bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological and molecular characterization of a distinct Citrus tristeza virus isolate originating from a lemon tree in Greece
Authors: Varveri C. , Olmos A. , Pina J. A. , Marroquín C. , Cambra M. 
Published: October 2014

A Citrus tristeza virus (CTV) isolate (L192GR) naturally occurring in lemon trees of more than 100 years old in Greece was fully characterized. Virus‐derived small interfering RNAs, induced by Dicer processing of dsRNAs formed during RNA virus replication, were isolated and used as targets for sequencing. Next‐generation high‐throughput sequencing using the Ion Torrent platform was performed. A total of 432 632 sequences, 94·05% of which corresponded to L192GR, were determined. Subsequent bioinformatics analysis enabled the determination of the full‐length 19 251 nt genome of the L192GR isolate (GenBank no. KC262793). Comparative analysis of complete genomes revealed molecular homology with CTV‐VT isolate FS2‐2 from Florida (GenBank no. EU937519) with 98·2% nucleotide sequence identity. Recombination events were detected in L192GR and they probably contribute to its unique characteristics. Specifically, although most isolates of the CTV‐VT group induce the seedling yellows syndrome and react positively with the monoclonal antibody MCA13, which is typically associated with severe CTV isolates, the MCA13‐positive L192GR gave very mild or even no symptoms in the seedling yellows indicator plants. Furthermore, experimental aphid transmissibility studies revealed a poor transmission efficiency of 20%. This is the first report of a CTV isolate originating from a lemon tree being fully characterized at biological, serological and molecular levels. The present study further confirms that, when the goal is the risk assessment associated with a new pathogen or isolate in a particular area, molecular data have to be combined with the biological properties of the pathogen.
Exaggerated Positivity in Self‐Evaluation: A Social Neuroscience Approach to Reconciling the Role of Self‐esteem Protection and Cognitive Bias
Authors: Beer Jennifer S. 
Published: October 2014

AbstractRecent neuroscience research provides new insight into why people tend to view themselves through rose‐colored glasses and suggests a different approach for improving self‐insight. Rose‐colored glasses (sometimes referred to as positive illusions, positivity bias, self‐serving bias, self‐enhancement, or overconfidence) are a pervasive characteristic of self‐evaluation. While it is intuitive to think about rose‐colored glasses as a self‐esteem protection tactic, research has shown that people tend to exaggerate their positive attributes even when self‐esteem is not at stake. This raises questions about the relation of the exaggerated positivity used to protect self‐esteem to the exaggerated positivity seen in other circumstances. Are people using a consistent thought pattern to overemphasize their positive attributes which generalizes across situations regardless of whether self‐esteem is at stake? Or is there something different about the way people go about overemphasizing their positive attributes when coping with a threat to self‐esteem? Recent neuroscience research supports the latter: inducing the need for self‐esteem protection changes the neural profile underlying exaggerated positivity. When self‐esteem is threatened, exaggerated positivity in self‐evaluation engages orbitofrontal cortex and a functional network of increased basal ganglia activation and decreased middle frontal gyrus activation. In contrast, exaggerated positivity arising in the absence of self‐esteem threat tends to reduce orbitofrontal cortex activation and its functional connectivity with the temporal, occipital, and frontal lobes. This discovery suggests that not all rose‐colored glasses are created equally and, therefore, curtailing them may require different interventions depending on whether self‐esteem protection is their underlying driving force.
The Vat locus encodes for a CC‐NBS‐LRR protein that confers resistance to Aphis gossypii infestation and A. gossypii‐mediated virus resistance
Authors: Dogimont Catherine , Chovelon Veronique , Pauquet Jerome , Boualem Adnane , Bendahmane Abdelhafid 
Published: October 2014

