bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aspects of anthocyanin absorption, metabolism and pharmacokinetics in humans
Authors: Kay Colin D 
Published: July 2006

AbstractInterest in the health-promoting properties of berry anthocyanins is intensifying; however, findings are primarily based onin vitrocharacteristics, leaving mechanisms associated with absorption, metabolism and pharmacokinetics largely unexplored. The present review integrates the available anthocyanin literature with that of similar flavonoids or polyphenols in order to form hypotheses regarding absorption, metabolism and clearance in humans. Of the limited available literature regarding the absorption and clearance kinetics of anthocyanins, maximum plasma concentrations are reported anywhere between 1·4 and 592 nmol/l and occur at 0·5–4 h post-consumption (doses; 68–1300 mg). Average urinary excretion is reported between 0·03 and 4 % of the ingested dose, having elimination half-lives of 1·5–3 h. In addition, much is unknown regarding the metabolism of anthocyanins. The most commonly cited conjugation reactions involved in the metabolism of other flavonoids include glucuronidation, methylation and sulfation. It is reasonable to suspect that anthocyanins are metabolised in much the same manner; however, until recently, there was little evidence to suggest that anthocyanins were metabolised to any significant extent. New evidence now suggests that anthocyanins are absorbed and transported in human serum and urine primarily as metabolites, with recent studies documenting as much as 68–80 % of anthocyanins as metabolised derivatives in human urine. Further research is required to resolve mechanisms associated with the absorption, metabolism and clearance of anthocyanins in order to establish their true biological activities and health effects. The presented evidence will hopefully focus future research, refining study design and propagating a more complete understanding of anthocyanins' biological significance in humans.
Different dietary strategies for weight loss in obesity: role of energy and macronutrient content
Authors: Abete I , Parra M. D , Zulet M. A , Martínez J. A 
Published: July 2006

AbstractObesity is a chronic disorder caused by an imbalance of the energy metabolism with high associated burdens. Therefore, huge efforts are being currently devoted in studying new types of hypoenergetic diets and their composition, in order to characterise more specific, long-lasting and safe slimming protocols. A number of investigations are trying to determine the specific influence of the macronutrient distribution in energy-restricted diets on the management of excessive body weight. In this context, very-low-energy diets supplying between 1670 and 3350 kJ (400 and 800 kcal)/d have been beneficial in short-term treatments causing a weight loss of 300–500 g/d. Such strategies place more emphasis on energy restriction than on the macronutrient composition of the diet prescription. Weight loss produced by either low-carbohydrate or low-fat moderately energy-restricted diets ranges from 0·5 to 1·0 kg/week, while diets with high or moderately high protein content have also been applied in weight-reducing programmes by inducing losses of 0·2–0·4 kg/week. Other factors that determine weight loss by dieting are sex, age, initial body weight, race, genetics, regional fat deposition, etc, which must be taken into account to explain the variability in the outcomes of different low-energy diets. Therefore, more research is needed about the impact of diets with different fuel substrates and foods on the characteristics of the weight-loss process.
Parameters controlling the glycaemic response to breads
Authors: Fardet Anthony , Leenhardt Fanny , Lioger Delphine , Scalbert Augustin , Rémésy Christian 
Published: July 2006

