Clustering of samples and variables with mixed-type data

PubMed Central

Edelmann, Dominic; Kopp-Schneider, Annette

2017-01-01

Analysis of data measured on different scales is a relevant challenge. Biomedical studies often focus on high-throughput datasets of, e.g., quantitative measurements. However, the need for integration of other features possibly measured on different scales, e.g. clinical or cytogenetic factors, becomes increasingly important. The analysis results (e.g. a selection of relevant genes) are then visualized, while adding further information, like clinical factors, on top. However, a more integrative approach is desirable, where all available data are analyzed jointly, and where also in the visualization different data sources are combined in a more natural way. Here we specifically target integrative visualization and present a heatmap-style graphic display. To this end, we develop and explore methods for clustering mixed-type data, with special focus on clustering variables. Clustering of variables does not receive as much attention in the literature as does clustering of samples. We extend the variables clustering methodology by two new approaches, one based on the combination of different association measures and the other on distance correlation. With simulation studies we evaluate and compare different clustering strategies. Applying specific methods for mixed-type data proves to be comparable and in many cases beneficial as compared to standard approaches applied to corresponding quantitative or binarized data. Our two novel approaches for mixed-type variables show similar or better performance than the existing methods ClustOfVar and bias-corrected mutual information. Further, in contrast to ClustOfVar, our methods provide dissimilarity matrices, which is an advantage, especially for the purpose of visualization. Real data examples aim to give an impression of various kinds of potential applications for the integrative heatmap and other graphical displays based on dissimilarity matrices. We demonstrate that the presented integrative heatmap provides more

Polyoxovanadate-alkoxide clusters as multi-electron charge carriers for symmetric non-aqueous redox flow batteries† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc05295b

PubMed Central

VanGelder, L. E.; Kosswattaarachchi, A. M.; Forrestel, P. L.

2018-01-01

Non-aqueous redox flow batteries have emerged as promising systems for large-capacity, reversible energy storage, capable of meeting the variable demands of the electrical grid. Here, we investigate the potential for a series of Lindqvist polyoxovanadate-alkoxide (POV-alkoxide) clusters, [V6O7(OR)12] (R = CH3, C2H5), to serve as the electroactive species for a symmetric, non-aqueous redox flow battery. We demonstrate that the physical and electrochemical properties of these POV-alkoxides make them suitable for applications in redox flow batteries, as well as the ability for ligand modification at the bridging alkoxide moieties to yield significant improvements in cluster stability during charge–discharge cycling. Indeed, the metal–oxide core remains intact upon deep charge–discharge cycling, enabling extremely high coulombic efficiencies (∼97%) with minimal overpotential losses (∼0.3 V). Furthermore, the bulky POV-alkoxide demonstrates significant resistance to deleterious crossover, which will lead to improved lifetime and efficiency in a redox flow battery. PMID:29675217

Spatial heterogeneity of type I error for local cluster detection tests

PubMed Central

2014-01-01

Background Just as power, type I error of cluster detection tests (CDTs) should be spatially assessed. Indeed, CDTs’ type I error and power have both a spatial component as CDTs both detect and locate clusters. In the case of type I error, the spatial distribution of wrongly detected clusters (WDCs) can be particularly affected by edge effect. This simulation study aims to describe the spatial distribution of WDCs and to confirm and quantify the presence of edge effect. Methods A simulation of 40 000 datasets has been performed under the null hypothesis of risk homogeneity. The simulation design used realistic parameters from survey data on birth defects, and in particular, two baseline risks. The simulated datasets were analyzed using the Kulldorff’s spatial scan as a commonly used test whose behavior is otherwise well known. To describe the spatial distribution of type I error, we defined the participation rate for each spatial unit of the region. We used this indicator in a new statistical test proposed to confirm, as well as quantify, the edge effect. Results The predefined type I error of 5% was respected for both baseline risks. Results showed strong edge effect in participation rates, with a descending gradient from center to edge, and WDCs more often centrally situated. Conclusions In routine analysis of real data, clusters on the edge of the region should be carefully considered as they rarely occur when there is no cluster. Further work is needed to combine results from power studies with this work in order to optimize CDTs performance. PMID:24885343

Bridging the opposite chemistries of tantalum and tungsten polyoxometalates.

PubMed

Molina, P I; Sures, D J; Miró, P; Zakharov, L N; Nyman, M

2015-09-28

The disparate solubility, redox activity, and pH stability of the group V and group VI polyoxometalates (POMs) confer very different functionality on these species, and tailoring cluster properties by varying the ratio of group V to group VI metals poses both an opportunity and a synthetic challenge. A classic series of studies reported over 40 years ago provided some insight into W/Nb POMs, from which researchers have built on to date. However, the analogous W/Ta series has never been addressed in a systematic manner. Three members of this W/Ta series are presented here, synthesized from simple oxo- and peroxocoltanate precursors. [Ta3W3O19](5-) displays the Lindqvist-type structure, while [TaW9O32](5-) and [Ta2W8O32](6-) are isostructural with decatungstate ([W10O32](4-)). Additionally, the use of peroxoniobate instead of hexaniobate as the starting material drives the formation of the decatungstate-type structure [NbW9O32](5-) instead of the Lindqvist ion that was established to be the foundational cluster geometry in prior work. The electronic structure of the Nb/Ta substituted decatungstates is directly related to the degree of substitution inasmuch as the HOMO-LUMO energy gap (Egap) slightly increases as more Nb/Ta atoms are incorporated into the structure. The poor mixing of the d-orbitals of Nb/Ta and W is responsible for the observed trends in the UV spectra and cyclic voltammetry. Moreover, the stability of the molecular frameworks in the gas phase is also related to the extent of substitution as revealed by electrospray mass-spectrometry (ESI-MS).

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.

Evolution of the early-type galaxy fraction in clusters since z = 0.8

NASA Astrophysics Data System (ADS)

Simard, L.; Clowe, D.; Desai, V.; Dalcanton, J. J.; von der Linden, A.; Poggianti, B. M.; White, S. D. M.; Aragón-Salamanca, A.; De Lucia, G.; Halliday, C.; Jablonka, P.; Milvang-Jensen, B.; Saglia, R. P.; Pelló, R.; Rudnick, G. H.; Zaritsky, D.

2009-12-01

We study the morphological content of a large sample of high-redshift clusters to determine its dependence on cluster mass and redshift. Quantitative morphologies are based on PSF-convolved, 2D bulge+disk decompositions of cluster and field galaxies on deep Very Large Telescope FORS2 images of eighteen, optically-selected galaxy clusters at 0.45 < z < 0.80 observed as part of the ESO Distant Cluster Survey (“EDisCS”). Morphological content is characterized by the early-type galaxy fraction f_et, and early-type galaxies are objectively selected based on their bulge fraction and image smoothness. This quantitative selection is equivalent to selecting galaxies visually classified as E or S0. Changes in early-type fractions as a function of cluster velocity dispersion, redshift and star-formation activity are studied. A set of 158 clusters extracted from the Sloan Digital Sky Survey is analyzed exactly as the distant EDisCS sample to provide a robust local comparison. We also compare our results to a set of clusters from the Millennium Simulation. Our main results are: (1) the early-type fractions of the SDSS and EDisCS clusters exhibit no clear trend as a function of cluster velocity dispersion. (2) Mid-z EDisCS clusters around σ = 500 km s-1 have f_et ≃ 0.5 whereas high-z EDisCS clusters have f_et ≃ 0.4. This represents a ~25% increase over a time interval of 2 Gyr. (3) There is a marked difference in the morphological content of EDisCS and SDSS clusters. None of the EDisCS clusters have early-type galaxy fractions greater than 0.6 whereas half of the SDSS clusters lie above this value. This difference is seen in clusters of all velocity dispersions. (4) There is a strong and clear correlation between morphology and star formation activity in SDSS and EDisCS clusters in the sense that decreasing fractions of [OII] emitters are tracked by increasing early-type fractions. This correlation holds independent of cluster velocity dispersion and redshift even

The Evolution of Globular Cluster Systems In Early-Type Galaxies

NASA Astrophysics Data System (ADS)

Grillmair, Carl

1999-07-01

We will measure structural parameters {core radii and concentrations} of globular clusters in three early-type galaxies using deep, four-point dithered observations. We have chosen globular cluster systems which have young, medium-age and old cluster populations, as indicated by cluster colors and luminosities. Our primary goal is to test the hypothesis that globular cluster luminosity functions evolve towards a ``universal'' form. Previous observations have shown that young cluster systems have exponential luminosity functions rather than the characteristic log-normal luminosity function of old cluster systems. We will test to see whether such young system exhibits a wider range of structural parameters than an old systems, and whether and at what rate plausible disruption mechanisms will cause the luminosity function to evolve towards a log-normal form. A simple observational comparison of structural parameters between different age cluster populations and between diff er ent sub-populations within the same galaxy will also provide clues concerning both the formation and destruction mechanisms of star clusters, the distinction between open and globular clusters, and the advisability of using globular cluster luminosity functions as distance indicators.

Merger types forming the Virgo cluster in recent gigayears

NASA Astrophysics Data System (ADS)

Olchanski, M.; Sorce, J. G.

2018-06-01

Context. As our closest cluster-neighbor, the Virgo cluster of galaxies is intensely studied by observers to unravel the mysteries of galaxy evolution within clusters. At this stage, cosmological numerical simulations of the cluster are useful to efficiently test theories and calibrate models. However, it is not trivial to select the perfect simulacrum of the Virgo cluster to fairly compare in detail its observed and simulated galaxy populations that are affected by the type and history of the cluster. Aims: Determining precisely the properties of Virgo for a later selection of simulated clusters becomes essential. It is still not clear how to access some of these properties, such as the past history of the Virgo cluster from current observations. Therefore, directly producing effective simulacra of the Virgo cluster is inevitable. Methods: Efficient simulacra of the Virgo cluster can be obtained via simulations that resemble the local Universe down to the cluster scale. In such simulations, Virgo-like halos form in the proper local environment and permit assessing the most probable formation history of the cluster. Studies based on these simulations have already revealed that the Virgo cluster has had a quiet merging history over the last seven gigayears and that the cluster accretes matter along a preferential direction. Results: This paper reveals that in addition such Virgo halos have had on average only one merger larger than about a tenth of their mass at redshift zero within the last four gigayears. This second branch (by opposition to main branch) formed in a given sub-region and merged recently (within the last gigayear). These properties are not shared with a set of random halos within the same mass range. Conclusions: This study extends the validity of the scheme used to produce the Virgo simulacra down to the largest sub-halos of the Virgo cluster. It opens up great prospects for detailed comparisons with observations, including substructures and

Monothiol glutaredoxins and A-type proteins: partners in Fe-S cluster trafficking.

PubMed

Mapolelo, Daphne T; Zhang, Bo; Randeniya, Sajini; Albetel, Angela-Nadia; Li, Haoran; Couturier, Jérémy; Outten, Caryn E; Rouhier, Nicolas; Johnson, Michael K

2013-03-07

Monothiol glutaredoxins (Grxs) are proposed to function in Fe-S cluster storage and delivery, based on their ability to exist as apo monomeric forms and dimeric forms containing a subunit-bridging [Fe(2)S(2)](2+) cluster, and to accept [Fe(2)S(2)](2+) clusters from primary scaffold proteins. In addition yeast cytosolic monothiol Grxs interact with Fra2 (Fe repressor of activation-2), to form a heterodimeric complex with a bound [Fe(2)S(2)](2+) cluster that plays a key role in iron sensing and regulation of iron homeostasis. In this work, we report on in vitro UV-visible CD studies of cluster transfer between homodimeric monothiol Grxs and members of the ubiquitous A-type class of Fe-S cluster carrier proteins ((Nif)IscA and SufA). The results reveal rapid, unidirectional, intact and quantitative cluster transfer from the [Fe(2)S(2)](2+) cluster-bound forms of A. thaliana GrxS14, S. cerevisiae Grx3, and A. vinelandii Grx-nif homodimers to A. vinelandii(Nif)IscA and from A. thaliana GrxS14 to A. thaliana SufA1. Coupled with in vivo evidence for interaction between monothiol Grxs and A-type Fe-S cluster carrier proteins, the results indicate that these two classes of proteins work together in cellular Fe-S cluster trafficking. However, cluster transfer is reversed in the presence of Fra2, since the [Fe(2)S(2)](2+) cluster-bound heterodimeric Grx3-Fra2 complex can be formed by intact [Fe(2)S(2)](2+) cluster transfer from (Nif)IscA. The significance of these results for Fe-S cluster biogenesis or repair and the cellular regulation of the Fe-S cluster status are discussed.

The Hubble Space Telescope Cluster Supernova Survey. II. The Type la Supernova rate in high-redshift galaxy clusters

DOE PAGES

Barbary, K.; Aldering, G.; Amanullah, R.; ...

2011-12-28

Here we report a measurement of the Type Ia supernova (SN Ia) rate in galaxy clusters at 0.9 < z < 1.46 from the Hubble Space Telescope Cluster Supernova Survey. This is the first cluster SN Ia rate measurement with detected z > 0.9 SNe. Finding 8 ± 1 cluster SNe Ia, we determine an SN Ia rate of 0.50 +0.23 -0.19 (stat) +0.10 -0.09 (sys) h 2 70 SNuB (SNuB ≡ 10 -12 SNe L -1 ⊙,B yr -1). In units of stellar mass, this translates to 0.36 + 0.16 -0.13 (stat) +0.07 -0.06 (sys) h 2 70 SNuMmore » (SNuM ≡ 10 -12 SNe M –1 ⊙ yr –1). This represents a factor of ≈ 5 ± 2 increase over measurements of the cluster rate at z < 0.2. We parameterize the late-time SN Ia delay time distribution (DTD) with a power law: Ψ(t)∝t s . Under the approximation of a single-burst cluster formation redshift of zf = 3, our rate measurement in combination with lower-redshift cluster SN Ia rates constrains s = –1.41 +0.47 –0.40, consistent with measurements of the DTD in the field. This measurement is generally consistent with expectations for the "double degenerate" scenario and inconsistent with some models for the "single degenerate" scenario predicting a steeper DTD at large delay times. We check for environmental dependence and the influence of younger stellar populations by calculating the rate specifically in cluster red-sequence galaxies and in morphologically early-type galaxies, finding results similar to the full cluster rate. Finally, the upper limit of one hostless cluster SN Ia detected in the survey implies that the fraction of stars in the intra-cluster medium is less than 0.47 (95% confidence), consistent with measurements at lower redshifts.« less

Language Learner Motivational Types: A Cluster Analysis Study

ERIC Educational Resources Information Center

Papi, Mostafa; Teimouri, Yasser

2014-01-01

The study aimed to identify different second language (L2) learner motivational types drawing on the framework of the L2 motivational self system. A total of 1,278 secondary school students learning English in Iran completed a questionnaire survey. Cluster analysis yielded five different groups based on the strength of different variables within…

Dwarf galaxy populations in present-day galaxy clusters - II. The history of early-type and late-type dwarfs

NASA Astrophysics Data System (ADS)

Lisker, Thorsten; Weinmann, Simone M.; Janz, Joachim; Meyer, Hagen T.

2013-06-01

How did the dwarf galaxy population of present-day galaxy clusters form and grow over time? We address this question by analysing the history of dark matter subhaloes in the Millennium II cosmological simulation. A semi-analytic model serves as the link to observations. We argue that a reasonable analogue to early morphological types or red-sequence dwarf galaxies are those subhaloes that experienced strong mass-loss, or alternatively those that have spent a long time in massive haloes. This approach reproduces well the observed morphology-distance relation of dwarf galaxies in the Virgo and Coma clusters, and thus provides insight into their history. Over their lifetime, present-day late types have experienced an amount of environmental influence similar to what the progenitors of dwarf ellipticals had already experienced at redshifts above 2. Therefore, dwarf ellipticals are more likely to be a result of early and continuous environmental influence in group- and cluster-size haloes, rather than a recent transformation product. The observed morphological sequences of late-type and early-type galaxies have developed in parallel, not consecutively. Consequently, the characteristics of today's late-type galaxies are not necessarily representative for the progenitors of today's dwarf ellipticals. Studies aiming to reproduce the present-day dwarf population thus need to start at early epochs, model the influence of various environments, and also take into account the evolution of the environments themselves.

Epidemiology Analysis of Streptococcus pyogenes in a Hospital in Southern Taiwan by Use of the Updated emm Cluster Typing System.

PubMed

Chiang-Ni, Chuan; Zheng, Po-Xing; Wang, Shu-Ying; Tsai, Pei-Jane; Chuang, Woei-Jer; Lin, Yee-Shin; Liu, Ching-Chuan; Wu, Jiunn-Jong

2016-01-01

emm typing is the most widely used molecular typing method for the human pathogen Streptococcus pyogenes (group A streptococcus [GAS]). emm typing is based on a small variable region of the emm gene; however, the emm cluster typing system defines GAS types according to the nearly complete sequence of the emm gene. Therefore, emm cluster typing is considered to provide more information regarding the functional and structural properties of M proteins in different emm types of GAS. In the present study, 677 isolates collected between 1994 and 2008 in a hospital in southern Taiwan were analyzed by the emm cluster typing system. emm clusters A-C4, E1, E6, and A-C3 were the most prevalent emm cluster types and accounted for 67.4% of total isolates. emm clusters A-C4 and E1 were associated with noninvasive diseases, whereas E6 was significantly associated with both invasive and noninvasive manifestations. In addition, emm clusters D4, E2, and E3 were significantly associated with invasive manifestations. Furthermore, we found that the functional properties of M protein, including low fibrinogen-binding and high IgG-binding activities, were correlated significantly with invasive manifestations. In summary, the present study provides updated epidemiological information on GAS emm cluster types in southern Taiwan. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Snapshot Survey of the Globular Cluster Populations of Isolated Early Type Galaxies

NASA Astrophysics Data System (ADS)

Gregg, Michael

2017-08-01

We propose WFC3/UVIS snapshot observations of a sample of 75 isolated early type galaxiesresiding in cosmic voids or extremely low density regions. The primary aim is to usetheir globular cluster populations to reconstruct their evolutionary history, revealingif, how, and why void ellipticals differ from cluster ellipticals. The galaxies span arange of luminosities, providing a varied sample for comparison with the well-documentedglobular cluster populations in denser environments. This proposed WFC3 study of isolatedearly type galaxies breaks new ground by targeting a sample which has thus far receivedlittle attention, and, significantly, this will be the first such study with HST.Characterizing early type galaxies in voids and their GC systems promises to increase ourunderstanding of galaxy formation and evolution of galaxies in general because isolatedobjects are the best approximation to a control sample that we have for understanding theinfluence of environment on formation and evolution. Whether these isolated objects turnout to be identical to or distinct from counterparts in other regions of the Universe,they will supply insight into the formation and evolution of all galaxies. Parallel ACSimaging will help to characterize the near field environments of the sample.

Analysis of Spectral-type A/B Stars in Five Open Clusters

NASA Astrophysics Data System (ADS)

Wilhelm, Ronald J.; Rafuil Islam, M.

2014-01-01

We have obtained low resolution (R = 1000) spectroscopy of N=68, spectral-type A/B stars in five nearby open star clusters using the McDonald Observatory, 2.1m telescope. The sample of blue stars in various clusters were selected to test our new technique for determining interstellar reddening and distances in areas where interstellar reddening is high. We use a Bayesian approach to find the posterior distribution for Teff, Logg and [Fe/H] from a combination of reddened, photometric colors and spectroscopic line strengths. We will present calibration results for this technique using open cluster star data with known reddening and distances. Preliminary results suggest our technique can produce both reddening and distance determinations to within 10% of cluster values. Our technique opens the possibility of determining distances for blue stars at low Galactic latitudes where extinction can be large and differential. We will also compare our stellar parameter determinations to previously reported MK spectral classifications and discuss the probability that some of our stars are not members of their reported clusters.

Late-Type Membership of the Open Cluster NGC 2232

NASA Technical Reports Server (NTRS)

Orban, Chris; Patten, Brian

2004-01-01

NGC 2232 is one of the nearest open clusters (approx.360 pc) with an age of approx.25 Myr. This places it in the unique position to study the transition from T Tauri activity to the Zero Age Main Sequence. In order for those studies to begin, late-type members must be identified for the cluster. X-ray observations combined with ground-based photometry and spectroscopy offers the best way to accomplish this goal. We present photometry in the VRI bands, 2MASS near-infrared measurements in the J, H , Ks bands and spectra for the suspected optical counterparts to the X-ray sources in the field of NGC 2232. 46 candidate members were identified through these efforts ranging from F5 to M5.

Bacillus cereus-type polyhydroxyalkanoate biosynthetic gene cluster contains R-specific enoyl-CoA hydratase gene.

PubMed

Kihara, Takahiro; Hiroe, Ayaka; Ishii-Hyakutake, Manami; Mizuno, Kouhei; Tsuge, Takeharu

2017-08-01

Bacillus cereus and Bacillus megaterium both accumulate polyhydroxyalkanoate (PHA) but their PHA biosynthetic gene (pha) clusters that code for proteins involved in PHA biosynthesis are different. Namely, a gene encoding MaoC-like protein exists in the B. cereus-type pha cluster but not in the B. megaterium-type pha cluster. MaoC-like protein has an R-specific enoyl-CoA hydratase (R-hydratase) activity and is referred to as PhaJ when involved in PHA metabolism. In this study, the pha cluster of B. cereus YB-4 was characterized in terms of PhaJ's function. In an in vitro assay, PhaJ from B. cereus YB-4 (PhaJ YB4 ) exhibited hydration activity toward crotonyl-CoA. In an in vivo assay using Escherichia coli as a host for PHA accumulation, the recombinant strain expressing PhaJ YB4 and PHA synthase led to increased PHA accumulation, suggesting that PhaJ YB4 functioned as a monomer supplier. The monomer composition of the accumulated PHA reflected the substrate specificity of PhaJ YB4 , which appeared to prefer short chain-length substrates. The pha cluster from B. cereus YB-4 functioned to accumulate PHA in E. coli; however, it did not function when the phaJ YB4 gene was deleted. The B. cereus-type pha cluster represents a new example of a pha cluster that contains the gene encoding PhaJ.

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants.

PubMed

Pasquali, Lorenzo; Gaulton, Kyle J; Rodríguez-Seguí, Santiago A; Mularoni, Loris; Miguel-Escalada, Irene; Akerman, İldem; Tena, Juan J; Morán, Ignasi; Gómez-Marín, Carlos; van de Bunt, Martijn; Ponsa-Cobas, Joan; Castro, Natalia; Nammo, Takao; Cebola, Inês; García-Hurtado, Javier; Maestro, Miguel Angel; Pattou, François; Piemonti, Lorenzo; Berney, Thierry; Gloyn, Anna L; Ravassard, Philippe; Skarmeta, José Luis Gómez; Müller, Ferenc; McCarthy, Mark I; Ferrer, Jorge

2014-02-01

Type 2 diabetes affects over 300 million people, causing severe complications and premature death, yet the underlying molecular mechanisms are largely unknown. Pancreatic islet dysfunction is central in type 2 diabetes pathogenesis, and understanding islet genome regulation could therefore provide valuable mechanistic insights. We have now mapped and examined the function of human islet cis-regulatory networks. We identify genomic sequences that are targeted by islet transcription factors to drive islet-specific gene activity and show that most such sequences reside in clusters of enhancers that form physical three-dimensional chromatin domains. We find that sequence variants associated with type 2 diabetes and fasting glycemia are enriched in these clustered islet enhancers and identify trait-associated variants that disrupt DNA binding and islet enhancer activity. Our studies illustrate how islet transcription factors interact functionally with the epigenome and provide systematic evidence that the dysregulation of islet enhancers is relevant to the mechanisms underlying type 2 diabetes.

Genome-Wide Analysis of Type VI System Clusters and Effectors in Burkholderia Species.

PubMed

Nguyen, Thao Thi; Lee, Hyun-Hee; Park, Inmyoung; Seo, Young-Su

2018-02-01

Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plant-associated and environmental Burkholderia species based on computational analyses. In total, 66 potential functional T6SS clusters were found in 30 target Burkholderia bacterial genomes, of which 33% possess three or four clusters. The core proteins in each cluster were specified and phylogenetic trees of three components (i.e., TssC, TssD, TssL) were constructed to elucidate the relationship among the identified T6SS clusters. Next, we identified 322 potential T6SEs in the target genomes based on homology searches and explored the important domains conserved in effector candidates. In addition, using the screening approach based on the profile hidden Markov model (pHMM) of T6SEs that possess markers for type VI effectors (MIX motif) (MIX T6SEs), 57 revealed proteins that were not included in training datasets were recognized as novel MIX T6SE candidates from the Burkholderia species. This approach could be useful to identify potential T6SEs from other bacterial genomes.

The kinematic properties of dwarf early-type galaxies in the Virgo cluster

NASA Astrophysics Data System (ADS)

Toloba, E.; Boselli, A.; Peletier, R. F.; Gorgas, J.

2011-11-01

We present new medium resolution kinematic data for a sample of 21 dwarf early-type galaxies (dEs) mainly in the Virgo cluster. These data are used to study the origin of dEs inhabiting clusters. Within them we detect two populations: half of the sample (52%) are rotationally supported and the other half are pressure supported. We also find that the rotationally supported dEs are located in the outer parts of the cluster, present disky morphological shapes and are younger than those pressure supported that are concentrated in the core of the cluster without any underlying structures. Our analysis reveals that the rotationally supported objects have rotation curves similarly shaped to those of star forming galaxies of similar luminosities and follow the Tully-Fisher relation. This is expected if dEs are the descendant of low luminosity star forming systems which recently entered the cluster and lost their gas due to a ram pressure stripping event, quenching their star formation activity and transforming them into quiescent systems, but conserving their angular momentum.

A comparison of the near-infrared spectral features of early-type galaxies in the Coma Cluster, the Virgo cluster and the field

NASA Technical Reports Server (NTRS)

Houdashelt, Mark L.; Frogel, Jay A.

1993-01-01

Earlier researchers derived the relative distance between the Coma and Virgo clusters from color-magnitude relations of the early-type galaxies in each cluster. They found that the derived distance was color-dependent and concluded that the galaxies of similar luminosity in the two clusters differ in their red stellar populations. More recently, the color-dependence of the Coma-Virgo distance modulus has been called into question. However, because these two clusters differ so dramatically in their morphologies and kinematics, it is plausible that the star formation histories of the member galaxies also differed. If the conclusions of earlier researchers are indeed correct, then some signature of the resulting stellar population differences should appear in the near-infrared and/or infrared light of the respective galaxies. We have collected near-infrared spectra of 17 Virgo and 10 Coma early-type galaxies; this sample spans about four magnitudes in luminosity in each cluster. Seven field E/S0 galaxies have been observed for comparison. Pseudo-equivalent widths have been measured for all of the field galaxies, all but one of the Virgo members, and five of the Coma galaxies. The features examined are sensitive to the temperature, metallicity, and surface gravity of the reddest stars. A preliminary analysis of these spectral features has been performed, and, with a few notable exceptions, the measured pseudo-equivalent widths agree well with previously published values.

Clustering Analysis of Antibiograms and Antibiogram Types of Streptococcus agalactiae Strains from Tilapia in China.

PubMed

Liu, Chan; Feng, Juan; Zhang, Defeng; Xie, Yundan; Li, Anxing; Wang, Jiangyong; Su, Youlu

2018-05-11

In view of the changing antibiotic-resistance profiles of Streptococcus agalactiae from tilapia in China, antimicrobial susceptibilities of 75 S. agalactiae strains were determined by the disc diffusion method, and cluster analyses of the antibiograms and antibiogram types were performed. All strains displayed multidrug resistance (MDR). The antimicrobial-resistance rates were highest (>90%) to aminoglycosides, sulfonamides, pipemidic acid, and norfloxacin, followed by penicillin, ampicillin, and ciprofloxacin (26.7-38.7%); those to furadantin, lincomycin, erythromycin, ofloxacin, tetracycline, and florfenicol were low (<10%), and no resistance to vancomycin, cefalexin, cefoxitin, amoxicillin, medemycin, doxitard, oxytetracycline, rifampin, chloramphenicol, or thiamphenicol was detected. Statistical analysis showed that the resistance rate to ciprofloxacin increased significantly in 2016 (p = 0.009), whereas that to trimethoprim/sulfamethoxazole decreased (p = 0.017). Cluster analyses identified that the strains had 23 antibiogram types (A-W) and clustered in five groups (Groups I-V). The strains with higher antimicrobial resistance mainly clustered in Groups I and II. Our results show that the antibiograms varied with time and by location and that antibiogram types are constantly updating and expanding. Effective measures must be taken to reduce the antimicrobial resistance and spread of MDR strains.

Deterministic Joint Remote Preparation of an Arbitrary Sevenqubit Cluster-type State

NASA Astrophysics Data System (ADS)

Ding, MengXiao; Jiang, Min

2017-06-01

In this paper, we propose a scheme for joint remotely preparing an arbitrary seven-qubit cluster-type state by using several GHZ entangled states as the quantum channel. The coefficients of the prepared states can be not only real, but also complex. Firstly, Alice performs a three-qubit projective measurement according to the amplitude coefficients of the target state, and then Bob carries out another three-qubit projective measurement based on its phase coefficients. Next, one three-qubit state containing all information of the target state is prepared with suitable operation. Finally, the target seven-qubit cluster-type state can be prepared by introducing four auxiliary qubits and performing appropriate local unitary operations based on the prepared three-qubit state in a deterministic way. The receiver's all recovery operations are summarized into a concise formula. Furthermore, it's worth noting that our scheme is more novel and feasible with the present technologies than most other previous schemes.

Recommendations for choosing an analysis method that controls Type I error for unbalanced cluster sample designs with Gaussian outcomes.

PubMed

Johnson, Jacqueline L; Kreidler, Sarah M; Catellier, Diane J; Murray, David M; Muller, Keith E; Glueck, Deborah H

2015-11-30

We used theoretical and simulation-based approaches to study Type I error rates for one-stage and two-stage analytic methods for cluster-randomized designs. The one-stage approach uses the observed data as outcomes and accounts for within-cluster correlation using a general linear mixed model. The two-stage model uses the cluster specific means as the outcomes in a general linear univariate model. We demonstrate analytically that both one-stage and two-stage models achieve exact Type I error rates when cluster sizes are equal. With unbalanced data, an exact size α test does not exist, and Type I error inflation may occur. Via simulation, we compare the Type I error rates for four one-stage and six two-stage hypothesis testing approaches for unbalanced data. With unbalanced data, the two-stage model, weighted by the inverse of the estimated theoretical variance of the cluster means, and with variance constrained to be positive, provided the best Type I error control for studies having at least six clusters per arm. The one-stage model with Kenward-Roger degrees of freedom and unconstrained variance performed well for studies having at least 14 clusters per arm. The popular analytic method of using a one-stage model with denominator degrees of freedom appropriate for balanced data performed poorly for small sample sizes and low intracluster correlation. Because small sample sizes and low intracluster correlation are common features of cluster-randomized trials, the Kenward-Roger method is the preferred one-stage approach. Copyright © 2015 John Wiley & Sons, Ltd.

The sensitivity of harassment to orbit: mass loss from early-type dwarfs in galaxy clusters

NASA Astrophysics Data System (ADS)

Smith, R.; Sánchez-Janssen, R.; Beasley, M. A.; Candlish, G. N.; Gibson, B. K.; Puzia, T. H.; Janz, J.; Knebe, A.; Aguerri, J. A. L.; Lisker, T.; Hensler, G.; Fellhauer, M.; Ferrarese, L.; Yi, S. K.

2015-12-01

We conduct a comprehensive numerical study of the orbital dependence of harassment on early-type dwarfs consisting of 168 different orbits within a realistic, Virgo-like cluster, varying in eccentricity and pericentre distance. We find harassment is only effective at stripping stars or truncating their stellar discs for orbits that enter deep into the cluster core. Comparing to the orbital distribution in cosmological simulations, we find that the majority of the orbits (more than three quarters) result in no stellar mass loss. We also study the effects on the radial profiles of the globular cluster systems of early-type dwarfs. We find these are significantly altered only if harassment is very strong. This suggests that perhaps most early-type dwarfs in clusters such as Virgo have not suffered any tidal stripping of stars or globular clusters due to harassment, as these components are safely embedded deep within their dark matter halo. We demonstrate that this result is actually consistent with an earlier study of harassment of dwarf galaxies, despite the apparent contradiction. Those few dwarf models that do suffer stellar stripping are found out to the virial radius of the cluster at redshift = 0, which mixes them in with less strongly harassed galaxies. However when placed on phase-space diagrams, strongly harassed galaxies are found offset to lower velocities compared to weakly harassed galaxies. This remains true in a cosmological simulation, even when haloes have a wide range of masses and concentrations. Thus phase-space diagrams may be a useful tool for determining the relative likelihood that galaxies have been strongly or weakly harassed.

Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing.

PubMed

Sun, Peng; Guo, Jiong; Baumbach, Jan

2012-07-17

The explosion of biological data has largely influenced the focus of today’s biology research. Integrating and analysing large quantity of data to provide meaningful insights has become the main challenge to biologists and bioinformaticians. One major problem is the combined data analysis of data from different types, such as phenotypes and genotypes. This data is modelled as bi-partite graphs where nodes correspond to the different data points, mutations and diseases for instance, and weighted edges relate to associations between them. Bi-clustering is a special case of clustering designed for partitioning two different types of data simultaneously. We present a bi-clustering approach that solves the NP-hard weighted bi-cluster editing problem by transforming a given bi-partite graph into a disjoint union of bi-cliques. Here we contribute with an exact algorithm that is based on fixed-parameter tractability. We evaluated its performance on artificial graphs first. Afterwards we exemplarily applied our Java implementation to data of genome-wide association studies (GWAS) data aiming for discovering new, previously unobserved geno-to-pheno associations. We believe that our results will serve as guidelines for further wet lab investigations. Generally our software can be applied to any kind of data that can be modelled as bi-partite graphs. To our knowledge it is the fastest exact method for weighted bi-cluster editing problem.

Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing.

PubMed

Sun, Peng; Guo, Jiong; Baumbach, Jan

2012-06-01

The explosion of biological data has largely influenced the focus of today's biology research. Integrating and analysing large quantity of data to provide meaningful insights has become the main challenge to biologists and bioinformaticians. One major problem is the combined data analysis of data from different types, such as phenotypes and genotypes. This data is modelled as bi-partite graphs where nodes correspond to the different data points, mutations and diseases for instance, and weighted edges relate to associations between them. Bi-clustering is a special case of clustering designed for partitioning two different types of data simultaneously. We present a bi-clustering approach that solves the NP-hard weighted bi-cluster editing problem by transforming a given bi-partite graph into a disjoint union of bi-cliques. Here we contribute with an exact algorithm that is based on fixed-parameter tractability. We evaluated its performance on artificial graphs first. Afterwards we exemplarily applied our Java implementation to data of genome-wide association studies (GWAS) data aiming for discovering new, previously unobserved geno-to-pheno associations. We believe that our results will serve as guidelines for further wet lab investigations. Generally our software can be applied to any kind of data that can be modelled as bi-partite graphs. To our knowledge it is the fastest exact method for weighted bi-cluster editing problem.

DDO 216-A1: A Central Globular Cluster in a Low-luminosity Transition-type Galaxy

NASA Astrophysics Data System (ADS)

Cole, Andrew A.; Weisz, Daniel R.; Skillman, Evan D.; Leaman, Ryan; Williams, Benjamin F.; Dolphin, Andrew E.; Johnson, L. Clifton; McConnachie, Alan W.; Boylan-Kolchin, Michael; Dalcanton, Julianne; Governato, Fabio; Madau, Piero; Shen, Sijing; Vogelsberger, Mark

2017-03-01

We confirm that the object DDO 216-A1 is a substantial globular cluster at the center of Local Group galaxy DDO 216 (the Pegasus dwarf irregular), using Hubble Space Telescope ACS imaging. By fitting isochrones, we find the cluster metallicity [M/H] = -1.6 ± 0.2, for reddening E(B-V) = 0.16 ± 0.02 the best-fit age is 12.3 ± 0.8 Gyr. There are ≈ 30 RR Lyrae variables in the cluster; the magnitude of the fundamental mode pulsators gives a distance modulus of 24.77 ± 0.08—identical to the host galaxy. The ratio of overtone to fundamental mode variables and their mean periods make DDO 216-A1 an Oosterhoff Type I cluster. We find a central surface brightness of 20.85 ± 0.17 F814W mag arcsec-2, a half-light radius of 3\\buildrel{\\prime\\prime}\\over{.} 1 (13.4 pc), and an absolute magnitude M814 = -7.90 ± 0.16 (M/{M}⊙ ≈ 105). King models fit to the cluster give the core radius and concentration index, r c = 2\\buildrel{\\prime\\prime}\\over{.} 1 ± 0\\buildrel{\\prime\\prime}\\over{.} 9 and c = 1.24 ± 0.39. The cluster is an “extended” cluster somewhat typical of some dwarf galaxies and the outer halo of the Milky Way. The cluster is projected ≲30 pc south of the center of DDO 216, unusually central compared to most dwarf galaxy globular clusters. Analytical models of dynamical friction and tidal destruction suggest that it probably formed at a larger distance, up to ˜1 kpc, and migrated inward. DDO 216 has an unexceptional specific cluster frequency, S N = 10. DDO 216 is the lowest-luminosity Local Group galaxy to host a 105 {M}⊙ globular cluster and the only transition-type (dSph/dIrr) galaxy in the Local Group with a globular cluster. Based on observations made with the NASA/ESA Hubble Space Telesope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. These observations were obtained under program GO-13768.

Long-Ranged Oppositely Charged Interactions for Designing New Types of Colloidal Clusters

NASA Astrophysics Data System (ADS)

Demirörs, Ahmet Faik; Stiefelhagen, Johan C. P.; Vissers, Teun; Smallenburg, Frank; Dijkstra, Marjolein; Imhof, Arnout; van Blaaderen, Alfons

2015-04-01

Getting control over the valency of colloids is not trivial and has been a long-desired goal for the colloidal domain. Typically, tuning the preferred number of neighbors for colloidal particles requires directional bonding, as in the case of patchy particles, which is difficult to realize experimentally. Here, we demonstrate a general method for creating the colloidal analogs of molecules and other new regular colloidal clusters without using patchiness or complex bonding schemes (e.g., DNA coating) by using a combination of long-ranged attractive and repulsive interactions between oppositely charged particles that also enable regular clusters of particles not all in close contact. We show that, due to the interplay between their attractions and repulsions, oppositely charged particles dispersed in an intermediate dielectric constant (4 <ɛ <10 ) provide a viable approach for the formation of binary colloidal clusters. Tuning the size ratio and interactions of the particles enables control of the type and shape of the resulting regular colloidal clusters. Finally, we present an example of clusters made up of negatively charged large and positively charged small satellite particles, for which the electrostatic properties and interactions can be changed with an electric field. It appears that for sufficiently strong fields the satellite particles can move over the surface of the host particles and polarize the clusters. For even stronger fields, the satellite particles can be completely pulled off, reversing the net charge on the cluster. With computer simulations, we investigate how charged particles distribute on an oppositely charged sphere to minimize their energy and compare the results with the solutions to the well-known Thomson problem. We also use the simulations to explore the dependence of such clusters on Debye screening length κ-1 and the ratio of charges on the particles, showing good agreement with experimental observations.

Studies of the Virgo cluster. VI - Morphological and kinematical structure of the Virgo cluster

NASA Technical Reports Server (NTRS)

Binggeli, Bruno; Tammann, G. A.; Sandage, Allan

1987-01-01

The structure of the Virgo cluster is analyzed on the basis of the positions, Hubble types, and radial velocities of 1277 Virgo cluster galaxies. The surface distribution of galaxies is considered according to type, and is discussed using maps, isopleths, strip counts, and radial-density distributions. It is found that the Virgo cluster shows pronounced double structure. The main concentration has a large velocity dispersion and is made up predominantly of early-type galaxies, while the secondary concentration has a much smaller velocity dispersion and contains late types. There is a strong spatial segregation of the Hubble types, the early-type galaxies being more concentrated toward the cluster center. There is significant substructure in the cluster core. The irregularity of the Virgo cluster in both configuration and velocity space shows that the core and the envelope are still forming, and hence that the cluster is young.

Hierarchical clusters in families with type 2 diabetes.

PubMed

García-Solano, Beatriz; Gallegos-Cabriales, Esther C; Gómez-Meza, Marco V; García-Madrid, Guillermina; Flores-Merlo, Marcela; García-Solano, Mauro

2015-01-01

Families represent more than a set of individuals; family is more than a sum of its individual members. With this classification, nurses can identify the family health-illness beliefs obey family as a unit concept, and plan family inclusion into the type 2 diabetes treatment, whom is not considered in public policy, despite families share diet, exercise, and self-monitoring with a member who suffers type 2 diabetes. The aim of this study was to determine whether the characteristics, functionality, routines, and family and individual health in type 2 diabetes describes the differences and similarities between families to consider them as a unit. We performed an exploratory, descriptive hierarchical cluster analysis of 61 families using three instruments and a questionnaire, in addition to weight, height, body fat percentage, hemoglobin A1c, total cholesterol, triglycerides, low-density lipoprotein and high-density lipoprotein. The analysis produced three groups of families. Wilk's lambda demonstrated statistically significant differences provided by age (Λ = 0.778, F = 2.098, p = 0.010) and family health (Λ = 0.813, F = 2.650, p = 0.023). A post hoc Tukey test coincided with the three subsets. Families with type 2 diabetes have common elements that make them similar, while sharing differences that make them unique.

Recent TB transmission, clustering and predictors of large clusters in London, 2010–2012: results from first 3 years of universal MIRU-VNTR strain typing

PubMed Central

Hamblion, Esther L; Le Menach, Arnaud; Anderson, Laura F; Lalor, Maeve K; Brown, Tim; Abubakar, Ibrahim; Anderson, Charlotte; Maguire, Helen; Anderson, Sarah R

2016-01-01

Background The incidence of TB has doubled in the last 20 years in London. A better understanding of risk groups for recent transmission is required to effectively target interventions. We investigated the molecular epidemiological characteristics of TB cases to estimate the proportion of cases due to recent transmission, and identify predictors for belonging to a cluster. Methods The study population included all culture-positive TB cases in London residents, notified between January 2010 and December 2012, strain typed using 24-loci multiple interspersed repetitive units-variable number tandem repeats. Multivariable logistic regression analysis was performed to assess the risk factors for clustering using sociodemographic and clinical characteristics of cases and for cluster size based on the characteristics of the first two cases. Results There were 10 147 cases of which 5728 (57%) were culture confirmed and 4790 isolates (84%) were typed. 2194 (46%) were clustered in 570 clusters, and the estimated proportion attributable to recent transmission was 34%. Clustered cases were more likely to be UK born, have pulmonary TB, a previous diagnosis, a history of substance abuse or alcohol abuse and imprisonment, be of white, Indian, black-African or Caribbean ethnicity. The time between notification of the first two cases was more likely to be <90 days in large clusters. Conclusions Up to a third of TB cases in London may be due to recent transmission. Resources should be directed to the timely investigation of clusters involving cases with risk factors, particularly those with a short period between the first two cases, to interrupt onward transmission of TB. PMID:27417280

The Effects of Presenting Different Types of Vocabulary Clusters on Very Young Learners' Foreign Language Learning

ERIC Educational Resources Information Center

Karabulut, Aslihan; Kesli Dollar, Yesim

2016-01-01

The main aim of this study was to find out which type of vocabulary cluster--semantic, thematic and unrelated--very young learners benefit from the most while learning foreign language vocabulary. The study also aimed at shedding light on the effects of these three vocabulary clusters on the immediate and delayed recall of foreign language…

Globular cluster systems as tracers of environmental effects on Virgo early-type dwarfs

NASA Astrophysics Data System (ADS)

Sánchez-Janssen, R.; Aguerri, J. A. L.

2012-08-01

Early-type dwarfs (dEs) are by far the most abundant galaxy population in nearby clusters. Whether these objects are primordial, or the recent end products of the different physical mechanisms that can transform galaxies once they enter these high-density environments, is still a matter of debate. Here we present a novel approach to test these scenarios by comparing the properties of the globular cluster systems (GCSs) of Virgo dEs and their potential progenitors with simple predictions from gravitational and hydrodynamical interaction models. We show that low-mass (M★ ≲ 2 × 108 M⊙) dEs have GCSs consistent with the descendants of gas-stripped late-type dwarfs. On the other hand, higher mass dEs have properties - including the high mass specific frequencies of their GCSs and their concentrated spatial distribution within Virgo - incompatible with a recent, environmentally driven evolution. They mostly comprise nucleated systems, but also dEs with recent star formation and/or disc features. Bright, nucleated dEs appear to be a population that has long resided within the cluster potential well, but have surprisingly managed to retain very rich and spatially extended GCSs - possibly an indication of high total masses. Our analysis does not favour violent evolutionary mechanisms that result in significant stellar mass-losses, but more gentle processes involving gas removal by a combination of internal and external factors, and highlights the relevant role of initial conditions. Additionally, we briefly comment on the origin of luminous cluster S0 galaxies.

Genetic homogeneity of Clostridium botulinum type A1 strains with unique toxin gene clusters.

PubMed

Raphael, Brian H; Luquez, Carolina; McCroskey, Loretta M; Joseph, Lavin A; Jacobson, Mark J; Johnson, Eric A; Maslanka, Susan E; Andreadis, Joanne D

2008-07-01

A group of five clonally related Clostridium botulinum type A strains isolated from different sources over a period of nearly 40 years harbored several conserved genetic properties. These strains contained a variant bont/A1 with five nucleotide polymorphisms compared to the gene in C. botulinum strain ATCC 3502. The strains also had a common toxin gene cluster composition (ha-/orfX+) similar to that associated with bont/A in type A strains containing an unexpressed bont/B [termed A(B) strains]. However, bont/B was not identified in the strains examined. Comparative genomic hybridization demonstrated identical genomic content among the strains relative to C. botulinum strain ATCC 3502. In addition, microarray data demonstrated the absence of several genes flanking the toxin gene cluster among the ha-/orfX+ A1 strains, suggesting the presence of genomic rearrangements with respect to this region compared to the C. botulinum ATCC 3502 strain. All five strains were shown to have identical flaA variable region nucleotide sequences. The pulsed-field gel electrophoresis patterns of the strains were indistinguishable when digested with SmaI, and a shift in the size of at least one band was observed in a single strain when digested with XhoI. These results demonstrate surprising genomic homogeneity among a cluster of unique C. botulinum type A strains of diverse origin.

ClusterCAD: a computational platform for type I modular polyketide synthase design

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

Eng, Clara H.; Backman, Tyler W H; Bailey, Constance B.

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKSmore » chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.« less

ClusterCAD: a computational platform for type I modular polyketide synthase design

DOE PAGES

Eng, Clara H.; Backman, Tyler W H; Bailey, Constance B.; ...

2017-10-11

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKSmore » chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.« less

Walking Away from Type 2 diabetes: a cluster randomized controlled trial.

PubMed

Yates, T; Edwardson, C L; Henson, J; Gray, L J; Ashra, N B; Troughton, J; Khunti, K; Davies, M J

2017-05-01

This study aimed to investigate whether an established behavioural intervention, Walking Away from Type 2 Diabetes, is effective at promoting and sustaining increased walking activity when delivered within primary care. Cluster randomized controlled trial involving 10 general practices recruited from Leicestershire, UK, in 2009-2010. Eight hundred and eight (36% female) individuals with a high risk of Type 2 diabetes mellitus, identified through a validated risk score, were included. Participants in five practices were randomized to Walking Away from Type 2 Diabetes, a pragmatic 3-h group-based structured education programme incorporating pedometer use with annual follow-on refresher sessions. The primary outcome was accelerometer assessed ambulatory activity (steps/day) at 12 months. Longer term maintenance was assessed at 24 and 36 months. Results were analysed using generalized estimating equation models, accounting for clustering. Complete accelerometer data for the primary outcome were available for 571 (71%) participants. Increases in ambulatory activity of 411 steps/day [95% confidence interval (CI): 117, 704] and self-reported vigorous-intensity physical activity of 218 metabolic equivalent min/week (95% CI: 6, 425) at 12 months were observed in the intervention group compared with control; differences between groups were not sustained at 36 months. No differences between groups were observed for markers of cardiometabolic health. Replacing missing data with multiple imputation did not affect the results. A pragmatic low-resource group-based structured education programme with pedometer use resulted in modest increases in ambulatory activity compared with control conditions after 12 months when implemented within a primary care setting to those at high risk of Type 2 diabetes mellitus; however, the results were not maintained over 36 months. © 2016 Diabetes UK.

On Iron Enrichment, Star Formation, and Type Ia Supernovae in Galaxy Clusters

NASA Technical Reports Server (NTRS)

Loewenstein, Michael

2006-01-01

The nature of star formation and Type Ia supernovae (SNIa) in galaxies in the field and in rich galaxy clusters are contrasted by juxtaposing the buildup of heavy metals in the universe inferred from observed star formation and supernovae rate histories with data on the evolution of Fe abundances in the intracluster medium (ICM). Models for the chemical evolution of Fe in these environments are constructed, subject to observational constraints, for this purpose. While models with a mean delay for SNIa of 3 Gyr and standard initial mass function (IMF) are fully consistent with observations in the field, cluster Fe enrichment immediately tracked a rapid, top-heavy phase of star formation - although transport of Fe into the ICM may have been more prolonged and star formation likely continued beyond redshift 1. The means of this prompt enrichment consisted of SNII yielding greater than or equal to 0.1 solar mass per explosion (if the SNIa rate normalization is scaled down from its value in the field according to the relative number of candidate progenitor stars in the 3 - 8 solar mass range) and/or SNIa with short delay times originating during the rapid star formation epoch. Star formation is greater than 3 times more efficient in rich clusters than in the field, mitigating the overcooling problem in numerical cluster simulations. Both the fraction of baryons cycled through stars, and the fraction of the total present-day stellar mass in the form of stellar remnants, are substantially greater in clusters than in the field.

A CCD Search for Variable Stars of Spectral Type B in the Northern Hemisphere Open Clusters. IX. NGC 457

NASA Astrophysics Data System (ADS)

Moździerski, D.; Pigulski, A.; Kopacki, G.; Kołaczkowski, Z.; Stęślicki, M.

2014-06-01

We present results of a BVIC variability survey in the young open cluster NGC 457 based on observations obtained during three separate runs spanning almost 20 years. In total, we found 79 variable stars, of which 66 are new. The BVIC photometry was transformed to the standard system and used to derive cluster parameters by means of isochrone fitting. The cluster is about 20 Myr old, the mean reddening amounts to about 0.48 mag in terms of the color excess E(B-V). Depending on the metallicity, the isochrone fitting yields a distance between 2.3 kpc and 2.9 kpc, which locates the cluster in the Perseus arm of the Galaxy. Using the complementary Hα photometry carried out in two seasons separated by over 10 years, we find that the cluster is very rich in Be stars. In total, 15 stars in the observed field of which 14 are cluster members showed Hα in emission either during our observations or in the past. Most of the Be stars vary in brightness on different time scales including short-period variability related most likely to g-mode pulsations. A single-epoch spectrum of NGC 457-6 shows that this Be star is presently in the shell phase. The inventory of variable stars in the observed field consists of a single β Cep-type star, NGC 457-8, 13 Be stars, 21 slowly pulsating B stars, seven δ Sct stars, one γ Dor star, 16 unclassified periodic stars, 8 eclipsing systems and a dozen of stars with irregular variability, of which six are also B-type stars. As many as 45 variable stars are of spectral type B which is the largest number in all open clusters presented in this series of papers. The most interesting is the discovery of a large group of slowly pulsating B stars which occupy the cluster main sequence in the range between V=11 mag and 14.5 mag, corresponding to spectral types B3 to B8. They all have very low amplitudes and about half show pulsations with frequencies higher than 3 d-1. We argue that these are most likely fast-rotating slowly pulsating B stars

Galaxy clusters, type Ia supernovae and the fine structure constant

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

Holanda, R.F.L.; Busti, V.C.; Colaço, L.R.

