bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics reveals cotton‐specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium
Authors: Chen Jie‐Yin , Liu Chun , Gui Yue‐Jing , Si Kai‐Wei , Zhang Dan‐Dan , Wang Jie , Short Dylan P. G. , Huang Jin‐Qun , Li Nan‐Yang , Liang Yong , Zhang Wen‐Qi , Yang Lin , Ma Xue‐Feng , Li Ting‐Gang , Zhou Lei , Wang Bao‐Li , Bao Yu‐Ming , Subbarao Krishna V. , Zhang Geng‐Yun , Dai Xiao‐Feng 
Published: October 2017

Summary

Verticillium dahliae isolates are most virulent on the host from which they were originally isolated. Mechanisms underlying these dominant host adaptations are currently unknown. We sequenced the genome of V. dahliae Vd991, which is highly virulent on its original host, cotton, and performed comparisons with the reference genomes of JR2 (from tomato) and VdLs.17 (from lettuce).

Pathogenicity‐related factor prediction, orthology and multigene family classification, transcriptome analyses, phylogenetic analyses, and pathogenicity experiments were performed.

The Vd991 genome harbored several exclusive, lineage‐specific (LS) genes within LS regions (LSRs). Deletion mutants of the seven genes within one LSR (G‐LSR2) in Vd991 were less virulent only on cotton. Integration of G‐LSR2 genes individually into JR2 and VdLs.17 resulted in significantly enhanced virulence on cotton but did not affect virulence on tomato or lettuce. Transcription levels of the seven LS genes in Vd991 were higher during the early stages of cotton infection, as compared with other hosts. Phylogenetic analyses suggested that G‐LSR2 was acquired from Fusarium oxysporum f. sp. vasinfectum through horizontal gene transfer.

Our results provide evidence that horizontal gene transfer from Fusarium to Vd991 contributed significantly to its adaptation to cotton and may represent a significant mechanism in the evolution of an asexual plant pathogen.
A Probabilistic Analysis of Surface Water Flood Risk in London
Authors: Jenkins Katie , Hall Jim , Glenis Vassilis , Kilsby Chris 
Published: October 2017

AbstractFlooding in urban areas during heavy rainfall, often characterized by short duration and high‐intensity events, is known as “surface water flooding.” Analyzing surface water flood risk is complex as it requires understanding of biophysical and human factors, such as the localized scale and nature of heavy precipitation events, characteristics of the urban area affected (including detailed topography and drainage networks), and the spatial distribution of economic and social vulnerability. Climate change is recognized as having the potential to enhance the intensity and frequency of heavy rainfall events. This study develops a methodology to link high spatial resolution probabilistic projections of hourly precipitation with detailed surface water flood depth maps and characterization of urban vulnerability to estimate surface water flood risk. It incorporates probabilistic information on the range of uncertainties in future precipitation in a changing climate. The method is applied to a case study of Greater London and highlights that both the frequency and spatial extent of surface water flood events are set to increase under future climate change. The expected annual damage from surface water flooding is estimated to be to be £171 million, £343 million, and £390 million/year under the baseline, 2030 high, and 2050 high climate change scenarios, respectively.
Non‐branched β‐1,3‐glucan oligosaccharides trigger immune responses in Arabidopsis
Authors: Mélida Hugo , Sopeña‐Torres Sara , Bacete Laura , Garrido‐Arandia María , Jordá Lucía , López Gemma , Muñoz‐Barrios Antonio , Pacios Luis F. , Molina Antonio 
Published: October 2017

