bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple power electronic controller for photovoltaic fed grid‐tied systems using line commutated inverter with fixed firing angle
Authors: Binu Ben Jose D.R. , Ammasai Gounden N. , Ravishankar Jayashri 
Published: February 2014

A power electronic interface with maximum power point tracking (MPPT) for grid connected photovoltaic (PV) systems using an integrated cascade boost converter (ICBC) and line commutated inverter (LCI) has been proposed. The variable dc voltage of the PV array is fed as input to the ICBC and the output voltage of the ICBC is maintained constant with the firing angle of the LCI being fixed at an appropriate value greater than 90°. The interesting feature of this scheme is that, it is not mandatory that the constant dc‐link voltage should be more than the peak value of the grid voltage. As the array voltage is now boosted and fixed at the dc link, any variation in the PV output power is reflected in the variation of the dc‐link current and hence only one parameter (the dc‐link current) sensing is required for the MPPT. Furthermore, the proposed controller has made it possible to dispense with the step up transformer between the LCI and the utility grid. The complete scheme has been constructed and experiments have been conducted on an 84 V, 10 A PV array feeding power to a three‐phase 230 V utility grid and the experimental results are compared with the MATLAB simulation results. The steady‐state analysis of the overall system and the experimental results confirm the validity of the proposed controller and the efficacy of the analysis.
Amperometric biosensor for cholesterol based on novel nanocomposite array gold nanoparticles/acetone‐extracted propolis/multiwall carbon nanotubes/gold
Authors: Molaei Rahim , Sabzi Reza Emamali , Farhadi Khalil , Kheiri Farshad , Forough Mehrdad 
Published: February 2014

In this reported work, the electrochemical behaviour of gold electrodes modified with gold nanoparticles, acetone‐extracted propolis, multiwall carbon nanotubes and cholesterol oxidase was established for the detection of hydrogen peroxide by using cyclic voltammetry and amperometric techniques. The obtained results confirmed that the current enzymatic biosensor exhibits a fast, highly sensitive, and cost‐effective detection of cholesterol. Cholesterol in the concentration range of 0.15–0.55 mmol l−1 was determined with a detection limit of 4.9 × 10−5 mol l−1 by the amperometric method, and the sensitivity of the proposed method was found to be 17.38 µA/mmol l−1. Normal electroactive species such as ascorbic acid and glucose in the presence of the constant concentration of cholesterol in the samples do not interfere with the determination.
Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology
Authors: Damrauer Jeffrey S. , Hoadley Katherine A. , Chism David D. , Fan Cheng , Tiganelli Christopher J. , Wobker Sara E. , Yeh Jen Jen , Milowsky Matthew I. , Iyer Gopa , Parker Joel S. , Kim William Y. 
Published: February 2014

Significance
The identification of molecular subtype heterogeneity in breast cancer has allowed a deeper understanding of breast cancer biology. We present evidence that there are two intrinsic subtypes of high-grade bladder cancer, basal-like and luminal, which reflect the hallmarks of breast biology. Moreover, we have developed an accurate gene set predictor of molecular subtype, the BASE47, that should allow the incorporation of subtype stratification into clinical trials. Further clinical, etiologic, and therapeutic response associations will be of interest in future investigations.
Outbreak ofTsukamurellaSpecies Bloodstream Infection among Patients at an Oncology Clinic, West Virginia, 2011–2012
Authors: See Isaac , Nguyen Duc B. , Chatterjee Somu , Shwe Thein , Scott Melissa , Ibrahim Sherif , Moulton-Meissner Heather , McNulty Steven , Noble-Wang Judith , Price Cindy , Schramm Kim , Bixler Danae , Guh Alice Y. 
Published: February 2014

Objective.To determine the source and identify control measures of an outbreak ofTsukamurellaspecies bloodstream infections at an outpatient oncology facility.Design.Epidemiologic investigation of the outbreak with a case-control study.Methods.A case was an infection in whichTsukamurellaspecies was isolated from a blood or catheter tip culture during the period January 2011 through June 2012 from a patient of the oncology clinic. Laboratory records of area hospitals and patient charts were reviewed. A case-control study was conducted among clinic patients to identify risk factors forTsukamurellaspecies bloodstream infection. Clinic staff were interviewed, and infection control practices were assessed.Results.Fifteen cases ofTsukamurella (Tsukamurella pulmonisorTsukamurella tyrosinosolvens) bloodstream infection were identified, all in patients with underlying malignancy and indwelling central lines. The median age of case patients was 68 years; 47% were male. The only significant risk factor for infection was receipt of saline flush from the clinic during the period September–October 2011 (P= .03), when the clinic had been preparing saline flush from a common-source bag of saline. Other infection control deficiencies that were identified at the clinic included suboptimal procedures for central line access and preparation of chemotherapy.Conclusion.Although multiple infection control lapses were identified, the outbreak was likely caused by improper preparation of saline flush syringes by the clinic. The outbreak demonstrates that bloodstream infections among oncology patients can result from improper infection control practices and highlights the critical need for increased attention to and oversight of infection control in outpatient oncology settings.
Identifying critical transitions of complex diseases based on a single sample
Authors: Liu Rui , Yu Xiangtian , Liu Xiaoping , Xu Dong , Aihara Kazuyuki , Chen Luonan 
Published: February 2014