2016-08-01

As is well known, measurements of the Sunyaev-Zeldovich effect can be combined with observations of the X-ray surface brightness of galaxy clusters to estimate the angular diameter distance to these structures. In this paper, we show that this technique depends on the fine structure constant, α. Therefore, if α is a time-dependent quantity, e.g., α = α{sub 0}φ( z ), where φ is a function of redshift, we argue that current data do not provide the real angular diameter distance, D {sub A}( z ), to the cluster, but instead D {sub A}{sup data}( z ) = φ( z ){supmore » 2} D {sub A}( z ). We use this result to derive constraints on a possible variation of α for a class of dilaton runaway models considering a sample of 25 measurements of D {sub A}{sup data}( z ) in redshift range 0.023 < z < 0.784 and estimates of D {sub A}( z ) from current type Ia supernovae observations. We find no significant indication of variation of α with the present data.« less

The Herschel Virgo Cluster Survey. XIII. Dust in early-type galaxies

NASA Astrophysics Data System (ADS)

di Serego Alighieri, S.; Bianchi, S.; Pappalardo, C.; Zibetti, S.; Auld, R.; Baes, M.; Bendo, G.; Corbelli, E.; Davies, J. I.; Davis, T.; De Looze, I.; Fritz, J.; Gavazzi, G.; Giovanardi, C.; Grossi, M.; Hunt, L. K.; Magrini, L.; Pierini, D.; Xilouris, E. M.

2013-04-01

Aims: We study the dust content of a large optical input sample of 910 early-type galaxies (ETG) in the Virgo cluster, also extending to the dwarf ETG, and examine the results in relation to those on the other cold ISM components. Methods: We have searched for far-infrared emission in all galaxies in the input sample using the 250 μm image of the Herschel Virgo Cluster Survey (HeViCS). This image covers a large fraction of the cluster with an area of ~55 square degrees. For the detected ETG we measured fluxes in five bands from 100 to 500 μm, and estimated the dust mass and temperature with modified black-body fits. Results: Dust is detected above the completeness limit of 25.4 mJy at 250 μm in 46 ETG, 43 of which are in the optically complete part of the input sample. In addition, dust is present at fainter levels in another six ETG. We detect dust in the four ETG with synchrotron emission, including M 87. Dust appears to be much more concentrated than stars and more luminous ETG have higher dust temperatures. Considering only the optically complete input sample and correcting for the contamination by background galaxies, dust detection rates down to the 25.4 mJy limit are 17% for ellipticals, about 40% for lenticulars (S0 + S0a), and around 3% for dwarf ETG. Dust mass does not correlate clearly with stellar mass and is often much greater than expected for a passive galaxy in a closed-box model. The dust-to-stars mass ratio anticorrelates with galaxy luminosity, and for some dwarf ETG reaches values as high as for dusty late-type galaxies. In the Virgo cluster slow rotators appear more likely to contain dust than fast ones. Comparing the dust results with those on Hi there are only eight ETG detected both in dust and in Hi in the HeViCS area; 39 have dust but only an upper limit on Hi, and eight have Hi but only an upper limit on dust. The locations of these galaxies in the cluster are different, with the dusty ETG concentrated in the densest regions, while the

Does the behavioural type-specific approach for type 2 diabetes promote changes in lifestyle? Protocol of a cluster randomised trial in Japan

PubMed Central

Adachi, Misa; Yamaoka, Kazue; Watanabe, Mariko; Nemoto, Asuka; Tango, Toshiro

2017-01-01

Introduction Type 2 diabetes (T2D) is a significant problem, and lifestyle modifications including self-management are important. We have developed a structured individual-based lifestyle education (SILE) programme for T2D. With attention now being paid to techniques to change behaviour, we recently developed a behavioural type-specific SILE (BETSILE) programme. We aimed to evaluate the effectiveness of the BETSILE programme compared with the SILE programme for reducing glycated haemoglobin (HbA1c) in patients with T2D and special behavioural types by a cluster randomised controlled trial. Methods and analysis This is a 6-month cluster randomised controlled trial with two intervention arms (BETSILE vs SILE) provided in a medical care setting by randomising registered dietitians for patients with T2D aged 20–79 years. Patients’ behavioural types were classified into four types (BT1 to BT4) using an assessment sheet. We will perform independent trials for BT1 and BT2. The primary endpoint is a change from the baseline HbA1c value at 6 months. Differences between the SILE and BETSILE groups will be primarily analysed following the intention-to-treat principle. Crude and multivariate adjusted effects will be examined after adjusting for covariates, using a general linear mixed-effects model for continuous variables and a logistic regression mixed-effects model for dichotomous variables. Sample sizes needed were calculated assuming effect sizes of 0.42 and 0.33 for BT1 and BT2, respectively, an intraclass correlation of 0.02, a significance level of 5% (two-sided), a power of 80%, and equal allocation of clusters to the two arms, with each cluster having three BT1 patients for the SILE and BETSILE arms and six BT2 patients for the SILE and BETSILE arms. We will need 16 dietitians for each arm, and a total 288 patients will be required. Ethics and dissemination This study has been approved by the Medical Ethical Committee of Teikyo University (No.15–222). Findings

Clustering and variable selection in the presence of mixed variable types and missing data.

PubMed

Storlie, C B; Myers, S M; Katusic, S K; Weaver, A L; Voigt, R G; Croarkin, P E; Stoeckel, R E; Port, J D

2018-05-17

We consider the problem of model-based clustering in the presence of many correlated, mixed continuous, and discrete variables, some of which may have missing values. Discrete variables are treated with a latent continuous variable approach, and the Dirichlet process is used to construct a mixture model with an unknown number of components. Variable selection is also performed to identify the variables that are most influential for determining cluster membership. The work is motivated by the need to cluster patients thought to potentially have autism spectrum disorder on the basis of many cognitive and/or behavioral test scores. There are a modest number of patients (486) in the data set along with many (55) test score variables (many of which are discrete valued and/or missing). The goal of the work is to (1) cluster these patients into similar groups to help identify those with similar clinical presentation and (2) identify a sparse subset of tests that inform the clusters in order to eliminate unnecessary testing. The proposed approach compares very favorably with other methods via simulation of problems of this type. The results of the autism spectrum disorder analysis suggested 3 clusters to be most likely, while only 4 test scores had high (>0.5) posterior probability of being informative. This will result in much more efficient and informative testing. The need to cluster observations on the basis of many correlated, continuous/discrete variables with missing values is a common problem in the health sciences as well as in many other disciplines. Copyright © 2018 John Wiley & Sons, Ltd.

Cluster analysis of the clinical histories of cattle affected with bovine anaemia associated with Theileria orientalis Ikeda type infection.

PubMed

Lawrence, K E; Forsyth, S F; Vaatstra, B L; McFadden, Amj; Pulford, D J; Govindaraju, K; Pomroy, W E

2017-11-01

AIM To determine the most commonly used words in the clinical histories of animals naturally infected with Theileria orientalis Ikeda type; whether these words differed between cases categorised by age, farm type or haematocrit (HCT), and if there was any clustering of the common words in relation to these categories. METHODS Clinical histories were transcribed for 605 cases of bovine anaemia associated with T. orientalis (TABA), that were submitted to laboratories with blood samples which tested positive for T. orientalis Ikeda type infection by PCR analysis, between October 2012 and November 2014. χ 2 tests were used to determine whether the proportion of submissions for each word was similar across the categories of HCT (normal, moderate anaemia or severe anaemia), farm type (dairy or beef) and age (young or old). Correspondence analysis (CA) was carried out on a contingency table of the frequency of the 28 most commonly used history words, cross-tabulated by age categories (young, old or unknown). Agglomerative hierarchical clustering, using Ward's method, was then performed on the coordinates from the correspondence analysis. RESULTS The six most commonly used history words were jaundice (204/605), lethargic (162/605), pale mucous membranes (161/605), cow (151/605), anaemia (147/605), and off milk (115/605). The proportion of cases with some history words differed between categories of age, farm type and HCT. The cluster analysis indicated that the recorded history words were grouped in two main clusters. The first included the words weight loss, tachycardia, pale mucous membranes, anaemia, lethargic and thin, and was associated with adult (p<0.001), severe anaemia (p<0.001) and dairy (p<0.001). The second cluster included the words deaths, ill-thrift, calves, calf and diarrhoea, and was associated with young (p<0.001), normal HCT (p<0.001), beef (p<0.001) and moderate anaemia (p<0.001). CONCLUSIONS AND CLINICAL RELEVANCE Cluster analysis of words recorded in

Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures.

PubMed

Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

2016-07-14

In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga.

From sticky-hard-sphere to Lennard-Jones-type clusters

NASA Astrophysics Data System (ADS)

Trombach, Lukas; Hoy, Robert S.; Wales, David J.; Schwerdtfeger, Peter

2018-04-01

A relation MSHS →LJ between the set of nonisomorphic sticky-hard-sphere clusters MSHS and the sets of local energy minima ML J of the (m ,n ) -Lennard-Jones potential Vmn LJ(r ) =ɛ/n -m [m r-n-n r-m] is established. The number of nonisomorphic stable clusters depends strongly and nontrivially on both m and n and increases exponentially with increasing cluster size N for N ≳10 . While the map from MSHS→MSHS →LJ is noninjective and nonsurjective, the number of Lennard-Jones structures missing from the map is relatively small for cluster sizes up to N =13 , and most of the missing structures correspond to energetically unfavorable minima even for fairly low (m ,n ) . Furthermore, even the softest Lennard-Jones potential predicts that the coordination of 13 spheres around a central sphere is problematic (the Gregory-Newton problem). A more realistic extended Lennard-Jones potential chosen from coupled-cluster calculations for a rare gas dimer leads to a substantial increase in the number of nonisomorphic clusters, even though the potential curve is very similar to a (6,12)-Lennard-Jones potential.

From sticky-hard-sphere to Lennard-Jones-type clusters.

PubMed

Trombach, Lukas; Hoy, Robert S; Wales, David J; Schwerdtfeger, Peter

2018-04-01

A relation M_{SHS→LJ} between the set of nonisomorphic sticky-hard-sphere clusters M_{SHS} and the sets of local energy minima M_{LJ} of the (m,n)-Lennard-Jones potential V_{mn}^{LJ}(r)=ɛ/n-m[mr^{-n}-nr^{-m}] is established. The number of nonisomorphic stable clusters depends strongly and nontrivially on both m and n and increases exponentially with increasing cluster size N for N≳10. While the map from M_{SHS}→M_{SHS→LJ} is noninjective and nonsurjective, the number of Lennard-Jones structures missing from the map is relatively small for cluster sizes up to N=13, and most of the missing structures correspond to energetically unfavorable minima even for fairly low (m,n). Furthermore, even the softest Lennard-Jones potential predicts that the coordination of 13 spheres around a central sphere is problematic (the Gregory-Newton problem). A more realistic extended Lennard-Jones potential chosen from coupled-cluster calculations for a rare gas dimer leads to a substantial increase in the number of nonisomorphic clusters, even though the potential curve is very similar to a (6,12)-Lennard-Jones potential.

Estimating global distribution of boreal, temperate, and tropical tree plant functional types using clustering techniques

NASA Astrophysics Data System (ADS)

Wang, Audrey; Price, David T.

2007-03-01

A simple integrated algorithm was developed to relate global climatology to distributions of tree plant functional types (PFT). Multivariate cluster analysis was performed to analyze the statistical homogeneity of the climate space occupied by individual tree PFTs. Forested regions identified from the satellite-based GLC2000 classification were separated into tropical, temperate, and boreal sub-PFTs for use in the Canadian Terrestrial Ecosystem Model (CTEM). Global data sets of monthly minimum temperature, growing degree days, an index of climatic moisture, and estimated PFT cover fractions were then used as variables in the cluster analysis. The statistical results for individual PFT clusters were found consistent with other global-scale classifications of dominant vegetation. As an improvement of the quantification of the climatic limitations on PFT distributions, the results also demonstrated overlapping of PFT cluster boundaries that reflected vegetation transitions, for example, between tropical and temperate biomes. The resulting global database should provide a better basis for simulating the interaction of climate change and terrestrial ecosystem dynamics using global vegetation models.

Rotational Periods and Starspot Activity of Young Solar-Type Dwarfs in the Open Cluster IC 4665

NASA Technical Reports Server (NTRS)

Allain, S.; Bouvier, J.; Prosser, C.; Marschall, L. A.; Laaksonen, B. D.

1995-01-01

We present the results of a V-band photometric monitoring survey of 15 late-type dwarfs in the young open cluster IC 4665. Low-amplitude periodic light variations are found for 8 stars and ascribed to the modulation by starspots that cover typically a few percent of the stellar disk. Periods range from 0.6 to 3.7 d, translating to equatorial velocities between 13 and 93 km/s. That no period longer than 4 d was detected suggests a relative paucity of extremely slow rotators (V(sub eq) much less than 10 km/s) among late-type dwarfs in IC 4665. The fractional number of slow rotators in IC 4665 is similar to that of Alpha Per cluster, suggesting that IC 4665 is close in age to Alpha Per (approx. 50 Myr).

Dynamic Fuzzy Model Development for a Drum-type Boiler-turbine Plant Through GK Clustering

NASA Astrophysics Data System (ADS)

Habbi, Ahcène; Zelmat, Mimoun

2008-10-01

This paper discusses a TS fuzzy model identification method for an industrial drum-type boiler plant using the GK fuzzy clustering approach. The fuzzy model is constructed from a set of input-output data that covers a wide operating range of the physical plant. The reference data is generated using a complex first-principle-based mathematical model that describes the key dynamical properties of the boiler-turbine dynamics. The proposed fuzzy model is derived by means of fuzzy clustering method with particular attention on structure flexibility and model interpretability issues. This may provide a basement of a new way to design model based control and diagnosis mechanisms for the complex nonlinear plant.

On Identifying Clusters Within the C-type Asteroids of the Sloan Digital Sky Survey

NASA Astrophysics Data System (ADS)

Poole, Renae; Ziffer, J.; Harvell, T.

2012-10-01

We applied AutoClass, a data mining technique based upon Bayesian Classification, to C-group asteroid colors in the Sloan Digital Sky Survey (SDSS). Previous taxonomic studies relied mostly on Principal Component Analysis (PCA) to differentiate asteroids within the C-group (e.g. B, G, F, Ch, Cg and Cb). AutoClass's advantage is that it calculates the most probable classification for us, removing the human factor from this part of the analysis. In our results, AutoClass divided the C-groups into two large classes and six smaller classes. The two large classes (n=4974 and 2033, respectively) display distinct regions with some overlap in color-vs-color plots. Each cluster's average spectrum is compared to 'typical' spectra of the C-group subtypes as defined by Tholen (1989) and each cluster's members are evaluated for consistency with previous taxonomies. Of the 117 asteroids classified as B-type in previous taxonomies, only 12 were found with SDSS colors that matched our criteria of having less than 0.1 magnitude error in u and 0.05 magnitude error in g, r, i, and z colors. Although this is a relatively small group, 11 of the 12 B-types were placed by AutoClass in the same cluster. By determining the C-group sub-classifications in the large SDSS database, this research furthers our understanding of the stratigraphy and composition of the main-belt.

Clustering of moderate luminosity X-ray-selected type 1 and type 2 AGNs at z ∼ 3

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

Allevato, V.; Finoguenov, A.; Civano, F.

2014-11-20

We investigate, for the first time at z ∼ 3, the clustering properties of 189 Type 1 and 157 Type 2 X-ray active galactic nuclei (AGNs) of moderate luminosity ((L {sub bol}) = 10{sup 45.3} erg s{sup –1}), with photometric or spectroscopic redshifts in the range 2.2 < z < 6.8. These samples are based on Chandra and XMM-Newton data in COSMOS. We find that Type 1 and Type 2 COSMOS AGNs at z ∼ 3 inhabit DMHs with typical mass of log M{sub h} = 12.84{sub −0.11}{sup +0.10} and 11.73{sub −0.45}{sup +0.39} h {sup –1} M {sub ☉}, respectively.more » This result requires a drop in the halo masses of Type 1 and 2 COSMOS AGNs at z ∼ 3 compared to z ≲ 2 XMM-COSMOS AGNs with similar luminosities. Additionally, we infer that unobscured COSMOS AGNs at z ∼ 3 reside in 10 times more massive halos compared to obscured COSMOS AGNs, at the 2.6σ level. This result extends to z ∼ 3 the results found in COSMOS at z ≲ 2, and rules out the picture in which obscuration is purely an orientation effect. A model which assumes that the AGNs activity is triggered by major mergers is quite successful in predicting both the low halo mass of COSMOS AGNs and the typical mass of luminous SDSS quasars at z ∼ 3, with the latter inhabiting more massive halos respect to moderate luminosity AGNs. Alternatively we can argue, at least for Type 1 COSMOS AGNs, that they are possibly representative of an early phase of fast (i.e., Eddington limited) BH growth induced by cosmic cold flows or disk instabilities. Given the moderate luminosity, these new fast growing BHs have masses of ∼10{sup 7-8} M {sub ☉} at z ∼ 3 which might evolve into ∼10{sup 8.5-9} M {sub ☉} mass BHs at z = 0. Following our clustering measurements, we argue that this fast BH growth at z ∼ 3 in AGNs with moderate luminosity occurs in DMHs with typical mass of ∼ 6× 10{sup 12} h {sup –1} M {sub ☉}.« less

Mg II Spectral Atlas and Flux Catalog for Late-Type Stars in the Hyades Cluster

NASA Technical Reports Server (NTRS)

Simon, Theodore

2001-01-01

In the course of a long-running IUE Guest Observer program, UV spectral images were obtained for more than 60 late-type members of the Hyades Cluster in order to investigate their chromospheric emissions. The emission line fluxes extracted from those observations were used to study the dependence of stellar dynamo activity upon age and rotation (IUE Observations of Rapidly Rotating Low-Mass Stars in Young Clusters: The Relation between Chromospheric Activity and Rotation). However, the details of those measurements, including a tabulation of the line fluxes, were never published. The purpose of the investigation summarized here was to extract all of the existing Hyades long-wavelength Mg II spectra in the IUE public archives in order to survey UV chromospheric emission in the cluster, thereby providing a consistent dataset for statistical and correlative studies of the relationship between stellar dynamo activity, rotation, and age over a broad range in mass.

Search and characterization of T-type planetary mass candidates in the σ Orionis cluster

NASA Astrophysics Data System (ADS)

Peña Ramírez, K.; Zapatero Osorio, M. R.; Béjar, V. J. S.; Rebolo, R.; Bihain, G.

2011-08-01

Context. The proper characterization of the least massive population of the young σ Orionis star cluster is required to understand the form of the cluster mass function and its impact on our comprehension of the substellar formation processes. S Ori 70 (T5.5 ± 1) and 73, two T-type cluster member candidates, are likely to have masses between 3 and 7 MJup if their age is 3 Myr. It awaits confirmation whether S Ori 73 has a methane atmosphere. Aims: We aim to: i) confirm the presence of methane absorption in S Ori 73 by performing methane imaging; ii) study S Ori 70 and 73 cluster membership via photometric colors and accurate proper motion analysis; and iii) perform a new search to identify additional T-type σ Orionis member candidates. Methods: We obtained HAWK-I (VLT) J, H, and CH4off photometry of an area of 119.15 arcmin2 in σ Orionis down to Jcomp = 21.7 and Hcomp = 21 mag. S Ori 70 and 73 are contained in the explored area. Near-infrared data were complemented with optical photometry using images acquired with OSIRIS (GTC) and VISTA as part of the VISTA Orion survey. Color-magnitude and color-color diagrams were constructed to characterize S Ori 70 and 73 photometrically, and to identify new objects with methane absorption and masses below 7 MJup. We derived proper motions by comparing of the new HAWK-I and VISTA images with published near-infrared data taken 3.4 - 7.9 yr ago. Results.S Ori 73 has a red H - CH4off color indicating methane absorption in the H-band and a spectral type of T4 ± 1. S Ori 70 displays a redder methane color than S Ori 73 in agreement with its latter spectral classification. Our proper motion measurements (μα cos δ = 26.7 ± 6.1, μδ = 21.3 ± 6.1 mas yr-1 for S Ori 70, and μα cos δ = 46.7 ± 4.9, μδ = -6.3 ± 4.7 mas yr-1 for S Ori 73) are larger than the motion of σ Orionis, rendering S Ori 70 and 73 cluster membership uncertain. From our survey, we identified one new photometric candidate with J = 21.69 ± 0.12 mag

NFκB-mediated activation of the cellular FUT3, 5 and 6 gene cluster by herpes simplex virus type 1.

PubMed

Nordén, Rickard; Samuelsson, Ebba; Nyström, Kristina

2017-11-01

Herpes simplex virus type 1 has the ability to induce expression of a human gene cluster located on chromosome 19 upon infection. This gene cluster contains three fucosyltransferases (encoded by FUT3, FUT5 and FUT6) with the ability to add a fucose to an N-acetylglucosamine residue. Little is known regarding the transcriptional activation of these three genes in human cells. Intriguingly, herpes simplex virus type 1 activates all three genes simultaneously during infection, a situation not observed in uninfected tissue, pointing towards a virus specific mechanism for transcriptional activation. The aim of this study was to define the underlying mechanism for the herpes simplex virus type 1 activation of FUT3, FUT5 and FUT6 transcription. The transcriptional activation of the FUT-gene cluster on chromosome 19 in fibroblasts was specific, not involving adjacent genes. Moreover, inhibition of NFκB signaling through panepoxydone treatment significantly decreased the induction of FUT3, FUT5 and FUT6 transcriptional activation, as did siRNA targeting of p65, in herpes simplex virus type 1 infected fibroblasts. NFκB and p65 signaling appears to play an important role in the regulation of FUT3, FUT5 and FUT6 transcriptional activation by herpes simplex virus type 1 although additional, unidentified, viral factors might account for part of the mechanism as direct interferon mediated stimulation of NFκB was not sufficient to induce the fucosyltransferase encoding gene cluster in uninfected cells. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular epidemiology demonstrated three emerging clusters of human immunodeficiency virus type 1 subtype B infection in Hong Kong.

PubMed

Leung, Tommy W C; Mak, Darwin; Wong, K H; Wang, Y; Song, Y H; Tsang, D N C; Wong, C; Shao, Y M; Lim, W L

2008-07-01

We conducted a molecular epidemiological study on newly diagnosed human immunodeficiency virus type 1 (HIV-1)-infected patients in Hong Kong to identify the epidemiological linkage of HIV-1 infection in the locality. Reverse transcription polymerase chain reaction (RT-PCR) for HIV-1 was performed on newly diagnosed HIV-1-positive sera collected from January 2002 to December 2006. PCR products correspond to the env C2V3V4 region and gag p17/p24 junction of the HIV-1 genome were nucleotide sequenced. Phylogenetic analyses performed on the acquired nucleotide sequences revealed that CRF01_AE and subtype B were the two dominant HIV-1 subtypes. Analyses also demonstrated the presence of three emerging HIV-1 clusters among the subtype B sequences in Hong Kong. Individual cluster possesses a unique cluster-specific amino acid signature for identification. Data show that one of the clusters (Cluster I) is rapidly expanding. In addition to the unique cluster-specific amino acid signature, the majority of sequences in Cluster I harbor a 6-amino acid insertion at the gag p17/p24 junction in a region that is thought to be closely associated with HIV-1 infectivity.

The ESO Nearby Abell Cluster Survey. VI. Spatial distribution and kinematics of early- and late-type galaxies

NASA Astrophysics Data System (ADS)

de Theije, P. A. M.; Katgert, P.

1999-01-01

Analysis of the data obtained in the ESO Nearby Abell Cluster Survey (ENACS) has shown that the space distribution and kinematics of galaxies with detectable emission lines in their spectra differ significantly from those of galaxies without emission lines. This result, and details of the kinematics, were considered as support for the idea that at least the spirals with emission lines are on orbits that are not isotropic. This might indicate that this subset of late-type galaxies either has `first approach'-orbits towards the dense core of their respective clusters, or has orbits that `avoid' the core. The galaxies with emission lines are essentially all late-type galaxies. On the other hand, the emission-line galaxies represent only about a third of the late-type galaxies, the majority of which do not show detectable emission lines. The galaxies without emission lines are therefore a mix of early- and late-type galaxies. In this paper we attempt to separate early- and late-type galaxies, and we study possible differences in distribution and kinematics of the two galaxy classes. For only about 10% of the galaxies in the ENACS, the morphology is known from imaging. Here, we describe our classification on the basis of the ENACS spectrum. The significant information in each spectrum is compressed into 15 Principal Components, which are used as input for an Artificial Neural Network. The latter is `trained' with 150 of the 270 galaxies for which a morphological type is available from Dressler, and subsequently used to classify each galaxy. This yields a classification for two-thirds of the ENACS galaxies. The Artificial Neural Network has two output classes: early-type (E+S0) and late-type (S+I) galaxies. We do not distinguish E and S0 galaxies, because these cannot be separated very robustly on the basis of the spectrum. The success rate of the classification is estimated from the sample of 120 galaxies with Dressler morphologies which were not used to train the ANN

Mass and size growth of early-type galaxies by dry mergers in cluster environments

NASA Astrophysics Data System (ADS)

Oogi, Taira; Habe, Asao; Ishiyama, Tomoaki

2016-02-01

We perform dry merger simulations to investigate the role of dry mergers in the size growth of early-type galaxies in high-density environments. We replace the virialized dark matter haloes obtained by a large cosmological N-body simulation with N-body galaxy models consisting of two components, a stellar bulge and a dark matter halo, which have higher mass resolution than the cosmological simulation. We then resimulate nine cluster-forming regions, whose masses range from 1 × 1014 to 5 × 1014 M⊙. Masses and sizes of stellar bulges are also assumed to satisfy the stellar mass-size relation of high-z compact massive early-type galaxies. We find that dry major mergers considerably contribute to the mass and size growth of central massive galaxies. One or two dry major mergers double the average stellar mass and quadruple the average size between z = 2 and 0. These growths favourably agree with observations. Moreover, the density distributions of our simulated central massive galaxies grow from the inside-out, which is consistent with recent observations. The mass-size evolution is approximated as R∝ M_{{ast }}^{α }, with α ˜ 2.24. Most of our simulated galaxies are efficiently grown by dry mergers, and their stellar mass-size relations match the ones observed in the local Universe. Our results show that the central galaxies in the cluster haloes are potential descendants of high-z (z ˜ 2-3) compact massive early-type galaxies. This conclusion is consistent with previous numerical studies which investigate the formation and evolution of compact massive early-type galaxies.

Distribution of Suicin Gene Clusters in Streptococcus suis Serotype 2 Belonging to Sequence Types 25 and 28.

PubMed

Athey, Taryn B T; Vaillancourt, Katy; Frenette, Michel; Fittipaldi, Nahuel; Gottschalk, Marcelo; Grenier, Daniel

2016-01-01

Recently, we reported the purification and characterization of three distinct lantibiotics (named suicin 90-1330, suicin 3908, and suicin 65) produced by Streptococcus suis . In this study, we investigated the distribution of the three suicin lantibiotic gene clusters among serotype 2 S. suis strains belonging to sequence type (ST) 25 and ST28, the two dominant STs identified in North America. The genomes of 102 strains were interrogated for the presence of suicin gene clusters encoding suicins 90-1330, 3908, and 65. The gene cluster encoding suicin 65 was the most prevalent and mainly found among ST25 strains. In contrast, none of the genes related to suicin 90-1330 production were identified in 51 ST25 strains nor in 35/51 ST28 strains. However, the complete suicin 90-1330 gene cluster was found in ten ST28 strains, although some genes in the cluster were truncated in three of these isolates. The vast majority (101/102) of S. suis strains did not possess any of the genes encoding suicin 3908. In conclusion, this study indicates heterogeneous distribution of suicin genes in S. suis .

Illuminating a Dark Lens : A Type Ia Supernova Magnified by the Frontier Fields Galaxy Cluster Abell 2744

NASA Astrophysics Data System (ADS)

Rodney, Steven A.; Patel, Brandon; Scolnic, Daniel; Foley, Ryan J.; Molino, Alberto; Brammer, Gabriel; Jauzac, Mathilde; Bradač, Maruša; Broadhurst, Tom; Coe, Dan; Diego, Jose M.; Graur, Or; Hjorth, Jens; Hoag, Austin; Jha, Saurabh W.; Johnson, Traci L.; Kelly, Patrick; Lam, Daniel; McCully, Curtis; Medezinski, Elinor; Meneghetti, Massimo; Merten, Julian; Richard, Johan; Riess, Adam; Sharon, Keren; Strolger, Louis-Gregory; Treu, Tommaso; Wang, Xin; Williams, Liliya L. R.; Zitrin, Adi

2015-09-01

SN HFF14Tom is a Type Ia SN discovered at z=1.3457+/- 0.0001 behind the galaxy cluster Abell 2744 (z = 0.308). In a cosmology-independent analysis, we find that HFF14Tom is 0.77 ± 0.15 mag brighter than unlensed Type Ia SNe at similar redshift, implying a lensing magnification of {μ }{obs}=2.03+/- 0.29. This observed magnification provides a rare opportunity for a direct empirical test of galaxy cluster lens models. Here we test 17 lens models, 13 of which were generated before the SN magnification was known, qualifying as pure “blind tests.” The models are collectively fairly accurate: 8 of the models deliver median magnifications that are consistent with the measured μ to within 1σ. However, there is a subtle systematic bias: the significant disagreements all involve models overpredicting the magnification. We evaluate possible causes for this mild bias, and find no single physical or methodological explanation to account for it. We do find that model accuracy can be improved to some extent with stringent quality cuts on multiply imaged systems, such as requiring that a large fraction have spectroscopic redshifts. In addition to testing model accuracies as we have done here, Type Ia SN magnifications could also be used as inputs for future lens models of Abell 2744 and other clusters, providing valuable constraints in regions where traditional strong- and weak-lensing information is unavailable.

Parity among interpretation methods of MLEE patterns and disparity among clustering methods in epidemiological typing of Candida albicans.

PubMed

Boriollo, Marcelo Fabiano Gomes; Rosa, Edvaldo Antonio Ribeiro; Gonçalves, Reginaldo Bruno; Höfling, José Francisco

2006-03-01

The typing of C. albicans by MLEE (multilocus enzyme electrophoresis) is dependent on the interpretation of enzyme electrophoretic patterns, and the study of the epidemiological relationships of these yeasts can be conducted by cluster analysis. Therefore, the aims of the present study were to first determine the discriminatory power of genetic interpretation (deduction of the allelic composition of diploid organisms) and numerical interpretation (mere determination of the presence and absence of bands) of MLEE patterns, and then to determine the concordance (Pearson product-moment correlation coefficient) and similarity (Jaccard similarity coefficient) of the groups of strains generated by three cluster analysis models, and the discriminatory power of such models as well [model A: genetic interpretation, genetic distance matrix of Nei (d(ij)) and UPGMA dendrogram; model B: genetic interpretation, Dice similarity matrix (S(D1)) and UPGMA dendrogram; model C: numerical interpretation, Dice similarity matrix (S(D2)) and UPGMA dendrogram]. MLEE was found to be a powerful and reliable tool for the typing of C. albicans due to its high discriminatory power (>0.9). Discriminatory power indicated that numerical interpretation is a method capable of discriminating a greater number of strains (47 versus 43 subtypes), but also pointed to model B as a method capable of providing a greater number of groups, suggesting its use for the typing of C. albicans by MLEE and cluster analysis. Very good agreement was only observed between the elements of the matrices S(D1) and S(D2), but a large majority of the groups generated in the three UPGMA dendrograms showed similarity S(J) between 4.8% and 75%, suggesting disparities in the conclusions obtained by the cluster assays.

Comparison of Molecular Typing Methods Useful for Detecting Clusters of Campylobacter jejuni and C. coli Isolates through Routine Surveillance

PubMed Central

Taboada, Eduardo; Grant, Christopher C. R.; Blakeston, Connie; Pollari, Frank; Marshall, Barbara; Rahn, Kris; MacKinnon, Joanne; Daignault, Danielle; Pillai, Dylan; Ng, Lai-King

2012-01-01

Campylobacter spp. may be responsible for unreported outbreaks of food-borne disease. The detection of these outbreaks is made more difficult by the fact that appropriate methods for detecting clusters of Campylobacter have not been well defined. We have compared the characteristics of five molecular typing methods on Campylobacter jejuni and C. coli isolates obtained from human and nonhuman sources during sentinel site surveillance during a 3-year period. Comparative genomic fingerprinting (CGF) appears to be one of the optimal methods for the detection of clusters of cases, and it could be supplemented by the sequencing of the flaA gene short variable region (flaA SVR sequence typing), with or without subsequent multilocus sequence typing (MLST). Different methods may be optimal for uncovering different aspects of source attribution. Finally, the use of several different molecular typing or analysis methods for comparing individuals within a population reveals much more about that population than a single method. Similarly, comparing several different typing methods reveals a great deal about differences in how the methods group individuals within the population. PMID:22162562

Globular clusters and environmental effects in galaxy clusters

NASA Astrophysics Data System (ADS)

Sales, Laura

2016-10-01

Globular clusters are old compact stellar systems orbiting around galaxies of all types. Tens of thousands of them can also be found populating the intra-cluster regions of nearby galaxy clusters like Virgo and Coma. Thanks to the HST Frontier Fields program, GCs are starting now to be detected also in intermediate redshift clusters. Yet, despite their ubiquity, a theoretical model for the formation and evolution of GCs is still missing, especially within the cosmological context.Here we propose to use cosmological hydrodynamical simulations of 18 galaxy clusters coupled to a post-processing GC formation model to explore the assembly of galaxies in clusters together with their expected GC population. The method, which has already been implemented and tested, will allow us to characterize for the first time the number, radial distribution and kinematics of GCs in clusters, with products directly comparable to observational maps. We will explore cluster-to-cluster variations and also characterize the build up of the intra-cluster component of GCs with time.As the method relies on a detailed study of the star-formation history of galaxies, we will jointly constrain the predicted quenching time-scales for satellites and the occurrence of starburst events associated to infall and orbital pericenters of galaxies in massive clusters. This will inform further studies on the distribution, velocity and properties of post-starburst galaxies in past, ongoing and future HST programs.

Protein sequences clustering of herpes virus by using Tribe Markov clustering (Tribe-MCL)

NASA Astrophysics Data System (ADS)

Bustamam, A.; Siswantining, T.; Febriyani, N. L.; Novitasari, I. D.; Cahyaningrum, R. D.

2017-07-01

The herpes virus can be found anywhere and one of the important characteristics is its ability to cause acute and chronic infection at certain times so as a result of the infection allows severe complications occurred. The herpes virus is composed of DNA containing protein and wrapped by glycoproteins. In this work, the Herpes viruses family is classified and analyzed by clustering their protein-sequence using Tribe Markov Clustering (Tribe-MCL) algorithm. Tribe-MCL is an efficient clustering method based on the theory of Markov chains, to classify protein families from protein sequences using pre-computed sequence similarity information. We implement the Tribe-MCL algorithm using an open source program of R. We select 24 protein sequences of Herpes virus obtained from NCBI database. The dataset consists of three types of glycoprotein B, F, and H. Each type has eight herpes virus that infected humans. Based on our simulation using different inflation factor r=1.5, 2, 3 we find a various number of the clusters results. The greater the inflation factor the greater the number of their clusters. Each protein will grouped together in the same type of protein.

Multiple populations within globular clusters in Early-type galaxies Exploring their effect on stellar initial mass function estimates

NASA Astrophysics Data System (ADS)

Chantereau, W.; Usher, C.; Bastian, N.

2018-05-01

It is now well-established that most (if not all) ancient globular clusters host multiple populations, that are characterised by distinct chemical features such as helium abundance variations along with N-C and Na-O anti-correlations, at fixed [Fe/H]. These very distinct chemical features are similar to what is found in the centres of the massive early-type galaxies and may influence measurements of the global properties of the galaxies. Additionally, recent results have suggested that M/L variations found in the centres of massive early-type galaxies might be due to a bottom-heavy stellar initial mass function. We present an analysis of the effects of globular cluster-like multiple populations on the integrated properties of early-type galaxies. In particular, we focus on spectral features in the integrated optical spectrum and the global mass-to-light ratio that have been used to infer variations in the stellar initial mass function. To achieve this we develop appropriate stellar population synthesis models and take into account, for the first time, an initial-final mass relation which takes into consideration a varying He abundance. We conclude that while the multiple populations may be present in massive early-type galaxies, they are likely not responsible for the observed variations in the mass-to-light ratio and IMF sensitive line strengths. Finally, we estimate the fraction of stars with multiple populations chemistry that come from disrupted globular clusters within massive ellipticals and find that they may explain some of the observed chemical patterns in the centres of these galaxies.

A Comparison of the Near-Infrared Spectral Features of Early-Type Galaxies in the Virgo and Coma Clusters

NASA Astrophysics Data System (ADS)

Houdashelt, M. L.

1992-05-01

Initial results are presented from an examination of near-infrared spectra (6800 - 9200 Angstroms) of 34 early-type galaxies - 17 in the Virgo cluster, 10 in the Coma cluster and seven field members. It has previously been speculated that E/S0 galaxies of similar luminosity in the Virgo and Coma clusters have different red stellar populations. To explore this possibility, pseudo-equivalent widths of a number of near-IR spectral features have been measured. The important features studied include the TiO bands near 7100, 7890, 8197, 8500 and 8950 Angstroms, which are mainly produced by the late-type stars whose flux contributes only about 10-20\\ the near-IR. The strengths of the Ca triplet (8498, 8542, 8662 Angstroms) and Na I doublet (8183, 8195 Angstroms) are also measured, since these features are affected by the relative contribution of dwarf stars to the red light. Although the main focus of this work is the search for spectral differences among the Coma, Virgo and field E/S0 populations, each subgroup of galaxies (and the sample as a whole) are also examined for correlations among the feature strengths, galaxy color and luminosity.

Optimal design of a plot cluster for monitoring

Treesearch

Charles T. Scott

1993-01-01

Traveling costs incurred during extensive forest surveys make cluster sampling cost-effective. Clusters are specified by the type of plots, plot size, number of plots, and the distance between plots within the cluster. A method to determine the optimal cluster design when different plot types are used for different forest resource attributes is described. The method...

Inhibition of type 1 fimbriae-mediated Escherichia coli adhesion and biofilm formation by trimeric cluster thiomannosides conjugated to diamond nanoparticles

NASA Astrophysics Data System (ADS)

Khanal, Manakamana; Larsonneur, Fanny; Raks, Victoriia; Barras, Alexandre; Baumann, Jean-Sébastien; Martin, Fernando Ariel; Boukherroub, Rabah; Ghigo, Jean-Marc; Ortiz Mellet, Carmen; Zaitsev, Vladimir; Garcia Fernandez, Jose M.; Beloin, Christophe; Siriwardena, Aloysius; Szunerits, Sabine

2015-01-01

Recent advances in nanotechnology have seen the development of a number of microbiocidal and/or anti-adhesive nanoparticles displaying activity against biofilms. In this work, trimeric thiomannoside clusters conjugated to nanodiamond particles (ND) were targeted for investigation. NDs have attracted attention as a biocompatible nanomaterial and we were curious to see whether the high mannose glycotope density obtained upon grouping monosaccharide units in triads might lead to the corresponding ND-conjugates behaving as effective inhibitors of E. coli type 1 fimbriae-mediated adhesion as well as of biofilm formation. The required trimeric thiosugar clusters were obtained through a convenient thiol-ene ``click'' strategy and were subsequently conjugated to alkynyl-functionalized NDs using a Cu(i)-catalysed ``click'' reaction. We demonstrated that the tri-thiomannoside cluster-conjugated NDs (ND-Man3) show potent inhibition of type 1 fimbriae-mediated E. coli adhesion to yeast and T24 bladder cells as well as of biofilm formation. The biofilm disrupting effects demonstrated here have only rarely been reported in the past for analogues featuring such simple glycosidic motifs. Moreover, the finding that the tri-thiomannoside cluster (Man3N3) is itself a relatively efficient inhibitor, even when not conjugated to any ND edifice, suggests that alternative mono- or multivalent sugar-derived analogues might also be usefully explored for E. coli-mediated biofilm disrupting properties.Recent advances in nanotechnology have seen the development of a number of microbiocidal and/or anti-adhesive nanoparticles displaying activity against biofilms. In this work, trimeric thiomannoside clusters conjugated to nanodiamond particles (ND) were targeted for investigation. NDs have attracted attention as a biocompatible nanomaterial and we were curious to see whether the high mannose glycotope density obtained upon grouping monosaccharide units in triads might lead to the corresponding

Nucleophilic substitution reaction for post-functionalization of polyoxometalates

DOE PAGES

Yin, Panchao; Li, Qiang; Zhang, Jin; ...

2015-07-06

In this study, a hexamolybdate-based organic inorganic hybrid molecule containing a chloralkane fragment is synthesized and its Cl atom can be substituted by iodine and nitrate through nucleophilic substitution reactions in high yields, which provide a post-functionalization protocol to bring in various additional functional groups into polyoxometalate-based hybrid materials under mild conditions.

Open clusters. III. Fundamental parameters of B stars in NGC 6087, NGC 6250, NGC 6383, and NGC 6530 B-type stars with circumstellar envelopes

NASA Astrophysics Data System (ADS)

Aidelman, Y.; Cidale, L. S.; Zorec, J.; Panei, J. A.

2018-02-01

Context. Stellar physical properties of star clusters are poorly known and the cluster parameters are often very uncertain. Methods: Our goals are to perform a spectrophotometric study of the B star population in open clusters to derive accurate stellar parameters, search for the presence of circumstellar envelopes, and discuss the characteristics of these stars. The BCD spectrophotometric system is a powerful method to obtain stellar fundamental parameters from direct measurements of the Balmer discontinuity. To this end, we wrote the interactive code MIDE3700. The BCD parameters can also be used to infer the main properties of open clusters: distance modulus, color excess, and age. Furthermore, we inspected the Balmer discontinuity to provide evidence for the presence of circumstellar disks and identify Be star candidates. We used an additional set of high-resolution spectra in the Hα region to confirm the Be nature of these stars. Results: We provide Teff, log g, Mv, Mbol, and spectral types for a sample of 68 stars in the field of the open clusters NGC 6087, NGC 6250, NGC 6383, and NGC 6530, as well as the cluster distances, ages, and reddening. Then, based on a sample of 230 B stars in the direction of the 11 open clusters studied along this series of three papers, we report 6 new Be stars, 4 blue straggler candidates, and 15 B-type stars (called Bdd) with a double Balmer discontinuity, which indicates the presence of circumstellar envelopes. We discuss the distribution of the fraction of B, Be, and Bdd star cluster members per spectral subtype. The majority of the Be stars are dwarfs and present a maximum at the spectral type B2-B4 in young and intermediate-age open clusters (<40 Myr). Another maximum of Be stars is observed at the spectral type B6-B8 in open clusters older than 40 Myr, where the population of Bdd stars also becomes relevant. The Bdd stars seem to be in a passive emission phase. Conclusions: Our results support previous statements that the

Are clusters of dietary patterns and cluster membership stable over time? Results of a longitudinal cluster analysis study.

PubMed

Walthouwer, Michel Jean Louis; Oenema, Anke; Soetens, Katja; Lechner, Lilian; de Vries, Hein

2014-11-01

Developing nutrition education interventions based on clusters of dietary patterns can only be done adequately when it is clear if distinctive clusters of dietary patterns can be derived and reproduced over time, if cluster membership is stable, and if it is predictable which type of people belong to a certain cluster. Hence, this study aimed to: (1) identify clusters of dietary patterns among Dutch adults, (2) test the reproducibility of these clusters and stability of cluster membership over time, and (3) identify sociodemographic predictors of cluster membership and cluster transition. This study had a longitudinal design with online measurements at baseline (N=483) and 6 months follow-up (N=379). Dietary intake was assessed with a validated food frequency questionnaire. A hierarchical cluster analysis was performed, followed by a K-means cluster analysis. Multinomial logistic regression analyses were conducted to identify the sociodemographic predictors of cluster membership and cluster transition. At baseline and follow-up, a comparable three-cluster solution was derived, distinguishing a healthy, moderately healthy, and unhealthy dietary pattern. Male and lower educated participants were significantly more likely to have a less healthy dietary pattern. Further, 251 (66.2%) participants remained in the same cluster, 45 (11.9%) participants changed to an unhealthier cluster, and 83 (21.9%) participants shifted to a healthier cluster. Men and people living alone were significantly more likely to shift toward a less healthy dietary pattern. Distinctive clusters of dietary patterns can be derived. Yet, cluster membership is unstable and only few sociodemographic factors were associated with cluster membership and cluster transition. These findings imply that clusters based on dietary intake may not be suitable as a basis for nutrition education interventions. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Scleroderma cluster among type-setters].

PubMed

Magnavita, N

2007-01-01

The etiology of systemic sclerosis, probably multifactorial, is not yet well defined. Among the many endogenous and exogenous factors probably involved, occupational elements may play an essential role. Here we report a cluster of local scleroderma and systemic sclerosis, which occurred in a small group of typography workers exposed to polyvinyl-acetate glues, containing up to 1% of vinyl-acetate. Vinyl acetate exposure has been associated with acidification of the intracellular environment, which is thought to produce cytotoxic and/or mitogenic responses that are the sentinel pharmacodynamic steps toward cancer. Autoantibody production in systemic sclerosis depends upon intracellular acidification. More studies are needed to clarify the relationship between vinyl acetate exposure and scleroderma.

The Solar-Type Hard-Binary Frequency and Distributions of Orbital Parameters in the Open Cluster M37

NASA Astrophysics Data System (ADS)

Geller, Aaron M.; Meibom, Soren; Barnes, Sydney A.; Mathieu, Robert D.

2014-02-01

Binary stars, and particularly the short-period ``hard'' binaries, govern the dynamical evolution of star clusters and determine the formation rates and mechanisms for exotic stars like blue stragglers and X-ray sources. Understanding the near-primordial hard-binary population of star clusters is of primary importance for dynamical models of star clusters, which have the potential to greatly advance our understanding of star cluster evolution. Yet the binary frequencies and distributions of binary orbital parameters (period, eccentricity, etc.) for young coeval stellar populations are poorly known, due to a lack of necessary observations. The young (~540 Myr) open cluster M37 hosts a rich binary population that can be used to empirically define these initial conditions. Importantly, this cluster has been the target of a comprehensive WIYN/Hydra radial-velocity (RV) survey, from which we have already identified a nearly complete sample of 329 solar-type (1.5 <=M [M_⊙] <=1.0) members in M37. Of these stars, 82 show significant RV variability, indicative of a binary companion. We propose to build upon these data with a multi-epoch RV survey using WIYN/Hydra to derive kinematic orbital solutions for these 82 binaries in M37. This project was granted time in 2013B and scheduled for later this year. We anticipate that about half of the detected binaries in M37 will acquire enough RV measurements (>=10) in 2013B to begin searching for orbital solutions. With this proposal and perhaps one additional semester we should achieve >=10 RV measurements for the remaining binaries.

Cluster dynamics and cluster size distributions in systems of self-propelled particles

NASA Astrophysics Data System (ADS)

Peruani, F.; Schimansky-Geier, L.; Bär, M.

2010-12-01

Systems of self-propelled particles (SPP) interacting by a velocity alignment mechanism in the presence of noise exhibit rich clustering dynamics. Often, clusters are responsible for the distribution of (local) information in these systems. Here, we investigate the properties of individual clusters in SPP systems, in particular the asymmetric spreading behavior of clusters with respect to their direction of motion. In addition, we formulate a Smoluchowski-type kinetic model to describe the evolution of the cluster size distribution (CSD). This model predicts the emergence of steady-state CSDs in SPP systems. We test our theoretical predictions in simulations of SPP with nematic interactions and find that our simple kinetic model reproduces qualitatively the transition to aggregation observed in simulations.

General Practitioners' Barriers to Prescribe Physical Activity: The Dark Side of the Cluster Effects on the Physical Activity of Their Type 2 Diabetes Patients.

PubMed

Lanhers, Charlotte; Duclos, Martine; Guttmann, Aline; Coudeyre, Emmanuel; Pereira, Bruno; Ouchchane, Lemlih

2015-01-01

To describe barriers to physical activity (PA) in type 2 diabetes patients and their general practitioners (GPs), looking for practitioner's influence on PA practice of their patients. We conducted a cross-sectional study on GPs (n = 48) and their type 2 diabetes patients (n = 369) measuring respectively barriers to prescribe and practice PA using a self-assessment questionnaire: barriers to physical activity in diabetes (BAPAD). Statistical analysis was performed accounting hierarchical data structure. Similar practitioner's patients were considered a cluster sharing common patterns. The higher the patient's BAPAD score, the higher the barriers to PA, the higher the risk to declare practicing no PA (p<0.001), low frequency and low duration of PA (p<0.001). A high patient's BAPAD score was also associated with a higher risk to have HbA1c ≥7% (53 mmol/mol) (p = 0.001). The intra-class correlation coefficient between type 2 diabetes patients and GPs was 34%, indicating a high cluster effect. A high GP's BAPAD score, regarding the PA prescription, is predictive of a high BAPAD score with their patients, regarding their practice (p = 0.03). Type 2 diabetes patients with lower BAPAD score, thus lower barriers to physical activity, have a higher PA level and a better glycemic control. An important and deleterious cluster effect between GPs and their patients is demonstrated: the higher the GP's BAPAD score, the higher the type 2 diabetes patients' BAPAD score. This important cluster effect might designate GPs as a relevant lever for future interventions regarding patient's education towards PA and type 2 diabetes management.

Isophote Shapes Of Early-Type Galaxies In Massive Clusters At Z 1 And 0

NASA Astrophysics Data System (ADS)

Mitsuda, Kazuma; Doi, Mamoru; Morokuma, Tomoki; Suzuki, Nao; Yasuda, Naoki; Perlmutter, Saul; Aldering, Greg; Meyers, Joshua

2017-06-01

Dynamics of early-type galaxies (ETGs), whether they are supported by rotation or dispersion, is a clue to understand their assembly history. We compare the isophote shape parameter a4 between z ˜ 1 and 0 as a proxy for dynamics to investigate the epoch at which the dynamical properties are established. We create cluster ETG samples with stellar masses of log(M✽/M⦿) ≥ 10.5 with spectroscopic redshifts. We have 130 ETGs from the Hubble Space Telescope Cluster Supernova Survey for z ˜ 1 and 355 ETGs from the Sloan Digital Sky Survey for z ˜ 0. We find similar dependence of the a4 parameter on the mass at z ˜ 1 and 0; the main population changes from disky (a4 > 0) to boxy (a4 ≤ 0) at a critical mass of log(M✽/M⦿) 11.5 with the massive end dominated by boxy ETGs. The disky ETG fraction is consistent between these redshifts. Although uncertainties are large, the results suggest that the isophote shapes and probably dynamical properties of cluster ETGs are already in place at z > 1 and do not significantly evolve in z < 1, despite significant size evolution. The constant disky fraction imply that the processes responsible for the size evolution is not enough violent to convert the dynamical properties of ETGs.

Clustering-based classification of road traffic accidents using hierarchical clustering and artificial neural networks.

PubMed

Taamneh, Madhar; Taamneh, Salah; Alkheder, Sharaf

2017-09-01

Artificial neural networks (ANNs) have been widely used in predicting the severity of road traffic crashes. All available information about previously occurred accidents is typically used for building a single prediction model (i.e., classifier). Too little attention has been paid to the differences between these accidents, leading, in most cases, to build less accurate predictors. Hierarchical clustering is a well-known clustering method that seeks to group data by creating a hierarchy of clusters. Using hierarchical clustering and ANNs, a clustering-based classification approach for predicting the injury severity of road traffic accidents was proposed. About 6000 road accidents occurred over a six-year period from 2008 to 2013 in Abu Dhabi were used throughout this study. In order to reduce the amount of variation in data, hierarchical clustering was applied on the data set to organize it into six different forms, each with different number of clusters (i.e., clusters from 1 to 6). Two ANN models were subsequently built for each cluster of accidents in each generated form. The first model was built and validated using all accidents (training set), whereas only 66% of the accidents were used to build the second model, and the remaining 34% were used to test it (percentage split). Finally, the weighted average accuracy was computed for each type of models in each from of data. The results show that when testing the models using the training set, clustering prior to classification achieves (11%-16%) more accuracy than without using clustering, while the percentage split achieves (2%-5%) more accuracy. The results also suggest that partitioning the accidents into six clusters achieves the best accuracy if both types of models are taken into account.

