bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and taxonomic reassessment of the box blight pathogen Calonectria pseudonaviculata, introducing Calonectria henricotiae sp. nov.
Authors: Gehesquière B. , Crouch J. A. , Marra R. E. , Van Poucke K. , Rys F. , Maes M. , Gobin B. , Höfte M. , Heungens K. 
Published: May 2015

Calonectria pseudonaviculata, the causal agent of the disease of Buxus spp. known as ‘box blight’, was first detected in the mid‐1990s in the UK and New Zealand. Since then, the geographic range of box blight has rapidly expanded to at least 21 countries throughout temperate regions of the world, causing significant losses in nurseries, gardens and wild boxwood populations. This study determined the genetic diversity in a collection of 234 Calonectria isolates from diseased Buxus plants, originating from 15 countries and four continents. Two genetic clades, G1 and G2, were identified within this sample using multilocus phylogenetic analysis. The application of genealogical concordance phylogenetic species recognition criteria using four independent nuclear loci determined that the Calonectria isolates in these two clades are separate phylogenetic species. The isolates in the G1 clade were upheld as C. pseudonaviculata sensu stricto. Based on phylogenetic distinctiveness and the lack of mating, a new species is proposed, Calonectria henricotiae sp. nov., for the Calonectria isolates in the G2 clade. A PCR‐RFLP assay and real‐time PCR assays were developed to easily and reproducibly differentiate these species. To assess the practical implications of the identification of the two species, their physiology, fungicide susceptibility and pathogenicity were compared. No differences in pathogenicity were observed. However, C. henricotiae isolates exhibited greater thermotolerance and reduced sensitivity to specific triazole as well as strobilurin fungicides. The identification of a second phylogenetic species causing box blight may have a substantial impact on the epidemiology and control of this destructive disease.
Water and sediment transport mechanisms in a large river‐connected lake
Authors: Wang Hua , Zhang Zhizhang , Song Depeng , Zhou Yiyi , Liu Xiaodong 
Published: May 2015

AbstractUsing the finite volume method, a 2‐D water‐sediment coupled model was developed to investigate the transport mechanisms of water and sediment in Poyang Lake, the largest river‐connected lake in China. Simulating water and sediment transport processes in an average water year revealed that the total volume of water and the amount of suspended sediment transported from the five main rivers upstream of Poyang Lake were approximately 1.56 × 1011 m3 and 1.25 × 107 t, respectively. The outputs of water and sediment from the lake to the downstream Yangtze River were approximately 2.17 × 1011 m3 and 1.53 × 107 t, respectively. During the wet season, especially between July and September, nearly 1.06 × 1010 m3 of water and 1.89 × 106 t of suspended sediment were transported upstream from the Yangtze River into the lake due to the high external water levels, which accounted for 4.88% and 12.35%, respectively, of the total annual transport from the lake into the Yangtze River.
Noise properties of CT images reconstructed by use of constrained total‐variation, data‐discrepancy minimization
Authors: Rose Sean , Andersen Martin S. , Sidky Emil Y. , Pan Xiaochuan 
Published: May 2015

Purpose:The authors develop and investigate iterative image reconstruction algorithms based on data‐discrepancy minimization with a total‐variation (TV) constraint. The various algorithms are derived with different data‐discrepancy measures reflecting the maximum likelihood (ML) principle. Simulations demonstrate the iterative algorithms and the resulting image statistical properties for low‐dose CT data acquired with sparse projection view angle sampling. Of particular interest is to quantify improvement of image statistical properties by use of the ML data fidelity term.Methods:An incremental algorithm framework is developed for this purpose. The instances of the incremental algorithms are derived for solving optimization problems including a data fidelity objective function combined with a constraint on the image TV. For the data fidelity term the authors, compare application of the maximum likelihood principle, in the form of weighted least‐squares (WLSQ) and Poisson‐likelihood (PL), with the use of unweighted least‐squares (LSQ).Results:The incremental algorithms are applied to projection data generated by a simulation modeling the breast computed tomography (bCT) imaging application. The only source of data inconsistency in the bCT projections is due to noise, and a Poisson distribution is assumed for the transmitted x‐ray photon intensity. In the simulations involving the incremental algorithms an ensemble of images, reconstructed from 1000 noise realizations of the x‐ray transmission data, is used to estimate the image statistical properties. The WLSQ and PL incremental algorithms are seen to reduce image variance as compared to that of LSQ without sacrificing image bias. The difference is also seen at few iterations—short of numerical convergence of the corresponding optimization problems.Conclusions:The proposed incremental algorithms prove effective and efficient for iterative image reconstruction in low‐dose CT applications particularly with sparse‐view projection data.
Variability in CT lung‐nodule volumetry: Effects of dose reduction and reconstruction methods
Authors: Young Stefano , Kim Hyun J. Grace , Ko Moe Moe , Ko War War , Flores Carlos , McNitt‐Gray Michael F. 
Published: May 2015

