bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modal and Nonmodal Symmetric Perturbations. Part II: Nonmodal Growths Measured by Total Perturbation Energy
Authors: Xu Qin , Lei Ting , Gao Shouting 
Published: June 2007

Maximum nonmodal growths of total perturbation energy are computed for symmetric perturbations constructed from the normal modes presented in Part I. The results show that the maximum nonmodal growths are larger than the energy growth produced by any single normal mode for a give optimization time, and this is simply because the normal modes are nonorthogonal (measured by the inner product associated with the total perturbation energy norm). It is shown that the maximum nonmodal growths are produced mainly by paired modes, and this can be explained by the fact that the streamfunction component modes are partially orthogonal between different pairs and parallel within each pair in the streamfunction subspace. When the optimization time is very short (compared with the inverse Coriolis parameter), the nonmodal growth is produced mainly by the paired fastest propagating modes. When the optimization time is not short, the maximum nonmodal growth is produced almost solely by the paired slowest propagating modes and the growth can be very large for a wide range of optimization time if the parameter point is near the boundary and outside the unstable region. If the parameter point is near the boundary but inside the unstable region, the paired slowest propagating modes can contribute significantly to the energy growth before the fastest growing mode becomes the dominant component. The maximum nonmodal growths produced by paired modes are derived analytically. The analytical solutions compare well with the numerical results obtained in the truncated normal mode space. The analytical solutions reveal the basic mechanisms for four types of maximum nonmodal energy growths: the PP1 and PP2 nonmodal growths produced by paired propagating modes and the GD1 and GD2 nonmodal growths produced by paired growing and decaying modes. The PP1 growth is characterized by the increase of the cross-band kinetic energy that excessively offsets the decrease of the along-band kinetic and buoyancy energy. The situation is opposite for the PP2 growth. The GD1 (or GD2) growth is characterized by the reduction of the initial cross-band kinetic energy (or initial along-band kinetic and buoyancy energy) due to the inclusion of the decaying mode.
Calibration of Sun Radiometer–Based Atmospheric Water Vapor Retrievals Using GPS Meteorology
Authors: Bokoye Amadou Idrissa , Royer Alain , Cliche Patrick , O’Neill Norm 
Published: June 2007

A study of the validation and calibration process for integrated water vapor (IWV) measurements derived from sun radiometry at the 940-nm solar absorption channel employed in the Aerosol Robotic Network (AERONET) Aerosol Canada (AEROCAN) is presented. The sun radiometer data are compared with GPS meteorology records used as a reference. Three Canadian sites from different climatic regimes covering the period 2000–04 are considered. The observations from five different sun radiometers (IWV-SUN) were processed using the initial AERONET IWV retrieval procedure (V1) whereas GPS-derived IWV (IWV-GPS) was retrieved using “GPSpace” software developed by the Geodetic Survey division of Natural Resources Canada. A sensitivity study is carried out to highlight the influence of both central wavelength and signal amplitude on the 940-nm filter characteristics, which are instrument dependent and can drift due to aging. The comparison between IWV-SUN (V1) and IWV-GPS shows an average rmse of 0.23 ± 0.11 g cm−2 (22%) and a mean bias of −0.09 ± 0.16 g cm−2 (9%). Furthermore, it is shown that the use of GPS for determining the 940-nm channel calibration constants for the solar radiometers improves IWV retrievals (rmse reduced by about 35% and bias by a factor of 3–10) without any knowledge of the 940-nm filter characteristics. These results are discussed within the context of the new AERONET IWV processing procedure (V2), which accounts for solar 940-nm region filter characteristics. The GPS receiver technique appears to be a powerful calibration tool because of its continuous observation capability, its robustness, and its operational simplicity.
Nonparametric Estimation of Raindrop Size Distributions from Dual-Polarization Radar Spectral Observations
Authors: Moisseev Dmitri N. , Chandrasekar V. 
Published: June 2007

This paper presents a method to retrieve raindrop size distributions (DSD) from slant profile dual-polarization Doppler spectra observations. It is shown that using radar measurements taken at a high elevation angle raindrop size distributions can be retrieved without making an assumption on the form of a DSD. In this paper it is shown that drop size distributions can be retrieved from Doppler power spectra by compensating for the effect of spectrum broadening and mean velocity shift. To accomplish that, spectrum deconvolution is used where the spectral broadening kernel width and wind velocity are estimated from spectral differential reflectivity measurements. Since convolution kernel is estimated from dual-polarization Doppler spectra observations and does not require observation of a clear-air signal, this method can be used by most radars capable of dual-polarization spectra measurements. To validate the technique, sensitivity of this method to the underlying assumptions and calibration errors is evaluated on realistic simulations of radar observations. Furthermore, performance of the method is illustrated on Colorado State University–University of Chicago–Illinois State Water Survey radar (CSU–CHILL) measurements of stratiform precipitation.
A Pressure-Sphere Anemometer for Measuring Turbulence and Fluxes in Hurricanes
Authors: Eckman Richard M. , Dobosy Ronald J. , Auble David L. , Strong Thomas W. , Crawford Timothy L. 
Published: June 2007

