Multi-­‐dimensional Protein Identification Technology

Before the rise of the Multidimentional Protein Identification Technology (MudPIT), protein and peptide mixtures were resolved using traditional proteomic technologies like the gel-­‐ based 2D chromatography that separates proteins by isoelectric point and molecular weight. This technique was tedious and limited, since the characterization of single proteins required isolation of protein gel spots, their subsequent proteolyzation and analysis using Matrix-­‐ assisted laser desorption/ionization-­‐time of flight (MALDI-­‐TOF) mass spectrometry.

Integer and Fractional Order Entropy Analysis of Earthquake Data-series

This paper studies the statistical distributions of worldwide earthquakes from year 1963 up to year 2012. A Cartesian grid, dividing Earth into geographic regions, is considered. Entropy and the Jensen–Shannon divergence are used to analyze and compare real-world data. Hierarchical clustering and multi-dimensional scaling techniques are adopted for data visualization. Entropy-based indices have the advantage of leading to a single parameter expressing the relationships between the seismic data. Classical and generalized (fractional) entropy and Jensen–Shannon divergence are tested. The generalized measures lead to a clear identification of patterns embedded in the data and contribute to better understand earthquake distributions.

Multidimensional Scalling Analysis of the World Economy During the Period 1972-2012

The last 40 years of the world economy are analyzed by means of computer visualization methods. Multidimensional scaling and the hierarchical clustering tree techniques are used. The current Western downturn in favor of Asian partners may still be reversed in the coming decades.

Visual data analysis in air traffic management

Visual data mining, multi-dimensional scaling, POLARMAP, Sammon's mapping, clustering, outlier detection

Ecology of sponge assemblages (Porifera) in the Wakatobi region, south-east Sulawesi, Indonesia: richness and abundance

The influence of sedimentation, depth and substratum angle on sponge assemblages in the Wakatobi region, south-eastern Sulawesi, Indonesia was considered. Sponge assemblages were sampled from two reef localities. The first reef (Sampela) was highly impacted by high sedimentation rates with fine sediment particles that settle slowly, while the second (Hoga) experienced only fast settling coarse sediment with lower overall sedimentation rates. Sponge assemblages were sampled (area occupied and numbers) on the reef fiat (0 m) and at 5 (reef crest), 10 and 15 m (15 m at Hoga only). Some significant (P < 0.001) differences were observed in the area occupied and the number of sponge patches between surface angles and sites. Significantly lower (t > 4.61, df = 9, P < 0.001) sponge numbers, percentage cover and richness were associated with the reef flat at both sites compared with all other depths at each site, with the exception of abundance of sponges on the reef flat at Sampela, which was much greater than at any other depth sampled. Species richness increased with depth at both sites but differences between surface angles were only recorded at Sampela, with higher species richness being found on vertical, inclined and horizontal surfaces respectively A total of 100 sponge species (total area sampled 52.5 m(2)) was reported from the two sites, with 58 species found at Sampela and 71 species at Hoga (41% of species shared). Multi-dimensional scaling (MDS) indicated differences in assemblage structure between sites and most depth intervals, but not substratum angles. A number of biological (e.g. competition and predation) and physical (e.g. sedimentation and aerial exposure) factors were considered to control sponge abundance and richness. Unexpectedly a significant (F-1,F-169 = 148.98, P < 0.001) positive linear relationship was found between sponge density and area occupied. In areas of high sponge coverage, the number of patches was also high, possibly due to fragmentation of large sponges produced as a result of predation and physical disturbance. The MDS results were also the same whether sponge numbers or percentage cover estimates were used, suggesting that although these different approaches yield different sorts of information, the same assemblage structure can be identified.

Temporal and spatial variability of mobile fauna on a submarine cliff and boulder scree complex: a community in flux

The mobile component of a community inhabiting a submarine boulder scree/cliff was investigated at Lough Hyne, Ireland at dawn, midday, dusk and night over a 1-week period. Line transects (50 m) were placed in the infralittoral (6 m) and circumlittoral (18 m) zones and also the interface between these two zones (12 m). The dominant mobile fauna of this cliff consisted of echinoderms (6 species), crustaceans (10 species) and fish (23 species). A different component community was identified at each time/depth interval using Multi-Dimensional Scaling (MDS) even though both species diversity (Shannon-Wiener indices) and richness (number of species) remained constant. These changes in community composition provided indirect evidence for migration by these mobile organisms. However, little evidence was found for migration between different zones with the exception of the several wrasse species. These species were observed to spend the daytime foraging in the deeper zone, but returned to the upper zone at night presumably for protection from predators. For the majority of species, migration was considered to occur to cryptic habitats such as holes and crevices. The number of organisms declined during the night, although crustacean numbers peaked, while fish and echinoderms were most abundant during day, possibly due to predator-prey interactions. This submarine community is in a state of flux, whereby, community characteristics, including trophic and energetic relationships, varied over small temporal (daily) and spatial (m) scales.

