Visualization methods for genealogical and RNA-sequencing studies: Pertinence, software, and applications

As is the case in many fields, biological disciplines are now facing the challenges of increasingly large and complex data. Biologists must now process and meaningfully interpret a deluge of data, and one necessary approach toward accomplishing this goal is through the use of visualization. Ultimately, the objective of developing visualization tools for biological data is to provide biologists with enhanced insight into the processes within organelles, cells, organs, and even whole organisms. R is a free interpretive programming language for statistical computing and graphics. It is widely used by statisticians to develop statistical software and data analysis tools, and has become even more popular in recent years for researchers across a wide range of disciplines. In this dissertation, we focus primarily on developing effective visualization tools for genealogical and RNA-sequencing datasets within the R framework. This work addresses the lack of modern and interactive visualization techniques in the fields of genealogy and RNA-sequencing through the following specific aims: (i) develop improved visualization techniques for genealogical datasets; (ii) generate comprehensive collections of examples underlining the importance of visualizing RNA-sequencing datasets; (iii) develop improved visualization methods for RNA-sequencing datasets; and (iv) perform an RNA-sequencing experiment that examines virus inoculation and nutrition in honey bees while applying the visualization tools we previously validated and developed. First, we present our software package ggenealogy that includes new visualization tools for genealogical datasets. In particular, we introduce a new method that provides unequivocal information about lineages in situations where intergenerational breeding occurs, as is often the case in agronomic applications. This was not previously possible with standard pedigree charts. Second, we create a compilation of reproducible examples using numerous public RNA-sequencing datasets that demonstrates uncommon visualization techniques detecting normalization issues, differential expression designation problems, and common analysis errors. We also show that these visualization tools can identify genes of interest in ways undetectable with models. Third, we introduce our software package bigPint that comprises visualization tools for RNA-sequencing datasets, many of which we previously showed to be beneficial through extensive testing. Fourth, we conduct the first RNA-sequencing study that examines the combined effects of monofloral diets and Israeli Acute Paralysis Virus (IAPV) inoculation on gene expression patterns in honey bees. These factors have been implicated as environmental stressors that pose heightened dangers to honey bee health, the decline of which has major implications for agricultural sustainability. Importantly, we use an extensive data visualization approach in our RNA-sequencing study that incorporates the methods we developed earlier and recommend such an avenue for researchers who have noisy RNA-sequencing data in the future

Cultural basis of social ‘deficits’ in autism spectrum disorders

There is very little research that specifically looks at how autism spectrum disorders are perceived in various communities. This qualitative research was conducted with parents who had children on the autistic spectrum belonging to four different ethnic communities (White British, Somali, West African and South Asian- 63 in total) and living in the UK. The study found that the importance that the parents give to various social skills varied on the basis of their cultural background and the gender of the parent. This is an important aspect to consider while providing support and services to individuals on the autism spectrum and their family members if the services have to be appropriate for their needs. This consideration would also enable the individuals on the autism spectrum to develop appropriate social skills required within their cultural groups. This is a preliminary study and further research on the topic is required

Bullying and school disruption assessment: studies with Portuguese adolescent students

Problem Statement: The question of bullying and school disruptive behavior has emerged as a powerful issue in Portuguese educational context. The lack of evaluation instruments, with studied psychometric characteristics, has constituted a problem. Purpose of Study: School disruption and bullying assessment, in Portuguese adolescents, was the focus of this research. Research Methods: The psychometric qualities — internal consistency and the external validity — were analyzed in different scales. Findings: The analyses carried out confirm the scales as reliable and valid instruments. Conclusions: These instruments may be a useful avenue for teachers, psychologists and other education professionals

Transcriptomic responses to diet qualityand viral infection in Apis mellifera

Background Parts of Europe and the United States have witnessed dramatic losses in commercially managed honey bees over the past decade to what is considered an unsustainable extent. The large-scale loss of bees has considerable implications for the agricultural economy because bees are one of the leading pollinators of numerous crops. Bee declines have been associated with several interactive factors. Recent studies suggest nutritional and pathogen stress can interactively contribute to bee physiological declines, but the molecular mechanisms underlying interactive effects remain unknown. In this study, we provide insight into this question by using RNA-sequencing to examine how monofloral diets and Israeli acute paralysis virus inoculation influence gene expression patterns in bees. Results We found a considerable nutritional response, with almost 2000 transcripts changing with diet quality. The majority of these genes were over-represented for nutrient signaling (insulin resistance) and immune response (Notch signaling and JaK-STAT pathways). In our experimental conditions, the transcriptomic response to viral infection was fairly limited. We only found 43 transcripts to be differentially expressed, some with known immune functions (argonaute-2), transcriptional regulation, and muscle contraction. We created contrasts to explore whether protective mechanisms of good diet were due to direct effects on immune function (resistance) or indirect effects on energy availability (tolerance). A similar number of resistance and tolerance candidate differentially expressed genes were found, suggesting both processes may play significant roles in dietary buffering from pathogen infection. Conclusions Through transcriptional contrasts and functional enrichment analysis, we contribute to our understanding of the mechanisms underlying feedbacks between nutrition and disease in bees. We also show that comparing results derived from combined analyses across multiple RNA-seq studies may allow researchers to identify transcriptomic patterns in bees that are concurrently less artificial and less noisy. This work underlines the merits of using data visualization techniques and multiple datasets to interpret RNA-sequencing studies.Ope

