Vertical transmission rates for HIV in the British Isles: estimates based on surveillance data

ObjectiveTo estimate and interpret time trends in vertical transmission rates for HIV using data from national obstetric and paediatric surveillance registers.DesignProspective study of HIV infected women reported through obstetric surveillance. HIV infection status of the child and onset of AIDS were reported through paediatric surveillance. Rates of vertical transmission and progression to AIDS rate were estimated by methods that take account of incomplete follow up of children with indeterminate infection status and delay in AIDS reporting.SettingBritish Isles.SubjectsPregnant women infected with HIV whose infection was diagnosed before delivery, and their babies.ResultsBy January 1999, 800 children born to diagnosed HIV infected women who had not breast fed had been reported. Vertical transmission rates rose to 19.6% (95% confidence interval 8.0% to 32.5%) in 1993 before falling to 2.2% (0% to 7.8%) in 1998. Between 1995 and 1998 use of antiretroviral treatment increased significantly each year, reaching 97% of live births in 1998. The rate of elective caesarean section remained constant, at around 40%, up to 1997 but increased to 62% in 1998. Caesarean section and antiretroviral treatment together were estimated to reduce risk of transmission from 31.6% (13.6% to 52.2%) to 4.2% (0.8% to 8.5%). The proportion of infected children developing AIDS in the first 6 months fell from 17.7% (6.8% to 30.8%) before 1994 to 7.2% (0% to 15.7%) after, coinciding with increased use of prophylaxis against Pneumocystis carinii pneumonia.ConclusionsIn the British Isles both HIV related morbidity and vertical transmission are being reduced through increased use of interventions.

Key messages

• Reliable estimates of HIV vertical transmission rates can be derived from surveillance data
• Infected pregnant women are increasingly taking up elective caesarean section and antiretroviral treatment to reduce the risk of transmitting HIV to their babies
• Vertical transmission rates have fallen greatly over the past four years and progression to AIDS among infected children may also have slowed
• These benefits can occur only if infected women are diagnosed before or during pregnancy

     

plot2groups: an R package to plot scatter points for two groups of values

Background

Researchers usually employ bar graphs to show two groups of data, which can be easily manipulated to yield false impressions. To some extent, scatterplot can retain the real data values and the spread of the data. However, for groups of numeric data, scatterplot may cause over-plotting problems. As a result, many values all stack on top of each other.

Results

We recently implemented an R package, plot2groups, to plot scatter points for two groups values, jittering the adjacent points side by side to avoid overlapping in the plot. The functions simultaneously calculate a P value of two group t- or rank-test and incorporated the P value into the plot.

Conclusions

plot2groups is a simple and flexible software package which can be used to visualize two groups of values within the statistical programming environment R.

     

APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools

Background

Mass spectrometry analyses of complex protein samples yield large amounts of data and specific expertise is needed for data analysis, in addition to a dedicated computer infrastructure. Furthermore, the identification of proteins and their specific properties require the use of multiple independent bioinformatics tools and several database search algorithms to process the same datasets. In order to facilitate and increase the speed of data analysis, there is a need for an integrated platform that would allow a comprehensive profiling of thousands of peptides and proteins in a single process through the simultaneous exploitation of multiple complementary algorithms.

Results

We have established a new proteomics pipeline designated as APP that fulfills these objectives using a complete series of tools freely available from open sources. APP automates the processing of proteomics tasks such as peptide identification, validation and quantitation from LC-MS/MS data and allows easy integration of many separate proteomics tools. Distributed processing is at the core of APP, allowing the processing of very large datasets using any combination of Windows/Linux physical or virtual computing resources.

Conclusions

APP provides distributed computing nodes that are simple to set up, greatly relieving the need for separate IT competence when handling large datasets. The modular nature of APP allows complex workflows to be managed and distributed, speeding up throughput and setup. Additionally, APP logs execution information on all executed tasks and generated results, simplifying information management and validation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0441-8) contains supplementary material, which is available to authorized users.     

Synthesis and application of two reagents for the introduction of sulfhydryl groups into proteins

Two reagents are described which can be used for the introduction of sulfhydryl groups into proteins. Mercaptopropionylhydrazide modifies specifically periodate-oxidized N termini of proteins, provided that the N-terminal residue is serine or threonine. 3-(Phenyldithio)propionimidate introduces a disulfide bond at lysine residues of proteins. Reduction converts the disulfide into a sulfhydryl group. The imidate compound was found to react with a high specificity with only one lysine residue of ribosomal protein L7/L12.     

