bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the use of haplotype phylogeny to detect disease susceptibility loci
Authors: Bardel Claire , Danjean Vincent , Hugot Jean-Pierre , Darlu Pierre , Génin Emmanuelle 
Published: May 2005

Abstract

Background
The cladistic approach proposed by Templeton has been presented as promising for the study of the genetic factors involved in common diseases. This approach allows the joint study of multiple markers within a gene by considering haplotypes and grouping them in nested clades. The idea is to search for clades with an excess of cases as compared to the whole sample and to identify the mutations defining these clades as potential candidate disease susceptibility sites. However, the performance of this approach for the study of the genetic factors involved in complex diseases has never been studied.

Results
In this paper, we propose a new method to perform such a cladistic analysis and we estimate its power through simulations. We show that under models where the susceptibility to the disease is caused by a single genetic variant, the cladistic test is neither really more powerful to detect an association nor really more efficient to localize the susceptibility site than an individual SNP testing. However, when two interacting sites are responsible for the disease, the cladistic analysis greatly improves the probability to find the two susceptibility sites. The impact of the linkage disequilibrium and of the tree characteristics on the efficiency of the cladistic analysis are also discussed. An application on a real data set concerning the CARD15 gene and Crohn disease shows that the method can successfully identify the three variant sites that are involved in the disease susceptibility.

Conclusion
The use of phylogenies to group haplotypes is especially interesting to pinpoint the sites that are likely to be involved in disease susceptibility among the different markers identified within a gene.
Selecting representative model micro-organisms
Authors: Holland BR , Schmid J 
Published: May 2005

Abstract

Background
Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.

Results
We develop the Best Total Coverage (BTC) method for selecting one or more representative model organisms from a group of interest, given that rough genetic distances between the members of the group are known. Software implementing a "greedy" version of the method can be used with large data sets, its effectiveness is tested using both constructed and biological data sets.

Conclusion
In both the simulated and biological examples the greedy-BTC method outperformed random selection of model organisms, and for two biological examples it outperformed selection of model strains based on phylogenetic structure. Although the method was designed with microbial species in mind, and is tested here on three microbial data sets, it will also be applicable to other types of organism.
Blood cultures in ambulatory outpatients
Authors: Laupland Kevin B , Church Deirdre L , Gregson Daniel B 
Published: May 2005

Abstract

Background
Blood cultures are a gold standard specific test for diagnosing many infections. However, the low yield may limit their usefulness, particularly in low-risk populations. This study was conducted to assess the utility of blood cultures drawn from ambulatory outpatients.

Methods
Blood cultures drawn at community-based collection sites in the Calgary Health Region (population 1 million) in 2001 and 2002 were included in this study. These patients were analyzed by linkages to acute care health care databases for utilization of acute care facilities within 2 weeks of blood culture draw.

Results
3102 sets of cultures were drawn from 1732 ambulatory outpatients (annual rate = 89.4 per 100,000 population). Significant isolates were identified from 73 (2.4%) sets of cultures from 51 patients, including Escherichia coli in 18 (35%) and seven (14%) each of Staphylococcus aureus and Streptococcus pneumoniae. Compared to patients with negative cultures, those with positive cultures were older (mean 49.6 vs. 40.1 years, p < 0.01), and more likely to subsequently receive care at a regional emergency department, outpatient antibiotic clinic, or hospital (35/51 vs. 296/1681, p < 0.0001). Of the 331 (19%) patients who received acute care treatment, those with positive cultures presented sooner after community culture draw (median 2 vs. 3 days, p < 0.01) and had longer median treatment duration (6 vs. 2 days, p < 0.01).

