Additional File Research Articles

Distribution and habitat characterization of the recently introduced invasive mosquito Aedes koreicus [Hulecoeteomyia koreica], a new potential vector and pest in north-eastern Italy

BackgroundThe container breeding species belonging to the genus Aedes (Meigen) are frequently recorded out of their place of origin. Invasive Aedes species are proven or potential vectors of important Arboviruses and their establishment in new areas pose a threat for human and animal health. A new species of exotic mosquito was recorded in 2011 in north-eastern Italy: Aedes (Finlaya) koreicus [Hulecoeteomyia koreica]. The aim of this study was to characterize the biology, the environment and the current distribution of this mosquito in north-eastern Italy. Morphological details useful to discriminate this species from other invasive Aedes mosquitoes are also given (see Additional files).MethodsAll possible breeding sites for larval development were monitored. In addition, ovitraps and traps for adults were used to collect eggs and adults. The mosquitoes (larvae and adults) were identified morphologically and molecularly. Environmental data and climatic variables during the period of mosquito activity (from April to October) were considered.ResultsAedes koreicus was found in 37 municipalities (39.4%) and was detected in 40.2% of places and in 37.3% of larval habitats monitored, in a range of altitude from 173 to 1250 m.a.s.l.. Garden centres were the most common locations (66.7%), followed by streets/squares (57.1%), private gardens (46.4%) and cemeteries (21.1%) (p < 0.01). The main larval habitats were catch basins (48.5%) and artificial water containers (41.8%). As for Aedes albopictus [Stegomyia albopicta], ovitraps were attractive for adult females resulting in the higher rate of positivity (15/21; 71.4%) among breeding sites. The period of Ae. koreicus activity ranged from March 29 to October 29.ConclusionThe species is clearly established in the area and is now overlapping with other vectors such as Ae. albopictus and colonizing areas over 800 m.a.s.l, not yet or sporadically reached by the tiger mosquito. The data collected are essential to assess the risk of colonization of other parts of Italy and Europe, as well as the risk of spreading of pathogens transmitted. These findings stress the importance of implementing entomological surveillance for early detection of invasive species, which is necessary for eradication or limitation of its further spread.

Effect of Phosphorus Amount on the Particle Size and Catalytic Performance of Heterogeneous Nickel(II) Schiff-Base Complex in Aldol Condensation Reaction

The organic–inorganic hybrid of citric acid, tetraethoxysilane (TEOS), and triethylphosphate (TEP) doped by a nickel Schiff-base complex was prepared by sol–gel method. The prepared composites were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmittance electron microscopy (TEM), scanning tunnelling microscopy (STM), and infrared spectroscopy (IR). In order to determine the phosphorus amount effect on the catalytic activity of the prepared composites, the aldol condensation was used as a model reaction. The results revealed that the composite with 10% phosphorus is a better catalyst in comparison with other composites. [Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the following free supplemental files: Additional figures file.]

Preparing to Work with Big Data in Proteomics - A Report on the HUPO-PSI Spring Workshop

The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. The 2013 annual spring workshop was hosted by the University of Liverpool, UK and concentrated on updating and refining the existing standards in the light of new methodologies and technologies. To control the inflation of file sizes, strategies for file compression, particularly for mzML files, were explored. Best practices for encoding information such as protein grouping and PTM localisation were refined and documented. Additional example files for the mzQuantML format were designed to provide support for selected reaction monitoring techniques. Enhancements to the PSI Common Query Interface (PSICQUIC) and PSI-MI XML were discussed. Finally, the group engaged in discussion on how the existing work of the HUPO-PSI can be leveraged by the Metabolomics Standards Initiative to improve the capture of metabolite data.

Correction: Ineffectiveness of Reverse Wording of Questionnaire Items: Let’s Learn from Cows in the Rain

As a result of an error by PLOS ONE, an incorrect version of the article was typeset. Below is a link to a version of the article based on the correct manuscript. Article: Click here for additional data file.(112K, pdf)

European and global approaches to survey ageing populations and perspectives for joint approaches to measure age-related health outcomes

European and global approaches to survey ageing populations and perspectives for joint approaches to measure age-related health outcomes

P271 Computerized Guidelines Analysis: 5-Years Experience And User Feedback

BackgroundIn 2007, HAS (Haute Autorité de Santé, France) started experimenting the use of computerised guidelines analysis with the G-DEE software as part of the guidelines production process. G-DEE uses shallow...

