bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpolation of Tidal Levels in the Coastal Zone for the Creation of a Hydrographic Datum
Authors: Turner J. F. , Iliffe J. C. , Ziebart M. K. , Wilson C. , Horsburgh K. J. 
Published: July 2009

Abstract
As part of the U.K. Hydrographic Office (UKHO)-sponsored Vertical Offshore Reference Frames (VORF) project, a high-resolution model of lowest astronomical tide (LAT) with respect to mean sea level has been developed for U.K.–Irish waters. In offshore areas the model relies on data from satellite altimetry, while in coastal areas data from a 3.5-km-resolution hydrodynamic tide-surge model and tide gauges have been included. To provide for a smooth surface and predict tidal levels in unobserved areas, the data have been merged and interpolated using the thin plate spline method, which has been appropriately tuned by an empirical prediction test whereby observed values at tide gauges were removed from the solution space and surrounding data used to predict its behavior. To allow for the complex coastal morphology, a sea distance function has been implemented within the data weighting, which is shown to significantly enhance the solution. The tuning process allows for independent validation giving a standard error of the resulting surface of 0.2 m for areas with no tidal observations.
Estimating Surface Divergence of Ocean Eddies Using Observed Trajectories from a Surface Drifting Buoy
Authors: Brassington Gary B. 
Published: July 2009

Abstract
A method is described that estimates the time evolution of surface divergence and other secondary circulation properties of an ocean eddy. The method is novel because it is applied to the observations of a single surface drifting buoy. Surface drifting buoys located on ocean eddies provide Lagrangian trajectories that orbit the local extremum in geopotential. At each instance, the position of the buoy lies on the boundary of a closed material surface over the eddy. Assuming, on an ocean eddy, that the material boundary points vary smoothly in time, a method is developed to estimate all points along this boundary. An ellipse is fitted to the approximated material boundary to provide a continuum of properties, including centroid, aspect ratio, orientation, and area. The time rate of change of these properties provides approximations to the eddy velocity, moment of inertia, secondary rotation, and surface divergence. Two surface drifting buoys deployed on an anticyclonic eddy in the East Australian Current are used to demonstrate the analysis method. The estimated surface divergence is compared and interpreted using the observed separation of the two drifting buoys and other independent observations.
A Method to Estimate Three-Dimensional Thermal Structure from Satellite Altimetry Data
Authors: Takano Akiko , Yamazaki Hidekatsu , Nagai Takeyoshi , Honda Osamu 
Published: July 2009

Abstract
A new empirical method to estimate mesoscale three-dimensional oceanic thermal structures from near-real-time satellite altimetry data is presented. The method uses a two-layer model with a novel set of empirical parameters for stratification. Empirical parameters, which are calculated from altimetry data and in situ temperature and salinity profiles obtained from globally distributed Argo floats, allowed for significant increases in the spatiotemporal mapping of mesoscale temperature distributions. The accuracy of the method was validated by comparing the estimated isothermal depths with in situ temperature data. Three case studies in different regions and seasons showed excellent agreement, with a strong linear correlation between the estimated and observed isothermal depths. The authors present the details of the method, discuss its limitations, and demonstrate the ecological relevance of the method for fisheries management by successfully predicting pelagic fish distributions.
Intercomparison of Spatial Forecast Verification Methods: Identifying Skillful Spatial Scales Using the Fractions Skill Score
Authors: Mittermaier Marion , Roberts Nigel 
Published: July 2009

