bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining risk factors and demographic surveillance: Potentials of WHO STEPS and INDEPTH methodologies for assessing epidemiological transition
Authors: Ng Nawi , Hoang Van Minh  , Tesfaye Fikru , Bonita Ruth , Byass Peter , Stenlund Hans , Weinehall Lars , Wall Stig
Published: January 2006

Aims: Demographic surveillance systems (DSSs) create platforms to monitor population dynamics. This paper discusses the potential of combining the WHO STEPwise approach to Surveillance (STEPS) within ongoing DSSs, to assess changes in non-communicable disease (NCD) risk factors. Methods: Three DSSs in Ethiopia, Vietnam, and Indonesia have collected NCD risk factors using WHO STEPS, focusing on self-reported lifestyle risk factors (Step 1) and measurement of blood pressure and anthropometric parameters (Step 2). Results: DSSs provide sampling frames for NCD risk factor surveillance, which reveals the distribution of risk factors and their dynamics at the population level. The WHO STEPS approach with its add-on modules is feasible and adaptable in DSS settings. Available mortality data in the DSSs enable mortality assessment by cause of death using verbal autopsy, which is relevant in estimating the impact of NCDs. DSSs as well as risk factor surveillance data may potentially be a lever for hypothesis-driven research to address specific a priori hypotheses or research questions. Conclusion: Combining DSSs with the WHO STEPS approach can potentially address basic epidemiological questions on NCDs, which can be used as a powerful advocacy tool in public health decision-making for NCD prevention.
Baseline prevalence of symptoms related to indoor environment
Authors: Eriksson Nils M. , Stenberg Berndt G.T.
Published: January 2006

Aims: Health problems associated with indoor environments have been reported and discussed extensively during the past few decades, not least in Sweden. There is, however, great uncertainty concerning the background prevalence of the symptoms in question. The main objective of the present study was to investigate the prevalence of general, mucosal, and skin symptoms in the Swedish population. Methods: A survey comprising 3,000 randomly selected Swedes, age 18—64, was carried out. The survey addressed 25 symptoms, principally general, mucosal, and skin symptoms. A number of other areas were covered and individual data registered at Statistics Sweden were added. The response rate was 70% (2,154 cases). Results: The prevalence of symptoms in the Swedish population was found to accord with results in studies based on different kinds of samples. Women reported significantly more single symptoms, as well as sets of symptoms, than men. There was no clear connection between age and symptoms. The prevalence of symptoms was slightly lower among employees compared with non-workers. Office workers did not report symptoms related to ``sick building syndrome'' (SBS) more frequently than employees not working in offices. SBS symptoms, skin symptoms, and symptoms similar to those reported by individuals with ``electric hypersensitivity'' were significantly more prevalent among employees with extensive VDU usage. Conclusions: The prevalence of reported health complaints accords with that which has been found in previous studies. The background prevalence reported here can serve as a reference for further studies. The high prevalence of symptoms among individuals with extensive VDU usage gives cause for further studies.
The significance of overweight and obesity for individual health behaviour: An economic analysis based on the Swedish surveys of living conditions 1980—81, 1988—89, and 1996—97
Authors: Bolin Kristian , Lindgren Björn , Rössner Stephan
Published: January 2006

Aims: The aim of the study was to examine whether being overweight (25≤BMI<30) or obese (BMI≥30) affect subsequent individual health behaviour, applying the framework of the individual-as-producer-of-health model. Methods: A set of panel data for 3,693 individuals interviewed repeatedly in 1980—81, 1988—89, and 1996—97 was created from the Swedish population-based biannual survey of living conditions. Self-assessed health was chosen as indicator of individual health capital and physical exercise as indicator of individual health investment. Results: (a) Men and women who suffered from obesity invested significantly less in their health in terms of physical exercise and reported significantly lower self-assessed health than the general male and female population, respectively. (b) Men who suffered from overweight invested less in their health and reported significantly lower self-assessed health than the general population, whereas women who were overweight — but not obese — did not differ from the general population. (c) Men and women who went from being obese to being overweight reported self-assessed health levels that did not differ from the general male and female population, respectively, but exercised less than men and women in general. Conclusions: The results imply (a) that the individual weight history must be taken into account in studies of the effect of obesity and overweight on health and health-related behaviour and (b) that men and women differ concerning the impact of obesity and overweight on health and health investments.
Health and healthcare utilization among single mothers and single fathers in Sweden
Authors: Westin Marcus , Westerling Ragnar
Published: January 2006

