Leipzig, one of the largest cities in Eastern Germany. We present a novel approach for the systematic analysis of this data which aims at identifying distinguishable clusters of body shapes called body types. In the first step, our method aggregates body measures provided by the scanner into meta-measures, each representing one relevant dimension of the body shape. In a next step, we stratified the cohort into body types and assessed their stability and dependence on the size of the underlying cohort. Using self-organizing maps (SOM) we identified thirteen robust meta-measures and fifteen body types comprising between 1 and 18 percent of the total cohort size. Thirteen of them are virtually gender specific (six for women and seven for men) and thus reflect most abundant body shapes of women and men. Two body types include both women and men, and describe androgynous body shapes that lack typical gender specific features. The body types disentangle a large variability of body shapes enabling distinctions which go beyond the traditional indices such as body mass index, the waist-to-height ratio, the waist-to-hip ratio and the mortality-hazard ABSI-index. In a next step, we will link the identified body types with disease predispositions to study how size and shape of the human body impact health and disease. PMID:27467550

Accounting for Multiple Births in Neonatal and Perinatal Trials: Systematic Review and Case Study

PubMed Central

Hibbs, Anna Maria; Black, Dennis; Palermo, Lisa; Cnaan, Avital; Luan, Xianqun; Truog, William E; Walsh, Michele C; Ballard, Roberta A

2010-01-01

Objectives To determine the prevalence in the neonatal literature of statistical approaches accounting for the unique clustering patterns of multiple births. To explore the sensitivity of an actual trial to several analytic approaches to multiples. Methods A systematic review of recent perinatal trials assessed the prevalence of studies accounting for clustering of multiples. The NO CLD trial served as a case study of the sensitivity of the outcome to several statistical strategies. We calculated odds ratios using non-clustered (logistic regression) and clustered (generalized estimating equations, multiple outputation) analyses. Results In the systematic review, most studies did not describe the randomization of twins and did not account for clustering. Of those studies that did, exclusion of multiples and generalized estimating equations were the most common strategies. The NO CLD study included 84 infants with a sibling enrolled in the study. Multiples were more likely than singletons to be white and were born to older mothers (p<0.01). Analyses that accounted for clustering were statistically significant; analyses assuming independence were not. Conclusions The statistical approach to multiples can influence the odds ratio and width of confidence intervals, thereby affecting the interpretation of a study outcome. A minority of perinatal studies address this issue. PMID:19969305

Characteristics of MAO coating obtained on ZK60 Mg alloy under two and three steps voltage-increasing modes in dual electrolyte

NASA Astrophysics Data System (ADS)

Yang, Jun; Wang, Ze-Xin; Lu, Sheng; Lv, Wei-gang; Jiang, Xi-zhi; Sun, Lei

2017-03-01

The micro-arc oxidation process was conducted on ZK60 Mg alloy under two and three steps voltage-increasing modes by DC pulse electrical source. The effect of each mode on current-time responses during MAO process and the coating characteristic were analysed and discussed systematically. The microstructure, thickness and corrosion resistance of MAO coatings were evaluated by scanning electron microscopy (SEM), energy disperse spectroscopy (EDS), microscope with super-depth of field and electrochemical impedance spectroscopy (EIS). The results indicate that two and three steps voltage-increasing modes can improve weak spark discharges with insufficient breakdown strength in later period during the MAO process. Due to higher value of voltage and voltage increment, the coating with maximum thickness of about 20.20μm formed under two steps voltage-increasing mode shows the best corrosion resistance. In addition, the coating fabricated under three steps voltage-increasing mode shows a smoother coating with better corrosion resistance due to the lower amplitude of voltage-increasing.

A comparative study of genome organization and inferences for the systematics of two large bushcricket genera of the tribe Barbitistini (Orthoptera: Tettigoniidae: Phaneropterinae)

PubMed Central

2014-01-01

Background Poecilimon and Isophya are the largest genera of the tribe Barbitistini and among the most systematically complicated and evolutionarily intriguing groups of Palearctic tettigoniids. We examined the genomic organization of 79 taxa with a stable chromosome number using classical (C–banding, silver and fluorochrome staining) and molecular (fluorescence in situ hybridization with 18S rDNA and (TTAGG) n telomeric probes) cytogenetic techniques. These tools were employed to establish genetic organization and differences or similarities between genera or species within the same genus and determine if cytogenetic markers can be used for identifying some taxonomic groups of species. Results Differences between the karyotypes of the studied genera include some general changes in the morphology of the X chromosome in Isophya (in contrast to Poecilimon). The number of major rDNA clusters per haploid genome divided Poecilimon into two main almost equal groups (with either one or two clusters), while two rDNA clusters predominated in Isophya. In both genera, rDNA loci were preferentially located in the paracentromeric region of the autosomes and rarely in the sex chromosomes. Our results demonstrate a coincidence between the location of rDNA loci and active NORs and GC-rich heterochromatin regions. The C/DAPI/CMA3 bands observed in most Poecilimon chromosomes suggest the presence of more families of repetitive DNA sequences as compared to the heterochromatin patterns in Isophya. Conclusions The results show both differences and similarities in genome organization among species of the same genus and between genera. Previous views on the systematics and phylogenetic grouping of certain lineages are discussed in light of the present cytogenetic results. In some cases, variation of chromosome markers was observed to correspond with variation in other evolutionary traits, which is related to the processes of ongoing speciation and hybridization in zones of secondary contact. It was concluded that the physical mapping of rDNA sequences and heterochromatin may be used as an additional marker for understanding interspecific relationships in these groups and their routes of speciation. PMID:24625118

Sample size calculations for stepped wedge and cluster randomised trials: a unified approach

PubMed Central

Hemming, Karla; Taljaard, Monica

2016-01-01

Objectives To clarify and illustrate sample size calculations for the cross-sectional stepped wedge cluster randomized trial (SW-CRT) and to present a simple approach for comparing the efficiencies of competing designs within a unified framework. Study Design and Setting We summarize design effects for the SW-CRT, the parallel cluster randomized trial (CRT), and the parallel cluster randomized trial with before and after observations (CRT-BA), assuming cross-sectional samples are selected over time. We present new formulas that enable trialists to determine the required cluster size for a given number of clusters. We illustrate by example how to implement the presented design effects and give practical guidance on the design of stepped wedge studies. Results For a fixed total cluster size, the choice of study design that provides the greatest power depends on the intracluster correlation coefficient (ICC) and the cluster size. When the ICC is small, the CRT tends to be more efficient; when the ICC is large, the SW-CRT tends to be more efficient and can serve as an alternative design when the CRT is an infeasible design. Conclusion Our unified approach allows trialists to easily compare the efficiencies of three competing designs to inform the decision about the most efficient design in a given scenario. PMID:26344808

Blood Vessel Extraction in Color Retinal Fundus Images with Enhancement Filtering and Unsupervised Classification

PubMed Central

2017-01-01

Retinal blood vessels have a significant role in the diagnosis and treatment of various retinal diseases such as diabetic retinopathy, glaucoma, arteriosclerosis, and hypertension. For this reason, retinal vasculature extraction is important in order to help specialists for the diagnosis and treatment of systematic diseases. In this paper, a novel approach is developed to extract retinal blood vessel network. Our method comprises four stages: (1) preprocessing stage in order to prepare dataset for segmentation; (2) an enhancement procedure including Gabor, Frangi, and Gauss filters obtained separately before a top-hat transform; (3) a hard and soft clustering stage which includes K-means and Fuzzy C-means (FCM) in order to get binary vessel map; and (4) a postprocessing step which removes falsely segmented isolated regions. The method is tested on color retinal images obtained from STARE and DRIVE databases which are available online. As a result, Gabor filter followed by K-means clustering method achieves 95.94% and 95.71% of accuracy for STARE and DRIVE databases, respectively, which are acceptable for diagnosis systems. PMID:29065611

Scalable and cost-effective NGS genotyping in the cloud.

PubMed

Souilmi, Yassine; Lancaster, Alex K; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J; Wall, Dennis P

2015-10-15

While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

Density functional study on structure and stability of bimetallic AuNZn (N<=6) clusters and their cations

NASA Astrophysics Data System (ADS)

Tanaka, Hiromasa; Neukermans, Sven; Janssens, Ewald; Silverans, Roger E.; Lievens, Peter

2003-10-01

A systematic study on the structure and stability of zinc doped gold clusters has been performed by density functional theory calculations. All the lowest-energy isomers found have a planar structure and resemble pure gold clusters in shape. Stable isomers tend to equally delocalize valence s electrons of the constituent atoms over the entire structure and maximize the number of Au-Zn bonds in the structure. This is because the Au-Zn bond is stronger than the Au-Au bond and gives an extra σ-bonding interaction by the overlap between vacant Zn 4p and valence Au 6s(5d) orbitals. No three-dimensional isomers were found for Au5Zn+ and Au4Zn clusters containing six delocalized valence electrons. This result reflects that these clusters have a magic number of delocalized electrons for two-dimensional systems. Calculated vertical ionization energies and dissociation energies as a function of the cluster size show odd-even behavior, in agreement with recent mass spectrometric observations [Tanaka et al., J. Am. Chem. Soc. 125, 2862 (2003)].

MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks on Multicore Clusters.

PubMed

Gonzalez-Dominguez, Jorge; Martin, Maria J

2017-10-10

In this work we present MPIGeneNet, a parallel tool that applies Pearson's correlation and Random Matrix Theory to construct gene co-expression networks. It is based on the state-of-the-art sequential tool RMTGeneNet, which provides networks with high robustness and sensitivity at the expenses of relatively long runtimes for large scale input datasets. MPIGeneNet returns the same results as RMTGeneNet but improves the memory management, reduces the I/O cost, and accelerates the two most computationally demanding steps of co-expression network construction by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on two different systems using three typical input datasets shows that MPIGeneNet is significantly faster than RMTGeneNet. As an example, our tool is up to 175.41 times faster on a cluster with eight nodes, each one containing two 12-core Intel Haswell processors. Source code of MPIGeneNet, as well as a reference manual, are available at https://sourceforge.net/projects/mpigenenet/.

Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae

PubMed Central

2017-01-01

Transferring the prokaryotic enzyme nitrogenase into a eukaryotic host with the final aim of developing N2 fixing cereal crops would revolutionize agricultural systems worldwide. Targeting it to mitochondria has potential advantages because of the organelle’s high O2 consumption and the presence of bacterial-type iron–sulfur cluster biosynthetic machinery. In this study, we constructed 96 strains of Saccharomyces cerevisiae in which transcriptional units comprising nine Azotobacter vinelandii nif genes (nifHDKUSMBEN) were integrated into the genome. Two combinatorial libraries of nif gene clusters were constructed: a library of mitochondrial leading sequences consisting of 24 clusters within four subsets of nif gene expression strength, and an expression library of 72 clusters with fixed mitochondrial leading sequences and nif expression levels assigned according to factorial design. In total, 29 promoters and 18 terminators were combined to adjust nif gene expression levels. Expression and mitochondrial targeting was confirmed at the protein level as immunoblot analysis showed that Nif proteins could be efficiently accumulated in mitochondria. NifDK tetramer formation, an essential step of nitrogenase assembly, was experimentally proven both in cell-free extracts and in purified NifDK preparations. This work represents a first step toward obtaining functional nitrogenase in the mitochondria of a eukaryotic cell. PMID:28221768

A mathematical programming approach for sequential clustering of dynamic networks

NASA Astrophysics Data System (ADS)

Silva, Jonathan C.; Bennett, Laura; Papageorgiou, Lazaros G.; Tsoka, Sophia

2016-02-01

A common analysis performed on dynamic networks is community structure detection, a challenging problem that aims to track the temporal evolution of network modules. An emerging area in this field is evolutionary clustering, where the community structure of a network snapshot is identified by taking into account both its current state as well as previous time points. Based on this concept, we have developed a mixed integer non-linear programming (MINLP) model, SeqMod, that sequentially clusters each snapshot of a dynamic network. The modularity metric is used to determine the quality of community structure of the current snapshot and the historical cost is accounted for by optimising the number of node pairs co-clustered at the previous time point that remain so in the current snapshot partition. Our method is tested on social networks of interactions among high school students, college students and members of the Brazilian Congress. We show that, for an adequate parameter setting, our algorithm detects the classes that these students belong more accurately than partitioning each time step individually or by partitioning the aggregated snapshots. Our method also detects drastic discontinuities in interaction patterns across network snapshots. Finally, we present comparative results with similar community detection methods for time-dependent networks from the literature. Overall, we illustrate the applicability of mathematical programming as a flexible, adaptable and systematic approach for these community detection problems. Contribution to the Topical Issue "Temporal Network Theory and Applications", edited by Petter Holme.

Prioritizing and synthesizing evidence to improve the health care of girls and women living with female genital mutilation: An overview of the process.

PubMed

Stein, Karin; Hindin, Michelle J; Chou, Doris; Say, Lale

2017-02-01

Female genital mutilation (FGM) constitutes a harmful traditional practice that can have a profound impact on the health and well-being of girls and women who undergo the procedure. In recent years, due to international migration, healthcare providers worldwide are increasingly confronted with the need to provide adequate health care to this population. Recognizing this situation the WHO recently developed the first evidence-based guidelines on the management of health complications from FGM. To inform the guideline recommendations, an expert-driven, two-step process was conducted. The first step consisted of developing and ranking a list of priority research questions for the evidence retrieval. The second step involved conducting a series of systematic reviews and qualitative data syntheses. In the present paper, we first provide the methodology used in the development and ranking of the research questions (step 1) and then detail the common methodology for each of the systematic reviews and qualitative evidence syntheses (step 2). © 2017 International Federation of Gynecology and Obstetrics. The World Health Organization retains copyright and all other rights in the manuscript of this article as submitted for publication.

Using preoperative unsupervised cluster analysis of chronic rhinosinusitis to inform patient decision and endoscopic sinus surgery outcome.

PubMed

Adnane, Choaib; Adouly, Taoufik; Khallouk, Amine; Rouadi, Sami; Abada, Redallah; Roubal, Mohamed; Mahtar, Mohamed

2017-02-01

The purpose of this study is to use unsupervised cluster methodology to identify phenotype and mucosal eosinophilia endotype subgroups of patients with medical refractory chronic rhinosinusitis (CRS), and evaluate the difference in quality of life (QOL) outcomes after endoscopic sinus surgery (ESS) between these clusters for better surgical case selection. A prospective cohort study included 131 patients with medical refractory CRS who elected ESS. The Sino-Nasal Outcome Test (SNOT-22) was used to evaluate QOL before and 12 months after surgery. Unsupervised two-step clustering method was performed. One hundred and thirteen subjects were retained in this study: 46 patients with CRS without nasal polyps and 67 patients with nasal polyps. Nasal polyps, gender, mucosal eosinophilia profile, and prior sinus surgery were the most discriminating factors in the generated clusters. Three clusters were identified. A significant clinical improvement was observed in all clusters 12 months after surgery with a reduction of SNOT-22 scores. There was a significant difference in QOL outcomes between clusters; cluster 1 had the worst QOL improvement after FESS in comparison with the other clusters 2 and 3. All patients in cluster 1 presented CRSwNP with the highest mucosal eosinophilia endotype. Clustering method is able to classify CRS phenotypes and endotypes with different associated surgical outcomes.

TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes.

PubMed

Jung, Inuk; Jo, Kyuri; Kang, Hyejin; Ahn, Hongryul; Yu, Youngjae; Kim, Sun

2017-12-01

Identifying biologically meaningful gene expression patterns from time series gene expression data is important to understand the underlying biological mechanisms. To identify significantly perturbed gene sets between different phenotypes, analysis of time series transcriptome data requires consideration of time and sample dimensions. Thus, the analysis of such time series data seeks to search gene sets that exhibit similar or different expression patterns between two or more sample conditions, constituting the three-dimensional data, i.e. gene-time-condition. Computational complexity for analyzing such data is very high, compared to the already difficult NP-hard two dimensional biclustering algorithms. Because of this challenge, traditional time series clustering algorithms are designed to capture co-expressed genes with similar expression pattern in two sample conditions. We present a triclustering algorithm, TimesVector, specifically designed for clustering three-dimensional time series data to capture distinctively similar or different gene expression patterns between two or more sample conditions. TimesVector identifies clusters with distinctive expression patterns in three steps: (i) dimension reduction and clustering of time-condition concatenated vectors, (ii) post-processing clusters for detecting similar and distinct expression patterns and (iii) rescuing genes from unclassified clusters. Using four sets of time series gene expression data, generated by both microarray and high throughput sequencing platforms, we demonstrated that TimesVector successfully detected biologically meaningful clusters of high quality. TimesVector improved the clustering quality compared to existing triclustering tools and only TimesVector detected clusters with differential expression patterns across conditions successfully. The TimesVector software is available at http://biohealth.snu.ac.kr/software/TimesVector/. sunkim.bioinfo@snu.ac.kr. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Clusters of Occupations Based on Systematically Derived Work Dimensions: An Exploratory Study.

ERIC Educational Resources Information Center

Cunningham, J. W.; And Others

The study explored the feasibility of deriving an educationally relevant occupational cluster structure based on Occupational Analysis Inventory (OAI) work dimensions. A hierarchical cluster analysis was applied to the factor score profiles of 814 occupations on 22 higher-order OAI work dimensions. From that analysis, 73 occupational clusters were…

Knowledge translation studies in paediatric emergency medicine: A systematic review of the literature.

PubMed

Wilson, Catherine L; Johnson, David; Oakley, Ed

2016-02-01

Systematic review of knowledge translation studies focused on paediatric emergency care to describe and assess the interventions used in emergency department settings. Electronic databases were searched for knowledge translation studies conducted in the emergency department that included the care of children. Two researchers independently reviewed the studies. From 1305 publications identified, 15 studies of varied design were included. Four were cluster-controlled trials, two patient-level randomised controlled trials, two interrupted time series, one descriptive study and six before and after intervention studies. Knowledge translation interventions were predominantly aimed at the treating clinician, with some targeting the organisation. Studies assessed effectiveness of interventions over 6-12 months in before and after studies, and 3-28 months in cluster or patient level controlled trials. Changes in clinical practice were variable, with studies on single disease and single treatments in a single site showing greater improvement. Evidence for effective methods to translate knowledge into practice in paediatric emergency medicine is fairly limited. More optimal study designs with more explicit descriptions of interventions are needed to facilitate other groups to effectively apply these procedures in their own setting. © 2016 The Authors Journal of Paediatrics and Child Health © 2016 Paediatrics and Child Health Division (Royal Australasian College of Physicians).

Patterns of Dysmorphic Features in Schizophrenia

PubMed Central

Scutt, L.E.; Chow, E.W.C.; Weksberg, R.; Honer, W.G.; Bassett, Anne S.

2011-01-01

Congenital dysmorphic features are prevalent in schizophrenia and may reflect underlying neurodevelopmental abnormalities. A cluster analysis approach delineating patterns of dysmorphic features has been used in genetics to classify individuals into more etiologically homogeneous subgroups. In the present study, this approach was applied to schizophrenia, using a sample with a suspected genetic syndrome as a testable model. Subjects (n = 159) with schizophrenia or schizoaffective disorder were ascertained from chronic patient populations (random, n=123) or referred with possible 22q11 deletion syndrome (referred, n = 36). All subjects were evaluated for presence or absence of 70 reliably assessed dysmorphic features, which were used in a three-step cluster analysis. The analysis produced four major clusters with different patterns of dysmorphic features. Significant between-cluster differences were found for rates of 37 dysmorphic features (P < 0.05), median number of dysmorphic features (P = 0.0001), and validating features not used in the cluster analysis: mild mental retardation (P = 0.001) and congenital heart defects (P = 0.002). Two clusters (1 and 4) appeared to represent more developmental subgroups of schizophrenia with elevated rates of dysmorphic features and validating features. Cluster 1 (n = 27) comprised mostly referred subjects. Cluster 4 (n= 18) had a different pattern of dysmorphic features; one subject had a mosaic Turner syndrome variant. Two other clusters had lower rates and patterns of features consistent with those found in previous studies of schizophrenia. Delineating patterns of dysmorphic features may help identify subgroups that could represent neurodevelopmental forms of schizophrenia with more homogeneous origins. PMID:11803519

The systematic review as a research process in music therapy.

PubMed

Hanson-Abromeit, Deanna; Sena Moore, Kimberly

2014-01-01

Music therapists are challenged to present evidence on the efficacy of music therapy treatment and incorporate the best available research evidence to make informed healthcare and treatment decisions. Higher standards of evidence can come from a variety of sources including systematic reviews. To define and describe a range of research review methods using examples from music therapy and related literature, with emphasis on the systematic review. In addition, the authors provide a detailed overview of methodological processes for conducting and reporting systematic reviews in music therapy. The systematic review process is described in five steps. Step 1 identifies the research plan and operationalized research question(s). Step 2 illustrates the identification and organization of the existing literature related to the question(s). Step 3 details coding of data extracted from the literature. Step 4 explains the synthesis of coded findings and analysis to answer the research question(s). Step 5 describes the strength of evidence evaluation and results presentation for practice recommendations. Music therapists are encouraged to develop and conduct systematic reviews. This methodology contributes to review outcome credibility and can determine how information is interpreted and used by clinicians, clients or patients, and policy makers. A systematic review is a methodologically rigorous research method used to organize and evaluate extant literature related to a clinical problem. Systematic reviews can assist music therapists in managing the ever-increasing literature, making well-informed evidence based practice and research decisions, and translating existing music-based and nonmusic based literature to clinical practice and research development. © the American Music Therapy Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Systematic Study on the Self-Assembled Hexagonal Au Voids, Nano-Clusters and Nanoparticles on GaN (0001).

PubMed

Pandey, Puran; Sui, Mao; Li, Ming-Yu; Zhang, Quanzhen; Kim, Eun-Soo; Lee, Jihoon

2015-01-01

Au nano-clusters and nanoparticles (NPs) have been widely utilized in various electronic, optoelectronic, and bio-medical applications due to their great potentials. The size, density and configuration of Au NPs play a vital role in the performance of these devices. In this paper, we present a systematic study on the self-assembled hexagonal Au voids, nano-clusters and NPs fabricated on GaN (0001) by the variation of annealing temperature and deposition amount. At relatively low annealing temperatures between 400 and 600°C, the fabrication of hexagonal shaped Au voids and Au nano-clusters are observed and discussed based on the diffusion limited aggregation model. The size and density of voids and nano-clusters can systematically be controlled. The self-assembled Au NPs are fabricated at comparatively high temperatures from 650 to 800°C based on the Volmer-Weber growth model and also the size and density can be tuned accordingly. The results are symmetrically analyzed and discussed in conjunction with the diffusion theory and thermodynamics by utilizing AFM and SEM images, EDS maps and spectra, FFT power spectra, cross-sectional line-profiles and size and density plots.

Systematic Study on the Self-Assembled Hexagonal Au Voids, Nano-Clusters and Nanoparticles on GaN (0001)

PubMed Central

Pandey, Puran; Sui, Mao; Li, Ming-Yu; Zhang, Quanzhen; Kim, Eun-Soo; Lee, Jihoon

2015-01-01

Au nano-clusters and nanoparticles (NPs) have been widely utilized in various electronic, optoelectronic, and bio-medical applications due to their great potentials. The size, density and configuration of Au NPs play a vital role in the performance of these devices. In this paper, we present a systematic study on the self-assembled hexagonal Au voids, nano-clusters and NPs fabricated on GaN (0001) by the variation of annealing temperature and deposition amount. At relatively low annealing temperatures between 400 and 600°C, the fabrication of hexagonal shaped Au voids and Au nano-clusters are observed and discussed based on the diffusion limited aggregation model. The size and density of voids and nano-clusters can systematically be controlled. The self-assembled Au NPs are fabricated at comparatively high temperatures from 650 to 800°C based on the Volmer-Weber growth model and also the size and density can be tuned accordingly. The results are symmetrically analyzed and discussed in conjunction with the diffusion theory and thermodynamics by utilizing AFM and SEM images, EDS maps and spectra, FFT power spectra, cross-sectional line-profiles and size and density plots. PMID:26285135

Optimization Strategies for Hardware-Based Cofactorization

NASA Astrophysics Data System (ADS)

Loebenberger, Daniel; Putzka, Jens

We use the specific structure of the inputs to the cofactorization step in the general number field sieve (GNFS) in order to optimize the runtime for the cofactorization step on a hardware cluster. An optimal distribution of bitlength-specific ECM modules is proposed and compared to existing ones. With our optimizations we obtain a speedup between 17% and 33% of the cofactorization step of the GNFS when compared to the runtime of an unoptimized cluster.

Robust Segmentation of Overlapping Cells in Histopathology Specimens Using Parallel Seed Detection and Repulsive Level Set

PubMed Central

Qi, Xin; Xing, Fuyong; Foran, David J.; Yang, Lin

2013-01-01

Automated image analysis of histopathology specimens could potentially provide support for early detection and improved characterization of breast cancer. Automated segmentation of the cells comprising imaged tissue microarrays (TMA) is a prerequisite for any subsequent quantitative analysis. Unfortunately, crowding and overlapping of cells present significant challenges for most traditional segmentation algorithms. In this paper, we propose a novel algorithm which can reliably separate touching cells in hematoxylin stained breast TMA specimens which have been acquired using a standard RGB camera. The algorithm is composed of two steps. It begins with a fast, reliable object center localization approach which utilizes single-path voting followed by mean-shift clustering. Next, the contour of each cell is obtained using a level set algorithm based on an interactive model. We compared the experimental results with those reported in the most current literature. Finally, performance was evaluated by comparing the pixel-wise accuracy provided by human experts with that produced by the new automated segmentation algorithm. The method was systematically tested on 234 image patches exhibiting dense overlap and containing more than 2200 cells. It was also tested on whole slide images including blood smears and tissue microarrays containing thousands of cells. Since the voting step of the seed detection algorithm is well suited for parallelization, a parallel version of the algorithm was implemented using graphic processing units (GPU) which resulted in significant speed-up over the C/C++ implementation. PMID:22167559

Subspace Clustering via Learning an Adaptive Low-Rank Graph.

PubMed

Yin, Ming; Xie, Shengli; Wu, Zongze; Zhang, Yun; Gao, Junbin

2018-08-01

By using a sparse representation or low-rank representation of data, the graph-based subspace clustering has recently attracted considerable attention in computer vision, given its capability and efficiency in clustering data. However, the graph weights built using the representation coefficients are not the exact ones as the traditional definition is in a deterministic way. The two steps of representation and clustering are conducted in an independent manner, thus an overall optimal result cannot be guaranteed. Furthermore, it is unclear how the clustering performance will be affected by using this graph. For example, the graph parameters, i.e., the weights on edges, have to be artificially pre-specified while it is very difficult to choose the optimum. To this end, in this paper, a novel subspace clustering via learning an adaptive low-rank graph affinity matrix is proposed, where the affinity matrix and the representation coefficients are learned in a unified framework. As such, the pre-computed graph regularizer is effectively obviated and better performance can be achieved. Experimental results on several famous databases demonstrate that the proposed method performs better against the state-of-the-art approaches, in clustering.

Longevity of Self-etch Dentin Bonding Adhesives Compared to Etch-and-rinse Dentin Bonding Adhesives: A Systematic Review.

PubMed

Masarwa, Nader; Mohamed, Ahmed; Abou-Rabii, Iyad; Abu Zaghlan, Rawan; Steier, Liviu

2016-06-01

A systematic review and meta-analysis were performed to compare longevity of Self-Etch Dentin Bonding Adhesives to Etch-and-Rinse Dentin Bonding Adhesives. The following databases were searched for PubMed, MEDLINE, Web of Science, CINAHL, the Cochrane Library complemented by a manual search of the Journal of Adhesive Dentistry. The MESH keywords used were: "etch and rinse," "total etch," "self-etch," "dentin bonding agent," "bond durability," and "bond degradation." Included were in-vitro experimental studies performed on human dental tissues of sound tooth structure origin. The examined Self-Etch Bonds were of two subtypes; Two Steps and One Step Self-Etch Bonds, while Etch-and-Rinse Bonds were of two subtypes; Two Steps and Three Steps. The included studies measured micro tensile bond strength (μTBs) to evaluate bond strength and possible longevity of both types of dental adhesives at different times. The selected studies depended on water storage as the aging technique. Statistical analysis was performed for outcome measurements compared at 24 h, 3 months, 6 months and 12 months of water storage. After 24 hours (p-value = 0.051), 3 months (p-value = 0.756), 6 months (p-value=0.267), 12 months (p-value=0.785) of water storage self-etch adhesives showed lower μTBs when compared to the etch-and-rinse adhesives, but the comparisons were statistically insignificant. In this study, longevity of Dentin Bonds was related to the measured μTBs. Although Etch-and-Rinse bonds showed higher values at all times, the meta-analysis found no difference in longevity of the two types of bonds at the examined aging times. Copyright © 2016 Elsevier Inc. All rights reserved.

Abstract Interpreters for Free

NASA Astrophysics Data System (ADS)

Might, Matthew

In small-step abstract interpretations, the concrete and abstract semantics bear an uncanny resemblance. In this work, we present an analysis-design methodology that both explains and exploits that resemblance. Specifically, we present a two-step method to convert a small-step concrete semantics into a family of sound, computable abstract interpretations. The first step re-factors the concrete state-space to eliminate recursive structure; this refactoring of the state-space simultaneously determines a store-passing-style transformation on the underlying concrete semantics. The second step uses inference rules to generate an abstract state-space and a Galois connection simultaneously. The Galois connection allows the calculation of the "optimal" abstract interpretation. The two-step process is unambiguous, but nondeterministic: at each step, analysis designers face choices. Some of these choices ultimately influence properties such as flow-, field- and context-sensitivity. Thus, under the method, we can give the emergence of these properties a graph-theoretic characterization. To illustrate the method, we systematically abstract the continuation-passing style lambda calculus to arrive at two distinct families of analyses. The first is the well-known k-CFA family of analyses. The second consists of novel "environment-centric" abstract interpretations, none of which appear in the literature on static analysis of higher-order programs.

Examining the Rule of Thumb of Not Using Multilevel Modeling: The "Design Effect Smaller than Two" Rule

ERIC Educational Resources Information Center

Lai, Mark H. C.; Kwok, Oi-man

2015-01-01

Educational researchers commonly use the rule of thumb of "design effect smaller than 2" as the justification of not accounting for the multilevel or clustered structure in their data. The rule, however, has not yet been systematically studied in previous research. In the present study, we generated data from three different models…

The void spectrum in two-dimensional numerical simulations of gravitational clustering

NASA Technical Reports Server (NTRS)

Kauffmann, Guinevere; Melott, Adrian L.

1992-01-01

An algorithm for deriving a spectrum of void sizes from two-dimensional high-resolution numerical simulations of gravitational clustering is tested, and it is verified that it produces the correct results where those results can be anticipated. The method is used to study the growth of voids as clustering proceeds. It is found that the most stable indicator of the characteristic void 'size' in the simulations is the mean fractional area covered by voids of diameter d, in a density field smoothed at its correlation length. Very accurate scaling behavior is found in power-law numerical models as they evolve. Eventually, this scaling breaks down as the nonlinearity reaches larger scales. It is shown that this breakdown is a manifestation of the undesirable effect of boundary conditions on simulations, even with the very large dynamic range possible here. A simple criterion is suggested for deciding when simulations with modest large-scale power may systematically underestimate the frequency of larger voids.

[Difficulties in emotion regulation and personal distress in young adults with social anxiety].

PubMed

Contardi, Anna; Farina, Benedetto; Fabbricatore, Mariantonietta; Tamburello, Stella; Scapellato, Paolo; Penzo, Ilaria; Tamburello, Antonino; Innamorati, Marco

2013-01-01

The aim of this study was to assess the association between social anxiety and difficulties in emotion regulation in a sample of Italian young adults. Our convenience sample was composed of 298 Italian young adults (184 women and 114 men) aged 18-34 years. Participants were administered the Interaction Anxiousness Scale (IAS), the Audience Anxiousness Scale (AAS), the Difficulties in Emotion Regulation Scale (DERS), and the Interpersonal Reactivity Index (IRI). A Two Step cluster analysis was used to group subjects according to their level of social anxiety. The cluster analysis indicated a two-cluster solution. The first cluster included 163 young adults with higher scores on the AAS and the IAS than those included in cluster 2 (n=135). A generalized linear model with groups as dependent variable indicated that people with higher social anxiety (compared to those with lower social anxiety) have higher scores on the dimension personal distress of the IRI (p<0.01), and on the DERS non acceptance of negative emotions (p<0.001) and lack of emotional clarity (p<0.05). The results are consistent with models of psychopathology, which hypothesize that people who cannot deal effectively with their emotions may develop depressive and anxious disorders.

Repair of Clustered Damage and DNA Polymerase Iota.

PubMed

Belousova, E A; Lavrik, O I

2015-08-01

Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

Systematic development of a self-help and motivational enhancement intervention to promote sexual health in HIV-positive men who have sex with men.

PubMed

Van Kesteren, Nicole M C; Kok, Gerjo; Hospers, Harm J; Schippers, Jan; De Wildt, Wencke

2006-12-01

The objective of this study was to describe the application of a systematic process-Intervention Mapping-to developing a theory- and evidence-based intervention to promote sexual health in HIV-positive men who have sex with men (MSM). Intervention Mapping provides a framework that gives program planners a systematic method for decision-making in each phase of intervention development. In Step 1, we focused on the improvement of two health-promoting behaviors: satisfactory sexual functioning and safer sexual behavior. These behaviors were then linked with selected personal and external determinants, such as attitudes and social support, to produce a set of proximal program objectives. In Step 2, theoretical methods were identified to influence the proximal program objectives and were translated into practical strategies. Although theoretical methods were derived from various theories, self-regulation theory and a cognitive model of behavior change provided the main framework for selecting the intervention methods. The main strategies chosen were bibliotherapy (i.e., the use of written material to help people solve problems or change behavior) and motivational interviewing. In Step 3, the theoretical methods and practical strategies were applied in a program that comprised a self-help guide, a motivational interviewing session and a motivational interviewing telephone call, both delivered by specialist nurses in HIV treatment centers. In Step 4, implementation was anticipated by developing a linkage group to ensure involvement of program users in the planning process and conducting additional research to understand how to implement our program better. In Step 5, program evaluation was anticipated based on the planning process from the previous Intervention Mapping steps.

Writing a Cochrane systematic review on preventive interventions to improve safety: the case of the construction industry.

PubMed

van der Molen, H F; Hoonakker, P L T; Lehtola, Marika M; Hsiao, H; Haslam, R A; Hale, A R; Verbeek, J H

2009-01-01

The objective of this paper is to describe the main steps and to conduct a systematic literature review on preventive interventions concerning work-related injuries and to illustrate the process. Based on the Cochrane handbook, a structured framework of six steps was outlined for the development of a systematic review. This framework was used to describe a Cochrane systematic review (CSR) on the effectiveness of interventions to prevent work related injuries in the construction industry. The 6 main steps to write a CSR were: formulating the problem and objectives; locating and selecting studies; assessing study quality; collecting data; analysing data and presenting results; and interpreting results. The CSR on preventing injuries in the construction industry yielded five eligible intervention studies. Re-analysis of original injury data of the studies on regulatory interventions, through correcting for pre-intervention injury trends led to different conclusions about the effectiveness of interventions than those reported in the original studies. The Cochrane handbook for systematic reviews of interventions provides a practical and feasible six-step framework for developing and reporting a systematic review for preventive interventions.

The Polar Cusp Observed by Cluster Under Constant Imf-Bz Southward

NASA Astrophysics Data System (ADS)

Escoubet, C. P.; Berchem, J.; Pitout, F.; Trattner, K. J.; Richard, R. L.; Taylor, M. G.; Soucek, J.; Grison, B.; Laakso, H. E.; Masson, A.; Dunlop, M. W.; Dandouras, I. S.; Reme, H.; Fazakerley, A. N.; Daly, P. W.

2011-12-01

The Earth's magnetic field is influenced by the interplanetary magnetic field (IMF), specially at the magnetopause where both magnetic fields enter in direct contact and magnetic reconnection can be initiated. In the polar regions, the polar cusp that extends from the magnetopause down to the ionosphere is also directly influenced. The reconnection not only allow ions and electrons from the solar wind to enter the polar cusp but also give an impulse to the magnetic field lines threading the polar cusp through the reconnection electric field. A dispersion in energy of the ions is subsequently produced by the motion of field lines and the time-of-flight effect on down-going ions. If reconnection is continuous and operates at constant rate, the ion dispersion is smooth and continuous. On the other hand if the reconnection rate varies, we expect interruption in the dispersion forming energy steps or staircase. Similarly, multiple entries near the magnetopause could also produce steps at low or mid-altitude when a spacecraft is crossing subsequently the field lines originating from these multiple sources. Cluster with four spacecraft following each other in the mid-altitude cusp can be used to distinguish between these "temporal" and "spatial" effects. We will show two Cluster cusp crossings where the spacecraft were separated by a few minutes. The energy dispersions observed in the first crossing were the same during the few minutes that separated the spacecraft. In the second crossing, two ion dispersions were observed on the first spacecraft and only one of the following spacecraft, about 10 min later. The detailed analysis indicates that these steps result from spatial structures.

Cluster Subcutaneous Allergen Specific Immunotherapy for the Treatment of Allergic Rhinitis: A Systematic Review and Meta-Analysis

PubMed Central

Sun, Yueqi; Luo, Xi; Li, Huabin

2014-01-01

Background Although allergen specific immunotherapy (SIT) represents the only immune- modifying and curative option available for patients with allergic rhinitis (AR), the optimal schedule for specific subcutaneous immunotherapy (SCIT) is still unknown. The objective of this study is to systematically assess the efficacy and safety of cluster SCIT for patients with AR. Methods By searching PubMed, EMBASE and the Cochrane clinical trials database from 1980 through May 10th, 2013, we collected and analyzed the randomized controlled trials (RCTs) of cluster SCIT to assess its efficacy and safety. Results Eight trials involving 567 participants were included in this systematic review. Our meta-analysis showed that cluster SCIT have similar effect in reduction of both rhinitis symptoms and the requirement for anti-allergic medication compared with conventional SCIT, but when comparing cluster SCIT with placebo, no statistic significance were found in reduction of symptom scores or medication scores. Some caution is required in this interpretation as there was significant heterogeneity between studies. Data relating to Rhinoconjunctivitis Quality of Life Questionnaire (RQLQ) in 3 included studies were analyzed, which consistently point to the efficacy of cluster SCIT in improving quality of life compared to placebo. To assess the safety of cluster SCIT, meta-analysis showed that no differences existed in the incidence of either local adverse reaction or systemic adverse reaction between the cluster group and control group. Conclusion Based on the current limited evidence, we still could not conclude affirmatively that cluster SCIT was a safe and efficacious option for the treatment of AR patients. Further large-scale, well-designed RCTs on this topic are still needed. PMID:24489740

Steps Toward Understanding Mitochondrial Fe/S Cluster Biogenesis.

