bluuebunny/crossref_metadata_2025 huggingface dataset:
Therapeutic efficacy test in malaria falciparum in Antioquia, Colombia
Authors: Blair Silvia , Carmona-Fonseca Jaime , Piñeros Juan G , Ríos Alexandra , Álvarez Tania , Álvarez Gonzalo , Tobón Alberto
Published: February 2006

Objective

Evaluate the frequency of failure of eight treatments for non-complicated malaria caused byPlasmodium falciparumin patients from Turbo (Urabá region), El Bagre and Zaragoza (Bajo Cauca region), applying the 1998 protocol of the World Health Organization (WHO). Monotherapies using chloroquine (CQ), amodiaquine (AQ), mefloquine (MQ) and sulphadoxine-pyrimethamine (SP), and combinations using chloroquine-sulphadoxine-pyrimethamine (CQ-SP), amodiaquine-sulphadoxine-pyrimethamine (AQ-SP), mefloquine-sulphadoxine-pyrimethamine (MQ-SP) and artesunate-sulphadoxine-pyrimethamine (AS-SP), were examined.

Methodology

A balanced experimental design with eight groups. Samples were selected based on statistical and epidemiological criteria. Patients were followed for 21 to 28 days, including seven or eight parasitological and clinical evaluations, with an active search for defaulting patients. A non-blinded evaluation of the antimalarial treatment response (early failure, late failure, adequate response) was performed.

Results

Initially, the loss of patients to follow-up was higher than 40%, but the immediate active search for the cases and the monetary help for transportation expenses of patients, reduced the loss to 6%. The treatment failure was: CQ 82%, AQ 30%, MQ 4%, SP 24%, CQ-SP 17%, AQ-SP 2%, MQ-S-P 0%, AS-SP 3%.

Conclusion

The characteristics of an optimal epidemiological monitoring system of antimalarial treatment response in Colombia are discussed. It is proposed to focus this on early failure detection, by applying a screening test every two to three years, based on a seven to 14-day follow-up. Clinical and parasitological assessment would be carried out by a general physician and a field microscopist from the local hospital, with active measures to search for defaulter patients at follow-up.
Are insecticide-treated bednets more protective against Plasmodium falciparum than Plasmodium vivax- infected mosquitoes?
Authors: Bockarie Moses J , Dagoro Henry
Published: February 2006

Background

The outcomes of insecticide-treated bednet (ITN) interventions for malaria control in Papua New Guinea tend to suggest a differential protective effect against Plasmodium falciparum and Plasmodium vivax. Little is known about the impact of ITNs on the relative abundance of mosquitoes infected with either P. falciparum or P. vivax. This paper describes the biting cycle of P. falciparum and P. vivax-infected mosquitoes and the impact of an ITN intervention on the proportion of mosquitoes infected with either parasite species.

Methods

Entomological investigations were performed in East Sepik (ESP) and New Ireland Provinces (NIP) of PNG. Mosquitoes were collected using the all-night (18:00 - 06:00) landing catch and CDC light-trap methods and species specific malaria sporozoite rates were determined by ELISA.

Results and discussion

The distribution of sporozoite positive mosquitoes in three four-hour periods (18:00-22:00, 22:00-02:00 & 02:00-06:00) showed that a higher proportion of P. vivax-infected mosquitoes were biting before people retired to bed under the protection of bednets. In the intervention village, the 308 mosquitoes collected before ITNs were introduced included eight (2.0%) P. falciparum-positive and four (1.0%) P. vivax- positive specimens, giving a parasite ratio of 2:1. The sporozoite rate determined from 908 mosquitoes caught after ITNs were introduced showed a significant decrease for P. falciparum (0.7%) and a slight increase for P. vivax (1.3%), resulting in a post intervention parasite ratio of 1:2. In the East Sepik Province, where ITNs were not used, P. falciparum remained the dominant species in 12 monthly mosquito collections and monthly P. falciparum:P. vivax formula varied from 8:1 to 1.2:1.

Conclusion

These findings suggest that people sleeping under treated bednets may be more exposed to P. vivax than P. falciparum-infected mosquitoes before going to sleep under the protection of bednets. This difference in the biting behaviour of mosquitoes infected with different malaria parasites may partly explain the change in the P. falciparum:P. vivax formula after the introduction of ITNs.
IL-4 alpha chain receptor (IL-4Rα) polymorphisms in allergic bronchopulmonary sspergillosis
Authors: Knutsen Alan P , Kariuki Barbara , Consolino Judy D , Warrier Manoj R
Published: February 2006

Background

Allergic bronchopulmonary aspergillosis occurs in 7–10% of cystic fibrosis (CF) and 1–2% of asthmatic patients. HLA-DR restriction and increased sensitivity to IL-4 stimulation have been proposed as risk factors in these populations.

Objective

We examined for the presence of IL-4 receptor alpha chain (IL-4Rα) single nucleotide polymorphisms (SNPs) in ABPA and whether these accounted for increased sensitivity to IL-4 stimulation.

Methods

One extracellular (ile75val) and four cytoplasmic IL-4Rα SNPs were analyzed in 40 CF and 22 asthmatic patients and in 56 non-ABPA CF and asthmatic patients. Sensitivity to IL-4 stimulation was measured by induction of CD23 expression on B cells.

