ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

Tracking performance with two breathing oxygen concentrations after high altitude rapid decompression

Current military aircraft Liquid Oxygen (LOX) systems supply 99.5 pct. gaseous Aviator's Breathing Oxygen (ABO) to aircrew. Newer Molecular Sieve Oxygen Generation Systems (MSOGS) supply breathing gas concentration of 93 to 95 pct. O2. The margin is compared of hypoxia protection afforded by ABO and MSOGS breathing gas after a 5 psi differential rapid decompression (RD) in a hypobaric research chamber. The barometric pressures equivalent to the altitudes of 46000, 52000, 56000, and 60000 ft were achieved from respective base altitudes in 1 to 1.5 s decompressions. During each exposure, subjects remained at the simulated peak altitude breathing either 100 or 94 pct. O2 with positive pressure for 60 s, followed by a rapid descent to 40000 ft. Subjects used the Tactical Life Support System (TLSS) for high altitude protection. Subcritical tracking task performance on the Performance Evaluation Device (PED) provided psychomotor test measures. Overall tracking task performance results showed no differences between the MSOGS breathing O2 concentration of 94 pct. and ABO. Significance RMS error differences were found between the ground level and base altitude trials compared to peak altitude trials. The high positive breathing pressures occurring at the peak altitudes explained the differences

The Use of a Book Club to Promote Biomedical Trainee Professional Development

Professional development for biomedical doctoral and postdoctoral trainees is vital, especially due to the increase in individuals pursuing non-faculty career paths. We created a professional development-focused discussion group between trainees and faculty/staff by utilizing a book club format in which monthly small group meetings occurred over an 8-month period. A pre- and post-survey consisting of Likert and free-response questions was completed by participants. Results demonstrated that after the book club, trainees: 1) were more knowledgeable about a variety of career paths; 2) had improved awareness of their interests in relation to their career; 3) were more knowledgeable of their transferrable skills; 4) were more comfortable engaging with their PI and completing/updating an Individual Development Plan; 5) were more likely to find mentors in addition to their PI to address career specific needs; and 6) were more likely to seek opportunities to conduct informational interviews or experiential learning. Additionally, we found that faculty/staff: 1) were more knowledgeable about careers outside of academia; 2) had greater consideration for their mentee\u27s values and interests in relation to their career; 3) had a better understanding of their mentee\u27s transferable skills; and 4) were more comfortable engaging with their mentee about their career path and addressing an Individual Development Plan. Overall, we found that the utilization of a book club consisting of trainees and faculty/staff as a professional development tool was beneficial for both groups of participants, and this format is feasible for use in biomedical education professional development

Kinetic and Spectroscopic Characterisation of Highly Reactive Methanesulfonates. Leaving Group Effects for Solvolyses and Comments on Geminal Electronic Effects Influencing SN_N1 Reactivity

Highly reactive methanesulfonates (mesylates, ROMs) have been prepared from 1-phenylethanol. cyclohex-2-en-1-ol, diphenylmethanol and p-methoxybenzyl alcohol by treatment with methanesulfonyl chloride and triethylamine in dichloro- or trichloro-methane at - 20 to 0 °C. The mesylates. characterised in solution by $^1$H and $^{13}$C NMR at -20 °C, were obtained in satisfactory purity (ca. 95%) in cold solutions but they decomposed by reaction with chloride, triethylamine or the parent alcohol. Rate constants for solvolyses in aqueous acetone and aqueous ethanol have been determined by a fast response conductimetric method. Product selectivities for solvolyses of pmethoxybenzyl mesylate in aqueous ethanol and methanol at 0 °C have been determined by HPLC. From additional new or Iiterature kinetic data for solvolyses of corresponding bromides. chlorides and p-nitrobenzoates (OPNB). Br/CI. OMs/Br and OMs/OPNB rate ratios were calculated; the results are consistent with electronic effects stabilising the carbocationic transition states and increasing OMs/Br rate ratios for these SN 1 solvolyses; none of the evidence supports a geminal electronic effect on Br/CI rate ratios (e.g. caused by stabilisation of the initial state in pmethoxybenzyl chloride). Steric effects on ester /halide rate ratios for solvolyses of tertiary substrates are confirmed. Relative rates over a 10$^{16}$ range for ester and halide leaving groups are evaluated for solvolyses of 1-phenylethyl substrates in 80% ethanol-water. updating previous work by Noyce et al. (1972)

Research and theory for nursing and midwifery: Rethinking the nature of evidence

Background and Rationale: The rise in the principles of evidence-based medicine in the 1990s heralded a re-emerging orthodoxy in research methodologies. The view of the randomised controlled trial (RCT) as a “gold standard” for evaluation of medical interventions has extended recently to evaluation of organisational forms and reforms and of change in complex systems—within health care and in other human services. Relatively little attention has been given to the epistemological assumptions underlying such a hierarchy of research evidence. Aims and Methods: Case studies from research in maternity care are used in this article to describe problems and limitations encountered in using RCTs to evaluate some recent policy-driven and consumer-oriented developments. These are discussed in relation to theory of knowledge and the epistemological assumptions, or paradigms, underpinning health services research. The aim in this discussion is not to advocate, or to reject, particular approaches to research but to advocate a more open and critical engagement with questions about the nature of evidence. Findings and Discussion: Experimental approaches are of considerable value in investigating deterministic and probabilistic cause and effect relationships, and in testing often well-established but unevaluated technologies. However, little attention has been paid to contextual and cultural factors in the effects of interventions, in the culturally constructed nature of research questions themselves, or of the data on which much research is based. More complex, and less linear, approaches to methodology are needed to address these issues. A simple hierarchical approach does not represent the complexity of evidence well and should move toward a more cyclical view of knowledge development