PubMed

Melber, Andrew; Winge, Dennis R

2018-01-01

Iron-sulfur clusters (Fe/S clusters) are essential cofactors required throughout the clades of biology for performing a myriad of unique functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. Although Fe/S clusters can be synthesized in vitro and transferred to a client protein without enzymatic assistance, biology has evolved intricate mechanisms to assemble and transfer Fe/S clusters within the cellular environment. In eukaryotes, the foundation of all cellular clusters starts within the mitochondria. The focus of this review is to detail the mitochondrial Fe/S biogenesis (ISC) pathway along with the Fe/S cluster transfer steps necessary to mature Fe/S proteins. New advances in our understanding of the mitochondrial Fe/S biogenesis machinery will be highlighted. Additionally, we will address various experimental approaches that have been successful in the identification and characterization of components of the ISC pathway. © 2018 Elsevier Inc. All rights reserved.

Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

DOEpatents

Alivisatos, A.P.; Colvin, V.L.

1998-05-12

Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed. 10 figs.

New clinical grading scales and objective measurement for conjunctival injection.

PubMed

Park, In Ki; Chun, Yeoun Sook; Kim, Kwang Gi; Yang, Hee Kyung; Hwang, Jeong-Min

2013-08-05

To establish a new clinical grading scale and objective measurement method to evaluate conjunctival injection. Photographs of conjunctival injection with variable ocular diseases in 429 eyes were reviewed. Seventy-three images with concordance by three ophthalmologists were classified into a 4-step and 10-step subjective grading scale, and used as standard photographs. Each image was quantified in four ways: the relative magnitude of the redness component of each red-green-blue (RGB) pixel; two different algorithms based on the occupied area by blood vessels (K-means clustering with LAB color model and contrast-limited adaptive histogram equalization [CLAHE] algorithm); and the presence of blood vessel edges, based on the Canny edge-detection algorithm. Area under the receiver operating characteristic curves (AUCs) were calculated to summarize diagnostic accuracies of the four algorithms. The RGB color model, K-means clustering with LAB color model, and CLAHE algorithm showed good correlation with the clinical 10-step grading scale (R = 0.741, 0.784, 0.919, respectively) and with the clinical 4-step grading scale (R = 0.645, 0.702, 0.838, respectively). The CLAHE method showed the largest AUC, best distinction power (P < 0.001, ANOVA, Bonferroni multiple comparison test), and high reproducibility (R = 0.996). CLAHE algorithm showed the best correlation with the 10-step and 4-step subjective clinical grading scales together with high distinction power and reproducibility. CLAHE algorithm can be a useful for method for assessment of conjunctival injection.

Cluster Detection Tests in Spatial Epidemiology: A Global Indicator for Performance Assessment

PubMed Central

Guttmann, Aline; Li, Xinran; Feschet, Fabien; Gaudart, Jean; Demongeot, Jacques; Boire, Jean-Yves; Ouchchane, Lemlih

2015-01-01

In cluster detection of disease, the use of local cluster detection tests (CDTs) is current. These methods aim both at locating likely clusters and testing for their statistical significance. New or improved CDTs are regularly proposed to epidemiologists and must be subjected to performance assessment. Because location accuracy has to be considered, performance assessment goes beyond the raw estimation of type I or II errors. As no consensus exists for performance evaluations, heterogeneous methods are used, and therefore studies are rarely comparable. A global indicator of performance, which assesses both spatial accuracy and usual power, would facilitate the exploration of CDTs behaviour and help between-studies comparisons. The Tanimoto coefficient (TC) is a well-known measure of similarity that can assess location accuracy but only for one detected cluster. In a simulation study, performance is measured for many tests. From the TC, we here propose two statistics, the averaged TC and the cumulated TC, as indicators able to provide a global overview of CDTs performance for both usual power and location accuracy. We evidence the properties of these two indicators and the superiority of the cumulated TC to assess performance. We tested these indicators to conduct a systematic spatial assessment displayed through performance maps. PMID:26086911

A Simple Model for the Earthquake Cycle Combining Self-Organized Criticality with Critical Point Behavior

NASA Astrophysics Data System (ADS)

Newman, W. I.; Turcotte, D. L.

2002-12-01

We have studied a hybrid model combining the forest-fire model with the site-percolation model in order to better understand the earthquake cycle. We consider a square array of sites. At each time step, a "tree" is dropped on a randomly chosen site and is planted if the site is unoccupied. When a cluster of "trees" spans the site (a percolating cluster), all the trees in the cluster are removed ("burned") in a "fire." The removal of the cluster is analogous to a characteristic earthquake and planting "trees" is analogous to increasing the regional stress. The clusters are analogous to the metastable regions of a fault over which an earthquake rupture can propagate once triggered. We find that the frequency-area statistics of the metastable regions are power-law with a negative exponent of two (as in the forest-fire model). This is analogous to the Gutenberg-Richter distribution of seismicity. This "self-organized critical behavior" can be explained in terms of an inverse cascade of clusters. Individual trees move from small to larger clusters until they are destroyed. This inverse cascade of clusters is self-similar and the power-law distribution of cluster sizes has been shown to have an exponent of two. We have quantified the forecasting of the spanning fires using error diagrams. The assumption that "fires" (earthquakes) are quasi-periodic has moderate predictability. The density of trees gives an improved degree of predictability, while the size of the largest cluster of trees provides a substantial improvement in forecasting a "fire."

Structural requirements and reaction pathways in dimethyl ether combustion catalyzed by supported Pt clusters.

PubMed

Ishikawa, Akio; Neurock, Matthew; Iglesia, Enrique

2007-10-31

The identity and reversibility of the elementary steps required for catalytic combustion of dimethyl ether (DME) on Pt clusters were determined by combining isotopic and kinetic analyses with density functional theory estimates of reaction energies and activation barriers to probe the lowest energy paths. Reaction rates are limited by C-H bond activation in DME molecules adsorbed on surfaces of Pt clusters containing chemisorbed oxygen atoms at near-saturation coverages. Reaction energies and activation barriers for C-H bond activation in DME to form methoxymethyl and hydroxyl surface intermediates show that this step is more favorable than the activation of C-O bonds to form two methoxides, consistent with measured rates and kinetic isotope effects. This kinetic preference is driven by the greater stability of the CH3OCH2* and OH* intermediates relative to chemisorbed methoxides. Experimental activation barriers on Pt clusters agree with density functional theory (DFT)-derived barriers on oxygen-covered Pt(111). Measured DME turnover rates increased with increasing DME pressure, but decreased as the O2 pressure increased, because vacancies (*) on Pt surfaces nearly saturated with chemisorbed oxygen are required for DME chemisorption. DFT calculations show that although these surface vacancies are required, higher oxygen coverages lead to lower C-H activation barriers, because the basicity of oxygen adatoms increases with coverage and they become more effective in hydrogen abstraction from DME. Water inhibits reaction rates via quasi-equilibrated adsorption on vacancy sites, consistent with DFT results indicating that water binds more strongly than DME on vacancies. These conclusions are consistent with the measured kinetic response of combustion rates to DME, O2, and H2O, with H/D kinetic isotope effects, and with the absence of isotopic scrambling in reactants containing isotopic mixtures of 18O2-16O2 or 12CH3O12CH3-13CH3O13CH3. Turnover rates increased with Pt cluster size, because small clusters, with more coordinatively unsaturated surface atoms, bind oxygen atoms more strongly than larger clusters and exhibit lower steady-state vacancy concentrations and a consequently smaller number of adsorbed DME intermediates involved in kinetically relevant steps. These effects of cluster size and metal-oxygen bond energies on reactivity are ubiquitous in oxidation reactions requiring vacancies on surfaces nearly saturated with intermediates derived from O2.

Automatic document classification of biological literature

PubMed Central

Chen, David; Müller, Hans-Michael; Sternberg, Paul W

2006-01-01

Background Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusion We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. PMID:16893465

Selective two-photon absorption in carbon dots: a piece of the photoluminescence emission puzzle.

PubMed

Santos, Carla I M; Mariz, Inês F A; Pinto, Sandra N; Gonçalves, Gil; Bdikin, Igor; Marques, Paula A A P; Neves, Maria Graça P M S; Martinho, José M G; Maçôas, Ermelinda M S

2018-06-22

Carbon nanodots (Cdots) are now emerging as promising nonlinear fluorophores for applications in biological environments. A thorough and systematic approach to the two-photon induced emission of Cdots that could provide design guidelines to control their nonlinear emission properties is still missing. In this work, we address the nonlinear optical spectroscopy of Cdots prepared by controlled chemical cutting of graphene oxide (GO). The two-photon absorption in the 700-1000 nm region and the corresponding emission spectrum are carefully investigated. The highest two-photon absorption cross-section estimated was 130 GM at 720 nm. This value is comparable with the one reported for graphene nanoribbons with push-pull architecture. The emission spectrum depends on the excitation mode. At the same excitation energy, nonlinear excitation results in excitation-wavelength independent emission, while upon linear excitation the emission is excitation-wavelength dependent. The biphotonic interaction seems to be selective towards sp2 clusters bearing electron donor and acceptor groups found in push-pull architectures. Both linear and nonlinear emission can be understood based on the existence of isolated sp2 clusters involved in π-π stacking interactions with clusters in adjacent layers.

Behavioral Health Risk Profiles of Undergraduate University Students in England, Wales, and Northern Ireland: A Cluster Analysis.

PubMed

El Ansari, Walid; Ssewanyana, Derrick; Stock, Christiane

2018-01-01

Limited research has explored clustering of lifestyle behavioral risk factors (BRFs) among university students. This study aimed to explore clustering of BRFs, composition of clusters, and the association of the clusters with self-rated health and perceived academic performance. We assessed (BRFs), namely tobacco smoking, physical inactivity, alcohol consumption, illicit drug use, unhealthy nutrition, and inadequate sleep, using a self-administered general Student Health Survey among 3,706 undergraduates at seven UK universities. A two-step cluster analysis generated: Cluster 1 (the high physically active and health conscious) with very high health awareness/consciousness, good nutrition, and physical activity (PA), and relatively low alcohol, tobacco, and other drug (ATOD) use. Cluster 2 (the abstinent) had very low ATOD use, high health awareness, good nutrition, and medium high PA. Cluster 3 (the moderately health conscious) included the highest regard for healthy eating, second highest fruit/vegetable consumption, and moderately high ATOD use. Cluster 4 (the risk taking) showed the highest ATOD use, were the least health conscious, least fruit consuming, and attached the least importance on eating healthy. Compared to the healthy cluster (Cluster 1), students in other clusters had lower self-rated health, and particularly, students in the risk taking cluster (Cluster 4) reported lower academic performance. These associations were stronger for men than for women. Of the four clusters, Cluster 4 had the youngest students. Our results suggested that prevention among university students should address multiple BRFs simultaneously, with particular focus on the younger students.

Cluster Stability Estimation Based on a Minimal Spanning Trees Approach

NASA Astrophysics Data System (ADS)

Volkovich, Zeev (Vladimir); Barzily, Zeev; Weber, Gerhard-Wilhelm; Toledano-Kitai, Dvora

2009-08-01

Among the areas of data and text mining which are employed today in science, economy and technology, clustering theory serves as a preprocessing step in the data analyzing. However, there are many open questions still waiting for a theoretical and practical treatment, e.g., the problem of determining the true number of clusters has not been satisfactorily solved. In the current paper, this problem is addressed by the cluster stability approach. For several possible numbers of clusters we estimate the stability of partitions obtained from clustering of samples. Partitions are considered consistent if their clusters are stable. Clusters validity is measured as the total number of edges, in the clusters' minimal spanning trees, connecting points from different samples. Actually, we use the Friedman and Rafsky two sample test statistic. The homogeneity hypothesis, of well mingled samples within the clusters, leads to asymptotic normal distribution of the considered statistic. Resting upon this fact, the standard score of the mentioned edges quantity is set, and the partition quality is represented by the worst cluster corresponding to the minimal standard score value. It is natural to expect that the true number of clusters can be characterized by the empirical distribution having the shortest left tail. The proposed methodology sequentially creates the described value distribution and estimates its left-asymmetry. Numerical experiments, presented in the paper, demonstrate the ability of the approach to detect the true number of clusters.

Using the intervention mapping protocol to develop a maintenance programme for the SLIMMER diabetes prevention intervention.

PubMed

Elsman, Ellen B M; Leerlooijer, Joanne N; Ter Beek, Josien; Duijzer, Geerke; Jansen, Sophia C; Hiddink, Gerrit J; Feskens, Edith J M; Haveman-Nies, Annemien

2014-10-27

Although lifestyle interventions have shown to be effective in reducing the risk for type 2 diabetes mellitus, maintenance of achieved results is difficult, as participants often experience relapse after the intervention has ended. This paper describes the systematic development of a maintenance programme for the extensive SLIMMER intervention, an existing diabetes prevention intervention for high-risk individuals, implemented in a real-life setting in the Netherlands. The maintenance programme was developed using the Intervention Mapping protocol. Programme development was informed by a literature study supplemented by various focus group discussions and feedback from implementers of the extensive SLIMMER intervention. The maintenance programme was designed to sustain a healthy diet and physical activity pattern by targeting knowledge, attitudes, subjective norms and perceived behavioural control of the SLIMMER participants. Practical applications were clustered into nine programme components, including sports clinics at local sports clubs, a concluding meeting with the physiotherapist and dietician, and a return session with the physiotherapist, dietician and physical activity group. Manuals were developed for the implementers and included a detailed time table and step-by-step instructions on how to implement the maintenance programme. The Intervention Mapping protocol provided a useful framework to systematically plan a maintenance programme for the extensive SLIMMER intervention. The study showed that planning a maintenance programme can build on existing implementation structures of the extensive programme. Future research is needed to determine to what extent the maintenance programme contributes to sustained effects in participants of lifestyle interventions.

A cross-sectional cluster analysis of the combined association of physical activity and sleep with sociodemographic and health characteristics in mid-aged and older adults.

PubMed

Rayward, Anna T; Duncan, Mitch J; Brown, Wendy J; Plotnikoff, Ronald C; Burton, Nicola W

2017-08-01

This study aimed to identify how different patterns of physical activity, sleep duration and sleep quality cluster together, and to examine how the identified clusters differ in terms of socio-demographic and health characteristics. Participants were adults from Brisbane, Australia, aged 42-72 years who reported their physical activity, sleep duration, sleep quality, socio-demographic and health characteristics in 2011 (n=5854). Two-step Cluster Analyses were used to identify clusters. Cluster differences in socio-demographic and health characteristics were examined using chi square tests (p<0.05). Four clusters were identified: 'Poor Sleepers' (31.2%), 'Moderate Sleepers' (30.7%), 'Mixed Sleepers/Highly Active' (20.5%), and 'Excellent Sleepers/Mixed Activity' (17.6%). The 'Poor Sleepers' cluster had the highest proportion of participants with less-than-recommended sleep duration and poor sleep quality, had the poorest health characteristics and a high proportion of participants with low physical activity. Physical activity, sleep duration and sleep quality cluster together in distinct patterns and clusters of poor behaviours are associated with poor health status. Multiple health behaviour change interventions which target both physical activity and sleep should be prioritised to improve health outcomes in mid-aged adults. Copyright © 2017 Elsevier B.V. All rights reserved.

Associations between Functional Milestones and Psychiatric Admissions in an Urban Area: Utility of a Cluster-Analytical Approach.

PubMed

Montemagni, Cristiana; Frieri, Tiziana; Villari, Vincenzo; Rocca, Paola

2018-06-01

The purpose of the study was to identify homogenous subgroups, based upon achievement of two functional milestones (marriage and employment) and Global Assessment of Functioning (GAF) score in a sample of 848 acute patients admitted to the Psychiatric Emergency Service (PES) of the Città della Salute e della Scienza di Torino, during a 24-months period. A two-step cluster-analysis, using GAF total score and the achievements in the two milestones as input data was performed. In order to examine whether the identified subgroups differed in external variables that were not included in the clustering process, and consequently to validate the found functional profiles, chi-square tests for categorical variables and analyses of variance (ANOVA) for continuous variables were performed. Five clusters were found. Employed patients (Clusters 4 and 5) had more years of education, less illness chronicity (shorter duration of illness and lower proportion of previous voluntary hospitalizations), lower use of mental health resources in the last year yet higher treatment adherence, larger network size, and higher ordinary discharge. Married inpatients (Clusters 3 and 5) had lower frequencies of substance abuse. The remarkably high rate of unemployment in this inpatients' sample, and the evidence of associations between unemployment and poorer functioning, argue for further research and development of evidence-based supported employment programs, that put forth diligent effort in helping people obtain work quickly and sustain; they may also help to reduce health care service use among that clientele.

Russian consumers' motives for food choice.

PubMed

Honkanen, Pirjo; Frewer, Lynn

2009-04-01

Knowledge about food choice motives which have potential to influence consumer consumption decisions is important when designing food and health policies, as well as marketing strategies. Russian consumers' food choice motives were studied in a survey (1081 respondents across four cities), with the purpose of identifying consumer segments based on these motives. These segments were then profiled using consumption, attitudinal and demographic variables. Face-to-face interviews were used to sample the data, which were analysed with two-step cluster analysis (SPSS). Three clusters emerged, representing 21.5%, 45.8% and 32.7% of the sample. The clusters were similar in terms of the order of motivations, but differed in motivational level. Sensory factors and availability were the most important motives for food choice in all three clusters, followed by price. This may reflect the turbulence which Russia has recently experienced politically and economically. Cluster profiles differed in relation to socio-demographic factors, consumption patterns and attitudes towards health and healthy food.

A real world study on the genetic, cognitive and psychopathological differences of obese patients clustered according to eating behaviours.

PubMed

Caroleo, Mariarita; Primerano, Amedeo; Rania, Marianna; Aloi, Matteo; Pugliese, Valentina; Magliocco, Fabio; Fazia, Gilda; Filippo, Andrea; Sinopoli, Flora; Ricchio, Marco; Arturi, Franco; Jimenez-Murcia, Susana; Fernandez-Aranda, Fernando; De Fazio, Pasquale; Segura-Garcia, Cristina

2018-02-01

Considering that specific genetic profiles, psychopathological conditions and neurobiological systems underlie human behaviours, the phenotypic differentiation of obese patients according to eating behaviours should be investigated. The aim of this study was to classify obese patients according to their eating behaviours and to compare these clusters in regard to psychopathology, personality traits, neurocognitive patterns and genetic profiles. A total of 201 obese outpatients seeking weight reduction treatment underwent a dietetic visit, psychological and psychiatric assessment and genotyping for SCL6A2 polymorphisms. Eating behaviours were clustered through two-step cluster analysis, and these clusters were subsequently compared. Two groups emerged: cluster 1 contained patients with predominantly prandial hyperphagia, social eating, an increased frequency of the long allele of the 5-HTTLPR and low scores in all tests; and cluster 2 included patients with more emotionally related eating behaviours (emotional eating, grazing, binge eating, night eating, post-dinner eating, craving for carbohydrates), dysfunctional personality traits, neurocognitive impairment, affective disorders and increased frequencies of the short (S) allele and the S/S genotype. Aside from binge eating, dysfunctional eating behaviours were useful symptoms to identify two different phenotypes of obese patients from a comprehensive set of parameters (genetic, clinical, personality and neuropsychology) in this sample. Grazing and emotional eating were the most important predictors for classifying obese patients, followed by binge eating. This clustering overcomes the idea that 'binging' is the predominant altered eating behaviour, and could help physicians other than psychiatrists to identify whether an obese patient has an eating disorder. Finally, recognising different types of obesity may not only allow a more comprehensive understanding of this illness, but also make it possible to tailor patient-specific treatment pathways. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Impact of constrained rewiring on network structure and node dynamics

NASA Astrophysics Data System (ADS)

Rattana, P.; Berthouze, L.; Kiss, I. Z.

2014-11-01

In this paper, we study an adaptive spatial network. We consider a susceptible-infected-susceptible (SIS) epidemic on the network, with a link or contact rewiring process constrained by spatial proximity. In particular, we assume that susceptible nodes break links with infected nodes independently of distance and reconnect at random to susceptible nodes available within a given radius. By systematically manipulating this radius we investigate the impact of rewiring on the structure of the network and characteristics of the epidemic. We adopt a step-by-step approach whereby we first study the impact of rewiring on the network structure in the absence of an epidemic, then with nodes assigned a disease status but without disease dynamics, and finally running network and epidemic dynamics simultaneously. In the case of no labeling and no epidemic dynamics, we provide both analytic and semianalytic formulas for the value of clustering achieved in the network. Our results also show that the rewiring radius and the network's initial structure have a pronounced effect on the endemic equilibrium, with increasingly large rewiring radiuses yielding smaller disease prevalence.

Maturation of nitrogenase cofactor—the role of a class E radical SAM methyltransferase NifB

PubMed Central

Hu, Yilin; Ribbe, Markus W.

2016-01-01

Nitrogenase catalyzes the important reactions of N2-, CO- and CO2-reduction at its active cofactor site. Designated the M-cluster, this complex metallocofactor is assembled through the generation of a characteristic 8Fe-core prior to the insertion of Mo and homocitrate that completes the stoichiometry of the M-cluster. NifB catalyzes the critical step of radical SAM-dependent carbide insertion that occurs concomitant with the insertion a “9th” sulfur and the rearrangement/coupling of two 4Fe-clusters into a complete 8Fe-core of the M-cluster. Further categorization of a family of NifB proteins as a new class of radical SAM methyltransferases suggests a general function of these proteins in complex metallocofactor assembly and provides a new platform for unveiling unprecedented chemical reactions catalyzed by biological systems. PMID:26969410

Automated detection of microcalcification clusters in mammograms

NASA Astrophysics Data System (ADS)

Karale, Vikrant A.; Mukhopadhyay, Sudipta; Singh, Tulika; Khandelwal, Niranjan; Sadhu, Anup

2017-03-01

Mammography is the most efficient modality for detection of breast cancer at early stage. Microcalcifications are tiny bright spots in mammograms and can often get missed by the radiologist during diagnosis. The presence of microcalcification clusters in mammograms can act as an early sign of breast cancer. This paper presents a completely automated computer-aided detection (CAD) system for detection of microcalcification clusters in mammograms. Unsharp masking is used as a preprocessing step which enhances the contrast between microcalcifications and the background. The preprocessed image is thresholded and various shape and intensity based features are extracted. Support vector machine (SVM) classifier is used to reduce the false positives while preserving the true microcalcification clusters. The proposed technique is applied on two different databases i.e DDSM and private database. The proposed technique shows good sensitivity with moderate false positives (FPs) per image on both databases.

A systematic approach to the Kansei factors of tactile sense regarding the surface roughness.

PubMed

Choi, Kyungmee; Jun, Changrim

2007-01-01

Designing products to satisfy customers' emotion requires the information gathered through the human senses, which are visual, auditory, olfactory, gustatory, or tactile senses. By controlling certain design factors, customers' emotion can be evaluated, designed, and satisfied. In this study, a systematic approach is proposed to study the tactile sense regarding the surface roughness. Numerous pairs of antonymous tactile adjectives are collected and clustered. The optimal number of adjective clusters is estimated based on the several criterion functions. The representative average preferences of the final clusters are obtained as the estimates of engineering parameters to control the surface roughness of the commercial polymer-based products.

Comparative Effectiveness of Two Walking Interventions on Participation, Step Counts, and Health.

PubMed

Smith-McLallen, Aaron; Heller, Debbie; Vernisi, Kristin; Gulick, Diana; Cruz, Samantha; Snyder, Richard L

2017-03-01

To (1) compare the effects of two worksite-based walking interventions on employee participation rates; (2) compare average daily step counts between conditions, and; (3) examine the effects of increases in average daily step counts on biometric and psychologic outcomes. We conducted a cluster-randomized trial in which six employer groups were randomly selected and randomly assigned to condition. Four manufacturing worksites and two office-based worksite served as the setting. A total of 474 employees from six employer groups were included. A standard walking program was compared to an enhanced program that included incentives, feedback, competitive challenges, and monthly wellness workshops. Walking was measured by self-reported daily step counts. Survey measures and biometric screenings were administered at baseline and 3, 6, and 9 months after baseline. Analysis used linear mixed models with repeated measures. During 9 months, participants in the enhanced condition averaged 726 more steps per day compared with those in the standard condition (p < .001). A 1000-step increase in average daily steps was associated with significant weight loss for both men (-3.8 lbs.) and women (-2.1 lbs.), and reductions in body mass index (-0.41 men, -0.31 women). Higher step counts were also associated with improvements in mood, having more energy, and higher ratings of overall health. An enhanced walking program significantly increases participation rates and daily step counts, which were associated with weight loss and reductions in body mass index.

Structural and morphological properties of mesoporous carbon coated molybdenum oxide films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dayal, Saurabh, E-mail: saurabhdayal153@gmail.com; Kumar, C. Sasi, E-mail: csasimv@gmail.com

2016-05-06

In the present study, we report the structural and morphological properties of mesoporous carbon coated molybdenum oxide films. The deposition of films was carried out in a two-step process, the first step involves deposition of molybdenum and carbon bilayer thin films using DC magnetron sputtering. In the second step the sample was ex-situ annealed in a muffle furnace at different temperatures (400°C to 600°C) and air cooled in the ambient atmosphere. The formation of the meso-porous carbon clusters on molybdenum oxide during the cooling step was investigated using FESEM and AFM techniques. The structural details were explored using XRD. Themore » meso-porous carbon were found growing over molybdenum oxide layer as a result of segregation phenomena.« less

Gravitational redshift and asymmetric redshift-space distortions for stacked clusters

NASA Astrophysics Data System (ADS)

Cai, Yan-Chuan; Kaiser, Nick; Cole, Shaun; Frenk, Carlos

2017-06-01

We derive the expression for the observed redshift in the weak field limit in the observer's past light cone, including all relativistic terms up to second order in velocity. We then apply it to compute the cluster-galaxy cross-correlation functions (CGCF) using N-body simulations. The CGCF is asymmetric along the line of sight owing to the presence of the small second-order terms such as the gravitational redshift (GRedshift). We identify two systematics in the modelling of the GRedshift signal in stacked clusters. First, it is affected by the morphology of dark matter haloes and the large-scale cosmic-web. The non-spherical distribution of galaxies around the central halo and the presence of neighbouring clusters systematically reduce the GRedshift signal. This bias is approximately 20 per cent for Mmin ≃ 1014 M⊙ h-1, and is more than 50 per cent for haloes with Mmin ≃ 2 × 1013 M⊙ h-1 at r > 4 Mpc h-1. Secondly, the best-fitting GRedshift profiles as well as the profiles of all other relativistic terms are found to be significantly different in velocity space compared to their real space versions. We find that the relativistic Doppler redshift effect, like other second-order effects, is subdominant to the GRedshift signal. We discuss some subtleties relating to these effects in velocity space. We also find that the S/N of the GRedshift signal increases with decreasing halo mass.

Study of multiband disordered systems using the typical medium dynamical cluster approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yi; Terletska, Hanna; Moore, C.

We generalize the typical medium dynamical cluster approximation to multiband disordered systems. Using our extended formalism, we perform a systematic study of the nonlocal correlation effects induced by disorder on the density of states and the mobility edge of the three-dimensional two-band Anderson model. We include interband and intraband hopping and an intraband disorder potential. Our results are consistent with those obtained by the transfer matrix and the kernel polynomial methods. We also apply the method to K xFe 2-ySe 2 with Fe vacancies. Despite the strong vacancy disorder and anisotropy, we find the material is not an Anderson insulator.more » Moreover our results demonstrate the application of the typical medium dynamical cluster approximation method to study Anderson localization in real materials.« less

Study of multiband disordered systems using the typical medium dynamical cluster approximation

DOE PAGES

Zhang, Yi; Terletska, Hanna; Moore, C.; ...

2015-11-06

We generalize the typical medium dynamical cluster approximation to multiband disordered systems. Using our extended formalism, we perform a systematic study of the nonlocal correlation effects induced by disorder on the density of states and the mobility edge of the three-dimensional two-band Anderson model. We include interband and intraband hopping and an intraband disorder potential. Our results are consistent with those obtained by the transfer matrix and the kernel polynomial methods. We also apply the method to K xFe 2-ySe 2 with Fe vacancies. Despite the strong vacancy disorder and anisotropy, we find the material is not an Anderson insulator.more » Moreover our results demonstrate the application of the typical medium dynamical cluster approximation method to study Anderson localization in real materials.« less

The effect of work-based mentoring on patient outcome in musculoskeletal physiotherapy: study protocol for a randomised controlled trial.

PubMed

Williams, Aled L; Phillips, Ceri J; Watkins, Alan; Rushton, Alison B

2014-10-25

Despite persistent calls to measure the effectiveness of educational interventions on patient outcomes, few studies have been conducted. Within musculoskeletal physiotherapy, the effects of postgraduate clinical mentoring on physiotherapist performance have been assessed, but the impact of this mentoring on patient outcomes remains unknown. The objective of this trial is to assess the effectiveness of a work-based mentoring programme to facilitate physiotherapist clinical reasoning on patient outcomes in musculoskeletal physiotherapy. A stepped wedge cluster randomised controlled trial (CRCT) has been designed to recruit a minimum of 12 senior physiotherapists who work in musculoskeletal outpatient departments of a large National Health Service (NHS) organization. Participating physiotherapists will be randomised by cluster to receive the intervention at three time periods. Patients will be blinded to whether their physiotherapist has received the intervention. The primary outcome measure will be the Patient-Specific Functional Scale; secondary outcome measures will include the EQ-5D, patient activation, patient satisfaction and physiotherapist performance. Sample size considerations used published methods describing stepped wedge designs, conventional values of 0.80 for statistical power and 0.05 for statistical significance, and pragmatic groupings of 12 participating physiotherapists in three clusters. Based on an intergroup difference of 1.0 on the PSFS with a standard deviation of 2.0, 10 patients are required to complete outcome measures per physiotherapist, at time period 1 (prior to intervention roll-out) and at each of time periods 2, 3 and 4, giving a sample size of 480 patients. To account for the potential loss to follow-up of 33%, 720 sets of patient outcomes will be collected.All physiotherapist participants will receive 150 hours of mentored clinical practice as the intervention and usual in-service training as control. Consecutive, consenting patients attending treatment by the participating physiotherapists during data collection periods will complete outcome measures at baseline, discharge and 12 months post-baseline. The lead researcher will be blinded to the allocation of the physiotherapist when analyzing outcome data; statistical analysis will involve classical linear models incorporating both an intervention effect and a random intercept term to reflect systematic differences among clusters. Assigned 31 July 2012: ISRCTN79599220.

Testing the Reliability of Cluster Mass Indicators with a Systematics Limited Dataset

NASA Technical Reports Server (NTRS)

Juett, Adrienne M.; Davis, David S.; Mushotzky, Richard

2009-01-01

We present the mass X-ray observable scaling relationships for clusters of galaxies using the XMM-Newton cluster catalog of Snowden et al. Our results are roughly consistent with previous observational and theoretical work, with one major exception. We find 2-3 times the scatter around the best fit mass scaling relationships as expected from cluster simulations or seen in other observational studies. We suggest that this is a consequence of using hydrostatic mass, as opposed to virial mass, and is due to the explicit dependence of the hydrostatic mass on the gradients of the temperature and gas density profiles. We find a larger range of slope in the cluster temperature profiles at radii 500 than previous observational studies. Additionally, we find only a weak dependence of the gas mass fraction on cluster mass, consistent with a constant. Our average gas mass fraction results also argue for a closer study of the systematic errors due to instrumental calibration and modeling method variations between analyses. We suggest that a more careful study of the differences between various observational results and with cluster simulations is needed to understand sources of bias and scatter in cosmological studies of galaxy clusters.

Interaction of tetraethoxysilane with OH-terminated SiO2 (0 0 1) surface: A first principles study

NASA Astrophysics Data System (ADS)

Deng, Xiaodi; Song, Yixu; Li, Jinchun; Pu, Yikang

2014-06-01

First principles calculates have been performed to investigate the surface reaction mechanism of tetraethoxysilane (TEOS) with fully hydroxylated SiO2(0 0 1) substrate. In semiconductor industry, this is the key step to understand and control the SiO2 film growth in chemical vapor deposition (CVD) and atomic layer deposition (ALD) processes. During the calculation, we proposed a model which breaks the surface dissociative chemisorption into two steps and we calculated the activation barriers and thermochemical energies for each step. Our calculation result for step one shows that the first half reaction is thermodynamically favorable. For the second half reaction, we systematically studied the two potential reaction pathways. The comparing result indicates that the pathway which is more energetically favorable will lead to formation of crystalline SiO2 films while the other will lead to formation of disordered SiO2 films.

Accounting for multiple births in neonatal and perinatal trials: systematic review and case study.

PubMed

Hibbs, Anna Maria; Black, Dennis; Palermo, Lisa; Cnaan, Avital; Luan, Xianqun; Truog, William E; Walsh, Michele C; Ballard, Roberta A

2010-02-01

To determine the prevalence in the neonatal literature of statistical approaches accounting for the unique clustering patterns of multiple births and to explore the sensitivity of an actual trial to several analytic approaches to multiples. A systematic review of recent perinatal trials assessed the prevalence of studies accounting for clustering of multiples. The Nitric Oxide to Prevent Chronic Lung Disease (NO CLD) trial served as a case study of the sensitivity of the outcome to several statistical strategies. We calculated odds ratios using nonclustered (logistic regression) and clustered (generalized estimating equations, multiple outputation) analyses. In the systematic review, most studies did not describe the random assignment of twins and did not account for clustering. Of those studies that did, exclusion of multiples and generalized estimating equations were the most common strategies. The NO CLD study included 84 infants with a sibling enrolled in the study. Multiples were more likely than singletons to be white and were born to older mothers (P < .01). Analyses that accounted for clustering were statistically significant; analyses assuming independence were not. The statistical approach to multiples can influence the odds ratio and width of confidence intervals, thereby affecting the interpretation of a study outcome. A minority of perinatal studies address this issue. Copyright 2010 Mosby, Inc. All rights reserved.

Dark Energy Survey Year 1 Results: Cross-Correlation Redshifts - Methods and Systematics Characterization

DOE PAGES

Gatti, M.

2018-02-22

We use numerical simulations to characterize the performance of a clustering-based method to calibrate photometric redshift biases. In particular, we cross-correlate the weak lensing (WL) source galaxies from the Dark Energy Survey Year 1 (DES Y1) sample with redMaGiC galaxies (luminous red galaxies with secure photometric red- shifts) to estimate the redshift distribution of the former sample. The recovered redshift distributions are used to calibrate the photometric redshift bias of standard photo-z methods applied to the same source galaxy sample. We also apply the method to three photo-z codes run in our simulated data: Bayesian Photometric Redshift (BPZ), Directional Neighborhoodmore » Fitting (DNF), and Random Forest-based photo-z (RF). We characterize the systematic uncertainties of our calibration procedure, and find that these systematic uncertainties dominate our error budget. The dominant systematics are due to our assumption of unevolving bias and clustering across each redshift bin, and to differences between the shapes of the redshift distributions derived by clustering vs photo-z's. The systematic uncertainty in the mean redshift bias of the source galaxy sample is z ≲ 0.02, though the precise value depends on the redshift bin under consideration. Here, we discuss possible ways to mitigate the impact of our dominant systematics in future analyses.« less

Dark Energy Survey Year 1 Results: Cross-Correlation Redshifts - Methods and Systematics Characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gatti, M.

We use numerical simulations to characterize the performance of a clustering-based method to calibrate photometric redshift biases. In particular, we cross-correlate the weak lensing (WL) source galaxies from the Dark Energy Survey Year 1 (DES Y1) sample with redMaGiC galaxies (luminous red galaxies with secure photometric red- shifts) to estimate the redshift distribution of the former sample. The recovered redshift distributions are used to calibrate the photometric redshift bias of standard photo-z methods applied to the same source galaxy sample. We also apply the method to three photo-z codes run in our simulated data: Bayesian Photometric Redshift (BPZ), Directional Neighborhoodmore » Fitting (DNF), and Random Forest-based photo-z (RF). We characterize the systematic uncertainties of our calibration procedure, and find that these systematic uncertainties dominate our error budget. The dominant systematics are due to our assumption of unevolving bias and clustering across each redshift bin, and to differences between the shapes of the redshift distributions derived by clustering vs photo-z's. The systematic uncertainty in the mean redshift bias of the source galaxy sample is z ≲ 0.02, though the precise value depends on the redshift bin under consideration. Here, we discuss possible ways to mitigate the impact of our dominant systematics in future analyses.« less

The stabilization mechanism of titanium cluster

NASA Astrophysics Data System (ADS)

Sun, Houqian; Ren, Yun; Hao, Yuhua; Wu, Zhaofeng; Xu, Ning

2015-05-01

A systematic and comparative theoretical study on the stabilization mechanism of titanium cluster has been performed by selecting the clusters Tin (n=3, 4, 5, 7, 13, 15 and 19) as representatives in the framework of density-functional theory. For small clusters Tin (n=3, 4 and 5), the binding energy gain due to spin polarization is substantially larger than that due to structural distortion. For medium clusters Ti13 and Ti15, both have about the same contribution. For Tin (n=4, 5, 13 and 15), when the undistorted high symmetric structure with spin-polarization is changed into the lowest energy structure, the energy level spelling due to distortion fails to reverse the level order of occupied and unoccupied molecular orbital (MO) of two type spin states, the spin configuration remains unchanged. In spin restricted and undistorted high symmetric structure, d orbitals participate in the hybridization in MOs, usually by way of a less distorted manner, and weak bonds are formed. In contrast, d orbitals take part in the formation of MOs in the ground state structure, usually in a distorted manner, and strong covalent metallic bonds are formed.

Measuring the Redshift Dependence of The Cosmic Microwave Background Monopole Temperature With Planck Data

NASA Technical Reports Server (NTRS)

De Martino, I.; Atrio-Barandela, F.; Da Silva, A.; Ebling, H.; Kashlinsky, A.; Kocevski, D.; Martins, C. J. A. P.

2012-01-01

We study the capability of Planck data to constrain deviations of the cosmic microwave background (CMB) blackbody temperature from adiabatic evolution using the thermal Sunyaev-Zeldovich anisotropy induced by clusters of galaxies. We consider two types of data sets depending on how the cosmological signal is removed: using a CMB template or using the 217 GHz map. We apply two different statistical estimators, based on the ratio of temperature anisotropies at two different frequencies and on a fit to the spectral variation of the cluster signal with frequency. The ratio method is biased if CMB residuals with amplitude approximately 1 microK or larger are present in the data, while residuals are not so critical for the fit method. To test for systematics, we construct a template from clusters drawn from a hydro-simulation included in the pre-launch Planck Sky Model. We demonstrate that, using a proprietary catalog of X-ray-selected clusters with measured redshifts, electron densities, and X-ray temperatures, we can constrain deviations of adiabatic evolution, measured by the parameter a in the redshift scaling T (z) = T0(1 + z)(sup 1-alpha), with an accuracy of sigma(sub alpha) = 0.011 in the most optimal case and with sigma alpha = 0.018 for a less optimal case. These results represent a factor of 2-3 improvement over similar measurements carried out using quasar spectral lines and a factor 6-20 with respect to earlier results using smaller cluster samples.

