bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Thinness of the Ocean in S–Θ–p Space and the Implications for Mean Diapycnal Advection
Authors: McDougall Trevor J. , Jackett David R. 
Published: June 2007

Abstract
It is shown that the ocean’s hydrography occupies little volume in the three-dimensional space defined by salinity–temperature–pressure (S–Θ–p), and the implications of this observation for the mean vertical transport across density surfaces are discussed. Although ocean data have frequently been analyzed in the two-dimensional temperature–salinity (S–Θ) diagram where casts of hydrographic data are often locally tight in S–Θ space, the relatively empty nature of the World Ocean in the three-dimensional S–Θ–p space seems not to have received attention. The World Ocean’s data lie close to a single surface in this three-dimensional space, and it is shown that this explains the known smallness of the ambiguity in defining neutral surfaces. The ill-defined nature of neutral surfaces means that lateral motion along neutral trajectories leads to mean vertical advection through density surfaces, even in the absence of small-scale mixing processes. The situation in which the ocean’s hydrography occupies a large volume in S–Θ–p space is also considered, and it is suggested that the consequent vertical diapycnal advection would be sufficiently large that the ocean would not be steady.
Use of Information by National Weather Service Forecasters and Emergency Managers during CALJET and PACJET-2001
Authors: Morss Rebecca E. , Ralph F. Martin 
Published: June 2007

Abstract
Winter storms making landfall in western North America can generate heavy precipitation and other significant weather, leading to floods, landslides, and other hazards that cause significant damage and loss of life. To help alleviate these negative impacts, the California Land-falling Jets (CALJET) and Pacific Land-falling Jets (PACJET) experiments took extra meteorological observations in the coastal region to investigate key research questions and aid operational West Coast 0–48-h weather forecasting. This article presents results from a study of how information provided by CALJET and PACJET was used by National Weather Service (NWS) forecasters and forecast users. The primary study methodology was analysis of qualitative data collected from observations of forecasters and from interviews with NWS personnel, CALJET–PACJET researchers, and forecast users. The article begins by documenting and discussing the many types of information that NWS forecasters combine to generate forecasts. Within this context, the article describes how forecasters used CALJET–PACJET observations to fill in key observational gaps. It then discusses researcher–forecaster interactions and examines how weather forecast information is used in emergency management decision making. The results elucidate the important role that forecasters play in integrating meteorological information and translating forecasts for users. More generally, the article illustrates how CALJET and PACJET benefited forecasts and society in real time, and it can inform future efforts to improve human-generated weather forecasts and future studies of the use and value of meteorological information.
Precipitation Forecast Verification of the Indian Summer Monsoon with Intercomparison of Three Diverse Regions
Authors: Mandal Vikramaditya , De Utpal K. , Basu Biplab K. 
Published: June 2007

AbstractThe Indian summer monsoon precipitation forecast, as well as its verification, are always of great interest because of their socioeconomic impact on the Indian subcontinent. The present work highlights the verification of quantitative precipitation forecasts of the Global Spectral Model, running at the National Center for Medium Range Weather Forecasting (NCMRWF), Noida, India. Studies like pattern correlation and anomaly correlation over all of India confirm that the model is applicable over the subcontinent. Some comparative studies are done for three diverse regions like West Bengal, Andhra Pradesh, and Rajasthan. Verification studies include both measure-oriented methods like root-mean-square error (RMSE) and Pearson’s correlation coefficient and distribution-oriented methods like bias score, false alarm ratio, probability of detection, and true skill score. The distribution-oriented verification (yes–no) is done for the daily threshold precipitation of 0.254, 2.54, 6.4, 12.8, 19.2, 32.0, 44.8, and 64.0 mm. Two years of data from 1997 and 1999 for Andhra Pradesh and Rajasthan and 5 yr of data from 1997 to 2001 are used for West Bengal. The distribution of model output during a severe rainfall situation over West Bengal is also examined to understand the usefulness of the model forecasts during those events. It can be concluded that the model is most efficient in predicting precipitation in the 2.54–12.8-mm range but the efficiency decreases rapidly for higher thresholds. Performance of the model during active and break phases of the monsoon is examined and it is found to be reasonably good. On the whole, it can be concluded that the performance of the NCMRWF model is reasonably good for day-1 forecasts and the weekly rainfall forecast is quite good for all forecast lead times.
Uncertainty and Inference for Verification Measures
Authors: Jolliffe Ian T. 
Published: June 2007

