bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subpolar High Anomaly Preconditioning Precipitation over South America
Authors: Solman Silvina A. , Orlanski Isidoro 
Published: January 2010

Abstract
The mechanisms associated with the intraseasonal variability of precipitation over South America during the spring season are investigated with emphasis on the influence of a quasi-stationary anomalous circulation over the southeastern South Pacific Ocean (SEP). A spectral analysis performed to the bandpass-filtered time series of daily precipitation anomalies for the La Plata Basin (LPB) and the South Atlantic convergence zone (SACZ) regions revealed several statistically relevant peaks corresponding to periods of roughly 23 days and 14–16 days—with the lower (higher) frequency peaks more prevalent for the SACZ (LPB). The large-scale circulation patterns preconditioning precipitation variability over both regions were explored by means of a regression analysis performed on the daily 500-hPa geopotential anomaly field provided by the NCEP–NCAR reanalysis dataset. The most prominent feature of the regression fields is the presence of a quasi-stationary anomalous anticyclonic (cyclonic) circulation over the southeastern South Pacific Ocean associated with positive rainfall anomalies over the LPB (SACZ) and, emanating from that high (low), an external Rossby wave propagating northeastward toward the South American continent. The synoptic-scale activity, quantified in terms of a frontal activity index, showed a strong influence on precipitation over the LPB and to a lesser extent over the SACZ. Moreover, the frontal activity is actually modulated by the anomalous high circulation over the SEP region. The behavior of this anomalous circulation may be supported by a positive feedback mechanism that can enhance the response of the high anomaly itself, which in turns reinforces the Rossby wave train propagating toward the South American continent.
The Climatology of the Middle Atmosphere in a Vertically Extended Version of the Met Office’s Climate Model. Part I: Mean State
Authors: Hardiman S. C. , Butchart N. , Osprey S. M. , Gray L. J. , Bushell A. C. , Hinton T. J. 
Published: January 2010

Abstract
The climatology of a stratosphere-resolving version of the Met Office’s climate model is studied and validated against ECMWF reanalysis data. Ensemble integrations are carried out at two different horizontal resolutions. Along with a realistic climatology and annual cycle in zonal mean zonal wind and temperature, several physical effects are noted in the model. The time of final warming of the winter polar vortex is found to descend monotonically in the Southern Hemisphere, as would be expected for purely radiative forcing. In the Northern Hemisphere, however, the time of final warming is driven largely by dynamical effects in the lower stratosphere and radiative effects in the upper stratosphere, leading to the earliest transition to westward winds being seen in the midstratosphere. A realistic annual cycle in stratospheric water vapor concentrations—the tropical “tape recorder”—is captured. Tropical variability in the zonal mean zonal wind is found to be in better agreement with the reanalysis for the model run at higher horizontal resolution because the simulated quasi-biennial oscillation has a more realistic amplitude. Unexpectedly, variability in the extratropics becomes less realistic under increased resolution because of reduced resolved wave drag and increased orographic gravity wave drag. Overall, the differences in climatology between the simulations at high and moderate horizontal resolution are found to be small.
Present-Day Arctic Sea Ice Variability in the Coupled ECHAM5/MPI-OM Model
Authors: Koldunov Nikolay V. , Stammer Detlef , Marotzke Jochem 
Published: January 2010

Abstract
As a contribution to a detailed evaluation of Intergovernmental Panel on Climate Change (IPCC)-type coupled climate models against observations, this study analyzes Arctic sea ice parameters simulated by the Max-Planck-Institute for Meteorology (MPI-M) fully coupled climate model ECHAM5/Max-Planck-Institute for Meteorology Hamburg Primitive Equation Ocean Model (MPI-OM) for the period from 1980 to 1999 and compares them with observations collected during field programs and by satellites. Results of the coupled run forced by twentieth-century CO2 concentrations show significant discrepancies during summer months with respect to observations of the spatial distribution of the ice concentration and ice thickness. Equally important, the coupled run lacks interannual variability in all ice and Arctic Ocean parameters. Causes for such big discrepancies arise from errors in the ECHAM5/MPI-OM atmosphere and associated errors in surface forcing fields (especially wind stress). This includes mean bias pattern caused by an artificial circulation around the geometric North Pole in its atmosphere, as well as insufficient atmospheric variability in the ECHAM5/MPI-OM model, for example, associated with Arctic Oscillation/North Atlantic Oscillation (AO/NAO). In contrast, the identical coupled ocean–ice model, when driven by NCEP–NCAR reanalysis fields, shows much increased skill in its ice and ocean circulation parameters. However, common to both model runs is too strong an ice export through the Fram Strait and a substantially biased heat content in the interior of the Arctic Ocean, both of which may affect sea ice budgets in centennial projections of the Arctic climate system.
Numerical Investigation of the Middle Atlantic Bight Shelfbreak Frontal Circulation Using a High-Resolution Ocean Hindcast Model
Authors: Chen Ke , He Ruoying 
Published: January 2010