Aims: To analyse self-rated health and healthcare utilization with regard to whether the respondents were single or couple parents, mothers or fathers. Methods: A postal questionnaire was distributed nationwide to 4,000 randomly chosen individuals 20—64 years of age, with a response rate of 66%. A total of 1,041 respondents had legal custody of a child (150 were single parents and 891 were couple parents), and thus met the definition of a parent used for this study. Analyses of self-rated health and health care utilization were performed according to sex, age, sociodemographic, and socioeconomic characteristics. Three different statistical methods were applied: Spearman correlation analyses, chi-square analyses and multivariate logistic regression. Results: Both single fathers and single mothers reported worse health than their couple counterparts. However, single fathers had contact with a physician more frequently (OR 1.84) than couple fathers, whereas single mothers did not. Furthermore, single mothers refrained from seeing a physician despite a medical need much more often (OR 2.07) than couple mothers. Conclusions: An uneven distribution of sociodemographic and socioeconomic characteristics might help us to understand why single parents, both mothers and fathers, have worse health than parents who live together. Previously recognized gender differences with regard to healthcare utilization were present in our study as well, and it is possible that these differences are related to the unequal distribution of sociodemographic and socioeconomic assets between single fathers and single mothers found here.
East—west health divide and east—west migration: Self-reported health of immigrants from Eastern Europe and the former Soviet Union in Sweden
Authors: Sungurova Yulia , Johansson Sven-Erik , Sundquist Jan
Published: January 2006

Aim: Research on the east—west health divide has provided extensive evidence of poorer health in Eastern Europe and the former Soviet Union than in Western Europe. This study focuses on immigrants from Eastern to Western Europe and analyses whether they have an increased risk of self-reported poor health compared with the host population and what determines that. Methods: This cross-sectional study is based on 373 immigrants from Poland, other East European countries, and the former Soviet Union, aged 25—84, who arrived in Sweden after 1944 and were interviewed during 1993— 2000 along with their 35,711 Swedish counterparts. Results: Age- and sex-adjusted unconditional logistic regression showed in general a 92% higher risk of reporting poor health among immigrants than among Swedish-born respondents. The risk also persisted after adjustment for several potential confounders (living singly, having a poor social network, low socioeconomic status, and smoking) and after an additional adjustment for acculturation (language at home), and years in Sweden. Conclusions: Being born in Eastern Europe or the former Soviet Union was an independent risk factor for reporting poor health. It is therefore suggested that it is important for primary and public care services to be aware of the health status and needs of immigrants from these countries.
Individual and contextual determinants of self-reported poor psychological health: A population-based multilevel analysis in southern Sweden
Authors: Lindström Martin , Moghaddassi Mahnaz , Merlo Juan
Published: January 2006

Objective: To investigate the influence of contextual and individual factors on self-reported psychological health. Design/ setting/participants/measurements: The 2000 public health survey in Scania is a cross-sectional postal questionnaire study with a 59% participation rate. A total of 13,715 persons aged 18—80 answered the questionnaire. A multilevel logistic regression model, with individuals at the first level and municipalities/city quarters at the second, was performed. The effect (intra-class correlation, cross-level modification, and odds ratios) of individual and municipality/city quarter factors on self-reported psychological health was analysed. Results: The crude variance between municipalities/city quarters was small but significant. It was particularly affected and lowered by individual civil status, country of origin, economic stress, and social participation. The inclusion of all individual factors age, sex, civil status, country of origin, education, economic stress, and social participation lowered the between municipality variance to not-significant levels, which is the reason why no contextual variables were included in the calculations. Conclusions: The results of this study suggest that poor self-reported psychological health is affected mainly by individual characteristics of the population and not by contextual factors at the municipality/city quarter level.
Data on height and weight from school health records as a national public health surveillance tool: The case of Sweden
Authors: Werner BO , Bodin Lennart , Bremberg Sven
Published: January 2006

Aim: To investigate the suitability of using routine height and weight data from records within a school health service system, for population monitoring of child and adolescent growth on a national level. Methods: A longitudinal study from age 7 to 18 years of all children born on the 15th of any month in 1973 and living in Sweden on 31 December 1989 (1,724 girls and 1,855 boys). Data were collected from school health records. Results: Descriptive statistics for height and weight calculated from data obtained from school health records are summarized and compared with previous Swedish studies. The effect of exclusion of children with chronic diseases involving major growth impairment and/or exclusion of children born outside Sweden have a minor impact on the results owing to the relatively small number of excluded children. Conclusion: Longitudinal data for somatic growth (height and weight) from age 7 to 18 years from a nationally representative sample of children in Sweden, collected from school health records, can be used for epidemiological monitoring of growth with fewer missing individuals and at lower costs compared with other dedicated studies. Data quality is comparable to similar national surveys. The data are suitable for descriptive analysis of growth and other forms of observational study.
Perspectives of midwives and doctors on adolescent sexuality and abortion care in Vietnam
Authors: Klingberg-Allvin Marie , Nguyen Thu Nga  , Ransjö-Arvidson Anna-Berit , Johansson Annika
Published: January 2006

