Age-related differences in pointing accuracy in familiar and unfamiliar environments

This study aimed to investigate age-related differences in spatial mental representations of familiar and unfamiliar places. Nineteen young adults (aged 18\u201323) and 19 older adults (aged 60\u201374), all living in the same Italian town, completed a set of visuospatial measures and then pointed in the direction of familiar landmarks in their town and in the direction of landmarks in an unknown environment studied on a map. Results showed that older adults were less accurate in the visuospatial tasks and in pointing at landmarks in an unfamiliar environment, but performed as well as the young adults when pointing to familiar places. Pointing performance correlated with visuospatial tests accuracy in both familiar and unfamiliar environments, while only pointing in an unknown environment correlated with visuospatial working memory (VSWM). The spatial representation of well-known places seems to be well preserved in older adults (just as well as in young adults), while it declines for unfamiliar environments. Spatial abilities sustain the mental representations of both familiar and unfamiliar environments, while the support of VSWM resources is only needed for the latter

Investigating the different domains of environmental knowledge acquired from virtual navigation and their relationship to cognitive factors and wayfinding inclinations

When learning an environment from virtual navigation people gain knowledge about landmarks, their locations, and the paths that connect them. The present study newly aimed to investigate all these domains of knowledge and how cognitive factors such as visuospatial abilities and wayfinding inclinations might support virtual passive navigation. A total of 270 participants (145 women) were tested online. They: (i) completed visuospatial tasks and answered questionnaires on their wayfinding inclinations; and (ii) learnt a virtual path. The environmental knowledge they gained was assessed on their free recall of landmarks, their egocentric and allocentric pointing accuracy (location knowledge), and their performance in route direction and landmark location tasks (path knowledge). Visuospatial abilities and wayfinding inclinations emerged as two separate factors, and environmental knowledge as a single factor. The SEM model showed that both visuospatial abilities and wayfinding inclinations support the environmental knowledge factor, with similar pattern of relationships in men and women. Overall, factors related to the individual are relevant to the environmental knowledge gained from an online virtual passive navigation

ncRNA orthologies in the vertebrate lineage.

Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the same time, methods such as PHASE or RAxML have implemented substitution models that consider pairs of sites to enable proper modelling of the loops and other features of RNA secondary structure. Here, we present a comprehensive analysis pipeline for the automatic detection of orthologues and paralogues for ncRNA genes. We focus on gene families represented in Rfam and for which a specific covariance model is provided. For each family ncRNA genes found in all Ensembl species are aligned using Infernal, and several trees are built using different substitution models. In parallel, a genomic alignment that includes the ncRNA genes and their flanking sequence regions is built with PRANK. This alignment is used to create two additional phylogenetic trees using the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The trees arising from both the ncRNA and genomic alignments are merged using TreeBeST, which reconciles them with the species tree in order to identify speciation and duplication events. The final tree is used to infer the orthologues and paralogues following Fitch's definition. We also determine gene gain and loss events for each family using CAFE. All data are accessible through the Ensembl Comparative Genomics ('Compara') API, on our FTP site and are fully integrated in the Ensembl genome browser, where they can be accessed in a user-friendly manner.Database URL: http://www.ensembl.org

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data

Virtual environments as memory training devices in navigational tasks for older adults.

Cognitive training approaches using virtual environments (VEs) might counter age-related visuospatial memory decline and associated difficulties in wayfinding. However, the effects of the visual design of a VE in route learning are not fully understood. Therefore, we created a custom-designed VE optimized for route learning, with adjusted levels of realism and highlighted landmark locations (MixedVE). Herein we tested participants' route recall performance in identifying direction of turn at the intersection with this MixedVE against two baseline alternatives (AbstractVE, RealisticVE). An older vs. a younger group solved the tasks in two stages (immediate vs. delayed recall by one week). Our results demonstrate that the MixedVE facilitates better recall accuracy than the other two VEs for both age groups. Importantly, this pattern persists a week later. Additionally, our older participants were mostly overconfident in their route recall performance, but the MixedVE moderated this potentially detrimental overconfidence. Before the experiment, participants clearly preferred the RealisticVE, whereas after the experiment, most of the younger, and many of the older participants, preferred the MixedVE. Taken together, our findings provide insights into the importance of tailoring visualization design in route learning with VEs. Furthermore, we demonstrate the great potential of the MixedVE and by extension, of similar VEs as memory training devices for route learning, especially for older participants

Database: The Journal of Biological Databases and Curation

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.Database URL: http://www.ensembl.org

Schools and the legacy of hybrid buildings

Learning from the past, collecting data on the Italian condition of school buildings, our R&D work aimed to question the design process of school buildings in Italy introducing an innovative model of school, which turned the conventional and isolated, mono-functional and rigid school buildings into interior urban public spaces and porous community hubs to empower the communities around them and to become manifestos of sustainability. Through some built examples of school buildings designed in Italy, the paper discusses the outputs and impact of the introduction of new design layouts, participation projects with different stakeholders and sustainability. The research has guided the introduction of the new Italian guide-lines for school building design, approved in 2013. A future perspective to be explored is the reconsideration of exporting the strategy in different contexts and to design reconsider other public infrastructures turning the mono-functional use of public buildings into hybrid and multifunctional ones

The Quest for Orthologs benchmark service and consensus calls in 2020.

The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases

Advances and Applications in the Quest for Orthologs

Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs) and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources