bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential Vorticity (PV) Thinking in Operations: The Utility of Nonconservation
Authors: Brennan Michael J. , Lackmann Gary M. , Mahoney Kelly M. 
Published: March 2008

AbstractThe use of the potential vorticity (PV) framework by operational forecasters is advocated through case examples that demonstrate its utility for interpreting and evaluating numerical weather prediction (NWP) model output for weather systems characterized by strong latent heat release (LHR). The interpretation of the dynamical influence of LHR is straightforward in the PV framework; LHR can lead to the generation of lower-tropospheric cyclonic PV anomalies. These anomalies can be related to meteorological phenomena including extratropical cyclones and low-level jets (LLJs), which can impact lower-tropospheric moisture transport.The nonconservation of PV in the presence of LHR results in a modification of the PV distribution that can be identified in NWP model output and evaluated through a comparison with observations and high-frequency gridded analyses. This methodology, along with the application of PV-based interpretation, can help forecasters identify aspects of NWP model solutions that are driven by LHR; such features are often characterized by increased uncertainty due to difficulties in model representation of precipitation amount and latent heating distributions, particularly for convective systems.Misrepresentation of the intensity and/or distribution of LHR in NWP model forecasts can generate errors that propagate through the model solution with time, potentially degrading the representation of cyclones and LLJs in the model forecast. The PV framework provides human forecasters with a means to evaluate NWP model forecasts in a way that facilitates recognition of when and how value may be added by modifying NWP guidance. This utility is demonstrated in case examples of coastal extratropical cyclogenesis and LLJ enhancement. Information is provided regarding tools developed for applying PV-based techniques in an operational setting.
A Statistical Comparison of the Properties of Flash Flooding and Nonflooding Precipitation Events in Portions of New York and Pennsylvania
Authors: Jessup Stephen M. , DeGaetano Arthur T. 
Published: March 2008

Abstract
Flash floods reported for the forecast area of the National Weather Service Forecast Office at Binghamton, New York (BGM), are compared with similar significant precipitation and flash flood watch events not corresponding to flash flood reports. These event types are characterized by measures of surface hydrological conditions, surface and upper-air variables, thermodynamic properties, and proxies for synoptic-scale features. Flash flood and nonflood events are compared quantitatively via discriminant analysis and cross validation, and qualitatively via scatterplots and composite soundings. Results are presented in the context of a flash flood checklist used at BGM prior to this study. Flash floods and nonfloods are found to differ most significantly in antecedent soil moisture. The wind direction at 850 hPa shows differences between flood and nonflood events, with flooding more common for an easterly to southeasterly direction and nonflooding more common for a northwesterly direction. Southwesterly wind direction is characteristic of both types. In general, nonflooding significant precipitation events are more commonly associated with a better-defined ridge axis of relatively high 850-hPa equivalent potential temperature and larger convective available potential energy as compared to the flash flood events. Several parameters included on the BGM flash flood checklist, though effective at distinguishing significant precipitation events and flash floods from random events, were found to be unable to separate flash floods from nonflooding significant rain events.
Hydrometeorological Accuracy Enhancement via Postprocessing of Numerical Weather Forecasts in Complex Terrain
Authors: McCollor Doug , Stull Roland 
Published: March 2008

