bluuebunny/crossref_metadata_2025 huggingface dataset:
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

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

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

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

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.
In-Orbit Performance of the MAXI/SSC onboard the ISS
Authors: Tsunemi Hiroshi , Tomida Hiroshi , Katayama Haruyoshi , Kimura Masashi , Daikyuji Arata , Miyaguchi Kazuhisa , Maeda Kentaro , Maeda Kentaro ,   the MAXI team
Published: February 2014

We report here the in-orbit performance of the CCD camera (MAXI/SSC) onboard the International Space Station (ISS). It was commissioned in 2009 August. This is the first all-sky survey mission employing X-ray CCDs. It consists of 32 CCDs, each of which is 1 inch square. It is a slit camera with a field of view of 1$^\circ\!\!\!.$5 $\times$ 90$^\circ$, and scans the sky as the rotation of the ISS. The CCD on the SSC is cooled down to the working temperature around $-$60$^\circ$C by the combination of a peltier cooler, a loop heat pipe and a radiator. The standard observation mode of the CCD is in a parallel sum mode (64-binning). The CCD functions properly, although it suffers an edge glow when the Sun is near the field of view (FOV), which reduces the observation efficiency of the SSC down to about 30%. The performance of the CCD is continuously monitored both by the Mn-K X-rays and by the Cu-K X-rays. There are many sources detected, not only point sources, but extended sources. Due to the lack of an effective observation time, we need more observation time to obtain an extended emission analysis extraction process.
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

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.
Observational Appearance and Spectrum of Black-Hole Winds
Authors: Fukue Jun , Iino Eriko
Published: February 2014

We examine the observational appearance of an optically thick, spherically symmetric, relativistic wind (a black-hole wind), focusing our attention on the emerging spectrum. In a relativistic flow, the apparent optical depth becomes small (large) in the downstream (upstream) direction due to the Lorentz-Fitzgerald contraction. As a result, the location of the apparent photosphere of the wind is remarkably modified, and there appears a relativistic limb-darkening (center-brightening) effect, where the comoving temperature distribution of the apparent photosphere is enhanced (reduced) at the center (in the limb). In addition, due to the usual Doppler boost, the observed temperature distribution is greatly changed. These relativistic effects modify the expected spectrum. When the wind speed is subrelativistic, the observed temperature distribution is almost uniform, and the spectra of the black-hole wind are blackbody-like. When the wind speed becomes relativistic, on the other hand, the observed temperature distribution, $T_{\rm obs}$, exhibits a power-law nature of $T_{\rm obs}$$\propto$$r^{-1}$, where $r$ is the distance from the disk center, and the observed spectra $S_{\nu}$ become a modified blackbody, which has a power-law part of $S_{\nu}$$\propto$$\nu$, where $\nu$ is the frequency. We briefly examine the effects of the spatial variation of the wind speed and the mass-loss rate.
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

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$$<$ 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

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

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

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

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

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$$<$ 6 $\times$ 10$^{15}\ $cm ($\delta/$10). These results are consistent with values previously reported. For the February flare, the rise time, $t_{ m r}$$<$ 1.3 $\times$ 10$^{5}\ $s, gives a loose upper limit on the size as $R$$<$ 4 $\times$ 10$^{16}\ $cm $(\delta/10)$, although the longer decay time, $t_{ m d}$$\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.
The Rossiter–McLaughlin Effect of the Transiting Exoplanet XO-4b
Authors: Narita Norio , Hirano Teruyuki , Sanchis-Ojeda Roberto , Winn Joshua N. , Holman Matthew J. , Sato Bun’ei , Aoki Wako , Tamura Motohide
Published: February 2014

