bluuebunny/crossref_metadata_2025_split huggingface dataset:
Respiratory heat and moisture loss is associated with eosinophilic inflammation in asthma
Authors: Noble D. D. , McCafferty J. B. , Greening A. P. , Innes J. A. 
Published: November 2006

Increased mucosal vascularity is a hallmark of airway inflammation in asthma. It was hypothesised that this would lead to a detectable increase in respiratory heat and moisture loss (RHML), which would reflect the degree of airway inflammation present.A total of 23 subjects with asthma and 18 healthy controls had RHML measured in a cross-sectional study. The measurements were made using a device that combines temperature and humidity measurement during inspiration and expiration and allows precise control over inspirate conditions and ventilatory pattern. The subjects with asthma underwent parallel measurements of exhaled nitric oxide, sputum eosinophil percentage and exhaled breath condensate pH.Mean±sdRHML was elevated in patients with asthma (98.1±7.3 J·L−1) compared with control subjects (91.9±4.5 J·L−1). RHML measurement in asthma correlated with sputum eosinophil percentage.This novel correlation between thermal and cellular measurements in asthma suggests that both of these noninvasive indices are sensitive to the degree of underlying chronic airway inflammation.
Treatment failure in tuberculosis
Authors: Panickar J. R. , Hoskyns W. 
Published: November 2006

Treatment of latent tuberculosis (TB) infection with 3 months of rifampicin/isoniazid is a major part of preventive TB programmes. The effectiveness of treatment of latent TB infection can only be assessed by rates of subsequent breakdown and there are few outcome data for this combination of rifampicin/isoniazid. Therefore, the aim of the present study was to estimate the failure rate following treatment for the latent TB infection.A questionnaire survey was carried out in all parents of children aged <16 yrs who completed treatment for latent TB infection at Leicester Royal Infirmary (Leicester, UK) over the period 1997–2003. Cases of treatment failure were identified by reviewing all re-referrals to the clinic, identifying children developing TB while on treatment and by postal questionnaire to all patients discharged.Of the 400 eligible children, 344 (86%) replied. Three children who had latent TB infection subsequently developed TB disease over the time period. Of those three patients, one developed chest radiograph signs at the end of treatment and two presented with symptoms within 2 yrs of completing treatment. Overall, the mean treatment failure rate was 0.87% (95% confidence interval 0.3–2.5) or 2.2 cases per 1,000 patient-yrs.In conclusion, rates of tuberculosis breakdown after treatment for latent tuberculosis infection with 3 months rifampicin/isoniazid are acceptably low.
NT-proBNP can be used to detect right ventricular systolic dysfunction in pulmonary hypertension
Authors: Blyth K. G. , Groenning B. A. , Mark P. B. , Martin T. N. , Foster J. E. , Steedman T. , Morton J. J. , Dargie H. J. , Peacock A. J. 
Published: November 2006

Right ventricular systolic dysfunction (RVSD) at baseline (pre-treatment) predicts early death in patients with pulmonary hypertension (PH). However, RVSD can only be detected reliably by prohibitively invasive or expensive techniques. N-terminal B-type natriuretic peptide concentration ([NT-proBNP]) correlates with RV function in PH; however, an [NT-proBNP] threshold that indicates RVSD in individual patients has not previously been determined.Twenty-five patients with PH (pulmonary arterial hypertension (n = 19) or chronic thromboembolic PH (n = 6)) underwent cardiovascular magnetic resonance (CMR) imaging and NT-proBNP measurement at baseline. [NT-proBNP] was correlated against RV dimensions and ejection fraction (RVEF) measured directly by CMR imaging. The ability of NT-proBNP to detect RVSD (defined as a CMR-derived RVEF >2sds below control values) was tested and predictors of [NT-proBNP] identified.[NT-proBNP] correlated negatively with RVEF. RVSD was present in nine out of 25 patients. An [NT-proBNP] threshold of 1,685 pg·mL−1was sensitive (100%) and specific (94%) in detecting RVSD. RVEF and RV mass index independently predicted [NT-proBNP].In pulmonary hypertension, a baseline N-terminal B-type natriuretic peptide concentration of >1,685 ng·L−1suggests right ventricular systolic dysfunction, and thus an increased risk of early death. N-terminal B-type natriuretic peptide could prove useful as an objective, noninvasive means of identifying patients with pulmonary hypertension who have right ventricular systolic dysfunction at presentation.
Mortality in COPD: role of comorbidities
Authors: Sin D. D. , Anthonisen N. R. , Soriano J. B. , Agusti A. G. 
Published: November 2006

