bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Smallmouth Bass Predation on Recruitment of Age-0 Yellow Perch in South Dakota Glacial Lakes
Authors: Dembkowski Daniel J. , Willis D. W. , Blackwell B. G. , Chipps S. R. , Bacula T. D. , Wuellner M. R. 
Published: July 2015

Abstract
We estimated the influence of predation by Smallmouth Bass Micropterus dolomieu on recruitment of age-0 Yellow Perch Perca flavescens in two northeastern South Dakota glacial lakes. We estimated a likely range in consumption of age-0 Yellow Perch using Smallmouth Bass diet information from two time periods when age-0 Yellow Perch constituted high (2008) and low (2012 and 2013) proportions of Smallmouth Bass diets, and bass population size estimates as inputs in a bioenergetics model. The proportion of age-0 Yellow Perch consumed by the Smallmouth Bass populations was determined by comparing estimates of consumption with estimates of age-0 perch production. During 2008, age-0 Yellow Perch constituted between 0% and 42% of Smallmouth Bass diets by weight, whereas during 2012 and 2013, age-0 perch constituted between 0% and 20% of bass diets by weight. Across both lakes and time periods, production of age-0 Yellow Perch ranged from 0.32 to 1.78 kg·ha−1·week−1. Estimates of Smallmouth Bass consumption measured during the same intervals ranged from 0.06 to 0.33 kg·ha−1·week−1, equating to consumption of between 1% and 34% of the available Yellow Perch biomass. Given current conditions relative to Smallmouth Bass abundance and consumption dynamics and production of age-0 Yellow Perch, it does not appear that Smallmouth Bass predation acts as a singular factor limiting recruitment of age-0 Yellow Perch in our study lakes. However, future research and management initiatives should recognize that the long-term impact of Smallmouth Bass predation is not static and will likely fluctuate depending on environmental (e.g., temperature) and biotic (e.g., trends in macrophyte abundance, predator and prey population structure and abundance, and predatory fish assemblage dynamics) characteristics.
Received December 19, 2014; accepted April 20, 2015
Contemplation of Smoking Cessation and Quit Attempts in Human Immunodeficiency Virus–Infected and Uninfected Veterans
Authors: Shahrir Shahida , Tindle Hilary A. , McGinnis Kathleen A. , Fiellin David A. , Goulet Joseph , Akgün Kathleen M. , Gibert Cynthia L. , Rodriguez-Barradas Maria C. , Crothers Kristina 
Published: July 2015

Background As antiretroviral treatments prolong life in human immunodeficiency virus (HIV)-infected patients, smoking cessation is now a top priority. However, studies of HIV-infected smokers have not been conducted with uninfected controls. In this study, researchers determined factors associated with contemplating smoking cessation and making a prior quit attempt among HIV-infected and uninfected smoking veterans. Methods Between 2005 and 2007, 1,027 HIV-infected and 794 uninfected smokers were identified as part of the Veterans Aging Cohort Study (VACS). Stratifying by HIV status, adjusted odds ratios (AORs) were calculated using logistic regression to identify factors associated with contemplating smoking cessation and making a prior quit attempt. Results Most participants (66 % of HIV-infected vs. 68 % of uninfected; P = .46) were contemplating cessation, and 56 % of both groups ( P = .99) had attempted to quit in the last year. In stratified multivariable analyses, HIV-infected smokers with recent pulmonary disease diagnoses were more likely to have made a quit attempt (AOR = 4.93, 95 % confidence interval [CI] = 1.41–17.17). Both HIV-infected and uninfected patients with unhealthy alcohol use were less likely to be contemplating cessation (AOR = 0.66, 95 % CI = 0.49–0.90 and 0.71, 95 % CI = 0.50–1.00). HIV-infected smokers who reported unhealthy alcohol use were also less likely to have made a quit attempt in the last year (AOR = 0.68, 95 % CI = 0.51–0.91). Conclusions Patient-level interest and motivation are not major barriers to smoking cessation among HIV-infected veterans. Targeting HIV-infected smokers with a recent pulmonary disease diagnosis may improve sustained smoking cessation. Unhealthy alcohol use appears to be a key modifiable risk factor. Smoking cessation rates may be improved by combining interventions for smoking and alcohol use for HIV-infected patients.
Candida biomarkers in patients with candidaemia and bacteraemia
Authors: Martínez-Jiménez M. Carmen , Muñoz Patricia , Valerio Maricela , Alonso Roberto , Martos Carmen , Guinea Jesús , Bouza Emilio 
Published: July 2015

