EvolveAGene 3: A DNA coding sequence evolution simulation program

EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches. Variation includes base substitutions, insertions and deletions. Output includes a log file, the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments

Barlow-Hall in vitro Evolution Protocol

The Barlow-Hall method for in vitro evolution is a simple alternative to methods such as DNA shuffling and is particularly applicable to predicting the evolution of target genes in nature. This detailed protocol includes the procedure itself and, as Appendices, describes particularly effective protocols for electroporation and for preparation of electrocompetent cells

A situational model development in hospitality retailing : the case of Irish pubs

Although importance of situational influences on consumer behaviour has been recognised for some time, little research has been conducted into their effects on hospitality retailing. Over the past decade the Irish theme pub sector has enjoyed extensive growth, which recent studies attribute to the situational components inherent within the environment. This study identities and evaluates the situational components that influence consumers within Irish theme pubs and gauges impact of each of the dimensions of an established situational model on customer behaviour using gender and age cohorts. A three phase, mixed method research design was used and respondents were selected from six Irish theme pubs in Melbourne. The study found that both physical and social situational components have a significant influence in attracting, serving and satisfying the needs of consumers.<br /

Irish theme pubs : an evaluation of environmental cues

A major phenomenon in hospitality retailing in recent years has been the growth in Irish theme pubs. These pubs consist of a collection of both tangible and intangible attributes referred to as environmental cues or atmospherics. Although environmental cues have been found to have a significant influence on consumer behaviour, little research has been conducted into their effects within Irish theme pubs. Using an established research framework, the aims of this study were to identify and evaluate environmental cues within Irish theme pubs and to establish how the dimensions of this framework influenced customers of Irish theme pubs in Melbourne. Qualitative interviews were conducted with customers of six selected Irish theme pubs and with the owners of these establishments. Whilst confirming the impOliance of environmental cues to Irish theme pub customers, the study also provides information that has application for hospitality retailers.<br /

An investigation into the influence of situational components in hospitality retailing

Although the importance of situational influences on consumer behaviour has been recognised for some time, little research has been conducted into their effects in hospitality retailing. Over the past decade the Irish theme pub sector has enjoyed extensive growth, which recent studies attribute to the situational components inherent within the environment. This study sought to identify and evaluate the situational components that influence consumers within Irish theme pubs and to gauge the influence of each of the dimensions of an established situational model on customer behaviour among gender and age cohorts. A three phase, mixed method research design was used and respondents were selected from six Irish theme pubs in Melbourne. The study found that both physical and social situational components have a significant influence in attracting, serving and satisfying the needs of consumers

Designing antibiotic cycling strategies by determining and understanding local adaptive landscapes

The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore susceptibility after resistance has arisen have been unsuccessful, including restrictions on prescribing [1] and antibiotic cycling [2,3]. Part of the problem may be that those efforts have implemented different classes of unrelated antibiotics, and relied on removal of resistance by random loss of resistance genes from bacterial populations (drift). Here, we show that alternating structurally similar antibiotics can restore susceptibility to antibiotics after resistance has evolved. We found that the resistance phenotypes conferred by variant alleles of the resistance gene encoding the TEM {\beta}-lactamase (blaTEM) varied greatly among 15 different {\beta}-lactam antibiotics. We captured those differences by characterizing complete adaptive landscapes for the resistance alleles blaTEM-50 and blaTEM-85, each of which differs from its ancestor blaTEM-1 by four mutations. We identified pathways through those landscapes where selection for increased resistance moved in a repeating cycle among a limited set of alleles as antibiotics were alternated. Our results showed that susceptibility to antibiotics can be sustainably renewed by cycling structurally similar antibiotics. We anticipate that these results may provide a conceptual framework for managing antibiotic resistance. This approach may also guide sustainable cycling of the drugs used to treat malaria and HIV

Geometric Interpretation of the Mixed Invariants of the Riemann Spinor

Mixed invariants are used to classify the Riemann spinor in the case of Einstein-Maxwell fields and perfect fluids. In the Einstein-Maxwell case these mixed invariants provide information as to the relative orientation of the gravitational and electromagnetic principal null directions. Consideration of the perfect fluid case leads to some results about the behaviour of the Bel-Robinson tensor regarded as a quartic form on unit timelike vectors.Comment: 31 pages, AMS-LaTe

