bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial community responses to a gradient of alkaline mountaintop mine drainage in Central Appalachian streams
Authors: Bier Raven L , Voss Kristofor A , Bernhardt Emily S 
Published: December 2014

Abstract
Microbial community composition and diversity change along chemical gradients, leading to the expectation that microbial community information might provide new gradient characterizations. Here we examine stream bacteria composition and diversity along a strong chemical gradient in Central Appalachian streams. Coal mining in the region generates alkaline mine drainage (AlkMD), causing dramatic increases in conductivity, alkalinity, sulfate and metals sufficient to degrade stream macrobiota communities throughout the ecoregion. In this study, we examined the relationship between water and biofilm chemistry and biofilm bacteria taxonomic composition in streams where active and reclaimed surface coal mines occupied 0–96% of watershed surface area. We incubated wood veneers in each stream site for 4 months to develop biofilms on similar substrates. We sampled water chemistry at the time of deployment and collection, and after 1 month. Following incubation, we collected biofilms for microbial and chemical characterization. Microbial composition was determined by pyrosequencing 16S rRNA amplicons. Biofilm subsamples were analyzed by inductively coupled plasma mass spectrometry to determine metal concentrations. Our results show that microbial community composition differed significantly between AlkMD-exposed and AlkMD-unexposed sites, and that compositional dissimilarity increased with AlkMD loading. Diversity was not correlated with pH or extent of upstream mining, but instead correlated with biofilm concentrations of Cd, Mn, Zn and Ni. Within mined sites, the extent of upstream mining was negatively correlated with taxonomic richness. Despite major compositional shifts, functional capacity predicted with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) correlated with mining in only 3 of 43 level-2 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology groups.
An integrated epigenomic analysis for type 2 diabetes susceptibility loci in monozygotic twins
Authors: Yuan Wei , Xia Yudong , Bell Christopher G. , Yet Idil , Ferreira Teresa , Ward Kirsten J. , Gao Fei , Loomis A. Katrina , Hyde Craig L. , Wu Honglong , Lu Hanlin , Liu Yuan , Small Kerrin S. , Viñuela Ana , Morris Andrew P. , Berdasco María , Esteller Manel , Brosnan M. Julia , Deloukas Panos , McCarthy Mark I. , John Sally L. , Bell Jordana T. , Wang Jun , Spector Tim D. 
Published: December 2014

AbstractDNA methylation has a great potential for understanding the aetiology of common complex traits such as Type 2 diabetes (T2D). Here we perform genome-wide methylated DNA immunoprecipitation sequencing (MeDIP-seq) in whole-blood-derived DNA from 27 monozygotic twin pairs and follow up results with replication and integrated omics analyses. We identify predominately hypermethylated T2D-related differentially methylated regions (DMRs) and replicate the top signals in 42 unrelated T2D cases and 221 controls. The strongest signal is in the promoter of theMALT1gene, involved in insulin and glycaemic pathways, and related to taurocholate levels in blood. Integrating the DNA methylome findings with T2D GWAS meta-analysis results reveals a strong enrichment for DMRs in T2D-susceptibility loci. We also detect signals specific to T2D-discordant twins in theGPR61andPRKCBgenes. These replicated T2D associations reflect both likely causal and consequential pathways of the disease. The analysis indicates how an integrated genomics and epigenomics approach, utilizing an MZ twin design, can provide pathogenic insights as well as potential drug targets and biomarkers for T2D and other complex traits.
Do good actions inspire good actions in others?
Authors: Capraro Valerio , Marcelletti Alessandra 
Published: December 2014