Abstract
A nested high-resolution ocean model is used to hindcast the Middle Atlantic Bight (MAB) shelfbreak circulation from December 2003 to June 2008. The model is driven by tidal harmonics, realistic atmospheric forcing, and dynamically consistent initial and open boundary conditions obtained from a large-scale circulation model. Simulated shelfbreak sea levels and tracer fields compare favorably with satellite observations and available in situ hydrographic climatology, demonstrating the utility of this nested ocean model for resolving the MAB shelfbreak circulation. The resulting time and space continuous hindcast solutions between January 2004 and December 2007 are used to describe the mean structures and temporal variations of the shelfbreak front and jet, the bottom boundary layer detachment, and the migration of the shelfbreak front. It is found that the shelfbreak jet and boundary convergence reach their maximum intensities in the spring, at which time the foot of the front also migrates to its farthest offshore position. Vorticity analyses reveal that the magnitude ratio of the mean relative vorticity between the seaward and the shoreward portions of the shelfbreak front is about 2:1. The shelfbreak ageostrophic circulation is largely controlled by the viscosity in the boundary layers and by the nonlinear advection in the flow interior. Simulated three-dimensional velocity and tracer fields are used to estimate the transport and heat and salt fluxes across the 200-m isobath. Within the model domain, the total cross-shelf water transport, the total eddy heat flux, and the total eddy salt flux are 0.035 ± 0.26 Sv (1 Sv ≡ 106 m3 s−1), 1.0 × 103 ± 4 × 104 W m−2, and 6.7 × 10−5 ± 7.0 × 10−4 kg m−2 s−1. The empirical orthogonal function (EOF) analysis on the 4-yr shelfbreak circulation hindcast solutions identifies two dominant modes. The first EOF mode accounts for 61% variance, confirming that the shelfbreak jet is a persistent year-round circulation feature. The second mode accounts for 13% variance, representing the baroclinic eddy passages across the shelf break.
Stability of the MSU-Derived Atmospheric Temperature Trend
Authors: Zou Cheng-Zhi , Wang Wenhui 
Published: January 2010

Abstract
Warm target effect and diurnal drift errors are the main sources of uncertainties in the trend determination from the NOAA Microwave Sounding Unit (MSU) observations. Currently, there are two methods to correct the warm target effect: 1) finding a best root-level (level-1c) calibration nonlinearity using simultaneous nadir overpass (SNO) matchups to minimize this effect for each scene radiance, and 2) finding a best-fit empirical relationship between the correction term of the end-level gridded brightness temperature and warm target temperature and then removing the best fit from the unadjusted time series. The former corrects the warm target effect before the diurnal drift adjustment and provides more accurate, warm target effect–minimized, level-1c scene radiances for reanalysis applications. The latter corrects the warm target effect at the end-level merging step, which depend on the diurnal drift correction that occurred at a previous step. Although minimized, the first method still leaves small residual warm target–related errors due to imperfect calibrations. This study demonstrates that when the diurnal drift effect is negligible, a combination of the two methods completely removes warm target effect and produces an invariant trend that is independent of the level-1c calibration in the SNO framework. The conclusion is directly applicable to the MSU channel-2 oceanic midtropospheric temperature (T2) and global channel-3 upper-tropospheric temperature (T3) and channel-4 lower-stratospheric temperature (T4), which satisfy the condition of negligible diurnal drift effect. On the basis of these results, version 1.2 of the National Environmental Satellite, Data, and Information Service (NESDIS)–Center for Satellite Applications and Research (STAR) multisatellite MSU time series was constructed, including all T2, T3, and T4 products. In addition, a diurnal drift correction based on the Remote Sensing Systems diurnal anomalies was applied to the T2 product, which produces consistent climate trends between land and ocean. The global long-term climate trends for T2 and T4 derived from the STAR V1.2 dataset are, respectively, 0.18 ± 0.05 and −0.39 ± 0.36 K decade−1 during 1979–2006; the T3 trend is 0.11 ± 0.08 K decade−1 for 1981–2006.
Rain Attenuation of Radar Echoes Considering Finite-Range Resolution and Using Drop Size Distributions
Authors: Peters Gerhard , Fischer Bernd , Clemens Marco 
Published: January 2010

