bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of Australian Precipitation by Meridional Gradients in East Indian Ocean Sea Surface Temperature
Authors: Ummenhofer Caroline C. , Sen Gupta Alexander , Taschetto Andréa S. , England Matthew H. 
Published: June 2009

Abstract
This study explores the impact of meridional sea surface temperature (SST) gradients across the eastern Indian Ocean on interannual variations in Australian precipitation. Atmospheric general circulation model (AGCM) experiments are conducted in which the sign and magnitude of eastern Indian Ocean SST gradients are perturbed. This results in significant rainfall changes for western and southeastern Australia. A reduction (increase) in the meridional SST gradient drives a corresponding response in the atmospheric thickness gradients and results in anomalous dry (wet) conditions over Australia. During simulated wet years, this seems to be due to westerly anomalies in the thermal wind over Australia and anomalous onshore moisture advection, with a suggestion that the opposite occurs during dry conditions. Thus, an asymmetry is seen in the magnitude of the forced circulation and precipitation response between the dry and wet simulations. To assess the relative contribution of the SST anomalies making up the meridional gradient, the SST pattern is decomposed into its constituent “poles,” that is, the eastern tropical pole off the northwest shelf of Australia versus the southern pole in the central subtropical Indian Ocean. Overall, the simulated Australian rainfall response is linear with regard to the sign and magnitude of the eastern Indian Ocean SST gradient. The tropical eastern pole has a larger impact on the atmospheric circulation and Australian precipitation changes relative to the southern subtropical pole. However, there is clear evidence of the importance of the southern pole in enhancing the Australian rainfall response, when occurring in conjunction with but of opposite sign to the eastern tropical pole. The observed relationship between the meridional SST gradient in the eastern Indian Ocean and rainfall over western and southeastern Australia is also analyzed for the period 1970–2005. The observed relationship is found to be consistent with the AGCM results.
Spatiotemporal Variability of Precipitation, Modeled Soil Moisture, and Vegetation Greenness in North America within the Recent Observational Record
Authors: Castro Christopher L. , Beltrán-Przekurat Adriana B. , Pielke Roger A. 
Published: June 2009

Abstract
Dominant spatiotemporal patterns of precipitation, modeled soil moisture, and vegetation are determined in North America within the recent observational record (late twentieth century onward). These data are from a gridded U.S.–Mexico precipitation product, retrospective long-term integrations of two land surface models, and satellite-derived vegetation greenness. The analysis procedure uses three statistical techniques. First, all the variables are normalized according to the standardized precipitation index procedure. Second, dominant patterns of spatiotemporal variability are determined using multitaper method–singular value decomposition for interannual and longer time scales. The dominant spatiotemporal patterns of precipitation generally conform to known and distinct Pacific SST forcing in the cool and warm seasons. Two specific time scales in precipitation at 9 and 6–7 yr correspond to significant variability in soil moisture and vegetation, respectively. The 9-yr signal is related to precipitation in late fall to early winter, whereas the 6–7-yr signal is related to earlysummer precipitation. Canonical correlation analysis is finally used to confirm that strong covariability between land surface variables and precipitation exists at these specific times of the year. Both signals are strongest in the central and western United States and are consistent with prior global modeling and paleoclimate studies that have investigated drought in North America.
Ebb-Tide Dynamics and Spreading of a Large River Plume*
Authors: McCabe Ryan M. , MacCready Parker , Hickey Barbara M. 
Published: June 2009

Abstract
Momentum balances in the near-field region of a large, tidally pulsed river plume are examined. The authors concentrate on a single ebb tide of the Columbia River plume, using the Regional Ocean Modeling System (ROMS) configured to hindcast flow conditions on the Washington and Oregon shelves and in the Columbia River estuary. During ebb, plume-interior streamwise balances are largely between advection, pressure gradient, and frictional forces. Stream-normal balances in this region reduce to centrifugal, cross-stream pressure gradient, and Coriolis terms (i.e., the “gradient wind” balance commonly assumed in river plume bulge investigations). Temporal derivatives are most important at the plume front and as the ebb progresses. Winds were light and contributed little to the force balance. Midebb stress and vertical salt flux were largest at a midplume depth, where stratification and vertical shear were also high, consistent with shear-induced mixing. Internal stress slows the spreading plume considerably. A kinematic description of the spreading process relates lateral spreading to the momentum dynamics and illustrates that plume spreading is largely a competition between the cross-stream pressure gradient and Coriolis forces. However, the very near-field dome of buoyant water is instrumental in setting initial flow pathways.
Ensemble Kalman Filter Configurations and Their Performance with the Logistic Map
Authors: Mitchell Herschel L. , Houtekamer P. L. 
Published: June 2009

