Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.)

Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.

CDKN2A is not the principal target of deletions on the short arm of chromosome 9 in neuroendocrine (Merkel cell) carcinoma of the skin

The majority of small-cell lung cancers (SCLCs) express p16 but not pRb. Given our previous study showing loss of pRb in Merkel cell carcinoma (MCC)/neuroendocrine carcinoma of the skin and the clinicopathological similarities between SCLC and MCC, we wished to determine if this was also the case in MCC. Twenty-nine MCC specimens from 23 patients were examined for deletions at 10 loci on 9p and 1 on 9q. No loss of heterozygosity (LOH) was seen in 9 patients including 2 for which tumour and cell line DNAs were examined. Four patients had LOH for all informative loci on 9p. Ten tumours showed more limited regions of loss on 9p, and from these 2 common regions of deletion were determined. Half of all informative cases had LOH at D9S168, the most telomeric marker examined, and 3 specimens showed loss of only D9S168. A second region (IFNA-D9S126) showed LOH in 10 (44%) cases, and case MCC26 showed LOH for only D9S126, implicating genes centromeric of the CDKN2A locus. No mutations in the coding regions of p16 were seen in 7 cell lines tested, and reactivity to anti-p16 antibody was seen in all 11 tumour specimens examined and in 6 of 7 cell lines from 6 patients. Furthermore, all cell lines examined reacted with anti-p14(ARF) antibody. These results suggest that neither transcript of the CDKN2A locus is the target of deletions on 9p in MCC and imply the existence of tumour-suppressor genes mapping both centromeric and telomeric of this locus.

Capturing affective experiences using the SMS experience sampling (SMS-ES) method

This paper reports the feasibility and methodological considerations of using the Short Message System Experience Sampling (SMS-ES) Method, which is an experience sampling research method developed to assist researchers to collect repeat measures of consumers’ affective experiences. The method combines SMS with web-based technology in a simple yet effective way. It is described using a practical implementation study that collected consumers’ emotions in response to using mobile phones in everyday situations. The method is further evaluated in terms of the quality of data collected in the study, as well as against the methodological considerations for experience sampling studies. These two evaluations suggest that the SMS-ES Method is both a valid and reliable approach for collecting consumers’ affective experiences. Moreover, the method can be applied across a range of for-profit and not-for-profit contexts where researchers want to capture repeated measures of consumers’ affective experiences occurring over a period of time. The benefits of the method are discussed to assist researchers who wish to apply the SMS-ES Method in their own research designs.

i-vector based speaker recognition on short utterances

Robust speaker verification on short utterances remains a key consideration when deploying automatic speaker recognition, as many real world applications often have access to only limited duration speech data. This paper explores how the recent technologies focused around total variability modeling behave when training and testing utterance lengths are reduced. Results are presented which provide a comparison of Joint Factor Analysis (JFA) and i-vector based systems including various compensation techniques; Within-Class Covariance Normalization (WCCN), LDA, Scatter Difference Nuisance Attribute Projection (SDNAP) and Gaussian Probabilistic Linear Discriminant Analysis (GPLDA). Speaker verification performance for utterances with as little as 2 sec of data taken from the NIST Speaker Recognition Evaluations are presented to provide a clearer picture of the current performance characteristics of these techniques in short utterance conditions.

The effectiveness of a short-term group music therapy intervention for young parents and their children

