bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of different exhaled nitric oxide multiple flow rate models in COPD
Authors: Roy K. , Borrill Z. L. , Starkey C. , Hazel A. L. , Morris J. , Vestbo J. , Singh D. 
Published: February 2007

Multiple flow rates of exhaled nitric oxide (eNO) fraction (Fe,NO) data can be modelled to estimate airway wall concentration of nitric oxide (Caw,NO), diffusing capacity of nitric oxide (Daw,NO), alveolar nitric oxide concentration (Calv,NO) and total maximal flux of nitric oxide in the airway compartment (J′aw,NO).Fe,NOat 10, 30, 50, 100 and 200 mL·s−1from 50 chronic obstructive pulmonary disease (COPD) patients and 35 healthy controls (smokers and nonsmokers) modelled using five different methods was compared and the effect of the number of flow rates was investigated.All methods showed that current smoking reducedC&SetFont Italic="0";aw,NOin COPD patients, with some methods showing that smoking reducedJ′aw,NO. Smoking did not affectCalv,NOorDaw,NO. The methods gave similar results forCaw,NObut there was variability between methods forJ′aw,NO,Calv,NOandDaw,NO&SetFont Italic="0";. The median error by least squares fitting between modelled and actual data was significantly lower for the nonlinear method (1.96) compared with the mixed methods (3.31 and 3.62). Parameters calculated using the nonlinear method using five and four flow rates were significantly different. The ratio (95% confidence interval) ofCaw,NOwas 2.02 (1.45–2.83).Nitric oxide models give different results, although airway conductance of nitric oxide is relatively model independent. Nonlinear modelling has the least error, suggesting it is the best method. The number of flow rates should be standardised.
Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence
Authors: Fisk Debra L , Latta Leigh C , Knapp Roland A , Pfrender Michael E 
Published: February 2007

Abstract

Background
Introduced species can have profound effects on native species, communities, and ecosystems, and have caused extinctions or declines in native species globally. We examined the evolutionary response of native zooplankton populations to the introduction of non-native salmonids in alpine lakes in the Sierra Nevada of California, USA. We compared morphological and life-history traits in populations of Daphnia with a known history of introduced salmonids and populations that have no history of salmonid introductions.

Results
Our results show that Daphnia populations co-existing with fish have undergone rapid adaptive reductions in body size and in the timing of reproduction. Size-related traits decreased by up to 13 percent in response to introduced fish. Rates of evolutionary change are as high as 4,238 darwins (0.036 haldanes).

Conclusion
Species introductions into aquatic habitats can dramatically alter the selective environment of native species leading to a rapid evolutionary response. Knowledge of the rates and limits of adaptation is an important component of understanding the long-term effects of alterations in the species composition of communities. We discuss the evolutionary consequences of species introductions and compare the rate of evolution observed in the Sierra Nevada Daphnia to published estimates of evolutionary change in ecological timescales.
Epidemiology and clinical findings associated with enteroviral acute flaccid paralysis in Pakistan
Authors: Saeed Mohsan , Zaidi Sohail Z , Naeem Asif , Masroor Muhammad , Sharif Salmaan , Shaukat Shahzad , Angez Mehar , Khan Anis 
Published: February 2007

Abstract

Background
Enteroviruses are among the most common viruses infecting humans worldwide and they are associated with diverse clinical syndromes. Acute flaccid paralysis (AFP) is a clinical manifestation of enteroviral neuropathy, transverse myelitis, Guillian-Barre Syndrome, Traumatic neuritis and many other nervous system disorders. The objective of this study was to understand the role of Non-Polio Enteroviruses (NPEV) towards this crippling disorder.

Methods
Stool specimens of 1775 children, aged less than 15 years, suffering from acute flaccid paralysis were collected after informed consent within 14 days of onset of symptoms during January 2003 to September 2003. The specimens were inoculated on RD and L20B cells using conventional tube cell culture while micro-neutralization test was used to identify the non-polio enterovirus (NPEV) serotypes. Detailed clinical information and 60-days follow-up reports were analyzed for NPEV-associated AFP cases.