SummaryAphis gossypii is a polyphagous sucking aphid and a vector for many viruses. In Cucumis melo, a dominant locus, Vat, confers a high level of resistance to Aphis gossypii infestation and to viruses transmitted by this vector. To investigate the mechanism underlying this double resistance, we first genetically dissected the Vat locus. We delimited the double resistance to a single gene that encodes for a coiled‐coil–nucleotide‐binding‐site–leucine‐rich repeat (CC‐NBS‐LRR) protein type. To validate the genetic data, transgenic lines expressing the Vat gene were generated and assessed for the double resistance. In this analysis, Vat‐transgenic plants were resistant to A. gossypii infestation as well as A. gossypii‐mediated virus transmission. When the plants were infected mechanically, virus infection occurred on both transgenic and non‐transgenic control plants. These results confirmed that the cloned CC‐NBS‐LRR gene mediates both resistance to aphid infestation and virus infection using A. gossypii as a vector. This resistance also invokes a separate recognition and response phases in which the recognition phase involves the interaction of an elicitor molecule from the aphid and Vat from the plant. The response phase is not specific and blocks both aphid infestation and virus infection. Sequence analysis of Vat alleles suggests a major role of an unusual conserved LRR repeat in the recognition of A. gossypii.
Probing formation of cargo/importin‐α transport complexes in plant cells using a pathogen effector
Authors: Wirthmueller Lennart , Roth Charlotte , Fabro Georgina , Caillaud Marie‐Cécile , Rallapalli Ghanasyam , Asai Shuta , Sklenar Jan , Jones Alexandra M. E. , Wiermer Marcel , Jones Jonathan D. G. , Banfield Mark J. 
Published: October 2014

SummaryImportin‐αs are essential adapter proteins that recruit cytoplasmic proteins destined for active nuclear import to the nuclear transport machinery. Cargo proteins interact with the importin‐α armadillo repeat domain via nuclear localization sequences (NLSs), short amino acids motifs enriched in Lys and Arg residues. Plant genomes typically encode several importin‐α paralogs that can have both specific and partially redundant functions. Although some cargos are preferentially imported by a distinct importin‐α it remains unknown how this specificity is generated and to what extent cargos compete for binding to nuclear transport receptors. Here we report that the effector protein HaRxL106 from the oomycete pathogen Hyaloperonospora arabidopsidis co‐opts the host cell's nuclear import machinery. We use HaRxL106 as a probe to determine redundant and specific functions of importin‐α paralogs from Arabidopsis thaliana. A crystal structure of the importin‐α3/MOS6 armadillo repeat domain suggests that five of the six Arabidopsis importin‐αs expressed in rosette leaves have an almost identical NLS‐binding site. Comparison of the importin‐α binding affinities of HaRxL106 and other cargos in vitro and in plant cells suggests that relatively small affinity differences in vitro affect the rate of transport complex formation in vivo. Our results suggest that cargo affinity for importin‐α, sequence variation at the importin‐α NLS‐binding sites and tissue‐specific expression levels of importin‐αs determine formation of cargo/importin‐α transport complexes in plant cells.
Arabidopsis acyl‐CoA‐binding protein ACBP3 participates in plant response to hypoxia by modulating very‐long‐chain fatty acid metabolism
Authors: Xie Li‐Juan , Yu Lu‐Jun , Chen Qin‐Fang , Wang Feng‐Zhu , Huang Li , Xia Fan‐Nv , Zhu Tian‐Ren , Wu Jian‐Xin , Yin Jian , Liao Bin , Yao Nan , Shu Wensheng , Xiao Shi 
Published: October 2014

SummaryIn Arabidopsis thaliana, acyl‐CoA‐binding proteins (ACBPs) are encoded by a family of six genes (ACBP1 to ACBP6), and are essential for diverse cellular activities. Recent investigations suggest that the membrane‐anchored ACBPs are involved in oxygen sensing by sequestration of group VII ethylene‐responsive factors under normoxia. Here, we demonstrate the involvement of Arabidopsis ACBP3 in hypoxic tolerance. ACBP3 transcription was remarkably induced following submergence under both dark (DS) and light (LS) conditions. ACBP3‐overexpressors (ACBP3‐OEs) showed hypersensitivity to DS, LS and ethanolic stresses, with reduced transcription of hypoxia‐responsive genes as well as accumulation of hydrogen peroxide in the rosettes. In contrast, suppression of ACBP3 in ACBP3‐KOs enhanced plant tolerance to DS, LS and ethanol treatments. By analyses of double combinations of OE‐1 with npr1‐5, coi1‐2, ein3‐1 as well as ctr1‐1 mutants, we observed that the attenuated hypoxic tolerance in ACBP3‐OEs was dependent on NPR1‐ and CTR1‐mediated signaling pathways. Lipid profiling revealed that both the total amounts and very‐long‐chain species of phosphatidylserine (C42:2‐ and C42:3‐PS) and glucosylinositolphosphorylceramides (C22:0‐, C22:1‐, C24:0‐, C24:1‐, and C26:1‐GIPC) were significantly lower in ACBP3‐OEs but increased in ACBP3‐KOs upon LS exposure. By microscale thermophoresis analysis, the recombinant ACBP3 protein bound VLC acyl‐CoA esters with high affinities in vitro. Further, a knockout mutant of MYB30, a master regulator of very‐long‐chain fatty acid (VLCFA) biosynthesis, exhibited enhanced sensitivities to LS and ethanolic stresses, phenotypes that were ameliorated by ACBP3‐RNAi. Taken together, these findings suggest that Arabidopsis ACBP3 participates in plant response to hypoxia by modulating VLCFA metabolism.
Assessing the Uncertainty in Projecting Local Mean Sea Level from Global Temperature
Authors: Guttorp Peter , Januzzi Alex , Novak Marie , Podschwit Harry , Richardson Lee , Sowder Colin D. , Zimmerman Aaron , Bolin David , Särkkä Aila 
Published: October 2014