We report photometric and radial velocity observations of the XO-4 transiting planetary system, conducted with the FLWO 1.2 m telescope and the 8.2 m Subaru Telescope. Based on the new light curves, the refined transit ephemeris of XO-4b is $P$$=$ 4.1250828$\ \pm\ $0.0000040 d and $T_{\rm c}$ [BJD$_{\rm TDB}$] $=$ 2454485.93323$\ \pm\ $0.00039. We measured the Rossiter–McLaughlin effect of XO-4b and estimated the sky-projected angle between the stellar spin axis and the planetary orbital axis to be $\lambda$$=$$-$46$^\circ\!\!\!.$7$\ ^{{+8^\circ\!\!\!.1}}_{{-6^\circ\!\!\!.1}}$. This measurement of $\lambda$ is less robust than in some other cases because the impact parameter of the transit is small, causing a strong degeneracy between $\lambda$ and the projected stellar rotational velocity. Nevertheless, our finding of a spin–orbit misalignment suggests that the migration process for XO-4b involved few-body dynamics rather than interaction with a gaseous disk. In addition, our result conforms with the pattern reported by Winn et al. (2010, ApJ, 718, L145) that high obliquities are preferentially found for stars with effective temperatures hotter than 6250 K.
MOIRCS Deep Survey. IX. Deep Near-Infrared Imaging Data and Source Catalog
Authors: Kajisawa Masaru , Ichikawa Takashi , Tanaka Ichi , Yamada Toru , Akiyama Masayuki , Suzuki Ryuji , Tokoku Chihiro , Uchimoto Yuka Katsuno , Konishi Masahiro , Yoshikawa Tomohiro , Nishimura Tetsuo , Omata Koji , Ouchi Masami , Iwata Ikuru , Hamana Takashi , Onodera Masato
Published: February 2014

We present deep $J$-, $H$-, and $K_{\rm s}$-band imaging data of the MOIRCS Deep Survey (MODS), which was carried out with the Multi-Object Infrared Camera and Spectrograph (MOIRCS) mounted on the Subaru Telescope in the GOODS-North region. The data reach 5$\ \sigma$ total limiting magnitudes for point sources of $J$$=$ 23.9, $H$$=$ 22.8, and $K_{\rm s}$$=$ 22.8 (Vega magnitude) over 103 arcmin$^{2}$ (wide field). In 28 arcmin$^{2}$ of the survey area, which is an ultra-deep field of the MODS (deep field), the data reach 5$\ \sigma$ depths of $J$$=$ 24.8, $H$$=$ 23.4, and $K_{\rm s}$$=$ 23.8. The spatial resolutions of the combined images are FWHM $\sim\ $0$''\!\!\!.$6 and $\sim\ $0$''\!\!\!.$5 for the wide and deep fields in all bands, respectively. Combining the MODS data with the multi-wavelength public data taken with the HST, Spitzer, and other ground-based telescopes in the GOODS field, we constructed a multi-wavelength photometric catalog of $K_{\rm s}$-selected sources. Using the catalog, we present $K_{\rm s}$-band number counts and near-infrared color distribution of the detected objects; we also demonstrate some selection techniques with the NIR colors for high redshift galaxies. These data and catalog are publicly available via Internet.
Outflow in Overlooked Luminous Quasar: Subaru Observations of AKARI J1757$+$5907
Authors: Aoki Kentaro , Oyabu Shinki , Dunn Jay P. , Arav Nahum , Edmonds Doug , Korista Kirk T. , Matsuhara Hideo , Toba Yoshiki
Published: February 2014

We present Subaru observations of the newly discovered luminous quasar AKARI J1757$+$5907, which shows an absorption outflow in its spectrum. The absorption consists of 9 distinct troughs, and our analysis focuses on the troughs at $\sim-$1000 km s$^{-1}$ for which we could measure accurate column densities of He I$^*$, Fe II, and Mg II. We used photoionization models to constrain the ionization parameter, total hydrogen column density, and number density of the outflowing gas. These constraints yielded lower limits for the distance, mass-flow rate, and kinetic luminosity for outflows of 3.7 kpc, 70 $M_{\odot}$ yr$^{-1}$, and 2.0 $\times$10$^{43}$ erg s$^{-1}$, respectively. Such a mass-flow rate value can contribute significantly to metal enrichment of the intra-cluster medium. We found that this moderate velocity outflow is similar to those recently discovered in massive post-starburst galaxies. Finally, we describe the scientific potential of future observations targeting this object.
An alternative numerical method for the stationary pulsar magnetosphere
Authors: Takamori Yohsuke , Okawa Hirotada , Takamoto Makoto , Suwa Yudai
Published: February 2014

