bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Terrestrial Photosynthesis Down Regulation on the Twentieth-Century Carbon Budget Simulated with the CCCma Earth System Model
Authors: Arora V. K. , Boer G. J. , Christian J. R. , Curry C. L. , Denman K. L. , Zahariev K. , Flato G. M. , Scinocca J. F. , Merryfield W. J. , Lee W. G. 
Published: June 2009

Abstract
The simulation of atmospheric–land–ocean CO2 exchange for the 1850–2000 period offers the possibility of testing and calibrating the carbon budget in earth system models by comparing the simulated changes in atmospheric CO2 concentration and in land and ocean uptake with observation-based information. In particular, some of the uncertainties associated with the treatment of land use change (LUC) and the role of down regulation in affecting the strength of CO2 fertilization for terrestrial photosynthesis are assessed using the Canadian Centre for Climate Modelling and Analysis Earth System Model (CanESM1). LUC emissions may be specified as an external source of CO2 or calculated interactively based on estimated changes in crop area. The evidence for photosynthetic down regulation is reviewed and an empirically based representation is implemented and tested in the model. Four fully coupled simulations are performed: with and without terrestrial photosynthesis down regulation and with interactively determined or specified LUC emissions. Simulations without terrestrial photosynthesis down regulation yield 15–20 ppm lower atmospheric CO2 by the end of the twentieth century, compared to observations, regardless of the LUC approach used because of higher carbon uptake by land. Implementation of down regulation brings simulated values of atmospheric CO2 and land and ocean carbon uptake closer to observation-based values. The use of specified LUC emissions yields a large source in the tropics during the 1981–2000 period, which is inconsistent with studies suggesting the tropics to be near-neutral or small carbon sinks. The annual cycle of simulated global averaged CO2, dominated by the Northern Hemisphere terrestrial photosynthesis and respiration cycles, is reasonably well reproduced, as is the latitudinal distribution of CO2 and the dependence of interhemispheric CO2 gradient on fossil fuel emissions. The empirical approach used here offers a reasonable method of implementing down regulation in coupled carbon–climate models in the absence of a more explicit biogeochemical representation.
Gap-Leaping Vortical Currents
Authors: McDonald N. Robb , Johnson E. R. 
Published: June 2009

Abstract
A one-parameter family of exact solutions describing the bifurcation of a steady two-dimensional current with uniform vorticity near a gap in a thin barrier is found. The unsteady evolution of source-driven flows toward these steady states is studied using a version of contour dynamics, appropriately modified to take into account the presence of a barrier with a single gap. It is shown that some of the steady solutions are realizable as large-time limits of the source-driven flows, although some are not owing to persistent eddy-shedding events in the vicinity of the gap. For the special case when there is zero net flux through the gap, numerical experiments show that the through-gap flux of vortical fluid increases with the width of the gap and that this flux approaches a steady limit with time.
Synoptic- and Frontal-Scale Influences on Tropical Transition Events in the Atlantic Basin. Part II: Tropical Transition of Hurricane Karen
Authors: Hulme Andrew L. , Martin Jonathan E. 
Published: June 2009