Purpose:Measuring the size of nodules on chest CT is important for lung cancer staging and measuring therapy response. 3D volumetry has been proposed as a more robust alternative to 1D and 2D sizing methods. There have also been substantial advances in methods to reduce radiation dose in CT. The purpose of this work was to investigate the effect of dose reduction and reconstruction methods on variability in 3D lung‐nodule volumetry.Methods:Reduced‐dose CT scans were simulated by applying a noise‐addition tool to the raw (sinogram) data from clinically indicated patient scans acquired on a multidetector‐row CT scanner (Definition Flash, Siemens Healthcare). Scans were simulated at 25%, 10%, and 3% of the dose of their clinical protocol (CTDIvol of 20.9 mGy), corresponding to CTDIvol values of 5.2, 2.1, and 0.6 mGy. Simulated reduced‐dose data were reconstructed with both conventional filtered backprojection (B45 kernel) and iterative reconstruction methods (SAFIRE: I44 strength 3 and I50 strength 3). Three lab technologist readers contoured “measurable” nodules in 33 patients under each of the different acquisition/reconstruction conditions in a blinded study design. Of the 33 measurable nodules, 17 were used to estimate repeatability with their clinical reference protocol, as well as interdose and inter‐reconstruction‐method reproducibilities. The authors compared the resulting distributions of proportional differences across dose and reconstruction methods by analyzing their means, standard deviations (SDs), and t‐test and F‐test results.Results:The clinical‐dose repeatability experiment yielded a mean proportional difference of 1.1% and SD of 5.5%. The interdose reproducibility experiments gave mean differences ranging from −5.6% to −1.7% and SDs ranging from 6.3% to 9.9%. The inter‐reconstruction‐method reproducibility experiments gave mean differences of 2.0% (I44 strength 3) and −0.3% (I50 strength 3), and SDs were identical at 7.3%. For the subset of repeatability cases, inter‐reconstruction‐method mean/SD pairs were (1.4%, 6.3%) and (−0.7%, 7.2%) for I44 strength 3 and I50 strength 3, respectively. Analysis of representative nodules confirmed that reader variability appeared unaffected by dose or reconstruction method.Conclusions:Lung‐nodule volumetry was extremely robust to the radiation‐dose level, down to the minimum scanner‐supported dose settings. In addition, volumetry was robust to the reconstruction methods used in this study, which included both conventional filtered backprojection and iterative methods.
Environmental Isolates of Azole-Resistant Aspergillus fumigatus in Germany
Authors: Bader Oliver , Tünnermann Jana , Dudakova Anna , Tangwattanachuleeporn Marut , Weig Michael , Groß Uwe 
Published: May 2015

ABSTRACT

Azole antifungal drug resistance in
Aspergillus fumigatus
is an emerging problem in several parts of the world. Here we investigated the distribution of such strains in soils from Germany. At a general positivity rate of 12%, most prevalently, we found strains with the TR
34
/L98H and TR
46
/Y121F/T289A alleles, dispersed along a corridor across northern Germany. Comparison of the distributions of resistance alleles and genotypes between environment and clinical samples suggests the presence of local clinical clusters.
A Mutation of RNA Polymerase β′ Subunit (RpoC) Converts Heterogeneously Vancomycin-Intermediate Staphylococcus aureus (hVISA) into “Slow VISA”
Authors: Matsuo Miki , Hishinuma Tomomi , Katayama Yuki , Hiramatsu Keiichi 
Published: May 2015