Background: Vietnam has one of the highest abortion rates in the world and adolescent abortions are thought to constitute at least one-third of all cases. Lack of balanced reproductive health information and services to adolescents and negative social attitudes towards adolescent sexuality are contributing factors to the high abortion rates. Health providers are important in guiding and counselling adolescents on how to protect their reproductive health. There is a lack of studies on health providers' perspectives on their work in adolescent reproductive health care. Aim: To explore the perspectives of midwives and doctors on adolescent sexuality and abortion, and what they considered to be quality abortion care for adolescents and the barriers to it, as well as to their own training needs. Methods: Observations of care in abortion clinics and focus-group discussions (FGD) were used to collect data. Doctors and midwives from three healthcare facilities in Quang Ninh province in Northern Vietnam participated in a total of eight FGDs. Data were analysed using latent content analysis. Findings: Major barriers identified for quality abortion care were of technical and managerial nature. Participants considered that counselling unmarried clients in connection with abortion should focus on warning against the risks and dangers of abortion and pre-marital sexual relations, which they strongly disapproved of. However, they also expressed a pragmatic and caring attitude towards the unmarried girls and couples coming for abortion. Adolescent sexuality and abortion are morally sensitive issues in the Vietnamese culture. The contradictions between cultural norms and the reality facing health providers while counselling unmarried adolescents need to be addressed in education and training programmes.
Socioeconomic aspects of fractures within universal public healthcare: A nationwide case-control study from Denmark
Authors: Vestergaard Peter , Rejnmark Lars , Mosekilde Leif
Published: January 2006

Aims: To investigate the effects of income and other socioeconomic variables on fracture risk adjusted for disease-related confounders as fractures are a major public health problem. Methods: Case-control study where all subjects in Denmark with a fracture during the year 2000 (n=124,655) served as cases. From the general population three age- and gender-matched subjects were selected as controls (n=373,962). Adjustment were made for income, living with someone vs. living alone, having a job vs. being out of work, education, comorbidity (Charlson index), number of bed days in hospital, number of contacts with general practitioner, use of corticosteroids, prior fracture, and alcoholism. Results: Income was not associated with fracture risk on adjustment for the other covariates. Living with someone was associated with a decreased risk of any fracture in all ages. A higher level of education was associated with a decreased fracture risk in the age groups<60 years, but an increased fracture risk among subjects≥60 years. Being at work was associated with a decreased hip fracture risk among subjects≥40 years. Alcoholism and a prior fracture were significant predictors of fracture in all age groups. Conclusions: Income does not predict fracture risk in Denmark after adjustment for other social and comorbidity variables. This may signal neutralization of the effect by socioeconomic compensation or that income was the product of underlying socioeconomic variables.
Cardiovascular risk factor burden has a stronger association with self-rated poor health in adults in the US than in Sweden, especially for the lower educated
Authors: Emmelin Maria , Nafziger Anne N. , Stenlund Hans , Weinehall Lars , Wall Stig
Published: January 2006

Background: There is an ongoing debate about the importance of biomedical and sociodemographic risk factors in the prediction of self-rated health. Objectives: To compare the association of sociodemographic and cardiovascular risk factors and self-rated health in Sweden and the US. Design: Data from two population-based cross-sectional health surveys, one in Sweden and one in the US. Subjects: The surveys included questionnaire and measured data from 5,461 adults in Sweden and 7,643 in the US. Participants were between 35 and 65 years of age. Results: The odds ratios for poor self-rated health for the included cardiovascular risk factors were greater in the US. Low education was significantly more prevalent among those with self-rated poor health in the US, but not in Sweden. Using Swedes with high education as reference group (OR=1), adults in the US with low education and 2+ risk factors had a greater than threefold risk (OR=6.3) of self-rated poor health compared with Swedish low-educated adults with the same risk factor burden (OR=1.9). The better-educated US adults with 2+ risk factors were significantly more likely to report poor health (OR=3.4) compared with their Swedish counterparts (OR=2.4). Conclusions: The interaction between risk factors, education, and self-rated health suggests a frightening picture, especially for the US. Public health interventions for reducing cardiovascular risk factors need to include both population and individual measures. Taking people's overall evaluation of their health into account when assessing total health risk is important.
Automated discovery of 3D motifs for protein function annotation
Authors: Polacco Benjamin J. , Babbitt Patricia C.
Published: January 2006

Motivation: Function inference from structure is facilitated by the use of patterns of residues (3D motifs), normally identified by expert knowledge, that correlate with function. As an alternative to often limited expert knowledge, we use machine-learning techniques to identify patterns of 3–10 residues that maximize function prediction. This approach allows us to test the assumption that residues that provide function are the most informative for predicting function.

