Leader sequence upstream of <i>patAB</i>.

<p>The graph represents the free energy of the most stable folded form of the 5′ region of the <i>patAB</i> transcript, as it extends from the promoter, in 4038 (black line) and 4039 (red line). The positions of the C1855761A polymorphism (PUS) distinguishing the two isolates and translation initiation site are indicated by the dashed lines, while the Shine-Dalgarno sequence is represented by the shaded region. The terminator-like hairpin structures formed by both transcripts as the RNA reaches the point at which the Shine-Dalgarno sequence is transcribed are displayed; it is evident that the mutation in 4039 is predicted to greatly weaken the hairpin loop of this secondary structure.</p

Differences in virulence of <i>S. pneumoniae</i> 4038 and 4039, clinical isolates in which the latter contains a SNP upregulating <i>patAB</i>.

<p>The results of three experiments are shown: (A) mice inoculated with 10² CFU intraperitoneally (n = 5), (B) mice inoculated with 10⁴ CFU intraperitoneally (n = 5) and (C) mice challenged with 10⁶ CFU intranasally (n = 5). For each, the displayed outcomes are: (i) survival curves, (ii) level of bacteraemia and (iii) counts of the two isolates in different organs. Significant differences between viable cell counts, calculated at a <i>p</i><0.05 level using a T test, are indicated by asterisks.</p

Distribution of accessory genome loci.

<p>(A) The non-prophage accessory genome loci, identified through comparison of genome assemblies, are displayed as blocks of alternating colours. The loci are coloured and grouped according to their functional annotation. All sequences are labelled with their position in a publicly available genome, or their ENA accession code; some have been trimmed to remove insertion sequences, to avoid read mapping artefacts. (B) The maximum likelihood phylogeny, as displayed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003868#pgen-1003868-g001" target="_blank">Figure 1</a>. (C) This panel is composed of one row per taxon, each representing the output of mapping the sequence reads from an individual sample against the accessory genome loci. This is displayed as a heatmap that is blue where there is no read mapping, indicating an absence of a locus, changing to red where there is read mapping indicating the locus is present (scaled to a maximum of 100 reads per million reads mapped).</p

Expression of the <i>patAB</i> locus.

<p>(A) Annotation of the <i>patAB</i> gene cluster, with the intervening IS element remnant on the opposite strand, and the upstream <i>mutS</i> gene. The position of the C1855761A polymorphism distinguishing <i>S. pneumoniae</i> 4038 and 4039 is indicated. (B) Graph showing Illumina read coverage, standardised as a plot of reads mapping per million reads mapped, from RNA-seq experiments. Each line shows the mean value from three replicates surrounded by a shaded area representing the minimum and maximum values. The red and orange lines represent transcription of the two strands of the genome in 4038, and the blue and green lines represent the transcription of the two strands of the genome in 4039.</p

Phylogenetic analysis of the clonal complex 180 isolates.

<p>(A) A simplified representation of the 2,036,867 bp genome of <i>S. pneumoniae</i> OXC141 with tick marks every 0.5 Mb. The loci encoding the proteinaceous antigens PspA and PspC, as well as the capsule biosynthesis locus, are labelled, as are the prophage φOXC141, a putative ICE-related sequence, the ∼22 kb bacteriocin island and Pneumococcal Pathogenicity Island 1 (PPI-1). (B) A maximum likelihood phylogeny of the serotype 3 isolates based on the vertically inherited substitutions not introduced through recombination events. The tree and taxa are coloured according to their geographical location. (C) The panel surrounded by the dotted line contains one row for each isolate in the tree, with a column for each base in the reference genome. Red blocks indicate recombination events reconstructed as occurring on an internal branch, hence are shared by more than one isolate through common descent, while blue blocks indicate recombinations unique to one particular isolate.</p

Effects of an interactive mHealth innovation for early detection of patient-reported symptom distress with focus on participatory care: protocol for a study based on prospective, randomised, controlled trials in patients with prostate and breast cancer

Abstract Background Cancer patients are predominantly treated as out-patients and as they often experience difficult symptoms and side effects it is important to facilitate and improve patient-clinician communication to support symptom management and self-care. Although the number of projects within supportive cancer care evaluating mobile health is increasing, few evidence-based interventions are described in the literature and thus there is a need for good quality clinical studies with a randomised design and sufficient power to guide future implementations. An interactive information and communications technology platform, including a smartphone/computer tablet app for reporting symptoms during cancer treatment was created in collaboration with a company specialising in health care management. The aim of this paper is to evaluate the effects of using the platform for patients with breast cancer during neo adjuvant chemotherapy treatment and patients with locally advanced prostate cancer during curative radiotherapy treatment. The main hypothesis is that the use of the platform will improve clinical management, reduce costs, and promote safe and participatory care. Method The study is a prospective, randomised, controlled trial for each patient group and it is based on repeated measurements. Patients are consecutively included and randomised. The intervention groups report symptoms via the app daily, during treatment and up to three weeks after end of treatment, as a complement to standard care. Patients in the control groups receive standard care alone. Outcomes targeted are symptom burden, quality of life, health literacy (capacity to understand and communicate health needs and promote healthy behaviours), disease progress and health care costs. Data will be collected before and after treatment by questionnaires, registers, medical records and biomarkers. Lastly, participants will be interviewed about participatory and meaningful care. Discussion Results will generate knowledge to enhance understanding about how to develop person-centred care using mobile technology. Supporting patients’ involvement in their care to identify problems early, promotes more timely initiation of necessary treatment. This can benefit patients treated outside the hospital setting in regard to maintaining their safety. Clinical trial registration June 12 2015 NCT02477137 (Prostate cancer) and June 12 2015 NCT02479607 (Breast cancer)