Developments in CLARA accelerator design and simulations

We present recent developments in the accelerator design of CLARA (Compact Linear Accelerator for Research and Applications), the proposed UK FEL test facility at Daresbury Laboratory. Updates on the electron beam simulations and code comparisons including wakefields are described. Simulations of the effects of geometric wakefields in the small-aperture FEL undulator are shown, as well as further simulations on potential FEL experiments using chirped beams. We also present the results of simulations on post-FEL diagnostics

The effect of nutrient limitation on bacterial wax ester production

Nutrient limitation is widely employed to alter the behaviour of micro-organisms. Here, the impact of nitrogen and, for the first time, phosphate limitation is investigated on the production of bacterial storage lipids; specifically wax esters, a class of storage lipids of industrial interest, by the bacterium Acinetobacter baylyi ADP1 grown on the low-cost substrate acetate. Studies determined the absolute and temporal effects of nutrient limitation and identified a maximum wax titre of 132 mg/L and content of 17 % of biomass. A 4-fold increase in wax production was achievable by manipulating carbon: phosphate ratio. Multivariable analysis identified a novel interaction effect between carbon: nitrogen and carbon: phosphate ratios on wax production. Extreme phosphate starvation shifted the dominant lipid class from wax esters to triacylglycerols, the first report of the potential of phosphate limitation to alter the type of lipid generated. These findings offer valuable insights for future microbial bioproduction studies

Sarcasm in written communication: emoticons are efficient markers of intention

Here we present two studies that investigate the use of emoticons in clarifying message intent. We look at sarcasm in particular, which can be especially hard to interpret correctly in written communication. In both studies, participants were required to make the intentions of their messages clear. In the first, they clarified the meaning of existing sentences without altering the wording; in the second, they produced their own sentences. Results provided clear evidence that tongue and wink emoticons are the principal indicators of sarcastic intent, and that ellipsis is associated more with criticism, rather than with sarcasm. These findings highlight the significant role emoticons play in clarifying message intention, compensating for the absence of non-verbal cues in written communicatio

Construct-level predictive validity of educational attainment and intellectual aptitude tests in medical student selection: meta-regression of six UK longitudinal studies

Background: Measures used for medical student selection should predict future performance during training. A problem for any selection study is that predictor-outcome correlations are known only in those who have been selected, whereas selectors need to know how measures would predict in the entire pool of applicants. That problem of interpretation can be solved by calculating construct-level predictive validity, an estimate of true predictor-outcome correlation across the range of applicant abilities. Methods: Construct-level predictive validities were calculated in six cohort studies of medical student selection and training (student entry, 1972 to 2009) for a range of predictors, including A-levels, General Certificates of Secondary Education (GCSEs)/O-levels, and aptitude tests (AH5 and UK Clinical Aptitude Test (UKCAT)). Outcomes included undergraduate basic medical science and finals assessments, as well as postgraduate measures of Membership of the Royal Colleges of Physicians of the United Kingdom (MRCP(UK)) performance and entry in the Specialist Register. Construct-level predictive validity was calculated with the method of Hunter, Schmidt and Le (2006), adapted to correct for right-censorship of examination results due to grade inflation. Results: Meta-regression analyzed 57 separate predictor-outcome correlations (POCs) and construct-level predictive validities (CLPVs). Mean CLPVs are substantially higher (.450) than mean POCs (.171). Mean CLPVs for first-year examinations, were high for A-levels (.809; CI: .501 to .935), and lower for GCSEs/O-levels (.332; CI: .024 to .583) and UKCAT (mean = .245; CI: .207 to .276). A-levels had higher CLPVs for all undergraduate and postgraduate assessments than did GCSEs/O-levels and intellectual aptitude tests. CLPVs of educational attainment measures decline somewhat during training, but continue to predict postgraduate performance. Intellectual aptitude tests have lower CLPVs than A-levels or GCSEs/O-levels. Conclusions: Educational attainment has strong CLPVs for undergraduate and postgraduate performance, accounting for perhaps 65% of true variance in first year performance. Such CLPVs justify the use of educational attainment measure in selection, but also raise a key theoretical question concerning the remaining 35% of variance (and measurement error, range restriction and right-censorship have been taken into account). Just as in astrophysics, ‘dark matter’ and ‘dark energy’ are posited to balance various theoretical equations, so medical student selection must also have its ‘dark variance’, whose nature is not yet properly characterized, but explains a third of the variation in performance during training. Some variance probably relates to factors which are unpredictable at selection, such as illness or other life events, but some is probably also associated with factors such as personality, motivation or study skills