Abstract

Objectives
Microbiological strategies are necessary to help clinicians discontinue empirical antifungal therapy in patients with suspected invasive candidiasis. Culture methods and biomarkers each show low sensitivity. We analysed the value of combining different biomarkers as a decision-making tool for discontinuing empirical antifungal treatment.

Methods
We studied stored serum samples from 31 patients with candidaemia (Candida albicans 40%, Candida tropicalis 20%, Candida parapsilosis 18%, Candida glabrata 12% and other 10%) and 50 patients with bacteraemia at Gregorio Marañón Hospital, Madrid, Spain. C. albicans germ tube antibody (CAGTA), mannan antigens (MN), antimannan antibodies (AMN) and (1→3)-β-d-glucan (BDG) were assayed using the manufacturer's and alternative cut-offs to improve the accuracy of the tests.

Results
The sensitivity of the biomarkers when used alone was low (58%−84%), but specificity was high (65.8%−92.0%). The best combinations were CAGTA and BDG using cut-offs of 1/80 and 80 pg/mL, respectively (sensitivity 96.8% and specificity 84%), and CAGTA and MN using cut-offs of 1/80 and 75 pg/mL, respectively (sensitivity 93.5% and specificity 86.0%). The sensitivity of both combinations was 100% for C. albicans, C. tropicalis and C. parapsilosis, but only combinations including BDG detected Candida krusei. The negative predictive values (NPVs) of both combinations were, respectively, 97.7% and 95.6% (prevalence of candidaemia, 23.6%). For a prevalence of candidaemia of 5% and 10%, the NPV reached 99.8% and 99.6%.

Conclusions
The combinations of CAGTA and BDG or CAGTA and MN had a very high NPV at the alternative cut-offs and could be used in antifungal stewardship programmes as a decision-making tool for discontinuing unnecessary empirical therapy in patients with suspected candidaemia.
Activity of ceftazidime/avibactam against isogenic strains of Escherichia coli containing KPC and SHV β-lactamases with single amino acid substitutions in the Ω-loop
Authors: Winkler Marisa L. , Papp-Wallace Krisztina M. , Bonomo Robert A. 
Published: July 2015

Abstract

Objectives
The objective of this study was to explore the activity of ceftazidime and ceftazidime/avibactam against a collection of isogenic strains of Escherichia coli DH10B possessing SHV and KPC β-lactamases containing single amino acid substitutions in the Ω-loop (residues 164–179).

Methods
Ceftazidime and ceftazidime/avibactam MICs were determined by the agar dilution method for a panel of isogenic E. coli strains expressing SHV-1 and KPC-2 with amino acid substitutions at positions 164, 167, 169 or 179. Two KPC-2 β-lactamase variants that possessed elevated MICs of ceftazidime/avibactam were selected for further biochemical analyses.

Results
Avibactam restored susceptibility to ceftazidime for all Ω-loop variants of SHV-1 with MICs &lt;8 mg/L. In contrast, several of the Arg164 and Asp179 variants of KPC-2 demonstrated MICs of ceftazidime/avibactam &gt;8 mg/L. β-Lactamase kinetics showed that the Asp179Asn variant of KPC-2 demonstrated enhanced kinetic properties against ceftazidime. The Ki app, k2/K and koff of the Arg164Ala and Asp179Asn variant KPC-2 β-lactamases indicated that avibactam effectively inhibited these enzymes.