Inhibition of type 1 fimbriae-mediated Escherichia coli adhesion and biofilm formation by trimeric cluster thiomannosides conjugated to diamond nanoparticles.

PubMed

Khanal, Manakamana; Larsonneur, Fanny; Raks, Victoriia; Barras, Alexandre; Baumann, Jean-Sébastien; Martin, Fernando Ariel; Boukherroub, Rabah; Ghigo, Jean-Marc; Ortiz Mellet, Carmen; Zaitsev, Vladimir; Garcia Fernandez, Jose M; Beloin, Christophe; Siriwardena, Aloysius; Szunerits, Sabine

2015-02-14

Recent advances in nanotechnology have seen the development of a number of microbiocidal and/or anti-adhesive nanoparticles displaying activity against biofilms. In this work, trimeric thiomannoside clusters conjugated to nanodiamond particles (ND) were targeted for investigation. NDs have attracted attention as a biocompatible nanomaterial and we were curious to see whether the high mannose glycotope density obtained upon grouping monosaccharide units in triads might lead to the corresponding ND-conjugates behaving as effective inhibitors of E. coli type 1 fimbriae-mediated adhesion as well as of biofilm formation. The required trimeric thiosugar clusters were obtained through a convenient thiol-ene "click" strategy and were subsequently conjugated to alkynyl-functionalized NDs using a Cu(I)-catalysed "click" reaction. We demonstrated that the tri-thiomannoside cluster-conjugated NDs (ND-Man3) show potent inhibition of type 1 fimbriae-mediated E. coli adhesion to yeast and T24 bladder cells as well as of biofilm formation. The biofilm disrupting effects demonstrated here have only rarely been reported in the past for analogues featuring such simple glycosidic motifs. Moreover, the finding that the tri-thiomannoside cluster (Man3N3) is itself a relatively efficient inhibitor, even when not conjugated to any ND edifice, suggests that alternative mono- or multivalent sugar-derived analogues might also be usefully explored for E. coli-mediated biofilm disrupting properties.

Metallicity Variations in the Type II Globular Cluster NGC 6934

NASA Astrophysics Data System (ADS)

Marino, A. F.; Yong, D.; Milone, A. P.; Piotto, G.; Lundquist, M.; Bedin, L. R.; Chené, A.-N.; Da Costa, G.; Asplund, M.; Jerjen, H.

2018-06-01

The Hubble Space Telescope photometric survey of Galactic globular clusters (GCs) has revealed a peculiar “chromosome map” for NGC 6934. In addition to a typical sequence, similar to that observed in Type I GCs, NGC 6934 displays additional stars on the red side, analogous to the anomalous Type II GCs, as defined in our previous work. We present a chemical abundance analysis of four red giants in this GC. Two stars are located on the chromosome map sequence common to all GCs, and another two lie on the additional sequence. We find (i) star-to-star Fe variations, with the two anomalous stars being enriched by ∼0.2 dex. Because of our small-size sample, this difference is at the ∼2.5σ level. (ii) There is no evidence for variations in the slow neutron-capture abundances over Fe, at odds with what is often observed in anomalous Type II GCs, e.g., M 22 and ω Centauri (iii) no large variations in light elements C, O, and Na, compatible with locations of the targets on the lower part of the chromosome map where such variations are not expected. Since the analyzed stars are homogeneous in light elements, the only way to reproduce the photometric splits on the sub-giant (SGB) and the red giant (RGB) branches is to assume that red RGB/faint SGB stars are enhanced in [Fe/H] by ∼0.2. This fact corroborates the spectroscopic evidence of a metallicity variation in NGC 6934. The observed chemical pattern resembles only partially the other Type II GCs, suggesting that NGC 6934 might belong either to a third class of GCs, or be a link between normal Type I and anomalous Type II GCs. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile, and Gemini Telescope at Canada–France–Hawaii Telescope.

Finding gene clusters for a replicated time course study

PubMed Central

2014-01-01

Background Finding genes that share similar expression patterns across samples is an important question that is frequently asked in high-throughput microarray studies. Traditional clustering algorithms such as K-means clustering and hierarchical clustering base gene clustering directly on the observed measurements and do not take into account the specific experimental design under which the microarray data were collected. A new model-based clustering method, the clustering of regression models method, takes into account the specific design of the microarray study and bases the clustering on how genes are related to sample covariates. It can find useful gene clusters for studies from complicated study designs such as replicated time course studies. Findings In this paper, we applied the clustering of regression models method to data from a time course study of yeast on two genotypes, wild type and YOX1 mutant, each with two technical replicates, and compared the clustering results with K-means clustering. We identified gene clusters that have similar expression patterns in wild type yeast, two of which were missed by K-means clustering. We further identified gene clusters whose expression patterns were changed in YOX1 mutant yeast compared to wild type yeast. Conclusions The clustering of regression models method can be a valuable tool for identifying genes that are coordinately transcribed by a common mechanism. PMID:24460656

Modeling of correlated data with informative cluster sizes: An evaluation of joint modeling and within-cluster resampling approaches.

PubMed

Zhang, Bo; Liu, Wei; Zhang, Zhiwei; Qu, Yanping; Chen, Zhen; Albert, Paul S

2017-08-01

Joint modeling and within-cluster resampling are two approaches that are used for analyzing correlated data with informative cluster sizes. Motivated by a developmental toxicity study, we examined the performances and validity of these two approaches in testing covariate effects in generalized linear mixed-effects models. We show that the joint modeling approach is robust to the misspecification of cluster size models in terms of Type I and Type II errors when the corresponding covariates are not included in the random effects structure; otherwise, statistical tests may be affected. We also evaluate the performance of the within-cluster resampling procedure and thoroughly investigate the validity of it in modeling correlated data with informative cluster sizes. We show that within-cluster resampling is a valid alternative to joint modeling for cluster-specific covariates, but it is invalid for time-dependent covariates. The two methods are applied to a developmental toxicity study that investigated the effect of exposure to diethylene glycol dimethyl ether.

Primordial binary populations in low-density star clusters as seen by Chandra: globular clusters versus old open clusters

NASA Astrophysics Data System (ADS)

van den Berg, Maureen C.

2015-08-01

The binaries in the core of a star cluster are the energy source that prevents the cluster from experiencing core collapse. To model the dynamical evolution of a cluster, it is important to have constraints on the primordial binary content. X-ray observations of old star clusters are very efficient in detecting the close interacting binaries among the cluster members. The X-ray sources in star clusters are a mix of binaries that were dynamically formed and primordial binaries. In massive, dense star clusters, dynamical encounters play an important role in shaping the properties and numbers of the binaries. In contrast, in the low-density clusters the impact of dynamical encounters is presumed to be very small, and the close binaries detected in X-rays represent a primordial population. The lowest density globular clusters have current masses and central densities similar to those of the oldest open clusters in our Milky Way. I will discuss the results of studies with the Chandra X-ray Observatory that have nevertheless revealed a clear dichotomy: far fewer (if any at all) X-ray sources are detected in the central regions of the low-density globular clusters compared to the number of secure cluster members that have been detected in old open clusters (above a limiting X-ray luminosity of typically 4e30 erg/s). The low stellar encounter rates imply that dynamical destruction of binaries can be ignored at present, therefore an explanation must be sought elsewhere. I will discuss several factors that can shed light on the implied differences between the primordial close binary populations in the two types of star clusters.

A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas.

PubMed

Radovich, Milan; Solzak, Jeffrey P; Hancock, Bradley A; Conces, Madison L; Atale, Rutuja; Porter, Ryan F; Zhu, Jin; Glasscock, Jarret; Kesler, Kenneth A; Badve, Sunil S; Schneider, Bryan P; Loehrer, Patrick J

2016-02-16

Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing. The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used. Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. A substantial differentiator was a large microRNA cluster on chr19q13.42 that was significantly overexpressed in all A and AB tumours and whose expression was virtually absent in the other thymomas and normal tissues. Overexpression of this microRNA cluster activates the PI3K/AKT/mTOR pathway. Treatment of a thymoma AB cell line with a panel of PI3K/AKT/mTOR inhibitors resulted in marked reduction of cell viability. A large microRNA cluster on chr19q13.42 is a transcriptional hallmark of type A and AB thymomas. Furthermore, this cluster activates the PI3K pathway, suggesting the possible exploration of PI3K inhibitors in patients with these subtypes of tumour. This work has led to the initiation of a phase II clinical trial of PI3K inhibition in relapsed or refractory thymomas (http://clinicaltrials.gov/ct2/show/NCT02220855).

STELLAR KINEMATICS AND STRUCTURAL PROPERTIES OF VIRGO CLUSTER DWARF EARLY-TYPE GALAXIES FROM THE SMAKCED PROJECT. III. ANGULAR MOMENTUM AND CONSTRAINTS ON FORMATION SCENARIOS

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

Toloba, E.; Guhathakurta, P.; Boselli, A.

2015-02-01

We analyze the stellar kinematics of 39 dwarf early-type galaxies (dEs) in the Virgo Cluster. Based on the specific stellar angular momentum λ{sub Re} and the ellipticity, we find 11 slow rotators and 28 fast rotators. The fast rotators in the outer parts of the Virgo Cluster rotate significantly faster than fast rotators in the inner parts of the cluster. Moreover, 10 out of the 11 slow rotators are located in the inner 3° (D < 1 Mpc) of the cluster. The fast rotators contain subtle disk-like structures that are visible in high-pass filtered optical images, while the slow rotatorsmore » do not exhibit these structures. In addition, two of the dEs have kinematically decoupled cores and four more have emission partially filling in the Balmer absorption lines. These properties suggest that Virgo Cluster dEs may have originated from late-type star-forming galaxies that were transformed by the environment after their infall into the cluster. The correlation between λ{sub Re} and the clustercentric distance can be explained by a scenario where low luminosity star-forming galaxies fall into the cluster, their gas is rapidly removed by ram-pressure stripping, although some of it can be retained in their core, their star formation is quenched but their stellar kinematics are preserved. After a long time in the cluster and several passes through its center, the galaxies are heated up and transformed into slow rotating dEs.« less

Trapping {BW12}2 tungstoborate: synthesis and crystal structure of hybrid [{(H2BW12O42)2O}{Mo6O6S6(OH)4(H2O)2}]14- anion.

PubMed

Korenev, V S; Abramov, P A; Vicent, C; Mainichev, D A; Floquet, S; Cadot, E; Sokolov, M N; Fedin, V P

2012-12-28

Reaction between monolacunary {BW(11)} tungstoborate and oxothiocationic building block, {Mo(2)O(2)S(2)}, results in the formation of a new polyoxothiometalate with a unique architecture in which two [H(2)BW(12)O(43)](9-) tungstoborate subunits are linked together with a hexamolybdate [Mo(V)(6)O(6)S(6)(OH)(4)(H(2)O)(2)](2+) bridge.

Evidence for Cluster Evolution from an Improved Measurement of the Velocity Dispersion and Morphological Fraction of Cluster 1324+3011 at z=0.76

NASA Astrophysics Data System (ADS)

Lubin, Lori M.; Oke, J. B.; Postman, Marc

2002-10-01

We have carried out additional spectroscopic observations in the field of cluster Cl 1324+3011 at z=0.76. Combined with the spectroscopy recently presented by Postman, Lubin, & Oke, we now have spectroscopically confirmed 47 cluster members. With this significant number of redshifts, we measure accurately the cluster velocity dispersion to be 1016+126-93 km s-1. The distribution of velocity offsets is consistent with a Gaussian, indicating no substantial velocity substructure. As previously noted for other optically selected clusters at redshifts of z>~0.5, a comparison between the X-ray luminosity (LX) and the velocity dispersion (σ) of Cl 1324+3011 implies that this cluster is underluminous in X-rays by a factor of ~3-40 when compared with the LX-σ relation for local and moderate-redshift clusters. We also examine the morphologies of those cluster members that have available high angular resolution imaging with the Hubble Space Telescope (HST). There are 22 spectroscopically confirmed cluster members within the HST field of view. Twelve of these are visually classified as early-type (elliptical or S0) galaxies, implying an early-type fraction of 0.55+0.17-0.14 in this cluster. This fraction is a factor of ~1.5 lower than that observed in nearby rich clusters. Confirming previous cluster studies, the results for cluster Cl 1324+3011, combined with morphological studies of other massive clusters at redshifts of 0<=z<~1, suggest that the galaxy population in massive clusters is strongly evolving with redshift. This evolution implies that early-type galaxies are forming out of the excess of late-type (spiral, irregular, and peculiar) galaxies over the ~7 Gyr timescale.

Assembly and Transfer of Iron–Sulfur Clusters in the Plastid

PubMed Central

Lu, Yan

2018-01-01

Iron-Sulfur (Fe-S) clusters and proteins are essential to many growth and developmental processes. In plants, they exist in the plastids, mitochondria, cytosol, and nucleus. Six types of Fe-S clusters are found in the plastid: classic 2Fe-2S, NEET-type 2Fe-2S, Rieske-type 2Fe-2S, 3Fe-4S, 4Fe-4S, and siroheme 4Fe-4S. Classic, NEET-type, and Rieske-type 2Fe-2S clusters have the same 2Fe-2S core; similarly, common and siroheme 4Fe-4S clusters have the same 4Fe-4S core. Plastidial Fe-S clusters are assembled by the sulfur mobilization (SUF) pathway, which contains cysteine desulfurase (EC 2.8.1.7), sulfur transferase (EC 2.8.1.3), Fe-S scaffold complex, and Fe-S carrier proteins. The plastidial cysteine desulfurase-sulfur transferase-Fe-S-scaffold complex system is responsible for de novo assembly of all plastidial Fe-S clusters. However, different types of Fe-S clusters are transferred to recipient proteins via respective Fe-S carrier proteins. This review focuses on recent discoveries on the molecular functions of different assembly and transfer factors involved in the plastidial SUF pathway. It also discusses potential points for regulation of the SUF pathway, relationships among the plastidial, mitochondrial, and cytosolic Fe-S assembly and transfer pathways, as well as several open questions about the carrier proteins for Rieske-type 2Fe-2S, NEET-type 2Fe-2S, and 3F-4S clusters. PMID:29662496

Cluster-cluster clustering

NASA Technical Reports Server (NTRS)

Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C. S.

1985-01-01

The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales.

Galaxy clusters in the cosmic web

NASA Astrophysics Data System (ADS)

Acebrón, A.; Durret, F.; Martinet, N.; Adami, C.; Guennou, L.

2014-12-01

Simulations of large scale structure formation in the universe predict that matter is essentially distributed along filaments at the intersection of which lie galaxy clusters. We have analysed 9 clusters in the redshift range 0.4clusters. Based on colour-magnitude diagrams, we have selected the galaxies likely to be in the cluster redshift range and studied their spatial distribution. We detect a number of structures and filaments around several clusters, proving that colour-magnitude diagrams are a reliable method to detect filaments around galaxy clusters. Since this method excludes blue (spiral) galaxies at the cluster redshift, we also apply the LePhare software to compute photometric redshifts from BVRIZ images to select galaxy cluster members and study their spatial distribution. We then find that, if only galaxies classified as early-type by LePhare are considered, we obtain the same distribution than with a red sequence selection, while taking into account late-type galaxies just pollutes the background level and deteriorates our detections. The photometric redshift based method therefore does not provide any additional information.

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.

A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas

PubMed Central

Radovich, Milan; Solzak, Jeffrey P; Hancock, Bradley A; Conces, Madison L; Atale, Rutuja; Porter, Ryan F; Zhu, Jin; Glasscock, Jarret; Kesler, Kenneth A; Badve, Sunil S; Schneider, Bryan P; Loehrer, Patrick J

2016-01-01

Background: Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing. Methods: The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used. Results: Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. A substantial differentiator was a large microRNA cluster on chr19q13.42 that was significantly overexpressed in all A and AB tumours and whose expression was virtually absent in the other thymomas and normal tissues. Overexpression of this microRNA cluster activates the PI3K/AKT/mTOR pathway. Treatment of a thymoma AB cell line with a panel of PI3K/AKT/mTOR inhibitors resulted in marked reduction of cell viability. Conclusions: A large microRNA cluster on chr19q13.42 is a transcriptional hallmark of type A and AB thymomas. Furthermore, this cluster activates the PI3K pathway, suggesting the possible exploration of PI3K inhibitors in patients with these subtypes of tumour. This work has led to the initiation of a phase II clinical trial of PI3K inhibition in relapsed or refractory thymomas (http://clinicaltrials.gov/ct2/show/NCT02220855). PMID:26766736

Selenium as a Structural Surrogate of Sulfur: Template-Assisted Assembly of Five Types of Tungsten-Iron-Sulfur/Selenium Clusters and the Structural Fate of Chalcogenide Reactants

PubMed Central

Zheng, Bo; Chen, Xu-Dong; Zheng, Shao-Liang; Holm, R. H.

2012-01-01

Syntheses of five types of tungsten-iron-sulfur/selenium clusters–incomplete cubanes, single cubanes, edge-bridged double cubanes (EBDCs), PN-type clusters, and double-cuboidal clusters–have been devised based on the concept of template-assisted assembly. The template reactant is six-coordinate [(Tp*)WVIS3]1−, which in the assembly systems organizes FeII,III and sulfide/selenide into cuboidal [(Tp*)WFe2S3] or cubane [(Tp*)WFe3S3Q] units. With appropriate terminal iron ligation, these units are capable of independent existence or may be transformed into higher nuclearity species. Selenide is used as a surrogate for sulfide in cluster assembly in order to determine by X-ray structures the position occupied by an external chalcogenide nucleophile or an internal chalcogenide atom in product clusters. Specific incorporation of selenide is demonstrated by formation of [WFe3S3Se]2+,3+ cubane cores. Reductive dimerization of the cubane leads to the EBDC core [W2Fe6S6Se2]2+ containing μ4-Se sites. Reaction of these species with HSe− affords the PN-type cores [W2Fe6S6Se3]1+ in which selenide occupies μ6-Se and μ2-Se sites. Reaction of [(Tp*)WS3]1−, FeCl2, and Na2Se results in the double cuboidal [W2Fe4S6Se3]2+,0 core with μ2-Se and μ4-Se bridges. It is highly probable that in analogous sulfide-only assembly systems, external and internal sulfide reactants occupy corresponding positions in cluster products. The results further demonstrate the viability of template-assisted cluster synthesis inasmuch as the reduced (Tp*)WS3 unit is present in all clusters. Structures, zero-field Mössbauer data, and redox potentials are presented for all cluster types. (Tp* = tris(pyrazolyl)hydroborate(1−)) PMID:22424175

A cluster of three cases of botulism due to Clostridium baratii type F, France, August 2015.

PubMed

Tréhard, Hélène; Poujol, Isabelle; Mazuet, Christelle; Blanc, Quentin; Gillet, Yves; Rossignol, Frédérique; Popoff, Michel-Robert; Jourdan Da Silva, Nathalie

2016-01-01

A cluster of three cases of food-borne botulism due to Clostridium baratii type F occurred in France in August 2015. All cases required respiratory assistance. Consumption of a Bolognese sauce at the same restaurant was the likely source of contamination. Clostridium baratii was isolated both from stool specimens from the three patients and ground meat used to prepare the sauce. This is the second episode reported in France caused by this rare pathogen.

STELLAR POPULATIONS AND EVOLUTION OF EARLY-TYPE CLUSTER GALAXIES: CONSTRAINTS FROM OPTICAL IMAGING AND SPECTROSCOPY OF z = 0.5-0.9 GALAXY CLUSTERS

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

Jorgensen, Inger; Chiboucas, Kristin, E-mail: ijorgensen@gemini.edu, E-mail: kchiboucas@gemini.edu

2013-03-15

indices and recent stellar population models from Thomas et al., we find that MS0451.6-0305 has a mean metallicity [M/H] approximately 0.2 dex below that of the other clusters and our low-redshift sample. We confirm our previous result that RXJ0152.7-1357 has a mean abundance ratio [{alpha}/Fe] approximately 0.3 dex higher than that of the other clusters. The differences in [M/H] and [{alpha}/Fe] between the high-redshift clusters and the low-redshift sample are inconsistent with a passive evolution scenario for early-type cluster galaxies over the redshift interval studied. Low-level star formation may be able to bring the metallicity of MS0451.6-0305 in agreement with the low-redshift sample, while we speculate whether galaxy mergers can lead to sufficiently large changes in the abundance ratios for the RXJ0152.7-1357 galaxies to allow them to reach the low-redshift sample values in the time available.« less

Genetic diversity of K-antigen gene clusters of Escherichia coli and their molecular typing using a suspension array.

PubMed

Yang, Shuang; Xi, Daoyi; Jing, Fuyi; Kong, Deju; Wu, Junli; Feng, Lu; Cao, Boyang; Wang, Lei

2018-04-01

Capsular polysaccharides (CPSs), or K-antigens, are the major surface antigens of Escherichia coli. More than 80 serologically unique K-antigens are classified into 4 groups (Groups 1-4) of capsules. Groups 1 and 4 contain the Wzy-dependent polymerization pathway and the gene clusters are in the order galF to gnd; Groups 2 and 3 contain the ABC-transporter-dependent pathway and the gene clusters consist of 3 regions, regions 1, 2 and 3. Little is known about the variations among the gene clusters. In this study, 9 serotypes of K-antigen gene clusters (K2ab, K11, K20, K24, K38, K84, K92, K96, and K102) were sequenced and correlated with their CPS chemical structures. On the basis of sequence data, a K-antigen-specific suspension array that detects 10 distinct CPSs, including the above 9 CPSs plus K30, was developed. This is the first report to catalog the genetic features of E. coli K-antigen variations and to develop a suspension array for their molecular typing. The method has a number of advantages over traditional bacteriophage and serum agglutination methods and lays the foundation for straightforward identification and detection of additional K-antigens in the future.

uvbyβ photometry of early type open cluster and field stars

NASA Astrophysics Data System (ADS)

Handler, G.

2011-04-01

Context. The β Cephei stars and slowly pulsating B (SPB) stars are massive main sequence variables. The strength of their pulsational driving strongly depends on the opacity of iron-group elements. As many of those stars naturally occur in young open clusters, whose metallicities can be determined in several fundamental ways, it is logical to study the incidence of pulsation in several young open clusters. Aims: To provide the foundation for such an investigation, Strömgren-Crawford uvbyβ photometry of open cluster target stars was carried out to determine effective temperatures, luminosities, and therefore cluster memberships. Methods: In the course of three observing runs, uvbyβ photometry for 168 target stars was acquired and transformed into the standard system by measurements of 117 standard stars. The list of target stars also included some known cluster and field β Cephei stars, as well as β Cephei and SPB candidates that are targets of the asteroseismic part of the Kepler satellite mission. Results: The uvbyβ photometric results are presented. The data are shown to be on the standard system, and the properties of the target stars are discussed: 140 of these are indeed OB stars, a total of 101 targets lie within the β Cephei and/or SPB star instability strips, and each investigated cluster contains such potential pulsators. Conclusions: These measurements will be taken advantage of in a number of subsequent publications. Based on measurements obtained at McDonald Observatory of the University of Texas at Austin.Tables 3-6 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/528/A148

Antibiotic Resistance and Single-Nucleotide Polymorphism Cluster Grouping Type in a Multinational Sample of Resistant Mycobacterium tuberculosis Isolates▿

PubMed Central

Brimacombe, M.; Hazbon, M.; Motiwala, A. S.; Alland, D.

2007-01-01

A single-nucleotide polymorphism-based cluster grouping (SCG) classification system for Mycobacterium tuberculosis was used to examine antibiotic resistance type and resistance mutations in relationship to specific evolutionary lineages. Drug resistance and resistance mutations were seen across all SCGs. SCG-2 had higher proportions of katG codon 315 mutations and resistance to four drugs. PMID:17846140

Studies of the Virgo Cluster. II - A catalog of 2096 galaxies in the Virgo Cluster area. V - Luminosity functions of Virgo Cluster galaxies

NASA Technical Reports Server (NTRS)

Binggeli, B.; Tammann, G. A.; Sandage, A.

1985-01-01

The present catalog of 2096 galaxies within an area of about 140 sq deg approximately centered on the Virgo cluster should be an essentially complete listing of all certain and possible cluster members, independent of morphological type. Cluster membership is essentially decided by galaxy morphology; for giants and the rare class of high surface brightness dwarfs, membership rests on velocity data. While 1277 of the catalog entries are considered members of the Virgo cluster, 574 are possible members and 245 appear to be background Zwicky galaxies. Major-to-minor axis ratios are given for all galaxies brighter than B(T) = 18, as well as for many fainter ones.

Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci.

PubMed

Zheng, Po-Xing; Chan, Yuen-Chi; Chiou, Chien-Shun; Chiang-Ni, Chuan; Wang, Shu-Ying; Tsai, Pei-Jane; Chuang, Woei-Jer; Lin, Yee-Shin; Liu, Ching-Chuan; Wu, Jiunn-Jong

2015-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas) and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson's index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.

Properties of highly clustered networks

NASA Astrophysics Data System (ADS)

Newman, M. E.

2003-08-01

We propose and solve exactly a model of a network that has both a tunable degree distribution and a tunable clustering coefficient. Among other things, our results indicate that increased clustering leads to a decrease in the size of the giant component of the network. We also study susceptible/infective/recovered type epidemic processes within the model and find that clustering decreases the size of epidemics, but also decreases the epidemic threshold, making it easier for diseases to spread. In addition, clustering causes epidemics to saturate sooner, meaning that they infect a near-maximal fraction of the network for quite low transmission rates.

Open clusters in Auriga OB2

NASA Astrophysics Data System (ADS)

Marco, Amparo; Negueruela, Ignacio

2016-06-01

We study the area around the H II region Sh 2-234, including the young open cluster Stock 8, to investigate the extent and definition of the association Aur OB2 and the possible role of triggering in massive cluster formation. We obtained Strömgren and J, H, KS photometry for Stock 8 and Strömgren photometry for two other cluster candidates in the area, which we confirm as young open clusters and name Alicante 11 and Alicante 12. We took spectroscopy of ˜33 early-type stars in the area, including the brightest cluster members. We calculate a common distance of 2.80^{+0.27}_{-0.24} kpc for the three open clusters and surrounding association. We derive an age 4-6 Ma for Stock 8, and do not find a significantly different age for the other clusters or the association. The star LS V +34°23, with spectral type O8 II(f), is likely the main source of ionization of Sh 2-234. We observe an important population of pre-main-sequence stars, some of them with discs, associated with the B-type members lying on the main sequence. We interpret the region as an area of recent star formation with some residual and very localized ongoing star formation. We do not find evidence for sequential star formation on a large scale. The classical definition of Aur OB2 has to be reconsidered, because its two main open clusters, Stock 8 and NGC 1893, are not at the same distance. Stock 8 is probably located in the Perseus arm, but other nearby H II regions whose distances also place them in this arm show quite different distances and radial velocities and, therefore, are not connected.

GENERAL: Teleportation of a Bipartite Entangled Coherent State via a Four-Partite Cluster-Type Entangled State

NASA Astrophysics Data System (ADS)

Chen, Hui-Na; Liu, Jin-Ming

2009-10-01

We present an optical scheme to almost completely teleport a bipartite entangled coherent state using a four-partite cluster-type entangled coherent state as quantum channel. The scheme is based on optical elements such as beam splitters, phase shifters, and photon detectors. We also obtain the average fidelity of the teleportation process. It is shown that the average fidelity is quite close to unity if the mean photon number of the coherent state is not too small.

Subspace K-means clustering.

PubMed

Timmerman, Marieke E; Ceulemans, Eva; De Roover, Kim; Van Leeuwen, Karla

2013-12-01

To achieve an insightful clustering of multivariate data, we propose subspace K-means. Its central idea is to model the centroids and cluster residuals in reduced spaces, which allows for dealing with a wide range of cluster types and yields rich interpretations of the clusters. We review the existing related clustering methods, including deterministic, stochastic, and unsupervised learning approaches. To evaluate subspace K-means, we performed a comparative simulation study, in which we manipulated the overlap of subspaces, the between-cluster variance, and the error variance. The study shows that the subspace K-means algorithm is sensitive to local minima but that the problem can be reasonably dealt with by using partitions of various cluster procedures as a starting point for the algorithm. Subspace K-means performs very well in recovering the true clustering across all conditions considered and appears to be superior to its competitor methods: K-means, reduced K-means, factorial K-means, mixtures of factor analyzers (MFA), and MCLUST. The best competitor method, MFA, showed a performance similar to that of subspace K-means in easy conditions but deteriorated in more difficult ones. Using data from a study on parental behavior, we show that subspace K-means analysis provides a rich insight into the cluster characteristics, in terms of both the relative positions of the clusters (via the centroids) and the shape of the clusters (via the within-cluster residuals).

Radiation-induced segregation and precipitation behaviours around cascade clusters under electron irradiation.

PubMed

Sueishi, Yuichiro; Sakaguchi, Norihito; Shibayama, Tamaki; Kinoshita, Hiroshi; Takahashi, Heishichiro

2003-01-01

We have investigated the formation of cascade clusters and structural changes in them by means of electron irradiation following ion irradiation in an austenitic stainless steel. Almost all of the cascade clusters, which were introduced by the ion irradiation, grew to form interstitial-type dislocation loops or vacancy-type stacking fault tetrahedra after electron irradiation at 623 K, whereas a few of the dot-type clusters remained in the matrix. It was possible to recognize the concentration of Ni and Si by radiation-induced segregation around the dot-type clusters. After electron irradiation at 773 K, we found that some cascade clusters became precipitates (delta-Ni2Si) due to radiation-induced precipitation. This suggests that the cascade clusters could directly become precipitation sites during irradiation.

Re-estimating sample size in cluster randomised trials with active recruitment within clusters.

PubMed

van Schie, S; Moerbeek, M

2014-08-30

Often only a limited number of clusters can be obtained in cluster randomised trials, although many potential participants can be recruited within each cluster. Thus, active recruitment is feasible within the clusters. To obtain an efficient sample size in a cluster randomised trial, the cluster level and individual level variance should be known before the study starts, but this is often not the case. We suggest using an internal pilot study design to address this problem of unknown variances. A pilot can be useful to re-estimate the variances and re-calculate the sample size during the trial. Using simulated data, it is shown that an initially low or high power can be adjusted using an internal pilot with the type I error rate remaining within an acceptable range. The intracluster correlation coefficient can be re-estimated with more precision, which has a positive effect on the sample size. We conclude that an internal pilot study design may be used if active recruitment is feasible within a limited number of clusters. Copyright © 2014 John Wiley & Sons, Ltd.

Creating Quasi Two-Dimensional Cluster-Assembled Materials through Self-Assembly of a Janus Polyoxometalate-Silsesquioxane Co-Cluster.

PubMed

Wu, Han; Zhang, Yu-Qi; Hu, Min-Biao; Ren, Li-Jun; Lin, Yue; Wang, Wei

2017-05-30

Clusters are an important class of nanoscale molecules or superatoms that exhibit an amazing diversity in structure, chemical composition, shape, and functionality. Assembling two types of clusters is creating emerging cluster-assembled materials (CAMs). In this paper, we report an effective approach to produce quasi two-dimensional (2D) CAMs of two types of spherelike clusters, polyhedral oligomeric silsesquioxanes (POSS), and polyoxometalates (POM). To avoid macrophase separation between the two clusters, they are covalently linked to form a POM-POSS cocluster with Janus characteristics and a dumbbell shape. This Janus characteristics enables the cocluster to self-assemble into diverse nanoaggregates, as conventional amphiphilic molecules and macromolecules do, in selective solvents. In our study, we obtained micelles, vesicles, nanosheets, and nanoribbons by tuning the n-hexane content in mixed solvents of acetone and n-hexane. Ordered packing of clusters in the nanosheets and nanoribbons were directly visualized using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) technique. We infer that the increase of packing order results in the vesicle-to-sheet transition and the change in packing mode causes the sheet-to-ribbon transitions. Our findings have verified the effectivity of creating quasi 2D cluster-assembled materials though the cocluster self-assembly as a new approach to produce novel CAMs.

Sexual Partnership Types as Determinant of HIV Risk in South African MSM: An Event-Level Cluster Analysis

PubMed Central

Sandfort, Theo; Yi, Huso; Knox, Justin; Reddy, Vasu

2012-01-01

While individual determinants of HIV risk among MSM have been widely studied, there is limited understanding of how relational characteristics determine sexual risk. Based on data collected among 300 South African men who have sex with men (MSM) and using cluster analysis, this study developed a typology of four partnership types: the “Race-Economic Similar,” “Age-Race-Economic Discordant,” “Non-regular Neighbourhood,” and “Familiar” partnership types. Support for the meaningfulness of these types was found through associations of these partnership types with participant characteristics and characteristics of the last anal sex event. Furthermore, in a multivariate analysis, only partnership type independently predicted whether the last anal sex event was unprotected. Findings of the study illustrate the importance of taking into account the relational context in understanding unprotected sexual practices and present ways to target intervention efforts as well as identify relationship specific determinants of unprotected sex. PMID:22956229

Vector dissimilarity and clustering.

PubMed

Lefkovitch, L P

1991-04-01

Based on the description of objects by m attributes, an m-element vector dissimilarity function is defined that, unlike scalar functions, retains the distinction among attributes. This function, which satisfies the conditions for a metric, allows the definition of betweenness, which can then be used for clustering. Applications to the subset-generation phase of conditional clustering and to nearest-neighbor-type algorithms are described.

Real & Simulated IFU Observations of Low-Mass Early-Type Galaxies: Environmental Influence Probed for Cluster Galaxies

NASA Astrophysics Data System (ADS)

Sybilska, Agnieszka; Łokas, Ewa Luiza; Fouquet, Sylvain

2017-03-01

We combine high-quality IFU data with a new set of numerical simulations to study low-mass early type galaxies (dEs) in dense environments. Our earlier study of dEs in the Virgo cluster has produced the first large-scale maps of kinematic and stellar population properties of dEs in those environments (Ryś et al. 2013, 2014, 2015). A quantitative discrimination between various (trans)formation processes proposed for these objects is, however, a complex issue, requiring a priori assumptions about the progenitors of galaxies we observe and study today. To bridge this gap between observations and theoretical predictions, we use the expertise gained in the IFU data analysis to look ``through the eye of SAURON'' at our new suite of high-resolution N-body simulations of dEs in the Virgo cluster. Mimicking the observers perspective as closely as possible, we can also indicate the existing instrumental and viewer limitations regarding what we are/are not able to detect as observers.

Photospheric carbon and oxygen abundances of F-G type stars in the Pleiades cluster*

NASA Astrophysics Data System (ADS)

Takeda, Yoichi; Hashimoto, Osamu; Honda, Satoshi

2017-02-01

In order to investigate the carbon-to-oxygen ratio of the young open cluster M 45 (Pleiades), the C and O abundances of 32 selected F-G type dwarfs (in the effective temperature range of Teff ˜ 5800-7600 K and projected rotational velocity range of vesin i ˜ 10-110 km s-1) belonging to this cluster were determined by applying the synthetic spectrum-fitting technique to C i 5380 and O i 6156-8 lines. The non-local thermodynamical equilibrium corrections for these C i and O i lines were found to be practically negligible (less than a few hundredths dex).The resulting C and O abundances (along with the Fe abundance) turned out nearly uniform without any systematic dependence upon Teff or vesin i. We found, however, in spite of almost solar Fe abundance ([Fe/H] ˜ 0), carbon turned out to be slightly subsolar ([C/H] ˜ -0.1) while that of oxygen was slightly supersolar ([O/H] ˜ +0.1). This leads to a conclusion that the [C/O] ratio was moderately subsolar (˜ -0.2) in the primordial gas from which these Pleiades stars were formed ˜ 120-130 Myr ago. Interestingly, similarly young B-type stars are reported to show just the same result ([C/O] ˜ -0.2), while rather aged (˜ 1-10 Gyr) field F-G stars of near-solar metallicity yield almost the solar value ([C/O] ˜ 0) on average. Such a difference in the C/O ratio between two star groups of distinctly different ages may be explained as a consequence of the orbit migration mechanism which Galactic stars may undergo over a long time.

Rare human leukocyte antigen genotype in two siblings with type 1 diabetes in a Japanese family clustered with type 1 diabetes.

PubMed

Ina, Yujiro; Kawabata, Yumiko; Sakamoto, Ryuichi; Sekiguchi, Naotaka; Ikegami, Hiroshi

2017-11-01

Multiplex families with type 1 diabetes are important for identification of rare variants that cannot be identified in case-control association studies. The very low incidence of type 1 diabetes in the Japanese population, however, makes identification of such families difficult. We identified a Japanese family in which three members developed type 1 diabetes, and studied the genotype of the human leukocyte antigen. All three members with type 1 diabetes had the DRB1*08:02-DQB1*03:02 haplotype, which is specific to the Asian population and strongly susceptible for type 1 diabetes. In particular, a proband and his sister had the same genotype, DRB1*08:02-DQB1*03:02/DRB1*08:02-DQB1*03:02, which is extremely rare even in the Japanese population. Both parents also had DRB1*08:02-DQB1*03:02, but in combination with different human leukocyte antigen haplotypes. Weakly susceptible DRB1*13:02-DQB1*06:04 was present in the affected mother, and resistant DRB1*15:01-DQB1*06:02 in the unaffected father. These data suggest DRB1*08:02-DQB1*03:02 to be a contributing factor for familial clustering of type 1 diabetes in this family. © 2017 The Authors. Journal of Diabetes Investigation published by Asian Association for the Study of Diabetes (AASD) and John Wiley & Sons Australia, Ltd.

An investigation of war trauma types, symptom clusters, and risk-factors associated with post-traumatic stress disorder: where does gender fit?

PubMed

Farhood, Laila; Fares, Souha; Hamady, Carmen

2018-05-25

The female-male ratio in the prevalence of post-traumatic stress disorder (PTSD) is approximately 2:1. Gender differences in experienced trauma types, PTSD symptom clusters, and PTSD risk factors are unclear. We aimed to address this gap using a cross-sectional design. A sample of 991 civilians (522 women, 469 men) from South Lebanon was randomly selected in 2007, after the 2006 war. Trauma types were grouped into disaster and accident, loss, chronic disease, non-malignant disease, and violence. PTSD symptom clusters involved re-experiencing, avoidance, negative cognitions and mood, and arousal. These were assessed using parts I and IV of the Arabic version of the Harvard Trauma Questionnaire (HTQ). Risk factors were assessed using data from a social support and life events questionnaire in multiple regression models. Females were twice as likely as males to score above PTSD threshold (24.3 vs. 10.4%, p ˂ 0.001). Total scores on all trauma types were similar across genders. Females scored higher on all symptom clusters (p < 0.001). Social support, social life events, witnessed traumas, and domestic violence significantly were associated with PTSD in both genders. Social support, social life events, witnessed traumas and domestic violence were significantly associated with PTSD in both genders. Conversely, gender difference in experienced traumas was not statistically significant. These findings accentuate the need to re-consider the role of gender in the assessment and treatment of PTSD.

The evolution of early-type galaxies in nearby clusters: breaking the age-metallicity degeneracy with Spitzer IRS Blue Peak-Up Imaging

NASA Astrophysics Data System (ADS)

Bressan, Alessandro; Buson, Lucio; Clemens, Marcel; Danese, Luigi; Granato, Gian Luigi; Panuzzo, Pasquale; Rampazzo, Roberto; Silva, Laura; Valdes, Jose Ramon

2005-06-01

We have shown with Cycle 1 observations that Spitzer has the capability of disentangling age and metallicity in old stellar populations. By looking to the broad emission feature left by dust enshrouded asymptotic giant branch stars above 9.7 microns, Spitzer IRS can provide direct evidence that the colour- magnitude relation of Virgo ellipticals is mainly driven by metallicity. However, with the IRS spectrograph we can only probe the bright tail of the colour-magnitude relation, and only in the nearest cluster. We propose to use IRS Blue Peak-Up, the only Spitzer band that looks directly in the core of that spectral feature, to reach fainter galaxies. We will perform a thorough investigation of early type galaxies along the colour-magnitude relation in Virgo and in Coma clusters. These observations, when coupled with already existing IRAC and Optical-NIR observations, will allow a) an unbiased census of the stellar populations in cluster early type galaxies; b) an estimate of the AGB material recycled into the ISM in these systems; c) a direct check of the universality of the colour- magnitude relation on a wide range of magnitudes; d) a spatial study of the stellar populations within the galaxies, e.g. investigating differences between bulge and disk populations within S0; e) the most secure reference frame with which to compare the evolution of early type galaxies in other environments (groups and field).

STAR FORMATION AND SUPERCLUSTER ENVIRONMENT OF 107 NEARBY GALAXY CLUSTERS

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

Cohen, Seth A.; Hickox, Ryan C.; Wegner, Gary A.

We analyze the relationship between star formation (SF), substructure, and supercluster environment in a sample of 107 nearby galaxy clusters using data from the Sloan Digital Sky Survey. Previous works have investigated the relationships between SF and cluster substructure, and cluster substructure and supercluster environment, but definitive conclusions relating all three of these variables has remained elusive. We find an inverse relationship between cluster SF fraction ( f {sub SF}) and supercluster environment density, calculated using the Galaxy luminosity density field at a smoothing length of 8 h {sup −1} Mpc (D8). The slope of f {sub SF} versus D8more » is −0.008 ± 0.002. The f {sub SF} of clusters located in low-density large-scale environments, 0.244 ± 0.011, is higher than for clusters located in high-density supercluster cores, 0.202 ± 0.014. We also divide superclusters, according to their morphology, into filament- and spider-type systems. The inverse relationship between cluster f {sub SF} and large-scale density is dominated by filament- rather than spider-type superclusters. In high-density cores of superclusters, we find a higher f {sub SF} in spider-type superclusters, 0.229 ± 0.016, than in filament-type superclusters, 0.166 ± 0.019. Using principal component analysis, we confirm these results and the direct correlation between cluster substructure and SF. These results indicate that cluster SF is affected by both the dynamical age of the cluster (younger systems exhibit higher amounts of SF); the large-scale density of the supercluster environment (high-density core regions exhibit lower amounts of SF); and supercluster morphology (spider-type superclusters exhibit higher amounts of SF at high densities).« less

MALDI-TOF typing highlights geographical and fluconazole resistance clusters in Candida glabrata.

PubMed

Dhieb, C; Normand, A C; Al-Yasiri, M; Chaker, E; El Euch, D; Vranckx, K; Hendrickx, M; Sadfi, N; Piarroux, R; Ranque, S

2015-06-01

Utilizing matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra for Candida glabrata typing would be a cost-effective and easy-to-use alternative to classical DNA-based typing methods. This study aimed to use MALDI-TOF for the typing of C. glabrata clinical isolates from various geographical origins and test its capacity to differentiate between fluconazole-sensitive and -resistant strains.Both microsatellite length polymorphism (MLP) and MALDI-TOF mass spectra of 58 C. glabrata isolates originating from Marseilles (France) and Tunis (Tunisia) as well as collection strains from diverse geographic origins were analyzed. The same analysis was conducted on a subset of C. glabrata isolates that were either susceptible (MIC ≤ 8 mg/l) or resistant (MIC ≥ 64 mg/l) to fluconazole.According to the seminal results, both MALDI-TOF and MLP classifications could highlight C. glabrata population structures associated with either geographical dispersal barriers (p < 10(-5)) or the selection of antifungal drug resistance traits (<10(-5)).In conclusion, MALDI-TOF geographical clustering was congruent with MPL genotyping and highlighted a significant population genetic structure according to fluconazole susceptibility in C. glabrata. Furthermore, although MALDI-TOF and MLP resulted in distinct classifications, MALDI-TOF also classified the isolates with respect to their fluconazole susceptibility profile. Further prospective studies are required to evaluate the capacity of MALDI-TOF typing to investigate C. glabrata infection outbreaks and predict the antifungal susceptibility profile of clinical laboratory isolates. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Lightcurves and Period Changes for Type II Cepheids in the Globular Cluster M13 (Abstract)

NASA Astrophysics Data System (ADS)

Smith, H. A.; Anderson, M.; Osborn, W.; Layden, A.; Kopacki, G.; Pritzl, B.; Kelley, A.; McBride, K.; Alexander, M.; Kuehn, C.; Kilian, A.; King, E.; Carbajal, D.; Lusting, R.; De Lee, N.

2015-12-01

(Abstract only) B, V, and Cousins I-band light curves have been observed for the type II Cepheids V1, V2, and V6 in the globular cluster M13. These are relatively short period, BL Her-type Cepheids, with periods of 1.5, 5.1, and 2.1 days, respectively. Additional observations of V2 have been obtained from early photographic plates in the Yerkes Observatory archive. Long term period changes of these Cepheids have been determined by combining recent photometry with earlier observations that now extend back for more than a century. The observed period changes for V1, V2, and V6 are compared with the predictions of stellar evolution theory, under the assumption that the progenitors of the Cepheids were stars that at one time were on the blue horizontal branch.

Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci

PubMed Central

Zheng, Po-Xing; Chan, Yuen-Chi; Chiou, Chien-Shun; Chiang-Ni, Chuan; Wang, Shu-Ying; Tsai, Pei-Jane; Chuang, Woei-Jer; Lin, Yee-Shin; Liu, Ching-Chuan; Wu, Jiunn-Jong

2015-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas) and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson’s index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type. PMID:26710228

Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein

PubMed Central

Thompson, Michael C.; Wheatley, Nicole M.; Jorda, Julien; Sawaya, Michael R.; Gidaniyan, Soheil D.; Ahmed, Hoda; Yang, Zhongyu; McCarty, Krystal N.; Whitelegge, Julian P.; Yeates, Todd O.

2014-01-01

Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein, whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date. PMID:25102080

Arrangement of the Clostridium baratii F7 Toxin Gene Cluster with Identification of a σ Factor That Recognizes the Botulinum Toxin Gene Cluster Promoters

DOE PAGES

Dover, Nir; Barash, Jason R.; Burke, Julianne N.; ...

2014-05-22

Botulinum neurotoxin (BoNT) is the most poisonous substances known and its eight toxin types (A to H) are distinguished by the inability of polyclonal antibodies that neutralize one toxin type to neutralize any of the other seven toxin types. Infant botulism, an intestinal toxemia orphan disease, is the most common form of human botulism in the United States. It results from swallowed spores of Clostridium botulinum (or rarely, neurotoxigenic Clostridium butyricum or Clostridium baratii) that germinate and temporarily colonize the lumen of the large intestine, where, as vegetative cells, they produce botulinum toxin. Botulinum neurotoxin is encoded by the bontmore » gene that is part of a toxin gene cluster that includes several accessory genes. In this paper, we sequenced for the first time the complete botulinum neurotoxin gene cluster of nonproteolytic C. baratii type F7. Like the type E and the nonproteolytic type F6 botulinum toxin gene clusters, the C. baratii type F7 had an orfX toxin gene cluster that lacked the regulatory botR gene which is found in proteolytic C. botulinum strains and codes for an alternative σ factor. In the absence of botR, we identified a putative alternative regulatory gene located upstream of the C. baratii type F7 toxin gene cluster. This putative regulatory gene codes for a predicted σ factor that contains DNA-binding-domain homologues to the DNA-binding domains both of BotR and of other members of the TcdR-related group 5 of the σ 70 family that are involved in the regulation of toxin gene expression in clostridia. We showed that this TcdR-related protein in association with RNA polymerase core enzyme specifically binds to the C. baratii type F7 botulinum toxin gene cluster promoters. Finally, this TcdR-related protein may therefore be involved in regulating the expression of the genes of the botulinum toxin gene cluster in neurotoxigenic C. baratii.« less

Abell 1142 and the Missing Central Galaxy – A Cluster in Transition?

NASA Astrophysics Data System (ADS)

Jones, Alexander; Su, Yuanyuan; Buote, David; Forman, William; van Weeren, Reinout; Jones, Christine; Gastaldello, Fabio; Kraft, Ralph; Randall, Scott

2018-01-01

Two types of galaxy clusters exist: cool core (CC) clusters which exhibit centrally-peaked metallicity and X-ray emission and non-cool core (NCC) clusters, possessing comparably homogeneous metallicity and X-ray emission distributions. However, the origin of this dichotomy is still unknown. The current prevailing theories state that either there is a primordial entropy limit, above which a CC is unable to form, or that clusters can change type through major mergers and radiative cooling. Abell 1142 is a galaxy cluster that can provide a unique probe of the root of this cluster-type division. It is formed of two merging sub-clusters, each with its own brightest cluster galaxies (BCG). Its enriched X-ray centroid (possible CC remnant) lies between these two BCGs. We present the thermal and chemical distributions of this system using deep (180ks) XMM-Newton observations to shed light on the role of mergers in the evolution of galaxy clusters.

Hybrid Collaborative Learning for Classification and Clustering in Sensor Networks

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri L.; Sosnowski, Scott; Lane, Terran

2012-01-01

Traditionally, nodes in a sensor network simply collect data and then pass it on to a centralized node that archives, distributes, and possibly analyzes the data. However, analysis at the individual nodes could enable faster detection of anomalies or other interesting events as well as faster responses, such as sending out alerts or increasing the data collection rate. There is an additional opportunity for increased performance if learners at individual nodes can communicate with their neighbors. In previous work, methods were developed by which classification algorithms deployed at sensor nodes can communicate information about event labels to each other, building on prior work with co-training, self-training, and active learning. The idea of collaborative learning was extended to function for clustering algorithms as well, similar to ideas from penta-training and consensus clustering. However, collaboration between these learner types had not been explored. A new protocol was developed by which classifiers and clusterers can share key information about their observations and conclusions as they learn. This is an active collaboration in which learners of either type can query their neighbors for information that they then use to re-train or re-learn the concept they are studying. The protocol also supports broadcasts from the classifiers and clusterers to the rest of the network to announce new discoveries. Classifiers observe an event and assign it a label (type). Clusterers instead group observations into clusters without assigning them a label, and they collaborate in terms of pairwise constraints between two events [same-cluster (mustlink) or different-cluster (cannot-link)]. Fundamentally, these two learner types speak different languages. To bridge this gap, the new communication protocol provides four types of exchanges: hybrid queries for information, hybrid "broadcasts" of learned information, each specified for classifiers-to-clusterers, and clusterers

Block Ignition Inertial Confinement Fusion (ICF) with Condensed Matter Cluster Type Targets for p-B11 Powered Space Propulsion

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

Miley, George H.; Hora, H.; Badziak, J.