Abstract
The classical rain attenuation correction scheme of Hitschfeld and Bordan (HIBO) and the newer iterative approach by Hildebrand (HL) are reconsidered. Although the motivation for the HL algorithm was an extension into ranges, where HIBO tends to be unstable, it is shown here that the contrary is the case. The finite-range resolution causes an intrinsic instability of HL already at moderate attenuation, where HIBO would still deliver stable results. Therefore, the authors concentrate the further analysis on HIBO, and confirm that the usual implementation of HIBO does not account correctly for finite-range resolution. They suggest a modified scheme that produces exact retrievals in the ideal case of perfect measurements.
For vertically pointing Doppler radars a new element is explored in the attenuation correction—namely, calculating rain attenuation κ and rainfall R from Doppler spectra via the raindrop size distributions (RSDs). Although this spectral scheme (SIBO) avoids the uncertainty of Z–R and Z–κ relations, the superiority of this approach is not a priori obvious because of its sensitivity to vertical wind. Therefore, radar rain rates, based on a Z–R relation and on RSDs, respectively, are compared with in situ measurements. The results indicate better agreement for RSD-based retrievals. Because κ is closely correlated with R, the authors assert the advantage of RSD-based retrievals of κ.
The application of HIBO and SIBO to real data shows that the uncertainty of standard Z–R relations is the main source of deviation between the two versions. In addition, the comparison of profiles suggests that the parameters of Z–R relations aloft can deviate considerably from near-surface values. Although artifacts cannot be excluded with certainty, there is some evidence that this observation actually reflects microphysical processes.
Numerical Simulations of Island Effects on Airflow and Weather during the Summer over the Island of Oahu
Authors: Van Nguyen Hiep , Chen Yi-Leng , Fujioka Francis 
Published: January 2010

Abstract
The high-resolution (1.5 km) nonhydrostatic fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) and an advanced land surface model (LSM) are used to study the island-induced airflow and weather for the island of Oahu, Hawaii, under summer trade wind conditions.
Despite Oahu’s relatively small area (1536 km2), there are considerable spatial variations in horizontal distribution of thermodynamic fields related to terrain, airflow, rain, cloud, and ground cover. The largest diurnal variations in temperature and moisture occur in the lee sides of mountains, especially along the western leeside coast. The island-scale surface airflow is also significantly affected by terrain and land surface forcing. The downslope winds above the leeside slopes of both the Ko’olau and Waianae Mountains are simulated with significant diurnal variations with the strongest downslope winds just before sunrise.
The timing of diurnal rainfall maxima over the Ko’olau Mountains is closely related to vertical motions. The early morning rainfall maximum on the windward side is caused by anomalous rising motion due to significant flow deceleration when the land surface is the coolest. The evening rainfall maximum after sunset is related to anomalous orographic lifting due to stronger winds aloft. In the early afternoon, winds aloft are relatively weak with a relatively high level of free convection (LFC) because of vertical mixing. As a result, the rainfall over the Ko’olau Mountains exhibits an afternoon minimum. The westerly reversed flow off the western leeside coast in the afternoon is mainly thermally driven and related to land surface heating superimposed by latent heat release of persistent orographic precipitation over the Ko’olau Mountains. Rainfall along the western leeside slopes has a late afternoon maximum due to the development of the onshore/upslope flow.
Non-Hookean Elastic Behavior and Crystallite Orientation in Carbon Fibers
Authors: Djordjević Isidor M. , Sekulić Danioela R. , Mitrić Midrog N. , Stevanović Momčilo M. 
Published: January 2010

Four different PAN-based carbon fibers (high strength, high modulus, and two enhanced strain fibers) were investigated in the standard single filament tensile tests. Nonlinear response was observed in all tested carbon fibers, but the nonlinearity in these fibers was not of the same extent. The tangential fiber modulus values for successive strain intervals (from zero up to failure strain) were fitted by linear as well as the second-order polynomial regression method. The coefficients of linear and square regression as well as the mean square deviation of experimental points from the points on a fitted curve were equal in all tested groups of fibers. The fitted square regression curve has a theoretical foundation, but the empirical expression is obtained by linear regression of modulus—strain data in carbon fibers. However, since the obtained linear relations include the coefficient γ, which can be a measure of elastic nonlinearity, deduced γ coefficient values were correlated to the parameters of carbon fiber crystallite structure as well as crystallites orientation.
Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates
Authors: Blakesley Robert W , Hansen Nancy F , Gupta Jyoti , McDowell Jennifer C , Maskeri Baishali , Barnabas Beatrice B , Brooks Shelise Y , Coleman Holly , Haghighi Payam , Ho Shi-Ling , Schandler Karen , Stantripop Sirintorn , Vogt Jennifer L , Thomas Pamela J ,   NISC Comparative Sequencing Program, Bouffard Gerard G , Green Eric D 
Published: January 2010

Abstract

Background
The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage.

