Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.

The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment.Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome.These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies

Discovery-led refinement in e-discovery investigations: sensemaking, cognitive ergonomics and system design.

Given the very large numbers of documents involved in e-discovery investigations, lawyers face a considerable challenge of collaborative sensemaking. We report findings from three workplace studies which looked at different aspects of how this challenge was met. From a sociotechnical perspective, the studies aimed to understand how investigators collectively and individually worked with information to support sensemaking and decision making. Here, we focus on discovery-led refinement; specifically, how engaging with the materials of the investigations led to discoveries that supported refinement of the problems and new strategies for addressing them. These refinements were essential for tractability. We begin with observations which show how new lines of enquiry were recursively embedded. We then analyse the conceptual structure of a line of enquiry and consider how reflecting this in e-discovery support systems might support scalability and group collaboration. We then focus on the individual activity of manual document review where refinement corresponded with the inductive identification of classes of irrelevant and relevant documents within a collection. Our observations point to the effects of priming on dealing with these efficiently and to issues of cognitive ergonomics at the human–computer interface. We use these observations to introduce visualisations that might enable reviewers to deal with such refinements more efficiently

A Qualitative Evaluation of an NHS Weight Management Programme for Obese Patients in Liverpool

Purpose – The increasing prevalence of obesity in the UK has been of concern for some time. This is particularly true in Liverpool and in response the Liverpool Weight Management Programme (LWMP) was devised. It offers a service involving dietitians and other expert agencies working towards facilitating dietary and lifestyle changes in obese NHS patients in Liverpool via a 12-week education programme. This qualitative study aims to investigate patients' experiences of the LWMP. Design/methodology/approach – Informed volunteers participated in focus groups exploring their experiences following the programme. Focus groups were audio recorded and transcribed verbatim, then analysed following a thematic approach utilising constant comparison analysis to allow a qualitative view of the LWMP to be formed. Findings – Participants described an increase in immediate self-confidence during the LWMP, as opposed to coercion and pressure experienced elsewhere. The results also show the implementation of dietary changes by participants and favourable opinions towards both the group settings and patient-centred care. Participants also positively described the LWMP regarding the programmes social approach and aspects of programme content; however, there were issues with over-dependence on healthcare professionals. Healthcare professionals also need to recognise that long-term empowerment may still be lacking and that follow-up support and the effectiveness of some areas of programme content need to be considered to ensure patients benefit from sustainable weight management. Originality/value – This paper addresses an identified need for qualitative research in the area of health service weight management programmes and highlights the importance of long-term support in empowering patients by exploring their lived experience of the LWMP

Period tracker applications: What menstrual cycle information are they giving women?

BACKGROUND: Period tracking applications (apps) allow women to track their menstrual cycles and receive a prediction for their period dates. The majority of apps also provide predictions of ovulation day and the fertile window. Research indicates apps are basing predictions on assuming women undergo a textbook 28-day cycle with ovulation occurring on day 14 and a fertile window between days 10 and 16. OBJECTIVE: To determine how the information period tracker apps give women on their period dates, ovulation day and fertile window compares to expected results from big data. METHODS: Five women's profiles for 6 menstrual cycles were created and entered into 10 apps. Cycle length and ovulation day for the sixth cycle were Woman 1-Constant 28 day cycle length, ovulation day 16; Woman 2-Average 23 day cycle length, ovulation day 13; Woman 3-Average 28 day cycle length, ovulation day 17; Woman 4-Average 33 day cycle length, ovulation day 20; and Woman 5-Irregular, average 31 day cycle length, ovulation day 14. RESULTS: The 10 period tracker apps examined gave conflicting information on period dates, ovulation day and the fertile window. For cycle length, the apps all predicted woman 1's cycles correctly but for women 2-5, the apps predicted 0 to 8 days shorter or longer than expected. For day of ovulation, for women 1-4, of the 36 predictions, 3 (8%) were exactly correct, 9 predicted 1 day too early (25%) and 67% of predictions were 2-9 days early. For woman 5, most of the apps predicted a later day of ovulation. CONCLUSION: Period tracker apps should ensure they only give women accurate information, especially for the day of ovulation and the fertile window which can only be predicted if using a marker of ovulation, such as basal body temperature, ovulation sticks or cervical mucus

Laser-driven acceleration of quasi-monoenergetic, near-collimated titanium ions via a transparency-enhanced acceleration scheme

Laser-driven ion acceleration has been an active research area in the past two decades with the prospects of designing novel and compact ion accelerators. Many potential applications in science and industry require high-quality, energetic ion beams with low divergence and narrow energy spread. Intense laser ion acceleration research strives to meet these challenges and may provide high charge state beams, with some successes for carbon and lighter ions. Here we demonstrate the generation of well collimated, quasi-monoenergetic titanium ions with energies ∼145 and 180 MeV in experiments using the high-contrast(<10-9) and high-intensity (6× 1020 W cm-2) Trident laser and ultra-Thin (∼100 nm) titanium foil targets. Numerical simulations show that the foils become transparent to the laser pulses, undergoing relativistically induced transparency (RIT), resulting in a two-stage acceleration process which lasts until ∼2 ps after the onset of RIT. Such long acceleration time in the self-generated electric fields in the expanding plasma enables the formation of the quasi-monoenergetic peaks. This work contributes to the better understanding of the acceleration of heavier ions in the RIT regime, towards the development of next generation laser-based ion accelerators for various applications