Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Evidence for time dependency of molecular rate estimates

Long-term changes in the genetic composition of a population occur by the fixation of new mutations, a process known as substitution. The rate at which mutations arise in a population and the rate at which they are fixed are expected to be equal under neutral conditions (Kimura, 1968). Between the appearance of a new mutation and its eventual fate of fixation or loss, there will be a period in which it exists as a transient polymorphism in the population (Kimura and Ohta, 1971). If the majority of mutations are deleterious (and nonlethal), the fixation probabilities of these transient polymorphisms are reduced and the mutation rate will exceed the substitution rate (Kimura, 1983). Consequently, different apparent rates may be observed on different time scales of the molecular evolutionary process (Penny, 2005; Penny and Holmes, 2001). The substitution rate of the mitochondrial protein-coding genes of birds and mammals has been traditionally recognized to be about 0.01 substitutions/site/million years (Myr) (Brown et al., 1979; Ho, 2007; Irwin et al., 1991; Shields and Wilson, 1987), with the noncoding D-loop evolving several times more quickly (e.g., Pesole et al., 1992; Quinn, 1992). Over the past decade, there has been mounting evidence that instantaneous mutation rates substantially exceed substitution rates, in a range of organisms (e.g., Denver et al., 2000; Howell et al., 2003; Lambert et al., 2002; Mao et al., 2006; Mumm et al., 1997; Parsons et al., 1997; Santos et al., 2005). The immediate reaction to the first of these findings was that the polymorphisms generated by the elevated mutation rate are short-lived, perhaps extending back only a few hundred years (Gibbons, 1998; Macaulay et al., 1997). That is, purifying selection was thought to remove these polymorphisms very rapidly.

Computationally efficient methods for solving time-variable-order time-space fractional reaction-diffusion equation

Fractional differential equations are becoming more widely accepted as a powerful tool in modelling anomalous diffusion, which is exhibited by various materials and processes. Recently, researchers have suggested that rather than using constant order fractional operators, some processes are more accurately modelled using fractional orders that vary with time and/or space. In this paper we develop computationally efficient techniques for solving time-variable-order time-space fractional reaction-diffusion equations (tsfrde) using the finite difference scheme. We adopt the Coimbra variable order time fractional operator and variable order fractional Laplacian operator in space where both orders are functions of time. Because the fractional operator is nonlocal, it is challenging to efficiently deal with its long range dependence when using classical numerical techniques to solve such equations. The novelty of our method is that the numerical solution of the time-variable-order tsfrde is written in terms of a matrix function vector product at each time step. This product is approximated efficiently by the Lanczos method, which is a powerful iterative technique for approximating the action of a matrix function by projecting onto a Krylov subspace. Furthermore an adaptive preconditioner is constructed that dramatically reduces the size of the required Krylov subspaces and hence the overall computational cost. Numerical examples, including the variable-order fractional Fisher equation, are presented to demonstrate the accuracy and efficiency of the approach.

Time-varying bispectral analysis of auditory evoked multi-channel scalp EEG

Time-varying bispectra, computed using a classical sliding window short-time Fourier approach, are analyzed for scalp EEG potentials evoked by an auditory stimulus and new observations are presented. A single, short duration tone is presented from the left or the right, direction unknown to the test subject. The subject responds by moving the eyes to the direction of the sound. EEG epochs sampled at 200 Hz for repeated trials are processed between -70 ms and +1200 ms with reference to the stimulus. It is observed that for an ensemble of correctly recognized cases, the best matching timevarying bispectra at (8 Hz, 8Hz) are for PZ-FZ channels and this is also largely the case for grand averages but not for power spectra at 8 Hz. Out of 11 subjects, the only exception for time-varying bispectral match was a subject with family history of Alzheimer’s disease and the difference was in bicoherence, not biphase.

Quality of work life and turnover intention in primary healthcare organisations : a cross-sectional study of registered nurses in Saudi Arabia

