bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stock Market Reaction to Court Decisions Related to Differential Treatment of In-State and Out-of-State Internet Wine Sales
Authors: Sharma Rajneesh 
Published: June 2012

AbstractThis paper analyzes stock market reaction to court decisions related to the differential treatment of in-state and out-of-state internet wine sales. Several states had differential laws governing internet sales of wine directly to consumers for in-state and out-of-state wineries. These laws were possibly more harmful to small wine producers as their products are less likely to be carried by retailers. In May of 2005, The Supreme Court of the United States declared these practices unconstitutional. Prior to the Supreme Court granting the writ of certiorari there was a circuit split on the issue. Our study seeks to measure the impact of the Courts' decisions on the stock returns of wineries using standard event study methodology. The results show a negative stock market reaction to publically traded large wineries to the Supreme Court ruling. It appears that differential treatment laws were, indeed, beneficial to the large wineries. (JEL Classification: G18, Q28)
Eco-Labels as a Signal of Quality
Authors: Kwong Lester M.K. 
Published: June 2012

AbstractUsing a canonical model of signaling, we show that if the cost of organic viticulture is strictly increasing in the quality dimension, then the use of eco-labels as a signal for quality cannot possibly occur as an equilibrium outcome. Conditions for the existence of such a signalling equilibrium as well as some general properties regarding its configuration are herein characterized. (JEL Classification: L15, L66, M3)
Utilizing the polar cap index to explore strong driving of polar cap dynamics
Authors: Gao Ye , Kivelson Margaret G. , Ridley Aaron J. , Weygand James M. , Walker Raymond J. 
Published: June 2012

The polar cap, defined as a region of open magnetic flux, is an ideal region in which to investigate how properties of the solar wind directly affect the magnetosphere. For such studies, the polar cap (PC) index provides a useful characterization of the state of the polar ionosphere. In this paper, we study how polar cap properties, quantified by the PC index, depend on solar wind parameters and other geomagnetic indices during intervals of exceptionally large (10 mV/m) merging electric field. Using 53 one to two‐day intervals that include such extreme fields, we find that the PC index correlates strongly with the modified electric field (EK‐R) proposed by Kivelson and Ridley (2008). Here, EK‐R is a form representative of several models in which the electric field imposed on the ionosphere by magnetopause reconnection saturates for extreme solar wind driving. However, there are anomalous events during which the auroral oval expanded poleward to the latitude of the PC index station and the index increased because of proximity to auroral zone currents. It is found that nightside magnetospheric processes, as represented by AL, make a significant contribution to the PC index. A linear regression analysis shows that the portion of the PC index directly driven by the solar wind electric field outweighs the contribution arising from energy release in the magnetotail by roughly a factor of 2. Neither the solar wind dynamic pressure (Pdyn) nor jumps in Pdyn are found to directly contribute to the PC index. However, there exists some correlation between the PC index and Pdyn, because of the common dependence of EK‐R and Pdyn on the solar wind number density.
Validation of remotely sensed evapotranspiration over the Hai River Basin, China
Authors: Jia Zhenzhen , Liu Shaomin , Xu Ziwei , Chen Yujie , Zhu Mingjia 
Published: June 2012

Ground‐based validation is crucial for ensuring the accuracy of remotely sensed evapotranspiration (RS_ET) and extending its application. This paper proposes an innovative validation method based on multisource evapotranspiration (ET) from ground measurements, with the validation results including the accuracy assessment, error source analysis, and uncertainty analysis of the validation process. It is a potentially useful approach to evaluate the accuracy and analyze the spatiotemporal properties of RS_ET at both the basin and local scales, and is appropriate to validate RS_ET in diverse resolutions at different time‐scales. An independent RS_ET validation using such a method was presented over the Hai River Basin in 2002–2009, China. In general, validation at the basin scale showed good agreements between the 1 km annual RS_ET and the validation data such as the water balance ET (root‐mean‐square error (RMSE): 50.73 mm), MODIS ET products (RMSE: 79.84 mm), precipitation, and land use types. At the local scale, multiscale ET measurements from large aperture scintillometer (LAS) and eddy covariance system (EC) with a footprint model were used for validation over three typical landscapes. In most cases, the 1 km RS_ET resulted in slight overestimation with the LAS measurements (RMSE: 10.75 mm for monthly results, 0.78 mm for daily results), while the 30 m RS_ET was underestimated compared to the EC measurements (RMSE: 16.28 mm for monthly results, 0.99 mm for daily results). Furthermore, error sources of RS_ET and uncertainties of the validation process were investigated in detail. The results showed that the proposed validation method was reasonable and feasible.
Ionospheric signatures of Tohoku‐Oki tsunami of March 11, 2011: Model comparisons near the epicenter
Authors: Galvan David A. , Komjathy Attila , Hickey Michael P. , Stephens Philip , Snively Jonathan , Tony Song Y. , Butala Mark D. , Mannucci Anthony J. 
Published: June 2012