Results: We apply our method, GASPS, to the haloacid dehalogenase, enolase, amidohydrolase and crotonase superfamilies and to the serine proteases. The motifs found by GASPS are as good at function prediction as 3D motifs based on expert knowledge. The GASPS motifs with the greatest ability to predict protein function consist mainly of known functional residues. However, several residues with no known functional role are equally predictive. For four groups, we show that the predictive power of our 3D motifs is comparable with or better than approaches that use the entire fold (Combinatorial-Extension) or sequence profiles (PSI-BLAST).

Availability: Source code is freely available for academic use by contacting the authors.

Contact:  babbitt@cgl.ucsf.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
OrthologID: automation of genome-scale ortholog identification within a parsimony framework
Authors: Chiu Joanna C. , Lee Ernest K. , Egan Mary G. , Sarkar Indra Neil , Coruzzi Gloria M. , DeSalle Rob
Published: January 2006

Motivation: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation.

Results: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.

Availability:  

Contact:  gloria.coruzzi@nyu.edu
Tools for the SBML Community
Authors: Gillespie Colin S. , Wilkinson Darren J. , Proctor Carole J. , Shanley Daryl P. , Boys Richard J. , Kirkwood Thomas B. L.
Published: January 2006

Motivation: SBML is quickly becoming the standard format to exchange biochemical models. The tools presented in this paper are loosely-coupled, and are intended to be incorporated into SBML aware applications. The rationale for this is to reduce the amount of repeated work carried out within the community and to create tools that offer a greater number of features to the end-user.

Availability: All tools described are available from and are licensed under GNU General Public License.

Contact:  c.gillespie@ncl.ac.uk
LSAT: learning about alternative transcripts in MEDLINE
Authors: Shah Parantu K. , Bork Peer
Published: January 2006

Motivation: Generation of alternative transcripts from the same gene is an important biological event due to their contribution in creating functional diversity in eukaryotes. In this work, we choose the task of extracting information around this complex topic using a two-step procedure involving machine learning and information extraction.

Results: In the first step, we trained a classifier that inductively learns to identify sentences about physiological transcript diversity from the MEDLINE abstracts. Using a large hand-built corpus, we compared the sentence classification performance of various text categorization methods. Support vector machines (SVMs) followed by the maximum entropy classifier outperformed other methods for the sentence classification task. The SVM with the radial basis function kernel and optimized parameters achieved Fβ-measure of 91% during the 4-fold cross validation and of 74% when applied to all sentences in more than 12 million abstracts of MEDLINE. In the second step, we identified eight frequently present semantic categories in the sentences and performed a limited amount of semantic role labeling. The role labeling step also achieved very high Fβ-measure for all eight categories.

Availability: The results of our two-step procedure are summarized in the LSAT database of alternative transcripts. LSAT is available at

Contact:  shah@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online
Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application
Authors: Xirasagar Sandhya , Gustafson Scott F. , Huang Cheng-Cheng , Pan Qinyan , Fostel Jennifer , Boyer Paul , Merrick B. Alex , Tomer Kenneth B. , Chan Denny D. , Yost Kenneth J. , Choi Danielle , Xiao Nianqing , Stasiewicz Stanley , Bushel Pierre , Waters Michael D.
Published: January 2006

Motivation: The CEBS data repository is being developed to promote a systems biology approach to understand the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein–protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner.

Results: An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source systems toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data () which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium () that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms, is presented here.

Availability: A universal modeling language (UML) depiction of the entire SysTox-OM is available at and the Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at . Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at

Contact:  xirasagars@saic.com

Supplementary information: Supplementary data are available at Bioinformatics online.
Comparison of Affymetrix GeneChip expression measures
Authors: Irizarry Rafael A. , Wu Zhijin , Jaffee Harris A.
Published: January 2006

Motivation: In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted.

