bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in cardiorespiratory fitness and coronary heart disease risk factors following 24 wk of moderate- or high-intensity exercise of equal energy cost
Authors: O'Donovan Gary , Owen Andrew , Bird Steve R. , Kearney Edward M. , Nevill Alan M. , Jones David W. , Woolf-May Kate
Published: January 2005

This study was designed to investigate the effect of exercise intensity on cardiorespiratory fitness and coronary heart disease risk factors. Maximum oxygen consumption (V̇o2 max), lipid, lipoprotein, and fibrinogen concentrations were measured in 64 previously sedentary men before random allocation to a nonexercise control group, a moderate-intensity exercise group (three 400-kcal sessions per week at 60% of V̇o2 max), or a high-intensity exercise group (three 400-kcal sessions per week at 80% of V̇o2 max). Subjects were instructed to maintain their normal dietary habits, and training heart rates were represcribed after monthly fitness tests. Forty-two men finished the study. After 24 wk, V̇o2 maxincreased by 0.38 ± 0.14 l/min in the moderate-intensity group and by 0.55 ± 0.27 l/min in the high-intensity group. Repeated-measures analysis of variance identified a significant interaction between monthly V̇o2 maxscore and exercise group ( F = 3.37, P < 0.05), indicating that V̇o2 maxresponded differently to moderate- and high-intensity exercise. Trend analysis showed that total cholesterol, low-density lipoprotein cholesterol, non-high-density lipoprotein cholesterol, and fibrinogen concentrations changed favorably across control, moderate-intensity, and high-intensity groups. However, significant changes in total cholesterol (−0.55 ± 0.81 mmol/l), low-density lipoprotein cholesterol (−0.52 ± 0.80 mmol/l), and non-high-density lipoprotein cholesterol (−0.54 ± 0.86 mmol/l) were only observed in the high-intensity group (all P < 0.05 vs. controls). These data suggest that high-intensity training is more effective in improving cardiorespiratory fitness than moderate-intensity training of equal energy cost. These data also suggest that changes in coronary heart disease risk factors are influenced by exercise intensity.
Influence of Renal Function on the Pharmacokinetics of Piperacillin/Tazobactam in Intensive Care Unit Patients During Continuous Venovenous Hemofiltration
Authors: Arzuaga Alazne , Maynar Javier , Gascón Alicia R. , Isla Arantxazu , Corral Esther , Fonseca Fernando , Sánchez‐Izquierdo José Ángel , Rello Jordi , Canut Andrés , Pedraz José Luis
Published: January 2005

The pharmacokinetics of piperacillin/tazobactam (4 g/0.5 g every 6 or 8 hours, by 20‐minute intravenous infusion) were studied in 14 patients with acute renal failure who underwent continuous venovenous hemofiltration with AN69 membranes. Patients were grouped according to severity (CLCR 10 mL/min, 10 < CLCR 50 mL/min, and CLCR > 50 mL/min). A noncompartmental analysis was performed. The sieving coefficient (0.78 ± 0.28) was similar to the unbound fraction (0.65 ± 0.24) for tazobactam, but it was significantly different (0.34 ± 0.25) from the unbound fraction (0.78 ± 0.14) for piperacillin. Extracorporeal clearance was 37.0% ± 28.8%, 12.7% ± 12.6%, and 2.8% ± 3.2% for piperacillin in each group and 62.5% ± 44.9%, 35.4% ± 17.0%, and 13.1% ± 8.0% for tazobactam. No patients presented tazobactam accumulation. In patients with CLCR < 50 mL/min, tss(%) > MIC90 values were 100% for a panel of 19 pathogens, but in those with CLCR > 50 mL/min, tss(%) > MIC90 indexes were 55.5% and 16.6% for pathogens with MIC90 values of 32 and 64. The extracorporeal clearance of piperacillin/tazobactam is clinically significant in patients with CLCR > 50 mL/min, in which the risk of underdosing and clinical failure is important and extra doses are required.
Pharmacokinetics and Acute Safety of Inhaled Testosterone in Postmenopausal Women
Authors: Davison Sonia , Thipphawong John , Blanchard Jim , Liu Kui , Morishige Richard , Gonda Igor , Okikawa Jerry , Adams Jennifer , Evans Allan , Otulana Babatunde , Davis Susan
Published: January 2005