Development of guidelines for the surveillance of invasive mosquitoes in Europe

BackgroundThe recent notifications of autochthonous cases of dengue and chikungunya in Europe prove that the region is vulnerable to these diseases in areas where known mosquito vectors (Aedes albopictus and Aedes aegypti) are present. Strengthening surveillance of these species as well as other invasive container-breeding aedine mosquito species such as Aedes atropalpus, Aedes japonicus, Aedes koreicus and Aedes triseriatus is therefore required. In order to support and harmonize surveillance activities in Europe, the European Centre for Disease Prevention and Control (ECDC) launched the production of ‘Guidelines for the surveillance of invasive mosquitoes in Europe’. This article describes these guidelines in the context of the key issues surrounding invasive mosquitoes surveillance in Europe.MethodsBased on an open call for tender, ECDC granted a pan-European expert team to write the guidelines draft. It content is founded on published and grey literature, contractor’s expert knowledge, as well as appropriate field missions. Entomologists, public health experts and end users from 17 EU/EEA and neighbouring countries contributed to a reviewing and validation process. The final version of the guidelines was edited by ECDC (Additional file 1).ResultsThe guidelines describe all procedures to be applied for the surveillance of invasive mosquito species. The first part addresses strategic issues and options to be taken by the stakeholders for the decision-making process, according to the aim and scope of surveillance, its organisation and management. As the strategy to be developed needs to be adapted to the local situation, three likely scenarios are proposed. The second part addresses all operational issues and suggests options for the activities to be implemented, i.e. key procedures for field surveillance of invasive mosquito species, methods of identification of these mosquitoes, key and optional procedures for field collection of population parameters, pathogen screening, and environmental parameters. In addition, methods for data management and analysis are recommended, as well as strategies for data dissemination and mapping. Finally, the third part provides information and support for cost estimates of the planned programmes and for the evaluation of the applied surveillance process.ConclusionThe ‘Guidelines for the surveillance of invasive mosquitoes in Europe’ aim at supporting the implementation of tailored surveillance of invasive mosquito species of public health importance. They are intended to provide support to professionals involved in mosquito surveillance or control, decision/policy makers, stakeholders in public health and non-experts in mosquito surveillance. Surveillance also aims to support control of mosquito-borne diseases, including integrated vector control, and the guidelines are therefore part of a tool set for managing mosquito-borne disease risk in Europe.

Clinical impact of biologic therapy in the treatment of SLE

Biologic therapies have generated substantial research interest for treating autoimmune diseases, resulting in several US Food and Drug Administration approvals. However, clinical trial results in systemic lupus erythematosus (SLE) populations have failed to meet efficacy expectations, primarily owing to methodological flaws in design, especially outcome measures. To address these issues, the US Food and Drug Administration published a guidance document for clinical trial design in SLE that included specific efficacy endpoints for measuring disease severity. Belimumab was the first biologic approved for SLE based on positive responses measured with the SLE Responder Index, which required a decrease in inflammation, no new organ domains being involved, and improvement in physician global assessment. Trials of other biologics have used other versions of SLE Responder Index responder indices. In addition to belimumab, a score of other biologic agents are being investigated, primarily those targeting T cells, B cells, complement, and tolerogen-targeting agents. Their development stages and clinical trial results vary. Belimumab has generated the greatest amount of clinical trials, as investigators try to further define its role in clinical practice. Results have been shared in many forums, including annual meetings of the American College of Rheumatology and European League Against Rheumatism, along with publications in the medical literature. These findings indicate that belimumab is effective in patients with more active disease who are able to wait up to 3 months for improvement. Additionally, it can be considered for patients with active disease despite therapy with NSAIDs, antimalarials, immunosuppressives, or corticosteroids, especially if the benefits of treatment outweigh its risks or if the patient is intolerant to steroids or immunosuppressives. Additional file 1 contains an edited transcript of the full presentation.

