Did you hear? Auditory prospective memory cues are more beneficial for autistic than for non-autistic children and adolescents.

BACKGROUND: The transition from primary to secondary school is particularly difficult for autistic children, a transition underpinned by an increase in prospective memory (PM) demands. AIMS: To better understand PM in autistic children of the relevant age range and its underlying processes, the current study investigated the impact of cue salience (distinctiveness) on PM in autistic and non-autistic children and adolescents. The study was unique in manipulating the visual and auditory salience of PM cues. Salient cues are assumed to put lower demands on executive control resources as compared to cues that blend in with the ongoing activity. METHODS AND PROCEDURES: The children completed a computer-based categorisation task in which an event-based PM task was embedded. The salience of PM cues was manipulated (low, high visual and high auditory salience). OUTCOMES AND RESULTS: Results revealed that both groups benefitted from an increase in visual and auditory salience, but only autistic participants were faster to respond to auditory cues. CONCLUSIONS AND IMPLICATIONS: Increased cue salience improved PM performance for all children. Positive effects of auditory cues were especially evident in autistic children.

Comparison of disaccharide donors for heparan sulfate synthesis: uronic acids vs. their pyranose equivalents.

Late oxidation of hexose based building blocks or the use of uronic acid containing building blocks are two complementary strategies in the synthesis of glycosaminoglycans, the latter simplifiying the later stages of the process. Here we report the synthesis and evaluation of various disaccharide donors-uronic acids and their pyranose equivalents-for the synthesis of heparan sulfate, using an established protective group strategy. Hexose based "imidate" type donors perform well in the studied glycosylations, while their corresponding uronate esters fall short; a uronate ester thioglycoside performs equal to, if not better than, a hexose thioglycoside equivalent.

Do importance instructions improve time-based prospective remembering in autism spectrum conditions?

This study explored the impact of motivation on the memory for delayed intentions (so-called, prospective memory, PM) in autistic individuals. Specifically, we were interested in the effects of personal (i.e., receiving a reward) as compared to social motivation (i.e., performing a favour for someone). Given the well-established theory of mind deficits in autism, we expected autistic individuals to benefit more strongly from personal than social importance manipulations, whereas the opposite pattern was predicted for controls. Sixty-one adolescents with autism and 61 typically developing adolescents participated, with each group distributed equally to one of the three motivation conditions of standard, social and personal reward. Participants worked on a 2-back picture-based ongoing task in which a time-based PM task was embedded. A mixed 2 (Group) x 3 (Motivation condition) analysis of covariance with age, verbal and non-verbal abilities as covariates and correct PM responses as dependent variable indicated solely a main effect of group, with controls outperforming the autism group. In contrast to our expectations, there was no main effect of condition, no significant interaction, and none of the covariates had any significant impact. However, further planned analyses revealed that controls only outperformed autistic individuals in the personal reward condition. Controls performed significantly best when a personal reward was promised, whereas there were no significant differences between the motivation conditions for autistic individuals. Findings are discussed in terms of underlying processes.

Prospective memory in autism: theory and literature review.

OBJECTIVE: The current article set out to review all research conducted to date investigating prospective memory (PM) in autism. METHOD: All studies on PM in autism are first described, followed by a critical review and discussion of experimental findings within the multiprocess framework. PM in autism is then considered through an embodied predictive-coding account of autism. RESULTS: Overall, despite somewhat inconsistent methodologies, a general deficit in PM in autism is observed, with evidence mostly in line with the multiprocess framework. That is, for tasks that are high in cognitive and attentional demand (e.g. time-based tasks; event-based cues of non-focality or low salience) PM performance of autistic participants is impaired. Building upon previous work in predictive-coding, and the way in which expected precision modulates attention, we postulate mechanisms that underpin PM and the potential deficits seen in autism. Furthermore, a unifying predictive-coding account of autism is extended under embodied predictive-coding models, to show how a predictive-coding impairment accounts not only for characteristic autistic difficulties, but also for commonly found differences in autistic movement. CONCLUSIONS: We show how differences in perception and action, core to the development of autism, lead directly to problems seen in PM. Using this link between movement and PM, we then put forward a number of holistic, embodied interventions to support PM in autism.

Ensembl 2017.

Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.

Ensembl 2016.

The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.

Event-based prospective memory in mildly and severely autistic children.