Sensory profile and preference mapping of orange cakes with addition of prebiotics inulin and oligofructose

Orange cakes with addition of inulin and oligofructose to justify a prebiotic claim (minimum of 3 g of fructans in a 60 g serving of cake) were investigated regarding sensory aspects. The sensory profile of cakes with inulin, with inulin/oligofructose and without prebiotics (standard cake) was evaluated using descriptive quantitative analysis. Preference mapping was assessed using multidimensional scaling on data obtained through an acceptability test with a nine-point hedonic scale. The cakes with prebiotics presented greater crust brownness, dough beigeness, hardness and stickiness than the standard cake and lower crumbliness. Principal Component Analysis (69.5 and 10.7% of explanation to the first and second principal components, respectively) showed that crust brownness, dough beigeness, hardness and stickiness contributed to distinguish the cakes with prebiotics from standard cakes. The sensory acceptability was similar for the three cakes and higher when compared to three commercial cakes, but the preference mapping showed that cakes with prebiotics were preferred to commercial cakes. Addition of prebiotics in orange cakes is feasible, based on the sensory results, which may facilitate marketing of this functional food with sensorial qualities equivalent to conventional products. © 2012 Elsevier Ltd.

Biodiversità malacologica degli ecosistemi a coralli bianchi del Mediterraneo, dall'ultimo glaciale ad oggi

Nello studio di questa tesi è stata descritta una ricerca condotta allo scopo di fornire un contributo alla conoscenza della biodiversità analizzando la componente macrofaunistica subfossile e recente del Phylum Mollusca del Canale di Sicilia e del Golfo di Cadice. Tali organismi sono già da tempo noti in questi ambienti poiché associati a biocostruzioni a coralli bianchi presenti lungo i margini continentali atlantici e mediterranei i cui costituenti principali sono gli sclerattiniari coloniali Lophelia pertusa e Madrepora oculata. Tuttavia ben poco si conosce sull’ecologia di queste specie che si ritrovano spesso influenzate da scambi idrologici e biologici attraverso lo Stretto di Gibilterra. Nel corso di questo studio sono state analizzate 7 carote sedimentarie marine campionate durante diverse campagne oceanografiche: 6 carotaggi atlantici prelevati durante la campagna oceanografica Meteor nel Golfo di Cadice e 1 carota campionata nel Canale di Sicilia durante la campagna oceanografica MARCOS guidata dall’ISMAR-CNR di Bologna, sulla quale si concentra l’attenzione di questo lavoro. I dati raccolti sono stati analizzati in maniere quantitativa, per questo è stato utilizzato il software per analisi statistiche “Past3” e sono stati combinati con l’analisi qualitativa dei campioni in modo da ottenere il maggior numero di informazioni. Tra le analisi statistiche sono state effettuate il calcolo di tutti gli indici di dominanza, diversità, di equiripartizione e ricchezza specifica (Simpson, Shannon, Evenness e Margalef) e l’analisi multivariata NMDS (Non-metric Multi-Dimensional Scaling). Infine è stata effettuata l’analisi delle associazioni trofiche distribuite in una carota. Il risultato ha evidenziato un’elevata biodiversità per campioni prelevati in profondità e il ritrovamento di organismi appartenenti all’ultimo glaciale.

Influence of white-tailed deer on nitrogen cycling and vegetative community change in canopy gaps in a hemlock-northern hardwood forest

Our research explored the influence of deer and gap size on nitrogen cycling, soil compaction, and vegetation trajectories in twelve canopy gaps of varying sizes in a hemlock-northern hardwood forest. Each gap contained two fenced and two unfenced plots. Gap size, soil compaction, winter deer use, and available nitrogen were measured in 2011. Vegetation was assessed in 2007 and 2011, and non-metric multi-dimensional scaling was used to determine vegetative change. Results show that winter deer use was greater in smaller gaps. Deer accessibility did not influence compaction but did significantly increase total available nitrogen in April. April ammonium, April nitrate, and May nitrate were positively related to gap size. The relationship between gap size and vegetative community change was positive for fenced plots but unrelated for unfenced plots. In conclusion, deer are positively contributing to nitrogen dynamics and altering the relationship between canopy gap size and vegetative community change.

