Multilevel modelling for inference of genetic regulatory networks

Time-course experiments with microarrays are often used to study dynamic biological systems and genetic regulatory networks (GRNs) that model how genes influence each other in cell-level development of organisms. The inference for GRNs provides important insights into the fundamental biological processes such as growth and is useful in disease diagnosis and genomic drug design. Due to the experimental design, multilevel data hierarchies are often present in time-course gene expression data. Most existing methods, however, ignore the dependency of the expression measurements over time and the correlation among gene expression profiles. Such independence assumptions violate regulatory interactions and can result in overlooking certain important subject effects and lead to spurious inference for regulatory networks or mechanisms. In this paper, a multilevel mixed-effects model is adopted to incorporate data hierarchies in the analysis of time-course data, where temporal and subject effects are both assumed to be random. The method starts with the clustering of genes by fitting the mixture model within the multilevel random-effects model framework using the expectation-maximization (EM) algorithm. The network of regulatory interactions is then determined by searching for regulatory control elements (activators and inhibitors) shared by the clusters of co-expressed genes, based on a time-lagged correlation coefficients measurement. The method is applied to two real time-course datasets from the budding yeast (Saccharomyces cerevisiae) genome. It is shown that the proposed method provides clusters of cell-cycle regulated genes that are supported by existing gene function annotations, and hence enables inference on regulatory interactions for the genetic network.

A multilevel investigation of inequalities in clinical and psychosocial outcomes for women after breast cancer

Background In Australia, breast cancer is the most common cancer affecting Australian women. Inequalities in clinical and psychosocial outcomes have existed for some time, affecting particularly women from rural areas and from areas of disadvantage. We have a limited understanding of how individual and area-level factors are related to each other, and their associations with survival and other clinical and psychosocial outcomes. Methods/Design This study will examine associations between breast cancer recurrence, survival and psychosocial outcomes (e.g. distress, unmet supportive care needs, quality of life). The study will use an innovative multilevel approach using area-level factors simultaneously with detailed individual-level factors to assess the relative importance of remoteness, socioeconomic and demographic factors, diagnostic and treatment pathways and processes, and supportive care utilization to clinical and psychosocial outcomes. The study will use telephone and self-administered questionnaires to collect individual-level data from approximately 3, 300 women ascertained from the Queensland Cancer Registry diagnosed with invasive breast cancer residing in 478 Statistical Local Areas Queensland in 2011 and 2012. Area-level data will be sourced from the Australian Bureau of Statistics census data. Geo-coding and spatial technology will be used to calculate road travel distances from patients' residence to diagnostic and treatment centres. Data analysis will include a combination of standard empirical procedures and multilevel modelling. Discussion The study will address the critical question of: what are the individual- or area-level factors associated with inequalities in outcomes from breast cancer? The findings will provide health care providers and policy makers with targeted information to improve the management of women with breast cancer, and inform the development of strategies to improve psychosocial care for women with breast cancer.

A multilevel investigation into the effects of the philosophical community of inquiry on 6th grade students' reading comprehension, interest in maths, self-esteem, pro-social behaviours and emotional well-being

This investigation measured the effects of a one year participation in an Australian Philosophical Community of Inquiry program on 280 sixth grade students' reading comprehension, interest in maths, self-esteem, social behaviours, and emotional well-being. A multilevel model for change was used to detect differences in the response variables, between a quasi-experimental group and comparison group. Results showed that, for participants, reading comprehension significantly increased while interest in maths decreased. No differences between the groups were found for pro-social behaviour and emotional well-being. Self esteem, however, declined for participants while nonparticipants' self esteem increased.

