bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil Initialization Strategy for Use in Limited-Area Weather Prediction Systems
Authors: Di Giuseppe Francesca , Cesari Davide , Bonafé Giovanni 
Published: February 2011

Abstract
Three diverse methods of initializing soil moisture and temperature in limited-area numerical weather prediction models are compared and assessed through the use of nonstandard surface observations to identify the approach that best combines ease of implementation, improvement in forecast skill, and realistic estimations of soil parameters. The first method initializes the limited-area model soil prognostic variables by a simple interpolation from a parent global model that is used to provide the lateral boundary conditions for the forecasts, thus ensuring that the limited-area model’s soil field cannot evolve far from the host model. The second method uses the soil properties generated by a previous limited-area model forecast, allowing the soil moisture to evolve over time to a new equilibrium consistent with the regional model’s hydrological cycle. The third method implements a new local soil moisture variational analysis system that uses screen-level temperature to adjust the soil water content, allowing the use of high-resolution station data that may be available to a regional meteorological service.
The methods are tested in a suite of short-term weather forecasts performed with the Consortium for Small Scale Modeling (COSMO) model over the period September–November 2008, using the ECMWF Integrated Forecast System (IFS) model to provide the lateral boundary conditions. Extensive comparisons to observations show that substantial improvements in forecast skills are achievable with improved soil temperature initialization while a smaller additional benefit in the prediction of surface fluxes is possible with the soil moisture analysis. The analysis suggests that keeping the model prognostic variables close to equilibrium with the soil state, especially for temperature, is more relevant than correcting the soil moisture initial values. In particular, if a local soil analysis system is not available, it seems preferable to adopt an “open loop” strategy rather than the interpolation from the host global model analysis. This appears to be especially true for the COSMO model in its current operational configuration since the soil–vegetation–atmosphere transfer (SVAT) scheme of the ECMWF global host model and that of COSMO are radically diverse.
Assessment of Assimilating ASCAT Surface Wind Retrievals in the NCEP Global Data Assimilation System
Authors: Bi Li , Jung James A. , Morgan Michael C. , Le Marshall John F. 
Published: February 2011

Abstract
A two-season Observing System Experiment (OSE) was used to quantify the impacts of assimilating the Advanced Scatterometer (ASCAT) surface winds product distributed by the European Organization for the Exploitation of Meteorological Satellites (EUMESAT) and the National Environmental Satellite, Data, and Information Service (NESDIS). The ASCAT wind retrievals were provided by the Royal Netherlands Meteorological Office (KNMI) and the 50-km resolution ASCAT products were assimilated. The impact of assimilating the ASCAT surface wind product in the National Centers for Environmental Prediction (NCEP) Global Data Assimilation/Global Forecast System (GDAS/GFS) was assessed by comparing the forecast results through 168 h for the months of August 2008 and January 2009. The NCEP GDAS/GFS was used, at a resolution of T382–64 layers, as the assimilation system and forecast model for these experiments.
A control simulation utilizing all the data types assimilated in the operational GDAS was compared to an experimental simulation that added the ASCAT surface winds. Quality control procedures required to assimilate the ASCAT surface winds are discussed. Anomaly correlations (ACs) of geopotential height forecasts as well as geographic distribution of AC of geopotential height forecasts at 1000 and 500 hPa were evaluated for the control and experiment during both seasons. The geographical distribution of forecast impact (FI) on the wind and temperature fields near the surface is also presented.
The results of this study show that assimilation of the surface wind retrievals from the ASCAT sensor improve the NCEP GFS wind and temperature forecasts. A positive FI, which suggests the error growth of the experiment is slower than the control, has been realized in the NCEP GDAS/GFS wind and temperature forecasts through 24 h. The ASCAT experiment AC scores show modest forecast improvements from days 4 through 7.
A Hybrid Background Error Covariance Model for Assimilating Glider Data into a Coastal Ocean Model
Authors: Yaremchuk Max , Nechaev Dmitri , Pan Chudong 
Published: February 2011

Abstract
A hybrid background error covariance (BEC) model for three-dimensional variational data assimilation of glider data into the Navy Coastal Ocean Model (NCOM) is introduced. Similar to existing atmospheric hybrid BEC models, the proposed model combines low-rank ensemble covariances with the heuristic Gaussian-shaped covariances to estimate forecast error statistics. The distinctive features of the proposed BEC model are the following: (i) formulation in terms of inverse error covariances, (ii) adaptive determination of the rank m of with information criterion based on the innovation error statistics, (iii) restriction of the heuristic covariance operator to the null space of , and (iv) definition of the BEC magnitudes through separate analyses of the innovation error statistics in the state space and the null space of .
The BEC model is validated by assimilation experiments with simulated and real data obtained during a glider survey of the Monterey Bay in August 2003. It is shown that the proposed hybrid scheme substantially improves the forecast skill of the heuristic covariance model.
Radiological Features of the Intraosseous Lipoma of the Sphenoid
Authors: Srubiski Aviva , Csillag Andrew , Timperley Daniel , Kalish Larry , Qiu Min Ru , Harvey Richard J. 
Published: February 2011

