A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.

Validating the use of intrinsic markers in body feathers to identify inter‑individual differences in non‑breeding areas of northern fulmars

Many wildlife studies use chemical analyses to explore spatio-temporal variation in diet, migratory patterns and contaminant exposure. Intrinsic markers are particularly valuable for studying non-breeding marine predators, when direct methods of investigation are rarely feasible. However, any inferences regarding foraging ecology are dependent upon the time scale over which tissues such as feathers are formed. In this study, we validate the use of body feathers for studying non-breeding foraging patterns in a pelagic seabird, the northern fulmar. Analysis of carcasses of successfully breeding adult fulmars indicated that body feathers moulted between September and March, whereas analyses of carcasses and activity patterns suggested that wing feather and tail feather moult occurred during more restricted periods (September to October and September to January, respectively). By randomly sampling relevant body feathers, average values for individual birds were shown to be consistent. We also integrated chemical analyses of body feather with geolocation tracking data to demonstrate that analyses of δ13C and δ15N values successfully assigned 88 % of birds to one of two broad wintering regions used by breeding adult fulmars from a Scottish study colony. These data provide strong support for the use of body feathers as a tool for exploring non-breeding foraging patterns and diet in wide-ranging, pelagic seabirds.

Sexual abuse of children in low-income settings:time for action

In this article, child sexual abuse in low-income settings is reviewed, including the extent of the problem, the way children present, and how they should be managed. Liaising with other agencies, training in all aspects of sexual abuse and creating an environment that is conducive to good care by all groups involved is essential. Technical details of medical examination are not covered as appropriate guidelines are accessible.

Efficient Key Generation by Exploiting Randomness from Channel Responses of Individual OFDM Subcarriers

Key generation from the randomness of wireless channels is a promising technique to establish a secret cryptographic key securely between legitimate users. This paper proposes a new approach to extract keys efficiently from channel responses of individual orthogonal frequency-division multiplexing (OFDM) subcarriers. The efficiency is achieved by (i) fully exploiting randomness from time and frequency domains and (ii) improving the cross-correlation of the channel measurements. Through the theoretical modelling of the time and frequency autocorrelation relationship of the OFDM subcarrier's channel responses, we can obtain the optimal probing rate and use multiple uncorrelated subcarriers as random sources. We also study the effects of non-simultaneous measurements and noise on the cross-correlation of the channel measurements. We find the cross-correlation is mainly impacted by noise effects in a slow fading channel and use a low pass filter (LPF) to reduce the key disagreement rate and extend the system's working signal-to-noise ratio range. The system is evaluated in terms of randomness, key generation rate, and key disagreement rate, verifying that it is feasible to extract randomness from both time and frequency domains of the OFDM subcarrier's channel responses.

Verification of Key Generation from Individual OFDM Subcarrier's Channel Response

This paper presents a key generation system derived from the channel response of individual subcarrier in orthogonal frequency-division multiplexing (OFDM) systems. Practical aspects of the security were investigated by implementing our key generation scheme on a wireless open-access research platform (WARP), which enables us to obtain channel estimation of individual OFDM subcarriers, a feature not currently available in most commercial wireless interface cards. Channel response of individual OFDM subcarrier is usually a wide sense stationary random process, which allows us to find the optimal probing period and maximize the key generation rate. The implementation requires cross layer design as it involves interaction between physical and MAC layer. We have experimentally verified the feasibility and principles of key generation, and also evaluated the performance of our system in terms of randomness, key generation rate and key disagreement rate, which proves that OFDM subcarrier's channel responses are valid for key generation.

Quantification of the smoking-associated cancer risk with rate advancement periods: meta-analysis of individual participant data from cohorts of the CHANCES consortium

BACKGROUND: Smoking is the most important individual risk factor for many cancer sites but its association with breast and prostate cancer is not entirely clear. Rate advancement periods (RAPs) may enhance communication of smoking related risk to the general population. Thus, we estimated RAPs for the association of smoking exposure (smoking status, time since smoking cessation, smoking intensity, and duration) with total and site-specific (lung, breast, colorectal, prostate, gastric, head and neck, and pancreatic) cancer incidence and mortality.

METHODS: This is a meta-analysis of 19 population-based prospective cohort studies with individual participant data for 897,021 European and American adults. For each cohort we calculated hazard ratios (HRs) for the association of smoking exposure with cancer outcomes using Cox regression adjusted for a common set of the most important potential confounding variables. RAPs (in years) were calculated as the ratio of the logarithms of the HRs for a given smoking exposure variable and age. Meta-analyses were employed to summarize cohort-specific HRs and RAPs.