SummaryFungal cell walls, which are essential for environmental adaptation and host colonization by the fungus, have been evolutionarily selected by plants and animals as a source of microbe‐associated molecular patterns (MAMPs) that, upon recognition by host pattern recognition receptors (PRRs), trigger immune responses conferring disease resistance. Chito‐oligosaccharides [β‐1,4‐N‐acetylglucosamine oligomers, (GlcNAc)n] are the only glycosidic structures from fungal walls that have been well‐demonstrated to function as MAMPs in plants. Perception of (GlcNAc)4–8 by Arabidopsis involves CERK1, LYK4 and LYK5, three of the eight members of the LysM PRR family. We found that a glucan‐enriched wall fraction from the pathogenic fungus Plectosphaerella cucumerina which was devoid of GlcNAc activated immune responses in Arabidopsis wild‐type plants but not in the cerk1 mutant. Using this differential response, we identified the non‐branched 1,3‐β‐d‐(Glc) hexasaccharide as a major fungal MAMP. Recognition of 1,3‐β‐d‐(Glc)6 was impaired in cerk1 but not in mutants defective in either each of the LysM PRR family members or in the PRR‐co‐receptor BAK1. Transcriptomic analyses of Arabidopsis plants treated with 1,3‐β‐d‐(Glc)6 further demonstrated that this fungal MAMP triggers the expression of immunity‐associated genes. In silico docking analyses with molecular mechanics and solvation energy calculations corroborated that CERK1 can bind 1,3‐β‐d‐(Glc)6 at effective concentrations similar to those of (GlcNAc)4. These data support that plants, like animals, have selected as MAMPs the linear 1,3‐β‐d‐glucans present in the walls of fungi and oomycetes. Our data also suggest that CERK1 functions as an immune co‐receptor for linear 1,3‐β‐d‐glucans in a similar way to its proposed function in the recognition of fungal chito‐oligosaccharides and bacterial peptidoglycan MAMPs.
Patient blood management knowledge and practice among clinicians from seven European university hospitals: a multicentre survey
Authors: Manzini P. M. , Dall'Omo A. M. , D'Antico S. , Valfrè A. , Pendry K. , Wikman A. , Fischer D. , Borg‐Aquilina D. , Laspina S. , van Pampus E. C. M. , van Kraaij M. , Bruun M. T. , Georgsen J. , Grant‐Casey J. , Babra P. S. , Murphy M. F. , Folléa G. , Aranko K. 
Published: October 2017

Background and ObjectivesThe aim of this survey was to evaluate the knowledge about Patient Blood Management (PBM) principles and practices amongst clinicians working in seven European hospitals participating in a European Blood Alliance (EBA) project.Materials and MethodsA web‐based questionnaire was sent to 4952 clinicians working in medical, surgery and anaesthesiology disciplines. The responses were analysed, and the overall results as well as a comparison between hospitals are presented.ResultsA total of 788 responses (16%) were obtained. About 24% of respondents were not aware of a correlation between preoperative anaemia (POA) and perioperative morbidity and mortality. For 22%, treatment of POA was unlikely to favourably influence morbidity and mortality even before surgery with expected blood loss. More than half of clinicians did not routinely treat POA. 29%, when asked which is the best way to treat deficiency anaemia preoperatively, answered that they did not have sufficient knowledge and 5% chose to ‘do nothing’. Amongst those who treated POA, 38% proposed red cell transfusion prior to surgery as treatment. Restrictive haemoglobin triggers for red blood cell transfusion, single unit policy and reduction of number and volumes of blood samples for diagnostic purposes were only marginally implemented.ConclusionOverall, the responses indicated poor knowledge about PBM. Processes to diagnose and treat POA were not generally and homogeneously implemented. This survey should provide further impetus to implement programmes to improve knowledge and practice of PBM.
Brexit and the future of English in Europe
Authors: BOLTON KINGSLEY , DAVIS DANIEL R. 
Published: October 2017

ABSTRACTIn this issue of the journal we present a forum on a current topic of key sociolinguistic interest to both linguists and the wider population in Europe and elsewhere, that is, the expected future of the English language in a reconfigured Europe after the impending British exit (or ‘Brexit’) from Europe. The key document discussed in this forum is a position paper from Marko Modiano, which has drawn a number of responses from leading linguists across the field of world Englishes. We are sincerely thankful to Modiano for initiating this forum, and grateful also to all those that have contributed their responses to his article, which has resulted, we believe, in an insightful and lively discussion of the sociolinguistics of English and multilingualism in contemporary Europe.
ICE vs GloWbE: Big data and corpus compilation
Authors: LOUREIRO‐PORTO LUCÍA 
Published: October 2017