Results: We benchmarked 31 probe set algorithms using a U95A dataset of spike in controls. Using this dataset, we found that background correction, one of the main steps in preprocessing, has the largest effect on performance. In particular, background correction appears to improve accuracy but, in general, worsen precision. The benchmark results put this balance in perspective. Furthermore, we have improved some of the original benchmark metrics to provide more detailed information regarding precision and accuracy. A handful of methods stand out as providing the best balance using spike-in data with the older U95A array, although different experiments on more current arrays may benchmark differently.

Availability: The affycomp package, now version 1.5.2, continues to be available as part of the Bioconductor project (). The webtool continues to be available at

Contact:  rafa@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Hierarchical multi-label prediction of gene function
Authors: Barutcuoglu Zafer , Schapire Robert E. , Troyanskaya Olga G.
Published: January 2006

Motivation: Assigning functions for unknown genes based on diverse large-scale data is a key task in functional genomics. Previous work on gene function prediction has addressed this problem using independent classifiers for each function. However, such an approach ignores the structure of functional class taxonomies, such as the Gene Ontology (GO). Over a hierarchy of functional classes, a group of independent classifiers where each one predicts gene membership to a particular class can produce a hierarchically inconsistent set of predictions, where for a given gene a specific class may be predicted positive while its inclusive parent class is predicted negative. Taking the hierarchical structure into account resolves such inconsistencies and provides an opportunity for leveraging all classifiers in the hierarchy to achieve higher specificity of predictions.

Results: We developed a Bayesian framework for combining multiple classifiers based on the functional taxonomy constraints. Using a hierarchy of support vector machine (SVM) classifiers trained on multiple data types, we combined predictions in our Bayesian framework to obtain the most probable consistent set of predictions. Experiments show that over a 105-node subhierarchy of the GO, our Bayesian framework improves predictions for 93 nodes. As an additional benefit, our method also provides implicit calibration of SVM margin outputs to probabilities. Using this method, we make function predictions for multiple proteins, and experimentally confirm predictions for proteins involved in mitosis.

Supplementary information: Results for the 105 selected GO classes and predictions for 1059 unknown genes are available at:

Contact:  ogt@cs.princeton.edu
Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting
Authors: Thomas Alun , Camp Nicola J.
Published: January 2006

Summary: Graphical modeling is used to extend the gene counting method to compute maximum likelihood estimates of allele frequencies for samples of individuals related in extended pedigrees. Genotypes may be missing or partially observed, and error rates can be simultaneously estimated.

Availability: The Java classes and Javadocs pages for GeneCountAllelescan be obtained from , which also has more information on its use and file formats.

Contact:  alun@genepi.med.utah.edu
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Authors: Kuhner Mary K.
Published: January 2006

Summary: We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters from genetic data. LAMARC can co-estimate subpopulation Θ = 4Neμ, immigration rates, subpopulation exponential growth rates and overall recombination rate, or a user-specified subset of these parameters. It can perform either maximum-likelihood or Bayesian analysis, and accomodates nucleotide sequence, SNP, microsatellite or elecrophoretic data, with resolved or unresolved haplotypes. It is available as portable source code and executables for all three major platforms.

Availability: LAMARC 2.0 is freely available at

Contact:  lamarc@gs.washington.edu
Extending the dynamic range of phase contrast magnetic resonance velocity imaging using advanced higher-dimensional phase unwrapping algorithms
Authors: Salfity M.F , Huntley J.M , Graves M.J , Marklund O , Cusack R , Beauregard D.A
Published: January 2006

Phase contrast magnetic resonance velocity imaging is a powerful technique for quantitative
in vivo
blood flow measurement. Current practice normally involves restricting the sensitivity of the technique so as to avoid the problem of the measured phase being ‘wrapped’ onto the range −
π
to +
π
. However, as a result, dynamic range and signal-to-noise ratio are sacrificed. Alternatively, the true phase values can be estimated by a phase unwrapping process which consists of adding integral multiples of 2
π
to the measured wrapped phase values. In the presence of noise and data undersampling, the phase unwrapping problem becomes non-trivial. In this paper, we investigate the performance of three different phase unwrapping algorithms when applied to three-dimensional (two spatial axes and one time axis) phase contrast datasets. A simple one-dimensional temporal unwrapping algorithm, a more complex and robust three-dimensional unwrapping algorithm and a novel velocity encoding unwrapping algorithm which involves unwrapping along a fourth dimension (the ‘velocity encoding’ direction) are discussed, and results from the three are presented and compared. It is shown that compared to the traditional approach, both dynamic range and signal-to-noise ratio can be increased by a factor of up to five times, which demonstrates considerable promise for a possible eventual clinical implementation. The results are also of direct relevance to users of any other technique delivering time-varying two-dimensional phase images, such as dynamic speckle interferometry and synthetic aperture radar.
The evolutionary outcome of sexual conflict
Authors: Lessells C(Kate). M
Published: January 2006