Oxidation catalysis by polyoxometalates fundamental electron-transfer phenomena

Treesearch

Yurii V. Geletii; Rajai H. Atalla; Alan J. Bailey; Laurent Delannoy; Craig L. Hill; Ira A. Weinstock

2002-01-01

Early transition-metal oxygen-anion clusters (polyoxometalates, POMs) are a large and rapidly growing class of versatile and tunable oxidation catalysts. All key molecular properties of these clusters (composition, size, shape, charge density, reduction potential, solubility, etc.) can be systematically altered, and the clusters themselves can serve as tunable ligands...

A biogenesis step upstream of Microprocessor controls miR-17~92 expression

PubMed Central

Du, Peng; Wang, Longfei; Sliz, Piotr; Gregory, Richard I.

2015-01-01

SUMMARY The precise control of miR-17~92 microRNA (miRNA) is essential for normal development and overexpression of certain miRNAs from this cluster is oncogenic. Here we find the relative expression of the six miRNAs processed from the primary (pri-miR-17~92) transcript is dynamically regulated during embryonic stem cell (ESC) differentiation. Pri-miR-17~92 is processed to a biogenesis intermediate, termed ‘progenitor-miRNA’ (pro-miRNA). Pro-miRNA is an efficient substrate for Microprocessor and is required to selectively license production of pre-miR-17, -18a, -19a, 20a, and -19b from this cluster. Two complementary cis-regulatory repression domains within pri-miR-17~92 are required for the blockade of miRNA processing through the formation of an autoinhibitory RNA conformation. The endonuclease CPSF3 (CPSF73), and the Spliceosome-associated ISY1 are responsible for pro-miRNA biogenesis and expression of all miRNAs within the cluster except miR-92. Thus, developmentally regulated pro-miRNA processing is key step controlling miRNA expression and explains the posttranscriptional control of miR-17~92 expression in development. PMID:26255770

Optimized data fusion for K-means Laplacian clustering

PubMed Central

Yu, Shi; Liu, Xinhai; Tranchevent, Léon-Charles; Glänzel, Wolfgang; Suykens, Johan A. K.; De Moor, Bart; Moreau, Yves

2011-01-01

Motivation: We propose a novel algorithm to combine multiple kernels and Laplacians for clustering analysis. The new algorithm is formulated on a Rayleigh quotient objective function and is solved as a bi-level alternating minimization procedure. Using the proposed algorithm, the coefficients of kernels and Laplacians can be optimized automatically. Results: Three variants of the algorithm are proposed. The performance is systematically validated on two real-life data fusion applications. The proposed Optimized Kernel Laplacian Clustering (OKLC) algorithms perform significantly better than other methods. Moreover, the coefficients of kernels and Laplacians optimized by OKLC show some correlation with the rank of performance of individual data source. Though in our evaluation the K values are predefined, in practical studies, the optimal cluster number can be consistently estimated from the eigenspectrum of the combined kernel Laplacian matrix. Availability: The MATLAB code of algorithms implemented in this paper is downloadable from http://homes.esat.kuleuven.be/~sistawww/bioi/syu/oklc.html. Contact: shiyu@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20980271

A 3D particle Monte Carlo approach to studying nucleation

NASA Astrophysics Data System (ADS)

Köhn, Christoph; Enghoff, Martin Bødker; Svensmark, Henrik

2018-06-01

The nucleation of sulphuric acid molecules plays a key role in the formation of aerosols. We here present a three dimensional particle Monte Carlo model to study the growth of sulphuric acid clusters as well as its dependence on the ambient temperature and the initial particle density. We initiate a swarm of sulphuric acid-water clusters with a size of 0.329 nm with densities between 107 and 108 cm-3 at temperatures between 200 and 300 K and a relative humidity of 50%. After every time step, we update the position of particles as a function of size-dependent diffusion coefficients. If two particles encounter, we merge them and add their volumes and masses. Inversely, we check after every time step whether a polymer evaporates liberating a molecule. We present the spatial distribution as well as the size distribution calculated from individual clusters. We also calculate the nucleation rate of clusters with a radius of 0.85 nm as a function of time, initial particle density and temperature. The nucleation rates obtained from the presented model agree well with experimentally obtained values and those of a numerical model which serves as a benchmark of our code. In contrast to previous nucleation models, we here present for the first time a code capable of tracing individual particles and thus of capturing the physics related to the discrete nature of particles.

Determining the Optimal Number of Clusters with the Clustergram

NASA Technical Reports Server (NTRS)

Fluegemann, Joseph K.; Davies, Misty D.; Aguirre, Nathan D.

2011-01-01

Cluster analysis aids research in many different fields, from business to biology to aerospace. It consists of using statistical techniques to group objects in large sets of data into meaningful classes. However, this process of ordering data points presents much uncertainty because it involves several steps, many of which are subject to researcher judgment as well as inconsistencies depending on the specific data type and research goals. These steps include the method used to cluster the data, the variables on which the cluster analysis will be operating, the number of resulting clusters, and parts of the interpretation process. In most cases, the number of clusters must be guessed or estimated before employing the clustering method. Many remedies have been proposed, but none is unassailable and certainly not for all data types. Thus, the aim of current research for better techniques of determining the number of clusters is generally confined to demonstrating that the new technique excels other methods in performance for several disparate data types. Our research makes use of a new cluster-number-determination technique based on the clustergram: a graph that shows how the number of objects in the cluster and the cluster mean (the ordinate) change with the number of clusters (the abscissa). We use the features of the clustergram to make the best determination of the cluster-number.

Associations between neighbourhood walkability and daily steps in adults: a systematic review and meta-analysis.

PubMed

Hajna, Samantha; Ross, Nancy A; Brazeau, Anne-Sophie; Bélisle, Patrick; Joseph, Lawrence; Dasgupta, Kaberi

2015-08-11

Higher street connectivity, land use mix and residential density (collectively referred to as neighbourhood walkability) have been linked to higher levels of walking. The objective of our study was to summarize the current body of knowledge on the association between neighbourhood walkability and biosensor-assessed daily steps in adults. We conducted a systematic search of PubMed, SCOPUS, and Embase (Ovid) for articles published prior to May 2014 on the association between walkability (based on Geographic Information Systems-derived street connectivity, land use mix, and/or residential density) and daily steps (pedometer or accelerometer-assessed) in adults. The mean differences in daily steps between adults living in high versus low walkable neighbourhoods were pooled across studies using a Bayesian hierarchical model. The search strategy yielded 8,744 unique abstracts. Thirty of these underwent full article review of which six met the inclusion criteria. Four of these studies were conducted in Europe and two were conducted in Asia. A meta-analysis of four of these six studies indicates that participants living in high compared to low walkable neighbourhoods accumulate 766 more steps per day (95 % credible interval 250, 1271). This accounts for approximately 8 % of recommended daily steps. The results of European and Asian studies support the hypothesis that higher neighbourhood walkability is associated with higher levels of biosensor-assessed walking in adults. More studies on this association are needed in North America.

Healthy Steps: a systematic review of a preventive practice-based model of pediatric care.

PubMed

Piotrowski, Caroline C; Talavera, Gregory A; Mayer, Joni A

2009-02-01

The preventive role of anticipatory guidance in pediatric practice has gained increasing importance over the last two decades, resulting in the development of competing models of practice-based care. Our goal was to systematically evaluate and summarize the literature pertaining to the Healthy Steps Program for Young Children, a widely cited and utilized preventive model of care and anticipatory guidance, Medline and the bibliographies of review articles for relevant studies were searched using the keywords: Healthy Steps, preventive care, pediatric practice and others. Other sources included references of retrieved publications, review articles, and books; government documents; and Internet sources. Relevant sources were selected on the basis of their empirical evaluation of some component of care (e.g., child outcomes, parent outcomes, quality of care). From 21 identified articles, 13 met the inclusion criteria of empirical evaluation. These evaluations were summarized and compared. Results indicated that the Healthy Steps program has been rigorously evaluated and shown to be effective in preventing negative child and parent outcomes and enhancing positive outcomes. Despite limited information concerning cost effectiveness, the Healthy Steps Program provides clear benefit through early screening, family-centered care, and evidence-based anticipatory guidance. It is recommended that the Healthy Steps program be more widely disseminated to relevant stakeholders, and further enhanced by improved linguistic and cultural sensitivity and long term evaluation of cost effectiveness.

Stepwise and stagewise approaches for spatial cluster detection

PubMed Central

Xu, Jiale

2016-01-01

Spatial cluster detection is an important tool in many areas such as sociology, botany and public health. Previous work has mostly taken either hypothesis testing framework or Bayesian framework. In this paper, we propose a few approaches under a frequentist variable selection framework for spatial cluster detection. The forward stepwise methods search for multiple clusters by iteratively adding currently most likely cluster while adjusting for the effects of previously identified clusters. The stagewise methods also consist of a series of steps, but with tiny step size in each iteration. We study the features and performances of our proposed methods using simulations on idealized grids or real geographic area. From the simulations, we compare the performance of the proposed methods in terms of estimation accuracy and power of detections. These methods are applied to the the well-known New York leukemia data as well as Indiana poverty data. PMID:27246273

Stepwise and stagewise approaches for spatial cluster detection.

PubMed

Xu, Jiale; Gangnon, Ronald E

2016-05-01

Spatial cluster detection is an important tool in many areas such as sociology, botany and public health. Previous work has mostly taken either a hypothesis testing framework or a Bayesian framework. In this paper, we propose a few approaches under a frequentist variable selection framework for spatial cluster detection. The forward stepwise methods search for multiple clusters by iteratively adding currently most likely cluster while adjusting for the effects of previously identified clusters. The stagewise methods also consist of a series of steps, but with a tiny step size in each iteration. We study the features and performances of our proposed methods using simulations on idealized grids or real geographic areas. From the simulations, we compare the performance of the proposed methods in terms of estimation accuracy and power. These methods are applied to the the well-known New York leukemia data as well as Indiana poverty data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Properties of star clusters - I. Automatic distance and extinction estimates

NASA Astrophysics Data System (ADS)

Buckner, Anne S. M.; Froebrich, Dirk

2013-12-01

Determining star cluster distances is essential to analyse their properties and distribution in the Galaxy. In particular, it is desirable to have a reliable, purely photometric distance estimation method for large samples of newly discovered cluster candidates e.g. from the Two Micron All Sky Survey, the UK Infrared Deep Sky Survey Galactic Plane Survey and VVV. Here, we establish an automatic method to estimate distances and reddening from near-infrared photometry alone, without the use of isochrone fitting. We employ a decontamination procedure of JHK photometry to determine the density of stars foreground to clusters and a galactic model to estimate distances. We then calibrate the method using clusters with known properties. This allows us to establish distance estimates with better than 40 per cent accuracy. We apply our method to determine the extinction and distance values to 378 known open clusters and 397 cluster candidates from the list of Froebrich, Scholz & Raftery. We find that the sample is biased towards clusters of a distance of approximately 3 kpc, with typical distances between 2 and 6 kpc. Using the cluster distances and extinction values, we investigate how the average extinction per kiloparsec distance changes as a function of the Galactic longitude. We find a systematic dependence that can be approximated by AH(l) [mag kpc-1] = 0.10 + 0.001 × |l - 180°|/° for regions more than 60° from the Galactic Centre.

A comparison of three clustering methods for finding subgroups in MRI, SMS or clinical data: SPSS TwoStep Cluster analysis, Latent Gold and SNOB.

PubMed

Kent, Peter; Jensen, Rikke K; Kongsted, Alice

2014-10-02

There are various methodological approaches to identifying clinically important subgroups and one method is to identify clusters of characteristics that differentiate people in cross-sectional and/or longitudinal data using Cluster Analysis (CA) or Latent Class Analysis (LCA). There is a scarcity of head-to-head comparisons that can inform the choice of which clustering method might be suitable for particular clinical datasets and research questions. Therefore, the aim of this study was to perform a head-to-head comparison of three commonly available methods (SPSS TwoStep CA, Latent Gold LCA and SNOB LCA). The performance of these three methods was compared: (i) quantitatively using the number of subgroups detected, the classification probability of individuals into subgroups, the reproducibility of results, and (ii) qualitatively using subjective judgments about each program's ease of use and interpretability of the presentation of results.We analysed five real datasets of varying complexity in a secondary analysis of data from other research projects. Three datasets contained only MRI findings (n = 2,060 to 20,810 vertebral disc levels), one dataset contained only pain intensity data collected for 52 weeks by text (SMS) messaging (n = 1,121 people), and the last dataset contained a range of clinical variables measured in low back pain patients (n = 543 people). Four artificial datasets (n = 1,000 each) containing subgroups of varying complexity were also analysed testing the ability of these clustering methods to detect subgroups and correctly classify individuals when subgroup membership was known. The results from the real clinical datasets indicated that the number of subgroups detected varied, the certainty of classifying individuals into those subgroups varied, the findings had perfect reproducibility, some programs were easier to use and the interpretability of the presentation of their findings also varied. The results from the artificial datasets indicated that all three clustering methods showed a near-perfect ability to detect known subgroups and correctly classify individuals into those subgroups. Our subjective judgement was that Latent Gold offered the best balance of sensitivity to subgroups, ease of use and presentation of results with these datasets but we recognise that different clustering methods may suit other types of data and clinical research questions.

Predicting radiologists' true and false positive decisions in reading mammograms by using gaze parameters and image-based features

NASA Astrophysics Data System (ADS)

Gandomkar, Ziba; Tay, Kevin; Ryder, Will; Brennan, Patrick C.; Mello-Thoms, Claudia

2016-03-01

Radiologists' gaze-related parameters combined with image-based features were utilized to classify suspicious mammographic areas ultimately scored as True Positives (TP) and False Positives (FP). Eight breast radiologists read 120 two-view digital mammograms of which 59 had biopsy proven cancer. Eye tracking data was collected and nearby fixations were clustered together. Suspicious areas on mammograms were independently identified based on thresholding an intensity saliency map followed by automatic segmentation and pruning steps. For each radiologist reported area, radiologist's fixation clusters in the area, as well as neighboring suspicious areas within 2.5° of the center of fixation, were found. A 45-dimensional feature vector containing gaze parameters of the corresponding cluster along with image-based characteristics was constructed. Gaze parameters included total number of fixations in the cluster, dwell time, time to hit the cluster for the first time, maximum number of consecutive fixations, and saccade magnitude of the first fixation in the cluster. Image-based features consisted of intensity, shape, and texture descriptors extracted from the region around the suspicious area, its surrounding tissue, and the entire breast. For each radiologist, a userspecific Support Vector Machine (SVM) model was built to classify the reported areas as TPs or FPs. Leave-one-out cross validation was utilized to avoid over-fitting. A feature selection step was embedded in the SVM training procedure by allowing radial basis function kernels to have 45 scaling factors. The proposed method was compared with the radiologists' performance using the jackknife alternative free-response receiver operating characteristic (JAFROC). The JAFROC figure of merit increased significantly for six radiologists.

Suzaku observations of the outskirts of the galaxy cluster Abell 3395, including a filament toward Abell 3391

NASA Astrophysics Data System (ADS)

Sugawara, Yuuki; Takizawa, Motokazu; Itahana, Madoka; Akamatsu, Hiroki; Fujita, Yutaka; Ohashi, Takaya; Ishisaki, Yoshitaka

2017-12-01

The results of Suzaku observations of the outskirts of Abell 3395, including a large-scale structure filament toward Abell 3391, are presented. We measured temperature and abundance distributions from the southern outskirt of A 3395 to the north at the virial radius, where a filament structure has been found in the former X-ray and Sunyaev-Zel'dovich (SZ) effect observations between A 3391 and A 3395. The overall temperature structure is consistent with the universal profile proposed by Okabe, N., et al. 2014, PASJ, 66, 99 for relaxed clusters, except for the filament region. A hint of intracluster medium heating is found between the two clusters, which might be due to their interaction in the early phase of a cluster merger. Although we obtained a relatively low metal abundance of Z=0.169^{+0.164+0.009+0.018}_{-0.150-0.004-0.015} solar, where the first, second, and third errors are statistical, cosmic X-ray background systematic, and non-X-ray background systematic, respectively, at the virial radius in the filament, our results are still consistent with previous results for other clusters (Z ˜ 0.3 solar) within errors. Therefore, our results are also consistent with the early enrichment scenario. We estimated Compton y parameters only from X-ray results in the region between A 3391 and A 3395 assuming a simple geometry. They are smaller than the previous SZ results with the Planck satellite. The difference could be attributed to a more elaborate geometry such as a filament inclined to the line-of-sight direction, or underestimation of the X-ray temperature because of the unresolved multi-temperature structures or undetected hot X-ray emission of the shock-heated gas.

YSOVAR: The Age of the Cepheus C Star Cluster

NASA Astrophysics Data System (ADS)

Luna, Jessica; Covey, K.; YSOVAR

2014-01-01

We constructed a spectroscopic Hertzsprung-Russell diagram for the Cepheus C (Ceph C) sub-cluster, which we use to generate the first quantitative measurement of this young cluster’s age. Using two TripleSpec spectrographs, on the 3.5m telescope at Apache Point Ob- servatory and the 200” telescope at Palomar Observatory, we obtained near infrared (NIR) spectra for 31 candidate Ceph C members. By comparing our target spectra to a large library of dwarf, sub-giant, and giant star templates, we measured spectral types for candidate Ceph C members ranging from F2 to M2.5. We converted each YSO’s ST into a Teff estimate using the ST to Teff relation recently published by Pecaut et al. (2013). Using our spectroscopically derived extinction estimates to deredden spectral energy distributions constructed from 2MASS and Spitzer photometry, we measured each YSO’s bolometric luminosity. Placing each candidate Ceph C member on an HR Dia- gram, we used Dartmouth pre-main sequence evolutionary tracks to estimate the mass and age of each YSO. We measure a median stellar age for the Ceph C cluster of ˜10 Myrs or less. We also detect a large systematic effect in our ages, however, such that cooler, low mass mem- bers have substantially smaller inferred ages than their higher mass counterparts. We are working to understand the root cause of this systematic effect, but this first estimate of Ceph C’s age will advance our understanding of the cluster’s relationship to other sub clusters in Cepheus, and place the Ceph C cluster in context among other local star forming regions. This research was funded by the NSF through grant number AST-1004107.

HICOSMO: cosmology with a complete sample of galaxy clusters - II. Cosmological results

NASA Astrophysics Data System (ADS)

Schellenberger, G.; Reiprich, T. H.

2017-10-01

The X-ray bright, hot gas in the potential well of a galaxy cluster enables systematic X-ray studies of samples of galaxy clusters to constrain cosmological parameters. HIFLUGCS consists of the 64 X-ray brightest galaxy clusters in the Universe, building up a local sample. Here, we utilize this sample to determine, for the first time, individual hydrostatic mass estimates for all the clusters of the sample and, by making use of the completeness of the sample, we quantify constraints on the two interesting cosmological parameters, Ωm and σ8. We apply our total hydrostatic and gas mass estimates from the X-ray analysis to a Bayesian cosmological likelihood analysis and leave several parameters free to be constrained. We find Ωm = 0.30 ± 0.01 and σ8 = 0.79 ± 0.03 (statistical uncertainties, 68 per cent credibility level) using our default analysis strategy combining both a mass function analysis and the gas mass fraction results. The main sources of biases that we correct here are (1) the influence of galaxy groups (incompleteness in parent samples and differing behaviour of the Lx-M relation), (2) the hydrostatic mass bias, (3) the extrapolation of the total mass (comparing various methods), (4) the theoretical halo mass function and (5) other physical effects (non-negligible neutrino mass). We find that galaxy groups introduce a strong bias, since their number density seems to be over predicted by the halo mass function. On the other hand, incorporating baryonic effects does not result in a significant change in the constraints. The total (uncorrected) systematic uncertainties (∼20 per cent) clearly dominate the statistical uncertainties on cosmological parameters for our sample.

Dispersed or clustered housing for adults with intellectual disability: a systematic review.

PubMed

Mansell, Jim; Beadle-Brown, Julie

2009-12-01

The purpose of this review was to evaluate the available research on the quality and costs of dispersed community-based housing when compared with clustered housing. Searches against specified criteria yielded 19 papers based on 10 studies presenting data comparing dispersed housing with some kind of clustered housing (village communities, residential campuses, or clusters of houses). The studies reported the experience of nearly 2,500 people from four different countries. In five of eight quality of life domains there were no studies reporting benefits of clustered settings. In respect of interpersonal relations, emotional, and physical well-being, clustered settings had some advantages. However, in many of these cases the better results refer only to village communities and not to campus housing or clustered housing. In terms of costs, clustered housing was usually less expensive because of lower staffing levels. In two of the three studies that examined costs controlling for user characteristics, there was no statistically significant difference. Dispersed housing appears to be superior to clustered housing on the majority of quality indicators studied. The only exception to this is that village communities for people with less severe disabilities have some benefits; this is not, however, a model which can be feasibly provided for everyone. Clustered housing is usually less expensive than dispersed housing but this is because it provides fewer staff hours per person. There is no evidence that clustered housing can deliver the same quality of life as dispersed housing at a lower cost.

Phenotypes Determined by Cluster Analysis in Moderate to Severe Bronchial Asthma.

PubMed

Youroukova, Vania M; Dimitrova, Denitsa G; Valerieva, Anna D; Lesichkova, Spaska S; Velikova, Tsvetelina V; Ivanova-Todorova, Ekaterina I; Tumangelova-Yuzeir, Kalina D

2017-06-01

Bronchial asthma is a heterogeneous disease that includes various subtypes. They may share similar clinical characteristics, but probably have different pathological mechanisms. To identify phenotypes using cluster analysis in moderate to severe bronchial asthma and to compare differences in clinical, physiological, immunological and inflammatory data between the clusters. Forty adult patients with moderate to severe bronchial asthma out of exacerbation were included. All underwent clinical assessment, anthropometric measurements, skin prick testing, standard spirometry and measurement fraction of exhaled nitric oxide. Blood eosinophilic count, serum total IgE and periostin levels were determined. Two-step cluster approach, hierarchical clustering method and k-mean analysis were used for identification of the clusters. We have identified four clusters. Cluster 1 (n=14) - late-onset, non-atopic asthma with impaired lung function, Cluster 2 (n=13) - late-onset, atopic asthma, Cluster 3 (n=6) - late-onset, aspirin sensitivity, eosinophilic asthma, and Cluster 4 (n=7) - early-onset, atopic asthma. Our study is the first in Bulgaria in which cluster analysis is applied to asthmatic patients. We identified four clusters. The variables with greatest force for differentiation in our study were: age of asthma onset, duration of diseases, atopy, smoking, blood eosinophils, nonsteroidal anti-inflammatory drugs hypersensitivity, baseline FEV1/FVC and symptoms severity. Our results support the concept of heterogeneity of bronchial asthma and demonstrate that cluster analysis can be an useful tool for phenotyping of disease and personalized approach to the treatment of patients.

User’s guide for GcClust—An R package for clustering of regional geochemical data

USGS Publications Warehouse

Ellefsen, Karl J.; Smith, David B.

2016-04-08

GcClust is a software package developed by the U.S. Geological Survey for statistical clustering of regional geochemical data, and similar data such as regional mineralogical data. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of the user’s guide are bundled together in R’s unit of sharable code, which is called a “package.” The user’s guide includes step-by-step instructions showing how the functions are used to cluster data and to evaluate the clustering results. These functions are demonstrated in this report using test data, which are included in the package.

Comparison of Poisson and Bernoulli spatial cluster analyses of pediatric injuries in a fire district

PubMed Central

Warden, Craig R

2008-01-01

Background With limited resources available, injury prevention efforts need to be targeted both geographically and to specific populations. As part of a pediatric injury prevention project, data was obtained on all pediatric medical and injury incidents in a fire district to evaluate geographical clustering of pediatric injuries. This will be the first step in attempting to prevent these injuries with specific interventions depending on locations and mechanisms. Results There were a total of 4803 incidents involving patients less than 15 years of age that the fire district responded to during 2001–2005 of which 1997 were categorized as injuries and 2806 as medical calls. The two cohorts (injured versus medical) differed in age distribution (7.7 ± 4.4 years versus 5.4 ± 4.8 years, p < 0.001) and location type of incident (school or church 12% versus 15%, multifamily residence 22% versus 13%, single family residence 51% versus 28%, sport, park or recreational facility 3% versus 8%, public building 8% versus 7%, and street or road 3% versus 30%, respectively, p < 0.001). Using the medical incident locations as controls, there was no significant clustering for environmental or assault injuries using the Bernoulli method while there were four significant clusters for all injury mechanisms combined, 13 clusters for motor vehicle collisions, one for falls, and two for pedestrian or bicycle injuries. Using the Poisson cluster method on incidence rates by census tract identified four clusters for all injuries, three for motor vehicle collisions, four for fall injuries, and one each for environmental and assault injuries. The two detection methods shared a minority of overlapping geographical clusters. Conclusion Significant clustering occurs overall for all injury mechanisms combined and for each mechanism depending on the cluster detection method used. There was some overlap in geographic clusters identified by both methods. The Bernoulli method allows more focused cluster mapping and evaluation since it directly uses location data. Once clusters are found, interventions can be targeted to specific geographic locations, location types, ages of victims, and mechanisms of injury. PMID:18808720

The Cluster Environment of Two High-mass Protostars

NASA Astrophysics Data System (ADS)

Montes, Virginie; Hofner, Peter

2017-06-01

Characterizing the environment and stellar population in which high-mass stars form is an important step to decide between the main massive star formation theories. In the monolithic collapse model, the mass of the core will determine the final stellar mass (e.g., McKee & Tan 2003). In contrast, in the competitive accretion model (e.g., Bonnell & Bate 2006), the mass of the high-mass star is related to the properties of the cluster. As dynamical processes substantially affect the appearance of a cluster, we study early stages of high-mass star formation. These regions often show extended emission from hot dust at infrared wavelengths, which can cause difficulties to define the cluster. We use a multi-wavelength technique to study nearby high-mass star clusters, based on X-ray observations with the Chandra X-Ray Telescope, in conjunction with infrared data and VLA data. The technique relies on the fact that YSOs are particularly bright in X-ray and that contamination is relatively small. X-ray observations allow us to determine the cluster size. The cluster membership and YSOs classification is established using infrared identification of the X-ray sources, and color-color and color-magnitude diagrams.In this talk, I will present our findings on the cluster study of two high-mass star forming regions: IRAS 20126+4104 and IRAS 16562-3959. While most massive stars appear to be formed in rich a cluster environment, those two sources are candidates for the formation of massive stars in a relatively poor cluster. In contrast to what was found in previous studies (Qiu et al. 2008), the dominant B0-type protostar in IRAS 20126+4104 is associated with a small cluster of low-mass stars. I will also show our current work on IRAS 16562-3959, which contains one of the most luminous O-type protostars in the Galaxy. In the vicinity of this particularly interesting region there is a multitude of small clusters, for which I will present how their stellar population differ from the high-mass star-forming cluster IRAS 16562-3959.

Comparison of Poisson and Bernoulli spatial cluster analyses of pediatric injuries in a fire district.

PubMed

Warden, Craig R

2008-09-22

With limited resources available, injury prevention efforts need to be targeted both geographically and to specific populations. As part of a pediatric injury prevention project, data was obtained on all pediatric medical and injury incidents in a fire district to evaluate geographical clustering of pediatric injuries. This will be the first step in attempting to prevent these injuries with specific interventions depending on locations and mechanisms. There were a total of 4803 incidents involving patients less than 15 years of age that the fire district responded to during 2001-2005 of which 1997 were categorized as injuries and 2806 as medical calls. The two cohorts (injured versus medical) differed in age distribution (7.7 +/- 4.4 years versus 5.4 +/- 4.8 years, p < 0.001) and location type of incident (school or church 12% versus 15%, multifamily residence 22% versus 13%, single family residence 51% versus 28%, sport, park or recreational facility 3% versus 8%, public building 8% versus 7%, and street or road 3% versus 30%, respectively, p < 0.001). Using the medical incident locations as controls, there was no significant clustering for environmental or assault injuries using the Bernoulli method while there were four significant clusters for all injury mechanisms combined, 13 clusters for motor vehicle collisions, one for falls, and two for pedestrian or bicycle injuries. Using the Poisson cluster method on incidence rates by census tract identified four clusters for all injuries, three for motor vehicle collisions, four for fall injuries, and one each for environmental and assault injuries. The two detection methods shared a minority of overlapping geographical clusters. Significant clustering occurs overall for all injury mechanisms combined and for each mechanism depending on the cluster detection method used. There was some overlap in geographic clusters identified by both methods. The Bernoulli method allows more focused cluster mapping and evaluation since it directly uses location data. Once clusters are found, interventions can be targeted to specific geographic locations, location types, ages of victims, and mechanisms of injury.

Mapping cellular Fe-S cluster uptake and exchange reactions - divergent pathways for iron-sulfur cluster delivery to human ferredoxins.

PubMed

Fidai, Insiya; Wachnowsky, Christine; Cowan, J A

2016-12-07

Ferredoxins are protein mediators of biological electron-transfer reactions and typically contain either [2Fe-2S] or [4Fe-4S] clusters. Two ferredoxin homologues have been identified in the human genome, Fdx1 and Fdx2, that share 43% identity and 69% similarity in protein sequence and both bind [2Fe-2S] clusters. Despite the high similarity, the two ferredoxins play very specific roles in distinct physiological pathways and cannot replace each other in function. Both eukaryotic and prokaryotic ferredoxins and homologues have been reported to receive their Fe-S cluster from scaffold/delivery proteins such as IscU, Isa, glutaredoxins, and Nfu. However, the preferred and physiologically relevant pathway for receiving the [2Fe-2S] cluster by ferredoxins is subject to speculation and is not clearly identified. In this work, we report on in vitro UV-visible (UV-vis) circular dichroism studies of [2Fe-2S] cluster transfer to the ferredoxins from a variety of partners. The results reveal rapid and quantitative transfer to both ferredoxins from several donor proteins (IscU, Isa1, Grx2, and Grx3). Transfer from Isa1 to Fdx2 was also observed to be faster than that of IscU to Fdx2, suggesting that Fdx2 could receive its cluster from Isa1 instead of IscU. Several other transfer combinations were also investigated and the results suggest a complex, but kinetically detailed map for cellular cluster trafficking. This is the first step toward building a network map for all of the possible iron-sulfur cluster transfer pathways in the mitochondria and cytosol, providing insights on the most likely cellular pathways and possible redundancies in these pathways.

Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Panchao; Wu, Bin; Li, Tao

A 2.9 nm molybdenum oxide cluster {Mo 132} (Formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH 3COOH/CH 3COO- buffers. This reaction has been monitored by time-resolved UV-Vis, 1H-NMR, small angle X-ray/neutron scattering, and X-ray absorption near edge structure spectroscopy. The growth of {Mo 132} cluster shows a typical sigmoid curve, suggesting a multi-step assembly mechanism for this reaction. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordinationmore » effect of the acetate groups. Once the concentration of {Mo V 2(acetate)} reaches a critical value, it triggers the assembly of Mo V and Mo VI species into {Mo 132} clusters. Parameters such as the type and amount of reducing agent, the pH, the type of cation, and the type of organic ligand in the reaction buffer, have been studied for the roles they play in the formation of the target clusters.Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo 132} (formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {Mo V 2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value, it triggers the co-assembly of Mo V and Mo VI species into the giant clusters.« less

Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters

DOE PAGES

Yin, Panchao; Wu, Bin; Li, Tao; ...

2016-07-26

A 2.9 nm molybdenum oxide cluster {Mo 132} (Formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH 3COOH/CH 3COO- buffers. This reaction has been monitored by time-resolved UV-Vis, 1H-NMR, small angle X-ray/neutron scattering, and X-ray absorption near edge structure spectroscopy. The growth of {Mo 132} cluster shows a typical sigmoid curve, suggesting a multi-step assembly mechanism for this reaction. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordinationmore » effect of the acetate groups. Once the concentration of {Mo V 2(acetate)} reaches a critical value, it triggers the assembly of Mo V and Mo VI species into {Mo 132} clusters. Parameters such as the type and amount of reducing agent, the pH, the type of cation, and the type of organic ligand in the reaction buffer, have been studied for the roles they play in the formation of the target clusters.Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo 132} (formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {Mo V 2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value, it triggers the co-assembly of Mo V and Mo VI species into the giant clusters.« less

The added value of a mobile application of Community Case Management on referral, re-consultation and hospitalization rates of children aged under 5 years in two districts in Northern Malawi: study protocol for a pragmatic, stepped-wedge cluster-randomized controlled trial.

PubMed

Hardy, Victoria; O'Connor, Yvonne; Heavin, Ciara; Mastellos, Nikolaos; Tran, Tammy; O'Donoghue, John; Fitzpatrick, Annette L; Ide, Nicole; Wu, Tsung-Shu Joseph; Chirambo, Griphin Baxter; Muula, Adamson S; Nyirenda, Moffat; Carlsson, Sven; Andersson, Bo; Thompson, Matthew

2017-10-11

There is evidence to suggest that frontline community health workers in Malawi are under-referring children to higher-level facilities. Integrating a digitized version of paper-based methods of Community Case Management (CCM) could strengthen delivery, increasing urgent referral rates and preventing unnecessary re-consultations and hospital admissions. This trial aims to evaluate the added value of the Supporting LIFE electronic Community Case Management Application (SL eCCM App) compared to paper-based CCM on urgent referral, re-consultation and hospitalization rates, in two districts in Northern Malawi. This is a pragmatic, stepped-wedge cluster-randomized trial assessing the added value of the SL eCCM App on urgent referral, re-consultation and hospitalization rates of children aged 2 months and older to up to 5 years, within 7 days of the index visit. One hundred and two health surveillance assistants (HSAs) were stratified into six clusters based on geographical location, and clusters randomized to the timing of crossover to the intervention using simple, computer-generated randomization. Training workshops were conducted prior to the control (paper-CCM) and intervention (paper-CCM + SL eCCM App) in assigned clusters. Neither participants nor study personnel were blinded to allocation. Outcome measures were determined by abstraction of clinical data from patient records 2 weeks after recruitment. A nested qualitative study explored perceptions of adherence to urgent referral recommendations and a cost evaluation determined the financial and time-related costs to caregivers of subsequent health care utilization. The trial was conducted between July 2016 and February 2017. This is the first large-scale trial evaluating the value of adding a mobile application of CCM to the assessment of children aged under 5 years. The trial will generate evidence on the potential use of mobile health for CCM in Malawi, and more widely in other low- and middle-income countries. ClinicalTrials.gov, ID: NCT02763345 . Registered on 3 May 2016.

Effectiveness of a two-step population-based osteoporosis screening program using FRAX: the randomized Risk-stratified Osteoporosis Strategy Evaluation (ROSE) study.

PubMed

Rubin, K H; Rothmann, M J; Holmberg, T; Høiberg, M; Möller, S; Barkmann, R; Glüer, C C; Hermann, A P; Bech, M; Gram, J; Brixen, K

2018-03-01

The Risk-stratified Osteoporosis Strategy Evaluation (ROSE) study investigated the effectiveness of a two-step screening program for osteoporosis in women. We found no overall reduction in fractures from systematic screening compared to the current case-finding strategy. The group of moderate- to high-risk women, who accepted the invitation to DXA, seemed to benefit from the program. The purpose of the ROSE study was to investigate the effectiveness of a two-step population-based osteoporosis screening program using the Fracture Risk Assessment Tool (FRAX) derived from a self-administered questionnaire to select women for DXA scan. After the scanning, standard osteoporosis management according to Danish national guidelines was followed. Participants were randomized to either screening or control group, and randomization was stratified according to age and area of residence. Inclusion took place from February 2010 to November 2011. Participants received a self-administered questionnaire, and women in the screening group with a FRAX score ≥ 15% (major osteoporotic fractures) were invited to a DXA scan. Primary outcome was incident clinical fractures. Intention-to-treat analysis and two per-protocol analyses were performed. A total of 3416 fractures were observed during a median follow-up of 5 years. No significant differences were found in the intention-to-treat analyses with 34,229 women included aged 65-80 years. The per-protocol analyses showed a risk reduction in the group that underwent DXA scanning compared to women in the control group with a FRAX ≥ 15%, in regard to major osteoporotic fractures, hip fractures, and all fractures. The risk reduction was most pronounced for hip fractures (adjusted SHR 0.741, p = 0.007). Compared to an office-based case-finding strategy, the two-step systematic screening strategy had no overall effect on fracture incidence. The two-step strategy seemed, however, to be beneficial in the group of women who were identified by FRAX as moderate- or high-risk patients and complied with DXA.

Mapping and simulating systematics due to spatially-varying observing conditions in DES science verification data

DOE PAGES

Leistedt, B.; Peiris, H. V.; Elsner, F.; ...

2016-10-17

Spatially-varying depth and characteristics of observing conditions, such as seeing, airmass, or sky background, are major sources of systematic uncertainties in modern galaxy survey analyses, in particular in deep multi-epoch surveys. We present a framework to extract and project these sources of systematics onto the sky, and apply it to the Dark Energy Survey (DES) to map the observing conditions of the Science Verification (SV) data. The resulting distributions and maps of sources of systematics are used in several analyses of DES SV to perform detailed null tests with the data, and also to incorporate systematics in survey simulations. Wemore » illustrate the complementarity of these two approaches by comparing the SV data with the BCC-UFig, a synthetic sky catalogue generated by forward-modelling of the DES SV images. We then analyse the BCC-UFig simulation to construct galaxy samples mimicking those used in SV galaxy clustering studies. We show that the spatially-varying survey depth imprinted in the observed galaxy densities and the redshift distributions of the SV data are successfully reproduced by the simulation and well-captured by the maps of observing conditions. The combined use of the maps, the SV data and the BCC-UFig simulation allows us to quantify the impact of spatial systematics on N(z), the redshift distributions inferred using photometric redshifts. We conclude that spatial systematics in the SV data are mainly due to seeing fluctuations and are under control in current clustering and weak lensing analyses. However, they will need to be carefully characterised in upcoming phases of DES in order to avoid biasing the inferred cosmological results. The framework presented is relevant to all multi-epoch surveys, and will be essential for exploiting future surveys such as the Large Synoptic Survey Telescope, which will require detailed null-tests and realistic end-to-end image simulations to correctly interpret the deep, high-cadence observations of the sky.« less

MAPPING AND SIMULATING SYSTEMATICS DUE TO SPATIALLY VARYING OBSERVING CONDITIONS IN DES SCIENCE VERIFICATION DATA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leistedt, B.; Peiris, H. V.; Elsner, F.