ObjectiveBenign intraosseous lesions of the skull base are often identified in the course of routine radiological investigation. Imaging features associated with suspected intraosseous lipoma (IOL) can mimic more aggressive pathology. The features of this poorly described entity in the skull base were analyzed to aid the otolaryngologist in differentiation from other pathology.Study DesignRetrospective analysis of computed tomography (CT) and magnetic resonance imaging (MRI) images over the period from March 2007 to March 2009.SettingRadiology service, tertiary hospital, Sydney, Australia.MethodsImages with diagnosis of incidental suspected IOL within the sphenoid were selected. Radiological features including trabecular pattern, secondary calcification, cortical bone thinning, and size and the presence of fat (defined as <−5 HU) were recorded.ResultsTen patients (5 male) were identified. Seventy percent had unilateral, single lesions occurring within the sphenoid bone. The mean size was 13.1 ± 5.6 mm (range, 4‐21 mm). Fat was demonstrated in all lesions. There were 3 cases of multiple lesions occurring within the sphenoid bone. In addition, 61.5% were associated with cortical bone thinning and 46.2% with secondary calcification within the lesion. Changes to normal trabecular bone occurred: 46.2% with a partial loss of and 53.8% with a complete absence of trabecular pattern. Histopathologic confirmation of IOL is presented.ConclusionIOL is believed to be a more common benign intraosseous lesion within the skull base than previously reported. Cortical bone thinning and other features normally suggestive of aggressive pathology commonly occur. Otolaryngologists should be aware of these common lesions to avoid unnecessary further investigation.
Evaluation of Second Look Procedures for Pediatric Cholesteatomas
Authors: McRackan Theodore R. , Abdellatif Walid M. , Wanna George B. , Rivas Alejandro , Gupta Nikita , Dietrich Mary S. , Haynes David S. 
Published: February 2011

ObjectiveThis study aims to identify factors that may help predict recurrence, the need for second‐look operations, and other outcomes in the pediatric population.Study DesignCase series with chart review.SettingTertiary medical center.Subjects and MethodsFive hundred and seventeen ears in 493 patients underwent primary acquired cholesteatoma resection over a 37‐year period. Demographic (age, sex, and other medical conditions), cholesteatoma laterality, presence of perforation or otorrhea on otoscopic exam, preoperative and most recent audiologic data, and detailed intraoperative data were collected.ResultsOverall, 47.2% of patients underwent second‐look operations, with 48.0% having recurrent cholesteatoma visualized with attic recurrence being the most common location. In total, 22.7% of all patients in this study had recurrent disease. Factors at initial operation associated with a statistically significant increased risk of recurrence included cholesteatoma in the sinus tympani (odds ratio = 2.09; 95% confidence interval, 1.36‐3.22) and incus destruction (1.65; 1.01‐2.71).ConclusionThe authors have successfully identified multiple factors at the time of initial operation that can have significant postoperative implications.
Nasal Skin Thickness Measured Using Computed Tomography and Its Effect on Tip Surgery Outcomes
Authors: Cho Gye Song , Kim Jeoung Hyun , Yeo Nam‐Kyung , Kim Soo Hyun , Jang Yong Ju 
Published: February 2011

ObjectiveSkin thickness can be a major factor affecting rhinoplasty outcomes. However, few studies have examined the impact of nasal skin thickness on rhinoplasty aesthetic results. The aim of this study is to determine the effect of nasal skin thickness on the tip surgery outcome objectively.Study DesignCase series with chart review.SettingAcademic tertiary care medical center.Subjects and MethodsThe study involved 77 patients who were evaluated using preoperative computed tomography scans and underwent rhinoplasty including tip surgery. Surgical outcomes were classified as excellent, good, or poor. Nasal skin thickness was measured at nasion, rhinion, nasal tip, and columella using computed tomography scans and was analyzed according to surgical outcomes.ResultsThe mean nasal skin thickness was 3.3 mm for nasion, 2.4 mm for rhinion, 2.9 mm for nasal tip, and 2.3 mm for columella. Postoperative outcomes were classified as excellent in 45, good in 17, and poor in 15 patients. The excellent outcome group had the thinnest nasal tip and columella nasal skin (2.8 mm and 2.2 mm), whereas the poor outcome group had the thickest skin in these regions (3.4 mm and 2.6 mm) (P <. 0001 and P = 0.01, respectively).ConclusionNasal skin is thickest over the nasofrontal angle, thins over the rhinion, is thick again in the nasal tip, and thins out over the columella. Thick skin at the nasal tip and columella was associated with poor surgical outcomes. Regional skin thickness appears to be an important prognostic factor for tip surgery success.
Analyzing the Effect of Anti-Abortion U.S. State Legislation in the Post-CaseyEra
Authors: New Michael J. 
Published: February 2011