The use of laser-driven Inertial Confinement Fusion (ICF) for space propulsion has been the subject of several earlier conceptual design studies, (see: Orth, 1998; and other references therein). However, these studies were based on older ICF technology using either 'direct' or 'in-direct x-ray driven' type target irradiation. Important new directions have opened for laser ICF in recent years following the development of 'chirped' lasers capable of ultra short pulses with powers of TW up to few PW which leads to the concept of 'fast ignition (FI)' to achieve higher energy gains from target implosions. In a recent publication the authorsmore » showed that use of a modified type of FI, termed 'block ignition' (Miley et al., 2008), could meet many of the requirements anticipated (but not then available) by the designs of the Vehicle for Interplanetary Space Transport Applications (VISTA) ICF fusion propulsion ship (Orth, 2008) for deep space missions. Subsequently the first author devised and presented concepts for imbedding high density condensed matter 'clusters' of deuterium into the target to obtain ultra high local fusion reaction rates (Miley, 2008). Such rates are possible due to the high density of the clusters (over an order of magnitude above cryogenic deuterium). Once compressed by the implosion, the yet higher density gives an ultra high reaction rate over the cluster volume since the fusion rate is proportional to the square of the fuel density. Most recently, a new discovery discussed here indicates that the target matrix could be composed of B{sup 11} with proton clusters imbedded. This then makes p-B{sup 11} fusion practical, assuming all of the physics issues such as stability of the clusters during compression are resolved. Indeed, p-B{sup 11} power is ideal for fusion propulsion since it has a minimum of unwanted side products while giving most of the reaction energy to energetic alpha particles which can be directed into an exhaust (propulsion

In-depth discrimination of aerosol types using multiple clustering techniques over four locations in Indo-Gangetic plains

NASA Astrophysics Data System (ADS)

Bibi, Humera; Alam, Khan; Bibi, Samina

2016-11-01

Discrimination of aerosol types is essential over the Indo-Gangetic plain (IGP) because several aerosol types originate from different sources having different atmospheric impacts. In this paper, we analyzed a seasonal discrimination of aerosol types by multiple clustering techniques using AERosol RObotic NETwork (AERONET) datasets for the period 2007-2013 over Karachi, Lahore, Jaipur and Kanpur. We discriminated the aerosols into three major types; dust, biomass burning and urban/industrial. The discrimination was carried out by analyzing different aerosol optical properties such as Aerosol Optical Depth (AOD), Angstrom Exponent (AE), Extinction Angstrom Exponent (EAE), Abortion Angstrom Exponent (AAE), Single Scattering Albedo (SSA) and Real Refractive Index (RRI) and their interrelationship to investigate the dominant aerosol types and to examine the variation in their seasonal distribution. The results revealed that during summer and pre-monsoon, dust aerosols were dominant while during winter and post-monsoon prevailing aerosols were biomass burning and urban industrial, and the mixed type of aerosols were present in all seasons. These types of aerosol discriminated from AERONET were in good agreement with CALIPSO (the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation) measurement.

Multilocus microsatellite typing shows three different genetic clusters of Leishmania major in Iran.

PubMed

Mahnaz, Tashakori; Al-Jawabreh, Amer; Kuhls, Katrin; Schönian, Gabriele

2011-10-01

Ten polymorphic microsatellite markers were used to analyse 25 strains of Leishmania major collected from cutaneous leishmaniasis cases in different endemic areas in Iran. Nine of the markers were polymorphic, revealing 21 different genotypes. The data displayed significant microsatellite polymorphism with rare allelic heterozygosity. Bayesian statistic and distance based analyses identified three genetic clusters among the 25 strains analysed. Cluster I represented mainly strains isolated in the west and south-west of Iran, with the exception of four strains originating from central Iran. Cluster II comprised strains from the central part of Iran, and cluster III included only strains from north Iran. The geographical distribution of L. major in Iran was supported by comparing the microsatellite profiles of the 25 Iranian strains to those of 105 strains collected in 19 Asian and African countries. The Iranian clusters I and II were separated from three previously described populations comprising strains from Africa, the Middle East and Central Asia whereas cluster III grouped together with the Central Asian population. The considerable genetic variability of L. major might be related to the existence of different populations of Phlebotomus papatasi and/or to differences in reservoir host abundance in different parts of Iran. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Analysis of earthquake clustering and source spectra in the Salton Sea Geothermal Field

NASA Astrophysics Data System (ADS)

Cheng, Y.; Chen, X.

2015-12-01

The Salton Sea Geothermal field is located within the tectonic step-over between San Andreas Fault and Imperial Fault. Since the 1980s, geothermal energy exploration has resulted with step-like increase of microearthquake activities, which mirror the expansion of geothermal field. Distinguishing naturally occurred and induced seismicity, and their corresponding characteristics (e.g., energy release) is important for hazard assessment. Between 2008 and 2014, seismic data recorded by a local borehole array were provided public access from CalEnergy through SCEC data center; and the high quality local recording of over 7000 microearthquakes provides unique opportunity to sort out characteristics of induced versus natural activities. We obtain high-resolution earthquake location using improved S-wave picks, waveform cross-correlation and a new 3D velocity model. We then develop method to identify spatial-temporally isolated earthquake clusters. These clusters are classified into aftershock-type, swarm-type, and mixed-type (aftershock-like, with low skew, low magnitude and shorter duration), based on the relative timing of largest earthquakes and moment-release. The mixed-type clusters are mostly located at 3 - 4 km depth near injection well; while aftershock-type clusters and swarm-type clusters also occur further from injection well. By counting number of aftershocks within 1day following mainshock in each cluster, we find that the mixed-type clusters have much higher aftershock productivity compared with other types and historic M4 earthquakes. We analyze detailed spatial variation of 'b-value'. We find that the mixed-type clusters are mostly located within high b-value patches, while large (M>3) earthquakes and other types of clusters are located within low b-value patches. We are currently processing P and S-wave spectra to analyze the spatial-temporal correlation of earthquake stress parameter and seismicity characteristics. Preliminary results suggest that the

Mutation Clusters from Cancer Exome.

PubMed

Kakushadze, Zura; Yu, Willie

2017-08-15

We apply our statistically deterministic machine learning/clustering algorithm *K-means (recently developed in https://ssrn.com/abstract=2908286) to 10,656 published exome samples for 32 cancer types. A majority of cancer types exhibit a mutation clustering structure. Our results are in-sample stable. They are also out-of-sample stable when applied to 1389 published genome samples across 14 cancer types. In contrast, we find in- and out-of-sample instabilities in cancer signatures extracted from exome samples via nonnegative matrix factorization (NMF), a computationally-costly and non-deterministic method. Extracting stable mutation structures from exome data could have important implications for speed and cost, which are critical for early-stage cancer diagnostics, such as novel blood-test methods currently in development.

Mutation Clusters from Cancer Exome

PubMed Central

Kakushadze, Zura; Yu, Willie

2017-01-01

We apply our statistically deterministic machine learning/clustering algorithm *K-means (recently developed in https://ssrn.com/abstract=2908286) to 10,656 published exome samples for 32 cancer types. A majority of cancer types exhibit a mutation clustering structure. Our results are in-sample stable. They are also out-of-sample stable when applied to 1389 published genome samples across 14 cancer types. In contrast, we find in- and out-of-sample instabilities in cancer signatures extracted from exome samples via nonnegative matrix factorization (NMF), a computationally-costly and non-deterministic method. Extracting stable mutation structures from exome data could have important implications for speed and cost, which are critical for early-stage cancer diagnostics, such as novel blood-test methods currently in development. PMID:28809811

The Ellipticities of Cluster Early-type Galaxies from z ~ 1 to z ~ 0: No Evolution in the Overall Distribution of Bulge-to-Disk Ratios

NASA Astrophysics Data System (ADS)

Holden, B. P.; Franx, M.; Illingworth, G. D.; Postman, M.; van der Wel, A.; Kelson, D. D.; Blakeslee, J. P.; Ford, H.; Demarco, R.; Mei, S.

2009-03-01

We have compiled a sample of early-type cluster galaxies from 0 < z < 1.3 and measured the evolution of their ellipticity distributions. Our sample contains 487 galaxies in 17 z>0.3 clusters with high-quality space-based imaging and a comparable sample of 210 galaxies in 10 clusters at z < 0.05. We select early-type galaxies (elliptical and S0 galaxies) that fall within the cluster R 200, and which lie on the red-sequence in the magnitude range -19.3>MB > - 21, after correcting for luminosity evolution as measured by the fundamental plane. Our ellipticity measurements are made in a consistent manner over our whole sample. We perform extensive simulations to quantify the systematic and statistical errors, and find that it is crucial to use point-spread function (PSF)-corrected model fits; determinations of the ellipticity from Hubble Space Telescope image data that do not account for the PSF "blurring" are systematically and significantly biased to rounder ellipticities at redshifts z>0.3. We find that neither the median ellipticity, nor the shape of the ellipticity distribution of cluster early-type galaxies evolves with redshift from z ~ 0 to z>1 (i.e., over the last ~8 Gyr). The median ellipticity at z>0.3 is statistically identical with that at z < 0.05, being higher by only 0.01 ± 0.02 or 3 ± 6%, while the distribution of ellipticities at z>0.3 agrees with the shape of the z < 0.05 distribution at the 1-2% level (i.e., the probability that they are drawn from the same distribution is 98-99%). These results are strongly suggestive of an unchanging overall bulge-to-disk ratio distribution for cluster early-type galaxies over the last ~8 Gyr from z ~ 1 to z ~ 0. This result contrasts with that from visual classifications which show that the fraction of morphologically-selected disk-dominated early-type galaxies, or S0s, is significantly lower at z>0.4 than at z ~ 0. We find that the median disk-dominated early-type, or S0, galaxy has a somewhat higher

Galaxy properties in clusters. II. Backsplash galaxies

NASA Astrophysics Data System (ADS)

Muriel, H.; Coenda, V.

2014-04-01

Aims: We explore the properties of galaxies on the outskirts of clusters and their dependence on recent dynamical history in order to understand the real impact that the cluster core has on the evolution of galaxies. Methods: We analyse the properties of more than 1000 galaxies brighter than M0.1r = - 19.6 on the outskirts of 90 clusters (1 < r/rvir < 2) in the redshift range 0.05 < z < 0.10. Using the line of sight velocity of galaxies relative to the cluster's mean, we selected low and high velocity subsamples. Theoretical predictions indicate that a significant fraction of the first subsample should be backsplash galaxies, that is, objects that have already orbited near the cluster centre. A significant proportion of the sample of high relative velocity (HV) galaxies seems to be composed of infalling objects. Results: Our results suggest that, at fixed stellar mass, late-type galaxies in the low-velocity (LV) sample are systematically older, redder, and have formed fewer stars during the last 3 Gyrs than galaxies in the HV sample. This result is consistent with models that assume that the central regions of clusters are effective in quenching the star formation by means of processes such as ram pressure stripping or strangulation. At fixed stellar mass, LV galaxies show some evidence of having higher surface brightness and smaller size than HV galaxies. These results are consistent with the scenario where galaxies that have orbited the central regions of clusters are more likely to suffer tidal effects, producing loss of mass as well as a re-distribution of matter towards more compact configurations. Finally, we found a higher fraction of ET galaxies in the LV sample, supporting the idea that the central region of clusters of galaxies may contribute to the transformation of morphological types towards earlier types.

Deterministic Joint Remote Preparation of Arbitrary Four-Qubit Cluster-Type State Using EPR Pairs

NASA Astrophysics Data System (ADS)

Li, Wenqian; Chen, Hanwu; Liu, Zhihao

2017-02-01

Using four Einstein-Podolsky-Rosen (EPR) pairs as the pre-shared quantum channel, an economic and feasible scheme for deterministic joint remote preparation of the four-particle cluster-type state is presented. In the scheme, one of the senders performs a four-qubit projective measurement based on a set of ingeniously constructed vectors with real coefficients, while the other performs the bipartite projective measurements in terms of the imaginary coefficients. Followed with some appropriate unitary operations and controlled-NOT operations, the receiver can reconstruct the desired state. Compared with other analogous JRSP schemes, our scheme can not only reconstruct the original state (to be prepared remotely) with unit successful probability, but also ensure greater efficiency.

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.

Using Cluster Analysis to Examine Husband-Wife Decision Making

ERIC Educational Resources Information Center

Bonds-Raacke, Jennifer M.

2006-01-01

Cluster analysis has a rich history in many disciplines and although cluster analysis has been used in clinical psychology to identify types of disorders, its use in other areas of psychology has been less popular. The purpose of the current experiments was to use cluster analysis to investigate husband-wife decision making. Cluster analysis was…

THE NEXT GENERATION VIRGO CLUSTER SURVEY XVI: THE ANGULAR MOMENTUM OF DWARF EARLY-TYPE GALAXIES FROM GLOBULAR CLUSTER SATELLITES

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

Toloba, Elisa; Guhathakurta, Puragra; Li, Biao

2016-05-01

We analyze the kinematics of six Virgo cluster dwarf early-type galaxies (dEs) from their globular cluster (GC) systems. We present new Keck/DEIMOS spectroscopy for three of them and re-analyze the data found in the literature for the remaining three. We use two independent methods to estimate the rotation amplitude ( V {sub rot}) and velocity dispersion ( σ {sub GC}) of the GC systems and evaluate their statistical significance by simulating non-rotating GC systems with the same number of GC satellites and velocity uncertainties. Our measured kinematics agree with the published values for the three galaxies from the literature and,more » in all cases, some rotation is measured. However, our simulations show that the null hypothesis of being non-rotating GC systems cannot be ruled out. In the case of VCC 1861, the measured V {sub rot} and the simulations indicate that it is not rotating. In the case of VCC 1528, the null hypothesis can be marginally ruled out, and thus it might be rotating although further confirmation is needed. In our analysis, we find that, in general, the measured V {sub rot} tends to be overestimated and the measured σ {sub GC} tends to be underestimated by amounts that depend on the intrinsic V {sub rot}/ σ {sub GC}, the number of observed GCs ( N {sub GC}), and the velocity uncertainties. The bias is negligible when N {sub GC} ≳ 20. In those cases where a large N {sub GC} is not available, it is imperative to obtain data with small velocity uncertainties. For instance, errors of ≤2 km s{sup −1} lead to V {sub rot} < 10 km s{sup −1} for a system that is intrinsically not rotating.« less

Intra-cluster Globular Clusters in a Simulated Galaxy Cluster

NASA Astrophysics Data System (ADS)

Ramos-Almendares, Felipe; Abadi, Mario; Muriel, Hernán; Coenda, Valeria

2018-01-01

Using a cosmological dark matter simulation of a galaxy-cluster halo, we follow the temporal evolution of its globular cluster population. To mimic the red and blue globular cluster populations, we select at high redshift (z∼ 1) two sets of particles from individual galactic halos constrained by the fact that, at redshift z = 0, they have density profiles similar to observed ones. At redshift z = 0, approximately 60% of our selected globular clusters were removed from their original halos building up the intra-cluster globular cluster population, while the remaining 40% are still gravitationally bound to their original galactic halos. As the blue population is more extended than the red one, the intra-cluster globular cluster population is dominated by blue globular clusters, with a relative fraction that grows from 60% at redshift z = 0 up to 83% for redshift z∼ 2. In agreement with observational results for the Virgo galaxy cluster, the blue intra-cluster globular cluster population is more spatially extended than the red one, pointing to a tidally disrupted origin.

BioCluster: tool for identification and clustering of Enterobacteriaceae based on biochemical data.

PubMed

Abdullah, Ahmed; Sabbir Alam, S M; Sultana, Munawar; Hossain, M Anwar

2015-06-01

Presumptive identification of different Enterobacteriaceae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochemical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is labor-intensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and similarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface (GUI) tool named BioCluster. This tool was designed for automated clustering and identification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering (HC) and the Improved Hierarchical Clustering (IHC), a modified algorithm that was developed specifically for the clustering and identification of Enterobacteriaceae species. IHC takes into account the variability in result of 1-47 biochemical tests within this Enterobacteriaceae family. This tool also provides different options to optimize the clustering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that BioCluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http://microbialgen.du.ac.bd/biocluster/. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Subtyping Salmonella enterica serovar enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs).

PubMed

Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M; Barrangou, Rodolphe; Gerner-Smidt, Peter; Ribot, Efrain M; Knabel, Stephen J; Dudley, Edward G

2011-07-01

Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.

THE YOUNG OPEN CLUSTER BERKELEY 55

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

Negueruela, Ignacio; Marco, Amparo, E-mail: ignacio.negueruela@ua.es, E-mail: amparo.marco@ua.es

We present UBV photometry of the highly reddened and poorly studied open cluster Berkeley 55, revealing an important population of B-type stars and several evolved stars of high luminosity. Intermediate-resolution far-red spectra of several candidate members confirm the presence of one F-type supergiant and six late supergiants or bright giants. The brightest blue stars are mid-B giants. Spectroscopic and photometric analyses indicate an age 50 {+-} 10 Myr. The cluster is located at a distance d Almost-Equal-To 4 kpc, consistent with other tracers of the Perseus Arm in this direction. Berkeley 55 is thus a moderately young open cluster withmore » a sizable population of candidate red (super)giant members, which can provide valuable information about the evolution of intermediate-mass stars.« less

Cognitive Deficits in Executive Functions and Decision-Making Impairments Cluster Gambling Disorder Sub-types.

PubMed

Mallorquí-Bagué, Núria; Tolosa-Sola, Iris; Fernández-Aranda, Fernándo; Granero, Roser; Fagundo, Ana Beatriz; Lozano-Madrid, María; Mestre-Bach, Gemma; Gómez-Peña, Mónica; Aymamí, Neus; Borrás-González, Indira; Sánchez-González, Jessica; Baño, Marta; Del Pino-Gutiérrez, Amparo; Menchón, José M; Jiménez-Murcia, Susana

2018-03-01

To identify Gambling Disorder (GD) subtypes, in a population of men seeking treatment for GD, according to specific executive function domains (i.e., cognitive flexibility, inhibition and working memory as well as decision making) which are usually impaired in addictive behaviors. A total of 145 males ranging from 18 to 65 years diagnosed with GD were included in this study. All participants completed: (a) a set of questionnaires to assess psychopathological symptoms, personality and impulsivity traits, and (b) a battery of neuropsychological measures to test different executive functioning domains. Two clusters were identified based on the individual performance on the neuropsychological assessment. Cluster 1 [n = 106; labeled as Low Impaired Executive Function (LIEF)] was composed by patients with poor results in the neuropsychological assessment; cluster 2 patients [n = 46; labeled as High Impaired Executive Function (HIEF)] presented significantly higher deficits on the assessed domains and performed worse than the ones of LIEF cluster. Regarding the characterization of these two clusters, patients in cluster 2 were significantly older, unemployed and registered higher mean age of GD onset than patients in cluster 1. Additionally, patients in cluster 2 also obtained higher psychopathological symptoms, impulsivity (in both positive and negative urgency as well as sensation seeking) and some specific personality traits (higher harm avoidance as well as lower self-directedness and cooperativeness) than patients in cluster 1. The results of this study describe two different GD subtypes based on different cognitive domains (i.e., executive function performance). These two GD subtypes display different impulsivity and personality traits as well as clinical symptoms. The results provide new insight into the etiology and characterization of GD and have the potential to help improving current treatments.

Effects of Cluster Environment on Chemical Abundances in Virgo Cluster Spirals

NASA Astrophysics Data System (ADS)

Kennicutt, R. C.; Skillman, E. D.; Shields, G. A.; Zaritsky, D.

1995-12-01

We have obtained new chemical abundance measurements of HII regions in Virgo cluster spiral galaxies, in order to test whether the cluster environment has significantly influenced the gas-phase abundances and chemical evolution of spiral disks. The sample of 9 Virgo spirals covers a narrow range of morphological type (Sbc - Sc) but shows broad ranges in HI deficiencies and radii in the cluster. This allows us to compare the Virgo sample as a whole to field spirals, using a large sample from Zaritsky, Kennicutt, & Huchra, and to test for systematic trends with HI content and location within the cluster. The Virgo spirals show a wide dispersion in mean disk abundances and abundance gradients. Strongly HI deficient spirals closest to the cluster core show anomalously high oxygen abundances (by 0.3 to 0.5 dex), while outlying spirals with normal HI content show abundances similar to those of field spirals. The most HI depleted spirals also show weaker abundance gradients on average, but the formal significance of this trend is marginal. We find a strong correlation between mean abundance and HI/optical diameter ratio that is quite distinct from the behavior seen in field galaxies. This suggests that dynamical processes associated with the cluster environment are more important than cluster membership in determining the evolution of chemical abundances and stellar populations in spiral galaxies. Simple chemical evolution models are calculated to predict the magnitude of the abundance enhancement expected if ram-pressure stripping or curtailment of infall is responsible for the gas deficiencies. The increased abundances of the spirals in the cluster core may have significant effects on their use as cosmological standard candles.

Profiling Local Optima in K-Means Clustering: Developing a Diagnostic Technique

ERIC Educational Resources Information Center

Steinley, Douglas

2006-01-01

Using the cluster generation procedure proposed by D. Steinley and R. Henson (2005), the author investigated the performance of K-means clustering under the following scenarios: (a) different probabilities of cluster overlap; (b) different types of cluster overlap; (c) varying samples sizes, clusters, and dimensions; (d) different multivariate…

Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation.

PubMed

Tang, Ping-Han; Wu, Ten-Ming; Yen, Tsung-Wen; Lai, S K; Hsu, P J

2011-09-07

We perform isothermal Brownian-type molecular dynamics simulations to obtain the velocity autocorrelation function and its time Fourier-transformed power spectral density for the metallic cluster Ag(17)Cu(2). The temperature dependences of these dynamical quantities from T = 0 to 1500 K were examined and across this temperature range the cluster melting temperature T(m), which we define to be the principal maximum position of the specific heat is determined. The instantaneous normal mode analysis is then used to dissect the cluster dynamics by calculating the vibrational instantaneous normal mode density of states and hence its frequency integrated value I(j) which is an ensemble average of all vibrational projection operators for the jth atom in the cluster. In addition to comparing the results with simulation data, we look more closely at the entities I(j) of all atoms using the point group symmetry and diagnose their temperature variations. We find that I(j) exhibit features that may be used to deduce T(m), which turns out to agree very well with those inferred from the power spectral density and specific heat. © 2011 American Institute of Physics

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.

Explanation of temporal clustering of tsunami sources using the epidemic-type aftershock sequence model

USGS Publications Warehouse

Geist, Eric L.

2014-01-01

Temporal clustering of tsunami sources is examined in terms of a branching process model. It previously was observed that there are more short interevent times between consecutive tsunami sources than expected from a stationary Poisson process. The epidemic‐type aftershock sequence (ETAS) branching process model is fitted to tsunami catalog events, using the earthquake magnitude of the causative event from the Centennial and Global Centroid Moment Tensor (CMT) catalogs and tsunami sizes above a completeness level as a mark to indicate that a tsunami was generated. The ETAS parameters are estimated using the maximum‐likelihood method. The interevent distribution associated with the ETAS model provides a better fit to the data than the Poisson model or other temporal clustering models. When tsunamigenic conditions (magnitude threshold, submarine location, dip‐slip mechanism) are applied to the Global CMT catalog, ETAS parameters are obtained that are consistent with those estimated from the tsunami catalog. In particular, the dip‐slip condition appears to result in a near zero magnitude effect for triggered tsunami sources. The overall consistency between results from the tsunami catalog and that from the earthquake catalog under tsunamigenic conditions indicates that ETAS models based on seismicity can provide the structure for understanding patterns of tsunami source occurrence. The fractional rate of triggered tsunami sources on a global basis is approximately 14%.

Deterministic Joint Remote Preparation of a Four-Qubit Cluster-Type State via GHZ States

NASA Astrophysics Data System (ADS)

Wang, Hai-bin; Zhou, Xiao-Yan; An, Xing-xing; Cui, Meng-Meng; Fu, De-sheng

2016-08-01

A scheme for the deterministic joint remote preparation of a four-qubit cluster-type state using only two Greenberger-Horne-Zeilinger (GHZ) states as quantum channels is presented. In this scheme, the first sender performs a two-qubit projective measurement according to the real coefficient of the desired state. Then, the other sender utilizes the measurement result and the complex coefficient to perform another projective measurement. To obtain the desired state, the receiver applies appropriate unitary operations to his/her own two qubits and two CNOT operations to the two ancillary ones. Most interestingly, our scheme can achieve unit success probability, i.e., P s u c =1. Furthermore, comparison reveals that the efficiency is higher than that of most other analogous schemes.

Canonical PSO Based K-Means Clustering Approach for Real Datasets.

PubMed

Dey, Lopamudra; Chakraborty, Sanjay

2014-01-01

"Clustering" the significance and application of this technique is spread over various fields. Clustering is an unsupervised process in data mining, that is why the proper evaluation of the results and measuring the compactness and separability of the clusters are important issues. The procedure of evaluating the results of a clustering algorithm is known as cluster validity measure. Different types of indexes are used to solve different types of problems and indices selection depends on the kind of available data. This paper first proposes Canonical PSO based K-means clustering algorithm and also analyses some important clustering indices (intercluster, intracluster) and then evaluates the effects of those indices on real-time air pollution database, wholesale customer, wine, and vehicle datasets using typical K-means, Canonical PSO based K-means, simple PSO based K-means, DBSCAN, and Hierarchical clustering algorithms. This paper also describes the nature of the clusters and finally compares the performances of these clustering algorithms according to the validity assessment. It also defines which algorithm will be more desirable among all these algorithms to make proper compact clusters on this particular real life datasets. It actually deals with the behaviour of these clustering algorithms with respect to validation indexes and represents their results of evaluation in terms of mathematical and graphical forms.

Hybrid fuzzy cluster ensemble framework for tumor clustering from biomolecular data.

PubMed

Yu, Zhiwen; Chen, Hantao; You, Jane; Han, Guoqiang; Li, Le

2013-01-01

Cancer class discovery using biomolecular data is one of the most important tasks for cancer diagnosis and treatment. Tumor clustering from gene expression data provides a new way to perform cancer class discovery. Most of the existing research works adopt single-clustering algorithms to perform tumor clustering is from biomolecular data that lack robustness, stability, and accuracy. To further improve the performance of tumor clustering from biomolecular data, we introduce the fuzzy theory into the cluster ensemble framework for tumor clustering from biomolecular data, and propose four kinds of hybrid fuzzy cluster ensemble frameworks (HFCEF), named as HFCEF-I, HFCEF-II, HFCEF-III, and HFCEF-IV, respectively, to identify samples that belong to different types of cancers. The difference between HFCEF-I and HFCEF-II is that they adopt different ensemble generator approaches to generate a set of fuzzy matrices in the ensemble. Specifically, HFCEF-I applies the affinity propagation algorithm (AP) to perform clustering on the sample dimension and generates a set of fuzzy matrices in the ensemble based on the fuzzy membership function and base samples selected by AP. HFCEF-II adopts AP to perform clustering on the attribute dimension, generates a set of subspaces, and obtains a set of fuzzy matrices in the ensemble by performing fuzzy c-means on subspaces. Compared with HFCEF-I and HFCEF-II, HFCEF-III and HFCEF-IV consider the characteristics of HFCEF-I and HFCEF-II. HFCEF-III combines HFCEF-I and HFCEF-II in a serial way, while HFCEF-IV integrates HFCEF-I and HFCEF-II in a concurrent way. HFCEFs adopt suitable consensus functions, such as the fuzzy c-means algorithm or the normalized cut algorithm (Ncut), to summarize generated fuzzy matrices, and obtain the final results. The experiments on real data sets from UCI machine learning repository and cancer gene expression profiles illustrate that 1) the proposed hybrid fuzzy cluster ensemble frameworks work well on real

The outskirts of the Coma cluster

NASA Astrophysics Data System (ADS)

Gavazzi, Giuseppe

Evolved Coma-like clusters of galaxies are constituted of relaxed cores composed of ''old'' early-type galaxies, embedded in large-scale structures, mostly constituted of unevolved (late-type) systems. According to the hierarchical theory of cluster formation the central regions are being fed with unevolved, low-mass systems infalling from the surroundings that are gradually transformed into elliptical/S0 galaxies by tidal galaxy-galaxy and galaxy-cluster interactions, taking place at some boundary distance. The Coma cluster, the most studied of all local clusters, provides us with the ideal test-bed for such an evolutionary study because of the completeness of the photometric and kinematic information already at hands. The field of view of the planned GALEX observations is not big enough to include the boundary interface where most transformations processes are expected to take place, including the truncation of the current star formation. We propose to complete the outskirt of Coma with an additional corona of 11 GALEX imaging fields of 1500 sec exposure each, matching the deepness (UV_{AB}=23.5 mag) of the fields observed in guarantee time. Given the priority of the target, we also propose one optional Central pointing that includes one bright star marginally exceeding the detector brightness limit.

Clustering, cosmology and a new era of black hole demographics- II. The conditional luminosity functions of Type 2 and Type 1 active galactic nuclei

NASA Astrophysics Data System (ADS)

Ballantyne, D. R.

2017-01-01

The orientation-based unification model of active galactic nuclei (AGNs) posits that the principle difference between obscured (Type 2) and unobscured (Type 1) AGNs is the line of sight into the central engine. If this model is correct then there should be no difference in many of the properties of AGN host galaxies (e.g. the mass of the surrounding dark matter haloes). However, recent clustering analyses of Type 1 and Type 2 AGNs have provided some evidence for a difference in the halo mass, in conflict with the orientation-based unified model. In this work, a method to compute the conditional luminosity function (CLF) of Type 2 and Type 1 AGNs is presented. The CLF allows many fundamental halo properties to be computed as a function of AGN luminosity, which we apply to the question of the host halo masses of Type 1 and 2 AGNs. By making use of the total AGN CLF, the Type 1 X-ray luminosity function, and the luminosity-dependent Type 2 AGN fraction, the CLFs of Type 1 and 2 AGNs are calculated at z ≈ 0 and 0.9. At both z, there is no statistically significant difference in the mean halo mass of Type 2 and 1 AGNs at any luminosity. There is marginal evidence that Type 1 AGNs may have larger halo masses than Type 2s, which would be consistent with an evolutionary picture where quasars are initially obscured and then subsequently reveal themselves as Type 1s. As the Type 1 lifetime is longer, the host halo will increase somewhat in mass during the Type 1 phase. The CLF technique will be a powerful way to study the properties of many AGNs subsets (e.g. radio-loud, Compton-thick) as future wide-area X-ray and optical surveys substantially increase our ability to place AGNs in their cosmological context.

Ag-ligand modified tungstovandates and their efficient catalysis degradation properties for methylene blue

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

Zheng, Ran; Zhang, Huixia; Liu, Yunping

Two polytungstovandates [Ag(mbpy){sub 2}][Ag{sub 2}(mbpy){sub 3}][VW{sub 5}O{sub 19}]·H{sub 2}O (1) and [Ag(mbpy)]{sub 2}[Ag(mbpy){sub 2}]{sub 4}[VW{sub 12}O{sub 40}] (2) (mbpy =4,4′-dimethyl-2,2′-bipyridyl), had been hydrothermally synthesized and characterized by IR, TG, and single-crystal X-ray diffraction techniques. Single-crystal structural analysis revealed that the polyanionic clusters in two compounds are different: Lindqvist-type in 1 and α-Keggin-type in 2, respectively, while the cationic moieties in them are Ag-mbpy units. The experiments showed that this kind of hybrid crystal materials possesses more efficiently catalytic performance for the degradation of organic dye methylene blue (MB) in water solution under the UV irradiation. The significant degradation rate ofmore » MB can reach 89.9%, 94.9% by crystals 1 and 2 (40 mg) in the course of about 5 min. - Graphical abstract: Two Ag-ligand modified polytungstovandates had been synthesized and characterized, which were active in the catalytic degradation of organic dye methylene blue under the UV irradiation. - Highlights: • Two Ag-ligand modified tungstovandates were synthesized and characterized. • Weak interactions play important roles in constructing crystal frameworks. • Compounds are active to catalyze the degradation of methylene blue.« less

Stability of vacancy-type defect clusters in Ni based on first-principles and molecular dynamics simulations

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-10-17

Using first-principles calculations based on density-functional theory, the energetics of different vacancy-type defects, including voids, stacking fault tetrahedra (SFT) and vacancy loops, in Ni are investigated. It is found that voids are more stable than SFT at 0 K, which is also the case after taking into account the volumetric strains. By carrying out ab initio molecular dynamics simulations at temperatures up to 1000 K, direct transformations from vacancy loops and voids into SFT are observed. Our results suggest the importance of temperature effects in determining thermodynamic stability of vacancy clusters in face-centered cubic metals.

Cluster randomization and political philosophy.

PubMed

Chwang, Eric

2012-11-01

In this paper, I will argue that, while the ethical issues raised by cluster randomization can be challenging, they are not new. My thesis divides neatly into two parts. In the first, easier part I argue that many of the ethical challenges posed by cluster randomized human subjects research are clearly present in other types of human subjects research, and so are not novel. In the second, more difficult part I discuss the thorniest ethical challenge for cluster randomized research--cases where consent is genuinely impractical to obtain. I argue that once again these cases require no new analytic insight; instead, we should look to political philosophy for guidance. In other words, the most serious ethical problem that arises in cluster randomized research also arises in political philosophy. © 2011 Blackwell Publishing Ltd.

The Size Distribution Of Cluster Galaxies

NASA Astrophysics Data System (ADS)

Kuchner, U.; Ziegler, B.; Bamford, S.; Verdugo, M.; Haeussler, B.

2017-06-01

We establish a sample of 560 spectroscopically confirmed cluster members of MACS J1206.2- 0847 at z = 0.45 and utilize multi-wavelength and multi-component Sersic profile fitting to provide luminosities and sizes for the key structural components bulge and disk. While the difference between field and cluster galaxy properties are mostly due to a preference for cluster members to be early-type (quiescent, bulge-dominated), we see evidence for an outer disk fading and a sharp rise in the number of red disks with smaller effective radii at the tidally active cluster region around R200. Even though red disks are already virialized according to their velocity distribution, they are clearly not part of the old population found in the innermost region; they represent an important population of transitional objects in clusters.

Classifying GABAergic interneurons with semi-supervised projected model-based clustering.

PubMed

Mihaljević, Bojan; Benavides-Piccione, Ruth; Guerra, Luis; DeFelipe, Javier; Larrañaga, Pedro; Bielza, Concha

2015-09-01

A recently introduced pragmatic scheme promises to be a useful catalog of interneuron names. We sought to automatically classify digitally reconstructed interneuronal morphologies according to this scheme. Simultaneously, we sought to discover possible subtypes of these types that might emerge during automatic classification (clustering). We also investigated which morphometric properties were most relevant for this classification. A set of 118 digitally reconstructed interneuronal morphologies classified into the common basket (CB), horse-tail (HT), large basket (LB), and Martinotti (MA) interneuron types by 42 of the world's leading neuroscientists, quantified by five simple morphometric properties of the axon and four of the dendrites. We labeled each neuron with the type most commonly assigned to it by the experts. We then removed this class information for each type separately, and applied semi-supervised clustering to those cells (keeping the others' cluster membership fixed), to assess separation from other types and look for the formation of new groups (subtypes). We performed this same experiment unlabeling the cells of two types at a time, and of half the cells of a single type at a time. The clustering model is a finite mixture of Gaussians which we adapted for the estimation of local (per-cluster) feature relevance. We performed the described experiments on three different subsets of the data, formed according to how many experts agreed on type membership: at least 18 experts (the full data set), at least 21 (73 neurons), and at least 26 (47 neurons). Interneurons with more reliable type labels were classified more accurately. We classified HT cells with 100% accuracy, MA cells with 73% accuracy, and CB and LB cells with 56% and 58% accuracy, respectively. We identified three subtypes of the MA type, one subtype of CB and LB types each, and no subtypes of HT (it was a single, homogeneous type). We got maximum (adapted) Silhouette width and ARI values of

Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures.

PubMed

Copp, Stacy M; Schultz, Danielle E; Swasey, Steven; Gwinn, Elisabeth G

2015-03-24

The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics.

Atomically precise cluster catalysis towards quantum controlled catalysts

PubMed Central

Watanabe, Yoshihide

2014-01-01

Catalysis of atomically precise clusters supported on a substrate is reviewed in relation to the type of reactions. The catalytic activity of supported clusters has generally been discussed in terms of electronic structure. Several lines of evidence have indicated that the electronic structure of clusters and the geometry of clusters on a support, including the accompanying cluster-support interaction, are strongly correlated with catalytic activity. The electronic states of small clusters would be easily affected by cluster–support interactions. Several studies have suggested that it is possible to tune the electronic structure through atomic control of the cluster size. It is promising to tune not only the number of cluster atoms, but also the hybridization between the electronic states of the adsorbed reactant molecules and clusters in order to realize a quantum-controlled catalyst. PMID:27877723

Iontophoretic transport of associates based on porous Keplerate-type cluster polyoxometalate Mo72Fe30 and containing biologically active substances

NASA Astrophysics Data System (ADS)

Ostroushko, A. A.; Gagarin, I. D.; Tonkushina, M. O.; Grzhegorzhevskii, K. V.; Danilova, I. G.; Gette, I. F.; Kim, G. A.

2017-09-01

The possibility of iontophoretic transport through the native membranes of biologically active substances (vitamin B1 and insulin) associated with porous clusters Mo72Fe30 polyoxometalate of the Keplerate type is demonstrated for the first time in an experimental setup. The diffusion coefficient is estimated. The possibility of transferring Keplerate ions with a protective coating of biocompatible polymer polyvinylpyrrolidone is also shown.

Testing the Large-scale Environments of Cool-core and Non-cool-core Clusters with Clustering Bias

NASA Astrophysics Data System (ADS)

Medezinski, Elinor; Battaglia, Nicholas; Coupon, Jean; Cen, Renyue; Gaspari, Massimo; Strauss, Michael A.; Spergel, David N.

2017-02-01

There are well-observed differences between cool-core (CC) and non-cool-core (NCC) clusters, but the origin of this distinction is still largely unknown. Competing theories can be divided into internal (inside-out), in which internal physical processes transform or maintain the NCC phase, and external (outside-in), in which the cluster type is determined by its initial conditions, which in turn leads to different formation histories (I.e., assembly bias). We propose a new method that uses the relative assembly bias of CC to NCC clusters, as determined via the two-point cluster-galaxy cross-correlation function (CCF), to test whether formation history plays a role in determining their nature. We apply our method to 48 ACCEPT clusters, which have well resolved central entropies, and cross-correlate with the SDSS-III/BOSS LOWZ galaxy catalog. We find that the relative bias of NCC over CC clusters is b = 1.42 ± 0.35 (1.6σ different from unity). Our measurement is limited by the small number of clusters with core entropy information within the BOSS footprint, 14 CC and 34 NCC clusters. Future compilations of X-ray cluster samples, combined with deep all-sky redshift surveys, will be able to better constrain the relative assembly bias of CC and NCC clusters and determine the origin of the bimodality.

Testing the Large-scale Environments of Cool-core and Non-cool-core Clusters with Clustering Bias

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

Medezinski, Elinor; Battaglia, Nicholas; Cen, Renyue

2017-02-10

There are well-observed differences between cool-core (CC) and non-cool-core (NCC) clusters, but the origin of this distinction is still largely unknown. Competing theories can be divided into internal (inside-out), in which internal physical processes transform or maintain the NCC phase, and external (outside-in), in which the cluster type is determined by its initial conditions, which in turn leads to different formation histories (i.e., assembly bias). We propose a new method that uses the relative assembly bias of CC to NCC clusters, as determined via the two-point cluster-galaxy cross-correlation function (CCF), to test whether formation history plays a role in determiningmore » their nature. We apply our method to 48 ACCEPT clusters, which have well resolved central entropies, and cross-correlate with the SDSS-III/BOSS LOWZ galaxy catalog. We find that the relative bias of NCC over CC clusters is b = 1.42 ± 0.35 (1.6 σ different from unity). Our measurement is limited by the small number of clusters with core entropy information within the BOSS footprint, 14 CC and 34 NCC clusters. Future compilations of X-ray cluster samples, combined with deep all-sky redshift surveys, will be able to better constrain the relative assembly bias of CC and NCC clusters and determine the origin of the bimodality.« less

Unifying principles in homodimeric type I photosynthetic reaction centers: properties of PscB and the FA, FB and FX iron-sulfur clusters in green sulfur bacteria.

PubMed

Jagannathan, Bharat; Golbeck, John H

2008-12-01

The photosynthetic reaction center from the green sulfur bacterium Chlorobium tepidum (CbRC) was solubilized from membranes using Triton X-100 and isolated by sucrose density ultra-centrifugation. The CbRC complexes were subsequently treated with 0.5 M NaCl and ultrafiltered over a 100 kDa cutoff membrane. The resulting CbRC cores did not exhibit the low-temperature EPR resonances from FA- and FB- and were unable to reduce NADP+. SDS-PAGE and mass spectrometric analysis showed that the PscB subunit, which harbors the FA and FB clusters, had become dissociated, and was now present in the filtrate. Attempts to rebind PscB onto CbRC cores were unsuccessful. Mössbauer spectroscopy showed that recombinant PscB contains a heterogeneous mixture of [4Fe-4S]2+,1+ and other types of Fe/S clusters tentatively identified as [2Fe-2S]2+,1+ clusters and rubredoxin-like Fe3+,2+ centers, and that the [4Fe-4S]2+,1+ clusters which were present were degraded at high ionic strength. Quantitative analysis confirmed that the amount of iron and sulfide in the recombinant protein was sub-stoichiometric. A heme-staining assay indicated that cytochrome c551 remained firmly attached to the CbRC cores. Low-temperature EPR spectroscopy of photoaccumulated CbRC complexes and CbRC cores showed resonances between g=5.4 and 4.4 assigned to a S=3/2 ground spin state [4Fe-4S]1+ cluster and at g=1.77 assigned to a S=1/2 ground spin state [4Fe-4S]1+ cluster, both from FX-. These results unify the properties of the acceptor side of the Type I homodimeric reaction centers found in green sulfur bacteria and heliobacteria: in both, the FA and FB iron-sulfur clusters are present on a salt-dissociable subunit, and FX is present as an interpolypeptide [4Fe-4S]2+,1+ cluster with a significant population in a S=3/2 ground spin state.

Comparison of 17 genome types of adenovirus type 3 identified among strains recovered from six continents.

PubMed Central

Li, Q G; Wadell, G

1988-01-01

Restriction endonucleases BamHI, BclI, BglI, BglII, BstEII, EcoRI, HindIII, HpaI, SalI, SmalI, XbalI, and XholI were used to analyze 61 selected strains of adenovirus type 3 (Ad3) isolated from Africa, Asia, Australia, Europe, North America, and South America. It was noted that the use of BamHI, BclI, BglII, HpaI, SalI, and SmaI was sufficient to distinguish 17 genome types; 13 of them were newly identified. All 17 Ad3 genome types could be divided into three genomic clusters. Genome types of Ad3 cluster 1 occurred in Africa, Europe, South America, and North America. Genomic cluster 2 was identified in Africa; genomic cluster 3 was identified in Africa, Asia, Australia, Europe (a few), and North America. This was of interest because 15 identified genome types of Ad7 could also be divided into three genomic clusters. The degree of genetic relatedness between the 17 Ad3 and the 15 Ad7 genome types was analyzed and was expressed in a three-dimensional model. Images PMID:2838500

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

PubMed Central

Poole, William; Leinonen, Kalle; Shmulevich, Ilya

2017-01-01

Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes. However, most approaches for identifying cancer mutations focus on either the entire-gene or single amino-acid level. We have bridged these two methodologies with a multiscale mutation clustering algorithm that identifies variable length mutation clusters in cancer genes. We ran our algorithm on 539 genes using the combined mutation data in 23 cancer types from The Cancer Genome Atlas (TCGA) and identified 1295 mutation clusters. The resulting mutation clusters cover a wide range of scales and often overlap with many kinds of protein features including structured domains, phosphorylation sites, and known single nucleotide variants. We statistically associated these multiscale clusters with gene expression and drug response data to illuminate the functional and clinical consequences of mutations in our clusters. Interestingly, we find multiple clusters within individual genes that have differential functional associations: these include PTEN, FUBP1, and CDH1. This methodology has potential implications in identifying protein regions for drug targets, understanding the biological underpinnings of cancer, and personalizing cancer treatments. Toward this end, we have made the mutation clusters and the clustering algorithm available to the public. Clusters and pathway associations can be interactively browsed at m2c.systemsbiology.net. The multiscale mutation clustering algorithm is available at https://github.com/IlyaLab/M2C. PMID:28170390

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.

PubMed

Poole, William; Leinonen, Kalle; Shmulevich, Ilya; Knijnenburg, Theo A; Bernard, Brady

2017-02-01

Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes. However, most approaches for identifying cancer mutations focus on either the entire-gene or single amino-acid level. We have bridged these two methodologies with a multiscale mutation clustering algorithm that identifies variable length mutation clusters in cancer genes. We ran our algorithm on 539 genes using the combined mutation data in 23 cancer types from The Cancer Genome Atlas (TCGA) and identified 1295 mutation clusters. The resulting mutation clusters cover a wide range of scales and often overlap with many kinds of protein features including structured domains, phosphorylation sites, and known single nucleotide variants. We statistically associated these multiscale clusters with gene expression and drug response data to illuminate the functional and clinical consequences of mutations in our clusters. Interestingly, we find multiple clusters within individual genes that have differential functional associations: these include PTEN, FUBP1, and CDH1. This methodology has potential implications in identifying protein regions for drug targets, understanding the biological underpinnings of cancer, and personalizing cancer treatments. Toward this end, we have made the mutation clusters and the clustering algorithm available to the public. Clusters and pathway associations can be interactively browsed at m2c.systemsbiology.net. The multiscale mutation clustering algorithm is available at https://github.com/IlyaLab/M2C.

Galaxy populations in the Antlia cluster - III. Properties of faint early-type galaxies

NASA Astrophysics Data System (ADS)

Smith Castelli, Analía. V.; Cellone, Sergio A.; Faifer, Favio R.; Bassino, Lilia P.; Richtler, Tom; Romero, Gisela A.; Calderón, Juan Pablo; Caso, Juan Pablo

2012-01-01

We present a new analysis of the early-type galaxy population in the central region of the Antlia cluster, focusing on the faint systems such as dwarf ellipticals (dEs) and dwarf spheroidals (dSphs). The colour-magnitude relation (CMR) and the relation between luminosity and mean effective surface brightness for galaxies in the central region of Antlia have been previously studied in Paper I of the present series. Now we confirm 22 early-type galaxies as Antlia members, using Gemini-GMOS and Magellan-MIKE spectra. Among them, 15 are dEs from the FS90 Antlia Group catalogue, two belong to the rare type of compact ellipticals (cEs) and five are new faint dwarfs that had never been catalogued before. In addition, we present 16 newly identified low-surface-brightness galaxy candidates, almost half of them displaying morphologies consistent with being Antlia's counterparts of Local Group dSphs, which extend the faint luminosity limit of our study down to MB=-10.1(BT= 22.6) mag. With these new data, we built an improved CMR in the Washington photometric system, i.e. integrated T1 magnitudes versus (C-T1) colours, which extends ˜4 mag faintwards the limit of spectroscopically confirmed Antlia members. When only confirmed early-type members are considered, this relation extends over 10 mag in luminosity with no apparent change in slope or increase in colour dispersion towards its faint end. The intrinsic colour scatter of the relation is compared with those reported for other clusters of galaxies; we argue that it is likely that the large scatter of the CMR, usually reported at faint magnitudes, is mostly due to photometric errors along with an improper membership/morphological classification. The distinct behaviour of the luminosity versus mean effective surface brightness relation at the bright and faint ends is analysed, while it is confirmed that dE galaxies on the same relation present a very similar effective radius, regardless of their colour. The projected spatial

Canonical PSO Based K-Means Clustering Approach for Real Datasets

PubMed Central

Dey, Lopamudra; Chakraborty, Sanjay

2014-01-01

“Clustering” the significance and application of this technique is spread over various fields. Clustering is an unsupervised process in data mining, that is why the proper evaluation of the results and measuring the compactness and separability of the clusters are important issues. The procedure of evaluating the results of a clustering algorithm is known as cluster validity measure. Different types of indexes are used to solve different types of problems and indices selection depends on the kind of available data. This paper first proposes Canonical PSO based K-means clustering algorithm and also analyses some important clustering indices (intercluster, intracluster) and then evaluates the effects of those indices on real-time air pollution database, wholesale customer, wine, and vehicle datasets using typical K-means, Canonical PSO based K-means, simple PSO based K-means, DBSCAN, and Hierarchical clustering algorithms. This paper also describes the nature of the clusters and finally compares the performances of these clustering algorithms according to the validity assessment. It also defines which algorithm will be more desirable among all these algorithms to make proper compact clusters on this particular real life datasets. It actually deals with the behaviour of these clustering algorithms with respect to validation indexes and represents their results of evaluation in terms of mathematical and graphical forms. PMID:27355083

An agglomerative hierarchical clustering approach to visualisation in Bayesian clustering problems

PubMed Central

Dawson, Kevin J.; Belkhir, Khalid

2009-01-01

Clustering problems (including the clustering of individuals into outcrossing populations, hybrid generations, full-sib families and selfing lines) have recently received much attention in population genetics. In these clustering problems, the parameter of interest is a partition of the set of sampled individuals, - the sample partition. In a fully Bayesian approach to clustering problems of this type, our knowledge about the sample partition is represented by a probability distribution on the space of possible sample partitions. Since the number of possible partitions grows very rapidly with the sample size, we can not visualise this probability distribution in its entirety, unless the sample is very small. As a solution to this visualisation problem, we recommend using an agglomerative hierarchical clustering algorithm, which we call the exact linkage algorithm. This algorithm is a special case of the maximin clustering algorithm that we introduced previously. The exact linkage algorithm is now implemented in our software package Partition View. The exact linkage algorithm takes the posterior co-assignment probabilities as input, and yields as output a rooted binary tree, - or more generally, a forest of such trees. Each node of this forest defines a set of individuals, and the node height is the posterior co-assignment probability of this set. This provides a useful visual representation of the uncertainty associated with the assignment of individuals to categories. It is also a useful starting point for a more detailed exploration of the posterior distribution in terms of the co-assignment probabilities. PMID:19337306

OSO-8 X-ray spectra of clusters of galaxies. 1. Observations of twenty clusters: Physical correlations

NASA Technical Reports Server (NTRS)

Mushotzky, R. F.; Serlemitsos, P. J.; Smith, B. W.; Boldt, E. A.; Holt, S. S.

1978-01-01

OSO-8 X-ray spectra from 2 to 20 keV were analyzed for 26 clusters of galaxies. Temperature, emission integrals, iron abundances, and low energy absorption measurements are given. Eight clusters have positive iron emission line detections at the 90% confidence level, and all twenty cluster spectra are consistent with Fe/H=0.000014 by number with the possible exception of Virgo. Physical correlations between X-ray spectral parameters and other cluster properties are examined. It is found that: (1) the X-ray temperature is approximately proportional to the square of the velocity dispersion of the galaxies; (2) the emission integral and therefore the bolometric X-ray luminosity is a strong function of the X-ray temperature; (3) the X-ray temperature and emission integral are better correlated with cluster central galaxy density than with richness; (4) temperature and emission integral are separately correlated with Rood-Sastry type; and (5) the fraction of galaxies which are spirals is correlated with the observed ram pressure in the cluster core.

Hierarchical clustering of HPV genotype patterns in the ASCUS-LSIL triage study

PubMed Central

Wentzensen, Nicolas; Wilson, Lauren E.; Wheeler, Cosette M.; Carreon, Joseph D.; Gravitt, Patti E.; Schiffman, Mark; Castle, Philip E.

2010-01-01

Anogenital cancers are associated with about 13 carcinogenic HPV types in a broader group that cause cervical intraepithelial neoplasia (CIN). Multiple concurrent cervical HPV infections are common which complicate the attribution of HPV types to different grades of CIN. Here we report the analysis of HPV genotype patterns in the ASCUS-LSIL triage study using unsupervised hierarchical clustering. Women who underwent colposcopy at baseline (n = 2780) were grouped into 20 disease categories based on histology and cytology. Disease groups and HPV genotypes were clustered using complete linkage. Risk of 2-year cumulative CIN3+, viral load, colposcopic impression, and age were compared between disease groups and major clusters. Hierarchical clustering yielded four major disease clusters: Cluster 1 included all CIN3 histology with abnormal cytology; Cluster 2 included CIN3 histology with normal cytology and combinations with either CIN2 or high-grade squamous intraepithelial lesion (HSIL) cytology; Cluster 3 included older women with normal or low grade histology/cytology and low viral load; Cluster 4 included younger women with low grade histology/cytology, multiple infections, and the highest viral load. Three major groups of HPV genotypes were identified: Group 1 included only HPV16; Group 2 included nine carcinogenic types plus non-carcinogenic HPV53 and HPV66; and Group 3 included non-carcinogenic types plus carcinogenic HPV33 and HPV45. Clustering results suggested that colposcopy missed a prevalent precancer in many women with no biopsy/normal histology and HSIL. This result was confirmed by an elevated 2-year risk of CIN3+ in these groups. Our novel approach to study multiple genotype infections in cervical disease using unsupervised hierarchical clustering can address complex genotype distributions on a population level. PMID:20959485

Clustervision: Visual Supervision of Unsupervised Clustering.