We observe ionospheric perturbations caused by the Tohoku earthquake and tsunami of March 11, 2011. Perturbations near the epicenter were found in measurements of ionospheric total electron content (TEC) from 1198 GPS receivers in the Japanese GEONET network. For the first time for this event, we compare these observations with the estimated magnitude and speed of a tsunami‐driven atmospheric gravity wave, using an atmosphere‐ionosphere‐coupling model and a tsunami model of sea‐surface height, respectively. Traveling ionospheric disturbances (TIDs) were observed moving away from the epicenter at approximate speeds of 3400 m/s, 1000 m/s and 200–300 m/s, consistent with Rayleigh waves, acoustic waves, and gravity waves, respectively. We focus our analysis on gravity waves moving south and east of the epicenter, since tsunamis propagating in the deep ocean have been shown to produce gravity waves detectable in ionospheric TEC in the past. Observed southeastward gravity wave perturbations, seen ∼60 min after the earthquake, are mostly between 0.5 to 1.5 TECU, representing up to ∼5% of the background vertical TEC (VTEC). Comparisons of observed TID gravity waves with the modeled tsunami speed in the ocean and the predicted VTEC perturbation amplitudes from an atmosphere‐ionosphere‐coupling model show the measurements and models to be in close agreement. Due to the dense GPS network and high earthquake magnitude, these are the clearest observations to date of the effect of a major earthquake and tsunami on the ionosphere near the epicenter. Such observations from a future real‐time GPS receiver network could be used to validate tsunami models, confirm the existence of a tsunami, or track its motion where in situ buoy data is not available.
Synchrotron-based ultrafast x-ray diffraction at high repetition rates
Authors: Navirian H. , Shayduk R. , Leitenberger W. , Goldshteyn J. , Gaal P. , Bargheer M. 
Published: June 2012

We present a setup for ultrafast x-ray diffraction (UXRD) based at the storage ring BESSY II, in particular, a pump laser that excites the sample using 250 fs laser-pulses at repetition rates ranging from 208 kHz to 1.25 MHz. We discuss issues connected to the high heat-load and spatio-temporal alignment strategies in the context of a UXRD experiment at high repetition rates. The spatial overlap between laser pump and x-ray probe pulse is obtained with 10 μm precision and transient lattice changes can be recorded with an accuracy of δa/a0 = 10−6. We also compare time-resolved x-ray diffraction signals from a laser excited LSMO/STO superlattice with phonon dynamics simulations. From the analysis we determine the x-ray pulse duration to 120 ps in standard operation mode and below 10 ps in low-α mode.
Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59
Authors: Khersonsky Olga , Kiss Gert , Röthlisberger Daniela , Dym Orly , Albeck Shira , Houk Kendall N. , Baker David , Tawfik Dan S. 
Published: June 2012