AbstractActions such as sharing food and cooperating to reach a common goal have played a fundamental role in the evolution of human societies. Despite the importance of suchgoodactions, little is known about if and how they can spread from person to person to person. For instance, does being recipient of an altruistic act increase your probability of being cooperative with a third party? We have conducted an experiment on Amazon Mechanical Turk to test this mechanism using economic games. We have measured willingness to be cooperative through a standard Prisoner's dilemma and willingness to act altruistically using a binary Dictator game. In the baseline treatments, the endowments needed to play were given by the experimenters, as usual; in the control treatments, they came from a good action made by someone else. Across four different comparisons and a total of 572 subjects, we have never found a significant increase of cooperation or altruism when the endowment came from a good action. We conclude that good actions do not necessarily inspire good actions in others. While this is consistent with the theoretical prediction, it challenges the majority of other experimental studies.
Soft switching high‐voltage gain dc–dc interleaved boost converter
Authors: e Silva Aquino Ranoyca Nayana Alencar Leão , Tofoli Fernando Lessa , Praca Paulo Peixoto , Oliveira Demercil de Souza , Barreto Luiz Henrique Silva Colado 
Published: December 2014

This study presents the qualitative and quantitative analyses, design procedure and experimental results on a soft switching cell applied to a high‐voltage gain interleaved boost converter. An active snubber cell is proposed as a possible solution for the increase of efficiency in a hard switching topology, where switching losses are drastically minimised. The main advantages of the introduced circuit are the common source terminal to all switches; zero‐voltage switching of the main switches; zero current switching of the auxiliary switches; low‐voltage stress across the switches; balanced voltage across the output capacitors; the presence of a magnetic coupling cell, which allows the gain to be significantly increased; and the magnetic components that are designed for twice the switching frequency. A prototype rated at 500 W is implemented and evaluated, where relevant issues are discussed to validate the theoretical assumptions.
How does crisis leadership influence effective crisis readiness (CR)?
Authors: Cronin J. , Parry K. 
Published: December 2014

Abstract

This chapter focuses on the need for a 'living' crisis management plan, which could be adapted over time for different crisis situations. The chapter draws on leadership theories and concepts to illustrate the importance of crisis leadership (CL) in effectively managing crises within the Thai hotel industry. It focuses on the relationship between CL and crisis readiness (CR), and on how the CL categories of crisis experience and experiential learning (EL) impact upon an organization's ability to prepare for a future crisis. It is then suggested that EL needs to be 'lived and breathed'. In addition, senior management should give high priority to a crisis management plan and should view the plan as a 'living manual' by incorporating it into the organization's day-to-day operations.
The development of a transnational tourism risk, crisis and recovery management network.
Authors: Beirman D. 
Published: December 2014

Abstract

This chapter outlines the development of a transnational tourism risk, crisis and recovery management network, using a case study of the Pacific Asia Travel Association (PATA)'s Rapid Response Taskforce (PRRT). The core paradigm in preparing contingency measures and crisis response necessarily focuses on collaborative approaches between private sector stakeholders and governments. Because risk to the viability of the tourism industry and the impact of a crisis event frequently extends beyond national frontiers, the PRRT builds collaborative alliances within and beyond the Asia-Pacific including (but not limited to) the United Nations World Tourism Organization (UNWTO), World Travel and Tourism Council (WTTC), Asia-Pacific Economic Cooperation (APEC) Tourism, and Association of Southeast Asian Nations (ASEAN) Tourism.
Climate change and global health: a new conceptual framework - Mini Review.
Authors: Butler C. D. 
Published: December 2014

Abstract
Climate change's burden of disease seems orders of magnitude too low to justify claims that it is this century's greatest threat to health. However, such claims can be more easily understood by considering how climate change acts as a risk multiplier, compounding pre-existing socially and politically-mediated drivers of adverse health consequences including conflict.
MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory
Authors: Marchetti Luca , Manca Vincenzo 
Published: December 2014

Abstract
Summary: MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R.
Availability and implementation: The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it.
Contact: luca.marchetti@univr.it, marchetti@cosbi.eu
Supplementary information: Supplementary data are available at Bioinformatics online.
The potential utility of parent-reported attention screening in survivors of childhood cancer to identify those in need of comprehensive neuropsychological evaluation
Authors: Hardy Kristina K. , Willard Victoria W. , Wigdor Alissa B. , Allen Taryn M. , Bonner Melanie J. 
Published: December 2014

Abstract

Background
Survivors of childhood cancer are at risk for neuropsychological late effects, yet identifying those in need of evaluation and obtaining needed services can be challenging for the medical team. Finding time- and cost-effective screening measures that can be used to identify children in need of evaluation is a clinical priority. Our objective was to investigate the association between parent-rated attention problems and related neuropsychological impairments in childhood cancer survivors as a means of identifying those at high risk for difficulties.

