bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a Wind-Wave System for Ensemble Tropical Cyclone Wave Forecasting. Part I: Winds
Authors: Lazarus Steven M. , Wilson Samuel T. , Splitt Michael E. , Zarillo Gary A. 
Published: November 2012

Abstract
A computationally efficient method of producing tropical cyclone (TC) wind analyses is developed and tested, using a hindcast methodology, for 12 Gulf of Mexico storms. The analyses are created by blending synthetic data, generated from a simple parametric model constructed using extended best-track data and climatology, with a first-guess field obtained from the NCEP–NCAR North American Regional Reanalysis (NARR). Tests are performed whereby parameters in the wind analysis and vortex model are varied in an attempt to best represent the TC wind fields. A comparison between nonlinear and climatological estimates of the TC size parameter indicates that the former yields a much improved correlation with the best-track radius of maximum wind rm. The analysis, augmented by a pseudoerror term that controls the degree of blending between the NARR and parametric winds, is tuned using buoy observations to calculate wind speed root-mean-square deviation (RMSD), scatter index (SI), and bias. The bias is minimized when the parametric winds are confined to the inner-core region. Analysis wind statistics are stratified within a storm-relative reference frame and by radial distance from storm center, storm intensity, radius of maximum wind, and storm translation speed. The analysis decreases the bias and RMSD in all quadrants for both moderate and strong storms and is most improved for storms with an rm of less than 20 n mi. The largest SI reductions occur for strong storms and storms with an rm of less than 20 n mi. The NARR impacts the analysis bias: when the bias in the former is relatively large, it remains so in the latter.
Weather and Individual Happiness
Authors: Tsutsui Yoshiro 
Published: November 2012

Abstract
This paper investigates the influence of weather on happiness. While previous studies have examined climatic influence by comparing the well-being of people living in different regions, this paper focuses on how daily changes in weather affect individuals living in a single location. The dataset consists of 516 days of data on 75 students from Osaka University. Daily information on outside events, as well as the daily physical condition and individual characteristics of the respondents, are used as controls. Subjective happiness is related to temperature: in a quadratic model, happiness is maximized at 13.9°C. The effects of other meteorological variables—humidity, wind speed, precipitation, and sunshine—are not significant. The sensitivity of happiness to temperature also depends on attributes such as sex, age, and academic department. Happiness is more strongly affected by current temperature than by average temperature over the day. While enjoyment (a positive affect measure) is affected by weather in a similar way to happiness, sadness and depression (negative affect measures) behave somewhat differently.
Statistical distributions of test statistics used for quantitative trait association mapping in structured populations
Authors: Teyssèdre Simon , Elsen Jean-Michel , Ricard Anne 
Published: November 2012

Abstract

Background
Spurious associations between single nucleotide polymorphisms and phenotypes are a major issue in genome-wide association studies and have led to underestimation of type 1 error rate and overestimation of the number of quantitative trait loci found. Many authors have investigated the influence of population structure on the robustness of methods by simulation. This paper is aimed at developing further the algebraic formalization of power and type 1 error rate for some of the classical statistical methods used: simple regression, two approximate methods of mixed models involving the effect of a single nucleotide polymorphism (SNP) and a random polygenic effect (GRAMMAR and FASTA) and the transmission/disequilibrium test for quantitative traits and nuclear families. Analytical formulae were derived using matrix algebra for the first and second moments of the statistical tests, assuming a true mixed model with a polygenic effect and SNP effects.

Results
The expectation and variance of the test statistics and their marginal expectations and variances according to the distribution of genotypes and estimators of variance components are given as a function of the relationship matrix and of the heritability of the polygenic effect. These formulae were used to compute type 1 error rate and power for any kind of relationship matrix between phenotyped and genotyped individuals for any level of heritability. For the regression method, type 1 error rate increased with the variability of relationships and with heritability, but decreased with the GRAMMAR method and was not affected with the FASTA and quantitative transmission/disequilibrium test methods.