Abstract
Motivation: Unlike traditional diagnosis of an existing disease state, detecting the pre-disease state just before the serious deterioration of a disease is a challenging task, because the state of the system may show little apparent change or symptoms before this critical transition during disease progression. By exploring the rich interaction information provided by high-throughput data, the dynamical network biomarker (DNB) can identify the pre-disease state, but this requires multiple samples to reach a correct diagnosis for one individual, thereby restricting its clinical application.
Results: In this article, we have developed a novel computational approach based on the DNB theory and differential distributions between the expressions of DNB and non-DNB molecules, which can detect the pre-disease state reliably even from a single sample taken from one individual, by compensating insufficient samples with existing datasets from population studies. Our approach has been validated by the successful identification of pre-disease samples from subjects or individuals before the emergence of disease symptoms for acute lung injury, influenza and breast cancer.
Contact: lnchen@sibs.ac.cn.
Supplementary information: Supplementary data are available at Bioinformatics online.
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
Authors: May Ali , Abeln Sanne , Crielaard Wim , Heringa Jaap , Brandt Bernd W. 
Published: February 2014

Abstract
Motivation: 16S rDNA pyrosequencing is a powerful approach that requires extensive usage of computational methods for delineating microbial compositions. Previously, it was shown that outcomes of studies relying on this approach vastly depend on the choice of pre-processing and clustering algorithms used. However, obtaining insights into the effects and accuracy of these algorithms is challenging due to difficulties in generating samples of known composition with high enough diversity. Here, we use in silico microbial datasets to better understand how the experimental data are transformed into taxonomic clusters by computational methods.
Results: We were able to qualitatively replicate the raw experimental pyrosequencing data after rigorously adjusting existing simulation software. This allowed us to simulate datasets of real-life complexity, which we used to assess the influence and performance of two widely used pre-processing methods along with 11 clustering algorithms. We show that the choice, order and mode of the pre-processing methods have a larger impact on the accuracy of the clustering pipeline than the clustering methods themselves. Without pre-processing, the difference between the performances of clustering methods is large. Depending on the clustering algorithm, the most optimal analysis pipeline resulted in significant underestimations of the expected number of clusters (minimum: 3.4%; maximum: 13.6%), allowing us to make quantitative estimations of the bacterial complexity of real microbiome samples.
Contact: a.may@vu.nl or b.brandt@acta.nl
Supplementary information: Supplementary data are available at Bioinformatics online. The simulated datasets are available via http://www.ibi.vu.nl/downloads.
HUM calculator and HUM package for R: easy-to-use software tools for multicategory receiver operating characteristic analysis
Authors: Novoselova Natalia , Della Beffa Cristina , Wang Junxi , Li Jialiang , Pessler Frank , Klawonn Frank 
Published: February 2014

Abstract
Summary: Receiver operating characteristic (ROC) analysis is usually applied in bioinformatics to evaluate the abilities of biological markers to differentiate between the presence or absence of a disease. It includes the derivation of the useful scalar performance measure area under the ROC curve for binary classification tasks. As real applications often deal with more than two classes, multicategory ROC analysis and the corresponding hypervolume under the manifold (HUM) measure have become a topic of growing interest. To support researchers in carrying out multicategory ROC analysis, we have developed two tools in different programming environments which feature user-friendly, object-oriented and flexible interfaces and enable the user to compute HUM values and plot 2D- and 3D-ROC curves.
Availability: The software is freely available from our Web site http://public.ostfalia.de/∼klawonn/HUM.htm
Contact: novos65@mail.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
Analysis of gene expression data using a linear mixed model/finite mixture model approach: application to regional differences in the human brain
Authors: Trabzuni Daniah ,   the United Kingdom Brain Expression Consortium (UKBEC), Thomson Peter C. 
Published: February 2014