Distance between home and work: A multilevel analysis of individual workers, neighbourhoods, and employment sites in Northern Ireland

Abstract. We explore the distances between home and work for employees at twenty-eight different employment sites across Northern Ireland. Substantively, this is important for better understanding the geography of labour catchments. Methodologically, with data on the distances between place of residence (566 wards) and place of work for some 15 000 workers, and the use of multilevel modelling (MLM), the analysis adds to the evidence derived from other census-based and survey-based studies. Descriptive analysis is supplemented with MLM that simultaneously explores individual, neighbourhood, and site variations in travel-to-work patterns using hierarchical and cross-classified model specifications, including individual and ecological predictor variables (and their cross-level interactions). In doing so we apportion variability to different levels and spatial contexts, and also outline the factors that shape spatial mobility. We find, as expected, that factors such as gender and occupation influence the distance between home and work, and also confirm the importance of neighbourhood characteristics (such as population density observed in ecological analyses at ward level) in shaping individual outcomes, with major differences found between urban and rural locations. Beyond this, the analysis of variability also points to the relative significance of residential location, with less individual variability in travel-to-work distance between workers within wards than within employment sites. We conclude by suggesting that, whilst some general ‘rules’ about the factors that shape labour catchments are possible (eg workers in rural areas and in higher occupations travel further than others), the complex variability between places highlighted by the MLM analysis illustrates the salience of place-specific uniqueness.

Socio-economic inequalities in women's fruit and vegetable intakes: a multilevel study of individual, social and environmental mediators

Objective: This study employed a multilevel design to test the contribution of individual, social and environmental factors to mediating socio-economic status (SES) inequalities in fruit and vegetable consumption among women. Design: A cross-sectional survey was linked with objective environmental data. Setting: A community sample involving 45 neighbourhoods. Subjects: In total, 1347 women from 45 neighbourhoods provided survey data on their SES (highest education level), nutrition knowledge, health considerations related to food purchasing, and social support for healthy eating. These data were linked with objective environmental data on the density of supermarkets and fruit and vegetable outlets in local neighbourhoods. Results: Multilevel modelling showed that individual and social factors partly mediated, but did not completely explain, SES variations in fruit and vegetable consumption. Store density did not mediate the relationship of SES with fruit or vegetable consumption. Conclusions: Nutrition promotion interventions should focus on enhancing nutrition knowledge and health considerations underlying food purchasing in order to promote healthy eating, particularly among those who are socio-economically disadvantaged. Further investigation is required to identify additional potential mediators of SES-diet relationships, particularly at the environmental level. © The Authors 2006.

The influence of neighbourhood formality status and socio-economic position on self-rated health among adult men and women: a multilevel, cross sectional, population study from Aleppo, Syria

Background There is substantial evidence from high income countries that neighbourhoods have an influence on health independent of individual characteristics. However, neighbourhood characteristics are rarely taken into account in the analysis of urban health studies from developing countries. Informal urban neighbourhoods are home to about half of the population in Aleppo, the second largest city in Syria (population>2.5 million). This study aimed to examine the influence of neighbourhood socioeconomic status (SES) and formality status on self-rated health (SRH) of adult men and women residing in formal and informal urban neighbourhoods in Aleppo. Methods The study used data from 2038 survey respondents to the Aleppo Household Survey, 2004 (age 18–65 years, 54.8% women, response rate 86%). Respondents were nested in 45 neighbourhoods. Five individual-level SES measures, namely education, employment, car ownership, item ownership and household density, were aggregated to the level of neighbourhood. Multilevel regression models were used to investigate associations. Results We did not find evidence of important SRH variation between neighbourhoods. Neighbourhood average of household item ownership was associated with a greater likelihood of reporting excellent SRH in women; odds ratio (OR) for an increase of one item on average was 2.3 (95% CI 1.3-4.4 (versus poor SRH)) and 1.7 (95% CI 1.1-2.5 (versus normal SRH)), adjusted for individual characteristics and neighbourhood formality. After controlling for individual and neighbourhood SES measures, women living in informal neighbourhoods were less likely to report poor SRH than women living in formal neighbourhoods (OR= 0.4; 95% CI (0.2- 0.8) (versus poor SRH) and OR=0.5; 95%; CI (0.3-0.9) (versus normal SRH). Conclusions Findings support evidence from high income countries that certain characteristic of neighbourhoods affect men and women in different ways. Further research from similar urban settings in developing countries is needed to understand the mechanisms by which informal neighbourhoods influence women’s health.