Conclusion
Blood cultures drawn in outpatient settings are uncommonly positive, but may define patients for increased intensity of therapy. Strategies to reduce utilization without excluding patients with positive cultures need to be developed for this patient population.
A mass vaccination campaign targeting adults and children to prevent typhoid fever in Hechi; Expanding the use of Vi polysaccharide vaccine in Southeast China: A cluster-randomized trial
Authors: Yang Jin , Acosta Camilo J , Si Guo-ai , Zeng Jun , Li Cui-yun , Liang Da-bin , Ochiai R Leon , Page Anne-Laure , Danovaro-Holliday M Carolina , Zhang Jie , Zhou Bao-de , Liao He-zhuang , Wang Ming-liu , Tan Dong-mei , Tang Zhen-zhu , Gong Jian , Park Jin-Kyung , Ali Mohammad , Ivanoff Bernard , Liang Gui-chen , Yang Hong-hui , Pang Tikki , Xu Zhi-yi , Donner Allan , Galindo Claudia M , Dong Bai-qing , Clemens John D 
Published: May 2005

Abstract
Background
One of the goals of this study was to learn the coverage, safety and logistics of a mass vaccination campaign against typhoid fever in children and adults using locally produced typhoid Vi polysaccharide (PS) and group A meningococcal PS vaccines in southern China.

Methods
The vaccination campaign targeted 118,588 persons in Hechi, Guangxi Province, aged between 5 to 60 years, in 2003. The study area was divided into 107 geographic clusters, which were randomly allocated to receive one of the single-dose parenteral vaccines. All aspects regarding vaccination logistics, feasibility and safety were documented and systematically recorded. Results of the logistics, feasibility and safety are reported.

Results
The campaign lasted 5 weeks and the overall vaccination coverage was 78%. On average, the 30 vaccine teams gave immunizations on 23 days. Vaccine rates were higher in those aged ≤ 15 years (90%) than in adolescents and young adults (70%). Planned mop-up activities increased the coverage by 17%. The overall vaccine wastage was 11%. The cold chain was maintained and documented. 66 individuals reported of adverse events out of all vaccinees, where fever (21%), malaise (19%) and local redness (19%) were the major symptoms; no life-threatening event occurred. Three needle-sharp events were reported.

Conclusion
The mass immunization proved feasible and safe, and vaccine coverage was high. Emphasis should be placed on: injection safety measures, community involvement and incorporation of mop-up strategies into any vaccination campaign. School-based and all-age Vi mass immunizations programs are potentially important public health strategies for prevention of typhoid fever in high-risk populations in southern China.
Influence of species and anatomical location on chondrocyte expansion
Authors: Akens Margarete K , Hurtig Mark B 
Published: May 2005

Abstract
Background
Bovine articular cartilage is often used to study chondrocytes in vitro. It is difficult to correlate in vitro studies using bovine chondrocytes with in vivo studies using other species such as rabbits and sheep. The aim of this investigation was to study the effect of species, anatomical location and exogenous growth factors on chondrocyte proliferation in vitro.

Methods
Equine (EQ), bovine (BO) and ovine (OV) articular chondrocytes from metacarpophalangeal (fetlock (F)), shoulder (S) and knee (K) joints were cultured in tissue culture flasks. Growth factors (rh-FGFb: 10 ng/ml; rh-TGFβ: 5 ng/ml) were added to the cultures at days 2 and 4. On day 6, cells were counted and flow cytometry analysis was performed to determine cell size and granularity. A three factor ANOVA with paired Tukey's correction was used for statistical analysis.

Results
After 6 days in culture, cell numbers had increased in control groups of EQ-F, OV-S, OV-F and BO-F chondrocytes. The addition of rh-FGFb led to the highest increase in cell numbers in the BO-F, followed by EQ-F and OV-S chondrocytes. The addition of rh-TGFβ increased cell numbers in EQ-S and EQ-F chondrocytes, but showed nearly no effect on EQ-K, OV-K, OV-S, OV-F and BO-F chondrocytes. There was an overall difference with the addition of growth factors between the different species and joints.