Abstract
Motivation: Gene expression data exhibit common information over the genome. This article shows how data can be analysed from an efficient whole-genome perspective. Further, the methods have been developed so that users with limited expertise in bioinformatics and statistical computing techniques could use and modify this procedure to their own needs. The method outlined first uses a large-scale linear mixed model for the expression data genome-wide, and then uses finite mixture models to separate differentially expressed (DE) from non-DE transcripts. These methods are illustrated through application to an exceptional UK Brain Expression Consortium involving 12 human frozen post-mortem brain regions.
Results: Fitting linear mixed models has allowed variation in gene expression between different biological states (e.g. brain regions, gender, age) to be investigated. The model can be extended to allow for differing levels of variation between different biological states. Predicted values of the random effects show the effects of each transcript in a particular biological state. Using the UK Brain Expression Consortium data, this approach yielded striking patterns of co-regional gene expression. Fitting the finite mixture model to the effects within each state provides a convenient method to filter transcripts that are DE: these DE transcripts can then be extracted for advanced functional analysis.
Availability: The data for all regions except HYPO and SPCO are available at the Gene Expression Omnibus (GEO) site, accession number GSE46706. R code for the analysis is available in the Supplementary file.
Contact: peter.thomson@sydney.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
An Abundance Analysis of the Primary Star of the Peculiar Eclipsing Binary $\epsilon$ Aurigae out of the Eclipsing Phase
Authors: Sadakane Kozo , Kambe Eiji , Sato Bun’ei , Honda Satoshi , Hashimoto Osamu 
Published: February 2014

Abstract
A detailed abundance analysis of the primary star of $\epsilon$ Aur before an eclipse was carried out using a very high signal-to-noise ratio optical-region spectrum. An A7 Iab supergiant HD 81471, presumably a member of the Vela OB1 association, was used as a reference. We obtained atmospheric parameters (T$_{\rm eff}$, log g, and $\xi_{\rm t}$) to be (8025 K, 1.0 and 10 km s$^{-1}$) and (8050 K, 1.0 and 7 km s$^{-1}$) for $\epsilon$ Aur and HD 81471, respectively. The abundances of Mg, Si, S, Ca, Sc, Ti, Cr, and Fe were very close to the solar abundances in both stars. Light elements C and O were under-abundant, while N and Na were over-abundant in both stars, after correcting for non-LTE effects. Definite under-abundances of Sr were detected in both stars. Slight, but definite, over-abundances were found in $\epsilon$ Aur for the s-process elements Y, Zr, and Ba, when compared with the results of HD 81471. Enhancements in the abundances of N, Na, and s-process elements might indicate the occurences of thermal dredge-up and the s-process nucleosynthesis in $\epsilon$ Aur during the past evolution.
Metallicity of the Fossil Group NGC 1550 Observed with Suzaku
Authors: Sato Kosuke , Kawaharada Madoka , Nakazawa Kazuhiro , Matsushita Kyoko , Ishisaki Yoshitaka , Yamasaki Noriko Y. , Ohashi Takaya 
Published: February 2014

Abstract
We studied the temperature and metal abundance distributions of the intra-cluster medium (ICM) in a group of galaxies, NGC 1550, observed with Suzaku. NGC 1550 is classified as a fossil group, which has few bright member galaxies, except for the central galaxy. Thus, such a type of galaxy is important to investigate how metals are enriched to the ICM. With the Suzaku XIS instrument, we directly measured not only the Si, S, and Fe lines, but also the O and Mg lines, and obtained those abundances to an outer region of $\sim\ $0.5$r_{180}$ for the first time, and confirmed that the metals in the ICM of such a fossil group are indeed extending to a large radius. We found steeper gradients for the Mg, Si, S, and Fe abundances, while O showed an almost flat abundance distribution. Abundance ratios of $\alpha$-elements to Fe were similar to those of the other groups and poor clusters. We calculated the number ratio of type II to type Ia supernovae for the ICM enrichment to be 2.9$\ \pm\ $0.5 within 0.1$r_{180}$; the value is consistent with those for the other groups and poor clusters observed with Suzaku. We also calculated the metal mass-to-light ratios (MLRs) for Fe, O, and Mg with the $B$-band and $K$-band luminosities of the member galaxies of NGC 1550. The derived MLRs are comparable to those of the NGC 5044 group in the $r$$&lt;$ 0.1$r_{180}$ region, while those of NGC 1550 are slightly higher than those of NGC 5044 in the outer region.
Chemical Variation in Molecular Cloud Cores in the Orion A Cloud
Authors: Tatematsu Ken'ichi , Hirota Tomoya , Kandori Ryo , Umemoto Tomofumi 
Published: February 2014