Abstract
A finescale simulation of the tropical transition of Atlantic Hurricane Karen in October 2001 is examined to determine the processes leading to the development of upshear convection and its effects on the process of tropical transition. The analysis shows that, as in marine extratropical cyclones, the area upshear of the pretransition cyclone is characterized by reduced stability. Lower-tropospheric frontogenesis leads to an intense burst of convection there and instigates three important processes that combine to produce a full-fledged tropical cyclone. First, the convection generates intense low-level vorticity on the western half of the cyclone, which quickly dominates the cyclone’s vorticity field eventually organizing the circulation into a small-scale, intense vortex. Second, the diabatically enhanced circulation hastens the isolation of the cyclone’s developing warm core by intensifying cold air advection on the northern and western sides of the storm and by placing evaporatively cooled air into the boundary layer to the south of the cyclone. Third, upshear convection vertically redistributes potential vorticity (PV) from the tropopause to the surface and introduces a component to the upper-level winds, which advects strong, shear-inducing PV gradients away from the column above the cyclone. These three processes transform the initial extratropical cyclone into a frontless vortex with tropical storm–force winds and a warm core in a low-shear environment. These features are sufficient, given a warm enough ocean surface, to allow self-amplification of the storm as a tropical cyclone.
The results further blur the distinction between tropical and extratropical cyclones as many of the processes identified as important to transition are similar to those that characterize ordinary marine cyclones and the extratropical occlusion process with the key distinctions being that here the convection is stronger and the initial upper-level feature is weaker. Thus, tropical transition of strong extratropical precursors follows the canonical midlatitude cyclone life cycle with upshear convection serving as the catalyst that both induces and organizes processes that favor tropical cyclogenesis in the postmature phase.
Dynamical Forecast of Inter–El Niño Variations of Tropical SST and Australian Spring Rainfall
Authors: Lim Eun-Pa , Hendon Harry H. , Hudson Debra , Wang Guomin , Alves Oscar 
Published: June 2009

Abstract
The relationship between variations of Indo-Pacific sea surface temperatures (SSTs) and Australian springtime rainfall over the last 30 years is investigated with a focus on predictability of inter–El Niño variations of SST and associated rainfall anomalies. Based on observed data, the leading empirical orthogonal function (EOF) of Indo-Pacific SST represents mature El Niño conditions, while the second and fourth modes depict major east–west shifts of individual El Niño events. These higher-order EOFs of SST explain more rainfall variance in Australia, especially in the southeast, than does the El Niño mode. Furthermore, intense springtime droughts tend to be associated with peak warming in the central Pacific, as captured by EOFs 2 and 4, together with warming in the eastern Pacific as depicted by EOF1.
The ability to predict these inter–El Niño variations of SST and Australian rainfall is assessed with the Australian Bureau of Meteorology dynamical coupled model seasonal forecast system, the Predictive Ocean and Atmospheric Model for Australia (POAMA). A 10-member ensemble of 9-month hindcasts was generated for the period 1980–2006. For the September–November season, the leading 2 EOFs of SST are predictable with lead times of 3–6 months, while SST EOF4 is predictable out to a lead time of 1 month. The teleconnection between the leading EOFs of SST and Australian rainfall is also well depicted in the model. Based on this ability to predict major east–west variations of El Niño and the teleconnection to Australian rainfall, springtime rainfall over eastern Australia, and major drought events are predictable up to a season in advance.
The Impact of Moisture on Mountain Waves during T-REX
Authors: Jiang Qingfang , Doyle James D. 
Published: June 2009

Abstract
The impact of moist processes on mountain waves over Sierra Nevada Mountain Range is investigated in this study. Aircraft measurements over Owens Valley obtained during the Terrain-induced Rotor Experiment (T-REX) indicate that mountain waves were generally weaker when the relative humidity maximum near the mountaintop level was above 70%. Four moist cases with a RH maximum near the mountaintop level greater than 90% have been further examined using a mesoscale model and a linear wave model. Two competing mechanisms governing the influence of moisture on mountain waves have been identified. The first mechanism involves low-level moisture that enhances flow–terrain interaction by reducing windward flow blocking. In the second mechanism, the moist airflow tends to damp mountain waves through destratifying the airflow and reducing the buoyancy frequency. The second mechanism dominates in the presence of a deep moist layer in the lower to middle troposphere, and the wave amplitude is significantly reduced associated with a smaller moist buoyancy frequency. With a shallow moist layer and strong low-level flow, the two mechanisms can become comparable in magnitude and largely offset each other.
Neighborhood Verification: A Strategy for Rewarding Close Forecasts
Authors: Ebert Elizabeth E. 
Published: June 2009