This was a preliminary feasibility study to assess the pharmacokinetics and acute safety of a single dose of orally inhaled testosterone via the AERx system, a novel handheld aerosol delivery system in postmenopausal women. Twelve postmenopausal women stabilized on oral estrogen therapy were treated with a single dose of testosterone (0.1, 0.2, or 0.3 mg) by inhalation. Plasma concentrations of sex steroids were measured between 1 and 360 minutes. Pulmonary and cardiovascular adverse events were monitored. Inhaled testosterone produced a dose‐dependent increase in plasma total and free testosterone. At the highest dose (0.3 mg), total and free testosterone increased from baseline (mean ± SD, 0.6 ± 0.3 nmol/L, 2.5 ± 1.0 pmol/L) to maximum levels of 62.6 ± 20.4 nmol/L (total) and 168.2 ± 50.2 pmol/L (free), occurring 1 to 2 minutes after dosing. A 2‐compartment model best described the free and total testosterone pharmacokinetic profile. Dihydrotestosterone levels were higher than baseline at 60 minutes (P < .0002). Estradiol did not vary, but sex hormone binding globulin and albumin fell. There were no adverse events related to the treatment. Administration of inhaled testosterone is safe and achieves a supraphysiologic “pulse” kinetic profile of total and free testosterone with a rapid return to pretreatment levels.
Short‐Term Exposure Evaluation of Adult Smokers Switching From Conventional to First‐Generation Electrically Heated Cigarettes During Controlled Smoking
Authors: Roethig Hans J. , Kinser Robin D. , Lau Raymond W. , Walk Ruediger‐A. , Wang Nancy
Published: January 2005

This randomized, controlled study in 110 male and female adult smokers evaluated biomarkers of tobacco smoke exposure (carbon monoxide [CO], carboxyhemoglobin [CO‐Hb], nicotine, urine mutagenicity) under controlled smoking conditions when adult smokers of 1 conventional cigarette brand (CC1) were switched to an electrically heated cigarette smoking system (EHCSS) or a low‐tar conventional cigarette (CC2). Baseline exposure was determined while all subjects smoked CC1. Subjects then were stratified for gender and cigarette consumption and randomized to 1 of 5 groups—EHCSS1, EHCSS2, CC1, CC2, or no smoking—and monitored for 8 days. Compared to baseline, biomarkers of exposure on day 8 decreased 53% to 93% (P < .0001) for EHCSS groups and 18% to 39% (P < .02) for CC2. Environmental tobacco smoke arising from the smoking activities of the different study groups was measured in the air of a separate smoking room over 1‐hour periods. Concentrations of respirable suspended particulates in both EHCSS groups were about 90% lower than in the CC1 and CC2 groups, similar to the 95% reduction in the no‐smoking group. CO was undetectable in the EHCSS and no‐smoking groups. Results from this short‐term clinical study indicate that switching from a conventional cigarette to a first‐generation EHCSS reduces the generation of environmental tobacco smoke and can reduce the exposure to the measured, potentially harmful constituents in tobacco smoke if smokers do not compensate by numbers of cigarettes. The study design was found to be suitable for the evaluation of the exposure of adult smokers to the measured smoke constituents and to allow the differentiation of different cigarette designs.
Levofloxacin Pharmacokinetics in Children
Authors: Chien Shuchean , Wells Thomas G. , Blumer Jeffrey L. , Kearns Gregory L. , Bradley John S. , Bocchini Joseph A. , Natarajan Jaya , Maldonado Samuel , Noel Gary J.
Published: January 2005

Levofloxacin is a broad‐spectrum fluoroquinolone antibiotic with activity against many pathogens that cause bacterial infections in children, including penicillin‐resistant pneumococci. To provide dosing guidance for children, 3 single‐dose, multicenter pharmacokinetic studies were conducted in 85 children in 5 age groups: 6 months to <2 years, 2 to <5 years, 5 to<10 years, 10 to <12 years, and 12 to 16 years. Each child received a single 7‐mg/kg dose of levofloxacin (not to exceed 500 mg) intravenously or orally. Plasma and urine samples were collected through 24 hours after dose. Pharmacokinetic parameters were estimated and compared among the 5 age groups and to previously collected adult data. Levofloxacin absorption (as indicated by Cmax and tmax) and distribution in children are not age dependent and are comparable to those in adults. Levofloxacin elimination (reflected by t1/2 and clearance), however, is age dependent. Children younger than 5 years of age clear levofloxacin nearly twice as fast (intravenous dose, 0.32 ± 0.08 L/h/kg; oral dose, 0.28 ± 0.05 L/h/kg) as adults and, as a result, have the total systemic exposure (area under the plasma drug concentration‐time curve) approximately one half that of adults. The levofloxacin area under the plasma drug concentration‐time curve (dose normalized) in children receiving a single dose of the oral liquid formulation is comparable to that in children receiving the intravenous formulation. To provide compatible levofloxacin exposures associated with clinical effectiveness and safety in adults, children <5 years need a daily dose of 10 mg/kg, whereas children 6 months to <5 years should receive 10 mg/kg every 12 hours.
Promoting Enterprise Development or Subsidizing Tradition?
Authors: Nitani Miwako , Riding Allan
Published: January 2005

Governments and trade associations have often intervened in credit markets to guarantee loans made by financial institutions to small and medium-sized enterprises (SMEs). The most active loan guarantee program in the world is the Japanese Credit Supplementation System yet the level of entrepreneurial activity in Japan is extremely low. This paradox suggests that lack of available capital may not be the only constraint on entrepreneurial activity. This empirical article examines the Japanese loan guarantee system. It reports on its strengths and weakness, finding that the Japanese Credit Supplementation System emphasizes the salvage of firms facing distress: financial support for new businesses appears to be a lower priority. This focus reflects cultural and social realities of the Japanese context. However, it arguably discourages entrepreneurial activity by both reducing the intensity of Schumpeter’s ‘creative destruction’ and also by artificially maintaining non-viable firms that then compete with unsupported firms.
Care Provision in Housing With Supportive Services: The Importance of Care Type, Individual Characteristics, and Care Site
Authors: Phillips Charles D. , Hawes Catherine
Published: January 2005