Methods
Cognitive and psychosocial data of survivors who completed neuropsychological evaluations were retrospectively abstracted. Parents of 70 survivors of pediatric cancer (mean age, 11.6 years) completed the Conners Parent Rating Scale and the Child Behavior Checklist. Children also completed a measure of intellectual functioning. The 18 symptoms of inattention and hyperactivity were abstracted from the Conners questionnaire, and participants were classified according to whether or not they met attention deficit/hyperactivity disorder (ADHD) symptom criteria (≥6 inattentive symptoms).

Results
Survivors who met symptom criteria for ADHD (27%) demonstrated greater impairments in IQ and working memory, but not processing speed, than survivors who did not. Meeting ADHD symptom criteria was also associated with greater externalizing and social problems but not more internalizing symptoms. ADHD symptom screening was associated with low sensitivity (range = 26.3%–69.2%) but stronger specificity (range = 75.0%–82.7%) for neuropsychological difficulties.

Conclusion
Parental ratings of attentional symptoms may be a useful way to screen survivors who may be in need of a full neuropsychological assessment.
Trigonometric parallax of IRAS 22555+6213 with VERA: Three-dimensional view of sources along the same line of sight
Authors: Chibueze James O. , Sakanoue Hirofumi , Nagayama Takumi , Omodaka Toshihiro , Handa Toshihiro , Kamezaki Tatsuya , Burns Ross A. , Kobayashi Hideyuki , Nakanishi Hiroyuki , Honma Mareki , Ueno Yuji , Kurayama Tomoharu , Matsuo Mitsuhiro , Sakai Nobuyuki 
Published: December 2014

Abstract
We report the results of the measurement of the trigonometric parallax of an H2O maser source in IRAS 22555+6213 with the VLBI Exploration of Radio Astrometry (VERA). The annual parallax was determined to be 0.314 ± 0.070 mas, corresponding to a distance of $3.18^{+0.90}_{-0.66}\,{\rm kpc}$. Our results confirm IRAS 22555+6213 to be located in the Perseus arm. We computed the peculiar motion of IRAS 22555+6213 to be (Usrc, Vsrc, Wsrc) = (4 ± 4, −32 ± 6, 8 ± 6) km s−1, where Usrc, Vsrc, and Wsrc are directed toward the Galactic center, in the direction of Galactic rotation and toward the Galactic north pole, respectively. IRAS 22555+6213, NGC 7538, and Cepheus A lie along the same line of sight, and are within 2° on the sky. Their parallax distances, with which we derived their absolute position in the Milky Way, show that IRAS 22555+6213 and NGC 7538 are associated with the Perseus Arm, while Cepheus A is located in the Local Arm. We compared the kinematic distances of IRAS 22198+6336, G108.18+05.51, G108.20−00.58, G108.47+02.81, G108.59+00.49, Cepheus A, NGC 7538, G111.23−01.23, G111.25−00.76, and IRAS 22555+6213 derived with flat and non-flat rotation curves with their parallax distance and found the kinematic distance derived from the non-flat rotation assumption (−5 to −39 km s−1 lag) to be consistent with the parallax distance.
Correlation between γ-ray and radio emissions in Fermi blazars
Authors: Wu De-Xiang , Fan Jun-Hui , Liu Yi , Yang Jiang-He , Hao Jing-Meng , Pei Zhi-Yuan , Lin Chao 
Published: December 2014