Purpose: The purpose of this study was to improve the retention of primary healthcare (PHC) nurses through exploring and assessing their quality of work life (QWL) and turnover intention. Design and methods: A cross-sectional survey design was used in this study. Data were collected using a questionnaire comprising four sections (Brooks’ survey of Quality of Nursing Work Life [QNWL], Anticipated Turnover Intention, open-ended questions and demographic characteristics). A convenience sample was recruited from 143 PHC centres in Jazan, Saudi Arabia. A response rate of 87% (n = 508/585) was achieved. The SPSS v17 for Windows and NVivo 8 were used for analysis purposes. Procedures and tests used in this study to analyse the quantitative data were descriptive statistics, t-test, ANOVA, General Linear Model (GLM) univariate analysis, standard multiple regression, and hierarchical multiple regression. Qualitative data obtained from responses to the open-ended questions were analysed using the NVivo 8. Findings: Quantitative findings suggested that PHC nurses were dissatisfied with their work life. Respondents’ scores ranged between 45 and 218 (mean = 139.45), which is lower than the average total score on Brooks’ Survey (147). Major influencing factors were classified under four dimensions. First, work life/home life factors: unsuitable working hours, lack of facilities for nurses, inability to balance work with family needs and inadequacy of vacations’ policy. Second, work design factors: high workload, insufficient workforce numbers, lack of autonomy and undertaking many non-nursing tasks. Third, work context factors: management practices, lack of development opportunities, and inappropriate working environment in terms of the level of security, patient care supplies and unavailability of recreation room. Finally, work world factors: negative public image of nursing, and inadequate payment. More positively, nurses were notably satisfied with their co-workers. Conversely, 40.4% (n = 205) of the respondents indicated that they intended to leave their current employment. The relationships between QWL and demographic variables of gender, age, marital status, dependent children, dependent adults, nationality, ethnicity, nursing tenure, organisational tenure, positional tenure, and payment per month were significant (p < .05). The eta squared test for these demographics indicates a small to medium effect size of the variation in QWL scores. Using the GLM univariate analysis, education level was also significantly related to the QWL (p < .05). The relationships between turnover intention and demographic variables including gender, age, marital status, dependent children, education level, nursing tenure, organisational tenure, positional tenure, and payment per month were significant (p < .05). The eta squared test for these demographics indicates a small to moderate effect size of the variation in the turnover intention scores. Using the GLM univariate analysis, the dependent adults’ variable was also significantly related to turnover intention (p < .05). Turnover intention was significantly related to QWL. Using standard multiple regression, 26% of the variance in turnover intention was explained by the QWL F (4,491), 43.71, p < .001, with R² = .263. Further analysis using hierarchical multiple regression found that the total variance explained by the model as a whole (demographics and QWL) was 32.1%, F (17.433) = 12.04, p < .001. QWL explained an additional 19% of the variance in turnover intention, after controlling for demographic variables, R squared change =.19, F change (4, 433) = 30.190, p < .001. The work context variable makes the strongest unique contribution (-.387) to explain the turnover intention, followed by the work design dimension (-.112). The qualitative findings reaffirmed the quantitative findings in terms of QWL and turnover intention. However, the home life/work life and work world dimensions were of great important to both QWL and turnover intention. The qualitative findings revealed a number of new factors that were not included in the survey questionnaire. These included being away from family, lack of family support, social and cultural aspects, accommodation facilities, transportation, building and infrastructure of PHC, nature of work, job instability, privacy at work, patients and community, and distance between home and workplace. Conclusion: Creating and maintaining a healthy work life for PHC nurses is very important to improve their work satisfaction, reduce turnover, enhance productivity and improve nursing care outcomes. Improving these factors could lead to a higher QWL and increase retention rates and therefore reinforcing the stabilisation of the nursing workforce. Significance of the research: Many countries are examining strategies to attract and retain the health care workforce, particularly nurses. This study identified factors that influence the QWL of PHC nurses as well as their turnover intention. It also determined the significant relationship between QWL and turnover intention. In addition, the present study tested Brooks’ survey of QNWL on PHC nurses for the first time. The qualitative findings of this study revealed a number of new variables regarding QWL and turnover intention of PHC nurses. These variables could be used to improve current survey instruments or to develop new research surveys. The study findings could be also used to develop and appropriately implement plans to improve QWL. This may help to enhance the home and work environments of PHC nurses, improve individual and organisational performance, and increase nurses’ commitment. This study contributes to the existing body of research knowledge by presenting new data and findings from a different country and healthcare system. It is the first of its kind in Saudi Arabia, especially in the field of PHC. It has examined the relationship between QWL and turnover intention of PHC nurses for the first time using nursing instruments. The study also offers a fresh explanation (new framework) of the relationship between QWL and turnover intention among PHC nurses, which could be used or tested by researchers in other settings. Implications for further research: Review of the extant literature reveals little in-depth research on the PHC workforce, especially in terms of QWL and organisational turnover in developing countries. Further research is required to develop a QWL tool for PHC nurses, taking into consideration the findings of the current study along with the local culture. Moreover, the revised theoretical framework of the current study could be tested in further research in other regions, countries or healthcare systems in order to identify its ability to predict the level of PHC nurses’ QWL and their intention to leave. There is a need to conduct longitudinal research on PHC organisations to gain an in-depth understanding of the determents of and changes in QWL and turnover intention of PHC nurses at various points of time. An intervention study is required to improve QWL and retention among PHC nurses using the findings of the current study. This would help to assess the impact of such strategies on reducing turnover of PHC nurses. Focusing on the location of the current study, it would be valuable to conduct another study in five years’ time to examine the percentage of actual turnover among PHC nurses compared with the reported turnover intention in the current study. Further in-depth research would also be useful to assess the impact of the local culture on the perception of expatriate nurses towards their QWL and their turnover intention. A comparative study is required between PHC centres and hospitals as well as the public and private health sector agencies in terms of QWL and turnover intention of nursing personnel. Findings may differ from sector to sector according to variations in health systems, working environments and the case mix of patients.