Spatially varying depth and the characteristics of observing conditions, such as seeing, airmass, or sky background, are major sources of systematic uncertainties in modern galaxy survey analyses, particularly in deep multi-epoch surveys. We present a framework to extract and project these sources of systematics onto the sky, and apply it to the Dark Energy Survey (DES) to map the observing conditions of the Science Verification (SV) data. The resulting distributions and maps of sources of systematics are used in several analyses of DES-SV to perform detailed null tests with the data, and also to incorporate systematics in survey simulations. Wemore » illustrate the complementary nature of these two approaches by comparing the SV data with BCC-UFig, a synthetic sky catalog generated by forward-modeling of the DES-SV images. We analyze the BCC-UFig simulation to construct galaxy samples mimicking those used in SV galaxy clustering studies. We show that the spatially varying survey depth imprinted in the observed galaxy densities and the redshift distributions of the SV data are successfully reproduced by the simulation and are well-captured by the maps of observing conditions. The combined use of the maps, the SV data, and the BCC-UFig simulation allows us to quantify the impact of spatial systematics on N(z), the redshift distributions inferred using photometric redshifts. We conclude that spatial systematics in the SV data are mainly due to seeing fluctuations and are under control in current clustering and weak-lensing analyses. However, they will need to be carefully characterized in upcoming phases of DES in order to avoid biasing the inferred cosmological results. The framework presented here is relevant to all multi-epoch surveys and will be essential for exploiting future surveys such as the Large Synoptic Survey Telescope, which will require detailed null tests and realistic end-to-end image simulations to correctly interpret the deep, high-cadence observations of the sky« less

Mapping and simulating systematics due to spatially-varying observing conditions in DES science verification data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leistedt, B.; Peiris, H. V.; Elsner, F.

Spatially-varying depth and characteristics of observing conditions, such as seeing, airmass, or sky background, are major sources of systematic uncertainties in modern galaxy survey analyses, in particular in deep multi-epoch surveys. We present a framework to extract and project these sources of systematics onto the sky, and apply it to the Dark Energy Survey (DES) to map the observing conditions of the Science Verification (SV) data. The resulting distributions and maps of sources of systematics are used in several analyses of DES SV to perform detailed null tests with the data, and also to incorporate systematics in survey simulations. Wemore » illustrate the complementarity of these two approaches by comparing the SV data with the BCC-UFig, a synthetic sky catalogue generated by forward-modelling of the DES SV images. We then analyse the BCC-UFig simulation to construct galaxy samples mimicking those used in SV galaxy clustering studies. We show that the spatially-varying survey depth imprinted in the observed galaxy densities and the redshift distributions of the SV data are successfully reproduced by the simulation and well-captured by the maps of observing conditions. The combined use of the maps, the SV data and the BCC-UFig simulation allows us to quantify the impact of spatial systematics on N(z), the redshift distributions inferred using photometric redshifts. We conclude that spatial systematics in the SV data are mainly due to seeing fluctuations and are under control in current clustering and weak lensing analyses. However, they will need to be carefully characterised in upcoming phases of DES in order to avoid biasing the inferred cosmological results. The framework presented is relevant to all multi-epoch surveys, and will be essential for exploiting future surveys such as the Large Synoptic Survey Telescope, which will require detailed null-tests and realistic end-to-end image simulations to correctly interpret the deep, high-cadence observations of the sky.« less

iso-Migrastatin, migrastatin, and dorrigocin production in Streptomyces platensis NRRL 18993 is governed by a single biosynthetic machinery featuring an acyltransferase-less type I polyketide synthase.

PubMed

Lim, Si-Kyu; Ju, Jianhua; Zazopoulos, Emmanuel; Jiang, Hui; Seo, Jeong-Woo; Chen, Yihua; Feng, Zhiyang; Rajski, Scott R; Farnet, Chris M; Shen, Ben

2009-10-23

iso-Migrastatin and related glutarimide-containing polyketides are potent inhibitors of tumor cell migration and their implied potential as antimetastatic agents for human cancers has garnered significant attention. Genome scanning of Streptomyces platensis NRRL 18993 unveiled two candidate gene clusters (088D and mgs); each encodes acyltransferase-less type I polyketide synthases commensurate with iso-migrastatin biosynthesis. Both clusters were inactivated by lambda-RED-mediated PCR-targeting mutagenesis in S. platensis; iso-migrastatin production was completely abolished in the DeltamgsF mutant SB11012 strain, whereas inactivation of 088D-orf7 yielded the SB11006 strain that exhibited no discernible change in iso-migrastatin biosynthesis. These data indicate that iso-migrastatin production is governed by the mgs cluster. Systematic gene inactivation allowed determination of the precise boundaries of the mgs cluster and the essentiality of the genes within the mgs cluster in iso-migrastatin production. The mgs cluster consists of 11 open reading frames that encode three acyltransferase-less type I polyketide synthases (MgsEFG), one discrete acyltransferase (MgsH), a type II thioesterase (MgsB), three post-PKS tailoring enzymes (MgsIJK), two glutarimide biosynthesis enzymes (MgsCD), and one regulatory protein (MgsA). A model for iso-migrastatin biosynthesis is proposed based on functional assignments derived from bioinformatics and is further supported by the results of in vivo gene inactivation experiments.

iso-Migrastatin, Migrastatin, and Dorrigocin Production in Streptomyces platensis NRRL 18993 Is Governed by a Single Biosynthetic Machinery Featuring an Acyltransferase-less Type I Polyketide Synthase*

PubMed Central

Lim, Si-Kyu; Ju, Jianhua; Zazopoulos, Emmanuel; Jiang, Hui; Seo, Jeong-Woo; Chen, Yihua; Feng, Zhiyang; Rajski, Scott R.; Farnet, Chris M.; Shen, Ben

2009-01-01

iso-Migrastatin and related glutarimide-containing polyketides are potent inhibitors of tumor cell migration and their implied potential as antimetastatic agents for human cancers has garnered significant attention. Genome scanning of Streptomyces platensis NRRL 18993 unveiled two candidate gene clusters (088D and mgs); each encodes acyltransferase-less type I polyketide synthases commensurate with iso-migrastatin biosynthesis. Both clusters were inactivated by λ-RED-mediated PCR-targeting mutagenesis in S. platensis; iso-migrastatin production was completely abolished in the ΔmgsF mutant SB11012 strain, whereas inactivation of 088D-orf7 yielded the SB11006 strain that exhibited no discernible change in iso-migrastatin biosynthesis. These data indicate that iso-migrastatin production is governed by the mgs cluster. Systematic gene inactivation allowed determination of the precise boundaries of the mgs cluster and the essentiality of the genes within the mgs cluster in iso-migrastatin production. The mgs cluster consists of 11 open reading frames that encode three acyltransferase-less type I polyketide synthases (MgsEFG), one discrete acyltransferase (MgsH), a type II thioesterase (MgsB), three post-PKS tailoring enzymes (MgsIJK), two glutarimide biosynthesis enzymes (MgsCD), and one regulatory protein (MgsA). A model for iso-migrastatin biosynthesis is proposed based on functional assignments derived from bioinformatics and is further supported by the results of in vivo gene inactivation experiments. PMID:19726666

Biosynthesis of actinorhodin and related antibiotics: discovery of alternative routes for quinone formation encoded in the act gene cluster.

PubMed

Okamoto, Susumu; Taguchi, Takaaki; Ochi, Kozo; Ichinose, Koji

2009-02-27

All known benzoisochromanequinone (BIQ) biosynthetic gene clusters carry a set of genes encoding a two-component monooxygenase homologous to the ActVA-ORF5/ActVB system for actinorhodin biosynthesis in Streptomyces coelicolor A3(2). Here, we conducted molecular genetic and biochemical studies of this enzyme system. Inactivation of actVA-ORF5 yielded a shunt product, actinoperylone (ACPL), apparently derived from 6-deoxy-dihydrokalafungin. Similarly, deletion of actVB resulted in accumulation of ACPL, indicating a critical role for the monooxygenase system in C-6 oxygenation, a biosynthetic step common to all BIQ biosyntheses. Furthermore, in vitro, we showed a quinone-forming activity of the ActVA-ORF5/ActVB system in addition to that of a known C-6 monooxygenase, ActVA-ORF6, by using emodinanthrone as a model substrate. Our results demonstrate that the act gene cluster encodes two alternative routes for quinone formation by C-6 oxygenation in BIQ biosynthesis.

Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence.

PubMed

Barczak, Amy K; Avraham, Roi; Singh, Shantanu; Luo, Samantha S; Zhang, Wei Ran; Bray, Mark-Anthony; Hinman, Amelia E; Thompson, Matthew; Nietupski, Raymond M; Golas, Aaron; Montgomery, Paul; Fitzgerald, Michael; Smith, Roger S; White, Dylan W; Tischler, Anna D; Carpenter, Anne E; Hung, Deborah T

2017-05-01

A key to the pathogenic success of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the capacity to survive within host macrophages. Although several factors required for this survival have been identified, a comprehensive knowledge of such factors and how they work together to manipulate the host environment to benefit bacterial survival are not well understood. To systematically identify Mtb factors required for intracellular growth, we screened an arrayed, non-redundant Mtb transposon mutant library by high-content imaging to characterize the mutant-macrophage interaction. Based on a combination of imaging features, we identified mutants impaired for intracellular survival. We then characterized the phenotype of infection with each mutant by profiling the induced macrophage cytokine response. Taking a systems-level approach to understanding the biology of identified mutants, we performed a multiparametric analysis combining pathogen and host phenotypes to predict functional relationships between mutants based on clustering. Strikingly, mutants defective in two well-known virulence factors, the ESX-1 protein secretion system and the virulence lipid phthiocerol dimycocerosate (PDIM), clustered together. Building upon the shared phenotype of loss of the macrophage type I interferon (IFN) response to infection, we found that PDIM production and export are required for coordinated secretion of ESX-1-substrates, for phagosomal permeabilization, and for downstream induction of the type I IFN response. Multiparametric clustering also identified two novel genes that are required for PDIM production and induction of the type I IFN response. Thus, multiparametric analysis combining host and pathogen infection phenotypes can be used to identify novel functional relationships between genes that play a role in infection.

Text mining to decipher free-response consumer complaints: insights from the NHTSA vehicle owner's complaint database.

PubMed

Ghazizadeh, Mahtab; McDonald, Anthony D; Lee, John D

2014-09-01

This study applies text mining to extract clusters of vehicle problems and associated trends from free-response data in the National Highway Traffic Safety Administration's vehicle owner's complaint database. As the automotive industry adopts new technologies, it is important to systematically assess the effect of these changes on traffic safety. Driving simulators, naturalistic driving data, and crash databases all contribute to a better understanding of how drivers respond to changing vehicle technology, but other approaches, such as automated analysis of incident reports, are needed. Free-response data from incidents representing two severity levels (fatal incidents and incidents involving injury) were analyzed using a text mining approach: latent semantic analysis (LSA). LSA and hierarchical clustering identified clusters of complaints for each severity level, which were compared and analyzed across time. Cluster analysis identified eight clusters of fatal incidents and six clusters of incidents involving injury. Comparisons showed that although the airbag clusters across the two severity levels have the same most frequent terms, the circumstances around the incidents differ. The time trends show clear increases in complaints surrounding the Ford/Firestone tire recall and the Toyota unintended acceleration recall. Increases in complaints may be partially driven by these recall announcements and the associated media attention. Text mining can reveal useful information from free-response databases that would otherwise be prohibitively time-consuming and difficult to summarize manually. Text mining can extend human analysis capabilities for large free-response databases to support earlier detection of problems and more timely safety interventions.

Towards a methodology for cluster searching to provide conceptual and contextual "richness" for systematic reviews of complex interventions: case study (CLUSTER).

PubMed

Booth, Andrew; Harris, Janet; Croot, Elizabeth; Springett, Jane; Campbell, Fiona; Wilkins, Emma

2013-09-28

Systematic review methodologies can be harnessed to help researchers to understand and explain how complex interventions may work. Typically, when reviewing complex interventions, a review team will seek to understand the theories that underpin an intervention and the specific context for that intervention. A single published report from a research project does not typically contain this required level of detail. A review team may find it more useful to examine a "study cluster"; a group of related papers that explore and explain various features of a single project and thus supply necessary detail relating to theory and/or context.We sought to conduct a preliminary investigation, from a single case study review, of techniques required to identify a cluster of related research reports, to document the yield from such methods, and to outline a systematic methodology for cluster searching. In a systematic review of community engagement we identified a relevant project - the Gay Men's Task Force. From a single "key pearl citation" we conducted a series of related searches to find contextually or theoretically proximate documents. We followed up Citations, traced Lead authors, identified Unpublished materials, searched Google Scholar, tracked Theories, undertook ancestry searching for Early examples and followed up Related projects (embodied in the CLUSTER mnemonic). Our structured, formalised procedure for cluster searching identified useful reports that are not typically identified from topic-based searches on bibliographic databases. Items previously rejected by an initial sift were subsequently found to inform our understanding of underpinning theory (for example Diffusion of Innovations Theory), context or both. Relevant material included book chapters, a Web-based process evaluation, and peer reviewed reports of projects sharing a common ancestry. We used these reports to understand the context for the intervention and to explore explanations for its relative lack of success. Additional data helped us to challenge simplistic assumptions on the homogeneity of the target population. A single case study suggests the potential utility of cluster searching, particularly for reviews that depend on an understanding of context, e.g. realist synthesis. The methodology is transparent, explicit and reproducible. There is no reason to believe that cluster searching is not generalizable to other review topics. Further research should examine the contribution of the methodology beyond improved yield, to the final synthesis and interpretation, possibly by utilizing qualitative sensitivity analysis.

Dark matter, long-range forces, and large-scale structure

NASA Technical Reports Server (NTRS)

Gradwohl, Ben-Ami; Frieman, Joshua A.

1992-01-01

If the dark matter in galaxies and clusters is nonbaryonic, it can interact with additional long-range fields that are invisible to experimental tests of the equivalence principle. We discuss the astrophysical and cosmological implications of a long-range force coupled only to the dark matter and find rather tight constraints on its strength. If the force is repulsive (attractive), the masses of galaxy groups and clusters (and the mean density of the universe inferred from them) have been systematically underestimated (overestimated). We explore the consequent effects on the two-point correlation function, large-scale velocity flows, and microwave background anisotropies, for models with initial scale-invariant adiabatic perturbations and cold dark matter.

Extension of lattice cluster theory to strongly interacting, self-assembling polymeric systems.

PubMed

Freed, Karl F

2009-02-14

A new extension of the lattice cluster theory is developed to describe the influence of monomer structure and local correlations on the free energy of strongly interacting and self-assembling polymer systems. This extension combines a systematic high dimension (1/d) and high temperature expansion (that is appropriate for weakly interacting systems) with a direct treatment of strong interactions. The general theory is illustrated for a binary polymer blend whose two components contain "sticky" donor and acceptor groups, respectively. The free energy is determined as an explicit function of the donor-acceptor contact probabilities that depend, in turn, on the local structure and both the strong and weak interactions.

A comparison of unsupervised classification procedures on LANDSAT MSS data for an area of complex surface conditions in Basilicata, Southern Italy

NASA Technical Reports Server (NTRS)

Justice, C.; Townshend, J. (Principal Investigator)

1981-01-01

Two unsupervised classification procedures were applied to ratioed and unratioed LANDSAT multispectral scanner data of an area of spatially complex vegetation and terrain. An objective accuracy assessment was undertaken on each classification and comparison was made of the classification accuracies. The two unsupervised procedures use the same clustering algorithm. By on procedure the entire area is clustered and by the other a representative sample of the area is clustered and the resulting statistics are extrapolated to the remaining area using a maximum likelihood classifier. Explanation is given of the major steps in the classification procedures including image preprocessing; classification; interpretation of cluster classes; and accuracy assessment. Of the four classifications undertaken, the monocluster block approach on the unratioed data gave the highest accuracy of 80% for five coarse cover classes. This accuracy was increased to 84% by applying a 3 x 3 contextual filter to the classified image. A detailed description and partial explanation is provided for the major misclassification. The classification of the unratioed data produced higher percentage accuracies than for the ratioed data and the monocluster block approach gave higher accuracies than clustering the entire area. The moncluster block approach was additionally the most economical in terms of computing time.

One-step generation of continuous-variable quadripartite cluster states in a circuit QED system

NASA Astrophysics Data System (ADS)

Yang, Zhi-peng; Li, Zhen; Ma, Sheng-li; Li, Fu-li

2017-07-01

We propose a dissipative scheme for one-step generation of continuous-variable quadripartite cluster states in a circuit QED setup consisting of four superconducting coplanar waveguide resonators and a gap-tunable superconducting flux qubit. With external driving fields to adjust the desired qubit-resonator and resonator-resonator interactions, we show that continuous-variable quadripartite cluster states of the four resonators can be generated with the assistance of energy relaxation of the qubit. By comparison with the previous proposals, the distinct advantage of our scheme is that only one step of quantum operation is needed to realize the quantum state engineering. This makes our scheme simpler and more feasible in experiment. Our result may have useful application for implementing quantum computation in solid-state circuit QED systems.

Dispersed or Clustered Housing for Adults with Intellectual Disability: A Systematic Review

ERIC Educational Resources Information Center

Mansell, Jim; Beadle-Brown, Julie

2009-01-01

Background: The purpose of this review was to evaluate the available research on the quality and costs of dispersed community-based housing when compared with clustered housing. Methods: Searches against specified criteria yielded 19 papers based on 10 studies presenting data comparing dispersed housing with some kind of clustered housing (village…

The nucleation and growth of uranium on the basal plane of graphite studied by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Tench, R. J.

1992-11-01

For the first time, nanometer scale uranium clusters were created on the basal plane of highly oriented pyrolytic graphite by laser ablation under ultra-high vacuum conditions. The physical and chemical properties of these clusters were investigated by scanning tunneling microscopy (STM) as well as standard surface science techniques. Auger electron and X-ray photoelectron spectroscopies found the uranium deposit to be free of contamination and showed that no carbide had formed with the underlying graphite. Clusters with sizes ranging from 42 to 630 sq A were observed upon initial room temperature deposition. Surface diffusion of uranium was observed after annealing the substrate above 800 K, as evidenced by the decreased number density and the increased size of the clusters. Preferential depletion of clusters on terraces near step edges as a result of annealing was observed. The activation energy for diffusion deduced from these measurements was found to be 15 Kcal/mole. Novel formation of ordered uranium thin films was observed for coverages greater than two monolayers after annealing above 900 K. These ordered films displayed islands with hexagonally faceted edges rising in uniform step heights characteristic of the unit cell of the P-phase of uranium. In addition, atomic resolution STM images of these ordered films indicated the formation of the (beta)-phase of uranium. The chemical properties of these surfaces were investigated and it was shown that these uranium films had a reduced oxidation rate in air as compared to bulk metal and that STM imaging in air induced a polarity-dependent enhancement of the oxidation rate.

Clustering Scientific Publications Based on Citation Relations: A Systematic Comparison of Different Methods.

PubMed

Šubelj, Lovro; van Eck, Nees Jan; Waltman, Ludo

2016-01-01

Clustering methods are applied regularly in the bibliometric literature to identify research areas or scientific fields. These methods are for instance used to group publications into clusters based on their relations in a citation network. In the network science literature, many clustering methods, often referred to as graph partitioning or community detection techniques, have been developed. Focusing on the problem of clustering the publications in a citation network, we present a systematic comparison of the performance of a large number of these clustering methods. Using a number of different citation networks, some of them relatively small and others very large, we extensively study the statistical properties of the results provided by different methods. In addition, we also carry out an expert-based assessment of the results produced by different methods. The expert-based assessment focuses on publications in the field of scientometrics. Our findings seem to indicate that there is a trade-off between different properties that may be considered desirable for a good clustering of publications. Overall, map equation methods appear to perform best in our analysis, suggesting that these methods deserve more attention from the bibliometric community.

Clustering Scientific Publications Based on Citation Relations: A Systematic Comparison of Different Methods

PubMed Central

Šubelj, Lovro; van Eck, Nees Jan; Waltman, Ludo

2016-01-01

Clustering methods are applied regularly in the bibliometric literature to identify research areas or scientific fields. These methods are for instance used to group publications into clusters based on their relations in a citation network. In the network science literature, many clustering methods, often referred to as graph partitioning or community detection techniques, have been developed. Focusing on the problem of clustering the publications in a citation network, we present a systematic comparison of the performance of a large number of these clustering methods. Using a number of different citation networks, some of them relatively small and others very large, we extensively study the statistical properties of the results provided by different methods. In addition, we also carry out an expert-based assessment of the results produced by different methods. The expert-based assessment focuses on publications in the field of scientometrics. Our findings seem to indicate that there is a trade-off between different properties that may be considered desirable for a good clustering of publications. Overall, map equation methods appear to perform best in our analysis, suggesting that these methods deserve more attention from the bibliometric community. PMID:27124610

Connecting with patients and instilling realism in an era of emerging communication possibilities: a review on palliative care communication heading to telecare practice.

PubMed

van Gurp, Jelle; Hasselaar, Jeroen; van Leeuwen, Evert; Hoek, Patrick; Vissers, Kris; van Selm, Martine

2013-12-01

Appropriate palliative care communication is pivotal to optimizing the quality of life in dying patients and their families. This review aims at describing communication patterns in palliative care and discussing potential relations between communication patterns and upcoming telecare in the practice of palliative care. This review builds on a systematic five-step qualitative analysis of the selected articles: 1. Development of a 'descriptive table of studies reviewed' based on the concept of genre, 2. Open coding of table content and first broad clustering of codes, 3. Intracluster categorization of inductive codes into substantive categories, 4. Constant inter- and intracluster comparison results in identification of genres, and 5. Labeling of genres. This review includes 71 articles. In the analysis, two communication genres in palliative care proved to be dominant: the conversation to connect, about creating and maintaining a professional-patient/family relationship, and the conversation to instill realism, about telling a clinical truth without diminishing hope. The abovementioned two genres clarify a logical intertwinement between communicative purposes, the socio-ethical background underlying palliative care practice and elements of form. Our study supports understanding of current communication in palliative care and anticipates future communicative actions in an era of new communication technologies. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Weak Lensing : Ground vs. Space in the Cosmos Field

NASA Astrophysics Data System (ADS)

Kasliwal, Mansi M.; Massey, R. J.; Ellis, R. S.; Rhodes, J.

2006-12-01

Weak lensing statistics are best for large numbers wide surveys with greater number of galaxies and deep surveys with a higher number density of galaxies. Although space-based surveys are unparalleled in their depth, ground-based surveys are the more cost-effective way to survey wide regions of the sky. We assess the relative merits of the two observing platforms, by using premier, multi-band, ground-based Subaru SuprimeCam data and space-based Hubble ACS data, in the 2 sq. degree COSMOS field in three ways. First, we compare shear measurements of individual galaxies and identify the relative calibration of the two datasets in terms of the largest subset in magnitude and size that is consistent. Second, we compare spaceand ground-based mass maps to quantify the relative completeness and contamination of the resulting cluster catalogs. We find that more clusters with XMM catalog counterparts are detected from space than ground and some ground-based clusters are possibly spurious detections. Third, we perform a detailed comparison of the precision with which it is possible to reconstruct the mass and size of four clusters at various redshifts identified from both ground and space. We find that the noise is much lower from space in all three investigations, but find no evidence for systematic overestimation or underestimation of the individual cluster properties by either survey.

Cosmology with EMSS Clusters of Galaxies

NASA Technical Reports Server (NTRS)

Donahue, Megan; Voit, G. Mark

1999-01-01

We use ASCA observations of the Extended Medium Sensitivity Survey sample of clusters of galaxies to construct the first z = 0.5 - 0.8 cluster temperature function. This distant cluster temperature function, when compared to local z approximately 0 and to a similar moderate redshift (z = 0.3 - 0.4) temperature function strongly constrains the matter density of the universe. Best fits to the distributions of temperatures and redshifts of these cluster samples results in Omega(sub M) = 0.45 +/- 0.1 if Lambda = 0 and Omega = 0.27 +/- 0.1 if Lambda + Omega(sub M) = 1. The uncertainties are 1sigma statistical. We examine the systematics of our approach and find that systematics, stemming mainly from model assumptions and not measurement errors, are about the same size as the statistical uncertainty +/- 0.1. In this poster proceedings, we clarify the issue of a8 as reported in our paper Donahue & Voit (1999), since this was a matter of discussion at the meeting.

Characteristics of Brazilian Offenders and Victims of Interpersonal Violence: An Exploratory Study.

PubMed

d'Avila, Sérgio; Campos, Ana Cristina; Bernardino, Ítalo de Macedo; Cavalcante, Gigliana Maria Sobral; Nóbrega, Lorena Marques da; Ferreira, Efigênia Ferreira E

2016-10-01

The aim of this study was to characterize the profile of Brazilian offenders and victims of interpersonal violence, following a medicolegal and forensic perspective. A cross-sectional and exploratory study was performed in a Center of Forensic Medicine and Dentistry. The sample was made up of 1,704 victims of nonlethal interpersonal violence with some type of trauma. The victims were subject to forensic examinations by a criminal investigative team that identified and recorded the extent of the injuries. For data collection, a specific form was designed consisting of four parts according to the information provided in the medicolegal and social records: sociodemographic data of the victims, offender's characteristics, aggression characteristics, and types of injuries. Descriptive and multivariate statistics using cluster analysis (CA) were performed. The two-step cluster method was used to characterize the profile of the victims and offenders. Most of the events occurred during the nighttime (50.9%) and on weekdays (66.3%). Soft tissue injuries were the most prevalent type (94.6%). Based on the CA results, two clusters for the victims and two for the offenders were identified. Victims: Cluster 1 was formed typically by women, aged 30 to 59 years, and married; Cluster 2 was composed of men, aged 20 to 29 years, and unmarried. Offenders: Cluster 1 was characterized by men, who perpetrated violence in a community environment. Cluster 2 was formed by men, who perpetrated violence in the familiar environment. These findings revealed different risk groups with distinct characteristics for both victims and offenders, allowing the planning of targeted measures of care, prevention, and health promotion. This study assesses the profile of violence through morbidity data and significantly contributes to building an integrated system of health surveillance in Brazil, as well as linking police stations, forensic services, and emergency hospitals.

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes.

PubMed

Xu, Jiajiong; Tang, Wei; Ma, Jun; Wang, Hong

2017-07-01

Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series. A large number of unique operational taxonomic units (OTUs) at these four treatment steps further illustrated their strong shaping power towards the drinking water microbial communities. Interestingly, multidimensional scaling analysis revealed tight clustering of biofilm samples collected from different treatment steps, with Nitrospira, the nitrite-oxidizing bacteria, noted at higher relative abundances in biofilm compared to water samples. Overall, this study provides a snapshot of step-to-step microbial evolvement in multi-step drinking water treatment systems, and the results provide insight to control and manipulation of the drinking water microbiome via optimization of DWTP design and operation.

SU-F-J-66: Anatomy Deformation Based Comparison Between One-Step and Two-Step Optimization for Online ART

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Z; Yu, G; Qin, S

Purpose: This study investigated that how the quality of adapted plan was affected by inter-fractional anatomy deformation by using one-step and two-step optimization for on line adaptive radiotherapy (ART) procedure. Methods: 10 lung carcinoma patients were chosen randomly to produce IMRT plan by one-step and two-step algorithms respectively, and the prescribed dose was set as 60 Gy on the planning target volume (PTV) for all patients. To simulate inter-fractional target deformation, four specific cases were created by systematic anatomy variation; including target superior shift 0.5 cm, 0.3cm contraction, 0.3 cm expansion and 45-degree rotation. Based on these four anatomy deformation,more » adapted plan, regenerated plan and non-adapted plan were created to evaluate quality of adaptation. Adapted plans were generated automatically by using one-step and two-step algorithms respectively to optimize original plans, and regenerated plans were manually created by experience physicists. Non-adapted plans were produced by recalculating the dose distribution based on corresponding original plans. The deviations among these three plans were statistically analyzed by paired T-test. Results: In PTV superior shift case, adapted plans had significantly better PTV coverage by using two-step algorithm compared with one-step one, and meanwhile there was a significant difference of V95 by comparison with adapted and non-adapted plans (p=0.0025). In target contraction deformation, with almost same PTV coverage, the total lung received lower dose using one-step algorithm than two-step algorithm (p=0.0143,0.0126 for V20, Dmean respectively). In other two deformation cases, there were no significant differences observed by both two optimized algorithms. Conclusion: In geometry deformation such as target contraction, with comparable PTV coverage, one-step algorithm gave better OAR sparing than two-step algorithm. Reversely, the adaptation by using two-step algorithm had higher efficiency and accuracy as target occurred position displacement. We want to thank Dr. Lei Xing and Dr. Yong Yang in the Stanford University School of Medicine for this work. This work was jointly supported by NSFC (61471226), Natural Science Foundation for Distinguished Young Scholars of Shandong Province (JQ201516), and China Postdoctoral Science Foundation (2015T80739, 2014M551949).« less

Cluster analysis of autoantibodies in 852 patients with systemic lupus erythematosus from a single center.

PubMed

Artim-Esen, Bahar; Çene, Erhan; Şahinkaya, Yasemin; Ertan, Semra; Pehlivan, Özlem; Kamali, Sevil; Gül, Ahmet; Öcal, Lale; Aral, Orhan; Inanç, Murat

2014-07-01

Associations between autoantibodies and clinical features have been described in systemic lupus erythematosus (SLE). Herein, we aimed to define autoantibody clusters and their clinical correlations in a large cohort of patients with SLE. We analyzed 852 patients with SLE who attended our clinic. Seven autoantibodies were selected for cluster analysis: anti-DNA, anti-Sm, anti-RNP, anticardiolipin (aCL) immunoglobulin (Ig)G or IgM, lupus anticoagulant (LAC), anti-Ro, and anti-La. Two-step clustering and Kaplan-Meier survival analyses were used. Five clusters were identified. A cluster consisted of patients with only anti-dsDNA antibodies, a cluster of anti-Sm and anti-RNP, a cluster of aCL IgG/M and LAC, and a cluster of anti-Ro and anti-La antibodies. Analysis revealed 1 more cluster that consisted of patients who did not belong to any of the clusters formed by antibodies chosen for cluster analysis. Sm/RNP cluster had significantly higher incidence of pulmonary hypertension and Raynaud phenomenon. DsDNA cluster had the highest incidence of renal involvement. In the aCL/LAC cluster, there were significantly more patients with neuropsychiatric involvement, antiphospholipid syndrome, autoimmune hemolytic anemia, and thrombocytopenia. According to the Systemic Lupus International Collaborating Clinics damage index, the highest frequency of damage was in the aCL/LAC cluster. Comparison of 10 and 20 years survival showed reduced survival in the aCL/LAC cluster. This study supports the existence of autoantibody clusters with distinct clinical features in SLE and shows that forming clinical subsets according to autoantibody clusters may be useful in predicting the outcome of the disease. Autoantibody clusters in SLE may exhibit differences according to the clinical setting or population.

Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.

PubMed

Ohtana, Yuki; Abdullah, Azian Azamimi; Altaf-Ul-Amin, Md; Huang, Ming; Ono, Naoaki; Sato, Tetsuo; Sugiura, Tadao; Horai, Hisayuki; Nakamura, Yukiko; Morita Hirai, Aki; Lange, Klaus W; Kibinge, Nelson K; Katsuragi, Tetsuo; Shirai, Tsuyoshi; Kanaya, Shigehiko

2014-12-01

Developing database systems connecting diverse species based on omics is the most important theme in big data biology. To attain this purpose, we have developed KNApSAcK Family Databases, which are utilized in a number of researches in metabolomics. In the present study, we have developed a network-based approach to analyze relationships between 3D structure and biological activity of metabolites consisting of four steps as follows: construction of a network of metabolites based on structural similarity (Step 1), classification of metabolites into structure groups (Step 2), assessment of statistically significant relations between structure groups and biological activities (Step 3), and 2-dimensional clustering of the constructed data matrix based on statistically significant relations between structure groups and biological activities (Step 4). Applying this method to a data set consisting of 2072 secondary metabolites and 140 biological activities reported in KNApSAcK Metabolite Activity DB, we obtained 983 statistically significant structure group-biological activity pairs. As a whole, we systematically analyzed the relationship between 3D-chemical structures of metabolites and biological activities. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nonclassical nucleation pathways in protein crystallization

NASA Astrophysics Data System (ADS)

Zhang, Fajun

2017-11-01

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.

Nonclassical nucleation pathways in protein crystallization.

PubMed

Zhang, Fajun

2017-11-08

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.

Spatial Correlation of Solar-Wind Turbulence from Two-Point Measurements

NASA Technical Reports Server (NTRS)

Matthaeus, W. H.; Milano, L. J.; Dasso, S.; Weygand, J. M.; Smith, C. W.; Kivelson, M. G.

2005-01-01

Interplanetary turbulence, the best studied case of low frequency plasma turbulence, is the only directly quantified instance of astrophysical turbulence. Here, magnetic field correlation analysis, using for the first time only proper two-point, single time measurements, provides a key step in unraveling the space-time structure of interplanetary turbulence. Simultaneous magnetic field data from the Wind, ACE, and Cluster spacecraft are analyzed to determine the correlation (outer) scale, and the Taylor microscale near Earth's orbit.

The balance between keystone clustering and bed roughness in experimental step-pool stabilization

NASA Astrophysics Data System (ADS)

Johnson, J. P.

2016-12-01

Predicting how mountain channels will respond to environmental perturbations such as floods requires an improved quantitative understanding of morphodynamic feedbacks among bed topography, surface grain size and sediment sorting. In boulder-rich gravel streams, transport and sorting often lead to the development of step pool morphologies, which are expressed both in bed topography and coarse grain clustering. Bed stability is difficult to measure, and is sometimes inferred from the presence of step pools. I use scaled flume experiments to explore feedbacks among surface grain sizes, coarse grain clustering, bed roughness and hydraulic roughness during progressive bed stabilization and over a range of sediment transport rates. While grain clusters are sometimes identified by subjective interpretation, I quantify the degree of coarse surface grain clustering using spatial statistics, including a novel normalization of Ripley's K function. This approach is objective and provides information on the strength of clustering over a range of length scales. Flume experiments start with an initial bed surface with a broad grain size distribution and spatially random positions. Flow causes the bed surface to progressively stabilize in response to erosion, surface coarsening, roughening and grain reorganization. At 95% confidence, many but not all beds stabilized with coarse grains becoming more clustered than complete spatial randomness (CSR). I observe a tradeoff between topographic roughness and clustering. Beds that stabilized with higher degrees of coarse-grain clustering were topographically smoother, and vice-versa. Initial conditions influenced the degree of clustering at stability: Beds that happened to have fewer initial coarse grains had more coarse grain reorganization during stabilization, leading to more clustering. Finally, regressions demonstrate that clustering statistics actually predict hydraulic roughness significantly better than does D84 (the size at which 84% of grains are smaller). In the experimental data, the spatial organization of surface grains is a stronger control on flow characteristics than the size of surface grains.

Nanoscale structure and morphology of sulfonated polyphenylenes via atomistic simulations

DOE PAGES

Abbott, Lauren J.; Frischknecht, Amalie L.

2017-01-23

We performed atomistic simulations on a series of sulfonated polyphenylenes systematically varying the degree of sulfonation and water content to determine their effect on the nanoscale structure, particularly for the hydrophilic domains formed by the ionic groups and water molecules. We found that the local structure around the ionic groups depended on the sulfonation and hydration levels, with the sulfonate groups and hydronium ions less strongly coupled at higher water contents. In addition, we characterized the morphology of the ionic domains employing two complementary clustering algorithms. At low sulfonation and hydration levels, clusters were more elongated in shape and poorlymore » connected throughout the system. As the degree of sulfonation and water content were increased, the clusters became more spherical, and a fully percolated ionic domain was formed. As a result, these structural details have important implications for ion transport.« less

Identification and characterization of near-fatal asthma phenotypes by cluster analysis.

PubMed

Serrano-Pariente, J; Rodrigo, G; Fiz, J A; Crespo, A; Plaza, V

2015-09-01

Near-fatal asthma (NFA) is a heterogeneous clinical entity and several profiles of patients have been described according to different clinical, pathophysiological and histological features. However, there are no previous studies that identify in a unbiased way--using statistical methods such as clusters analysis--different phenotypes of NFA. Therefore, the aim of the present study was to identify and to characterize phenotypes of near fatal asthma using a cluster analysis. Over a period of 2 years, 33 Spanish hospitals enrolled 179 asthmatics admitted for an episode of NFA. A cluster analysis using two-steps algorithm was performed from data of 84 of these cases. The analysis defined three clusters of patients with NFA: cluster 1, the largest, including older patients with clinical and therapeutic criteria of severe asthma; cluster 2, with an high proportion of respiratory arrest (68%), impaired consciousness level (82%) and mechanical ventilation (93%); and cluster 3, which included younger patients, characterized by an insufficient anti-inflammatory treatment and frequent sensitization to Alternaria alternata and soybean. These results identify specific asthma phenotypes involved in NFA, confirming in part previous findings observed in studies with a clinical approach. The identification of patients with a specific NFA phenotype could suggest interventions to prevent future severe asthma exacerbations. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Traditional birth attendant training for improving health behaviours and pregnancy outcomes

PubMed Central

Sibley, Lynn M; Sipe, Theresa Ann; Barry, Danika

2014-01-01

Background Between the 1970s and 1990s, the World Health Organization promoted traditional birth attendant (TBA) training as one strategy to reduce maternal and neonatal mortality. To date, evidence in support of TBA training is limited but promising for some mortality outcomes. Objectives To assess the effects of TBA training on health behaviours and pregnancy outcomes. Search methods We searched the Cochrane Pregnancy and Childbirth Group’s Trials Register (18 June 2012), citation alerts from our work and reference lists of studies identified in the search. Selection criteria Published and unpublished randomised controlled trials (RCT), comparing trained versus untrained TBAs, additionally trained versus trained TBAs, or women cared for/living in areas served by TBAs. Data collection and analysis Three authors independently assessed study quality and extracted data in the original and first update review. Three authors and one external reviewer independently assessed study quality and two extracted data in this second update. Main results Six studies involving over 1345 TBAs, more than 32,000 women and approximately 57,000 births that examined the effects of TBA training for trained versus untrained TBAs (one study) and additionally trained TBA training versus trained TBAs (five studies) are included in this review. These studies consist of individual randomised trials (two studies) and cluster-randomised trials (four studies). The primary outcomes across the sample of studies were perinatal deaths, stillbirths and neonatal deaths (early, late and overall). Trained TBAs versus untrained TBAs: one cluster-randomised trial found a significantly lower perinatal death rate in the trained versus untrained TBA clusters (adjusted odds ratio (OR) 0.70, 95% confidence interval (CI) 0.59 to 0.83), lower stillbirth rate (adjusted OR 0.69, 95% CI 0.57 to 0.83) and lower neonatal death rate (adjusted OR 0.71, 95% CI 0.61 to 0.82). This study also found the maternal death rate was lower but not significant (adjusted OR 0.74, 95% CI 0.45 to 1.22). Additionally trained TBAs versus trained TBAs: three large cluster-randomised trials compared TBAs who received additional training in initial steps of resuscitation, including bag-valve-mask ventilation, with TBAs who had received basic training in safe, clean delivery and immediate newborn care. Basic training included mouth-to-mouth resuscitation (two studies) or bag-valve-mask resuscitation (one study). There was no significant difference in the perinatal death rate between the intervention and control clusters (one study, adjusted OR 0.79, 95% CI 0.61 to 1.02) and no significant difference in late neonatal death rate between intervention and control clusters (one study, adjusted risk ratio (RR) 0.47, 95% CI 0.20 to 1.11). The neonatal death rate, however, was 45% lower in intervention compared with the control clusters (one study, 22.8% versus 40.2%, adjusted RR 0.54, 95% CI 0.32 to 0.92). We conducted a meta-analysis on two outcomes: stillbirths and early neonatal death. There was no significant difference between the additionally trained TBAs versus trained TBAs for stillbirths (two studies, mean weighted adjusted RR 0.99, 95% CI 0.76 to 1.28) or early neonatal death rate (three studies, mean weighted adjusted RR 0.83, 95% CI 0.68 to 1.01). Authors’ conclusions The results are promising for some outcomes (perinatal death, stillbirth and neonatal death). However, most outcomes are reported in only one study. A lack of contrast in training in the intervention and control clusters may have contributed to the null result for stillbirths and an insufficient number of studies may have contributed to the failure to achieve significance for early neonatal deaths. Despite the additional studies included in this updated systematic review, there remains insufficient evidence to establish the potential of TBA training to improve peri-neonatal mortality. PMID:22895949

On evaluating clustering procedures for use in classification

NASA Technical Reports Server (NTRS)

Pore, M. D.; Moritz, T. E.; Register, D. T.; Yao, S. S.; Eppler, W. G. (Principal Investigator)

1979-01-01

The problem of evaluating clustering algorithms and their respective computer programs for use in a preprocessing step for classification is addressed. In clustering for classification the probability of correct classification is suggested as the ultimate measure of accuracy on training data. A means of implementing this criterion and a measure of cluster purity are discussed. Examples are given. A procedure for cluster labeling that is based on cluster purity and sample size is presented.