Computational design is a test of our understanding of enzyme catalysis and a means of engineering novel, tailor-made enzymes. While the de novo computational design of catalytically efficient enzymes remains a challenge, designed enzymes may comprise unique starting points for further optimization by directed evolution. Directed evolution of two computationally designed Kemp eliminases, KE07 and KE70, led to low to moderately efficient enzymes (
k
cat
/
K
m
values of ≤ 5 × 10
4
M
-1
s
-1
). Here we describe the optimization of a third design, KE59. Although KE59 was the most catalytically efficient Kemp eliminase from this design series (by
k
cat
/
K
m
, and by catalyzing the elimination of nonactivated benzisoxazoles), its impaired stability prevented its evolutionary optimization. To boost KE59’s evolvability, stabilizing consensus mutations were included in the libraries throughout the directed evolution process. The libraries were also screened with less activated substrates. Sixteen rounds of mutation and selection led to > 2,000-fold increase in catalytic efficiency, mainly via higher
k
cat
values. The best KE59 variants exhibited
k
cat
/
K
m
values up to 0.6 × 10
6
M
-1
s
-1
, and
k
cat
/
k
uncat
values of ≤ 10
7
almost regardless of substrate reactivity. Biochemical, structural, and molecular dynamics (MD) simulation studies provided insights regarding the optimization of KE59. Overall, the directed evolution of three different designed Kemp eliminases, KE07, KE70, and KE59, demonstrates that computational designs are highly evolvable and can be optimized to high catalytic efficiencies.
Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle
Authors: Barnes Jonathan C. , Fahrenbach Albert C. , Dyar Scott M. , Frasconi Marco , Giesener Marc A. , Zhu Zhixue , Liu Zhichang , Hartlieb Karel J. , Carmieli Ranaan , Wasielewski Michael R. , Stoddart J. Fraser 
Published: June 2012

The kinetics and thermodynamics of intramolecular electron transfer (IET) can be subjected to redox control in a bistable [2]rotaxane comprised of a dumbbell component containing an electron-rich 1,5-dioxynaphthalene (DNP) unit and an electron-poor phenylene-bridged bipyridinium (P-BIPY2+) unit and a cyclobis (paraquat-p-phenylene) (CBPQT4+) ring component. The [2]rotaxane exists in the ground-state co-conformation (GSCC) wherein the CBPQT4+ring encircles the DNP unit. Reduction of the CBPQT4+leads to the CBPQT2(•+)diradical dication while the P-BIPY2+unit is reduced to its P-BIPY•+radical cation. A radical-state co-conformation (RSCC) results from movement of the CBPQT2(•+)ring along the dumbbell to surround the P-BIPY•+unit. This shuttling event induces IET to occur between the pyridinium redox centers of the P-BIPY•+unit, a property which is absent between these redox centers in the free dumbbell and in the 1∶1 complex formed between the CBPQT2(•+)ring and the radical cation of methyl-phenylene-viologen (MPV•+). Using electron paramagnetic resonance (EPR) spectroscopy, the process of IET was investigated by monitoring the line broadening at varying temperatures and determining the rate constant (kET = 1.33 × 107 s-1) and activation energy (ΔG‡ = 1.01 kcal mol-1) for electron transfer. These values were compared to the corresponding values predicted, using the optical absorption spectra and Marcus–Hush theory.
Statistical model-based testing to evaluate the recurrence of genomic aberrations
Authors: Niida Atushi , Imoto Seiya , Shimamura Teppei , Miyano Satoru 
Published: June 2012

Abstract
Motivation: In cancer genomes, chromosomal regions harboring cancer genes are often subjected to genomic aberrations like copy number alteration and loss of heterozygosity. Given this, finding recurrent genomic aberrations is considered an apt approach for screening cancer genes. Although several permutation-based tests have been proposed for this purpose, none of them are designed to find recurrent aberrations from the genomic dataset without paired normal sample controls. Their application to unpaired genomic data may lead to false discoveries, because they retrieve pseudo-aberrations that exist in normal genomes as polymorphisms.
Results: We develop a new parametric method named parametric aberration recurrence test (PART) to test for the recurrence of genomic aberrations. The introduction of Poisson-binomial statistics allow us to compute small P-values more efficiently and precisely than the previously proposed permutation-based approach. Moreover, we extended PART to cover unpaired data (PART-up) so that there is a statistical basis for analyzing unpaired genomic data. PART-up uses information from unpaired normal sample controls to remove pseudo-aberrations in unpaired genomic data. Using PART-up, we successfully predict recurrent genomic aberrations in cancer cell line samples whose paired normal sample controls are unavailable. This article thus proposes a powerful statistical framework for the identification of driver aberrations, which would be applicable to ever-increasing amounts of cancer genomic data seen in the era of next generation sequencing.
Availability: Our implementations of PART and PART-up are available from http://www.hgc.jp/~niiyan/PART/manual.html.
Contact: aniida@ims.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
GenomeRing: alignment visualization based on SuperGenome coordinates
Authors: Herbig A. , Jäger G. , Battke F. , Nieselt K. 
Published: June 2012