Housing with supportive services is an important long-term sector, but information about care provision to residents in these settings is largely unavailable. The role of individual characteristics versus facility identity in determining how care is provided is completely unexplored. Data from 60 facilities in a single state were used to investigate the degree to which individual characteristics and facility identity determined how much care was provided to residents. Individual characteristics had the greatest impact on the amount of direct care time received by individuals. Care that was dementia oriented (i.e., cueing), however, was more strongly affected by the identity of the facility than by individual characteristics. These results have important implications for how consumers should think about seeking, and policy makers should think about supporting, care for those with impaired cognitive status who utilize housing with supportive services.
Ex vivo culture of Fancc-/- stem/progenitor cells predisposes cells to undergo apoptosis, and surviving stem/progenitor cells display cytogenetic abnormalities and an increased risk of malignancy
Authors: Li Xiaxin , Le Beau Michelle M. , Ciccone Samantha , Yang Feng-Chun , Freie Brian , Chen Shi , Yuan Jin , Hong Ping , Orazi Attilio , Haneline Laura S. , Clapp D. Wade
Published: January 2005

Current strategies for genetic therapy using Moloney retroviruses require ex vivo manipulation of hematopoietic cells to facilitate stable integration of the transgene. While many studies have evaluated the impact of ex vivo culture on normal murine and human stem/progenitor cells, the cellular consequences of ex vivo manipulation of stem cells with intrinsic defects in genome stability are incompletely understood. Here we show that ex vivo culture of Fancc-/- bone marrow cells results in a time-dependent increase in apoptosis of primitive Fancc-/- progenitor cells in conditions that promote the proliferation of wild-type stem/progenitor cells. Further, recipients reconstituted with the surviving Fancc-/- cells have a high incidence of cytogenetic abnormalities and myeloid malignancies that are associated with an acquired resistance to tumor necrosis factor α (TNF-α). Collectively, these data indicate that the intrinsic defects in the genomic stability of Fancc-/- stem/progenitor cells provide a selective pressure for cells that are resistant to apoptosis and have a propensity for the evolution to clonal hematopoiesis and malignancy. These studies could have implications for the design of genetic therapies for treatment of Fanconi anemia and potentially other genetic diseases with intrinsic defects in genome stability.
B-cell kinetics in humans: rapid turnover of peripheral blood memory cells
Authors: Macallan Derek C. , Wallace Diana L. , Zhang Yan , Ghattas Hala , Asquith Becca , de Lara Catherine , Worth Andrew , Panayiotakopoulos George , Griffin George E. , Tough David F. , Beverley Peter C. L.
Published: January 2005

Information about the kinetic behavior and lifespan of lymphocytes is crucial to understanding the mechanisms that regulate processes such as immunologic memory. We have used in vivo labeling of dividing cells with 6,6-2H2-glucose, combined with cell sorting and gas-chromatography-mass spectrometry for deuterium enrichment, in order to analyze the kinetics of human total, naive, or memory B lymphocytes, separated from peripheral blood using monoclonal antibodies. We show that total blood B cells of young adults divide at an average rate of 1.9% (±1.0%) per day and at a similar though slightly slower rate, 1.5% (±1.3%) per day, in the elderly. Separation of naive and memory B cells according to expression of CD27 indicates that naive peripheral blood B cells divide slowly (0.46% per day), while memory cells proliferate more rapidly (2.66% per day). These data are compatible with the view that B-cell memory may be maintained by clones of proliferating B cells.
Effects of PM10 in human peripheral blood monocytes and J774 macrophages
Authors: Brown DM , Donaldson K , Stone V
Published: January 2005

The effects of PM10, one of the components of particulate air pollution, was investigated using human monocytes and a mouse macrophage cell line (J774). The study aimed to investigate the role of these nanoparticles on the release of the pro-inflammatory cytokine TNF-α and IL-1α gene expression. We also investigated the role of intracellular calcium signalling events and oxidative stress in control of these cytokines and the effect of the particles on the functioning of the cell cytoskeleton. We showed that there was an increase in intracellular calcium concentration in J774 cells on treatment with PM10 particles which could be significantly reduced with concomitant treatment with the calcium antagonists verapamil, the intracellular calcium chelator BAPTA-AM but not with the antioxidant nacystelyn or the calmodulin inhibitor W-7. In human monocytes, PM10 stimulated an increase in intracellular calcium which was reduced by verapamil, BAPTA-AM and nacystelyn. TNF-α release was increased with particle treatment in human monocytes and reduced by only verapamil and BAPTA-AM. IL-1α gene expression was increased with particle treatment and reduced by all of the inhibitors. There was increased F-actin staining in J774 cells after treatment with PM10 particles, which was significantly reduced to control levels with all the antagonists tested. The present study has shown that PM10 particles may exert their pro-inflammatory effects by modulating intracellular calcium signalling in macrophages leading to expression of pro-inflammatory cytokines. Impaired motility and phagocytic ability as shown by changes in the F-actin cytoskeleton is likely to play a key role in particle clearance from the lung.
The "Transport Specificity Ratio": a structure-function tool to search the protein fold for loci that control transition state stability in membrane transport catalysis
Authors: King Steven C
Published: January 2005