PubMed

Kwon, Bum Chul; Eysenbach, Ben; Verma, Janu; Ng, Kenney; De Filippi, Christopher; Stewart, Walter F; Perer, Adam

2018-01-01

Clustering, the process of grouping together similar items into distinct partitions, is a common type of unsupervised machine learning that can be useful for summarizing and aggregating complex multi-dimensional data. However, data can be clustered in many ways, and there exist a large body of algorithms designed to reveal different patterns. While having access to a wide variety of algorithms is helpful, in practice, it is quite difficult for data scientists to choose and parameterize algorithms to get the clustering results relevant for their dataset and analytical tasks. To alleviate this problem, we built Clustervision, a visual analytics tool that helps ensure data scientists find the right clustering among the large amount of techniques and parameters available. Our system clusters data using a variety of clustering techniques and parameters and then ranks clustering results utilizing five quality metrics. In addition, users can guide the system to produce more relevant results by providing task-relevant constraints on the data. Our visual user interface allows users to find high quality clustering results, explore the clusters using several coordinated visualization techniques, and select the cluster result that best suits their task. We demonstrate this novel approach using a case study with a team of researchers in the medical domain and showcase that our system empowers users to choose an effective representation of their complex data.

Rotation Periods of Open Cluster Stars. IV.

NASA Astrophysics Data System (ADS)

Prosser, Charles F.; Grankin, Konstantin N.

We present the results from a photometric monitoring program of primarily solar-type open cluster stars obtained during 1994 and 1995. Several members of the α Persei cluster have been monitored and the corresponding relation between coronal x-ray activity and rotation period derived. The relation among mid-G/K type members illustrates both the previously noticed downturn in L_X/L_bol at high rotation rates and the sharp decrease in coronal activity at long rotation periods as seen among Pleiades stars. Intensive observation of one slowly rotating G-type member of IC 4665 has enabled a period determination of 8-10 days to be made and illustrates the need for (and limitations of) high quality observations.

The Clusters - Collaborative Models of Sustainable Regional Development

NASA Astrophysics Data System (ADS)

Mănescu, Gabriel; Kifor, Claudiu

2014-12-01

The clusters are the subject of actions and of whole series of documents issued by national and international organizations, and, based on experience, many authorities promote the idea that because of the clusters, competitiveness increases, the workforce specializes, regional businesses and economies grow. The present paper is meant to be an insight into the initiatives of forming clusters in Romania. Starting from a comprehensive analysis of the development potential offered by each region of economic development, we present the main types of clusters grouped according to fields of activity and their overall objectives

Clustering performance comparison using K-means and expectation maximization algorithms.

PubMed

Jung, Yong Gyu; Kang, Min Soo; Heo, Jun

2014-11-14

Clustering is an important means of data mining based on separating data categories by similar features. Unlike the classification algorithm, clustering belongs to the unsupervised type of algorithms. Two representatives of the clustering algorithms are the K -means and the expectation maximization (EM) algorithm. Linear regression analysis was extended to the category-type dependent variable, while logistic regression was achieved using a linear combination of independent variables. To predict the possibility of occurrence of an event, a statistical approach is used. However, the classification of all data by means of logistic regression analysis cannot guarantee the accuracy of the results. In this paper, the logistic regression analysis is applied to EM clusters and the K -means clustering method for quality assessment of red wine, and a method is proposed for ensuring the accuracy of the classification results.

The Cluster AgeS Experiment (CASE). Variable Stars in the Field of the Globular Cluster M22

NASA Astrophysics Data System (ADS)

Rozyczka, M.; Thompson, I. B.; Pych, W.; Narloch, W.; Poleski, R.; Schwarzenberg-Czerny, A.

2017-09-01

The field of the globular cluster M22 (NGC 6656) was monitored between 2000 and 2008 in a search for variable stars. BV light curves were obtained for 359 periodic, likely periodic, and long-term variables, 238 of which are new detections. 39 newly detected variables, and 63 previously known ones are members or likely members of the cluster, including 20 SX Phe, 10 RRab and 16 RRc type pulsators, one BL Her type pulsator, 21 contact binaries, and 9 detached or semi-detached eclipsing binaries. The most interesting among the identified objects are V112 - a bright multimode SX Phe pulsator, V125 - a β Lyr type binary on the blue horizontal branch, V129 - a blue/yellow straggler with a W UMa-like light curve, located halfway between the extreme horizontal branch and red giant branch, and V134 - an extreme horizontal branch object with P=2.33 d and a nearly sinusoidal light curve. All four of them are proper motion members of the cluster. Among nonmembers, a P=2.83 d detached eclipsing binary hosting a δ Sct type pulsator was found, and a peculiar P=0.93 d binary with ellipsoidal modulation and narrow minimum in the middle of one of the descending shoulders of the sinusoid. We also collected substantial new data for previously known variables. In particular we revise the statistics of the occurrence of the Blazhko effect in RR Lyr type variables of M22.

Young, metal-enriched cores in early-type dwarf galaxies in the Virgo cluster based on colour gradients

NASA Astrophysics Data System (ADS)

Urich, Linda; Lisker, Thorsten; Janz, Joachim; van de Ven, Glenn; Leaman, Ryan; Boselli, Alessandro; Paudel, Sanjaya; Sybilska, Agnieszka; Peletier, Reynier F.; den Brok, Mark; Hensler, Gerhard; Toloba, Elisa; Falcón-Barroso, Jesús; Niemi, Sami-Matias

2017-10-01

Early-type dwarf galaxies are not simply featureless, old objects, but were found to be much more diverse, hosting substructures and a variety of stellar population properties. To explore the stellar content of faint early-type galaxies, and to investigate in particular those with recent central star formation, we study colours and colour gradients within one effective radius in optical (g - r) and near-infrared (I - H) bands for 120 Virgo cluster early-type galaxies with - 19 mag type galaxies. The metallicity gradients of these blue-cored early-type dwarf galaxies are, however, in the range of most normal faint early-type galaxies, which we find to have non-zero gradients with higher central metallicity. The blue central regions are consistent with star formation activity within the last few 100 Myr. We discuss whether these galaxies could be explained by environmental quenching of star formation in the outer galaxy regions while the inner star formation activity continued.

Dynamic multifactor clustering of financial networks

NASA Astrophysics Data System (ADS)

Ross, Gordon J.

2014-02-01

We investigate the tendency for financial instruments to form clusters when there are multiple factors influencing the correlation structure. Specifically, we consider a stock portfolio which contains companies from different industrial sectors, located in several different countries. Both sector membership and geography combine to create a complex clustering structure where companies seem to first be divided based on sector, with geographical subclusters emerging within each industrial sector. We argue that standard techniques for detecting overlapping clusters and communities are not able to capture this type of structure and show how robust regression techniques can instead be used to remove the influence of both sector and geography from the correlation matrix separately. Our analysis reveals that prior to the 2008 financial crisis, companies did not tend to form clusters based on geography. This changed immediately following the crisis, with geography becoming a more important determinant of clustering structure.

Cluster Beam Deposition Technology for Optical Coatings. Phase 1

DTIC Science & Technology

1987-05-01

Particles 55 5.4.3 Growth of Ultrafine Particles or 61 Clusters by Gas Quenching 6.0 REFERENCES 67 APPENDIX: SUPPLEMENTARY INFORMATION 69 COP TR-407/5-87...approach, based on growth and transport of ultrafine particles or clusters in a quenching gas, appears more promising in our view and has been proposed for... Ultrafine Particles or Clusters by Gas quenching The apparent difficulty of making metal clusters with a Takagi-type source led us to explore other

The distribution of mass for spiral galaxies in clusters and in the field

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

Forbes, D.A.; Whitmore, B.C.

1989-04-01

A comparison is made between the mass distributions of spiral galaxies in clusters and in the field using Burstein's mass-type methodology. Both the H-alpha emission-line rotation curves and more extended H I rotation curves are used. The fitting technique for determining mass types used by Burstein and coworkers has been replaced by an objective chi-sq method. Mass types are shown to be a function of both the Hubble type and luminosity, contrary to earlier results. The present data show a difference in the distribution of mass types for spiral galaxies in the field and in clusters, in the sense thatmore » mass type I galaxies, where the inner and outer velocity gradients are similar, are generally found in the field rather than in clusters. This can be understood in terms of the results of Whitmore, Forbes, and Rubin (1988), who find that the rotation curves of galaxies in the central region of clusters are generally failing, while the outer galaxies in a cluster and field galaxies tend to have flat or rising rotation curves. 15 refs.« less

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

NASA Astrophysics Data System (ADS)

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-01

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with xTBA ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at xTBA ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, xTBA ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies.

PubMed

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-21

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

Buckets, Clusters and Dienst

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

1997-01-01

In this paper we describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 80 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets." We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information. We show that the overhead for these additional capabilities is minimal to both the author and the user when compared to the equivalent process within NCSTRL.

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.

Using cluster analysis and a classification and regression tree model to developed cover types in the Sky Islands of southeastern Arizona

Treesearch

Jose M. Iniguez; Joseph L. Ganey; Peter J. Daughtery; John D. Bailey

2005-01-01

The objective of this study was to develop a rule based cover type classification system for the forest and woodland vegetation in the Sky Islands of southeastern Arizona. In order to develop such a system we qualitatively and quantitatively compared a hierarchical (Ward’s) and a non-hierarchical (k-means) clustering method. Ecologically, unique groups represented by...

Giant mini-clusters as possible origin of halo phenomena observed in super-families

NASA Technical Reports Server (NTRS)

1985-01-01

Among 91 mini-clusters from 30 high energy Chiron-type families in Chacaltaya emulsion chambers, there were observed several extremely large multiplicity clusters in the highest energy range, far beyond the average of ordinary type clusters. Some details of microscopic observation of those giant mini-clusters in nuclear emulsion plates and some phenomenological regularity found in common among them are described. Such giant mini-clusters are possible candidates for the origin of narrow symmetric single halo phenomena in X-ray films which are frequently observed in super-families of visible energy greater than 1,000 TeV.

Concept design and cluster control of advanced space connectable intelligent microsatellite

NASA Astrophysics Data System (ADS)

Wang, Xiaohui; Li, Shuang; She, Yuchen

2017-12-01

In this note, a new type of advanced space connectable intelligent microsatellite is presented to extend the range of potential application of microsatellite and improve the efficiency of cooperation. First, the overall concept of the micro satellite cluster is described, which is characterized by autonomously connecting with each other and being able to realize relative rotation through the external interfaces. Second, the multi-satellite autonomous assembly algorithm and control algorithm of the cluster motion are developed to make the cluster system combine into a variety of configurations in order to achieve different types of functionality. Finally, the design of the satellite cluster system is proposed, and the possible applications are discussed.

The effectiveness of the Austrian disease management programme for type 2 diabetes: a cluster-randomised controlled trial.

PubMed

Sönnichsen, Andreas C; Winkler, Henrike; Flamm, Maria; Panisch, Sigrid; Kowatsch, Peter; Klima, Gert; Fürthauer, Bernhard; Weitgasser, Raimund

2010-11-05

Disease management programmes (DMPs) are costly and impose additional work load on general practitioners (GPs). Data on their effectiveness are inconclusive. We therefore conducted a cluster-randomised controlled trial to evaluate the effectiveness of the Austrian DMP for diabetes mellitus type 2 on HbA1c and quality of care for adult patients in primary care. All GPs of Salzburg-province were invited to participate. After cluster-randomisation by district, all patients with diabetes type 2 were recruited consecutively from 7-11/2007. The DMP, consisting mainly of physician and patient education, standardised documentation and agreement on therapeutic goals, was implemented in the intervention group while the control group received usual care. We aimed to show superiority of the intervention regarding metabolic control and process quality. The primary outcome measure was a change in HbA1c after one year. Secondary outcomes were days in the hospital, blood pressure, lipids, body mass index (BMI), enrolment in patient education and regular guideline-adherent examination. Blinding was not possible. 92 physicians recruited 1489 patients (649 intervention, 840 control). After 401 ± 47 days, 590 intervention-patients and 754 controls had complete data. In the intention to treat analysis (ITT) of all 1489 patients, HbA1c decreased 0.41% in the intervention group and 0.28% in controls. The difference of -0.13% (95% CI -0.24; -0.02) was significant at p = 0.026. Significance was lost in mixed models adjusted for baseline value and cluster-effects (adjusted mean difference -0.03 (95% CI -0.15; 0.09, p = 0.607). Of the secondary outcome measures, BMI and cholesterol were significantly reduced in the intervention group compared to controls in ITT after adjustments (-0.53 kg/m²; 95% CI -1.03;-0.02; p = 0.014 and -0.10 mmol/l; 95% CI -0.21; -0.003; p = 0.043). Additionally, more patients received patient education (49.5% vs. 20.1%, p < 0.0001), eye- (71.0% vs. 51.2%, p < 0

Applications of cluster analysis to satellite soundings

NASA Technical Reports Server (NTRS)

Munteanu, M. J.; Jakubowicz, O.; Kalnay, E.; Piraino, P.

1984-01-01

The advantages of the use of cluster analysis in the improvement of satellite temperature retrievals were evaluated since the use of natural clusters, which are associated with atmospheric temperature soundings characteristic of different types of air masses, has the potential for improving stratified regression schemes in comparison with currently used methods which stratify soundings based on latitude, season, and land/ocean. The method of discriminatory analysis was used. The correct cluster of temperature profiles from satellite measurements was located in 85% of the cases. Considerable improvement was observed at all mandatory levels using regression retrievals derived in the clusters of temperature (weighted and nonweighted) in comparison with the control experiment and with the regression retrievals derived in the clusters of brightness temperatures of 3 MSU and 5 IR channels.

Cloning, Sequencing, and Functional Analysis of an Iterative Type I Polyketide Synthase Gene Cluster for Biosynthesis of the Antitumor Chlorinated Polyenone Neocarzilin in “Streptomyces carzinostaticus”

PubMed Central

Otsuka, Miyuki; Ichinose, Koji; Fujii, Isao; Ebizuka, Yutaka

2004-01-01

Neocarzilins (NCZs) are antitumor chlorinated polyenones produced by “Streptomyces carzinostaticus” var. F-41. The gene cluster responsible for the biosynthesis of NCZs was cloned and characterized. DNA sequence analysis of a 33-kb region revealed a cluster of 14 open reading frames (ORFs), three of which (ORF4, ORF5, and ORF6) encode type I polyketide synthase (PKS), which consists of four modules. Unusual features of the modular organization is the lack of an obvious acyltransferase domain on modules 2 and 4 and the presence of longer interdomain regions more than 200 amino acids in length on each module. Involvement of the PKS genes in NCZ biosynthesis was demonstrated by heterologous expression of the cluster in Streptomyces coelicolor CH999, which produced the apparent NCZ biosynthetic intermediates dechloroneocarzillin A and dechloroneocarzilin B. Disruption of ORF5 resulted in a failure of NCZ production, providing further evidence that the cluster is essential for NCZ biosynthesis. Mechanistic consideration of NCZ formation indicates the iterative use of at least one module of the PKS, which subsequently releases its product by decarboxylation to generate an NCZ skeleton, possibly catalyzed by a type II thioesterase encoded by ORF7. This is a novel type I PKS system of bacterial origin for the biosynthesis of a reduced polyketide chain. Additionally, the protein encoded by ORF3, located upstream of the PKS genes, closely resembles the FADH2-dependent halogenases involved in the formation of halometabolites. The ORF3 protein could be responsible for the halogenation of NCZs, presenting a unique example of a halogenase involved in the biosynthesis of an aliphatic halometabolite. PMID:15328113

Cardiovascular Disease-Related Lifestyle Factors among People with Type 2 Diabetes in Pakistan: A Multicentre Study for the Prevalence, Clustering, and Associated Sociodemographic Determinants

PubMed Central

Khuwaja, Ali Khan; Lalani, Saima; Azam, Iqbal Syed; Ali, Badar Sabir; Jabbar, Abdual; Dhanani, Raheem

2011-01-01

Background. We evaluated the prevalence and clustering pattern of cardiovascular disease (CVD) related lifestyle factors and their association with CVD among patients with type 2 diabetes. We also examined the association of these factors with various socio-demographic characteristics. Methods. A total of 1000 patients with type 2 diabetes were interviewed in a cross-sectional, multi-center study in out-patient clinics in Karachi, Pakistan. Results. In this study 30.3% study participants had CVD. Majority of the patients were physically inactive and had adverse psychosocial factors. Forty percent of the study participants were exposed to passive smoking while 12.7% were current smokers. Only 8.8% of study subjects had none of the studied lifestyle factor, 27.5% had one, while 63.7% had two or three factors. CVDs were independently associated with physical inactivity, adverse psychosocial factors, passive smoking and clustering of two or three lifestyle factors. Physical inactivity was more prevalent among females and patients with no/less education. Proportion of adverse psychosocial factors were higher among females, elders and patients with no/less education. Clustering of these lifestyle factors was significantly higher among females, elderly and no/less educated patients. Conclusion. These results suggest the need of comprehensive and integrated interventions to reduce the prevalence of lifestyle factors. PMID:21837274

Power Calculations for Moderators in Multi-Site Cluster Randomized Trials

ERIC Educational Resources Information Center

Spybrook, Jessaca; Kelcey, Ben; Dong, Nianbo

2016-01-01

Cluster randomized trials (CRTs), or studies in which intact groups of individuals are randomly assigned to a condition, are becoming more common in evaluation studies of educational programs. A specific type of CRT in which clusters are randomly assigned to treatment within blocks or sites, known as multisite cluster randomized trials (MSCRTs),…

Salient concerns in using analgesia for cancer pain among outpatients: A cluster analysis study.

PubMed

Meghani, Salimah H; Knafl, George J

2017-02-10

To identify unique clusters of patients based on their concerns in using analgesia for cancer pain and predictors of the cluster membership. This was a 3-mo prospective observational study ( n = 207). Patients were included if they were adults (≥ 18 years), diagnosed with solid tumors or multiple myelomas, and had at least one prescription of around-the-clock pain medication for cancer or cancer-treatment-related pain. Patients were recruited from two outpatient medical oncology clinics within a large health system in Philadelphia. A choice-based conjoint (CBC) analysis experiment was used to elicit analgesic treatment preferences (utilities). Patients employed trade-offs based on five analgesic attributes (percent relief from analgesics, type of analgesic, type of side-effects, severity of side-effects, out of pocket cost). Patients were clustered based on CBC utilities using novel adaptive statistical methods. Multiple logistic regression was used to identify predictors of cluster membership. The analyses found 4 unique clusters: Most patients made trade-offs based on the expectation of pain relief (cluster 1, 41%). For a subset, the main underlying concern was type of analgesic prescribed, i.e ., opioid vs non-opioid (cluster 2, 11%) and type of analgesic side effects (cluster 4, 21%), respectively. About one in four made trade-offs based on multiple concerns simultaneously including pain relief, type of side effects, and severity of side effects (cluster 3, 28%). In multivariable analysis, to identify predictors of cluster membership, clinical and socioeconomic factors (education, health literacy, income, social support) rather than analgesic attitudes and beliefs were found important; only the belief, i.e ., pain medications can mask changes in health or keep you from knowing what is going on in your body was found significant in predicting two of the four clusters [cluster 1 (-); cluster 4 (+)]. Most patients appear to be driven by a single salient concern

Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators.

PubMed

O'Connell, Kerry Joan; Motherway, Mary O'Connell; Liedtke, Andrea; Fitzgerald, Gerald F; Paul Ross, R; Stanton, Catherine; Zomer, Aldert; van Sinderen, Douwe

2014-06-01

Members of the genus Bifidobacterium are commonly found in the gastrointestinal tracts of mammals, including humans, where their growth is presumed to be dependent on various diet- and/or host-derived carbohydrates. To understand transcriptional control of bifidobacterial carbohydrate metabolism, we investigated two genetic carbohydrate utilization clusters dedicated to the metabolism of raffinose-type sugars and melezitose. Transcriptomic and gene inactivation approaches revealed that the raffinose utilization system is positively regulated by an activator protein, designated RafR. The gene cluster associated with melezitose metabolism was shown to be subject to direct negative control by a LacI-type transcriptional regulator, designated MelR1, in addition to apparent indirect negative control by means of a second LacI-type regulator, MelR2. In silico analysis, DNA-protein interaction, and primer extension studies revealed the MelR1 and MelR2 operator sequences, each of which is positioned just upstream of or overlapping the correspondingly regulated promoter sequences. Similar analyses identified the RafR binding operator sequence located upstream of the rafB promoter. This study indicates that transcriptional control of gene clusters involved in carbohydrate metabolism in bifidobacteria is subject to conserved regulatory systems, representing either positive or negative control.

Transcription of Two Adjacent Carbohydrate Utilization Gene Clusters in Bifidobacterium breve UCC2003 Is Controlled by LacI- and Repressor Open Reading Frame Kinase (ROK)-Type Regulators

PubMed Central

O'Connell, Kerry Joan; O'Connell Motherway, Mary; Liedtke, Andrea; Fitzgerald, Gerald F.; Ross, R. Paul; Stanton, Catherine; Zomer, Aldert

2014-01-01

Members of the genus Bifidobacterium are commonly found in the gastrointestinal tracts of mammals, including humans, where their growth is presumed to be dependent on various diet- and/or host-derived carbohydrates. To understand transcriptional control of bifidobacterial carbohydrate metabolism, we investigated two genetic carbohydrate utilization clusters dedicated to the metabolism of raffinose-type sugars and melezitose. Transcriptomic and gene inactivation approaches revealed that the raffinose utilization system is positively regulated by an activator protein, designated RafR. The gene cluster associated with melezitose metabolism was shown to be subject to direct negative control by a LacI-type transcriptional regulator, designated MelR1, in addition to apparent indirect negative control by means of a second LacI-type regulator, MelR2. In silico analysis, DNA-protein interaction, and primer extension studies revealed the MelR1 and MelR2 operator sequences, each of which is positioned just upstream of or overlapping the correspondingly regulated promoter sequences. Similar analyses identified the RafR binding operator sequence located upstream of the rafB promoter. This study indicates that transcriptional control of gene clusters involved in carbohydrate metabolism in bifidobacteria is subject to conserved regulatory systems, representing either positive or negative control. PMID:24705323

Galaxy clusters in the SDSS Stripe 82 based on photometric redshifts

DOE PAGES

Durret, F.; Adami, C.; Bertin, E.; ...

2015-06-10

Based on a recent photometric redshift galaxy catalogue, we have searched for galaxy clusters in the Stripe ~82 region of the Sloan Digital Sky Survey by applying the Adami & MAzure Cluster FInder (AMACFI). Extensive tests were made to fine-tune the AMACFI parameters and make the cluster detection as reliable as possible. The same method was applied to the Millennium simulation to estimate our detection efficiency and the approximate masses of the detected clusters. Considering all the cluster galaxies (i.e. within a 1 Mpc radius of the cluster to which they belong and with a photoz differing by less thanmore » 0.05 from that of the cluster), we stacked clusters in various redshift bins to derive colour-magnitude diagrams and galaxy luminosity functions (GLFs). For each galaxy with absolute magnitude brighter than -19.0 in the r band, we computed the disk and spheroid components by applying SExtractor, and by stacking clusters we determined how the disk-to-spheroid flux ratio varies with cluster redshift and mass. We also detected 3663 clusters in the redshift range 0.1513 and a few 10 14 solar masses. Furthermore, by stacking the cluster galaxies in various redshift bins, we find a clear red sequence in the (g'-r') versus r' colour-magnitude diagrams, and the GLFs are typical of clusters, though with a possible contamination from field galaxies. The morphological analysis of the cluster galaxies shows that the fraction of late-type to early-type galaxies shows an increase with redshift (particularly in high mass clusters) and a decrease with detection level, i.e. cluster mass. From the properties of the cluster galaxies, the majority of the candidate clusters detected here seem to be real clusters with typical cluster properties.« less

Galaxy clusters in the SDSS Stripe 82 based on photometric redshifts

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

Durret, F.; Adami, C.; Bertin, E.

Based on a recent photometric redshift galaxy catalogue, we have searched for galaxy clusters in the Stripe ~82 region of the Sloan Digital Sky Survey by applying the Adami & MAzure Cluster FInder (AMACFI). Extensive tests were made to fine-tune the AMACFI parameters and make the cluster detection as reliable as possible. The same method was applied to the Millennium simulation to estimate our detection efficiency and the approximate masses of the detected clusters. Considering all the cluster galaxies (i.e. within a 1 Mpc radius of the cluster to which they belong and with a photoz differing by less thanmore » 0.05 from that of the cluster), we stacked clusters in various redshift bins to derive colour-magnitude diagrams and galaxy luminosity functions (GLFs). For each galaxy with absolute magnitude brighter than -19.0 in the r band, we computed the disk and spheroid components by applying SExtractor, and by stacking clusters we determined how the disk-to-spheroid flux ratio varies with cluster redshift and mass. We also detected 3663 clusters in the redshift range 0.1513 and a few 10 14 solar masses. Furthermore, by stacking the cluster galaxies in various redshift bins, we find a clear red sequence in the (g'-r') versus r' colour-magnitude diagrams, and the GLFs are typical of clusters, though with a possible contamination from field galaxies. The morphological analysis of the cluster galaxies shows that the fraction of late-type to early-type galaxies shows an increase with redshift (particularly in high mass clusters) and a decrease with detection level, i.e. cluster mass. From the properties of the cluster galaxies, the majority of the candidate clusters detected here seem to be real clusters with typical cluster properties.« less

Application of hybrid clustering using parallel k-means algorithm and DIANA algorithm

NASA Astrophysics Data System (ADS)

Umam, Khoirul; Bustamam, Alhadi; Lestari, Dian

2017-03-01

DNA is one of the carrier of genetic information of living organisms. Encoding, sequencing, and clustering DNA sequences has become the key jobs and routine in the world of molecular biology, in particular on bioinformatics application. There are two type of clustering, hierarchical clustering and partitioning clustering. In this paper, we combined two type clustering i.e. K-Means (partitioning clustering) and DIANA (hierarchical clustering), therefore it called Hybrid clustering. Application of hybrid clustering using Parallel K-Means algorithm and DIANA algorithm used to clustering DNA sequences of Human Papillomavirus (HPV). The clustering process is started with Collecting DNA sequences of HPV are obtained from NCBI (National Centre for Biotechnology Information), then performing characteristics extraction of DNA sequences. The characteristics extraction result is store in a matrix form, then normalize this matrix using Min-Max normalization and calculate genetic distance using Euclidian Distance. Furthermore, the hybrid clustering is applied by using implementation of Parallel K-Means algorithm and DIANA algorithm. The aim of using Hybrid Clustering is to obtain better clusters result. For validating the resulted clusters, to get optimum number of clusters, we use Davies-Bouldin Index (DBI). In this study, the result of implementation of Parallel K-Means clustering is data clustered become 5 clusters with minimal IDB value is 0.8741, and Hybrid Clustering clustered data become 13 sub-clusters with minimal IDB values = 0.8216, 0.6845, 0.3331, 0.1994 and 0.3952. The IDB value of hybrid clustering less than IBD value of Parallel K-Means clustering only that perform at 1ts stage. Its means clustering using Hybrid Clustering have the better result to clustered DNA sequence of HPV than perform parallel K-Means Clustering only.

Detection of CO emission in Hydra 1 cluster galaxies

NASA Technical Reports Server (NTRS)

Huchtmeier, W. K.

1990-01-01

A survey of bright Hydra cluster spiral galaxies for the CO(1-0) transition at 115 GHz was performed with the 15m Swedish-ESO submillimeter telescope (SEST). Five out of 15 galaxies observed have been detected in the CO(1-0) line. The largest spiral galaxy in the cluster, NGC 3312, got more CO than any spiral of the Virgo cluster. This Sa-type galaxy is optically largely distorted and disrupted on one side. It is a good candidate for ram pressure stripping while passing through the cluster's central region. A comparison with global CO properties of Virgo cluster spirals shows a relatively good agreement with the detected Hydra cluster galaxies.

Using cluster analysis and a classification and regression tree model to developed cover types in the Sky Islands of southeastern Arizona [Abstract

Treesearch

Jose M. Iniguez; Joseph L. Ganey; Peter J. Daugherty; John D. Bailey

2005-01-01

The objective of this study was to develop a rule based cover type classification system for the forest and woodland vegetation in the Sky Islands of southeastern Arizona. In order to develop such system we qualitatively and quantitatively compared a hierarchical (Ward’s) and a non-hierarchical (k-means) clustering method. Ecologically, unique groups and plots...

Vacancy clustering and acceptor activation in nitrogen-implanted ZnO

NASA Astrophysics Data System (ADS)

Børseth, Thomas Moe; Tuomisto, Filip; Christensen, Jens S.; Monakhov, Edouard V.; Svensson, Bengt G.; Kuznetsov, Andrej Yu.

2008-01-01

The role of vacancy clustering and acceptor activation on resistivity evolution in N ion-implanted n -type hydrothermally grown bulk ZnO has been investigated by positron annihilation spectroscopy, resistivity measurements, and chemical profiling. Room temperature 220keV N implantation using doses in the low 1015cm-2 range induces small and big vacancy clusters containing at least 2 and 3-4 Zn vacancies, respectively. The small clusters are present already in as-implanted samples and remain stable up to 1000°C with no significant effect on the resistivity evolution. In contrast, formation of the big clusters at 600°C is associated with a significant increase in the free electron concentration attributed to gettering of amphoteric Li impurities by these clusters. Further annealing at 800°C results in a dramatic decrease in the free electron concentration correlated with activation of 1016-1017cm-3 acceptors likely to be N and/or Li related. The samples remain n type, however, and further annealing at 1000°C results in passivation of the acceptor states while the big clusters dissociate.

Generic, network schema agnostic sparse tensor factorization for single-pass clustering of heterogeneous information networks

PubMed Central

Meng, Qinggang; Deng, Su; Huang, Hongbin; Wu, Yahui; Badii, Atta

2017-01-01

Heterogeneous information networks (e.g. bibliographic networks and social media networks) that consist of multiple interconnected objects are ubiquitous. Clustering analysis is an effective method to understand the semantic information and interpretable structure of the heterogeneous information networks, and it has attracted the attention of many researchers in recent years. However, most studies assume that heterogeneous information networks usually follow some simple schemas, such as bi-typed networks or star network schema, and they can only cluster one type of object in the network each time. In this paper, a novel clustering framework is proposed based on sparse tensor factorization for heterogeneous information networks, which can cluster multiple types of objects simultaneously in a single pass without any network schema information. The types of objects and the relations between them in the heterogeneous information networks are modeled as a sparse tensor. The clustering issue is modeled as an optimization problem, which is similar to the well-known Tucker decomposition. Then, an Alternating Least Squares (ALS) algorithm and a feasible initialization method are proposed to solve the optimization problem. Based on the tensor factorization, we simultaneously partition different types of objects into different clusters. The experimental results on both synthetic and real-world datasets have demonstrated that our proposed clustering framework, STFClus, can model heterogeneous information networks efficiently and can outperform state-of-the-art clustering algorithms as a generally applicable single-pass clustering method for heterogeneous network which is network schema agnostic. PMID:28245222

Generic, network schema agnostic sparse tensor factorization for single-pass clustering of heterogeneous information networks.

PubMed

Wu, Jibing; Meng, Qinggang; Deng, Su; Huang, Hongbin; Wu, Yahui; Badii, Atta

2017-01-01

Heterogeneous information networks (e.g. bibliographic networks and social media networks) that consist of multiple interconnected objects are ubiquitous. Clustering analysis is an effective method to understand the semantic information and interpretable structure of the heterogeneous information networks, and it has attracted the attention of many researchers in recent years. However, most studies assume that heterogeneous information networks usually follow some simple schemas, such as bi-typed networks or star network schema, and they can only cluster one type of object in the network each time. In this paper, a novel clustering framework is proposed based on sparse tensor factorization for heterogeneous information networks, which can cluster multiple types of objects simultaneously in a single pass without any network schema information. The types of objects and the relations between them in the heterogeneous information networks are modeled as a sparse tensor. The clustering issue is modeled as an optimization problem, which is similar to the well-known Tucker decomposition. Then, an Alternating Least Squares (ALS) algorithm and a feasible initialization method are proposed to solve the optimization problem. Based on the tensor factorization, we simultaneously partition different types of objects into different clusters. The experimental results on both synthetic and real-world datasets have demonstrated that our proposed clustering framework, STFClus, can model heterogeneous information networks efficiently and can outperform state-of-the-art clustering algorithms as a generally applicable single-pass clustering method for heterogeneous network which is network schema agnostic.

Spectroscopic and functional characterization of iron-sulfur cluster-bound forms of Azotobacter vinelandii (Nif)IscA.

PubMed

Mapolelo, Daphne T; Zhang, Bo; Naik, Sunil G; Huynh, Boi Hanh; Johnson, Michael K

2012-10-16

The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of (Nif)IscA in the maturation of nitrogen fixation proteins are currently unknown. To address these questions, in vitro spectroscopic studies (UV-visible absorption/CD, resonance Raman and Mössbauer) have been used to investigate the mechanism of [4Fe-4S] cluster assembly on Azotobacter vinelandii(Nif)IscA, and the ability of (Nif)IscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that (Nif)IscA can rapidly and reversibly cycle between forms containing one [2Fe-2S](2+) and one [4Fe-4S](2+) cluster per homodimer via DTT-induced two-electron reductive coupling of two [2Fe-2S](2+) clusters and O(2)-induced [4Fe-4S](2+) oxidative cleavage. This unique type of cluster interconversion in response to cellular redox status and oxygen levels is likely to be important for the specific role of A-type proteins in the maturation of [4Fe-4S] cluster-containing proteins under aerobic growth or oxidative stress conditions. Only the [4Fe-4S](2+)-(Nif)IscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-(Nif)IscA was shown to accept clusters from [4Fe-4S] cluster-bound NifU via rapid intact cluster transfer, indicating a potential role as a cluster carrier for delivery of clusters assembled on NifU. Overall the results support the proposal that A-type proteins can function as carrier proteins for clusters assembled on U-type proteins and suggest that they are likely to supply [2Fe-2S] clusters rather than [4Fe-4S] for the maturation of [4Fe-4S] cluster-containing proteins under aerobic or oxidative stress growth conditions.

Spectroscopic and Functional Characterization of Iron-Sulfur Cluster-Bound Forms of Azotobacter vinelandii NifIscA†

PubMed Central

Mapolelo, Daphne T.; Zhang, Bo; Naik, Sunil G.; Huynh, Boi Hanh; Johnson, Michael K.

2012-01-01

The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of NifIscA in the maturation of nitrogen fixation proteins are currently unknown. To address these questions, in vitro spectroscopic studies (UV–visible absorption/CD, resonance Raman and Mössbauer) have been used to investigate the mechanism of [4Fe-4S] cluster assembly on Azotobacter vinelandii NifIscA, and the ability of NifIscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that NifIscA can rapidly and reversibly cycle between forms containing one [2Fe-2S]2+ and one [4Fe-4S]2+ cluster per homodimer via DTT-induced two-electron reductive coupling of two [2Fe-2S]2+ clusters and O2-induced [4Fe-4S]2+ oxidative cleavage. This unique type of cluster interconversion in response to cellular redox status and oxygen levels is likely to be important for the specific role of A-type proteins in the maturation of [4Fe-4S] cluster-containing proteins under aerobic growth or oxidative stress conditions. Only the [4Fe-4S]2+-NifIscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-NifIscA was shown to accept clusters from [4Fe-4S] cluster-bound NifU via rapid intact cluster transfer, indicating a potential role as a cluster carrier for delivery of clusters assembled on NifU. Overall the results support the proposal that A-type proteins can function as carrier proteins for clusters assembled on U-type proteins and suggest that they are likely to supply [2Fe-2S] clusters rather than [4Fe-4S] for the maturation of [4Fe-4S] cluster-containing proteins under aerobic or oxidative stress growth conditions. PMID:23003323

Detection of X-ray emission from distant clusters of galaxies

NASA Technical Reports Server (NTRS)

Henry, J. P.; Branduardi, G.; Fabricant, D.; Feigelson, E.; Murray, S.; Tananbaum, H.; Briel, U.; Soltan, A.

1979-01-01

The paper reports the first extensive detection of X-ray emission from clusters of galaxies at cosmological distances. The properties of these objects are similar to those observed in objects at low redshifts. The 0.5-4.5 keV luminosities are in the range of less than 1 x 10 to the 43rd to 2 x 10 to the 45th ergs/s; the core radii are on the order of 0.5 Mpc; and Bautz-Morgan type I clusters are more luminous than types II or III. The observations are consistent with models assuming an evolving cluster potential and moderately efficient galaxy formation, but do not require them when observational selection is considered. X-ray observations of the 3C 295 cluster indicate that there is sufficient intergalactic medium to cause stripping of the cluster spirals, but the colors of these galaxies imply that they have not been stripped. A possible explanation of this discrepancy is discussed.

Spiral Arm Morphology in Cluster Environment

NASA Astrophysics Data System (ADS)

Choi, Isaac Yeoun-Gyu; Ann, Hong Bae

2011-10-01

We examine the dependence of the morphology of spiral galaxies on the environment using the KIAS Value Added Galaxy Catalog (VAGC) which is derived from the Sloan Digital Sky Survey (SDSS) DR7. Our goal is to understand whether the local environment or global conditions dominate in determining the morphology of spiral galaxies. For the analysis, we conduct a morphological classification of galaxies in 20 X-ray selected Abell clusters up to z˜0.06, using SDSS color images and the X-ray data from the Northern ROSAT All-Sky (NORAS) catalog. We analyze the distribution of arm classes along the clustercentric radius as well as that of Hubble types. To segregate the effect of local environment from the global environment, we compare the morphological distribution of galaxies in two X-lay luminosity groups, the low-Lx clusters (Lx < 0.15×1044erg/s) and high-Lx clusters (Lx > 1.8×1044erg/s). We find that the morphology-clustercentric relation prevails in the cluster envirnment although there is a brake near the cluster virial radius. The grand design arms comprise about 40% of the cluster spiral galaxies with a weak morphology-clustercentric radius relation for the arm classes, in the sense that flocculent galaxies tend to increase outward, regardless of the X-ray luminosity. From the cumulative radial distribution of cluster galaxies, we found that the low-Lx clusters are fully virialized while the high-Lx clusters are not.

Blind Quantum Signature with Controlled Four-Particle Cluster States

NASA Astrophysics Data System (ADS)

Li, Wei; Shi, Jinjing; Shi, Ronghua; Guo, Ying

2017-08-01

A novel blind quantum signature scheme based on cluster states is introduced. Cluster states are a type of multi-qubit entangled states and it is more immune to decoherence than other entangled states. The controlled four-particle cluster states are created by acting controlled-Z gate on particles of four-particle cluster states. The presented scheme utilizes the above entangled states and simplifies the measurement basis to generate and verify the signature. Security analysis demonstrates that the scheme is unconditional secure. It can be employed to E-commerce systems in quantum scenario.

Clustering self-organizing maps (SOM) method for human papillomavirus (HPV) DNA as the main cause of cervical cancer disease

NASA Astrophysics Data System (ADS)

Bustamam, A.; Aldila, D.; Fatimah, Arimbi, M. D.

2017-07-01

One of the most widely used clustering method, since it has advantage on its robustness, is Self-Organizing Maps (SOM) method. This paper discusses the application of SOM method on Human Papillomavirus (HPV) DNA which is the main cause of cervical cancer disease, the most dangerous cancer in developing countries. We use 18 types of HPV DNA-based on the newest complete genome. By using open-source-based program R, clustering process can separate 18 types of HPV into two different clusters. There are two types of HPV in the first cluster while 16 others in the second cluster. The analyzing result of 18 types HPV based on the malignancy of the virus (the difficultness to cure). Two of HPV types the first cluster can be classified as tame HPV, while 16 others in the second cluster are classified as vicious HPV.

Peer support for patients with type 2 diabetes: cluster randomised controlled trial.

PubMed

Smith, S M; Paul, G; Kelly, A; Whitford, D L; O'Shea, E; O'Dowd, T

2011-02-15

To test the effectiveness of peer support for patients with type 2 diabetes. Cluster randomised controlled. 20 general practices in the east of the Republic of Ireland. 395 patients (192 in intervention group, 203 in control group) and 29 peer supporters with type 2 diabetes. All practices introduced a standardised diabetes care system. The peer support intervention ran over a two year period and contained four elements: the recruitment and training of peer supporters, nine group meetings led by peer supporters in participant's own general practice, and a retention plan for the peer supporters. HbA(1c); cholesterol concentration; systolic blood pressure; and wellbeing score. There was no difference between intervention and control patients at baseline. All practices and 85% (337) of patients were followed up. At two year follow-up, there were no significant differences in HbA(1c) (mean difference -0.08%, 95% confidence interval -0.35% to 0.18%), systolic blood pressure (-3.9 mm Hg, -8.9 to 1.1 mm Hg), total cholesterol concentration (-0.03 mmol/L, -0.28 to 0.22 mmol/L), or wellbeing scores (-0.7, -2.3 to 0.8). While there was a trend towards decreases in the proportion of patients with poorly controlled risk factors at follow-up, particularly for systolic blood pressure (52% (87/166) >130 mm Hg in intervention v 61% (103/169) >130 mm Hg in control), these changes were not significant. The process evaluation indicated that the intervention was generally delivered as intended, though 18% (35) of patients in the intervention group never attended any group meetings. A group based peer support intervention is feasible in general practice settings, but the intervention was not effective when targeted at all patients with type 2 diabetes. While there was a trend towards improvements of clinical outcomes, the results do not support the widespread adoption of peer support. Trial registration Current Controlled Trials ISRCTN42541690.

Momentum-space cluster dual-fermion method

NASA Astrophysics Data System (ADS)

Iskakov, Sergei; Terletska, Hanna; Gull, Emanuel

2018-03-01

Recent years have seen the development of two types of nonlocal extensions to the single-site dynamical mean field theory. On one hand, cluster approximations, such as the dynamical cluster approximation, recover short-range momentum-dependent correlations nonperturbatively. On the other hand, diagrammatic extensions, such as the dual-fermion theory, recover long-ranged corrections perturbatively. The correct treatment of both strong short-ranged and weak long-ranged correlations within the same framework is therefore expected to lead to a quick convergence of results, and offers the potential of obtaining smooth self-energies in nonperturbative regimes of phase space. In this paper, we present an exact cluster dual-fermion method based on an expansion around the dynamical cluster approximation. Unlike previous formulations, our method does not employ a coarse-graining approximation to the interaction, which we show to be the leading source of error at high temperature, and converges to the exact result independently of the size of the underlying cluster. We illustrate the power of the method with results for the second-order cluster dual-fermion approximation to the single-particle self-energies and double occupancies.

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

Linear clusters of galaxies - A999 and A1016

NASA Astrophysics Data System (ADS)

Chapman, G. N. F.; Geller, M. J.; Huchra, J. P.

1987-09-01

The authors have measured 44 new redshifts in A 999 and 40 in A 1016: these clusters are both "linear" according to Rood and Sastry (1971) and Struble and Rood (1982, 1984). With 20 cluster members in A 999 and 22 in A 1016, the authors can estimate the probability that these clusters are actually drawn from spherically symmetric distributions. By comparing the clusters with Monte Carlo King models, they find that A 999 is probably intrinsically spherically symmetric, but A 1016 is probably linear. The authors estimate that ⪆2% of a catalog of spherically symmetric clusters might be erroneously classified as linear. They use the data to estimate the virial masses for these systems. The authors reassess the cluster-galaxy alignment analysis of Adams, Strom, and Strom (1980) and examine the relationship between the luminosity and morphological type of the cluster members and the cluster itself.

Clustering of Tuberculosis Cases Based on Variable-Number Tandem-Repeat Typing in Relation to the Population Structure of Mycobacterium tuberculosis in the Netherlands

PubMed Central

Sloot, Rosa; Borgdorff, Martien W.; de Beer, Jessica L.; van Ingen, Jakko; Supply, Philip

2013-01-01

The population structure of 3,776 Mycobacterium tuberculosis isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmission is overestimated if based on identical VNTR patterns. PMID:23658260

UV SEDs of early-type cluster galaxies: a new look at the UV upturn

NASA Astrophysics Data System (ADS)

Ali, S. S.; Bremer, M. N.; Phillipps, S.; De Propris, R.

2018-05-01

Using GALEX, Ultraviolet Optical Telescope (UVOT), and optical photometry, we explore the prevalence and strength of the Ultraviolet (UV) upturn in the spectra of quiescent early-type galaxies in several nearby clusters. Even for galaxies with completely passive optical colours, there is a large spread in vacuum UV colour consistent with almost all having some UV upturn component. Combining GALEX and UVOT data below 3000 Å, we generate for the first time comparatively detailed UV spectral energy distributions for Coma cluster galaxies. Fitting the UV upturn component with a blackbody, 26 of these show a range of characteristic temperatures (10 000-21 000K) for the UV upturn population. Assuming a single temperature to explain GALEX-optical colours could underestimate the fraction of galaxies with UV upturns and mis-classify some as systems with residual star formation. The UV upturn phenomenon is not an exclusive feature found only in giant galaxies; we identify galaxies with similar (or even bluer) FUV - V colours to the giants with upturns over a range of fainter luminosities. The temperature and strength of the UV upturn are correlated with galaxy mass. Under the plausible hypothesis that the sources of the UV upturn are blue horizontal branch stars, the most likely mechanism for this is the presence of a substantial (between 4 per cent and 20 per cent) Helium-rich (Y > 0.3) population of stars in these galaxies, potentially formed at z ˜ 4 and certainly at z > 2; this plausibly sets a lower limit of {˜ } {0.3- 0.8} × 10^{10} M⊙ to the in situ stellar mass of ˜L* galaxies at this redshift.

The Clusters AgeS Experiment (CASE). Variable Stars in the Field of the Globular Cluster NGC 6362

NASA Astrophysics Data System (ADS)

Kaluzny, J.; Thompson, I. B.; Rozyczka, M.; Pych, W.; Narloch, W.

2014-12-01

The field of the globular cluster NGC 6362 was monitored between 1995 and 2009 in a search for variable stars. BV light curves were obtained for 69 periodic variable stars including 34 known RR Lyr stars, 10 known objects of other types and 25 newly detected variable stars. Among the latter we identified 18 proper-motion members of the cluster: seven detached eclipsing binaries (DEBs), six SX Phe stars, two W UMa binaries, two spotted red giants, and a very interesting eclipsing binary composed of two red giants - the first example of such a system found in a globular cluster. Five of the DEBs are located at the turnoff region, and the remaining two are redward of the lower main sequence. Eighty-four objects from the central 9×9 arcmin2 of the cluster were found in the region of cluster blue stragglers. Of these 70 are proper motion (PM) members of NGC 6362 (including all SX Phe and two W UMa stars), and five are field stars. The remaining nine objects lacking PM information are located at the very core of the cluster, and as such they are likely genuine blue stragglers.

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

Entropy-based consensus clustering for patient stratification.

PubMed

Liu, Hongfu; Zhao, Rui; Fang, Hongsheng; Cheng, Feixiong; Fu, Yun; Liu, Yang-Yu

2017-09-01

Patient stratification or disease subtyping is crucial for precision medicine and personalized treatment of complex diseases. The increasing availability of high-throughput molecular data provides a great opportunity for patient stratification. Many clustering methods have been employed to tackle this problem in a purely data-driven manner. Yet, existing methods leveraging high-throughput molecular data often suffers from various limitations, e.g. noise, data heterogeneity, high dimensionality or poor interpretability. Here we introduced an Entropy-based Consensus Clustering (ECC) method that overcomes those limitations all together. Our ECC method employs an entropy-based utility function to fuse many basic partitions to a consensus one that agrees with the basic ones as much as possible. Maximizing the utility function in ECC has a much more meaningful interpretation than any other consensus clustering methods. Moreover, we exactly map the complex utility maximization problem to the classic K -means clustering problem, which can then be efficiently solved with linear time and space complexity. Our ECC method can also naturally integrate multiple molecular data types measured from the same set of subjects, and easily handle missing values without any imputation. We applied ECC to 110 synthetic and 48 real datasets, including 35 cancer gene expression benchmark datasets and 13 cancer types with four molecular data types from The Cancer Genome Atlas. We found that ECC shows superior performance against existing clustering methods. Our results clearly demonstrate the power of ECC in clinically relevant patient stratification. The Matlab package is available at http://scholar.harvard.edu/yyl/ecc . yunfu@ece.neu.edu or yyl@channing.harvard.edu. 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

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

Molecular growth from a Mo176 to a Mo248 cluster

NASA Astrophysics Data System (ADS)

Müller, A.; Shah, Syed Q. N.; Bögge, H.; Schmidtmann, M.

1999-01-01

In polyoxometalate chemistry a large variety of compounds, clusters and solid-state structures can be formed by the linking together of well-defined metal-oxygen building blocks, . These species exhibit unusual topological and electronic properties, andfind applications ranging from medicine to industrial processes. The recently reported ring-shaped mixed-valence polyoxomolybdates of the type {Mo154} (refs 5, 6) and {Mo176} (refs 7, 8) represent a new class of giant clusters with nanometre-sized cavities and interesting properties for host-guest chemistry. Here we describe the formation of related clusters of the type {Mo248} formed by addition of further units to the inner surface of the {Mo176 } `wheel'. The additional units arrange themselves into two {Mo36} `hub-caps' on the initial wheel-clusters that are not stable in isolation. These findings reveal a new pathway to the development of complex coordination clusters.

PREFACE: Nuclear Cluster Conference; Cluster'07

NASA Astrophysics Data System (ADS)

Freer, Martin

2008-05-01

The Cluster Conference is a long-running conference series dating back to the 1960's, the first being initiated by Wildermuth in Bochum, Germany, in 1969. The most recent meeting was held in Nara, Japan, in 2003, and in 2007 the 9th Cluster Conference was held in Stratford-upon-Avon, UK. As the name suggests the town of Stratford lies upon the River Avon, and shortly before the conference, due to unprecedented rainfall in the area (approximately 10 cm within half a day), lay in the River Avon! Stratford is the birthplace of the `Bard of Avon' William Shakespeare, and this formed an intriguing conference backdrop. The meeting was attended by some 90 delegates and the programme contained 65 70 oral presentations, and was opened by a historical perspective presented by Professor Brink (Oxford) and closed by Professor Horiuchi (RCNP) with an overview of the conference and future perspectives. In between, the conference covered aspects of clustering in exotic nuclei (both neutron and proton-rich), molecular structures in which valence neutrons are exchanged between cluster cores, condensates in nuclei, neutron-clusters, superheavy nuclei, clusters in nuclear astrophysical processes and exotic cluster decays such as 2p and ternary cluster decay. The field of nuclear clustering has become strongly influenced by the physics of radioactive beam facilities (reflected in the programme), and by the excitement that clustering may have an important impact on the structure of nuclei at the neutron drip-line. It was clear that since Nara the field had progressed substantially and that new themes had emerged and others had crystallized. Two particular topics resonated strongly condensates and nuclear molecules. These topics are thus likely to be central in the next cluster conference which will be held in 2011 in the Hungarian city of Debrechen. Martin Freer Participants and Cluster'07

Alpha-cluster preformation factor within cluster-formation model for odd-A and odd-odd heavy nuclei

NASA Astrophysics Data System (ADS)

Saleh Ahmed, Saad M.

