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.

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

The perceived importance of mall retail categories and its effect on likelihood of purchase during a recession

Recessions impact the retail sector and as such research into consumer decision making during such times is imperative. In response to this, our study takes an innovative approach to examining how the perceived importance of retail store categories in a shopping mall influences the relationship between consumers' shopping attitudes and likelihood of purchasing in those categories during a recession. The overall findings show the importance of a product category to a consumer, which is often overlooked, has a strong explanatory influence on consumer purchase intentions for that specific retail store categories in a shopping mall under recession conditions. Findings also show that for consumers’ who have altered their shopping behaviour the perceived importance of a retail store category fully mediates the relationship for: Majors, Leisure, Food Catered and Mini Majors categories, and partial mediation for Apparel. Importance has no mediating effect for: Food Retail, General Retail, Mobile Phone Services, Home wares, and Retail Services. Our study makes a key contribution to the retail management literature with the findings suggesting that redefining and articulating the importance of the value offering for specific retail store categories can help reduce the impact of changes in consumers' recessionary shopping intentions across the mall tenant mix. Such actions can then help preserve the image of the shopping mall in the minds of the consumers when the economic recovery begins.

Hearing voice and silence during stressful economic times

Purpose - It is ironic that in stressful economic times, when new ideas and positive behaviors could be most valuable, employees may not speak up, leading to reduced employee participation, less organizational learning, less innovation and less receptiveness to change. The supervisor is the organization’s first line of defense against a culture of silence and towards a culture of openness. This research asks what helps supervisors to hear prosocial voice and notice defensive silence. Design/methodology/approach - We conducted a cross-sectional field study of 142 supervisors. Findings - Our results indicate that prosocial voice is increased by supervisor tension and trust in employees, while defensive silence is increased by supervisor tension but reduced by unionization of employees and trust in employees. This indicates that, as hypothesized by others, voice and silence are orthogonal and not opposites of the same construct. Research limitations/implications - The data is measured at one point in time, and further longitudinal study would be helpful to further understand the phenomena. Practical implications - This research highlights the potential for supervisors in stressful situations to selectively hear voice and silence from employees. Originality/value - This study adds to our knowledge of prosocial voice and defensive silence by testing supervisors’ perceptions of these constructs during difficult times. It provides valuable empirical insights to a literature dominated by conceptual non-empirical papers. Limited research on silence might reflect how difficult it is to study such an ambiguous and passive construct as silence (often simply viewed as a lack of speech). also contribute to trust literature by identifying its role in increasing supervisor’s perceptions of prosocial voice and reducing perceptions of defensive silence.

PLDA based speaker recognition on short utterances

This paper investigates the effects of limited speech data in the context of speaker verification using a probabilistic linear discriminant analysis (PLDA) approach. Being able to reduce the length of required speech data is important to the development of automatic speaker verification system in real world applications. When sufficient speech is available, previous research has shown that heavy-tailed PLDA (HTPLDA) modeling of speakers in the i-vector space provides state-of-the-art performance, however, the robustness of HTPLDA to the limited speech resources in development, enrolment and verification is an important issue that has not yet been investigated. In this paper, we analyze the speaker verification performance with regards to the duration of utterances used for both speaker evaluation (enrolment and verification) and score normalization and PLDA modeling during development. Two different approaches to total-variability representation are analyzed within the PLDA approach to show improved performance in short-utterance mismatched evaluation conditions and conditions for which insufficient speech resources are available for adequate system development. The results presented within this paper using the NIST 2008 Speaker Recognition Evaluation dataset suggest that the HTPLDA system can continue to achieve better performance than Gaussian PLDA (GPLDA) as evaluation utterance lengths are decreased. We also highlight the importance of matching durations for score normalization and PLDA modeling to the expected evaluation conditions. Finally, we found that a pooled total-variability approach to PLDA modeling can achieve better performance than the traditional concatenated total-variability approach for short utterances in mismatched evaluation conditions and conditions for which insufficient speech resources are available for adequate system development.

