Benthic habitat mapping in the Olympic Coast National Marine Sanctuary: Classification of side scan sonar data from survey HMPR-108-2002-01: Version I

In September 2002, side scan sonar was used to image a portion of the sea floor in the northern OCNMS and was mosaiced at 1-meter pixel resolution using 100 kHz data collected at 300-meter range scale. Video from a remotely-operated vehicle (ROV), bathymetry data, sedimentary samples, and sonar mapping have been integrated to describe geological and biological aspects of habitat and polygon features have been created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). The data can be used with geographic information system (GIS) software for display, query, and analysis. Textural analysis of the sonar images provided a relatively automated method for delineating substrate into three broad classes representing soft, mixed sediment, and hard bottom. Microhabitat and presence of certain biologic attributes were also populated into the polygon features, but strictly limited to areas where video groundtruthing occurred. Further groundtruthing work in specific areas would improve confidence in the classified habitat map. (PDF contains 22 pages.)

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.

An evaluation of geographic and annual variation in morphometric characters and gill-raker counts of yellowfin tuna, Thunnus albacares, from the Pacific Ocean

ENGLISH: Samples of yellowfin tuna, Thunnus albacares, collected from five areas of the Pacific Ocean (Mexico, Ecuador, Australia, Japan, and Hawaii) between January and May of 1988 and 1990 were examined for spatiotemporal variation in morphometric characters and gill-raker counts. 'Iwo-factor analysis of variance, with area and year treated as grouping factors, indicated a significant difference in the means of the total gill-raker counts among fish from different areas, but no significant difference between fish caught in different years. The morphometric data were adjusted by allometric formulae to remove size effects. The correct classification rates for the five groups, using discriminant function analysis, based on adjusted morphometric characters, were 77.60/0 for the samples from 1988 and 74.40/0 for those from 1990. These are 72.00/0 and 68.00/0 (Cohen's kappa statistic) better than would have occurred chance. The pattern of geographic variability, however, is unstable for these two years, thus requiring separate discriminant functions for each year. Although there is annual variability in the morphometric characters, these results demonstrate that the stocks examined are morphometrically distinguishable and that their phenetic relationships reflect their geographic origin. SPANISH: Se examinaron muestras de atún aleta amarilla, Thunnus albacares, tomadas de cinco áreas del Océano Pacífico (México, Ecuador, Australia, Japón, y Hawaii) entre enero y mayo de 1988 y 1990, para descubrir variaciones espaciotemporales en las características morfométricas y los conteos de branquiespinas. Un análisis de varianza de dos factores, con área y año como factores de agrupación, indicó una diferencia significativa en los promedios de los conteos de branquiespinas totales entre peces de distintas áreas, pero ninguna entre peces capturados en distintos años. Se ajustaron los datos morfométricos con fórmulas alométricas para eliminar los efectos de la talla del pez. En un análisis de función discriminante, las tasas de clasificación correcta de los cinco grupos, basadas en características morfométricas ajustadas, fueron 77.60/0 para las muestras de 1988 y 74.40/0 para aquellas de 1990. Estas cifras son 72.00/0 y 68.00/0 (estadístico de kappa de Cohen) mejores de lo que se hubiera obtenido al azar. Sin embargo, la variabilidad geográfica es inestable en estos dos años, requiriendo por lo tanto funciones discriminantes separadas para cada año. Aunque existe variabilidad anual en las características morfométricas, estos resultados demuestran que los stocks examinados son morfamétricamente distinguibles, y que su relación fenética refleja su origen geográfico. (PDF contains 31 pages.)

Economic Valuation of Ecosystem Services: Conflicts in Classification

4 p.

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.

Advantages and Versatility of Fluorescence-Based Methodology to Characterize the Functionality of LDLR and Class Mutation Assignment

Familial hypercholesterolemia (FH) is a common autosomal codominant disease with a frequency of 1:500 individuals in its heterozygous form. The genetic basis of FH is most commonly mutations within the LDLR gene. Assessing the pathogenicity of LDLR variants is particularly important to give a patient a definitive diagnosis of FH. Current studies of LDLR activity ex vivo are based on the analysis of I-125-labeled lipoproteins (reference method) or fluorescent-labelled LDL. The main purpose of this study was to compare the effectiveness of these two methods to assess LDLR functionality in order to validate a functional assay to analyse LDLR mutations. LDLR activity of different variants has been studied by flow cytometry using FITC-labelled LDL and compared with studies performed previously with I-125-labeled lipoproteins. Flow cytometry results are in full agreement with the data obtained by the I-125 methodology. Additionally confocal microscopy allowed the assignment of different class mutation to the variants assayed. Use of fluorescence yielded similar results than I-125-labeled lipoproteins concerning LDLR activity determination, and also allows class mutation classification. The use of FITC-labelled LDL is easier in handling and disposal, cheaper than radioactivity and can be routinely performed by any group doing LDLR functional validations.

