bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics identifies the Magnaporthe oryzae avirulence effector AvrPi9 that triggers Pi9‐mediated blast resistance in rice
Authors: Wu Jun , Kou Yanjun , Bao Jiandong , Li Ya , Tang Mingzhi , Zhu Xiaoli , Ponaya Ariane , Xiao Gui , Li Jinbin , Li Chenyun , Song Min‐Young , Cumagun Christian Joseph R. , Deng Qiyun , Lu Guodong , Jeon Jong‐Seong , Naqvi Naweed I. , Zhou Bo 
Published: February 2015

Summary

We identified the Magnaporthe oryzae avirulence effector AvrPi9 cognate to rice blast resistance gene Pi9 by comparative genomics of requisite strains derived from a sequential planting method.

AvrPi9 encodes a small secreted protein that appears to localize in the biotrophic interfacial complex and is translocated to the host cell during rice infection. AvrPi9 forms a tandem gene array with its paralogue proximal to centromeric region of chromosome 7. AvrPi9 is expressed highly at early stages during initiation of blast disease.

Virulent isolate strains contain Mg‐SINE within the AvrPi9 coding sequence. Loss of AvrPi9 did not lead to any discernible defects during growth or pathogenesis in M. oryzae. This study reiterates the role of diverse transposable elements as off‐switch agents in acquisition of gain‐of‐virulence in the rice blast fungus.

The prevalence of AvrPi9 correlates well with the avirulence pathotype in diverse blast isolates from the Philippines and China, thus supporting the broad‐spectrum resistance conferred by Pi9 in different rice growing areas. Our results revealed that Pi9 and Piz‐t at the Pi2/9 locus activate race specific resistance by recognizing sequence‐unrelated AvrPi9 and AvrPiz‐t genes, respectively.
Consumer–plant interaction strength: importance of body size, density and metabolic biomass
Authors: Atkins Rebecca L. , Griffin John N. , Angelini Christine , O'Connor Mary I. , Silliman Brian R. 
Published: February 2015

Explaining variability in the strength and sign of trophic interactions between primary consumers and plants is a long‐standing research challenge. Consumer density and body size vary widely in space and time and are predicted to have interactive effects on consumer–plant interactions. In a southern US salt marsh, we used replicate field enclosures to orthogonally manipulate the body size (mass) and density of a dominant consumer (a snail). We investigated impacts (leaf damage and biomass) on monocultures of cordgrass, the foundation species, over three months. Increasing consumer density and body size increased leaf damage additively and, as predicted, multiplicatively reduced plant biomass. Notably, size and density determined the sign of consumer impact on plants: low to medium densities of small consumers enhanced, while high densities of large consumers strongly suppressed, plant biomass. Finally, total consumer metabolic biomass (mass0.75) within an enclosure parsimoniously explained plant biomass response, supporting theoretical predictions and suggesting that multiplicative effects of density and body size resulted from their effects on total metabolic biomass. The consequences of changes in consumer density and body size resulting from anthropogenic perturbations may therefore be predicted based on metabolic biomass.SynthesisConsumer size, density and biomass can all strongly affect consumer–plant interactions. Though density and body size have been extensively studied as drivers of variation in interaction strength, the role of biomass as the ultimate driver has been less appreciated. We manipulated body size and density of a single consumer species and, based on metabolic theory, integrated these into a single variable: total metabolic biomass. Our results suggest that changes in interaction strength attributed to size or density may in fact be due to changes in metabolic biomass. This metric could thus serve as a useful tool in further understanding species interactions.
Enhanced waterlogging tolerance in barley by manipulation of expression of the N‐end rule pathway E3 ligase PROTEOLYSIS6
Authors: Mendiondo Guillermina M. , Gibbs Daniel J. , Szurman‐Zubrzycka Miriam , Korn Arnd , Marquez Julietta , Szarejko Iwona , Maluszynski Miroslaw , King John , Axcell Barry , Smart Katherine , Corbineau Francoise , Holdsworth Michael J. 
Published: February 2015