Reporting non-adherence in cluster randomised trials: A systematic review.

PubMed

Agbla, Schadrac C; DiazOrdaz, Karla

2018-06-01

Treatment non-adherence in randomised trials refers to situations where some participants do not receive their allocated treatment as intended. For cluster randomised trials, where the unit of randomisation is a group of participants, non-adherence may occur at the cluster or individual level. When non-adherence occurs, randomisation no longer guarantees that the relationship between treatment receipt and outcome is unconfounded, and the power to detect the treatment effects in intention-to-treat analysis may be reduced. Thus, recording adherence and estimating the causal treatment effect adequately are of interest for clinical trials. To assess the extent of reporting of non-adherence issues in published cluster trials and to establish which methods are currently being used for addressing non-adherence, if any, and whether clustering is accounted for in these. We systematically reviewed 132 cluster trials published in English in 2011 previously identified through a search in PubMed. One-hundred and twenty three cluster trials were included in this systematic review. Non-adherence was reported in 56 cluster trials. Among these, 19 reported a treatment efficacy estimate: per protocol in 15 and as treated in 4. No study discussed the assumptions made by these methods, their plausibility or the sensitivity of the results to deviations from these assumptions. The year of publication of the cluster trials included in this review (2011) could be considered a limitation of this study; however, no new guidelines regarding the reporting and the handling of non-adherence for cluster trials have been published since. In addition, a single reviewer undertook the data extraction. To mitigate this, a second reviewer conducted a validation of the extraction process on 15 randomly selected reports. Agreement was satisfactory (93%). Despite the recommendations of the Consolidated Standards of Reporting Trials statement extension to cluster randomised trials, treatment adherence is under-reported. Among the trials providing adherence information, there was substantial variation in how adherence was defined, handled and reported. Researchers should discuss the assumptions required for the results to be interpreted causally and whether these are scientifically plausible in their studies. Sensitivity analyses to study the robustness of the results to departures from these assumptions should be performed.

Estimation of a cover-type change matrix from error-prone data

Treesearch

Steen Magnussen

2009-01-01

Coregistration and classification errors seriously compromise per-pixel estimates of land cover change. A more robust estimation of change is proposed in which adjacent pixels are grouped into 3x3 clusters and treated as a unit of observation. A complete change matrix is recovered in a two-step process. The diagonal elements of a change matrix are recovered from...

DNA-Mediated Patterning of Single Quantum Dot Nanoarrays: A Reusable Platform for Single-Molecule Control

NASA Astrophysics Data System (ADS)

Huang, Da; Freeley, Mark; Palma, Matteo

2017-03-01

We present a facile strategy of general applicability for the assembly of individual nanoscale moieties in array configurations with single-molecule control. Combining the programming ability of DNA as a scaffolding material with a one-step lithographic process, we demonstrate the patterning of single quantum dots (QDs) at predefined locations on silicon and transparent glass surfaces: as proof of concept, clusters of either one, two, or three QDs were assembled in highly uniform arrays with a 60 nm interdot spacing within each cluster. Notably, the platform developed is reusable after a simple cleaning process and can be designed to exhibit different geometrical arrangements.

Universal quantum computation with temporal-mode bilayer square lattices

NASA Astrophysics Data System (ADS)

Alexander, Rafael N.; Yokoyama, Shota; Furusawa, Akira; Menicucci, Nicolas C.

2018-03-01

We propose an experimental design for universal continuous-variable quantum computation that incorporates recent innovations in linear-optics-based continuous-variable cluster state generation and cubic-phase gate teleportation. The first ingredient is a protocol for generating the bilayer-square-lattice cluster state (a universal resource state) with temporal modes of light. With this state, measurement-based implementation of Gaussian unitary gates requires only homodyne detection. Second, we describe a measurement device that implements an adaptive cubic-phase gate, up to a random phase-space displacement. It requires a two-step sequence of homodyne measurements and consumes a (non-Gaussian) cubic-phase state.

Manipulation of surface morphology of flower-like Ag/ZnO nanorods to enhance photocatalytic performance

NASA Astrophysics Data System (ADS)

U-thaipan, Kasira; Tedsree, Karaked

2018-06-01

The surface morphology of flower-like Ag/ZnO nanorod can be manipulated by adopting different synthetic routes and also loading different levels of Ag in order to alter their surface structures to achieve the maximum photocatalytic efficiency. In a single-step preparation method Ag/ZnO was prepared by heating directly a mixture of Zn2+ and Ag+ precursors in an aqueous NaOH-ethylene glycol solution, while in the two-step preparation method an intermediate of flower-shaped ZnO nanorod was obtained by a hydrothermal process before depositing Ag particles on the ZnO surfaces by chemical reduction. The structure, morphology and optical properties of the synthesized samples were characterized using TEM, SEM, XRD, DRS and PL techniques. The sample prepared by single-step method are characterized with agglomeration of Ag atoms as clusters on the surface of ZnO, whereas in the sample prepared by two-step method Ag atoms are found uniformly dispersed and deposited as discrete Ag nanoparticles on the surface of ZnO. A significant enhancement in the adsorption of visible light was evident for Ag/ZnO samples prepared by two-step method especially with low Ag content (0.5 mol%). The flower-like Ag/ZnO nanorod prepared with 0.5 mol% Ag by two-step process was found to be the most efficient photocatalyst for the degradation of phenol, which can decompose 90% of phenol within 120 min.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanfilippo, Antonio P.; Chikkagoudar, Satish

We describe an approach to analyzing trade data which uses clustering to detect similarities across shipping manifest records, classification to evaluate clustering results and categorize new unseen shipping data records, and visual analytics to provide to support situation awareness in dynamic decision making to monitor and warn against the movement of radiological threat materials through search, analysis and forecasting capabilities. The evaluation of clustering results through classification and systematic inspection of the clusters show the clusters have strong semantic cohesion and offer novel ways to detect transactions related to nuclear smuggling.

Blue emitting undecaplatinum clusters

NASA Astrophysics Data System (ADS)

Chakraborty, Indranath; Bhuin, Radha Gobinda; Bhat, Shridevi; Pradeep, T.

2014-07-01

A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents.A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents. Electronic supplementary information (ESI) available: Details of experimental procedures, instrumentation, chromatogram of the crude cluster; SEM/EDAX, DLS, PXRD, TEM, FT-IR, and XPS of the isolated Pt11 cluster; UV/Vis, MALDI MS and SEM/EDAX of isolated 2 and 3; and 195Pt NMR of the K2PtCl6 standard. See DOI: 10.1039/c4nr02778g

Coordinating the Provision of Health Services in Humanitarian Crises: a Systematic Review of Suggested Models.

PubMed

Lotfi, Tamara; Bou-Karroum, Lama; Darzi, Andrea; Hajjar, Rayan; El Rahyel, Ahmed; El Eid, Jamale; Itani, Mira; Brax, Hneine; Akik, Chaza; Osman, Mona; Hassan, Ghayda; El-Jardali, Fadi; Akl, Elie

2016-08-03

Our objective was to identify published models of coordination between entities funding or delivering health services in humanitarian crises, whether the coordination took place during or after the crises. We included reports describing models of coordination in sufficient detail to allow reproducibility. We also included reports describing implementation of identified models, as case studies. We searched Medline, PubMed, EMBASE, Cochrane Central Register of Controlled Trials, CINAHL, PsycINFO, and the WHO Global Health Library. We also searched websites of relevant organizations. We followed standard systematic review methodology. Our search captured 14,309 citations. The screening process identified 34 eligible papers describing five models of coordination of delivering health services: the "Cluster Approach" (with 16 case studies), the 4Ws "Who is Where, When, doing What" mapping tool (with four case studies), the "Sphere Project" (with two case studies), the "5x5" model (with one case study), and the "model of information coordination" (with one case study). The 4Ws and the 5x5 focus on coordination of services for mental health, the remaining models do not focus on a specific health topic. The Cluster approach appears to be the most widely used. One case study was a mixed implementation of the Cluster approach and the Sphere model. We identified no model of coordination for funding of health service. This systematic review identified five proposed coordination models that have been implemented by entities funding or delivering health service in humanitarian crises. There is a need to compare the effect of these different models on outcomes such as availability of and access to health services.

Identification of Loci and Functional Characterization of Trichothecene Biosynthesis Genes in Filamentous Fungi of the Genus Trichoderma▿†

PubMed Central

Cardoza, R. E.; Malmierca, M. G.; Hermosa, M. R.; Alexander, N. J.; McCormick, S. P.; Proctor, R. H.; Tijerino, A. M.; Rumbero, A.; Monte, E.; Gutiérrez, S.

2011-01-01

Trichothecenes are mycotoxins produced by Trichoderma, Fusarium, and at least four other genera in the fungal order Hypocreales. Fusarium has a trichothecene biosynthetic gene (TRI) cluster that encodes transport and regulatory proteins as well as most enzymes required for the formation of the mycotoxins. However, little is known about trichothecene biosynthesis in the other genera. Here, we identify and characterize TRI gene orthologues (tri) in Trichoderma arundinaceum and Trichoderma brevicompactum. Our results indicate that both Trichoderma species have a tri cluster that consists of orthologues of seven genes present in the Fusarium TRI cluster. Organization of genes in the cluster is the same in the two Trichoderma species but differs from the organization in Fusarium. Sequence and functional analysis revealed that the gene (tri5) responsible for the first committed step in trichothecene biosynthesis is located outside the cluster in both Trichoderma species rather than inside the cluster as it is in Fusarium. Heterologous expression analysis revealed that two T. arundinaceum cluster genes (tri4 and tri11) differ in function from their Fusarium orthologues. The Tatri4-encoded enzyme catalyzes only three of the four oxygenation reactions catalyzed by the orthologous enzyme in Fusarium. The Tatri11-encoded enzyme catalyzes a completely different reaction (trichothecene C-4 hydroxylation) than the Fusarium orthologue (trichothecene C-15 hydroxylation). The results of this study indicate that although some characteristics of the tri/TRI cluster have been conserved during evolution of Trichoderma and Fusarium, the cluster has undergone marked changes, including gene loss and/or gain, gene rearrangement, and divergence of gene function. PMID:21642405

Systematic review of universal school-based resilience interventions targeting adolescent tobacco, alcohol or illicit drug use: review protocol

PubMed Central

Hodder, Rebecca Kate; Freund, Megan; Wolfenden, Luke; Bowman, Jenny; Gillham, Karen; Dray, Julia; Wiggers, John

2014-01-01

Introduction Tobacco, alcohol and illicit drug use contribute significantly to global rates of morbidity and mortality. Despite evidence suggesting interventions designed to increase adolescent resilience may represent a means of reducing adolescent substance use, and schools providing a key opportunity to implement such interventions, existing systematic reviews assessing the effectiveness of school-based interventions targeting adolescent substance use have not examined this potential. Methods and analysis The aim of the systematic review is to determine whether universal interventions focused on enhancing the resilience of adolescents are effective in reducing adolescent substance use. Eligible studies will: include participants 5–18 years of age; report tobacco use, alcohol consumption or illicit drug use as outcomes; and implement a school-based intervention designed to promote internal (eg, self-esteem) and external (eg, school connectedness) resilience factors. Eligible study designs include randomised controlled trials, cluster randomised controlled trials, staggered enrolment trials, stepped wedged trials, quasi-randomised trials, quasi-experimental trials, time series/interrupted time-series trials, preference trials, regression discontinuity trials and natural experiment studies with a parallel control group. A search strategy including criteria for participants, study design, outcome, setting and intervention will be implemented in various electronic databases and information sources. Two reviewers will independently screen studies to assess eligibility, as well as extract data from, and assess risk of bias of included studies. A third reviewer will resolve any discrepancies. Attempts will be made to quantify trial effects by meta-analysis. Binary outcomes will be pooled and effect size reported using ORs. For continuous data, effect size of trials will be reported using a mean difference where trial outcomes report the same outcome using a consistent measure, or standardised mean difference where trials report a comparable measure. Otherwise, trial outcomes will be described narratively. Dissemination Review findings will be disseminated via peer-reviewed journals and conferences. PMID:24861548

Particle-like structure of coaxial Lie algebras

NASA Astrophysics Data System (ADS)

Vinogradov, A. M.

2018-01-01

This paper is a natural continuation of Vinogradov [J. Math. Phys. 58, 071703 (2017)] where we proved that any Lie algebra over an algebraically closed field or over R can be assembled in a number of steps from two elementary constituents, called dyons and triadons. Here we consider the problems of the construction and classification of those Lie algebras which can be assembled in one step from base dyons and triadons, called coaxial Lie algebras. The base dyons and triadons are Lie algebra structures that have only one non-trivial structure constant in a given basis, while coaxial Lie algebras are linear combinations of pairwise compatible base dyons and triadons. We describe the maximal families of pairwise compatible base dyons and triadons called clusters, and, as a consequence, we give a complete description of the coaxial Lie algebras. The remarkable fact is that dyons and triadons in clusters are self-organised in structural groups which are surrounded by casings and linked by connectives. We discuss generalisations and applications to the theory of deformations of Lie algebras.

Registered nurses' experiences of caring for pregnant and postpartum women in general hospital settings: a systematic review and meta-synthesis of qualitative data.

PubMed

Bayes, Sara; Ewens, Beverley

2017-03-01

To understand how nurses view and experience caring for pregnant and postpartum women in nonmaternity care settings. A degree of apprehension is perceived to exist among nurses in relation to caring for pregnant or postpartum women in nonmaternity care settings. The nature of nonmidwife nurses' concerns about caring for this group of women in these contexts, however, is not known. A six-step systematic approach was employed for this review. In Step 1, the research question was developed; Step 2 involved developing the inclusion criteria for articles; the literature search strategy was devised in Step 3; Step 4 comprised the conduct of the literature search and selection of articles for review; in Step 5, the critical appraisal of selected studies and synthesis of data was undertaken; interpretation of the findings occurred in Step 6. Following a process of elimination, the final number of articles retained for this review was three. Fifty-four Level 1 findings were extracted from these three articles which were subsequently collapsed into four Level 2 categories. Two Level 3 synthesised findings that characterise what is known about the topic of interest were then derived from these four Level two categories. Nurses are reportedly ill prepared for the experience of caring for pregnant and postpartum women in general care settings. A combination of a lack of education and a need to 'learn on the job' reportedly evokes stress, trauma and a sense of professional inadequacy. This review identifies lack of knowledge and of adequate supervision for nurses in this context, which in turn poses a clinical risk to pregnant and postpartum women in their care. Effective strategies to establish initial and ongoing collaborative education and clinical practice guidelines are required. © 2016 John Wiley & Sons Ltd.

Constraining the baryon-dark matter relative velocity with the large-scale 3-point correlation function of the SDSS BOSS DR12 CMASS galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slepian, Zachary; Slosar, Anze; Eisenstein, Daniel J.

We search for a galaxy clustering bias due to a modulation of galaxy number with the baryon-dark matter relative velocity resulting from recombination-era physics. We find no detected signal and place the constraint bv <0.01 on the relative velocity bias for the CMASS galaxies. This bias is an important potential systematic of Baryon Acoustic Oscillation (BAO) method measurements of the cosmic distance scale using the 2-point clustering. Our limit on the relative velocity bias indicates a systematic shift of no more than 0.3% rms in the distance scale inferred from the BAO feature in the BOSS 2-point clustering, well belowmore » the 1% statistical error of this measurement. In conclusion, this constraint is the most stringent currently available and has important implications for the ability of upcoming large-scale structure surveys such as DESI to self-protect against the relative velocity as a possible systematic.« less

Constraining the baryon-dark matter relative velocity with the large-scale 3-point correlation function of the SDSS BOSS DR12 CMASS galaxies

DOE PAGES

Slepian, Zachary; Slosar, Anze; Eisenstein, Daniel J.; ...

2017-10-24

We search for a galaxy clustering bias due to a modulation of galaxy number with the baryon-dark matter relative velocity resulting from recombination-era physics. We find no detected signal and place the constraint bv <0.01 on the relative velocity bias for the CMASS galaxies. This bias is an important potential systematic of Baryon Acoustic Oscillation (BAO) method measurements of the cosmic distance scale using the 2-point clustering. Our limit on the relative velocity bias indicates a systematic shift of no more than 0.3% rms in the distance scale inferred from the BAO feature in the BOSS 2-point clustering, well belowmore » the 1% statistical error of this measurement. In conclusion, this constraint is the most stringent currently available and has important implications for the ability of upcoming large-scale structure surveys such as DESI to self-protect against the relative velocity as a possible systematic.« less

Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins†

PubMed Central

Gao, Huanyao; Subramanian, Sowmya; Couturier, Jérémy; Naik, Sunil; Kim, Sung-Kun; Leustek, Thomas; Knaff, David B.; Wu, Hui-Chen; Vignols, Florence; Huynh, Boi Hanh; Rouhier, Nicolas; Johnson, Michael K.

2013-01-01

Nfu-type proteins are essential in the biogenesis of iron-sulfur (Fe-S) clusters in numerous organisms. A number of phenotypes including low levels of Fe-S cluster incorporation are associated with deletion of the gene encoding a chloroplast-specific Nfu-type protein, Nfu2 from Arabidopsis thaliana (AtNfu2). Here we report that recombinant AtNfu2 is able to assemble both [2Fe-2S] and [4Fe-4S] clusters. Analytical data and gel filtration studies support cluster/protein stoichiometries of one [2Fe-2S] cluster/homotetramer and one [4Fe-4S] cluster/homodimer. The combination of UV-visible absorption and circular dichroism, resonance Raman and Mössbauer spectroscopies has been employed to investigate the nature, properties and transfer of the clusters assembled on Nfu2. The results are consistent with subunit-bridging [2Fe-2S]2+ and [4Fe-4S]2+ clusters coordinated by the cysteines in the conserved CXXC motif. The results also provided insight into the specificity of Nfu2 for maturation of chloroplastic Fe-S proteins via intact, rapid and quantitative cluster transfer. [2Fe-2S] cluster-bound Nfu2 is shown to be an effective [2Fe-2S]2+ cluster donor for glutaredoxin S16, but not glutaredoxin S14. Moreover, [4Fe-4S] cluster-bound Nfu2 is shown to be a very rapid and efficient [4Fe-4S]2+ cluster donor for adenosine 5′-phosphosulfate reductase (APR1) and yeast two-hybrid studies indicate that APR1 forms a complex with Nfu2, but not with Nfu1 and Nfu3, the two other chloroplastic Nfu proteins. This cluster transfer is likely to be physiologically relevant and is particularly significant for plant metabolism as APR1 catalyzes the second step in reductive sulfur assimilation which ultimately results in the biosynthesis of cysteine, methionine, glutathione, and Fe-S clusters. PMID:24032747

Gravitational Lensing by Clusters of Galaxies

NASA Astrophysics Data System (ADS)

Tyson, J.; Murdin, P.

2000-11-01

CLUSTERS OF GALAXIES are massive and relatively rare objects containing hundreds of galaxies. Their huge mass—dominated by DARK MATTER—bends light from all background objects, systematically distorting the images of thousands of distant galaxies (shear). This observed gravitational lens distortion can be inverted to produce an `image' of the mass in the foreground cluster of galaxies. Most of the...

In vivo [Fe-S] cluster acquisition by IscR and NsrR, two stress regulators in Escherichia coli.

PubMed

Vinella, Daniel; Loiseau, Laurent; Ollagnier de Choudens, Sandrine; Fontecave, Marc; Barras, Frédéric

2013-02-01

The multi-proteins Isc and Suf systems catalyse the biogenesis of [Fe-S] proteins. Here we investigate how NsrR and IscR, transcriptional regulators that sense NO and [Fe-S] homeostasis, acquire their [Fe-S] clusters under both normal and iron limitation conditions. Clusters directed at the apo-NsrR and apo-IscR proteins are built on either of the two scaffolds, IscU or SufB. However, differences arise in [Fe-S] delivery steps. In the case of NsrR, scaffolds deliver clusters to either one of the two ATCs, IscA and SufA, and, subsequently, to the 'non-Isc non-Suf' ATC, ErpA. Nevertheless, a high level of SufA can bypass the requirement for ErpA. In the case of IscR, several routes occur. One does not include assistance of any ATC. Others implicate ATCs IscA or ErpA, but, surprisingly, SufA was totally absent from any IscR maturation pathways. Both IscR and NsrR have the intrinsic capacity to sense iron limitation. However, NsrR appeared to be efficiently matured by Isc and Suf, thereby preventing NsrR to act as a physiologically relevant iron sensor. This work emphasizes that different maturation pathways arise as a function of the apo-target considered, possibly in relation with the type of cluster, [2Fe-2S] versus [4Fe-4S], it binds. © 2013 Blackwell Publishing Ltd.

The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: theoretical systematics and Baryon Acoustic Oscillations in the galaxy correlation function

NASA Astrophysics Data System (ADS)

Vargas-Magaña, Mariana; Ho, Shirley; Cuesta, Antonio J.; O'Connell, Ross; Ross, Ashley J.; Eisenstein, Daniel J.; Percival, Will J.; Grieb, Jan Niklas; Sánchez, Ariel G.; Tinker, Jeremy L.; Tojeiro, Rita; Beutler, Florian; Chuang, Chia-Hsun; Kitaura, Francisco-Shu; Prada, Francisco; Rodríguez-Torres, Sergio A.; Rossi, Graziano; Seo, Hee-Jong; Brownstein, Joel R.; Olmstead, Matthew; Thomas, Daniel

2018-06-01

We investigate the potential sources of theoretical systematics in the anisotropic Baryon Acoustic Oscillation (BAO) distance scale measurements from the clustering of galaxies in configuration space using the final Data Release (DR12) of the Baryon Oscillation Spectroscopic Survey (BOSS). We perform a detailed study of the impact on BAO measurements from choices in the methodology such as fiducial cosmology, clustering estimators, random catalogues, fitting templates, and covariance matrices. The theoretical systematic uncertainties in BAO parameters are found to be 0.002 in the isotropic dilation α and 0.003 in the quadrupolar dilation ɛ. The leading source of systematic uncertainty is related to the reconstruction techniques. Theoretical uncertainties are sub-dominant compared with the statistical uncertainties for BOSS survey, accounting 0.2σstat for α and 0.25σstat for ɛ (σα, stat ˜ 0.010 and σɛ, stat ˜ 0.012, respectively). We also present BAO-only distance scale constraints from the anisotropic analysis of the correlation function. Our constraints on the angular diameter distance DA(z) and the Hubble parameter H(z), including both statistical and theoretical systematic uncertainties, are 1.5 per cent and 2.8 per cent at zeff = 0.38, 1.4 per cent and 2.4 per cent at zeff = 0.51, and 1.7 per cent and 2.6 per cent at zeff = 0.61. This paper is part of a set that analyses the final galaxy clustering data set from BOSS. The measurements and likelihoods presented here are cross-checked with other BAO analysis in Alam et al. The systematic error budget concerning the methodology on post-reconstruction BAO analysis presented here is used in Alam et al. to produce the final cosmological constraints from BOSS.

Sloan Digital Sky Survey III photometric quasar clustering: probing the initial conditions of the Universe

NASA Astrophysics Data System (ADS)

Ho, Shirley; Agarwal, Nishant; Myers, Adam D.; Lyons, Richard; Disbrow, Ashley; Seo, Hee-Jong; Ross, Ashley; Hirata, Christopher; Padmanabhan, Nikhil; O'Connell, Ross; Huff, Eric; Schlegel, David; Slosar, Anže; Weinberg, David; Strauss, Michael; Ross, Nicholas P.; Schneider, Donald P.; Bahcall, Neta; Brinkmann, J.; Palanque-Delabrouille, Nathalie; Yèche, Christophe

2015-05-01

The Sloan Digital Sky Survey has surveyed 14,555 square degrees of the sky, and delivered over a trillion pixels of imaging data. We present the large-scale clustering of 1.6 million quasars between z=0.5 and z=2.5 that have been classified from this imaging, representing the highest density of quasars ever studied for clustering measurements. This data set spans 0~ 11,00 square degrees and probes a volume of 80 h-3 Gpc3. In principle, such a large volume and medium density of tracers should facilitate high-precision cosmological constraints. We measure the angular clustering of photometrically classified quasars using an optimal quadratic estimator in four redshift slices with an accuracy of ~ 25% over a bin width of δl ~ 10-15 on scales corresponding to matter-radiation equality and larger (0l ~ 2-3). Observational systematics can strongly bias clustering measurements on large scales, which can mimic cosmologically relevant signals such as deviations from Gaussianity in the spectrum of primordial perturbations. We account for systematics by employing a new method recently proposed by Agarwal et al. (2014) to the clustering of photometrically classified quasars. We carefully apply our methodology to mitigate known observational systematics and further remove angular bins that are contaminated by unknown systematics. Combining quasar data with the photometric luminous red galaxy (LRG) sample of Ross et al. (2011) and Ho et al. (2012), and marginalizing over all bias and shot noise-like parameters, we obtain a constraint on local primordial non-Gaussianity of fNL = -113+154-154 (1σ error). We next assume that the bias of quasar and galaxy distributions can be obtained independently from quasar/galaxy-CMB lensing cross-correlation measurements (such as those in Sherwin et al. (2013)). This can be facilitated by spectroscopic observations of the sources, enabling the redshift distribution to be completely determined, and allowing precise estimates of the bias parameters. In this paper, if the bias and shot noise parameters are fixed to their known values (which we model by fixing them to their best-fit Gaussian values), we find that the error bar reduces to 1σ simeq 65. We expect this error bar to reduce further by at least another factor of five if the data is free of any observational systematics. We therefore emphasize that in order to make best use of large scale structure data we need an accurate modeling of known systematics, a method to mitigate unknown systematics, and additionally independent theoretical models or observations to probe the bias of dark matter halos.

Carbon Fibers Conductivity Studies

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Butkus, A. M.

1980-01-01

In an attempt to understand the process of electrical conduction in polyacrylonitrile (PAN)-based carbon fibers, calculations were carried out on cluster models of the fiber consisting of carbon, nitrogen, and hydrogen atoms using the modified intermediate neglect of differential overlap (MINDO) molecular orbital (MO) method. The models were developed based on the assumption that PAN carbon fibers obtained with heat treatment temperatures (HTT) below 1000 C retain nitrogen in a graphite-like lattice. For clusters modeling an edge nitrogen site, analysis of the occupied MO's indicated an electron distribution similar to that of graphite. A similar analysis for the somewhat less stable interior nitrogen site revealed a partially localized II electron distribution around the nitrogen atom. The differences in bonding trends and structural stability between edge and interior nitrogen clusters led to a two-step process proposed for nitrogen evolution with increasing HTT.

Dynamic evolution of nearby galaxy clusters

NASA Astrophysics Data System (ADS)

Biernacka, M.; Flin, P.

2011-06-01

A study of the evolution of 377 rich ACO clusters with redshift z<0.2 is presented. The data concerning galaxies in the investigated clusters were obtained using FOCAS packages applied to Digital Sky Survey I. The 377 galaxy clusters constitute a statistically uniform sample to which visual galaxy/star reclassifications were applied. Cluster shape within 2.0 h-1 Mpc from the adopted cluster centre (the mean and the median of all galaxy coordinates, the position of the brightest and of the third brightest galaxy in the cluster) was determined through its ellipticity calculated using two methods: the covariance ellipse method (hereafter CEM) and the method based on Minkowski functionals (hereafter MFM). We investigated ellipticity dependence on the radius of circular annuli, in which ellipticity was calculated. This was realized by varying the radius from 0.5 to 2 Mpc in steps of 0.25 Mpc. By performing Monte Carlo simulations, we generated clusters to which the two ellipticity methods were applied. We found that the covariance ellipse method works better than the method based on Minkowski functionals. We also found that ellipticity distributions are different for different methods used. Using the ellipticity-redshift relation, we investigated the possibility of cluster evolution in the low-redshift Universe. The correlation of cluster ellipticities with redshifts is undoubtly an indicator of structural evolution. Using the t-Student statistics, we found a statistically significant correlation between ellipticity and redshift at the significance level of α = 0.95. In one of the two shape determination methods we found that ellipticity grew with redshift, while the other method gave opposite results. Monte Carlo simulations showed that only ellipticities calculated at the distance of 1.5 Mpc from cluster centre in the Minkowski functional method are robust enough to be taken into account, but for that radius we did not find any relation between e and z. Since CEM pointed towards the existence of the e(z) relation, we conclude that such an effect is real though rather weak. A detailed study of the e(z) relation showed that the observed relation is nonlinear, and the number of elongated structures grows rapidly for z>0.14.

Binary-corrected velocity dispersions from single- and multi-epoch radial velocities: massive stars in R136 as a test case

NASA Astrophysics Data System (ADS)

Cottaar, M.; Hénault-Brunet, V.

2014-02-01

Orbital motions from binary stars can broaden the observed line-of-sight velocity distribution of a stellar system and artificially inflate the measured line-of-sight velocity dispersion, which can in turn lead to erroneous conclusions about the dynamical state of the system. Recently, a maximum-likelihood procedure was proposed to recover the intrinsic velocity dispersion of a resolved star cluster from a single epoch of radial velocity data of individual stars, which was achieved by simultaneously fitting the intrinsic velocity distribution of the single stars and the centers of mass of the binaries along with the velocity shifts caused by binary orbital motions. Assuming well-characterized binary properties, this procedure can accurately reproduce intrinsic velocity dispersions below 1 km s-1 for solar-type stars. Here we investigate the systematic offsets induced when the binary properties are uncertain and we show that two epochs of radial velocity data with an appropriate baseline can help to mitigate these systematic effects. We first test the method described above using Monte Carlo simulations, taking into account the large uncertainties in the binary properties of OB stars. We then apply it to radial velocity data in the young massive cluster R136 for which the intrinsic velocity dispersion of O-type stars is known from an intensive multi-epoch approach. For typical velocity dispersions of young massive clusters (≳4 km s-1) and with a single epoch of data, we demonstrate that the method can just about distinguish between a cluster in virial equilibrium and an unbound cluster. This is due to the higher spectroscopic binary fraction and more loosely constrained distributions of orbital parameters of OB stars compared to solar-type stars. By extending the maximum-likelihood method to multi-epoch data, we show that the accuracy on the fitted velocity dispersion can be improved by only a few percent by using only two epochs of radial velocities. This procedure offers a promising method of accurately measuring the intrinsic stellar velocity dispersion in other systems for which the binary properties are poorly constrained, for example, young clusters and associations whose luminosity is dominated by OB stars. Appendix A is available in electronic form at http://www.aanda.org

A first principles investigation of the oxygen adsorption on Zr(0001) surface using cluster expansions

NASA Astrophysics Data System (ADS)

Samin, Adib J.; Taylor, Christopher D.

2017-11-01

The design of corrosion resistant zircalloys is important for a variety of technological applications ranging from medicine to the nuclear industry. Since corrosion resistance is mainly attributed to the formation of a surface oxide layer, developing a detailed understanding of this process may assist in future corrosion resistance design. In this work, we conduct a systematic multi-scale investigation of the early stages of oxide formation. This was accomplished by first using a database of fully relaxed DFT calculations to build a cluster-expansion description of the potential function. The developed potential was reasonably good at predicting DFT energies as evidenced by the cross-validation score of 4.4 meV/site. The effective cluster expansion parameters were indicative of repulsive adsorbate interactions in the adlayer in agreement with the literature. The potential then allowed for a systematic investigation of the oxygen configurations on the Zr(0001) surface via Monte Carlo simulations. The adsorption energy was recorded as a function of coverage and an increasing trend was observed in agreement with DFT predictions and the repulsive nature of interactions in the adlayer. The convex hull diagram was recorded indicating the most stable configuration to occur around a coverage of 0.6 ML. The adsorption isotherm was also recorded and contrasted for two temperatures relevant for different applications.

VizieR Online Data Catalog: Star clusters distances and extinctions (Buckner+, 2013)

NASA Astrophysics Data System (ADS)

Buckner, A. S. M.; Froebrich, D.

2014-10-01

Determining star cluster distances is essential to analyse their properties and distribution in the Galaxy. In particular, it is desirable to have a reliable, purely photometric distance estimation method for large samples of newly discovered cluster candidates e.g. from the Two Micron All Sky Survey, the UK Infrared Deep Sky Survey Galactic Plane Survey and VVV. Here, we establish an automatic method to estimate distances and reddening from near-infrared photometry alone, without the use of isochrone fitting. We employ a decontamination procedure of JHK photometry to determine the density of stars foreground to clusters and a galactic model to estimate distances. We then calibrate the method using clusters with known properties. This allows us to establish distance estimates with better than 40 percent accuracy. We apply our method to determine the extinction and distance values to 378 known open clusters and 397 cluster candidates from the list of Froebrich, Scholz & Raftery (2007MNRAS.374..399F, Cat. J/MNRAS/374/399). We find that the sample is biased towards clusters of a distance of approximately 3kpc, with typical distances between 2 and 6kpc. Using the cluster distances and extinction values, we investigate how the average extinction per kiloparsec distance changes as a function of the Galactic longitude. We find a systematic dependence that can be approximated by AH(l)[mag/kpc]=0.10+0.001x|l-180°|/° for regions more than 60° from the Galactic Centre. (1 data file).

A Systematic Approach to Subgroup Classification in Intellectual Disability

ERIC Educational Resources Information Center

Schalock, Robert L.; Luckasson, Ruth

2015-01-01

This article describes a systematic approach to subgroup classification based on a classification framework and sequential steps involved in the subgrouping process. The sequential steps are stating the purpose of the classification, identifying the classification elements, using relevant information, and using clearly stated and purposeful…

Hydration of Atmospheric Molecular Clusters: Systematic Configurational Sampling.

PubMed

Kildgaard, Jens; Mikkelsen, Kurt V; Bilde, Merete; Elm, Jonas

2018-05-09

We present a new systematic configurational sampling algorithm for investigating the potential energy surface of hydrated atmospheric molecular clusters. The algo- rithm is based on creating a Fibonacci sphere around each atom in the cluster and adding water molecules to each point in 9 different orientations. To allow the sam- pling of water molecules to existing hydrogen bonds, the cluster is displaced along the hydrogen bond and a water molecule is placed in between in three different ori- entations. Generated redundant structures are eliminated based on minimizing the root mean square distance (RMSD) of different conformers. Initially, the clusters are sampled using the semiempirical PM6 method and subsequently using density func- tional theory (M06-2X and ωB97X-D) with the 6-31++G(d,p) basis set. Applying the developed algorithm we study the hydration of sulfuric acid with up to 15 water molecules. We find that the additions of the first four water molecules "saturate" the sulfuric acid molecule and are more thermodynamically favourable than the addition of water molecule 5-15. Using the large generated set of conformers, we assess the performance of approximate methods (ωB97X-D, M06-2X, PW91 and PW6B95-D3) in calculating the binding energies and assigning the global minimum conformation compared to high level CCSD(T)-F12a/VDZ-F12 reference calculations. The tested DFT functionals systematically overestimates the binding energies compared to cou- pled cluster calculations, and we find that this deficiency can be corrected by a simple scaling factor.

Critical behavior of the quantum spin- {1}/{2} anisotropic Heisenberg model

NASA Astrophysics Data System (ADS)

Sousa, J. Ricardo de

A two-step renormalization group approach - a decimation followed by an effective field renormalization group (EFRG) - is proposed in this work to study the critical behavior of the quantum spin- {1}/{2} anisotropic Heisenberg model. The new method is illustrated by employing approximations in which clusters with one, two and three spins are used. The values of the critical parameter and critical exponent, in two- and three-dimensional lattices, for the Ising and isotropic Heisenberg limits are calculated and compared with other renormalization group approaches and exact (or series) results.

Symptom clusters and treatment time delay in Korean patients with ST-elevation myocardial infarction on admission.

PubMed

Kim, Hee-Sook; Eun, Sang Jun; Hwang, Jin Yong; Lee, Kun-Sei; Cho, Sung-Il

2018-05-01

Most patients with acute myocardial infarction (AMI) experience more than one symptom at onset. Although symptoms are an important early indicator, patients and physicians may have difficulty interpreting symptoms and detecting AMI at an early stage. This study aimed to identify symptom clusters among Korean patients with ST-elevation myocardial infarction (STEMI), to examine the relationship between symptom clusters and patient-related variables, and to investigate the influence of symptom clusters on treatment time delay (decision time [DT], onset-to-balloon time [OTB]). This was a prospective multicenter study with a descriptive design that used face-to-face interviews. A total of 342 patients with STEMI were included in this study. To identify symptom clusters, two-step cluster analysis was performed using SPSS software. Multinomial logistic regression to explore factors related to each cluster and multiple logistic regression to determine the effect of symptom clusters on treatment time delay were conducted. Three symptom clusters were identified: cluster 1 (classic MI; characterized by chest pain); cluster 2 (stress symptoms; sweating and chest pain); and cluster 3 (multiple symptoms; dizziness, sweating, chest pain, weakness, and dyspnea). Compared with patients in clusters 2 and 3, those in cluster 1 were more likely to have diabetes or prior MI. Patients in clusters 2 and 3, who predominantly showed other symptoms in addition to chest pain, had a significantly shorter DT and OTB than those in cluster 1. In conclusion, to decrease treatment time delay, it seems important that patients and clinicians recognize symptom clusters, rather than relying on chest pain alone. Further research is necessary to translate our findings into clinical practice and to improve patient education and public education campaigns.