Abstract
We have observed molecular cloud cores in the Orion A giant molecular cloud (GMC) in CCS, HC$_3$N, DNC, and HN$^{13}$C to study their chemical characteristics. We detected CCS in the Orion A GMC for the first time. CCS was detected in about a third of the observed cores. The cores detected in CCS are not localized, but widely distributed over the Orion A GMC. The CCS peak intensity of the core tends to be high in the southern region of the Orion A GMC. The HC$_3$N peak intensity of the core also tends to be high in the southern region, while there are HC$_3$N intense cores near Orion KL, which is not seen in CCS. The core associated with Orion KL shows a broad HC$_3$N line profile, and the star-formation activity near to Orion KL seems to enhance the HC$_3$N emission. The column density ratio of NH$_3$ to CCS is lower near the middle of the filament, and higher toward the northern and southern regions along the Orion A GMC filament. This ratio is known to trace the chemical evolution in nearby dark cloud cores, but seems to be affected by the core gas temperature in the Orion A GMC: cores with low NH$_3$ to CCS column density ratios tend to have a warmer gas temperature. The value of the column density ratio of DNC to HN$^{13}$C is generally similar to that in dark cloud cores, but becomes lower around Orion KL due to a higher gas temperature.
Possible Origins of Dispersion of the Peak Energy–Brightness Correlations of Gamma-Ray Bursts
Authors: Yonetoku Daisuke , Murakami Toshio , Tsutsui Ryo , Nakamura Takashi , Morihara Yoshiyuki , Takahashi Keitaro 
Published: February 2014

Abstract
We collected and reanalyzed about 200 GRB data of prompt-emission with known redshift observed until the end of 2009, and selected 101 GRBs that were well-observed to have good spectral parameters in order to determine the spectral peak energy ($E_{\rm p}$), 1-second peak luminosity ($L_{\rm p}$) and isotropic energy ($E_{\rm iso}$). Using our newly constructed database with 101 GRBs, we first revised the $E_{\rm p}$–$L_{\rm p}$ and $E_{\rm p}$–$E_{\rm iso}$ correlations. The correlation coefficients of the revised correlations were 0.889 for 99 degrees of freedom for the $E_{\rm p}$–$L_{\rm p}$ correlation and 0.867 for 96 degrees of freedom for the $E_{\rm p}$–$E_{\rm iso}$ correlation. These values correspond to a chance probability of 2.18 $\times$ 10$^{-35}$ and 4.27 $\times$ 10$^{-31}$, respectively. It is a very important issue whether these tight correlations are an intrinsic property of GRBs, or are caused by some selection effect of observations. In this paper, we examine how the truncation of the detector sensitivity affects the correlations, and conclude they are surely intrinsic properties of GRBs. Next we investigate origins of the dispersion of the correlations by studying their brightness and redshift dependence. Here, the brightness (flux or fluence) dependence would be regarded as being an estimator of the bias due to the detector threshold. We found a weak fluence-dependence in the $E_{\rm p}$–$E_{\rm iso}$ correlations and a redshift dependence in the $E_{\rm p}$–$L_{\rm p}$ correlation both at the 2$\ \sigma$ statistical level. These two effects may contribute to the dispersion of the correlations, which is larger than the statistical uncertainty. We discuss a possible reason of these dependences and give a future prospect to improve the correlations.
Comparison of AGN and Nuclear Starburst Activity in Seyfert 1 and 2 Galaxies over a Wide Luminosity Range Based on Near-Infrared 2–4μm Spectroscopy
Authors: Oi Nagisa , Imanishi Masatoshi , Imase Keisuke 
Published: February 2014