AbstractMuch of the academic literature that analyzes U.S. state-level restrictions on abortion focuses on parental involvement laws and the extent to which abortion is publicly funded through Medicaid. However, one shortcoming common to all of these studies is that they fail to analyze informed consent laws and other types of anti-abortion legislation that received constitutional protection through the U.S. Supreme Court's decision inPlanned Parenthood of Southeastern Pennsylvania v. Casey(1992). In this study, a series of regressions on a comprehensive time series cross-sectional data set provides evidence that several types of state-level anti-abortion legislation result in statistically significant declines in both the abortion rate and the abortion ratio. Furthermore, a series of natural experiments provide further evidence that abortion restrictions are correlated with reductions in the incidence of abortion.
Formal and Perceived Leadership Power in U.S. State Legislatures
Authors: Battista James Coleman 
Published: February 2011

AbstractWhile there is a growing literature on the factors linked to the power held by leaders in state legislatures, the complexity of leadership power as a concept makes assessing it difficult. The author demonstrates that measures of formal leadership power derived from the written rules are uncorrelated with survey measures capturing legislators' own assessments of their leader's strength. These differences have practical importance, with each type of measure yielding different substantive findings in models predicting leadership power.
Adding value to clinical trial registries: insights from Australian Cancer Trials Online, a website for consumers
Authors: Dear Rachel , Barratt Alexandra , Askie Lisa , McGeechan Kevin , Arora Sheena , Crossing Sally , Currow David , Tattersall Martin 
Published: February 2011

Background Clinical trials registries are now operating in the USA, Europe, Australia, China, and India and more are planned. Trial registries could be an excellent source of information about clinical trials for patients and others affected by cancer as well as health care professionals, but may be difficult for patients to navigate and use. Purpose An opportunity arose in Australia to develop a consumer friendly cancer clinical trials website (Australian Cancer Trials Online (ACTO), www.australiancancertrials.gov.au ) using an automated data feed from two large clinical trial registries. In this article, we describe aspects of this new website, and explore ways in which such a website may add value to clinical trial data which are already collected and held by trial registries. Methods The development of ACTO was completed by a Web company working in close association with staff at the Australian New Zealand Clinical Trials Registry (ANZCTR), and with consumer representatives. Data for the website were sourced directly and only from clinical trial registries, thus avoiding the creation of an additional trials database. It receives an automated, daily data feed of newly registered cancer clinical trials from both the ANZCTR and Clinical Trials.gov. Results The development of ACTO exemplifies the advantage of a local clinical trial registry working with consumers to provide accessible information about cancer clinical trials to meet consumers’ information needs. We found that the inclusion of a lay summary added substantial value for consumers, and recommend that consideration be given to adding a lay summary to the mandatory data items collected by all trial registries. Furthermore, improved navigation, decision support tools, and consistency in data collection between clinical trial registries will also enable consumer websites to provide additional value for users. Limitations Clinical trial registration is not compulsory in Australia. If the additional cancer items (including a lay summary) are not provided by registrants of cancer trials on ANZCTR, this can compromise the quality and usefulness of the data for the end-user, in this case consumers, as they may encounter gaps in the data. Conclusion Expanding the World Health Organization Trial Registration Data Set to include this additional information, particularly the lay summary, would be valuable. A well-coordinated system of clinical trial registration is critical to the success of efforts to provide better access for all to inform about clinical trials.
Treosulfan-based conditioning regimens for hematopoietic stem cell transplantation in children with primary immunodeficiency: United Kingdom experience
Authors: Slatter Mary A. , Rao Kanchan , Amrolia Persis , Flood Terry , Abinun Mario , Hambleton Sophie , Nademi Zohreh , Goulden Nick , Davies Graham , Qasim Waseem , Gaspar Hubert B. , Cant Andrew , Gennery Andrew R. , Veys Paul 
Published: February 2011