Abstract
High-resolution forecasts may be quite useful even when they do not match the observations exactly. Neighborhood verification is a strategy for evaluating the “closeness” of the forecast to the observations within space–time neighborhoods rather than at the grid scale. Various properties of the forecast within a neighborhood can be assessed for similarity to the observations, including the mean value, fractional coverage, occurrence of a forecast event sufficiently near an observed event, and so on. By varying the sizes of the neighborhoods, it is possible to determine the scales for which the forecast has sufficient skill for a particular application. Several neighborhood verification methods have been proposed in the literature in the last decade. This paper examines four such methods in detail for idealized and real high-resolution precipitation forecasts, highlighting what can be learned from each of the methods. When applied to idealized and real precipitation forecasts from the Spatial Verification Methods Intercomparison Project, all four methods showed improved forecast performance for neighborhood sizes larger than grid scale, with the optimal scale for each method varying as a function of rainfall intensity.
Differences in Sonographic Characteristics of the Vastus Medialis Obliquus between Patients with Patellofemoral Pain Syndrome and Healthy Adults
Authors: Jan Mei-Hwa , Lin Da-Hon , Lin Jiu-Jenq , Lin Chien-Ho Janice , Cheng Cheng-Kung , Lin Yeong-Fwu 
Published: June 2009

Background There is controversy regarding the relationship between patellofemoral pain syndrome (PFPS) and insufficiency of the vastus medialis obliquus (VMO). The conventional clinical practice of VMO strengthening for PFPS has been challenged for lack of evidence. The purpose of this study was to observe the difference in sonographic findings of the VMO between patients with PFPS and healthy adults. Hypothesis The morphological characteristics of the VMO are different between patients with PFPS and healthy adults. Study Design Case-control study; Level of evidence, 3. Methods Fifty-four patients with PFPS and 54 age-, gender-, body height—, and body weight—matched healthy adults as controls were enrolled in the study to measure by sonography the insertion level, fiber angle, and volume of the VMO at its insertional portion to detect differences between patients with PFPS and healthy controls. Results The insertion level, fiber angle, and VMO volume were all significantly smaller in the PFPS group than in the control group (P < .05). Multivariate analysis of variance has revealed a Wilks λ value of .845 and an F value of 5.640 (P = .001). Conclusion There was a significant difference in the 3 VMO measures between patients with PFPS and the healthy controls. Individuals might be predisposed to PFPS by different VMO characteristics, including insertion level and fiber angle. The current study cannot determine whether the observed morphological differences were the results of atrophy in response to pain or if they represent dysplasia that was predisposed to pain development. The clinical manifestations of VMO characteristics should be thoroughly investigated in other populations. Clinical Relevance The function of the VMO is important to consider in the rehabilitation of patients with PFPS.
Activation of Wnt5A signaling is required for CXC chemokine ligand 12–mediated T-cell migration
Authors: Ghosh Manik C. , Collins Gary D. , Vandanmagsar Bolormaa , Patel Kalpesh , Brill Margaret , Carter Arnell , Lustig Ana , Becker Kevin G. , Wood William W. , Emeche Chineye D. , French Amanda D. , O'Connell Michael P. , Xu Mai , Weeraratna Ashani T. , Taub Dennis D. 
Published: June 2009