Results

IL-4Rα SNPs were observed in 95% of ABPA patients. The predominant IL-4Rα SNP was the extracellular IL-4Rα SNP, ile75val, observed in 80% of ABPA patients.

Conclusion

The presence of IL-4Rα SNPs, principally ile75val, appears to be a genetic risk for the development of ABPA.
Macrophage metalloelastase (MMP-12) deficiency does not alter bleomycin-induced pulmonary fibrosis in mice
Authors: Manoury Boris , Nenan Soazig , Guenon Isabelle , Boichot Elisabeth , Planquois Jean-Michel , Bertrand Claude P , Lagente Vincent
Published: February 2006

Background

Pulmonary fibrosis is characterized by excessive deposition of extracellular matrix in the interstitium resulting in respiratory failure. The role of remodeling mediators such as metalloproteinases (MMPs) and their inhibitors (TIMPs) in the fibrogenic process remains misunderstood. In particular, macrophage metalloelastase, also identified as MMP-12, is known to be involved in remodeling processes under pathological conditions. However, MMP-12 involvement in pulmonary fibrosis is unknown. Here we investigated fibrotic response to bleomycin in MMP-12 deficient mice.

Materials and methods

C57BL/6 mice, Balb/c mice and MMP-12 -/- mice with a C57BL/6 background received 0.3 mg bleomycin by intranasal administration. 14 days after, mice were anesthetized and underwent either bronchoalveolear lavage (BAL) or lung removal. Collagen deposition in lung tissue was determined by Sircol™ collagen assay, MMP activity in BAL fluid was analyzed by zymography, and other mediators were quantified in BAL fluid by ELISA. Real time PCR was performed to assess gene expression in lung removed one or 14 days after bleomycin administration. Student t test or Mann & Whitney tests were used when appropriate for statistical analysis.

Results

The development of pulmonary fibrosis in "fibrosis prone" (C57BL/6) mice was associated with prominent MMP-12 expression in lung, whereas MMP-12 expression was weak in lung tissue of "fibrosis resistant" (Balb/c) mice. MMP-12 mRNA was not detected in MMP-12 -/- mice, in conformity with their genotype. Bleomycin elicited macrophage accumulation in BAL of MMP-12 -/- and wild type (WT) mice, and MMP-12 deficiency had no significant effect on BAL cells composition. Collagen content of lung was increased similarly in MMP-12 -/- and WT mice 14 days after bleomycin administration. Bleomycin elicit a raise of TGF-β protein, MMP-2 and TIMP-1 protein and mRNA in BAL fluids and lung respectively, and no significant difference was observed between MMP-12 -/- and WT mice considering those parameters.

Conclusion

The present study shows that MMP-12 deficiency has no significant effect on bleomycin-induced fibrosis.
Predictors of job satisfaction among doctors, nurses and auxiliaries in Norwegian hospitals: relevance for micro unit culture
Authors: Krogstad Unni , Hofoss Dag , Veenstra Marijke , Hjortdahl Per
Published: February 2006

Objective

To explore what domains of work are important for job satisfaction among doctors, nurses and auxiliaries and to discuss differences between professional groups in the perspective of micro team culture.

Design

Cross-sectional survey data from hospital staff working clinically at inpatient hospital wards in Norway in 2000.

Measures

Linear regression models predicting job satisfaction for the three professions were compared. First, five domains of hospital work were examined for general job satisfaction. Based on the result of the first regression, five items concerning local leadership were explored in a second regression.

Results

A total of 1814 doctors, nurses and auxiliaries working at 11 Norwegian hospitals responded (overall response rate: 65%). The only domain of work that significantly predicted high job satisfaction important for all groups was positive evaluation of local leadership. Both steps of analyses suggested that professional development is most important for doctors. For registered nurses, experiencing support and feedback from the nearest superior was the main explanatory variable for job satisfaction. Job satisfaction of auxiliaries was equally predicted by professional development and local leadership. The results are discussed and interpreted as reflections of cultural values, loyalties and motivation.

Conclusion

The professional values of medicine, the organizational and holistic skills of nurses and the practical experience of auxiliaries should all be valued in the building of interdependent micro teams.
Distinguishing between linear and exponential cell growth during the division cycle: Single-cell studies, cell-culture studies, and the object of cell-cycle research
Authors: Cooper Stephen
Published: February 2006

Background

Two approaches to understanding growth during the cell cycle are single-cell studies, where growth during the cell cycle of a single cell is measured, and cell-culture studies, where growth during the cell cycle of a large number of cells as an aggregate is analyzed. Mitchison has proposed that single-cell studies, because they show variations in cell growth patterns, are more suitable for understanding cell growth during the cell cycle, and should be preferred over culture studies. Specifically, Mitchison argues that one can glean the cellular growth pattern by microscopically observing single cells during the division cycle. In contrast to Mitchison's viewpoint, it is argued here that the biological laws underlying cell growth are not to be found in single-cell studies. The cellular growth law can and should be understood by studying cells as an aggregate.