BACKGROUND: There is a growing body of research into the development of prospective memory (PM) in typically developing children but research is limited in autistic children (Aut) and rarely includes children with more severe symptoms. AIMS: This study is the first to specifically compare event-based PM in severely autistic children to mildly autistic and typically developing children. METHODS AND PROCEDURES: Fourteen mildly autistic children and 14 severely autistic children, aged 5-13 years, were matched for educational attainment with 26 typically developing children aged 5-6 years. Three PM tasks and a retrospective memory task were administered. OUTCOMES AND RESULTS: Results showed that severely autistic children performed less well than typically developing children on two PM tasks but mildly autistic children did not differ from either group. No group differences were found on the most motivating (a toy reward) task. CONCLUSIONS AND IMPLICATIONS: The findings suggest naturalistic tasks and motivation are important factors in PM success in severely autistic children and highlights the need to consider the heterogeneity of autism and symptom severity in relation to performance on event-based PM tasks.

The Role of Extrinsic Rewards and Cue-Intention Association in Prospective Memory in Young Children.

The current study examined, for the first time, the effect of cue-intention association, as well as the effects of promised extrinsic rewards, on prospective memory in young children, aged 5-years-old (n = 39) and 7-years-old (n = 40). Children were asked to name pictures for a toy mole, whilst also having to remember to respond differently to certain target pictures (prospective memory task). The level to which the target picture was associated with the intention was manipulated across two conditions (low- or high-association) for all participants, whilst half of the participants were promised a reward for good prospective memory performance. Results showed a main effect of age, with the 7-year-olds outperforming the 5-year-olds. Furthermore, there was a main effect of reward, with those promised a reward performing better than those who were not. No effect was found for cue-association, with the participants of both age groups performing equally well in both association conditions. No significant interactions were found between any of the variables. The potentially important role of reward in young children's everyday prospective memory tasks, and possible reasons for the lack of a reflexive-associative effect, are discussed.

Ensembl 2015.

Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.

Solid-state dimer method for calculating solid-solid phase transitions.

The dimer method is a minimum mode following algorithm for finding saddle points on a potential energy surface of atomic systems. Here, the dimer method is extended to include the cell degrees of freedom for periodic solid-state systems. Using this method, reaction pathways of solid-solid phase transitions can be determined without having to specify the final state structure or reaction mechanism. Example calculations include concerted phase transitions between CdSe polymorphs and a nucleation and growth mechanism for the A15 to BCC transition in Mo.

Ensembl 2014.

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.

Combining Kohn-Sham and orbital-free density-functional theory for Hugoniot calculations to extreme pressures.

The shock Hugoniot for lithium 6 deuteride ((6)LiD) was calculated via first principles using Kohn-Sham density-functional theory molecular dynamics (KSMD) for temperatures of 0.5-25 eV. The upper limit of 25 eV represents a practical limit where KSMD is no longer computationally feasible due to the number of electronic bands which are required to be populated. To push the Hugoniot calculations to higher temperatures we make use of orbital-free density-functional theory molecular dynamics (OFMD). Thomas-Fermi-Dirac-based OFMD gives a poor description of the electronic structure at low temperatures so the initial state is not well defined. We propose a method of bootstrapping the Hugoniot from OFMD to the Hugoniot from KSMD between 10 and 20 eV, where the two methods are in agreement. The combination of KSMD and OFMD allows construction of a first-principles Hugoniot from the initial state to 1000 eV. Theoretical shock-compression results are in good agreement with available experimental data and exhibit the appropriate high-temperature limits. We show that a unified KSMD-OFMD Hugoniot can be used to assess the quality of the existing equation-of-state (EOS) models and inform better EOS models based on justifiable physics.

Ensembl 2013.

The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.

Optimizing transition states via kernel-based machine learning.

We present a method for optimizing transition state theory dividing surfaces with support vector machines. The resulting dividing surfaces require no a priori information or intuition about reaction mechanisms. To generate optimal dividing surfaces, we apply a cycle of machine-learning and refinement of the surface by molecular dynamics sampling. We demonstrate that the machine-learned surfaces contain the relevant low-energy saddle points. The mechanisms of reactions may be extracted from the machine-learned surfaces in order to identify unexpected chemically relevant processes. Furthermore, we show that the machine-learned surfaces significantly increase the transmission coefficient for an adatom exchange involving many coupled degrees of freedom on a (100) surface when compared to a distance-based dividing surface.

A generalized solid-state nudged elastic band method.

A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid-solid transformations involving both atomic and unit-cell degrees of freedom. We combine atomic and cell degrees of freedom into a unified description of the crystal structure so that calculated reaction paths are insensitive to the choice of periodic cell. For the rock-salt to wurtzite transition in CdSe, we demonstrate that the method is robust for mechanisms dominated either by atomic motion or by unit-cell deformation; notably, the lowest-energy transition mechanism found by our G-SSNEB changes with cell size from a concerted transformation of the cell coordinates in small cells to a nucleation event in large cells. The method is efficient and can be applied to systems in which the force and stress tensor are calculated using density functional theory.