Chronic obstructive pulmonary disease (COPD) represents an increasing burden throughout the world. COPD-related mortality is probably underestimated because of the difficulties associated with identifying the precise cause of death. Respiratory failure is considered the major cause of death in advanced COPD. Comorbidities such as cardiovascular disease and lung cancer are also major causes and, in mild-to-moderate COPD, are the leading causes of mortality.The links between COPD and these conditions are not fully understood. However, a link through the inflammation pathway has been suggested, as persistent low-grade pulmonary and systemic inflammation, both known risk factors for cardiovascular disease and cancer, are present in COPD independent of cigarette smoking.Lung-specific measurements, such as forced expiratory volume in one second (FEV1), predict mortality in COPD and in the general population. However, composite tools, such as health-status measurements (e.g.St George's Respiratory Questionnaire) and the BODE index, which incorporates Body mass index, lung function (airflow Obstruction), Dyspnoea and Exercise capacity, predict mortality better than FEV1alone. These multidimensional tools may be more valuable because, unlike predictive approaches based on single parameters, they can reflect the range of comorbidities and the complexity of underlying mechanisms associated with COPD.The current paper reviews the role of comorbidities in chronic obstructive pulmonary disease mortality, the putative underlying pathogenic link between chronic obstructive pulmonary disease and comorbid conditions (i.e.inflammation), and the tools used to predict chronic obstructive pulmonary disease mortality.
Evolution and respiratory genetics
Authors: Le Souëf P. N. , Candelaria P. , Goldblatt J. 
Published: November 2006

Evolution is a plausible explanation for between-population differences in particular allele frequencies if: the genes involved have related functions; the heterogeneous alleles involved have similar functional consequences; the involved genes are not linked chromosomally; and the patterns observed would result in a biologically plausible, survival-enhancing gene–environment interaction. However, possible evolutionary effects have to be differentiated from founder effects and random genetic drift.The current authors have noted the existence of a consistent pattern of allelic frequencies in genes related to T-helper 2 (Th2) immune responses in humans of different ancestral backgrounds, residing in climatically similar regions. Th2 responses are thought to have evolved in mammals to resist infection by parasites, particularly helminths. Modern man arose in tropical Africa where helminths thrived. Relatively recently, humans migrated to cooler or drier climates where most helminths struggled to reproduce. The genetic tendency to strong Th2 responses may have become a health liability, the reduction in risk from parasites being counterbalanced by an increased inherited propensity to atopic or allergic diseases.The pattern noted by the present authors includes specific alleles of interleukin-4 and its receptor, interleukin-13, interleukin-10, the β chain of the high-affinity receptor for immunoglobulin E, the β1-adrenergic receptor, and the alpha chain of tumour necrosis factor. These population-specific polymorphism profiles are likely to be relevant in current disease patterns. The high incidence of asthma in migrants from tropical locations to affluent temperate countries is likely to be related to these patterns. Of even more concern is the possibility that increasing westernisation among the ∼2 billion people living in the tropics will produce rapidly increasing levels of asthma, as these populations have a high genetic predisposition to allergic disease.
Dynamic variable selection in SNP genotype autocalling from APEX microarray data
Authors: Podder Mohua , Welch William J , Zamar Ruben H , Tebbutt Scott J 
Published: November 2006

Abstract

Background
Single nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide – adenine (A), thymine (T), cytosine (C) or guanine (G) – is altered. Arguably, SNPs account for more than 90% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX). This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger-based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system (known as SNP Chart) is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias.

Results
Using a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully-automated genotyping algorithm based on simple linear discriminant analysis (LDA) using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU) of St. Paul's Hospital (plus one negative PCR control sample). Our method achieves a concordance rate of 98.9% with a 99.6% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9% with a higher concordance rate of 99.6%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8%.

Conclusion
The strength of this APEX chemistry-based platform is its unique redundancy having multiple probes for a single SNP. Our model-based genotype calling algorithm captures the redundancy in the system considering all the underlying probe features of a particular SNP, automatically down-weighting any 'bad data' corresponding to image artifacts on the microarray slide or failure of a specific chemistry. In this regard, our method is able to automatically select the probes which work well and reduce the effect of other so-called bad performing probes in a sample-specific manner, for any number of SNPs.
BioMoby extensions to the Taverna workflow management and enactment software
Authors: Kawas Edward , Senger Martin , Wilkinson Mark D 
Published: November 2006

Abstract

Background
As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface.

Results
The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate.