Conclusions
The formulae can be easily used to provide the correct threshold of type 1 error rate and to calculate the power when designing experiments or data collection protocols. The results concerning the efficacy of each method agree with simulation results in the literature but were generalized in this work. The power of the GRAMMAR method was equal to the power of the FASTA method at the same type 1 error rate. The power of the quantitative transmission/disequilibrium test was low. In conclusion, the FASTA method, which is very close to the full mixed model, is recommended in association mapping studies.
iMS2Flux– a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis
Authors: Poskar C Hart , Huege Jan , Krach Christian , Franke Mathias , Shachar-Hill Yair , Junker Björn H 
Published: November 2012

Abstract

Background
Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in combination with stable isotope labeling experiments. However, before the mass spectrometric data can be used it has to be corrected for biases caused by naturally occurring stable isotopes, by the analytical technique(s) employed, or by the biological sample itself. Finally the MS data and the labeling information it contains have to be assembled into a data format usable by flux analysis software (of which several dedicated packages exist). Currently the processing of mass spectrometric data is time-consuming and error-prone requiring peak by peak cut-and-paste analysis and manual curation. In order to facilitate high-throughput metabolic flux analysis, the automation of multiple steps in the analytical workflow is necessary.

Results
Here we describe iMS2Flux, software developed to automate, standardize and connect the data flow between mass spectrometric measurements and flux analysis programs. This tool streamlines the transfer of data from extraction via correction tools to 13C-Flux software by processing MS data from stable isotope labeling experiments. It allows the correction of large and heterogeneous MS datasets for the presence of naturally occurring stable isotopes, initial biomass and several mass spectrometry effects. Before and after data correction, several checks can be performed to ensure accurate data. The corrected data may be returned in a variety of formats including those used by metabolic flux analysis software such as 13CFLUX, OpenFLUX and 13CFLUX2.

Conclusion

iMS2Flux is a versatile, easy to use tool for the automated processing of mass spectrometric data containing isotope labeling information. It represents the core framework for a standardized workflow and data processing. Due to its flexibility it facilitates the inclusion of different experimental datasets and thus can contribute to the expansion of flux analysis applications.
Testing of human papillomavirus in lung cancer and non-tumor lung tissue
Authors: Galvan Antonella , Noci Sara , Taverna Francesca , Lombardo Claudia , Franceschi Silvia , Pastorino Ugo , Dragani Tommaso A 
Published: November 2012

Abstract

Background
Risk factors for lung cancer, such as cigarette smoking, environmental pollution, asbestos, and genetic determinants, are well-known, whereas involvement of the human papillomavirus (HPV) is still unclear.

Methods
We examined a series of 100 lung cancer patients from Italy and the UK for the presence of HPV DNA in both lung tumor specimens and adjacent non-tumoral specimens from the same patients. Thirty-five of the most clinically relevant HPV types were assayed using PCR amplification of the highly conserved L1 region of the viral genome followed by hybridization with specific probes.

Results
No HPV was detected in tumor specimens nor in normal lung tissue of any patient.

Conclusions
These data indicate that, in this Western series, HPV is not associated with the risk of lung cancer. Our findings will help refine estimates of lung cancer risk in patients affected by a common viral infection involved in other types of human cancer.
Reliability and validity of self-assessment of mouth opening: a validation study
Authors: Saund Daniel Satnam Singh , Pearson David , Dietrich Thomas 
Published: November 2012

Abstract

Background
The objective of this study was to evaluate the reproducibility and validity of patients’ mouth opening measurements in a research setting.

Methods
Firstly, 68 patients made repeated self-measurements of mouth opening using a cardboard scale (Therabite Range of Motion Scale – TRMS). Secondly, 80 patients enrolled in a clinical trial on morbidity after lower third molar surgery, made daily assessments during the postoperative week. Patients’ measurements were then compared to gold-standard clinicians’ measurements.