Abstract
Blazars as a special subclass of Active Galactic Nuclei (AGNs) consist of two classes, namely Flat Spectrum Radio Quasars (FSRQs) and BL Lacertae objects (BL Lacs). We compiled information about core and extended radio emissions of 124 γ-ray (0.1–100 GeV) loud blazars (79 FSRQs and 45 BL Lacs). Correlation is found between γ-ray and 5 GHz radio luminosities when the dependence of these two parameters on redshift is taken into account. The correlation suggests that, as well as the radio emission, the γ-ray emission may be strongly beamed. We find no correlation between the γ-ray luminosity (Lγ) and the core-dominance parameter R = Lcore/Lext, where Lcore is the VLBI core emission at 5 GHz, Lext is the extended (lobe) radio emissions at 5 GHz, but there is a strong correlation between log(Lγ/Lext) and log(1 + R).
Stacking analysis of 12CO and 13CO spectra of NGC 3627: Existence of non-optically thick 12CO emission?
Authors: Morokuma-Matsui Kana , Sorai Kazuo , Watanabe Yoshimasa , Kuno Nario 
Published: December 2014

Abstract
We stacked 12CO and 13CO spectra of NGC 3627 after redefining the velocity axis of each spectrum of the mapping data so that the zero corresponds to the local mean velocity of the 12CO spectra. The signal-to-noise ratios of the resulting spectra are improved by a factor of up to 3.2 compared to those obtained with normal stacking analysis. We successfully detect a weak 13CO emission from the interarm region where the emission was not detected in the individual pointings. We compare the integrated intensity ratios $I_{^{12}\rm {CO}}/I_{^{13}{\rm CO}}$ among six characteristic regions (center, bar, bar-end, offset, arm, and interarm). We find that $I_{^{12}\rm {CO}}/I_{^{13}{\rm CO}}$ in the bar and interarm are higher than those in the other regions by a factor of ∼ 2 and $I_{^{12}\rm {CO}}/I_{^{13}{\rm CO}}$ in the center is moderately high. These high $I_{^{12}\rm {CO}}/I_{^{13}{\rm CO}}$ ratios in the bar and center are attributed to a high intensity ratio ($T_{^{12}\rm {CO}}/T_{^{13}{\rm CO}}$), and that in the interarm is attributed to a high ratio of the full width at half maximum of spectra (FWHM$_{^{12}\rm {CO}}/$FWHM$_{^{13}{\rm CO}}$). The difference between FWHM$_{^{12}{\rm CO}}$ and FWHM$_{^{13}{\rm CO}}$ of the interarm indicates the existence of two components, one with a narrow line width (∼ FWHM$_{\rm ^{13}CO}$) and the other with a broad line width (∼ FWHM$_{\rm ^{12}CO}$). Additionally, the $T_{^{12}\rm {CO}}/T_{^{13}{\rm CO}}$ ratio in the broad-line-width component of the interarm is higher than the other regions. The high $T_{^{12}\rm {CO}}/T_{^{13}{\rm CO}}$ in the center and bar and of the broad-line-width component in the interarm suggest the existence of non-optically thick 12CO components. We find that more than half of the 12CO emissions of the interarm are likely to be radiated from the diffuse component. Our result suggests that the use of a universal CO-to-H2 conversion factor might lead to an overestimation of molecular gas mass and underestimation of star-formation efficiency in the interarm by a factor of a few.
Reconstruction of Gene Regulatory Networks based on Repairing Sparse Low-rank Matrices
Authors: Chang Young Hwan , Dobbe Roel , Bhushan Palak , Gray Joe W. , Tomlin Claire J. 
Published: December 2014

AbstractWith the growth of high-throughput proteomic data, in particular time series gene expression data from various perturbations, a general question that has arisen is how to organize inherently heterogenous data into meaningful structures. Since biological systems such as breast cancer tumors respond differently to various treatments, little is known about exactly how these gene regulatory networks (GRNs) operate under different stimuli. For example, when we apply a drug-induced perturbation to a target protein, we often only know that the dynamic response of the specific protein may be affected. We do not know by how much, how long and even whether this perturbation affects other proteins or not. Challenges due to the lack of such knowledge not only occur in modeling the dynamics of a GRN but also cause bias or uncertainties in identifying parameters or inferring the GRN structure. This paper describes a new algorithm which enables us to estimate bias error due to the effect of perturbations and correctly identify the common graph structure among biased inferred graph structures. To do this, we retrieve common dynamics of the GRN subject to various perturbations. We refer to the task as “repairing” inspired by “image repairing” in computer vision. The method can automatically correctly repair the common graph structure across perturbed GRNs, even without precise information about the effect of the perturbations. We evaluate the method on synthetic data sets and demonstrate advantages over C-regularized graph inference by advancing our understanding of how these networks respond across different targeted therapies. Also, we demonstrate an application to the DREAM data sets and discuss its implications to experiment design.
Influence of edaphic and management factors on the diversity and abundance of ammonia‐oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars
Authors: Bertagnolli Anthony D. , Meinhardt Kelley A. , Pannu Manmeet , Brown Sally , Strand Stuart , Fransen Steven C. , Stahl David A. 
Published: December 2014