A multimembership catalogue for 1876 open clusters using UCAC4 data

NASA Astrophysics Data System (ADS)

Sampedro, L.; Dias, W. S.; Alfaro, E. J.; Monteiro, H.; Molino, A.

2017-10-01

The main objective of this work is to determine the cluster members of 1876 open clusters, using positions and proper motions of the astrometric fourth United States Naval Observatory (USNO) CCD Astrograph Catalog (UCAC4). For this purpose, we apply three different methods, all based on a Bayesian approach, but with different formulations: a purely parametric method, another completely non-parametric algorithm and a third, recently developed by Sampedro & Alfaro, using both formulations at different steps of the whole process. The first and second statistical moments of the members' phase-space subspace, obtained after applying the three methods, are compared for every cluster. Although, on average, the three methods yield similar results, there are also specific differences between them, as well as for some particular clusters. The comparison with other published catalogues shows good agreement. We have also estimated, for the first time, the mean proper motion for a sample of 18 clusters. The results are organized in a single catalogue formed by two main files, one with the most relevant information for each cluster, partially including that in UCAC4, and the other showing the individual membership probabilities for each star in the cluster area. The final catalogue, with an interface design that enables an easy interaction with the user, is available in electronic format at the Stellar Systems Group (SSG-IAA) web site (http://ssg.iaa.es/en/content/sampedro-cluster-catalog).

Sulfur mobilization for Fe-S cluster assembly by the essential SUF pathway in the Plasmodium falciparum apicoplast and its inhibition.

PubMed

Charan, Manish; Singh, Nidhi; Kumar, Bijay; Srivastava, Kumkum; Siddiqi, Mohammad Imran; Habib, Saman

2014-06-01

The plastid of the malaria parasite, the apicoplast, is essential for parasite survival. It houses several pathways of bacterial origin that are considered attractive sites for drug intervention. Among these is the sulfur mobilization (SUF) pathway of Fe-S cluster biogenesis. Although the SUF pathway is essential for apicoplast maintenance and parasite survival, there has been limited biochemical investigation of its components and inhibitors of Plasmodium SUFs have not been identified. We report the characterization of two proteins, Plasmodium falciparum SufS (PfSufS) and PfSufE, that mobilize sulfur in the first step of Fe-S cluster assembly and confirm their exclusive localization to the apicoplast. The cysteine desulfurase activity of PfSufS is greatly enhanced by PfSufE, and the PfSufS-PfSufE complex is detected in vivo. Structural modeling of the complex reveals proximal positioning of conserved cysteine residues of the two proteins that would allow sulfide transfer from the PLP (pyridoxal phosphate) cofactor-bound active site of PfSufS. Sulfide release from the l-cysteine substrate catalyzed by PfSufS is inhibited by the PLP inhibitor d-cycloserine, which forms an adduct with PfSufS-bound PLP. d-Cycloserine is also inimical to parasite growth, with a 50% inhibitory concentration close to that reported for Mycobacterium tuberculosis, against which the drug is in clinical use. Our results establish the function of two proteins that mediate sulfur mobilization, the first step in the apicoplast SUF pathway, and provide a rationale for drug design based on inactivation of the PLP cofactor of PfSufS. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Clustering-based spot segmentation of cDNA microarray images.

PubMed

Uslan, Volkan; Bucak, Ihsan Ömür

2010-01-01

Microarrays are utilized as that they provide useful information about thousands of gene expressions simultaneously. In this study segmentation step of microarray image processing has been implemented. Clustering-based methods, fuzzy c-means and k-means, have been applied for the segmentation step that separates the spots from the background. The experiments show that fuzzy c-means have segmented spots of the microarray image more accurately than the k-means.

Tailoring Ion Charge State Distribution in Tetramethyltin Clusters under Influence of Moderate Intensity Picosecond Laser Pulse: Role of Laser Wavelength and Rate of Energy Deposition

NASA Astrophysics Data System (ADS)

Sharma, Pramod; Das, Soumitra; Vatsa, Rajesh K.

2017-07-01

Systematic manipulation of ionic-outcome in laser-cluster interaction process has been realized for studies carried out on tetramethyltin (TMT) clusters under picosecond laser conditions, determined by choice of laser wavelength and intensity. As a function of laser intensity, TMT clusters exhibit gradual enhancement in overall ionization of its cluster constituents, up to a saturation level of ionization, which was distinct for different wavelengths (266, 355, and 532 nm). Simultaneously, systematic appearance of higher multiply charged atomic ions and shift in relative abundance of multiply charged atomic ions towards higher charge state was observed, using time-of-flight mass spectrometer. At saturation level, multiply charged atomic ions up to (C2+, Sn2+) at 266 nm, (C4+, Sn4+) at 355 nm, and (C4+, Sn6+) at 532 nm were detected. In addition, at 355 nm intra-cluster ion chemistry within the ionized cluster leads to generation of molecular hydrogen ion (H2 +) and triatomic molecular hydrogen ion (H3 +). Generation of multiply charged atomic ions is ascribed to efficient coupling of laser pulse with the cluster media, facilitated by inner-ionized electrons produced within the cluster, at the leading edge of laser pulse. Role of inner-ionized electrons is authenticated by measuring kinetic energy distribution of electrons liberated upon disintegration of excessively ionized cluster, under the influence of picosecond laser pulse.

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

PubMed

Lee, Woojoo; Alexeyenko, Andrey; Pernemalm, Maria; Guegan, Justine; Dessen, Philippe; Lazar, Vladimir; Lehtiö, Janne; Pawitan, Yudi

2015-01-01

Biological heterogeneity is common in many diseases and it is often the reason for therapeutic failures. Thus, there is great interest in classifying a disease into subtypes that have clinical significance in terms of prognosis or therapy response. One of the most popular methods to uncover unrecognized subtypes is cluster analysis. However, classical clustering methods such as k-means clustering or hierarchical clustering are not guaranteed to produce clinically interesting subtypes. This could be because the main statistical variability--the basis of cluster generation--is dominated by genes not associated with the clinical phenotype of interest. Furthermore, a strong prognostic factor might be relevant for a certain subgroup but not for the whole population; thus an analysis of the whole sample may not reveal this prognostic factor. To address these problems we investigate methods to identify and assess clinically interesting subgroups in a heterogeneous population. The identification step uses a clustering algorithm and to assess significance we use a false discovery rate- (FDR-) based measure. Under the heterogeneity condition the standard FDR estimate is shown to overestimate the true FDR value, but this is remedied by an improved FDR estimation procedure. As illustrations, two real data examples from gene expression studies of lung cancer are provided.

'Team up against TB': promoting involvement in Thibela TB, a trial of community-wide tuberculosis preventive therapy.

PubMed

Grant, Alison D; Coetzee, Leonie; Fielding, Katherine L; Lewis, James J; Ntshele, Smanga; Luttig, Mariëtha M; Mngadi, Kathryn T; Muller, Dorothy; Popane, Flora; Mdluli, John; Mngadi, Nkosinathi; Sefuthi, Clement; Clark, David A; Churchyard, Gavin

2010-11-01

To describe a programme of community education and mobilization to promote uptake in a cluster-randomized trial of tuberculosis preventive therapy offered to all members of intervention clusters. Gold mines in South Africa, where tuberculosis incidence is extremely high, despite conventional control measures. All employees in intervention clusters (mine shaft and associated hostel) were invited to enrol. Cumulative enrolment in the study in intervention clusters. Key steps in communicating information relevant to the study included extensive consultation with key stakeholders; working with a communication company to develop a project 'brand'; developing a communication strategy tailored to each intervention site; and involving actors from a popular television comedy series to help inform communities about the study. One-to-one communications used peer educators along with study staff, and participant advisory groups facilitated two-way communication between study staff and participants. By contrast, treatment 'buddies' and text messaging to promote adherence proved less successful. Mean cumulative enrolment in the first four intervention clusters was 61.9%, increasing to 83.0% in the final four clusters. A tailored communication strategy can facilitate a high level of enrolment in a community health intervention.

A two-step patterning process increases the robustness of periodic patterning in the fly eye.

PubMed

Gavish, Avishai; Barkai, Naama

2016-06-01

Complex periodic patterns can self-organize through dynamic interactions between diffusible activators and inhibitors. In the biological context, self-organized patterning is challenged by spatial heterogeneities ('noise') inherent to biological systems. How spatial variability impacts the periodic patterning mechanism and how it can be buffered to ensure precise patterning is not well understood. We examine the effect of spatial heterogeneity on the periodic patterning of the fruit fly eye, an organ composed of ∼800 miniature eye units (ommatidia) whose periodic arrangement along a hexagonal lattice self-organizes during early stages of fly development. The patterning follows a two-step process, with an initial formation of evenly spaced clusters of ∼10 cells followed by a subsequent refinement of each cluster into a single selected cell. Using a probabilistic approach, we calculate the rate of patterning errors resulting from spatial heterogeneities in cell size, position and biosynthetic capacity. Notably, error rates were largely independent of the desired cluster size but followed the distributions of signaling speeds. Pre-formation of large clusters therefore greatly increases the reproducibility of the overall periodic arrangement, suggesting that the two-stage patterning process functions to guard the pattern against errors caused by spatial heterogeneities. Our results emphasize the constraints imposed on self-organized patterning mechanisms by the need to buffer stochastic effects. Author summary Complex periodic patterns are common in nature and are observed in physical, chemical and biological systems. Understanding how these patterns are generated in a precise manner is a key challenge. Biological patterns are especially intriguing, as they are generated in a noisy environment; cell position and cell size, for example, are subject to stochastic variations, as are the strengths of the chemical signals mediating cell-to-cell communication. The need to generate a precise and robust pattern in this 'noisy' environment restricts the space of patterning mechanisms that can function in the biological setting. Mathematical modeling is useful in comparing the sensitivity of different mechanisms to such variations, thereby highlighting key aspects of their design.We use mathematical modeling to study the periodic patterning of the fruit fly eye. In this system, a highly ordered lattice of differentiated cells is generated in a two-dimensional cell epithelium. The pattern is first observed by the appearance of evenly spaced clusters of ∼10 cells that express specific genes. Each cluster is subsequently refined into a single cell, which initiates the formation and differentiation of a miniature eye unit, the ommatidium. We formulate a mathematical model based on the known molecular properties of the patterning mechanism, and use a probabilistic approach to calculate the errors in cluster formation and refinement resulting from stochastic cell-to-cell variations ('noise') in different quantitative parameters. This enables us to define the parameters most influencing noise sensitivity. Notably, we find that this error is roughly independent of the desired cluster size, suggesting that large clusters are beneficial for ensuring the overall reproducibility of the periodic cluster arrangement. For the stage of cluster refinement, we find that rapid communication between cells is critical for reducing error. Our work provides new insights into the constraints imposed on mechanisms generating periodic patterning in a realistic, noisy environment, and in particular, discusses the different considerations in achieving optimal design of the patterning network.

Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways

PubMed Central

Čavužić, Mirela; Liu, Yuchen

2017-01-01

Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s2U) derivatives, 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A). Their biosynthetic pathways have two major types depending on the requirement of iron–sulfur (Fe–S) clusters. In all cases, the first step in bacteria and eukaryotes is to activate the sulfur atom of free l-cysteine by cysteine desulfurases, generating a persulfide (R-S-SH) group. In some archaea, a cysteine desulfurase is missing. The following steps of the bacterial s2U and s4U formation are Fe–S cluster independent, and the activated sulfur is transferred by persulfide-carrier proteins. By contrast, the biosynthesis of bacterial s2C and ms2A require Fe–S cluster dependent enzymes. A recent study shows that the archaeal s4U synthetase (ThiI) and the eukaryotic cytosolic 2-thiouridine synthetase (Ncs6) are Fe–S enzymes; this expands the role of Fe–S enzymes in tRNA thiolation to the Archaea and Eukarya domains. The detailed reaction mechanisms of Fe–S cluster depend s2U and s4U formation await further investigations. PMID:28287455

Evidence for biasing in the CfA survey

NASA Technical Reports Server (NTRS)

Hamilton, A. J. S.

1988-01-01

Intrinsically bright galaxies appear systematically more correlated than faint galaxies in the Center for Astrophysics redshift survey. The amplification of the two-point correlation function behaves exponentially with luminosity, being essentially flat up to the knee of the luminosity function, then increasing markedly. The amplification reaches a factor of 3.5e + or - 0.4 in the very brightest galaxies. The effect is dominated by spirals rather than ellipticals, so that the correlation function of bright spirals becomes comparable to that of normal ellipticals. Similar results are obtained whether the correlation function is measured in two or three dimensions. The effect persists to separations of a correlation length or more, and is not confined to the cores of the Virgo, Coma, and Abell 1367 clusters, suggesting that the effect is caused by biasing, that is, galaxies kindle preferentially in more clustered regions, rather than by gravitational relaxation.

Stepwise Assembly and Characterization of DNA Linked Two-Color Quantum Dot Clusters.

PubMed

Coopersmith, Kaitlin; Han, Hyunjoo; Maye, Mathew M

2015-07-14

The DNA-mediated self-assembly of multicolor quantum dot (QD) clusters via a stepwise approach is described. The CdSe/ZnS QDs were synthesized and functionalized with an amphiphilic copolymer, followed by ssDNA conjugation. At each functionalization step, the QDs were purified via gradient ultracentrifugation, which was found to remove excess polymer and QD aggregates, allowing for improved conjugation yields and assembly reactivity. The QDs were then assembled and disassembled in a stepwise manner at a ssDNA functionalized magnetic colloid, which provided a convenient way to remove unreacted QDs and ssDNA impurities. After assembly/disassembly, the clusters' optical characteristics were studied by fluorescence spectroscopy and the assembly morphology and stoichiometry was imaged via electron microscopy. The results indicate that a significant amount of QD-to-QD energy transfer occurred in the clusters, which was studied as a function of increasing acceptor-to-donor ratios, resulting in increased QD acceptor emission intensities compared to controls.

Adolescents' physical activity in physical education, school recess, and extra-curricular sport by motivational profiles.

PubMed

Mayorga-Vega, Daniel; Viciana, Jesús

2014-06-01

The main purpose of this study was to evaluate the differences in adolescents´ objective physical activity levels and perceived effort in physical education, school recess, and extra-curricular organized sport by motivational profiles in physical education. A sample of 102 students 11-16 yr. old completed a self-report questionnaire assessing self-determined motivation toward physical education. Subsequently, students' objective physical activity levels (steps/min., METs, and moderate-to-vigorous physical activity) and perceived effort were evaluated for each situation. Cluster analysis identified a two-cluster structure: "Moderate motivation toward physical education profile" and "High motivation toward physical education profile." Adolescents in the second cluster had higher physical activity and perceived effort values than adolescents in the first cluster, except for METs and moderate-to-vigorous physical activity in extra-curricular sport. These results support the importance of physical education teachers who should promote self-determined motivation toward physical education so that students can reach the recommended physical activity levels.

Organizational-Level Strategies With or Without an Activity Tracker to Reduce Office Workers’ Sitting Time: Rationale and Study Design of a Pilot Cluster-Randomized Trial

PubMed Central

Fjeldsoe, Brianna S; Young, Duncan C; Winkler, Elisabeth A H; Dunstan, David W; Straker, Leon M; Brakenridge, Christian J; Healy, Genevieve N

2016-01-01

Background The office workplace is a key setting in which to address excessive sitting time and inadequate physical activity. One major influence on workplace sitting is the organizational environment. However, the impact of organizational-level strategies on individual level activity change is unknown. Further, the emergence of sophisticated, consumer-targeted wearable activity trackers that facilitate real-time self-monitoring of activity, may be a useful adjunct to support organizational-level strategies, but to date have received little evaluation in this workplace setting. Objective The aim of this study is to evaluate the feasibility, acceptability, and effectiveness of organizational-level strategies with or without an activity tracker on sitting, standing, and stepping in office workers in the short (3 months, primary aim) and long-term (12 months, secondary aim). Methods This study is a pilot, cluster-randomized trial (with work teams as the unit of clustering) of two interventions in office workers: organizational-level support strategies (eg, visible management support, emails) or organizational-level strategies plus the use of a waist-worn activity tracker (the LUMOback) that enables self-monitoring of sitting, standing, and stepping time and enables users to set sitting and posture alerts. The key intervention message is to ‘Stand Up, Sit Less, and Move More.’ Intervention elements will be implemented from within the organization by the Head of Workplace Wellbeing. Participants will be recruited via email and enrolled face-to-face. Assessments will occur at baseline, 3, and 12 months. Time spent sitting, sitting in prolonged (≥30 minute) bouts, standing, and stepping during work hours and across the day will be measured with activPAL3 activity monitors (7 days, 24 hours/day protocol), with total sitting time and sitting time during work hours the primary outcomes. Web-based questionnaires, LUMOback recorded data, telephone interviews, and focus groups will measure the feasibility and acceptability of both interventions and potential predictors of behavior change. Results Baseline and follow-up data collection has finished. Results are expected in 2016. Conclusions This pilot, cluster-randomized trial will evaluate the feasibility, acceptability, and effectiveness of two interventions targeting reductions in sitting and increases in standing and stepping in office workers. Few studies have evaluated these intervention strategies and this study has the potential to contribute both short and long-term findings. PMID:27226457

Structural and electronic properties of U{sub n}O{sub m} (n=1-3,m=1-3n) clusters: A theoretical study using screened hybrid density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yu; Liu, Haitao; Zhang, Ping, E-mail: zhang-ping@iapcm.ac.cn

The structural and electronic properties of small uranium oxide clusters U{sub n}O{sub m} (n=1-3, m=1-3n) are systematically studied within the screened hybrid density functional theory. It is found that the formation of U–O–U bondings and isolated U–O bonds are energetically more stable than U–U bondings. As a result, no uranium cores are observed. Through fragmentation studies, we find that the U{sub n}O{sub m} clusters with the m/n ratio between 2 and 2.5 are very stable, hinting that UO{sub 2+x} hyperoxides are energetically stable. Electronically, we find that the O-2p states always distribute in the deep energy range, and the U-5fmore » states always distribute at the two sides of the Fermi level. The U-6d states mainly hybridize with the U-5f states in U-rich clusters, while hybridizing with O-2p states in O-rich clusters. Our work is the first one on the screened hybrid density functional theory level studying the atomic and electronic properties of the actinide oxide clusters.« less

[Fe-S] cluster assembly in the apicoplast and its indispensability in mosquito stages of the malaria parasite.

PubMed

Charan, Manish; Choudhary, Hadi Hasan; Singh, Nidhi; Sadik, Mohammad; Siddiqi, Mohammad Imran; Mishra, Satish; Habib, Saman

2017-08-01

The relict plastid (apicoplast) of the malaria parasite is the site for important biochemical pathways and is essential for parasite survival. The sulfur mobilization (SUF) pathway of iron-sulfur [Fe-S] cluster assembly in the apicoplast of Plasmodium spp. is of interest due to its absence in the human host suggesting the possibility of antimalarial intervention through apicoplast [Fe-S] biogenesis. We report biochemical characterization of components of the Plasmodium falciparum apicoplast SUF pathway after the first step of SUF. In vitro interaction experiments and in vivo cross-linking showed that apicoplast-encoded PfSufB and apicoplast-targeted PfSufC and PfSufD formed a complex. The PfSufB-C 2 -D complex could function as a scaffold to assemble [4Fe-4S] clusters in vitro and activity of the PfSufC ATPase was enhanced by PfSufD. Two carrier proteins, the NifU-like protein PfNfu and the A-type carrier PfSufA are homodimers, the former mediating transfer of [4Fe-4S] from the scaffold to a model [4Fe-4S] target protein with higher efficiency. Conditional knockout of SufS, the enzyme catalyzing the first step of SUF, by selective excision in the mosquito stages of Plasmodium berghei severely impaired development of sporozoites in oocysts establishing essentiality of the SUF machinery in the vector. Our results delineate steps of the complete apicoplast SUF pathway and demonstrate its critical role in the parasite life cycle. © 2017 Federation of European Biochemical Societies.

Canopy1, a positive feedback regulator of FGF signaling, controls progenitor cell clustering during Kupffer's vesicle organogenesis

PubMed Central

Matsui, Takaaki; Thitamadee, Siripong; Murata, Tomoko; Kakinuma, Hisaya; Nabetani, Takuji; Hirabayashi, Yoshio; Hirate, Yoshikazu; Okamoto, Hitoshi; Bessho, Yasumasa

2011-01-01

The assembly of progenitor cells is a crucial step for organ formation during vertebrate development. Kupffer's vesicle (KV), a key organ required for the left–right asymmetric body plan in zebrafish, is generated from a cluster of ∼20 dorsal forerunner cells (DFCs). Although several genes are known to be involved in KV formation, how DFC clustering is regulated and how cluster formation then contributes to KV formation remain unclear. Here we show that positive feedback regulation of FGF signaling by Canopy1 (Cnpy1) controls DFC clustering. Cnpy1 positively regulates FGF signals within DFCs, which in turn promote Cadherin1-mediated cell adhesion between adjacent DFCs to sustain cell cluster formation. When this FGF positive feedback loop is disrupted, the DFC cluster fails to form, eventually leading to KV malformation and defects in the establishment of laterality. Our results therefore uncover both a previously unidentified role of FGF signaling during vertebrate organogenesis and a regulatory mechanism underlying cell cluster formation, which is an indispensable step for formation of a functional KV and establishment of the left–right asymmetric body plan. PMID:21628557

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory

NASA Astrophysics Data System (ADS)

Jensen, Christian H.; Nerukh, Dmitry; Glen, Robert C.

2008-03-01

We investigate the sensitivity of a Markov model with states and transition probabilities obtained from clustering a molecular dynamics trajectory. We have examined a 500ns molecular dynamics trajectory of the peptide valine-proline-alanine-leucine in explicit water. The sensitivity is quantified by varying the boundaries of the clusters and investigating the resulting variation in transition probabilities and the average transition time between states. In this way, we represent the effect of clustering using different clustering algorithms. It is found that in terms of the investigated quantities, the peptide dynamics described by the Markov model is sensitive to the clustering; in particular, the average transition times are found to vary up to 46%. Moreover, inclusion of nonphysical sparsely populated clusters can lead to serious errors of up to 814%. In the investigation, the time step used in the transition matrix is determined by the minimum time scale on which the system behaves approximately Markovian. This time step is found to be about 100ps. It is concluded that the description of peptide dynamics with transition matrices should be performed with care, and that using standard clustering algorithms to obtain states and transition probabilities may not always produce reliable results.

Iron-sulfur clusters as biological sensors: the chemistry of reactions with molecular oxygen and nitric oxide.

PubMed

Crack, Jason C; Green, Jeffrey; Thomson, Andrew J; Le Brun, Nick E

2014-10-21

Iron-sulfur cluster proteins exhibit a range of physicochemical properties that underpin their functional diversity in biology, which includes roles in electron transfer, catalysis, and gene regulation. Transcriptional regulators that utilize iron-sulfur clusters are a growing group that exploit the redox and coordination properties of the clusters to act as sensors of environmental conditions including O2, oxidative and nitrosative stress, and metabolic nutritional status. To understand the mechanism by which a cluster detects such analytes and then generates modulation of DNA-binding affinity, we have undertaken a combined strategy of in vivo and in vitro studies of a range of regulators. In vitro studies of iron-sulfur cluster proteins are particularly challenging because of the inherent reactivity and fragility of the cluster, often necessitating strict anaerobic conditions for all manipulations. Nevertheless, and as discussed in this Account, significant progress has been made over the past decade in studies of O2-sensing by the fumarate and nitrate reduction (FNR) regulator and, more recently, nitric oxide (NO)-sensing by WhiB-like (Wbl) and FNR proteins. Escherichia coli FNR binds a [4Fe-4S] cluster under anaerobic conditions leading to a DNA-binding dimeric form. Exposure to O2 converts the cluster to a [2Fe-2S] form, leading to protein monomerization and hence loss of DNA binding ability. Spectroscopic and kinetic studies have shown that the conversion proceeds via at least two steps and involves a [3Fe-4S](1+) intermediate. The second step involves the release of two bridging sulfide ions from the cluster that, unusually, are not released into solution but rather undergo oxidation to sulfane (S(0)) subsequently forming cysteine persulfides that then coordinate the [2Fe-2S] cluster. Studies of other [4Fe-4S] cluster proteins that undergo oxidative cluster conversion indicate that persulfide formation and coordination may be more common than previously recognized. This remarkable feature suggested that the original [4Fe-4S] cluster can be restored using persulfide as the source of sulfide ion. We have demonstrated that only iron and a source of electrons are required to promote efficient conversion back from the [2Fe-2S] to the [4Fe-4S] form. We propose this as a novel in vivo repair mechanism that does not require the intervention of an iron-sulfur cluster biogenesis pathway. A number of iron-sulfur regulators have evolved to function as sensors of NO. Although it has long been known that the iron-sulfur clusters of many phylogenetically unrelated proteins are vulnerable to attack by NO, our recent studies of Wbl proteins and FNR have provided new insights into the mechanism of cluster nitrosylation, which overturn the commonly accepted view that the product is solely a mononuclear iron dinitrosyl complex (known as a DNIC). The major reaction is a rapid, multiphase process involving stepwise addition of up to eight NO molecules per [4Fe-4S] cluster. The major iron nitrosyl product is EPR silent and has optical characteristics similar to Roussin's red ester, [Fe2(NO)4(RS)2] (RRE), although a species similar to Roussin's black salt, [Fe4(NO)7(S)3](-) (RBS) cannot be ruled out. A major future challenge will be to clarify the nature of these species.

Calibrating First-Order Strong Lensing Mass Estimates in Clusters of Galaxies

NASA Astrophysics Data System (ADS)

Reed, Brendan; Remolian, Juan; Sharon, Keren; Li, Nan; SPT Clusters Cooperation

2018-01-01

We investigate methods to reduce the statistical and systematic errors inherent to using the Einstein Radius as a first-order mass estimate in strong lensing galaxy clusters. By finding an empirical universal calibration function, we aim to enable a first-order mass estimate of large cluster data sets in a fraction of the time and effort of full-scale strong lensing mass modeling. We use 74 simulated cluster data from the Argonne National Laboratory in a lens redshift slice of [0.159, 0.667] with various source redshifts in the range of [1.23, 2.69]. From the simulated density maps, we calculate the exact mass enclosed within the Einstein Radius. We find that the mass inferred from the Einstein Radius alone produces an error width of ~39% with respect to the true mass. We explore an array of polynomial and exponential correction functions with dependence on cluster redshift and projected radii of the lensed images, aiming to reduce the statistical and systematic uncertainty. We find that the error on the the mass inferred from the Einstein Radius can be reduced significantly by using a universal correction function. Our study has implications for current and future large galaxy cluster surveys aiming to measure cluster mass, and the mass-concentration relation.

Clustering of brain tumor cells: a first step for understanding tumor recurrence

NASA Astrophysics Data System (ADS)

Khain, Evgeniy; Nowicki, M. O.; Chiocca, E. A.; Lawler, S. E.; Schneider-Mizell, C. M.; Sander, L. M.

2012-02-01

Glioblastoma tumors are highly invasive; therefore the overall prognosis of patients remains poor, despite major improvements in treatment techniques. Cancer cells detach from the inner tumor core and actively migrate away [1]; eventually these invasive cells might form clusters, which can develop to recurrent tumors. In vitro experiments in collagen gel [1] followed the clustering dynamics of different glioma cell lines. Based on the experimental data, we formulated a stochastic model for cell dynamics, which identified two mechanisms of clustering. First, there is a critical value of the strength of adhesion; above the threshold, large clusters grow from a homogeneous suspension of cells; below it, the system remains homogeneous, similarly to the ordinary phase separation. Second, when cells form a cluster, there is evidence that their proliferation rate increases. We confirmed the theoretical predictions in a separate cell migration experiment on a substrate and found that both mechanisms are crucial for cluster formation and growth [2]. In addition to their medical importance, these phenomena present exciting examples of pattern formation and collective cell behavior in intrinsically non-equilibrium systems [3]. [4pt] [1] A. M. Stein et al, Biophys. J., 92, 356 (2007). [0pt] [2] E. Khain et al, EPL 88, 28006 (2009). [0pt] [3] E. Khain et al, Phys. Rev. E. 83, 031920 (2011).

Opening the Window on Galaxy Assembly: Ages and Structural Parameters of Globular Clusters Towards the Galactic Bulge

NASA Astrophysics Data System (ADS)

Cohen, Roger

2015-10-01

The primary aim of this program is to undertake a systematic investigation of highly reddened Galactic globular clusters (GGCs) located towards the Galactic bulge. These clusters have been excluded from deep space-based photometric surveys due to their severe total and differential extinction. We will exploit the photometric depth and homogeneity of two existing Treasury programs (the ACS GGC Treasury Survey and the WFC3 Bulge Treasury Program) along with the unique optical+IR parallel imaging capabilities of HST to finally place the bulge GGCs in the context of their optically well-studied counterparts. Specifically, by leveraging ACS/WFC together with WFC3/IR, we first exploit the reddening sensitivity at optical wavelengths to map severe, small-scale differential reddening in the cluster cores. Corrected two-color WFC3/IR photometry will then be used to measure cluster ages to better than 1 Gyr relative precision, finally completing the age-metallicity relation of the Milky Way GGC system. Ages are obtained using a demonstrated procedure which is strictly differential, and therefore insensitive to total distance, reddening, reddening law, or photometric calibration uncertainties. At the same time, deep archival Treasury survey imaging of the Galactic bulge will be used to decontaminate cluster luminosity functions, yielding measurements of bulge GGC mass functions and mass segregation on par with results from the ACS GGC Treasury survey. Finally, the imaging which we propose will be combined with existing wide-field near-IR PSF photometry, yielding complete radial number density profiles, structural and morphological parameters.

Accurate Modeling of Galaxy Clustering on Small Scales: Testing the Standard ΛCDM + Halo Model

NASA Astrophysics Data System (ADS)

Sinha, Manodeep; Berlind, Andreas A.; McBride, Cameron; Scoccimarro, Roman

2015-01-01

The large-scale distribution of galaxies can be explained fairly simply by assuming (i) a cosmological model, which determines the dark matter halo distribution, and (ii) a simple connection between galaxies and the halos they inhabit. This conceptually simple framework, called the halo model, has been remarkably successful at reproducing the clustering of galaxies on all scales, as observed in various galaxy redshift surveys. However, none of these previous studies have carefully modeled the systematics and thus truly tested the halo model in a statistically rigorous sense. We present a new accurate and fully numerical halo model framework and test it against clustering measurements from two luminosity samples of galaxies drawn from the SDSS DR7. We show that the simple ΛCDM cosmology + halo model is not able to simultaneously reproduce the galaxy projected correlation function and the group multiplicity function. In particular, the more luminous sample shows significant tension with theory. We discuss the implications of our findings and how this work paves the way for constraining galaxy formation by accurate simultaneous modeling of multiple galaxy clustering statistics.

Method of identifying clusters representing statistical dependencies in multivariate data

NASA Technical Reports Server (NTRS)

Borucki, W. J.; Card, D. H.; Lyle, G. C.

1975-01-01

Approach is first to cluster and then to compute spatial boundaries for resulting clusters. Next step is to compute, from set of Monte Carlo samples obtained from scrambled data, estimates of probabilities of obtaining at least as many points within boundaries as were actually observed in original data.

New detections of embedded clusters in the Galactic halo

NASA Astrophysics Data System (ADS)

Camargo, D.; Bica, E.; Bonatto, C.

2016-09-01

Context. Until recently it was thought that high Galactic latitude clouds were a non-star-forming ensemble. However, in a previous study we reported the discovery of two embedded clusters (ECs) far away from the Galactic plane (~ 5 kpc). In our recent star cluster catalogue we provided additional high and intermediate latitude cluster candidates. Aims: This work aims to clarify whether our previous detection of star clusters far away from the disc represents just an episodic event or whether star cluster formation is currently a systematic phenomenon in the Galactic halo. We analyse the nature of four clusters found in our recent catalogue and report the discovery of three new ECs each with an unusually high latitude and distance from the Galactic disc midplane. Methods: The analysis is based on 2MASS and WISE colour-magnitude diagrams (CMDs), and stellar radial density profiles (RDPs). The CMDs are built by applying a field-star decontamination procedure, which uncovers the cluster's intrinsic CMD morphology. Results: All of these clusters are younger than 5 Myr. The high-latitude ECs C 932, C 934, and C 939 appear to be related to a cloud complex about 5 kpc below the Galactic disc, under the Local arm. The other clusters are above the disc, C 1074 and C 1100 with a vertical distance of ~3 kpc, C 1099 with ~ 2 kpc, and C 1101 with ~1.8 kpc. Conclusions: According to the derived parameters ECs located below and above the disc occur, which gives evidence of widespread star cluster formation throughout the Galactic halo. This study therefore represents a paradigm shift, by demonstrating that a sterile halo must now be understood as a host for ongoing star formation. The origin and fate of these ECs remain open. There are two possibilities for their origin, Galactic fountains or infall. The discovery of ECs far from the disc suggests that the Galactic halo is more actively forming stars than previously thought. Furthermore, since most ECs do not survive the infant mortality, stars may be raining from the halo into the disc, and/or the halo may be harbouring generations of stars formed in clusters like those detected in our survey.

Clustering performances in the NBA according to players' anthropometric attributes and playing experience.

PubMed

Zhang, Shaoliang; Lorenzo, Alberto; Gómez, Miguel-Angel; Mateus, Nuno; Gonçalves, Bruno; Sampaio, Jaime

2018-04-20

The aim of this study was: (i) to group basketball players into similar clusters based on a combination of anthropometric characteristics and playing experience; and (ii) explore the distribution of players (included starters and non-starters) from different levels of teams within the obtained clusters. The game-related statistics from 699 regular season balanced games were analyzed using a two-step cluster model and a discriminant analysis. The clustering process allowed identifying five different player profiles: Top height and weight (HW) with low experience, TopHW-LowE; Middle HW with middle experience, MiddleHW-MiddleE; Middle HW with top experience, MiddleHW-TopE; Low HW with low experience, LowHW-LowE; Low HW with middle experience, LowHW-MiddleE. Discriminant analysis showed that TopHW-LowE group was highlighted by two-point field goals made and missed, offensive and defensive rebounds, blocks, and personal fouls; whereas the LowHW-LowE group made fewest passes and touches. The players from weaker teams were mostly distributed in LowHW-LowE group, whereas players from stronger teams were mainly grouped in LowHW-MiddleE group; and players that participated in the finals were allocated in the MiddleHW-MiddleE group. These results provide alternative references for basketball staff concerning the process of evaluating performance.

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.

PubMed

Wagner, Tristan; Koch, Jürgen; Ermler, Ulrich; Shima, Seigo

2017-08-18

In methanogenic archaea, the carbon dioxide (CO 2 ) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferredoxin and the heterodisulfide of coenzymes M and B. Here, we present the structure of the native heterododecameric HdrABC-MvhAGD complex at 2.15-angstrom resolution. HdrB contains two noncubane [4Fe-4S] clusters composed of fused [3Fe-4S]-[2Fe-2S] units sharing 1 iron (Fe) and 1 sulfur (S), which were coordinated at the CCG motifs. Soaking experiments showed that the heterodisulfide is clamped between the two noncubane [4Fe-4S] clusters and homolytically cleaved, forming coenzyme M and B bound to each iron. Coenzymes are consecutively released upon one-by-one electron transfer. The HdrABC-MvhAGD atomic model serves as a structural template for numerous HdrABC homologs involved in diverse microbial metabolic pathways. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Delivery of Iron-Sulfur Clusters to the Hydrogen-Oxidizing [NiFe]-Hydrogenases in Escherichia coli Requires the A-Type Carrier Proteins ErpA and IscA

PubMed Central

Pinske, Constanze; Sawers, R. Gary

2012-01-01

During anaerobic growth Escherichia coli synthesizes two membrane-associated hydrogen-oxidizing [NiFe]-hydrogenases, termed hydrogenase 1 and hydrogenase 2. Each enzyme comprises a catalytic subunit containing the [NiFe] cofactor, an electron-transferring small subunit with a particular complement of [Fe-S] (iron-sulfur) clusters and a membrane-anchor subunit. How the [Fe-S] clusters are delivered to the small subunit of these enzymes is unclear. A-type carrier (ATC) proteins of the Isc (iron-sulfur-cluster) and Suf (sulfur mobilization) [Fe-S] cluster biogenesis pathways are proposed to traffic pre-formed [Fe-S] clusters to apoprotein targets. Mutants that could not synthesize SufA had active hydrogenase 1 and hydrogenase 2 enzymes, thus demonstrating that the Suf machinery is not required for hydrogenase maturation. In contrast, mutants devoid of the IscA, ErpA or IscU proteins of the Isc machinery had no detectable hydrogenase 1 or 2 activities. Lack of activity of both enzymes correlated with the absence of the respective [Fe-S]-cluster-containing small subunit, which was apparently rapidly degraded. During biosynthesis the hydrogenase large subunits receive their [NiFe] cofactor from the Hyp maturation machinery. Subsequent to cofactor insertion a specific C-terminal processing step occurs before association of the large subunit with the small subunit. This processing step is independent of small subunit maturation. Using western blotting experiments it could be shown that although the amount of each hydrogenase large subunit was strongly reduced in the iscA and erpA mutants, some maturation of the large subunit still occurred. Moreover, in contrast to the situation in Isc-proficient strains, these processed large subunits were not membrane-associated. Taken together, our findings demonstrate that both IscA and ErpA are required for [Fe-S] cluster delivery to the small subunits of the hydrogen-oxidizing hydrogenases; however, delivery of the Fe atom to the active site might have different requirements. PMID:22363723

a Three-Step Spatial-Temporal Clustering Method for Human Activity Pattern Analysis

NASA Astrophysics Data System (ADS)

Huang, W.; Li, S.; Xu, S.