Conclusion
Different proliferation profiles of chondrocytes from the various joints were found. Therefore, we recommend performing in vitro studies using the species and site where subsequent in vivo studies are planned.
Intercellular communication, NO and the biology of Chinese medicine
Authors: Ralt Dina 
Published: May 2005

Abstract
New multiple categories of health disciplines have become popular in the west and integration between the medicinal approaches has become essential.
The hypothesis presented here suggests a novel integrative view that combines Western biochemistry with the Chinese medicinal concept of qi.
The core for this hypothesis is that transmission of qi along the meridians is based on informational molecules that travel via an intercellular communication system. Acupuncture at specific points enhances the flow of the signaling molecules through this communication system.
Nitric oxide is suggested as a prime candidate for such a signaling molecule in the meridian system. The biochemistry of nitric oxide can shed light on the biology underlying Chinese medicine while Chinese medicinal data can provide a clue to the sought after framework for nitric oxide.
A novel function for spumaretrovirus integrase: an early requirement for integrase-mediated cleavage of 2 LTR circles
Authors: Delelis Olivier , Petit Caroline , Leh Herve , Mbemba Gladys , Mouscadet Jean-François , Sonigo Pierre 
Published: May 2005

Abstract
Retroviral integration is central to viral persistence and pathogenesis, cancer as well as host genome evolution. However, it is unclear why integration appears essential for retrovirus production, especially given the abundance and transcriptional potential of non-integrated viral genomes. The involvement of retroviral endonuclease, also called integrase (IN), in replication steps apart from integration has been proposed, but is usually considered to be accessory. We observe here that integration of a retrovirus from the spumavirus family depends mainly on the quantity of viral DNA produced. Moreover, we found that IN directly participates to linear DNA production from 2-LTR circles by specifically cleaving the conserved palindromic sequence found at LTR-LTR junctions. These results challenge the prevailing view that integrase essential function is to catalyze retroviral DNA integration. Integrase activity upstream of this step, by controlling linear DNA production, is sufficient to explain the absolute requirement for this enzyme.
The novel role of IN over 2-LTR circle junctions accounts for the pleiotropic effects observed in cells infected with IN mutants. It may explain why 1) 2-LTR circles accumulate in vivo in mutants carrying a defective IN while their linear and integrated DNA pools decrease; 2) why both LTRs are processed in a concerted manner. It also resolves the original puzzle concerning the integration of spumaretroviruses. More generally, it suggests to reassess 2-LTR circles as functional intermediates in the retrovirus cycle and to reconsider the idea that formation of the integrated provirus is an essential step of retrovirus production.
Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues
Authors: Ndunguru Joseph , Taylor Nigel J , Yadav Jitender , Aly Haytham , Legg James P , Aveling Terry , Thompson Graham , Fauquet Claude M 
Published: May 2005

Abstract

Background
Plant viral diseases present major constraints to crop production. Effective sampling of the viruses infecting plants is required to facilitate their molecular study and is essential for the development of crop protection and improvement programs. Retaining integrity of viral pathogens within sampled plant tissues is often a limiting factor in this process, most especially when sample sizes are large and when operating in developing counties and regions remote from laboratory facilities. FTA is a paper-based system designed to fix and store nucleic acids directly from fresh tissues pressed into the treated paper. We report here the use of FTA as an effective technology for sampling and retrieval of DNA and RNA viruses from plant tissues and their subsequent molecular analysis.

Results
DNA and RNA viruses were successfully recovered from leaf tissues of maize, cassava, tomato and tobacco pressed into FTA® Classic Cards. Viral nucleic acids eluted from FTA cards were found to be suitable for diagnostic molecular analysis by PCR-based techniques and restriction analysis, and for cloning and nucleotide sequencing in a manner equivalent to that offered by tradition isolation methods. Efficacy of the technology was demonstrated both from sampled greenhouse-grown plants and from leaf presses taken from crop plants growing in farmer's fields in East Africa. In addition, FTA technology was shown to be suitable for recovery of viral-derived transgene sequences integrated into the plant genome.