Linear combination test for gene set analysis of a continuous phenotype

BackgroundGene set analysis (GSA) methods test the association of sets of genes with a phenotype in gene expression microarray studies. Many GSA methods have been proposed, especially methods for use with a binary phenotype. Equally, if not more importantly however, is the ability to test the enrichment of a gene signature or pathway against the continuous phenotypes which are routinely and commonly observed in, for example, clinicopathological measurements. It is not always easy or meaningful to dichotomize continuous phenotypes into two classes, and attempting to do this may lead to the inaccurate classification of samples, which would affect the downstream enrichment analysis. In the present study, we have build on recent efforts to incorporate correlation structure within gene sets and pathways into the GSA test statistic. To address the issue of continuous phenotypes directly without the need for artificial discrete classification and thus increase the power of the test while ensuring computational efficiency and rigor, new GSA methods that can incorporate a covariance matrix estimator for a continuous phenotype may present an effective approach.ResultsWe have designed a new method by extending the GSA approach called Linear Combination Test (LCT) from a binary to a continuous phenotype. Simulation studies and a real microarray dataset were used to compare the proposed LCT for a continuous phenotype, a modification of LCT (referred to as LCT2), and two publicly available GSA methods for continuous phenotypes.ConclusionsWe found that the LCT methods performed better than the other two GSA methods; however, this finding should be understood in the context of our specific simulation studies and the real microarray dataset that were used to compare the methods. Free R-codes to perform LCT for binary and continuous phenotypes are available at http://www.ualberta.ca/~yyasui/homepage.html. The R-code to perform LCT for a continuous phenotype is available as Additional file 1.

Unmet needs: therapeutic standards of care

Many unmet needs exist for practitioners caring for patients with systemic lupus erythematosus (SLE). The top need is for a blockbuster drug with glucocorticoid efficacy but fewer side effects. They also need better markers to identify responders without waiting 3 to 6 months to see clinical improvement. Current therapeutic goals are to induce and maintain responses while minimizing side effects. Therapy selection varies depending on disease severity and response to previous therapies. Therapies for SLE target different areas in the immunologic process, primarily T-cell and B-cell lymphocytes for mycophenolate mofetil (MMF), azathioprine, and anti-B-lymphocyte stimulator, and a wider array of cells for glucocorticoids. The American College of Rheumatology recently published treatment guidelines for the use of adjunctive therapies in patients with lupus nephritis that recommend hydroxychloroquine as background therapy in all of these patients, and it established target levels for blood pressure, and low-density lipoprotein to reduce complications. Data were inadequate to make recommendations regarding glucocorticoid doses for induction of improvement (thus 0.5 to 1 mg/kg/day is the recommendation) or for tapering or discontinuing prednisone. Renal biopsy is recommended for all patients with active lupus nephritis, previously untreated, to provide data for classification of glomerular disease and thus enable selection of appropriate therapy. Recommendations for induction therapy include either MMF or cyclophosphamide (CYC). MMF has the advantage of being equally effective in all races and being formulated for oral administration. CYC is less effective in African Americans and Latinos but is equivalent in Caucasians and Asians. Low-dose CYC is an option for Caucasians. Teratogenicity is a concern with MMF, CYC, and methotrexate, but hydroxychloroquine, glucocorticoids, and azathioprine can be used during pregnancy, if necessary. New evidence suggests that improvements in proteinuria and C3/C4 blood levels may predict response as early as 8 weeks. Clinical trials with belimumab for lupus nephritis are not yet available although it did not appear to worsen renal disease in patients without active lupus nephritis. Belimumab is approved by the US Food and Drug Administration for use in antinuclear antibodies and/or anti-DNA-positive SLE patients with active disease that persists despite standard treatments. Investigators continue to research other targeted therapies for high response rates, less toxicity, and less need for chronic glucocorticoid treatment. Additional file 1 contains an edited transcript of the full presentation.

Measuring disease activity and severity in clinical trials and the clinic: same or different?

Standardized criteria to classify systemic lupus erythematosus (SLE) disease activity provide a well-defined methodology to accurately assess SLE. These criteria were recently revised to reflect new knowledge of SLE, both clinical and immunologic. Although developed to classify SLE, these criteria can help with the diagnosis in clinical practice. Research has also provided additional evidence of elevated morbidity and mortality associated with high-dose prednisone therapy, defined as greater than 6 mg/day. At these doses, significant increases in organ damage and cardiovascular events occur. Use of NSAIDs is also known to raise cardiovascular risk. Better options include intermittent intramuscular triamcinolone and hydroxychloroquine. The question of how often to monitor patients with stable SLE is confounded by the many variables showing clinical activity and their average frequency of occurrence. Nevertheless, the evidence suggests that 3 months is the ideal time for follow-up testing. Although there is no confirmed technical standard for measuring SLE disease activity, two primary instruments are available in the clinic: the Physicians Global Assessment and the SELENA-SLEDAI instrument. Each has varying degrees of ability to detect changes in disease activity as well as clinical usefulness. In clinical trials, outcomes are measured by the SLE Responder Index, an instrument that defines response based on criteria from SELENA-SLEDAI, Physicians Global Assessment, and British Isles Lupus Assessment Group index. In clinical practice, responses are primarily based on improvements in disease activity, especially reduced flares. Improvements in serology also matter, as patients with high anti-DNA or low complement are twice as likely to flare during the next year. Quality-of-life criteria are important to patients. Overall, the goal is to accurately measure clinical improvement in the patient's SLE disease activity. Additional file 1 contains an edited transcript of the full presentation.