Results
NPEV were isolated from 474 samples. The male to female ratio was 1.4:1. The isolation of NPEV decreased significantly with the increase in age. Cases associated with fever at the onset of NPEV-associated AFP were found to be 62%. The paralysis was found asymmetrical in 67% cases, the progression of paralysis to peak within 4 days was found in 72% cases and residual paralysis after 60 days of paralysis onset was observed in 39% cases associated with NPEV. A clinical diagnosis of Guillian-Barre syndrome was made in 32% cases. On Microneutralization assay, echo-6 (13%) and coxsackievirus B (13%) were the most commonly isolated serotypes of NPEV along with E-7, E-13, E-11, E-4 and E-30. The isolates (n = 181) found untypable by the antiserum pools were confirmed as NPEV by PCR using Pan-Enterovirus primers.

Conclusion
The present study suggests that NPEV are a dominant cause of AFP and different serotypes of NPEV are randomly distributed in Pakistan. The untypable isolates need further characterization and analysis in order to determine their association with clinical presentation of a case.
An adenovirus prime/plasmid boost strategy for induction of equipotent immune responses to two dengue virus serotypes
Authors: Khanam Saima , Rajendra Pilankatta , Khanna Navin , Swaminathan Sathyamangalam 
Published: February 2007

Abstract

Background
Dengue is a public health problem of global significance for which there is neither an effective antiviral therapy nor a preventive vaccine. It is a mosquito-borne viral disease, caused by dengue (DEN) viruses, which are members of the Flaviviridae family. There are four closely related serotypes, DEN-1, DEN-2, DEN-3 and DEN-4, each of which is capable of causing disease. As immunity to any one serotype can potentially sensitize an individual to severe disease during exposure to a heterologous serotype, the general consensus is that an effective vaccine should be tetravalent, that is, it must be capable of affording protection against all four serotypes. The current strategy of creating tetravalent vaccine formulations by mixing together four monovalent live attenuated vaccine viruses has revealed the phenomenon of viral interference leading to the manifestation of immune responses biased towards a single serotype.

Results
This work stems from the emergence of (i) the DEN virus envelope (E) domain III (EDIII) as the most important region of the molecule from a vaccine perspective and (ii) the adenovirus (Ad) as a promising vaccine vector platform. We describe the construction of a recombinant, replication-defective Ad (rAd) vector encoding a chimeric antigen made of in-frame linked EDIIIs of DEN virus serotypes 2 and 4. Using this rAd vector, in conjunction with a plasmid vector encoding the same chimeric bivalent antigen, in a prime-boost strategy, we show that it is possible to elicit equipotent neutralizing and T cell responses specific to both DEN serotypes 2 and 4.

Conclusion
Our data support the hypothesis that a DEN vaccine targeting more than one serotype may be based on a single DNA-based vector to circumvent viral interference. This work lays the foundation for developing a single Ad vector encoding EDIIIs of all four DEN serotypes to evoke a balanced immune response against each one of them. Thus, this work has implications for the development of safe and effective tetravalent dengue vaccines.
Evaluating antibiotics for use in medicine using a poloxamer biofilm model
Authors: Clutterbuck Abi L , Cochrane Christine A , Dolman Jayne , Percival Steven L 
Published: February 2007

Abstract

Background
Wound infections, due to biofilms, are a constant problem because of their recalcitrant nature towards antibiotics. Appropriate antibiotic selection for the treatment of these biofilm infections is important. The traditional in vitro disc diffusion method for antibiotic selection uses bacterial cultures grown on agar plates. However, the form of bacterial growth on agar is not representative of how bacteria grow in wounds and other tissue sites as here bacteria grow naturally in a biofilm. The aim of this research was to test a more appropriate method for testing antimicrobial efficacy on biofilms and compare with the standard methods used for antibiotic sensitivity testing.