Chromospheric activity as age indicator

Chromospheric activity has been calibrated and widely used as an age indicator. However, it has been suggested that the viability of this age indicator is, in the best case, limited to stars younger than about 1.5 Gyr. I aim to define the age range for which chromospheric activity is a robust astrophysical clock. I collected literature measurements of the S-index in field stars, which is a measure of the strength of the H and K lines of the Ca II and a proxy for chromospheric activity, and exploited the homogeneous database of temperature and age determinations for field stars provided by the Geneva-Copenhagen survey of the solar neighbourhood. Field data, inclusive data previously used to calibrate chromospheric ages, confirm the result found using open cluster data, i.e. there is no decay of chromospheric activity after about 2 Gyr. The only existing indication supporting the viability of chromospheric ages older than 2 Gyr is the similarity of chromospheric activity levels in the components of 35 dwarf binaries. However, even in the most optimistic scenario, uncertainty in age determination for field stars and lack of sufficient data in open clusters make any attempt of calibrating an age activity relationship for old stars premature. The hypothesis that chromospheric activity follows the Skumanich law, i.e. that it is proportional to the inverse square root of the age, should be relaxed.Comment: 5 pages, 2 figures, A&A letters, accepte

Performance of the Tinnitus Functional Index as a diagnostic instrument in a UK clinical population

Objectives: The Tinnitus Functional Index (TFI) has been optimised as a diagnostic tool for quantifying the functional impact of tinnitus in US veteran and civilian groups. However, the TFI has not been evaluated for use in other English-speaking clinical populations despite its increasingly popular uptake. Here, a prospective multi-site longitudinal validation study was conducted to evaluate psychometric properties relevant to the UK clinical population. Guided by quality criteria for the measurement properties of health-related questionnaires, we specifically evaluated three diagnostic properties relating to the degree to which the TFI (i) covers the eight dimensions proposed to be important for diagnosis, (ii) reliably distinguishes individual differences in severity of tinnitus, and (iii) reliably measures the functional impact of tinnitus. We also examine whether clinically meaningful interpretations of the scores can be produced for the UK population. Methods: Twelve National Health Service audiology clinics across the UK recruited 255 tinnitus patients to complete questionnaires at four time-intervals, from initial clinical assessment and then over a nine-month period. Patients completed the TFI, the Tinnitus Handicap Inventory (THI), tinnitus case history questions, a Global rating of Perceived Problem with tinnitus and a Clinical Global Impression of perceived change in tinnitus. Baseline TFI data were used to examine the factor structure, construct validity and interpretability of the TFI. Follow-up TFI data were used to examine reliability. Results: Confirmatory factor analysis suggested that of the eight subscales (factors) initially established for the TFI, the ‘Auditory’ subscale did not contribute to the overall construct ‘functional impact of tinnitus’, and a modified seven-factor model (TFI-22) better fit the variance in the patient scores. Both the global 25-item TFI and the global TFI-22 scores showed exceptionally high internal consistency (α ≥ 0.95), high construct validity with the THI (r = 0.80) and high test-retest reliability (ICC = 0.87). Test-retest agreement however was only deemed to be borderline acceptable (89%). Receiver Operator Characteristic analysis indicated the 25-item TFI and TFI-22 has excellent ability to distinguish between different levels of impact (Area under the curve > 0.7). Conclusion: The TFI was confirmed to cover multiple symptom domains, measuring a multi-domain construct of tinnitus, and satisfies a range of psychometric requirements for a good clinical measure, including having excellent reliability, stability over time and sensitivity to individual differences in tinnitus severity. However, a modified seven-factor structure without the Auditory subscale (TFI-22) is recommended for calculating a global composite score for UK patients. Using patients’ experience and Receiver Operator Characteristic analysis, a grading system was presented which identifies the distinct grades of tinnitus impact in the UK clinical population that is broadly comparable to the US-based system