AbstractThe process of moving from an ensemble of global climate model temperature projections to local sea level projections requires several steps. Sea level was estimated in Olympia, Washington (a city that is very concerned with sea level rise because parts of downtown are barely above mean highest high tide), by relating global mean temperature to global sea level; relating global sea level to sea levels at Seattle, Washington; and finally relating Seattle to Olympia. There has long been a realization that accurate assessment of the precision of projections is needed for science-based policy decisions. When a string of statistical and/or deterministic models is connected, the uncertainty of each individual model needs to be accounted for. Here the uncertainty is quantified for each model in the described system and the total uncertainty is assessed in a cascading effect throughout the system. The projected sea level rise over time and its total estimated uncertainty are visualized simultaneously for the years 2000–2100, the increased uncertainty due to each of the component models at a particular projection year is identified, and estimates of the time at which a certain sea level rise will first be reached are made.
Satellite-Based Precipitation Estimation and Its Application for Streamflow Prediction over Mountainous Western U.S. Basins
Authors: Behrangi Ali , Andreadis Konstantinos , Fisher Joshua B. , Turk F. Joseph , Granger Stephanie , Painter Thomas , Das Narendra 
Published: October 2014

AbstractRecognizing the importance and challenges inherent to the remote sensing of precipitation in mountainous areas, this study investigates the performance of the commonly used satellite-based high-resolution precipitation products (HRPPs) over several basins in the mountainous western United States. Five HRPPs [Tropical Rainfall Measuring Mission 3B42 and 3B42-RT algorithms, the Climate Prediction Center morphing technique (CMORPH), Precipitation Estimation from Remotely Sensed Imagery Using Artificial Neural Networks (PERSIANN), and the PERSIANN Cloud Classification System (PERSIANN-CCS)] are analyzed in the present work using ground gauge, gauge-adjusted radar, and CloudSat precipitation products. Using ground observation of precipitation and streamflow, the skill of HRPPs and the resulting streamflow simulations from the Variable Infiltration Capacity hydrological model are cross-compared. HRPPs often capture major precipitation events but seldom capture the observed magnitude of precipitation over the studied region and period (2003–09). Bias adjustment is found to be effective in enhancing the HRPPs and resulting streamflow simulations. However, if not bias adjusted using gauges, errors are typically large as in the lower-level precipitation inputs to HRPPs. The results using collocated Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E) and CloudSat precipitation data show that missing data, often over frozen land, and limitations in retrieving precipitation from systems that lack frozen hydrometeors contribute to the observed microwave-based precipitation errors transferred to HRPPs. Over frozen land, precipitation retrievals from infrared sensors and microwave sounders show some skill in capturing the observed precipitation climatology maps. However, infrared techniques often show poor detection skill, and microwave sounding in dry atmosphere remains challenging. By recognizing the sources of precipitation error and in light of the operation of the Global Precipitation Measurement mission, further opportunity for enhancing the current status of precipitation retrievals and the hydrology of cold and mountainous regions becomes available.
Further Development of the Regional Boundary Layer Model to Study the Impacts of Greenery on the Urban Thermal Environment
Authors: Yang Jianbo , Liu Hongnian , Sun Jianning , Zhu Yan , Wang Xueyuan , Xiong Zhe , Jiang Weimei 
Published: October 2014