AbstractBread is one of the most widely consumed staple foods worldwide. White-wheat bread, largely consumed in France, is made from highly refined flour, which leads to a low nutrient density. Due to a highly porous structure and gelatinised starch, it is easily broken down during digestion, leading to a rapid increase of glucose released into the bloodstream. Low glycaemic responses are considered favourable to health, especially against a background of diabetes. Literature reports show that selection of raw material is an essential factor in decreasing the glycaemic index (GI) of white bread. There are two means of decreasing the rate of starch degradation: either (i) slowing gastric emptying rate and/or glucose diffusion–absorption through the intestinal mucosa, which can be achieved by incorporating soluble fibre or organic acid in bread, or (ii) limiting starch accessibility to α-amylase by using high-amylose cereal varieties and/or incorporating intact cereal grains. Studies on cereal products show that preservation of the food structure during digestion seems to be a more important GI-reducing factor than the degree of starch crystallinity or the presence of soluble fibre. Thus, we should look to produce bread with a more compact food structure or higher density, which is the case in leavened wholewheat bread or bread with intact cereal grains. The baking process should also be improved to achieve this goal, by using, for example, a reduced kneading time or less yeast than usual.
Evolving enzyme technology: impact on commercial poultry nutrition
Authors: Cowieson A. J , Hruby M , Pierson E. E. M 
Published: July 2006

AbstractThe use of exogenous enzymes to improve the nutritional value of poultry diets is a relatively new concept. The technology is rapidly evolving, with new enzymes, enzyme combinations, and novel applications being developed as rapidly as regulatory restrictions will allow. Most researchers in the field of poultry nutrition would consider phytase to be the last significant leap forward in terms of enzyme use in the animal feed industry. However, there is a great deal of ongoing research into the next generation of enzymes with a focus on ingredient quality, predictability of response via least-square models, improvements in food safety, effect of bird age, effect of various side activities and enzyme dose, maximisation of net income and reduction in environmental pollution. It is the purpose of the present review article to summarise the current research in the area of feed enzymes for poultry and to speculate on future applications of enzymes and new enzyme technologies that may be of value to the industry in the coming years.
Nutritional supplements: prevalence of use and contamination with doping agents
Authors: Van Thuyne W , Van Eenoo P , Delbeke F. T 
Published: July 2006

AbstractBased upon recent sales numbers, nutritional supplements play a key role in the lifestyle of a substantial proportion of the population. As well as products such as vitamins or minerals, several precursors of anabolic steroids are marketed as nutritional supplements. Another group of commercially available supplements are products for weight loss based upon herbal formulations originating fromEphedraspecies. Apart from supplements indicating the presence of these active compounds, numerous non-hormonal nutritional supplements were found that were contaminated with non-labelled anabolic steroids. Stimulating agents other than naturally occurring analogues of ephedrine were detected. A major group using dietary supplements are sportsmen, ranging from amateur level to elite athletes. Besides the possible health risks associated with the use of dietary supplements, athletes should take care not to violate the rules of the World Anti-Doping Agency because athletes remain responsible for substances detected in their biofluids, irrespective of their origin. Several analytical methods have been developed to determine the presence of doping agents as contaminants. The present review attempts to address the issues concerning the use of nutritional supplements and the detection of doping agents as contaminants in dietary supplements.
Influence of dietary components on development of the microbiota in single-stomached species
Authors: Bauer Eva , Williams Barbara A , Smidt Hauke , Mosenthin Rainer , Verstegen Martin W. A 
Published: July 2006

AbstractAfter birth, development of a normal microbial community occurs gradually, and is affected by factors such as the composition of the maternal gut microbiota, the environment, and the host genome. Diet also has a direct influence, both on composition and activity of this community. This influence begins with the milk, when specific components exert their growth-promoting effect on a beneficial microbiota, thereby suppressing potential pathogens. For example, breast-fed infants compared with formula-fed babies usually have a microbial community dominated by bifidobacteria. When solid food is introduced (weaning), dramatic changes in microbial composition occur, so pathogens can gain access to the disturbed gastrointestinal (GI) ecosystem. However, use of specific dietary components can alter the composition and activity of the microbiota positively. Of all dietary components, fermentable carbohydrates seem to be most promising in terms of promoting proliferation of beneficial bacterial species. Carbohydrate fermentation results in the production of SCFA which are known for their trophic and health-promoting effects. Fermentation of proteins, on the other hand, is often associated with growth of potential pathogens, and results in production of detrimental substances including NH3and amines. In terms of the GI microbiota, lipids are often associated with the antimicrobial activity of medium-chain fatty acids and their derivatives. The present review aims to provide deeper insights into the composition and development of the neonatal GI microbiota, how this microbiota can be influenced by certain dietary components, and how this might ultimately lead to improvements in host health.
Changes in the initiation of heroin use after a reduction in heroin supply
Authors: DAY CAROLYN , DEGENHARDT LOUISA , HALL WAYNE 
Published: July 2006

