bluuebunny/crossref_metadata_2025_split huggingface dataset:
Holiday Breaks for Adults with Intellectual Disabilities Living with Older Carers
Authors: McConkey Roy , McCullough Joanne 
Published: April 2006

• Summary: The evaluation of a project instigated by a voluntary group provided an opportunity to investigate the benefits of holiday breaks to both carers and participants. Feedback was obtained from over 100 people with intellectual disabilities through individual and group interviews, as well as from their carers using self-completed questionnaires. • Findings: Overall, the breaks were thoroughly enjoyed by the project members, providing them with a range of activities and leisure pursuits in the company of their friends and, on certain breaks, with non-disabled people as well. Carers reported more benefits to their relative in the later years of the project and became more willing for their relative to attend. • Applications: Three main issues are discussed: the use of mainstream settings and services, rather than specialist facilities, to provide short breaks; how best to encourage other carers of people with more significant needs to avail themselves of these opportunities; and ways of improving the social and leisure networks of people living with families so that the benefits of the ‘holiday’ experience could be recreated more locally and more frequently.
Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway
Authors: Wjst Matthias , Altmüller Janine , Faus-Kessler Theresia , Braig Christine , Bahnweg Margret , André Elisabeth 
Published: April 2006

Abstract
The vitamin D prophylaxis of rickets in pregnant women and newborns may play a role in early allergic sensitization. We now asked if an already diseased population may have inherited genetic variants in the vitamin D turnover or signalling pathway.
Serum levels of calcidiol (25-OH-D3) and calcitriol (1,25-(OH)2-D3) were retrospectively assessed in 872 partipants of the German Asthma Family Study. 96 DNA single base variants in 13 different genes were genotyped with MALDI-TOF and a bead array system. At least one positive SNP with a TDT of p < 0.05 for asthma or total IgE and calcidiol or calcitriol was seen in IL10, GC, IL12B, CYP2R1, IL4R, and CYP24A1. Consistent strong genotypic association could not be observed. Haplotype association were found only for CYP24A1, the main calcidiol degrading enzyme, where a frequent 5-point-haplotype was associated with asthma (p = 0,00063), total IgE (p = 0,0014), calcidiol (p = 0,0043) and calcitriol (p = 0,0046).
Genetic analysis of biological pathways seem to be a promising approach where this may be a first entry point into effects of a polygenic inherited vitamin D sensitivity that may affect also other metabolic, immunological and cancerous diseases.
Exhaled breath condensate cysteinyl leukotrienes and airway remodeling in childhood asthma: a pilot study
Authors: Lex Christiane , Zacharasiewicz Angela , Payne Donald NR , Wilson Nicola M , Nicholson Andrew G , Kharitonov Sergei A , Barnes Peter J , Bush Andrew 
Published: April 2006

Abstract

Background
It has been suggested that cysteinyl leukotrienes (cysLTs) play an important role in airway remodeling. Previous reports have indicated that cysLTs augment human airway smooth muscle cell proliferation. Recently, cysLTs have been measured in exhaled breath condensate (EBC). The aim of this study was to evaluate the relationship between cysLTs in EBC and another marker of airway remodeling, reticular basement membrane (RBM) thickening, in endobronchial biopsies in children.

Methods
29 children, aged 4–15 years, with moderate to severe persistent asthma, who underwent bronchoscopy as part of their clinical assessment, were included. Subjects underwent spirometry and EBC collection for cysLTs analysis, followed by bronchoscopy and endobronchial biopsy within 24 hours.

Results
EBC cysLTs were significantly lower in asthmatic children who were treated with montelukast than in those who were not (median (interquartile range) 36.62 (22.60–101.05) versus 249.1 (74.21–526.36) pg/ml, p = 0.004). There was a significant relationship between EBC cysLTs and RBM thickness in the subgroup of children who were not treated with montelukast (n = 13, r = 0.75, p = 0.003).

Conclusion
EBC cysLTs appear to be associated with RBM thickening in asthma.
Performance of a new hand-held device for exhaled nitric oxide measurement in adults and children
Authors: Alving K , Janson C , Nordvall L 
Published: April 2006

