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.

Monitoring and classification of lakes in Finland

In Finland, as in other member countries of the European Union, preparations for implementing the EC Water Framework Directive (WFD) have begun. The article describes the current monitoring and classification strategies for Finnish Lakes.

A preliminary classification of lake types in Northern Ireland

The EC Water Framework Directive (WFD) introduces the concept of the ecological status of surface waters. The WFD requires that water bodies within an ecoregion are divided into waterbody "types" or "ecotypes". The waterbody type is determined by physico-chemical descriptors. A group of representatives from two government environmental agencies (Environment and Heritage Service and the Industrial Research and Technology Unit) and the two universities (Queen's University Belfast and the University of Ulster) in Northern Ireland, has been established to develop methods for measuring the ecological status of lakes, for the purposes of the WFD. The work here is that contributing to the first objective classification into waterbody types.

On the classification of lakes and lake-like bodies of the Ukraine [Translation from: Gidrobiologicheskie Zhurnal, Kiev 19(2) 100-101, 1983]

In the Ukraine there are several thousand large, medium and small lakes and lake-like reservoirs, distinguished by origin, salinity, regional position, productivity and by construction a significant number of large and small water bodies, ponds and industrial reservoirs of variable designation. The problem of national systems necessitates the creation of specific schemes and classifications. Classifying into specific types of reservoir by means of suitable specifications is required for planning national measures with the objective of the rational utilisation of natural resources. It is now necessary to consider the present-day characteristics of Ukranian lakes. In the case of the Ukraine it is possible to use two approaches - genetical and ecological. This paper uses the genetical system to classify the lake-like water bodies of the Ukraine.

Comparison of systems of biological indication approved during the course of the joint Anglo-Soviet investigations held under the auspices of the Institute of Hydrobiology of the Academy of Sciences of the Ukrainian SSR

In accordance with the plan for joint Anglo-Soviet scientific and technical collaboration on environmental problems, the comparative evaluation of systems of hydrobiological analysis of the surface water quality started in 1977 at the Regional Laboratory of the Severn-Trent Water Authority in Nottingham were continued in the spring of 1978. The investigations were carried out under the auspices of the Institute of Hydrobiology of the Academy of Sciences of the Ukrainian SSR. Hydrobiological and hydrochemical samples were collected by Soviet and British specialists from the Kiev reservoir and the rivers Dnieper, Sozh, Desna and Snov. The samples were processed on the expedition ships and in the Laboratory for the Hydrobiology of Small Water Bodies of the Institute of Hydrobiology of the Academy of Sciences of the Ukrainian SSR. The possible approved methods to be adopted were evaluated from the samples using the phytoperiphyton, phytoplankton, zooplankton and zoobenthos against a background of hydrochemical characteristics. The study concludes that weather conditions complicated the work on testing the systems of biological indication of water quality and made it inadvisable to use those methods of comparison which were used when similar work was carried out in Nottingham.

Image-Based Delineation and Classification of Built Heritage Masonry

Fundacion 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.

Classification of Coastal Communities Reporting Commercial Fish Landings in the U.S. Northeast Region: Developing and Testing a Methodology

The National Marine Fisheries Service is required by law to conduct social impact assessments of communities impacted by fishery management plans. To facilitate this process, we developed a technique for grouping communities based on common sociocultural attributes. Multivariate data reduction techniques (e.g. principal component analyses, cluster analyses) were used to classify Northeast U.S. fishing communities based on census and fisheries data. The comparisons indicate that the clusters represent real groupings that can be verified with the profiles. We then selected communities representative of different values on these multivariate dimensions for in-depth analysis. The derived clusters are then compared based on more detailed data from fishing community profiles. Ground-truthing (e.g. visiting the communities and collecting primary information) a sample of communities from three clusters (two overlapping geographically) indicates that the more remote techniques are sufficient for typing the communities for further in-depth analyses. The in-depth analyses provide additional important information which we contend is representative of all communities within the cluster.

Lakes - Classification & Monitoring: a strategy for the classification of lakes

This is the report on Lakes – Classification and Monitoring, a strategy for the classification of lakes by the National Rivers Authority. This report describes a scheme for the assessment and monitoring of water and ecological quality in standing waters, greater than about 1ha in area, in England and Wales although it is generally relevant to Northwest Europe. Thirteen hydrological, chemical and biological variables are used to characterize the standing water body in any current sampling. Statistical testing on the chemical variables showed that at least six samples during a year would be needed to produce a representative sampling mean; but in this scheme the choice of variables minimizes logistic cost by not using boat sampling and time costs by not demanding extensive taxonomic work. Standing waters are classified in a state-changed system in which the contemporary values of the variables are compared with a reference baseline state and then placed in categories of percentage change from this baseline. The scheme is presently designed for use at about five year intervals on all lakes greater than 2ha area plus additional lakes of significant amenity or conservation interest.