Correction: The Timing Statistics of Spontaneous Calcium Release in Cardiac Myocytes

The Supporting Information files were erroneously supplied as LaTeX files. Please see Appendix S1 and Appendix S2 at the following links: Click here for additional data file.(149K, pdf) Click here for additional data file.(102K, pdf)

PiDNA: predicting protein–DNA interactions with structural models

Predicting binding sites of a transcription factor in the genome is an important, but challenging, issue in studying gene regulation. In the past decade, a large number of protein–DNA co-crystallized structures available in the Protein Data Bank have facilitated the understanding of interacting mechanisms between transcription factors and their binding sites. Recent studies have shown that both physics-based and knowledge-based potential functions can be applied to protein–DNA complex structures to deliver position weight matrices (PWMs) that are consistent with the experimental data. To further use the available structural models, the proposed Web server, PiDNA, aims at first constructing reliable PWMs by applying an atomic-level knowledge-based scoring function on numerous in silico mutated complex structures, and then using the PWM constructed by the structure models with small energy changes to predict the interaction between proteins and DNA sequences. With PiDNA, the users can easily predict the relative preference of all the DNA sequences with limited mutations from the native sequence co-crystallized in the model in a single run. More predictions on sequences with unlimited mutations can be realized by additional requests or file uploading. Three types of information can be downloaded after prediction: (i) the ranked list of mutated sequences, (ii) the PWM constructed by the favourable mutated structures, and (iii) any mutated protein–DNA complex structure models specified by the user. This study first shows that the constructed PWMs are similar to the annotated PWMs collected from databases or literature. Second, the prediction accuracy of PiDNA in detecting relatively high-specificity sites is evaluated by comparing the ranked lists against in vitro experiments from protein-binding microarrays. Finally, PiDNA is shown to be able to select the experimentally validated binding sites from 10 000 random sites with high accuracy. With PiDNA, the users can design biological experiments based on the predicted sequence specificity and/or request mutated structure models for further protein design. As well, it is expected that PiDNA can be incorporated with chromatin immunoprecipitation data to refine large-scale inference of in vivo protein–DNA interactions. PiDNA is available at: http://dna.bime.ntu.edu.tw/pidna.

Correction: Pharmacological Inhibition of Glycogen Synthase Kinase 3 Regulates T Cell Development In Vitro

There were errors in Figure 5 and Supporting Figures S4, S5, and S6. The correct versions of these Figures can be viewed here: Figure 5: Supporting Figure S4: Click here for additional data file.(15M, tif) Supporting Figure S5: Click here for additional data file.(7.9M, tif) Supporting Figure S6: Click here for additional data file.(15M, tif)

Correction: Differential Expression Analysis for Pathways

A minor correction has been made to the function “meanExpDict”, where the conditional statement was flipped during code refactoring. Further, the instructions have been made more clear. Please view the correct File S3 here: Click here for additional data file.(140K, gz) You can also access the source code repository directly via this link: https://sourceforge.net/projects/deapathways/

Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks

BackgroundThe usefulness of the data from Affymetrix microarray analysis depends largely on the reliability of the files describing the correspondence between probe sets, genes and transcripts. Particularly, when a gene is targeted by several probe sets, these files should give information about the similarity of each alternative probe set pair. Transcriptional networks integrate the multiple correlations that exist between all probe sets and supply much more information than a simple correlation coefficient calculated for two series of signals. In this study, we used the PSAWN (Probe Set Assignment With Networks) programme we developed to investigate whether similarity of alternative probe sets resulted in some specific properties.FindingsPSAWNpy delivered a full textual description of each probe set and information on the number and properties of secondary targets. PSAWNml calculated the similarity of each alternative probe set pair and allowed finding relationships between similarity and localisation of probes in common transcripts or exons. Similar alternative probe sets had very low negative correlation, high positive correlation and similar neighbourhood overlap. Using these properties, we devised a test that allowed grouping similar probe sets in a given network. By considering several networks, additional information concerning the similarity reproducibility was obtained, which allowed defining the actual similarity of alternative probe set pairs. In particular, we calculated the common localisation of probes in exons and in known transcripts and we showed that similarity was correctly correlated with them. The information collected on all pairs of alternative probe sets in the most popular 3’ IVT Affymetrix chips is available in tabular form at http://bns.crbm.cnrs.fr/download.html.ConclusionsThese processed data can be used to obtain a finer interpretation when comparing microarray data between biological conditions. They are particularly well adapted for searching 3’ alternative poly-adenylation events and can be also useful for studying the structure of transcriptional networks. The PSAWNpy, (in Python) and PSAWNml (in Matlab) programmes are freely available and can be downloaded at http://code.google.com/p/arraymatic. Tutorials and reference manuals are available at BMC Research Notes online (Additional file 1) or from http://bns.crbm.cnrs.fr/softwares.html.