AbstractChemokines mediate the signaling and migration of T cells, but little is known about the transcriptional events involved therein. Microarray analysis of CXC chemokine ligand (CXCL) 12−treated T cells revealed that Wnt ligands are significantly up-regulated during CXCL12 treatment. Real-time polymerase chain reaction and Western blot analysis confirmed that the expression of noncanonical Wnt pathway members (eg, Wnt5A) was specifically up-regulated during CXCL12 stimulation, whereas β-catenin and canonical Wnt family members were selectively down-regulated. Wnt5A augmented signaling through the CXCL12-CXCR4 axis via the activation of protein kinase C. Moreover, Wnt5A expression was required for CXCL12–mediated T-cell migration, and rWnt5A sensitized human T cells to CXCL12-induced migration. Furthermore, Wnt5A expression was also required for the sustained expression of CXCR4. These results were further supported in vivo using EL4 thymoma metastasis as a model of T-cell migration. Together, these data demonstrate that Wnt5A is a critical mediator of CXCL12-CXCR4 signaling and migration in human and murine T cells.
Src homology 2 domain–containing inositol-5-phosphatase and CCAAT enhancer-binding protein β are targeted by miR-155 in B cells of Eμ-MiR-155 transgenic mice
Authors: Costinean Stefan , Sandhu Sukhinder K. , Pedersen Irene M. , Tili Esmerina , Trotta Rossana , Perrotti Danilo , Ciarlariello David , Neviani Paolo , Harb Jason , Kauffman Lauren Rachel , Shidham Aaditya , Croce Carlo Maria 
Published: June 2009

AbstractWe showed that Eμ-MiR-155 transgenic mice develop acute lymphoblastic leukemia/high-grade lymphoma. Most of these leukemias start at approximately 9 months irrespective of the mouse strain. They are preceded by a polyclonal pre–B-cell proliferation, have variable clinical presentation, are transplantable, and develop oligo/monoclonal expansion. In this study, we show that in these transgenic mice the B-cell precursors have the highest MiR-155 transgene expression and are at the origin of the leukemias. We determine that Src homology 2 domain–containing inositol-5-phosphatase (SHIP) and CCAAT enhancer-binding protein β (C/EBPβ), 2 important regulators of the interleukin-6 signaling pathway, are direct targets of MiR-155 and become gradually more down-regulated in the leukemic than in the preleukemic mice. We hypothesize that miR-155, by down-modulating Ship and C/EBPβ, initiates a chain of events that leads to the accumulation of large pre-B cells and acute lymphoblastic leukemia/high-grade lymphoma.
An efficient variance component approach implementing an average information REML suitable for combined LD and linkage mapping with a general complex pedigree
Authors: Lee Sang Hong , van der Werf Julius H.J. 
Published: June 2009

Abstract
Variance component (VC) approaches based on restricted maximum likelihood (REML) have been used as an attractive method for positioning of quantitative trait loci (QTL). Linkage disequilibrium (LD) information can be easily implemented in the covariance structure among QTL effects (e.g. genotype relationship matrix) and mapping resolution appears to be high. Because of the use of LD information, the covariance structure becomes much richer and denser compared to the use of linkage information alone. This makes an average information (AI) REML algorithm based on mixed model equations and sparse matrix techniques less useful. In addition, (near-) singularity problems often occur with high marker densities, which is common in fine-mapping, causing numerical problems in AIREML based on mixed model equations. The present study investigates the direct use of the variance covariance matrix of all observations in AIREML for LD mapping with a general complex pedigree. The method presented is more efficient than the usual approach based on mixed model equations and robust to numerical problems caused by near-singularity due to closely linked markers. It is also feasible to fit multiple QTL simultaneously in the proposed method whereas this would drastically increase computing time when using mixed model equation-based methods.
The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations
Authors: De Kovel Carolien Gerda Franciska 
Published: June 2009

Abstract
Recently, inter-population comparisons of allele frequencies to detect past selection haven gained popularity. Data from genome-wide scans are used to detect the number and position of genes that have responded to unknown selection pressures in natural populations, or known selection pressures in experimental lines. Yet, the limitations and possibilities of these methods have not been well studied. In this paper, the objectives were (1) to investigate the distance over which a signal of directional selection is detectable under various scenarios, and (2) to study the power of the method depending on the properties of the used markers, for both natural populations and experimental set-ups. A combination of recurrence equations and simulations was used. The results show that intermediate strength selection on new mutations can be detected with a marker spacing of about 0.5 cM in large natural populations, 200 to 400 generations after the divergence of subpopulations. In experimental situations, only strong selection will be detectable, while markers can be spaced a few cM apart. Adaptation from standing variation in the base population will be hard to detect, though some solutions are presented for experimental designs.
Validation of an approximate approach to compute genetic correlations between longevity and linear traits
Authors: Tarrés Joaquim , Piedrafita Jesús , Ducrocq Vincent 
Published: June 2009