Alone against the crowd: Individual differences in referees' ability to cope under pressure

This paper contributes to the recent debate about the role of referees in the home advantage phenomenon. Specifically, it aims to provide a convincing answer to the newly posed question of the existence of individual differences among referees in terms of the home advantage (Boyko, Boyko, & Boyko, 2007; Johnston, 2008). Using multilevel modelling on a large and representative dataset we find that (1) the home advantage effect differs significantly among referees, and (2) this relationship is moderated by the size of the crowd. These new results suggest that a part of the home advantage is due to the effect of the crowd on the referees, and that some referees are more prone to be influenced by the crowd than others. This provides strong evidence to indicate that referees are a significant contributing factor to the home advantage. The implications of these findings are discussed both in terms of the relevant social psychological research, and with respect to the selection, assessment, and training of referees.

Promoting posttraumatic growth in police recruits : preliminary results of a randomised controlled resilience intervention trial

Recent research has demonstrated that the same experiences that may elicit symptoms of post-traumatic stress disorder (PTSD) in emergency service personnel can also provide a catalyst for positive personal changes such as posttraumatic growth (PTG). In this research newly recruited police officers (N = 412) participated in a randomised control trial of a program specifically designed to promote mental health. On entry to the academy, new recruits were randomly allocated, by classrooms, to either a treatment as usual condition (i.e., existing psychoeducation program) or to the intervention group. The Promoting Resilient Officers (PRO) program is a resilience building intervention adapted from an earlier resilience building program in collaboration with the police service. The PRO program also includes additional components on trauma and PTG. The current research included the participants who had experienced trauma prior to or during the research period (N = 246). It was hypothesised that participation in the PRO program would increase levels of PTG and lower levels of PTSD when compared to recruits in the control condition. Using multilevel modelling and post-hoc analyses, results indicated there were significantly higher levels of PTG across multiple dimensions when compared to the control group. There was no effect on PTSD symptoms with both conditions showing a floor effect. The research indicated the potential value of developing interventions that elicit reflections on the potential for positive as well as negative outcomes of experiencing traumatic and other highly challenging events.

The effect of temperature on height growth of Scots pine in northern Finland

The effect of temperature on height growth of Scots pine in the northern boreal zone in Lapland was studied in two different time scales. Intra-annual growth was monitored in four stands in up to four growing seasons using an approximately biweekly measurement interval. Inter-annual growth was studied using growth records representing seven stands and five geographical locations. All the stands were growing on a dry to semi-dry heath that is a typical site type for pine stands in Finland. The applied methodology is based on applied time-series analysis and multilevel modelling. Intra-annual elongation of the leader shoot correlated with temperature sum accumulation. Height growth ceased when, on average, 41% of the relative temperature sum of the site was achieved (observed minimum and maximum were 38% and 43%). The relative temperature sum was calculated by dividing the actual temperature sum by the long-term mean of the total annual temperature sum for the site. Our results suggest that annual height growth ceases when a location-specific temperature sum threshold is attained. The positive effect of the mean July temperature of the previous year on annual height increment proved to be very strong at high latitudes. The mean November temperature of the year before the previous had a statistically significantly effect on height increment in the three northernmost stands. The effect of mean monthly precipitation on annual height growth was statistically insignificant. There was a non-linear dependence between length and needle density of annual shoots. Exceptionally low height growth results in high needle-density, but the effect is weaker in years of average or good height growth. Radial growth and next year s height growth are both largely controlled by current July temperature. Nevertheless, their growth variation in terms of minimum and maximum is not necessarily strongly correlated. This is partly because height growth is more sensitive to changes in temperature. In addition, the actual effective temperature period is not exactly the same for these two growth components. Yet, there is a long-term balance that was also statistically distinguishable; radial growth correlated significantly with height growth with a lag of 2 years. Temperature periods shorter than a month are more effective variables than mean monthly values, but the improvement is on the scale of modest to good when applying Julian days or growing-degree-days as pointers.

一种基于区域分割的多级环境建模方法

针对现有移动机器人路径规划中各种环境建模方法存在使用范围有限、复杂问题处理能力不足和运行效率低、缺乏灵活性等问题，结合二维半描述和知识利用原理，提出了一种可以比较圆满地解决诸如建筑物内不同楼层连接、室内室外环境交替出现等实用结构性空间问题的基于区域分割的多级环境建模方法。