AbstractWhen a forecast is assessed, a single value for a verification measure is often quoted. This is of limited use, as it needs to be complemented by some idea of the uncertainty associated with the value. If this uncertainty can be quantified, it is then possible to make statistical inferences based on the value observed. There are two main types of inference: confidence intervals can be constructed for an underlying “population” value of the measure, or hypotheses can be tested regarding the underlying value. This paper will review the main ideas of confidence intervals and hypothesis tests, together with the less well known “prediction intervals,” concentrating on aspects that are often poorly understood. Comparisons will be made between different methods of constructing confidence intervals—exact, asymptotic, bootstrap, and Bayesian—and the difference between prediction intervals and confidence intervals will be explained. For hypothesis testing, multiple testing will be briefly discussed, together with connections between hypothesis testing, prediction intervals, and confidence intervals.
Ceiling and Visibility Forecasts via Neural Networks
Authors: Marzban Caren , Leyton Stephen , Colman Brad 
Published: June 2007

Abstract
Statistical postprocessing of numerical model output can improve forecast quality, especially when model output is combined with surface observations. In this article, the development of nonlinear postprocessors for the prediction of ceiling and visibility is discussed. The forecast period is approximately 2001–05, involving data from hourly surface observations, and from the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model. The statistical model for mapping these data to ceiling and visibility is a neural network. A total of 39 such neural networks are developed for each of 39 terminal aerodrome forecast stations in the northwest United States. These postprocessors are compared with a number of alternatives, including logistic regression, and model output statistics (MOS) derived from the Aviation Model/Global Forecast System. It is found that the performance of the neural networks is generally superior to logistic regression and MOS. Depending on the comparison, different measures of performance are examined, including the Heidke skill statistic, cross-entropy, relative operating characteristic curves, discrimination plots, and attributes diagrams. The extent of the improvement brought about by the neural network depends on the measure of performance, and the specific station.
An Assessment of Marine Surface Winds from the Australian Bureau of Meteorology Numerical Weather Prediction Systems
Authors: Schulz Eric W. , Kepert Jeffrey D. , Greenslade Diana J. M. 
Published: June 2007

AbstractA method for routinely verifying numerical weather prediction surface marine winds with satellite scatterometer winds is introduced. The marine surface winds from the Australian Bureau of Meteorology’s operational global and regional numerical weather prediction systems are evaluated. The model marine surface layer is described. Marine surface winds from the global and limited-area models are compared with observations, both in situ (anemometer) and remote (scatterometer). A 2-yr verification shows that wind speeds from the regional model are typically underestimated by approximately 5%, with a greater bias in the meridional direction than the zonal direction. The global model also underestimates the surface winds by around 5%–10%. A case study of a significant marine storm shows that where larger errors occur, they are due to an underestimation of the storm intensity, rather than to biases in the boundary layer parameterizations.
Influence of Initial Conditions on the WRF–ARW Model QPF Response to Physical Parameterization Changes
Authors: Jankov Isidora , Gallus William A. , Segal Moti , Koch Steven E. 
Published: June 2007