Results
To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain.

Conclusion
Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.
High-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation
Authors: Azorsa David O , Robeson RiLee H , Frost Danielle , hoovet Bessie Meec , Brautigam Gillian R , Dickey Chad , Beaudry Christian , Basu Gargi D , Holz David R , Hernandez Joseph A , Bisanz Kristen M , Gwinn Leslie , Grover Andrew , Rogers Joseph , Reiman Eric M , Hutton Michael , Stephan Dietrich A , Mousses Spyro , Dunckley Travis 
Published: January 2010

Abstract

Background
Neurofibrillary tangles (NFT), a cardinal neuropathological feature of Alzheimer's disease (AD) that is highly correlated with synaptic loss and dementia severity, appear to be partly attributable to increased phosphorylation of the microtubule stabilizing protein tau at certain AD-related residues. Identifying the kinases involved in the pathologic phosphorylation of tau may provide targets at which to aim new AD-modifying treatments.

Results
We report results from a screen of 572 kinases in the human genome for effects on tau hyperphosphorylation using a loss of function, high-throughput RNAi approach. We confirm effects of three kinases from this screen, the eukaryotic translation initiation factor 2 α kinase 2 (EIF2AK2), the dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and the A-kinase anchor protein 13 (AKAP13) on tau phosphorylation at the 12E8 epitope (serine 262/serine 356). We provide evidence that EIF2AK2 effects may result from effects on tau protein expression, whereas DYRK1A and AKAP13 are likely more specifically involved in tau phosphorylation pathways.

Conclusions
These findings identify novel kinases that phosphorylate tau protein and provide a valuable reference data set describing the kinases involved in phosphorylating tau at an AD-relevant epitope.
Characterization of a variant vlhA gene of Mycoplasma synoviae, strain WVU 1853, with a highly divergent haemagglutinin region
Authors: Béjaoui Khiari Awatef , Guériri Ibtissem , Ben Mohammed Radhia , Ben Abdelmoumen Mardassi Boutheina 
Published: January 2010

Abstract

Background
In Mycoplasma synoviae, type strain WVU 1853, a single member of the haemaglutinin vlhA gene family has been previously shown to be expressed. Variants of vlhA are expressed from the same unique vlhA promoter by recruiting pseudogene sequences via site-specific recombination events, thus generating antigenic variability. Using a bacterial stock of M. synoviae WVU 1853 that had been colony purified thrice and maintained in our laboratory at low passage level, we previously identified a vlhA gene-related partial coding sequence, referred to as MS2/28.1. The E. coli-expressed product of this partial coding sequence was found to be immunodominant, suggesting that it might be expressed.

Results
Reverse transcription-PCR amplification (RT-PCR), using a sense primer located at the 5'-end region of the expected vlhA transcript and a reverse primer located at the 3' end of MS2/28.1 coding sequence, yielded a consistent amplification product showing that MS2/28.1 was indeed transcribed. Nucleotide sequence analysis of the RT-PCR product identified an 1815-nucleotide full-length open reading frame (ORF), immediately preceded by a nucleotide sequence identical to that previously reported for expressed vlhA genes. PCR amplifications using genomic DNA isolated from single colonies further confirmed that the full-length ORF of MS2/28.1 was located downstream of the unique vlhA promoter sequence. The deduced 604-amino acid (aa) sequence showed a perfect sequence identity to the previously reported vlhA expressed genes along the first 224 residues, then highly diverged with only 37.6% aa identity. Despite the fact that this M. synoviae clone expressed a highly divergent and considerably shorter C-terminal haemagglutinin product, it was found to be expressed at the surface of the bacterium and was able to haemagglutinate chicken erythrocytes. Importantly, the E. coli-expressed C-terminal highly divergent 60 residues of MS2/28.1 proved haemagglutination competent.

Conclusions
In contrast to the previously characterized vlhA expressed variants, MS2/28.1 displayed a highly divergent sequence, while still able to haemagglutinate erythrocytes. Overall, the data provide an indication as to which extent the M. synoviae
vlhA gene could vary its antigenic repertoire.