AbstractIncreasing heroin use in Australia over the past 30 years has been associated with a decline in the age of initiation to heroin use. The 2001 Australian heroin shortage was used to assess the effects of a reduction in heroin supply on age of initiation into heroin injecting. Data collected from regular injecting drug users (IDU) over the period 1996–2004 as part of the Australian Illicit Drug Reporting System were examined for changes in self‐reported age of first heroin use after the onset of the heroin shortage. Estimates were also made of the number of young people who may not have commenced injecting heroin during the heroin shortage. The proportion of IDU interviewed in the IDRS who were aged ≤24 years decreased from 46% in 1996 to 12% in 2004, with the most marked drop in 2001, the year in which there was an abrupt and marked reduction in heroin availability. Of those who reported first injecting between 1993 and 2000, similar proportions reported heroin and amphetamine as the first drug injected. After 2000, methamphetamine was the drug most often reported as being the first injected. Estimates suggested that between 2745 and 10 560 young people may not have begun to inject heroin in 2001 as a result of reduced heroin supply. If around one in four of these young users had progressed to regular or dependent heroin use, then there may have been a reduction of between 700 and 2500 dependent heroin users. There was an increase in amphetamine injecting but it is unclear to what extent any reduction in heroin injecting has been offset by increased amphetamine injecting. Reduced heroin availability probably resulted in a reduction in the number of new heroin injectors in Australia. Efforts need to be made to reduce the chances that young people who have initiated methamphetamine injecting do not move to heroin injecting when the heroin supply returns.
Unusual presentations for pharmacotherapy—poppy seed dependence*
Authors: LLOYD‐JONES D. M. , BONOMO Y. 
Published: July 2006

AbstractTwo cases of patients presenting with opioid dependence who maintained their dependence with poppy tea are described. There appears to have been an increase in this practice in some groups, although dependent use is uncommon. These cases illustrate significant levels of dependence on a licit, and readily available, source of opiates requiring high doses of pharmacotherapy that match those typically required by individuals who are treated for heroin dependence.
Identification of transcription factor cooperativity via stochastic system model
Authors: Chang Yu-Hsiang , Wang Yu-Chao , Chen Bor-Sen 
Published: July 2006

Abstract
Motivation: Transcription factor binding sites are known to co-occur in the same gene owing to cooperativity of the transcription factors (TFs) that bind to them. Genome-wide location data can help us understand how an individual TF regulates its target gene. Nevertheless, how TFs cooperate to regulate their target genes still needs further study. In this study, genome-wide location data and expression profiles are integrated to reveal how TFs cooperate to regulate their target genes from the stochastic system perspective.
Results: Based on a stochastic dynamic model, a new measurement of TF cooperativity is developed according to the regulatory abilities of cooperative TF pairs and the number of their occurrences. Our method is employed to the yeast cell cycle and reveals successfully many cooperative TF pairs confirmed by previous experiments, e.g. Swi4-Swi6 in G1/S phase and Ndd1-Fkh2 in G2/M phase. Other TF pairs with potential cooperativity mentioned in our results can provide new directions for future experiments. Finally, a cooperative TF network of cell cycle is constructed from significant cooperative TF pairs.
Contact: bschen@ee.nthu.edu.tw
Supplementary information:
Scoring of predicted GRK2 phosphorylation sites in Nedd4-2
Authors: Arthur Jonathan W. , Sanchez-Perez Angeles , Cook David I. 
Published: July 2006