Background

In establishing structure-function relationships for membrane transport proteins, the interpretation of phenotypic changes can be problematic, owing to uncertainties in protein expression levels, sub-cellular localization, and protein-folding fidelity. A dual-label competitive transport assay called "Transport Specificity Ratio" (TSR) analysis has been developed that is simple to perform, and circumvents the "expression problem," providing a reliable TSR phenotype (a constant) for comparison to other transporters.

Results

Using the Escherichia coli GABA (4-aminobutyrate) permease (GabP) as a model carrier, it is demonstrated that the TSR phenotype is largely independent of assay conditions, exhibiting: (i) indifference to the particular substrate concentrations used, (ii) indifference to extreme changes (40-fold) in transporter expression level, and within broad limits (iii) indifference to assay duration. The theoretical underpinnings of TSR analysis predict all of the above observations, supporting that TSR has (i) applicability in the analysis of membrane transport, and (ii) particular utility in the face of incomplete information on protein expression levels and initial reaction rate intervals (e.g., in high-throughput screening situations). The TSR was used to identify gab permease (GabP) variants that exhibit relative changes in catalytic specificity (kcat/Km) for [14C]GABA (4-aminobutyrate) versus [3H]NA (nipecotic acid).

Conclusions

The TSR phenotype is an easily measured constant that reflects innate molecular properties of the transition state, and provides a reliable index of the difference in catalytic specificity that a carrier exhibits toward a particular pair of substrates. A change in the TSR phenotype, called a Δ(TSR), represents a specificity shift attributable to underlying changes in the intrinsic substrate binding energy (ΔGb) that translocation catalysts rely upon to decrease activation energy ("Equation missing"). TSR analysis is therefore a structure-function tool that enables parsimonious scanning for positions in the protein fold that couple to the transition state, creating stability and thereby serving as functional determinants of catalytic power (efficiency, or specificity).
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
Authors: Martin David MA , Berriman Matthew , Barton Geoffrey J
Published: January 2005

Background

The function of a novel gene product is typically predicted by transitive assignment of annotation from similar sequences. We describe a novel method, GOtcha, for predicting gene product function by annotation with Gene Ontology (GO) terms. GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. Term-specific probabilities are a novel feature of GOtcha and allow the identification of conflicts or uncertainty in annotation.

Results

The GOtcha method was applied to the recently sequenced genome for Plasmodium falciparum and six other genomes. GOtcha was compared quantitatively for retrieval of assigned GO terms against direct transitive assignment from the highest scoring annotated BLAST search hit (TOPBLAST). GOtcha exploits information deep into the 'twilight zone' of similarity search matches, making use of much information that is otherwise discarded by more simplistic approaches.

At a P-score cutoff of 50%, GOtcha provided 60% better recovery of annotation terms and 20% higher selectivity than annotation with TOPBLAST at an E-value cutoff of 10-4.

Conclusions

The GOtcha method is a useful tool for genome annotators. It has identified both errors and omissions in the original Plasmodium falciparum annotation and is being adopted by many other genome sequencing projects.
A functional hierarchical organization of the protein sequence space
Authors: Kaplan Noam , Friedlich Moriah , Fromer Menachem , Linial Michal
Published: January 2005

Background

It is a major challenge of computational biology to provide a comprehensive functional classification of all known proteins. Most existing methods seek recurrent patterns in known proteins based on manually-validated alignments of known protein families. Such methods can achieve high sensitivity, but are limited by the necessary manual labor. This makes our current view of the protein world incomplete and biased. This paper concerns ProtoNet, a automatic unsupervised global clustering system that generates a hierarchical tree of over 1,000,000 proteins, based solely on sequence similarity.

Results

In this paper we show that ProtoNet correctly captures functional and structural aspects of the protein world. Furthermore, a novel feature is an automatic procedure that reduces the tree to 12% its original size. This procedure utilizes only parameters intrinsic to the clustering process. Despite the substantial reduction in size, the system's predictive power concerning biological functions is hardly affected. We then carry out an automatic comparison with existing functional protein annotations. Consequently, 78% of the clusters in the compressed tree (5,300 clusters) get assigned a biological function with a high confidence. The clustering and compression processes are unsupervised, and robust.