Conclusion
Results demonstrate that FTA is a practical, economical and sensitive method for sampling, storage and retrieval of viral pathogens and plant genomic sequences, when working under controlled conditions and in the field. Application of this technology has the potential to significantly increase ability to bring modern analytical techniques to bear on the viral pathogens infecting crop plants.
Increased Fas ligand expression of CD4+ T cells by HCV core induces T cell-dependent hepatic inflammation
Authors: Cruise Michael W , Melief Hendrikje M , Lukens John , Soguero Carolina , Hahn Young S 
Published: May 2005

AbstractHepatitis C virus (HCV) infection is associated with a high rate of viral persistence and the development of chronic liver disease. The expression of HCV core protein in T cells has previously been reported to alter T cell activation and has been linked to the development of liver inflammation. However, the molecular and cellular basis for the role of HCV core-expressing T cells in liver inflammation is not understood. Here, using double-transgenic mice of CD2/HCV-core transgenic mice and ovalbumin (OVA)-specific T cell receptor transgenic mice, we demonstrated that in vivo antigenic stimulation (OVA peptide administration) triggers a marked influx of core-expressing, antigen-specific, transgenic CD4+ T cells into the liver of these mice. Phenotypic analysis of the liver-infiltrating T cells revealed high expression levels of CD44 and Fas ligand (FasL). Adoptive transfer of liver-infiltrating, core-expressing CD4+ T cells into severe combined immunodeficiency mice directly demonstrated the capacity of these activated T cells to induce liver inflammation. It is important that anti-FasL antibody treatment of the mice at the time of cell transfer abrogated the liver inflammation induced by core-expressing CD4+ T cells. These findings suggest that activated T lymphocytes expressing elevated levels of FasL may be involved in the bystander killing of hepatocyte, as well as the induction of chronic liver inflammation, by promoting recruitment of proinflammatory cells to the liver.
Effect of chitosan on the intranasal absorption of salmon calcitonin in sheep
Authors: Hinchcliffe Michael , Jabbal-Gill Inderjit , Smith Alan 
Published: May 2005

Abstract
The effects of a chitosan-based delivery system on the pharmacokinetics of intranasally administered salmon calcitonin (sCT) were investigated in a sheep model. In particular, the feasibility of producing a formulation with a comparable or improved bioavailability and/or less variability than the currently marketed nasal product (Miacalcin nasal spray, Novartis Pharmaceuticals) was assessed. A comparator (control) formulation comprising sCT solution was also tested. Sheep (n = 6) were dosed intranasally according to a randomized crossover design. The intranasal sCT dose was 1100 IU (equivalent to approximately 17 IU kg−1). After completion of the nasal dosing legs, five of the sheep received 300 IU sCT (equivalent to approximately 5 IU kg−1) by subcutaneous injection to estimate relative bioavailability. After intranasal or subcutaneous dosing, serial blood samples were taken and plasma separated by centrifugation before measuring sCT concentrations by ELISA. Pharmacokinetic (non-compartmental) and statistical (analysis of variance or non-parametric alternative) analyses were performed. No systemic or local adverse effects were observed following intranasal or subcutaneous administration of sCT. The mean relative bioavailability of sCT from the chitosan solution was improved twofold compared with Miacalcin nasal spray and threefold compared with sCT control solution. Inter-animal variability in sCT absorption appeared to be lower with use of the chitosan-based solution compared with the control solution or commercial product. Based on the reported sheep data, a chitosan delivery system could offer the potential to significantly improve the intranasal absorption of sCT and reduce the variability in absorption. In the clinical setting, this may allow relatively lower doses of the drug to be given intranasally and/or lead to improvements in the efficacy or quality of intranasal therapy.
Interaction of water with different cellulose ethers: a Raman spectroscopy and environmental scanning electron microscopy study
Authors: Fechner P M , Wartewig S , Kiesow A , Heilmann A , Kleinebudde P , Neubert R H H 
Published: May 2005

Abstract
Different non-ionic cellulose ethers like methyl cellulose (MC), hydroxypropyl cellulose (HPC) and hydroxypropylmethyl cellulose (HPMC) were investigated. The characterization of the cellulose ethers was carried out by thermogravimetry and sorption/desorption isotherms. Differences in the properties of the cellulose ether films were described by time-dependent contact angle measurements. Changes in molecular structure of the raw materials, gels and films caused by water contact were studied using Raman spectroscopy. Differences between the substitution types and changes due to the gel or film formation were observed. An environmental scanning electron microscopy (ESEM) technique was used to distinguish the morphological behaviour of the cellulose ether films in contact with water. Based on in-situ ESEM experiments, the swelling and drying behaviour of the various stages of cellulose ether films (film-hydrated film-dried film) were quantified by using image analysis.
Effect of micafungin on cytochrome P450 3A4 and multidrug resistance protein 1 activities, and its comparison with azole antifungal drugs
Authors: Sakaeda Toshiyuki , Iwaki Koichi , Kakumoto Mikio , Nishikawa Mika , Niwa Toshiro , Jin Jiang-shu , Nakamura Tsutomu , Nishiguchi Kohshi , Okamura Noboru , Okumura Katsuhiko 
Published: May 2005