Stationary pulsar magnetospheres in the force-free system are governed by the pulsar equation. In 1999, Contopoulos, Kazanas, and Fendt (hereafter CKF) numerically solved the pulsar equation and obtained a pulsar magnetosphere model called the CKF solution that has both closed and open magnetic field lines. The CKF solution is a successful solution, but it contains a poloidal current sheet that flows along the last open field line. This current sheet is artificially added to make the current system closed. In this paper, we suggest an alternative method to solve the pulsar equation and construct pulsar magnetosphere models without a current sheet. In our method, the pulsar equation is decomposed into Ampère's law and the force-free condition. We numerically solve these equations simultaneously with a fixed poloidal current. As a result, we obtain a pulsar magnetosphere model without a current sheet, which is similar to the CKF solution near the neutron star and has a jet-like structure at a distance along the pole. In addition, we discuss physical properties of the model and find that the force-free condition breaks down in a vicinity of the light cylinder due to dissipation that is included implicitly in the numerical method.
Agricultural Decisions after Relaxing Credit and Risk Constraints *
Authors: Karlan Dean , Osei Robert , Osei-Akoto Isaac , Udry Christopher
Published: February 2014

The investment decisions of small-scale farmers in developing countries are conditioned by their financial environment. Binding credit market constraints and incomplete insurance can limit investment in activities with high expected profits. We conducted several experiments in northern Ghana in which farmers were randomly assigned to receive cash grants, grants of or opportunities to purchase rainfall index insurance, or a combination of the two. Demand for index insurance is strong, and insurance leads to significantly larger agricultural investment and riskier production choices in agriculture. The binding constraint to farmer investment is uninsured risk: when provided with insurance against the primary catastrophic risk they face, farmers are able to find resources to increase expenditure on their farms. Demand for insurance in subsequent years is strongly increasing with the farmer’s own receipt of insurance payouts, with the receipt of payouts by others in the farmer’s social network and with recent poor rain in the village. Both investment patterns and the demand for index insurance are consistent with the presence of important basis risk associated with the index insurance, imperfect trust that promised payouts will be delivered and overweighting recent events.
StoS, a Hybrid Histidine Kinase Sensor of Xanthomonas oryzae pv. oryzae, Is Activated by Sensing Low O2 Concentration and Is Involved in Stress Tolerance and Virulence
Authors: Ikawa Yumi , Furutani Ayako , Ochiai Hirokazu , Tsuge Seiji
Published: February 2014

Bacteria have two-component signal transduction systems (TCSTS), which are important devices for receiving various environmental signals. A TCSTS generally consists of a sensor histidine kinase (HK) and a response regulator (RR) that contains a receiver domain. There are also hybrid-type HK (HyHK) that comprise a HK with a receiver domain within one molecule. In this study, we show that the deletion mutant of a HyHK XOO_0635 (StoS) of Xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight of rice, had decreased stress tolerance to high osmolarity, sodium, and H2O2. Growth of the StoS mutant was delayed, and viability was lower than the wild type in medium and in rice leaves. We found that StoS regulates the expression of various genes including XOO_3715, XOO_0131, and stoS itself. A domain search revealed a PAS domain with a heme pocket in StoS, implying that the HyHK functions as an O2 sensor. When the bacteria were incubated in low oxygen, the StoS-dependent expression of XOO_0131 and XOO_3715 became higher. Therefore, StoS is activated by sensing a low O2 concentration in its environs and is involved in gene expression for adapting to various stressful conditions.
Histochemical Characterization of Early Response to Cochliobolus sativus Infection in Selected Barley Genotypes
Authors: Rodríguez-Decuadro Susana , Silva Paula , Bentancur Oscar , Gamba Fernanda , Pritsch Clara
Published: February 2014

