Outputs from the Manchester Metropolitan University distance learning think tank event

An overview of, and the emergent themes from, the Manchester Metropolitan University distance learning think tank event which took place on 10th July 2014 and aimed to provide a forum to explore and discuss some of the key issues for colleagues across the university involved in planning, setting-up and delivering such programmes at MMU.

Poster: Outputs from the Manchester Metropolitan University online distance learning think tank event

Poster from the overview of, and the emergent themes from, the Manchester Metropolitan University distance learning think tank event which took place on 10th July 2014 and aimed to provide a forum to explore and discuss some of the key issues for colleagues across the university involved in planning, setting-up and delivering such programmes at MMU.

Designing marine fishery reserves using passive acoustic telemetry

Marine Fishery Reserves (MFRs) are being adopted, in part, as a strategy to replenish depleted fish stocks and serve as a source for recruits to adjacent fisheries. By necessity, their design must consider the biological parameters of the species under consideration to ensure that the spawning stock is conserved while simultaneously providing propagules for dispersal. We describe how acoustic telemetry can be employed to design effective MFRs by elucidating important life-history parameters of the species under consideration, including home range, and ecological preferences, including habitat utilization. We then designed a reserve based on these parameters using data from two acoustic telemetry studies that examined two closely-linked subpopulations of queen conch (Strombus gigas) at Conch Reef in the Florida Keys. The union of the home ranges of the individual conch (aggregation home range: AgHR) within each subpopulation was used to construct a shape delineating the area within which a conch would be located with a high probability. Together with habitat utilization information acquired during both the spawning and non-spawning seasons, as well as landscape features (i.e., corridors), we designed a 66.5 ha MFR to conserve the conch population. Consideration was also given for further expansion of the population into suitable habitats.

Report from the Knowledge Exchange Event: Pathways to Open Scholarship

The report on the ‘Pathways to Open Scholarship’ conference, organised by Knowledge Exchange to celebrate its 10th anniversary, contains an overview of the views that invited speakers and experts in the audience expressed on Open Scholarship developments. Open Scholarship is not yet a reality of everyday research and education. The event reported on, addressed the concept of "open scholarship" by debating issues and key challenges with the aim to identify pathways forward. Four central themes which represent crucial dimensions of open scholarship have been explored: Benefits, risks and limitations of Open Scholarship; Success as a researcher; Technology; and Publishing and publication services. The report contains views, expectations, wishes and frustrations that experts have on open scholarship, as well as new and promising initiatives and approaches. The report is a starting point for future planning of KE activity and input for a range of consultation talks with respected experts and leaders in the research community in KE countries and beyond.

Stocks of Dolphins (Stenella spp. and Delphinus delphis) in the Eastern Tropical Pacific: A Phylogeographic Classification

Current information is reviewed that provides clues to the intraspecific structure of dolphin species incidently killed in the yellowfin tuna purse-seine fishery of the eastern tropical Pacific (ETP). Current law requires that management efforts are focused on the intraspecific level, attempting to preserve local and presumably locally adapted populations. Four species are reviewed: pantropical spotted, Stenella attenuata; spinner, S. longirostTis; striped, S. coeruleoalba; and common, Delphinus delphis, dolphins. For each species, distributional, demographic, phenotypic, and genotypic data are summarized, and the putative stocks are categorized based on four hierarchal phylogeographic criteria relative to their probability of being evolutionarily significant units. For spotted dolphins, the morphological similarity of animals from the south and the west argues that stock designations (and boundaries) be changed from the current northern offshore and southern offshore to northeastern offshore and a combined western and southern offshore. For the striped dolphin, we find little reason to continue the present division into geographical stocks. For common dolphins, we reiterate an earlier recommendation that the long-beaked form (Baja neritic) and the northern short-beaked form be managed separately; recent morphological and genetic work provides evidence that they are probably separate species. Finally, we note that the stock structure of ETP spinner dolphins is complex, with the whitebelly form exhibiting characteristics of a hybrid swarm between the eastern and pantropical subspecies. There is little morphological basis at present for division of the whitebelly spinner dolphin into northern and southern stocks. However, we recommend continued separate management of the pooled whitebelly forms, despite their hybrid/intergrade status. Steps should be taken to ensure that management practices do not reduce the abundance of eastern relative to whitebelly spinner dolphins. To do so may lead to increased invasion of the eastern's stock range and possible replacement of the eastern spinner dolphin genome.(PDF file contains 24 pages.)

