bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hayek, The Road to Serfdom, and the British Conservatives
Authors: Shearmur Jeremy 
Published: August 2006

Over the years, Friedrich Hayek has received a generous response from some members of the British Conservative Party. One immediately thinks of endorsements of his work by Mrs. Thatcher in the 1970s and '80s.Those with longer memories—and teeth—might also recall the controversy around Winston Churchill's first election broadcast in 1945, and the response to it by the Labour leader Clement Attlee, the following evening. Churchill spoke of the dangers of planning, and raised the idea that it would, in the end, require the powers of a Gestapo to put the ideal of a planned society into practice. Attlee criticized these ideas, and Hayek as the source of the theoretical conceptions behind them. This led to a fair bit of attention being paid to Hayek by the press, and to his being described as an economic adviser to Churchill. But Hayek himself has downplayed his direct contacts with Churchill (cf. Hayek 1994, pp. 106–107). Indeed, in Hayek on Hayek (Hayek 1994), Hayek indicates that he met Churchill only once. On that occasion he was struck by Churchill's being the worse for drink and then recovering, to Hayek's surprise, to make a first-rate speech.
Text similarity: an alternative way to search MEDLINE
Authors: Lewis James , Ossowski Stephan , Hicks Justin , Errami Mounir , Garner Harold R. 
Published: August 2006

Abstract
Motivation: The most widely used literature search techniques, such as those offered by NCBI's PubMed system, require significant effort on the part of the searcher, and inexperienced searchers do not use these systems as effectively as experienced users. Improved literature search engines can save researchers time and effort by making it easier to locate the most important and relevant literature.
Results: We have created and optimized a new, hybrid search system for Medline that takes natural text as input and then delivers results with high precision and recall. The combination of a fast, low-sensitivity weighted keyword-based first pass algorithm to cast a wide net to gather an initial set of literature, followed by a unique sentence-alignment based similarity algorithm to rank order those results was developed that is sensitive, fast and easy to use. Several text similarity search algorithms, both standard and novel, were implemented and tested in order to determine which obtained the best results in information retrieval exercises.
Availability: Literature searching algorithms are implemented in a system called eTBLAST, freely accessible over the web at . A variety of other derivative systems and visualization tools provides the user with an enhanced experience and additional capabilities.
Contact: Harold.Garner@UTSouthwestern.edu
Systematic component selection for gene-network refinement
Authors: Radde Nicole , Gebert Jutta , Forst Christian V. 
Published: August 2006

Abstract
Motivation: A quantitative description of interactions between cell components is a major challenge in Computational Biology. As a method of choice, differential equations are used for this purpose, because they provide a detailed insight into the dynamic behavior of the system. In most cases, the number of time points of experimental time series is usually too small to estimate the parameters of a model of a whole gene regulatory network based on differential equations, such that one needs to focus on subnetworks consisting of only a few components. For most approaches, the set of components of the subsystem is given in advance and only the structure has to be estimated. However, the set of components that influence the system significantly are not always known in advance, making a method desirable that determines both, the components that are included into the model and the parameters.
Results: We have developed a method that uses gene expression data as well as interaction data between cell components to define a set of genes that we use for our modeling. In a subsequent step, we estimate the parameters of our model of piecewise linear differential equations and evaluate the results simulating the behavior of the system with our model.
We have applied our method to the DNA repair system of Mycobacterium tuberculosis. Our analysis predicts that the gene Rv2719c plays an important role in this system.
Contact: {radde.gebert}@zpr.uni-koeln.de, chris@lanl.gov
Eigengene-based linear discriminant model for tumor classification using gene expression microarray data
Authors: Shen Ronglai , Ghosh Debashis , Chinnaiyan Arul , Meng Zhaoling 
Published: August 2006