Inter-locus sexual conflict occurs by definition when there is sexually antagonistic selection on a trait so that the optimal trait value differs between the sexes. As a result, there is selection on each sex to manipulate the trait towards its own optimum and resist such manipulation by the other sex. Sexual conflict often leads additionally to the evolution of harmful behaviour and to self-reinforcing and even perpetual sexually antagonistic coevolution. In an attempt to understand the determinants of these different outcomes, I compare two groups of traits—those related to parental investment (PI) and to mating—over which there is sexual conflict, but which have to date been explored by largely separate research traditions. A brief review suggests that sexual conflict over PI, particularly over PI per offspring, leads less frequently to the evolution of manipulative behaviour, and rarely to the evolution of harmful behaviour or to the rapid evolutionary changes which may be symptomatic of sexually antagonistic coevolution. The chief determinants of the evolutionary outcome of sexual conflict are the benefits of manipulation and resistance, the costs of manipulation and resistance, and the feasibility of manipulation. All three of these appear to contribute to the differences in the evolutionary outcome of conflicts over PI and mating. A detailed dissection of the evolutionary changes following from sexual conflict exposes greater complexity than a simple adaptation–counter-adaptation cycle and clarifies the role of harm. Not all of the evolutionary changes that follow from sexual conflict are sexually antagonistic, and harm is not necessary for sexually antagonistic coevolution to occur. In particular, whereas selection on the trait over which there is conflict is by definition sexually antagonistic, collateral harm is usually in the interest of neither sex. This creates the opportunity for palliative adaptations which reduce collateral harm. Failure to recognize that such adaptations are in the interest of both sexes can hinder our understanding of the evolutionary outcome of sexual conflict.
Classification of cutaneous T‐cell lymphoma: from Alibert to WHO‐EORTC
Authors: Willemze Rein , J. L. M. Meijer Chris
Published: January 2006

Cutaneous T‐cell lymphomas (CTCLs) represent a heterogeneous group of neoplasms originating from skin‐homing T cells that show considerable variation in clinical presentation, histological appearance, immuno‐ phenotype, and prognosis. This review provides a historic overview of the classification of CTCLs from the first description of a patient with mycosis fungoides in 1806 to the recently published WHO‐EORTC classification. Practical guidelines for the usage of the WHO‐EORTC classification and relevant features of new or newly defined entities such as subcutaneous panniculitis‐like T‐cell lymphoma, extranodal NK/T‐cell lymphoma, nasal type, primary cutaneous aggressive CD8‐positive cytotoxic T‐cell lymphoma, and cutaneous γ/δ T‐cell lymphoma are presented. The aim of this review is to contribute to a better communication between dermatologist and pathologist and in this way to a better diagnosis and classification of CTCLs.
Standard and experimental therapy in cutaneous T‐cell lymphomas
Authors: Dummer Reinhard , Cozzio Antonio , Meier Sibylle , Beyeler Mirjam , Laetsch Barbara , Doebbeling Udo , Urosevic Mirjana
Published: January 2006

Abstract  Cutaneous T‐cell lymphomas are a heterogeneous group of lymphoproliferative disorders, characterized by the accumulation of clonal lymphocytes in the skin. Skin‐directed therapies are the preferred first‐line modalities. There are interesting new developments in topical therapy using retinoids and gene‐therapy products such as adenovirus‐ interferon (IFN)‐γ. Systemic treatment uses biologicals such as fusion molecules, monoclonal antibodies and immune response modifiers (IFNs and retinoids), and well‐tolerated antiproliferative drugs such as methotrexate. Evidence‐based treatment recommendation exists but is hampered by the lack of large multicenter randomized trials.
Pathobiology of CD30+ cutaneous T‐cell lymphomas
Authors: Kadin Marshall E.
Published: January 2006

Abstract:  CD30+ cutaneous lymphoproliferative disorders include lymphomatoid papulosis (LyP) and anaplastic large cell lymphoma (ALCL). LyP is associated with development of lymphoma in nearly 20% of patients. Herein is reviewed the clonal relationship of LyP to malignant lymphoma, the concept of a common stem cell for LyP and associated lymphomas, and the role of genetic instability in lymphomagenesis. The possible role of the CD30+ cell as a regulatory T‐cell is introduced and a model for progression of LyP to ALCL is illustrated.
Primary cutaneous B‐cell lymphomas: then and now
Authors: Kerl Helmut , Cerroni Lorenzo
Published: January 2006