Real-time detection of concealed chemical hazards under ambient light conditions using Raman spectroscopy

Current concerns regarding terrorism and international crime highlight the need for new techniques for detecting unknown and hazardous substances. A novel Raman spectroscopy-based technique, spatially offset Raman spectroscopy (SORS), was recently devised for non-invasively probing the contents of diffusely scattering and opaque containers. Here, we demonstrate a modified portable SORS sensor for detecting concealed substances in-field under different background lighting conditions. Samples including explosive precursors, drugs and an organophosphate insecticide (chemical warfare agent surrogate) were concealed inside diffusely scattering packaging including plastic, paper and cloth. Measurements were carried out under incandescent and fluorescent light as well as under daylight to assess the suitability of the probe for different real-life conditions. In each case, it was possible to identify the substances against their reference Raman spectra in less than one minute. The developed sensor has potential for rapid detection of concealed hazardous substances in airports, mail distribution centers and customs checkpoints.

Exposure to hot and cold temperatures and ambulance attendances in Brisbane, Australia: A time series study

ABSTRACT Objectives: To investigate the effect of hot and cold temperatures on ambulance attendances. Design: An ecological time series study. Setting and participants: The study was conducted in Brisbane, Australia. We collected information on 783 935 daily ambulance attendances, along with data of associated meteorological variables and air pollutants, for the period of 2000–2007. Outcome measures: The total number of ambulance attendances was examined, along with those related to cardiovascular, respiratory and other non-traumatic conditions. Generalised additive models were used to assess the relationship between daily mean temperature and the number of ambulance attendances. Results: There were statistically significant relationships between mean temperature and ambulance attendances for all categories. Acute heat effects were found with a 1.17% (95% CI: 0.86%, 1.48%) increase in total attendances for 1 °C increase above threshold (0–1 days lag). Cold effects were delayed and longer lasting with a 1.30% (0.87%, 1.73%) increase in total attendances for a 1 °C decrease below the threshold (2–15 days lag). Harvesting was observed following initial acute periods of heat effects, but not for cold effects. Conclusions: This study shows that both hot and cold temperatures led to increases in ambulance attendances for different medical conditions. Our findings support the notion that ambulance attendance records are a valid and timely source of data for use in the development of local weather/health early warning systems.

Repeat speeding offenders : time to stop thinking of them as just ‘unlucky normal’ drivers

- Speeding and crash involvement in Australia - Speeding recidivist research in Queensland - Challenges from an Australian perspective - Defining speeding - Community attitudes to speeding - Auditor-General reviews of speed camera programs - Implications for future speed management

Identifying customer behaviour and dwell time using soft biometrics

In a commercial environment, it is advantageous to know how long it takes customers to move between different regions, how long they spend in each region, and where they are likely to go as they move from one location to another. Presently, these measures can only be determined manually, or through the use of hardware tags (i.e. RFID). Soft biometrics are characteristics that can be used to describe, but not uniquely identify an individual. They include traits such as height, weight, gender, hair, skin and clothing colour. Unlike traditional biometrics, soft biometrics can be acquired by surveillance cameras at range without any user cooperation. While these traits cannot provide robust authentication, they can be used to provide identification at long range, and aid in object tracking and detection in disjoint camera networks. In this chapter we propose using colour, height and luggage soft biometrics to determine operational statistics relating to how people move through a space. A novel average soft biometric is used to locate people who look distinct, and these people are then detected at various locations within a disjoint camera network to gradually obtain operational statistics

A stranger's touch : effects of accidental interpersonal touch on consumer evaluations and shopping time

This article examines an unexplored area of consumer research—the effect of accidental interpersonal touch (AIT) from a stranger on consumer evaluations and shopping times. The research presents a field experiment in a retail setting. This study shows that men and women who have been touched by another consumer when examining products report more negative brand evaluations, negative product beliefs, less willingness to pay, and spend less time in-store than their control (no-touch) counterparts. Our findings indicate that the AIT effect is especially negative for touch from a male stranger for both men (same-sex touch) and women (opposite-sex touch). Directions are provided for future study that highlight potential moderators and process explanations underlying the AIT effect.