Abstract
Motivation: The nearest shrunken centroids classifier has become a popular algorithm in tumor classification problems using gene expression microarray data. Feature selection is an embedded part of the method to select top-ranking genes based on a univariate distance statistic calculated for each gene individually. The univariate statistics summarize gene expression profiles outside of the gene co-regulation network context, leading to redundant information being included in the selection procedure.
Results: We propose an Eigengene-based Linear Discriminant Analysis (ELDA) to address gene selection in a multivariate framework. The algorithm uses a modified rotated Spectral Decomposition (SpD) technique to select ‘hub’ genes that associate with the most important eigenvectors. Using three benchmark cancer microarray datasets, we show that ELDA selects the most characteristic genes, leading to substantially smaller classifiers than the univariate feature selection based analogues. The resulting de-correlated expression profiles make the gene-wise independence assumption more realistic and applicable for the shrunken centroids classifier and other diagonal linear discriminant type of models. Our algorithm further incorporates a misclassification cost matrix, allowing differential penalization of one type of error over another. In the breast cancer data, we show false negative prognosis can be controlled via a cost-adjusted discriminant function.
Availability: R code for the ELDA algorithm is available from author upon request.
Contact: zhaoling.meng@sanofi-aventis.com
Supplementary information: Supplementary data are available at Bioinformatics online.
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool
Authors: Zi Zhike , Klipp Edda 
Published: August 2006

Abstract
Summary: The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system.
Availability: . The website also contains detailed documentation for SBML-PET.
Contact: klipp@molgen.mpg.de, zhike_zi@molgen.mpg.de
Cost‐effectiveness analysis of screening modalities for breast cancer in Japan with special reference to women aged 40–49 years
Authors: Ohnuki Koji , Kuriyama Shinichi , Shoji Narumi , Nishino Yoshikazu , Tsuji Ichiro , Ohuchi Noriaki 
Published: August 2006

Although the introduction of screening mammography in Japan would be expected to reduce mortality from breast cancer, the optimal screening modality in terms of cost‐effectiveness remains unclear. We compared the cost‐effectiveness ratio, defined as the cost required for a life‐year saved, among the following three strategies: (1) annual clinical breast examination; (2) annual clinical breast examination combined with mammography; and (3) biennial clinical breast examination combined with mammography for women aged 30–79 years using a hypothetical cohort of 100 000. The sensitivity, specificity and early breast cancer rates were derived from studies conducted from 1995 to 2000 in Miyagi Prefecture. The treatment costs were based on a questionnaire survey conducted at 13 institutions in Japan. We used updated parameters that were needed in the analysis. Although the effectiveness of treatment in terms of the number of expected survival years was highest for annual combined modality, biennial combined modality had a higher cost‐effectiveness ratio, followed by annual combined modality and annual clinical breast examination in all age groups. In women aged 40–49 years, annual combined modality saved 852.9 lives and the cost/survival duration was 3 394 300 yen/year, whereas for biennial combined modality the corresponding figures were 833.8 and 2 025 100 yen/year, respectively. Annual clinical breast examination did not confer any advantages in terms of effectiveness (815.5 lives saved) or cost‐effectiveness (3 669 900 yen/year). While the annual combined modality was the most effective with respect to life‐years saved among women aged 40–49 years, biennial combined modality was found to provide the highest cost‐effectiveness. (Cancer Sci 2006; 97: 1242–1247)
Nutrition and allergic disease
Authors: Tricon S. , Willers S. , Smit H. A. , Burney P. G. , Devereux G. , Frew A. J. , Halken S. , Høst A. , Nelson M. , Shaheen S. , Warner J. O. , Calder P. C. 
Published: August 2006