Abstract
The fractions skill score (FSS) was one of the measures that formed part of the Intercomparison of Spatial Forecast Verification Methods project. The FSS was used to assess a common dataset that consisted of real and perturbed Weather Research and Forecasting (WRF) model precipitation forecasts, as well as geometric cases. These datasets are all based on the NCEP 240 grid, which translates to approximately 4-km resolution over the contiguous United States.
The geometric cases showed that the FSS can provide a truthful assessment of displacement errors and forecast skill. In addition, the FSS can be used to determine the scale at which an acceptable level of skill is reached and this usage is perhaps more helpful than interpreting the actual FSS value. This spatial-scale approach is becoming more popular for monitoring operational forecast performance.
The study also shows how the FSS responds to forecast bias. A more biased forecast always gives lower FSS values at large scales and usually at smaller scales. It is possible, however, for a more biased forecast to give a higher score at smaller scales, when additional rain overlaps the observed rain. However, given a sufficiently large sample of forecasts, a more biased forecast system will score lower. The use of percentile thresholds can remove the impacts of the bias.
When the proportion of the domain that is “wet” (the wet-area ratio) is small, subtle differences introduced through near-threshold misses can lead to large changes in FSS magnitude in individual cases (primarily because the bias is changed). Reliable statistics for small wet-area ratios require a larger sample of forecasts.
Care needs to be taken in the choice of verification domain. For high-resolution models, the domain should be large enough to encompass the length scale of the typical mesoscale forcing (e.g., upper-level troughs or squall lines). If the domain is too large, the wet-area ratios will always be small. If the domain is too small, fluctuations in the wet-area ratio can be large and larger spatial errors may be missed.
The FSS is a good measure of the spatial accuracy of precipitation forecasts. Different methods are needed to determine other patterns of behavior.
Can a chronic disease management pulmonary rehabilitation program for COPD reduce acute rural hospital utilization?
Authors: Rasekaba TM , Williams E , Hsu-Hage B 
Published: July 2009

Chronic obstructive pulmonary disease (COPD) imposes a costly burden on healthcare. Pulmonary rehabilitation (PR) is the best practice to better manage COPD to improve patient outcomes and reduce acute hospital care utilization. To evaluate the impact of a once-weekly, eight-week multidisciplinary PR program as an integral part of the COPD chronic disease management (CDM) Program at Kyabram District Health Services. The study compared two cohorts of COPD patients: CDM-PR Cohort (4–8 weeks) and Opt-out Cohort (0–3 weeks) between February 2006 and March 2007. The CDM-PR Program involved multidisciplinary patient education and group exercise training. Nonparametric statistical tests were used to compare acute hospital care utilization 12 months before and after the introduction of CDM-PR. The number of patients involved in the CDM-PR Cohort was 29 (n = 29), and that in the Opt-out Cohort was 24 ( n = 24). The CDM-PR Cohort showed significant reductions in cumulative acute hospital care utilization indicators (95% emergency department presentations, 95% inpatient admissions, 99% length of stay; effect sizes = 0.62–0.66, P < 0.001) 12 months after the introduction of the CDM Program; in contrast, changes in the cumulative indicators were statistically insignificant for the Opt-out Cohort (emergency department presentations decreased by 5%, inpatient admissions decreased by 12%, length of stay increased by 30%; effect size = 0.14–0.40, P > 0.05). Total costs associated with the hospital care utilization decreased from $130,000 to $7,500 for the CDM-PR Cohort and increased from $77,700 to $101,200 for the Opt-out Cohort. Participation in the CDM-PR for COPD patients can significantly reduce acute hospital care utilization and associated costs in a small rural health service.
Cor pulmonale
Authors: Weitzenblum E , Chaouat A 
Published: July 2009

The term “cor pulmonale” is still popular but there is presently no consensual definition and it seems more appropriate to define the condition by the presence of pulmonary hypertension (PH) resulting from diseases affecting the structure and/or the function of the lungs: PH results in right ventricular enlargement and may lead with time to right heart failure (RHF). Chronic obstructive pulmonary disease (COPD) is the first cause of cor pulmonale, far before idiopathic pulmonary fibrosis and obesity–hypoventilation syndrome. In chronic respiratory disease (CRD) PH is “pre-capillary,” due to an increase of pulmonary vascular resistance (PVR). The first cause of increased PVR is chronic long-standing alveolar hypoxia which induces pulmonary vascular remodeling. The main characteristic of PH in CRD and particularly in COPD is its mild to moderate degree, resting pulmonary artery mean pressure (PAP) in a stable state of the disease usually ranging between 20 and 35 mmHg. However, PH may worsen during exercise, sleep, and exacerbations of the disease. These acute increases in afterload can favor the development of RHF. A minority (<5%) of COPD patients exhibit severe or “disproportionate” PH (PAP >40 mmHg), the mechanism of which is not well understood. At present long-term oxygen therapy (LTOT) is the logical treatment of PH since alveolar hypoxia is considered to be the major determinant of the elevation of PAP and PVR. LTOT stabilizes or at least attenuates and sometimes reverses the progression of PH, but PAP seldom returns to normal. Vasodilators (prostacyclin, endothelin receptor antagonists, sildenafil, nitric oxide) could be considered in patients with severe PH but controlled studies in this field are presently lacking.
The importance of bone marrow examination in determining complete response to therapy in patients with multiple myeloma
Authors: Chee Cheng E. , Kumar Shaji , Larson Dirk R. , Kyle Robert A. , Dispenzieri Angela , Gertz Morie A. , Colby Colin L. , Rajkumar S. Vincent 
Published: July 2009

