Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting from short DNA reads. However, the performance of each of these tools is contingent on the length and quality of the sequencing data, the structure and complexity of the genome sequence, and the resolution and quality of long-range information. Furthermore, in the absence of any metric that captures the most fundamental "features" of a high-quality assembly, there is no obvious recipe for users to select the most desirable assembler/assembly. International competitions such as Assemblathons or GAGE tried to identify the best assembler(s) and their features. Some what circuitously, the only available approach to gauge de novo assemblies and assemblers relies solely on the availability of a high-quality fully assembled reference genome sequence. Still worse, reference-guided evaluations are often both difficult to analyze, leading to conclusions that are difficult to interpret. In this paper, we circumvent many of these issues by relying upon a tool, dubbed FRCbam, which is capable of evaluating de novo assemblies from the read-layouts even when no reference exists. We extend the FRCurve approach to cases where lay-out information may have been obscured, as is true in many deBruijn-graph-based algorithms. As a by-product, FRCurve now expands its applicability to a much wider class of assemblers -- thus, identifying higher-quality members of this group, their inter-relations as well as sensitivity to carefully selected features, with or without the support of a reference sequence or layout for the reads. The paper concludes by reevaluating several recently conducted assembly competitions and the datasets that have resulted from them.Comment: Submitted to PLoS One. Supplementary material available at http://www.nada.kth.se/~vezzi/publications/supplementary.pdf and http://cs.nyu.edu/mishra/PUBLICATIONS/12.supplementaryFRC.pd

'You Were Born Again With Us': Narratives of Italian Families Formed Through International Adoption

This thesis presents a qualitative study of adoptive parents, childrens, young adults and experts’ accounts of communication within families about a child’s past. Until now, this particular aspect of international adoption in Italy has received little attention. The aims of this study are to understand how both parents and adoptees’ deal with and manage the origins of adoptees, and also experts’ views of this communication. In addition, this research explores the potentiality of the use of 'life-story work’ amongst this specific sample. This study uses in-depth interviews to unravel the experiences of ten adoptive parents with their five adopted children and five young adopted adults. It also includes the perspectives of seven experts. The findings are embedded in the Italian social and cultural context, which contributes to shaping the meaning of the accounts collected. The findings show that all of the families had developed an adoption story. Visual aids and documents help and support the telling of these stories. Furthermore, the various stories served different functions: they enabled communication, they presented challenges, and they emphasised the relationships with the actors involved in international adoption. The findings show diversity in the approaches to communicative openness: the practices presented by the sample families in this research are organised according to four different approaches to communication. The differences amongst the families, children and young adults are linked to the amount of information available to the families; the child’s attitude to his or her past; the influence of the actors involved in the adoption; the way in which adoptive kinship is understood; the way in which the laws are applied, and the ways in which children’s voices and needs are accounted for by families and accredited bodies

Inhibitory mechanisms in the LGN: A possible substrate for amblyopia?

Inhibitory mechanisms in the LGN: A possible substrate for amblyopia

Interventions that prevent or reduce obesity in children from birth to five years of age: A systematic review

Childhood obesity worldwide affects 5.6% or 38.3 million children under five years of age. The longer children are overweight or obese, the more likely they are to become obese adults with all the contingent morbidity involved. An extensive number of preventive interventions to combat childhood obesity have been carried out worldwide. This article reports a systematic review of interventions aimed to reducing or preventing obesity under-fives. The search was performed with six different databases: Web of Science, PsycINFO, Cochrane, PubMed, Medline, and CINAHL. Studies meeting the inclusion criteria were independently assessed using Joanna Briggs Institute methodology. Thirty studies involving 23,185 children across nine countries were included. Twenty-two were randomised controlled trials, and 8 quasi-experimental pretest/post-test design with comparison. These studies fell into four different categories: home-based interventions with family involvement (n = 12), preschool/early childhood settings (n = 9), multicomponent interventions across multiple settings (n = 6) and healthcare setting (n = 3). Future research should focus on increasing the accessibility of education on diet and physical activity for deprived families as well as the cultural acceptability of interventions to prevent childhood obesity

Autism and children: diagnosis, functional profiles and intervention

In the last forty years, approaches to and the social perception of autism have changed significantly [...