Results

The purpose or objective of cell cycle analysis is presented and discussed. These ideas are applied to the controversy between proponents of linear growth as a possible growth pattern during the cell cycle and the proponents of exponential growth during the cell cycle. Differential (pulse) and integral (single cell) experiments are compared with regard to cell cycle analysis and it is concluded that pulse-labeling approaches are preferred over microscopic examination of cell growth for distinguishing between linear and exponential growth patterns. Even more to the point, aggregate experiments are to be preferred to single-cell studies.

Conclusion

The logical consistency of exponential growth – integrating and accounting for biochemistry, cell biology, and rigorous experimental analysis – leads to the conclusion that proposals of linear growth are the result of experimental perturbations and measurement limitations. It is proposed that the universal pattern of cell growth during the cell cycle is exponential.
Glutathione and growth inhibition of Mycobacterium tuberculosis in healthy and HIV infected subjects
Authors: Venketaraman Vishwanath , Rodgers Tatanisha , Linares Rafael , Reilly Nancy , Swaminathan Shobha , Hom David , Millman Ariel C , Wallis Robert , Connell Nancy D
Published: February 2006

Intracellular levels of glutathione are depleted in patients with acquired immunodeficiency syndrome in whom the risk of tuberculosis, particularly disseminated disease is many times that of healthy individuals. In this study, we examined the role of glutathione in immunity against tuberculosis infection in samples derived from healthy and human immunodeficiency virus infected subjects. Our studies confirm that glutathione levels are reduced in peripheral blood mononuclear cells and in red blood cells isolated from human immunodeficiency virus-infected subjects (CD4>400/cumm). Furthermore, treatment of blood cultures from human immunodeficiency virus infected subjects with N-acetyl cysteine, a glutathione precursor, caused improved control of intracellularM. tuberculosisinfection. N-acetyl cysteine treatment decreased the levels of IL-1, TNF-α, and IL-6, and increased the levels of IFN-γ in blood cultures derived from human immunodeficiency virus-infected subjects, promoting the host immune responses to containM. tuberculosisinfection successfully.
Cytokine expression in mice exposed to diesel exhaust particles by inhalation. Role of tumor necrosis factor
Authors: Saber Anne T , Jacobsen Nicklas R , Bornholdt Jette , Kjær Sanna L , Dybdahl Marianne , Risom Lotte , Loft Steffen , Vogel Ulla , Wallin Håkan
Published: February 2006

Background

Particulate air pollution has been associated with lung and cardiovascular disease, for which lung inflammation may be a driving mechanism. The pro-inflammatory cytokine, tumor necrosis factor (TNF) has been suggested to have a key-role in particle-induced inflammation.

We studied the time course of gene expression of inflammatory markers in the lungs of wild type mice andTnf-/-mice after exposure to diesel exhaust particles (DEPs). Mice were exposed to either a single or multiple doses of DEP by inhalation. We measured the mRNA level of the cytokinesTnfand interleukin-6(Il-6)and the chemokines, monocyte chemoattractant protein(Mcp-1), macrophage inflammatory protein-2(Mip-2)and keratinocyte derived chemokine(Kc)in the lung tissue at different time points after exposure.

Results

TnfmRNA expression levels increased late after DEP-inhalation, whereas the expression levels ofIl-6,Mcp-1andKcincreased early. The expression ofMip-2was independent of TNF if the dose was above a certain level. The expression levels of the cytokinesKc,Mcp-1andIl-6, were increased in the absence of TNF.

Conclusion

Our data demonstrate thatTnfis not important in early DEP induced inflammation and rather exerts negative influence onMcp-1andKcmRNA levels. This suggests that other signalling pathways are important, a candidate being one involvingMcp-1.
Quantitative analysis of the epithelial lining architecture in radicular cysts and odontogenic keratocysts
Authors: Landini Gabriel
Published: February 2006

Background

This paper describes a quantitative analysis of the cyst lining architecture in radicular cysts (of inflammatory aetiology) and odontogenic keratocysts (thought to be developmental or neoplastic) including its 2 counterparts: solitary and associated with the Basal Cell Naevus Syndrome (BCNS).

Methods

Epithelial linings from 150 images (from 9 radicular cysts, 13 solitary keratocysts and 8 BCNS keratocysts) were segmented into theoretical cells using a semi-automated partition based on the intensity of the haematoxylin stain which defined exclusive areas relative to each detected nucleus. Various morphometrical parameters were extracted from these "cells" and epithelial layer membership was computed using a systematic clustering routine.

Results

Statistically significant differences were observed across the 3 cyst types both at the morphological and architectural levels of the lining. Case-wise discrimination between radicular cysts and keratocyst was highly accurate (with an error of just 3.3%). However, the odontogenic keratocyst subtypes could not be reliably separated into the original classes, achieving discrimination rates slightly above random allocations (60%).