Abstract
We present near-infrared $K$- (1.9–2.5$\ \mu$m) and $L$- (2.8–4.2$\ \mu$m) band spectroscopy of 22 Seyfert nuclei. We used two methods to investigate the presence of nuclear starbursts: (1) the Polycyclic Aromatic Hydrocarbon (PAH) emission feature at $\lambda_{\rm rest}$$=$ 3.3$\ \mu$m in the rest frame of the $L$-band spectrum (a starburst indicator) and (2) the CO absorption feature at $\lambda_{\rm rest}$$=$ 2.3–2.4$\ \mu$m in the rest frame of the $K$-band spectrum, originating in the CO molecule. We clearly detected the 3.3$\ \mu$m PAH emission features in five objects and the CO absorption features in 17 objects. Seyfert 2 galaxies tend to show bluer $K$$-$$L$ colors compared with Seyfert 1 galaxies. We interpret the discrepancy as resulting from the relative strength of stellar emission because AGN emission is affected by dust extinction. The 3.3$\ \mu$m PAH emission luminosity ($L_{\rm 3.3PAH}$) distributions for the Seyfert 1s and Seyfert 2s are very similar when normalized to the AGN power. The star-formation rates estimated from $L_{\rm 3.3PAH}$ could be large enough to inflate the dusty torus by a supernova explosion. We find that $L_{\rm 3.3PAH}$ positively correlates with the $N$-band luminosity with small aperture over a wide AGN luminosity range, and is independent of the physical area we probed. The results suggest that the nuclear region has a concentration of star formation and it would control the AGN activity.
Explosion Geometry of a Rotating 13 $\ M_{\odot}$ Star Driven by the SASI-Aided Neutrino-Heating Supernova Mechanism
Authors: Suwa Yudai , Kotake Kei , Takiwaki Tomoya , Whitehouse Stuart C. , LiebendÖrfer Matthias , Sato Katsuhiko 
Published: February 2014

Abstract
By performing axisymmetric hydrodynamic simulations of core-collapse supernovae with spectral neutrino transport based on the isotropic diffusion source approximation scheme, we support the assumption that the neutrino-heating mechanism aided by the standing accretion shock instability (SASI) and convection can initiate an explosion of a 13$\ M_{\odot}$ star. Our results show that bipolar explosions are more likely to be associated with models that include rotation. We point out that models that form a north–south symmetric bipolar explosion can lead to larger explosion energies than the corresponding unipolar explosions can.
Bright X-Ray Flares from the BL Lac Object Markarian 421, Detected with MAXI in 2010 January and February
Authors: Isobe Naoki , Sugimori Kousuke , Kawai Nobuyuki , Ueda Yoshihiro , Negoro Hitoshi , Sugizaki Mutsumi , Matsuoka Masaru , Daikyuji Arata , Eguchi Satoshi , Hiroi Kazuo , Ishikawa Masaki , Ishiwata Ryoji , Kawasaki Kazuyoshi , Kimura Masashi , Kohama Mitsuhiro , Mihara Tatehiro , Miyoshi Sho , Morii Mikio , Nakagawa Yujin E. , Nakahira Satoshi , Nakajima Motoki , Ozawa Hiroshi , Sootome Tetsuya , Suzuki Motoko , Tomida Hiroshi , Tsunemi Hiroshi , Ueno Shiro , Yamamoto Takayuki , Yamaoka Kazutaka , Yoshida Atsumasa ,   the MAXI Team
Published: February 2014

Abstract
Strong X-ray flares from the blazar Mrk 421 were detected in 2010 January and February through 7-month monitoring with the MAXI GSC. The maximum 2–10 keV flux in the January and February flares was measured to be 120$\ \pm\ $10 mCrab and 164$\ \pm\ $17 mCrab, respectively; the latter is the highest among those reported from the object. A comparison of the MAXI and Swift BAT data suggests a convex X-ray spectrum with an approximated photon index of $\Gamma$$\gtrsim$ 2. This spectrum is consistent with a picture that MAXI is observing near the synchrotron peak frequency. The source exhibited a spectral variation during these flares, slightly different from those in previous observations, in which the positive correlation between the flux and hardness was widely reported. By equating the halving decay timescale in the January flare, $t_{ m d}$$\sim$ 2.5 $\times$ 10$^{4}\ $s, to the synchrotron cooling time, the magnetic field was evaluated to be $B$$\sim$ 4.5 $\times$ 10$^{-2}\ $G ($\delta/$10)$^{-1/3}$, where $\delta$ is the jet beaming factor. Assuming that the light crossing time of the emission region is shorter than the doubling rise time, $t_{ m r}$$\lesssim$ 2 $\times$ 10$^{4}\ $s, the region size was roughly estimated as $R$$&lt;$ 6 $\times$ 10$^{15}\ $cm ($\delta/$10). These results are consistent with values previously reported. For the February flare, the rise time, $t_{ m r}$$&lt;$ 1.3 $\times$ 10$^{5}\ $s, gives a loose upper limit on the size as $R$$&lt;$ 4 $\times$ 10$^{16}\ $cm $(\delta/10)$, although the longer decay time, $t_{ m d}$$\sim$ 1.4 $\times$ 10$^{5}\ $s, indicates $B$$\sim$ 1.5 $\times$ 10$^{-2}\ $G ($\delta/$10)$^{-1/3}$, which is weaker than the previous results. This could be reconciled by invoking a scenario that this flare is a superposition of unresolved events with a shorter timescale.