Abstract
Statistical postprocessing techniques such as model output statistics are used by national weather centers to improve the skill of numerical forecasts. However, many of these techniques require an extensive database to develop, maintain, and update the postprocessed forecasts. This paper explores alternative postprocessing techniques for temperature and precipitation based on weighted-average and recursive formulations of forecast–observation paired data that do not require extensive database management, yet provide distinct error reduction over direct model output.
For maximum and minimum daily temperatures, seven different postprocessing methods were tested based on direct model output error for forecast days 1–8. The methods were tested on a 1-yr series of daily temperature values averaged over 19 stations in complex terrain in southwestern British Columbia, Canada. For daily quantitative precipitation forecasts, three different postprocessing methods were tested over a 6-month wet season period.
The different postprocessing methods were compared using several verification metrics, including mean error (for temperature), degree of mass balance (for precipitation), mean absolute error, and threshold error. All of the postprocessing methods improved forecast skill over direct model output. The postprocessing methods for temperature forecasts require a much shorter training period (14 days) than precipitation forecasts (40 days) to accomplish error reduction over direct model output forecasts. The postprocessing methods that weight recent error estimates most heavily perform better in the short term (days 1–4) while methods that weight recent and earlier error estimates more evenly show improving relative performance in the midterm (days 5–8).
For temperature forecasts, Kalman filtering produced slightly better verification scores than the other methods. For precipitation forecasts, a 40-day moving-average weighting function and the best easy systematic estimator method produced the best degree of mass balance results, while a seasonally averaged method produced the lowest mean absolute errors and lowest threshold errors. The methods described in this paper require minimal database management or computer resources to update forecasts, and are especially viable for hydrometeorological applications that require calibrated daily temperature and precipitation forecasts.
Objective Identification of Annular Hurricanes
Authors: Knaff John A. , Cram Thomas A. , Schumacher Andrea B. , Kossin James P. , DeMaria Mark 
Published: March 2008

Abstract
Annular hurricanes are a subset of intense tropical cyclones that have been shown in previous work to be significantly stronger, to maintain their peak intensities longer, and to weaken more slowly than average tropical cyclones. Because of these characteristics, they represent a significant forecasting challenge. This paper updates the list of annular hurricanes to encompass the years 1995–2006 in both the North Atlantic and eastern–central North Pacific tropical cyclone basins. Because annular hurricanes have a unique appearance in infrared satellite imagery, and form in a specific set of environmental conditions, an objective real-time method of identifying these hurricanes is developed. However, since the occurrence of annular hurricanes is rare (∼4% of all hurricanes), a special algorithm to detect annular hurricanes is developed that employs two steps to identify the candidates: 1) prescreening the data and 2) applying a linear discriminant analysis. This algorithm is trained using a dependent dataset (1995–2003) that includes 11 annular hurricanes. The resulting algorithm is then independently tested using datasets from the years 2004–06, which contained an additional three annular hurricanes. Results indicate that the algorithm is able to discriminate annular hurricanes from tropical cyclones with intensities greater than 84 kt (43.2 m s−1). The probability of detection or hit rate produced by this scheme is shown to be ∼96% with a false alarm rate of ∼6%, based on 1363 six-hour time periods with a tropical cyclone with an intensity greater than 84 kt (1995–2006).
A Cloud and Precipitation Feature Database from Nine Years of TRMM Observations
Authors: Liu Chuntao , Zipser Edward J. , Cecil Daniel J. , Nesbitt Stephen W. , Sherwood Steven 
Published: March 2008

Abstract
An event-based method of analyzing the measurements from multiple satellite sensors is presented by using observations of the Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR), Microwave Imager (TMI), Visible and Infrared Scanner (VIRS), and Lightning Imaging System (LIS). First, the observations from PR, VIRS, TMI, and LIS are temporally and spatially collocated. Then the cloud and precipitation features are defined by grouping contiguous pixels using various criteria, including surface rain, cold infrared, or microwave brightness temperature. The characteristics of measurements from different sensors inside these features are summarized. Then, climatological descriptions of many properties of the identified features are generated. This analysis method condenses the original information of pixel-level measurements into the properties of events, which can greatly increase the efficiency of searching and sorting the observed historical events. Using the TRMM cloud and precipitation feature database, the regional variations of rainfall contribution by features with different size, intensity, and PR reflectivity vertical structure are shown. Above the freezing level, land storms tend to have larger 20-dBZ area and reach higher altitude than is the case for oceanic storms, especially those land storms over central Africa. Horizontal size and the maximum reflectivity of oceanic storms decrease with altitude. For land storms, these intensity measures increase with altitude between 2 km and the freezing level and decrease more slowly with altitude above the freezing level than for ocean storms.
Prognostic Factors and Treatment Outcome in Mesenteric Vein Thrombosis
Authors: Hedayati Nasim , Riha Gordon M. , Kougias Panagiotis , Huynh Tam T. , Cheng Charlie , Bechara Carlos , Bismuth Jean , Dardik Alan , Lin Peter H. 
Published: March 2008