SummaryThe prevalence of asthma and allergic diseases has increased dramatically over the past few decades with the highest incidence occurring in children. Most asthma and related atopic disorders have their origins in early life. Thus, it is imperative to understand the early life origins of the disease in order to identify targets for prevention and early intervention. Although atopic diseases have genetic determinants, the increased incidence of these diseases has occurred far too rapidly for genetic changes to explain the increase. This, most likely, results from changes in environmental influences acting on a pre‐existent genetic susceptibility. One of the environmental changes over the last 20–40 years that could have contributed to the recent increase in atopic diseases is diet. Food allergy is often one of the earliest manifestations of atopy, and sensitization to food is a risk factor for the subsequent appearance of respiratory allergy and asthma. However, studies investigating the effects of dietary restrictions on the prevention of allergy have been disappointing. On the other hand, current data suggests that exclusive breastfeeding should be encouraged for at least 4–6 months in infants at both high and low risk of atopy. Increased risk of asthma has also been observed in low birth weight infants, suggesting that under‐nutrition can detrimentally alter foetal development. Epidemiological and immunological studies also suggest that dietary modification or supplementation in the foetal and early life could reduce the development of atopic diseases. The current dietary hypotheses relate to antioxidants, lipids, electrolytes and probiotics. The aims of this report are: (i) to assess the best methods to analyse nutrient intake and nutrient status; (ii) to review the existing epidemiological evidence for an association between dietary intake (nutrients and food) and allergic diseases; and (iii) to define the windows of opportunity for nutritional supplementation to be used as a preventative strategy for asthma and allergy.
Influence of stream geomorphic condition on fish communities in Vermont, U.S.A.
Authors: SULLIVAN S. MAŽEIKA P. , WATZIN MARY C. , HESSION W. CULLY 
Published: August 2006

Summary1. Evaluations of stream geomorphic condition may increase our understanding of the composite effects of human‐induced habitat change on fish communities. Using systematic sampling of 44 reaches spread across 26 rivers in Vermont from 2002 through 2004, we tested the hypothesis that stream reaches in reference geomorphic condition would support fish assemblages that differed in diversity and productivity from fish communities found in reaches of poorer geomorphic condition.2. At each study reach, we sampled the fish community, identified the morphological unit according to common stream classification systems and then evaluated the extent of deviation from reference geomorphic condition using a regionally adapted geomorphic assessment methodology.3. We used principal component analysis (PCA) and linear regression to build exploratory models linking stream geomorphic condition to fish community characteristics.4. Our results suggest that geomorphic condition significantly influences fish community diversity, productivity and condition. Geomorphic condition was a significant factor in all of our fish community models. In conjunction with additional reach characteristics, geomorphic condition explained up to 31% of the total variance observed in models for species diversity of fish communities, 44% of the variance in assemblage biomass and 45% of the variance in a regional index of biotic integrity.5. Our work builds on single‐species evidence that geomorphic characteristics represent important local‐scale fish‐habitat variables, showing that stream geomorphic condition is a dominant factor affecting entire fish communities. Our results enhance our understanding of the hierarchy of factors that influences fish community diversity and organisation and support the use of geomorphic condition assessments in stream management.
The effect of whey protein concentrates and hydrocolloids on the texture and colour characteristics of chicken sausages
Authors: Andrès Silvina , Zaritzky Noemí , Califano Alicia 
Published: August 2006

SummaryThe effects of fat reduction by increasing water content and the addition of whey protein and hydrocolloids on the instrumental texture profile, microstructure and water holding capacity of low‐fat chicken sausages were analysed. Low‐fat sausages were prepared with fresh breast chicken meat; in all formulations, a 3:7 ratio guar/xanthan gum was used. A factorial design with three levels of added fat (0%, 1.98% and 4.96%), two levels of whey protein concentrate (0.64% and 1.94%), and two levels of the hydrocolloids (0.13% and 0.32%) was applied. Samples were heat‐processed (73 °C final internal temperature) and, after cooling, chemical composition of the sausages was determined and scanning electron microscopic images were obtained. Colour was measured with a tristimulus reflectance colorimeter. Texture profile analysis of sausages was performed and the results were related to sample formulations. Extra‐lean products with a fat content lower than 0.5 g/100 g product showed very good quality attributes determined by a sensory panel.
Heat transfer coefficients to canned green peas during end‐over‐end sterilisation
Authors: Garrote Raúl L. , Silva Enrique R. , Roa Rubén D. , Bertone Ricardo A. 
Published: August 2006