Abstract
The effects of micafungin on cytochrome P450 3A4 (CYP3A4) metabolic and multidrug resistance protein 1 (MDR1) transport activities were investigated and compared with those of amphotericin B and four azole antifungal drugs (ketoconazole, itraconazole, fluconazole and miconazole). The effects on the metabolic activity of CYP3A4 were examined by measuring nifedipine oxidase activity in human liver microsomes and the effects on MDR1 transport activity were evaluated using [3H]digoxin in MDR1-overexpressing LLC-GA5-COL150 cells. An inhibitory effect on CYP3A4 activity was found for ketoconazole, itraconazole and miconazole, with 50% inhibitory concentrations of 11.7, 32.6 and 74.2 nM, respectively. Fluconazole and micafungin had only slight inhibitory effects and amphotericin B had no effect. The MDR1-mediated transport of [3H]digoxin was inhibited by ketoconazole and itraconazole, and slightly by miconazole. It is suggested that micafungin and amphotericin B would be unlikely to cause drug-drug interactions by inhibition of CYP3A4 and MDR1. A positive correlation between the inhibitory effects on CYP3A4 and MDR1 activities was observed, and the physicochemical mechanisms involved and impact on clinical treatment should be studied further.
Bridging the gap: ageing, pharmacokinetics and pharmacodynamics
Authors: Burton Dominick G A , Allen Marcus C , Bird Joseph L E , Faragher Richard G A 
Published: May 2005

Abstract
Changes in pharmacokinetics and pharmacodynamics in elderly patients generally result in an increase in the incidence of drug toxicity and adverse drug reactions. Molecular alterations associated with ageing could bring about biological changes, a consequence of which is an altered response to pharmacological agents. Unfortunately, research in this area has yet to progress beyond the cataloguing of the pharmacokinetic and pharmacodynamic changes observed in the elderly. Therefore, real progress in our understanding of pharmacogerontology could be achieved if it were possible to merge pharmacokinetic and pharmacodynamic studies with recent advances in our understanding of the causal processes bringing about ageing changes at the cellular level. Therefore, this review will focus on the mechanisms of ageing in the hope that the information will be of value to those planning independent studies.
Delivery of nebulized budesonide is affected by nebulizer type and breathing pattern
Authors: O'Callaghan C , White J , Jackson J , Barry P W , Kantar A 
Published: May 2005

Abstract
The aim of this study was to determine the output in-vitro of budesonide from two different nebulizers under simulated breathing conditions. The BimboNeb and Nebula nebulizers were used to nebulize 2 mL of budesonide (500 μg) suspension. Particle size was determined by inertial impaction after a 5-min nebulization. Total outputs of the drug from both nebulizers were measured using a sinus flow pump to create simulated breathing conditions. Paediatric and adult breathing patterns were used, with drug output measured after 5 and 10 min nebulization. The mass median aerodynamic diameter of budesonide using the BimboNeb (4.5 μm) was significantly greater than that from the Nebula (3.4 μm) (P &lt; 0.01). With the simulated adult breathing pattern, the total drug output after 5 min with the BimboNeb (61.5 μg) was twice that from the Nebula (30.7 μg). For the paediatric breathing pattern, total outputs were very similar for both nebulizers. In all cases, nebulizing for 10 min produced greater drug outputs compared with those after 5 min, particularly for the paediatric breathing pattern. The amount of aerosolized drug available for inhalation needs to be assessed for each nebuliser used and the effect of the patient's breathing pattern should also be taken into account.