Abstract
To assist in optimizing a mixed-physics ensemble for warm season mesoscale convective system rainfall forecasting, the impact of various physical schemes as well as their interactions on rainfall when different initializations were used has been investigated. For this purpose, high-resolution Weather Research and Forecasting (WRF) model simulations of eight International H2O Project events were performed. For each case, three different treatments of convection, three different microphysical schemes, and two different planetary boundary layer (PBL) schemes were used. All cases were initialized with both Local Analyses and Prediction System (LAPS) “hot” start analyses and 40-km Eta Model analyses. To evaluate the impacts of the variation of two different physical schemes and their interaction on the simulated rainfall under the two different initial conditions, the factor separation method was used. The sensitivity to the use of various physical schemes and their interactions was found to be dependent on the initialization dataset. Runs initialized with Eta analyses appeared to be influenced by the use of the Betts–Miller–Janjić scheme in that model’s assimilation system, which tended to reduce the WRF’s sensitivity to changes in the microphysical scheme compared with that present when LAPS analyses were used for initialization. In addition, differences in initialized thermodynamics resulted in changes in sensitivity to PBL and convective schemes. With both initialization datasets, the greatest sensitivity to the simulated rain rate was due to changes in the convective scheme. However, for rain volume, substantial sensitivity was present due to changes in both the physical parameterizations and the initial datasets.
Moving towards evidence-based healthcare for musculoskeletal injuries: featuring the work of the Cochrane Bone, Joint and Muscle Trauma Group
Authors: Handoll Helen Hanora Georgina , Gillespie William John , Gillespie Lesley Diane , Madhok Rajan 
Published: June 2007

Due to their high incidence and associated morbidity and mortality, musculoskeletal injuries place an enormous burden on society. For example, in the 2004 to 2005 period 62,000 people with hip fracture accounted for 2.9% of the total number of hospital bed days in England. Between 12% and 37% of people with hip fracture die in the first year. Of the survivors, most are less mobile and many lose their independence. Soft-tissue joint injuries during sports and exercise-related activities in young adults constitute another important group. Of these, ankle sprain is the most common single injury and it predisposes people to further recurrence. Members of the Cochrane Bone, Joint and Muscle Trauma Group prepare systematic reviews (Cochrane Reviews) of the evidence for interventions used in the prevention and management of musculoskeletal injuries. These reviews serve to facilitate evidence-based decision making by policy makers, healthcare professionals and consumers, and to guide future research. This article focuses on two major groups of injuries: osteoporotic fractures and soft-tissue joint injuries, and discusses some of the fundamental issues and questions associated with the prevention and management of these. Drawing insights from relevant Cochrane Reviews, this article examines the different approaches used for preventing, and the role of surgery and immobilisation for treating, these injuries. Brief illustrations of the inherent complexity of rehabilitation are also provided. This article also gives examples of how these reviews are helping to inform healthcare choices and practice, and guide research in this area.
Intracellular mediators of transforming growth factor β superfamily signaling localize to endosomes in chicken embryo and mouse lenses in vivo
Authors: Rajagopal Ramya , Ishii Shunsuke , Beebe David C 
Published: June 2007

Abstract

Background
Endocytosis is a key regulator of growth factor signaling pathways. Recent studies showed that the localization to endosomes of intracellular mediators of growth factor signaling may be required for their function. Although there is substantial evidence linking endocytosis and growth factor signaling in cultured cells, there has been little study of the endosomal localization of signaling components in intact tissues or organs.

Results
Proteins that are downstream of the transforming growth factor-β superfamily signaling pathway were found on endosomes in chicken embryo and postnatal mouse lenses, which depend on signaling by members of the TGFβ superfamily for their normal development. Phosphorylated Smad1 (pSmad1), pSmad2, Smad4, Smad7, the transcriptional repressors c-Ski and TGIF and the adapter molecules Smad anchor for receptor activation (SARA) and C184M, localized to EEA-1- and Rab5-positive vesicles in chicken embryo and/or postnatal mouse lenses. pSmad1 and pSmad2 also localized to Rab7-positive late endosomes. Smad7 was found associated with endosomes, but not caveolae. Bmpr1a conditional knock-out lenses showed decreased nuclear and endosomal localization of pSmad1. Many of the effectors in this pathway were distributed differently in vivo from their reported distribution in cultured cells.