Conclusion

The methodology presented is able to provide new measures of epithelial architecture and may help to characterise and compare tissue spatial organisation as well as provide useful procedures for automating certain aspects of histopathological diagnosis.
Methotrexate in rheumatoid arthritis is frequently effective, even if re-employed after a previous failure
Authors: Kapral Theresa , Stamm Tanja , Machold Klaus P , Montag Karin , Smolen Josef S , Aletaha Daniel
Published: February 2006

Effectiveness of therapy with individual disease-modifying antirheumatic drugs (DMARDs) in rheumatoid arthritis (RA) is limited, and the number of available DMARDs is finite. Therefore, at some stage during the lengthy course of RA, institution of traditional DMARDs that have previously been applied may have to be reconsidered. In the present study we investigated the effectiveness of re-employed methotrexate in patients with a history of previous methotrexate failure (original course). A total of 1,490 RA patients (80% female, 59% rheumatoid factor positive) were followed from their first presentation, yielding a total of 6,470 patient-years of observation. We identified patients in whom methotrexate was re-employed after at least one intermittent course of a different DMARD. We compared reasons for discontinuation, improvement in acute phase reactants, and cumulative retention rates of methotrexate therapy between the original course of methotrexate and its re-employment. Similar analyses were peformed for other DMARDs. Methotrexate was re-employed in 86 patients. Compared with the original courses, re-employment was associated with a reduced risk for treatment termination because of ineffectiveness (P= 0.02, by McNemar test), especially if the maximum methotrexate dose of the original course had been low (<12.5 mg/week;P= 0.02, by logistic regression). In a Cox regression model, re-employed MTX was associated with a significantly reduced hazard of treatment termination compared with the original course of methotrexate, adjusting for dose and year of employment (hazard ratio 0.64, 95% confidence interval 0.42–0.97;P= 0.04). These findings were not recapitulated in analyses of re-employment of other DMARDs. Re-employment of MTX despite prior inefficacy, but not re-employment of other DMARDs, is an effective therapeutic option, especially in those patients in whom the methotrexate dose of the original course was low.
Vitamin D receptor gene BsmIpolymorphisms in Thai patients with systemic lupus erythematosus
Authors: Sakulpipatsin Wilaiporn , Verasertniyom Oravan , Nantiruj Kanokrat , Totemchokchyakarn Kitti , Lertsrisatit Porntawee , Janwityanujit Suchela
Published: February 2006

The immunomodulatory role of 1,25-dihydroxyvitamin D3 is well known. An association between vitamin D receptor (VDR) gene BsmI polymorphisms and systemic lupus erythematosus (SLE) has been reported. To examine the characteristics of VDR gene BsmI polymorphisms in patients with SLE and the relationship of polymorphisms to the susceptibility and clinical manifestations of SLE, VDR genotypings of 101 Thai patients with SLE and 194 healthy controls were performed based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The relationship between VDR gene BsmI polymorphisms and clinical manifestations of SLE was evaluated. The distribution of VDR genotyping in patients with SLE was 1.9% for BB (non-excisable allele homozygote), 21.78% for Bb (heterozygote), and 76.23% for bb (excisable allele homozygote). The distribution of VDR genotyping in the control group was 1.03% for BB, 15.98% for Bb, and 82.99% for bb. There was no statistically significant difference between the two groups (p = 0.357). The allelic distribution of B and b was similar within the groups (p = 0.173). The relationship between VDR genotype and clinical manifestation or laboratory profiles of SLE also cannot be statistically demonstrated. In conclusion, we cannot verify any association between VDR gene BsmI polymorphism and SLE. A larger study examining other VDR gene polymorphisms is proposed.
Clinical relevance of Aspergillus isolation from respiratory tract samples in critically ill patients
Authors: Vandewoude Koenraad H , Blot Stijn I , Depuydt Pieter , Benoit Dominique , Temmerman Werner , Colardyn Francis , Vogelaers Dirk
Published: February 2006

Introduction

The diagnosis of invasive pulmonary aspergillosis, according to the criteria as defined by the European Organisation for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG), is difficult to establish in critically ill patients. The aim of this study is to address the clinical significance of isolation of Aspergillus spp. from lower respiratory tract samples in critically ill patients on the basis of medical and radiological files using an adapted diagnostic algorithm to discriminate proven and probable invasive pulmonary aspergillosis from Aspergillus colonisation.

Methods

Using a historical cohort (January 1997 to December 2003), all critically ill patients with respiratory tract samples positive for Aspergillus were studied. In comparison to the EORTC/MSG criteria, a different appreciation was given to radiological features and microbiological data, including semiquantitative cultures and direct microscopic examination of broncho-alveolar lavage samples.

Results

Over a 7 year period, 172 patients were identified with a positive culture. Of these, 83 patients were classified as invasive aspergillosis. In 50 of these patients (60%), no high risk predisposing conditions (neutropenia, hematologic cancer and stem cell or bone marrow transplantation) were found. Typical radiological imaging (halo and air-crescent sign) occurred in only 5% of patients. In 26 patients, histological examination either by ante-mortem lung biopsy (n = 10) or necropsy (n = 16) was performed, allowing a rough estimation of the predictive value of the diagnostic algorithm. In all patients with histology, all cases of clinical probable pulmonary aspergillosis were confirmed (n = 17). Conversely, all cases classified as colonisation had negative histology (n = 9).