SummaryIncreased tolerance of crops to low oxygen (hypoxia) during flooding is a key target for food security. In Arabidopsis thaliana (L.) Heynh., the N‐end rule pathway of targeted proteolysis controls plant responses to hypoxia by regulating the stability of group VII ethylene response factor (ERFVII) transcription factors, controlled by the oxidation status of amino terminal (Nt)‐cysteine (Cys). Here, we show that the barley (Hordeum vulgare L.) ERFVII BERF1 is a substrate of the N‐end rule pathway in vitro. Furthermore, we show that Nt‐Cys acts as a sensor for hypoxia in vivo, as the stability of the oxygen‐sensor reporter protein MCGGAIL‐GUS increased in waterlogged transgenic plants. Transgenic RNAi barley plants, with reduced expression of the N‐end rule pathway N‐recognin E3 ligase PROTEOLYSIS6 (HvPRT6), showed increased expression of hypoxia‐associated genes and altered seed germination phenotypes. In addition, in response to waterlogging, transgenic plants showed sustained biomass, enhanced yield, retention of chlorophyll, and enhanced induction of hypoxia‐related genes. HvPRT6 RNAi plants also showed reduced chlorophyll degradation in response to continued darkness, often associated with waterlogged conditions. Barley Targeting Induced Local Lesions IN Genomes (TILLING) lines, containing mutant alleles of HvPRT6, also showed increased expression of hypoxia‐related genes and phenotypes similar to RNAi lines. We conclude that the N‐end rule pathway represents an important target for plant breeding to enhance tolerance to waterlogging in barley and other cereals.
Protein accumulation and rumen stability of wheat γ‐gliadin fusion proteins in tobacco and alfalfa
Authors: Sun Xiaodong , Chi‐Ham Cecilia L. , Cohen‐Davidyan Tamar , DeBen Christopher , Getachow Girma , DePeters Edward , Putnam Daniel , Bennett Alan 
Published: February 2015

SummaryThe nutritional value of various crops can be improved by engineering plants to produce high levels of proteins. For example, because methionine deficiency limits the protein quality of Medicago Sativa (alfalfa) forage, producing alfalfa plants that accumulate high levels of a methionine‐rich protein could increase the nutritional value of that crop. We used three strategies in designing methionine‐rich recombinant proteins that could accumulate to high levels in plants and thereby serve as candidates for improving the protein quality of alfalfa forage. In tobacco, two fusion proteins, γ‐gliadin‐δ‐zein and γ‐δ‐zein, as well as δ‐zein co‐expressed with β‐zein, all formed protein bodies. However, the γ‐gliadin‐δ‐zein fusion protein accumulated to the highest level, representing up to 1.5% of total soluble protein (TSP) in one transformant. In alfalfa, γ‐gliadin‐δ‐zein accumulated to 0.2% of TSP, and in an in vitro rumen digestion assay, γ‐gliadin‐δ‐zein was more resistant to microbial degradation than Rubisco. Additionally, although it did not form protein bodies, a γ‐gliadin‐GFP fusion protein accumulated to much higher levels, 7% of TSP, than a recombinant protein comprised of an ER localization signal fused to GFP in tobacco. Based on our results, we conclude that γ‐gliadin‐δ‐zein is a potential candidate protein to use for enhancing methionine levels in plants and for improving rumen stability of forage protein. γ‐gliadin fusion proteins may provide a general platform for increasing the accumulation of recombinant proteins in transgenic plants.
Experiences of working as an advanced practice nurse in Finland – the substance of advanced nursing practice and promoting and inhibiting factors
Authors: Wisur‐Hokkanen Carola , Glasberg Ann‐Louise , Mäkelä Carita , Fagerström Lisbeth 
Published: February 2015

