bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying the transtheoretical model to eating behaviour change: challenges and opportunities
Authors: Horwath Caroline C. 
Published: September 2005

AbstractThis review provides a rigorous investigation of the question of whether the transtheoretical model (TTM) (or stages of change model) is applicable to eating behaviour change. The TTM is currently the most popular of a number of stage theories being used to examine health behaviour change. Stage theories specify an ordered set of ‘stages of readiness to change’ into which people can be classified and identify the factors that can facilitate movement from one stage to the next. If eating behaviour change follows a stage process, then nutritionists could identify the predominant stage or stages in a population and focus resources on those issues most likely to move people to the next stage (e.g. from no intention of changing, to thinking about changing). In addressing this question, the review draws on the defining characteristics of stage theories as clarified by Weinstein et al. (1998), provides an in-depth coverage of methodological considerations, and a detailed summary table of dietary studies applying the TTM. Specific recommendations are made for improving the accuracy of dietary stage classifications. Among the key conclusions are: (1) dietary studies using the TTM have been hampered by a focus on nutritional outcomes such as dietary fat reduction, rather than clearly understood food behaviours (e.g. five servings of fruit and vegetables per day); (2) accurate stage classification systems are possible for food-based goals, but major misclassification problems occur with nutrient-based goals; (3) observation of an association between stage and dietary intake is not sufficient to demonstrate the validity of the model for dietary behaviour; (4) there is a need for valid questionnaires to measure all aspects of the TTM, and more research on the whole model, particularly the ‘processes of change’, rather than on single constructs such as ‘stage’ (5) cross-sectional studies generally support the predicted patterns of between-stage differences in decisional balance, self-efficacy, and processes of change; (6) studies which test the key hypothesis that different factors are important in distinguishing different stages are rare, as are prospective studies and stage-matched interventions. Only such studies can conclusively determine whether the TTM is applicable to eating behaviour. Since the ultimate test of the TTM will be the effectiveness of stage-matched dietary interventions, the review ends by exploring the requirements for such studies.
Using information theory to search for co-evolving residues in proteins
Authors: Martin L. C. , Gloor G. B. , Dunn S. D. , Wahl L. M. 
Published: September 2005

Abstract
Motivation: Some functionally important protein residues are easily detected since they correspond to conserved columns in a multiple sequence alignment (MSA). However important residues may also mutate, with compensatory mutations occurring elsewhere in the protein, which serve to preserve or restore functionality. It is difficult to distinguish these co-evolving sites from other non-conserved sites.
Results: We used Mutual Information (MI) to identify co-evolving positions. Using in silico evolved MSAs, we examined the effects of the number of sequences, the size of amino acid alphabet and the mutation rate on two sources of background MI: finite sample size effects and phylogenetic influence. We then assessed the performance of various normalizations of MI in enhancing detection of co-evolving positions and found that normalization by the pair entropy was optimal. Real protein alignments were analyzed and co-evolving isolated pairs were often found to be in contact with each other.
Availability: All data and program files can be found at
Contact: lwahl@uwo.ca
Supplementary information:
Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation
Authors: Zwir Igor , Huang Henry , Groisman Eduardo A. 
Published: September 2005

Abstract
Motivation: A critical challenge of the post-genomic era is to understand how genes are differentially regulated even when they belong to a given network. Because the fundamental mechanism controlling gene expression operates at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features and map such features into expression patterns to classify genes into distinct networks. However, these methods are not focused on distinguishing between differentially regulated genes within a given network. Here we describe an unsupervised machine learning method, termed GPS for gene promoter scan, that discriminates among co-regulated promoters by simultaneously considering both cis-acting regulatory features and gene expression. GPS is particularly useful for knowledge discovery in environments with reduced datasets and high levels of uncertainty.
Results: Application of this method to the enteric bacteria Escherichia coli and Salmonella enterica uncovered novel members, as well as regulatory interactions in the regulon controlled by the PhoP protein that were not discovered using previous approaches. The predictions made by GPS were experimentally validated to establish that the PhoP protein uses multiple mechanisms to control gene transcription, and is a central element in a highly connected network.
Availability: The scripts and programs used in this work are accessible from the gps-tools.wustl.edu website. Data and predictions are available by request.
Contact: groisman@borcim.wustl.edu
Supplementary information:
Design of long oligonucleotide probes for functional gene detection in a microbial community
Authors: Chung Won-Hyong , Rhee Sung-Keun , Wan Xiu-Feng , Bae Jin-Woo , Quan Zhe-Xue , Park Yong-Ha 
Published: September 2005