Conclusions
Several KPC-2 variants demonstrating ceftazidime resistance as a result of single amino acid substitutions in the Ω-loop were not susceptible to ceftazidime/avibactam (MICs &gt;8 mg/L). We hypothesize that this observation is due to the stabilizing interactions (e.g. hydrogen bonds) of ceftazidime within the active site of variant β-lactamases that prevent avibactam from binding to and inhibiting the β-lactamase. As ceftazidime/avibactam is introduced into the clinic, monitoring for new KPC-2 variants that may exhibit increased ceftazidime kinetics as well as resistance to this novel antibiotic combination will be important.
Within-host diversity of MRSA antimicrobial resistances
Authors: Stanczak-Mrozek Kinga I. , Manne Anusha , Knight Gwenan M. , Gould Katherine , Witney Adam A. , Lindsay Jodi A. 
Published: July 2015

Abstract

Objectives
MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and potential mechanisms of resistance gene transfer in vivo.

Methods
Nasal swabs from 38 MRSA carriers admitted to hospital were plated and 20 individual colonies from each patient tested for phenotypic antibiotic susceptibility and genetically for lineage, carriage of four prophages and three plasmid families. Free bacteriophages were detected in swabs as well as their capacity for transducing resistance genes.

Results
Nine (24%) patients carried phenotypic AMR variants and 24 (63%) carried prophage and plasmid variants. If a single colony was selected for testing, the probability of detecting all AMR in that patient was 87%. Sixty-four different AMR and mobile genetic element (MGE) profiles were detected, mostly in the MRSA CC22 background (where CC stands for clonal complex), with up to 8 profiles per patient. Nearly half of the patients carried detectable free bacteriophages and phages successfully transduced resistance genes between laboratory and patient isolates in vitro. WGS showed MRSA core genomes were stable, while AMR and MGEs varied.

Conclusions
‘Clouds’ of MRSA variants that have acquired or lost AMR and MGEs are common in nasal colonizing populations and bacteriophages may play an important role in gene transfer. Accurate estimation of AMR and genetic variability has implications for diagnostics, epidemiology, antimicrobial stewardship and understanding the evolutionary selection of AMR in colonizing populations.
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation
Authors: Jin Minliang , Liu Haijun , He Cheng , Fu Junjie , Xiao Yingjie , Wang Yuebin , Xie Weibo , Wang Guoying , Yan Jianbing 
Published: July 2015

ABSTRACTVariation in gene expression contributes to the diversity of phenotype. The construction of the pan-transcriptome is especially necessary for species with complex genomes, such as maize. However, knowledge of the regulation mechanisms and functional consequences of the pan-transcriptome is limited. In this study, we identified 13,382 nuclear expression presence and absence variation candidates (ePAVs, expressed in 5%~95% lines; based on the reference genome) by re-analyzing the RNA sequencing data from the kernels (15 days after pollination) of 368 maize diverse inbreds. It was estimated that only ~1% of the ePAVs are explained by DNA sequence presence and absence variations (PAV). The ePAV genes tend to be regulated by distant eQTLs when compared with non-ePAV genes (called here core expression genes, expressed in more than 95% lines). When the expression presence/absence status was used as the “ genotype” to perform genome-wide association study, 56 (0.42%) ePAVs were significantly associated with 15 agronomic traits and 1,967 (14.74%) with 526 metabolic traits, measured from the mature kernels. While the above was majorly based on the reference genome, by using a modified ‘assemble-then-align’ strategy, 2,355 high confidence novel sequences with a total length of 1.9Mb were found absent in the current B73 reference genome (v2). Ten randomly selected novel sequences were validated with genomic PCR. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes. Two novel validated sequences annotated as NBS_LRR like genes were found to associate with flavonoid content and their homologs in rice were also found to affect flavonoids and disease-resistance. Novel sequences absent in the present reference genome might be functionally important and deserve more attentions. This study provides novel perspectives and resources to discover maize quantitative trait variations and help us to better understand the kernel regulation networks, thus enhancing maize breeding.
Haplotypes of common SNPs can explain missing heritability of complex diseases
Authors: Bhatia Gaurav , Gusev Alexander , Loh Po-Ru , Vilhjálmsson Bjarni J. , Ripke Stephan ,   Schizophrenia Working Group of the Psychiatric Genomics Consortium, Purcell Shaun , Stahl Eli , Daly Mark , Candia Teresa R de , Kendler Kenneth S. , O’Donovan Michael C , Lee Sang Hong , Wray Naomi R. , Neale Benjamin M , Keller Matthew C. , Zaitlen Noah A. , Pasaniuc Bogdan , Yang Jian , Price Alkes L. 
Published: July 2015