AbstractA forest canopy model is developed and coupled into the Regional Boundary Layer Model (RBLM) to fully consider the vertical structure of tree morphology. Instead of a slab surface model formerly used to represent trees in RBLM, the new version allows refinement of the radiation budgets as well as sensible and latent heat fluxes and, hence, more precise simulation of the thermal impacts of tree plantings on urban meteorological behavior. By applying this new version of RBLM, sensitivity tests are conducted to explore the potential impacts of different greenery scenarios on the thermal environment in an eastern Chinese city, Suzhou, during hot summer days. Greenings, both tree planting and grass surfacing, are beneficial in cooling the ambient air temperature. In general, tree planting is more beneficial than grass surfacing with the same coverage. In terms of surface energy balance, with tree coverage increasing from 0% to 20%, and then to 40%, the average surface net radiation fluxes at noon (1200 LST) are 591, 512, and 421 W m−2, respectively. Correspondingly, the Bowen ratio is reduced from 8.78 to 1.20 and then to 0.43 as result of the redistribution of solar energy absorbed at the ground. The cooling effect of trees is more significant at noontime and can remarkably lower the daily maximum air temperature in urban areas. The cooling effect of urban greenery increases with its coverage. Using the study results, a tree coverage of around 40% may be a feasible and optimized urban greenery scheme.
A Closer Look at Boundary Layer Inversion in Large-Eddy Simulations and Bulk Models: Buoyancy-Driven Case
Authors: Gentine Pierre , Bellon Gilles , van Heerwaarden Chiel C. 
Published: October 2014

Abstract
The inversion layer (IL) of a clear-sky, buoyancy-driven convective boundary layer is investigated using large-eddy simulations covering a wide range of convective Richardson numbers. A new model of the IL is suggested and tested. The model performs better than previous first-order models of the entrainment and provides physical insights into the main controls of the mixed-layer and IL growths. A consistent prognostic equation of the IL growth is derived, with explicit dependence on the position of the minimum buoyancy flux, convective Richardson number, and relative stratification across the inversion G. The IL model expresses the interrelationship between the position and magnitude of the minimum buoyancy flux and inversion-layer depth. These relationships emphasize why zero-order jump models of the convective boundary layer perform well under a strong inversion and show that these models miss the additional parameter G to fully characterize the entrainment process under a weak inversion. Additionally, the position of the minimum buoyancy flux within the new IL model is shown to be a key component of convective boundary layer entrainment. The new IL model is sufficiently simple to be used in numerical weather prediction or general circulation models as a way to resolve the IL in a low-vertical-resolution model.
A Dynamically Constrained Method for Determining the Vortex Centers of Tropical Cyclones Predicted by High-Resolution Models
Authors: Xu Qin , Wei Li , Jin Yi , Zhao Qingyun , Cao Jie 
Published: October 2014

Abstract
This paper proposes a new method to properly define and accurately determine the vortex center of a model-predicted tropical cyclone (TC) from a dynamic perspective. Ideally, a dynamically determined TC vortex center should maximize the gradient wind balance or, equivalently, minimize the gradient wind imbalance measured by an energy norm over the TC vortex. In practice, however, such an energy norm cannot be used to easily and unambiguously determine the TC vortex center. An alternative yet practical approach is developed to dynamically and unambiguously define the TC vortex center. In this approach, the TC vortex core of near-solid-body rotation is modeled by a simple parametric vortex constrained by the gradient wind balance. Therefore, the modeled vortex can fit simultaneously the perturbation pressure and streamfunction of the TC vortex part (extracted from the model-predicted fields) over the TC vortex core area (within the radius of maximum tangential wind), while the misfit is measured by a properly defined cost function. Minimizing this cost function yields the desired dynamic optimality condition that can uniquely define the TC vortex center. Using this dynamic optimality condition, a new method is developed in the form of iterative least squares fit to accurately determine the TC vortex center. The new method is shown to be efficient and effective for finding the TC vortex center that accurately satisfies the dynamic optimality condition.
Does the ECMWF IFS Convection Parameterization with Stochastic Physics Correctly Reproduce Relationships between Convection and the Large-Scale State?
Authors: Watson Peter A. G. , Christensen H. M. , Palmer T. N. 
Published: October 2014

