On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles

Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian cancers profiled by microarray (p<0.01). We also identified 12 miRNAs that are associated with survival when miRNAs were profiled in the same specimens using Next Generation Sequencing (miRNA-Seq) (p<0.01). Surprisingly, only 1 miRNA transcript is associated with ovarian cancer survival in both datasets. Our analyses indicate that this discrepancy is due to the fact that miRNA levels reported by the two platforms correlate poorly, even after correcting for potential issues inherent to signal detection algorithms. Further investigation is warranted

The azimuthal component of Poynting's vector and the angular momentum of light

The usual description in basic electromagnetic theory of the linear and angular momenta of light is centred upon the identification of Poynting's vector as the linear momentum density and its cross product with position, or azimuthal component, as the angular momentum density. This seemingly reasonable approach brings with it peculiarities, however, in particular with regards to the separation of angular momentum into orbital and spin contributions, which has sometimes been regarded as contrived. In the present paper, we observe that densities are not unique, which leads us to ask whether the usual description is, in fact, the most natural choice. To answer this, we adopt a fundamental rather than heuristic approach by first identifying appropriate symmetries of Maxwell's equations and subsequently applying Noether's theorem to obtain associated conservation laws. We do not arrive at the usual description. Rather, an equally acceptable one in which the relationship between linear and angular momenta is nevertheless more subtle and in which orbital and spin contributions emerge separately and with transparent forms

Recent results in the decoding of Algebraic geometry codes

Objectives: The aim of this study was to examine the relationships between perceived teacher autonomy support versus control and students’ life skills development in PE, and whether students’ basic need satisfaction and frustration mediated these relationships. Design: Cross-sectional study. Method: English and Irish students (N = 407, Mage = 13.71, SD = 1.23) completed measures assessing perceived autonomy-supportive and controlling teaching, basic need satisfaction and frustration (autonomy, competence, and relatedness), and life skills development in PE (teamwork, goal setting, social skills, problem solving and decision making, emotional skills, leadership, time management, and interpersonal communication). Results: On the bright side of Self-Determination Theory (SDT), correlations revealed that perceived teacher autonomy support was positively associated with students’ basic need satisfaction and life skills development in PE. On the dark side of SDT, perceived controlling teaching was positively related to students’ basic need frustration, but not significantly related to their life skills development. Mediational analyses revealed that autonomy and relatedness satisfaction mediated the relationships between perceived teacher autonomy support and students’ development of all eight life skills. Competence satisfaction mediated the relationships between perceived teacher autonomy support and students’ development of teamwork, goal setting, and leadership skills. Conclusions: Our findings indicate that satisfaction of the needs for autonomy, competence, and relatedness are important mechanisms that in part explain the relationships between perceived teacher autonomy support and life skills development in PE. Therefore, teachers may look to promote students’ perceptions of an autonomy-supportive climate that satisfies their three basic needs and helps to develop their life skills

"Live” (stained) benthic foraminiferal living depths, stable isotopes, and taxonomy offshore South Georgia, Southern Ocean: implications for calcification depths

It is widely held that benthic foraminifera exhibit species-specific calcification depth preferences, with their tests recording sediment pore water chemistry at that depth (i.e. stable isotope and trace metal compositions). This assumed depth habitat-specific pore water chemistry relationship has been used to reconstruct various palaeoenvironmental parameters, such as bottom water oxygenation. However, many deep-water foraminiferal studies show wide intra-species variation in sediment living depth but relatively narrow intra-species variation in stable isotope composition. To investigate this depth habitat- stable isotope relationship on the shelf we analysed depth distribution and stable isotopes of “living” (Rose Bengal stained) benthic foraminifera from two box cores collected on the South Georgia shelf (ranging from 250–300 m water depth). We provide a comprehensive taxonomic analysis of the benthic fauna, comprising 79 taxonomic groupings. The fauna shows close affinities with shelf assemblages from around Antarctica. We find “live” specimens of a number calcareous species from a range of depths in the sediment column. Stable isotope ratios (δ13C and δ18O) were measured on stained specimens of three species, Astrononion echolsi, Cassidulinoides porrectus and Buccella sp. 1, at 1 cm depth intervals within the down-core sediment sequences. In agreement with studies in deep water settings, we find no significant intraspecies variability in either δ13C foram or δ18O foram with sediment living depth on the South Georgia shelf. Our findings add to the growing evidence that infaunal benthic foraminiferal species calcify at a fixed depth. Given the wide range of depths that we find “living” ‘infaunal’ species, we speculate that they may actually calcify predominantly at the sediment-seawater interface, where carbonate ion concentration and organic carbon availability is at a maximum