The quality of early life experiences are known to influence a child’s capacities for emotional, social, cognitive and physical competence throughout their life (Peterson, 1996; Zubrick et al., 2008). These early life experiences are directly affected by parenting and family environments. A lack of positive parenting has significant implications both for children, and the broader communities in which they live (Davies & Cummings, 1994; Dryfoos, 1990; Sanders, 1995). Young parents are known to be at risk of experiencing adverse circumstances that affect their ability to provide positive parenting to their children (Milan et al., 2004; Trad, 1995). There is a need to provide parenting support programs to young parents that offer opportunities for them to come together, support each other and learn ways to provide for their children’s developmental needs in a friendly, engaging and non-judgemental environment. This research project examines the effectiveness of a 10 week group music therapy program Sing & Grow as an early parenting intervention for 535 young parents. Sing & Grow is a national early parenting intervention program funded by the Australian Government and delivered by Playgroup Queensland. It is designed and delivered by Registered Music Therapists for families at risk of marginalisation with children aged from birth to three years. The aim of the program is to improve parenting skills and parent-child interactions, and increase social support networks through participation in a group that is strengths-based and structured in a way that lends itself to modelling, peer learning and facilitated learning. During the 10 weeks parents have opportunities to learn practical, hands-on ways to interact and play with their children that are conducive to positive parent-child relationships and ongoing child development. A range of interactive, nurturing, stimulating and developmental music activities provide the framework for parents to interact and play with their children. This research uses data collected through the Sing & Grow National Evaluation Study to examine outcomes for all participants aged 25 years and younger, who attended programs during the Sing & Grow pilot study and main study from mid-2005 to the end of 2007. The research examines the change from pre to post in self-reported parent behaviours, parent mental health and parent social support, and therapist observed parent-child interactions. A range of statistical analyses are used to address each Research Objective for the young parent population, and for subgroups within this population. Research Objective 1 explored the patterns of attendance in the Sing & Grow program for young parents, and for subgroups within this population. Results showed that levels of attendance were lower than expected and influenced by Indigenous status and source of family income. Patterns of attendance showed a decline over time and incomplete data rates were high which may indicate high dropout rates. Research Objective 2 explored perceived satisfaction, benefits and social support links made. Satisfaction levels with the program and staff were very high. Indigenous status was associated with lower levels of reported satisfaction with both the program and staff. Perceived benefits from participation in the program were very high. Employment status was associated with perceived benefits: parents who were not employed were more likely than employed parents to report that their understanding of child development had increased as a result of participation in the program. Social support connections were reported for participants with other professionals, services and parents. In particular, families were more likely to link up with playgroup staff and services. Those parents who attended six or more sessions were significantly more likely to attend a playgroup than those who attended five sessions or less. Social support connections were related to source of family income, level of education, Indigenous status and language background. Research Objective 3 investigated pre to post change on self-report parenting skills and parent mental health. Results indicated that participation in the Sing & Grow program was associated with improvements in parent mental health. No improvements were found for self-reported parenting skills. Research Objective 4 investigated pre to post change in therapist observation measures of parent-child interactions. Results indicated that participation in the Sing & Grow program was associated with large and significant improvements in parent sensitivity to, engagement with and acceptance of the child. There were significant interactions across time (pre to post) for the parent characteristics of Indigenous status, family income and level of education. Research Objective 5 explored the relationship between the number of sessions attended and extent of change on self-report outcomes and therapist observed outcomes, respectively. For each, an overall change score was devised to ascertain those parents who had made any positive changes over time. Results showed that there was no significant relationship between high attendance and positive change in either the self-report or therapist observed behavioural measures. A risk index was also constructed to test for a relationship between the risk status of the parent. Parents with the highest risk status were significantly more likely to attend six or more sessions than other parents, but risk status was not associated with any differences in parent reported outcomes or therapist observations. The results of this research study indicate that Sing & Grow is effective in improving outcomes for young parents’ mental health, parent-child interactions and social support connections. High attendance by families in the highest category for risk factors may indicate that the program is effective at engaging and retaining parents who are most at-risk and therefore traditionally hard to reach. Very high levels of satisfaction and perceived benefits support this. Further research is required to help confirm the promising evidence from the current study that a short term group music therapy program can support young parents and improve their parenting outcomes. In particular, this needs to address the more disappointing outcomes of the current research study to improve attendance and engagement of all young parents in the program and especially the needs of young Indigenous parents.

Evaluation of novel Streptococcus pyogenes vaccine candidates incorporating multiple conserved sequences from the C-repeat region of the M-protein

A major challenge for Streptococcus pyogenes vaccine development is the identification of epitopes that confer protection from infection by multiple S. pyogenes M-types. Here we have identified and characterised the distribution of common variant sequences from individual repeat units of the C-repeat region (CRR) of M-proteins representing 77 different M-types. Three polyvalent fusion vaccine candidates (SV1, SV2 and SV3) incorporating the most common variants were subsequently expressed and purified, and demonstrated to be alpha-helical by Circular Dichroism (CD), a secondary conformational characteristic of the CRR in the M-protein. Antibodies raised against each of these constructs recognise M-proteins that vary in their CRR, and bind to the surface of multiple S. pyogenes isolates. Antibodies raised against SV1, containing five variant sequences, also kill heterologous S. pyogenes isolates in in vitro bactericidal assays. Further structural characterisation of this construct demonstrated the conformation of SV1 was stable at different pHs, and thermal unfolding of SV1 a reversible process. Our findings demonstrate that linkage of multiple variant sequences into a single recombinant construct overcomes the need to embed the variant sequences in foreign helix promoting flanking sequences for conformational stability, and demonstrates the viability of the polyvalent candidates as global S. pyogenes vaccine candidates.