2016-06-01

How people move in cities and what they do in various locations at different times form human activity patterns. Human activity pattern plays a key role in in urban planning, traffic forecasting, public health and safety, emergency response, friend recommendation, and so on. Therefore, scholars from different fields, such as social science, geography, transportation, physics and computer science, have made great efforts in modelling and analysing human activity patterns or human mobility patterns. One of the essential tasks in such studies is to find the locations or places where individuals stay to perform some kind of activities before further activity pattern analysis. In the era of Big Data, the emerging of social media along with wearable devices enables human activity data to be collected more easily and efficiently. Furthermore, the dimension of the accessible human activity data has been extended from two to three (space or space-time) to four dimensions (space, time and semantics). More specifically, not only a location and time that people stay and spend are collected, but also what people "say" for in a location at a time can be obtained. The characteristics of these datasets shed new light on the analysis of human mobility, where some of new methodologies should be accordingly developed to handle them. Traditional methods such as neural networks, statistics and clustering have been applied to study human activity patterns using geosocial media data. Among them, clustering methods have been widely used to analyse spatiotemporal patterns. However, to our best knowledge, few of clustering algorithms are specifically developed for handling the datasets that contain spatial, temporal and semantic aspects all together. In this work, we propose a three-step human activity clustering method based on space, time and semantics to fill this gap. One-year Twitter data, posted in Toronto, Canada, is used to test the clustering-based method. The results show that the approximate 55% spatiotemporal clusters distributed in different locations can be eventually grouped as the same type of clusters with consideration of semantic aspect.

Molecular clustering of patients with diabetes and pulmonary tuberculosis: A systematic review and meta-analysis.

PubMed

Blanco-Guillot, Francles; Delgado-Sánchez, Guadalupe; Mongua-Rodríguez, Norma; Cruz-Hervert, Pablo; Ferreyra-Reyes, Leticia; Ferreira-Guerrero, Elizabeth; Yanes-Lane, Mercedes; Montero-Campos, Rogelio; Bobadilla-Del-Valle, Miriam; Torres-González, Pedro; Ponce-de-León, Alfredo; Sifuentes-Osornio, José; Garcia-Garcia, Lourdes

2017-01-01

Many studies have explored the relationship between diabetes mellitus (DM) and tuberculosis (TB) demonstrating increased risk of TB among patients with DM and poor prognosis of patients suffering from the association of DM/TB. Owing to a paucity of studies addressing this question, it remains unclear whether patients with DM and TB are more likely than TB patients without DM to be grouped into molecular clusters defined according to the genotype of the infecting Mycobacterium tuberculosis bacillus. That is, whether there is convincing molecular epidemiological evidence for TB transmission among DM patients. Objective: We performed a systematic review and meta-analysis to quantitatively evaluate the propensity for patients with DM and pulmonary TB (PTB) to cluster according to the genotype of the infecting M. tuberculosis bacillus. We conducted a systematic search in MEDLINE and LILACS from 1990 to June, 2016 with the following combinations of key words "tuberculosis AND transmission" OR "tuberculosis diabetes mellitus" OR "Mycobacterium tuberculosis molecular epidemiology" OR "RFLP-IS6110" OR "Spoligotyping" OR "MIRU-VNTR". Studies were included if they met the following criteria: (i) studies based on populations from defined geographical areas; (ii) use of genotyping by IS6110- restriction fragment length polymorphism (RFLP) analysis and spoligotyping or mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) or other amplification methods to identify molecular clustering; (iii) genotyping and analysis of 50 or more cases of PTB; (iv) study duration of 11 months or more; (v) identification of quantitative risk factors for molecular clustering including DM; (vi) > 60% coverage of the study population; and (vii) patients with PTB confirmed bacteriologically. The exclusion criteria were: (i) Extrapulmonary TB; (ii) TB caused by nontuberculous mycobacteria; (iii) patients with PTB and HIV; (iv) pediatric PTB patients; (v) TB in closed environments (e.g. prisons, elderly homes, etc.); (vi) diabetes insipidus and (vii) outbreak reports. Hartung-Knapp-Sidik-Jonkman method was used to estimate the odds ratio (OR) of the association between DM with molecular clustering of cases with TB. In order to evaluate the degree of heterogeneity a statistical Q test was done. The publication bias was examined with Begg and Egger tests. Review Manager 5.3.5 CMA v.3 and Biostat and Software package R were used. Selection criteria were met by six articles which included 4076 patients with PTB of which 13% had DM. Twenty seven percent of the cases were clustered. The majority of cases (48%) were reported in a study in China with 31% clustering. The highest incidence of TB occurred in two studies from China. The global OR for molecular clustering was 0.84 (IC 95% 0.40-1.72). The heterogeneity between studies was moderate (I2 = 55%, p = 0.05), although there was no publication bias (Beggs test p = 0.353 and Eggers p = 0.429). There were very few studies meeting our selection criteria. The wide confidence interval indicates that there is not enough evidence to draw conclusions about the association. Clustering of patients with DM in TB transmission chains should be investigated in areas where both diseases are prevalent and focus on specific contexts.

Cosmological Studies with Galaxy Clusters, Active Galactic Nuclei, and Strongly Lensed Quasars

NASA Astrophysics Data System (ADS)

Rumbaugh, Nicholas Andrew

The large-scale structure (LSS) of the universe provides scientists with one of the best laboratories for studying Lambda Cold Dark Matter (LambdaCDM) cosmology. Especially at high redshift, we see increased rates of galaxy cluster and galaxy merging in LSS relative to the field, which is useful for studying the hierarchical merging predicted by LambdaCDM. The largest identified bound structures, superclusters, have not yet virialized. Despite the wide range of dynamical states of their constituent galaxies, groups, and clusters, they are all still actively evolving, providing an ideal laboratory in which to study cluster and galaxy evolution. In this dissertation, I present original research on several aspects of LSS and LambdaCDM cosmology. Three separate studies are included, each one focusing on a different aspect. In the first study, we use X-ray and optical observations from nine galaxy clusters at high redshift, some embedded in larger structures and some isolated, to study their evolutionary states. We extract X-ray gas temperatures and luminosities as well as optical velocity dispersions. These cluster properties are compared using low-redshift scaling relations. In addition, we employ several tests of substructure, using velocity histograms, Dressler-Shectman tests, and centroiding offsets. We conclude that two clusters out of our sample are most likely unrelaxed, and find support for deviations from self-similarity in the redshift evolution of the Lx-T relation. Our numerous complementary tests of the evolutionary state of clusters suggest potential under-estimations of systematic error in studies employing only a single such test. In the second study, we use multi-band imaging and spectroscopy to study active galactic nuclei (AGN) in high-redshift LSS. The AGN were identified using X-ray imaging and matched to optical catalogs that contained spectroscopic redshifts to identify members of the structures. AGN host galaxies tended to be associated with the transitional `green valley' on a color-magnitude diagram. Spectral analysis of the AGN hosts showed that the average host galaxy had either on-going or recent star formation, and was younger than the average galaxy, across all LSS in our sample. We further subdivided our sample in two based on the average evolutionary state of the LSS. The AGN in the more evolved structures had lower X-ray luminosities and longer times since last starburst. These results provide some evidence for merger-based AGN triggering, although other mechanisms, and possibly more than one, could be responsible. In the third study, we probed LambdaCDM cosmology from a different angle. An important part of the model is the cosmological parameters that define our universe. As such, probes that can more accurately and precisely measure these parameters, such as H0 and the dark energy equation of state, w, can allow us to more closely inspect the model. Strongly-lensed quasars provide one such probe, and we sought to perform the first step in using them for cosmological inference, which is to measure the time delays between strongly lensed images. We performed radio monitoring campaigns on six strongly lensed quasars using the Very Large Array. Lightcurves were extracted for each lensed image and analyzed for intrinsic variability. Two lensed quasars showed strong time variations, but the variations were linear in time, preventing precise time delay measurements due to a degeneracy with the magnifications. These results suggest most of the systems should be targeted for followup monitoring, and we estimate that time delays can be measured for the most variable systems with precision of 0.5 to 3.5 days with two more seasons of monitoring. In a joint fit with previously studied systems, these measurements could tighten constraints on H 0 by up to ~1.4.

Effectiveness of en masse versus two-step retraction: a systematic review and meta-analysis.

PubMed

Rizk, Mumen Z; Mohammed, Hisham; Ismael, Omar; Bearn, David R

2018-01-05

This review aims to compare the effectiveness of en masse and two-step retraction methods during orthodontic space closure regarding anchorage preservation and anterior segment retraction and to assess their effect on the duration of treatment and root resorption. An electronic search for potentially eligible randomized controlled trials and prospective controlled trials was performed in five electronic databases up to July 2017. The process of study selection, data extraction, and quality assessment was performed by two reviewers independently. A narrative review is presented in addition to a quantitative synthesis of the pooled results where possible. The Cochrane risk of bias tool and the Newcastle-Ottawa Scale were used for the methodological quality assessment of the included studies. Eight studies were included in the qualitative synthesis in this review. Four studies were included in the quantitative synthesis. En masse/miniscrew combination showed a statistically significant standard mean difference regarding anchorage preservation - 2.55 mm (95% CI - 2.99 to - 2.11) and the amount of upper incisor retraction - 0.38 mm (95% CI - 0.70 to - 0.06) when compared to a two-step/conventional anchorage combination. Qualitative synthesis suggested that en masse retraction requires less time than two-step retraction with no difference in the amount of root resorption. Both en masse and two-step retraction methods are effective during the space closure phase. The en masse/miniscrew combination is superior to the two-step/conventional anchorage combination with regard to anchorage preservation and amount of retraction. Limited evidence suggests that anchorage reinforcement with a headgear produces similar results with both retraction methods. Limited evidence also suggests that en masse retraction may require less time and that no significant differences exist in the amount of root resorption between the two methods.

Performance map of a cluster detection test using extended power

PubMed Central

2013-01-01

Background Conventional power studies possess limited ability to assess the performance of cluster detection tests. In particular, they cannot evaluate the accuracy of the cluster location, which is essential in such assessments. Furthermore, they usually estimate power for one or a few particular alternative hypotheses and thus cannot assess performance over an entire region. Takahashi and Tango developed the concept of extended power that indicates both the rate of null hypothesis rejection and the accuracy of the cluster location. We propose a systematic assessment method, using here extended power, to produce a map showing the performance of cluster detection tests over an entire region. Methods To explore the behavior of a cluster detection test on identical cluster types at any possible location, we successively applied four different spatial and epidemiological parameters. These parameters determined four cluster collections, each covering the entire study region. We simulated 1,000 datasets for each cluster and analyzed them with Kulldorff’s spatial scan statistic. From the area under the extended power curve, we constructed a map for each parameter set showing the performance of the test across the entire region. Results Consistent with previous studies, the performance of the spatial scan statistic increased with the baseline incidence of disease, the size of the at-risk population and the strength of the cluster (i.e., the relative risk). Performance was heterogeneous, however, even for very similar clusters (i.e., similar with respect to the aforementioned factors), suggesting the influence of other factors. Conclusions The area under the extended power curve is a single measure of performance and, although needing further exploration, it is suitable to conduct a systematic spatial evaluation of performance. The performance map we propose enables epidemiologists to assess cluster detection tests across an entire study region. PMID:24156765

Clustering of Farsi sub-word images for whole-book recognition

NASA Astrophysics Data System (ADS)

Soheili, Mohammad Reza; Kabir, Ehsanollah; Stricker, Didier

2015-01-01

Redundancy of word and sub-word occurrences in large documents can be effectively utilized in an OCR system to improve recognition results. Most OCR systems employ language modeling techniques as a post-processing step; however these techniques do not use important pictorial information that exist in the text image. In case of large-scale recognition of degraded documents, this information is even more valuable. In our previous work, we proposed a subword image clustering method for the applications dealing with large printed documents. In our clustering method, the ideal case is when all equivalent sub-word images lie in one cluster. To overcome the issues of low print quality, the clustering method uses an image matching algorithm for measuring the distance between two sub-word images. The measured distance with a set of simple shape features were used to cluster all sub-word images. In this paper, we analyze the effects of adding more shape features on processing time, purity of clustering, and the final recognition rate. Previously published experiments have shown the efficiency of our method on a book. Here we present extended experimental results and evaluate our method on another book with totally different font face. Also we show that the number of the new created clusters in a page can be used as a criteria for assessing the quality of print and evaluating preprocessing phases.

Automated segmentation of comet assay images using Gaussian filtering and fuzzy clustering.

PubMed

Sansone, Mario; Zeni, Olga; Esposito, Giovanni

2012-05-01

Comet assay is one of the most popular tests for the detection of DNA damage at single cell level. In this study, an algorithm for comet assay analysis has been proposed, aiming to minimize user interaction and providing reproducible measurements. The algorithm comprises two-steps: (a) comet identification via Gaussian pre-filtering and morphological operators; (b) comet segmentation via fuzzy clustering. The algorithm has been evaluated using comet images from human leukocytes treated with a commonly used DNA damaging agent. A comparison of the proposed approach with a commercial system has been performed. Results show that fuzzy segmentation can increase overall sensitivity, giving benefits in bio-monitoring studies where weak genotoxic effects are expected.

A Systematic, Inquiry-Based 7-Step Virtual Worlds Teacher Training

ERIC Educational Resources Information Center

Nussli, Natalie Christina; Oh, Kevin

2015-01-01

Eighteen special education teachers explored one prominent example of three-dimensional virtual worlds, namely Second Life. This study aimed to (a) determine their perception of the effectiveness of a systematic 7-Step Virtual Worlds Teacher Training workshop in terms of enabling them to make informed decisions about the usability of virtual…

Machine Learning for Discriminating Quantum Measurement Trajectories and Improving Readout.

PubMed

Magesan, Easwar; Gambetta, Jay M; Córcoles, A D; Chow, Jerry M

2015-05-22

Current methods for classifying measurement trajectories in superconducting qubit systems produce fidelities systematically lower than those predicted by experimental parameters. Here, we place current classification methods within the framework of machine learning (ML) algorithms and improve on them by investigating more sophisticated ML approaches. We find that nonlinear algorithms and clustering methods produce significantly higher assignment fidelities that help close the gap to the fidelity possible under ideal noise conditions. Clustering methods group trajectories into natural subsets within the data, which allows for the diagnosis of systematic errors. We find large clusters in the data associated with T1 processes and show these are the main source of discrepancy between our experimental and ideal fidelities. These error diagnosis techniques help provide a path forward to improve qubit measurements.

A Hierarchical Framework for State-Space Matrix Inference and Clustering.

PubMed

Zuo, Chandler; Chen, Kailei; Hewitt, Kyle J; Bresnick, Emery H; Keleş, Sündüz

2016-09-01

In recent years, a large number of genomic and epigenomic studies have been focusing on the integrative analysis of multiple experimental datasets measured over a large number of observational units. The objectives of such studies include not only inferring a hidden state of activity for each unit over individual experiments, but also detecting highly associated clusters of units based on their inferred states. Although there are a number of methods tailored for specific datasets, there is currently no state-of-the-art modeling framework for this general class of problems. In this paper, we develop the MBASIC ( M atrix B ased A nalysis for S tate-space I nference and C lustering) framework. MBASIC consists of two parts: state-space mapping and state-space clustering. In state-space mapping, it maps observations onto a finite state-space, representing the activation states of units across conditions. In state-space clustering, MBASIC incorporates a finite mixture model to cluster the units based on their inferred state-space profiles across all conditions. Both the state-space mapping and clustering can be simultaneously estimated through an Expectation-Maximization algorithm. MBASIC flexibly adapts to a large number of parametric distributions for the observed data, as well as the heterogeneity in replicate experiments. It allows for imposing structural assumptions on each cluster, and enables model selection using information criterion. In our data-driven simulation studies, MBASIC showed significant accuracy in recovering both the underlying state-space variables and clustering structures. We applied MBASIC to two genome research problems using large numbers of datasets from the ENCODE project. The first application grouped genes based on transcription factor occupancy profiles of their promoter regions in two different cell types. The second application focused on identifying groups of loci that are similar to a GATA2 binding site that is functional at its endogenous locus by utilizing transcription factor occupancy data and illustrated applicability of MBASIC in a wide variety of problems. In both studies, MBASIC showed higher levels of raw data fidelity than analyzing these data with a two-step approach using ENCODE results on transcription factor occupancy data.

A detailed comparison of analysis processes for MCC-IMS data in disease classification—Automated methods can replace manual peak annotations

PubMed Central

Horsch, Salome; Kopczynski, Dominik; Kuthe, Elias; Baumbach, Jörg Ingo; Rahmann, Sven

2017-01-01

Motivation Disease classification from molecular measurements typically requires an analysis pipeline from raw noisy measurements to final classification results. Multi capillary column—ion mobility spectrometry (MCC-IMS) is a promising technology for the detection of volatile organic compounds in the air of exhaled breath. From raw measurements, the peak regions representing the compounds have to be identified, quantified, and clustered across different experiments. Currently, several steps of this analysis process require manual intervention of human experts. Our goal is to identify a fully automatic pipeline that yields competitive disease classification results compared to an established but subjective and tedious semi-manual process. Method We combine a large number of modern methods for peak detection, peak clustering, and multivariate classification into analysis pipelines for raw MCC-IMS data. We evaluate all combinations on three different real datasets in an unbiased cross-validation setting. We determine which specific algorithmic combinations lead to high AUC values in disease classifications across the different medical application scenarios. Results The best fully automated analysis process achieves even better classification results than the established manual process. The best algorithms for the three analysis steps are (i) SGLTR (Savitzky-Golay Laplace-operator filter thresholding regions) and LM (Local Maxima) for automated peak identification, (ii) EM clustering (Expectation Maximization) and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) for the clustering step and (iii) RF (Random Forest) for multivariate classification. Thus, automated methods can replace the manual steps in the analysis process to enable an unbiased high throughput use of the technology. PMID:28910313

Increasing the doping efficiency by surface energy control for ultra-transparent graphene conductors.

PubMed

Chang, Kai-Wen; Hsieh, Ya-Ping; Ting, Chu-Chi; Su, Yen-Hsun; Hofmann, Mario

2017-08-22

Graphene's attractiveness in many applications is limited by its high resistance. Extrinsic doping has shown promise to overcome this challenge but graphene's performance remains below industry requirements. This issue is caused by a limited charge transfer efficiency (CTE) between dopant and graphene. Using AuCl 3 as a model system, we measure CTE as low as 5% of the expected values due to the geometrical capacitance of small adsorbate clusters. We here demonstrate a strategy for enhancing the CTE by a two-step optimization of graphene's surface energy prior to AuCl 3 doping. First, exposure to UV ozone modified the hydrophilicity of graphene and was found to decrease the cluster's geometric capacitance, which had a direct effect on the CTE. Occurrence of lattice defects at high UV exposure, however, deteriorated graphene's transport characteristics and limited the effectiveness of this pretreatment step. Thus, prior to UV exposure, a functionalized polymer layer was introduced that could further enhance graphene's surface energy while protecting it from damage. Combination of these treatment steps were found to increase the AuCl 3 charge transfer efficiency to 70% and lower the sheet resistance to 106 Ω/γ at 97% transmittance which represents the highest reported performance for doped single layer graphene and is on par with commercially available transparent conductors.

densityCut: an efficient and versatile topological approach for automatic clustering of biological data

PubMed Central

Ding, Jiarui; Shah, Sohrab; Condon, Anne

2016-01-01

Motivation: Many biological data processing problems can be formalized as clustering problems to partition data points into sensible and biologically interpretable groups. Results: This article introduces densityCut, a novel density-based clustering algorithm, which is both time- and space-efficient and proceeds as follows: densityCut first roughly estimates the densities of data points from a K-nearest neighbour graph and then refines the densities via a random walk. A cluster consists of points falling into the basin of attraction of an estimated mode of the underlining density function. A post-processing step merges clusters and generates a hierarchical cluster tree. The number of clusters is selected from the most stable clustering in the hierarchical cluster tree. Experimental results on ten synthetic benchmark datasets and two microarray gene expression datasets demonstrate that densityCut performs better than state-of-the-art algorithms for clustering biological datasets. For applications, we focus on the recent cancer mutation clustering and single cell data analyses, namely to cluster variant allele frequencies of somatic mutations to reveal clonal architectures of individual tumours, to cluster single-cell gene expression data to uncover cell population compositions, and to cluster single-cell mass cytometry data to detect communities of cells of the same functional states or types. densityCut performs better than competing algorithms and is scalable to large datasets. Availability and Implementation: Data and the densityCut R package is available from https://bitbucket.org/jerry00/densitycut_dev. Contact: condon@cs.ubc.ca or sshah@bccrc.ca or jiaruid@cs.ubc.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153661

[Information system for supporting the Nursing Care Systematization].

PubMed

Malucelli, Andreia; Otemaier, Kelly Rafaela; Bonnet, Marcel; Cubas, Marcia Regina; Garcia, Telma Ribeiro

2010-01-01

It is an unquestionable fact, the importance, relevance and necessity of implementing the Nursing Care Systematization in the different environments of professional practice. Considering it as a principle, emerged the motivation for the development of an information system to support the Nursing Care Systematization, based on Nursing Process steps and Human Needs, using the diagnoses language, nursing interventions and outcomes for professional practice documentation. This paper describes the methodological steps and results of the information system development - requirements elicitation, modeling, object-relational mapping, implementation and system validation.

Formation of the young compact cluster GM 24 triggered by a cloud-cloud collision

NASA Astrophysics Data System (ADS)

Fukui, Yasuo; Kohno, Mikito; Yokoyama, Keiko; Nishimura, Atsushi; Torii, Kazufumi; Hattori, Yusuke; Sano, Hidetoshi; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo

2018-05-01

High-mass star formation is an important step which controls galactic evolution. GM 24 is a heavily obscured star cluster including a single O9 star with more than ˜100 lower-mass stars within a 0.3 pc radius toward (l, b) ˜ (350.5°, 0.96°), close to the Galactic mini-starburst NGC 6334. We found two velocity components associated with the cluster by new observations of 12CO J =2-1 emission, whereas the cloud was previously considered to be single. We found that the distribution of the two components of 5 {km}s-1 separation shows complementary distribution; the two fit well with each other if a relative displacement of 3 pc is applied along the Galactic plane. A position-velocity diagram of the GM 24 cloud is explained by a model based on numerical simulations of two colliding clouds, where an intermediate velocity component created by the collision is taken into account. We estimate the collision time scale to be ˜Myr in projection of a relative motion tilted to the line of sight by 45°. The results lend further support for cloud-cloud collision as an important mechanism of high-mass star formation in the Carina-Sagittarius Arm.

Molecular Tracing of Hepatitis C Virus Genotype 1 Isolates in Iran: A NS5B Phylogenetic Analysis with Systematic Review.

PubMed

Hesamizadeh, Khashayar; Alavian, Seyed Moayed; Najafi Tireh Shabankareh, Azar; Sharafi, Heidar

2016-12-01

Hepatitis C virus (HCV) is characterized by a high degree of genetic heterogeneity and classified into 7 genotypes and different subtypes. It heterogeneously distributed through various risk groups and geographical regions. A well-established phylogenetic relationship can simplify the tracing of HCV hierarchical strata into geographical regions. The current study aimed to find genetic phylogeny of subtypes 1a and 1b of HCV isolates based on NS5B nucleotide sequences in Iran and other members of Eastern Mediterranean regional office of world health organization, as well as other Middle Eastern countries, with a systematic review of available published and unpublished studies. The phylogenetic analyses were performed based on the nucleotide sequences of NS5B gene of HCV genotype 1 (HCV-1), which were registered in the GenBank database. The literature review was performed in two steps: 1) searching studies evaluating the NS5B sequences of HCV-1, on PubMed, Scopus, and Web of Science, and 2) Searching sequences of unpublished studies registered in the GenBank database. In this study, 442 sequences from HCV-1a and 232 from HCV-1b underwent phylogenetic analysis. Phylogenetic analysis of all sequences revealed different clusters in the phylogenetic trees. The results showed that the proportion of HCV-1a and -1b isolates from Iranian patients probably originated from domestic sources. Moreover, the HCV-1b isolates from Iranian patients may have similarities with the European ones. In this study, phylogenetic reconstruction of HCV-1 sequences clearly indicated for molecular tracing and ancestral relationships of the HCV genotypes in Iran, and showed the likelihood of domestic origin for HCV-1a and various origin for HCV-1b.

Cooperative inversion of magnetotelluric and seismic data sets

NASA Astrophysics Data System (ADS)

Markovic, M.; Santos, F.

2012-04-01

Cooperative inversion of magnetotelluric and seismic data sets Milenko Markovic,Fernando Monteiro Santos IDL, Faculdade de Ciências da Universidade de Lisboa 1749-016 Lisboa Inversion of single geophysical data has well-known limitations due to the non-linearity of the fields and non-uniqueness of the model. There is growing need, both in academy and industry to use two or more different data sets and thus obtain subsurface property distribution. In our case ,we are dealing with magnetotelluric and seismic data sets. In our approach,we are developing algorithm based on fuzzy-c means clustering technique, for pattern recognition of geophysical data. Separate inversion is performed on every step, information exchanged for model integration. Interrelationships between parameters from different models is not required in analytical form. We are investigating how different number of clusters, affects zonation and spatial distribution of parameters. In our study optimization in fuzzy c-means clustering (for magnetotelluric and seismic data) is compared for two cases, firstly alternating optimization and then hybrid method (alternating optimization+ Quasi-Newton method). Acknowledgment: This work is supported by FCT Portugal

Reddenings, Metallicities, and Possible Abundance Anomalies in Young Globular Clusters

NASA Astrophysics Data System (ADS)

Sarajedini, Ata; Layden, Andrew

1997-01-01

We present new photometry in the VI passbands for the ``young'' globular clusters Rup 106, Ter 7, and Arp 2. After formulating the simultaneous reddening and metallicity (SRM) method of Sarajedini (1994) in the BV passbands, we apply it, along with the SRM method in VI, to the red giant branches (RGBs) of these clusters using B-V photometry from the literature and the V-I data presented herein. We find [Fe/H] = -1.90 +/- 0.10, E(B-V) = 0.18 +/- 0.02 for Rup 106, [Fe/H] = -0.82 +/- 0.15, E(B-V) = 0.07 +/- 0.03 for Ter 7, and [Fe/H] = -1.84 +/- 0.09, E(B-V) = 0.10 +/- 0.02 for Arp 2. Furthermore, in light of this new abundance for Ter 7 and recent work on the luminosity of the red horizontal branch, we rederive the age of Ter 7 finding it to be some 6 Gyr younger than 47 Tuc. We show that the SRM method is insensitive to age for clusters with purely red HBs and ages as young as ~ 5 Gyr; for clusters with bluer HBs, the SRM method is only mildly sensitive to age differences between such clusters and the calibrating (standard) clusters. From these metallicity estimates, we conclude that the photometric abundances of the program clusters based on the properties of the RGB are systematically lower (Delta [Fe/H] = 0.1-0.4 dex) than those derived using other indicators, in particular the Ca 2 triplet method. We note that the young globular clusters Pal 12 and possibly IC 4499 also exhibit this behavior. We suggest that this discrepancy is due to systematic differences in the [alpha /Fe] ratios between the young clusters and the ``normal'' Galactic globulars used to calibrate the abundance determination methods. However, we are unable to completely reconcile all the observations of Rup 106 using this approach. Systematic differences in [alpha /Fe] between the young clusters and the rest of the Galactic globulars may indicate differences in their chemical enrichment histories, perhaps due to differing environments at the times of their formation. Interestingly, both Ter 7 and Arp 2 are believed to be memebers of the Sagittarius dwarf galaxy, while Rup 106 and (perhaps) Pal 12 are suspected of being captured from the Magellanic Clouds.

Desorption electrospray ionization mass spectrometry of DNA nucleobases: implications for a liquid film model.

PubMed

Qiu, Bo; Luo, Hai

2009-05-01

Desorption electrospray ionization (DESI) mass spectrometry has been implemented on a commercial ion-trap mass spectrometer and used to optimize mass spectrometric conditions for DNA nucleobases: adenine, cytosine, thymine, and guanine. Experimental parameters including spray voltage, distance between mass spectrometer inlet and the sampled spot, and nebulizing gas inlet pressure were optimized. Cluster ions including some magic number clusters of nucleobases were observed for the first time using DESI mass spectrometry. The formation of the cluster species was found to vary with the nucleobases, acidification of the spray solvent, and the deposited sample amount. All the experimental results can be explained well using a liquid film model based on the two-step droplet pick-up mechanism. It is further suggested that solubility of the analytes in the spray solvent is an important factor to consider for their studies by using DESI. 2009 John Wiley & Sons, Ltd.

How to write a systematic review.

PubMed

Harris, Joshua D; Quatman, Carmen E; Manring, M M; Siston, Robert A; Flanigan, David C

2014-11-01

The role of evidence-based medicine in sports medicine and orthopaedic surgery is rapidly growing. Systematic reviews and meta-analyses are also proliferating in the medical literature. To provide the outline necessary for a practitioner to properly understand and/or conduct a systematic review for publication in a sports medicine journal. Review. The steps of a successful systematic review include the following: identification of an unanswered answerable question; explicit definitions of the investigation's participant(s), intervention(s), comparison(s), and outcome(s); utilization of PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines and PROSPERO registration; thorough systematic data extraction; and appropriate grading of the evidence and strength of the recommendations. An outline to understand and conduct a systematic review is provided, and the difference between meta-analyses and systematic reviews is described. The steps necessary to perform a systematic review are fully explained, including the study purpose, search methodology, data extraction, reporting of results, identification of bias, and reporting of the study's main findings. Systematic reviews or meta-analyses critically appraise and formally synthesize the best existing evidence to provide a statement of conclusion that answers specific clinical questions. Readers and reviewers, however, must recognize that the quality and strength of recommendations in a review are only as strong as the quality of studies that it analyzes. Thus, great care must be used in the interpretation of bias and extrapolation of the review's findings to translation to clinical practice. Without advanced education on the topic, the reader may follow the steps discussed herein to perform a systematic review. © 2013 The Author(s).

Indicators to facilitate the early identification of patients with major depressive disorder in need of highly specialized care: A concept mapping study.

PubMed

van Krugten, F C W; Goorden, M; van Balkom, A J L M; Spijker, J; Brouwer, W B F; Hakkaart-van Roijen, L

2018-04-01

Early identification of the subgroup of patients with major depressive disorder (MDD) in need of highly specialized care could enhance personalized intervention. This, in turn, may reduce the number of treatment steps needed to achieve and sustain an adequate treatment response. The aim of this study was to identify patient-related indicators that could facilitate the early identification of the subgroup of patients with MDD in need of highly specialized care. Initial patient indicators were derived from a systematic review. Subsequently, a structured conceptualization methodology known as concept mapping was employed to complement the initial list of indicators by clinical expertise and develop a consensus-based conceptual framework. Subject-matter experts were invited to participate in the subsequent steps (brainstorming, sorting, and rating) of the concept mapping process. A final concept map solution was generated using nonmetric multidimensional scaling and agglomerative hierarchical cluster analyses. In total, 67 subject-matter experts participated in the concept mapping process. The final concept map revealed the following 10 major clusters of indicators: 1-depression severity, 2-onset and (treatment) course, 3-comorbid personality disorder, 4-comorbid substance use disorder, 5-other psychiatric comorbidity, 6-somatic comorbidity, 7-maladaptive coping, 8-childhood trauma, 9-social factors, and 10-psychosocial dysfunction. The study findings highlight the need for a comprehensive assessment of patient indicators in determining the need for highly specialized care, and suggest that the treatment allocation of patients with MDD to highly specialized mental healthcare settings should be guided by the assessment of clinical and nonclinical patient factors. © 2018 Wiley Periodicals, Inc.

One-step estimation of networked population size: Respondent-driven capture-recapture with anonymity.

PubMed

Khan, Bilal; Lee, Hsuan-Wei; Fellows, Ian; Dombrowski, Kirk

2018-01-01

Size estimation is particularly important for populations whose members experience disproportionate health issues or pose elevated health risks to the ambient social structures in which they are embedded. Efforts to derive size estimates are often frustrated when the population is hidden or hard-to-reach in ways that preclude conventional survey strategies, as is the case when social stigma is associated with group membership or when group members are involved in illegal activities. This paper extends prior research on the problem of network population size estimation, building on established survey/sampling methodologies commonly used with hard-to-reach groups. Three novel one-step, network-based population size estimators are presented, for use in the context of uniform random sampling, respondent-driven sampling, and when networks exhibit significant clustering effects. We give provably sufficient conditions for the consistency of these estimators in large configuration networks. Simulation experiments across a wide range of synthetic network topologies validate the performance of the estimators, which also perform well on a real-world location-based social networking data set with significant clustering. Finally, the proposed schemes are extended to allow them to be used in settings where participant anonymity is required. Systematic experiments show favorable tradeoffs between anonymity guarantees and estimator performance. Taken together, we demonstrate that reasonable population size estimates are derived from anonymous respondent driven samples of 250-750 individuals, within ambient populations of 5,000-40,000. The method thus represents a novel and cost-effective means for health planners and those agencies concerned with health and disease surveillance to estimate the size of hidden populations. We discuss limitations and future work in the concluding section.

The [(AI 2O 3) 2] - Anion Cluster: Electron Localization-Delocalization Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sierka, Marek; Dobler, Jens; Sauer, Joachim

2009-10-05

Three-dimensional bulk alumina and its two-dimensional thin films show great structural diversity, posing considerable challenges to their experimental structural characterization and computational modeling. Recently, structural diversity has also been demonstrated for zerodimensional gas phase aluminum oxide clusters. Mass-selected clusters not only make systematic studies of the structural and electronic properties as a function of size possible, but lately have also emerged as powerful molecular models of complex surfaces and solid catalysts. In particular, the [(Al 2O 3) 3-5] + clusters were the first example of polynuclear maingroup metal oxide cluster that are able to thermally activate CH 4. Over themore » past decades gas phase aluminum oxide clusters have been extensively studied both experimentally and computationally, but definitive structural assignments were made for only a handful of them: the planar [Al 3O 3] - and [Al 5O 4] - cluster anions, and the [(Al 2O 3) 1-4(AlO)] + cluster cations. For stoichiometric clusters only the atomic structures of [(Al 2O 3) 4] +/0 have been nambiguously resolved. Here we report on the structures of the [(Al 2O 3) 2] -/0 clusters combining photoelectron spectroscopy (PES) and quantum chemical calculations employing a genetic algorithm as a global optimization technique. The [(Al 2O 3) 2] - cluster anion show energetically close lying but structurally distinct cage and sheet-like isomers which differ by delocalization/localization of the extra electron. The experimental results are crucial for benchmarking the different computational methods applied with respect to a proper description of electron localization and the relative energies for the isomers which will be of considerable value for future computational studies of aluminum oxide and related systems.« less

The nature, origin and evolution of embedded star clusters

NASA Technical Reports Server (NTRS)

Lada, Charles J.; Lada, Elizabeth A.

1991-01-01

The recent development of imaging infrared array cameras has enabled the first systematic studies of embedded protoclusters in the galaxy. Initial investigations suggest that rich embedded clusters are quite numerous and that a significant fraction of all stars formed in the galaxy may begin their lives in such stellar systems. These clusters contain extremely young stellar objects and are important laboratories for star formation research. However, observational and theoretical considerations suggest that most embedded clusters do not survive emergence from molecular clouds as bound clusters. Understanding the origin, nature, and evolution of embedded clusters requires understanding the intimate physical relation between embedded clusters and the dense molecular cloud cores from which they form.

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

Structures in magnetohydrodynamic turbulence: Detection and scaling

NASA Astrophysics Data System (ADS)

Uritsky, V. M.; Pouquet, A.; Rosenberg, D.; Mininni, P. D.; Donovan, E. F.

2010-11-01

We present a systematic analysis of statistical properties of turbulent current and vorticity structures at a given time using cluster analysis. The data stem from numerical simulations of decaying three-dimensional magnetohydrodynamic turbulence in the absence of an imposed uniform magnetic field; the magnetic Prandtl number is taken equal to unity, and we use a periodic box with grids of up to 15363 points and with Taylor Reynolds numbers up to 1100. The initial conditions are either an X -point configuration embedded in three dimensions, the so-called Orszag-Tang vortex, or an Arn’old-Beltrami-Childress configuration with a fully helical velocity and magnetic field. In each case two snapshots are analyzed, separated by one turn-over time, starting just after the peak of dissipation. We show that the algorithm is able to select a large number of structures (in excess of 8000) for each snapshot and that the statistical properties of these clusters are remarkably similar for the two snapshots as well as for the two flows under study in terms of scaling laws for the cluster characteristics, with the structures in the vorticity and in the current behaving in the same way. We also study the effect of Reynolds number on cluster statistics, and we finally analyze the properties of these clusters in terms of their velocity-magnetic-field correlation. Self-organized criticality features have been identified in the dissipative range of scales. A different scaling arises in the inertial range, which cannot be identified for the moment with a known self-organized criticality class consistent with magnetohydrodynamics. We suggest that this range can be governed by turbulence dynamics as opposed to criticality and propose an interpretation of intermittency in terms of propagation of local instabilities.

MAPS OF MASSIVE CLUMPS IN THE EARLY STAGE OF CLUSTER FORMATION: TWO MODES OF CLUSTER FORMATION, COEVAL OR NON-COEVAL?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Higuchi, Aya E.; Saito, Masao; Mauersberger, Rainer

2013-03-10

We present maps of seven young massive molecular clumps within five target regions in C{sup 18}O (J = 1-0) line emission, using the Nobeyama 45 m telescope. These clumps, which are not associated with clusters, lie at distances between 0.7 and 2.1 kpc. We find C{sup 18}O clumps with radii of 0.5-1.7 pc, masses of 470-4200 M{sub Sun }, and velocity widths of 1.4-3.3 km s{sup -1}. All of the clumps are massive and approximately in virial equilibrium, suggesting they will potentially form clusters. Three of our target regions are associated with H II regions (CWHRs), while the other twomore » are unassociated with H II regions (CWOHRs). The C{sup 18}O clumps can be classified into two morphological types: CWHRs with a filamentary or shell-like structure and spherical CWOHRs. The two CWOHRs have systematic velocity gradients. Using the publicly released WISE database, Class I and Class II protostellar candidates are identified within the C{sup 18}O clumps. The fraction of Class I candidates among all YSO candidates (Class I+Class II) is {>=}50% in CWHRs and {<=}50% in CWOHRs. We conclude that effects from the H II regions can be seen in (1) the spatial distributions of the clumps: filamentary or shell-like structure running along the H II regions; (2) the velocity structures of the clumps: large velocity dispersion along shells; and (3) the small age spreads of YSOs. The small spreads in age of the YSOs show that the presence of H II regions tends to trigger coeval cluster formation.« less

A practical Bayesian stepped wedge design for community-based cluster-randomized clinical trials: The British Columbia Telehealth Trial.