Conclusion

A respiratory tract sample positive for Aspergillus spp. in the critically ill should always prompt further diagnostic assessment, even in the absence of the typical hematological and immunological host risk factors. In a minority of patients, the value of the clinical diagnostic algorithm was confirmed by histological findings, supporting its predictive value. The proposed diagnostic algorithm needs prospective validation.
Effect of oral decontamination with chlorhexidine on the incidence of nosocomial pneumonia: a meta-analysis
Authors: Pineda Lilibeth A , Saliba Ranime G , El Solh Ali A
Published: February 2006

Introduction

Nosocomial pneumonia is a significant cause of in-hospital morbidity and mortality. Oral care interventions have great potential to reduce the occurrence of nosocomial pneumonia. Studies using topical antiseptic agents yielded mixed results. We hypothesized that the use of chlorhexidine for oral decontamination would reduce the incidence of nosocomial pneumonia in patients requiring mechanical ventilation.

Methods

This study is a meta-analysis of randomized controlled trials assessing the effect of chlorhexidine on the incidence of nosocomial pneumonia. Data sources were Medline, EMBASE, Cochrane library, citation review of relevant primary and review articles, and contact with expert informants. Out of 1,251 articles screened, 4 randomized, controlled trials were identified that included a total of 1,202 patients. Descriptive and outcome data were extracted by two reviewers independently. Main outcome measures were the incidence of nosocomial pneumonia, and mortality. A random effects model was used.

Results

The incidence of nosocomial pneumonia in the control group was 7% (41 out of 615) compared to 4% (24 out of 587) in the treatment group. Gram-negative bacteria accounted for 78% of the total isolates, with Pseudomonas aeruginosa being the most frequently isolated pathogen irrespective of the intervention provided. Duration of mechanical ventilation and intensive care unit length of stay were comparable between the two groups. Overall, the use of oral decontamination with chlorhexidine did not affect the incidence of nosocomial pneumonia (odds ratio of 0.42; 95% confidence interval 0.16–1.06) or the mortality rate (odds ratio 0.77, 95% confidence interval 0.28–2.11).

Conclusion

The use of oral decontamination with chlorhexidine did not result in significant reduction in the incidence of nosocomial pneumonia in patients who received mechanical ventilation, nor altered the mortality rate. The lack of benefit may reflect the few studies conducted in this area. Future trials should focus on a combination strategy of mechanical and pharmacological interventions.
Natriuretic peptide testing for the evaluation of critically ill patients with shock in the intensive care unit: a prospective cohort study
Authors: Januzzi James L , Morss Alexander , Tung Roderick , Pino Richard , Fifer Michael A , Thompson B Taylor , Lee-Lewandrowski Elizabeth
Published: February 2006

Introduction

Amino-terminal pro-brain natriuretic peptide (NT-proBNP) is useful in evaluating heart failure, but its role in evaluating patients with shock in the intensive care unit (ICU) is not clear.

Method

Forty-nine consecutive patients in four different ICUs with shock of various types and with an indication for pulmonary artery catheter placement were evaluated. Analyses for NT-proBNP were performed on blood obtained at the time of catheter placement and results were correlated with pulmonary artery catheter findings. Logistic regression identified independent predictors of mortality.

Results

A wide range of NT-proBNP levels were observed (106 to >35,000 pg/ml). There was no difference in median NT-proBNP levels between patients with a cardiac and those with a noncardiac origin to their shock (3,046 pg/ml versus 2,959 pg/ml; P = 0.80), but an NT-proBNP value below 1,200 pg/ml had a negative predictive value of 92% for cardiogenic shock. NT-proBNP levels did not correlate with filling pressures or hemodynamics (findings not significant). NT-proBNP concentrations were higher in patients who died in the ICU (11,859 versus 2,534 pg/ml; P = 0.03), and the mortality rate of patients in the highest log-quartile of NT-proBNP (66.7%) was significantly higher than those in other log-quartiles (P < 0.001); NT-proBNP independently predicted ICU mortality (odds ratio 14.8, 95% confidence interval 1.8–125.2; P = 0.013), and was superior to Acute Physiology and Chronic Health Evaluation II score and brain natriuretic peptide in this regard.

Conclusion

Elevated levels of NT-proBNP do not necessarily correlate with high filling pressures among patients with ICU shock, but marked elevation in NT-proBNP is strongly associated with ICU death. Low NT-proBNP values in patients with ICU shock identifed those at lower risk for death, and may be useful in excluding the need for pulmonary artery catheter placement in such patients.
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana
Authors: Casneuf Tineke , De Bodt Stefanie , Raes Jeroen , Maere Steven , Van de Peer Yves
Published: February 2006

Background

Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide duplication events. Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence.

Results

Duplicates that have been created by large-scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. Moreover, the former tend to have highly redundant or overlapping expression patterns and are mostly expressed in the same tissues, while the latter show asymmetric divergence. In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in.