Turbulence and air-surface exchange are important factors throughout the life cycle of a tropical cyclone. Conventional turbulence instruments are not designed to function in the extreme environment encountered in such storms. A new instrument called the Extreme Turbulence (ET) probe has been developed specifically for measuring turbulence on a fixed tower in hurricane conditions. Although the probe is designed for surface deployment, it is based on the same pressure-sphere technology used for aircraft gust probes. The ET probe is designed around a 43-cm-diameter sphere with 30 pressure ports distributed over its surface. A major obstacle during development was finding a method to prevent water from fouling the pressure ports. Two approaches were investigated: a passive approach using gravity drainage and an active approach using an air pump to flush water from the ports. The probes were tested in both dry and wet conditions by mounting them on a vehicle side by side with more conventional instruments. In dry conditions, test data from the ET probes were in good agreement with the conventional instruments. In rain, probes using the passive rain defense performed about as well as in dry conditions, with the exception of some water intrusion into the temperature sensors. The active rain defense has received only limited attention so far, mainly because of the success and simplicity of the passive defense.
Acute First-Time Hamstring Strains during Slow-Speed Stretching
Authors: Askling Carl M. , Tengvar Magnus , Saartok Tönu , Thorstensson Alf 
Published: June 2007

Background Hamstring strains can be of 2 types with different injury mechanisms, 1 occurring during high-speed running and the other during stretching exercises. Hypothesis A stretching type of injury to the proximal rear thigh may involve specific muscle-tendon structures that could affect recovery time. Study Design Case series (prognosis); Level of evidence, 2. Methods Fifteen professional dancers with acute first-time hamstring strains were prospectively included in the study. All subjects were examined, clinically and with magnetic resonance imaging, on 4 occasions after injury: at day 2 to 4, 10, 21, and 42. The clinical follow-up period was 2 years. Results All dancers were injured during slow hip-flexion movements with extended knee and experienced relatively mild acute symptoms. All injuries were located proximally in the posterior thigh close to the ischial tuberosity. The injury involved the semimembranosus (87%), quadratus femoris (87%), and adductor magnus (33%). All injuries to the semimembranosus involved its proximal free tendon. There were no significant correlations between clinical or magnetic resonance imaging parameters and the time to return to preinjury level (median, 50 weeks; range, 30-76 weeks). Conclusion Stretching exercises can give rise to a specific type of strain injury to the posterior thigh. A precise history and careful palpation provide the clinician enough information to predict a prolonged time until return to preinjury level. One factor underlying prolonged recovery time could be the involvement of the free tendon of the semimembranosus muscle.
Impaired expression of Toll-like receptor 2 in nontuberculous mycobacterial lung disease
Authors: Ryu Y. J. , Kim E. J. , Lee S-H. , Kim S. Y. , Suh G. Y. , Chung M. P. , Kim H. , Kwon O. J. , Koh W-J. 
Published: June 2007

The aims of the present study were to investigate the expression of Toll-like receptor (TLR)2 on the peripheral blood monocytes of patients with nontuberculous mycobacterial (NTM) lung disease and healthy controls, and to assess the responses of these monocytes to TLR2 agonists such asMycobacterium aviumand lipoteichoic acid (LTA).Reverse transcriptase–PCR was used to analyse TLR2 mRNA expression in peripheral blood monocytes from 17 NTM patients and 10 healthy controls. mRNA and protein secretion levels were also determined for the cytokines interleukin (IL)-12 p40 and tumour necrosis factor (TNF)-α.Expression of TLR2 mRNA by peripheral blood monocytes after stimulation withM. aviumor LTA was lower in NTM patients than in healthy controls. IL-12 p40 and TNF-α mRNA and cytokine secretion levels were also lower in patients than in healthy controls. Treatment with anti-TLR antibody decreasedM. avium- and LTA-induced IL-12 p40 and TNF-α production in healthy controls, but not in NTM patients.The present results suggest that the downregulation of Toll-like receptor 2 and the resulting decreased production of interleukin-12 p40 and tumour necrosis factor-α followingMycobacterium aviumor lipoteichoic acid stimulation may contribute to host susceptibility to nontuberculous mycobacterial lung disease.
Effect of genioglossus contraction on pharyngeal lumen and airflow in sleep apnoea patients
Authors: Oliven A. , Tov N. , Geitini L. , Steinfeld U. , Oliven R. , Schwartz A. R. , Odeh M. 
Published: June 2007