Commentary on Spence et al. : "Problem solving programme implemented by teachers may prevent depression in the short term, but longer term benefits are unclear"

This is a methodologically exemplary trial of a population based (universal) approach to preventing depression in young people. The programme used teachers in a classroom setting to deliver cognitive behavioural problem solving skills to a cohort of students. We have little knowledge about “best practice” to prevent depression in adolescence. Classroom-based universal approaches appear to offer advantages in recruitment rates and lack of stigmatisation over approaches that target specific groups of at risk students. Earlier research on a universal school-based approach to preventing depression in adolescents showed promise, but employed mental health professionals to teach cognitive behavioural coping skills in small groups.1 Using such an approach routinely would be economically unsustainable. Spence’s trial, with teachers as facilitators, therefore represents a “real world” intervention that could be routinely disseminated.

Taking a leap of faith : are investors left short changed?

This dissertation examines the compliance and performance of a large sample of faith based (religious) ethical funds - the Shari'ah-compliant equity funds (SEFs), which may be viewed as a form of ethical investing. SEFs screen their investment for compliance with Islamic law, where riba (conventional interest expense), maysir (gambling), gharar (excessive uncertainty), and non-halal (non-ethical) products are prohibited. Using a set of stringent Shari'ah screens similar to those of MSCI Islamic, we first examine the extent to which SEFs comply with the Shari'ah law. Results show that only about 27% of the equities held by SEFs are Shari'ah-compliant. While most of the fund holdings pass the business screens, only about 42% pass the total debt to total assets ratio screen. This finding suggests that, in order to overcome a significant reduction in the investment opportunity, Shari'ah principles are compromised, with SEFs adopting lax screening rules so as to achieve a financial performance. While younger funds and funds that charge higher fees and are domiciled in more Muslim countries are more Shari'ah-compliant, we find little evidence of a positive relationship between fund disclosure of the Shari'ah compliance framework and Shari'ah-compliance. Clearly, Shari'ah compliance remains a major challenge for fund managers and SEF investors should be aware of Shari'ah-compliance risk since the fund managers do not always fulfill their fiduciary obligation, as promised in their prospectus. Employing a matched firm approach for a survivorship free sample of 387 SEFs, we then examine an issue that has been heavily debated in the literature: Does ethical screening reduce investment performance? Results show that it does but only by an average of 0.04% per month if benchmarked against matched conventional funds - this is a relatively small price to pay for religious faith. Cross-sectional regressions show an inverse relationship between Shari'ah compliance and fund performance: every one percentage increase in total compliance decreases fund performance by 0.01% per month. However, compliance fails to explain differences in the performance between SEFs and matched funds. Although SEFs do not generally perform better during crisis periods, further analysis shows evidence of better performance relative to conventional funds only during the recent Global Financial Crisis; the latter is consistent with popular media claims.