Conclusion

By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication.
A review and classification of the existing models of cyanobacteria
Authors: Guven Basak , Howard Alan
Published: February 2006

Bloom-forming and toxin-producing cyanobacteria remain a persistent nuisance across the world. Modelling of cyanobacteria in freshwaters is an important tool for understanding their population dynamics and predicting bloom occurrence in lakes and rivers. In this paper existing key models of cyanobacteria are reviewed, evaluated and classified. Two major groups emerge: deterministic mathematical and artificial neural network models. Mathematical models can be further subcategorized into those models concerned with impounded water bodies and those concerned with rivers. Most existing models focus on a single aspect such as the growth of transport mechanisms, but there are a few models which couple both.
Progress in invasive plants research
Authors: Henderson Scott , Dawson Terence P. , Whittaker Robert J.
Published: February 2006

This paper identifies the historical precedents and recent advances in descriptive and analytical aspects of invasive plant ecology. The paper takes a global perspective that focuses primarily on natural and semi-natural systems. The dynamics of plant invasions depend on the unique combination of species and recipient environments in light of short-lived, but highly influential, stochastic events. Spreading from the original point of establishment can be virtually instantaneous or follow a prolonged timelag. Range extension proceeds according to a variety of patterns dependent on the interplay between dispersal modes and landscape characteristics. The impacts of plant invasions are all-encompassing: biodiversity loss, economic impacts and aesthetic impacts occasioned by the loss of traditional cultural or natural landscapes. From the conservation perspective, costs are incalculable, but undoubtedly high. The impacts of invasive plants on natural ecosystems occur across all levels of biotic organization and, in the worst case, result in global extinctions and modification of fundamental ecosystem properties that make restoration practically impossible. Plant invasions occur across all habitat types and have spawned complementary theories, which are briefly presented within particular contexts.
Spatial modelling of vegetation change in dynamic landscapes: a review of methods and applications
Authors: Perry George L.W. , Enright Neal J.
Published: February 2006

Because of the spatiotemporal scales involved and the logistical constraints in collecting landscape-level data, spatially explicit simulation models have become important tools in ecological and biogeographical studies conducted over broad extents. Here we review the methods used and some of the applications of landscape-level models of succession and disturbance dynamics. Mechanistic and stochastic models are compared and contrasted and the development, over the last 15 years, of spatial landscape models of ecological change is discussed. Coarse-grained spatial landscape models are compared with finer-grained individual-based approaches (eg, forest gap models). Management and monitoring applications of landscape models are considered alongside a discussion of the appropriate use of models in this context. A key area where spatial landscape models of the type described here need to develop is improved integration with the social sciences - both in terms of the parameters and the processes that the models incorporate. Finally issues related to scale and scaling are outlined and, in particular, the utility of methods for linking ecological models operating at disparate scales (eg, forest gap models versus landscape models) is examined.
Climate change, biodiversity and the urban environment: a critical review based on London, UK
Authors: Wilby Robert L. , Perry George L.W.
Published: February 2006

According to projections by the United Nations, 60% of the world’s population will reside in urban areas by 2030. Studies of the ecology of cities and ecology in cities will therefore assume increasing relevance as urban communities seek to protect and/or enhance their ecological resources. Presently, the most serious threats to wildlife include the degradation and/or loss of habitats, the introduction and spread of problem species, water pollution, unsympathetic management, and the encroachment of inappropriate development. Climate change could add to these problems through competition from exotic species, the spread of disease and pests, increased summer drought stress for wetlands and woodland, and sea-level rise threatening rare coastal habitats. Earlier springs, longer frost-free seasons, and reduced snowfall could further affect the dates of egg-laying, as well as the emergence, first flowering and health of leafing or flowering plants. Small birds and naturalized species could thrive in the warmer winters associated with the combined effect of regional climate change and enhanced urban heat island. This article reviews the range of climate-related threats to biodiversity in the aquatic, intertidal and terrestrial habitats of urban areas. London is used as a case study to illustrate potential impacts, and to contend that ‘green spaces’ in cities could be used by planners to counter climate-related threats to biodiversity, as well as to improve flood control and air quality, and reduce urban heat island effects.
The Information Machine Letters to Nemirovich-Danchenko
Authors: Bokshanskaya Olga
Published: February 2006

Introduced by Anatoly Smeliansky

Translated by Ryan McKittrick and Julia Smeliansky
sall4acts downstream oftbx5and is required for pectoral fin outgrowth
Authors: Harvey Steven A. , Logan Malcolm P. O.
Published: February 2006

Okihiro syndrome (OS) is defined by forelimb defects associated with the eye disorder Duane anomaly and results from mutations in the gene SALL4. Forelimb defects in individuals with OS range from subtle thumb abnormalities to truncated limbs. Mutations in the T-box transcription factor TBX5 cause Holt-Oram syndrome (HOS), which results in forelimb and heart defects. Although mutations in TBX5 result in HOS, it has been predicted that these mutations account for only ∼30% of all individuals with HOS. Individuals with OS and HOS limb defects are very similar, in fact, individuals with mutations in SALL4 have in some cases previously been diagnosed with HOS. Using zebrafish as a model, we have investigated the function of sall4 and the relationship between sall4 and tbx5, during forelimb development. We demonstrate that sall4 and a related gene sall1 act downstream of tbx5 and are required for pectoral fin development. Our studies of Sall gene family redundancy and tbx5 offer explanations for the similarity of individuals with OS and HOS limb defects.
RNA-binding proteins SOP-2 and SOR-1 form a novel PcG-like complex inC. elegans
Authors: Zhang Tingting , Sun Yinyan , Tian E , Deng Hansong , Zhang Yuxia , Luo Xin , Cai Qingchun , Wang Huayi , Chai Jijie , Zhang Hong
Published: February 2006