AbstractWhile genome-wide significant associations generally explain only a small proportion of the narrow-sense heritability of complex disease (h2), recent work has shown that more heritability is explained by all genotyped SNPs (hg2). However, much of the heritability is still missing (hg2<h2). For example, for schizophrenia,h2is estimated at 0.7-0.8 buthg2is estimated at ∼0.3. Efforts at increasing coverage through accurately imputed variants have yielded only small increases in the heritability explained, and poorly imputed variants can lead to assay artifacts for case-control traits. We propose to estimate the heritability explained by a set of haplotype variants (haploSNPs) constructed directly from the study sample (hhap2). Our method constructs a set of haplotypes from phased genotypes by extending shared haplotypes subject to the 4-gamete test. In a large schizophrenia data set (PGC2-SCZ), haploSNPs with MAF > 0.1% explained substantially more phenotypic variance (hhap2= 0.64 (S.E. 0.084)) than genotyped SNPs alone (hg2= 0.32 (S.E. 0.029)). These estimates were based on cross-cohort comparisons, ensuring that cohort-specific assay artifacts did not contribute to our estimates. In a large multiple sclerosis data set (WTCCC2-MS), we observed an even larger difference betweenhhap2andhg2, though data from other cohorts will be required to validate this result. Overall, our results suggest that haplotypes of common SNPs can explain a large fraction of missing heritability of complex disease, shedding light on genetic architecture and informing disease mapping strategies.
How strategy changes in different monetary policy conditions
Authors: Yang Yan , Wang Fengli , Chen Shou 
Published: July 2015

Purpose– The paper aims to address how firms make strategic adjustment to the changing resource availability in different monetary policy conditions and how the stickiness of cost influences the strategic adjustment, and to dig out the major internal and industrial factors that influence the relationship between strategic change and monetary policy conditions.Design/methodology/approach– The mechanism of how monetary policy affects strategic change is expounded by resource-based view and transaction cost theory. The balanced panel data of 422 companies of manufacturing industry listed in Chinese A share market before the end of 2003 from 2004-2013 are selected as sample to test the theoretic hypotheses.Findings– It was found that looser monetary policy results in greater strategic change than the tighter one for the high adjustment cost. External capital dependence and industrial competition intensity strengthen the positive correlation between monetary policy condition and strategic change. Private firms are more susceptible to money supply condition change compared with state-owned enterprises. Companies tend to expand investment on fixed asset but to shrink investment on R & D and trademark in looser money supply condition.Practical implications– Companies make bigger strategic adjustment in looser monetary policy condition for the greater availability of financial resources and lower market risk, but smaller adjustment in the tight one. However, owing to the sunk cost and the high adjustment cost, companies are not suggested to make aggressive strategic adjustment in the loose monetary conditions so as to avoid overcapacity and financial risk in tight monetary policy condition. For the policy-maker, as loose monetary policy cannot stimulate innovation but boost expansion on capacity, it is better to strengthen the resources configuration mechanism of monetary policy when making monetary policy.Originality/value– This paper fulfils a theoretic gap to study the mechanism of how monetary policy influence corporate strategic resource reconfiguration via affecting the resource base of a company by combining resource-based view and transaction cost theory.
Mandatory and voluntary information disclosure and the effects on financial analysts
Authors: Wang Shengnian , Han Liang , Gao Weiting 
Published: July 2015

Purpose
– This paper aims to make a comparison, different from existing literature solely focusing on voluntary earnings forecasts and ex post earnings surprise, between the effects of mandatory earnings surprise warnings and voluntary information disclosure issued by management teams on financial analysts in terms of the number of followings and the accuracy of earnings forecasts.