Much effort is being made to breed barley with durable resistance to leaf spot blotch incited by Bipolaris sorokiniana (teleomorph: Cochliobolus sativus). We hypothesized that susceptibility and resistance traits in 11 diverse barley genotypes inoculated with a single C. sativus isolate might specify a range of distinct host cell responses. Quantitative descriptions of interaction microphenotypes exhibited by different barley genotype seedlings after infection with C. sativus are provided. Early oxidative responses occurring in epidermis and mesophyll leaf tissue were monitored by histochemical analysis of H2O2 accumulation at 8, 24, and 48 h after inoculation. Cell wall apposition (CWA) in epidermal cells and hypersensitive reaction (HR) of epidermal or mesophyll tissue were early defenses in both resistant and susceptible genotypes. There were differences in level, duration, and frequency of occurrence for CWA and HR for the different barley genotypes. Occurrence of HR in epidermal cells at post-penetration stages was indicative of compatibility. Patterns of cell responses were microphenotypically diverse between different resistant and susceptible genotypes. This suggests that timing and level of response are key features of microphenotypic diversity that distinguish different functional mechanisms of resistance and susceptibility present in barley.
Setting Up a Patient Care Call Center After Potential HCV Exposure
Authors: Friedman Candace , Bucholz Brigette , Anderson Susan G. , Dwyer Shon A. , Aguirre Josephine
Published: February 2014

Objectives

Notify patients of a potential exposure to hepatitis C virus, coordinate testing, and provide follow-up counseling.

Methods

A team was convened to identify various needs in developing a patient care call center. The areas addressed included the following: location, hours, and duration; telephone accessibility; tracking calls and test results; billing; staffing; notification; and potential issues requiring additional evaluation.

Results

Disclosure letters were sent to 1275 patients; 57 letters were not deliverable. There were 245 calls to the helpline from October 25 through November 15. Lessons learned centered on hours of availability, staffing, use of an automated phone system and email communication, tracking results, and billing issues.

Conclusions

A successful patient notification and follow-up effort requires a multidisciplinary team, internal and external communication, collection of data over an extended period, and coordination of patient information.
Stochastic analysis of biochemical reaction networks with absolute concentration robustness
Authors: Anderson David F. , Enciso Germán A. , Johnston Matthew D.
Published: February 2014

It has recently been shown that structural conditions on the reaction network, rather than a ‘fine-tuning’ of system parameters, often suffice to impart ‘absolute concentration robustness’ (ACR) on a wide class of biologically relevant, deterministically modelled mass-action systems. We show here that fundamentally different conclusions about the long-term behaviour of such systems are reached if the systems are instead modelled with stochastic dynamics and a discrete state space. Specifically, we characterize a large class of models that exhibit convergence to a positive robust equilibrium in the deterministic setting, whereas trajectories of the corresponding stochastic models are necessarily absorbed by a set of states that reside on the boundary of the state space, i.e. the system undergoes an extinction event. If the time to extinction is large relative to the relevant timescales of the system, the process will appear to settle down to a stationary distribution long before the inevitable extinction will occur. This quasi-stationary distribution is considered for two systems taken from the literature, and results consistent with ACR are recovered by showing that the quasi-stationary distribution of the robust species approaches a Poisson distribution.
New model diagnostics for spatio-temporal systems in epidemiology and ecology
Authors: Lau Max S. Y. , Marion Glenn , Streftaris George , Gibson Gavin J.
Published: February 2014

A cardinal challenge in epidemiological and ecological modelling is to develop effective and easily deployed tools for model assessment. The availability of such methods would greatly improve understanding, prediction and management of disease and ecosystems. Conventional Bayesian model assessment tools such as Bayes factors and the deviance information criterion (DIC) are natural candidates but suffer from important limitations because of their sensitivity and complexity. Posterior predictive checks, which use summary statistics of the observed process simulated from competing models, can provide a measure of model fit but appropriate statistics can be difficult to identify. Here, we develop a novel approach for diagnosing mis-specifications of a general spatio-temporal transmission model by embedding classical ideas within a Bayesian analysis. Specifically, by proposing suitably designed non-centred parametrization schemes, we construct latent residuals whose sampling properties are known given the model specification and which can be used to measure overall fit and to elicit evidence of the nature of mis-specifications of spatial and temporal processes included in the model. This model assessment approach can readily be implemented as an addendum to standard estimation algorithms for sampling from the posterior distributions, for example Markov chain Monte Carlo. The proposed methodology is first tested using simulated data and subsequently applied to data describing the spread ofHeracleum mantegazzianum(giant hogweed) across Great Britain over a 30-year period. The proposed methods are compared with alternative techniques including posterior predictive checking and the DIC. Results show that the proposed diagnostic tools are effective in assessing competing stochastic spatio-temporal transmission models and may offer improvements in power to detect model mis-specifications. Moreover, the latent-residual framework introduced here extends readily to a broad range of ecological and epidemiological models.
Effects of densitometry, material mapping and load estimation uncertainties on the accuracy of patient-specific finite-element models of the scapula
Authors: Campoli Gianni , Bolsterlee Bart , van der Helm Frans , Weinans Harrie , Zadpoor Amir A.
Published: February 2014