RESULTS: Overall, 140,205 subjects had a first incident cancer, and 53,164 died from cancer, during an average follow-up of 12 years. Current smoking advanced the overall risk of developing and dying from cancer by eight and ten years, respectively, compared with never smokers. The greatest advancements in cancer risk and mortality were seen for lung cancer and the least for breast cancer. Smoking cessation was statistically significantly associated with delays in the risk of cancer development and mortality compared with continued smoking.

CONCLUSIONS: This investigation shows that smoking, even among older adults, considerably advances, and cessation delays, the risk of developing and dying from cancer. These findings may be helpful in more effectively communicating the harmful effects of smoking and the beneficial effect of smoking cessation.

Representações sociais dos valores dos estudantes universitários portugueses

O trabalho de investigação que desenvolvemos situa-se no âmbito das representações sociais dos valores dos estudantes universitários em Portugal. Os estudantes universitários espelham os valores e as representações sociais da sociedade a que pertencem mas de uma forma filtrada por valores individuais próprios de indivíduos com um nível educacional mais elevado, a autonomia de pensamento em detrimento da conformidade, e a flexibilidade intelectual. E no caso português, são a primeira geração que nasceu e cresceu num período de prosperidade económica fruto da entrada na União Europeia. Considerando que procurámos situar-nos nos níveis de análise posicional e ideológico, ou seja, partir de um grupo concreto e definido e estudar as atitudes e valores desse grupo, procurámos seguir uma metodologia com referenciais teóricos no âmbito da investigação em Ciências Sociais, utilizando instrumentos típicos da abordagem sociológica e da psicologia social, pois procurámos caraterizar uma realidade de cariz sociocultural, a questão das representações sociais dos valores. Nesse sentido, procedemos à preparação de um questionário, baseado no European Values Survey (EVS), que visava revelar quais os valores dos estudantes universitários em Portugal onde procurámos saber como se posicionam os jovens universitários nas questões relacionadas com a família, o trabalho, a politica, a sociedade e a religião, verificando se as variações valorativas no interior da amostra dependem de determinadas variáveis sociodemográficas (género, estrato social, etc.) e utilizando os resultados da amostra portuguesa da vaga do EVS 2008 para identificar possíveis variações entre os estudantes e a população portuguesa em geral. As entrevistas que realizámos complementarmente forneceram informações interessantes sobre as representações sociais dos estudantes sobre esta problemática.

Physical activity in deprived communities in London: examining individual and neighbourhood-level factors

Introduction: The objectives of this study were to examine relationships between neighbourhood-level and individual-level characteristics and physical activity in deprived London neighbourhoods. Methods: In 40 of the most deprived neighbourhoods in London (ranked in top 11% in London by Index of Multiple Deprivation) a cross-sectional survey (n = 4107 adults aged > = 16 years), neighbourhood audit tool, GIS measures and routine data measured neighbourhood and individual-level characteristics. The binary outcome was meeting the minimum recommended (CMO, UK) 5×30 mins moderate physical activity per week. Multilevel modelling was used to examine associations between physical activity and individual and neighbourhood-level characteristics. Results: Respondents living more than 300 m away from accessible greenspace had lower odds of achieving recommended physical activity levels than those who lived within 300 m; from 301–600 m (OR = 0.7; 95% CI 0.5–0.9) and from 601–900 m (OR = 0.6; 95% CI 0.4–0.8). There was substantial residual between-neighbourhood variance in physical activity (median odds ratio = 1.7). Other objectively measured neighbourhood-level characteristics were not associated with physical activity levels. Conclusions Distance to nearest greenspace is associated with meeting recommended physical activity levels in deprived London neighbourhoods. Despite residual variance in physical activity levels between neighbourhoods, we found little evidence for the influence of other measured neighbourhood-level characteristics.

Brain responses and looking behavior during audiovisual speech integration in infants predict auditory speech comprehension in the second year of life

The use of visual cues during the processing of audiovisual (AV) speech is known to be less efficient in children and adults with language difficulties and difficulties are known to be more prevalent in children from low-income populations. In the present study, we followed an economically diverse group of thirty-seven infants longitudinally from 6–9 months to 14–16 months of age. We used eye-tracking to examine whether individual differences in visual attention during AV processing of speech in 6–9 month old infants, particularly when processing congruent and incongruent auditory and visual speech cues, might be indicative of their later language development. Twenty-two of these 6–9 month old infants also participated in an event-related potential (ERP) AV task within the same experimental session. Language development was then followed-up at the age of 14–16 months, using two measures of language development, the Preschool Language Scale and the Oxford Communicative Development Inventory. The results show that those infants who were less efficient in auditory speech processing at the age of 6–9 months had lower receptive language scores at 14–16 months. A correlational analysis revealed that the pattern of face scanning and ERP responses to audiovisually incongruent stimuli at 6–9 months were both significantly associated with language development at 14–16 months. These findings add to the understanding of individual differences in neural signatures of AV processing and associated looking behavior in infants.