Abstract:  In the past, concepts of cutaneous lymphomas were based on careful clinical and classical histopathological descriptions. Most primary cutaneous B‐cell lymphomas (pCBCL) were designated as lymphosarcoma, follicular lymphoma, histiocytic lymphoma, reticulum‐cell sarcoma or skin reticuloses. Today, pCBCL are classified as a fully recognized and well‐defined group of extranodal lymphomas according to the criteria of the World Health Organization–European Organization for Research and Treatment of Cancer classification. Better understanding of the mechanisms of the pathogenesis in pCBCL will hopefully stimulate investigative research and provide further improvement of diagnosis and treatment.
On the diagnosis of erythrodermic cutaneous T‐cell lymphoma
Authors: Vonderheid Eric C.
Published: January 2006

Abstract:  Erythrodermic cutaneous T‐cell lymphoma (E‐CTCL) is the cause of less than 5% of all cases of generalized erythroderma. A methodical evaluation of skin, blood, and lymph node samples using standard histology, immunohistochemistry (IHC), flow cytometry (FC), and molecular analysis for evidence of a dominant T‐cell clone has been recommended in a recently published diagnostic algorithm. In this commentary, the author discusses available information regarding the role of these diagnostic methods for the diagnosis of E‐CTCL with emphasis on personal observations regarding skin IHC and polymerase chain reaction (PCR)‐based molecular studies as adjunct diagnostic studies on a series of 55 patients with erythrodermic mycosis fungoides and 50 patients with Sézary syndrome compared to 50 patients with extensive benign inflammatory skin disease. The conclusions are (1) IHC of the skin does not reliably differentiate E‐CTCL from benign simulants, (2) presence of phenotypically abnormal T cells in the blood or expanded subsets of CD4+CD7– or CD4+CD26– cells by FC is particularly helpful as a diagnostic study, (3) the presence of an identical T‐cell clone in the skin and blood also is a specific diagnostic criterion for E‐CTCL, but exceptions may occur, and (4) the PCRγ‐denaturing gradient gel electrophoresis technique appears to be more reliable than PCRγ‐single‐stranded conformational polymorphism for diagnostic purposes.
Standard and new treatments in cutaneous B‐cell lymphomas
Authors: Dreno Brigitte
Published: January 2006

Background:  Primary cutaneous B‐cell lymphomas (PCBCL) are cutaneous non‐Hodgkin lymphomas and can be classified clinically and by prognosis. The aim of this paper is to perform a review of standard and new treatments.

Method:  This paper provides a literature review of the different treatments of PCBCL.

Results:  Surgery and radiotherapy remain the standard therapies in isolated cutaneous lesions. Systemic or intralesional interferon (IFN)‐α may be an alternative in PCBCL with diffuse cutaneous lesions. In aggressive forms with poor prognosis, polychemotherapy is the first line of treatment although rituximab and radioimmunotherapy are evolving therapeutic options.

Conclusion:  In the majority of cases, the treatment of CBCL is straightforward. In aggressive forms, new therapies and biologic therapies may be of real interest.
New aspects in the biology of cutaneous B‐cell lymphomas
Authors: Pimpinelli Nicola
Published: January 2006

Immunologic and molecular genetic studies greatly contributed to a better understanding and interpretation of the distinct clinico‐pathologic features of primary cutaneous B‐cell lymphomas (CBCL), which are the basis for the consensus WHO‐EORTC classification. There is increasingly accumulating evidence that these well defined clinico‐pathologic entities of CBCL have specific immunologic and molecular features, which further support their nosologic categorization as well as either interesting similarities with other extranodal B‐cell lymphomas or definite peculiarities as compared to nodal B‐cell lymphomas of similar histotype (specifically, follicle center lymphoma and diffuse large B‐cell lymphoma).
CD30+ lymphoproliferative disorders: histopathology, differential diagnosis, new variants, and simulators
Authors: Kempf Werner
Published: January 2006

Summary:  CD30+ lymphoproliferative disorders of the skin (CD30+ LPD) represent a well‐defined spectrum of primary cutaneous T‐cell lymphomas which have been recognized as distinct entities in recent lymphoma classifications. Lymphomatoid papulosis and anaplastic large‐cell lymphoma share the expression of CD30 antigen as a common phenotypic hallmark but differ in regard to their clinical and histologic features as well as their biologic behavior. This article summarizes the histologic features of CD30+ LPD and presents recently identified new clinicopathologic variants of CD30+ LPD. There is an increasing number of reactive inflammatory disorders and neoplastic diseases which are composed of or contain a significant number of CD30+ cells and mimic LyP or anaplastic large cell lymphoma clinically or histologically. Differential diagnostic considerations focus on other lymphoproliferative processes with CD30+ tumor cells as well as non‐lymphoid neoplasms and inflammatory simulators. The term CD30+ pseudolymphoma is proposed to designate inflammatory processes with CD30+ T cells. The final diagnosis of CD30+ LPD is based on a synthesis of clinical, histologic, phenotypic, and molecular genetic findings.
Irradiation therapy: from UV light to electron beam
Authors: Panizzon Renato G.
Published: January 2006