Methods
Outer Membrane Protein analysis was performed on E.coli, Staphylococcus aureus, Pseudomonas aeruginosa, Proteus mirabilis and Acinetobacter juni when grown on Mueller Hinton agar ('quasi-biofilm state') and 30% Poloxamer hydrogel ('true- biofilm state). Susceptibility to antibiotics on 28 clinical isolates was determined using the modified Kirby Bauer disc diffusion method, on agar and 30% Poloxamer.

Results
Similar outer membrane proteins [OMPs] were identified in bacteria grown in a biofilm state and on a 30% poloxamer hydrogel, which were very different to the OMPs identified in bacteria grown on Mueller-Hinton agar and broth. There was a significant difference between the means of the clearance zones around the antibiotic discs on standard agar and poloxamer gels [P < 0.05]. The zones of clearance were generally smaller for poloxamer-grown bacteria than those grown on standard agar. Diffusion distances of various antibiotics through agar and 30% poloxamer showed no significant difference [P > 0.05].

Conclusion
The findings of this experiment suggest that poloxamer gel could be used as an appropriate medium on which to conduct biofilm antibiotic susceptibility tests as it enables bacteria to be grown in a state representative of the infected surface from which the culture was taken.
Determining client need in a multi-state fetal alcohol syndrome consortium: from training to practice
Authors: Christopher Suzanne , Dunnagan Tim , Haynes George , Stiff Lili 
Published: February 2007

Abstract

Background
A multi-state consortium was developed in the US to conduct baseline data collection and intervention research on fetal alcohol syndrome. Each state employed support specialists whose job it was to reduce or eliminate alcohol consumption in women who were at high risk for drinking alcohol during their pregnancy. The purpose of this paper is to report how support specialists in three primarily rural/frontier states were trained to assess client need and how client need was actually assessed in the field.

Methods
A qualitative process evaluation was conducted using semi-structured interviews. Interviews were conducted with state staff involved in support specialist training and consortium activities and the support specialists themselves. Inductive analyses were conducted with interview data.

Results
Need determination varied by state and for one state within the state. How support specialists were trained to assess need and how need was assessed in the field was mostly congruent.

Conclusion
Process evaluation is an effective method for providing practical and useful answers to questions that cannot be answered by outcome evaluation alone.
On the performances of different IMRT treatment planning systems for selected paediatric cases
Authors: Fogliata Antonella , Nicolini Giorgia , Alber Markus , Åsell Mats , Clivio Alessandro , Dobler Barbara , Larsson Malin , Lohr Frank , Lorenz Friedlieb , Muzik Jan , Polednik Martin , Vanetti Eugenio , Wolff Dirk , Wyttenbach Rolf , Cozzi Luca 
Published: February 2007

Abstract

Background
To evaluate the performance of seven different TPS (Treatment Planning Systems: Corvus, Eclipse, Hyperion, KonRad, Oncentra Masterplan, Pinnacle and PrecisePLAN) when intensity modulated (IMRT) plans are designed for paediatric tumours.

Methods
Datasets (CT images and volumes of interest) of four patients were used to design IMRT plans. The tumour types were: one extraosseous, intrathoracic Ewing Sarcoma; one mediastinal Rhabdomyosarcoma; one metastatic Rhabdomyosarcoma of the anus; one Wilm's tumour of the left kidney with multiple liver metastases. Prescribed doses ranged from 18 to 54.4 Gy. To minimise variability, the same beam geometry and clinical goals were imposed on all systems for every patient. Results were analysed in terms of dose distributions and dose volume histograms.

Results
For all patients, IMRT plans lead to acceptable treatments in terms of conformal avoidance since most of the dose objectives for Organs At Risk (OARs) were met, and the Conformity Index (averaged over all TPS and patients) ranged from 1.14 to 1.58 on primary target volumes and from 1.07 to 1.37 on boost volumes. The healthy tissue involvement was measured in terms of several parameters, and the average mean dose ranged from 4.6 to 13.7 Gy. A global scoring method was developed to evaluate plans according to their degree of success in meeting dose objectives (lower scores are better than higher ones). For OARs the range of scores was between 0.75 ± 0.15 (Eclipse) to 0.92 ± 0.18 (Pinnacle3 with physical optimisation). For target volumes, the score ranged from 0.05 ± 0.05 (Pinnacle3 with physical optimisation) to 0.16 ± 0.07 (Corvus).