Transfer of two Helicoma species to Troposporella based on molecular and morphological data

Previous molecular data demonstrated that, although Helicoma is polyphyletic, most species in the genus, including the type Helicoma muelleri, are in the Tubeufiaceae. Here, we use analysis of the small subunit and internal transcribed spacers (ITS) rDNA regions to show that two species, H. monilipes and H. olivaceum, are phylogenetically distant from the type, branching outside of the Tubeufiaceae near Troposporella fumosa in a basal clade of the Dothideomycetes. The phylogeny does not support the recent transfer of T. fumosa to Helicoma. Instead, based on the molecular evidence as well as the examination of cultures and type specimens, Troposporella is reinstated at the generic level, and Helicoma monilipes and Helicoma olivaceum are transferred to Troposporella. All three Troposporella species share the production of helicoid conidia borne on sporodochial conidiomata from blastic conidiogenous cells. A key to accepted species is provided.     

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data

SUMMARY: New additional methods are presented for processing and visualizing mass spectrometry based molecular profile data, implemented as part of the recently introduced MZmine software. They include new features and extensions such as support for mzXML data format, capability to perform batch processing for large number of files, support for parallel processing, new methods for calculating peak areas using post-alignment peak picking algorithm and implementation of Sammon's mapping and curvilinear distance analysis for data visualization and exploratory analysis. AVAILABILITY: MZmine is available under GNU Public license from http://mzmine.sourceforge.net/.     

Specific targeting of ultrasound contrast agent (USCA) for diagnostic application: an in vitro feasibility study based on SAW biosensor

The present study described a new strategy to examine the interaction between the targeted ultrasound contrast agent (USCA) and its target under flow conditions with a surface acoustic wave (SAW) transducer. The sensing principle is based on the measurement of the phase change on the sensing element upon the binding of specific biomolecules. Love-wave biosensor array was consisting of sensor elements and reference elements. The sensor elements have been prepared by coating the sensor surface with tumor marker EDB-fibronectin by means of SAM technique and carbodiimide chemistry. Reference elements were left blank or coated with fibronectin and used to eliminate thermal drift, unspecific binding, and turbulence from injection of liquids by calculating the differential phase shift with respect to the sensor elements. The binding of targeted USCA to the sensor surface was constantly recorded by monitoring the phase shift on the sensor element. The binding of targeted USCA generated a high phase shift on the sensor elements, but almost no change on the reference elements. Control experiments using non-targeted and isotype-targeted USCA confirmed the specificity of binding due to anti-EDB-fibronectin scFv-antibody-fragment-EDB-fibronectin antigen interaction. The suitability of the SAW technique to monitor the specific binding behavior of targeted micron-sized USCA in real time has been well established.     

The dagestan gene pool: The genetic structure of the nine largest ethnic groups: Analysis based on data on the AB0 and Rhesus blood groups

Detailed analysis of the population structure of Dagestan ethnic groups based on data on the AB0 and Rhesus blood groups has been carried out. A total of 32101 representatives of the nine largest ethnic groups of Dagestan (from 682 auls in 46 raions) have been examined. This allows a comprehensive genetic landscape of the Dagestan population to be drawn. Comparison of the ethnic groups studied with other Caucasian ethnic groups makes it possible to determine the position of the Dagestan gene pool in the total structure of the Caucasian gene pool.     

h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data

Background  

An ever increasing number of techniques are being used to find genes with similar profiles from microarray studies. Visualization of gene expression profiles can aid this process, potentially contributing to the identification of co-regulated genes and gene function as well as network development.     

Reduction, classification and ranking of motion analysis data: an application to osteoarthritic and normal knee function data

There are certain major obstacles to using motion analysis as an aid to clinical decision making. These include: the difficulty in comprehending large amounts of both corroborating and conflicting information; the subjectivity of data interpretation; the need for visualization; and the quantitative comparison of temporal waveform data. This paper seeks to overcome these obstacles by applying a hybrid approach to the analysis of motion analysis data using principal component analysis (PCA), the Dempster-Shafer (DS) theory of evidence and simplex plots. Specifically, the approach is used to characterise the differences between osteoarthritic (OA) and normal (NL) knee function data and to produce a hierarchy of those variables that are most discriminatory in the classification process. Comparisons of the results obtained with the hybrid approach are made with results from artificial neural network analyses.