Patient centric intervention for children with high functioning autism spectrum disorder. Can ICT solutions improve the state of the art ?

In my PhD research we developed an integrated technological platform for the acquisition of neurophysiologic signals in a semi-naturalistic setting where children are free to move around, play with different objects and interact with the examiner. The interaction with the examiner rather than with a screen is another very important feature of the present research, and allows recreating a more real situation with social interactions and cues. In this paradigm, we can assume that the signals acquired from the brain and the autonomic system, are much more similar to what is generated while the child interacts in common life situations. This setting, with a relatively simple technical implementation, can be considered as one step towards a more behaviorally driven analysis of neurophysiologic activity. Within the context of a pilot open trial, we showed the feasibility of the technological platform applied to the classical intervention solutions for the autism. We found that (1) the platform was useful during both children-therapist interaction at hospital as well as children-parents interaction at home, (2) tailored intervention was compatible with at home use and non-professional therapist/parents. Going back to the title of my thesis: 'Can ICT solution improve the state-of-the-art ?' the answer could be: 'Yes it can be an useful support for a skilled professional in the field of autis

The social effect of "being imitated" in children with autism spectrum disorder

There is evidence that "being imitated" has social effects, and that the imitation of the child's actions may be used as a strategy to promote social engagement in children with autism spectrum disorder (ASD). The observation of someone that imitates us recruits, indeed, neural areas involved in social cognition. We reviewed studies exploring the behavioral consequences of "being imitated" in children with ASD. We aimed at assessing what are the social skills targeted by this strategy, and the factors that may improve the response. The "being imitated" strategy improves social gazes, proximal social behaviors, and play skills, particularly in children with low developmental level, and also when the strategy is implemented by children's mothers. The "being imitated" may be used as a tool in early intervention to improve social skills, helping to assess the effects of intervention at both behavioral and neural level

Creating Community and Belonging in a Designated Housing Estate for Disabled People

In recent years there has been an ideological push within social care away from segregated housing provision towards supported housing integrated within the wider community (McConkey, Keogh, Bunting, Iriarte, & Watson, 2016; Merrells, Buchanan, & Waters, 2019; Overmars-Marx, Thomése, Verdonschot, & Meininger, 2014). Despite this, many housing solutions for older and disabled people continue to be built on a designated basis, with physical and emotional wellbeing outcomes being both contested and mixed. After reviewing key policy relating to social care housing alongside some of the theoretical and ideological positions, this article explores the social and emotional outcomes of a diverse group of disabled people living with mental health difficulties, physical and intellectual impairments, illnesses and age-related conditions, who moved into a small, purpose-built estate of smart homes. Drawing primarily on qualitative data collected from tenants prior to moving and again seven months following relocation, the impact of moving into the estate on tenants’ sense of wellbeing and feelings of inclusion will be analysed and discussed in relation to efforts to build a new community

How attention to faces and objects changes over time in toddlers with autism spectrum disorders: Preliminary evidence from an eye tracking study

Further understanding of the longitudinal changes in visual pattern of toddlers with autism spectrum disorders (ASDs) is needed. We examined twelve 19 to 33-month-old toddlers at their first diagnosis (mean age: 25.1 months) and after six months (mean age: 31.7 months) during two initiating joint attention (IJA) tasks using eye tracking. Results were compared with the performance of age-matched typically developing (TD) toddlers evaluated at a single time-point. Autistic toddlers showed longitudinal changes in the visual sensory processing of the IJA tasks, approaching TD performance with an improvement in the ability to disengage and to explore the global space. Findings suggest the use of eye tracking technology as an objective, non-intrusive, adjunctive tool to measure outcomes in toddlers with ASD