Brain responses to audiovisual speech mismatch in infants are associated with individual differences in looking behaviour

Research on audiovisual speech integration has reported high levels of individual variability, especially among young infants. In the present study we tested the hypothesis that this variability results from individual differences in the maturation of audiovisual speech processing during infancy. A developmental shift in selective attention to audiovisual speech has been demonstrated between 6 and 9 months with an increase in the time spent looking to articulating mouths as compared to eyes (Lewkowicz & Hansen-Tift. (2012) Proc. Natl Acad. Sci. USA, 109, 1431–1436; Tomalski et al. (2012) Eur. J. Dev. Psychol., 1–14). In the present study we tested whether these changes in behavioural maturational level are associated with differences in brain responses to audiovisual speech across this age range. We measured high-density event-related potentials (ERPs) in response to videos of audiovisually matching and mismatched syllables /ba/ and /ga/, and subsequently examined visual scanning of the same stimuli with eye-tracking. There were no clear age-specific changes in ERPs, but the amplitude of audiovisual mismatch response (AVMMR) to the combination of visual /ba/ and auditory /ga/ was strongly negatively associated with looking time to the mouth in the same condition. These results have significant implications for our understanding of individual differences in neural signatures of audiovisual speech processing in infants, suggesting that they are not strictly related to chronological age but instead associated with the maturation of looking behaviour, and develop at individual rates in the second half of the first year of life.

Physical Activity in Deprived Communities in London: Examining Individual and Neighbourhood-Level Factors

Introduction The objectives of this study were to examine relationships between neighbourhood-level and individual-level characteristics and physical activity in deprived London neighbourhoods. Methods In 40 of the most deprived neighbourhoods in London (ranked in top 11% in London by Index of Multiple Deprivation) a cross-sectional survey (n = 4107 adults aged > = 16 years), neighbourhood audit tool, GIS measures and routine data measured neighbourhood and individual-level characteristics. The binary outcome was meeting the minimum recommended (CMO, UK) 5×30 mins moderate physical activity per week. Multilevel modelling was used to examine associations between physical activity and individual and neighbourhood-level characteristics. Results Respondents living more than 300 m away from accessible greenspace had lower odds of achieving recommended physical activity levels than those who lived within 300 m; from 301–600 m (OR = 0.7; 95% CI 0.5–0.9) and from 601–900 m (OR = 0.6; 95% CI 0.4–0.8). There was substantial residual between-neighbourhood variance in physical activity (median odds ratio = 1.7). Other objectively measured neighbourhood-level characteristics were not associated with physical activity levels. Conclusions Distance to nearest greenspace is associated with meeting recommended physical activity levels in deprived London neighbourhoods. Despite residual variance in physical activity levels between neighbourhoods, we found little evidence for the influence of other measured neighbourhood-level characteristics.

Beach quality assessment and management in the Sotavento (Eastern) Algarve, Portugal

The purpose of this study on beach quality assessment and management was to evaluate the quality of five beaches in the Algarve Sotavento region of Portugal and to identify beach users’ preferences and priorities regarding their visit to a beach. The Algarve is one of the country’s most internationally known regions and it is generally perceived as a major tourist destination. Because of the increasing level of tourists, there is a specific need to address beach quality, as overcrowding can result in excessive litter, reduce water quality and consequently reduce the socio-economic value of the area. The main methodology for the evaluation of the beach quality in this pilot project was the Bathing Area Registration and Evaluation framework (BARE), which recognizes five beach types (rural, remote, resort, urban and village) through five main priority issues of concern to beach users (water quality, scenery, litter, safety, facilities) and evaluates the beach quality, ranging from one (low) to five (high) stars. After overall bathing area classification, Quarteira-Vilamoura, Ilha do Farol, Ilha Deserta and Ilha da Armona received three-star rating and Quinta do Lago site obtained a one-star rating. The quantitative research data on beach users’ preferences and priorities was obtained through administration of 50 questionnaires per beach and showed that beach users at all sites expressed the need for improved cleanliness, safety and facilities on the beach. The BARE framework, together with the questionnaire surveys, allowed the identification of management priorities required to improve the quality of individual beaches and therefore increase income from tourism.