SummaryAmmonia‐oxidizing thaumarcheota (AOA) and ammonia‐oxidizing bacteria (AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene (amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass (Panicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. Nitrosotalea‐like and Nitrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with Nitrososphaera and Nitrosospira cluster 3A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high‐throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses.
Environmental tobacco smoke exposure, urine CC‐16 levels, and asthma outcomes among Chinese children
Authors: Ma Y.‐N. , Qian Z. , Wang J. , Rodemich E. , Lee Y. L. , Lv X.‐F. , Liu Y.‐Q. , Zhao Y. , Huang M.‐M. , Liu Y. , Sun J. , He Q.‐C. , Dong G.‐H. 
Published: December 2014

AbstractBackgroundPrevious studies have shown the relationship between club cell secretory protein (Clara) (CC‐16) and respiratory diseases. However, few studies have explored the associations between urine CC‐16 levels and environmental tobacco smoke (ETS) exposure in children. The objective of this study was to evaluate whether ETS exposure is associated with CC‐16 when stratified by asthma status.MethodsIn our study, CC‐16 was measured on 537 children aged 9–15 from northeast China in 2011–2012 using the Human Clara Cell Protein ELISA kits. Doctor‐diagnosed asthma was defined as having ever been diagnosed with asthma by a physician. The relationship between ETS exposure and urine CC‐16 level was assessed using linear regression.ResultsWhen stratified by asthma status, a negative association between ETS exposure and urine CC‐16 was observed after adjusting for the effects of the related covariates, with an adjusted β coefficient [P value] = −0.31 [0.006] in the first 2 years of life and with an adjusted β coefficient [P value] = −0.68 [0.004] in the first 2 years of life and current.ConclusionsOur study shows long‐term exposure to ETS was associated with urinary CC‐16 among children without asthma.
Epidemiology of 411 140 cataract operations performed in public hospitals and private hospitals/clinics in Denmark between 2004 and 2012
Authors: Solborg Bjerrum Søren , Mikkelsen Kim Lyngby , la Cour Morten 
Published: December 2014

AbstractPurposeTo study the epidemiology and mortality in patients who had cataract surgery in public hospitals and private hospitals/clinics in Denmark between 2004 and 2012 and to assess the validity of the Danish cataract registries.MethodsRegister‐ and chart‐based study.ResultsA total of 411 140 cataract operations were performed in 243 856 patients. Patients who had cataract surgery in public hospitals had an overall statistically significantly 62% higher mortality compared to patients who had cataract surgery in private hospitals/clinics. The decrease in mean age at first eye cataract surgery in private hospitals/clinics was statistically significantly greater compared to the decrease in mean age at first eye cataract surgery in public hospitals (p < 0.001). The median time interval between first and second eye cataract surgery decreased statistically significantly during the study period (p < 0.001) and was statistically significantly shorter in all calendar years for patients operated in private hospitals/clinics compared to patients operated in public hospitals (p < 0.001). In all, 46% of the cataract operations performed in private hospitals/clinics that led to cases of postoperative endophthalmitis were not registered in any registry.ConclusionIn general, patients who had cataract surgery in private hospitals/clinics were healthier, had first eye cataract surgery at an increasingly younger age and had a reduced time interval between cataract surgeries in the two eyes compared to patients who had cataract surgery in public hospitals. The lack of registration of cataract surgery by the private hospitals/clinics limits the quality of the registries.