Abstract
Motivation: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes.
Results: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set.
Availability:
Contact: yhpark@kribb.re.kr
Supplementary information:
A comparison study: applying segmentation to array CGH data for downstream analyses
Authors: Willenbrock Hanni , Fridlyand Jane 
Published: September 2005

Abstract
Motivation: Array comparative genomic hybridization (CGH) allows detection and mapping of copy number of DNA segments. A challenge is to make inferences about the copy number structure of the genome. Several statistical methods have been proposed to determine genomic segments with different copy number levels. However, to date, no comprehensive comparison of various characteristics of these methods exists. Moreover, the segmentation results have not been utilized in downstream analyses.
Results: We describe a comparison of three popular and publicly available methods for the analysis of array CGH data and we demonstrate how segmentation results may be utilized in the downstream analyses such as testing and classification, yielding higher power and prediction accuracy. Since the methods operate on individual chromosomes, we also propose a novel procedure for merging segments across the genome, which results in an interpretable set of copy number levels, and thus facilitate identification of copy number alterations in each genome.
Availability:
Contact: jfridlyand@cc.ucsf.edu
Supplementary Information:
BADASP: predicting functional specificity in protein families using ancestral sequences
Authors: Edwards Richard J. , Shields Denis C. 
Published: September 2005

Abstract
Summary: Burst After Duplication with Ancestral Sequence Predictions (BADASP) is a software package for identifying sites that may confer subfamily-specific biological functions in protein families following functional divergence of duplicated proteins. A given protein phylogeny is grouped into subfamilies based on orthology/paralogy relationships and/or user definitions. Ancestral sequences are then predicted from the sequence alignment and the functional specificity is calculated using variants of the Burst After Duplication method, which tests for radical amino acid substitutions following gene duplications that are subsequently conserved. Statistics are output along with subfamily groupings and ancestral sequences for an easy analysis with other packages.
Availability: BADASP is freely available from
Contact: redwards@rcsi.ie
Supplementary information: A manual with further details can be downloaded from
Functional stability of microbial communities in contaminated soils
Authors: Tobor‐Kapłon M. A. , Bloem J. , Römkens P. F. A. M. , Ruiter P. C. de 
Published: September 2005

Functional stability, measured in terms of resistance and resilience of respiration and growth rate of bacteria and fungi, was studied in soils that have been exposed to copper and low pH for more than twenty years. We used treatments, consisting of soil with no or high copper load (0 or 750 kg ha−1) and low or neutral pH (4.0 or 6.1). Stability was examined by applying an additional stress in the form of lead or salt. After addition of lead, respiration (decomposition of freshly added lucerne meal) showed lower resistance at low than at neutral pH and at high copper than at low copper. The most acid and contaminated soil was the least resistant. Respiration showed no resilience after addition of lead. Bacterial growth rate (thymidine incorporation) also showed resistance at low pH but only in soils that were not contaminated with copper.After addition of salt, respiration showed no differences in resistance but the soils without copper contamination showed higher resilience. Bacterial growth rate showed lower resistance at low pH than at neutral pH, the latter in which the growth rate increased by on average 123%. This increase at high pH was faster in soil without copper than in soil with copper contamination in which the growth rate initially decreased and then increased. The effects of secondary stress depended on the nature of the stress (lead or salt) and on the parameter measured (respiration or bacterial growth rate). In general the highest resistance and/or resilience were found in the least contaminated soils with neutral pH and/or no copper contamination. Thus, the microbial communities in the cleaner soils showed the highest functional stability. The results seem to confirm the notion that environmental stress alters ecosystems such that supplementary stress will have stronger impacts than in an unstressed system. The results may also confirm the insurance‐hypothesis that reduced biodiversity due to the first stress negatively affected community stability. As an alternative, we discuss the observed effects in terms of altered energy budget.
Relieving substrate limitation‐soil moisture and temperature determine gross N transformation rates
Authors: Bengtson Per , Falkengren‐Grerup Ursula , Bengtsson Göran 
Published: September 2005