Conclusion
With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.
Gelatinases, endonuclease and Vascular Endothelial Growth Factor during development and regression of swine luteal tissue
Authors: Ribeiro Luciana Andrea , Turba Maria Elena , Zannoni Augusta , Bacci Maria Laura , Forni Monica 
Published: November 2006

Abstract

Background
The development and regression of corpus luteum (CL) is characterized by an intense angiogenesis and angioregression accompanied by luteal tissue and extracellular matrix (ECM) remodelling. Vascular Endothelial Growth Factor (VEGF) is the main regulator of angiogenesis, promoting endothelial cell mitosis and differentiation. After the formation of neovascular tubes, the remodelling of ECM is essential for the correct development of CL, particularly by the action of specific class of proteolytic enzymes known as matrix metalloproteinases (MMPs). During luteal regression, characterized by an apoptotic process and successively by an intense ECM and luteal degradation, the activation of Ca++/Mg++-dependent endonucleases and MMPs activity are required. The levels of expression and activity of VEGF, MMP-2 and -9, and Ca++/Mg++-dependent endonucleases throughout the oestrous cycle and at pregnancy were analyzed.

Results
Different patterns of VEGF, MMPs and Ca++/Mg++-dependent endonuclease were observed in swine CL during different luteal phases and at pregnancy. Immediately after ovulation, the highest levels of VEGF mRNA/protein and MMP-9 activity were detected. On days 5–14 after ovulation, VEGF expression and MMP-2 and -9 activities are at basal levels, while Ca++/Mg++-dependent endonuclease levels increased significantly in relation to day 1. Only at luteolysis (day 17), Ca++/Mg++-dependent endonuclease and MMP-2 spontaneous activity increased significantly. At pregnancy, high levels of MMP-9 and VEGF were observed.

Conclusion
Our findings, obtained from a precisely controlled in vivo model of CL development and regression, allow us to determine relationships among VEGF, MMPs and endonucleases during angiogenesis and angioregression. Thus, CL provides a very interesting model for studying factors involved in vascular remodelling.
Identification of a gonadotropin-releasing hormone receptor orthologue in Caenorhabditis elegans
Authors: Vadakkadath Meethal Sivan , Gallego Miguel J , Haasl Ryan J , Petras Stephen J , Sgro Jean-Yves , Atwood Craig S 
Published: November 2006

Abstract

Background
The Caenorhabditis elegans genome is known to code for at least 1149 G protein-coupled receptors (GPCRs), but the GPCR(s) critical to the regulation of reproduction in this nematode are not yet known. This study examined whether GPCRs orthologous to human gonadotropin-releasing hormone receptor (GnRHR) exist in C. elegans.

Results
Our sequence analyses indicated the presence of two proteins in C. elegans, one of 401 amino acids [GenBank: NP_491453; WormBase: F54D7.3] and another of 379 amino acids [GenBank: NP_506566; WormBase: C15H11.2] with 46.9% and 44.7% nucleotide similarity to human GnRHR1 and GnRHR2, respectively. Like human GnRHR1, structural analysis of the C. elegans GnRHR1 orthologue (Ce-GnRHR) predicted a rhodopsin family member with 7 transmembrane domains, G protein coupling sites and phosphorylation sites for protein kinase C. Of the functionally important amino acids in human GnRHR1, 56% were conserved in the C. elegans orthologue. Ce-GnRHR was actively transcribed in adult worms and immunoanalyses using antibodies generated against both human and C. elegans GnRHR indicated the presence of a 46-kDa protein, the calculated molecular mass of the immature Ce-GnRHR. Ce-GnRHR staining was specifically localized to the germline, intestine and pharynx. In the germline and intestine, Ce-GnRHR was localized specifically to nuclei as revealed by colocalization with a DNA nuclear stain. However in the pharynx, Ce-GnRHR was localized to the myofilament lattice of the pharyngeal musculature, suggesting a functional role for Ce-GnRHR signaling in the coupling of food intake with reproduction. Phylogenetic analyses support an early evolutionary origin of GnRH-like receptors, as evidenced by the hypothesized grouping of Ce-GnRHR, vertebrate GnRHRs, a molluscan GnRHR, and the adipokinetic hormone receptors (AKHRs) and corazonin receptors of arthropods.

Conclusion
This is the first report of a GnRHR orthologue in C. elegans, which shares significant similarity with insect AKHRs. In vertebrates, GnRHRs are central components of the reproductive endocrine system, and the identification of a GnRHR orthologue in C. elegans suggests the potential use of C. elegans as a model system to study reproductive endocrinology.
Genomewide identification of pheromone-targeted transcription in fission yeast
Authors: Xue-Franzén Yongtao , Kjærulff Søren , Holmberg Christian , Wright Anthony , Nielsen Olaf 
Published: November 2006

Abstract

Background
Fission yeast cells undergo sexual differentiation in response to nitrogen starvation. In this process haploid M and P cells first mate to form diploid zygotes, which then enter meiosis and sporulate. Prior to mating, M and P cells communicate with diffusible mating pheromones that activate a signal transduction pathway in the opposite cell type. The pheromone signalling orchestrates mating and is also required for entry into meiosis.