Integration of aquaculture and agriculture: a route to sustainable farming systems

The integration of agriculture and aquaculture as a means of intensifying resource use and improving the productivity of many current farming practices in Southeast Asian and African countries is discussed. A brief account is given of work undertaken by ICLARM in Malawi and India regarding the improved use of marginal lands to integrate crops, vegetables, trees, livestock and fish, outlining also the various problems involved in the extension of such integrated fish farming systems.

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.

The Cheshire Meres an analysis of data and a prioritisation of sites

This is a report on the Analysis of Data and a Prioritisation of Sites at the Cheshire Meres by the Institute of Freshwater Ecology. The report addresses data collected by the Agency for 24 basin sites in Cheshire. At least two samples were collected from each site, though not simultaneously. Sites were visited in May/June and in November. The determinands are standard and they included: water, temperature, conductivity, pH, DO, fractional white light penetration, TSS, chlorophyll, TP, ortho-phosphate, nitrate-, nitrite-, ammonium and silicate. Though concentrations were often higher than for other lakes in the region, rather exceeding criteria for classification as eutrophic lakes, the results confirmed that the series of lakes is, naturally, highly eutrophic and nothing in the present data differs so far from expectation that is persuasive that the ecosystems are reacting adversely to environmental stress. The data set is review and summarised, site-by-site, in an appendix. The grounds for prioritisation are discussed. Whether or not this preferred prioritised option is adopted, the Agency is recommended to review the way it carries out monitoring. The determinands and the sampling frequency need to be geared to the information that is required.

Status of the shrimp sector in Bangladesh in the context of HACCP and trade issues: a review

Shrimp culture in Bangladesh has emerged as an important aquaculture industry over the last three decades although its culture in greater parts of the farming area is done in traditional ways. In the meantime, the government of Bangladesh has taken necessary measures along with the private sectors to increase production, upgrade processing industries and to promote export performance. Long supply chain in raw material collection, inadequate infrastructure facilities, poor level of cool chain and lack of adequate HACCP-based training on hygiene and sanitation of different groups of people involved in the field level are the main problems of quality loss of raw materials. Shortage of raw materials results in poor capacity utilization of the processing plants. The growth of bagda (P. monodon) hatchery has expanded rapidly over the last few years, remaining mostly concentrated in Cox's Bazar region is enough to meet the target production. However, there is a shortage of pelleted shrimp feed in Bangladesh. A large number of export processors are now producing increasing amounts of value-added products such as individually quick-frozen, peeled and divined, butterfly cut shrimp, as well as cooked products. The export earnings from value added products is about half of the total export value. About 95% of total fish products are exported to European countries, USA and Japan and the remaining to the Southeast Asia and the Middle East. Most of the EU approved shrimp processing industries have been upgraded with laboratory facilities and provided HACCP training to their workers. As of now, HACCP is applied on the processing plants, but to ensure the quality of raw materials and to reduce risks, shrimp farms are also required to adopt HACCP plan. There is increased pressure time to time from importing countries for fish processors to establish effective quality assurance system in processing plants. Fish Inspection and Quality Control (FIQC) of the Department of Fisheries while having moderately equipped laboratories with chemical, bio-chemical and microbiological testing facilities and qualified technical personnel, the creation of facilities for testing of antibiotics is underway. FIQC mainly supervises quality aspects of the processing plants and has little or no control over raw material supply chains from farm to processing plants. Bangladesh export consignments sometimes face rejection due to reported poor quality of the products. Three types of barriers are reported for export of shrimp to EU countries. These are:(1) government participation in trade and restrictive practices (state aid, countervailing duties, state trading enterprises, government monopoly practices), customs and administrative entry procedures (anti-dumping duties, customs valuation, classification, formalities, rules of origin); (2) technical barriers to trade or TBT (technical regulations, standards, testing, certification arrangement); (3) specific limitations (quantitative restrictions, import licensing, embargoes, exchange control, discriminatory sourcing, export restraints, measures to regulate domestic prices, requirements concerning marking, labeling and packaging).