Patient-specific biomechanical models including patient-specific finite-element (FE) models are considered potentially important tools for providing personalized healthcare to patients with musculoskeletal diseases. A multi-step procedure is often needed to generate a patient-specific FE model. As all involved steps are associated with certain levels of uncertainty, it is important to study how the uncertainties of individual components propagate to final simulation results. In this study, we considered a specific case of this problem where the uncertainties of the involved steps were known and the aim was to determine the uncertainty of the predicted strain distribution. The effects of uncertainties of three important components of patient-specific models, including bone density, musculoskeletal loads and the parameters of the material mapping relationship on the predicted strain distributions, were studied. It was found that the number of uncertain components and the level of their uncertainty determine the uncertainty of simulation results. The ‘average’ uncertainty values were found to be relatively small even for high levels of uncertainty in the components of the model. The ‘maximum’ uncertainty values were, however, quite high and occurred in the areas of the scapula that are of the greatest clinical relevance. In addition, the uncertainty of the simulation result was found to be dependent on the type of movement analysed, with abduction movements presenting consistently lower uncertainty values than flexion movements.
The evolution of fairness through spite
Authors: Forber Patrick , Smead Rory
Published: February 2014

The presence of apparently irrational fair play in the ultimatum game remains a focal point for studies in the evolution of social behaviour. We investigate the role of negative assortment in the evolution of fair play in the ultimatum game. Spite—social behaviour that inflicts harm with no direct benefit to the actor—can evolve when it is disproportionally directed at individuals playing different strategies. The introduction of negative assortment alters the dynamics in a way that increases the chance fairness evolves, but at a cost: spite also evolves. Fairness is usually linked to cooperation and prosocial behaviour, but this study shows that it may have evolutionary links to harmful antisocial behaviour.
Methylation and worker reproduction in the bumble-bee (Bombus terrestris)
Authors: Amarasinghe Harindra E. , Clayton Crisenthiya I. , Mallon Eamonn B.
Published: February 2014

Insects are at the dawn of an epigenetics era. Numerous social insect species have been found to possess a functioning methylation system, previously not thought to exist in insects. Methylation, an epigenetic tag, may be vital for the sociality and division of labour for which social insects are renowned. In the bumble-beeBombus terrestris, we found methylation differences between the genomes of queenless reproductive workers and queenless non-reproductive workers. In a follow up experiment, queenless workers whose genomes had experimentally altered methylation were more aggressive and more likely to develop ovaries compared with control queenless workers. This shows methylation is important in this highly plastic reproductive division of labour. Methylation is an epigenetic tag for genomic imprinting (GI). It is intriguing that the main theory to explain the evolution of GI predicts that GI should be important in this worker reproduction behaviour.
Mechanisms of plant–plant interactions: concealment from herbivores is more important than abiotic-stress mediation in an African savannah
Authors: Louthan Allison M. , Doak Daniel F. , Goheen Jacob R. , Palmer Todd M. , Pringle Robert M.
Published: February 2014

Recent work on facilitative plant–plant interactions has emphasized the importance of neighbours’ amelioration of abiotic stress, but the facilitative effects of neighbours in reducing plant apparency to herbivores have received less attention. Whereas theory on stress reduction predicts that competition should be more important in less stressful conditions, with facilitation becoming more important in harsh environments, apparency theory suggests that facilitation should be greater in the presence of herbivores, where it is disadvantageous to be conspicuous regardless of abiotic stress level. We tested the relative strength of neighbours’ stress reduction versus apparency reduction on survival, growth, reproduction and lifetime fitness ofHibiscus meyeri, a common forb in central Kenya, using neighbour removals conducted inside and outside large-herbivore exclosures replicated in arid and mesic sites. In the absence of herbivores, neighbours competed withH. meyeriin mesic areas and facilitatedH. meyeriin arid areas, as predicted by stress-reduction mechanisms. By contrast, neighbours facilitatedH. meyeriin the presence of herbivory, regardless of aridity level, consistent with plant apparency. Our results show that the facilitative effects arising from plant apparency are stronger than the effects arising from abiotic stress reduction in this system, suggesting that plant-apparency effects may be particularly important in systems with extant large-herbivore communities.
Stability versus diversity of the dentition during evolutionary radiation in cyprinine fish
Authors: Pasco-Viel Emmanuel , Yang Lei , Veran Monette , Balter Vincent , Mayden Richard L. , Laudet Vincent , Viriot Laurent
Published: February 2014