SummaryThe effect of temperature (110, 120 and 130 °C), rotation speed (5, 10 and 15 r.p.m.) and headspace (4, 8 and 12 mm) on heat transfer coefficients to canned green peas during end‐over‐end sterilisation was studied using response surface methodology. The models developed for fluid‐to‐particle heat transfer coefficient, hfp, and overall heat transfer coefficient, U, were adequate, showing no significant lack of fit and satisfactory correlation coefficients. For the two responses, temperature, rotation speed and headspace have a significant effect. U, ranged between 477 and 905 W m−2 °C−1, while hfp, fluctuated between 480 and 1950 W m−2 °C−1. The highest hfp and U values are obtained at high temperatures, rotation speeds and headspaces. The verification of the prediction models was satisfactory. Dimensionless correlations were developed for hfp and U, with equations showing a good agreement with the experimental data. Heat transfer to liquids and particles was modelled using the Reynolds number, the Prandtl number and adimensional headspace.
Lipase‐catalysed acidolysis of lard with caprylic acid to produce structured lipid
Authors: Zhao Haizhen , Lu Zhaoxin , Lu Fengxia , Bie Xiaomei , Liu Zhanmin , Zeng Xiaoxiong 
Published: August 2006

SummaryEnzymatic acidolysis of lard with caprylic acid was investigated. Of the five lipases that were tested in the initial screening, immobilised lipase TL IM from Thermomyces lanuginosus resulted in the highest incorporation of caprylic acid into lard. This enzyme was further studied for the effect of enzyme load, organic solvent, substrate ratio, reaction time and temperature. HPLC was used to analyse the products from the acidolysis reaction. The highest incorporation was attained at 15% enzyme load. Among the solvents tested, n‐hexane was the best reaction medium for the acidolysis of lard with caprylic acid. Time course studied suggests that the incorporation of caprylic acid into lard was increased up to 37.7 mol% after 24 h. Desirable mole ratio of lard to caprylic acid was 1:2, caprylic acid incorporation up to 34.2 mol%. Temperature had no significant effect on enzyme activity in the range of 40–80 °C.
Improvement of the functionality of a potential fruit insoluble fibre by micron technology
Authors: Chau Chi‐Fai , Wen Yu‐Ling , Wang Yi‐Ting 
Published: August 2006

SummaryAn insoluble food fibre was micronised to different microsizes (6.77–29.5 μm) by three different micron technologies using optimised conditions. The effects of different micronisation treatments and particle sizes on the characteristics and various physicochemical properties of this insoluble fibre were studied. As particle size decreased, the bulk density of the insoluble fibre was significantly (P < 0.05) decreased. A redistribution of fibre components from insoluble to soluble fractions was observed. The treatments, especially the high‐pressure micronisation, effectively (P < 0.05) increased the physicochemical properties (e.g. water‐holding capacity, swelling capacity, oil‐holding capacity, cation‐exchange capacity and glucose‐adsorption capacity) and also the inhibitory activity towards α‐amylase and pancreatic lipase of the insoluble fibre to different extent (from several up to c. fifteenfold). Our results suggested that micronisation treatments would provide an opportunity to improve the functionality of the insoluble fibre and exploit its potential applications as a functional ingredient in fibre‐rich products.
Partial purification and characterisation of polyphenol oxidase from celery root (Apium graveolens L.) and the investigation of the effects on the enzyme activity of some inhibitors
Authors: Aydemir Tülin , Akkanlı Gülay 
Published: August 2006