Results
Here we use DNA microarrays to identify genes that are induced by M-factor in P cells and by P-factor in M-cells. The use of a cyr1 genetic background allowed us to study pheromone signalling independently of nitrogen starvation. We identified a total of 163 genes that were consistently induced more than two-fold by pheromone stimulation. Gene disruption experiments demonstrated the involvement of newly discovered pheromone-induced genes in the differentiation process. We have mapped Gene Ontology (GO) categories specifically associated with pheromone induction. A direct comparison of the M- and P-factor induced expression pattern allowed us to identify cell-type specific transcripts, including three new M-specific genes and one new P-specific gene.

Conclusion
We found that the pheromone response was very similar in M and P cells. Surprisingly, pheromone control extended to genes fulfilling their function well beyond the point of entry into meiosis, including numerous genes required for meiotic recombination. Our results suggest that the Ste11 transcription factor is responsible for the majority of pheromone-induced transcription. Finally, most cell-type specific genes now appear to be identified in fission yeast.
Male circumcision, religion, and infectious diseases: an ecologic analysis of 118 developing countries
Authors: Drain Paul K , Halperin Daniel T , Hughes James P , Klausner Jeffrey D , Bailey Robert C 
Published: November 2006

AbstractBackgroundBoth religious practices and male circumcision (MC) have been associated with HIV and other sexually-transmitted infectious diseases. Most studies have been limited in size and have not adequately controlled for religion, so these relationships remain unclear.MethodsWe evaluated relationships between MC prevalence, Muslim and Christian religion, and 7 infectious diseases using country-specific data among 118 developing countries. We used multivariate linear regression to describe associations between MC and cervical cancer incidence, and between MC and HIV prevalence among countries with primarily sexual HIV transmission.ResultsFifty-three, 14, and 51 developing countries had a high (>80%), intermediate (20–80%), and low (<20%) MC prevalence, respectively. In univariate analyses, MC was associated with lower HIV prevalence and lower cervical cancer incidence, but not with HSV-2, syphilis, nor, as expected, with Hepatitis C, tuberculosis, or malaria. In multivariate analysis after stratifying the countries by religious groups, each categorical increase of MC prevalence was associated with a 3.65/100,000 women (95% CI 0.54-6.76, p = 0.02) decrease in annual cervical cancer incidence, and a 1.84-fold (95% CI 1.36-2.48, p < 0.001) decrease in the adult HIV prevalence among sub-Saharan African countries. In separate multivariate analyses among non-sub-Saharan African countries controlling for religion, higher MC prevalence was associated with a 8.94-fold (95% CI 4.30-18.60) decrease in the adult HIV prevalence among countries with primarily heterosexual HIV transmission, but not, as expected, among countries with primarily homosexual or injection drug use HIV transmission (p = 0.35).ConclusionMale circumcision was significantly associated with lower cervical cancer incidence and lower HIV prevalence in sub-Saharan Africa, independent of Muslim and Christian religion. As predicted, male circumcision was also strongly associated with lower HIV prevalence among countries with primarily heterosexual HIV transmission, but not among countries with primarily homosexual or injection drug use HIV transmission. These findings strengthen the reported biological link between MC and some sexually transmitted infectious diseases, including HIV and cervical cancer.
In vitro antibacterial activity of some plant essential oils
Authors: Prabuseenivasan Seenivasan , Jayakumar Manickkam , Ignacimuthu Savarimuthu 
Published: November 2006

AbstractBackground:To evaluate the antibacterial activity of 21 plant essential oils against six bacterial species.Methods:The selected essential oils were screened against four gram-negative bacteria (Escherichia coli,Klebsiella pneumoniae,Pseudomonas aeruginosa,Proteus vulgaris) and two gram-positive bacteriaBacillus subtilisandStaphylococcus aureusat four different concentrations (1:1, 1:5, 1:10 and 1:20) using disc diffusion method. The MIC of the active essential oils were tested using two fold agar dilution method at concentrations ranging from 0.2 to 25.6 mg/ml.Results:Out of 21 essential oils tested, 19 oils showed antibacterial activity against one or more strains. Cinnamon, clove, geranium, lemon, lime, orange and rosemary oils exhibited significant inhibitory effect. Cinnamon oil showed promising inhibitory activity even at low concentration, whereas aniseed, eucalyptus and camphor oils were least active against the tested bacteria. In general,B. subtiliswas the most susceptible. On the other hand,K. pneumoniaeexhibited low degree of sensitivity.Conclusion:Majority of the oils showed antibacterial activity against the tested strains. However Cinnamon, clove and lime oils were found to be inhibiting both gram-positive and gram-negative bacteria. Cinnamon oil can be a good source of antibacterial agents.