Abstract
This paper examines ensemble Kalman filter (EnKF) performance for a number of different EnKF configurations. The study is performed in a perfect-model context using the logistic map as forecast model. The focus is on EnKF performance when the ensemble is small. In accordance with theory, it is found that those configurations that maintain an appropriate ensemble spread are indeed those with the smallest ensemble mean error in a data assimilation cycle. Thus, the deficient ensemble spread produced by the single-ensemble EnKF results in increased ensemble mean error for this configuration. This problem with the conceptually simplest EnKF motivates an examination of a variety of other configurations. These include the configuration with a pair of ensembles and several configurations with overlapping ensembles, such as the four-subensemble configuration (used operationally at the Canadian Meteorological Centre) and the configuration in which observations are assimilated into each member using a gain computed from all of the other members. Also examined is a configuration that uses the jackknife estimator to obtain an estimate of the gain and an estimate of its uncertainty. Using these estimates, a different perturbed gain is then produced for each ensemble member. In general, it is found that these latter configurations outperform both the single-ensemble EnKF and the configuration with a pair of ensembles. In addition to these “stochastic” filters, the performance of a “deterministic” filter (which does not use perturbed observations) is also examined.
Analysis of Intense Poleward Water Vapor Transports into High Latitudes of Western North America
Authors: Roberge Alain , Gyakum John R. , Atallah Eyad H. 
Published: June 2009

Abstract
Significant cool season precipitation along the western coast of North America is often associated with intense water vapor transport (IWVT) from the Pacific Ocean during favorable synoptic-scale flow regimes. These relatively narrow and intense regions of water vapor transport can originate in either the tropical or subtropical oceans, and sometimes have been referred to as Pineapple Express events in previous literature when originating near Hawaii. However, the focus of this paper will be on diagnosing the synoptic-scale signatures of all significant water vapor transport events associated with poleward moisture transport impacting the western coast of Canada, regardless of the exact points of origin of the associated atmospheric river. A trajectory analysis is used to partition the events as a means of creating coherent and meaningful synoptic-scale composites. The results indicate that these IWVT events can be clustered by the general area of origin of the majority of the saturated parcels impacting British Columbia and the Yukon Territories. IWVT events associated with more zonal trajectories are characterized by a strong and mature Aleutian low, whereas IWVT events associated with more meridional trajectories are often characterized by an anticyclone situated along the California or Oregon coastline, and a relatively mature poleward-traveling cyclone, commonly originating in the central North Pacific.
Epidemiology of Severe Injuries among United States High School Athletes
Authors: Darrow Cory J. , Collins Christy L. , Yard Ellen E. , Comstock R. Dawn 
Published: June 2009

Background Over 7 million students participate in high school athletics annually. Despite numerous health benefits, high school athletes are at risk for injury. Hypothesis Severe injury rates and patterns differ by gender and type of exposure. Study Design Descriptive epidemiology study. Methods Sports-related injury data were collected during the 2005-2007 academic years from 100 nationally representative United States high schools via RIO (Reporting Information Online). Severe injury was defined as any injury that resulted in the loss of more than 21 days of sports participation. Results Participating certified athletic trainers (ATCs) reported 1378 severe injuries during 3 550 141 athlete-exposures (0.39 severe injuries per 1000 athletic exposures). Football had the highest severe injury rate (0.69), followed by wrestling (0.52), girls’ basketball (0.34), and girls’ soccer (0.33). The rate in all boys’ sports (0.45) was higher than all girls’ sports (0.26) (rate ratio [RR], 1.74; 95% confidence interval [CI], 1.54-1.98; P < .001). However, among directly comparable sports (soccer, basketball, and baseball/softball), girls sustained a higher severe injury rate (0.29) than boys (0.23) (RR, 1.28; 95% CI, 1.08-1.52; P = .006). More specifically, girls’ basketball had a higher rate (0.34) than boys’ basketball (0.24) (RR, 1.43; 95% CI, 1.10-1.86; P = .009). Differences between boys’ and girls’ soccer and baseball/softball were not statistically significant. The severe injury rate was greater in competition (0.79) than practice (0.24) (RR, 3.30; 95% CI, 2.97-3.67; P < .001). Nationally, high school athletes sustained an estimated 446 715 severe injuries from 2005-2007. The most commonly injured body sites were the knee (29.0%), ankle (12.3%), and shoulder (10.9%). The most common diagnoses were fractures (36.0%), complete ligament sprains (15.3%), and incomplete ligament sprains (14.3%). Of severe sports injuries, 0.3% resulted in medical disqualification for the athletes’ career, and an additional 56.8% resulted in medical disqualification for the entire season. One in 4 (28.3%) severe injuries required surgery, with over half (53.9%) being knee surgeries. Conclusion Severe injury rates and patterns varied by sport, gender, and type of exposure. Because severe injuries negatively affect athletes’ health and often place an increased burden on the health care system, future research should focus on developing interventions to decrease the incidence and severity of sports-related injuries.
Arthroscopic Rotator Cuff Repair
Authors: Nho Shane J. , Adler Ronald S. , Tomlinson Daniel P. , Allen Answorth A. , Cordasco Frank A. , Warren Russell F. , Altchek David W. , MacGillivray John D. 
Published: June 2009