Conclusion
Based on the findings reported here and data from other signaling systems, we suggest that the localization of activated intracellular mediators of the transforming growth factor-β superfamily to endosomes is important for the regulation of growth factor signaling.
Protein Kinase D regulates several aspects of development in Drosophila melanogaster
Authors: Maier Dieter , Nagel Anja C , Gloc Helena , Hausser Angelika , Kugler Sabrina J , Wech Irmgard , Preiss Anette 
Published: June 2007

Abstract

Background
Protein Kinase D (PKD) is an effector of diacylglycerol-regulated signaling pathways. Three isoforms are known in mammals that have been linked to diverse cellular functions including regulation of cell proliferation, differentiation, motility and secretory transport from the trans-Golgi network to the plasma membrane. In Drosophila, there is a single PKD orthologue, whose broad expression implicates a more general role in development.

Results
We have employed tissue specific overexpression of various PKD variants as well as tissue specific RNAi, in order to investigate the function of the PKD gene in Drosophila. Apart from a wild type (WT), a kinase dead (kd) and constitutively active (SE) Drosophila PKD variant, we also analyzed two human isoforms hPKD2 and hPKD3 for their capacity to substitute PKD activity in the fly. Overexpression of either WT or kd-PKD variants affected primarily wing vein development. However, overexpression of SE-PKD and PKD RNAi was deleterious. We observed tissue loss, wing defects and degeneration of the retina. The latter phenotype conforms to a role of PKD in the regulation of cytoskeletal dynamics. Strongest phenotypes were larval to pupal lethality. RNAi induced phenotypes could be rescued by a concurrent overexpression of Drosophila wild type PKD or either human isoform hPKD2 and hPKD3.

Conclusion
Our data confirm the hypothesis that Drosophila PKD is a multifunctional kinase involved in diverse processes such as regulation of the cytoskeleton, cell proliferation and death as well as differentiation of various fly tissues.
The identity, distribution, and impacts of non-native apple snails in the continental United States
Authors: Rawlings Timothy A , Hayes Kenneth A , Cowie Robert H , Collins Timothy M 
Published: June 2007

AbstractBackgroundSince the mid 1990s populations of non-native apple snails (Ampullariidae) have been discovered with increasing frequency in the continental United States. Given the dramatic effects that introduced apple snails have had on both natural habitats and agricultural areas in Southeast Asia, their introduction to the mainland U.S. is cause for concern. We combine phylogenetic analyses of mtDNA sequences with examination of introduced populations and museum collections to clarify the identities, introduced distributions, geographical origins, and introduction histories of apple snails.ResultsBased on sampling to date, we conclude there are five species of non-native apple snails in the continental U.S. Most significantly, we recognize three species within what has been called the channeled apple snail:Pomacea canaliculata(California and Arizona),Pomacea insularum, (Florida, Texas, and Georgia) andPomacea haustrum(Florida). The first established populations ofP. haustrumwere discovered in the late 1970s in Palm Beach County Florida, and have not spread appreciably in 30 years. In contrast, populations ofP. insularumwere established in Texas by 1989, in Florida by the mid to late 1990s, and in Georgia by 2005, and this species continues to spread rapidly. Most introducedP. insularumhaplotypes are a close match to haplotypes from the Río Uruguay near Buenos Aires, indicating cold tolerance, with the potential to spread from Florida, Georgia, and Texas through Louisiana, Alabama, Mississippi, and South Carolina.Pomacea canaliculatapopulations were first discovered in California in 1997. Haplotypes of introducedP. canaliculatamatch native-range haplotypes from near Buenos Aires, Argentina, also indicating cold tolerance and the potential to establish farther north.ConclusionThe term "channeled apple snail" is descriptive of a morphology found in many apple snail species. It does not identify a single species or a monophyletic group. Clarifying species identifications permits a more accurate assessment of introduction histories and distributions, and provides a very different picture of the tempo and pattern of invasions than was inferred when the three species with channeled sutures were considered one. Matching introduced and native-range haplotypes suggests the potential for range expansion, with implications for native aquatic ecosystems and species, agriculture, and human health.
Sequence analysis of coding and 3' and 5' flanking regions of the epithelial sodium channel α, β, and γ genes in Dahl S versus R rats
Authors: Shehata Marlene F , Leenen Frans HH , Tesson Frédérique 
Published: June 2007

Abstract

Background
To test whether epithelial sodium channel (ENaC) genes' variants contribute to salt sensitive hypertension in Dahl rats, we screened ENaC α, β, and γ genes entire coding regions, intron-exon junctions, and the 3' and 5' flanking regions in Dahl S, R and Wistar rats using both Denaturing High Performance Liquid Chromatography (DHPLC) and sequencing.