Development and Pilot Test of the Workplace Readiness Questionnaire, a Theory-Based Instrument to Measure Small Workplaces’ Readiness to Implement Wellness Programs

To develop a theory-based questionnaire to assess readiness for change in small workplaces adopting wellness programs

Herpes Simplex Virus-1 Infection in Human Primary Corneal Epithelial Cells is Blocked by a Stapled Peptide that Targets Processive DNA Synthesis

Purpose: Acyclovir is most commonly used for treating ocular Herpes Keratitis, a leading cause of infectious blindness. However, emerging resistance to Acyclovir resulting from mutations in the thymidine kinase gene of Herpes Simplex Virus −1 (HSV-1), has prompted the need for new therapeutics directed against a different viral protein. One novel target is the HSV-1 Processivity Factor which is essential for tethering HSV-1 Polymerase to the viral genome to enable long-chain DNA synthesis. Methods: A series of peptides, based on the crystal structure of the C-terminus of HSV-1 Polymerase, were constructed with hydrocarbon staples to retain their alpha-helical conformation. The stapled peptides were tested for blocking both HSV-1 DNA synthesis and infection. The most effective peptide was further optimized by replacing its negative N-terminus with two hydrophobic valine residues. This di-valine stapled peptide was tested for inhibiting HSV-1 infection of human primary corneal epithelial cells. Results: The stapled peptides blocked HSV-1 DNA synthesis and HSV-1 infection. The unstapled control peptide had no inhibitory effects. Specificity of the stapled peptides was confirmed by their inabilities to block infection by an unrelated virus. Significantly, the optimized di-valine stapled peptide effectively blocked HSV-1 infection in human primary corneal epithelial cells with selectivity index of 11.6. Conclusions: Hydrocarbon stapled peptides that simulate the α-helix from the C-terminus of HSV-1 DNA polymerase can specifically block DNA synthesis and infection of HSV-1 in human primary corneal epithelial cells. These stapled peptides provide a foundation for developing a topical therapeutic for treating human ocular Herpes Keratitis. © 202

Non‐invasive measurement of retinal permeability in a diabetic rat model

Objective: The gold standard for measuring blood-retinal barrier permeability is the Evans blue assay. However, this technique has limitations in vivo, including non-specific tissue binding and toxicity. This study describes a non-toxic, high throughput and cost effective alternative technique that minimizes animal usage. Methods: Sodium fluorescein fundus angiography was performed in non- and diabetic Brown Norway rats on days 0, 7, 14, 21 and 28. Sodium fluorescein intensity in the retinal interstitium and a main retinal vessel were measured over time. The intensity gradients were used to quantify retinal vascular permeability. Post study eyes were fixed, dissected and stained (isolectin B4) to measure required parameters for permeability quantification including: Total vessel length per retinal volume, radius and thickness. Results: In the non-diabetic cohort retinal permeability remained constant over the 28-day study period. However, in the diabetic cohort there was a significant and progressive increase in retinal permeability from day 14 to 28 (p [less than] 0.01, p [less than] 0.001, p [less than] 0.0001). Conclusions: This novel imaging methodology in combination with mathematical quantification allows retinal permeability to be non-invasively and accurately measured at multiple time points in the same animal. In addition, this technique is a non-toxic, rapid, sensitive and cost-effective alternative to the Evans blue assay