We describe the identification and characterization of a novel PcGgene in C. elegans, sor-1, which is involved in global repression of Hox genes. sor-1 encodes a novel protein with an RNA-binding activity. We provide evidence that SOR-1 and the previously identified RNA-binding protein SOP-2 may constitute an RNA-binding complex in Hox gene repression. SOR-1 and SOP-2 directly interact with each other and are colocalized in nuclear bodies. The localization of SOR-1 depends on SOP-2. Surprisingly, homologs of SOR-1 and SOP-2 are not found in other organisms,including the congeneric species C. briggsae, suggesting an unexpected lack of evolutionary constraint on an essential global gene regulatory system.
Study of the Dynamic Strength of Reticulated Domes under Severe Earthquake Loading
Authors: Fan F. , Shen S. Z. , Parke G. A. R.
Published: February 2006

The behaviour of selected steel domes subject to severe earthquake loading has been investigated and reported. Particular attention has been given to assess the development and spread of plasticity throughout these structures. Several dome configurations have been considered, both perfect and imperfect, together with a range of varying rise to span ratios. Finite element analysis of these structures has been undertaken to determine the rate of spread of plasticity and the rate of increase in node displacement under seismic loading. The dynamic strength failure acceleration (DSFA) has been defined as the acceleration at which the rate of spread of plasticity and node displacement reaches a runaway level and the structure becomes dynamically unstable. For the dome structures under consideration DSFA occurred at an acceleration of approximately 8 m/s2. In addition, the DSFA decreased by 15%–50% for the imperfect structures when compared with the perfect domes and was lower for the multi-directional seismic input. Also, the DSFA decreased gradually with a corresponding increase in the rise to span ratio.
Evaluation of Biological Deployable Systems
Authors: Hachem Caroline , Karni Eyal , Hanaor Ariel
Published: February 2006

The paper presents a survey of deployable structural systems found in some biological organisms. Four biological systems are presented and analysed in terms of their morphology, kinematics and structural characteristics. This presentation is followed by an evaluation of the similarity of the biological systems with existing deployable structures and of potential applications. The four biological systems surveyed are two types of insect wings – Coleoptera (beetles) and locust; locomotion of the earthworm; and the jaw of the egg eater snake ( Dasypeltis). These systems represent a diversity of deployable mechanisms. The paper concludes by associating the surveyed and other biological systems with known deployable structural systems such as: folded plates, tensioned membrane, pneumatic tubes ( pneus) and structures composed of articulated rigid members.
Mechanism of Collapse of Space Trusses with Steel Hollow Circular Bars with Flattened Ends
Authors: de Souza Alex Sander Clemente , Gonçalves Roberto Martins
Published: February 2006

This paper presents the results of experimental analysis of space trusses using steel tubular bars with flattened ends. The connections are formed by overlapped bars connected by single bolt. Such system has been used due to the low cost and assembly facilities. The behavior and collapse modes were determined by experimental analysis on six space trusses with 1.5 m height and spans of 7.5 m × 7.5 m and 7.5 m × 15 m. Structures with steel nodes in the top corner and supports points were also tested. The structural collapse was caused by either connection collapse or yielding in the bar ends. Traditional theoretical analysis models (linear truss model) are not suitable for these structures.
The Potential for Wider Application of Small Scale Low-Tech Membranes Explored through Interactive Workshops
Authors: Gutierrez Elisa , Larsen Olga Popovic
Published: February 2006

Cost effective low tech membrane structures have the potential for wider application and if promoted could become in certain cases a valid alternative to traditional built form. It is possible that their development might depend not only on high-tech resources but on creative designs, use of simple tools and simple techniques. Based on these two statements, the paper presents the outcome of 4 workshops in which a free flow and interactive form-finding, space-formation and use-definition process is put forward as a divergent design exploration strategy taking part at the conceptual design stage with a main aim of exploring the potential for expanding the applicability of small scale membranes. From producing simple ideas to building low-tech prototypes, the proposed approach shifts emphasis away from initial technical and rigid concerns and instead concentrates on knowledge gain and fostering creativity through exploration. The contribution of 180 non-experts ( potential designers and potential users) drew the approach prospective usefulness: knowledge, sensibility and insight were gained and skills were developed. They also raised issues that led to ideas for further research. The research showed that this approach is valid and one that could be taken up by experts and non-experts, which could have great impact on the future small-scale membrane architecture.
Buckling Load of Elliptic Paraboloidal Single Layer Reticulated Roofs with Simple Supports under Uniform Load
Authors: Kato Shiro , Yamauchi Yoshiro , Ueki Takashi , Okuhira Kazune
Published: February 2006