Results
Reliability of patients’ measurements was excellent with an intraclass correlation coefficient of 0.92. The patient’s measurements correlated well with the gold-standard clinician’s measurements, both for the first 68 patients (Pearson’s rho ranging from 0.86 to 0.90, p < 0.0001) as well as for the 80 patients enrolled in the clinical trial (rho = 0.82, p < 0.0001 at day 2, rho = 0.83, p < 0.0001 at final visit).

Conclusions
TRMS can be used by patients to produce reproducible and valid mouth opening measurements.
The effect of acupuncture on stroke recovery: study protocol for a randomized controlled trial
Authors: Liu Huilin , Zhang Dangsheng , Tan Xiuge , Yang Daqing , Wang Guiling , Zhao Yin , Wen Yali , Shi Guangxia , Wang Linpeng 
Published: November 2012

Abstract

Background
Stroke is one of the leading causes of death and disability in China. Current treatments for stroke are limited and achieve no optimal effect. Acupuncture is widely used in the treatment of stroke and in improving the quality of life for patients in China. In most previous clinical studies, the effects of acupuncture have been diverse, and few well-designed randomized controlled trials have been conducted to investigate the long-term effect of acupuncture on acute stroke recovery.

Method
Three hundred and twenty eight subjects with acute cerebral apoplexy will be recruited. The patients will be randomized into two different groups: the intervention group will receive acupuncture treatment together with Western standard treatment for 2 weeks plus the secondary prevention treatment for 22 weeks; the control group will receive only the Western standard treatment for 2 weeks and the secondary prevention treatment for 22 weeks. The primary outcome measures are Barthel Index and the Stroke-Specific Quality Of Life. The secondary outcome measures are the National Institutes of Health Stroke Scale and Modified Rankin Scale. All assessments will be conducted at the baseline and at weeks 4, 12 and 24 of follow-up.

Discussion
This study will evaluate the effects of acupuncture on the long-term recovery of acute stroke and on improving the quality of life of the patients. The results of this study will help establish optimal integrated therapeutic strategies for patients with stroke.

Trial registration
Current Controlled Trials ISRCTN29932220
Best proximity point theorems for reckoning optimal approximate solutions
Authors: Basha S Sadiq , Shahzad N , Jeyaraj R 
Published: November 2012

Abstract
Given a non-self mapping from A to B, where A and B are subsets of a metric space, in order to compute an optimal approximate solution of the equation

S
x
=
x

, a best proximity point theorem probes into the global minimization of the error function

x
⟶
d
(
x
,
S
x
)

corresponding to approximate solutions of the equation

S
x
=
x

. This paper presents a best proximity point theorem for generalized contractions, thereby furnishing optimal approximate solutions, called best proximity points, to some non-linear equations. Also, an iterative algorithm is presented to compute such optimal approximate solutions.

MSC:90C26, 90C30, 41A65, 46B20, 47H10, 54H25.
Serological and molecular investigation into the role of wild birds in the epidemiology of West Nile virus in Greece
Authors: Valiakos George , Touloudi Antonia , Athanasiou Labrini V , Giannakopoulos Alexios , Iacovakis Christos , Birtsas Periklis , Spyrou Vassiliki , Dalabiras Zisis , Petrovska Liljana , Billinis Charalambos 
Published: November 2012

Abstract

Background
A West Nile virus (WNV) disease outbreak occurred in 2010 in northern Greece with a total of 262 laboratory-confirmed human cases and 35 deaths. A serological and molecular surveillance was conducted on samples of hunter-harvested wild birds prior to and during the outbreak.

Findings
Serum and tissue samples from 295 resident and migratory wild birds, hunter-harvested during the 2009–2010 and 2010–2011 hunting seasons at the epicenter of the outbreak in northern Greece, were tested for the presence of WNV-specific antibodies by immunofluorescence assay and virus neutralization test. WNV neutralizing antibodies were detected in 53 avian samples. Fourteen positive sera were obtained from birds hunter-harvested up to 8 months prior to the human outbreak. Specific genetic determinants of virulence (His249Pro NS3 mutation, E-glycosylation motif) were recognized in a WNV lineage 2 strain isolated from a hunter-harvested Eurasian magpie and a nucleotide mismatch was revealed between this strain and a mosquito WNV strain isolated one month earlier in the same area.

