Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination.

BACKGROUND: Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis of normal and abnormal behaviour. In this study, we considered an existing neurobiological model of fast eye movements (saccades), capable of generating realistic simulations of: (i) normal horizontal saccades; and (ii) infantile nystagmus - pathological ocular oscillations that can be subdivided into different waveform classes. By developing appropriate fitness functions, we optimised the model to existing experimental saccade and nystagmus data, using a well-established multi-objective genetic algorithm. This algorithm required the model to be numerically integrated for very large numbers of parameter combinations. To address this computational bottleneck, we implemented a master-slave parallelisation, in which the model integrations were distributed across the compute units of a GPU, under the control of a CPU. RESULTS: While previous nystagmus fitting has been based on reproducing qualitative waveform characteristics, our optimisation protocol enabled us to perform the first direct fits of a model to experimental recordings. The fits to normal eye movements showed that although saccades of different amplitudes can be accurately simulated by individual parameter sets, a single set capable of fitting all amplitudes simultaneously cannot be determined. The fits to nystagmus oscillations systematically identified the parameter regimes in which the model can reproduce a number of canonical nystagmus waveforms to a high accuracy, whilst also identifying some waveforms that the model cannot simulate. Using a GPU to perform the model integrations yielded a speedup of around 20 compared to a high-end CPU. CONCLUSIONS: The results of both optimisation problems enabled us to quantify the predictive capacity of the model, suggesting specific modifications that could expand its repertoire of simulated behaviours. In addition, the optimal parameter distributions we obtained were consistent with previous computational studies that had proposed the saccadic braking signal to be the origin of the instability preceding the development of infantile nystagmus oscillations. Finally, the master-slave parallelisation method we developed to accelerate the optimisation process can be readily adapted to fit other highly parametrised computational biology models to experimental data

SODECL: An Open-Source Library for Calculating Multiple Orbits of a System of Stochastic Differential Equations in Parallel

This is the final version. Available on open access from ACM via the DOI in this recordStochastic differential equations (SDEs) are widely used to model systems affected by random processes. In general, the analysis of an SDE model requires numerical solutions to be generated many times over multiple parameter combinations. However, this process often requires considerable computational resources to be practicable. Due to the embarrassingly parallel nature of the task, devices such as multi-core processors and graphics processing units (GPUs) can be employed for acceleration. Here, we present SODECL (https://github.com/avramidis/sodecl), a software library that utilizes such devices to calculate multiple orbits of an SDE model. To evaluate the acceleration provided by SODECL, we compared the time required to calculate multiple orbits of an exemplar stochastic model when one CPU core is used, to the time required when using all CPU cores or a GPU. In addition, to assess scalability, we investigated how model size affected execution time on different parallel compute devices. Our results show that when using all 32 CPU cores of a high-end high-performance computing node, the task is accelerated by a factor of up to ≈ 6.7, compared to when using a single CPU core. Executing the task on a high-end GPU yielded accelerations of up to ≈ 4.5, compared to a single CPU core.Engineering and Physical Sciences Research Council (EPSRC

Environmental life cycle assessment of Mediterranean sea bass and sea bream

The aquaculture sector is the fastest growing food production industry, with sea bass and sea bream consisting important exporting goods in the Mediterranean region. This work presents results of a life cycle assessment of Mediterranean sea bass and sea bream, based on primary data collected from a Greek producer. The system boundary included fish feed production and the rearing operation, as well as the packaging and delivery processes, which were neglected in preceding literature studies. The life cycle inventory developed addressed previous data gaps in the production of Mediterranean aquaculture species. Comparison to preceding studies revealed differences on the production inventories and identified methodological choices leading to variability. Packaging and delivery processes were found to contribute approximately 40% towards the global warming score. The production of both sea bass and sea bream was shown to come with high eutrophication impacts occurring from the rearing stage. The feed production was identified as the most environmental impact intensive process throughout the life cycle. Sea bass came with lower environmental impacts per unit live mass, which was reversed when the species were compared on a protein basis. The replicable and transparent model presented here, contributes towards the more accurate quantification of the environmental impacts associated with Mediterranean aquaculture species and supports efforts aiming to promote environmental protection through dietary change