Conclusions

We present an automatically generated unbiased method that provides a hierarchical classification of all currently known proteins.
Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
Authors: Ma Hong-Wu , Buer Jan , Zeng An-Ping
Published: January 2005

Background

Cellular functions are coordinately carried out by groups of genes forming functional modules. Identifying such modules in the transcriptional regulatory network (TRN) of organisms is important for understanding the structure and function of these fundamental cellular networks and essential for the emerging modular biology. So far, the global connectivity structure of TRN has not been well studied and consequently not applied for the identification of functional modules. Moreover, network motifs such as feed forward loop are recently proposed to be basic building blocks of TRN. However, their relationship to functional modules is not clear.

Results

In this work we proposed a top-down approach to identify modules in the TRN of E. coli. By studying the global connectivity structure of the regulatory network, we first revealed a five-layer hierarchical structure in which all the regulatory relationships are downward. Based on this regulatory hierarchy, we developed a new method to decompose the regulatory network into functional modules and to identify global regulators governing multiple modules. As a result, 10 global regulators and 39 modules were identified and shown to have well defined functions. We then investigated the distribution and composition of the two basic network motifs (feed forward loop and bi-fan motif) in the hierarchical structure of TRN. We found that most of these network motifs include global regulators, indicating that these motifs are not basic building blocks of modules since modules should not contain global regulators.

Conclusion

The transcriptional regulatory network of E. coli possesses a multi-layer hierarchical modular structure without feedback regulation at transcription level. This hierarchical structure builds the basis for a new and simple decomposition method which is suitable for the identification of functional modules and global regulators in the transcriptional regulatory network of E. coli. Analysis of the distribution of feed forward loops and bi-fan motifs in the hierarchical structure suggests that these network motifs are not elementary building blocks of functional modules in the transcriptional regulatory network of E. coli.
Clustering under the line graph transformation: application to reaction network
Authors: Nacher Jose C , Ueda Nobuhisa , Yamada Takuji , Kanehisa Minoru , Akutsu Tatsuya
Published: January 2005

Background

Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. In general, the second network may be related to the first one by a technique called line graph transformation (i.e., edges in an initial network are transformed into nodes). Recently, the main topological properties of the metabolic networks have been properly described by means of a hierarchical model. While the chemical compound network has been classified as hierarchical network, a detailed study of the chemical reaction network had not been carried out.

Results

We have applied the line graph transformation to a hierarchical network and the degree-dependent clustering coefficient C(k) is calculated for the transformed network. C(k) indicates the probability that two nearest neighbours of a vertex of degree k are connected to each other. While C(k) follows the scaling law C(k) ~ k-1.1 for the initial hierarchical network, C(k) scales weakly as k0.08 for the transformed network. This theoretical prediction was compared with the experimental data of chemical reactions from the KEGG database finding a good agreement.

Conclusions

The weak scaling found for the transformed network indicates that the reaction network can be identified as a degree-independent clustering network. By using this result, the hierarchical classification of the reaction network is discussed.
The two neutrophil members of the formylpeptide receptor family activate the NADPH-oxidase through signals that differ in sensitivity to a gelsolin derived phosphoinositide-binding peptide
Authors: Fu Huamei , Björkman Lena , Janmey Paul , Karlsson Anna , Karlsson Jennie , Movitz Charlotta , Dahlgren Claes
Published: January 2005

Background

The formylpeptide receptor family members FPR and FPRL1, expressed in myeloid phagocytes, belong to the G-protein coupled seven transmembrane receptor family (GPCRs). They share a high degree of sequence similarity, particularly in the cytoplasmic domains involved in intracellular signaling. The established model of cell activation through GPCRs states that the receptors isomerize from an inactive to an active state upon ligand binding, and this receptor transformation subsequently activates the signal transducing G-protein. Accordingly, the activation of human neutrophil FPR and FPRL1 induces identical, pertussis toxin-sensitive functional responses and a transient increase in intracellular calcium is followed by a secretory response leading to mobilization of receptors from intracellular stores, as well as a release of reactive oxygen metabolites.

Results

We report that a cell permeable ten amino acid peptide (PBP10) derived from the phosphatidylinositol 4,5-bisphosphate (PIP2) binding region of gelsolin (an uncapper of actin filaments) blocks granule mobilization as well as secretion of oxygen radicals. The inhibitory effect of PBP10 is, however, receptor specific and affects the FPRL1-, but not the FPR-, induced cellular response. The transient rise in intracellular calcium induced by the active receptors is not affected by PBP10, suggesting that the blockage occurs in a parallel, novel signaling pathway used by FPRL1 to induce oxygen radical production and secretion. Also the FPR can activate neutrophils through a PBP10-sensitive signaling pathway, but this signal is normally blocked by the cytoskeleton.

Conclusions

This study demonstrates that the two very closely related chemoattractant receptors, FPR and FPRL1, use distinct signaling pathways in activation of human neutrophils. The PIP2-binding peptide PBP10 selectively inhibits FPRL1-mediated superoxide production and granule mobilization. Furthermore, the activity of this novel PBP10 sensitive pathway in neutrophils is modulated by the actin cytoskeleton network.
Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife
Authors: Manen Jean-François
Published: January 2005

Background

Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae) and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of Ilex. With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands), I. perado and I. canariensis, were studied in detail. Introgression between these two species was previously never reported. One plastid marker (the atpB-rbcL spacer) and two nuclear markers, the ribosomal internal transcribed spacer (ITS) and the nuclear encoded plastid glutamine synthetase (nepGS) were analyzed for 13 and 27 individuals of I. perado and I. canariensis, respectively.