Abstract
The current definition of complete response in multiple myeloma includes a requirement for a bone marrow (BM) examination showing less than 5% plasma cells in addition to negative serum and urine immunofixation. There have been suggestions to eliminate the need for BM examinations when defining complete response. We evaluated 92 patients with multiple myeloma who achieved negative immunofixation in the serum and urine after therapy and found that 14% had BM plasma cells more than or equal to 5%. Adding a requirement for normalization of the serum-free light chain ratio to negative immunofixation studies did not negate the need for BM studies; 10% with a normal serum-free light chain ratio had BM plasma cells more than or equal to 5%. We also found that, on achieving immunofixation-negative status, patients with less than 5% plasma cells in the BM had improved overall survival compared with those with 5% or more BM plasma cells (6.2 years vs 2.3 years, respectively; P = .01).
Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia
Authors: Russell Lisa J. , Capasso Melania , Vater Inga , Akasaka Takashi , Bernard Olivier A. , Calasanz Maria Jose , Chandrasekaran Thiruppavaii , Chapiro Elise , Gesk Stephan , Griffiths Mike , Guttery David S. , Haferlach Claudia , Harder Lana , Heidenreich Olaf , Irving Julie , Kearney Lyndal , Nguyen-Khac Florence , Machado Lee , Minto Lynne , Majid Aneela , Moorman Anthony V. , Morrison Heather , Rand Vikki , Strefford Jonathan C. , Schwab Claire , Tönnies Holger , Dyer Martin J. S. , Siebert Reiner , Harrison Christine J. 
Published: July 2009

AbstractWe report 2 novel, cryptic chromosomal abnormalities in precursor B-cell acute lymphoblastic leukemia (BCP-ALL): a translocation, either t(X;14)(p22;q32) or t(Y;14)(p11;q32), in 33 patients and an interstitial deletion, either del(X)(p22.33p22.33) or del(Y)(p11.32p11.32), in 64 patients, involving the pseudoautosomal region (PAR1) of the sex chromosomes. The incidence of these abnormalities was 5% in childhood ALL (0.8% with the translocation, 4.2% with the deletion). Patients with the translocation were older (median age, 16 years), whereas the patients with the deletion were younger (median age, 4 years). The 2 abnormalities result in deregulated expression of the cytokine receptor, cytokine receptor-like factor 2, CRLF2 (also known as thymic stromal-derived lymphopoietin receptor, TSLPR). Overexpression of CRLF2 was associated with activation of the JAK-STAT pathway in cell lines and transduced primary B-cell progenitors, sustaining their proliferation and indicating a causal role of CRLF2 overexpression in lymphoid transformation. In Down syndrome (DS) ALL and 2 non-DS BCP-ALL cell lines, CRLF2 deregulation was associated with mutations of the JAK2 pseudokinase domain, suggesting oncogenic cooperation as well as highlighting a link between non-DS ALL and JAK2 mutations.
Mer receptor tyrosine kinase is a novel therapeutic target in pediatric B-cell acute lymphoblastic leukemia
Authors: Linger Rachel M. A. , DeRyckere Deborah , Brandão Luis , Sawczyn Kelly K. , Jacobsen Kristen M. , Liang Xiayuan , Keating Amy K. , Graham Douglas K. 
Published: July 2009

Abstract
Acute lymphoblastic leukemia (ALL) is currently treated with an intense regimen of chemotherapy yielding cure rates near 80%. However, additional changes using available drugs are unlikely to provide significant improvement in survival. New therapies are warranted given the risk of severe therapy-associated toxicities including infertility, organ damage, and secondary malignancy. Here, we report ectopic expression of the receptor tyrosine kinase Mer in pediatric B-cell ALL. Inhibition of Mer prevented Erk 1/2 activation, increased the sensitivity of B-ALL cells to cytotoxic agents in vitro by promoting apoptosis, and delayed disease onset in a mouse model of leukemia. In addition, we discovered cross-talk between the Mer and mammalian target of rapamycin (mTOR) signaling pathways. Our results identify Mer as a novel therapeutic target in ALL and suggest that inhibitors of Mer will interact synergistically with currently used therapies. This strategy may allow for dose reduction resulting in decreased toxicity and increased survival rates. Mer is aberrantly expressed in numerous other malignancies suggesting that this approach may have broad applications.
Allogeneic hematopoietic cell transplantation for chronic lymphocytic leukemia: ready for prime time?
Authors: Delgado Julio , Milligan Donald W. , Dreger Peter 
Published: July 2009