A pragmatic cluster randomised trial evaluating three implementation interventions

Background Implementation research is concerned with bridging the gap between evidence and practice through the study of methods to promote the uptake of research into routine practice. Good quality evidence has been summarised into guideline recommendations to show that peri-operative fasting times could be considerably shorter than patients currently experience. The objective of this trial was to evaluate the effectiveness of three strategies for the implementation of recommendations about peri-operative fasting. Methods A pragmatic cluster randomised trial underpinned by the PARIHS framework was conducted during 2006 to 2009 with a national sample of UK hospitals using time series with mixed methods process evaluation and cost analysis. Hospitals were randomised to one of three interventions: standard dissemination (SD) of a guideline package, SD plus a web-based resource championed by an opinion leader, and SD plus plan-do-study-act (PDSA). The primary outcome was duration of fluid fast prior to induction of anaesthesia. Secondary outcomes included duration of food fast, patients' experiences, and stakeholders' experiences of implementation, including influences. ANOVA was used to test differences over time and interventions. Results Nineteen acute NHS hospitals participated. Across timepoints, 3,505 duration of fasting observations were recorded. No significant effect of the interventions was observed for either fluid or food fasting times. The effect size was 0.33 for the web-based intervention compared to SD alone for the change in fluid fasting and was 0.12 for PDSA compared to SD alone. The process evaluation showed different types of impact, including changes to practices, policies, and attitudes. A rich picture of the implementation challenges emerged, including inter-professional tensions and a lack of clarity for decision-making authority and responsibility. Conclusions This was a large, complex study and one of the first national randomised controlled trials conducted within acute care in implementation research. The evidence base for fasting practice was accepted by those participating in this study and the messages from it simple; however, implementation and practical challenges influenced the interventions' impact. A set of conditions for implementation emerges from the findings of this study, which are presented as theoretically transferable propositions that have international relevance. Trial registration ISRCTN18046709 - Peri-operative Implementation Study Evaluation (POISE

Learning to prescribe - pharmacists' experiences of supplementary prescribing training in England

Background: The introduction of non-medical prescribing for professions such as pharmacy and nursing in recent years offers additional responsibilities and opportunities but attendant training issues. In the UK and in contrast to some international models, becoming a non-medical prescriber involves the completion of an accredited training course offered by many higher education institutions, where the skills and knowledge necessary for prescribing are learnt. Aims: to explore pharmacists' perceptions and experiences of learning to prescribe on supplementary prescribing (SP) courses, particularly in relation to inter-professional learning, course content and subsequent use of prescribing in practice. Methods: A postal questionnaire survey was sent to all 808 SP registered pharmacists in England in April 2007, exploring demographic, training, prescribing, safety culture and general perceptions of SP. Results: After one follow-up, 411 (51%) of pharmacists responded. 82% agreed SP training was useful, 58% agreed courses provided appropriate knowledge and 62% agreed that the necessary prescribing skills were gained. Clinical examination, consultation skills training and practical experience with doctors were valued highly; pharmacology training and some aspects of course delivery were criticised. Mixed views on inter-professional learning were reported – insights into other professions being valued but knowledge and skills differences considered problematic. 67% believed SP and recent independent prescribing (IP) should be taught together, with more diagnostic training wanted; few pharmacists trained in IP, but many were training or intending to train. There was no association between pharmacists' attitudes towards prescribing training and when they undertook training between 2004 and 2007 but earlier cohorts were more likely to be using supplementary prescribing in practice. Conclusion: Pharmacists appeared to value their SP training and suggested improvements that could inform future courses. The benefits of inter-professional learning, however, may conflict with providing professionspecific training. SP training may be perceived to be an instrumental 'stepping stone' in pharmacists' professional project of gaining full IP status