2017-06-01

The alpha-cluster probability that represents the preformation of alpha particle in alpha-decay nuclei was determined for high-intensity alpha-decay mode odd-A and odd-odd heavy nuclei, 82 < Z < 114, 111 < N < 174. This probability was calculated using the energy-dependent formula derived from the formulation of clusterisation states representation (CSR) and the hypothesised cluster-formation model (CFM) as in our previous work. Our previous successful determination of phenomenological values of alpha-cluster preformation factors for even-even nuclei motivated us to expand the work to cover other types of nuclei. The formation energy of interior alpha cluster needed to be derived for the different nuclear systems with considering the unpaired-nucleon effect. The results showed the phenomenological value of alpha preformation probability and reflected the unpaired nucleon effect and the magic and sub-magic effects in nuclei. These results and their analyses presented are very useful for future work concerning the calculation of the alpha decay constants and the progress of its theory.

*K-means and cluster models for cancer signatures.

PubMed

Kakushadze, Zura; Yu, Willie

2017-09-01

We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data without using nonnegative matrix factorization (NMF). *K-means' computational cost is a fraction of NMF's. Using 1389 published samples for 14 cancer types, we find that 3 cancers (liver cancer, lung cancer and renal cell carcinoma) stand out and do not have cluster-like structures. Two clusters have especially high within-cluster correlations with 11 other cancers indicating common underlying structures. Our approach opens a novel avenue for studying such structures. *K-means is universal and can be applied in other fields. We discuss some potential applications in quantitative finance.

Renormalized coupled cluster approaches in the cluster-in-molecule framework: predicting vertical electron binding energies of the anionic water clusters (H2O)(n)(-).

PubMed

Xu, Peng; Gordon, Mark S

2014-09-04

Anionic water clusters are generally considered to be extremely challenging to model using fragmentation approaches due to the diffuse nature of the excess electron distribution. The local correlation coupled cluster (CC) framework cluster-in-molecule (CIM) approach combined with the completely renormalized CR-CC(2,3) method [abbreviated CIM/CR-CC(2,3)] is shown to be a viable alternative for computing the vertical electron binding energies (VEBE). CIM/CR-CC(2,3) with the threshold parameter ζ set to 0.001, as a trade-off between accuracy and computational cost, demonstrates the reliability of predicting the VEBE, with an average percentage error of ∼15% compared to the full ab initio calculation at the same level of theory. The errors are predominantly from the electron correlation energy. The CIM/CR-CC(2,3) approach provides the ease of a black-box type calculation with few threshold parameters to manipulate. The cluster sizes that can be studied by high-level ab initio methods are significantly increased in comparison with full CC calculations. Therefore, the VEBE computed by the CIM/CR-CC(2,3) method can be used as benchmarks for testing model potential approaches in small-to-intermediate-sized water clusters.

Effects of lifestyle education program for type 2 diabetes patients in clinics: study design of a cluster randomized trial.

PubMed

Adachi, Misa; Yamaoka, Kazue; Watanabe, Mariko; Nishikawa, Masako; Hida, Eisuke; Kobayashi, Itsuro; Tango, Toshiro

2010-11-30

The number of patients with type 2 diabetes is drastically increasing worldwide. It is a serious health problem in Japan as well. Lifestyle interventions can reduce progression from impaired glucose tolerance to type 2 diabetes, and glycemic control has been shown to improve postprandial plasma glucose levels. Moreover, several studies have suggested that continuous interventions (combined diet and exercise) can improve the plasma glucose level and reduce dosage of hypoglycemic agents.Although many interventional studies of lifestyle education for persons with diabetes in hospitals have been reported, only a few have been clinic-based studies employing an evidence-based lifestyle education program. This article describes the design of a cluster randomized controlled trial of the effectiveness of lifestyle education for patients with type 2 diabetes in clinics by registered dietitians. In Japan, general practitioners generally have their own medical clinics to provide medical care for outpatients in the community, including those with type 2 diabetes. With the collaboration of such general practitioners, the study patients were enrolled in the present study. Twenty general practitioners were randomly allocated to each provide patients for entry into either an intervention group (10) or a control group (10). In total, 200 participants will be included in the study. The intervention group will receive intensive education on lifestyle improvement related to type 2 diabetes by registered dietitians in clinics. Lifestyle education will be conducted several times during the study period. The control group will receive information on dietary intake and standard advice on glycemic control by registered dietitians. The primary endpoint is the change from the baseline value of HbA1c at 6 months. Data on health behavior and related issues will be gathered continuously over a 6-month period. This is the first study to evaluate lifestyle education in clinics by a cluster

Heteronuclear Metal Cluster Compounds Synthesis and Reactivity

DTIC Science & Technology

1990-08-10

important role in the formation of complexes with heteronuclear metal - metal bonds. Since this is our Final Report recent results are reported and...DTe FL’ Copy AFOSR-86-0125 Lfl X’ HETERONUCLEAR METAL CLUSTER COMPOUNDS00 SYNTHESIS AND REACTIVITY F. Gordon A. Stone, IDepartment of Inorganic...Security Classification) HETERONUCLEAR METAL CLUSTER COMPOUNDS: SYNTHESIS AND REACTIVITY 12. PERSONAL AUTHOR(S) F. GORDON A. STONE 13a. TYPE OF REPORT

Clustered DNA damages induced in human hematopoietic cells by low doses of ionizing radiation

NASA Technical Reports Server (NTRS)

Sutherland, Betsy M.; Bennett, Paula V.; Cintron-Torres, Nela; Hada, Megumi; Trunk, John; Monteleone, Denise; Sutherland, John C.; Laval, Jacques; Stanislaus, Marisha; Gewirtz, Alan

2002-01-01

Ionizing radiation induces clusters of DNA damages--oxidized bases, abasic sites and strand breaks--on opposing strands within a few helical turns. Such damages have been postulated to be difficult to repair, as are double strand breaks (one type of cluster). We have shown that low doses of low and high linear energy transfer (LET) radiation induce such damage clusters in human cells. In human cells, DSB are about 30% of the total of complex damages, and the levels of DSBs and oxidized pyrimidine clusters are similar. The dose responses for cluster induction in cells can be described by a linear relationship, implying that even low doses of ionizing radiation can produce clustered damages. Studies are in progress to determine whether clusters can be produced by mechanisms other than ionizing radiation, as well as the levels of various cluster types formed by low and high LET radiation.

Prevalence and risk factors of seizure clusters in adult patients with epilepsy.

PubMed

Chen, Baibing; Choi, Hyunmi; Hirsch, Lawrence J; Katz, Austen; Legge, Alexander; Wong, Rebecca A; Jiang, Alfred; Kato, Kenneth; Buchsbaum, Richard; Detyniecki, Kamil

2017-07-01

In the current study, we explored the prevalence of physician-confirmed seizure clusters. We also investigated potential clinical factors associated with the occurrence of seizure clusters overall and by epilepsy type. We reviewed medical records of 4116 adult (≥16years old) outpatients with epilepsy at our centers for documentation of seizure clusters. Variables including patient demographics, epilepsy details, medical and psychiatric history, AED history, and epilepsy risk factors were then tested against history of seizure clusters. Patients were then divided into focal epilepsy, idiopathic generalized epilepsy (IGE), or symptomatic generalized epilepsy (SGE), and the same analysis was run. Overall, seizure clusters were independently associated with earlier age of seizure onset, symptomatic generalized epilepsy (SGE), central nervous system (CNS) infection, cortical dysplasia, status epilepticus, absence of 1-year seizure freedom, and having failed 2 or more AEDs (P<0.0026). Patients with SGE (27.1%) were more likely to develop seizure clusters than patients with focal epilepsy (16.3%) and IGE (7.4%; all P<0.001). Analysis by epilepsy type showed that absence of 1-year seizure freedom since starting treatment at one of our centers was associated with seizure clustering in patients across all 3 epilepsy types. In patients with SGE, clusters were associated with perinatal/congenital brain injury. In patients with focal epilepsy, clusters were associated with younger age of seizure onset, complex partial seizures, cortical dysplasia, status epilepticus, CNS infection, and having failed 2 or more AEDs. In patients with IGE, clusters were associated with presence of an aura. Only 43.5% of patients with seizure clusters were prescribed rescue medications. Patients with intractable epilepsy are at a higher risk of developing seizure clusters. Factors such as having SGE, CNS infection, cortical dysplasia, status epilepticus or an early seizure onset, can also

The PhytoClust tool for metabolic gene clusters discovery in plant genomes

PubMed Central

Fuchs, Lisa-Maria

2017-01-01

Abstract The existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs, computational approaches are essential. Here, we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes. Our tool accurately identifies previously characterized plant MGCs. An exhaustive search of 31 plant genomes detected 1232 and 5531 putative gene cluster types and candidates, respectively. Clustering analysis of putative MGCs types by species reflected plant taxonomy. Furthermore, enrichment analysis revealed taxa- and species-specific enrichment of certain enzyme families in MGCs. When operating through our web-interface, PhytoClust users can mine a genome either based on a list of known cluster types or by defining new cluster rules. Moreover, for selected plant species, the output can be complemented by co-expression analysis. Altogether, we envisage PhytoClust to enhance novel MGCs discovery which will in turn impact the exploration of plant metabolism. PMID:28486689

Self consistency grouping: a stringent clustering method

PubMed Central

2012-01-01

Background Numerous types of clustering like single linkage and K-means have been widely studied and applied to a variety of scientific problems. However, the existing methods are not readily applicable for the problems that demand high stringency. Methods Our method, self consistency grouping, i.e. SCG, yields clusters whose members are closer in rank to each other than to any member outside the cluster. We do not define a distance metric; we use the best known distance metric and presume that it measures the correct distance. SCG does not impose any restriction on the size or the number of the clusters that it finds. The boundaries of clusters are determined by the inconsistencies in the ranks. In addition to the direct implementation that finds the complete structure of the (sub)clusters we implemented two faster versions. The fastest version is guaranteed to find only the clusters that are not subclusters of any other clusters and the other version yields the same output as the direct implementation but does so more efficiently. Results Our tests have demonstrated that SCG yields very few false positives. This was accomplished by introducing errors in the distance measurement. Clustering of protein domain representatives by structural similarity showed that SCG could recover homologous groups with high precision. Conclusions SCG has potential for finding biological relationships under stringent conditions. PMID:23320864

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.

SAR image segmentation using skeleton-based fuzzy clustering

NASA Astrophysics Data System (ADS)

Cao, Yun Yi; Chen, Yan Qiu

2003-06-01

SAR image segmentation can be converted to a clustering problem in which pixels or small patches are grouped together based on local feature information. In this paper, we present a novel framework for segmentation. The segmentation goal is achieved by unsupervised clustering upon characteristic descriptors extracted from local patches. The mixture model of characteristic descriptor, which combines intensity and texture feature, is investigated. The unsupervised algorithm is derived from the recently proposed Skeleton-Based Data Labeling method. Skeletons are constructed as prototypes of clusters to represent arbitrary latent structures in image data. Segmentation using Skeleton-Based Fuzzy Clustering is able to detect the types of surfaces appeared in SAR images automatically without any user input.

Witnessing the Formation of a Brightest Cluster Galaxy in a Nearby X-ray Cluster

NASA Astrophysics Data System (ADS)

Rasmussen, Jesper; Mulchaey, John S.; Bai, Lei; Ponman, Trevor J.; Raychaudhury, Somak; Dariush, Ali

2010-07-01

The central dominant galaxies in galaxy clusters constitute the most massive and luminous galaxies in the universe. Despite this, the formation of these brightest cluster galaxies (BCGs) and the impact of this on the surrounding cluster environment remain poorly understood. Here we present multiwavelength observations of the nearby poor X-ray cluster MZ 10451, in which both processes can be studied in unprecedented detail. Chandra observations of the intracluster medium (ICM) in the cluster core, which harbors two optically bright early-type galaxies in the process of merging, show that the system has retained a cool core and a central metal excess. This suggests that any merger-induced ICM heating and mixing remain modest at this stage. Tidally stripped stars seen around either galaxy likely represent an emerging intracluster light component, and the central ICM abundance enhancement may have a prominent contribution from in situ enrichment provided by these stars. The smaller of the merging galaxies shows evidence for having retained a hot gas halo, along with tentative evidence for some obscured star formation, suggesting that not all BCG major mergers at low redshift are completely dissipationless. Both galaxies are slightly offset from the peak of the ICM emission, with all three lying on an axis that roughly coincides with the large-scale elongation of the ICM. Our data are consistent with a picture in which central BCGs are built up by mergers close to the cluster core, by galaxies infalling on radial orbits aligned with the cosmological filaments feeding the cluster. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture

DOEpatents

Sanfilippo, Antonio [Richland, WA; Calapristi, Augustin J [West Richland, WA; Crow, Vernon L [Richland, WA; Hetzler, Elizabeth G [Kennewick, WA; Turner, Alan E [Kennewick, WA

2009-12-22

Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture are described. In one aspect, a document clustering method includes providing a document set comprising a plurality of documents, providing a cluster comprising a subset of the documents of the document set, using a plurality of terms of the documents, providing a cluster label indicative of subject matter content of the documents of the cluster, wherein the cluster label comprises a plurality of word senses, and selecting one of the word senses of the cluster label.

Typing and Clustering of Yersinia pseudotuberculosis Isolates by Restriction Fragment Length Polymorphism Analysis Using Insertion Sequences

PubMed Central

Voskresenskaya, E.; Savin, C.; Leclercq, A.; Tseneva, G.

2014-01-01

Yersinia pseudotuberculosis is an enteropathogen that has an animal reservoir and causes human infections, mostly in temperate and cold countries. Most of the methods previously used to subdivide Y. pseudotuberculosis were performed on small numbers of isolates from a specific geographical area. One aim of this study was to evaluate the typing efficiency of restriction fragment length polymorphism of insertion sequence hybridization patterns (IS-RFLP) compared to other typing methods, such as serotyping, ribotyping, and multilocus sequence typing (MLST), on the same set of 80 strains of Y. pseudotuberculosis of global origin. We found that IS100 was not adequate for IS-RFLP but that both IS285 and IS1541 efficiently subtyped Y. pseudotuberculosis. The discriminatory index (DI) of IS1541-RFLP (0.980) was superior to those of IS285-RFLP (0.939), ribotyping (0.944), MLST (0.861), and serotyping (0.857). The combination of the two IS (2IS-RFLP) further increased the DI to 0.998. Thus, IS-RFLP is a powerful tool for the molecular typing of Y. pseudotuberculosis and has the advantage of exhibiting well-resolved banding patterns that allow for a reliable comparison of strains of worldwide origin. The other aim of this study was to assess the clustering power of IS-RFLP. We found that 2IS-RFLP had a remarkable capacity to group strains with similar genotypic and phenotypic markers, thus identifying robust populations within Y. pseudotuberculosis. Our study thus demonstrates that 2IS- and even IS1541-RFLP alone might be valuable tools for the molecular typing of global isolates of Y. pseudotuberculosis and for the analysis of the population structure of this species. PMID:24671793

Efficient Remote Preparation of Four-Qubit Cluster-Type Entangled States with Multi-Party Over Partially Entangled Channels

NASA Astrophysics Data System (ADS)

Wang, Dong; Hoehn, Ross D.; Ye, Liu; Kais, Sabre

2016-07-01

We present a strategy for realizing multiparty-controlled remote state preparation (MCRSP) for a family of four-qubit cluster-type states by taking a pair of partial entanglements as the quantum channels. In this scenario, the encoded information is transmitted from the sender to a spatially separated receiver with control of the transmission by multiple parties. Predicated on the collaboration of all participants, the desired state can be faithfully restored at the receiver's location with high success probability by application of additional appropriate local operations and necessary classical communication. Moreover, this proposal for MCRSP can be faithfully achieved with unit total success probability when the quantum channels are distilled to maximally entangled ones.

Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks.

PubMed

Wang, Chenguang; Song, Yangqiu; El-Kishky, Ahmed; Roth, Dan; Zhang, Ming; Han, Jiawei

2015-08-01

One of the key obstacles in making learning protocols realistic in applications is the need to supervise them, a costly process that often requires hiring domain experts. We consider the framework to use the world knowledge as indirect supervision. World knowledge is general-purpose knowledge, which is not designed for any specific domain. Then the key challenges are how to adapt the world knowledge to domains and how to represent it for learning. In this paper, we provide an example of using world knowledge for domain dependent document clustering. We provide three ways to specify the world knowledge to domains by resolving the ambiguity of the entities and their types, and represent the data with world knowledge as a heterogeneous information network. Then we propose a clustering algorithm that can cluster multiple types and incorporate the sub-type information as constraints. In the experiments, we use two existing knowledge bases as our sources of world knowledge. One is Freebase, which is collaboratively collected knowledge about entities and their organizations. The other is YAGO2, a knowledge base automatically extracted from Wikipedia and maps knowledge to the linguistic knowledge base, Word-Net. Experimental results on two text benchmark datasets (20newsgroups and RCV1) show that incorporating world knowledge as indirect supervision can significantly outperform the state-of-the-art clustering algorithms as well as clustering algorithms enhanced with world knowledge features.

Mainshock-Aftershock Clustering in Volcanic Regions

NASA Astrophysics Data System (ADS)

Garza-Giron, Ricardo; Brodsky, Emily E.; Prejean, Stephanie G.

2018-02-01

Earthquakes break their general Poissonean behavior through two types of seismic bursts: swarms and mainshock-aftershock sequences. The former is commonly thought to dominate in volcanic and geothermal regions, but aftershock production, including within swarms, is not well studied in volcanic regions. Here we compare mainshock-aftershock clustering in active volcanic regions in Japan to nearby nonvolcanic regions. We find that aftershock production is similar in both areas by two separate metrics: (1) Both volcanic and nonvolcanic regions have similar proportions of areas that cluster into mainshock-aftershock sequences. (2) Volcanic areas with mainshock-aftershock sequences have aftershock productivity at least as high as nonvolcanic regions. We also find that volcano-tectonic events that are precursors to an eruption are more common at volcanoes without mainshock-aftershock clusters than at volcanoes with well-defined mainshock-aftershock clusters. This last finding hints at a strategy to identify volcanic systems where cataloged earthquakes are good predictors of behavior.

Android Malware Classification Using K-Means Clustering Algorithm

NASA Astrophysics Data System (ADS)

Hamid, Isredza Rahmi A.; Syafiqah Khalid, Nur; Azma Abdullah, Nurul; Rahman, Nurul Hidayah Ab; Chai Wen, Chuah

2017-08-01

Malware was designed to gain access or damage a computer system without user notice. Besides, attacker exploits malware to commit crime or fraud. This paper proposed Android malware classification approach based on K-Means clustering algorithm. We evaluate the proposed model in terms of accuracy using machine learning algorithms. Two datasets were selected to demonstrate the practicing of K-Means clustering algorithms that are Virus Total and Malgenome dataset. We classify the Android malware into three clusters which are ransomware, scareware and goodware. Nine features were considered for each types of dataset such as Lock Detected, Text Detected, Text Score, Encryption Detected, Threat, Porn, Law, Copyright and Moneypak. We used IBM SPSS Statistic software for data classification and WEKA tools to evaluate the built cluster. The proposed K-Means clustering algorithm shows promising result with high accuracy when tested using Random Forest algorithm.

The SWIFT AGN and Cluster Survey. I. Number Counts of AGNs and Galaxy Clusters

NASA Astrophysics Data System (ADS)

Dai, Xinyu; Griffin, Rhiannon D.; Kochanek, Christopher S.; Nugent, Jenna M.; Bregman, Joel N.

2015-05-01

The Swift active galactic nucleus (AGN) and Cluster Survey (SACS) uses 125 deg2 of Swift X-ray Telescope serendipitous fields with variable depths surrounding γ-ray bursts to provide a medium depth (4× {{10}-15} erg cm-2 s-1) and area survey filling the gap between deep, narrow Chandra/XMM-Newton surveys and wide, shallow ROSAT surveys. Here, we present a catalog of 22,563 point sources and 442 extended sources and examine the number counts of the AGN and galaxy cluster populations. SACS provides excellent constraints on the AGN number counts at the bright end with negligible uncertainties due to cosmic variance, and these constraints are consistent with previous measurements. We use Wide-field Infrared Survey Explorer mid-infrared (MIR) colors to classify the sources. For AGNs we can roughly separate the point sources into MIR-red and MIR-blue AGNs, finding roughly equal numbers of each type in the soft X-ray band (0.5-2 keV), but fewer MIR-blue sources in the hard X-ray band (2-8 keV). The cluster number counts, with 5% uncertainties from cosmic variance, are also consistent with previous surveys but span a much larger continuous flux range. Deep optical or IR follow-up observations of this cluster sample will significantly increase the number of higher-redshift (z\\gt 0.5) X-ray-selected clusters.

SC3 - consensus clustering of single-cell RNA-Seq data

PubMed Central

Kiselev, Vladimir Yu.; Kirschner, Kristina; Schaub, Michael T.; Andrews, Tallulah; Yiu, Andrew; Chandra, Tamir; Natarajan, Kedar N; Reik, Wolf; Barahona, Mauricio; Green, Anthony R; Hemberg, Martin

2017-01-01

Single-cell RNA-seq (scRNA-seq) enables a quantitative cell-type characterisation based on global transcriptome profiles. We present Single-Cell Consensus Clustering (SC3), a user-friendly tool for unsupervised clustering which achieves high accuracy and robustness by combining multiple clustering solutions through a consensus approach. We demonstrate that SC3 is capable of identifying subclones based on the transcriptomes from neoplastic cells collected from patients. PMID:28346451

A Survey of Popular R Packages for Cluster Analysis

ERIC Educational Resources Information Center

Flynt, Abby; Dean, Nema

2016-01-01

Cluster analysis is a set of statistical methods for discovering new group/class structure when exploring data sets. This article reviews the following popular libraries/commands in the R software language for applying different types of cluster analysis: from the stats library, the kmeans, and hclust functions; the mclust library; the poLCA…

Progeny Clustering: A Method to Identify Biological Phenotypes

PubMed Central

Hu, Chenyue W.; Kornblau, Steven M.; Slater, John H.; Qutub, Amina A.

2015-01-01

Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset. PMID:26267476

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

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

Search for Carbon-Rich Asymptotic Giant Branch Stars in Milky Way Globular Clusters

NASA Astrophysics Data System (ADS)

Indahl, Briana; Pessev, P.

2014-01-01

From our current understanding of stellar evolution, it would not be expected to find carbon rich asymptotic giant branch (AGB) stars in Milky Way globular clusters. Due to the low metallicity of the population II stars making up the globular clusters and their age, stars large enough to fuse carbon should have already evolved off of the asymptotic giant branch. Recently, however, there have been serendipitous discoveries of these types of stars. Matsunaga et al. (2006) discovered a Mira variable in the globular cluster Lynga 7. It was later confirmed by Feast et al. (2012) that the star is a member of the cluster and must be a product of a stellar merger. In the same year, Sharina et al. (2012) discovered a carbon star in the low metallicity globular cluster NGC6426 and reports it to be a CH star. Five more of these types of stars have been made as serendipitous discoveries and have been reported by Harding (1962), Dickens (1972), Cote et al. (1997), and Van Loon (2007). The abundance of these types of carbon stars in Milky Way globular clusters has been unknown because the discovery of these types of objects has only ever been a serendipitous discovery. These stars could have been easily overlooked in the past as they are outside the typical parameter space of galactic globular clusters. Also advances in near-infrared instruments and observing techniques have made it possible to detect the fainter carbon stars in binary systems. Having an understanding of the abundances of carbon stars in galactic globular clusters will aid in the modeling of globular cluster and galaxy formation leading to a better understanding of these processes. To get an understanding of the abundances of these stars we conducted the first comprehensive search for AGB carbon stars into all Milky Way globular clusters listed in the Harris Catalog (expect for Pyxis). I have found 128 carbon star candidates using methods of comparing color magnitude diagrams of the clusters with the carbon

Suppression of vacancy cluster growth in concentrated solid solution alloys

DOE PAGES

Zhao, Shijun; Velisa, Gihan; Xue, Haizhou; ...

2016-12-13

Large vacancy clusters, such as stacking-fault tetrahedra, are detrimental vacancy-type defects in ion-irradiated structural alloys. Suppression of vacancy cluster formation and growth is highly desirable to improve the irradiation tolerance of these materials. In this paper, we demonstrate that vacancy cluster growth can be inhibited in concentrated solid solution alloys by modifying cluster migration pathways and diffusion kinetics. The alloying effects of Fe and Cr on the migration of vacancy clusters in Ni concentrated alloys are investigated by molecular dynamics simulations and ion irradiation experiment. While the diffusion coefficients of small vacancy clusters in Ni-based binary and ternary solid solutionmore » alloys are higher than in pure Ni, they become lower for large clusters. This observation suggests that large clusters can easily migrate and grow to very large sizes in pure Ni. In contrast, cluster growth is suppressed in solid solution alloys owing to the limited mobility of large vacancy clusters. Finally, the differences in cluster sizes and mobilities in Ni and in solid solution alloys are consistent with the results from ion irradiation experiments.« less

Understanding the physical processes driving galaxy evolution in clusters : a case study of two z~0.5 galaxy clusters

NASA Astrophysics Data System (ADS)

Moran, Sean M.

Clusters of galaxies represent the largest laboratories in the universe for testing the incredibly chaotic physics governing the collapse of baryons into the stars, galaxies, groups, and diffuse clouds that we see today. Within the cluster environment, there are a wide variety of physical processes that may be acting to transform galaxies.In this thesis, we combine extensive Keck spectroscopy with wide-field HST imaging to perform a detailed case study of two intermediate redshift galaxy clusters, Cl 0024+1654 (z=0.395) and MS 0451-03 (z=0.540). Leveraging a comprehensive multiwavelength data set that spans the X-ray to infrared, and with spectral-line measurements serving as the key to revealing both the recent star-formation histories and kinematics of infalling galaxies, we aim to shed light on the environmental processes that could be acting to transform galaxies in clusters.We adopt a strategy to make maximal use of our HST-based morphologies by splitting our sample of cluster galaxies according to morphological type, characterizing signs of recent evolution in spirals and early types separately. This approach proves to be powerful in identifying galaxies that are currently being altered by an environmental interaction: early-type galaxies that have either been newly transformed or prodded back into an active phase, and spiral galaxies where star formation is being suppressed or enhanced all stand out in our sample.We begin by using variations in the early-type galaxy population as indicators of recent activity. Because ellipticals and S0s form such a homogeneous class in the local universe, we are sensitive to even very subtle signatures of recent and current environmental interactions. This study has yielded two key results: By constructing the Fundamental Plane (FP) of Cl 0024, we observe that elliptical and S0 galaxies exhibit a high scatter in their FP residuals, which occurs only among galaxies in the cluster core, suggesting a turbulent assembly history

The Nature of Red-Sequence Cluster Spiral Galaxies

NASA Astrophysics Data System (ADS)

Kashur, Lane; Barkhouse, Wayne; Sultanova, Madina; Kalawila Vithanage, Sandanuwa; Archer, Haylee; Foote, Gregory; Mathew, Elijah; Rude, Cody; Lopez-Cruz, Omar

2017-01-01

Preliminary analysis of the red-sequence galaxy population from a sample of 57 low-redshift galaxy clusters observed using the KPNO 0.9m telescope and 74 clusters from the WINGS dataset, indicates that a small fraction of red-sequence galaxies have a morphology consistent with spiral systems. For spiral galaxies to acquire the color of elliptical/S0s at a similar luminosity, they must either have been stripped of their star-forming gas at an earlier epoch, or contain a larger than normal fraction of dust. To test these ideas we have compiled a sample of red-sequence spiral galaxies and examined their infrared properties as measured by 2MASS, WISE, Spitzer, and Herschel. These IR data allows us to estimate the amount of dust in each of our red-sequence spiral galaxies. We compare the estimated dust mass in each of these red-sequence late-type galaxies with spiral galaxies located in the same cluster field but having colors inconsistent with the red-sequence. We thus provide a statistical measure to discriminate between purely passive spiral galaxy evolution and dusty spirals to explain the presence of these late-type systems in cluster red-sequences.

Choosing appropriate analysis methods for cluster randomised cross-over trials with a binary outcome.

PubMed

Morgan, Katy E; Forbes, Andrew B; Keogh, Ruth H; Jairath, Vipul; Kahan, Brennan C

2017-01-30

In cluster randomised cross-over (CRXO) trials, clusters receive multiple treatments in a randomised sequence over time. In such trials, there is usual correlation between patients in the same cluster. In addition, within a cluster, patients in the same period may be more similar to each other than to patients in other periods. We demonstrate that it is necessary to account for these correlations in the analysis to obtain correct Type I error rates. We then use simulation to compare different methods of analysing a binary outcome from a two-period CRXO design. Our simulations demonstrated that hierarchical models without random effects for period-within-cluster, which do not account for any extra within-period correlation, performed poorly with greatly inflated Type I errors in many scenarios. In scenarios where extra within-period correlation was present, a hierarchical model with random effects for cluster and period-within-cluster only had correct Type I errors when there were large numbers of clusters; with small numbers of clusters, the error rate was inflated. We also found that generalised estimating equations did not give correct error rates in any scenarios considered. An unweighted cluster-level summary regression performed best overall, maintaining an error rate close to 5% for all scenarios, although it lost power when extra within-period correlation was present, especially for small numbers of clusters. Results from our simulation study show that it is important to model both levels of clustering in CRXO trials, and that any extra within-period correlation should be accounted for. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Automated classification of mouse pup isolation syllables: from cluster analysis to an Excel-based "mouse pup syllable classification calculator".

PubMed

Grimsley, Jasmine M S; Gadziola, Marie A; Wenstrup, Jeffrey J

2012-01-01

Mouse pups vocalize at high rates when they are cold or isolated from the nest. The proportions of each syllable type produced carry information about disease state and are being used as behavioral markers for the internal state of animals. Manual classifications of these vocalizations identified 10 syllable types based on their spectro-temporal features. However, manual classification of mouse syllables is time consuming and vulnerable to experimenter bias. This study uses an automated cluster analysis to identify acoustically distinct syllable types produced by CBA/CaJ mouse pups, and then compares the results to prior manual classification methods. The cluster analysis identified two syllable types, based on their frequency bands, that have continuous frequency-time structure, and two syllable types featuring abrupt frequency transitions. Although cluster analysis computed fewer syllable types than manual classification, the clusters represented well the probability distributions of the acoustic features within syllables. These probability distributions indicate that some of the manually classified syllable types are not statistically distinct. The characteristics of the four classified clusters were used to generate a Microsoft Excel-based mouse syllable classifier that rapidly categorizes syllables, with over a 90% match, into the syllable types determined by cluster analysis.

Quantum cluster algebras and quantum nilpotent algebras.

PubMed

Goodearl, Kenneth R; Yakimov, Milen T

2014-07-08

A major direction in the theory of cluster algebras is to construct (quantum) cluster algebra structures on the (quantized) coordinate rings of various families of varieties arising in Lie theory. We prove that all algebras in a very large axiomatically defined class of noncommutative algebras possess canonical quantum cluster algebra structures. Furthermore, they coincide with the corresponding upper quantum cluster algebras. We also establish analogs of these results for a large class of Poisson nilpotent algebras. Many important families of coordinate rings are subsumed in the class we are covering, which leads to a broad range of applications of the general results to the above-mentioned types of problems. As a consequence, we prove the Berenstein-Zelevinsky conjecture [Berenstein A, Zelevinsky A (2005) Adv Math 195:405-455] for the quantized coordinate rings of double Bruhat cells and construct quantum cluster algebra structures on all quantum unipotent groups, extending the theorem of Geiß et al. [Geiß C, et al. (2013) Selecta Math 19:337-397] for the case of symmetric Kac-Moody groups. Moreover, we prove that the upper cluster algebras of Berenstein et al. [Berenstein A, et al. (2005) Duke Math J 126:1-52] associated with double Bruhat cells coincide with the corresponding cluster algebras.

Quantum cluster algebras and quantum nilpotent algebras

PubMed Central

Goodearl, Kenneth R.; Yakimov, Milen T.

2014-01-01

A major direction in the theory of cluster algebras is to construct (quantum) cluster algebra structures on the (quantized) coordinate rings of various families of varieties arising in Lie theory. We prove that all algebras in a very large axiomatically defined class of noncommutative algebras possess canonical quantum cluster algebra structures. Furthermore, they coincide with the corresponding upper quantum cluster algebras. We also establish analogs of these results for a large class of Poisson nilpotent algebras. Many important families of coordinate rings are subsumed in the class we are covering, which leads to a broad range of applications of the general results to the above-mentioned types of problems. As a consequence, we prove the Berenstein–Zelevinsky conjecture [Berenstein A, Zelevinsky A (2005) Adv Math 195:405–455] for the quantized coordinate rings of double Bruhat cells and construct quantum cluster algebra structures on all quantum unipotent groups, extending the theorem of Geiß et al. [Geiß C, et al. (2013) Selecta Math 19:337–397] for the case of symmetric Kac–Moody groups. Moreover, we prove that the upper cluster algebras of Berenstein et al. [Berenstein A, et al. (2005) Duke Math J 126:1–52] associated with double Bruhat cells coincide with the corresponding cluster algebras. PMID:24982197

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

The PhytoClust tool for metabolic gene clusters discovery in plant genomes.

PubMed

Töpfer, Nadine; Fuchs, Lisa-Maria; Aharoni, Asaph

2017-07-07

The existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs, computational approaches are essential. Here, we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes. Our tool accurately identifies previously characterized plant MGCs. An exhaustive search of 31 plant genomes detected 1232 and 5531 putative gene cluster types and candidates, respectively. Clustering analysis of putative MGCs types by species reflected plant taxonomy. Furthermore, enrichment analysis revealed taxa- and species-specific enrichment of certain enzyme families in MGCs. When operating through our web-interface, PhytoClust users can mine a genome either based on a list of known cluster types or by defining new cluster rules. Moreover, for selected plant species, the output can be complemented by co-expression analysis. Altogether, we envisage PhytoClust to enhance novel MGCs discovery which will in turn impact the exploration of plant metabolism. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

An optical/NIR survey of globular clusters in early-type galaxies. III. On the colour bimodality of globular cluster systems

NASA Astrophysics Data System (ADS)

Chies-Santos, A. L.; Larsen, S. S.; Cantiello, M.; Strader, J.; Kuntschner, H.; Wehner, E. M.; Brodie, J. P.

2012-03-01

Context. The interpretation that bimodal colour distributions of globular clusters (GCs) reflect bimodal metallicity distributions has been challenged. Non-linearities in the colour to metallicity conversions caused for example by the horizontal branch (HB) stars may be responsible for transforming a unimodal metallicity distribution into a bimodal (optical) colour distribution. Aims: We study optical/near-infrared (NIR) colour distributions of the GC systems in 14 E/S0 galaxies. Methods: We test whether the bimodal feature, generally present in optical colour distributions, remains in the optical/NIR ones. The latter colour combination is a better metallicity proxy than the former. We use KMM and GMM tests to quantify the probability that different colour distributions are better described by a bimodal, as opposed to a unimodal distribution. Results: We find that double-peaked colour distributions are more commonly seen in optical than in optical/NIR colours. For some of the galaxies where the optical (g - z) distribution is clearly bimodal, a bimodal distribution is not preferred over a unimodal one at a statistically significant level for the (g - K) and (z - K) distributions. The two most cluster-rich galaxies in our sample, NGC 4486 and NGC 4649, show some interesting differences. The (g - K) distribution of NGC 4649 is better described by a bimodal distribution, while this is true for the (g - K) distribution of NGC 4486 GCs only if restricted to a brighter sub-sample with small K-band errors (<0.05 mag). Formally, the K-band photometric errors cannot be responsible for blurring bimodal metallicity distributions to unimodal (g - K) colour distributions. However, simulations including the extra scatter in the colour-colour diagrams (not fully accounted for in the photometric errors) show that such scatter may contribute to the disappearance of bimodality in (g - K) for the full NGC 4486 sample. For the less cluster-rich galaxies results are inconclusive due to

Comparison of Se and Te clusters produced by ion bombardment

NASA Astrophysics Data System (ADS)

Trzyna, Małgorzata

2017-01-01

Nanostructures based on tellurium and selenium are materials used as components for the manufacturing topological insulators. Therefore it is crucial to precisely characterize these materials. In this work the emission of selenium and tellurium cluster ions, sputtered by Bi+ primary ion guns, was investigated by using Time-of-Flight Secondary Ion Mass Spectrometry (TOF SIMS). It has been found that BixTex and BixSex clusters appear in addition to Sex and Tex clusters in the mass range up to 1300 m/z. Local maxima or minima (magic numbers) are observed in the ion intensity versus a number of atoms per cluster for both positive and negative ions spectra for all types of clusters and primary ions used. These extrema can be attributed to different yield and stability of certain clusters but also to fragmentation of high-mass clusters.

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

PubMed

Han, Kyungreem; Venable, Richard M; Bryant, Anne-Marie; Legacy, Christopher J; Shen, Rong; Li, Hui; Roux, Benoît; Gericke, Arne; Pastor, Richard W

2018-02-01

All-atom molecular dynamics simulations combined with graph-theoretic analysis reveal that clustering of monomethyl phosphate dianion (MMP 2- ) is strongly influenced by the types and combinations of cations in the aqueous solution. Although Ca 2+ promotes the formation of stable and large MMP 2- clusters, K + alone does not. Nonetheless, clusters are larger and their link lifetimes are longer in mixtures of K + and Ca 2+ . This "synergistic" effect depends sensitively on the Lennard-Jones interaction parameters between Ca 2+ and the phosphorus oxygen and correlates with the hydration of the clusters. The pronounced MMP 2- clustering effect of Ca 2+ in the presence of K + is confirmed by Fourier transform infrared spectroscopy. The characterization of the cation-dependent clustering of MMP 2- provides a starting point for understanding cation-dependent clustering of phosphoinositides in cell membranes.

Membership and Coronal Activity in the NGC 2232 and Cr 140 Open Clusters

NASA Technical Reports Server (NTRS)

Oliversen, Ronald J. (Technical Monitor); Patten, Brian M.

2004-01-01

Making use of eight archival ROSAT HRI images in the regions of the NGC 2232 and Cr 140, this project's primary focus is to identify X-ray sources and to extract net source counts for these sources in these two open clusters. These X-ray data would be combined with ground-based photometry and spectroscopy in order to identify G, K, and early-M type cluster members. Such membership data are important because, at present, no members later than spectral type approx. F5 are currently known for either cluster. With ages estimated to be approx. 25 Myr and at distances of just approx. 350 pc, the combined late-type membership of the NGC 2232 and Cr 140 clusters would yield an almost unique sample of solar-type stars in the post-T Tauri/pre-main sequence phase of evolution. These stars could be used to assess the level and dispersion of coronal activity levels, as a part of a probe of the importance of magnetic braking and the level of magnetic dynamo activity, for solar-type stars just before they reach the zero-age main sequence.

Relative efficiency of unequal versus equal cluster sizes in cluster randomized trials using generalized estimating equation models.

PubMed

Liu, Jingxia; Colditz, Graham A

2018-05-01

There is growing interest in conducting cluster randomized trials (CRTs). For simplicity in sample size calculation, the cluster sizes are assumed to be identical across all clusters. However, equal cluster sizes are not guaranteed in practice. Therefore, the relative efficiency (RE) of unequal versus equal cluster sizes has been investigated when testing the treatment effect. One of the most important approaches to analyze a set of correlated data is the generalized estimating equation (GEE) proposed by Liang and Zeger, in which the "working correlation structure" is introduced and the association pattern depends on a vector of association parameters denoted by ρ. In this paper, we utilize GEE models to test the treatment effect in a two-group comparison for continuous, binary, or count data in CRTs. The variances of the estimator of the treatment effect are derived for the different types of outcome. RE is defined as the ratio of variance of the estimator of the treatment effect for equal to unequal cluster sizes. We discuss a commonly used structure in CRTs-exchangeable, and derive the simpler formula of RE with continuous, binary, and count outcomes. Finally, REs are investigated for several scenarios of cluster size distributions through simulation studies. We propose an adjusted sample size due to efficiency loss. Additionally, we also propose an optimal sample size estimation based on the GEE models under a fixed budget for known and unknown association parameter (ρ) in the working correlation structure within the cluster. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Globular Cluster Contributions to the Galactic Halo

NASA Astrophysics Data System (ADS)

Martell, Sarah; Grebel, Eva; Lai, David

2010-08-01

The goal of this project is to confirm chemically that globular clusters are the source of as much as half the population of the Galactic halo. Using moderate-resolution spectroscopy from the SEGUE survey, we have identified a previously unknown population of halo field giants with distinctly strong CN features. CN variations are typically only observed in globular clusters, so these stars are interpreted as immigrants to the halo that originally formed in globular clusters. In one night of Keck/HIRES time, we will obtain high-quality, high- resolution spectra for five such stars, and determine abundances of O, Na, Mg, Al, alpha, iron-peak and neutron-capture elements. With this information we can state clearly whether these unusual CN-strong halo stars carry the full abundance pattern seen in CN-strong globular cluster stars, with depleted C, O, and Mg and enhanced N, Na, and Al. This type of coarse ``chemical tagging'' will allow a clearer division of the Galactic halo into contributions from globular clusters and from dwarf galaxies, and will place constraints on theoretical models of globular cluster formation and evolution.

Seizure clusters: A common, understudied and undertreated phenomenon in refractory epilepsy.

PubMed

Komaragiri, Arpitha; Detyniecki, Kamil; Hirsch, Lawrence J

2016-06-01

Epilepsy is widely prevalent globally and has emerged as a well-studied neurological condition in the recent past. Seizure clusters, a type of seizures, and several aspects pertaining to the etiopathogenesis and management of clusters are yet to be elucidated. This review is an attempt to recapitulate the current understanding of seizure clusters based on the research that has been performed on seizure clusters. This article will provide a comprehensive review of various aspects of clusters, and discusses definitions, prevalence, risk factors, impact on quality of life, approved treatment modalities, and recent advances in management. Copyright © 2016 Elsevier Inc. All rights reserved.

Comprehensive cluster analysis with Transitivity Clustering.

PubMed

Wittkop, Tobias; Emig, Dorothea; Truss, Anke; Albrecht, Mario; Böcker, Sebastian; Baumbach, Jan

2011-03-01

Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.

Cluster Physics with Merging Galaxy Clusters

NASA Astrophysics Data System (ADS)

Molnar, Sandor

Collisions between galaxy clusters provide a unique opportunity to study matter in a parameter space which cannot be explored in our laboratories on Earth. In the standard ΛCDM model, where the total density is dominated by the cosmological constant (Λ) and the matter density by cold dark matter (CDM), structure formation is hierarchical, and clusters grow mostly by merging. Mergers of two massive clusters are the most energetic events in the universe after the Big Bang, hence they provide a unique laboratory to study cluster physics. The two main mass components in clusters behave differently during collisions: the dark matter is nearly collisionless, responding only to gravity, while the gas is subject to pressure forces and dissipation, and shocks and turbulence are developed during collisions. In the present contribution we review the different methods used to derive the physical properties of merging clusters. Different physical processes leave their signatures on different wavelengths, thus our review is based on a multifrequency analysis. In principle, the best way to analyze multifrequency observations of merging clusters is to model them using N-body/HYDRO numerical simulations. We discuss the results of such detailed analyses. New high spatial and spectral resolution ground and space based telescopes will come online in the near future. Motivated by these new opportunities, we briefly discuss methods which will be feasible in the near future in studying merging clusters.

Clustering in complex directed networks

NASA Astrophysics Data System (ADS)

Fagiolo, Giorgio

2007-08-01

Many empirical networks display an inherent tendency to cluster, i.e., to form circles of connected nodes. This feature is typically measured by the clustering coefficient (CC). The CC, originally introduced for binary, undirected graphs, has been recently generalized to weighted, undirected networks. Here we extend the CC to the case of (binary and weighted) directed networks and we compute its expected value for random graphs. We distinguish between CCs that count all directed triangles in the graph (independently of the direction of their edges) and CCs that only consider particular types of directed triangles (e.g., cycles). The main concepts are illustrated by employing empirical data on world-trade flows.

Identification of natural killer cell receptor clusters in the platypus genome reveals an expansion of C-type lectin genes.

PubMed

Wong, Emily S W; Sanderson, Claire E; Deakin, Janine E; Whittington, Camilla M; Papenfuss, Anthony T; Belov, Katherine

2009-08-01

Natural killer (NK) cell receptors belong to two unrelated, but functionally analogous gene families: the immunoglobulin superfamily, situated in the leukocyte receptor complex (LRC) and the C-type lectin superfamily, located in the natural killer complex (NKC). Here, we describe the largest NK receptor gene expansion seen to date. We identified 213 putative C-type lectin NK receptor homologs in the genome of the platypus. Many have arisen as the result of a lineage-specific expansion. Orthologs of OLR1, CD69, KLRE, CLEC12B, and CLEC16p genes were also identified. The NKC is split into at least two regions of the genome: 34 genes map to chromosome 7, two map to a small autosome, and the remainder are unanchored in the current genome assembly. No NK receptor genes from the LRC were identified. The massive C-type lectin expansion and lack of Ig-domain-containing NK receptors represents the most extreme polarization of NK receptors found to date. We have used this new data from platypus to trace the possible evolutionary history of the NK receptor clusters.

Internal Cluster Validation on Earthquake Data in the Province of Bengkulu

NASA Astrophysics Data System (ADS)

Rini, D. S.; Novianti, P.; Fransiska, H.

2018-04-01

K-means method is an algorithm for cluster n object based on attribute to k partition, where k < n. There is a deficiency of algorithms that is before the algorithm is executed, k points are initialized randomly so that the resulting data clustering can be different. If the random value for initialization is not good, the clustering becomes less optimum. Cluster validation is a technique to determine the optimum cluster without knowing prior information from data. There are two types of cluster validation, which are internal cluster validation and external cluster validation. This study aims to examine and apply some internal cluster validation, including the Calinski-Harabasz (CH) Index, Sillhouette (S) Index, Davies-Bouldin (DB) Index, Dunn Index (D), and S-Dbw Index on earthquake data in the Bengkulu Province. The calculation result of optimum cluster based on internal cluster validation is CH index, S index, and S-Dbw index yield k = 2, DB Index with k = 6 and Index D with k = 15. Optimum cluster (k = 6) based on DB Index gives good results for clustering earthquake in the Bengkulu Province.

Cluster-cluster correlations and constraints on the correlation hierarchy

NASA Technical Reports Server (NTRS)

Hamilton, A. J. S.; Gott, J. R., III

1988-01-01

The hypothesis that galaxies cluster around clusters at least as strongly as they cluster around galaxies imposes constraints on the hierarchy of correlation amplitudes in hierachical clustering models. The distributions which saturate these constraints are the Rayleigh-Levy random walk fractals proposed by Mandelbrot; for these fractal distributions cluster-cluster correlations are all identically equal to galaxy-galaxy correlations. If correlation amplitudes exceed the constraints, as is observed, then cluster-cluster correlations must exceed galaxy-galaxy correlations, as is observed.

Topic modeling for cluster analysis of large biological and medical datasets

PubMed Central

2014-01-01

Background The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, foster biological interpretation, and build validated predictors. Although multivariate techniques such as cluster analysis may allow researchers to identify groups, or clusters, of related variables, the accuracies and effectiveness of traditional clustering methods diminish for large and hyper dimensional datasets. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Its ability to reduce high dimensionality to a small number of latent variables makes it suitable as a means for clustering or overcoming clustering difficulties in large biological and medical datasets. Results In this study, three topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, are proposed and tested on the cluster analysis of three large datasets: Salmonella pulsed-field gel electrophoresis (PFGE) dataset, lung cancer dataset, and breast cancer dataset, which represent various types of large biological or medical datasets. All three various methods are shown to improve the efficacy/effectiveness of clustering results on the three datasets in comparison to traditional methods. A preferable cluster analysis method emerged for each of the three datasets on the basis of replicating known biological truths. Conclusion Topic modeling could be advantageously applied to the large datasets of biological or medical research. The three proposed topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, yield clustering improvements for the three different data types. Clusters more efficaciously represent truthful groupings and subgroupings in the data than

Topic modeling for cluster analysis of large biological and medical datasets.

PubMed

Zhao, Weizhong; Zou, Wen; Chen, James J

2014-01-01

The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, foster biological interpretation, and build validated predictors. Although multivariate techniques such as cluster analysis may allow researchers to identify groups, or clusters, of related variables, the accuracies and effectiveness of traditional clustering methods diminish for large and hyper dimensional datasets. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Its ability to reduce high dimensionality to a small number of latent variables makes it suitable as a means for clustering or overcoming clustering difficulties in large biological and medical datasets. In this study, three topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, are proposed and tested on the cluster analysis of three large datasets: Salmonella pulsed-field gel electrophoresis (PFGE) dataset, lung cancer dataset, and breast cancer dataset, which represent various types of large biological or medical datasets. All three various methods are shown to improve the efficacy/effectiveness of clustering results on the three datasets in comparison to traditional methods. A preferable cluster analysis method emerged for each of the three datasets on the basis of replicating known biological truths. Topic modeling could be advantageously applied to the large datasets of biological or medical research. The three proposed topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, yield clustering improvements for the three different data types. Clusters more efficaciously represent truthful groupings and subgroupings in the data than traditional methods, suggesting

Cluster analysis of sputum cytokine-high profiles reveals diversity in T(h)2-high asthma patients.

PubMed

Seys, Sven F; Scheers, Hans; Van den Brande, Paul; Marijsse, Gudrun; Dilissen, Ellen; Van Den Bergh, Annelies; Goeminne, Pieter C; Hellings, Peter W; Ceuppens, Jan L; Dupont, Lieven J; Bullens, Dominique M A

2017-02-23

Asthma is characterized by a heterogeneous inflammatory profile and can be subdivided into T(h)2-high and T(h)2-low airway inflammation. Profiling of a broader panel of airway cytokines in large unselected patient cohorts is lacking. Patients (n = 205) were defined as being "cytokine-low/high" if sputum mRNA expression of a particular cytokine was outside the respective 10 th /90 th percentile range of the control group (n = 80). Unsupervised hierarchical clustering was used to determine clusters based on sputum cytokine profiles. Half of patients (n = 108; 52.6%) had a classical T(h)2-high ("IL-4-, IL-5- and/or IL-13-high") sputum cytokine profile. Unsupervised cluster analysis revealed 5 clusters. Patients with an "IL-4- and/or IL-13-high" pattern surprisingly did not cluster but were equally distributed among the 5 clusters. Patients with an "IL-5-, IL-17A-/F- and IL-25- high" profile were restricted to cluster 1 (n = 24) with increased sputum eosinophil as well as neutrophil counts and poor lung function parameters at baseline and 2 years later. Four other clusters were identified: "IL-5-high or IL-10-high" (n = 16), "IL-6-high" (n = 8), "IL-22-high" (n = 25). Cluster 5 (n = 132) consists of patients without "cytokine-high" pattern or patients with only high IL-4 and/or IL-13. We identified 5 unique asthma molecular phenotypes by biological clustering. Type 2 cytokines cluster with non-type 2 cytokines in 4 out of 5 clusters. Unsupervised analysis thus not supports a priori type 2 versus non-type 2 molecular phenotypes. www.clinicaltrials.gov NCT01224938. Registered 18 October 2010.

Mapping the formation areas of giant molybdenum blue clusters: a spectroscopic study

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

Botar, Bogdan; Ellern, Arkady; Kogerler, Paul

2012-05-18

The self-assembly of soluble molybdenum blue species from simple molybdate solutions has primarily been associated with giant mixed-valent wheel-shaped cluster anions, derived from the {MoV/VI154/176} archetypes, and a {MoV/VI368} lemon-shaped cluster. The combined use of Raman spectroscopy and kinetic precipitation as self-assembly monitoring techniques and single-crystal X-ray diffraction is key to mapping the realm of molybdenum blue species by establishing spherical {MoV/VI102}-type Keplerates as an important giant molybdenum blue-type species. We additionally rationalize the empirical effect of reducing agent concentration on the formation of all three relevant skeletal types: wheel, lemon and spheres. Whereas both wheels and the lemon-shaped {MoV/VI368}more » cluster are obtained from weakly reduced molybdenum blue solutions, considerably higher reduced solutions lead to {MoV/VI102}-type Keplerates.« less

Word-initial /r/-clusters in Swedish speaking children with typical versus protracted phonological development.