Background Mesenteric vein thrombosis (MVT) can result in intestinal ischemia and is associated with high morbidity and mortality due in part to its frequent delay in diagnosis. The purpose of this study was to evaluate clinical presentation, diagnostic evaluation, and treatment outcome of MVT. Methods Hospital records and clinical data of all patients treated for MVT were reviewed during a recent 14-year period. Clinical outcome and factors affecting survival were analyzed. Results A total of 68 patients were included in the study. Abdominal exploration was performed in 23 patients (34%), and second-look operation was necessary in 18 patients (26%). Three patients (4%) underwent unsuccessful operative mesenteric vein thrombectomy, whereas percutaneous transhepatic mesenteric thrombectomy was performed successfully in 3 patients (4%). The 30-day mortality rate was 20%. Forty-six of the 54 survivors were treated with long-term oral anticoagulation therapy. Actuarial survival at 2, 4, 6, and 10 years was 68%, 57%, 43%, and 22%, respectively. Risk factor analysis showed malignancy ( P < .002), age >60 years ( P < .005), cirrhosis ( P < .02), symptom duration ( P < .005), and bowel resection ( P < .03) were associated with mortality. Logistic regression analysis showed age >60 years (odds ratio [OR], 3.64; P = .03), malignancy (OR, 3.88; P = .02), and prolonged symptom duration (OR, 5.62; P = .01) were independent predictors of mortality. Conclusions MVT is associated with significant mortality. Prompt diagnostic evaluation with computed tomography may reduce potential treatment delay. Underlying malignancy, advanced age, and prolonged symptom duration are predictive of poor outcome.
No Gender Influences on Clinical Outcomes or Durability of Repair Following Carotid Angioplasty With Stenting and Carotid Endarterectomy
Authors: Park Brian , Aiello Francesco , Dahn Michael S. , Menzoian James O. , Mavanur Arun 
Published: March 2008

Introduction To determine if gender influences clinical outcomes and durability of repair after carotid angioplasty with stenting (CAS) or carotid endartercetomy (CEA), an analysis of patient records was performed. Methods This study included 89 CAS patients (47 men and 42 women) and 93 CEA patients (53 men and 40 women). Patients underwent duplex scans 6, 12, 24 months postprocedure. The outcomes of periprocedural mortality, major adverse events, strokes, and myocardial infarctions were assessed. Incidence of critical restenosis and recurrence of symptoms was also assessed. Results No significant differences were noted between men and women who had undergone either CAS or CEA ( P > .05) for clinical outcomes and durability of repair. No differences for periprocedural mortality, major adverse events, critical restenosis, recurrent neurologic symptoms, and adverse event free survival were found. Conclusions These results do not indicate substantial gender influences on clinical outcomes or durability of repair following CAS and CEA.
Multiple myeloma
Authors: Kyle Robert A. , Rajkumar S. Vincent 
Published: March 2008

AbstractMultiple myeloma is a clonal plasma cell malignancy that accounts for slightly more than 10% of all hematologic cancers. In this paper, we present a historically focused review of the disease, from the description of the first case in 1844 to the present. The evolution of drug therapy and stem-cell transplantation for the treatment of myeloma, as well as the development of new agents, is discussed. We also provide an update on current concepts of diagnosis and therapy, with an emphasis on how treatments have emerged from a historical perspective after certain important discoveries and the results of experimental studies.
Conditional clustering of temporal expression profiles
Authors: Wang Ling , Montano Monty , Rarick Matt , Sebastiani Paola 
Published: March 2008

Abstract

Background
Many microarray experiments produce temporal profiles in different biological conditions but common cluster techniques are not able to analyze the data conditional on the biological conditions.