AbstractThe development of reduced intensity conditioning regimens has increased the number of patients diagnosed with chronic lymphocytic leukemia that are referred for allogeneic hematopoietic cell transplantation (allo-HCT). However, given the toxicity of allo-HCT, it should only be offered to eligible patients whose life expectancy is significantly reduced by the disease. Accordingly, the European Group of Blood and Marrow Transplantation has recently identified those patients in whom allo-HCT could be a reasonable therapeutic approach. In this review, we have evaluated the outcome of chronic lymphocytic leukemia patients undergoing allo-HCT, either after conventional or reduced intensity conditioning regimens, in the context of current nontransplantation strategies. We have also analyzed the most important predisposing factors that might interfere with the procedure as well as posttransplantation complications that are particularly common in these patients. Finally, we have addressed the most relevant factors when deciding what patients should be considered for allo-HCT and the timing of the procedure.
Eosinophil viability is increased by acidic pH in a cAMP- and GPR65-dependent manner
Authors: Kottyan Leah C. , Collier Ann R. , Cao Khanh H. , Niese Kathryn A. , Hedgebeth Megan , Radu Caius G. , Witte Owen N. , Khurana Hershey Gurjit K. , Rothenberg Marc E. , Zimmermann Nives 
Published: July 2009

AbstractThe microenvironment of the lung in asthma is acidic, yet the effect of acidity on inflammatory cells has not been well established. We now demonstrate that acidity inhibits eosinophil apoptosis and increases cellular viability in a dose-dependent manner between pH 7.5 and 6.0. Notably, acidity induced eosinophil cyclic adenosine 5′-monophosphate (cAMP) production and enhanced cellular viability in an adenylate cyclase–dependent manner. Furthermore, we identify G protein-coupled receptor 65 (GPR65) as the chief acid-sensing receptor expressed by eosinophils, as GPR65-deficient eosinophils were resistant to acid-induced eosinophil cAMP production and enhanced viability. Notably, GPR65−/− mice had attenuated airway eosinophilia and increased apoptosis in 2 distinct models of allergic airway disease. We conclude that eosinophil viability is increased in acidic microenvironments in a cAMP- and GPR65-dependent manner.
Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush
Authors: Templeton Justin P , Nassr Mohamed , Vazquez-Chona Felix , Freeman-Anderson Natalie E , Orr William E , Williams Robert W , Geisert Eldon E 
Published: July 2009

AbstractBackgroundRetinal ganglion cell (RGC) death is the final consequence of many blinding diseases, where there is considerable variation in the time course and severity of RGC loss. Indeed, this process appears to be influenced by a wide variety of genetic and environmental factors. In this study we explored the genetic basis for differences in ganglion cell death in two inbred strains of mice.ResultsWe found that RGCs are more susceptible to death following optic nerve crush in C57BL/6J mice (54% survival) than in DBA/2J mice (62% survival). Using the Illumina Mouse-6 microarray, we identified 1,580 genes with significant change in expression following optic nerve crush in these two strains of mice. Our analysis of the changes occurring after optic nerve crush demonstrated that the greatest amount of change (44% of the variance) was due to the injury itself. This included changes associated with ganglion cell death, reactive gliosis, and abortive regeneration. The second pattern of gene changes (23% of the variance) was primarily related to differences in gene expressions observed between the C57BL/6J and DBA/2J mouse strains. The remaining changes in gene expression represent interactions between the effects of optic nerve crush and the genetic background of the mouse. We extracted one genetic network from this dataset that appears to be related to tissue remodeling. One of the most intriguing sets of changes included members of the crystallin family of genes, which may represent a signature of pathways modulating the susceptibility of cells to death.ConclusionDifferential responses to optic nerve crush between two widely used strains of mice were used to define molecular networks associated with ganglion cell death and reactive gliosis. These results form the basis for our continuing interest in the modifiers of retinal injury.
Citrus auraptene suppresses cyclin D1 and significantly delays N-methyl nitrosourea induced mammary carcinogenesis in female Sprague-Dawley rats
Authors: Krishnan Prasad , Yan Karen J , Windler David , Tubbs Jesse , Grand Robert , Li Benjamin DL , Aldaz C Marcelo , McLarty Jerry , Kleiner-Hancock Heather E 
Published: July 2009