AbstractBackgroundExhaled nitric oxide (NO) measurement has been shown to be a valuable tool in the management of patients with asthma. Up to now, most measurements have been done with stationary, chemiluminescence-based NO analysers, which are not suitable for the primary health care setting. A hand-held NO analyser which simplifies the measurement would be of value both in specialized and primary health care. In this study, the performance of a new electrochemical hand-held device for exhaled NO measurements (NIOX MINO) was compared with a standard stationary chemiluminescence unit (NIOX).MethodsA total of 71 subjects (6–60 years; 36 males), both healthy controls and atopic patients with and without asthma were included. The mean of three approved exhalations (50 ml/s) in each device, and the first approved measurement in the hand-held device, were compared with regard to NO readings (Bland-Altman plots), measurement feasibility (success rate with 6 attempts) and repeatability (intrasubject SD).ResultsSuccess rate was high (≥ 84%) in both devices for both adults and children. The subjects represented a FENOrange of 8–147 parts per billion (ppb). When comparing the mean of three measurements (n = 61), the median of the intrasubject difference in exhaled NO for the two devices was -1.2 ppb; thus generally the hand-held device gave slightly higher readings. The Bland-Altman plot shows that the 95% limits of agreement were -9.8 and 8.0 ppb. The intrasubject median difference between the NIOX and the first approved measurement in the NIOX MINO was -2.0 ppb, and limits of agreement were -13.2 and 10.2 ppb. The median repeatability for NIOX and NIOX MINO were 1.1 and 1.2 ppb, respectively.ConclusionThe hand-held device (NIOX MINO) and the stationary system (NIOX) are in clinically acceptable agreement both when the mean of three measurements and the first approved measurement (NIOX MINO) is used. The hand-held device shows good repeatability, and it can be used successfully on adults and most children. The new hand-held device will enable the introduction of exhaled NO measurements into the primary health care.
An interactive tool for visualization of relationships between gene expression profiles
Authors: Ruzanov Peter , Jones Steven JM 
Published: April 2006

Abstract

Background
Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques.

Results
We designed and built TreeBuilder3D, an interactive viewer for visualizing the hierarchical relationships between expression profiles such as SAGE libraries or microarrays. The program allows loading expression data as plain text files and visualizing the relative differences of the analyzed datasets in 3-dimensional space using various distance metrics.

Conclusion
TreeBuilder3D provides a simple interface and has a small size. Written in Java, TreeBuilder3D is a platform-independent, open source application, which may be useful in analysis of large-scale gene expression data.
Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables
Authors: Van Belle Werner , Ånensen Nina , Haaland Ingvild , Bruserud Øystein , Høgda Kjell-Arild , Gjertsen Bjørn Tore 
Published: April 2006

Abstract

Background
Two-dimensional gel electrophoresis (2DE) is a powerful technique to examine post-translational modifications of complexly modulated proteins. Currently, spot detection is a necessary step to assess relations between spots and biological variables. This often proves time consuming and difficult when working with non-perfect gels. We developed an analysis technique to measure correlation between 2DE images and biological variables on a pixel by pixel basis. After image alignment and normalization, the biological parameters and pixel values are replaced by their specific rank. These rank adjusted images and parameters are then put into a standard linear Pearson correlation and further tested for significance and variance.

Results
We validated this technique on a set of simulated 2DE images, which revealed also correct working under the presence of normalization factors. This was followed by an analysis of p53 2DE immunoblots from cancer cells, known to have unique signaling networks. Since p53 is altered through these signaling networks, we expected to find correlations between the cancer type (acute lymphoblastic leukemia and acute myeloid leukemia) and the p53 profiles. A second correlation analysis revealed a more complex relation between the differentiation stage in acute myeloid leukemia and p53 protein isoforms.

Conclusion
The presented analysis method measures relations between 2DE images and external variables without requiring spot detection, thereby enabling the exploration of biosignatures of complex signaling networks in biological systems.
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
Authors: Altaf-Ul-Amin Md , Shinbo Yoko , Mihara Kenji , Kurokawa Ken , Kanaya Shigehiko 
Published: April 2006

Abstract

Background
After complete sequencing of a number of genomes the focus has now turned to proteomics. Advanced proteomics technologies such as two-hybrid assay, mass spectrometry etc. are producing huge data sets of protein-protein interactions which can be portrayed as networks, and one of the burning issues is to find protein complexes in such networks. The enormous size of protein-protein interaction (PPI) networks warrants development of efficient computational methods for extraction of significant complexes.

Results
This paper presents an algorithm for detection of protein complexes in large interaction networks. In a PPI network, a node represents a protein and an edge represents an interaction. The input to the algorithm is the associated matrix of an interaction network and the outputs are protein complexes. The complexes are determined by way of finding clusters, i. e. the densely connected regions in the network. We also show and analyze some protein complexes generated by the proposed algorithm from typical PPI networks of Escherichia coli and Saccharomyces cerevisiae. A comparison between a PPI and a random network is also performed in the context of the proposed algorithm.