Paths to which the nudged elastic band converges.

A recent letter to the editor (Quapp and Bofill, J Comput Chem 2010, 31, 2526) claims that the nudged elastic band (NEB) method can converge toward gradient extremal paths and not to steepest descent paths, as has been assumed. Here, we show that the NEB does in fact converge to steepest descent paths and that the observed tendency for the NEB to approach gradient extremal paths was a consequence of implementation errors. We also note that while the NEB finds steepest descent paths, these are not necessarily minimum energy paths in the sense of being a set of points which are minima in the potential energy surface perpendicular to the path. An example is given where segments of steepest descent paths follow potential energy ridges.

Kinetic and thermodynamic evaluation of the reversible N-heterocyclic carbene-isothiocyanate coupling reaction: applications in latent catalysis.

Using stopped flow and other spectroscopic techniques, the thermodynamic parameters of the coupling reaction between 1,3-dimesitylimidazolylidene and phenyl isothiocyanate were determined (H(o) = -96.1 kJ mol(-1) and ΔS(o) = -39.6 J mol(-1) K(-1)). On the basis of these data which indicated that the reaction was reversible (K(eq) = 5.94 × 10(14) M(-1) at 25 °C; k(f) = 252 M(-1) s(-1); k(r) = 4.24 × 10(-13) s(-1)), the adduct formed from the two aforementioned coupling partners was used as a latent catalyst to facilitate the [2 + 2 + 2] cyclotrimerization of phenyl isocyanate and the polymerization of DL-lactide.

Alchemical derivatives of reaction energetics.

Based on molecular grand canonical ensemble density functional theory, we present a theoretical description of how reaction barriers and enthalpies change as atoms in the system are subjected to alchemical transformations, from one element into another. The change in the energy barrier for the umbrella inversion of ammonia is calculated along an alchemical path in which the molecule is transformed into water, and the change in the enthalpy of protonation for methane is calculated as the molecule is transformed into a neon atom via ammonia, water, and hydrogen fluoride. Alchemical derivatives are calculated analytically from the electrostatic potential in the unperturbed system, and compared to numerical derivatives calculated with finite difference interpolation of the pseudopotentials for the atoms being transformed. Good agreement is found between the analytical and numerical derivatives. Alchemical derivatives are also shown to be predictive for integer changes in atomic numbers for oxygen binding to a 79 atom palladium nanoparticle, illustrating their potential use in gradient-based optimization algorithms for the rational design of catalysts.

Intrinsic diffusion of hydrogen on rutile TiO2(110).

The combined experimental and theoretical study of intrinsic hydrogen diffusion on bridge-bonded oxygen (BBO) rows of TiO 2(110) is presented. Sequences of isothermal scanning tunneling microscopy images demonstrate a complex behavior of hydrogen formed by water dissociation on BBO vacancies. Different diffusion rates are observed for the two hydrogens in the original geminate OH pair suggesting the presence of a long-lived polaronic state. For the case of separated hydroxyls, both theory and experiment yield comparable temperature-dependent diffusion rates. Density functional theory calculations show that there are two comparable low energy diffusion pathways for hydrogen motion along the BBO from one BBO to its neighbor, one by a direct hop and the other by an intermediate minimum at a terrace O. The values of kinetic parameters (prefactors and diffusion barriers) determined experimentally and theoretically are significantly different and indicate the presence of a more complex diffusion mechanism. We speculate that the hydrogen diffusion proceeds via a two-step mechanism: the initial diffusion of localized charge, followed by the diffusion of hydrogen. Both experiment and theory show the presence of repulsive OH-OH interactions.

Optimization methods for finding minimum energy paths.

A comparison of chain-of-states based methods for finding minimum energy pathways (MEPs) is presented. In each method, a set of images along an initial pathway between two local minima is relaxed to find a MEP. We compare the nudged elastic band (NEB), doubly nudged elastic band, string, and simplified string methods, each with a set of commonly used optimizers. Our results show that the NEB and string methods are essentially equivalent and the most efficient methods for finding MEPs when coupled with a suitable optimizer. The most efficient optimizer was found to be a form of the limited-memory Broyden-Fletcher-Goldfarb-Shanno method in which the approximate inverse Hessian is constructed globally for all images along the path. The use of a climbing-image allows for finding the saddle point while representing the MEP with as few images as possible. If a highly accurate MEP is desired, it is found to be more efficient to descend from the saddle to the minima than to use a chain-of-states method with many images. Our results are based on a pairwise Morse potential to model rearrangements of a heptamer island on Pt(111), and plane-wave based density functional theory to model a rollover diffusion mechanism of a Pd tetramer on MgO(100) and dissociative adsorption and diffusion of oxygen on Au(111).