Abstract
The estimation of genetic correlations between a nonlinear trait such as longevity and linear traits is computationally difficult on large datasets. A two-step approach was proposed and was checked via simulation. First, univariate analyses were performed to get genetic variance estimates and to compute pseudo-records and their associated weights. These pseudo-records were virtual performances free of all environmental effects that can be used in a BLUP animal model, leading to the same breeding values as in the (possibly nonlinear) initial analyses. By combining these pseudo-records in a multiple trait model and fixing the genetic and residual variances to their values computed during the first step, we obtained correlation estimates by AI-REML and approximate MT-BLUP predicted breeding values that blend direct and indirect information on longevity. Mean genetic correlations and reliabilities obtained on simulated data confirmed the suitability of this approach in a wide range of situations. When nonzero residual correlations exist between traits, a sire model gave nearly unbiased estimates of genetic correlations, while the animal model estimates were biased upwards. Finally, when an incorrect genetic trend was simulated to lead to biased pseudo-records, a joint analysis including a time effect could adequately correct for this bias.
Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness
Authors: Lagarrigue Sandrine , Pitel Frédérique , Carré Wilfrid , Abasht Behnam , Le Roy Pascale , Neau André , Amigues Yves , Sourdioux Michel , Simon Jean , Cogburn Larry , Aggrey Sammy , Leclercq Bernard , Vignal Alain , Douaire Madeleine 
Published: June 2009

Abstract
Quantitative trait loci (QTL) for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.
Prediction of genetic gain from quadratic optimisation with constrained rates of inbreeding
Authors: Villanueva Beatriz , Avendaño Santiago , Woolliams John A 
Published: June 2009

Abstract
There are selection methods available that allow the optimisation of genetic contributions of selection candidates for maximising the rate of genetic gain while restricting the rate of inbreeding. These methods imply selection on quadratic indices as the selection merit of a particular individual is a quadratic function of its estimated breeding value. This study provides deterministic predictions of genetic gain from selection on quadratic indices for a given set of resources (the number of candidates), heritability, and target rate of inbreeding. The rate of gain was obtained as a function of the accuracy of the Mendelian sampling term at the time of convergence of long-term contributions of selected candidates and the theoretical ideal rate of gain for a given rate of inbreeding after an exact allocation of long-term contributions to Mendelian sampling terms. The expected benefits from quadratic indices over traditional linear indices (i.e. truncation selection), both using BLUP breeding values, were quantified. The results clearly indicate higher gains from quadratic optimisation than from truncation selection. With constant rate of inbreeding and number of candidates, the benefits were generally largest for intermediate heritabilities but evident over the entire range. The advantage of quadratic indices was not highly sensitive to the rate of inbreeding for the constraints considered.
Optimization of a crossing system using mate selection
Authors: Li Yongjun , Werf Julius HJ van der , Kinghorn Brian P 
Published: June 2009

Abstract
A simple model based on one single identified quantitative trait locus (QTL) in a two-way crossing system was used to demonstrate the power of mate selection algorithms as a natural means of opportunistic line development for optimization of crossbreeding programs over multiple generations. Mate selection automatically invokes divergent selection in two parental lines for an over-dominant QTL and increased frequency of the favorable allele toward fixation in the sire-line for a fully-dominant QTL. It was concluded that an optimal strategy of line development could be found by mate selection algorithms for a given set of parameters such as genetic model of QTL, breeding objective and initial frequency of the favorable allele in the base populations, etc. The same framework could be used in other scenarios, such as programs involving crossing to exploit breed effects and heterosis. In contrast to classical index selection, this approach to mate selection can optimize long-term responses.