The purpose of the present study was to quantify the mechanical effect of genioglossus stimulation on flow mechanics and pharyngeal cross-sectional area in patients with obstructive sleep apnoea, and to identify variables that determine the magnitude of the respiratory effect of tongue protrusion.The pressure/flow and pressure/cross-sectional area relationships of the velo- and oropharynx were assessed in spontaneously breathing propofol-anaesthetised subjects before and during genioglossus stimulation.Genioglossus contraction decreased the critical pressure significantly from 1.2±3.3 to -0.7±3.8 cmH2O, with individual decreases ranging -0.6–5.9 cmH2O. Pharyngeal compliance was not affected by genioglossus contraction. The pharyngeal response to genioglossus stimulation was related to the magnitude of advancement of the posterior side of the tongue, but not to the severity of sleep apnoea, critical pressure, compliance or the shape and other characteristics of the velopharynx.Genioglossus contraction enlarges both the velo- and the oropharynx and lowers the critical pressure without affecting pharyngeal stiffness. The response to genioglossus stimulation depends upon the magnitude of tongue protrusion achieved rather than on inherent characteristics of the patient and their airway.
Factors determining early adherence to a lung cancer screening protocol
Authors: Montes U. , Seijo L. M. , Campo A. , Alcaide A. B. , Bastarrika G. , Zulueta J. J. 
Published: June 2007

Lung cancer screening using computed tomography (CT) is effective in detecting early stage disease. However, concerns regarding adherence have been raised.The current authors conducted a retrospective observational study of 641 asymptomatic smokers enrolled in a lung cancer screening programme between 2000 and 2003. Adherent subjects were compared with nonadherent subjects with regard to lung function, sex, age, motivation for enrolment, smoking status, distance to the referral centre, family history of lung cancer, asbestos exposure, education, the presence and type of nodule(s) seen on initial CT, and exposure to a nursing intervention designed to improve adherence.Overall, early adherence to the study protocol was 65%. Multivariate analysis confirmed the importance of sex, proximity to the referral centre, the presence of noncalcified nodules, and the nursing intervention as factors conditioning adherence to the study protocol. Patients encouraged to participate in the study were more adherent, as were former smokers. Sex interactions were observed in multivariate analysis. The nursing intervention was significant for females, while abnormal lung function improved male adherence.Adherence to lung cancer screening is particularly good among females and subjects living near the referral centre. The present study suggests the need to develop new strategies, especially those targeting males and subjects with low risk perception, in order to improve adherence.
A Three Stage Integrative Pathway Search (TIPS©) framework to identify toxicity relevant genes and pathways
Authors: Li Zheng , Srivastava Shireesh , Mittal Sheenu , Yang Xuerui , Sheng Lufang , Chan Christina 
Published: June 2007

Abstract

Background
The ability to obtain profiles of gene expressions, proteins and metabolites with the advent of high throughput technologies has advanced the study of pathway and network reconstruction. Genome-wide network reconstruction requires either interaction measurements or large amount of perturbation data, often not available for mammalian cell systems. To overcome these shortcomings, we developed a Three Stage Integrative Pathway Search (TIPS
©) approach to reconstruct context-specific active pathways involved in conferring a specific phenotype, from limited amount of perturbation data. The approach was tested on human liver cells to identify pathways that confer cytotoxicity.

Results
This paper presents a systems approach that integrates gene expression and cytotoxicity profiles to identify a network of pathways involved in free fatty acid (FFA) and tumor necrosis factor-α (TNF-α) induced cytotoxicity in human hepatoblastoma cells (HepG2/C3A). Cytotoxicity relevant genes were first identified and then used to reconstruct a network using Bayesian network (BN) analysis. BN inference was used subsequently to predict the effects of perturbing a gene on the other genes in the network and on the cytotoxicity. These predictions were subsequently confirmed through the published literature and further experiments.

Conclusion
The TIPS
© approach is able to reconstruct active pathways that confer a particular phenotype by integrating gene expression and phenotypic profiles. A web-based version of TIPS
© that performs the analysis described herein can be accessed at http://www.egr.msu.edu/tips.
Using expression arrays for copy number detection: an example from E. coli
Authors: Skvortsov Dmitriy , Abdueva Diana , Stitzer Michael E , Finkel Steven E , Tavaré Simon 
Published: June 2007

Abstract

Background
The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. While many of the methods and algorithms developed for the analysis microarrays have focused on expression analysis, the same technology can be used to detect genetic alterations, using for example standard commercial Affymetrix arrays. Due to the nature of the resultant data, standard techniques for processing GeneChip expression experiments are inapplicable.

Results
We have developed a robust and flexible methodology for high-resolution analysis of DNA copy number of whole genomes, using Affymetrix high-density expression oligonucleotide microarrays. Copy number is obtained from fluorescence signals after processing with novel normalization, spatial artifact correction, data transformation and deletion/duplication detection. We applied our approach to identify deleted and amplified regions in E. coli mutants obtained after prolonged starvation.