Spanish-English Codeswitching in Email Communication

While spoken codeswitching (CS) among Latinos has received significant scholarly attention, few studies have examined written CS, specifically naturally-occurring CS in email. This study contributes to an under-studied area of Latino linguistic practices by reporting the results of a study of CS in the emails of five Spanish-English bilingual Latinos. Methods are employed that are not often used in discourse analysis of email texts, namely multi-dimensional scaling and tree diagrams, to explore the contextual parameters of written Spanish-English CS systematically. Consistent with the findings of other studies of CS in CMC, English use was most associated with professional or formal contacts, and use of Spanish, the participants’ native language, was linked to intimacy, informality, and group identification. Switches to Spanish functioned to personalize otherwise transactional or work-related English-dominant emails. The article also discusses novel orthographic and linguistic forms specific to the CMC context.

Block GTM: Incorporating prior knowledge of covariance structure in data visualisation

Visualising data for exploratory analysis is a big challenge in scientific and engineering domains where there is a need to gain insight into the structure and distribution of the data. Typically, visualisation methods like principal component analysis and multi-dimensional scaling are used, but it is difficult to incorporate prior knowledge about structure of the data into the analysis. In this technical report we discuss a complementary approach based on an extension of a well known non-linear probabilistic model, the Generative Topographic Mapping. We show that by including prior information of the covariance structure into the model, we are able to improve both the data visualisation and the model fit.

Data visualisation and exploration with prior knowledge

Visualising data for exploratory analysis is a major challenge in many applications. Visualisation allows scientists to gain insight into the structure and distribution of the data, for example finding common patterns and relationships between samples as well as variables. Typically, visualisation methods like principal component analysis and multi-dimensional scaling are employed. These methods are favoured because of their simplicity, but they cannot cope with missing data and it is difficult to incorporate prior knowledge about properties of the variable space into the analysis; this is particularly important in the high-dimensional, sparse datasets typical in geochemistry. In this paper we show how to utilise a block-structured correlation matrix using a modification of a well known non-linear probabilistic visualisation model, the Generative Topographic Mapping (GTM), which can cope with missing data. The block structure supports direct modelling of strongly correlated variables. We show that including prior structural information it is possible to improve both the data visualisation and the model fit. These benefits are demonstrated on artificial data as well as a real geochemical dataset used for oil exploration, where the proposed modifications improved the missing data imputation results by 3 to 13%.

Visualisation and browsing of image databases

In this chapter we provide a comprehensive overview of the emerging field of visualising and browsing image databases. We start with a brief introduction to content-based image retrieval and the traditional query-by-example search paradigm that many retrieval systems employ. We specify the problems associated with this type of interface, such as users not being able to formulate a query due to not having a target image or concept in mind. The idea of browsing systems is then introduced as a means to combat these issues, harnessing the cognitive power of the human mind in order to speed up image retrieval.We detail common methods in which the often high-dimensional feature data extracted from images can be used to visualise image databases in an intuitive way. Systems using dimensionality reduction techniques, such as multi-dimensional scaling, are reviewed along with those that cluster images using either divisive or agglomerative techniques as well as graph-based visualisations. While visualisation of an image collection is useful for providing an overview of the contained images, it forms only part of an image database navigation system. We therefore also present various methods provided by these systems to allow for interactive browsing of these datasets. A further area we explore are user studies of systems and visualisations where we look at the different evaluations undertaken in order to test usability and compare systems, and highlight the key findings from these studies. We conclude the chapter with several recommendations for future work in this area. © 2011 Springer-Verlag Berlin Heidelberg.

Spatial scale and abundance patterns of large fish communities in freshwater marshes of the Florida Everglades

Anthropogenic habitat alterations and water-management practices have imposed an artificial spatial scale onto the once contiguous freshwater marshes of the Florida Everglades. To gain insight into how these changes may affect biotic communities, we examined whether variation in the abundance and community structure of large fishes (SL . 8 cm) in Everglades marshes varied more at regional or intraregional scales, and whether this variation was related to hydroperiod, water depth, floating mat volume, and vegetation density. From October 1997 to October 2002, we used an airboat electrofisher to sample large fishes at sites within three regions of the Everglades. Each of these regions is subject to unique watermanagement schedules. Dry-down events (water depth , 10 cm) occurred at several sites during spring in 1999, 2000, 2001, and 2002. The 2001 dry-down event was the most severe and widespread. Abundance of several fishes decreased significantly through time, and the number of days post-dry-down covaried significantly with abundance for several species. Processes operating at the regional scale appear to play important roles in regulating large fishes. The most pronounced patterns in abundance and community structure occurred at the regional scale, and the effect size for region was greater than the effect size for sites nested within region for abundance of all species combined, all predators combined, and each of the seven most abundant species. Non-metric multi-dimensional scaling revealed distinct groupings of sites corresponding to the three regions. We also found significant variation in community structure through time that correlated with the number of days post-dry-down. Our results suggest that hydroperiod and water management at the regional scale influence large fish communities of Everglades marshes.