Abstract

Background
Breast cancer is a major problem in the United States leading to tens of thousands of deaths each year. Although citrus auraptene suppresses cancer in numerous rodent models, its role in breast cancer prevention previously has not been reported. Thus, our goal was to determine the anticarcinogenic effects of auraptene against breast cancer.

Methods
The effects of auraptene on cell proliferation of MCF-7 and MDA-MB-231 human breast carcinoma cells in culture was assessed by measuring metabolism of a substrate to a formazan dye. Dietary effects of auraptene on tumor incidence, multiplicity and latency were studied in the N-methyl nitrosourea (MNU) induced mammary carcinogenesis model in female Sprague Dawley rats. The concentration of auraptene in rat tissues was analyzed by reverse phase HPLC. Cyclin D1 expression in MCF-7 cells and rat tumors was measured by western blot.

Results
Auraptene (500 ppm) significantly delayed median time to tumor by 39 days compared to the MNU only group (p < 0.05, n = 24–26). Auraptene (10 μM) reduced Insulin like Growth Factor-1 (IGF-1, 10 ng/mL)-induced cyclin D1 expression by 40% in MCF-7 cells. In comparison, western blot analysis of rat mammary tumors (n = 10 per group) confirmed that auraptene (500 ppm) significantly reduced (p < 0.05) cyclin D1 expression by 49% compared to the MNU only group. Analysis of rat mammary tissue extract by HPLC with fluorescence detection indicated an average concentration (means ± S.E.) of 1.4 ± 0.5 μM and 1.8 ± 0.3 μM in the normal mammary glands of the auraptene 200 ppm and 500 ppm groups, respectively. The concentration (means ± S.E.) of auraptene in the mammary tumors of the auraptene 200 ppm group was 0.31 ± 0.98 μM.

Conclusion
Overall, these observations suggest that the predominant effect of auraptene was to delay the development of tumors possibly through the suppression of cyclin D1 expression. These results point to the potential chemopreventive effects of auraptene in mammary carcinogenesis.
Malignant transformation of oral potentially malignant disorders in males: a retrospective cohort study
Authors: Ho Pei-Shan , Chen Pai-Li , Warnakulasuriya Saman , Shieh Tien-Yu , Chen Yun-Kwan , Huang I-Yueh 
Published: July 2009

Abstract

Background
Oral squamous cell carcinoma could be preceded by clinically evident oral potentially malignant disorders (OPMDs). Transformation of OPMDs to cancer has been studied in several population groups. It is difficult to undertake comparisons across populations due to variations in the methods of computation of malignancy rates among different studies. The aim of our study was to estimate the rate of malignant transformation of OPMDs taking into account the duration of follow-up and to identify the significant factors indicative of malignant potential.

Methods
A total of 148 male patients with OPMDs were included. They were selected among all consecutive subjects registered at the maxillofacial clinic at a medical hospital in Kaohsiung, Taiwan. The mean follow up period was 37.8 months.

Results
The malignant transformation rate was highest in subjects diagnosed with oral epithelial dysplasia. In this group the transformation rate was 7.62 per 100 persons-year. The rate in the group with verrucous hyperplasia (VH) was 5.21 per 100 persons-year, and in those with hyperkeratosis or epithelial hyperplasia was 3.26 per 100 persons-year. The anatomical site of OPMDs was the only statistically significant variable associated with malignancy. The hazard rate ratio (HRR) was 2.41 times for tongue lesions when compared with buccal lesions.

Conclusion
The reported discrepancies of malignant transformation of OPMDs involve the follow-up time to cancer development and hence it is preferable to use a time-to-event estimation for comparisons. We found that malignant transformation of OPMDs involving the tongue was significantly higher than in other anatomical subsites after adjusting for the clinicopathological type or lifestyle factors at diagnosis.