Abstract
Motivation: Epithelial Na+ channels (ENaC) mediate the transport of sodium (Na) across epithelia in the kidney, gut and lungs and are required for blood pressure regulation. They are inhibited by ubiquitin protein ligases, such as Nedd4-2. These ligases bind to proline-rich motifs (PY motifs) present in the C-termini of ENaC subunits. Loss of this inhibition leads to hypertension. We have previously reported that ENaC channels are maintained in the active state by the G protein coupled receptor kinase, GRK2. The enzyme has been implicated in the development of essential hypertension [R. D. Feldman (2002)Mol. Pharmacol., 61, 707–709]. Additional findings in our lab pointed towards a possible role for GRK2 in the phosphorylation and inactivation of Nedd4-2.
Results: We have predicted GRK2 phosphorylation sites on Nedd4-2 by combining sequence analysis, homology modeling and surface accessibility calculations. A total of 24 potential phosphorylation sites were predicted by sequence analysis. Of these, 16 could be modeled using homology modeling and 6 of these were found to have sufficient surface exposure to be accessible to the GRK2 enzyme responsible for the phosphorylation of Nedd4-2. The method provides an ordered list of the most probable GRK2 phosphorylation sites on Nedd4-2 providing invaluable guidance to future experimental studies aimed at mutating certain Nedd4-2 residues in order to prevent phosphorylation by GRK2. The method developed could be applied in a wide variety of biological applications involving the binding of one molecule to a protein. The relative effectiveness of the technique is determined mainly by the quality of the homology model built for the protein of interest.
Contact: jarthur@med.usyd.edu.au
CART variance stabilization and regularization for high-throughput genomic data
Authors: Papana Ariadni , Ishwaran Hemant 
Published: July 2006

Abstract
Motivation: mRNA expression data obtained from high-throughput DNA microarrays exhibit strong departures from homogeneity of variances. Often a complex relationship between mean expression value and variance is seen. Variance stabilization of such data is crucial for many types of statistical analyses, while regularization of variances (pooling of information) can greatly improve overall accuracy of test statistics.
Results: A Classification and Regression Tree (CART) procedure is introduced for variance stabilization as well as regularization. The CART procedure adaptively clusters genes by variances. Using both local and cluster wide information leads to improved estimation of population variances which improves test statistics. Whereas making use of cluster wide information allows for variance stabilization of data.
Availability: Sufficient details for our CART procedure are given so that the interested reader can program the method for themselves. The algorithm is also accessible within the Java software package BAMarrayTM, which is freely available to non-commercial users at
Contact: hemant.ishwaran@gmail.com
OrderedList—a bioconductor package for detecting similarity in ordered gene lists
Authors: Lottaz Claudio , Yang Xinan , Scheid Stefanie , Spang Rainer 
Published: July 2006

Abstract
Summary: OrderedList is a Bioconductor compliant package for meta-analysis based on ordered gene lists like those resulting from differential gene expression analysis. Our package quantifies the similarity between gene lists. The significance of the similarity score is estimated from random scores computed on perturbed data. OrderedList illustrates list similarity in intuitive plots and determines the score-driving genes for further analysis.
Availability:
Contact: claudio.lottaz@molgen.mpg.de
Supplementary information: Please visit our webpage on
Gene selection in cancer classification using sparse logistic regression with Bayesian regularization
Authors: Cawley Gavin C. , Talbot Nicola L. C. 
Published: July 2006

