Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource.

Response to Comment on "An excess of massive stars in the local 30 Doradus starburst".

Farr and Mandel reanalyze our data, finding initial mass function slopes for high-mass stars in 30 Doradus that agree with our results. However, their reanalysis appears to underpredict the observed number of massive stars. Their technique results in more precise slopes than in our work, strengthening our conclusion that there is an excess of massive stars (>30 solar masses) in 30 Doradus.

Experimental determination of configurational entropy in a two-dimensional liquid under random pinning.

A quasi two-dimensional colloidal suspension is studied under the influence of immobilisation (pinning) of a random fraction of its particles. We introduce a novel experimental method to perform random pinning and, with the support of numerical simulation, we find that increasing the pinning concentration smoothly arrests the system, with a cross-over from a regime of high mobility and high entropy to a regime of low mobility and low entropy. At the local level, we study fluctuations in area fraction and concentration of pins and map them to entropic structural signatures and local mobility, obtaining a measure for the local entropic fluctuations of the experimental system.

An excess of massive stars in the local 30 Doradus starburst.

The 30 Doradus star-forming region in the Large Magellanic Cloud is a nearby analog of large star-formation events in the distant universe. We determined the recent formation history and the initial mass function (IMF) of massive stars in 30 Doradus on the basis of spectroscopic observations of 247 stars more massive than 15 solar masses ([Formula: see text]). The main episode of massive star formation began about 8 million years (My) ago, and the star-formation rate seems to have declined in the last 1 My.

Bridging the gap: from massive stars to supernovae.

Almost since the beginning, massive stars and their resultant supernovae have played a crucial role in the Universe. These objects produce tremendous amounts of energy and new, heavy elements that enrich galaxies, encourage new stars to form and sculpt the shapes of galaxies that we see today. The end of millions of years of massive star evolution and the beginning of hundreds or thousands of years of supernova evolution are separated by a matter of a few seconds, in which some of the most extreme physics found in the Universe causes the explosive and terminal disruption of the star.

Weak temperature dependence of ageing of structural properties in atomistic model glassformers.

Ageing phenomena are investigated from a structural perspective in two binary Lennard-Jones glassformers, the Kob-Andersen and Wahnström mixtures. In both, the geometric motif assumed by the glassformer upon supercooling, the locally favoured structure (LFS), has been established. The Kob-Andersen mixture forms bicapped square antiprisms; the Wahnström model forms icosahedra.

The nature of geometric frustration in the Kob-Andersen mixture.

Geometric frustration is an approach to the glass transition based upon the consideration of locally favoured structures (LFS), which are geometric motifs which minimise the local free energy. Geometric frustration proposes that a transition to a crystalline state is frustrated because these LFS do not tile space. However, this concept is based on icosahedra which are not always the LFS for a given system.

Puzzling accretion onto a black hole in the ultraluminous X-ray source M 101 ULX-1.

There are two proposed explanations for ultraluminous X-ray sources (ULXs) with luminosities in excess of 10(39) erg s(-1). They could be intermediate-mass black holes (more than 100-1,000 solar masses, M sun symbol) radiating at sub-maximal (sub-Eddington) rates, as in Galactic black-hole X-ray binaries but with larger, cooler accretion disks. Alternatively, they could be stellar-mass black holes radiating at Eddington or super-Eddington rates.

Genotypic and demographic characterization of invasive isolates of Salmonella Typhimurium in HIV co-infected patients in South Africa.

Background: Non-typhoidal Salmonella are frequently food-borne zoonotic pathogens that may cause invasive disease in HIV-positive individuals.

Methodology: Invasive isolates (n = 652) of Salmonella Typhimurium from human patients in Gauteng Province of South Africa were investigated for the years 2006 and 2007. Bacteria were identified using standard microbiological techniques and serotyping was performed using commercially available antisera.

A software tool to aid long-term care budget planning at local authority level.

Objective: Local authorities face real challenges when it comes to annual budget planning for funding the system of long-term care. Uncertainty about the long-term cost of caring for current residents in the system, in addition to unknown future admissions, have made the tasks of local authority budget managers very complex and demanding. In this paper, we present a software implementation of a novel forecasting framework developed by the authors to provide useful information to local authority budget planners involved in long-term care.

A software tool to aid budget planning for long-term care at local authority level.

In this paper, we present a software tool that implements a novel modelling framework developed by the authors to provide useful information to budget planners for long-term care at local authority level. By combining unit costs of care with an underlying survival model for publicly funded residents in long-term care, the software tool is able to provide forecasts on the cost of maintaining the group of elderly who are currently in long-term care (referred to as known commitments) for a period of time. User interacts with the tool via a friendly graphical interface that guides them through a set of screens of options in a familiar wizard fashion.

Involving older people in research: methodological issues.

The policy imperative to increase public participation in health and social care research, planning and service delivery raises significant questions about optimum approaches, methods and the extent to which this policy can influence change in practice. This paper highlights the key policy literature on user involvement and participatory research methods to establish the context for a partnership research project exploring perceptions of risk in relation to falls from the perspectives of older people, carers, and health and social care professionals. The paper reports the methods used in developing user involvement in the research at a number of levels, including project management, and a consumer panel working alongside the research team and influencing the dissemination in local falls prevention strategies.