ABSTRACTICE and GloWbE are the two main corpora available for the study of world Englishes, and as such they share several features. However, they also differ in a number of respects owing to the different techniques adopted during compilation: while ICE is a traditional corpus with 32 text types represented, GloWbE only contains material from the Internet. This article compares the two corpora from a number of perspectives: (i) frequency and collocation of modal verbs of necessity, (ii) degree of orality and informality of the blogs included in GloWbE versus the spoken component of ICE; and (iii) the vernacular and globalised nature of both corpora. Findings show that big data cannot be considered as an alternative source to corpus compilation. Rather, the new text type(s) found in Internet material should be included in traditional corpora.
Liquidity Risk under The New Basel Global Regulatory Framework
Authors: Hlebik Sviatlana 
Published: October 2017

This paper contributes to understanding liquidity risk and its role in systemic financial crises. It focuses on the new banking regulation Basel III, in particularly on the Liquidity risk ratio that measures long-term liquidity positions of European banks. It emphasizes the importance and the issues relating to the Net Stable Funding Ratio (NSFR) which will become a minimum standard by 1 January 2018. Application at a level of 100% to credit institutions and systemic investment firms is not however expected before 2020, two years after the date of entry into force of the proposed Regulation. The paper aims to analyze the relationship between NSFR and banking stability, financial markets factors and central bank operations, in order to understand the potential impact of the key components of the new Basel global regulatory framework.
Reviewer Acknowledgements
Authors: Young James 
Published: October 2017

Reviewer AcknowledgementsInternational Journal of Social Science Studies (IJSSS) would like to acknowledge the following reviewers for their assistance with peer review of manuscripts for this issue. Many authors, regardless of whether IJSSS publishes their work, appreciate the helpful feedback provided by the reviewers. Their comments and suggestions were of great help to the authors in improving the quality of their papers. Each of the reviewers listed below returned at least one review for this issue.Reviewers for Volume 5, Number 11 Adrienne L. Edwards, University of Nevada, USAAhmet Yıkmış, Abant Izzet Baysal Univeersity, TurkeyAyşegül Sili Kalem, Necmettin Erbakan Universitesi, TurkeyE.Ozan Aksoz, Anadolu University, TurkeyGülsüm Depeli, Hacettepe University, TurkeyHenry Poduthas, West Texas A&M University, USAJehu Onyekwere Nnaji, University of Naples II, Italy and Globe Visions Network Italy, ItalyRasa Poceviciene, Siauliai University, LithuaniaYanzhe Zhang, Jilin University, China, China/AustraliaZlatan Begić, University of Tuzla, Bosnia and Herzegovina
Optimum Design of a BLDC Motor for Electric Continuous Variable Valve Timing System
Authors: Baek Soo-Whang 
Published: October 2017

In order to save resources and prevent global warming, it has been urgently needed to reduce CO2 emissions and decrease automobile fuel consumption in recent years. The trend in automotive applications are being studied to improve fuel efficiency and to reduce volume and weight. For these reasons, the mechanical parts of the automobile are being replaced by electric components.
This paper deals with the optimum design process for a small Brushless DC (BLDC) motor used in Electric-Continuous Variable Valve Timing (E-CVVT) system in automobiles with internal combustion engines. It is also proposed to improve the rated efficiency and the maximum torque and reduce the cogging torque to improve the characteristics of the BLDC motor. To maximize the maximum torque as well as to maintain the rated efficiency, the radial basis function based on latin hypercube sampling and genetic algorithm are utilized. The design variables, objective functions, and constraints are selected for the optimum design of the BLDC motor, which is divided into three steps. Step I and step II are calculated to improve the rated efficiency and the maximum torque respectively, while step III utilizes to reduce cogging torque. To verify the proposed optimum design process, the improvement of characteristic is suggested with FE-analysis.
Mechanical Feasibility of Airfoil Shaped Energy Harvesting Device Based on Aerodynamic Instability Phenomena
Authors: Yun Gangsik , Oh Dongho , Kim Youngjin , Kim JiHyeon , Kim TaeHyeong 
Published: October 2017

Unsteady aerodynamic forces generally have been treated as subjects to avoid or control. However, more energy resources could be gained if humans could use the unsteady aerodynamic force that can destroy massive structures.
In this paper, an energy harvesting device was proposed using the flutter phenomenon, which is one of the phenomena of aerodynamic instability. Unlike existing flutter-based energy harvesting devices, the proposed device can be operated regardless of wind direction. A prototype was developed for a performance evaluation in a wind tunnel, and displacement measurements were taken over varying wind speeds.
Development of a Novel Multipenicillin Assay and Assessment of the Impact of Analyte Degradation: Lessons for Scavenged Sampling in Antimicrobial Pharmacokinetic Study Design
Authors: Kipper Karin , Barker Charlotte I. S. , Standing Joseph F. , Sharland Mike , Johnston Atholl 
Published: October 2017