Conclusion
The availability of Affymetrix expression chips for a wide variety of organisms makes the proposed array CGH methodology useful more generally.
Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor
Authors: Joshi Saurabh , Davies Holly , Sims Lauren Porter , Levy Shawn E , Dean Jurrien 
Published: June 2007

AbstractBackgroundOvarian folliculogenesis in mammals is a complex process involving interactions between germ and somatic cells. Carefully orchestrated expression of transcription factors, cell adhesion molecules and growth factors are required for success. We have identified a germ-cell specific, basic helix-loop-helix transcription factor, FIGLA (FactorIn theGermLine,Alpha) and demonstrated its involvement in two independent developmental processes: formation of the primordial follicle and coordinate expression of zona pellucida genes.ResultsTaking advantage ofFiglanull mouse lines, we have used a combined approach of microarray andSerialAnalysis ofGeneExpression (SAGE) to identify potential downstream target genes. Using high stringent cutoffs, we find that FIGLA functions as a key regulatory molecule in coordinating expression of the NALP family of genes, genes of known oocyte-specific expression and a set of functionally un-annotated genes. FIGLA also inhibits expression of male germ cell specific genes that might otherwise disrupt normal oogenesis.ConclusionThese data implicate FIGLA as a central regulator of oocyte-specific genes that play roles in folliculogenesis, fertilization and early development.
Oxygen restriction increases the infective potential of Listeria monocytogenes in vitro in Caco-2 cells and in vivo in guinea pigs
Authors: Bo Andersen Jens , Roldgaard Bent B , Christensen Bjarke Bak , Licht Tine Rask 
Published: June 2007

Abstract

Background
Listeria monocytogenes has been implicated in several food borne outbreaks as well as sporadic cases of disease. Increased understanding of the biology of this organism is important in the prevention of food borne listeriosis.
The infectivity of Listeria monocytogenes ScottA, cultivated with and without oxygen restriction, was compared in vitro and in vivo. Fluorescent protein labels were applied to allow certain identification of Listeria cells from untagged bacteria in in vivo samples, and to distinguish between cells grown under different conditions in mixed infection experiments.

Results
Infection of Caco-2 cells revealed that Listeria cultivated under oxygen-restricted conditions were approximately 100 fold more invasive than similar cultures grown without oxygen restriction. This was observed for exponentially growing bacteria, as well as for stationary-phase cultures.
Oral dosage of guinea pigs with Listeria resulted in a significantly higher prevalence (p < 0.05) of these bacteria in jejunum, liver and spleen four and seven days after challenge, when the bacterial cultures had been grown under oxygen-restricted conditions prior to dosage. Additionally, a 10–100 fold higher concentration of Listeria in fecal samples was observed after dosage with oxygen-restricted bacteria. These differences were seen after challenge with single Listeria cultures, as well as with a mixture of two cultures grown with and without oxygen restriction.

Conclusion
Our results show for the first time that the environmental conditions to which L. monocytogenes is exposed prior to ingestion are decisive for its in vivo infective potential in the gastrointestinal tract after passage of the gastric barrier. This is highly relevant for safety assessment of this organism in food.
Performance of the EQ-5D and the EQ-5D+C in elderly patients with cognitive impairments
Authors: Wolfs Claire AG , Dirksen Carmen D , Kessels Alfons , Willems Daniëlle CM , Verhey Frans RJ , Severens Johan L 
Published: June 2007

Abstract

Background
The EQ-5D is a reliable tool for measuring Health-Related Quality of Life (HRQoL). However, concern has been expressed that it may ignore elements of HRQoL, particularly cognition. In response to this concern, the EQ-5D has been extended with a cognitive dimension (EQ-5D+C). The aim of this study was to compare the performance of the EQ-5D and the EQ-5D+C in elderly patients with cognitive impairments by assessing their construct validity and responsiveness.

Methods
Data from the MEDICIE study (n = 196) were used, in which all questionnaires were rated by proxies.

Results
Regarding construct validity, we found similar correlations between the EQ-5D and the Mini Mental State Examination (MMSE) and between the EQ-5D+C and the MMSE. Furthermore, both the EQ-5D and the EQ-5D+C were responsive to changes in the MMSE, with the EQ-5D performing slightly better.

Conclusion
We conclude that the EQ-5D performs well for evaluating HRQoL in a population with cognitive impairments. Based on the results of this explorative study, it does not seem necessary to adjust the current classification system by adding a cognitive dimension. However, in order to compare both instruments regarding utility values, it is necessary to develop a new scoring algorithm for the EQ-5D+C by conducting a general population study. Considering the explorative nature of this study, it is recommended that more aspects of the validity of both the EQ-5D and the EQ-5D+C are explored in patients with cognitive impairments using a more tailored study design.