Evolutionary radiations, especially adaptive radiations, have been widely studied but mainly for recent events such as in cichlid fish orAnolislizards. Here, we investigate the radiation of the subfamily Cyprininae, which includes more than 1300 species and is estimated to have originated from Southeast Asia around 55 Ma. In order to decipher a potential adaptive radiation, within a solid phylogenetic framework, we investigated the trophic apparatus, and especially the pharyngeal dentition, as teeth have proved to be important markers of ecological specialization. We compared two tribes within Cyprininae, Poropuntiini and Labeonini, displaying divergent dental patterns, as well as other characters related to their trophic apparatus. Our results suggest that the anatomy of the trophic apparatus and diet are clearly correlated and this explains the difference in dental patterns observed between these two tribes. Our results illustrate the diversity of mechanisms that account for species diversity in this very diverse clade: diversification of dental characters from an ancestral pattern on the one hand, conservation of a basal synapomorphy leading to ecological specialization on the other hand. By integrating morphological, ecological and phylogenetic analyses, it becomes possible to investigate ancient radiation events that have shaped the present diversity of species.
The evolution of traditional knowledge: environment shapes medicinal plant use in Nepal
Authors: Saslis-Lagoudakis C. Haris , Hawkins Julie A. , Greenhill Simon J. , Pendry Colin A. , Watson Mark F. , Tuladhar-Douglas Will , Baral Sushim R. , Savolainen Vincent
Published: February 2014

Traditional knowledge is influenced by ancestry, inter-cultural diffusion and interaction with the natural environment. It is problematic to assess the contributions of these influences independently because closely related ethnic groups may also be geographically close, exposed to similar environments and able to exchange knowledge readily. Medicinal plant use is one of the most important components of traditional knowledge, since plants provide healthcare for up to 80% of the world's population. Here, we assess the significance of ancestry, geographical proximity of cultures and the environment in determining medicinal plant use for 12 ethnic groups in Nepal. Incorporating phylogenetic information to account for plant evolutionary relatedness, we calculate pairwise distances that describe differences in the ethnic groups' medicinal floras and floristic environments. We also determine linguistic relatedness and geographical separation for all pairs of ethnic groups. We show that medicinal uses are most similar when cultures are found in similar floristic environments. The correlation between medicinal flora and floristic environment was positive and strongly significant, in contrast to the effects of shared ancestry and geographical proximity. These findings demonstrate the importance of adaptation to local environments, even at small spatial scale, in shaping traditional knowledge during human cultural evolution.
Radiocarbon evidence for the presence of mice on Madeira Island (North Atlantic) one millennium ago
Authors: Rando Juan Carlos , Pieper Harald , Alcover Josep Antoni
Published: February 2014

Owing to the catastrophic extinction events that occurred following the Holocene arrival of alien species, extant oceanic island biotas are a mixture of recently incorporated alien fauna and remnants of the original fauna. Knowledge of the Late Quaternary pristine island faunas and a reliable chronology of the earliest presence of alien species on each archipelago are critical in understanding the magnitude and tempo of Quaternary island extinctions. Until now, two successive waves of human arrivals have been identified in the North Atlantic Macaronesian archipelagos (Azores, Madeira, Selvagens, Canary and Cape Verde Islands): ‘aboriginal’, which is limited to the Canary Islands around two millennia ago, and ‘colonial’, from the fourteenth century onwards. New surveys in Ponta de São Lourenço (Madeira Island) have allowed us to obtain and date ancient bones of mice. The date obtained (1033 ± 28 BP) documents the earliest evidence for the presence of mice on the island. This date extends the time frame in which the most significant ecological changes occurred on the island. It also suggests that humans could have reached Madeira before 1036 cal AD, around four centuries before Portugal officially took possession of the island.