Conclusions
This is the first report regarding exposure of wild birds to WNV prior to the 2010 outbreak, in Greece. Results provide evidence of the implication of wild birds in a local enzootic cycle that could allow maintenance and amplification of the virus before and during the outbreak. Findings of past exposure of migratory birds to WNV upon their arrival in Greece during autumn migration, suggest avian species with similar migration traits as candidates for the introduction of WNV into Greece. The possibility that an endemic circulation of WNV could have caused the outbreak, after an amplification cycle due to favorable conditions cannot be excluded.
Metabonomic analysis of water extracts from Chinese and American ginsengs by 1H nuclear magnetic resonance: identification of chemical profile for quality control
Authors: Chan Pui Hei , Zheng Ken YZ , Tsim Karl WK , Lam Henry 
Published: November 2012

Abstract

Background
With the gaining popularity of commercially prepared decoctions of herbal medicines on the market, an objective and efficient way to reveal the authenticity of such products is urgently needed. Previous attempts to use chromatographic or spectroscopic methods to identify ginseng samples made use of components derived from methanol extracts of the herb. It was not established that these herbs can be distinguished solely from consumable components, which are responsible for the clinical efficacy of the herb.
In this study, metabonomics, or metabolic profiling, based on the application of 1H-Nuclear Magnetic Resonance (NMR), is applied to distinguish the water extracts of three closely related ginseng species: P. ginseng (from two different cultivated regions in China), P. notoginseng and P. quinquefolius.

Methods
A water extraction protocol that mimics how ginseng decoctions are made for consumption was used to prepare triplicate samples from each herb for analysis. High-resolution 1H NMR spectroscopy was used to acquire metabolic profiles of the four ginseng samples. The spectral data were subjected to multivariate and univariate analysis to identify metabolites that were able to distinguish different types of ginseng.

Results
H NMR metabolic profiling was performed to distinguish the water extracts of P. ginseng cultivated in Hebei and Jilin of China, both of which were distinguished from extracts of P. notoginseng and P. quinquefolius, by unsupervised principle component analysis based on the entire 1H NMR spectral fingerprint Statistically significant differences were found for several discriminating features traced to common metabolites and the ginsenosides Rg1 and Rd, in the 1H NMR spectra.

Conclusion
This study demonstrated that 1H NMR metabonomics can simultaneously distinguish different ginseng species and multiple samples of the same species that were cultivated in different regions. This technique is applicable to the authentication and quality control of ginseng products.
Use of response surface methodology for development of new microwell-based spectrophotometric method for determination of atrovastatin calcium in tablets
Authors: Wani Tanveer A , Ahmad Ajaz , Zargar Seema , Khalil Nasr Y , Darwish Ibrahim A 
Published: November 2012

Abstract

Background
Response surface methodology by Box–Behnken design employing the multivariate approach enables substantial improvement in the method development using fewer experiments, without wastage of large volumes of organic solvents, which leads to high analysis cost. This methodology has not been employed for development of a method for analysis of atorvastatin calcium (ATR-Ca).

Results
The present research study describes the use of in optimization and validation of a new microwell-based UV-Visible spectrophotometric method of for determination of ATR-Ca in its tablets. By the use of quadratic regression analysis, equations were developed to describe the behavior of the response as simultaneous functions of the selected independent variables. Accordingly, the optimum conditions were determined which included concentration of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), time of reaction and temperature. The absorbance of the colored-CT complex was measured at 460 nm by microwell-plate absorbance reader. The method was validated, in accordance with ICH guidelines for accuracy, precision, selectivity and linearity (r² = 0.9993) over the concentration range of 20–200 μg/ml. The assay was successfully applied to the analysis of ATR-Ca in its pharmaceutical dosage forms with good accuracy and precision.