ABSTRACT
Penicillins are widely used to treat infections in children; however, the evidence is continuing to evolve in defining the optimal dosing. Modern pediatric pharmacokinetic study protocols frequently favor opportunistic, “scavenged” sampling. This study aimed to develop a small-volume single assay for five major penicillins and to assess the influence of sample degradation on inferences made using pharmacokinetic modeling, to investigate the suitability of scavenged sampling strategies. Using a rapid ultrahigh-performance liquid chromatographic-tandem mass spectrometric method, an assay for five penicillins (amoxicillin, ampicillin, benzylpenicillin, piperacillin, and flucloxacillin) in blood plasma was developed and validated. Penicillin stabilities were evaluated under different conditions. Using these data, the impact of drug degradation on inferences made during pharmacokinetic modeling was evaluated. All evaluated penicillins indicated good stability at room temperature (23 ± 2°C) over 1 h, remaining in the range of 98 to 103% of the original concentration. More-rapid analyte degradation had already occurred after 4 h, with stability ranging from 68% to 99%. Stability over longer periods declined: degradation of up to 60% was observed with delayed sample processing of up to 24 h. Modeling showed that analyte degradation can lead to a 30% and 28% bias in clearance and volume of distribution, respectively, and falsely show nonlinearity in clearance. Five common penicillins can now be measured in a single low-volume blood sample. Beta-lactam chemical instability in plasma can cause misleading pharmacokinetic modeling results, which could impact upon model-based dosing recommendations and the forthcoming era of beta-lactam therapeutic drug monitoring.
In Vitro
Antiviral Activity and Resistance Profile of the Next-Generation Hepatitis C Virus NS3/4A Protease Inhibitor Glecaprevir
Authors: Ng Teresa I. , Tripathi Rakesh , Reisch Thomas , Lu Liangjun , Middleton Timothy , Hopkins Todd A. , Pithawalla Ron , Irvin Michelle , Dekhtyar Tatyana , Krishnan Preethi , Schnell Gretja , Beyer Jill , McDaniel Keith F. , Ma Jun , Wang Guoqiang , Jiang Li-Juan , Or Yat Sun , Kempf Dale , Pilot-Matias Tami , Collins Christine 
Published: October 2017

ABSTRACT

Glecaprevir (formerly ABT-493) is a novel hepatitis C virus (HCV) NS3/4A protease inhibitor (PI) with pangenotypic activity. It inhibited the enzymatic activity of purified NS3/4A proteases from HCV genotypes 1 to 6
in vitro
(half-maximal [50%] inhibitory concentration = 3.5 to 11.3 nM) and the replication of stable HCV subgenomic replicons containing proteases from genotypes 1 to 6 (50% effective concentration [EC
50
] = 0.21 to 4.6 nM). Glecaprevir had a median EC
50
of 0.30 nM (range, 0.05 to 3.8 nM) for HCV replicons containing proteases from 40 samples from patients infected with HCV genotypes 1 to 5. Importantly, glecaprevir was active against the protease from genotype 3, the most-difficult-to-treat HCV genotype, in both enzymatic and replicon assays demonstrating comparable activity against the other HCV genotypes. In drug-resistant colony selection studies, glecaprevir generally selected substitutions at NS3 amino acid position A156 in replicons containing proteases from genotypes 1a, 1b, 2a, 2b, 3a, and 4a and substitutions at position D/Q168 in replicons containing proteases from genotypes 3a, 5a, and 6a. Although the substitutions A156T and A156V in NS3 of genotype 1 reduced susceptibility to glecaprevir, replicons with these substitutions demonstrated a low replication efficiency
in vitro
. Glecaprevir is active against HCV with most of the common NS3 amino acid substitutions that are associated with reduced susceptibility to other currently approved HCV PIs, including those at positions 155 and 168. Combination of glecaprevir with HCV inhibitors with other mechanisms of action resulted in additive or synergistic antiviral activity. In summary, glecaprevir is a next-generation HCV PI with potent pangenotypic activity and a high barrier to the development of resistance.
Hypo-osmolar Formulation of Tenofovir (TFV) Enema Promotes Uptake and Metabolism of TFV in Tissues, Leading to Prevention of SHIV/SIV Infection
Authors: Xiao Peng , Gumber Sanjeev , Marzinke Mark A. , Date Abhijit A. , Hoang Thuy , Hanes Justin , Ensign Laura M. , Wang Lin , Rohan Lisa , Fuchs Edward J. , Hendrix Craig , Villinger Francois 
Published: October 2017