SummaryPolyphenol oxidase (PPO) of celery root was extracted and partially purified by (NH4)2SO4 fractionation and dialysis. Optimum pH and temperature were found at pH 7.0 and 30 °C, and Km and Vmax values were 29 mm and 5560 U mL−1 min−1 with catechol, respectively. The activation energy of the enzyme with catechol was 17.9 kJ mol−1 at pH 7.0. In electrophoretic seperation, six isoenzymes were detected with dl‐dopa substrate. PPO showed activity to catechol, 4‐methylcatechol, pyrogallol, gallic acid, dl‐dopa. l‐Tyrosine was also tested but was not oxidised by celery root PPO. β‐Mercaptoethanol was found to be the most effective inhibitor. (NH4)2SO4, NaCl, KCl and sucrose appeared to be protective agents of celery root PPO against thermal denaturation. Metal ions (Cu2+, Zn2+, Mn2+) were poor inhibitors of the celery root PPO at 1 mm. PPO activity was also inhibited by CaCl2, NaCl, BaCl2, FeSO4 and NiCl2.
Hydrological disturbance benefits a native fish at the expense of an exotic fish
Authors: LEPRIEUR F. , HICKEY M. A. , ARBUCKLE C. J. , CLOSS G. P. , BROSSE S. , TOWNSEND C. R. 
Published: August 2006

SummarySome native fish in New Zealand do not coexist with introduced salmonids. Previous studies of disjunct distributions of exotic brown troutSalmo truttaand native galaxiids demonstrated native extirpation except where major waterfalls prevented upstream migration of trout. In the Manuherikia River system, we predicted that water abstraction might be a further factor controlling the spatial distribution of both the invader and a native fish.We applied multiple discriminant function analyses to test for differences in environmental conditions (catchment and instream scales) at sites with roundhead galaxiasGalaxias anomalusand brown trout in sympatry and allopatry. We then used a supervised artificial neural network (ANN) to predict the presence–absence ofG. anomalusand brown trout (135 sites). The quantification of contributions of environmental variables to ANN models allowed us to identify factors controlling their spatial distribution.Brown trout can reach most locations in the Manuherikia catchment, and often occur upstream ofG. anomalus. Their largely disjunct distributions in this river are mediated by water abstraction for irrigation, together with pool habitat availability and valley slope. Trout are more susceptible than the native fish to stresses associated with low flows, and seem to be prevented from eliminating galaxiid populations from sites in low gradient streams where there is a high level of water abstraction.Synthesis and applications. In contrast to many reports in the literature, our results show that hydrological disturbance associated with human activities benefits a native fish at the expense of an exotic in the Manuherikia River, New Zealand. Water abstraction is also known to have negative impacts on native galaxiids, therefore we recommend restoring natural low flows to maintain sustainable habitats for native galaxiids, implementing artificial barriers in selected tributaries to limit trout predation on native fish, and removing trout upstream.
Line‐intercept laboratory subsampling estimates periphyton biovolumes more efficiently than standard methods
Authors: FRAPPIER BRIAN , DUCEY MARK J. 
Published: August 2006

Summary

Algal assemblages have been included in biological monitoring in a number of national, large‐scale and long‐term biological monitoring and assessment programmes of streams, lakes and wetlands. However, there has been no substantial investigation of alternative enumeration strategies.
We compared the sampling efficiency of the common periphyton subsampling strategies of counting 300 cells by strip counts or random fields and measuring 10 cells per taxon for biovolume, with line‐intercept sampling (LIS), using samples collected from four streams differing in canopy cover and discharge. We also simulated the optimum ratio of cells tallied to cells measured for biovolume for all approaches.
LIS was 1·6–5·5 times more efficient at estimating algal taxa biovolume than the 300‐cell count methods. LIS performed best relative to conventional 300‐cell count methods in streams with high biovolume, although efficiency gains were still noticeable in low biovolume streams. In addition, LIS tended to detect more taxa than the conventional 300‐cell target biological assessment methods.
In simulations, LIS was more efficient than the conventional methods for nearly all combinations of target cell count and cells measured for biovolume. No single optimal ratio of cells counted to cells measured was found. The target cell count that resulted in the greatest efficiency was higher in assemblages with large variation in cell density. Likewise, assemblages with high variance in taxa biovolume were most efficiently sampled by measuring more cells.
Synthesis and applications. An increase in sampling efficiency as a result of greater adoption of LIS sampling may result in more accurate estimation of the relationships between periphyton community composition and environmental factors, and more sensitive detection of impacts using stream periphyton. Additionally, LIS may improve estimates in other ecological research fields employing microscopic counting chambers.