ABSTRACT

Various mutations in the
rpoB
gene, which encodes the RNA polymerase β subunit, are associated with increased vancomycin (VAN) resistance in vancomycin-intermediate
Staphylococcus aureus
(VISA) and heterogeneously VISA (hVISA) strains. We reported that
rpoB
mutations are also linked to the expression of the recently found “slow VISA” (sVISA) phenotype (M. Saito, Y. Katayama, T. Hishinuma, A. Iwamoto, Y. Aiba, K Kuwahara-Arai, L. Cui, M. Matsuo, N. Aritaka, and K. Hiramatsu, Antimicrob Agents Chemother 58:5024–5035, 2014,
http://dx.doi.org/10.1128/AAC.02470-13
). Because RpoC and RpoB are components of RNA polymerase, we examined the effect of the
rpoC
(P440L) mutation on the expression of the sVISA phenotype in the Mu3
fdh2
*V6-5 strain (V6-5), which was derived from a previously reported hVISA strain with the VISA phenotype. V6-5 had an extremely prolonged doubling time (DT) (72 min) and high vancomycin MIC (16 mg/liter). However, the phenotype of V6-5 was unstable, and the strain frequently reverted to hVISA with concomitant loss of low growth rate, cell wall thickness, and reduced autolysis. Whole-genome sequencing of phenotypic revertant strain V6-5-L1 and comparison with V6-5 revealed a second mutation, F562L, in
rpoC
. Introduction of the wild-type (WT)
rpoC
gene using a multicopy plasmid resolved the sVISA phenotype of V6-5, indicating that the
rpoC
(P440L) mutant expressed the sVISA phenotype in hVISA. To investigate the mechanisms of resistance in the sVISA strain, we independently isolated an additional 10 revertants to hVISA and VISA. In subsequent whole-genome analysis, we identified compensatory mutations in the genes of three distinct functional categories: the
rpoC
gene itself as regulatory mutations, peptidoglycan biosynthesis genes, and
relQ
, which is involved in the stringent response. It appears that the
rpoC
(P440L) mutation causes the sVISA phenotype by augmenting cell wall peptidoglycan synthesis and through the control of the stringent response.
Determination of MIC Distribution and Epidemiological Cutoff Values for Bedaquiline and Delamanid in Mycobacterium tuberculosis Using the MGIT 960 System Equipped with TB eXiST
Authors: Keller Peter M. , Hömke Rico , Ritter Claudia , Valsesia Giorgia , Bloemberg Guido V. , Böttger Erik C. 
Published: May 2015

ABSTRACT
Bedaquiline (Sirturo) and delamanid (Deltyba) have recently been approved by the regulatory authorities for treatment of multidrug-resistant tuberculosis (MDR-TB). Antimicrobial susceptibility testing is not established for either substance. On the basis of the use of the MGIT 960 system equipped with EpiCenter/TB eXiST, we determined a mean bedaquiline MIC for wild-type strains of 0.65 mg/liter (median, 0.4 mg/liter) and an epidemiological cutoff (ECOFF) of 1.6 mg/liter; for delamanid, a mean wild-type drug MIC of 0.013 mg/liter (median, 0.01 mg/liter) and an ECOFF of 0.04 mg/liter were determined.
Outbreak of NDM-1-Producing Klebsiella pneumoniae Causing Neonatal Infection in a Teaching Hospital in Mainland China
Authors: Zhang XiaoYu , Li XianPing , Wang Min , Yue HeJia , Li PengLing , Liu YaPing , Cao Wei , Yao DongMei , Liu Li , Zhou XiaoLan , Zheng Rong , Bo Tao 
Published: May 2015

ABSTRACT

The emergence and spread of bacteria carrying the
bla
NDM-1
gene has become a worldwide concern. Here, we report eight cases of
Klebsiella pneumoniae
with
bla
NDM-1
in the neonatal ward of a teaching hospital in mainland China. Multilocus sequence typing showed that seven isolates were clonally related and confirmed them as sequence type 17 (ST17). One isolate belonged to ST433. These findings suggest continuous spread of
bla
NDM-1
in mainland China and emphasize the need for intensive surveillance and precautions.
Rationale, secondary outcome scores and 1-year follow-up of a randomised trial of platelet-rich plasma injections in acute hamstring muscle injury: the Dutch Hamstring Injection Therapy study
Authors: Reurink Gustaaf , Goudswaard Gert Jan , Moen Maarten H , Weir Adam , Verhaar Jan A N , Bierma-Zeinstra Sita M A , Maas Mario , Tol Johannes L 
Published: May 2015