AbstractMotivation: Gene selection algorithms for cancer classification, based on the expression of a small number of biomarker genes, have been the subject of considerable research in recent years. Shevade and Keerthi propose a gene selection algorithm based on sparse logistic regression (SLogReg) incorporating a Laplace prior to promote sparsity in the model parameters, and provide a simple but efficient training procedure. The degree of sparsity obtained is determined by the value of a regularization parameter, which must be carefully tuned in order to optimize performance. This normally involves a model selection stage, based on a computationally intensive search for the minimizer of the cross-validation error. In this paper, we demonstrate that a simple Bayesian approach can be taken to eliminate this regularization parameter entirely, by integrating it out analytically using an uninformative Jeffrey's prior. The improved algorithm (BLogReg) is then typically two or three orders of magnitude faster than the original algorithm, as there is no longer a need for a model selection step. The BLogReg algorithm is also free from selection bias in performance estimation, a common pitfall in the application of machine learning algorithms in cancer classification.Results: The SLogReg, BLogReg and Relevance Vector Machine (RVM) gene selection algorithms are evaluated over the well-studied colon cancer and leukaemia benchmark datasets. The leave-one-out estimates of the probability of test error and cross-entropy of the BLogReg and SLogReg algorithms are very similar, however the BlogReg algorithm is found to be considerably faster than the original SLogReg algorithm. Using nested cross-validation to avoid selection bias, performance estimation for SLogReg on the leukaemia dataset takes almost 48 h, whereas the corresponding result for BLogReg is obtained in only 1 min 24 s, making BLogReg by far the more practical algorithm. BLogReg also demonstrates better estimates of conditional probability than the RVM, which are of great importance in medical applications, with similar computational expense.Availability: A MATLAB implementation of the sparse logistic regression algorithm with Bayesian regularization (BLogReg) is available fromContact: gcc@cmp.uea.ac.uk
Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network
Authors: Buendia Patricia , Narasimhan Giri 
Published: July 2006

AbstractSummary: Serial NetEvolve is a flexible simulation program that generates DNA sequences evolved along a tree or recombinant network. It offers a user-friendly Windows graphical interface and a Windows or Linux simulator with a diverse selection of parameters to control the evolutionary model. Serial NetEvolve is a modification of the Treevolve program with the following additional features: simulation of serially-sampled data, the choice of either a clock-like or a variable rate model of sequence evolution, sampling from the internal nodes and the output of the randomly generated tree or network in our newly proposed NeTwick format.Availability: From websiteContacts: giri@cis.fiu.eduSupplementary information: Manual and examples available from
SynView: a GBrowse-compatible approach to visualizing comparative genome data
Authors: Wang Haiming , Su Yanqi , Mackey Aaron J. , Kraemer Eileen T. , Kissinger Jessica C. 
Published: July 2006

Abstract
Summary: We present SynView, a simple and generic approach to dynamically visualize multi-species comparative genome data. It is a light-weight application based on the popular and configurable web-based GBrowse framework. It can be used with a variety of databases and provides the user with a high degree of interactivity. The tool is written in Perl and runs on top of the GBrowse framework. It is in use in the PlasmoDB () and the CryptoDB () projects and can be easily integrated into other cross-species comparative genome projects.
Availability: The program and instructions are freely available at
Contact: jkissing@uga.edu
Global topological features of cancer proteins in the human interactome
Authors: Jonsson Pall F. , Bates Paul A. 
Published: July 2006

Abstract
Motivation: The study of interactomes, or networks of protein-protein interactions, is increasingly providing valuable information on biological systems. Here we report a study of cancer proteins in an extensive human protein-protein interaction network constructed by computational methods.
Results: We show that human proteins translated from known cancer genes exhibit a network topology that is different from that of proteins not documented as being mutated in cancer. In particular, cancer proteins show an increase in the number of proteins they interact with. They also appear to participate in central hubs rather than peripheral ones, mirroring their greater centrality and participation in networks that form the backbone of the proteome. Moreover, we show that cancer proteins contain a high ratio of highly promiscuous structural domains, i.e., domains with a high propensity for mediating protein interactions. These observations indicate an underlying evolutionary distinction between the two groups of proteins, reflecting the central roles of proteins, whose mutations lead to cancer.
Contact: paul.bates@cancer.org.uk
Supplementary information: The interactome data are available though the PIP (Potential Interactions of Proteins) web server at . Further additional material is available at