BackgroundEvaluation of new advanced practice nursing roles, from different angles, is strongly recommended in the literature. New nurses' experiences of working in an advanced role may highlight problems and/or factors that promote or inhibit a successful implementation of new advanced nursing roles.AimTo explore advanced practice nurses' experiences of the content of their nursing care and to describe promoting or inhibiting factors for working with a full scope of advanced nursing practice.MethodsThe study design was explorative and descriptive. A total of 24 advanced practice nurses participated in focus group interviews (two were interviewed individually) about the processes, structure and outcome of working as advanced practice nurses. Qualitative manifest content analysis was used for data analysis.FindingsThe substance of advanced practice nursing can be described with three main themes: a broader and deeper holistic view of patients' state of health, an independent and responsible manner of working and knowing own limits. Promoting factors were an identity as a nurse with advanced competency, feedback from satisfied patients and fruitful teamwork is a necessity. Inhibiting factors were a lack of organisational understanding for advanced nursing practice, poor planning leads to unsatisfactory advanced practice nursing models and advanced practice nurses' lack of courage in adopting new advanced roles.ConclusionThe participants experienced both a personal inner transition and a role transition that were either supported or opposed. Vague or nonexistent definitions and concepts, insufficient knowledge, insufficient support and undefined roles hindered participants' role transition. Two main strategies should be employed. The first is the realisation of more strategic leadership and support from organisations on all management levels, including nursing organisations/unions, while the second is to more realistically prepare future advanced practice nurses for the challenges they will face, through mentorship programmes and continuous further training.
Prospective Associations between Peer Aggression and Victimization: The Moderating Roles of Physiological Stress Reactivity and Gender
Authors: Pitula Clio E. , Murray‐Close Dianna , Banny Adrienne M. , Crick Nicki R. 
Published: February 2015

AbstractThe present investigation examined whether heightened skin conductance reactivity (SCLR) to peer stress strengthened the prospective associations between physical and relational aggression and victimization, and whether associations were stronger for physical forms of aggression and victimization among boys and relational forms of aggression and victimization among girls. A total of 91 children [M age = 10.18 years, standard deviation (SD) = .68] were assessed twice over 1 year. At the first assessment, SCLR in response to recounting a relational stressor (e.g., exclusion; SCLR‐R) and an instrumental stressor (e.g., property theft; SCLR‐I), and teacher‐reported aggression were measured. Parents reported on child victimization at both time points. Among youth with heightened SCLR‐I, physical aggression was associated with increases in physical victimization for boys and decreases in physical victimization for girls. Among youth with heightened SCLR‐R, relational aggression was associated with increases in physical victimization for girls only. Results were largely consistent with the hypothesis that aggressors with a propensity to exhibit negative displays of emotion, as indexed by heightened sympathetic nervous system (SNS) reactivity to peer stress, may be especially likely to suffer peer victimization. Gender‐specific effects highlight the importance of including both physical and relational forms of aggression and victimization to capture victimization risk among aggressive boys and girls.
Genetic polymorphisms of serum amyloid A1 and coronary artery disease risk
Authors: Xie X. , Ma Y‐T. , Yang Y‐N. , Li X‐M. , Zheng Y‐Y. , Liu F. , Ma X. , Fu Z‐Y. , Yu Z‐X. , Chen Y. , Chen B‐D. , Huang Y. 
Published: February 2015

AbstractSerum amyloid A (SAA) protein is not only an inflammatory factor but also an apolipoprotein that can replace apolipoprotein A1 (apoA1) as the major apolipoprotein of high‐density lipoprotein cholesterol (HDL‐C). However, the relationship between genetic polymorphisms of SAA and coronary artery disease (CAD) remains unclear. A total of four single nucleotide polymorphisms (rs12218, rs4638289, rs7131332, and rs11603089) of the SAA gene were genotyped using the polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) method in two independent case–control studies, one of the Han population (1416 CAD patients and 1373 control subjects) and the other of the Uygur population (588 CAD patients and 529 control subjects). We found that the rs12218 CC genotype was more frequent among the CAD patients than among the controls in both the Han (8.3% vs. 4.8%, P < 0.001) and Uygur populations (15.5% vs. 11.3%, P < 0.05). After adjustments for confounding factors, such as sex, age, smoking, drinking, hypertension, diabetes, and serum levels of triglycerides, total cholesterol, HDL, and plasma SAA, the differences remained significant in the Han (CC vs. CT+TT, P < 0.001, OR = 3.863, 95% CI: 1.755–12.477) and Uygur groups (CC vs. CT+TT, P = 0.031, OR = 3.022, 95% CI: 1.033–8.840). Genetic polymorphisms in SAA1 are associated with CAD in the Han and Uygur populations in western China.
Area‐preservation Simplification of Polygonal Boundaries by the Use of the Structured Total Least Squares Method with Constraints
Authors: Tong Xiaohua , Jin Yanmin , Li Lingyun , Ai Tinghua 
Published: February 2015