Conservative management for postprostatectomy urinary incontinence

BACKGROUND: Urinary incontinence is common after radical prostatectomy and can also occur in some circumstances after transurethral resection of the prostate (TURP). Conservative management includes pelvic floor muscle training with or without biofeedback, electrical stimulation, extra-corporeal magnetic innervation (ExMI), compression devices (penile clamps), lifestyle changes, or a combination of methods.   OBJECTIVES: To determine the effectiveness of conservative management for urinary incontinence up to 12 months after transurethral, suprapubic, laparoscopic, radical retropubic or perineal prostatectomy, including any single conservative therapy or any combination of conservative therapies.  SEARCH METHODS: We searched the Cochrane Incontinence Group Specialised Register (5 February 2014), CENTRAL (2014, Issue 1), EMBASE (January 2010 to Week 3 2014), CINAHL (January 1982 to 18 January 2014), ClinicalTrials.gov and World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (both searched 29 January 2014), and the reference lists of relevant articles.  SELECTION CRITERIA: Randomised or quasi-randomised controlled trials evaluating conservative interventions for urinary continence in men after prostatectomy.  DATA COLLECTION AND ANALYSIS: Two or more review authors assessed the methodological quality of the trials and abstracted data. We tried to contact several authors of included studies to obtain extra information.  MAIN RESULTS: Fifty trials met the inclusion criteria, 45 in men after radical prostatectomy, four trials after TURP and one trial after either operation. The trials included 4717 men of whom 2736 had an active conservative intervention. There was considerable variation in the interventions, populations and outcome measures. Data were not available for many of the pre-stated outcomes. Men's symptoms improved over time irrespective of management.There was no evidence from eight trials that pelvic floor muscle training with or without biofeedback was better than control for men who had urinary incontinence up to 12 months after radical prostatectomy; the quality of the evidence was judged to be moderate (for example 57% with urinary incontinence in the intervention group versus 62% in the control group, risk ratio (RR) for incontinence after 12 months 0.85, 95% confidence interval (CI) 0.60 to 1.22). One large multi-centre trial of one-to-one therapy showed no difference in any urinary or quality of life outcome measures and had narrow CIs. It seems unlikely that men benefit from one-to-one PFMT therapy after TURP. Individual small trials provided data to suggest that electrical stimulation, external magnetic innervation, or combinations of treatments might be beneficial but the evidence was limited. Amongst trials of conservative treatment for all men after radical prostatectomy, aimed at both treatment and prevention, there was moderate evidence of an overall benefit from pelvic floor muscle training versus control management in terms of reduction of urinary incontinence (for example 10% with urinary incontinence after one year in the intervention groups versus 32% in the control groups, RR for urinary incontinence 0.32, 95% CI 0.20 to 0.51). However, this finding was not supported by other data from pad tests. The findings should be treated with caution because the risk of bias assessment showed methodological limitations. Men in one trial were more satisfied with one type of external compression device, which had the lowest urine loss, compared to two others or no treatment. The effect of other conservative interventions such as lifestyle changes remained undetermined as no trials involving these interventions were identified.  AUTHORS' CONCLUSIONS: The value of the various approaches to conservative management of postprostatectomy incontinence after radical prostatectomy remains uncertain. The evidence is conflicting and therefore rigorous, adequately powered randomised controlled trials (RCTs) which abide by the principles and recommendations of the CONSORT statement are still needed to obtain a definitive answer. The trials should be robustly designed to answer specific well constructed research questions and include outcomes which are important from the patient's perspective in decision making and are also relevant to the healthcare professionals. Long-term incontinence may be managed by an external penile clamp, but there are safety problems