Parenting-by-gender interactions in child psychopathology: attempting to address inconsistencies with a Canadian national database

<p>Abstract</p> <p>Background</p> <p>Research has shown strong links between parenting and child psychopathology. The moderating role of child gender is of particular interest, due to gender differences in socialization history and in the prevalence of psychiatric disorders. Currently there is little agreement on how gender moderates the relationship between parenting and child psychopathology. This study attempts to address this lack of consensus by drawing upon two theories (self-salience vs. gender stereotyped misbehaviour) to determine how child gender moderates the role of parenting, if at all.</p> <p>Methods</p> <p>Using generalized estimating equations (GEE) associations between three parenting dimensions (hostile-ineffective parenting, parental consistency, and positive interaction) were examined in relationship to child externalizing (physical aggression, indirect aggression, and hyperactivity-inattention) and internalizing (emotional disorder-anxiety) dimensions of psychopathology. A sample 4 and 5 year olds from the National Longitudinal Survey of Children and Youth (NLSCY) were selected for analysis and followed over 6 years (N = 1214). Two models with main effects (Model 1) and main effects plus interactions (Model 2) were tested.</p> <p>Results</p> <p>No child gender-by-parenting interactions were observed for child physical aggression and indirect aggression. The association between hostile-ineffective parenting and child hyperactivity was stronger for girls, though this effect did not reach conventional levels of statistical significance (<it>p </it>= .059). The associations between parenting and child emotional disorder did vary as a function of gender, where influences of parental consistency and positive interaction were stronger for boys.</p> <p>Discussion</p> <p>Despite the presence of a few significant interaction effects, hypotheses were not supported for either theory (i.e. self-salience or gender stereotyped misbehaviour). We believe that the inconsistencies in the literature regarding child gender-by-parenting interactions is due to the reliance on gender as an indicator of a different variable which is intended to explain the interactions. This may be problematic because there is likely within-gender and between-sample variability in such constructs. Future research should consider measuring and modelling variables that are assumed to explain such interactions when conducting gender-by-parenting research.</p

Learning and consolidation of new spoken words in autism spectrum disorder

Autism spectrum disorder (ASD) is characterized by rich heterogeneity in vocabulary knowledge and word knowledge that is not well accounted for by current cognitive theories. This study examines whether individual differences in vocabulary knowledge in ASD might be partly explained by a difficulty with consolidating newly learned spoken words and/or integrating them with existing knowledge. Nineteen boys with ASD and 19 typically developing (TD) boys matched on age and vocabulary knowledge showed similar improvements in recognition and recall of novel words (e.g. 'biscal') 24 hours after training, suggesting an intact ability to consolidate explicit knowledge of new spoken word forms. TD children showed competition effects for existing neighbors (e.g. 'biscuit') after 24 hours, suggesting that the new words had been integrated with existing knowledge over time. In contrast, children with ASD showed immediate competition effects that were not significant after 24 hours, suggesting a qualitative difference in the time course of lexical integration. These results are considered from the perspective of the dual-memory systems framework

Routine omics collection is a golden opportunity for European human research in space and analog environments

Widespread generation and analysis of omics data have revolutionized molecular medicine on Earth, yet its power to yield new mechanistic insights and improve occupational health during spaceflight is still to be fully realized in humans. Nevertheless, rapid technological advancements and ever-regular spaceflight programs mean that longitudinal, standardized, and cost-effective collection of human space omics data are firmly within reach. Here, we consider the practicality and scientific return of different sampling methods and omic types in the context of human spaceflight. We also appraise ethical and legal considerations pertinent to omics data derived from European astronauts and spaceflight participants (SFPs). Ultimately, we propose that a routine omics collection program in spaceflight and analog environments presents a golden opportunity. Unlocking this bright future of artificial intelligence (AI)-driven analyses and personalized medicine approaches will require further investigation into best practices, including policy design and standardization of omics data, metadata, and sampling methods

Anticipating and addressing event-specific alcohol consumption among adolescents.

Background: Various specific events and celebrations are associated with excessive alcohol consumption and related harms. End-of-school celebrations such as Schoolies in Australia are of particular concern given high levels of documented harm among underage and young drinkers. The present study investigated high school students’ expectations of their Schoolies celebrations to inform future interventions to reduce adverse outcomes among members of this vulnerable group and other young people involved in similar rites of passage. Methods: A link to an online survey was distributed via high schools and Schoolies-related websites. The survey included qualitative questions that invited respondents to discuss (i) aspects of Schoolies they were looking forward to most and least and (ii) their perceptions of the likely consequences if they refrained from consuming alcohol during the event. In total, 435 students provided responses. Results: Respondents discussed the role of Schoolies in marking their transition to adulthood. Their comments revealed a cross-temporal focus indicating that Schoolies is simultaneously symbolic of the past, present, and future. Through its ability to enhance social interaction, alcohol was perceived to have a vital role in realising the potential of this event to signify and facilitate this temporal progression. Conclusions: Results suggest interventions that treat Schoolies as an isolated event that occurs in specific locations may fail to appreciate the extent to which these events transcend time for those involved. Instead, harm reduction is likely to involve a reconceptualisation of the event among both participants and authority figures to facilitate the provision of alternative pastimes to drinking during Schoolies that yield similar social benefits