Abstract
Motivation: The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.
Results: Here, we present two complementary approaches to tackle this problem. First, we propose the SuperGenome concept for the computation of a common coordinate system for all genomes in a multiple alignment. This coordinate system allows for the consistent placement of genome annotations in the presence of insertions, deletions and rearrangements. Second, we present the GenomeRing visualization that, based on the SuperGenome, creates an interactive overview visualization of the multiple genome alignment in a circular layout. We demonstrate our methods by applying them to an alignment of Campylobacter jejuni strains for the discovery of genomic islands as well as to an alignment of Helicobacter pylori, which we visualize in combination with gene expression data.
Availability: GenomeRing and example data is available at http://it.inf.uni-tuebingen.de/software/genomering/
Contact: kay.nieselt@uni-tuebingen.de
Shifts in soil organic carbon for plantation and pasture establishment in native forests and grasslands of South America
Authors: Eclesia Roxana P. , Jobbagy Esteban G. , Jackson Robert B. , Biganzoli Fernando , Piñeiro Gervasio 
Published: June 2012

AbstractThe replacement of native vegetation by pastures or tree plantations is increasing worldwide. Contradictory effects of these land use transitions on the direction of changes in soil organic carbon (SOC) stocks, quality, and vertical distribution have been reported, which could be explained by the characteristics of the new or prior vegetation, time since vegetation replacement, and environmental conditions. We used a series of paired‐field experiments and a literature synthesis to evaluate how these factors affectSOCcontents in transitions between tree‐ and grass‐dominated (grazed) ecosystems in South America. Both our field and literature approaches showed thatSOCchanges (0–20 cm of depth) were independent of the initial native vegetation (forest, grassland, or savanna) but strongly dependent on the characteristics of the new vegetation (tree plantations or pastures), its age, and precipitation. Pasture establishment increasedSOCcontents across all our precipitation gradient and C gains were greater as pastures aged. In contrast, tree plantations increasedSOCstocks in arid sites but decreased them in humid ones. However,SOClosses in humid sites were counterbalanced by the effect of plantation age, as plantations increased theirSOCstocks as plantations aged. A multiple regression model including age and precipitation explained more than 50% (p < 0.01) ofSOCchanges observed after sowing pastures or planting trees. The only clear shift observed in the vertical distribution ofSOCoccurred when pastures replaced native forests, withSOCgains in the surface soil but losses at greater depths. The changes inSOCstocks occurred mainly in the silt+clay soil size fraction (MAOM), whileSOCstocks in labile (POM) fraction remained relatively constant. Our results can be considered in designing strategies to increaseSOCstorage and soil fertility and highlight the importance of precipitation, soil depth, and age in determiningSOCchanges across a range of environments and land‐use transitions.
Do nitrogen fertilizers stimulate or inhibit methane emissions from rice fields?
Authors: Banger Kamaljit , Tian Hanqin , Lu Chaoqun 
Published: June 2012