Results
This article presents a novel technique to cluster data from time course microarray experiments performed across several experimental conditions. Our algorithm uses polynomial models to describe the gene expression patterns over time, a full Bayesian approach with proper conjugate priors to make the algorithm invariant to linear transformations, and an iterative procedure to identify genes that have a common temporal expression profile across two or more experimental conditions, and genes that have a unique temporal profile in a specific condition.

Conclusion
We use simulated data to evaluate the effectiveness of this new algorithm in finding the correct number of clusters and in identifying genes with common and unique profiles. We also use the algorithm to characterize the response of human T cells to stimulations of antigen-receptor signaling gene expression temporal profiles measured in six different biological conditions and we identify common and unique genes. These studies suggest that the methodology proposed here is useful in identifying and distinguishing uniquely stimulated genes from commonly stimulated genes in response to variable stimuli. Software for using this clustering method is available from the project home page.
Insertion-deletion polymorphisms (indels) as genetic markers in natural populations
Authors: Väli Ülo , Brandström Mikael , Johansson Malin , Ellegren Hans 
Published: March 2008

Abstract

Background
We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations.

Results
Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n = 7) and wolves (n = 18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci were highly correlated.

Conclusion
With an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations.
Can subtle changes in gene expression be consistently detected with different microarray platforms?
Authors: Pedotti Paola , 't Hoen Peter AC , Vreugdenhil Erno , Schenk Geert J , Vossen Rolf HAM , Ariyurek Yavuz , de Hollander Mattias , Kuiper Rowan , van Ommen Gertjan JB , den Dunnen Johan T , Boer Judith M , de Menezes Renée X 
Published: March 2008

AbstractBackgroundThe comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle.ResultsGene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms.ConclusionThe different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression.
Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis
Authors: Eichner Christiane , Frost Petter , Dysvik Bjarte , Jonassen Inge , Kristiansen Bjørn , Nilsen Frank 
Published: March 2008

Abstract

Background

Lepeophtheirus salmonis is an ectoparasitic copepod feeding on skin, mucus and blood from salmonid hosts. Initial analysis of EST sequences from pre adult and adult stages of L. salmonis revealed a large proportion of novel transcripts. In order to link unknown transcripts to biological functions we have combined EST sequencing and microarray analysis to characterize female salmon louse transcriptomes during post molting maturation and egg production.

Results
EST sequence analysis shows that 43% of the ESTs have no significant hits in GenBank. Sequenced ESTs assembled into 556 contigs and 1614 singletons and whenever homologous genes were identified no clear correlation with homologous genes from any specific animal group was evident. Sequence comparison of 27 L. salmonis proteins with homologous proteins in humans, zebrafish, insects and crustaceans revealed an almost identical sequence identity with all species.
Microarray analysis of maturing female adult salmon lice revealed two major transcription patterns; up-regulation during the final molting followed by down regulation and female specific up regulation during post molting growth and egg production. For a third minor group of ESTs transcription decreased during molting from pre-adult II to immature adults. Genes regulated during molting typically gave hits with cuticula proteins whilst transcripts up regulated during post molting growth were female specific, including two vitellogenins.

Conclusion
The copepod L.salmonis contains high a level of novel genes. Among analyzed L.salmonis proteins, sequence identities with homologous proteins in crustaceans are no higher than to homologous proteins in humans. Three distinct processes, molting, post molting growth and egg production correlate with transcriptional regulation of three groups of transcripts; two including genes related to growth, one including genes related to egg production. The function of the regulated transcripts is discussed in relation to post molting morphological changes in adult female salmon louse. There is clear evidence that transcription of the major yolk proteins is not induced before some of the post molting growth of abdomen and the genital segment has occurred. A hallmark for the observed growth is transcription of many putative cuticula proteins prior to the size increase.