A field experiment was designed with the objective to reveal the interactions between soil moisture, temperature, total, dissolved, and phosphate buffer extractable C and N, and microbial activity in the control of in situ gross N mineralization and immobilization rates in a deciduous forest. We had three alternative hypotheses to explain variations of the gross N transformations: 1) microorganisms are C limited, 2) microorganisms are N limited, or 3) neither C nor N limit the microorganisms but moisture and temperature conditions. Each hypothesis had specific criteria to be fulfilled for its acceptance. The results demonstrated that gross N transformation rates were more dependent on and variable with soil moisture and temperature than the size of the different C and N pools. The immobilization of N was dependent on the gross mineralization rate, suggesting that the production of enzymes for mineralization of organic N and the immobilization of N from the surrounding soil is disconfirmed when the intracellular N content of the microorganisms is sufficiently high. If the microorganisms are starved for N, enzyme systems involved in both the assimilation and mineralization of N are activated.The mean in situ gross N mineralization rate was two orders of magnitude higher than the natural N deposition in the area and the N addition in the NITREX experiments, meaning that a reduction in the gross N mineralization rate of about 1% would be enough to compensate for the addition of inorganic N. This decrease would hardly be detectable given the great spatial and temporal variability of N transformation rates.
Among population variation in specialist and generalist seed predation – the importance of host plant distribution, alternative hosts and environmental variation
Authors: Östergård Hannah , Ehrlén Johan 
Published: September 2005

Pre‐dispersal seed predators can have important effects on population dynamics and trait selection in their host plants. However, the factors determining spatial variation in predation intensity are poorly known. We assessed the relative importance of host plant distribution, alternative hosts and environmental factors for among‐population variation in predation in a system with three host plants, a specialist and a generalist pre‐dispersal seed predator.Effects of host plant population size were relatively more important in the specialist than in the generalist seed predator. The specialist seed predatorApion opeticum, utilizing onlyLathyrus vernusoccurred in less than half of the patches, and specialist seed predation was influenced only by host plant population size. The generalistBruchus atomariuswas present in nearly all patches, and generalist predation was influenced by environmental factors and availability of alternative hosts. Predation on alternative hosts was not affected byL. vernuspresence.The results suggest that a wide range of factors influences the strength of plant–seed–predator interactions, and that the relative importance of different factors depend on the degree of specialization. This will result in highly complex selection mosaics and coevolutionary trajectories.
Optimizing therapy for myeloid disorders of Down syndrome
Authors: Webb David K. H. 
Published: September 2005

SummaryChildren with Down syndrome (DS) are at increased risk of leukaemia. Myeloid disorders include transient abnormal myelopoiesis (TAM), myelodysplasia (MDS) and acute myeloid leukaemia (AML). Mutations in the GATA‐1 gene, which encodes for a transcription factor central to the normal development of the erythroid and megakaryocytic lineages, are found in cases of TAM, MDS and AML in DS children. DS children with MDS/AML mostly present between the ages of 1 and 4 years, and have a large predominance of megakaryoblastic disease (French–American–British type M7). The MDS and AML are part of a single disease entity (myeloid leukaemia of Down syndrome) that is extremely sensitive to chemotherapy. Resistant disease and relapse are rare, but treatment‐related toxicity is high, and deaths in remission have exceeded those due to disease in most series. Accordingly, controlled dosage reduction is the focus of contemporary treatment studies.
Central nervous system‐directed preventative therapy in adults with lymphoma
Authors: McMillan Andrew 
Published: September 2005

SummaryAll adult patients with Burkitt lymphoma or lymphoblastic lymphoma should receive central nervous system (CNS)‐directed therapy with both intrathecal and high‐dose systemic chemotherapy. There is no evidence to support the routine use of prophylactic CNS‐directed therapy in any specific subgroup of adult patients with ‘low grade’ lymphomas. There are some anatomical sites where involvement by lymphoma is associated with a higher risk of CNS relapse. These probably include testis, breast, paranasal sinuses and the epidural space. Multivariate analyses strongly support a raised serum lactate dehydrogenase level and the involvement of more than one extranodal site as the strongest predictors of subsequent CNS relapse. A high International Prognostic Index score may replace the use of the above two factors in combination. There is evidence of good efficacy when intrathecal chemotherapy and high‐dose systemic chemotherapy are used in combination. It is not clear how the best balance between the ‘sensitivity’ and ‘specificity’ of the choice of patients to receive CNS‐directed therapy can be achieved.
Does severity of low‐dose, double‐blind, placebo‐controlled food challenges reflect severity of allergic reactions to peanut in the community?
Authors: Hourihane J. O'B. , Grimshaw K. E. C. , Lewis S. A. , Briggs R. A. , Trewin J. B. , King R. M. , Kilburn S. A. , Warner J. O. 
Published: September 2005