Gender and educational leadership in England: a comparison of secondary headteachers' views over time

In the context of gender being a barrier to accessing leadership, this paper presents a comparison of the views of men and women head teacher (principals) of secondary schools in England in the 1990s and in 2004. The same survey instrument was used on both occasions. The perceptions of the head teachers show change in some areas and no change in others. Overall, women are more likely to become head teachers and are now less likely to be categorised into pastoral roles, but in some cases women still meet prejudice from governors and others in the wider community. Women head teachers are more likely to have partners and children than in the 1990s, sharing equally or carrying most of the domestic responsibilities, whereas male colleagues are most likely to have partners who take the majority of responsibility in the home. Essentialist stereotypes about women and men as leaders still prevail, although both the women and men head teachers see themselves as adopting a traditionally ‘feminine’ style of leadership. Women head teachers are likely to see some benefits in being a woman in a role stereotypically associated with men. However, there has been an increase in the proportion of women who feel that they have to prove their worth as a leader, and this may be linked with increased levels of accountability in schools

Ocular and Extraocular Expression of Opsins in the Rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa)

A growing body of work on the neuroethology of cubozoans is based largely on the capabilities of the photoreceptive tissues, and it is important to determine the molecular basis of their light sensitivity. The cubozoans rely on 24 special purpose eyes to extract specific information from a complex visual scene to guide their behavior in the habitat. The lens eyes are the most studied photoreceptive structures, and the phototransduction in the photoreceptor cells is based on light sensitive opsin molecules. Opsins are photosensitive transmembrane proteins associated with photoreceptors in eyes, and the amino acid sequence of the opsins determines the spectral properties of the photoreceptors. Here we show that two distinct opsins (Tripedalia cystophora-lens eye expressed opsin and Tripedalia cystophora-neuropil expressed opsin, or Tc-leo and Tc-neo) are expressed in the Tripedalia cystophora rhopalium. Quantitative PCR determined the level of expression of the two opsins, and we found Tc-leo to have a higher amount of expression than Tc-neo. In situ hybridization located Tc-leo expression in the retinal photoreceptors of the lens eyes where the opsin is involved in image formation. Tc-neo is expressed in a confined part of the neuropil and is probably involved in extraocular light sensation, presumably in relation to diurnal activity

Early high flow nasal cannula therapy in bronchiolitis, a prospective randomised control trial (protocol): A Paediatric Acute Respiratory Intervention Study (PARIS)

Background Bronchiolitis imposes the largest health care burden on non-elective paediatric hospital admissions worldwide, with up to 15 % of cases requiring admission to intensive care. A number of previous studies have failed to show benefit of pharmaceutical treatment in respect to length of stay, reduction in PICU admission rates or intubation frequency. The early use of non-invasive respiratory support devices in less intensive scenarios to facilitate earlier respiratory support may have an impact on outcome by avoiding progression of the disease process. High Flow Nasal Cannula (HFNC) therapy has emerged as a new method to provide humidified air flow to deliver a non-invasive form of positive pressure support with titratable oxygen fraction. There is a lack of high-grade evidence on use of HFNC therapy in bronchiolitis. Methods/Design Prospective multi-centre randomised trial comparing standard treatment (standard subnasal oxygen) and High Flow Nasal Cannula therapy in infants with bronchiolitis admitted to 17 hospitals emergency departments and wards in Australia and New Zealand, including 12 non-tertiary regional/metropolitan and 5 tertiary centres. The primary outcome is treatment failure; defined as meeting three out of four pre-specified failure criteria requiring escalation of treatment or higher level of care; i) heart rate remains unchanged or increased compared to admission/enrolment observations, ii) respiratory rate remains unchanged or increased compared to admission/enrolment observations, iii) oxygen requirement in HFNC therapy arm exceeds FiO2 ≥ 40 % to maintain SpO2 ≥ 92 % (or ≥94 %) or oxygen requirement in standard subnasal oxygen therapy arm exceeds >2L/min to maintain SpO2 ≥ 92 % (or ≥94 %), and iv) hospital internal Early Warning Tool calls for medical review and escalation of care. Secondary outcomes include transfer to tertiary institution, admission to intensive care, length of stay, length of oxygen treatment, need for non-invasive/invasive ventilation, intubation, adverse events, and cost. Discussion This large multicenter randomised trial will allow the definitive assessment of the efficacy of HFNC therapy as compared to standard subnasal oxygen in the treatment of bronchiolitis

Sequential design of computer experiments for the estimation of a probability of failure

This paper deals with the problem of estimating the volume of the excursion set of a function $f:\mathbb{R}^d \to \mathbb{R}$ above a given threshold, under a probability measure on $\mathbb{R}^d$ that is assumed to be known. In the industrial world, this corresponds to the problem of estimating a probability of failure of a system. When only an expensive-to-simulate model of the system is available, the budget for simulations is usually severely limited and therefore classical Monte Carlo methods ought to be avoided. One of the main contributions of this article is to derive SUR (stepwise uncertainty reduction) strategies from a Bayesian-theoretic formulation of the problem of estimating a probability of failure. These sequential strategies use a Gaussian process model of $f$ and aim at performing evaluations of $f$ as efficiently as possible to infer the value of the probability of failure. We compare these strategies to other strategies also based on a Gaussian process model for estimating a probability of failure.Comment: This is an author-generated postprint version. The published version is available at http://www.springerlink.co