Anaerobic co-digestion of Euphorbia tirucalli with pig blood for volatile fatty acid production

Acidogenic fermentation of biomass to produce volatile fatty acids provides a renewable pathway to industrial chemicals ordinarily derived from petrochemicals. Crassulacean acid metabolism plants such as Euphorbia tirucalli are cultivable on marginal land and offer promising feedstocks for this purpose. This study investigated how the refining of E. tirucalli biomass to fatty acids could be augmented with a high-protein co-substrate, pig blood. Blood mono-digestions provided the highest titres of total fatty acid (up to 38 ± 2 g/L), while at high substrate concentrations, acetic acid was maximal in co-digestions. 75 % blood with 25 % E. tirucalli produced acetic acid titres 40.8 % (p < 0.001) and 30.8 % (p = 0.001) higher than those in mono-digestions of E. tirucalli and blood, respectively. Where acetate is the desired product, inclusion of blood as a co-substrate offers significant benefit for Euphorbia biorefining

Observing a column-dependent zeta in dense interstellar sources: the case of the Horsehead Nebula

Context: Observations of small carbon-bearing molecules such as CCH, C4H, c-C3H2, and HCO in the Horsehead Nebula have shown these species to have higher abundances towards the edge of the source than towards the center. Aims: Given the determination of a wide range of values for zeta (s-1), the total ionization rate of hydrogen atoms, and the proposal of a column-dependent zeta(N_H), where N_H is the total column of hydrogen nuclei, we desire to determine if the effects of zeta(N_H) in a single object with spatial variation can be observable. We chose the Horsehead Nebula because of its geometry and high density. Method: We model the Horsehead Nebula as a near edge-on photon dominated region (PDR), using several choices for zeta, both constant and as a function of column. The column-dependent zeta functions are determined by a Monte Carlo model of cosmic ray penetration, using a steep power-law spectrum and accounting for ionization and magnetic field effects. We consider a case with low-metal elemental abundances as well as a sulfur-rich case. Results: We show that use of a column-dependent zeta(N_H) of 5(-15) s-1 at the surface and 7.5(-16) s-1 at Av = 10 on balance improves agreement between measured and theoretical molecular abundances, compared with constant values of zeta.Comment: 12 pages, 6 figures, 5 tables, accepted in A&

Evaluation of the current knowledge limitations in breast cancer research: a gap analysis

BACKGROUND A gap analysis was conducted to determine which areas of breast cancer research, if targeted by researchers and funding bodies, could produce the greatest impact on patients. METHODS Fifty-six Breast Cancer Campaign grant holders and prominent UK breast cancer researchers participated in a gap analysis of current breast cancer research. Before, during and following the meeting, groups in seven key research areas participated in cycles of presentation, literature review and discussion. Summary papers were prepared by each group and collated into this position paper highlighting the research gaps, with recommendations for action. RESULTS Gaps were identified in all seven themes. General barriers to progress were lack of financial and practical resources, and poor collaboration between disciplines. Critical gaps in each theme included: (1) genetics (knowledge of genetic changes, their effects and interactions); (2) initiation of breast cancer (how developmental signalling pathways cause ductal elongation and branching at the cellular level and influence stem cell dynamics, and how their disruption initiates tumour formation); (3) progression of breast cancer (deciphering the intracellular and extracellular regulators of early progression, tumour growth, angiogenesis and metastasis); (4) therapies and targets (understanding who develops advanced disease); (5) disease markers (incorporating intelligent trial design into all studies to ensure new treatments are tested in patient groups stratified using biomarkers); (6) prevention (strategies to prevent oestrogen-receptor negative tumours and the long-term effects of chemoprevention for oestrogen-receptor positive tumours); (7) psychosocial aspects of cancer (the use of appropriate psychosocial interventions, and the personal impact of all stages of the disease among patients from a range of ethnic and demographic backgrounds). CONCLUSION Through recommendations to address these gaps with future research, the long-term benefits to patients will include: better estimation of risk in families with breast cancer and strategies to reduce risk; better prediction of drug response and patient prognosis; improved tailoring of treatments to patient subgroups and development of new therapeutic approaches; earlier initiation of treatment; more effective use of resources for screening populations; and an enhanced experience for people with or at risk of breast cancer and their families. The challenge to funding bodies and researchers in all disciplines is to focus on these gaps and to drive advances in knowledge into improvements in patient care