AbstractThis article presents an area‐preservation approach for polygonal boundary simplification by the use of structured total least squares adjustment with constraints (STLSC), with the aim being to maintain the area of the original polygons after the simplification. Traditionally, a simplified line is represented by critical points selected from the original one. However, this study focuses on maintaining the areas of the polygons in the process of simplification of polygonal boundaries. Therefore, the proposed method in this article is a supplement to the existing line simplification methods, and it improves the quality of the simplification of polygonal boundaries in terms of positional and area errors. Based on the sub‐divisions of the original polyline, using the critical points detected from the polyline by the use of line simplification methods, the framework of the proposed method includes three main components, as follows: (1) establishment of the straight‐line‐segment fitting model based on both the critical and intermediate points on the sub‐polyline; (2) introduction of both area and end‐point constraints to reduce the geometric distortions due to the line simplification; and (3) derivation of the solution of boundary simplification by the use of STLSC.An empirical example was conducted to test the applicability of the proposed method. The results showed that: (1) by imposing the linear fitting model on both the critical and intermediate points on the sub‐polylines in the proposed STLSC method, the positional differences between the original points and the simplified line are approximately in a normal distribution; and (2) by introducing both end‐point and area constraints in the proposed STLSC method, the areas of the simplified polygons are the same as those of the original ones at different scales, and the two neighboring fitted lines are connected to each other at the optimized position.
Voriconazole exposure and the risk of cutaneous squamous cell carcinoma in allogeneic hematopoietic stem cell transplant patients
Authors: Wojenski D.J. , Bartoo G.T. , Merten J.A. , Dierkhising R.A. , Barajas M.R. , el‐Azhary R.A. , Wilson J.W. , Plevak M.F. , Hogan W.J. , Litzow M.R. , Patnaik M.M. , Wolf R.C. , Hashmi S.K. 
Published: February 2015

AbstractBackgroundVoriconazole is a commonly used antifungal medication in allogeneic hematopoietic stem cell transplantation (allo‐HSCT) patients. In solid organ transplantation, voriconazole use has been associated with the development of cutaneous squamous cell carcinoma (SCC). We sought to determine if voriconazole use was associated with SCC in patients undergoing allo‐HSCT.MethodsWe retrospectively reviewed consecutive adult patients who underwent allo‐HSCT at Mayo Clinic from January 2007 through July 2012. Multivariable Cox models were created to assess the relationship of SCC with two time‐dependent voriconazole exposure variables: (i) history of voriconazole exposure (yes/no), and (ii) cumulative days of voriconazole use.ResultsIn our cohort of 381 allo‐HSCT patients, SCC developed in 26 of 312 patients exposed to voriconazole (25 post‐voriconazole) and in 1 of 69 patients who received alternative antifungal agent(s). Cumulative incidence of SCC was estimated to be 19% at 5 years post allo‐transplant. Cumulative days of voriconazole use was found to be a risk factor for SCC, and this relationship persisted in a multivariable model using previously identified risk factors as covariates (hazard ratio 1.859 for each 180 days of use, P < 0.001).ConclusionThis is the first study, to our knowledge, to identify cumulative days of voriconazole use as a risk factor for SCC development following allo‐HSCT, and may help guide appropriate antifungal use in this patient population.
Changes in mitochondrial perilipin 3 and perilipin 5 protein content in rat skeletal muscle following endurance training and acute stimulated contraction
Authors: Ramos S. V. , Turnbull P. C. , MacPherson R. E. K. , LeBlanc P. J. , Ward W. E. , Peters S. J. 
Published: February 2015

New Findings

What is the central question of this study?
The aim was to determine whether mitochondrial protein content of perilipin 3 (PLIN3) and perilipin 5 (PLIN5) is increased following endurance training and whether mitochondrial PLIN5 protein is increased to a greater extent in endurance‐trained rats when compared with sedentary rats following acute contraction.

What is the main finding and its importance?
Mitochondrial PLIN3 but not PLIN5 protein was increased in endurance‐trained compared with sedentary rats, suggesting a mitochondrial role for PLIN3 due to chronic exercise. Contrary to our hypothesis, acute mitochondrial PLIN5 protein was similar in both sedentary and endurance‐trained rats.