PubMed

Lundeborg Hammarström, Inger

2018-01-01

The present study investigated word-initial (WI) /r/-clusters in Central Swedish-speaking children with and without protracted phonological development (PPD). Data for WI singleton /r/ and singleton and cluster /l/ served as comparisons. Participants were twelve 4-year-olds with PPD and twelve age- and gender-matched typically developing (TD) controls. Native speakers audio-recorded and transcribed 109 target single words using a Swedish phonology test with 12 WI C+/r/-clusters and three WI CC+/r/-clusters. The results showed significantly higher match scores for the TD children, a lower match proportion for the /r/ targets and for singletons compared with clusters, and differences in mismatch patterns between the groups. There were no matches for /r/-cluster targets in the PPD group, with all children except two in that group showing deletions for both /r/-cluster types. The differences in mismatch proportions and types between the PPD group and controls suggests new directions for future clinical practice.

Circulation Clusters--An Empirical Approach to Decentralization of Academic Libraries.

ERIC Educational Resources Information Center

McGrath, William E.

1986-01-01

Discusses the issue of centralization or decentralization of academic library collections, and describes a statistical analysis of book circulation at the University of Southwestern Louisiana that yielded subject area clusters as a compromise solution to the problem. Applications of the cluster model for all types of library catalogs are…

Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks

PubMed Central

Wang, Chenguang; Song, Yangqiu; El-Kishky, Ahmed; Roth, Dan; Zhang, Ming; Han, Jiawei

2015-01-01

One of the key obstacles in making learning protocols realistic in applications is the need to supervise them, a costly process that often requires hiring domain experts. We consider the framework to use the world knowledge as indirect supervision. World knowledge is general-purpose knowledge, which is not designed for any specific domain. Then the key challenges are how to adapt the world knowledge to domains and how to represent it for learning. In this paper, we provide an example of using world knowledge for domain dependent document clustering. We provide three ways to specify the world knowledge to domains by resolving the ambiguity of the entities and their types, and represent the data with world knowledge as a heterogeneous information network. Then we propose a clustering algorithm that can cluster multiple types and incorporate the sub-type information as constraints. In the experiments, we use two existing knowledge bases as our sources of world knowledge. One is Freebase, which is collaboratively collected knowledge about entities and their organizations. The other is YAGO2, a knowledge base automatically extracted from Wikipedia and maps knowledge to the linguistic knowledge base, Word-Net. Experimental results on two text benchmark datasets (20newsgroups and RCV1) show that incorporating world knowledge as indirect supervision can significantly outperform the state-of-the-art clustering algorithms as well as clustering algorithms enhanced with world knowledge features. PMID:26705504

Host Cell Contact-Induced Transcription of the Type IV Fimbria Gene Cluster of Actinobacillus pleuropneumoniae

PubMed Central

Boekema, Bouke K. H. L.; Van Putten, Jos P. M.; Stockhofe-Zurwieden, Norbert; Smith, Hilde E.

2004-01-01

Type IV pili (Tfp) of gram-negative species share many characteristics, including a common architecture and conserved biogenesis pathway. Much less is known about the regulation of Tfp expression in response to changing environmental conditions. We investigated the diversity of Tfp regulatory systems by searching for the molecular basis of the reported variable expression of the Tfp gene cluster of the pathogen Actinobacillus pleuropneumoniae. Despite the presence of an intact Tfp gene cluster consisting of four genes, apfABCD, no Tfp were formed under standard growth conditions. Sequence analysis of the predicted major subunit protein ApfA showed an atypical alanine residue at position −1 from the prepilin peptidase cleavage site in 42 strains. This alanine deviates from the consensus glycine at this position in Tfp from other species. Yet, cloning of the apfABCD genes under a constitutive promoter in A. pleuropneumoniae resulted in pilin and Tfp assembly. Tfp promoter-luxAB reporter gene fusions demonstrated that the Tfp promoter was intact but tightly regulated. Promoter activity varied with bacterial growth phase and was detected only when bacteria were grown in chemically defined medium. Infection experiments with cultured epithelial cells demonstrated that Tfp promoter activity was upregulated upon adherence of the pathogen to primary cultures of lung epithelial cells. Nonadherent bacteria in the culture supernatant exhibited virtually no promoter activity. A similar upregulation of Tfp promoter activity was observed in vivo during experimental infection of pigs. The host cell contact-induced and in vivo-upregulated Tfp promoter activity in A. pleuropneumoniae adds a new dimension to the diversity of Tfp regulation. PMID:14742510

Basic Hemorheology Advan Physiology Ed v37 n2 p129-134 Usingclassic.pdfC

ERIC Educational Resources Information Center

Toksvang, Linea Natalie; Berg, Ronan M.G.

2013-01-01

"The viscosity of the blood in narrow capillary tubes" by Robin Fahraeus and Torsten Lindqvist ("Am J Physiol" 96: 562--568, 1931) can be a valuable opportunity for teaching basic hemorheological principles in undergraduate cardiovascular physiology. This classic paper demonstrates that a progressive decline in apparent…

Astrophysics. Multiple images of a highly magnified supernova formed by an early-type cluster galaxy lens.

PubMed

Kelly, Patrick L; Rodney, Steven A; Treu, Tommaso; Foley, Ryan J; Brammer, Gabriel; Schmidt, Kasper B; Zitrin, Adi; Sonnenfeld, Alessandro; Strolger, Louis-Gregory; Graur, Or; Filippenko, Alexei V; Jha, Saurabh W; Riess, Adam G; Bradac, Marusa; Weiner, Benjamin J; Scolnic, Daniel; Malkan, Matthew A; von der Linden, Anja; Trenti, Michele; Hjorth, Jens; Gavazzi, Raphael; Fontana, Adriano; Merten, Julian C; McCully, Curtis; Jones, Tucker; Postman, Marc; Dressler, Alan; Patel, Brandon; Cenko, S Bradley; Graham, Melissa L; Tucker, Bradley E

2015-03-06

In 1964, Refsdal hypothesized that a supernova whose light traversed multiple paths around a strong gravitational lens could be used to measure the rate of cosmic expansion. We report the discovery of such a system. In Hubble Space Telescope imaging, we have found four images of a single supernova forming an Einstein cross configuration around a redshift z = 0.54 elliptical galaxy in the MACS J1149.6+2223 cluster. The cluster's gravitational potential also creates multiple images of the z = 1.49 spiral supernova host galaxy, and a future appearance of the supernova elsewhere in the cluster field is expected. The magnifications and staggered arrivals of the supernova images probe the cosmic expansion rate, as well as the distribution of matter in the galaxy and cluster lenses. Copyright © 2015, American Association for the Advancement of Science.

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

PubMed Central

Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

2015-01-01

The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

Convex clustering: an attractive alternative to hierarchical clustering.

PubMed

Chen, Gary K; Chi, Eric C; Ranola, John Michael O; Lange, Kenneth

2015-05-01

The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/.

Molecular Subtyping to Detect Human Listeriosis Clusters

PubMed Central

Sauders, Brian D.; Fortes, Esther D.; Morse, Dale L.; Dumas, Nellie; Kiehlbauch, Julia A.; Schukken, Ynte; Hibbs, Jonathan R.

2003-01-01

We analyzed the diversity (Simpson’s Index, D) and distribution of Listeria monocytogenes in human listeriosis cases in New York State (excluding New York City) from November 1996 to June 2000 by using automated ribotyping and pulsed-field gel electrophoresis (PFGE). We applied a scan statistic (p<0.05) to detect listeriosis clusters caused by a specific Listeria monocytogenes subtype. Of 131 human isolates, 34 (D=0.923) ribotypes and 74 (D=0.975) PFGE types were found. Nine (31% of cases) clusters were identified by ribotype or PFGE; five (18% of cases) clusters were identified by using both methods. Two of the nine clusters (13% of cases) identified corresponded with investigated multistate listeriosis outbreaks. While most human listeriosis cases are considered sporadic, highly discriminatory molecular subtyping approaches thus indicated that 13% to 31% of cases reported in New York State may represent single-source clusters. Listeriosis control and reduction efforts should include broad-based subtyping of human isolates and consider that a large number of cases may represent outbreaks. PMID:12781006

Grain Cluster Microstructure and Grain Boundary Character Distribution in Alloy 690

NASA Astrophysics Data System (ADS)

Xia, Shuang; Zhou, Bangxin; Chen, Wenjue

2009-12-01

The effects of thermal-mechanical processing (TMP) on microstructure evolution during recrystallization and grain boundary character distribution (GBCD) in aged Alloy 690 were investigated by the electron backscatter diffraction (EBSD) technique and optical microscopy. The original grain boundaries of the deformed microstructure did not play an important role in the manipulation of the proportion of the Σ3 n ( n = 1, 2, 3…) type boundaries. Instead, the grain cluster formed by multiple twinning starting from a single nucleus during recrystallization was the key microstructural feature affecting the GBCD. All of the grains in this kind of cluster had Σ3 n mutual misorientations regardless of whether they were adjacent. A large grain cluster containing 91 grains was found in the sample after a small-strain (5 pct) and a high-temperature (1100 °C) recrystallization anneal, and twin relationships up to the ninth generation (Σ39) were found in this cluster. The ratio of cluster size over grain size (including all types of boundaries as defining individual grains) dictated the proportion of Σ3 n boundaries.

Percolation technique for galaxy clustering

NASA Technical Reports Server (NTRS)

Klypin, Anatoly; Shandarin, Sergei F.

1993-01-01

We study percolation in mass and galaxy distributions obtained in 3D simulations of the CDM, C + HDM, and the power law (n = -1) models in the Omega = 1 universe. Percolation statistics is used here as a quantitative measure of the degree to which a mass or galaxy distribution is of a filamentary or cellular type. The very fast code used calculates the statistics of clusters along with the direct detection of percolation. We found that the two parameters mu(infinity), characterizing the size of the largest cluster, and mu-squared, characterizing the weighted mean size of all clusters excluding the largest one, are extremely useful for evaluating the percolation threshold. An advantage of using these parameters is their low sensitivity to boundary effects. We show that both the CDM and the C + HDM models are extremely filamentary both in mass and galaxy distribution. The percolation thresholds for the mass distributions are determined.

Clustered star formation and the origin of stellar masses.

PubMed

Pudritz, Ralph E

2002-01-04

Star clusters are ubiquitous in galaxies of all types and at all stages of their evolution. We also observe them to be forming in a wide variety of environments, ranging from nearby giant molecular clouds to the supergiant molecular clouds found in starburst and merging galaxies. The typical star in our galaxy and probably in others formed as a member of a star cluster, so star formation is an intrinsically clustered and not an isolated phenomenon. The greatest challenge regarding clustered star formation is to understand why stars have a mass spectrum that appears to be universal. This review examines the observations and models that have been proposed to explain these fundamental issues in stellar formation.

A General Class of Signed Rank Tests for Clustered Data when the Cluster Size is Potentially Informative.

PubMed

Datta, Somnath; Nevalainen, Jaakko; Oja, Hannu

2012-09-01

Rank based tests are alternatives to likelihood based tests popularized by their relative robustness and underlying elegant mathematical theory. There has been a serge in research activities in this area in recent years since a number of researchers are working to develop and extend rank based procedures to clustered dependent data which include situations with known correlation structures (e.g., as in mixed effects models) as well as more general form of dependence.The purpose of this paper is to test the symmetry of a marginal distribution under clustered data. However, unlike most other papers in the area, we consider the possibility that the cluster size is a random variable whose distribution is dependent on the distribution of the variable of interest within a cluster. This situation typically arises when the clusters are defined in a natural way (e.g., not controlled by the experimenter or statistician) and in which the size of the cluster may carry information about the distribution of data values within a cluster.Under the scenario of an informative cluster size, attempts to use some form of variance adjusted sign or signed rank tests would fail since they would not maintain the correct size under the distribution of marginal symmetry. To overcome this difficulty Datta and Satten (2008; Biometrics, 64, 501-507) proposed a Wilcoxon type signed rank test based on the principle of within cluster resampling. In this paper we study this problem in more generality by introducing a class of valid tests employing a general score function. Asymptotic null distribution of these tests is obtained. A simulation study shows that a more general choice of the score function can sometimes result in greater power than the Datta and Satten test; furthermore, this development offers the user a wider choice. We illustrate our tests using a real data example on spinal cord injury patients.

Cluster management.

PubMed

Katz, R

1992-11-01

Cluster management is a management model that fosters decentralization of management, develops leadership potential of staff, and creates ownership of unit-based goals. Unlike shared governance models, there is no formal structure created by committees and it is less threatening for managers. There are two parts to the cluster management model. One is the formation of cluster groups, consisting of all staff and facilitated by a cluster leader. The cluster groups function for communication and problem-solving. The second part of the cluster management model is the creation of task forces. These task forces are designed to work on short-term goals, usually in response to solving one of the unit's goals. Sometimes the task forces are used for quality improvement or system problems. Clusters are groups of not more than five or six staff members, facilitated by a cluster leader. A cluster is made up of individuals who work the same shift. For example, people with job titles who work days would be in a cluster. There would be registered nurses, licensed practical nurses, nursing assistants, and unit clerks in the cluster. The cluster leader is chosen by the manager based on certain criteria and is trained for this specialized role. The concept of cluster management, criteria for choosing leaders, training for leaders, using cluster groups to solve quality improvement issues, and the learning process necessary for manager support are described.

Termination of seizure clusters is related to the duration of focal seizures.

PubMed

Ferastraoaru, Victor; Schulze-Bonhage, Andreas; Lipton, Richard B; Dümpelmann, Matthias; Legatt, Alan D; Blumberg, Julie; Haut, Sheryl R

2016-06-01

Clustered seizures are characterized by shorter than usual interseizure intervals and pose increased morbidity risk. This study examines the characteristics of seizures that cluster, with special attention to the final seizure in a cluster. This is a retrospective analysis of long-term inpatient monitoring data from the EPILEPSIAE project. Patients underwent presurgical evaluation from 2002 to 2009. Seizure clusters were defined by the occurrence of at least two consecutive seizures with interseizure intervals of <4 h. Other definitions of seizure clustering were examined in a sensitivity analysis. Seizures were classified into three contextually defined groups: isolated seizures (not meeting clustering criteria), terminal seizure (last seizure in a cluster), and intracluster seizures (any other seizures within a cluster). Seizure characteristics were compared among the three groups in terms of duration, type (focal seizures remaining restricted to one hemisphere vs. evolving bilaterally), seizure origin, and localization concordance among pairs of consecutive seizures. Among 92 subjects, 77 (83%) had at least one seizure cluster. The intracluster seizures were significantly shorter than the last seizure in a cluster (p = 0.011), whereas the last seizure in a cluster resembled the isolated seizures in terms of duration. Although focal only (unilateral), seizures were shorter than seizures that evolved bilaterally and there was no correlation between the seizure type and the seizure position in relation to a cluster (p = 0.762). Frontal and temporal lobe seizures were more likely to cluster compared with other localizations (p = 0.009). Seizure pairs that are part of a cluster were more likely to have a concordant origin than were isolated seizures. Results were similar for the 2 h definition of clustering, but not for the 8 h definition of clustering. We demonstrated that intracluster seizures are short relative to isolated seizures and terminal seizures. Frontal

Clustering cancer gene expression data by projective clustering ensemble

PubMed Central

Yu, Xianxue; Yu, Guoxian

2017-01-01

Gene expression data analysis has paramount implications for gene treatments, cancer diagnosis and other domains. Clustering is an important and promising tool to analyze gene expression data. Gene expression data is often characterized by a large amount of genes but with limited samples, thus various projective clustering techniques and ensemble techniques have been suggested to combat with these challenges. However, it is rather challenging to synergy these two kinds of techniques together to avoid the curse of dimensionality problem and to boost the performance of gene expression data clustering. In this paper, we employ a projective clustering ensemble (PCE) to integrate the advantages of projective clustering and ensemble clustering, and to avoid the dilemma of combining multiple projective clusterings. Our experimental results on publicly available cancer gene expression data show PCE can improve the quality of clustering gene expression data by at least 4.5% (on average) than other related techniques, including dimensionality reduction based single clustering and ensemble approaches. The empirical study demonstrates that, to further boost the performance of clustering cancer gene expression data, it is necessary and promising to synergy projective clustering with ensemble clustering. PCE can serve as an effective alternative technique for clustering gene expression data. PMID:28234920

Vacuum ultraviolet imagery of the Virgo cluster region

NASA Astrophysics Data System (ADS)

Onaka, T.; Tanaka, W.; Watanabe, T.; Watanabe, J.; Yamaguchi, A.; Nakagiri, M.; Kodaira, K.; Nakano, M.; Sasaki, M.; Tsujimura, T.; Yamashita, K.

1989-07-01

The results are reported of an experiment using the UV imager aboard an attitude-controlled S520 type sounding rocket. The total UV fluxes of galaxies in the Virgo Cluster as well as the flux level of the diffuse UV background around the cluster were measured. The data on NGC 4486 and NGC 4472 confirm the variation in the degree of the 'turnup' below 200 nm in the energy spectrum of the total light of elliptical galaxies. At two-color diagram of galaxies of visual/near-UV/vacuum UV indicates that colors of spiral galaxies are distributed within a strip and well-correlated with the morphological type, while elliptical galaxies are located differently from spiral galaxies.

Seizure clustering.

PubMed

Haut, Sheryl R

2006-02-01

Seizure clusters, also known as repetitive or serial seizures, occur commonly in epilepsy. Clustering implies that the occurrence of one seizure may influence the probability of a subsequent seizure; thus, the investigation of the clustering phenomenon yields insights into both specific mechanisms of seizure clustering and more general concepts of seizure occurrence. Seizure clustering has been defined clinically as a number of seizures per unit time and, statistically, as a deviation from a random distribution, or interseizure interval dependence. This review explores the pathophysiology, epidemiology, and clinical implications of clustering, as well as other periodic patterns of seizure occurrence. Risk factors for experiencing clusters and potential precipitants of clustering are also addressed.

XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data

PubMed Central

2015-01-01

Background Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. Results In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. Conclusions Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results. PMID:26328893

Data Clustering

NASA Astrophysics Data System (ADS)

Wagstaff, Kiri L.

2012-03-01

On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained

Locality-Aware CTA Clustering For Modern GPUs

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

Li, Ang; Song, Shuaiwen; Liu, Weifeng

2017-04-08

In this paper, we proposed a novel clustering technique for tapping into the performance potential of a largely ignored type of locality: inter-CTA locality. We first demonstrated the capability of the existing GPU hardware to exploit such locality, both spatially and temporally, on L1 or L1/Tex unified cache. To verify the potential of this locality, we quantified its existence in a broad spectrum of applications and discussed its sources of origin. Based on these insights, we proposed the concept of CTA-Clustering and its associated software techniques. Finally, We evaluated these techniques on all modern generations of NVIDIA GPU architectures. Themore » experimental results showed that our proposed clustering techniques could significantly improve on-chip cache performance.« less

A Wide Variety of Clostridium perfringens Type A Food-Borne Isolates That Carry a Chromosomal cpe Gene Belong to One Multilocus Sequence Typing Cluster

PubMed Central

Xiao, Yinghua; Wagendorp, Arjen; Moezelaar, Roy; Abee, Tjakko

2012-01-01

Of 98 suspected food-borne Clostridium perfringens isolates obtained from a nationwide survey by the Food and Consumer Product Safety Authority in The Netherlands, 59 strains were identified as C. perfringens type A. Using PCR-based techniques, the cpe gene encoding enterotoxin was detected in eight isolates, showing a chromosomal location for seven isolates and a plasmid location for one isolate. Further characterization of these strains by using (GTG)5 fingerprint repetitive sequence-based PCR analysis distinguished C. perfringens from other sulfite-reducing clostridia but did not allow for differentiation between various types of C. perfringens strains. To characterize the C. perfringens strains further, multilocus sequence typing (MLST) analysis was performed on eight housekeeping genes of both enterotoxic and non-cpe isolates, and the data were combined with a previous global survey covering strains associated with food poisoning, gas gangrene, and isolates from food or healthy individuals. This revealed that the chromosomal cpe strains (food strains and isolates from food poisoning cases) belong to a distinct cluster that is significantly distant from all the other cpe plasmid-carrying and cpe-negative strains. These results suggest that different groups of C. perfringens have undergone niche specialization and that a distinct group of food isolates has specific core genome sequences. Such findings have epidemiological and evolutionary significance. Better understanding of the origin and reservoir of enterotoxic C. perfringens may allow for improved control of this organism in foods. PMID:22865060

Polyhydrido Copper Clusters: Synthetic Advances, Structural Diversity, and Nanocluster-to-Nanoparticle Conversion.

PubMed

Dhayal, Rajendra S; van Zyl, Werner E; Liu, C W

2016-01-19

Metal hydride clusters have historically been studied to unravel their aesthetically pleasing molecular structures and interesting properties, especially toward hydrogen related applications. Central to this work is the hydride ligand, H¯, the smallest closed-shell spherical anion known. Two new developments in polyhydrido nanocluster chemistry include the determination of heretofore unknown hydride coordination modes and novel structural constructs, and conversion from the molecular entities to rhombus-shaped copper nanoparticles (CuNPs). These advances, together with hydrogen evolution and catalysis, have provided both experimentalists and theorists with a rich scientific directive to further explore. The isolation of hexameric [{(Ph3P)CuH}6] (Stryker reagent) could be regarded as the springboard for the recent emergence of polyhydrido copper cluster chemistry due to its utilization in a variety of organic chemical transformations. The stability of clusters of various nuclearity was improved through phosphine, pyridine, and carbene type ligands. Our focus lies with the isolation of novel copper (poly)hydride clusters using mostly the phosphor-1,1-dithiolato type ligands. We found such chalcogen-stabilized clusters to be exceptionally air and moisture stable over a wide range of nuclearities (Cu7 to Cu32). In this Account, we (i) report on state-of-the-art copper hydride cluster chemistry, especially with regards to the diverse and novel structural types generally, and newly discovered hydride coordination modes in particular, (ii) demonstrate the indispensable power of neutron diffraction for the unambiguous assignment and location of hydride ligand(s) within a cluster, and (iii) prove unique transformations that can occur not only between well characterized high nuclearity clusters, but also how such clusters can transform to uniquely shaped nanoparticles of several nanometers in diameter through copper hydride reduction. The increase in the number of low- to

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.

The cluster-cluster correlation function. [of galaxies

NASA Technical Reports Server (NTRS)

Postman, M.; Geller, M. J.; Huchra, J. P.

1986-01-01

The clustering properties of the Abell and Zwicky cluster catalogs are studied using the two-point angular and spatial correlation functions. The catalogs are divided into eight subsamples to determine the dependence of the correlation function on distance, richness, and the method of cluster identification. It is found that the Corona Borealis supercluster contributes significant power to the spatial correlation function to the Abell cluster sample with distance class of four or less. The distance-limited catalog of 152 Abell clusters, which is not greatly affected by a single system, has a spatial correlation function consistent with the power law Xi(r) = 300r exp -1.8. In both the distance class four or less and distance-limited samples the signal in the spatial correlation function is a power law detectable out to 60/h Mpc. The amplitude of Xi(r) for clusters of richness class two is about three times that for richness class one clusters. The two-point spatial correlation function is sensitive to the use of estimated redshifts.

"Student Lab"-on-a-Chip: Integrating Low-Cost Microfluidics into Undergraduate Teaching Labs to Study Multiphase Flow Phenomena in Small Vessels

ERIC Educational Resources Information Center

Young, Edmond W. K.; Simmons, Craig A.

2009-01-01

We describe a simple, low-cost laboratory session to demonstrate the Fahraeus-Lindqvist effect, a microphase flow phenomenon that occurs in small blood vessels and alters the effective rheological properties of blood. The experiments are performed by flowing cells through microchannels fabricated by soft lithography and characterization of cell…

Co-clustering directed graphs to discover asymmetries and directional communities

PubMed Central

Rohe, Karl; Qin, Tai; Yu, Bin

2016-01-01

In directed graphs, relationships are asymmetric and these asymmetries contain essential structural information about the graph. Directed relationships lead to a new type of clustering that is not feasible in undirected graphs. We propose a spectral co-clustering algorithm called di-sim for asymmetry discovery and directional clustering. A Stochastic co-Blockmodel is introduced to show favorable properties of di-sim. To account for the sparse and highly heterogeneous nature of directed networks, di-sim uses the regularized graph Laplacian and projects the rows of the eigenvector matrix onto the sphere. A nodewise asymmetry score and di-sim are used to analyze the clustering asymmetries in the networks of Enron emails, political blogs, and the Caenorhabditis elegans chemical connectome. In each example, a subset of nodes have clustering asymmetries; these nodes send edges to one cluster, but receive edges from another cluster. Such nodes yield insightful information (e.g., communication bottlenecks) about directed networks, but are missed if the analysis ignores edge direction. PMID:27791058

Co-clustering directed graphs to discover asymmetries and directional communities.

PubMed

Rohe, Karl; Qin, Tai; Yu, Bin

2016-10-21

In directed graphs, relationships are asymmetric and these asymmetries contain essential structural information about the graph. Directed relationships lead to a new type of clustering that is not feasible in undirected graphs. We propose a spectral co-clustering algorithm called di-sim for asymmetry discovery and directional clustering. A Stochastic co-Blockmodel is introduced to show favorable properties of di-sim To account for the sparse and highly heterogeneous nature of directed networks, di-sim uses the regularized graph Laplacian and projects the rows of the eigenvector matrix onto the sphere. A nodewise asymmetry score and di-sim are used to analyze the clustering asymmetries in the networks of Enron emails, political blogs, and the Caenorhabditis elegans chemical connectome. In each example, a subset of nodes have clustering asymmetries; these nodes send edges to one cluster, but receive edges from another cluster. Such nodes yield insightful information (e.g., communication bottlenecks) about directed networks, but are missed if the analysis ignores edge direction.

Cluster formation in liverwort-associated methylobacteria and its implications.

PubMed

Kutschera, U; Thomas, J; Hornschuh, M

2007-08-01

Pink-pigmented methylotropic bacteria of the genus Methylobacterium inhabit the surfaces of plant organs. In bryophytes, these methylobacteria enhance cell growth, but the nature of this plant-microbe interaction is largely unknown. In this study, methylobacteria were isolated from the upper surface of the free-living thalli of the liverwort Marchantia polymorpha L. Identification of one strain by 16S ribosomal RNA (rRNA) gene-targeted polymerase chain reaction (PCR) and other data show that these microbes represent an undescribed species of the genus Methylobacterium (Methylobacterium sp.). The growth-promoting activity of these wild-type methylobacteria was tested and compared with that of the type strain Methylobacterium mesophilicum. Both types of methylobacteria stimulated surface expansion of isolated gemmae from Marchantia polymorpha by about 350%. When suspended in water, the liverwort-associated bacteria (Methylobacterium sp.) formed dense clusters of up to 600 cells. In liquid cultures of Methylobacterium mesophilicum, single cells were observed, but no clustering occurred. We suggest that the liverwort-associated methylobacteria are co-evolved symbionts of the plants: Cluster formation may be a behavior that enhances the survival of the epiphytic microbes during periods of drought of these desiccation-tolerant lower plants.

Cluster formation in liverwort-associated methylobacteria and its implications

NASA Astrophysics Data System (ADS)

Kutschera, U.; Thomas, J.; Hornschuh, M.

2007-08-01

Pink-pigmented methylotropic bacteria of the genus Methylobacterium inhabit the surfaces of plant organs. In bryophytes, these methylobacteria enhance cell growth, but the nature of this plant-microbe interaction is largely unknown. In this study, methylobacteria were isolated from the upper surface of the free-living thalli of the liverwort Marchantia polymorpha L. Identification of one strain by 16S ribosomal RNA (rRNA) gene-targeted polymerase chain reaction (PCR) and other data show that these microbes represent an undescribed species of the genus Methylobacterium ( Methylobacterium sp.). The growth-promoting activity of these wild-type methylobacteria was tested and compared with that of the type strain Methylobacterium mesophilicum. Both types of methylobacteria stimulated surface expansion of isolated gemmae from Marchantia polymorpha by about 350%. When suspended in water, the liverwort-associated bacteria ( Methylobacterium sp.) formed dense clusters of up to 600 cells. In liquid cultures of Methylobacterium mesophilicum, single cells were observed, but no clustering occurred. We suggest that the liverwort-associated methylobacteria are co-evolved symbionts of the plants: Cluster formation may be a behavior that enhances the survival of the epiphytic microbes during periods of drought of these desiccation-tolerant lower plants.

Computer program documentation: ISOCLS iterative self-organizing clustering program, program C094

NASA Technical Reports Server (NTRS)

Minter, R. T. (Principal Investigator)

1972-01-01

The author has identified the following significant results. This program implements an algorithm which, ideally, sorts a given set of multivariate data points into similar groups or clusters. The program is intended for use in the evaluation of multispectral scanner data; however, the algorithm could be used for other data types as well. The user may specify a set of initial estimated cluster means to begin the procedure, or he may begin with the assumption that all the data belongs to one cluster. The procedure is initiatized by assigning each data point to the nearest (in absolute distance) cluster mean. If no initial cluster means were input, all of the data is assigned to cluster 1. The means and standard deviations are calculated for each cluster.

Unrepaired clustered DNA lesions induce chromosome breakage in human cells

PubMed Central

Asaithamby, Aroumougame; Hu, Burong; Chen, David J.

2011-01-01

Clustered DNA damage induced by ionizing radiation is refractory to repair and may trigger carcinogenic events for reasons that are not well understood. Here, we used an in situ method to directly monitor induction and repair of clustered DNA lesions in individual cells. We showed, consistent with biophysical modeling, that the kinetics of loss of clustered DNA lesions was substantially compromised in human fibroblasts. The unique spatial distribution of different types of DNA lesions within the clustered damages, but not the physical location of these damages within the subnuclear domains, determined the cellular ability to repair the damage. We then examined checkpoint arrest mechanisms and yield of gross chromosomal aberrations. Induction of nonrepairable clustered damage affected only G2 accumulation but not the early G2/M checkpoint. Further, cells that were released from the G2/M checkpoint with unrepaired clustered damage manifested a spectrum of chromosome aberrations in mitosis. Difficulties associated with clustered DNA damage repair and checkpoint release before the completion of clustered DNA damage repair appear to promote genome instability that may lead to carcinogenesis. PMID:21527720

Fission and fusion scenarios for magnetic microswimmer clusters

PubMed Central

Guzmán-Lastra, Francisca; Kaiser, Andreas; Löwen, Hartmut

2016-01-01

Fission and fusion processes of particle clusters occur in many areas of physics and chemistry from subnuclear to astronomic length scales. Here we study fission and fusion of magnetic microswimmer clusters as governed by their hydrodynamic and dipolar interactions. Rich scenarios are found that depend crucially on whether the swimmer is a pusher or a puller. In particular a linear magnetic chain of pullers is stable while a pusher chain shows a cascade of fission (or disassembly) processes as the self-propulsion velocity is increased. Contrarily, magnetic ring clusters show fission for any type of swimmer. Moreover, we find a plethora of possible fusion (or assembly) scenarios if a single swimmer collides with a ringlike cluster and two rings spontaneously collide. Our predictions are obtained by computer simulations and verifiable in experiments on active colloidal Janus particles and magnetotactic bacteria. PMID:27874006

Geometric structure of percolation clusters.

PubMed

Xu, Xiao; Wang, Junfeng; Zhou, Zongzheng; Garoni, Timothy M; Deng, Youjin

2014-01-01

We investigate the geometric properties of percolation clusters by studying square-lattice bond percolation on the torus. We show that the density of bridges and nonbridges both tend to 1/4 for large system sizes. Using Monte Carlo simulations, we study the probability that a given edge is not a bridge but has both its loop arcs in the same loop and find that it is governed by the two-arm exponent. We then classify bridges into two types: branches and junctions. A bridge is a branch iff at least one of the two clusters produced by its deletion is a tree. Starting from a percolation configuration and deleting the branches results in a leaf-free configuration, whereas, deleting all bridges produces a bridge-free configuration. Although branches account for ≈43% of all occupied bonds, we find that the fractal dimensions of the cluster size and hull length of leaf-free configurations are consistent with those for standard percolation configurations. By contrast, we find that the fractal dimensions of the cluster size and hull length of bridge-free configurations are given by the backbone and external perimeter dimensions, respectively. We estimate the backbone fractal dimension to be 1.643 36(10).

Keeping the ball rolling: fullerene-like molecular clusters.

PubMed

Kong, Xiang-Jian; Long, La-Sheng; Zheng, Zhiping; Huang, Rong-Bin; Zheng, Lan-Sun

2010-02-16

The discovery of fullerenes in 1985 opened a new chapter in the chemistry of highly symmetric molecules. Fullerene-like metal clusters, characterized by (multi)shell-like structures, are one rapidly developing class of molecules that share this shape. In addition to creating aesthetically pleasing molecular structures, the ordered arrangement of metal atoms within such frameworks provides the opportunity to develop materials with properties not readily achieved in corresponding mononuclear or lower-nuclearity complexes. In this Account, we survey the great variety of fullerene-like metal-containing clusters with an emphasis on their synthetic and structural chemistry, a first step in the discussion of this fascinating field of cluster chemistry. We group the compounds of interest into three categories based on the atomic composition of the cluster core: those with formal metal-metal bonding, those characterized by ligand participation, and those supported by polyoxometalate building blocks. The number of clusters in the first group, containing metal-metal bonds, is relatively small. However, because of the unique and complex bonding scenarios observed for some of these species, these metalloid clusters present a number of research questions with significant ramifications. Because these cores contain molecular clusters of precious metals at the nanoscale, they offer an opportunity to study chemical properties at size ranges from the molecular to nanoscale and to gain insights into the electronic structures and properties of nanomaterials of similar chemical compositions. Clusters of the second type, whose core structures are facilitated by ligand participation, could aid in the development of functional materials. Of particular interest are the magnetic clusters containing both transition and lanthanide elements. A series of such heterometallic clusters that we prepared demonstrates diverse magnetic properties including antiferromagnetism, ferrimagnetism, and

Condensed Matter Cluster Reactions in LENR Power Cells for a Radical New Type of Space Power Source

NASA Astrophysics Data System (ADS)

Yang, Xiaoling; Miley, George H.; Hora, Heinz

2009-03-01

This paper reviews previous theoretical and experimental study on the possibility of nuclear events in multilayer thin film electrodes (Lipson et al., 2004 and 2005; Miley et al., 2007), including the correlation between excess heat and transmutations (Miley and Shrestha, 2003) and the cluster theory that predicts it. As a result of this added understanding of cluster reactions, a new class of electrodes is under development at the University of Illinois. These electrodes are designed to enhance cluster formation and subsequent reactions. Two approaches are under development. The first employs improved loading-unloading techniques, intending to obtain a higher volumetric density of sites favoring cluster formation. The second is designed to create nanostructures on the electrode where the cluster state is formed by electroless deposition of palladium on nickel micro structures. Power units employing these electrodes should offer unique advantages for space applications. This is a fundamental new nuclear energy source that is environmentally compatible with a minimum of radiation involvement, high specific power, very long lifetime, and scalable from micro power to kilowatts.

An X-Ray Survey of the Open Cluster NGC 6475 (M7) with ROSAT

NASA Technical Reports Server (NTRS)

Prosser, Charles F.; Stauffer, John R.; Caillault, J.-P.; Balachandran, Suchitra; Stern, Robert A.; Randich, Sofia

1995-01-01

A ROSAT x-ray survey, with complimentary optical photometry, of the open cluster NGC 6475 has enabled the detection of approx. 50 late-F to K0 and approx. 70 K/M dwarf new candidate members, providing the first reliable detection of low-mass stars in this low. galactic latitude, 220 Myr old cluster. The x-ray observations reported here have a typical limiting sensitivity of L(sub x) approx. equal to 10(exp 29) erg/s. The detection frequency of early type cluster members is consistent with the hypothesis that the x-ray emitting early type stars are binary systems with an unseen, low-mass secondary producing the x rays. The ratio between x-ray and bolometric luminosity among NGC 6475 members saturates at a spectral-type/color which is intermediate between that in much younger and in much older clusters, consistent with rotational spindown of solar-type stars upon their arrival on the ZAMS. The upper envelope of x-ray luminosity as a function of spectral type is comparable to that of the Pleiades, with the observed spread in x-ray luminosity among low-mass members being likely due to the presence of binaries and relatively rapid rotators. However, the list of x-ray selected candidate members is likely biased against low-mass, slowly rotating single stars. While some preliminary spectroscopic information is given in an appendix, further spectroscopic observations of the new candidate members will aid in interpreting the coronal activity among solar-type NGC 6475 members and their relation to similar stars in older and younger open clusters.

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

Comparing the performance of biomedical clustering methods.

PubMed

Wiwie, Christian; Baumbach, Jan; Röttger, Richard

2015-11-01

Identifying groups of similar objects is a popular first step in biomedical data analysis, but it is error-prone and impossible to perform manually. Many computational methods have been developed to tackle this problem. Here we assessed 13 well-known methods using 24 data sets ranging from gene expression to protein domains. Performance was judged on the basis of 13 common cluster validity indices. We developed a clustering analysis platform, ClustEval (http://clusteval.mpi-inf.mpg.de), to promote streamlined evaluation, comparison and reproducibility of clustering results in the future. This allowed us to objectively evaluate the performance of all tools on all data sets with up to 1,000 different parameter sets each, resulting in a total of more than 4 million calculated cluster validity indices. We observed that there was no universal best performer, but on the basis of this wide-ranging comparison we were able to develop a short guideline for biomedical clustering tasks. ClustEval allows biomedical researchers to pick the appropriate tool for their data type and allows method developers to compare their tool to the state of the art.

Galaxy clusters and cold dark matter - A low-density unbiased universe?

NASA Technical Reports Server (NTRS)

Bahcall, Neta A.; Cen, Renyue

1992-01-01

Large-scale simulations of a universe dominated by cold dark matter (CDM) are tested against two fundamental properties of clusters of galaxies: the cluster mass function and the cluster correlation function. We find that standard biased CDM models are inconsistent with these observations for any bias parameter b. A low-density, low-bias CDM-type model, with or without a cosmological constant, appears to be consistent with both the cluster mass function and the cluster correlations. The low-density model agrees well with the observed correlation function of the Abell, Automatic Plate Measuring Facility (APM), and Edinburgh-Durham cluster catalogs. The model is in excellent agreement with the observed dependence of the correlation strength on cluster mean separation, reproducing the measured universal dimensionless cluster correlation. The low-density model is also consistent with other large-scale structure observations, including the APM angular galaxy-correlations, and for lambda = 1-Omega with the COBE results of the microwave background radiation fluctuations.

Cluster randomised trials in the medical literature: two bibliometric surveys

PubMed Central

Bland, J Martin

2004-01-01

Background Several reviews of published cluster randomised trials have reported that about half did not take clustering into account in the analysis, which was thus incorrect and potentially misleading. In this paper I ask whether cluster randomised trials are increasing in both number and quality of reporting. Methods Computer search for papers on cluster randomised trials since 1980, hand search of trial reports published in selected volumes of the British Medical Journal over 20 years. Results There has been a large increase in the numbers of methodological papers and of trial reports using the term 'cluster random' in recent years, with about equal numbers of each type of paper. The British Medical Journal contained more such reports than any other journal. In this journal there was a corresponding increase over time in the number of trials where subjects were randomised in clusters. In 2003 all reports showed awareness of the need to allow for clustering in the analysis. In 1993 and before clustering was ignored in most such trials. Conclusion Cluster trials are becoming more frequent and reporting is of higher quality. Perhaps statistician pressure works. PMID:15310402

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.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, James F.; Furuya, Frederic R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

Nuclear Rings in the IR: Hidden Super Star Clusters

NASA Astrophysics Data System (ADS)

Maoz, Dan

1997-07-01

We propose NICMOS broad-band {F160W, F187W} and Paschen Alpha {F187N} imaging of nuclear starburst rings in two nearby galaxies. We already have UV {F220W} FOC data, and are scheduled to obtain WFPC2 images in U, V, I, and Halpha+[NII] of these rings. The rings contain large populations of super star clusters similar to those recently discovered in other types of starburst systems. Nuclear rings contain large numbers of these clusters in relatively unobscured starburst environments. Measurement of the age, size, and stellar contents of the clusters can test the hypothesis that super star clusters are young globular clusters. Together with our UV and optical data, NICMOS images will provide the SED of numerous super star clusters over a decade in wavelength. Our already-approved observations will allow us to estimate, by comparison with evolutionary synthesis models, the masses and ages of the clusters. The proposed IR data will be sensitive to the number of supergiants {1.6 micron} and O-stars {Paschen Alpha} in each of the clusters. The observations will provide an independent determination of the reddening, mass, and age of each cluster. We expect to see in the IR numerous clusters that are obscured in the UV and optical. These clusters may be the younger ones, which are still embedded in their molecular clouds. By measuring the mass, age, and size of a large number of clusters, we can actually obtain an evolutionary picture of these objects at different stages in their lives.

The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies.

PubMed

Prosperi, Mattia C F; De Luca, Andrea; Di Giambenedetto, Simona; Bracciale, Laura; Fabbiani, Massimiliano; Cauda, Roberto; Salemi, Marco

2010-10-25

Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation. The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initial conditions, the algorithm can produce different partitions. We describe a procedure that selects a prime partition among a set of candidate ones and calculates a measure of cluster reliability. TBC was successfully tested for the identification of type-1 human immunodeficiency and hepatitis C virus subtypes, and compared with previously established methodologies. It was also evaluated in the problem of HIV-1 intra-patient quasispecies clustering, and for transmission cluster identification, using a set of sequences from patients with known transmission event histories. TBC has been shown to be effective for the subtyping of HIV and HCV, and for identifying intra-patient quasispecies. To some extent, the algorithm was able also to infer clusters corresponding to events of infection transmission. The computational complexity of TBC is quadratic in the number of taxa, lower than other established methods; in addition, TBC has been enhanced with a measure of cluster reliability. The TBC can be useful to characterise molecular quasipecies in a broad context.

Gas Dynamics in Galaxy Clusters

NASA Astrophysics Data System (ADS)

McCourt, Michael Kingsley, Jr.

Galaxy clusters are the most massive structures in the universe and, in the hierarchical pattern of cosmological structure formation, the largest objects in the universe form last. Galaxy clusters are thus interesting objects for a number of reasons. Three examples relevant to this thesis are: 1. Constraining the properties of dark energy: Due to the hierarchical nature of structure formation, the largest objects in the universe form last. The cluster mass function is thus sensitive to the entire expansion history of the universe and can be used to constrain the properties of dark energy. This constraint complements others derived from the CMB or from Type Ia supernovae and provides an important, independent confirmation of such methods. In particular, clusters provide detailed information about the equation of state parameter w because they sample a large redshift range z ˜ 0 - 1. 2. Probing galaxy formation: Clusters contain the most massive galaxies in the uni- verse, and the most massive black holes; because clusters form so late, we can still witness the assembly of these objects in the nearby universe. Clusters thus provide a more detailed view of galaxy formation than is possible in studies of lower-mass ob- jects. An important example comes from x-ray studies of clusters, which unexpectedly found that star formation in massive galaxies in clusters is closely correlated with the properties of the hot, virialized gas in their halos. This correlation persists despite the enormous separation in temperature, in dynamical time-scales, and in length-scales between the virialized gas in the halo and the star-forming regions in the galaxy. This remains a challenge to interpret theoretically. 3. Developing our knowledge of dilute plasmas: The masses and sizes of galaxy clusters imply that the plasma which permeates them is both very hot (˜ 108 K) and very dilute (˜ 10 -2 cm-3). This plasma is collisional enough to be considered a fluid, but collisionless enough to

Site-specific polarizabilities as descriptors of metallic behavior in atomic clusters

NASA Astrophysics Data System (ADS)

Jackson, Koblar; Jellinek, Julius

The electric dipole polarizability of a cluster is a measure of its response to an applied electric field. The site specific polarizability method decomposes the total cluster polarizability into contributions from individual atoms and also allows it to be partitioned into charge transfer and electric dipole contributions. By systematically examining the trends in these quantities for several types of metal atom clusters over a wide range of cluster sizes, we find common characteristics that uniquely link the behavior of the clusters to that of the corresponding bulk metals for clusters as small as 10 atoms. We discuss these trends and compare and contrast them with results for non-metal clusters. This work was supported by the Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences, U.S. Department of Energy under Grant SC0001330 (KAJ) and Contract No. DE-AC02-06CH11357 (JJ).

Pre-processing and post-processing in group-cluster mergers

NASA Astrophysics Data System (ADS)

Vijayaraghavan, R.; Ricker, P. M.

2013-11-01

Galaxies in clusters are more likely to be of early type and to have lower star formation rates than galaxies in the field. Recent observations and simulations suggest that cluster galaxies may be `pre-processed' by group or filament environments and that galaxies that fall into a cluster as part of a larger group can stay coherent within the cluster for up to one orbital period (`post-processing'). We investigate these ideas by means of a cosmological N-body simulation and idealized N-body plus hydrodynamics simulations of a group-cluster merger. We find that group environments can contribute significantly to galaxy pre-processing by means of enhanced galaxy-galaxy merger rates, removal of galaxies' hot halo gas by ram pressure stripping and tidal truncation of their galaxies. Tidal distortion of the group during infall does not contribute to pre-processing. Post-processing is also shown to be effective: galaxy-galaxy collisions are enhanced during a group's pericentric passage within a cluster, the merger shock enhances the ram pressure on group and cluster galaxies and an increase in local density during the merger leads to greater galactic tidal truncation.

Diametrical clustering for identifying anti-correlated gene clusters.

PubMed

Dhillon, Inderjit S; Marcotte, Edward M; Roshan, Usman

2003-09-01

Clustering genes based upon their expression patterns allows us to predict gene function. Most existing clustering algorithms cluster genes together when their expression patterns show high positive correlation. However, it has been observed that genes whose expression patterns are strongly anti-correlated can also be functionally similar. Biologically, this is not unintuitive-genes responding to the same stimuli, regardless of the nature of the response, are more likely to operate in the same pathways. We present a new diametrical clustering algorithm that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i). re-partitioning the genes and (ii). computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a 'diametric' cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method. We present systems whose mRNA expression patterns, and likely their functions, oppose the yeast ribosome and proteosome, along with evidence for the inverse transcriptional regulation of a number of cellular systems.

Inference from clustering with application to gene-expression microarrays.

PubMed

Dougherty, Edward R; Barrera, Junior; Brun, Marcel; Kim, Seungchan; Cesar, Roberto M; Chen, Yidong; Bittner, Michael; Trent, Jeffrey M

2002-01-01

There are many algorithms to cluster sample data points based on nearness or a similarity measure. Often the implication is that points in different clusters come from different underlying classes, whereas those in the same cluster come from the same class. Stochastically, the underlying classes represent different random processes. The inference is that clusters represent a partition of the sample points according to which process they belong. This paper discusses a model-based clustering toolbox that evaluates cluster accuracy. Each random process is modeled as its mean plus independent noise, sample points are generated, the points are clustered, and the clustering error is the number of points clustered incorrectly according to the generating random processes. Various clustering algorithms are evaluated based on process variance and the key issue of the rate at which algorithmic performance improves with increasing numbers of experimental replications. The model means can be selected by hand to test the separability of expected types of biological expression patterns. Alternatively, the model can be seeded by real data to test the expected precision of that output or the extent of improvement in precision that replication could provide. In the latter case, a clustering algorithm is used to form clusters, and the model is seeded with the means and variances of these clusters. Other algorithms are then tested relative to the seeding algorithm. Results are averaged over various seeds. Output includes error tables and graphs, confusion matrices, principal-component plots, and validation measures. Five algorithms are studied in detail: K-means, fuzzy C-means, self-organizing maps, hierarchical Euclidean-distance-based and correlation-based clustering. The toolbox is applied to gene-expression clustering based on cDNA microarrays using real data. Expression profile graphics are generated and error analysis is displayed within the context of these profile graphics. A

Effectiveness of a PLISSIT model intervention in patients with type 2 diabetes mellitus in primary care: design of a cluster-randomised controlled trial.

PubMed

Rutte, Anne; van Oppen, Patricia; Nijpels, Giel; Snoek, Frank J; Enzlin, Paul; Leusink, Peter; Elders, Petra J M

2015-06-02

Sexual dysfunction is prevalent in patients with type 2 diabetes mellitus, but remains one of the most frequently neglected complications in diabetes care. Both patients and care providers appear to have difficulty with discussing sexual problems in diabetes care. A sexual counselling model for care providers, such as the PLISSIT model, might be a useful tool to improve the discussion of sexual issues in patients with type 2 diabetes mellitus. PLISSIT stands for Permission, Limited Information, Specific Suggestions, and Intensive Therapy. Even though the use of the PLISSIT model has often been recommended in diabetes care, no evidence with regards to its effectiveness in patients with type 2 diabetes mellitus exists. This study describes the design of a cluster-randomised controlled trial evaluating the effectiveness of a PLISSIT-model intervention in men and women with type 2 diabetes mellitus in primary care. Patients with type 2 diabetes mellitus, aged 40-75 years, who indicate to be dissatisfied about their sexual functioning and that they would like to talk about their sexual problem(s) with their general practitioner are recruited. All participants receive an information leaflet from the practice nurse. In the intervention group, each participant will also receive sexual counselling based on the PLISSIT model from their general practitioner. In the control group, usual care will be provided to those participants requesting an appointment with their general practitioner when the information leaflet was not deemed sufficient. Primary outcomes include sexual functioning, satisfaction about sexual function, and quality of life. Secondary outcomes are depressive symptoms, sexual distress, emotional well-being, and treatment satisfaction. Outcomes will be measured by means of self-report questionnaires at baseline, and after 3 and 12 months post-baseline. Treatment satisfaction will be assessed in telephone interviews. This paper describes the design of a cluster

Morphology of size-selected Ptn clusters on CeO2(111)

NASA Astrophysics Data System (ADS)

Shahed, Syed Mohammad Fakruddin; Beniya, Atsushi; Hirata, Hirohito; Watanabe, Yoshihide

2018-03-01

Supported Pt catalysts and ceria are well known for their application in automotive exhaust catalysts. Size-selected Pt clusters supported on a CeO2(111) surface exhibit distinct physical and chemical properties. We investigated the morphology of the size-selected Ptn (n = 5-13) clusters on a CeO2(111) surface using scanning tunneling microscopy at room temperature. Ptn clusters prefer a two-dimensional morphology for n = 5 and a three-dimensional (3D) morphology for n ≥ 6. We further observed the preference for a 3D tri-layer structure when n ≥ 10. For each cluster size, we quantitatively estimated the relative fraction of the clusters for each type of morphology. Size-dependent morphology of the Ptn clusters on the CeO2(111) surface was attributed to the Pt-Pt interaction in the cluster and the Pt-O interaction between the cluster and CeO2(111) surface. The results obtained herein provide a clear understanding of the size-dependent morphology of the Ptn clusters on a CeO2(111) surface.

Morphology of size-selected Ptn clusters on CeO2(111).

PubMed

Shahed, Syed Mohammad Fakruddin; Beniya, Atsushi; Hirata, Hirohito; Watanabe, Yoshihide

2018-03-21

Supported Pt catalysts and ceria are well known for their application in automotive exhaust catalysts. Size-selected Pt clusters supported on a CeO 2 (111) surface exhibit distinct physical and chemical properties. We investigated the morphology of the size-selected Pt n (n = 5-13) clusters on a CeO 2 (111) surface using scanning tunneling microscopy at room temperature. Pt n clusters prefer a two-dimensional morphology for n = 5 and a three-dimensional (3D) morphology for n ≥ 6. We further observed the preference for a 3D tri-layer structure when n ≥ 10. For each cluster size, we quantitatively estimated the relative fraction of the clusters for each type of morphology. Size-dependent morphology of the Pt n clusters on the CeO 2 (111) surface was attributed to the Pt-Pt interaction in the cluster and the Pt-O interaction between the cluster and CeO 2 (111) surface. The results obtained herein provide a clear understanding of the size-dependent morphology of the Pt n clusters on a CeO 2 (111) surface.