Results

The plastid marker is intra-specifically constant and correlated with species identity. On the other hand, whereas the nuclear markers are conserved in I. perado, they are highly polymorphic in I. canariensis. The presence of pseudogenes and recombination in ITS sequences of I. canariensis explain this polymorphism. Ancestral sequence polymorphism with incomplete lineage sorting, or past or recent hybridization with an unknown species could explain this polymorphism, not resolved by concerted evolution. However, as already reported for many other plants, past or recent introgression of an alien genotype seem the most probable explanation for such a tremendous polymorphism.

Conclusions

Data do not allow the determination with certitude of the putative species introgressing I. canariensis, but I. perado is suspected. The introgression would be unilateral, with I. perado as the male donor, and the paternal sequences would be rapidly converted in highly divergent and consequently unidentifiable pseudogenes. At least, this study allows the establishment of precautionary measures when nuclear markers are used in phylogenetic studies of genera having experienced introgression such as the genus Ilex.
Screening large-scale association study data: exploiting interactions using random forests
Authors: Lunetta Kathryn L , Hayward L Brooke , Segal Jonathan , Van Eerdewegh Paul
Published: January 2005

Background

Genome-wide association studies for complex diseases will produce genotypes on hundreds of thousands of single nucleotide polymorphisms (SNPs). A logical first approach to dealing with massive numbers of SNPs is to use some test to screen the SNPs, retaining only those that meet some criterion for futher study. For example, SNPs can be ranked by p-value, and those with the lowest p-values retained. When SNPs have large interaction effects but small marginal effects in a population, they are unlikely to be retained when univariate tests are used for screening. However, model-based screens that pre-specify interactions are impractical for data sets with thousands of SNPs. Random forest analysis is an alternative method that produces a single measure of importance for each predictor variable that takes into account interactions among variables without requiring model specification. Interactions increase the importance for the individual interacting variables, making them more likely to be given high importance relative to other variables. We test the performance of random forests as a screening procedure to identify small numbers of risk-associated SNPs from among large numbers of unassociated SNPs using complex disease models with up to 32 loci, incorporating both genetic heterogeneity and multi-locus interaction.

Results

Keeping other factors constant, if risk SNPs interact, the random forest importance measure significantly outperforms the Fisher Exact test as a screening tool. As the number of interacting SNPs increases, the improvement in performance of random forest analysis relative to Fisher Exact test for screening also increases. Random forests perform similarly to the univariate Fisher Exact test as a screening tool when SNPs in the analysis do not interact.

Conclusions

In the context of large-scale genetic association studies where unknown interactions exist among true risk-associated SNPs or SNPs and environmental covariates, screening SNPs using random forest analyses can significantly reduce the number of SNPs that need to be retained for further study compared to standard univariate screening methods.
The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.
Authors: An Hyeong Jun , Lee Doheon , Lee Kwang Hyung , Bhak Jonghwa
Published: January 2005

Background

A significant portion (about 8% in the human genome) of mammalian mRNA sequences contains AU (Adenine and Uracil) rich elements or AREs at their 3' untranslated regions (UTR). These mRNA sequences are usually stable. However, an increasing number of observations have been made of unstable species, possibly depending on certain elements such as Alu repeats. ARE motifs are repeats of the tetramer AUUU and a monomer A at the end of the repeats ((AUUU)nA). The importance of AREs in biology is that they make certain mRNA unstable. Proto-oncogene, such as c-fos, c-myc, and c-jun in humans, are associated with AREs. Although it has been known that the increased number of ARE motifs caused the decrease of the half-life of mRNA containing ARE repeats, the exact mechanism is as of yet unknown. We analyzed the occurrences of AREs and Alu and propose a possible mechanism for how human mRNA could acquire and keep AREs at its 3' UTR originating from Alu repeats.

Results

Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A) regions at its end, which lead to poly-thymine (poly-T) regions at the end of its complementary Alu. It has been found that AREs are present at the poly-T regions. From the 3' UTR of the NCBI's reference mRNA sequence database, we found nearly 40% (38.5%) of ARE (Class I) were associated with Alu sequences (Table 1) within one mismatch allowance in ARE sequences. Other ARE classes had statistically significant associations as well. This is far from a random occurrence given their limited quantity. At each ARE class, random distribution was simulated 1,000 times, and it was shown that there is a special relationship between ARE patterns and the Alu repeats.Table 1

Defined ARE classes. (Symbol marks are used in this study instead of full sequences.)