Efficacy of reciprocating and rotary techniques for removing filling material during root canal retreatment

To compare the efficacy of reciprocating and rotary techniques with that of hand files for removing gutta-percha and sealer from root canals. The root canals of fifty-four human extracted maxillary central incisors were cleaned and shaped using a crown-down technique to a size 40 and filled with gutta-percha and a zinc oxide-eugenol-based sealer using a lateral compaction technique. Teeth were divided into three groups according to the technique used for removing the root filling material: group I - Gates-Glidden burs and stainless steel hand files up to size 50; group II - rotary technique with NiTi Mtwo R files and additional Mtwo files to size 50, 0.04 taper; group III - reciprocating technique with the Reciproc instrument R50, size 50, 0.05 taper. Chloroform was used as a solvent in all groups. Teeth were then split longitudinally and photographed under 8× magnification. The images were transferred to a computer, and the total canal space and remaining filling material were quantified. The ratio of remaining filling material to root canal periphery was computed with the aid of Image Tool 3.0 software. The mean percentages of remaining filling material and time required to remove it were compared using the Kruskal-Wallis and Mann-Whitney tests (P < 0.05). The mean percentage of remaining filling material was significantly higher (P < 0.05) in group II, with Mtwo rotary files (12.17%), than in group I, with the hand file technique (7.19%), and group III, with Reciproc instruments (4.57%), which were statistically similar (P > 0.05). The time required to remove filling material was significantly shorter (P < 0.05) in group III (194 s), followed by group II (365 s) and group I (725 s) (P < 0.05). Remaining endodontic filling material was observed on the canal walls of all teeth regardless of the technique used. Hand files combined with Gates-Glidden burs (group I) and the reciprocating technique (group III) removed more filling material from the canal walls than the Mtwo R files. The reciprocating technique was the most rapid method for removing gutta-percha and sealer, followed by the rotary technique and the hand file technique.

Correction: Genetic Diversity within Schistosoma haematobium: DNA Barcoding Reveals Two Distinct Groups

The cox1 accession number for Kenya on page 6 ({type:entrez-nucleotide,attrs:{text:JQ397340,term_id:384871862,term_text:JQ397340}}JQ397340) is incorrect. The correct accession number is {type:entrez-nucleotide,attrs:{text:JQ397370,term_id:384871922,term_text:JQ397370}}JQ397370. Additionally, this line is incorrectly printed twice. The correct Supporting Information, Table 1 can be viewed here: Click here for additional data file.(137K, doc)

Correction: Blood Meal-Derived Heme Decreases ROS Levels in the Midgut of Aedes aegypti and Allows Proliferation of Intestinal Microbiota

Table S1 does not appear. Please view Table S1 here: Click here for additional data file.(11K, xlsx)

Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses

As next generation sequencing technologies are getting more efficient and less expensive, RNA-Seq is becoming a widely used technique for transcriptome studies. Computational analysis of RNA-Seq data often starts with the mapping of millions of short reads back to the genome or transcriptome, a process in which some reads are found to map equally well to multiple genomic locations (multimapping reads). We have developed the Minimum Unique Length Tool (MULTo), a framework for efficient and comprehensive representation of mappability information, through identification of the shortest possible length required for each genomic coordinate to become unique in the genome and transcriptome. Using the minimum unique length information, we have compared different uniqueness compensation approaches for transcript expression level quantification and demonstrate that the best compensation is achieved by discarding multimapping reads and correctly adjusting gene model lengths. We have also explored uniqueness within specific regions of the mouse genome and enhancer mapping experiments. Finally, by making MULTo available to the community we hope to facilitate the use of uniqueness compensation in RNA-Seq analysis and to eliminate the need to make additional mappability files.