Alternating direction implicit numerical method for the space and time fractional Bloch-Torrey equation in 3-D

Recently, some authors have considered a new diffusion model–space and time fractional Bloch-Torrey equation (ST-FBTE). Magin et al. (2008) have derived analytical solutions with fractional order dynamics in space (i.e., _ = 1, β an arbitrary real number, 1 < β ≤ 2) and time (i.e., 0 < α < 1, and β = 2), respectively. Yu et al. (2011) have derived an analytical solution and an effective implicit numerical method for solving ST-FBTEs, and also discussed the stability and convergence of the implicit numerical method. However, due to the computational overheads necessary to perform the simulations for nuclear magnetic resonance (NMR) in three dimensions, they present a study based on a two-dimensional example to confirm their theoretical analysis. Alternating direction implicit (ADI) schemes have been proposed for the numerical simulations of classic differential equations. The ADI schemes will reduce a multidimensional problem to a series of independent one-dimensional problems and are thus computationally efficient. In this paper, we consider the numerical solution of a ST-FBTE on a finite domain. The time and space derivatives in the ST-FBTE are replaced by the Caputo and the sequential Riesz fractional derivatives, respectively. A fractional alternating direction implicit scheme (FADIS) for the ST-FBTE in 3-D is proposed. Stability and convergence properties of the FADIS are discussed. Finally, some numerical results for ST-FBTE are given.

A new implicit numerical method for the space and time fractional Bloch-Torrey equation

In recent years, it has been found that many phenomena in engineering, physics, chemistry and other sciences can be described very successfully by models using mathematical tools from fractional calculus. Recently, noted a new space and time fractional Bloch-Torrey equation (ST-FBTE) has been proposed (see Magin et al. (2008)), and successfully applied to analyse diffusion images of human brain tissues to provide new insights for further investigations of tissue structures. In this paper, we consider the ST-FBTE on a finite domain. The time and space derivatives in the ST-FBTE are replaced by the Caputo and the sequential Riesz fractional derivatives, respectively. Firstly, we propose a new effective implicit numerical method (INM) for the STFBTE whereby we discretize the Riesz fractional derivative using a fractional centered difference. Secondly, we prove that the implicit numerical method for the ST-FBTE is unconditionally stable and convergent, and the order of convergence of the implicit numerical method is ( T2 - α + h2 x + h2 y + h2 z ). Finally, some numerical results are presented to support our theoretical analysis.

Numerical methods for solving the multi-term time-fractional wave-diffusion equations

In this paper, the multi-term time-fractional wave diffusion equations are considered. The multiterm time fractional derivatives are defined in the Caputo sense, whose orders belong to the intervals [0,1], [1,2), [0,2), [0,3), [2,3) and [2,4), respectively. Some computationally effective numerical methods are proposed for simulating the multi-term time-fractional wave-diffusion equations. The numerical results demonstrate the effectiveness of theoretical analysis. These methods and techniques can also be extended to other kinds of the multi-term fractional time-space models with fractional Laplacian.

A finite volume method for solving the two-sided time-space fractional advection-dispersion equation

The field of fractional differential equations provides a means for modelling transport processes within complex media which are governed by anomalous transport. Indeed, the application to anomalous transport has been a significant driving force behind the rapid growth and expansion of the literature in the field of fractional calculus. In this paper, we present a finite volume method to solve the time-space two-sided fractional advection dispersion equation on a one-dimensional domain. Such an equation allows modelling different flow regime impacts from either side. The finite volume formulation provides a natural way to handle fractional advection-dispersion equations written in conservative form. The novel spatial discretisation employs fractionally-shifted Gr¨unwald formulas to discretise the Riemann-Liouville fractional derivatives at control volume faces in terms of function values at the nodes, while the L1-algorithm is used to discretise the Caputo time fractional derivative. Results of numerical experiments are presented to demonstrate the effectiveness of the approach.