Irradiation therapy represents one of the mainstay treatment modalities in cutaneous T‐cell lymphomas. For the patch and plaque stages UV therapy is mostly used. Among UV light treatment broadband UVB is less effective than narrow band UVB. If these modalities are not sufficient, then PUVA therapy is indicated and might be used in even more advanced stages, including the erythrodermic stage of the disease. For resistant cases and remaining tumors, conventional radiotherapy or electron beam therapy is the treatment of a choice. If the disease is widespread, total skin electron beam radiation gives excellent results. One should not forget the possibility of combining UV therapy with radiotherapy or electron beam radiation, or with chemo‐ and immunotherapy respectively.
Patterns of frugivory of the Budongo Forest chimpanzees, Uganda
Authors: Tweheyo Mnason , Lye Kåre A.
Published: January 2006

Frugivory patterns of the chimpanzees in the Budongo Forest Reserve, Uganda were studied between June 2000 and August 2001. Chimpanzee feeding habitats, movement, group size and food eaten were assessed using focal and scan sampling. It was found that fruits were scarce during the dry season, when chimpanzees appeared and moved in large groups over long distances and raided farms at the forest edge. Chimpanzee movement out of the forest to forage was influenced by seasonal fluctuations in availability of preferred foods as some cultivated crops are perennial. Presence of chimpanzees in a specific feeding habitat was related to the availability of edible fruits both within and between months, suggesting that the presence of food may influence chimpanzee movement patterns. Therefore, a good understanding of patterns of frugivory is essential for making informed decisions about conservation of chimpanzees and other frugivores like birds and monkeys in Budongo as different forest habitats are under varying human pressure because of logging and other forms of utilization.
Stand structure, species diversity and regeneration of an endemic palm forest on the Seychelles
Authors: Fleischmann Karl , Edwards Peter J. , Ramseier Dieter , Kollmann Johannes
Published: January 2006

The ‘Vallée de Mai’ on the island of Praslin in the Seychelles group is a World Heritage Site because of its unique forest vegetation dominated by the palmLodoicea maldivica. However, despite its great conservation importance, the stand structure, species diversity and regeneration of this forest have not previously been studied. Moreover, the conservation value of the reserve is currently threatened by invading alien plants and limited regeneration of some native species. The species composition of the forest was studied in six permanent plots (1985 and 1998) and along seven trail transects (1997). To explain potential variation in tree regeneration, the light climate within all plots was investigated using hemispherical photographs. The results reveal little change in forest structure, species diversity and regeneration in the permanent plots over the 13‐year period, but some regeneration of most woody species, presence of some alien species and a relatively high species turnover. We found no significant influence of local light climate upon forest structure, species diversity or regeneration. Although the stand characteristics seem to be relatively stable, the permanent plots and transects should be monitored in order to detect future changes in stand structure and to optimize the protection of this unique forest reserve.
Shifts in native ungulate communities on a former cattle ranch in Tanzania
Authors: Treydte Anna C. , Edwards Peter J. , Suter Werner
Published: January 2006

When an area is brought under protection, current animal populations and their habitat preferences need to be assessed to predict population trends and future habitat availability. Using data from walking transects, we estimated the size of native ungulate populations on an abandoned cattle ranch in a coastal savannah in Tanzania, now included in the new Saadani National Park. Data were analysed withdistancesampling and conventional strip transect techniques and were compared with results of previous wildlife counts. Few individuals of mainly browsing species were present in former cattle grazing areas exhibiting high bush‐encroachment while a ten times higher biomass of browsers and grazers was found in the cattle‐unmodified savannah. Population sizes of some species increased twofold between 1991 and 2001 within the entire area but neither population size nor species richness increased in the abandoned rangeland during our 3‐year study period from 2001 to 2003. We conclude that the former ranch has potential for future recolonization by wild ungulates. Resettlement will take place gradually with ‘pioneer‐species’ facilitating the entry of more demanding species. Habitat restoration through wildlife can be observed and quantified on Mkwaja Ranch which will be of importance for future management of native ungulates reclaiming abandoned rangeland.