Background Recent studies have demonstrated predictable healing after arthroscopic rotator cuff repair at a single time point, but few studies have evaluated tendon healing over time. Hypothesis Rotator cuff tears that are intact on ultrasound at 1 time point will remain intact, and clinical results will improve regardless of healing status. Study Design Cohort study; Level of evidence, 3. Methods The Arthroscopic Rotator Cuff Registry was established to determine the effectiveness of arthroscopic rotator cuff repair with clinical outcomes using the American Shoulder and Elbow Surgeons score and ultrasound at 1 and 2 years, postoperatively. Patients were assigned to 1 of 3 groups based on ultrasound appearance: group 1, rotator cuff tendon intact at 1 and 2 years (n = 63); group 2, rotator cuff tendon defect at 1 and 2 years (n = 23); group 3, rotator cuff tendon defect at 1 year but no defect at 2 years (n = 7). Results The ultrasound appearance was consistent at 1 and 2 years for 86 of the 93 patients (92.5%). The patients in group 1 had a significantly lower mean age (57.8 ± 9.8 years) than the patients of group 2 (63.6 ± 8.6 years; P = .04). Group 2 had a significantly greater rotator cuff tear size (4.36 ± 1.6 cm) than group 1 (2.84 ± 1.1 cm; P = .00025). Each group had a significant improvement in American Shoulder and Elbow Surgeons scores from baseline to 2-year follow-up. Conclusion All intact rotator cuff tendons at 1 year remained intact at 2 years. A small group of patients with postoperative imaging did not appear healed by ultrasound at 1 year but did so at 2 years. Patients demonstrated improvement in American Shoulder and Elbow Surgeons shoulder scores, range of motion, and strength, regardless of tendon healing status on ultrasound.
Control of allergic rhinitis and asthma test – a formal approach to the development of a measuring tool
Authors: Nogueira-Silva Luis , Martins Sonia V , Cruz-Correia Ricardo , Azevedo Luis F , Morais-Almeida Mario , Bugalho-Almeida António , Vaz Marianela , Costa-Pereira Altamiro , Fonseca Joao A 
Published: June 2009

Abstract

Background
The concurrent management of allergic rhinitis and asthma (ARA) has been recommended by Allergic Rhinitis and its Impact on Asthma (ARIA) guidelines. However, a tool capable of assessing simultaneously the control of upper and lower airways diseases is lacking.

Aim
To describe the studies conducted to design the control of ARA test (CARAT) questionnaire.

Methods
We performed a literature review to generate a list of potentially important items for the assessment of control of ARA. A formal consensus development process, that used an innovative web-based application, was designed – 111 experts in ARA and 60 patients participated. At the final consensus meeting, 25 primary and secondary care physicians formulated the questions and response options. A qualitative feasibility study (n = 31 patients) was conducted to evaluate the comprehensibility of the questionnaire while testing two different designs.

Results
Thirty-four potentially important items were identified. All the steps of the consensus process were completed in 2.5 months. The opinions of experts and patients lead to the formulation of 17 questions. At the feasibility study the instructions and wording problems were corrected and a semi-tabular format was chosen.

Conclusion
A tool to measure the control of allergic rhinitis and asthma was developed using a comprehensive set of methodological steps ensuring the design quality and the face and content validity. Additional validation studies to assess the psychometric properties of the questionnaire have started.
Nuclear accumulation and activation of p53 in embryonic stem cells after DNA damage
Authors: Solozobova Valeriya , Rolletschek Alexandra , Blattner Christine 
Published: June 2009

Abstract

Background
P53 is a key tumor suppressor protein. In response to DNA damage, p53 accumulates to high levels in differentiated cells and activates target genes that initiate cell cycle arrest and apoptosis. Since stem cells provide the proliferative cell pool within organisms, an efficient DNA damage response is crucial.

Results
In proliferating embryonic stem cells, p53 is localized predominantly in the cytoplasm. DNA damage-induced nuclear accumulation of p53 in embryonic stem cells activates transcription of the target genes mdm2, p21, puma and noxa. We observed bi-phasic kinetics for nuclear accumulation of p53 after ionizing radiation. During the first wave of nuclear accumulation, p53 levels were increased and the p53 target genes mdm2, p21 and puma were transcribed. Transcription of noxa correlated with the second wave of nuclear accumulation. Transcriptional activation of p53 target genes resulted in an increased amount of proteins with the exception of p21. While p21 transcripts were efficiently translated in 3T3 cells, we failed to see an increase in p21 protein levels after IR in embryonal stem cells.