SummaryBackground
The severity of allergic reactions to food appears to be affected by many interacting factors. It is uncertain whether challenge‐based reactions reflect the severity of past reactions or can predict future risk.Objective
To explore the relationship of a subject's clinical history of past reactions to the severity of reaction elicited by a low‐dose, double‐blind, placebo‐controlled food challenge (DBPCFC) with peanut.Method
Cross‐sectional questionnaire assessment of community‐based allergic reactions and low‐dose DBPCFC in self‐selected peanut‐allergic subjects. Reaction severity was assessed using a novel scoring system, taking account of the dose of allergen ingested.Results
Forty subjects (15 males, 23 children, 23 asthmatics by history) were studied. Only the most recent community reaction predicted the severity of reaction in the DBPCFC, but even this association was weak (r=0.37, P=0.03). Peanut‐specific IgE (PsIgE) and skin prick test (SPT) weal size were not associated with community score but PsIgE level correlated well with the challenge score (r=0.6, P=0.001). Asthma did not affect the eliciting dose or challenge score directly but the association of PsIgE and challenge score was stronger in those without asthma (r=0.72, P=0.001) than in those with asthma (r=0.48, P=0.02).Conclusions
The scoring system developed appears to improve the sensitivity of assessment of reactions induced by DBPCFC. This is the first prospective study showing an association between PsIgE levels and clinical reactivity in DBPCFC, an effect that is more pronounced in non‐asthmatics. This finding has important implications for the clinical care of subjects with food allergy. There is a poor correlation between the severity of reported reactions in the community and the severity of reaction elicited during low‐dose DBPCFC with peanut.
Effects of glutathione S‐transferase M1, T1 and P1 on lung function in asthmatic families
Authors: Carroll W. D. , Lenney W. , Jones P. W. , Strange R. C. , Child F. , Whyte M. K. , Primhak R. A. , Fryer A. A. 
Published: September 2005

SummaryRationale
Previous data have suggested that glutathione‐S‐transferase (GST) genotypes are important in determining the rate of lung function growth in childhood. This effect was most marked in Caucasian children with asthma.Objectives
We investigated the association of lung function with GSTM1, GSTP1 and GSTT1 genotypes in Caucasian families with asthma.Methods
Four hundred and eighteen children and 316 parents from 224 Caucasian families were recruited via a child with asthma, the proband. Associations between lung function and GST genotype were determined using multilevel models.Results
There were no observed associations between lung function and GST genotype in parents. However, in the children, the GSTP1 val105/val105 and GSTM1 null genotypes were associated with significantly higher forced expiratory volume in 1 s (FEV1) and FVC values as percentage of predicted. This effect was not statistically significant in the probands but was marked in their siblings in whom GSTP1 val105/val105 was associated with 9.4% higher FEV1 and 10.7% higher FVC (P=0.005 and 0.001, respectively). The GSTM1 null genotype was associated with a 6.7% higher FEV1 and 4.1% higher FVC (P=0.003 and 0.063, respectively). These effects remained significant after correcting for the confounders of individual atopic status, tobacco smoke exposure and familial aggregation of lung function values.Conclusions
GSTM1 and GSTP1 genotypes are important determinants of lung function in childhood. The smaller differences seen in probands are predicted by a simple model in which more rapid decline in lung function is seen in these individuals.
The use of exhaled nitric oxide concentration to identify eosinophilic airway inflammation: an observational study in adults with asthma
Authors: Berry M. A. , Shaw D. E. , Green R. H. , Brightling C. E. , Wardlaw A. J. , Pavord I. D. 
Published: September 2005

SummaryBackground
Assessment of eosinophilic airway inflammation may be helpful in the management of asthma. Nitric oxide (NO) has potential advantages as a tool to monitor airway inflammation although little is known about the relationship between NO and eosinophilic airway inflammation and the factors which influence it.Methods
We set out to define the relationship between exhaled NO and the sputum eosinophil count, identify the exhaled NO concentration that best identified a sputum eosinophil count >3% and investigate the impact of several potential confounding factors in 566 consecutive patients with varying severity of asthma. Finally we examined the ability of exhaled NO concentrations measured at differing exhalation flows to identify the presence of a sputum eosinophilia.Results
We found a significant positive relationship between exhaled NO and sputum eosinophil count (R2=0.26, P<0.001) which was best described using a non‐linear model. There were no clinically important confounding factors to this model. In non‐smokers an exhaled NO concentration of >8.3 p.p.b. at 250 mL/s gave 71% sensitivity and 72% specificity for identifying a sputum eosinophil count of >3%.Conclusions
This value of exhaled NO would seem to be the best for identifying significant eosinophilic airway inflammation. It is applicable to a wide range of non‐smoking patients with asthma; exhalation flow does not alter the ability of exhaled NO concentration to detect a sputum eosinophilia.