Conclusion
The proposed algorithm makes it possible to detect clusters of proteins in PPI networks which mostly represent molecular biological functional units. Therefore, protein complexes determined solely based on interaction data can help us to predict the functions of proteins, and they are also useful to understand and explain certain biological processes.
Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids
Authors: Jansen Robert K , Kaittanis Charalambos , Saski Christopher , Lee Seung-Bum , Tomkins Jeffrey , Alverson Andrew J , Daniell Henry 
Published: April 2006

AbstractBackgroundThe Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome ofVitis viniferaand used these data to assess relationships among 27 angiosperms, including nine taxa of rosids.ResultsTheVitis viniferachloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order ofVitisis identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion ofGossypiumis necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses placeCucumisas sister to the Myrtales and therefore do not support the monophyly of the eurosid I clade.ConclusionPhylogenies based on DNA sequences from complete chloroplast genome sequences provide strong support for the position of the Vitaceae as the earliest diverging lineage of rosids. Our phylogenetic analyses support recent assertions that inadequate taxon sampling and incorrect model specification for concatenated multi-gene data sets can mislead phylogenetic inferences when using whole chloroplast genomes for phylogeny reconstruction.
Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation
Authors: McKenzie Patrick , Chadalavada Seetharam C , Bohrer Justin , Adams Josephine C 
Published: April 2006

Abstract

Background
Thrombospondins (TSPs) are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tissue organisation. Five TSPs, designated TSP-1 through TSP-5, are encoded in the human genome. All but one have known roles in acquired or inherited human diseases. To further understand the roles of TSPs in human physiology and pathology, it would be advantageous to extend the repertoire of relevant vertebrate models. In general the zebrafish is proving an excellent model organism for vertebrate biology, therefore we set out to evaluate the status of TSPs in zebrafish and two species of pufferfish.

Results
We identified by bioinformatics that three fish species encode larger numbers of TSPs than vertebrates, yet all these sequences group as homologues of TSP-1 to -4. By phylogenomic analysis of neighboring genes, we uncovered that, in fish, a TSP-4-like sequence is encoded from the gene corresponding to the tetrapod TSP-5 gene. Thus, all TSP genes show conservation of synteny between fish and tetrapods. In the human genome, the TSP-1, TSP-3, TSP-4 and TSP-5 genes lie within paralogous regions that provide insight into the ancestral genomic context of vertebrate TSPs.

Conclusion
A new model for TSP evolution in vertebrates is presented. The TSP-5 protein sequence has evolved rapidly from a TSP-4-like sequence as an innovation in the tetrapod lineage. TSP biology in fish is complicated by the presence of additional lineage- and species-specific TSP paralogues. These novel results give deeper insight into the evolution of TSPs in vertebrates and open new directions for understanding the physiological and pathological roles of TSP-4 and TSP-5 in humans.
Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression
Authors: Richter Karin , Wirta Valtteri , Dahl Lina , Bruce Sara , Lundeberg Joakim , Carlsson Leif , Williams Cecilia 
Published: April 2006

AbstractBackgroundExpression of the LIM-homeobox geneLhx2in murine hematopoietic cells allows for the generation of hematopoietic stem cell (HSC)-like cell lines. To address the molecular basis ofLhx2function, we generated HSC-like cell lines whereLhx2expression is regulated by a tet-on system and hence dependent on the presence of doxycyclin (dox). These cell lines efficiently down-regulateLhx2expression upon dox withdrawal leading to a rapid differentiation into various myeloid cell types.ResultsGlobal gene expression of these cell lines cultured in dox was compared to different time points after dox withdrawal using microarray technology. We identified 267 differentially expressed genes. The majority of the genes overlapping with HSC-specific databases were those down-regulated after turning offLhx2expression and a majority of the genes overlapping with those defined as late progenitor-specific genes were the up-regulated genes, suggesting that these cell lines represent a relevant model system for normal HSCs also at the level of global gene expression. Moreover,in situhybridisations of several genes down-regulated after dox withdrawal showed overlapping expression patterns withLhx2in various tissues during embryonic development.ConclusionGlobal gene expression analysis of HSC-like cell lines with inducible Lhx2 expression has identified genes putatively linked to self-renewal / differentiation of HSCs, and function ofLhx2in organ development and stem / progenitor cells of non-hematopoietic origin.
Chlamydia pneumoniae, heat shock proteins 60 and risk of secondary cardiovascular events in patients with coronary heart disease under special consideration of diabetes: a prospective study
Authors: Guech-Ongey Mercy , Brenner Hermann , Twardella Dorothee , Rothenbacher Dietrich 
Published: April 2006

Abstract

Background
There have been suggestions of an association between Chlamydia pneumoniae, chlamydial heat shock protein (Ch-hsp) 60 and human heat shock protein (h-hsp) 60 infection sero-status and development of secondary cardiovascular events. Patients with diabetes might be at higher risk since they are prone to infections. The objective of this study was to investigate prospectively the role of Chlamydia pneumoniae (CP), chlamydial heat shock protein (Ch-hsp) 60 and a possible intermediate role of human heat shock protein (h-hsp) 60 sero-status in the development of secondary cardiovascular disease (CVD) events in patients with coronary heart disease (CHD) under special consideration of diabetes mellitus.