PubMed

Cunanan, Kristen M; Carlin, Bradley P; Peterson, Kevin A

2016-12-01

Many clinical trial designs are impractical for community-based clinical intervention trials. Stepped wedge trial designs provide practical advantages, but few descriptions exist of their clinical implementational features, statistical design efficiencies, and limitations. Enhance efficiency of stepped wedge trial designs by evaluating the impact of design characteristics on statistical power for the British Columbia Telehealth Trial. The British Columbia Telehealth Trial is a community-based, cluster-randomized, controlled clinical trial in rural and urban British Columbia. To determine the effect of an Internet-based telehealth intervention on healthcare utilization, 1000 subjects with an existing diagnosis of congestive heart failure or type 2 diabetes will be enrolled from 50 clinical practices. Hospital utilization is measured using a composite of disease-specific hospital admissions and emergency visits. The intervention comprises online telehealth data collection and counseling provided to support a disease-specific action plan developed by the primary care provider. The planned intervention is sequentially introduced across all participating practices. We adopt a fully Bayesian, Markov chain Monte Carlo-driven statistical approach, wherein we use simulation to determine the effect of cluster size, sample size, and crossover interval choice on type I error and power to evaluate differences in hospital utilization. For our Bayesian stepped wedge trial design, simulations suggest moderate decreases in power when crossover intervals from control to intervention are reduced from every 3 to 2 weeks, and dramatic decreases in power as the numbers of clusters decrease. Power and type I error performance were not notably affected by the addition of nonzero cluster effects or a temporal trend in hospitalization intensity. Stepped wedge trial designs that intervene in small clusters across longer periods can provide enhanced power to evaluate comparative effectiveness, while offering practical implementation advantages in geographic stratification, temporal change, use of existing data, and resource distribution. Current population estimates were used; however, models may not reflect actual event rates during the trial. In addition, temporal or spatial heterogeneity can bias treatment effect estimates. © The Author(s) 2016.

Structural evolutions and hereditary characteristics of icosahedral nano-clusters formed in Mg70Zn30 alloys during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liang, Yong-Chao; Liu, Rang-Su; Xie, Quan; Tian, Ze-An; Mo, Yun-Fei; Zhang, Hai-Tao; Liu, Hai-Rong; Hou, Zhao-Yang; Zhou, Li-Li; Peng, Ping

2017-02-01

To investigate the structural evolution and hereditary mechanism of icosahedral nano-clusters formed during rapid solidification, a molecular dynamics (MD) simulation study has been performed for a system consisting of 107 atoms of liquid Mg70Zn30 alloy. Adopting Honeycutt-Anderson (HA) bond-type index method and cluster type index method (CTIM-3) to analyse the microstructures in the system it is found that for all the nano-clusters including 2~8 icosahedral clusters in the system, there are 62 kinds of geometrical structures, and those can be classified, by the configurations of the central atoms of basic clusters they contained, into four types: chain-like, triangle-tailed, quadrilateral-tailed and pyramidal-tailed. The evolution of icosahedral nano-clusters can be conducted by perfect heredity and replacement heredity, and the perfect heredity emerges when temperature is slightly less than Tm then increase rapidly and far exceeds the replacement heredity at Tg; while for the replacement heredity, there are three major modes: replaced by triangle (3-atoms), quadrangle (4-atoms) and pentagonal pyramid (6-atoms), rather than by single atom step by step during rapid solidification processes.

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

NASA Technical Reports Server (NTRS)

Dhaeseleer, Patrik; Liang, Shoudan; Somogyi, Roland

2000-01-01

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Minimal Model of Quantum Kinetic Clusters for the Energy-Transfer Network of a Light-Harvesting Protein Complex.

PubMed

Wu, Jianlan; Tang, Zhoufei; Gong, Zhihao; Cao, Jianshu; Mukamel, Shaul

2015-04-02

The energy absorbed in a light-harvesting protein complex is often transferred collectively through aggregated chromophore clusters. For population evolution of chromophores, the time-integrated effective rate matrix allows us to construct quantum kinetic clusters quantitatively and determine the reduced cluster-cluster transfer rates systematically, thus defining a minimal model of energy-transfer kinetics. For Fenna-Matthews-Olson (FMO) and light-havrvesting complex II (LCHII) monomers, quantum Markovian kinetics of clusters can accurately reproduce the overall energy-transfer process in the long-time scale. The dominant energy-transfer pathways are identified in the picture of aggregated clusters. The chromophores distributed extensively in various clusters can assist a fast and long-range energy transfer.

Detecting space-time cancer clusters using residential histories

NASA Astrophysics Data System (ADS)

Jacquez, Geoffrey M.; Meliker, Jaymie R.

2007-04-01

Methods for analyzing geographic clusters of disease typically ignore the space-time variability inherent in epidemiologic datasets, do not adequately account for known risk factors (e.g., smoking and education) or covariates (e.g., age, gender, and race), and do not permit investigation of the latency window between exposure and disease. Our research group recently developed Q-statistics for evaluating space-time clustering in cancer case-control studies with residential histories. This technique relies on time-dependent nearest neighbor relationships to examine clustering at any moment in the life-course of the residential histories of cases relative to that of controls. In addition, in place of the widely used null hypothesis of spatial randomness, each individual's probability of being a case is instead based on his/her risk factors and covariates. Case-control clusters will be presented using residential histories of 220 bladder cancer cases and 440 controls in Michigan. In preliminary analyses of this dataset, smoking, age, gender, race and education were sufficient to explain the majority of the clustering of residential histories of the cases. Clusters of unexplained risk, however, were identified surrounding the business address histories of 10 industries that emit known or suspected bladder cancer carcinogens. The clustering of 5 of these industries began in the 1970's and persisted through the 1990's. This systematic approach for evaluating space-time clustering has the potential to generate novel hypotheses about environmental risk factors. These methods may be extended to detect differences in space-time patterns of any two groups of people, making them valuable for security intelligence and surveillance operations.

A novel glucuronosyltransferase has an unprecedented ability to catalyse continuous two-step glucuronosylation of glycyrrhetinic acid to yield glycyrrhizin.

PubMed

Xu, Guojie; Cai, Wei; Gao, Wei; Liu, Chunsheng

2016-10-01

Glycyrrhizin is an important bioactive compound that is used clinically to treat chronic hepatitis and is also used as a sweetener world-wide. However, the key UDP-dependent glucuronosyltransferases (UGATs) involved in the biosynthesis of glycyrrhizin remain unknown. To discover unknown UGATs, we fully annotated potential UGATs from Glycyrrhiza uralensis using deep transcriptome sequencing. The catalytic functions of candidate UGATs were determined by an in vitro enzyme assay. Systematically screening 434 potential UGATs, we unexpectedly found one unique GuUGAT that was able to catalyse the glucuronosylation of glycyrrhetinic acid to directly yield glycyrrhizin via continuous two-step glucuronosylation. Expression analysis further confirmed the key role of GuUGAT in the biosynthesis of glycyrrhizin. Site-directed mutagenesis revealed that Gln-352 may be important for the initial step of glucuronosylation, and His-22, Trp-370, Glu-375 and Gln-392 may be important residues for the second step of glucuronosylation. Notably, the ability of GuUGAT to catalyse a continuous two-step glucuronosylation reaction was determined to be unprecedented among known glycosyltransferases of bioactive plant natural products. Our findings increase the understanding of traditional glycosyltransferases and pave the way for the complete biosynthesis of glycyrrhizin. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The divided communities of shared concerns: mapping the intellectual structure of e-Health research in social science journals.

PubMed

Jiang, L Crystal; Wang, Zhen-Zhen; Peng, Tai-Quan; Zhu, Jonathan J H

2015-01-01

Social scientific approach has become an important approach in e-Health studies over the past decade. However, there has been little systematical examination of what aspects of e-Health social scientists have studied and how relevant and informative knowledge has been produced and diffused by this line of inquiry. This study performed a systematic review of the body of e-Health literature in mainstream social science journals over the past decade by testing the applicability of a 5A categorization (i.e., access, availability, appropriateness, acceptability, and applicability), proposed by the U.S. Department of Health and Human Services, as a framework for understanding social scientific research in e-Health. This study used a quantitative, bottom-up approach to review the e-Health literature in social sciences published from 2000 to 2009. A total of 3005 e-Health studies identified from two social sciences databases (i.e., Social Sciences Citation Index and Arts & Humanities Citation Index) were analyzed with text topic modeling and structural analysis of co-word network, co-citation network, and scientific food web. There have been dramatic increases in the scale of e-Health studies in social sciences over the past decade in terms of the numbers of publications, journal outlets and participating disciplines. The results empirically confirm the presence of the 5A clusters in e-Health research, with the cluster of applicability as the dominant research area and the cluster of availability as the major knowledge producer for other clusters. The network analysis also reveals that the five distinctive clusters share much more in common in research concerns than what e-Health scholars appear to recognize. It is time to explicate and, more importantly, tap into the shared concerns cutting across the seemingly divided scholarly communities. In particular, more synergy exercises are needed to promote adherence of the field. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Formation history of open clusters constrained by detailed asteroseismology of red giant stars observed by Kepler

NASA Astrophysics Data System (ADS)

Corsaro, Enrico; Lee, Yueh-Ning; García, Rafael A.; Hennebelle, Patrick; Mathur, Savita; Beck, Paul G.; Mathis, Stephane; Stello, Dennis; Bouvier, Jérôme

2017-10-01

Stars originate by the gravitational collapse of a turbulent molecular cloud of a diffuse medium, and are often observed to form clusters. Stellar clusters therefore play an important role in our understanding of star formation and of the dynamical processes at play. However, investigating the cluster formation is diffcult because the density of the molecular cloud undergoes a change of many orders of magnitude. Hierarchical-step approaches to decompose the problem into different stages are therefore required, as well as reliable assumptions on the initial conditions in the clouds. We report for the first time the use of the full potential of NASA Kepler asteroseismic observations coupled with 3D numerical simulations, to put strong constraints on the early formation stages of open clusters. Thanks to a Bayesian peak bagging analysis of about 50 red giant members of NGC 6791 and NGC 6819, the two most populated open clusters observed in the nominal Kepler mission, we derive a complete set of detailed oscillation mode properties for each star, with thousands of oscillation modes characterized. We therefore show how these asteroseismic properties lead us to a discovery about the rotation history of stellar clusters. Finally, our observational findings will be compared with hydrodynamical simulations for stellar cluster formation to constrain the physical processes of turbulence, rotation, and magnetic fields that are in action during the collapse of the progenitor cloud into a proto-cluster.

Effectiveness of a stepped-care intervention to prevent major depression in patients with type 2 diabetes mellitus and/or coronary heart disease and subthreshold depression: A pragmatic cluster randomized controlled trial.

PubMed

Pols, Alide D; van Dijk, Susan E; Bosmans, Judith E; Hoekstra, Trynke; van Marwijk, Harm W J; van Tulder, Maurits W; Adriaanse, Marcel C

2017-01-01

Given the public health significance of poorly treatable co-morbid major depressive disorders (MDD) among patients with type 2 diabetes mellitus (DM2) and coronary heart disease (CHD), we need to investigate whether strategies to prevent the development of major depression could reduce its burden of disease. We therefore evaluated the effectiveness of a stepped-care program for subthreshold depression in comparison with usual care in patients with DM2 and/or CHD. A cluster randomized controlled trial, with 27 primary care centers serving as clusters. A total of 236 DM2 and/or CHD patients with subthreshold depression (nine item Patient Health Questionnaire (PHQ-9) score ≥ 6, no current MDD according to DSM-IV criteria) were allocated to the intervention group (N = 96) or usual care group (n = 140). The stepped-care program was delivered by trained practice nurses during one year and consisted of four sequential treatment steps: watchful waiting, guided self-help, problem solving treatment and referral to the general practitioner. The primary outcome was the 12-month cumulative incidence of MDD as measured with the Mini International Neuropsychiatric Interview (MINI). Secondary outcomes included severity of depression (measured by PHQ-9) at 3, 6, 9 and 12 months. Of 236 patients (mean age, 67,5 (SD 10) years; 54.7% men), 210 (89%) completed the MINI at 12 months. The cumulative incidence of MDD was 9 of 89 (10.1%) participants in the intervention group and 12 of 121 (9.9%) participants in the usual care group. We found no statistically significant overall effect of the intervention (OR = 1.21; 95% confidence interval (0.12 to 12.41)) and there were no statistically significant differences in the course or severity of depressive symptoms between the two groups. This study suggest that Step-Dep was not more effective in preventing MDD than usual care in a primary care population with DM2 and/or CHD and subthreshold depression.

Evaluation of Second-Level Inference in fMRI Analysis

PubMed Central

Roels, Sanne P.; Loeys, Tom; Moerkerke, Beatrijs

2016-01-01

We investigate the impact of decisions in the second-level (i.e., over subjects) inferential process in functional magnetic resonance imaging on (1) the balance between false positives and false negatives and on (2) the data-analytical stability, both proxies for the reproducibility of results. Second-level analysis based on a mass univariate approach typically consists of 3 phases. First, one proceeds via a general linear model for a test image that consists of pooled information from different subjects. We evaluate models that take into account first-level (within-subjects) variability and models that do not take into account this variability. Second, one proceeds via inference based on parametrical assumptions or via permutation-based inference. Third, we evaluate 3 commonly used procedures to address the multiple testing problem: familywise error rate correction, False Discovery Rate (FDR) correction, and a two-step procedure with minimal cluster size. Based on a simulation study and real data we find that the two-step procedure with minimal cluster size results in most stable results, followed by the familywise error rate correction. The FDR results in most variable results, for both permutation-based inference and parametrical inference. Modeling the subject-specific variability yields a better balance between false positives and false negatives when using parametric inference. PMID:26819578

Collective behavior in two-dimensional biological systems: Receptor clustering and beta-sheet aggregation

NASA Astrophysics Data System (ADS)

Guo, Chinlin

We studied two particular biomedical systems which exhibit collective molecular behavior. One is clustering of tumor necrosis factor receptor I (TNFR1), and another is β-sheet folding and aggregation. Receptor clustering has been shown to be a crucial step in many signaling events but its biological meaning has not been adequately addressed. Here, via a simple lattice model, we show how cells use this clustering machinery to enhance sensitivity as well as robustness. On the other hand, intracellular deposition of aggregated protein rich in β-sheet is a prominent cytopathological feature of most neurodegenerative diseases. How this aggregation occurs and how it responds to therapy is not completely understood. Here, we started from a reconstruction of the H-bond potential and carry out a full investigation of β-sheet thermodynamics as well as kinetics. We show that β-sheet aggregation is most likely due to molecular stacking and found that the minimal length of an aggregate mutant polymer corresponds well with the number observed in adult Huntington's disease. We have also shown that molecular agents such as dendrimers might fail at high-dose therapy; instead, a potential therapy strategy is to block β-turn formation. Our predictions can be used for future experimental tests and clinical trials.

Identification and Characterization of Unique Subgroups of Chronic Pain Individuals with Dispositional Personality Traits.

PubMed

Mehta, S; Rice, D; McIntyre, A; Getty, H; Speechley, M; Sequeira, K; Shapiro, A P; Morley-Forster, P; Teasell, R W

2016-01-01

Objective. The current study attempted to identify and characterize distinct CP subgroups based on their level of dispositional personality traits. The secondary objective was to compare the difference among the subgroups in mood, coping, and disability. Methods. Individuals with chronic pain were assessed for demographic, psychosocial, and personality measures. A two-step cluster analysis was conducted in order to identify distinct subgroups of patients based on their level of personality traits. Differences in clinical outcomes were compared using the multivariate analysis of variance based on cluster membership. Results. In 229 participants, three clusters were formed. No significant difference was seen among the clusters on patient demographic factors including age, sex, relationship status, duration of pain, and pain intensity. Those with high levels of dispositional personality traits had greater levels of mood impairment compared to the other two groups (p < 0.05). Significant difference in disability was seen between the subgroups. Conclusions. The study identified a high risk group of CP individuals whose level of personality traits significantly correlated with impaired mood and coping. Use of pharmacological treatment alone may not be successful in improving clinical outcomes among these individuals. Instead, a more comprehensive treatment involving psychological treatments may be important in managing the personality traits that interfere with recovery.

Stabilization of Small Boron Cage by Transition Metal Encapsulation

NASA Astrophysics Data System (ADS)

Zhang, Lijun; Lv, Jian; Wang, Yanchao; Ma, Yanming

2015-03-01

The discovery of chemically stable fullerene-like structures formed by elements other than carbon has been long-standing desired. On this aspect significant efforts have centered around boron, only one electron deficient compared with carbon. However, during the past decade a large number of experimental and theoretical studies have established that small boron clusters are either planar/quasi-planar or forming double-ring tubular structures. Until recently, two all-boron fullerenes have been independently discovered: B38 proposed by our structure searching calculations and B40 observed in a joint experimental and theoretical study. Here we extend our work to the even smaller boron clusters and propose an effective routine to stabilize them by transition metal encapsulation. By combining swarm-intelligence structure searching and first-principles calculations, we have systematically investigated the energy landscapes of transition-metal-doped MB24 clusters (M = Ti, Zr, Hf, Cr, Mo, W, Fe, Ru and Os). Two stable symmetric endohedral boron cages, MoB24 and WB24 are identified. The stability of them can be rationalized in terms of their unique 18-electron closed-shell electronic structures. Funded by Recruitment Program of Global Experts of China and China Postdoctoral Science Foundation.

Classic Nuclear Localization Signals and a Novel Nuclear Localization Motif Are Required for Nuclear Transport of Porcine Parvovirus Capsid Proteins

PubMed Central

Boisvert, Maude; Bouchard-Lévesque, Véronique; Fernandes, Sandra

2014-01-01

ABSTRACT Nuclear targeting of capsid proteins (VPs) is important for genome delivery and precedes assembly in the replication cycle of porcine parvovirus (PPV). Clusters of basic amino acids, corresponding to potential nuclear localization signals (NLS), were found only in the unique region of VP1 (VP1up, for VP1 unique part). Of the five identified basic regions (BR), three were important for nuclear localization of VP1up: BR1 was a classic Pat7 NLS, and the combination of BR4 and BR5 was a classic bipartite NLS. These NLS were essential for viral replication. VP2, the major capsid protein, lacked these NLS and contained no region with more than two basic amino acids in proximity. However, three regions of basic clusters were identified in the folded protein, assembled into a trimeric structure. Mutagenesis experiments showed that only one of these three regions was involved in VP2 transport to the nucleus. This structural NLS, termed the nuclear localization motif (NLM), is located inside the assembled capsid and thus can be used to transport trimers to the nucleus in late steps of infection but not for virions in initial infection steps. The two NLS of VP1up are located in the N-terminal part of the protein, externalized from the capsid during endosomal transit, exposing them for nuclear targeting during early steps of infection. Globally, the determinants of nuclear transport of structural proteins of PPV were different from those of closely related parvoviruses. IMPORTANCE Most DNA viruses use the nucleus for their replication cycle. Thus, structural proteins need to be targeted to this cellular compartment at two distinct steps of the infection: in early steps to deliver viral genomes to the nucleus and in late steps to assemble new viruses. Nuclear targeting of proteins depends on the recognition of a stretch of basic amino acids by cellular transport proteins. This study reports the identification of two classic nuclear localization signals in the minor capsid protein (VP1) of porcine parvovirus. The major protein (VP2) nuclear localization was shown to depend on a complex structural motif. This motif can be used as a strategy by the virus to avoid transport of incorrectly folded proteins and to selectively import assembled trimers into the nucleus. Structural nuclear localization motifs can also be important for nuclear proteins without a classic basic amino acid stretch, including multimeric cellular proteins. PMID:25078698

Real-time observation of formation and relaxation dynamics of NH4 in (CH3OH)m(NH3)n clusters.

PubMed

Yamada, Yuji; Nishino, Yoko; Fujihara, Akimasa; Ishikawa, Haruki; Fuke, Kiyokazu

2009-03-26

The formation and relaxation dynamics of NH4(CH3OH)m(NH3)n clusters produced by photolysis of ammonia-methanol mixed clusters has been observed by a time-resolved pump-probe method with femtosecond pulse lasers. From the detailed analysis of the time evolutions of the protonated cluster ions, NH4(+)(CH3OH)m(NH3)n, the kinetic model has been constructed, which consists of sequential three-step reaction: ultrafast hydrogen-atom transfer producing the radical pair (NH4-NH2)*, the relaxation process of radical-pair clusters, and dissociation of the solvated NH4 clusters. The initial hydrogen transfer hardly occurs between ammonia and methanol, implying the unfavorable formation of radical pair, (CH3OH2-NH2)*. The remarkable dependence of the time constants in each step on the number and composition of solvents has been explained by the following factors: hydrogen delocalization within the clusters, the internal conversion of the excited-state radical pair, and the stabilization of NH4 by solvation. The dependence of the time profiles on the probe wavelength is attributed to the different ionization efficiency of the NH4(CH3OH)m(NH3)n clusters.

Stepping Stones Triple P-Positive Parenting Program for Children with Disability: A Systematic Review and Meta-Analysis

ERIC Educational Resources Information Center

Tellegen, Cassandra L.; Sanders, Matthew R.

2013-01-01

This systematic review and meta-analysis evaluated the treatment effects of a behavioral family intervention, Stepping Stones Triple P (SSTP) for parents of children with disabilities. SSTP is a system of five intervention levels of increasing intensity and narrowing population reach. Twelve studies, including a total of 659 families, met…

Characterization of bafilomycin biosynthesis in Kitasatospora setae KM-6054 and comparative analysis of gene clusters in Actinomycetales microorganisms.

PubMed

Nara, Ayako; Hashimoto, Takuya; Komatsu, Mamoru; Nishiyama, Makoto; Kuzuyama, Tomohisa; Ikeda, Haruo

2017-05-01

Bafilomycins A 1 , C 1 and B 1 (setamycin) produced by Kitasatospora setae KM-6054 belong to the plecomacrolide family, which exhibit antibacterial, antifungal, antineoplastic and immunosuppressive activities. An analysis of gene clusters from K. setae KM-6054 governing the biosynthesis of bafilomycins revealed that it contains five large open reading frames (ORFs) encoding the multifunctional polypeptides of bafilomycin polyketide synthases (PKSs). These clustered PKS genes, which are responsible for bafilomycin biosynthesis, together encode 11 homologous sets of enzyme activities, each catalyzing a specific round of polyketide chain elongation. The region contains an additional 13 ORFs spanning a distance of 73 287 bp, some of which encode polypeptides governing other key steps in bafilomycin biosynthesis. Five ORFs, BfmB, BfmC, BfmD, BfmE and BfmF, were involved in the formation of methoxymalonyl-acyl carrier protein (ACP). Two possible regulatory genes, bfmR and bfmH, were found downstream of the above genes. A gene-knockout analysis revealed that BfmR was only a transcriptional regulator for the transcription of bafilomycin biosynthetic genes. Two genes, bfmI and bfmJ, were found downstream of bfmH. An analysis of these gene-disruption mutants in addition to an enzymatic analysis of BfmI and BfmJ revealed that BfmJ activated fumarate and BfmI functioned as a catalyst to form a fumaryl ester at the C21 hydroxyl residue of bafilomycin A 1 . A comparative analysis of bafilomycin gene clusters in K. setae KM-6054, Streptomyces lohii JCM 14114 and Streptomyces griseus DSM 2608 revealed that each ORF of both gene clusters in two Streptomyces strains were quite similar to each other. However, each ORF of gene cluster in K. setae KM-6054 was of lower similarity to that of corresponding ORF in the two Streptomyces species.

Generation of gas-phase ions from charged clusters: an important ionization step causing suppression of matrix and analyte ions in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Lou, Xianwen; van Dongen, Joost L J; Milroy, Lech-Gustav; Meijer, E W

2016-12-30

Ionization in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a very complicated process. It has been reported that quaternary ammonium salts show extremely strong matrix and analyte suppression effects which cannot satisfactorily be explained by charge transfer reactions. Further investigation of the reasons causing these effects can be useful to improve our understanding of the MALDI process. The dried-droplet and modified thin-layer methods were used as sample preparation methods. In the dried-droplet method, analytes were co-crystallized with matrix, whereas in the modified thin-layer method analytes were deposited on the surface of matrix crystals. Model compounds, tetrabutylammonium iodide ([N(Bu) 4 ]I), cesium iodide (CsI), trihexylamine (THA) and polyethylene glycol 600 (PEG 600), were selected as the test analytes given their ability to generate exclusively pre-formed ions, protonated ions and metal ion adducts respectively in MALDI. The strong matrix suppression effect (MSE) observed using the dried-droplet method might disappear using the modified thin-layer method, which suggests that the incorporation of analytes in matrix crystals contributes to the MSE. By depositing analytes on the matrix surface instead of incorporating in the matrix crystals, the competition for evaporation/ionization from charged matrix/analyte clusters could be weakened resulting in reduced MSE. Further supporting evidence for this inference was found by studying the analyte suppression effect using the same two sample deposition methods. By comparing differences between the mass spectra obtained via the two sample preparation methods, we present evidence suggesting that the generation of gas-phase ions from charged matrix/analyte clusters may induce significant suppression of matrix and analyte ions. The results suggest that the generation of gas-phase ions from charged matrix/analyte clusters is an important ionization step in MALDI-MS. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Feature Clustering for Accelerating Parallel Coordinate Descent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scherrer, Chad; Tewari, Ambuj; Halappanavar, Mahantesh

2012-12-06

We demonstrate an approach for accelerating calculation of the regularization path for L1 sparse logistic regression problems. We show the benefit of feature clustering as a preconditioning step for parallel block-greedy coordinate descent algorithms.

Conversion treatment of thin titanium layer deposited on carbon steel

NASA Astrophysics Data System (ADS)

Benarioua, Younes; Wendler, Bogdan; Chicot, Didier

2018-05-01

The present study has been conducted in order to obtain titanium carbide layer using a conversion treatment consisting of two main steps. In the first step a thin pure titanium layer was deposited on 120C4 carbon steel by PVD. In the second step, the carbon atoms from the substrate diffuse to the titanium coating due to a vacuum annealing treatment and the Ti coating transforms into titanium carbide. Depending on the annealing temperature a partial or complete conversion into TiC is obtained. The hardness of the layer can be expected to differ depending on the processing temperatures. By a systematic study of the hardness as a function of the applied load, we confirm the process of growth of the layer.

Planck 2015 results. XXVII. The second Planck catalogue of Sunyaev-Zeldovich sources

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Arnaud, M.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Barrena, R.; Bartlett, J. G.; Bartolo, N.; Battaner, E.; Battye, R.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bikmaev, I.; Böhringer, H.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Bucher, M.; Burenin, R.; Burigana, C.; Butler, R. C.; Calabrese, E.; Cardoso, J.-F.; Carvalho, P.; Catalano, A.; Challinor, A.; Chamballu, A.; Chary, R.-R.; Chiang, H. C.; Chon, G.; Christensen, P. R.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Combet, C.; Comis, B.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Dahle, H.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Désert, F.-X.; Dickinson, C.; Diego, J. M.; Dolag, K.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Ducout, A.; Dupac, X.; Efstathiou, G.; Eisenhardt, P. R. M.; Elsner, F.; Enßlin, T. A.; Eriksen, H. K.; Falgarone, E.; Fergusson, J.; Feroz, F.; Ferragamo, A.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A. A.; Franceschi, E.; Frejsel, A.; Galeotta, S.; Galli, S.; Ganga, K.; Génova-Santos, R. T.; Giard, M.; Giraud-Héraud, Y.; Gjerløw, E.; González-Nuevo, J.; Górski, K. M.; Grainge, K. J. B.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J. E.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Hempel, A.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Hurier, G.; Jaffe, A. H.; Jaffe, T. R.; Jin, T.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Khamitov, I.; Kisner, T. S.; Kneissl, R.; Knoche, J.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lamarre, J.-M.; Lasenby, A.; Lattanzi, M.; Lawrence, C. R.; Leonardi, R.; Lesgourgues, J.; Levrier, F.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maggio, G.; Maino, D.; Mak, D. S. Y.; Mandolesi, N.; Mangilli, A.; Martin, P. G.; Martínez-González, E.; Masi, S.; Matarrese, S.; Mazzotta, P.; McGehee, P.; Mei, S.; Melchiorri, A.; Melin, J.-B.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nastasi, A.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Noviello, F.; Novikov, D.; Novikov, I.; Olamaie, M.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Patanchon, G.; Pearson, T. J.; Perdereau, O.; Perotto, L.; Perrott, Y. C.; Perrotta, F.; Pettorino, V.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Reach, W. T.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Renzi, A.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Rossetti, M.; Roudier, G.; Rozo, E.; Rubiño-Martín, J. A.; Rumsey, C.; Rusholme, B.; Rykoff, E. S.; Sandri, M.; Santos, D.; Saunders, R. D. E.; Savelainen, M.; Savini, G.; Schammel, M. P.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Shimwell, T. W.; Spencer, L. D.; Stanford, S. A.; Stern, D.; Stolyarov, V.; Stompor, R.; Streblyanska, A.; Sudiwala, R.; Sunyaev, R.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tramonte, D.; Tristram, M.; Tucci, M.; Tuovinen, J.; Umana, G.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vielva, P.; Villa, F.; Wade, L. A.; Wandelt, B. D.; Wehus, I. K.; White, S. D. M.; Wright, E. L.; Yvon, D.; Zacchei, A.; Zonca, A.

2016-09-01

We present the all-sky Planck catalogue of Sunyaev-Zeldovich (SZ) sources detected from the 29 month full-mission data. The catalogue (PSZ2) is the largest SZ-selected sample of galaxy clusters yet produced and the deepest systematic all-sky surveyof galaxy clusters. It contains 1653 detections, of which 1203 are confirmed clusters with identified counterparts in external data sets, and is the first SZ-selected cluster survey containing >103 confirmed clusters. We present a detailed analysis of the survey selection function in terms of its completeness and statistical reliability, placing a lower limit of 83% on the purity. Using simulations, we find that the estimates of the SZ strength parameter Y5R500are robust to pressure-profile variation and beam systematics, but accurate conversion to Y500 requires the use of prior information on the cluster extent. We describe the multi-wavelength search for counterparts in ancillary data, which makes use of radio, microwave, infra-red, optical, and X-ray data sets, and which places emphasis on the robustness of the counterpart match. We discuss the physical properties of the new sample and identify a population of low-redshift X-ray under-luminous clusters revealed by SZ selection. These objects appear in optical and SZ surveys with consistent properties for their mass, but are almost absent from ROSAT X-ray selected samples.

Planck 2015 results: XXVII. The second Planck catalogue of Sunyaev-Zeldovich sources

DOE PAGES

Ade, P. A. R.; Aghanim, N.; Arnaud, M.; ...

2016-09-20

Here, we present the all-sky Planck catalogue of Sunyaev-Zeldovich (SZ) sources detected from the 29 month full-mission data. The catalogue (PSZ2) is the largest SZ-selected sample of galaxy clusters yet produced and the deepest systematic all-sky surveyof galaxy clusters. It contains 1653 detections, of which 1203 are confirmed clusters with identified counterparts in external data sets, and is the first SZ-selected cluster survey containing >103 confirmed clusters. We present a detailed analysis of the survey selection function in terms of its completeness and statistical reliability, placing a lower limit of 83% on the purity. Using simulations, we find that themore » estimates of the SZ strength parameter Y5R500are robust to pressure-profile variation and beam systematics, but accurate conversion to Y500 requires the use of prior information on the cluster extent. We describe the multi-wavelength search for counterparts in ancillary data, which makes use of radio, microwave, infra-red, optical, and X-ray data sets, and which places emphasis on the robustness of the counterpart match. We discuss the physical properties of the new sample and identify a population of low-redshift X-ray under-luminous clusters revealed by SZ selection. These objects appear in optical and SZ surveys with consistent properties for their mass, but are almost absent from ROSAT X-ray selected samples.« less

Optical spectroscopy and velocity dispersions of galaxy clusters from the SPT-SZ survey

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruel, J.; Bayliss, M.; Bazin, G.

2014-09-01

We present optical spectroscopy of galaxies in clusters detected through the Sunyaev-Zel'dovich (SZ) effect with the South Pole Telescope (SPT). We report our own measurements of 61 spectroscopic cluster redshifts, and 48 velocity dispersions each calculated with more than 15 member galaxies. This catalog also includes 19 dispersions of SPT-observed clusters previously reported in the literature. The majority of the clusters in this paper are SPT-discovered; of these, most have been previously reported in other SPT cluster catalogs, and five are reported here as SPT discoveries for the first time. By performing a resampling analysis of galaxy velocities, we findmore » that unbiased velocity dispersions can be obtained from a relatively small number of member galaxies (≲ 30), but with increased systematic scatter. We use this analysis to determine statistical confidence intervals that include the effect of membership selection. We fit scaling relations between the observed cluster velocity dispersions and mass estimates from SZ and X-ray observables. In both cases, the results are consistent with the scaling relation between velocity dispersion and mass expected from dark-matter simulations. We measure a ∼30% log-normal scatter in dispersion at fixed mass, and a ∼10% offset in the normalization of the dispersion-mass relation when compared to the expectation from simulations, which is within the expected level of systematic uncertainty.« less

Tracking a Solar Wind Dynamic Pressure Pulses' Impact Through the Magnetosphere Using the Heliophysics System Observatory

NASA Astrophysics Data System (ADS)

Vidal-Luengo, S.; Moldwin, M.

2017-12-01

During northward Interplanetary Magnetic Field (IMF) Bz conditions, the magnetosphere acts as a closed "cavity" and reacts to solar wind dynamic pressure pulses more simply than during southward IMF conditions. Effects of solar wind dynamic pressure have been observed as geomagnetic lobe compressions depending on the characteristics of the pressure pulse and the spacecraft location. One of the most important aspects of this study is the incorporation of simultaneous observations by different missions, such as WIND, CLUSTER, THEMIS, MMS, Van Allen Probes and GOES as well as magnetometer ground stations that allow us to map the magnetosphere response at different locations during the propagation of a pressure pulse. In this study we used the SYM-H as an indicator of dynamic pressure pulses occurrence from 2007 to 2016. The selection criteria for events are: (1) the increase in the index must be bigger than 10 [nT] and (2) the rise time must be in less than 5 minutes. Additionally, the events must occur under northward IMF and at the same time at least one spacecraft has to be located in the magnetosphere nightside. Using this methodology we found 66 pressure pulse events for analysis. Most of them can be classified as step function pressure pulses or as sudden impulses (increase followed immediately by a decrease of the dynamic pressure). Under these two categories the results show some systematic signatures depending of the location of the spacecraft. For both kind of pressure pulse signatures, compressions are observed on the dayside. However, on the nightside compressions and/or South-then-North magnetic signatures can be observed for step function like pressure pulses, meanwhile for the sudden impulse kind of pressure pulses the magnetospheric response seems to be less global and more dependent on the local conditions.

Spin-wave wavelength down-conversion at thickness steps

NASA Astrophysics Data System (ADS)

Stigloher, Johannes; Taniguchi, Takuya; Madami, Marco; Decker, Martin; Körner, Helmut S.; Moriyama, Takahiro; Gubbiotti, Gianluca; Ono, Teruo; Back, Christian H.

2018-05-01

We report a systematic experimental study on the refraction and reflection of magnetostatic spin-waves at a thickness step between two Permalloy films of different thickness. The transmitted spin-waves for the transition from a thick film to a thin film have a higher wave vector compared to the incoming waves. Consequently, such systems may find use as passive wavelength transformers in magnonic networks. We investigate the spin-wave transmission behavior by studying the influence of the external magnetic field, incident angle, and thickness ratio of the films using time-resolved scanning Kerr microscopy and micro-focused Brillouin light scattering.

Plant metabolic clusters - from genetics to genomics.

PubMed

Nützmann, Hans-Wilhelm; Huang, Ancheng; Osbourn, Anne

2016-08-01

Contents 771 I. 771 II. 772 III. 780 IV. 781 V. 786 786 References 786 SUMMARY: Plant natural products are of great value for agriculture, medicine and a wide range of other industrial applications. The discovery of new plant natural product pathways is currently being revolutionized by two key developments. First, breakthroughs in sequencing technology and reduced cost of sequencing are accelerating the ability to find enzymes and pathways for the biosynthesis of new natural products by identifying the underlying genes. Second, there are now multiple examples in which the genes encoding certain natural product pathways have been found to be grouped together in biosynthetic gene clusters within plant genomes. These advances are now making it possible to develop strategies for systematically mining multiple plant genomes for the discovery of new enzymes, pathways and chemistries. Increased knowledge of the features of plant metabolic gene clusters - architecture, regulation and assembly - will be instrumental in expediting natural product discovery. This review summarizes progress in this area. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Effect of study design and setting on tuberculosis clustering estimates using Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR): a systematic review.

PubMed

Mears, Jessica; Abubakar, Ibrahim; Cohen, Theodore; McHugh, Timothy D; Sonnenberg, Pam

2015-01-21

To systematically review the evidence for the impact of study design and setting on the interpretation of tuberculosis (TB) transmission using clustering derived from Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) strain typing. MEDLINE, EMBASE, CINHAL, Web of Science and Scopus were searched for articles published before 21st October 2014. Studies in humans that reported the proportion of clustering of TB isolates by MIRU-VNTR were included in the analysis. Univariable meta-regression analyses were conducted to assess the influence of study design and setting on the proportion of clustering. The search identified 27 eligible articles reporting clustering between 0% and 63%. The number of MIRU-VNTR loci typed, requiring consent to type patient isolates (as a proxy for sampling fraction), the TB incidence and the maximum cluster size explained 14%, 14%, 27% and 48% of between-study variation, respectively, and had a significant association with the proportion of clustering. Although MIRU-VNTR typing is being adopted worldwide there is a paucity of data on how study design and setting may influence estimates of clustering. We have highlighted study design variables for consideration in the design and interpretation of future studies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Hypersexuality and high sexual desire: exploring the structure of problematic sexuality.

PubMed

Carvalho, Joana; Štulhofer, Aleksandar; Vieira, Armando L; Jurin, Tanja

2015-06-01

The concept of hypersexuality has been accompanied by fierce debates and conflicting conclusions about its nature. One of the central questions under the discussion is a potential overlap between hypersexuality and high sexual desire. With the relevant research in its early phase, the structure of hypersexuality remains largely unknown. The aim of the present study was to systematically explore the overlap between problematic sexuality and high sexual desire. A community online survey was carried out in Croatia in 2014. The data were first cluster analyzed (by gender) based on sexual desire, sexual activity, perceived lack of control over one's sexuality, and negative behavioral consequences. Participants in the meaningful clusters were then compared for psychosocial characteristics. To complement cluster analysis (CA), multigroup confirmatory factor analysis (CFA) of the same four constructs was carried out. Indicators representing the proposed structure of hypersexuality were included: sexual desire, frequency of sexual activity, lack of control over one's sexuality, and negative behavioral outcomes. Psychosocial characteristics such as religiosity, attitudes toward pornography, and general psychopathology were also evaluated. CA pointed to the existence of two meaningful clusters, one representing problematic sexuality, that is, lack of control over one's sexuality and negative outcomes (control/consequences cluster), and the other reflecting high sexual desire and frequent sexual activity (desire/activity cluster). Compared with the desire/activity cluster, individuals from the control/consequences cluster reported more psychopathology and were characterized by more traditional attitudes. Complementing the CA findings, CFA pointed to two distinct latent dimensions-problematic sexuality and high sexual desire/activity. Our study supports the distinctiveness of hypersexuality and high sexual desire/activity, suggesting that problematic sexuality might be more associated with the perceived lack of personal control over sexuality and moralistic attitudes than with high levels of sexual desire and activity. © 2015 International Society for Sexual Medicine.