Hypercalcitoninaemia in pseudohypo-parathyroidism type 1A and type 1B

Pseudohypoparathyroidism (PHP) is a heterogeneous group of rare endocrine disorders characterised by normal renal function and renal resistance to the action of the parathyroid hormone. Type 1A (PHP1A), which is the most common variant, also include developmental and skeletal defects named as Albright hereditary osteodystrophy (AHO). We present two cases, a 54- and a 33-year-old male diagnosed with PHP who were referred to us for persistently high levels of serum calcitonin. AHO and multinodular goitre were present in the 54-year-old male, while the second patient was free of skeletal deformities and his thyroid gland was of normal size and without nodular appearance. We performed GNAS molecular analysis (methylation status and copy number analysis by MS-MLPA) in genomic DNA samples for both patients. The analysis revealed a novel missense variant c.131T>G p.(Leu44Pro) affecting GNAS exon 1, in the patient with the clinical diagnosis of PHP1A. This amino acid change appears to be in accordance with the clinical diagnosis of the patient. The genomic DNA analysis of the second patient revealed the presence of the recurrent 3-kb deletion affecting the imprinting control region localised in the STX16 region associated with the loss of methylation (LOM) at the GNAS A/B differentially methylated region and consistent with the diagnosis of an autosomal dominant form of PHP type 1B (PHP1B). In conclusion, hypercalcitoninaemia may be encountered in PHP1A and PHP1B even in the absence of thyroid pathology. Learning points: We describe a novel missense variant c.131T>G p.(Leu44Pro) affecting GNAS exon 1 as the cause of PHP1A. Hypercalcitoninaemia in PHP1A is considered an associated resistance to calcitonin, as suggested by the generalised impairment of Gs\u3b1-mediated hormone signalling. GNAS methylation defects, as in type PHP1B, without thyroid pathology can also present with hypercalcitoninaemia

Improving Students’ Social Participation in Primary and Secondary Schools Across Europe

This handbook is the product of collaboration within the “FRIEND-SHIP—Improving Students’ Social Participation in Primary and Secondary Schools Across Europe” Project, funded by the European Commission—Erasmus+ Programme, Project No.: 2019-1-AT01-KA201-05 1226. One of the main outputs of this Project consisted of the development of the FRIEND-SHIP Program, a school-based intervention aimed at improving social participation of all students between 8 and 11 years of age. The FRIEND-SHIP Program is intended to be implemented by teachers and consists of 12 sessions, each with the duration of 45–60 minutes, implemented twice a week over six weeks. The activities that comprise this program are essentially experiential. Students are invited to take an active and involved role by participating in group activities, role-playing, social stories, arts, and physical activities. The main purpose of this handbook is to support teachers in implementing the FRIEND-SHIP program with their classes. This handbook is divided in three parts: • CHAPTERS 1, 2 and 3 cover background information about social participation and inclusion, as well as the description of the target audience of this handbook and the digital tool for evaluating the FRIEND-SHIP Program effects. • CHAPTER 4 covers the FRIEND-SHIP Intervention Program, including guiding principles, aims, and detailed descriptions of sessions. • CHAPTER 5 covers the information gathered with the implementation of the FRIEND-SHIP Intervention Program throughout the Project life.This handbook is the product of collaboration within the “FRIEND-SHIP—Improving Students’ Social Participation in Primary and Secondary Schools Across Europe” Project, funded by the European Commission—Erasmus+ Programme, Project No.: 2019-1-AT01-KA201-05 1226.info:eu-repo/semantics/publishedVersio

The influence of teaching experience and professional development on Greek teachers' attitudes towards inclusion

This is a postprint of an article whose final and definitive form has been published in the European Journal of Special Needs Education© 2007 Copyright Taylor & Francis; European Journal of Special Needs Education is available online at http://www.informaworld.comOn the assumption that the successful implementation of any inclusive policy is largely dependent on educators being positive about it, a survey was undertaken into the attitudes of Greek teachers to inclusion. The 155 respondents were general education primary teachers drawn from one region of Northern Greece, with a proportion deliberately selected from schools identified as actively implementing inclusive programmes. The analysis revealed positive attitudes towards the general concept of inclusion but variable views on the difficulty of accommodating different types of disabilities in mainstream classrooms. Teachers who had been actively involved in teaching pupils with SEN held significantly more positive attitudes than their counterparts with little or no such experience. The analysis also demonstrated the importance of substantive long-term training in the formation of positive teacher attitudes towards inclusion. The paper concludes with recommendations for developing critical professional development courses that can result in attitudinal change and the formulation of genuinely inclusive practices