Endurance training results in an increased association between skeletal muscle lipid droplets and mitochondria. This association is likely to be important for the expected increase in intramuscular fatty acid oxidation that occurs with endurance training. The perilipin family of lipid droplet proteins, PLIN(2–5), are thought to play a role in skeletal muscle lipolysis. Recently, results from our laboratory demonstrated that skeletal muscle mitochondria contain PLIN3 and PLIN5 protein. Furthermore, 30 min of stimulated contraction induces an increased mitochondrial PLIN5 content. To determine whether mitochondrial content of PLIN3 and PLIN5 is altered with endurance training, Sprague–Dawley rats were randomized into sedentary or endurance‐trained groups for 8 weeks of treadmill running followed by an acute (30 min) sciatic nerve stimulation to induce lipolysis. Mitochondrial PLIN3 protein was ∼1.5‐fold higher in red gastrocnemius of endurance‐trained rats compared with sedentary animals, with no change in mitochondrial PLIN5 protein. In addition, there was an increase in plantaris intramuscular lipid storage. Acute electrically stimulated contraction in red gastrocnemius from sedentary and endurance‐trained rats resulted in a similar increase of mitochondrial PLIN5 between these two groups, with no net change in PLIN3 in either group. Plantaris intramuscular lipid content decreased to a similar extent in sedentary and endurance‐trained rats. These results suggest that while total mitochondrial PLIN5 content is not altered by endurance training, PLIN5 does have an acute role in the mitochondrial fraction during muscle contraction. Conversely, mitochondrial PLIN3 does not change acutely with muscle contraction, but PLIN3 content was increased following endurance training, indicating a role in chronic adaptations of skeletal muscle.
Government/Industry Partnership: A Revolutionary Approach in Global Leadership of Advanced Gas Turbines
Authors: Ali Sy A. , Zeh Charles M. 
Published: February 2015

The U.S. Department of Energy (DOE) has established a government/industry partnership program to greatly improve the capabilities of U.S. gas turbine technology. A new and challenging program named the Advanced Turbine Systems Program (ATS) has been initiated by DOE. The technical and business objectives of this initiative are to challenge the bounds of high performance capabilities of gas turbines, meet stringent environmental requirements, and produce lower cost electric power and cogeneration steam. This program will also yield greater societal benefits through continued expansion of high skilled U.S. jobs and export of U.S. products world wide.
A progress report on the ATS program pertaining to program status at DOE will be presented and reviewed in this paper. A preliminary design of an industrial advanced turbine system configuration will also be outlined in the paper. The technical challenges; advanced critical technologies incorporation, analytical and experimental solutions, and test results of an advanced gas turbine meeting the DOE goals will be described and discussed.
Comparison of a TVD-Upwind Scheme and a Central Difference Scheme for Navier-Stokes Turbine Stage Flow Calculation
Authors: Raif Markus , Mayer Jürgen F. , Stetter Heinz 
Published: February 2015

The differences of two distinct numerical schemes implemented in one code called ITSM3D are presented for a turbine stage test case. Thus both schemes are used with exactly the same computational infrastructure, e. g, same grids, boundary conditions, acceleration strategies, time-stepping, turbulence model etc. The two methods are based on an explicit Runge-Kutta-type finite volume scheme expressed in cylindrical coordinates and have been developed at the Institut für Thermische Strömungsmaschinen und Maschinenlaboratorium of the University of Stuttgart. One scheme is a node centered 3rd order TVD scheme according to Osher and the other belongs to the cell vertex central difference type with the concept of artificial viscosity. The model of Baldwin-Lomax is used in order to simulate turbulent effects. Non-reflective boundary conditions are taken at stator inlet and rotor outlet to avoid non-physical reflections. A multigrid technique in combination with implicit residual smoothing and local time-stepping is employed to accelerate the computation.
The test case for this comparison is the last stage of a low-pressure turbine. The computational results obtained are discussed and compared to each other as well as to experimental data. They are presented as pressure and Mach number isoline contours and diagrams of circumferential averaged quantities at inlet and outlet planes of stator and rotor versus radial position.