Solid-liquid interfacial free energy out of equilibrium

The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred outperforms the approach of pruning followed by thresholding, particularly at large sample sizes. Accordingly, predicted R(2) increased from 20.1% to 25.3% in a large schizophrenia dataset and from 9.8% to 12.0% in a large multiple sclerosis dataset. A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase.

General, PDB-based collective variables for protein folding

New, automated forms of data-analysis are required in order to understand the high-dimensional trajectories that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-dimensional representations of the trajectory using only the information encoded in the trajectory. The downside of this approach is that different sets of coordinates are required for each different chemical systems under study precisely because the coordinates are constructed using information from the trajectory. In this paper we show how one can resolve this problem by using the sketch-map algorithm that we recently proposed to construct a low-dimensional representation of the structures contained in the protein data bank (PDB). We show that the resulting coordinates are as useful for analysing trajectory data as coordinates constructed using landmark configurations taken from the trajectory and that these coordinates can thus be used for understanding protein folding across a range of systems.

Novel functional interaction between the plasma membrane Ca2+ pump 4b and the proapoptotic tumor suppressor Ras-associated factor 1 (RASSF1)

Plasma membrane calmodulin-dependent calcium ATPases (PMCAs) are enzymatic systems implicated in the extrusion of calcium from the cell. We and others have previously identified molecular interactions between the cytoplasmic COOH-terminal end of PMCA and PDZ domain-containing proteins. These interactions suggested a new role for PMCA as a modulator of signal transduction pathways. The existence of other intracellular regions in the PMCA molecule prompted us to investigate the possible participation of other domains in interactions with different partner proteins. A two-hybrid screen of a human fetal heart cDNA library, using the region 652-840 of human PMCA4b (located in the catalytic, second intracellular loop) as bait, revealed a novel interaction between PMCA4b and the tumor suppressor RASSF1, a Ras effector protein involved in H-Ras-mediated apoptosis. Immunofluorescence co-localization, immunoprecipitation, and glutathione S-transferase pull-down experiments performed in mammalian cells provided further confirmation of the physical interaction between the two proteins. The interaction domain has been narrowed down to region 74-123 of RASSF1C (144-193 in RASSF1A) and 652-748 of human PMCA4b. The functionality of this interaction was demonstrated by the inhibition of the epidermal growth factor-dependent activation of the Erk pathway when PMCA4b and RASSF1 were co-expressed. This inhibition was abolished by blocking PMCA/RASSSF1 association with an excess of a green fluorescent protein fusion protein containing the region 50-123 of RASSF1C. This work describes a novel protein-protein interaction involving a domain of PMCA other than the COOH terminus. It suggests a function for PMCA4b as an organizer of macromolecular protein complexes, where PMCA4b could recruit diverse proteins through interaction with different domains. Furthermore, the functional association with RASSF1 indicates a role for PMCA4b in the modulation of Ras-mediated signaling.

Behavioural and physiological responses of shelter dogs to long-term confinement

In Italy, National Law (281/1991) prohibits euthanasia of shelter dogs if they are not dangerous or suffering seriously. Adoption rates in rescue shelters are often lower than entrance rates, leading inevitably to overcrowded facilities where animals are likely to spend the rest of their lives in kennels. In this situation, housing conditions (i.e. space provided, environmental, and social stimulation) may have an impact on canine welfare. In this research project, the effects of two different forms of housing (group- and pair housing) on long-term shelter dogs were compared using behavioural and physiological parameters. Observational data and saliva samples were collected from dogs exposed to both experimental settings; behaviour and cortisol concentration levels were used as welfare indicators. Pair housing offered fewer social and environmental stimuli and behavioural analysis showed a significant decrease in locomotor, exploratory, and social behaviour. Cortisol levels show that this parameter varied independently of housing conditions. Although this study found no evidence suggesting that one form of confinement reduced animal welfare more than the other (e.g. in terms of abnormal behaviour, or higher cortisol concentrations), the type of confinement did affect the expression of a variety of behaviours and these variations should not be ignored with respect to housing decisions for long-term shelter dogs.

Laterality as an indicator of emotional stress in ewes and lambs during a separation test

We assessed motor laterality in sheep to explore species-specific brain hemi-field dominance and how this could be affected by genetic or developmental factors. Further, we investigated whether directionality and strength of laterality could be linked to emotional stress in ewes and their lambs during partial separation. Forty-three ewes and their singleton lambs were scored on the (left/right) direction of turn in a y-maze to rejoin a conspecific (laterality test). Further, their behavioural response (i.e. time spent near the fence, vocalisations, and activity level) during forced separation by an open-mesh fence was assessed (separation test). Individual laterality was recorded for 44.2 % ewes (significant right bias) and 81.4 % lambs (equally biased to the left and the right). There was no significant association in side bias between dams and offspring. The Chi-squared test revealed a significant population bias for both groups (p < 0.05). Evolutionary adaptive strategies or stimuli-related visual laterality may provide explanation for this decision-making process. Absolute strength of laterality (irrespective of side) was high (Kolmogorov–Smirnov test, dams: D = 0.2; p < 0.001; lambs: D = 0.36, p < 0.0001). The Wilcoxon test showed that lateralised lambs and dams spent significantly more time near each other during separation than non-lateralised animals (p < 0.05), and that lateralised dams were also more active than non-lateralised ones. Arguably, the lateralised animals showed a greater attraction to their pair because they were more disturbed and thus required greater reassurance. The data show that measures of laterality offer a potential novel non-invasive indicator of separation stress.