AbstractIn rice cultivation, there are controversial reports on net impacts of nitrogen (N) fertilizers on methane (CH
4) emissions. Nitrogen fertilizers increase crop growth as well as alter CH
4 producing (Methanogens) and consuming (Methanotrophs) microbes, and thereby produce complex effects on CH
4 emissions. Objectives of this study were to determine net impact of N fertilizers on CH
4 emissions and to identify their underlying mechanisms in the rice soils. Database was obtained from 33 published papers that contained CH
4 emissions observations from N fertilizer (28–406 kg N ha−1) treatment and its control. Results have indicated that N fertilizers increased CH
4 emissions in 98 of 155 data pairs in rice soils. Response of CH
4 emissions per kg N fertilizer was significantly (P < 0.05) greater at < 140 kg N ha−1 than > 140 kg N ha−1 indicating that substrate switch from CH
4 to ammonia by Methanotrophs may not be a dominant mechanism for increased CH
4 emissions. On the contrary, decreased CH
4 emission in intermittent drainage by N fertilizers has suggested the stimulation of Methanotrophs in rice soils. Effects of N fertilizer stimulated Methanotrophs in reducing CH
4 emissions were modified by the continuous flood irrigation due to limitation of oxygen to Methanotrophs. Greater response of CH
4 emissions per kg N fertilizer in urea than ammonia sulfate probably indicated the interference of sulfate in the CH
4 production process. Overall, response of CH
4 emissions to N fertilizers was correlated with N‐induced crop yield (r = +0.39; P < 0.01), probably due to increased carbon substrates for Methanogens. Using CH
4 emission observations, this meta‐analysis has identified dominant microbial processes that control net effects of N fertilizers on CH
4 emissions in rice soils. Finally, we have provided a conceptual model that included microbial processes and controlling factors to predict effects of N fertilizers on CH
4 emissions in rice soils.
Validating the personal health records adoption model using a modified e‐Delphi
Authors: Logue Melanie D. , Effken Judith A. 
Published: June 2012

logue m.d. & effken j.a. (2013) Validating the personal health records adoption model using a modified e‐Delphi. Journal of Advanced Nursing69(3), 685–696. doi: 10.1111/j.1365‐2648.2012.06056.xAbstractAim.  To report the results of a preliminary test of validity of a proposed theoretical framework of electronic personal health record adoption by older adults.Background.  Personal health records can assist older adults in managing or co‐managing their chronic health conditions. Although there is interest by this population, their adoption of this technology has been slow. Without a comprehensive understanding of the reasons for this phenomenon, facilitating adoption will be difficult. Therefore, we developed a theoretical framework of adoption barriers and facilitators.Design.  Survey.Methods.  A modified e‐Delphi methodology was used to validate the framework by obtaining consensus from a panel of experts in related healthcare fields. These data were collected over 3 months in 2010. Of 16 expert panellists, 13 completed Round 1, 12 completed Rounds 2 and 3, and 9 completed Round 4. Central tendencies and percent agreement were computed to establish consensus.Findings.  The e‐Delphi resulted in expert consensus on the concepts, variables, and empirical indicators that were retained in (or added to) the framework to describe barriers and/or facilitators to older adults’ adoption of personal health records for self‐management of chronic disease.Conclusion.  The validated model will be used as the basis for developing an instrument to identify barriers and facilitators to personal health records adoption and use by older adults with chronic disease. With better understanding of the factors that influence personal health record adoption in this population, more effective strategies may be developed to increase adoption and thus improve chronic disease management.
A Plating‐PCR Technique for Detection and Quantification of the Biological Control Agent Agrobacterium vitis Strain E26 in Soil under Controlled Conditions
Authors: Bi Zhen , Li Jinyun , Guo Yanbin , Zheng Hui , Hu Bin , Wang Jianhui , Wang Huimin 
Published: June 2012

AbstractAgrobacterium vitis strain E26 is a promising biocontrol agent of grapevine crown gall, an economically important disease of grape worldwide. In this report, we developed a Plating‐PCR method that allows specific detection and quantification of E26 by combining classical microbiological techniques with molecular tools. Random amplified polymorphic DNA fingerprints were used to differentiate E26 from other A. vitis strains. A differentially amplified fragment from E26 was sequenced and characterized as a sequence characterized amplified region (SCAR) marker. Two primer pairs were then designed and evaluated for their specificity against E26. One of the two SCAR primer pairs, 740F/R, was further selected for specific detection of strain E26. A plating assay coupled to PCR with the SCAR primers 740F/R allowed the assessment of population dynamics of E26 in non‐sterile grape rhizosphere soil under controlled conditions.