Conclusion
In embryonic stem cells where (anti-proliferative) p53 activity is not necessary, or even unfavorable, p53 is retained in the cytoplasm and prevented from activating its target genes. However, if its activity is beneficial or required, p53 is allowed to accumulate in the nucleus and activates its target genes, even in embryonic stem cells.
The DEAD-box protein MEL-46 is required in the germ line of the nematode Caenorhabditis elegans
Authors: Minasaki Ryuji , Puoti Alessandro , Streit Adrian 
Published: June 2009

AbstractBackgroundIn the hermaphrodite of the nematodeCaenorhabditis elegans, the first germ cells differentiate as sperm. Later the germ line switches to the production of oocytes. This process requires the activity of a genetic regulatory network that includes among others thefem,fogandmoggenes. The function of some of these genes is germline specific while others also act in somatic tissues. DEAD box proteins have been shown to be involved in the control of gene expression at different steps such as transcription and pre-mRNA processing.ResultsWe show that theCaenorhabditis elegansgenemel-46(maternaleffectlethal) encodes a DEAD box protein that is related to the mammalian DDX20/Gemin3/DP103 genes.mel-46is expressed throughout development and mutations inmel-46display defects at multiple developmental stages. Here we focus on the role ofmel-46in the hermaphrodite germ line.mel-46(yt5)mutant hermaphrodites are partially penetrant sterile and fully penetrant maternal effect lethal. The germ line of mutants shows variable defects in oogenesis. Further,mel-46(yt5)suppresses the complete feminization caused by mutations infog-2andfem-3, two genes that are at the top and the center, respectively, of the genetic germline sex determining cascade, but notfog-1that is at the bottom of this cascade.ConclusionTheC. elegansgenemel-46encodes a DEAD box protein that is required maternally for early embryogenesis and zygotically for postembryonic development. In the germ line, it is required for proper oogenesis. Although it interacts genetically with genes of the germline sex determination machinery its primary function appears to be in oocyte differentiation rather than sex determination.
Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays
Authors: Bernardo Amy N , Bradbury Peter J , Ma Hongxiang , Hu Shengwa , Bowden Robert L , Buckler Edward S , Bai Guihua 
Published: June 2009

AbstractBackgroundWheat (Triticum aestivumL.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (~17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome.ResultsSix wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data.ConclusionThe Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.
Improved long-term expression from helper virus-free HSV-1 vectors packaged using combinations of mutated HSV-1 proteins that include the UL13 protein kinase and specific components of the VP16 transcriptional complex
Authors: Liu Meng , Wang Xiaodan , Geller Alfred I 
Published: June 2009

Abstract

Background
Herpes Simplex Virus (HSV-1) gene expression is thought to shut off recombinant gene expression from HSV-1 vectors; however, in a helper virus-free HSV-1 vector system, a number of promoters support only short-term expression. These results raise the paradox that recombinant gene expression remains short-term even in the absence of almost all (~99%) of the HSV-1 genome, HSV-1 genes, and HSV-1 gene expression. To resolve this paradox, we hypothesized that specific proteins in the HSV-1 virus particle shut off recombinant gene expression. In two earlier studies, we examined the effects on recombinant gene expression of packaging vectors using specific mutated HSV-1 proteins. We found that vectors packaged using mutated UL13 (a protein kinase), or VP16, or UL46 and/or UL47 (components of the VP16 transcriptional complex) supported improved long-term expression, and vectors packaged using mutated UL46 and/or UL47 also supported improved gene transfer (numbers of cells at 4 days). These results suggested the hypothesis that specific proteins in the HSV-1 particle act by multiple pathways to reduce recombinant gene expression. To test this hypothesis, we examined combinations of mutated proteins that included both UL13 and specific components of the VP16 transcriptional complex.

Results
A HSV-1 vector containing a neuronal-specific promoter was packaged using specific combinations of mutated proteins, and the resulting vector stocks were tested in the rat striatum. For supporting long-term expression, the preferred combination of mutated HSV-1 proteins was mutated UL13, UL46, and UL47. Vectors packaged using this combination of mutated proteins supported a higher efficiency of gene transfer and high levels expression for 3 months, the longest time examined.

Conclusion
Vector particles containing this combination of mutated HSV-1 proteins improve recombinant gene expression. Implications of these results for strategies to further improve long-term expression are discussed. Moreover, long-term expression will benefit specific gene therapy applications.