Symbol
ARE sequence

Class I
(AUUU)5A
AUUUAUUUAUUUAUUUAUUUA

Class II
(AUUU)4A
AUUUAUUUAUUUAUUUA

Class III
U(AUUU)3AU
UAUUUAUUUAUUUAU

Class IV
UU(AUUU)2AUU
UUAUUUAUUUAUU

Class V
U4AUUUAU4
UUUUAUUUAUUUU

Class VI
W3UAUUUAUW3
WWWUAUUUAWWW

Conclusion

AREs are mediating sequence elements affecting the stabilization or degradation of mRNA at the 3' untranslated regions. However, AREs' mechanism and origins are unknown. We report that Alu is a source of ARE. We found that half of the longest AREs were derived from the poly-T regions of the complementary Alu.
High-throughput sequencing: a failure mode analysis
Authors: Yang George S , Stott Jeffery M , Smailus Duane , Barber Sarah A , Balasundaram Miruna , Marra Marco A , Holt Robert A
Published: January 2005

Background

Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating costs. While high-throughput centres report failure rates typically on the order of 10%, the causes of sporadic sequencing failures are seldom analyzed in detail and have not, in the past, been formally reported.

Results

Here we report the results of a failure mode analysis of our production sequencing facility based on detailed evaluation of 9,216 ESTs generated from two cDNA libraries. Two categories of failures are described; process-related failures (failures due to equipment or sample handling) and template-related failures (failures that are revealed by close inspection of electropherograms and are likely due to properties of the template DNA sequence itself).

Conclusions

Preventative action based on a detailed understanding of failure modes is likely to improve the performance of other production sequencing pipelines.
Gene expression in the brain and kidney of rainbow trout in response to handling stress
Authors: Krasnov Aleksei , Koskinen Heikki , Pehkonen Petri , Rexroad Caird E , Afanasyev Sergey , Mölsä Hannu
Published: January 2005

Background

Microarray technologies are rapidly becoming available for new species including teleost fishes. We constructed a rainbow trout cDNA microarray targeted at the identification of genes which are differentially expressed in response to environmental stressors. This platform included clones from normalized and subtracted libraries and genes selected through functional annotation. Present study focused on time-course comparisons of stress responses in the brain and kidney and the identification of a set of genes which are diagnostic for stress response.

Results

Fish were stressed with handling and samples were collected 1, 3 and 5 days after the first exposure. Gene expression profiles were analysed in terms of Gene Ontology categories. Stress affected different functional groups of genes in the tissues studied. Mitochondria, extracellular matrix and endopeptidases (especially collagenases) were the major targets in kidney. Stress response in brain was characterized with dramatic temporal alterations. Metal ion binding proteins, glycolytic enzymes and motor proteins were induced transiently, whereas expression of genes involved in stress and immune response, cell proliferation and growth, signal transduction and apoptosis, protein biosynthesis and folding changed in a reciprocal fashion. Despite dramatic difference between tissues and time-points, we were able to identify a group of 48 genes that showed strong correlation of expression profiles (Pearson r > |0.65|) in 35 microarray experiments being regulated by stress. We evaluated performance of the clone sets used for preparation of microarray. Overall, the number of differentially expressed genes was markedly higher in EST than in genes selected through Gene Ontology annotations, however 63% of stress-responsive genes were from this group.

Conclusions

1. Stress responses in fish brain and kidney are different in function and time-course. 2. Identification of stress-regulated genes provides the possibility for measuring stress responses in various conditions and further search for the functionally related genes.
Mapping and mutation of the conserved DNA polymerase interaction motif (DPIM) located in the C-terminal domain of fission yeast DNA polymerase δ subunit Cdc27
Authors: Gray Fiona C , Pohler J Richard G , Warbrick Emma , MacNeill Stuart A
Published: January 2005

Background

DNA polymerases α and δ play essential roles in the replication of chromosomal DNA in eukaryotic cells. DNA polymerase α (Pol α)-primase is required to prime synthesis of the leading strand and each Okazaki fragment on the lagging strand, whereas DNA polymerase δ (Pol δ) is required for the elongation stages of replication, a function it appears capable of performing on both leading and lagging strands, at least in the absence of DNA polymerase ε (Pol ε).

Results

Here it is shown that the catalytic subunit of Pol α, Pol1, interacts with Cdc27, one of three non-catalytic subunits of fission yeast Pol δ, both in vivo and in vitro. Pol1 interacts with the C-terminal domain of Cdc27, at a site distinct from the previously identified binding sites for Cdc1 and PCNA. Comparative protein sequence analysis identifies a protein sequence motif, called the DNA polymerase interaction motif (DPIM), in Cdc27 orthologues from a wide variety of eukaryotic species, including mammals. Mutational analysis shows that the DPIM in fission yeast Cdc27 is not required for effective DNA replication, repair or checkpoint function.

Conclusions

The absence of any detectable phenotypic consequences arising from mutation of the DPIM suggests that despite its evolutionary conservation, the interaction between the two polymerases mediated by this motif is a non-essential one.
Quality of care for hypertension in the United States
Authors: Asch Steven M , McGlynn Elizabeth A , Hiatt Liisa , Adams John , Hicks Jennifer , DeCristofaro Alison , Chen Roland , LaPuerta Pablo , Kerr Eve A
Published: January 2005

Background

Despite heavy recent emphasis on blood pressure (BP) control, many patients fail to meet widely accepted goals. While access and adherence to therapy certainly play a role, another potential explanation is poor quality of essential care processes (QC). Yet little is known about the relationship between QC and BP control.