Conclusion
A set of complex paediatric cases presented a variety of individual treatment planning challenges. Despite the large spread of results, inverse planning systems offer promising results for IMRT delivery, hence widening the treatment strategies for this very sensitive class of patients.
Genome display tool: visualizing features in complex data sets
Authors: Viswanath Lalitha , Lu Yue , Fox George E 
Published: February 2007

Abstract

Background
The enormity of the information contained in large data sets makes it difficult to develop intuitive understanding. It would be useful to have software that allows visualization of possible correlations between properties that can be associated with a core data set. In the case of bacterial genomes, existing visualization tools focus on either global properties such as variations in composition or detailed local displays of the features that comprise the annotation. It is not easy to visualize other information in the context of this core information.

Results
A Java based software known as the Genome Display Tool (GDT), allows the user to simultaneously view the distribution of multiple attributes pertaining to genes and intragenic regions in a single bacterial genome using different colours and shapes on a single screen. The display represents each gene by small boxes that correlate with physical position in the genome. The size of the boxes is dynamically allocated based on the number of genes and a zoom feature allows close-up inspection of regions of interest. The display is interfaced with a MS-Access relational database and can display any feature in the database that can be represented by discrete values. Data is readily added to the database from an MS-Excel spread sheet. The functionality of GDT is demonstrated by comparing the results of two predictions of recent horizontal transfer events in the genome of Synechocystis PCC-6803. The resulting display allows the user to immediately see how much agreement exists between the two methods and also visualize how genes in various categories (e.g. predicted in both methods, one method etc) are distributed in the genome.

Conclusion
The GDT software provides the user with a powerful tool that allows development of an intuitive understanding of the relative distribution of features in a large data set. As additional features are added to the data set, the number of possible correlations that can be visualized grows rapidly. Although described here for use in bacterial genomics, the principle is general and similar software might be useful in other contexts such as patient studies.
Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis
Authors: Yetukuri Laxman , Katajamaa Mikko , Medina-Gomez Gema , Seppänen-Laakso Tuulikki , Vidal-Puig Antonio , Orešič Matej 
Published: February 2007

Abstract

Background
Lipids are an important and highly diverse class of molecules having structural, energy storage and signaling roles. Modern analytical technologies afford screening of many lipid molecular species in parallel. One of the biggest challenges of lipidomics is elucidation of important pathobiological phenomena from the integration of the large amounts of new data becoming available.

Results
We present computational and informatics approaches to study lipid molecular profiles in the context of known metabolic pathways and established pathophysiological responses, utilizing information obtained from modern analytical technologies. In order to facilitate identification of lipids, we compute the scaffold of theoretically possible lipids based on known lipid building blocks such as polar head groups and fatty acids. Each compound entry is linked to the available information on lipid pathways and contains the information that can be utilized for its automated identification from high-throughput UPLC/MS-based lipidomics experiments. The utility of our approach is demonstrated by its application to the lipidomic characterization of the fatty liver of the genetically obese insulin resistant ob/ob mouse model. We investigate the changes of correlation structure of the lipidome using multivariate analysis, as well as reconstruct the pathways for specific molecular species of interest using available lipidomic and gene expression data.

Conclusion
The methodology presented herein facilitates identification and interpretation of high-throughput lipidomics data. In the context of the ob/ob mouse liver profiling, we have identified the parallel associations between the elevated triacylglycerol levels and the ceramides, as well as the putative activated ceramide-synthesis pathways.
A minimal set of dynamic equations in systems modelled with bond graphs
Authors: Romero G , Felez J , Maroto J , Cabanellas J. M. 
Published: February 2007