Conclusion
The assay described herein has great practical value in the routine analysis of ATR-Ca in quality control laboratories, as it has high throughput property, consumes minimum volume of organic solvent thus it offers the reduction in the exposures of the analysts to the toxic effects of organic solvents, environmentally friendly "Green" approach) and reduction in the analysis cost by 50-fold.
Molecular confirmation of the occurrence in Germany of Anopheles daciae (Diptera, Culicidae)
Authors: Kronefeld Mandy , Dittmann Marko , Zielke Dorothee , Werner Doreen , Kampen Helge 
Published: November 2012

Abstract

Background

Anopheles daciae, a newly described member of the Maculipennis group, was recently reported from western, southern and eastern Europe. Before its recognition, it had commonly been listed under the name of An. messeae, due to its extreme morphological and genetic similarities. As the sibling species of the Maculipennis group are known to differ in their vector competences for malaria parasites and other pathogens, the occurrence of An. daciae in a given region might have an impact on the epidemiology of mosquito-borne diseases. Mosquito collections from different localities in Germany were therefore screened for An. daciae.

Methods
Adult and immature Maculipennis group mosquitoes were collected between May 2011 and June 2012 at 23 different sites in eight federal states of Germany. A standard PCR assay was used to differentiate the previously known sibling species while the ITS2 rDNA of specimens preliminarily identified as An. messeae/daciae was sequenced and analysed for species-specific nucleotide differences.

Results
Four hundred and seventy-seven Anopheles specimens were successively identified to Maculipennis group level by morphology and to species level by DNA-based methods. Four species of the Maculipennis group were registered: An. messeae (n = 384), An. maculipennis (n = 82), An. daciae (n = 10) and An. atroparvus (n = 1). Anopheles daciae occurred at four sites in three federal states of Germany, three of the sites being located in north-eastern Germany (federal states of Brandenburg and Saxony) while one collection site was situated in the northern Upper Rhine Valley in the federal state of Hesse, south-western Germany.

Conclusions
The detection of An. daciae represents the first recognition of this species in Germany where it was found to occur in sympatry with An. messeae and An. maculipennis. As the collection sites were in both north-eastern and south-western parts of Germany, the species is probably even more widely distributed in Germany than demonstrated, albeit apparently with low population densities. Research is needed that confirms the species status of An. daciae and elucidates its vector competence as compared to An. messeae and the other species of the Maculipennis group, in order to optimize management of possible future outbreaks of diseases caused by pathogen transmission through Maculipennis group mosquitoes.
Mitochondrial peroxidase TPx-2 is not essential in the blood and insect stages of Plasmodium berghei
Authors: Masuda-Suganuma Hirono , Usui Miho , Fukumoto Shinya , Inoue Noboru , Kawazu Shin-ichiro 
Published: November 2012

Abstract

Background
Malaria parasites actively proliferate in the body of their vertebrate and insect hosts, and are subjected to the toxic effects of reactive oxygen species. The antioxidant defenses of malaria parasites are considered to play essential roles in their survival and are thus considered promising targets for intervention. We sought to identify the cellular function of thioredoxin peroxidase-2 (TPx-2), which is expressed in the mitochondria, by disrupting the TPx-2 gene (pbtpx-2) of the rodent malaria parasite Plasmodium berghei.

Findings
In three independent experiments, two disruptant populations (TPx-2 KO) and three wild-type parasite populations with pyrimethamine resistance (dhfr-ts/mt at the DHFR-TS locus) and intact pbtpx-2 (TPx-2 WT) were obtained and cloned. Null expression of TPx-2 in the KO population was confirmed by RT-PCR and Western blot analyses. The TPx-2 KO parasite developed normally in mouse erythrocytes and multiplied at a rate similar to that of the TPx-2 WT parasite during the experimental period. The peak period of gametocytemia was delayed by 1 day in the TPx-2 KO compared with that of the TPx-2 WT and the parent parasite, however, the highest gametocyte number was comparable. The number of midgut oocysts in the TPx-2 KO at 14 days post feeding was comparable to that of the TPx-2 WT.

Conclusions
The present finding suggests that mitochondrial Prx TPx-2 is not essential for asexual and the insect stage development of the malaria parasite.