Detecting cancer clusters in a regional population with local cluster tests and Bayesian smoothing methods: a simulation study

PubMed Central

2013-01-01

Background There is a rising public and political demand for prospective cancer cluster monitoring. But there is little empirical evidence on the performance of established cluster detection tests under conditions of small and heterogeneous sample sizes and varying spatial scales, such as are the case for most existing population-based cancer registries. Therefore this simulation study aims to evaluate different cluster detection methods, implemented in the open soure environment R, in their ability to identify clusters of lung cancer using real-life data from an epidemiological cancer registry in Germany. Methods Risk surfaces were constructed with two different spatial cluster types, representing a relative risk of RR = 2.0 or of RR = 4.0, in relation to the overall background incidence of lung cancer, separately for men and women. Lung cancer cases were sampled from this risk surface as geocodes using an inhomogeneous Poisson process. The realisations of the cancer cases were analysed within small spatial (census tracts, N = 1983) and within aggregated large spatial scales (communities, N = 78). Subsequently, they were submitted to the cluster detection methods. The test accuracy for cluster location was determined in terms of detection rates (DR), false-positive (FP) rates and positive predictive values. The Bayesian smoothing models were evaluated using ROC curves. Results With moderate risk increase (RR = 2.0), local cluster tests showed better DR (for both spatial aggregation scales > 0.90) and lower FP rates (both < 0.05) than the Bayesian smoothing methods. When the cluster RR was raised four-fold, the local cluster tests showed better DR with lower FPs only for the small spatial scale. At a large spatial scale, the Bayesian smoothing methods, especially those implementing a spatial neighbourhood, showed a substantially lower FP rate than the cluster tests. However, the risk increases at this scale were mostly diluted by data

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

The Globular Cluster NGC 6402 (M14). II. Variable Stars

NASA Astrophysics Data System (ADS)

Contreras Peña, C.; Catelan, M.; Grundahl, F.; Stephens, A. W.; Smith, H. A.

2018-03-01

We present time-series BVI photometry for the Galactic globular cluster NGC 6402 (M14). The data consist of ∼137 images per filter, obtained using the 0.9 and 1.0 m SMARTS telescopes at the Cerro Tololo Inter-American Observatory. The images were obtained during two observing runs in 2006–2007. The image-subtraction package ISIS, along with DAOPHOT II/ALLFRAME, was used to perform crowded-field photometry and search for variable stars. We identified 130 variables, eight of which are new discoveries. The variable star population is comprised of 56 ab-type RR Lyrae stars, 54 c-type RR Lyrae, 6 type II Cepheids, 1 W UMa star, 1 detached eclipsing binary, and 12 long-period variables. We provide Fourier decomposition parameters for the RR Lyrae, and discuss the physical parameters and photometric metallicity derived therefrom. The M14 distance modulus is also discussed, based on different approaches for the calibration of the absolute magnitudes of RR Lyrae stars. The possible presence of second-overtone RR Lyrae in M14 is critically addressed, with our results arguing against this possibility. By considering all of the RR Lyrae stars as members of the cluster, we derive < {P}ab > =0.589 {{d}}{{a}}{{y}}{{s}}. This, together with the position of the RR Lyrae stars of both Bailey types in the period–amplitude diagram, suggests an Oosterhoff-intermediate classification for the cluster. Such an intermediate Oosterhoff type is much more commonly found in nearby extragalactic systems, and we critically discuss several other possible indications that may point to an extragalactic origin for this cluster. Based on observations obtained with the 0.9 m and 1 m telescopes at the Cerro Tololo Inter-American Observatory, Chile, operated by the SMARTS consortium.

The HectoMAP Cluster Survey. II. X-Ray Clusters

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

Sohn, Jubee; Chon, Gayoung; Bohringer, Hans

Here, we apply a friends-of-friends algorithm to the HectoMAP redshift survey and cross-identify associated X-ray emission in the ROSAT All-Sky Survey data (RASS). The resulting flux-limited catalog of X-ray cluster surveys is complete to a limiting flux of ~3 × 10 –13 erg s –1 cm –2 and includes 15 clusters (7 newly discovered) with redshifts z ≤ 0.4. HectoMAP is a dense survey (~1200 galaxies deg –2) that provides ~50 members (median) in each X-ray cluster. We provide redshifts for the 1036 cluster members. Subaru/Hyper Suprime-Cam imaging covers three of the X-ray systems and confirms that they are impressivemore » clusters. The HectoMAP X-ray clusters have an L X–σ cl scaling relation similar to that of known massive X-ray clusters. The HectoMAP X-ray cluster sample predicts ~12,000 ± 3000 detectable X-ray clusters in RASS to the limiting flux, comparable with previous estimates.« less

The HectoMAP Cluster Survey. II. X-Ray Clusters

DOE PAGES

Sohn, Jubee; Chon, Gayoung; Bohringer, Hans; ...

2018-03-10

Here, we apply a friends-of-friends algorithm to the HectoMAP redshift survey and cross-identify associated X-ray emission in the ROSAT All-Sky Survey data (RASS). The resulting flux-limited catalog of X-ray cluster surveys is complete to a limiting flux of ~3 × 10 –13 erg s –1 cm –2 and includes 15 clusters (7 newly discovered) with redshifts z ≤ 0.4. HectoMAP is a dense survey (~1200 galaxies deg –2) that provides ~50 members (median) in each X-ray cluster. We provide redshifts for the 1036 cluster members. Subaru/Hyper Suprime-Cam imaging covers three of the X-ray systems and confirms that they are impressivemore » clusters. The HectoMAP X-ray clusters have an L X–σ cl scaling relation similar to that of known massive X-ray clusters. The HectoMAP X-ray cluster sample predicts ~12,000 ± 3000 detectable X-ray clusters in RASS to the limiting flux, comparable with previous estimates.« less

Cluster optical coding: from biochips to counterfeit security

NASA Astrophysics Data System (ADS)

Haglmueller, Jakob; Alguel, Yilmaz; Mayer, Christian; Matyushin, Viacheslav; Bauer, Georg; Pittner, Fritz; Leitner, Alfred; Aussenegg, Franz R.; Schalkhammer, Thomas G.

2004-07-01

Spatially tuned resonant nano-clusters allow high local field enhancement when exited by electromagnetic radiation. A number of phenomena had been described and subsequently applied to novel nano- and bionano-devices. Decisive for these types of devices and sensors is the precise nanometric assembly, coupling the local field surrounding a cluster to allow resonance with other elements interacting with this field. In particular, the distance cluster-mirror or cluster-fluorophore gives rise to a variety of enhancement phenomena. High throughput transducers using metal cluster resonance technology are based on surface-enhancement of metal cluster light absorption (SEA). The optical property for the analytical application of metal cluster films is the so-called anomalous absorption. At a well defined nanometric distance of a cluster to a mirror the reflected electromagnetic field has the same phase at the position of the absorbing cluster as the incident fields. This feedback mechanism strongly enhances the effective cluster absorption coefficient. The system is characterised by a narrow reflection minimum. Based on this SEA-phenomenon (licensed to and further developed and optimized by NovemberAG, Germany Erlangen) a number of commercial products have been constructed. Brandsealing(R) uses the patented SEA cluster technology to produce optical codings. Cluster SEA thin film systems show a characteristic color-flip effect and are extremely mechanically and thermally robust. This is the basis for its application as an unique security feature. The specific spectroscopic properties as e.g. narrow band multi-resonance of the cluster layers allow the authentication of the optical code which can be easily achieved with a mobile hand-held reader developed by november AG and Siemens AG. Thus, these features are machine-readable which makes them superior to comparable technologies. Cluster labels are available in two formats: as a label for tamper-proof product packaging, and

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.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, J.F.; Furuya, F.R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

A General Class of Signed Rank Tests for Clustered Data when the Cluster Size is Potentially Informative

PubMed Central

Datta, Somnath; Nevalainen, Jaakko; Oja, Hannu

2012-01-01

SUMMARY Rank based tests are alternatives to likelihood based tests popularized by their relative robustness and underlying elegant mathematical theory. There has been a serge in research activities in this area in recent years since a number of researchers are working to develop and extend rank based procedures to clustered dependent data which include situations with known correlation structures (e.g., as in mixed effects models) as well as more general form of dependence. The purpose of this paper is to test the symmetry of a marginal distribution under clustered data. However, unlike most other papers in the area, we consider the possibility that the cluster size is a random variable whose distribution is dependent on the distribution of the variable of interest within a cluster. This situation typically arises when the clusters are defined in a natural way (e.g., not controlled by the experimenter or statistician) and in which the size of the cluster may carry information about the distribution of data values within a cluster. Under the scenario of an informative cluster size, attempts to use some form of variance adjusted sign or signed rank tests would fail since they would not maintain the correct size under the distribution of marginal symmetry. To overcome this difficulty Datta and Satten (2008; Biometrics, 64, 501–507) proposed a Wilcoxon type signed rank test based on the principle of within cluster resampling. In this paper we study this problem in more generality by introducing a class of valid tests employing a general score function. Asymptotic null distribution of these tests is obtained. A simulation study shows that a more general choice of the score function can sometimes result in greater power than the Datta and Satten test; furthermore, this development offers the user a wider choice. We illustrate our tests using a real data example on spinal cord injury patients. PMID:23074359

Fission and fusion scenarios for magnetic microswimmer clusters

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

Guzmán-Lastra, Francisca; Kaiser, Andreas; Löwen, Hartmut

Fission and fusion processes of particle clusters occur in many areas of physics and chemistry from subnuclear to astronomic length scales. Here we study fission and fusion of magnetic microswimmer clusters as governed by their hydrodynamic and dipolar interactions. Rich scenarios are found that depend crucially on whether the swimmer is a pusher or a puller. In particular a linear magnetic chain of pullers is stable while a pusher chain shows a cascade of fission (or disassembly) processes as the self-propulsion velocity is increased. Contrarily, magnetic ring clusters show fission for any type of swimmer. Moreover, we find a plethoramore » of possible fusion (or assembly) scenarios if a single swimmer collides with a ringlike cluster and two rings spontaneously collide. Lastly, our predictions are obtained by computer simulations and verifiable in experiments on active colloidal Janus particles and magnetotactic bacteria.« less

Fission and fusion scenarios for magnetic microswimmer clusters

DOE PAGES

Guzmán-Lastra, Francisca; Kaiser, Andreas; Löwen, Hartmut

2016-11-22

Fission and fusion processes of particle clusters occur in many areas of physics and chemistry from subnuclear to astronomic length scales. Here we study fission and fusion of magnetic microswimmer clusters as governed by their hydrodynamic and dipolar interactions. Rich scenarios are found that depend crucially on whether the swimmer is a pusher or a puller. In particular a linear magnetic chain of pullers is stable while a pusher chain shows a cascade of fission (or disassembly) processes as the self-propulsion velocity is increased. Contrarily, magnetic ring clusters show fission for any type of swimmer. Moreover, we find a plethoramore » of possible fusion (or assembly) scenarios if a single swimmer collides with a ringlike cluster and two rings spontaneously collide. Lastly, our predictions are obtained by computer simulations and verifiable in experiments on active colloidal Janus particles and magnetotactic bacteria.« less

Early-type galaxies in the Antlia cluster: catalogue and isophotal analysis

NASA Astrophysics Data System (ADS)

Calderón, Juan P.; Bassino, Lilia P.; Cellone, Sergio A.; Gómez, Matías

2018-06-01

We present a statistical isophotal analysis of 138 early-type galaxies in the Antlia cluster, located at a distance of ˜ 35 Mpc. The observational material consists of CCD images of four 36 × 36 arcmin2 fields obtained with the MOSAIC II camera at the Blanco 4-m telescope at Cerro Tololo Interamerican Observatory. Our present work supersedes previous Antlia studies in the sense that the covered area is four times larger, the limiting magnitude is MB ˜ -9.6 mag, and the surface photometry parameters of each galaxy are derived from Sérsic model fits extrapolated to infinity. In a companion previous study we focused on the scaling relations obtained by means of surface photometry, and now we present the data, on which the previous paper is based, the parameters of the isophotal fits as well as an isophotal analysis. For each galaxy, we derive isophotal shape parameters along the semimajor axis and search for correlations within different radial bins. Through extensive statistical tests, we also analyse the behaviour of these values against photometric and global parameters of the galaxies themselves. While some galaxies do display radial gradients in their ellipticity (ɛ) and/or their Fourier coefficients, differences in mean values between adjacent regions are not statistically significant. Regarding Fourier coefficients, dwarf galaxies usually display gradients between all adjacent regions, while non-dwarfs tend to show this behaviour just between the two outermost regions. Globally, there is no obvious correlation between Fourier coefficients and luminosity for the whole magnitude range (-12 ≳ MV ≳ -22); however, dwarfs display much higher dispersions at all radii.

Reactivity of Cubane-Type [(OC)(3)MFe(3)S(4)(SR)(3)](3-) Clusters (M = Mo, W): Interconversion with Cuboidal [Fe(3)S(4)](0) Clusters and Electron Transfer.

PubMed

Raebiger, James W.; Crawford, Charles A.; Zhou, Jian; Holm, R. H.

1997-03-12

The title clusters, several examples of which have been reported earlier, have been prepared by two different methods and subjected to structural and reactivity studies. The compounds (Et(4)N)(3)[(OC)(3)MFe(3)S(4)(Smes)(3)].MeCN (M = Mo/W) are isomorphous and crystallize in monoclinic space group P2(1)/n with a = 13.412(1)/13.297(1) Å, b = 19.0380(1)/18.9376(3) Å, c = 26.4210(1)/26.2949(1) Å, beta = 97.87(1)/97.549(1) degrees, and Z = 4. The clusters contain long M-S (2.62/2.59 Å) and M-Fe (3.22/3.19 Å) bonds, consistent with the reported structure of [(OC)(3)MoFe(3)S(4)(SEt)(3)](3-) (3). Reaction of [(OC)(3)MoFe(3)S(4)(LS(3))](3-) (7) with CO in the presence of NaPF(6) affords cuboidal [Fe(3)S(4)(LS(3))](3-) (9), also prepared in this laboratory by another route as a synthetic analogue of protein-bound [Fe(3)S(4)](0) clusters. The clusters [Fe(3)S(4)(SR)(3)](3-) (R = mes, Et), of limited stability, were generated by the same reaction. Treatment of 9 with [M(CO)(3)(MeCN)(3)] affords 7 and its M = W analogue. The clusters [(OC)(3)MFe(3)S(4)(SR)(3)](3-) form a four-member electron transfer series in which the 3- cluster can be once reduced (4-) and twice oxidized (2-, 1-) to afford clusters of the indicated charges. The correct assignment of redox couple to potential in the redox series of six clusters is presented, correcting an earlier misassignment of the redox series of 3. Carbonyl stretching frequencies are shown to be sensitive to cluster oxidation state, showing that the M sites and Fe(3)S(4) fragments are electronically coupled despite the long bond distances. (LS(3) = 1,3,5-tris((4,6-dimethyl-3-mercaptophenyl)thio)-2,4,6-tris(p-tolylthio)benzenate(3-); mes = mesityl.)

Photodissociation of nitromethane cluster anions.

PubMed

Goebbert, Daniel J; Khuseynov, Dmitry; Sanov, Andrei

2010-08-28

Three types of anionic fragments are observed in the photodissociation of nitromethane cluster anions, (CH(3)NO(2))(n)(-), n=1-6, at 355 nm: NO(2)(-)(CH(3)NO(2))(k), (CH(3)NO(2))(k)(-), and OH(-) (kclusters containing a monomer-anion core, CH(3)NO(2)(-), solvated by n-1 neutral nitromethane molecules. The NO(2)(-)(CH(3)NO(2))(k) and OH(-) fragments formed from these clusters are described as core-dissociation products, while the (CH(3)NO(2))(k)(-) fragments are attributed to energy transfer from excited CH(3)NO(2)(-) into the solvent network or a core-dissociation-recombination (caging) mechanism. As with other cluster families, the fraction of caged photofragments shows an overall increase with increasing cluster size. The low-lying A(2)A' and/or B(2)A' electronic states of CH(3)NO(2)(-) are believed responsible for photoabsorption leading to dissociation to NO(2)(-) based fragments, while the C(2)A" state is a candidate for the OH(-) pathway. Compared to neutral nitromethane, the photodissociation of CH(3)NO(2)(-) requires lower energy photons because the photochemically active electron occupies a high energy pi* orbital (which is vacant in the neutral). Although the electronic states in the photodissociation of CH(3)NO(2) and CH(3)NO(2)(-) are different, the major fragments, CH(3)+NO(2) and CH(3)+NO(2)(-), respectively, both form via C-N bond cleavage.

A nonparametric clustering technique which estimates the number of clusters

NASA Technical Reports Server (NTRS)

Ramey, D. B.

1983-01-01

In applications of cluster analysis, one usually needs to determine the number of clusters, K, and the assignment of observations to each cluster. A clustering technique based on recursive application of a multivariate test of bimodality which automatically estimates both K and the cluster assignments is presented.

Cluster formation by allelomimesis in real-world complex adaptive systems

NASA Astrophysics Data System (ADS)

Juanico, Dranreb Earl; Monterola, Christopher; Saloma, Caesar

2005-04-01

Animal and human clusters are complex adaptive systems and many organize in cluster sizes s that obey the frequency distribution D(s)∝s-τ . The exponent τ describes the relative abundance of the cluster sizes in a given system. Data analyses reveal that real-world clusters exhibit a broad spectrum of τ values, 0.7 (tuna fish schools) ⩽τ⩽4.61 (T4 bacteriophage gene family sizes). Allelomimesis is proposed as an underlying mechanism for adaptation that explains the observed broad τ spectrum. Allelomimesis is the tendency of an individual to imitate the actions of others and two cluster systems have different τ values when their component agents display unequal degrees of allelomimetic tendencies. Cluster formation by allelomimesis is shown to be of three general types: namely, blind copying, information-use copying, and noncopying. Allelomimetic adaptation also reveals that the most stable cluster size is formed by three strongly allelomimetic individuals. Our finding is consistent with available field data taken from killer whales and marmots.

Galaxy Clusters

NASA Astrophysics Data System (ADS)

Miller, Christopher J. Miller

2012-03-01

There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations

Testing Numerical Models of Cool Core Galaxy Cluster Formation with X-Ray Observations

NASA Astrophysics Data System (ADS)

Henning, Jason W.; Gantner, Brennan; Burns, Jack O.; Hallman, Eric J.

2009-12-01

Using archival Chandra and ROSAT data along with numerical simulations, we compare the properties of cool core and non-cool core galaxy clusters, paying particular attention to the region beyond the cluster cores. With the use of single and double β-models, we demonstrate a statistically significant difference in the slopes of observed cluster surface brightness profiles while the cluster cores remain indistinguishable between the two cluster types. Additionally, through the use of hardness ratio profiles, we find evidence suggesting cool core clusters are cooler beyond their cores than non-cool core clusters of comparable mass and temperature, both in observed and simulated clusters. The similarities between real and simulated clusters supports a model presented in earlier work by the authors describing differing merger histories between cool core and non-cool core clusters. Discrepancies between real and simulated clusters will inform upcoming numerical models and simulations as to new ways to incorporate feedback in these systems.

Subtype-specific differentiation of cardiac pacemaker cell clusters from human induced pluripotent stem cells.

PubMed

Schweizer, Patrick A; Darche, Fabrice F; Ullrich, Nina D; Geschwill, Pascal; Greber, Boris; Rivinius, Rasmus; Seyler, Claudia; Müller-Decker, Karin; Draguhn, Andreas; Utikal, Jochen; Koenen, Michael; Katus, Hugo A; Thomas, Dierk

2017-10-16

Human induced pluripotent stem cells (hiPSC) harbor the potential to differentiate into diverse cardiac cell types. Previous experimental efforts were primarily directed at the generation of hiPSC-derived cells with ventricular cardiomyocyte characteristics. Aiming at a straightforward approach for pacemaker cell modeling and replacement, we sought to selectively differentiate cells with nodal-type properties. hiPSC were differentiated into spontaneously beating clusters by co-culturing with visceral endoderm-like cells in a serum-free medium. Subsequent culturing in a specified fetal bovine serum (FBS)-enriched cell medium produced a pacemaker-type phenotype that was studied in detail using quantitative real-time polymerase chain reaction (qRT-PCR), immunocytochemistry, and patch-clamp electrophysiology. Further investigations comprised pharmacological stimulations and co-culturing with neonatal cardiomyocytes. hiPSC co-cultured in a serum-free medium with the visceral endoderm-like cell line END-2 produced spontaneously beating clusters after 10-12 days of culture. The pacemaker-specific genes HCN4, TBX3, and TBX18 were abundantly expressed at this early developmental stage, while levels of sarcomeric gene products remained low. We observed that working-type cardiomyogenic differentiation can be suppressed by transfer of early clusters into a FBS-enriched cell medium immediately after beating onset. After 6 weeks under these conditions, sinoatrial node (SAN) hallmark genes remained at high levels, while working-type myocardial transcripts (NKX2.5, TBX5) were low. Clusters were characterized by regular activity and robust beating rates (70-90 beats/min) and were triggered by spontaneous Ca 2+ transients recapitulating calcium clock properties of genuine pacemaker cells. They were responsive to adrenergic/cholinergic stimulation and able to pace neonatal rat ventricular myocytes in co-culture experiments. Action potential (AP) measurements of cells individualized

Anharmonic effects in large-amplitude vibrations of metal clusters

NASA Astrophysics Data System (ADS)

Karpeshin, F. F.; da Providência, J.; Providência, C.; da Providência, J., Jr.

2002-03-01

Two types of extreme collective motion, large-amplitude many-phonon vibration of the ionic core and rotation of the cluster with high angular momenta, are considered. The interplay between vibration and collective motion towards fission is discussed. A new mechanism of formation and rupture of the neck is proposed which is based on the Franck-Condon principle, and accounts for the interplay between vibration and fission. Under rotation, the change of the shape of the cluster and a phase transition from axially symmetric to triaxial ellipsoid are predicted. For studying the effects, vibrational motion can be induced by laser radiation. Rotational motion may arise in collisions of clusters.

Investigating a tuberculosis cluster among Filipino health care workers in a low-incidence country.

PubMed

Davidson, J A; Fulton, N; Thomas, H L; Lalor, M K; Zenner, D; Brown, T; Murphy, S; Anderson, L F

2018-03-01

Nearly 8% of adult tuberculosis (TB) cases in England, Wales and Northern Ireland (EW&NI) occur among health care workers (HCWs), the majority of whom are from high TB incidence countries. To determine if a TB cluster containing multiple HCWs was due to nosocomial transmission. A cluster of TB cases notified in EW&NI from 2009 to 2014, with indistinguishable 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) profiles, was identified through routine national cluster review. Cases were investigated to identify epidemiological links, and occupational health (OH) information was collected for HCW cases. To further discriminate strains, typing of eight additional loci was conducted. Of the 53 cases identified, 22 were HCWs. The majority (n = 43), including 21 HCWs, were born in the Philippines. Additional typing split the cluster into three subclusters and seven unique strains. No epidemiological links were identified beyond one household and a common residential area. HCWs in this cluster received no or inadequate OH assessment. The MIRU-VNTR profile of this cluster probably reflects common endemic strains circulating in the Philippines, with reactivation occurring in the UK. Furthermore, 32-locus typing showed that 24-locus MIRU-VNTR failed to distinguish strain diversity. The lack of OH assessment indicates that latent tuberculous infection could have been identified and treated, thereby preventing active cases from occurring.

Composition of clusters and building blocks in amylopectins from maize mutants deficient in starch synthase III.

PubMed

Zhu, Fan; Bertoft, Eric; Seetharaman, Koushik

2013-12-18

Branches in amylopectin are distributed along the backbone. Units of the branches are building blocks (smaller) and clusters (larger) based on the distance between branches. In this study, composition of clusters and building blocks of amylopectins from dull1 maize mutants deficient in starch synthase III (SSIII) with a common genetic background (W64A) were characterized and compared with the wild type. Clusters were produced from amylopectins by partial hydrolysis using α-amylase of Bacillus amyloliquefaciens and were subsequently treated with phosphorylase a and β-amylase to produce φ,β-limit dextrins. Clusters were further extensively hydrolyzed with the α-amylase to produce building blocks. Structures of clusters and building blocks were analyzed by diverse chromatographic techniques. The results showed that the dull1 mutation resulted in larger clusters with more singly branched building blocks. The average cluster contained ~5.4 blocks in dull1 mutants and ~4.2 blocks in the wild type. The results are compared with previous results from SSIII-deficient amo1 barley and suggest fundamental differences in the cluster structures.

Narcolepsy with and without cataplexy, idiopathic hypersomnia with and without long sleep time: a cluster analysis.

PubMed

Šonka, Karel; Šusta, Marek; Billiard, Michel

2015-02-01

The successive editions of the International Classification of Sleep Disorders (ICSD) reflect the evolution of the concepts of various sleep disorders. This is particularly the case for central disorders of hypersomnolence, with continuous changes in terminology and divisions of narcolepsy, idiopathic hypersomnia, and recurrent hypersomnia. According to the ICSD 2nd Edition (ICSD-2), narcolepsy with cataplexy (NwithC), narcolepsy without cataplexy (Nw/oC), idiopathic hypersomnia with long sleep time (IHwithLST), and idiopathic hypersomnia without long sleep time (IHw/oLST) are four, well-defined hypersomnias of central origin. However, in the absence of biological markers, doubts have been raised as to the relevance of a division of idiopathic hypersomnia into two forms, and it is not yet clear whether Nw/oC and IHw/oLST are two distinct entities. With this in mind, it was decided to empirically review the ICSD-2 classification by using a hierarchical cluster analysis to see whether this division has some relevance, even though the terms "with long sleep time" and "without long sleep time" are inappropriate. The cluster analysis differentiated three main clusters: Cluster 1, "combined monosymptomatic hypersomnia/narcolepsy type 2" (people initially diagnosed with IHw/oLST and Nw/oC); Cluster 2 "polysymptomatic hypersomnia" (people initially diagnosed with IHwithLST); and Cluster 3, narcolepsy type 1 (people initially diagnosed with NwithC). Cluster analysis confirmed that narcolepsy type 1 and polysymptomatic hypersomnia are independent sleep disorders. People who were initially diagnosed with Nw/oC and IHw/oLST formed a single cluster, referred to as "combined monosymptomatic hypersomnia/narcolepsy type 2." Copyright © 2014 Elsevier B.V. All rights reserved.

The origin of dwarf early-type galaxies

NASA Astrophysics Data System (ADS)

Toloba, E.

2013-05-01

We have conducted a spectrophotometric study of dwarf early-type galaxies (dEs) in the Virgo cluster and in regions of lower density. We have found that these galaxies show many properties in common with late-type galaxies but not with more massive early-types (E/S0). The properties of the dEs in Virgo show gradients within the cluster. dEs in the outer parts of the Virgo cluster are kinematically supported by rotation, while those in the center are supported by the random motions of their stars (i.e. pressure supported). The rotationally supported dEs have disky isophotes and faint underlying spiral/irregular substructures, they also show younger ages than those pressure supported, which have boxy isophotes and are smooth and regular, without any substructure. We compare the position of these dEs with massive early-type galaxies in the Faber-Jackson and Fundamental Plane relations, and we find that, although there is no difference between the position of rotationally and pressure supported dEs, both deviate from the relations of massive early-type galaxies in the direction of dwarf spheroidal systems (dSphs). We have used their offset with respect to the Fundamental Plane of E/S0 galaxies to estimate their dark matter fraction. All the properties studied in this work agree with a ram pressure stripping scenario, where late-type galaxies infall into the cluster, their interaction with the intergalactic medium blows away their gas and, as a result, they are quenched in a small amount of time. However, those dEs in the center of the cluster seem to have been fully transformed leaving no trace of their possible spiral origin, thus, if that is the case, they must have experienced a more violent mechanism in combination with ram pressure stripping, the open problem is that even galaxy harassment does not fully explain the observed properties for the pressure supported dEs in the center of the Virgo cluster.

ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network.

PubMed

Wang, Jianxin; Zhong, Jiancheng; Chen, Gang; Li, Min; Wu, Fang-xiang; Pan, Yi

2015-01-01

Cluster analysis of biological networks is one of the most important approaches for identifying functional modules and predicting protein functions. Furthermore, visualization of clustering results is crucial to uncover the structure of biological networks. In this paper, ClusterViz, an APP of Cytoscape 3 for cluster analysis and visualization, has been developed. In order to reduce complexity and enable extendibility for ClusterViz, we designed the architecture of ClusterViz based on the framework of Open Services Gateway Initiative. According to the architecture, the implementation of ClusterViz is partitioned into three modules including interface of ClusterViz, clustering algorithms and visualization and export. ClusterViz fascinates the comparison of the results of different algorithms to do further related analysis. Three commonly used clustering algorithms, FAG-EC, EAGLE and MCODE, are included in the current version. Due to adopting the abstract interface of algorithms in module of the clustering algorithms, more clustering algorithms can be included for the future use. To illustrate usability of ClusterViz, we provided three examples with detailed steps from the important scientific articles, which show that our tool has helped several research teams do their research work on the mechanism of the biological networks.

Techniques and computations for mapping plot clusters that straddle stand boundaries

Treesearch

Charles T. Scott; William A. Bechtold

1995-01-01

Many regional (extensive) forest surveys use clusters of subplots or prism points to reduce survey costs. Two common methods of handling clusters that straddle stand boundaries entail: (1) moving all subplots into a single forest cover type, or (2)"averaging" data across multiple conditions without regard to the boundaries. these methods result in biased...

Upgrading of the LGD cluster at JINR to support DLNP experiments

NASA Astrophysics Data System (ADS)

Bednyakov, I. V.; Dolbilov, A. G.; Ivanov, Yu. P.

2017-01-01

Since its construction in 2005, the Computing Cluster of the Dzhelepov Laboratory of Nuclear Problems has been mainly used to perform calculations (data analysis, simulation, etc.) for various scientific collaborations in which DLNP scientists take an active part. The Cluster also serves to train specialists. Much has changed in the past decades, and the necessity has arisen to upgrade the cluster, increasing its power and replacing the outdated equipment to maintain its reliability and modernity. In this work we describe the experience of performing this upgrading, which can be helpful for system administrators to put new equipment for clusters of this type into operation quickly and efficiently.

GibbsCluster: unsupervised clustering and alignment of peptide sequences.

PubMed

Andreatta, Massimo; Alvarez, Bruno; Nielsen, Morten

2017-07-03

Receptor interactions with short linear peptide fragments (ligands) are at the base of many biological signaling processes. Conserved and information-rich amino acid patterns, commonly called sequence motifs, shape and regulate these interactions. Because of the properties of a receptor-ligand system or of the assay used to interrogate it, experimental data often contain multiple sequence motifs. GibbsCluster is a powerful tool for unsupervised motif discovery because it can simultaneously cluster and align peptide data. The GibbsCluster 2.0 presented here is an improved version incorporating insertion and deletions accounting for variations in motif length in the peptide input. In basic terms, the program takes as input a set of peptide sequences and clusters them into meaningful groups. It returns the optimal number of clusters it identified, together with the sequence alignment and sequence motif characterizing each cluster. Several parameters are available to customize cluster analysis, including adjustable penalties for small clusters and overlapping groups and a trash cluster to remove outliers. As an example application, we used the server to deconvolute multiple specificities in large-scale peptidome data generated by mass spectrometry. The server is available at http://www.cbs.dtu.dk/services/GibbsCluster-2.0. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Elucidation of the Pattern of the Onset of Male Lower Urinary Tract Symptoms Using Cluster Analysis: Efficacy of Tamsulosin in Each Symptom Group.

PubMed

Aikawa, Ken; Kataoka, Masao; Ogawa, Soichiro; Akaihata, Hidenori; Sato, Yuichi; Yabe, Michihiro; Hata, Junya; Koguchi, Tomoyuki; Kojima, Yoshiyuki; Shiragasawa, Chihaya; Kobayashi, Toshimitsu; Yamaguchi, Osamu

2015-08-01

To present a new grouping of male patients with lower urinary tract symptoms (LUTS) based on symptom patterns and clarify whether the therapeutic effect of α1-blocker differs among the groups. We performed secondary analysis of anonymous data from 4815 patients enrolled in a postmarketing surveillance study of tamsulosin in Japan. Data on 7 International Prostate Symptom Score (IPSS) items at the initial visit were used in the cluster analysis. IPSS and quality of life (QOL) scores before and after tamsulosin treatment for 12 weeks were assessed in each cluster. Partial correlation coefficients were also obtained for IPSS and QOL scores based on changes before and after treatment. Five symptom groups were identified by cluster analysis of IPSS. On their symptom profile, each cluster was labeled as minimal type (cluster 1), multiple severe type (cluster 2), weak stream type (cluster 3), storage type (cluster 4), and voiding type (cluster 5). Prevalence and the mean symptom score were significantly improved in almost all symptoms in all clusters by tamsulosin treatment. Nocturia and weak stream had the strongest effect on QOL in clusters 1, 2, and 4 and clusters 3 and 5, respectively. The study clarified that 5 characteristic symptom patterns exist by cluster analysis of IPSS in male patients with LUTS. Tamsulosin improved various symptoms and QOL in each symptom group. The study reports many male patients with LUTS being satisfied with monotherapy using tamsulosin and suggests the usefulness of α1-blockers as a drug of first choice. Copyright © 2015 Elsevier Inc. All rights reserved.

Perspectives on seizure clusters: Gaps in lexicon, awareness, and treatment.

PubMed

Buelow, Janice M; Shafer, Patricia; Shinnar, Ruth; Austin, Joan; Dewar, Sandra; Long, Lucretia; O'Hara, Kathryn; Santilli, Nancy

2016-04-01

Seizure clusters in epilepsy can result in serious outcomes such as missed work or school, postictal psychosis, emergency room visits, or hospitalizations, and yet they are often not included in discussions between health-care professionals (HCPs) and their patients. The purpose of this paper was to describe and compare consumer (patient and caregivers) and professional understanding of seizure clusters and to describe how consumers and HCPs communicate regarding seizure clusters. We reviewed social media discussion sites to explore consumers' understanding of seizure clusters. We analyzed professional (medical) literature to explore the HCPs' understanding of seizure clusters. Major themes were revealed in one or both groups, including: communication about diagnosis; frequency, duration, and time frame; seizure type and pattern; severity; and self-management. When comparing discussions of professionals and consumers, both consumers and clinicians discussed the definition of seizure clusters. Discussions of HCPs were understandably clinically focused, and consumer discussions reflected the experience of seizure clusters; however, both groups struggled with a common lexicon. Seizure cluster events remain a problem associated with serious outcomes. Herein, we outline the lack of a common understanding and recommend the development of a common lexicon to improve communication regarding seizure clusters. Copyright © 2016 Upsher-Smith Laboratories, Inc. Published by Elsevier Inc. All rights reserved.

The impact of radiation feedback on the assembly of star clusters in a galactic context

NASA Astrophysics Data System (ADS)

Guillard, Nicolas; Emsellem, Eric; Renaud, Florent

2018-07-01

Massive star clusters are observed in galaxies spanning a broad range of luminosities and types, and are assumed to form in dense gas-rich environments. Using a parsec-resolution hydrodynamical simulation of an isolated gas-rich low-mass galaxy, we discuss here the non-linear effects of stellar feedback on the properties of star clusters with a focus on the progenitors of nuclear clusters. Our simulation shows two categories of star clusters: those for which feedback expels gas leftovers associated with their formation sites, and those, in a denser environment, around which feedback fails to totally clear the gas. We confirm that radiation feedback (photoionization and radiative pressure) plays a more important role than Type II supernovae in destroying dense gas structures, and in altering or quenching the subsequent cluster formation. Radiation feedback also disturbs the cluster mass growth, by increasing the internal energy of the gas component to the point at which radiation pressure overcomes the cluster gravity. We discuss how these effects may depend on the local properties of the interstellar medium, and also on the details of the subgrid recipes, which can affect the available cluster gas reservoirs, the evolution of potential nuclear cluster progenitors, and the overall galaxy morphology.

Type-Ia Supernova Rates to Redshift 2.4 from Clash: The Cluster Lensing and Supernova Survey with Hubble

NASA Technical Reports Server (NTRS)

Graur, O.; Rodney, S. A.; Maoz, D.; Riess, A. G.; Jha, S. W.; Postman, M.; Dahlen, T.; Holoien, T. W.-S.; McCully, C.; Patel, B.;

Type-Ia supernova rates to redshift 2.4 from clash: The cluster lensing and supernova survey with Hubble

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

Graur, O.; Rodney, S. A.; Riess, A. G.

2014-03-01

We present the supernova (SN) sample and Type-Ia SN (SN Ia) rates from the Cluster Lensing And Supernova survey with Hubble (CLASH). Using the Advanced Camera for Surveys and the Wide Field Camera 3 on the Hubble Space Telescope (HST), we have imaged 25 galaxy-cluster fields and parallel fields of non-cluster galaxies. We report a sample of 27 SNe discovered in the parallel fields. Of these SNe, ∼13 are classified as SN Ia candidates, including four SN Ia candidates at redshifts z > 1.2. We measure volumetric SN Ia rates to redshift 1.8 and add the first upper limit onmore » the SN Ia rate in the range 1.8 < z < 2.4. The results are consistent with the rates measured by the HST/GOODS and Subaru Deep Field SN surveys. We model these results together with previous measurements at z < 1 from the literature. The best-fitting SN Ia delay-time distribution (DTD; the distribution of times that elapse between a short burst of star formation and subsequent SN Ia explosions) is a power law with an index of −1.00{sub −0.06(0.10)}{sup +0.06(0.09)} (statistical){sub −0.08}{sup +0.12} (systematic), where the statistical uncertainty is a result of the 68% and 95% (in parentheses) statistical uncertainties reported for the various SN Ia rates (from this work and from the literature), and the systematic uncertainty reflects the range of possible cosmic star-formation histories. We also test DTD models produced by an assortment of published binary population synthesis (BPS) simulations. The shapes of all BPS double-degenerate DTDs are consistent with the volumetric SN Ia measurements, when the DTD models are scaled up by factors of 3-9. In contrast, all BPS single-degenerate DTDs are ruled out by the measurements at >99% significance level.« less

Classification of microvascular patterns via cluster analysis reveals their prognostic significance in glioblastoma.

PubMed

Chen, Long; Lin, Zhi-Xiong; Lin, Guo-Shi; Zhou, Chang-Fu; Chen, Yu-Peng; Wang, Xing-Fu; Zheng, Zong-Qing

2015-01-01

There are limited researches focusing on microvascular patterns (MVPs) in human glioblastoma and their prognostic impact. We evaluated MVPs of 78 glioblastomas by CD34/periodic acid-Schiff dual staining and by cluster analysis of the percentage of microvascular area for distinct microvascular formations. The distribution of 5 types of basic microvascular formations, that is, microvascular sprouting (MS), vascular cluster (VC), vascular garland (VG), glomeruloid vascular proliferation (GVP), and vasculogenic mimicry (VM), was variable. Accordingly, cluster analysis classified MVPs into 2 types: type I MVP displayed prominent MSs and VCs, whereas type II MVP had numerous VGs, GVPs, and VMs. By analyzing the proportion of microvascular area for each type of formation, we determined that glioblastomas with few MSs and VCs had many GVPs and VMs, and vice versa. VG seemed to be a transitional type of formation. In case of type I MVP, expression of Ki-67 and p53 but not MGMT was significantly higher as compared with those of type II MVP (P < .05). Survival analysis showed that the type of MVPs presented as an independent prognostic factor of progression-free survival (PFS) and overall survival (OS) (both P < .001). Type II MVP had a more negative influence on PFS and OS than did type I MVP. We conclude that the heterogeneous MVPs in glioblastoma can be categorized properly by certain histopathologic and statistical analyses and may influence clinical outcome. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

X-Ray source populations in old open clusters: Collinder 261

NASA Astrophysics Data System (ADS)

Vats, Smriti; van den Berg, Maureen; Wijnands, Rudy

2014-09-01

We are carrying out an X-ray survey of old open clusters with the Chandra X-ray Observatory. Single old stars, being slow rotators, are very faint in X-rays (L_X < 1×10^27 erg/s). Hence, X-rays produced by mass transfer in cataclysmic variables (CVs) or by rapid rotation of the stars in tidally locked, detached binaries (active binaries; ABs) can be detected, without contamination from single stars. By comparing the properties of various types of interacting binaries in different environments (the Galactic field, old open clusters, globular clusters), we aim to study binary evolution and how it may be affected by dynamical encounters with other cluster stars. Stellar clusters are good targets to study binaries, as age, distance, chemical composition, are well constrained. Collinder (Cr) 261 is an old open cluster (age ~ 7 Gyr), with one of the richest populations inferred of close binaries and blue stragglers of all open clusters and is therefore an obvious target to study the products of close encounters in open clusters. We will present the first results of this study, detailing the low-luminosity X-ray population of Cr 261, in conjunction with other open clusters in our survey (NGC 188, Berkeley 17, NGC 6253, M67, NGC 6791) and in comparison with populations in globular clusters.

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

Membership determination of open clusters based on a spectral clustering method

NASA Astrophysics Data System (ADS)

Gao, Xin-Hua

2018-06-01

We present a spectral clustering (SC) method aimed at segregating reliable members of open clusters in multi-dimensional space. The SC method is a non-parametric clustering technique that performs cluster division using eigenvectors of the similarity matrix; no prior knowledge of the clusters is required. This method is more flexible in dealing with multi-dimensional data compared to other methods of membership determination. We use this method to segregate the cluster members of five open clusters (Hyades, Coma Ber, Pleiades, Praesepe, and NGC 188) in five-dimensional space; fairly clean cluster members are obtained. We find that the SC method can capture a small number of cluster members (weak signal) from a large number of field stars (heavy noise). Based on these cluster members, we compute the mean proper motions and distances for the Hyades, Coma Ber, Pleiades, and Praesepe clusters, and our results are in general quite consistent with the results derived by other authors. The test results indicate that the SC method is highly suitable for segregating cluster members of open clusters based on high-precision multi-dimensional astrometric data such as Gaia data.

Cluster Analysis of Indonesian Province Based on Household Primary Cooking Fuel Using K-Means

NASA Astrophysics Data System (ADS)

Huda, S. N.

2017-03-01

Each household definitely provides installations for cooking. Kerosene, which is refined from petroleum products once dominated types of primary fuel for cooking in Indonesia, whereas kerosene has an expensive cost and small efficiency. Other household use LPG as their primary cooking fuel. However, LPG supply is also limited. In addition, with a very diverse environments and cultures in Indonesia led to diversity of the installation type of cooking, such as wood-burning stove brazier. The government is also promoting alternative fuels, such as charcoal briquettes, and fuel from biomass. The use of other fuels is part of the diversification of energy that is expected to reduce community dependence on petroleum-based fuels. The use of various fuels in cooking that vary from one region to another reflects the distribution of fuel basic use by household. By knowing the characteristics of each province, the government can take appropriate policies to each province according each character. Therefore, it would be very good if there exist a cluster analysis of all provinces in Indonesia based on the type of primary cooking fuel in household. Cluster analysis is done using K-Means method with K ranging from 2-5. Cluster results are validated using Silhouette Coefficient (SC). The results show that the highest SC achieved from K = 2 with SC value 0.39135818388151. Two clusters reflect provinces in Indonesia, one is a cluster of more traditional provinces and the other is a cluster of more modern provinces. The cluster results are then shown in a map using Google Map API.

Globular Cluster Variable Stars—Atlas and Coordinate Improvement using AAVSOnet Telescopes (Abstract)

NASA Astrophysics Data System (ADS)

Welch, D.; Henden, A.; Bell, T.; Suen, C.; Fare, I.; Sills, A.

2015-12-01

(Abstract only) The variable stars of globular clusters have played and continue to play a significant role in our understanding of certain classes of variable stars. Since all stars associated with a cluster have the same age, metallicity, distance and usually very similar (if not identical reddenings), such variables can produce uniquely powerful constraints on where certain types of pulsation behaviors are excited. Advanced amateur astronomers are increasingly well-positioned to provide long-term CCD monitoring of globular cluster variable star but are hampered by a long history of poor or inaccessible finder charts and coordinates. Many of variable-rich clusters have published photographic finder charts taken in relatively poor seeing with blue-sensitive photographic plates. While useful signal-to-noise ratios are relatively straightforward to achieve for RR Lyrae, Type 2 Cepheids, and red giant variables, correct identification remains a difficult issue—particularly when images are taken at V or longer wavelengths. We describe the project and report its progress using the OC61, TMO61, and SRO telescopes of AAVSOnet after the first year of image acquisition and demonstrate several of the data products being developed for globular cluster variables.

Cancer detection based on Raman spectra super-paramagnetic clustering

NASA Astrophysics Data System (ADS)

González-Solís, José Luis; Guizar-Ruiz, Juan Ignacio; Martínez-Espinosa, Juan Carlos; Martínez-Zerega, Brenda Esmeralda; Juárez-López, Héctor Alfonso; Vargas-Rodríguez, Héctor; Gallegos-Infante, Luis Armando; González-Silva, Ricardo Armando; Espinoza-Padilla, Pedro Basilio; Palomares-Anda, Pascual

2016-08-01

The clustering of Raman spectra of serum sample is analyzed using the super-paramagnetic clustering technique based in the Potts spin model. We investigated the clustering of biochemical networks by using Raman data that define edge lengths in the network, and where the interactions are functions of the Raman spectra's individual band intensities. For this study, we used two groups of 58 and 102 control Raman spectra and the intensities of 160, 150 and 42 Raman spectra of serum samples from breast and cervical cancer and leukemia patients, respectively. The spectra were collected from patients from different hospitals from Mexico. By using super-paramagnetic clustering technique, we identified the most natural and compact clusters allowing us to discriminate the control and cancer patients. A special interest was the leukemia case where its nearly hierarchical observed structure allowed the identification of the patients's leukemia type. The goal of this study is to apply a model of statistical physics, as the super-paramagnetic, to find these natural clusters that allow us to design a cancer detection method. To the best of our knowledge, this is the first report of preliminary results evaluating the usefulness of super-paramagnetic clustering in the discipline of spectroscopy where it is used for classification of spectra.

The Origin of Dwarf Early-Type Galaxies

NASA Astrophysics Data System (ADS)

Toloba, Elisa

2012-10-01

Abridge. We have conducted a spectrophotometric study of dwarf early-type galaxies (dEs) in the Virgo cluster and in regions of lower density. We have found that these galaxies show many properties in common with late-type galaxies but not with more massive early-types (E/S0). The properties of the dEs in Virgo show gradients within the cluster. dEs in the outer parts of the Virgo cluster are kinematically supported by rotation, while those in the center are supported by the random motions of their stars (i.e. pressure supported). The rotationally supported dEs have disky isophotes and faint underlying spiral/irregular substructures, they also show younger ages than those pressure supported, which have boxy isophotes and are smooth and regular, without any substructure. We compare the position of these dEs with massive early-type galaxies in the Faber-Jackson and Fundamental Plane relations, and we find that, although there is no difference between the position of rotationally and pressure supported dEs, both deviate from the relations of massive early-type galaxies in the direction of dwarf spheroidal systems (dSphs). We have used their offset with respect to the Fundamental Plane of E/S0 galaxies to estimate their dark matter fraction. All the properties studied in this work agree with a ram pressure stripping scenario, where late-type galaxies infall into the cluster, their interaction with the intergalactic medium blows away their gas and, as a result, they are quenched in a small amount of time. However, those dEs in the center of the cluster seem to have been fully transformed leaving no trace of their possible spiral origin, thus, if that is the case, they must have experienced a more violent mechanism in combination with ram pressure stripping.

Lithium Abundances in the Young Open Cluster IC 2602

NASA Technical Reports Server (NTRS)

Randich, S.; Aharpour, N.; Pallavicini, R.; Prosser, C. F.; Stauffer, J. R.

1997-01-01

We have obtained high-resolution spectra for 28 candidate late-type stars in the 30 Myr old cluster IC 2602. NLTE Li abundances have been derived from measured equivalent widths. The log n(Li) - T(sub eff) and log n(Li) - mass distributions for our sample stars have been compared with those of the Pleiades and alpha Persei. Our data show that F stars in the three clusters have the same lithium content, which corresponds to the initial content for Pop. I stars. G and early-K IC 2602 stars are, on average, somewhat more Li-rich than their counterparts in the two slightly older clusters. Finally, the latest-type IC 2602 stars are heavily Li depleted, with their Li content being as low as the lowest measured among the Pleiades. As in the Pleiades and alpha Per, a star-to-star scatter in lithium is observed among 30 Myr old late-K/early-K dwarfs in IC 2602, indicating that this spread develops in the pre-main sequence phases.

Quenching of the star formation activity in cluster galaxies

NASA Astrophysics Data System (ADS)

Boselli, A.; Roehlly, Y.; Fossati, M.; Buat, V.; Boissier, S.; Boquien, M.; Burgarella, D.; Ciesla, L.; Gavazzi, G.; Serra, P.

2016-11-01

We study the star formation quenching mechanism in cluster galaxies by fitting the spectral energy distribution (SED) of the Herschel Reference Survey, a complete volume-limited K-band-selected sample of nearby galaxies including objects in different density regions, from the core of the Virgo cluster to the general field. The SEDs of the target galaxies were fitted using the CIGALE SED modelling code. The truncated activity of cluster galaxies was parametrised using a specific star formation history with two free parameters, the quenching age QA and the quenching factor QF. These two parameters are crucial for the identification of the quenching mechanism, which acts on long timescales when starvation processes are at work, but is rapid and efficient when ram pressure occurs. To be sensitive to an abrupt and recent variation of the star formation activity, we combined twenty photometric bands in the UV to far-infrared in a new way with three age-sensitive Balmer line absorption indices extracted from available medium-resolution (R 1000) integrated spectroscopy and with Hα narrow-band imaging data. The use of a truncated star formation history significantly increases the quality of the fit in HI-deficient galaxies of the sample, that is to say, in those objects whose atomic gas content has been removed during the interaction with the hostile cluster environment. The typical quenching age of the perturbed late-type galaxies is QA ≲ 300 Myr whenever the activity of star formation is reduced by 50% < QF ≤ 80% and QA ≲ 500 Myr for QF > 80%, while that of the quiescent early-type objects is QA ≃ 1-3 Gyr. The fraction of late-type galaxies with a star formation activity reduced by QF > 80% and with an HI-deficiency parameter HI-def > 0.4 drops by a factor of 5 from the inner half virial radius of the Virgo cluster (R/Rvir < 0.5), where the hot diffuse X-ray emitting gas of the cluster is located, to the outer regions (R/Rvir > 4). The efficient quenching of the

Whole-Genome Sequencing of Recent Listeria monocytogenes Isolates from Germany Reveals Population Structure and Disease Clusters.

PubMed

Halbedel, Sven; Prager, Rita; Fuchs, Stephan; Trost, Eva; Werner, Guido; Flieger, Antje

2018-06-01

Listeria monocytogenes causes foodborne outbreaks with high mortality. For improvement of outbreak cluster detection, the German consiliary laboratory for listeriosis implemented whole-genome sequencing (WGS) in 2015. A total of 424 human L. monocytogenes isolates collected in 2007 to 2017 were subjected to WGS and core-genome multilocus sequence typing (cgMLST). cgMLST grouped the isolates into 38 complexes, reflecting 4 known and 34 unknown disease clusters. Most of these complexes were confirmed by single nucleotide polymorphism (SNP) calling, but some were further differentiated. Interestingly, several cgMLST cluster types were further subtyped by pulsed-field gel electrophoresis, partly due to phage insertions in the accessory genome. Our results highlight the usefulness of cgMLST for routine cluster detection but also show that cgMLST complexes require validation by methods providing higher typing resolution. Twelve cgMLST clusters included recent cases, suggesting activity of the source. Therefore, the cgMLST nomenclature data presented here may support future public health actions. Copyright © 2018 American Society for Microbiology.