BackgroundPlatelet-rich plasma (PRP) injections are an experimental treatment for acute muscle injuries. We examined whether PRP injections would accelerate return to play after hamstring injury. The methods and the primary outcome measure were published in theNew England Journal of Medicine(NEJM) as ‘Platelet-rich plasma injections in acute muscle injury’ (2014). This article shares information not available in theNEJMletter or online supplement, especially the rationale behind the study and the secondary outcome measures including 1 year re-injury data.MethodsWe performed a multicentre, randomised, double-blind, placebo-controlled trial in 80 competitive and recreational athletes with acute hamstring muscle injuries. Details can be found in theNEJM(http://www.nejm.org/doi/full/10.1056/NEJMc1402340). The primary outcome measure was the time needed to return to play during 6 months of follow-up. Not previously reported secondary outcome scores included re-injury at 1 year, alteration in clinical and MRI parameters, subjective patient satisfaction and the hamstring outcome score.ResultsIn the earlierNEJMpublication, we reported that PRP did not accelerate return to play; nor did we find a difference in the 2-month re-injury rate. We report no significant between-group difference in the 1-year re-injury rate (HR=0.89; 95% CI, 0.38 to 2.13; p=0.80) or any other secondary outcome measure.ConclusionsAt 1-year postinjection, we found no benefit of intramuscular PRP compared with placebo injections in patients with acute hamstring injuries in the time to return to play, re-injury rate and alterations of subjective, clinical or MRI measures.
Sex differences in the association of fasting and postchallenge glucose levels with grip strength among older adults: the Rancho Bernardo Study
Authors: Kalyani Rita Rastogi , Kim Catherine , Ferrucci Luigi , Laughlin Gail A , Kritz-Silverstein Donna , Kong Shengchun , Nan Bin , Barrett-Connor Elizabeth 
Published: May 2015

ObjectivePersons with diabetes have accelerated muscle loss. The association of fasting and postchallenge glucose levels per se to grip strength, a clinical marker of poor physical function, and potential sex differences in this relationship has not been previously described.DesignLongitudinal cohort.SettingUSA.ParticipantsParticipants were community-dwelling older adults (mean age 71.3 years) without self-reported diabetes and/or use of diabetes medication with glucose measured at baseline (1992–1996).MeasurementsFasting plasma glucose (FPG) was measured in 1019 women and 636 men. Two-hour glucose (2HG) levels after a 75 g oral glucose tolerance test were also available (women, n=870; men, n=559). Dominant hand grip strength was assessed using a hand-held dynamometer at 3.0±1.6 visits over a median 7.0 years. Mixed linear models examined the association of baseline glucose levels with grip strength, accounting for repeated visits, and adjusting for covariates.ResultsSex-specific FPG quartiles were associated with unadjusted differences in grip strength among women (p=0.03) but not men (p=0.50). However, in men, adjusting for age, education, height, weight, peripheral neuropathy, physical activity, and comorbidities, each SD (SD=17 mg/dL) higher FPG was associated with persistently lower grip strength (−0.44±0.22 kg, p=0.049); 2HG (SD=50 mg/dL) was unrelated to grip strength (−0.39±0.25 kg, p=0.13). In women, neither FPG (SD=16 mg/dL) nor 2HG (SD=45 mg/dL) was associated with grip strength (0.02±0.12 kg, p=0.90; and −0.20±0.14 kg, p=0.14; respectively) after adjustment. The rate of change in grip strength did not differ across FPG or 2HG quartiles in either sex.ConclusionsIn age-adjusted analyses, elevated fasting glucose levels are associated with persistently lower grip strength in older men, but not women. Future studies are needed to elucidate reasons for these sex differences and may provide further insight into accelerated loss of muscle function as a complication of diabetes in older adults.
Exposure to air pollution and meteorological factors associated with children’s primary care visits at night due to asthma attack: case-crossover design for 3-year pooled patients
Authors: Yamazaki Shin , Shima Masayuki , Yoda Yoshiko , Oka Katsumi , Kurosaka Fumitake , Shimizu Shigeta , Takahashi Hironobu , Nakatani Yuji , Nishikawa Jittoku , Fujiwara Katsuhiko , Mizumori Yasuyuki , Mogami Akira , Yamada Taku , Yamamoto Nobuharu 
Published: May 2015