Abstract
Children with primary immunodeficiency diseases, particularly those less than 1 year of age, experience significant toxicity after hematopoietic stem cell transplantation, with busulfan- or melphalan-based conditioning. Treosulfan causes less veno-occlusive disease than busulfan and does not require pharmacokinetic monitoring. We report its use in 70 children. Children received 42 g/m2 or 36 g/m2 with cyclophosphamide 200 mg/kg (n = 30) or fludarabine 150 mg/m2 (n = 40), with alemtuzumab in most. Median age at transplantation was 8.5 months (range, 1.2-175 months); 46 (66%) patients were 12 months of age or younger. Donors were as follows: matched sibling donor, 8; matched family donor, 13; haploidentical, 4; and unrelated, 45. Median follow-up was 19 months (range, 1-47 months). Overall survival was 81%, equivalent in those age less or greater than 1 year. Skin toxicity was common. Veno-occlusive disease occurred twice with cyclophosphamide. Eighteen patients (26%) had graft-versus-host disease, and only 7 (10%) greater than grade 2. Two patients rejected; 24 of 42 more than 1 year after transplantation had 100% donor chimerism. The remainder had stable mixed chimerism. T-cell chimerism was significantly better with fludarabine. Long-term follow-up is required, but in combination with fludarabine, treosulfan is a good choice of conditioning for hematopoietic stem cell transplantation in primary immunodeficiency disease.
Genome-wide discovery of missing genes in biological pathways of prokaryotes
Authors: Chen Yong , Mao Fenglou , Li Guojun , Xu Ying 
Published: February 2011

Abstract

Background
Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called “missing gene” problem.

Methods
We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping, to fill holes caused by missing genes as well as to expand the mapped pathway model. The basic idea of the algorithm is to identify genes in the target genome whose homologous genes share common operons with homologs of any mapped pathway genes in some reference genome, and to add such genes to the target pathway if their functions are consistent with the cellular function of the target pathway.

Results
We have implemented this idea using a graph-theoretic approach and demonstrated the effectiveness of the algorithm on known pathways of E. coli in the KEGG database. On all KEGG pathways containing at least 5 genes, our method achieves an average of 60% positive predictive value (PPV) and the performance is increased with more seed genes added. Analysis shows that our method is highly robust.

Conclusions
An effective method is presented to find missing genes in biological pathways of prokaryotes, which achieves high prediction reliability on E. coli at a genome level. Numerous missing genes are found to be related to knwon E. coli pathways, which can be further validated through biological experiments. Overall this method is robust and can be used for functional inference.
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures
Authors: Fukagawa Daiji , Tamura Takeyuki , Takasu Atsuhiro , Tomita Etsuji , Akutsu Tatsuya 
Published: February 2011

Abstract

Background
Measuring similarities between tree structured data is important for analysis of RNA secondary structures, phylogenetic trees, glycan structures, and vascular trees. The edit distance is one of the most widely used measures for comparison of tree structured data. However, it is known that computation of the edit distance for rooted unordered trees is NP-hard. Furthermore, there is almost no available software tool that can compute the exact edit distance for unordered trees.

Results
In this paper, we present a practical method for computing the edit distance between rooted unordered trees. In this method, the edit distance problem for unordered trees is transformed into the maximum clique problem and then efficient solvers for the maximum clique problem are applied. We applied the proposed method to similar structure search for glycan structures. The result suggests that our proposed method can efficiently compute the edit distance for moderate size unordered trees. It also suggests that the proposed method has the accuracy comparative to those by the edit distance for ordered trees and by an existing method for glycan search.

Conclusions
The proposed method is simple but useful for computation of the edit distance between unordered trees. The object code is available upon request.
High-throughput peptide quantification using mTRAQ reagent triplex
Authors: Yoon Joo Young , Yeom Jeonghun , Lee Heebum , Kim Kyutae , Na Seungjin , Park Kunsoo , Paek Eunok , Lee Cheolju 
Published: February 2011

Abstract

Background
Protein quantification is an essential step in many proteomics experiments. A number of labeling approaches have been proposed and adopted in mass spectrometry (MS) based relative quantification. The mTRAQ, one of the stable isotope labeling methods, is amine-specific and available in triplex format, so that the sample throughput could be doubled when compared with duplex reagents.

Methods and results
Here we propose a novel data analysis algorithm for peptide quantification in triplex mTRAQ experiments. It improved the accuracy of quantification in two features. First, it identified and separated triplex isotopic clusters of a peptide in each full MS scan. We designed a schematic model of triplex overlapping isotopic clusters, and separated triplex isotopic clusters by solving cubic equations, which are deduced from the schematic model. Second, it automatically determined the elution areas of peptides. Some peptides have similar atomic masses and elution times, so their elution areas can have overlaps. Our algorithm successfully identified the overlaps and found accurate elution areas. We validated our algorithm using standard protein mixture experiments.

Conclusions
We showed that our algorithm was able to accurately quantify peptides in triplex mTRAQ experiments. Its software implementation is compatible with Trans-Proteomic Pipeline (TPP), and thus enables high-throughput analysis of proteomics data.