Behavioural reactivity of ewes and lambs during partial and total social isolation

This work investigated the differences in the reactivity of Sarda (primiparous n= 18, multiparous n= 17) and Dorset (multiparous n= 8) breeds of sheep and their singleton lambs to two challenging test situations involving a mother-lamb partial separation test and an isolation test. Non-parametric analysis used single behavioural variables and fear scores to evaluate the effect of parity, sex of lambs, and the association between mother-lamb behaviour. Amongst ewes, Dorset were characterised by a more calm temperament while Sarda (especially primiparous ewes) were more active in their response to challenge (i.e. more attempts to escape). As with their dams, lambs reflected to a certain extent this divergence and overall during isolation lamb fear score was on average significantly higher than dams. Correlations between measures of behavioural reactivity across tests were carried out to search for predictive measures of fear. A very strong correlation emerged linking vocalisation to locomotor activity. Vocalisation could be a good candidate as predictor factor of an active reaction of sheep to a fearful situation.

Supporting Mothers Bereaved by Suicide in Northern Ireland:Integrating Research and Practice

Nurturing attachments in looked after children: a feasibility study of a group-based programme for carers

Introduction: The attachment related difficulties of Looked after Children are well recognised in literature with difficulties linked to early experiences hypothesised to be perpetuated by experiences of the care system itself. Recent policy guidelines have emphasised the importance of relationships for children in care, one of the most important being with their primary carer. Golding (2014) published a group format training resource entitled ‘Nurturing Attachments’ which aims to promote ‘therapeutic parenting’; however there is limited knowledge on the feasibility of this intensive approach.
Aims: To assess the feasibility of Nurturing Attachments through exploring (i.) recruitment, retention and attrition, (ii.) initial outcomes, (iii.) acceptability and (iv.) ability of the programme to be delivered in line with the manual content and structure.
Method Two Health and Social Care Trusts in NI participated in the study by facilitating a Nurturing Attachments group in each site with adoptive parents, foster carers and kinship carers (N = 26). Carers completed pre and post measures to explore initial outcome, completing an evaluation questionnaire to explore acceptability. Acceptability was also explored with Trust stakeholders and group facilitators through focus group and interview. To explore if the manual can be delivered as intended, each group completed debrief tools.
Results: The overall response rate for uptake was 13.9%, which impacted on engagement for a ‘treatment as usual’ group. Once engaged in the programme, attrition was low and attendance was high. Initial outcomes have shown positive effects for both young person and carers. Feedback suggests a positive response regarding acceptability with limited expressed concern. The manual can be delivered in a standardised way; however can be flexible enough to allow for group processes.
Conclusions: Further research is needed to continue to explore efficacy, however the current study has provided supporting evidence that Nurturing Attachments as an intervention has positively impacted on many levels of the LAAC system.

Use of negative information in positioning and tracking algorithms

To avoid additional hardware deployment, indoor localization systems have to be designed in such a way that they rely on existing infrastructure only. Besides the processing of measurements between nodes, localization procedure can include the information of all available environment information. In order to enhance the performance of Wi-Fi based localization systems, the innovative solution presented in this paper considers also the negative information. An indoor tracking method inspired by Kalman filtering is also proposed.

Convergence of Smart Grid ICT architectures for the last mile

The evolution of the electrical grid into a smart grid, allowing user production, storage and exchange of energy, remote control of appliances, and in general optimizations over how the energy is managed and consumed, is also an evolution into a complex Information and Communication Technology (ICT) system. With the goal of promoting an integrated and interoperable smart grid, a number of organizations all over the world started uncoordinated standardization activities, which caused the emergence of a large number of incompatible architectures and standards. There are now new standardization activities which have the goal of organizing existing standards and produce best practices to choose the right approach(es) to be employed in specific smart grid designs. This paper follows the lead of NIST and ETSI/CEN/CENELEC approaches in trying to provide taxonomy of existing solutions; our contribution reviews and relates current ICT state-of-the-art, with the objective of forecasting future trends based on the orientation of current efforts and on relationships between them. The resulting taxonomy provides guidelines for further studies of the architectures, and highlights how the standards in the last mile of the smart grid are converging to common solutions to improve ICT infrastructure interoperability.

Relatório de estágio Câmara Municipal do Porto

Relatório de Estágio apresentado ao Instituto de Contabilidade e Administração do Porto para a obtenção do grau de Mestre em Tradução e Interpretação Especializadas, sob orientação de Doutora Clara Sarmento (ISCAP) e Dra. Michele Pinto (Coordenadora do Gabinete da Juventude)