Abstract
Important questions concerning parameterization of tropical convection are how should subgrid-scale variability be represented and which large-scale variables should be used in the parameterizations? Here the statistics of observational data in Darwin, Australia, are compared with those of short-term forecasts of convection made by the European Centre for Medium-Range Weather Forecasts Integrated Forecast System. The forecasts use multiplicative-noise stochastic physics (MNSP) that has led to many improvements in weather forecast skill. However, doubts have recently been raised about whether MNSP is consistent with observations of tropical convection. It is shown that the model can reproduce the variability of convection intensity for a given large-scale state, both with and without MNSP. Therefore MNSP is not inconsistent with observations, and much of the modeled variability arises from nonlinearity of the deterministic part of the convection scheme. It is also shown that the model can reproduce the lack of correlation between convection intensity and large-scale CAPE and an entraining CAPE, even though the convection parameterization assumes that deep convection is more intense when the vertical temperature profile is more unstable, with entrainment taken into account. Relationships between convection and large-scale convective inhibition and vertical velocity are also correctly captured.
Attribution and Characteristics of Wet and Dry Seasons in the Upper Colorado River Basin
Authors: Bolinger Rebecca A. , Kummerow Christian D. , Doesken Nolan J. 
Published: October 2014

Abstract
Previous research has shown that the temperature and precipitation variability in the Upper Colorado River basin (UCRB) is correlated with large-scale climate variability [i.e., El Niño–Southern Oscillation (ENSO) and Pacific decadal oscillation (PDO)]. But this correlation is not very strong, suggesting the need to look beyond the statistics. Looking at monthly contributions across the basin, results show that February is least sensitive to variability, and a wet October could be a good predictor for a wet season. A case study of a wet and a dry year (with similar ENSO/PDO conditions) shows that the occurrence of a few large accumulating events is what drives the seasonal variability, and these large events can happen under a variety of synoptic conditions. Looking at several physical factors that can impact the amount of accumulation in any given event, it is found that large accumulating events (&gt;10 mm in one day) are associated with westerly winds at all levels, higher wind speeds at all levels, and greater amounts of total precipitable water. The most important difference between a large accumulating and small accumulating event is the presence of a strong (&gt;4 m s−1) low-level westerly wind. Because much more emphasis should be given to this more local feature, as opposed to large-scale variability, an accurate seasonal forecast for the basin is not producible at this time.
Different Modes of Variability over the Tasman Sea: Implications for Regional Climate*
Authors: Liess Stefan , Kumar Arjun , Snyder Peter K. , Kawale Jaya , Steinhaeuser Karsten , Semazzi Frederick H. M. , Ganguly Auroop R. , Samatova Nagiza F. , Kumar Vipin 
Published: October 2014

Abstract
A new approach is used to detect atmospheric teleconnections without being bound by orthogonality (such as empirical orthogonal functions). This method employs negative correlations in a global dataset to detect potential teleconnections. One teleconnection occurs between the Tasman Sea and the Southern Ocean. It is related to El Niño–Southern Oscillation (ENSO), the Indian Ocean dipole (IOD), and the southern annular mode (SAM). This teleconnection is significantly correlated with SAM during austral summer, fall, and winter, with IOD during spring, and with ENSO in summer. It can thus be described as a hybrid between these modes. Given previously found relationships between IOD and ENSO, and IOD’s proximity to the teleconnection centers, correlations to IOD are generally stronger than to ENSO.
Increasing pressure over the Tasman Sea leads to higher (lower) surface temperature over eastern Australia (the southwestern Pacific) in all seasons and is related to reduced surface temperature over Wilkes Land and Adélie Land in Antarctica during fall and winter. Precipitation responses are generally negative over New Zealand. For one standard deviation of the teleconnection index, precipitation anomalies are positive over Australia in fall, negative over southern Australia in winter and spring, and negative over eastern Australia in summer. When doubling the threshold, the size of the anomalous high-pressure center increases and annual precipitation anomalies are negative over southeastern Australia and northern New Zealand. Eliassen–Palm fluxes quantify the seasonal dependence of SAM, ENSO, and IOD influences. Analysis of the dynamical interactions between these teleconnection patterns can improve prediction of seasonal temperature and precipitation patterns in Australia and New Zealand.