A comparison of two methods of assessing orthodontic treatment need in the mixed dentition: DAI and IOTN.

This paper assesses the unmet orthodontic treatment need in a random sample of 10-year-old schoolchildren, using two indices: the Dental Aesthetic Index (DAI) and the Index of Orthodontic Treatment Need (IOTN). The DAI scores were adjusted by omitting the missing teeth component of the index because many children were in the mixed dentition with unerupted permanent teeth. Although both indices assessed the same number of children with malocclusions requiring orthodontic treatment, not all were ranked similarly by each index.

A longitudinal study of orthodontic treatment need in Dunedin schoolchildren.

The Index of Orthodontic Treatment Need (IOTN) was used to assess unmet orthodontic treatment need in 152 13-year-old Dunedin schoolchildren, and to compare the findings with those obtained in the same children 3 years previously. The children were randomly selected from Dunedin schools as 10-year-olds, and had not received orthodontic treatment. Approximately 86 percent of the 13-year-old children had "No-little" need for orthodontic treatment when assessed by the child-assessed Aesthetic Component (AC) and the examiner-assessed AC.

Orthodontic treatment need in 10-year-old Dunedin schoolchildren.

The prevalence of unmet orthodontic treatment need was assessed in a random sample of 294 10-year-old Dunedin schoolchildren using the Index of Orthodontic Treatment Need. Approximately one-third of the children from this mainly mixed-dentition sample were assessed as having a need for orthodontic treatment. No children needed orthodontic treatment on the basis of the Aesthetic Component alone, but slightly more than a quarter did on the basis of the Dental Health Component alone.

Cytotoxicity of 5-aza-2'-deoxycytidine in a mammalian cell system.

After the addition of 5-aza-2'-deoxycytidine, a potent inhibitor of DNA methylation and S-phase-specific cytotoxic agent, metaphase chromosomes of Chinese hamster ovary (CHO) cells exhibited a highly decondensed and extended morphology (numerous "fragile sites") at the first mitotic division. However, when a lethal dose of this drug was added in early G1 phase to cells synchronised by mitotic selection, the majority subsequently divided at the same time as an untreated control cell population with few division abnormalities and with few of the more usual types of chromosome aberrations such as gaps, breaks and exchanges. The drug-treated cells also entered and completed the second S-phase without significant delay and it was only at the second mitosis after addition of 5-azadeoxycytidine that cells showed delays in entering mitosis and significant increases in abnormal divisions concomitant with a modest increase in chromosome aberrations.

A sizing artifact of DNA restriction fragments with unusually long single-stranded termini.

The restriction endonucleases (ENases) BstNI (CCATGG) and EcoRII (CCATGG) both cleave DNA at the same time sequences, but only EcoRII produces 5-nucleotide (nt) cohesive ends and is inhibited by 5-methylation of the inner cytosine. The low-Mr fragments in digests of mouse DNA made with these two ENases exhibit different mobilities during agarose-gel electrophoresis. The difference in the mobilities of the BstNI and EcoRII fragments from mouse DNA was not due to closely spaced, differentially methylated sites, or to alternate mechanisms such as circularization of the long cohesive ends of the EcoRII fragments, or to residual bound protein.

Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains.

Efficient recovery of clones from the 5' end of the human L1 dispersed repetitive elements necessitates the use of deletion mcr- host strains since this region contains a CpG island which is hypermethylated in vivo. Clones recovered with conventional mcr+ hosts seem to have been derived preferentially from L1 members which have accumulated mutations that have removed sites of methylation. We present a revised consensus from the 5' presumptive control region of these elements.

Effects of mcr restriction of methylated CpG islands of the L1 transposons during packaging and plating stages of mammalian genomic library construction.

The use of optimally methylation-tolerant mcrA- mcrB- strains has been shown to produce an over tenfold increase in the plating efficiencies of mammalian genomic libraries, compared to a superior conventional phage host strain LE392 which is mcrB+. However, there is an even more significant effect of mcr restriction. Amongst the recombinants recovered with an mcrB+ host, we have found that there is an additional 30-fold reduction in the frequencies of clones containing the heavily methylated 5'-CpG island sequences of both the human and rat L1 repetitive elements.

Reversal of the multidrug resistance phenotype with cremophor EL, a common vehicle for water-insoluble vitamins and drugs.

A polyethoxylated castor oil, Cremophor EL, which is used as a vehicle for p.o. and i.

The effect of E. coli host strain on the consensus sequence of regions of the human L1 transposon.

We have used highly methylation tolerant host strains to clone hyper- and hypo-methylated genomic elements from different regions of the same family of long interspersed repetitive elements from human DNA, specifically the 1.8 kilobase (kb) and 1.2kb KpnI fragments from members of the L1 family of transposable elements in which respectively some 18% and 2.

Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants.

Many strains of E. coli K12 restrict DNA containing cytosine methylation such as that present in plant and animal genomes. Such restriction can severely inhibit the efficiency of cloning genomic DNAs.