The present paper discusses buckling strength of elliptic paraboloidal reticular roofs under uniform load with a rectangular plan. The roofs are assumed as three way single layers with a simple support at all peripheries of a rectangular plan. The buckling analyses are performed for linear buckling, elastic buckling, and elastic-plastic buckling. The results of buckling loads are formulated based on two procedures for practical design use. One is an explicit formula for elastic buckling loads using a knock down factor and the other one is an implicit expression for buckling loads interpreted as a column buckling strength in terms of generalized slenderness ratio.
Monovalent cations use multiple mechanisms to resolve ribozyme misfolding
Authors: JIANG YAN-FEI , XIAO MU , YIN PING , ZHANG YI
Published: February 2006

Recent efforts have been made to unravel the independent roles of monovalent cations in RNA folding, primarily using the Tetrahymena ribozyme as a model. Here we report how monovalent cations impact the folding of the Candida ribozyme. Interestingly, this ribozyme requires an order of magnitude less monovalent cations (Na+ and Tris+) to commit to a new folding starting state in which the J3/4:P6 base triple is partially formed and mispairing in the L2.1 and L6 terminal loops is resolved. When Mg2+-induced ribozyme folding proceeded on the same energy landscape, the altered starting state led to a rapid assembly of the correct ribozyme core and a fivefold to 10-fold increase in the ribozyme activity. Moreover, when the ribozyme folding was started from a misfolding-prone state, high millimolar concentrations of monovalent cations moderately elevated the ribozyme activity by efficiently resolving the misfolding of a peripheral element, P5abc.
AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II
Authors: GULLEROVA MONIKA , BARTA ANDREA , LORKOVIĆ ZDRAVKO J.
Published: February 2006

AtCyp59 and its orthologs from different organisms belong to a family of modular proteins consisting of a peptidyl-prolyl cis–trans isomerase (PPIase) domain, followed by an RNA recognition motif (RRM), and a C-terminal domain enriched in charged amino acids. AtCyp59 was identified in a yeast two-hybrid screen as an interacting partner of the Arabidopsis SR protein SCL33/SR33. The interaction with SCL33/SR33 and with a majority of Arabidopsis SR proteins was confirmed by in vitro pull-down assays. Consistent with these interactions, AtCyp59 localizes to the cell nucleus, but it does not significantly colocalize with SR proteins in nuclear speckles. Rather, it shows a punctuate localization pattern resembling transcription sites. Indeed, by using yeast two-hybrid, in vitro pull-down, and immunoprecipitation assays, we found that AtCyp59 interacts with the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. Ectopic expression of the tagged protein in Arabidopsis cell suspension resulted in highly reduced growth that is most probably due to reduced phosphorylation of the CTD. Together our data suggest a possible function of AtCyp59 in activities connecting transcription and pre-mRNA processing. We discuss our data in the context of a dynamic interplay between transcription and pre-mRNA processing.
Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans
Authors: LEE ROSALIND C. , HAMMELL CHRISTOPHER M. , AMBROS VICTOR
Published: February 2006

C. elegans contains numerous small RNAs of ~21–24 nt in length. The microRNAs (miRNAs) are small noncoding RNAs produced by DCR-1- and ALG-dependent processing of self-complementary hairpin transcripts. Endogenous small interfering RNAs (endo-siRNAs), associated with ongoing silencing of protein-coding genes in normal worms, are produced by mechanisms that involve DCR-1 but, unlike miRNAs, also involve RDE-2, RDE-3, RDE-4, RRF-1, and RRF-3. The tiny noncoding (tncRNAs) are similar to endo-siRNAs in their biogenesis except that they are derived from noncoding sequences. These endo-siRNA- and tncRNA-based endogenous RNAi pathways involve some components, including DCR-1 and RDE-4, that are shared with exogenous RNAi, and some components, including RRF-3 and ERI-1, that are specific to endogenous RNAi. rrf-3 and eri-1 mutants are enhanced for some silencing processes and defective for others, suggesting cross-regulatory interactions between RNAi pathways in C. elegans. Microarray expression profiling of RNAi-defective mutant worms further suggests diverse endogenous RNAi pathways for silencing different sets of genes.
Ribose 2′-hydroxyl groups in the 5′ strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation
Authors: FEINBERG JASON S. , JOSEPH SIMPSON
Published: February 2006

The coupled movement of tRNA–mRNA complex through the ribosome is a fundamental step during the protein elongation process. We demonstrate that the ribosome will translocate a P-site–bound tRNAMet with a break in the phosphodiester backbone between positions 17 and 18 in the D-loop. Crystallographic data showed that the acceptor arms of P- and E-site tRNA interact extensively with the ribosomal large subunit. Therefore, we used this fragmented P-site–bound tRNAMet to investigate the contributions of single 2′-hydroxyl groups in the 5′ strand of the acceptor arm for translocation into the ribosomal E-site. EF-G–dependent translocation of the tRNAs was monitored using a toeprinting assay and a fluorescence-based rapid kinetic method. Surprisingly, our results show that none of the 2′-hydroxyl groups in the 5′ strand of the acceptor arm of P-site–bound tRNAMet between positions 1–17 play a critical role during translocation. This suggests that either these 2′-hydroxyl groups are not important for translocation or they are redundant and the three-dimensional shape of the P-site tRNA is more important for translocation.