ABSTRACT

Oral preexposure prophylaxis (PrEP) has been approved for prophylaxis of HIV-1 transmission but is associated with high costs and issues of adherence. Protection from anal transmission of HIV using topical microbicides and methods congruent with sexual behavior offers the promise of improved adherence. We compared the pharmacokinetics (PK) and
ex vivo
efficacy of iso-osmolar (IOsm) and hypo-osmolar (HOsm) rectal enema formulations of tenofovir (TFV) in rhesus macaques. Single-dose PK of IOsm or HOsm high-dose (5.28 mg/ml) and low-dose (1.76 mg/ml) formulations of TFV enemas were evaluated for systemic uptake in blood, colorectal biopsy specimens, and rectal CD4
+
T cells. Markedly higher TFV concentrations were observed in plasma and tissues after administration of the HOsm high-dose formulation than with all other formulations tested. TFV and TFV diphosphate (TFV-DP) concentrations in tissue correlated for the HOsm high-dose formulation, demonstrating rapid uptake and transformation of TFV to TFV-DP in tissues. TFV-DP amounts in tissues collected at 1 and 24 h were 7 times and 5 times higher, respectively (
P
< 0.01), than the ones collected in tissues with the IOsm formulation. The HOsm high-dose formulation prevented infection in
ex vivo
challenges of rectal tissues collected at 1, 24, and 72 h after the intrarectal dosing, whereas the same TFV dose formulated as an IOsm enema was less effective.
Use of Calgary and Microfluidic BioFlux Systems To Test the Activity of Fosfomycin and Tobramycin Alone and in Combination against Cystic Fibrosis Pseudomonas aeruginosa Biofilms
Authors: Díez-Aguilar María , Morosini María Isabel , Köksal Emin , Oliver Antonio , Ekkelenkamp Miquel , Cantón Rafael 
Published: October 2017

ABSTRACT

Pseudomonas aeruginosa
is a major cause of morbidity and mortality in chronically infected cystic fibrosis patients. Novel
in vitro
biofilm models which reliably predict the therapeutic success of antimicrobial therapies against biofilm bacteria should be implemented. The activity of fosfomycin, tobramycin, and the fosfomycin-tobramycin combination against 6 susceptible
P. aeruginosa
strains isolated from respiratory samples from cystic fibrosis patients was tested by using two
in vitro
biofilm models: a closed system (Calgary device) and an open model based on microfluidics (BioFlux). All but one of the isolates formed biofilms. The fosfomycin and tobramycin minimal biofilm inhibitory concentrations (MBIC) were 1,024 to >1,024 μg/ml and 8 to 32 μg/ml, respectively. According to fractional inhibitory concentration analysis, the combination behaved synergistically against all the isolates except the
P. aeruginosa
ATCC 27853 strain. The dynamic formation of the biofilm was also studied with the BioFlux system, and the MIC and MBIC of each antibiotic were tested. For the combination, the lowest tobramycin concentration that was synergistic with fosfomycin was used. The captured images were analyzed by measuring the intensity of the colored pixels, which was proportional to the biofilm biomass. A statistically significant difference was found when the intensity of the inoculum was compared with the intensity of the microchannel in which the MBIC of tobramycin, fosfomycin, or their combination was used (
P
< 0.01) but not when the MIC was applied (
P
> 0.01). Fosfomycin-tobramycin was demonstrated to be synergistic against cystic fibrosis
P. aeruginosa
strains in the biofilm models when both the Calgary and the microfluidic BioFlux systems were tested. These results support the clinical use of this combination.