133Cs relaxation times in rat tissues

133Cs relaxation-time studies of tissues from rats into which cesium has been incorporated by dietary loading have been carried out in vivo and in vitro. Whereas tissue T1 values are on the order of seconds, T2 values are as low as a few tens of milliseconds, 133Cs tissue relaxation times are analogous to those of 39K in the same tissues, but are more readily measured because of the greater sensitivity of 133Cs compared with 39K, T1 and T2 data of excised tissue at two resonance frequencies (65.60 and 39.37 MHz) and temperatures (302 and 278 K) have been analyzed in terms of a general description of spin- relaxation. The results are consistent with most of the cesium ions being in a free state, undergoing fast exchange with bound ions having long correlation times located in one or more intracellular compartments,

SeqSLAM : visual route-based navigation for sunny summer days and stormy winter nights

Learning and then recognizing a route, whether travelled during the day or at night, in clear or inclement weather, and in summer or winter is a challenging task for state of the art algorithms in computer vision and robotics. In this paper, we present a new approach to visual navigation under changing conditions dubbed SeqSLAM. Instead of calculating the single location most likely given a current image, our approach calculates the best candidate matching location within every local navigation sequence. Localization is then achieved by recognizing coherent sequences of these “local best matches”. This approach removes the need for global matching performance by the vision front-end - instead it must only pick the best match within any short sequence of images. The approach is applicable over environment changes that render traditional feature-based techniques ineffective. Using two car-mounted camera datasets we demonstrate the effectiveness of the algorithm and compare it to one of the most successful feature-based SLAM algorithms, FAB-MAP. The perceptual change in the datasets is extreme; repeated traverses through environments during the day and then in the middle of the night, at times separated by months or years and in opposite seasons, and in clear weather and extremely heavy rain. While the feature-based method fails, the sequence-based algorithm is able to match trajectory segments at 100% precision with recall rates of up to 60%.

Clinical performance of a new silicone hydrogel contact lens over 6 months of extended wear

Purpose: Silicone hydrogel contact lenses (CLs) are becoming increasingly popular for daily wear (DW), extended wear (EW) and continuous wear (CW), due to their higher oxygen transmissibility compared to hydrogel CLs. The aim of this study was to investigate the clinical and subjective performance of asmofilcon A (Menicon Co., Ltd), a new surface treated silicone hydrogel CL, during 6-night EW over 6 months (M). Methods: A prospective, randomised, single-masked, monadic study was conducted. N=60 experienced DW soft CL wearers were randomly assigned to wear either asmofilcon A (test: Dk=129, water content (WC)=40%, Nanogloss surface treatment) or senofilcon A (control: Dk=103, WC=38%, PVP internal wetting agent, Vistakon, Johnson & Johnson Vision Care) CLs bilaterally for 6 M on an EW basis. A PHMB-preserved solution (Menicon Co., Ltd) was dispensed for CL care. Evaluations were conducted at CL delivery and after 1 week (W), 4 W, 3 M and 6 M of EW. At each visit, a range of objective and subjective clinical performance measures were assessed. Results: N=50 subjects (83%) successfully completed the study, with the majority of discontinuations due to loss to follow-up (n=3) or moving away/travel (n=5). N=2 subjects experienced adverse events; n=1 unilateral red eye with asmofilcon A and n=1 asymptomatic infiltrate with senofilcon A. There were no significant differences in high or low contrast distance visual acuity (HCDVA or LCDVA) between asmofilcon A and senofilcon A; however, LCDVA decreased significantly over time with both CL types (p<0.05). The two CL types did not vary significantly with respect to any of the objective and subjective measures assessed (p>0.05); CL fitting characteristics and CL surface measurements were very similar and mean bulbar and limbal redness measures were always less than grade 1.0. Superior palpebral conjunctival injection showed a statistically, but not clinically, significant increase over time with both CL types (p<0.05). Corneal staining did not vary significantly between asmofilcon A and senofilcon A (p>0.05), with low median gradings of less than 0.5 observed for all areas assessed. There were no solution-related staining reactions observed with either CL type. The asmofilcon A and senofilcon A CLs were both rated highly with respect to overall comfort, with medians of 14 or 15 hours of comfortable lens wearing time per day reported at each of the study visits (p>0.05). Conclusions: Over 6 months of EW, the asmofilcon A and senofilcon A CLs performed in a similar manner with respect to visual acuity, ocular health and CL performance measures. Some changes over time were observed with both CL types, including reduced LCDVA and increased superior palpebral injection, which warrant further investigation in longer-term EW studies. Asmofilcon A appeared to be equivalent in performance to senofilcon A.