Design/methodology/approach
– This paper uses panel data analysis with fixed effects on data collected from Chinese public firms between 2006 and 2010. It uses an exogenous regulation enforcement to minimise the endogeneity problem.

Findings
– This paper finds that financial analysts are less likely to follow firms which mandatorily issue earnings surprise warnings ex ante than those voluntarily issue earnings forecasts. Moreover, ex post, they issue less accurate and more dispersed forecasts on former firms. The results support Brown et al.’s (2009) finding in the USA and suggest that the earnings surprise warnings affect information asymmetries.

Practical implications
– This paper justifies the mandatory earnings surprise warnings policy issued by Chinese Securities Regulatory Commission in 2006.

Originality/value
– Mandatory earnings surprise is a unique practical regulation for publicly listed firms in China. This paper, for the first time, provides empirical evaluation on the effectiveness of a mandatory information disclosure policy in China. Consistent with existing literature on information disclosure by public firms in other countries, this paper finds that, in China, voluntary information disclosure captures more private information than mandatory information disclosure on corporate earnings ability.
Dynamics between currency and equity in Chinese markets
Authors: Aftab Muhammad , Ahmad Rubi , Ismail Izlin 
Published: July 2015

Purpose
– This study aims to examine the dynamics between exchange rate and equities contextualizing the current liberal currency regime in China. This investigation also extends the analysis to explore the potential important factors influencing the interactions between these two markets. After exchange rate reforms, currency issue has emerged as a new dimension in portfolio decisions and diversification strategies in Chinese equity markets.

Design/methodology/approach
– This research uses the dynamic conditional correlation generalized autoregressive conditional heteroskedasticity model proposed by Engle (2002) to explore the dynamic interactions between the currency and stock markets. Further, the paper uses regression analysis to explore the explanatory channels of the correlation. The sample comprises 1,265 listed companies over the period 2005-2012 with daily, weekly and monthly observations. To make analysis robust, the study also considers different exchange rates and equities belonging to different industries.

Findings
– The findings suggest that exchange rate and stock price are related negatively. This conduit increases during the financial crisis period. This association is more prominent at monthly frequency than that of daily and weekly frequencies, which may refer to the noise factor in the high-frequency data. For a portfolio diversification point of view, currency may be considered an alternative diversifier against equity in China. The results also suggest a weak influence of market forces on the association between the currency and stock markets.

Originality/value
– Much of the related past research is based on co-integration approaches and limited to the relationship between currency and equity markets without exploring the determining channels of this important connection. This study uses a more suitable approach to examine the topic and also investigates the determinants. Besides, previous studies take index data which may be poor to depict the overall market outlook. This paper proceeds with firm-level data which are more appropriate to expose the overall market outlook and investor behavior. This research also draws valuable implications.
Business strategy, market competition and earnings management
Authors: Wu Peng , Gao Lei , Gu Tingting 
Published: July 2015

Purpose– The purpose of this study is to explore the relationships among business strategy, market competition and earnings management.Design/methodology/approach– This paper uses 2,037 Chinese A-share listed firms from 2010 to 2012 to test the research questions using regression analyses.Findings– The firms that follow cost leadership strategy (cost leaders) are more likely to have a higher level of real earnings management. The firms that follow differentiation strategy (differentiators) are less likely to use real earnings management. For cost leaders, the market competition further increases the level of real earnings management, whereas the level of earnings management of differentiators is not significantly impacted by the market competition.Practical implications– Results of this study indicate the feasibility of differentiation strategy in China and suggest that management should be encouraged to use such a strategy or to use a hybrid strategy to achieve its operational and financial goals.Originality/value– The study contributes to the research of earning management by providing evidence on that business strategy has significant impacts on earnings management. It also shows an incremental influence of market competition on earnings management through its impacts on business strategy.