Ocular surface changes with short-term contact lens wear

Contact lenses are a common method for the correction of refractive errors of the eye. While there have been significant advancements in contact lens designs and materials over the past few decades, the lenses still represent a foreign object in the ocular environment and may lead to physiological as well as mechanical effects on the eye. When contact lenses are placed in the eye, the ocular anatomical structures behind and in front of the lenses are directly affected. This thesis presents a series of experiments that investigate the mechanical and physiological effects of the short-term use of contact lenses on anterior and posterior corneal topography, corneal thickness, the eyelids, tarsal conjunctiva and tear film surface quality. The experimental paradigm used in these studies was a repeated measures, cross-over study design where subjects wore various types of contact lenses on different days and the lenses were varied in one or more key parameters (e.g. material or design). Both, old and newer lens materials were investigated, soft and rigid lenses were used, high and low oxygen permeability materials were tested, toric and spherical lens designs were examined, high and low powers and small and large diameter lenses were used in the studies. To establish the natural variability in the ocular measurements used in the studies, each experiment also contained at least one “baseline” day where an identical measurement protocol was followed, with no contact lenses worn. In this way, changes associated with contact lens wear were considered in relation to those changes that occurred naturally during the 8 hour period of the experiment. In the first study, the regional distribution and magnitude of change in corneal thickness and topography was investigated in the anterior and posterior cornea after short-term use of soft contact lenses in 12 young adults using the Pentacam. Four different types of contact lenses (Silicone hydrogel/ Spherical/–3D, Silicone Hydrogel/Spherical/–7D, Silicone Hydrogel/Toric/–3D and HEMA/Toric/–3D) of different materials, designs and powers were worn for 8 hours each, on 4 different days. The natural diurnal changes in corneal thickness and curvature were measured on two separate days before any contact lens wear. Significant diurnal changes in corneal thickness and curvature within the duration of the study were observed and these were taken into consideration for calculating the contact lens induced corneal changes. Corneal thickness changed significantly with lens wear and the greatest corneal swelling was seen with the hydrogel (HEMA) toric lens with a noticeable regional swelling of the cornea beneath the stabilization zones, the thickest regions of the lenses. The anterior corneal surface generally showed a slight flattening with lens wear. All contact lenses resulted in central posterior corneal steepening, which correlated with the relative degree of corneal swelling. The corneal swelling induced by the silicone hydrogel contact lenses was typically less than the natural diurnal thinning of the cornea over this same period (i.e. net thinning). This highlights why it is important to consider the natural diurnal variations in corneal thickness observed from morning to afternoon to accurately interpret contact lens induced corneal swelling. In the second experiment, the relative influence of lenses of different rigidity (polymethyl methacrylate – PMMA, rigid gas permeable – RGP and silicone hydrogel – SiHy) and diameters (9.5, 10.5 and 14.0) on corneal thickness, topography, refractive power and wavefront error were investigated. Four different types of contact lenses (PMMA/9.5, RGP/9.5, RGP/10.5, SiHy/14.0), were worn by 14 young healthy adults for a period of 8 hours on 4 different days. There was a clear association between fluorescein fitting pattern characteristics (i.e. regions of minimum clearance in the fluorescein pattern) and the resulting corneal shape changes. PMMA lenses resulted in significant corneal swelling (more in the centre than periphery) along with anterior corneal steepening and posterior flattening. RGP lenses, on the other hand, caused less corneal swelling (more in the periphery than centre) along with opposite effects on corneal curvature, anterior corneal flattening and posterior steepening. RGP lenses also resulted in a clinically and statistically significant decrease in corneal refractive power (ranging from 0.99 to 0.01 D), large enough to affect vision and require adjustment in the lens power. Wavefront analysis also showed a significant increase in higher order aberrations after PMMA lens wear, which may partly explain previous reports of "spectacle blur" following PMMA lens wear. We further explored corneal curvature, thickness and refractive changes with back surface toric and spherical RGP lenses in a group of 6 subjects with toric corneas. The lenses were worn for 8 hours and measurements were taken before and after lens wear, as in previous experiments. Both lens types caused anterior corneal flattening and a decrease in corneal refractive power but the changes were greater with the spherical lens. The spherical lens also caused a significant decrease in WTR astigmatism (WRT astigmatism defined as major axis within 30 degrees of horizontal). Both the lenses caused slight posterior corneal steepening and corneal swelling, with a greater effect in the periphery compared to the central cornea. Eyelid position, lid-wiper and tarsal conjunctival staining were also measured in Experiment 2 after short-term use of the rigid and SiHy contact lenses. Digital photos of the external eyes were captured for lid position analysis. The lid-wiper region of the marginal conjunctiva was stained using fluorescein and lissamine green dyes and digital photos were graded by an independent masked observer. A grading scale was developed in order to describe the tarsal conjunctival staining. A significant decrease in the palpebral aperture height (blepharoptosis) was found after wearing of PMMA/9.5 and RGP/10.5 lenses. All three rigid contact lenses caused a significant increase in lid-wiper and tarsal staining after 8 hours of lens wear. There was also a significant diurnal increase in tarsal staining, even without contact lens wear. These findings highlight the need for better contact lens edge design to minimise the interactions between the lid and contact lens edge during blinking and more lubricious contact lens surfaces to reduce ocular surface micro-trauma due to friction and for. Tear film surface quality (TFSQ) was measured using a high-speed videokeratoscopy technique in Experiment 2. TFSQ was worse with all the lenses compared to baseline (PMMA/9.5, RGP/9.5, RGP/10.5, and SiHy/14) in the afternoon (after 8 hours) during normal and suppressed blinking conditions. The reduction in TFSQ was similar with all the contact lenses used, irrespective of their material and diameter. An unusual pattern of change in TFSQ in suppressed blinking conditions was also found. The TFSQ with contact lens was found to decrease until a certain time after which it improved to a value even better than the bare eye. This is likely to be due to the tear film drying completely over the surface of the contact lenses. The findings of this study also show that there is still a scope for improvement in contact lens materials in terms of better wettability and hydrophilicity in order to improve TFSQ and patient comfort. These experiments showed that a variety of changes can occur in the anterior eye as a result of the short-term use of a range of commonly used contact lens types. The greatest corneal changes occurred with lenses manufactured from older HEMA and PMMA lens materials, whereas modern SiHy and rigid gas permeable materials caused more subtle changes in corneal shape and thickness. All lenses caused signs of micro-trauma to the eyelid wiper and palpebral conjunctiva, although rigid lenses appeared to cause more significant changes. Tear film surface quality was also significantly reduced with all types of contact lenses. These short-term changes in the anterior eye are potential markers for further long term changes and the relative differences between lens types that we have identified provide an indication of areas of contact lens design and manufacture that warrant further development.