The current paper presents a procedure for converting to a minimal set the dynamic equations of a system modelled with bond graphs starting from a large set of differential-algebraic equations including any type of topological loops and zero-order causal paths (ZCPs). This minimal set is composed only of differential equations expressed in terms of the degrees of freedom of the system. These equations are suitable for use in real-time simulations. Initially, flows corresponding to inertances and displacements associated with compliances are used to establish the dynamic equations and to find the ZCPs of the system. Two different methods are used to solve the ZCPs. With the first method, Lagrange multipliers are introduced by means of new flows and efforts as break variables of causal paths, adding constraint equations. With the second method, break variables are used directly to open the ZCPs. The procedure developed in the present paper solves the problem originated by the use of Lagrange multipliers with the introduction of break variables that imply the presence of new variables and constraint equations. This procedure, before numerical integration of the dynamic equations, converts the equations to a minimal set in order to gain computational efficiency. Several examples are also provided to illustrate the conversion steps.
Evaluation of Assigned-Value Uncertainty for Complex Calibrator Value Assignment Processes: A Prealbumin Example
Authors: Middleton John , Vaks Jeffrey E 
Published: February 2007

Abstract
Background: Errors of calibrator-assigned values lead to errors in the testing of patient samples. The ability to estimate the uncertainties of calibrator-assigned values and other variables minimizes errors in testing processes. International Organization of Standardization guidelines provide simple equations for the estimation of calibrator uncertainty with simple value-assignment processes, but other methods are needed to estimate uncertainty in complex processes.
Methods: We estimated the assigned-value uncertainty with a Monte Carlo computer simulation of a complex value-assignment process, based on a formalized description of the process, with measurement parameters estimated experimentally. This method was applied to study uncertainty of a multilevel calibrator value assignment for a prealbumin immunoassay.
Results: The simulation results showed that the component of the uncertainty added by the process of value transfer from the reference material CRM470 to the calibrator is smaller than that of the reference material itself (&lt;0.8% vs 3.7%). Varying the process parameters in the simulation model allowed for optimizing the process, while keeping the added uncertainty small. The patient result uncertainty caused by the calibrator uncertainty was also found to be small.
Conclusions: This method of estimating uncertainty is a powerful tool that allows for estimation of calibrator uncertainty for optimization of various value assignment processes, with a reduced number of measurements and reagent costs, while satisfying the requirements to uncertainty. The new method expands and augments existing methods to allow estimation of uncertainty in complex processes.
Systematic review of clinical trials of treatments for osteoarthritis in dogs
Authors: Aragon Carlos L. , Hofmeister Erik H. , Budsberg Steven C. 
Published: February 2007

Abstract
Objective—To identify and critically evaluate the quality of evidence of the most commonly used pharmacologic, nutraceutical, and purported slow-acting drugs of osteoarthritis for the management of osteoarthritis in dogs by use of the FDA's evidence-based medicine scoring system.
Design—Systematic review.
Sample Population—16 clinical trials.
Procedures—A broad bibliographic search was performed prior to May 2006. Inclusion criteria focused on prospective trials evaluating commonly used medical treatment interventions for the management of osteoarthritis in dogs and published in peer-reviewed journals. The analysis consisted of the following: study design rating, quality factor rating, quantity rating, consistency rating, relevance to disease risk reduction rating, and cumulative strength of evidence ranking.
Results—4 trials evaluating meloxicam were rated as type I.Three trials evaluating carprofen were rated as type I, and 2 trials were rated as type III. One trial evaluating each of the following agents was rated as type 1: etodolac; P54FP; polysulfated glycosaminoglycan; and a combination of chondroitin sulfate, glucosamine hydrochloride, and manganese ascorbate. Two trials evaluating pentosan polysulphate and 2 trails evaluating green-lipped mussels were rated as type I. One trial evaluating hyaluronan was rated as type III.
Conclusions and Clinical Relevance—A high level of comfort exists for meloxicam that the claimed relationship is scientifically valid and that its use is clinically efficacious for the treatment of osteoarthritis in dogs.A moderate level of comfort exists for carprofen; etodolac; pentosan polysulphate; green-lipped mussels; P54FP; polysulfated glycosaminoglycans; and a combination of chondroitin sulfate, glucosamine hydrochloride, and manganese ascorbate. An extremely low level of comfort exists for hyaluronan.