Conjugated docosahexaenoic acid suppresses KPL-1 human breast cancer cell growth in vitro and in vivo: potential mechanisms of action

Introduction The present study was conducted to examine the effect of conjugated docosahexaenoic acid (CDHA) on cell growth, cell cycle progression, mode of cell death, and expression of cell cycle regulatory and/or apoptosis-related proteins in KPL-1 human breast cancer cell line. This effect of CDHA was compared with that of docosahexaenoic acid (DHA). Methods KPL-1 cell growth was assessed by colorimetric 3- (4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay; cell cycle progression and mode of cell death were examined by flow cytometry; and levels of expression of p53, p21Cip1/Waf1, cyclin D1, Bax, and Bcl-2 proteins were examined by Western blotting analysis. In vivo tumor growth was examined by injecting KPL-1 cells subcutaneously into the area of the right thoracic mammary fat pad of female athymic mice fed a CDHA diet. Results CDHA inhibited KPL-1 cells more effectively than did DHA (50% inhibitory concentration for 72 hours: 97 μmol/l and 270 μmol/l, respectively). With both CDHA and DHA growth inhibition was due to apoptosis, as indicated by the appearance of a sub-G1 fraction. The apoptosis cascade involved downregulation of Bcl-2 protein; Bax expression was unchanged. Cell cycle progression was due to G0/G1 arrest, which involved increased expression of p53 and p21Cip1/Waf1, and decreased expression of cyclin D1. CDHA modulated cell cycle regulatory proteins and apoptosis-related proteins in a manner similar to that of parent DHA. In the athymic mouse system 1.0% dietary CDHA, but not 0.2%, significantly suppressed growth of KPL-1 tumor cells; CDHA tended to decrease regional lymph node metastasis in a dose dependent manner. Conclusion CDHA inhibited growth of KPL-1 human breast cancer cells in vitro more effectively than did DHA. The mechanisms of action involved modulation of apoptosis cascade and cell cycle progression. Dietary CDHA at 1.0% suppressed KPL-1 cell growth in the athymic mouse system.</p

Using hyperosmolar stress to measure biologic and stress-activated protein kinase responses in preimplantation embryos

We used hyperosmolar stress to test blastocysts for their biologic and enzymatic responses to culture stress. Embryos mount dose- and time-dependent responses to hyperosmolar stress. Biological responses included slowed cavitation and cell accumulation and increased apoptosis at increasing doses. These responses were preceded by stress-activated protein kinase (SAPK) phosphorylation and nuclear translocation consistent with its causal role. For cavitation and new cell cycle initiation, 200 mM sorbitol caused stasis. Above 200 mM, sorbitol was ultimately lethal and below 200 mM, its embryos had milder effects. Phosphorylated SAPK was induced rapidly in embryos at 0.5 h in a dose-dependent manner from 0 to 600 mM sorbitol. Higher hyperosmolarity caused a biphasic peak of phosphorylated SAPK, but there was no return to baseline through 3 h. At 24 h, a dose-dependent response persisted that was linear from 0 to 200 mM sorbitol. Hyperosmolar stress rapidly induced, within 0.5 h, phosphorylated, nuclear c-Jun and decreased phosphorylated, nuclear c-Myc in a SAPK-dependent manner. The data suggest that SAPK is induced and functions on down-stream effector molecules in a temporal and quantitative manner consistent with its function in the embryonic homeostatic response to stress. The remarkable resistance of embryos to high concentrations of sorbitol suggests that part of its homeostatic response is different from that of somatic cells