Methods

We assessed QC in 12 U.S. communities by reviewing the medical records of a randomly selected group of patients for the two years preceding our study. We included patients with either a diagnosis of hypertension or two visits with BPs of ≥140/90 in their medical records. We used 28 process indicators based on explicit evidence to assess QC. The indicators covered a broad spectrum of care and were developed through a modified Delphi method. We considered patients who received all indicated care to have optimal QC. We defined control of hypertension as BP < 140/90 in the most recent reading.

Results

Of 1,953 hypertensive patients, only 57% received optimal care and 42% had controlled hypertension. Patients who had received optimal care were more likely to have their BP under control at the end of the study (45% vs. 35%, p = .0006). Patients were more likely to receive optimal care if they were over age 50 (76% vs. 63%, p < .0001), had diabetes (77% vs. 71%, p = .0038), coronary artery disease (87% vs. 69%, p < .0001), or hyperlipidemia (80% vs. 68%, p < .0001), and did not smoke (73% vs. 66%, p = .0005).

Conclusions

Higher QC for hypertensive patients is associated with better BP control. Younger patients without cardiac risk factors are at greatest risk for poor care. Quality measurement systems like the one presented in this study can guide future quality improvement efforts.
Observed intra-cluster correlation coefficients in a cluster survey sample of patient encounters in general practice in Australia
Authors: Knox Stephanie A , Chondros Patty
Published: January 2005

Background

Cluster sample study designs are cost effective, however cluster samples violate the simple random sample assumption of independence of observations. Failure to account for the intra-cluster correlation of observations when sampling through clusters may lead to an under-powered study. Researchers therefore need estimates of intra-cluster correlation for a range of outcomes to calculate sample size. We report intra-cluster correlation coefficients observed within a large-scale cross-sectional study of general practice in Australia, where the general practitioner (GP) was the primary sampling unit and the patient encounter was the unit of inference.

Methods

Each year the Bettering the Evaluation and Care of Health (BEACH) study recruits a random sample of approximately 1,000 GPs across Australia. Each GP completes details of 100 consecutive patient encounters. Intra-cluster correlation coefficients were estimated for patient demographics, morbidity managed and treatments received. Intra-cluster correlation coefficients were estimated for descriptive outcomes and for associations between outcomes and predictors and were compared across two independent samples of GPs drawn three years apart.

Results

Between April 1999 and March 2000, a random sample of 1,047 Australian general practitioners recorded details of 104,700 patient encounters. Intra-cluster correlation coefficients for patient demographics ranged from 0.055 for patient sex to 0.451 for language spoken at home. Intra-cluster correlations for morbidity variables ranged from 0.005 for the management of eye problems to 0.059 for management of psychological problems. Intra-cluster correlation for the association between two variables was smaller than the descriptive intra-cluster correlation of each variable. When compared with the April 2002 to March 2003 sample (1,008 GPs) the estimated intra-cluster correlation coefficients were found to be consistent across samples.

Conclusions

The demonstrated precision and reliability of the estimated intra-cluster correlations indicate that these coefficients will be useful for calculating sample sizes in future general practice surveys that use the GP as the primary sampling unit.
Development of a questionnaire weighted scoring system to target diagnostic examinations for asthma in adults: a modelling study
Authors: Hirsch Sybil , Frank Timothy L , Shapiro Jonathan L , Hazell Michelle L , Frank Peter I
Published: January 2005

Background

Identification and treatment of unrecognised asthmatics in the community is important for improving the health of the individual and minimising cost and quality of life burden. It is not practical to offer clinical diagnostic assessment to whole communities, and a simple tool such as a questionnaire is required to identify a smaller target group. Conventional questionnaire screening methods which separate individuals into positive and negative categories have resulted in large numbers of individuals requiring clinical assessment. This study has therefore developed and tested a weighted scoring system that prioritises those most urgently in need, based on their questionnaire responses.

Methods

A stratified random sample of adult respondents to a general practice postal questionnaire survey were categorised 'asthmatic' or 'non-asthmatic' according to three expert physicians' opinions. Based on this categorisation, logistic regression was used to derive weights reflecting the relative importance of each question in predicting asthma, allowing calculation of weighted scores reflecting likelihood of asthma. Respondents scoring higher than a chosen threshold would be offered diagnostic examination.

Results

Age and presence of wheeze were most influential (weight 3) and overall weighted scores ranged from -1 to 13. Positive predictive values (PPV) were estimated. For example, setting the threshold score at nine gave an estimated PPV for asthma diagnosis of 93.5%, a threshold score of seven corresponded to PPV 78.8%. PPV estimates were supported by examining 145 individuals from a new survey.

Conclusion

Weighted scoring of questionnaire responses provides a method for evaluating the priority level of an individual 'at a glance', minimising the resource wastage of examining false positives.