A detailed investigation of classification methods for vowel speech imagery recognition

Accurate and fast decoding of speech imagery from electroencephalographic (EEG) data could serve as a basis for a new generation of brain computer interfaces (BCIs), more portable and easier to use. However, decoding of speech imagery from EEG is a hard problem due to many factors. In this paper we focus on the analysis of the classification step of speech imagery decoding for a three-class vowel speech imagery recognition problem. We empirically show that different classification subtasks may require different classifiers for accurately decoding and obtain a classification accuracy that improves the best results previously published. We further investigate the relationship between the classifiers and different sets of features selected by the common spatial patterns method. Our results indicate that further improvement on BCIs based on speech imagery could be achieved by carefully selecting an appropriate combination of classifiers for the subtasks involved.

Classification of neocortical interneurons using affinity propagation

In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. Neuronal classification has been a difficult problem because it is unclear what a neuronal cell class actually is and what are the best characteristics are to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological or molecular characteristics, when applied to selected datasets, have provided quantitative and unbiased identification of distinct neuronal subtypes. However, better and more robust classification methods are needed for increasingly complex and larger datasets. We explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. In fact, using a combined anatomical/physiological dataset, our algorithm differentiated parvalbumin from somatostatin interneurons in 49 out of 50 cases. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

Evidence for classification of c.1852_1853AA > GC in MLH1 as a neutral variant for Lynch syndrome

Background: Lynch syndrome (LS) is an autosomal dominant inherited cancer syndrome characterized by early onset cancers of the colorectum, endometrium and other tumours. A significant proportion of DNA variants in LS patients are unclassified. Reports on the pathogenicity of the c.1852_1853AA>GC (p.Lys618Ala) variant of the MLH1 gene are conflicting. In this study, we provide new evidence indicating that this variant has no significant implications for LS. Methods: The following approach was used to assess the clinical significance of the p.Lys618Ala variant: frequency in a control population, case-control comparison, co-occurrence of the p.Lys618Ala variant with a pathogenic mutation, co-segregation with the disease and microsatellite instability in tumours from carriers of the variant. We genotyped p.Lys618Ala in 1034 individuals (373 sporadic colorectal cancer [CRC] patients, 250 index subjects from families suspected of having LS [revised Bethesda guidelines] and 411 controls). Three well-characterized LS families that fulfilled the Amsterdam II Criteria and consisted of members with the p.Lys618Ala variant were included to assess co-occurrence and co-segregation. A subset of colorectal tumour DNA samples from 17 patients carrying the p.Lys618Ala variant was screened for microsatellite instability using five mononucleotide markers. Results: Twenty-seven individuals were heterozygous for the p.Lys618Ala variant; nine had sporadic CRC (2.41%), seven were suspected of having hereditary CRC (2.8%) and 11 were controls (2.68%). There were no significant associations in the case-control and case-case studies. The p.Lys618Ala variant was co-existent with pathogenic mutations in two unrelated LS families. In one family, the allele distribution of the pathogenic and unclassified variant was in trans, in the other family the pathogenic variant was detected in the MSH6 gene and only the deleterious variant co-segregated with the disease in both families. Only two positive cases of microsatellite instability (2/17, 11.8%) were detected in tumours from p.Lys618Ala carriers, indicating that this variant does not play a role in functional inactivation of MLH1 in CRC patients. Conclusions: The p.Lys618Ala variant should be considered a neutral variant for LS. These findings have implications for the clinical management of CRC probands and their relatives.

Image-based delineation and classification of built heritage masonry

[EN]Fundación Zain is developing new built heritage assessment protocols. The goal is to objectivize and standardize the analysis and decision process that leads to determining the degree of protection of built heritage in the Basque Country. The ultimate step in this objectivization and standardization effort will be the development of an information and communication technology (ICT) tool for the assessment of built heritage. This paper presents the ground work carried out to make this tool possible: the automatic, image-based delineation of stone masonry. This is a necessary first step in the development of the tool, as the built heritage that will be assessed consists of stone masonry construction, and many of the features analyzed can be characterized according to the geometry and arrangement of the stones. Much of the assessment is carried out through visual inspection. Thus, this process will be automated by applying image processing on digital images of the elements under inspection. The principal contribution of this paper is the automatic delineation the framework proposed. The other contribution is the performance evaluation of this delineation as the input to a classifier for a geometrically characterized feature of a built heritage object. The element chosen to perform this evaluation is the stone arrangement of masonry walls. The validity of the proposed framework is assessed on real images of masonry walls.