Methods
Patients aged 30–70 undergoing an in-patient rehabilitation program after acute manifestation of coronary heart disease (International Classification of Disease, 9th Rev. pos. 410–414) between January 1999 and May 2000 in one of two participating rehabilitation clinics in Germany were included in this analysis. Chlamydia pneumoniae (CP), chlamydial heat shock protein (Ch-hsp) 60 and human heat shock protein (h-hsp) 60 status at baseline were measured by serum immunoglobulin G and A antibodies. Secondary CVD events (myocardial infarction, stroke, and cardiovascular death) were recorded during a mean follow-up period of 33.5 months (response = 87%).

Results
Among the 1052 subjects 37.4% and 39.3% were sero-positive to CP IgA and IgG respectively, 22.2% were sero-positive to Ch-hsp 60 IgG and 8.4% were positive to h-hsp 60 IgG at baseline. During follow-up, secondary CVD events occurred among 71 (6.8%) participants. Occurrence of a secondary CVD event was more common among CP (IgA) and CP (IgG) sero-positive than among sero-negative patients (p-values 0.04 and 0.1, respectively). The risk of secondary CVD events was increased among patients with both a positive CP sero-status and diabetes compared to infection negative, non-diabetic patients and in general, sero-positivity added a hazard to diabetes. The interaction term between infection sero-status and diabetes was not statistically significant. We were not able to show an intermediate role of human heat shock protein (h-hsp) 60 sero-status in the development of secondary CVD events in patients with CHD.

Conclusion
Results from this cohort of 1052 patients with pre-existing CHD cannot exclude a possible moderate increase in risk of secondary CVD events among patients with a positive infection sero-status. However, our study showed no intermediate role of human heat shock protein (h-hsp) 60 sero-status in the development of secondary CVD events in patients with CHD. Larger studies or meta-analysis of multiple studies are needed to address the interaction between infection sero-status and diabetes with adequate power.
Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer
Authors: Tan Duan-Jun , Chang Julia , Liu Ling-Ling , Bai Ren-Kui , Wang Yu-Fen , Yeh Kun-Tu , Wong Lee-Jun C 
Published: April 2006

AbstractBackgroundThe roles of mitochondria in energy metabolism, the generation of ROS, aging, and the initiation of apoptosis have implicated their importance in tumorigenesis. In this study we aim to establish the mutation spectrum and to understand the role of somatic mtDNA mutations in esophageal cancer.MethodsThe entire mitochondrial genome was screened for somatic mutations in 20 pairs (18 esophageal squamous cell carcinomas, one adenosquamous carcinoma and one adenocarcinoma) of tumor/surrounding normal tissue of esophageal cancers, using temporal temperature gradient gel electrophoresis (TTGE), followed by direct DNA sequencing to identify the mutations.ResultsFourteen somatic mtDNA mutations were identified in 55% (11/20) of tumors analyzed, including 2 novel missense mutations and a frameshift mutation in ND4L, ATP6 subunit, and ND4 genes respectively. Nine mutations (64%) were in the D-loop region. Numerous germline variations were found, at least 10 of them were novel and five were missense mutations, some of them occurred in evolutionarily conserved domains. Using real-time quantitative PCR analysis, the mtDNA content was found to increase in some tumors and decrease in others. Analysis of molecular and other clinicopathological findings does not reveal significant correlation between somatic mtDNA mutations and mtDNA content, or between mtDNA content and metastatic status.ConclusionOur results demonstrate that somatic mtDNA mutations in esophageal cancers are frequent. Some missense and frameshift mutations may play an important role in the tumorigenesis of esophageal carcinoma. More extensive biochemical and molecular studies will be necessary to determine the pathological significance of these somatic mutations.
Attitudes to smoking cessation and triggers to relapse among Chinese male smokers
Authors: Yang Tingzhong , Fisher K John , Li Fuzhong , Danaher Brian G 
Published: April 2006

Abstract

Background
Smoking is related to many diseases, and the relapse to smoking after cessation in China is noticeable. We examined the attitudes of Chinese male smokers regarding smoking cessation and reasons for relapse.

Methods
We interviewed 201 male smokers in Hangzhou City, Zhejiang province, China who had tried to quit smoking at least once in order to identify reasons for quitting and situations triggering relapse.

Results
The most significant reported reasons for quitting included personal health (77.1%), the cost of cigarettes (53.7%), and family pressures to quit (29.9%). The most common factors triggering relapse were social situations (34.3%), feeling negative or down (13.4%) and times of being alone (8.4%).

Conclusion
Health and family concerns, personal factors, the influence of others and a lack of cessation resources were cited as salient factors concerning smoking cessation among male smokers in this study. Effective smoking control efforts in China will require attention to these influences if China is to curb its current smoking epidemic.