ObjectiveWe examined the association of outdoor air pollution and meteorological parameters with primary care visits (PCVs) at night due to asthma attack.SettingA case-crossover study was conducted in a primary care clinic in Himeji City, Japan.ParticipantsParticipants were 1447 children aged 0–14 years who visited the clinic with an asthma attack from April 2010 until March 2013.ExposureDaily concentrations of air pollutants and meteorological parameters were measured.Primary outcomePCVs at night due to asthma attack. A conditional logistic regression model was used to estimate ORs of PCVs per unit increment of air pollutants or meteorological parameters (the per-unit increments of particulate matter with an aerodynamic diameter ≤2.5 µm (PM2.5) and ozone were 10 μg/m3and 10 ppb, respectively). Analyses took into consideration the effects of seasonality.ResultsWe noted an association between PCVs and daily ozone levels on the day before a PCV (OR=1.17; 95% CI 1.01 to 1.35; p=0.04), as well as between PCVs and 3-day mean ozone levels before a PCV (OR=1.29; 95% CI 1.00 to 1.46; p=0.04), from April until June. We also observed an association between PCVs and daily PM2.5levels on the day before a PCV from December until March (OR=1.16; 95% CI 1.01 to 1.33; p=0.05). Meteorological parameters, such as hours of sunshine from September until November, atmospheric pressure from April until June, and temperature from April until August, were also found to be associated with PCVs.ConclusionsThe findings in the present study supported an association between ozone and PCVs and suggest that certain meteorological items may be associated with PCVs.
Health gains and financial risk protection: an extended cost-effectiveness analysis of treatment and prevention of diarrhoea in Ethiopia
Authors: Pecenka Clinton J , Johansson Kjell Arne , Memirie Solomon Tessema , Jamison Dean T , Verguet Stéphane 
Published: May 2015

ObjectivesPolicymakers face many decisions when considering public financing for health, including the kind of health interventions to include in a publically financed package. The consequences of these choices will influence health outcomes as well as the financial risk protection provided to different segments of the population. The purpose of this study is to illustrate the size and distribution of benefits due to treatment and prevention of diarrhoea (ie, rotavirus vaccination).MethodsWe use an economic model to examine the impacts of universal public finance (UPF) of diarrhoeal treatment alone, as opposed to diarrhoeal treatment along with rotavirus vaccination in Ethiopia using extended cost-effectiveness analysis (ECEA). ECEA allows us to measure the health gains and financial risk protection provided by these interventions for each wealth quintile. Our model compares a baseline situation with diarrhoeal treatment seeking of 32% (overall) and no rotavirus vaccination, to a situation where UPF increases treatment seeking by 20 percentage points for each quintile and rotavirus vaccination reaches DTP (diphteria, pertussis, tetanus) 2 levels for each quintile (overall rate of 52%). We calculate deaths averted, private expenditures averted and costs incurred by the government under the baseline situation and with UPF.ResultsWe find that diarrhoeal treatment paired with rotavirus vaccination is more cost effective than diarrhoeal treatment alone for the metrics we examine in this paper (deaths and private expenditures averted). Per US$1 million invested, diarrhoeal treatment saves 44 lives and averts US$115 000 in private expenditures. For the same investment, diarrhoeal treatment and rotavirus vaccination save 61 lives and avert US$150 000 in private expenditures. The health benefits of these interventions tend to benefit the poor, while the financial benefits favour the better-off.ConclusionsPolicymakers should consider multiple benefit streams as well as their scale and incidence when considering public finance of health interventions.
Managing work–family conflict in the medical profession: working conditions and individual resources as related factors
Authors: Mache Stefanie , Bernburg Monika , Vitzthum Karin , Groneberg David A , Klapp Burghard F , Danzer Gerhard 
Published: May 2015

ObjectivesThis study developed and tested a research model that examined the effects of working conditions and individual resources on work–family conflict (WFC) using data collected from physicians working at German clinics.Material and methodsThis is a cross-sectional study of 727 physicians working in German hospitals. The work environment, WFC and individual resources were measured by the Copenhagen Psychosocial Questionnaire, the WFC Scale, the Brief Resilient Coping Scale and the Questionnaire for Self-efficacy, Optimism and Pessimism. Descriptive, correlation and linear regression analyses were applied.ResultsClinical doctors working in German hospitals perceived high levels of WFC (mean=76). Sociodemographic differences were found for age, marital status and presence of children with regard to WFC. No significant gender differences were found. WFCs were positively related to high workloads and quantitative job demands. Job resources (eg, influence at work, social support) and personal resources (eg, resilient coping behaviour and self-efficacy) were negatively associated with physicians’ WFCs. Interaction terms suggest that job and personal resources buffer the effects of job demands on WFC.ConclusionsIn this study, WFC was prevalent among German clinicians. Factors of work organisation as well as factors of interpersonal relations at work were identified as significant predictors for WFC. Our results give a strong indication that both individual and organisational factors are related to WFC. Results may play an important role in optimising clinical care. Practical implications for physicians’ career planning and recommendations for future research are discussed.