Results
Our analysis revealed no sequence variability in the three genes encoding ENaC in Dahl S versus R rats. One homozygous sequence variation predicted to result in a D75E substitution was identified in Dahl and Wistar rat ENaC α compared to Brown Norway. Six and two previously reported polymorphic sites in Brown Norway sequences were lost in Dahl and Wistar rats, respectively. In the 5' flanking regions, we found a deletion of 5GCTs in Dahl and Wistar rat ENaC α gene, five new polymorphic sites in ENaC β and γ genes, one homozygous sequence variation in Dahl and Wistar rat ENaC γ gene, as well as one Dahl rat specific homozygous insertion of -1118CCCCCA in ENaC γ gene. This insertion created additional binding sites for Sp1 and Oct-1. Five and three Brown Norway polymorphic sites were lost in Dahl and Wistar rats, respectively. No sequence variability in ENaC 3' flanking regions was identified in Dahl compared to Brown Norway rats.

Conclusion
The first comprehensive sequence analysis of ENaC genes did not reveal any differences between Dahl S and R rats that were isogenic in the regions screened. Mutations in ENaC genes intronic sequence or in ENaC-regulatory genes might possibly account for increased ENaC activity in Dahl S versus R rats.
Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells
Authors: Sokolov Mykyta V , Neumann Ronald D , Panyutin Igor G 
Published: June 2007

Abstract

Background
This study assesses the whole-genome gene expression changes in a panel of primary human cell lines in response to DNA damage mediated by decay of DNA-incorporated radioiodinated thymidine analog 5-[125I]iodo-2'-deoxyuridine (125I-IUdR). Three normal human cell lines of different origin, namely, gingival fibroblasts AG09319, fetal skin fibroblasts GM05388 and neonatal foreskin epidermal keratinocytes (NHFK) were used in this study. DNA molecules were radiolabeled by incubation of cells in culture in a medium supplemented with either 3.7 kBq/ml or 18.5 kBq/ml of 125I-IUdR for 24 h followed by incubation in IUdR-free medium for additional 24 hours. Each experiment was carried out in quadruplicate. 125I-IUdR uptake was monitored by measuring DNA-associated radioactivity. The whole-genome gene expression changes were evaluated using Agilent Human Whole Genome oligo microarrays containing 44,290 elements representing all known and predicted human genes. DNA microarray dataset was independently partially validated with quantitative real-time PCR (RT-PCR).

Results
AG09319 gingival cells in culture responded to 125I-IUdR treatment by changing the expression level of 335 genes in total, whereas under the same conditions GM05388 and NHFK cells differentially expressed 49 genes and 27 genes, respectively. However, for GM05388 cells the number of differentially expressed genes increases with the rise of 125I-IUdR concentrations in cell culture media. The key up-regulated biological processes in a chosen panel of cell lines concern the regulation of protein kinase activities and/or cell death. Genes repressed in response to 125I-IUdR treatment are involved in cytokinesis, M phase of the cell cycle, chromosome architecture and organization, DNA metabolism, DNA packaging, DNA repair and response to DNA damage. Despite the disparate nature of the gene patterns elicited by 125I-induced DNA damage among the different cell lines, the differentially expressed transcripts reveal strikingly non-random chromosomal distribution in all the cell lines we used.

Conclusion
Our data suggest that DNA-targeted ionizing radiation produced by 125I-IUdR results in changes in expression of only a limited subset of genes in primary human cells. The responsive genes are distributed non-randomly among the chromosomes; and a significant fraction of them is p53-dependent in the transcriptional regulation.