The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a nonlinear, topology preserving projection for the visualization of the input data and their similarities. The core algorithm in the BioDICE plugin is Fast Learning Self Organizing Map (FLSOM), which is an improved variant of the Self Organizing Map (SOM) algorithm. The plugin generates an interactive 2D map that allows the visual exploration of multidimensional data and the identification of groups of similar objects. The effectiveness of the plugin is demonstrated on a case study related to chemical compounds. Conclusions: The number and variety of available tools and its extensibility have made Taverna a popular choice for the development of scientific data workflows. This work presents a novel plugin, BioDICE, which adds a data-driven knowledge discovery component to Taverna. BioDICE provides an effective and powerful clustering tool, which can be adopted for the explorative analysis of biological datasets.

Exploration of the neural correlates of cerebral palsy for sensorimotor BCI control

Cerebral palsy (CP) includes a broad range of disorders, which can result in impairment of posture and movement control. Brain-computer interfaces (BCIs) have been proposed as assistive devices for individuals with CP. Better understanding of the neural processing underlying motor control in affected individuals could lead to more targeted BCI rehabilitation and treatment options. We have explored well-known neural correlates of movement, including event-related desynchronization (ERD), phase synchrony, and a recently-introduced measure of phase dynamics, in participants with CP and healthy control participants. Although present, significantly less ERD and phase locking were found in the group with CP. Additionally, inter-group differences in phase dynamics were also significant. Taken together these findings suggest that users with CP exhibit lower levels of motor cortex activation during motor imagery, as reflected in lower levels of ongoing mu suppression and less functional connectivity. These differences indicate that development of BCIs for individuals with CP may pose additional challenges beyond those faced in providing BCIs to healthy individuals.

Exploration of relational factors: Sino-foreign joint-venture partnering

Purpose – Despite recent threats of economic contraction, China still offers attractive opportunities for foreign companies seeking to expand their business activities through joint venturing (JV) partnering entry strategies. Recent research has indicated a growing recognition of the importance of relational factors in JV partnering. The purpose of this paper is to build on recent research findings that identify critical relation success factors in JVs and explores these in the context of a Hong Kong-based civil aviation services company seeking to expand business activities in Greater China. Design/methodology/approach – While the extant management literature focuses primarily on factors relevant to the inter-partner relationship between partners in the formation stage of a joint venture, this research takes a dynamic stakeholder perspective in respect of the relevant relational factors over the evolution of a partnership. The research described in this paper is based on a case-based study that identifies and examines the relevance and importance of uniquely Chinese factors such as guanxi, renqing and mianzi in the specific context of a strategic partnering relationship. Findings – This phenomenological study provides empirical evidence of critical linkages of these to intrinsically Chinese notions of guanxi, mianzi and renqing – it links these to key strategic partnering success factors identified to be trust, conflict resolution, commitment and cooperation. This study thereby reinforces the importance of the uniquely Chinese relational context in cross-border JVs. Moreover, the research findings suggest that these factors underpin the dynamic bi-directional stakeholder relationship in a Sino-foreign strategic partnership. Originality/value – This study conceptually links the uniquely Chinese relational factors (guanxi, mianzi and renqing) to key success factors supporting the establishment of a strategic partnership in a Sino-foreign context; moreover, it contributes empirical evidence substantiating the proposed conceptual linkage.

An exploration of the role duality experienced by HR professionals as both implementers and recipients of HR practices: evidence from the Indian railways

This study provides an innovative perspective on empirically assessing HR by focusing on the duality of HR professionals’ experiences as both implementers and recipients or internal customers of HR practices given that they are also employees of the organization. We hypothesize that HR professionals experience HR practices more favorably from an implementer perspective as compared to an internal customer perspective. These differences in experiences are likely to be influenced by HR professionals’ hierarchical position in the HR department. Our analyses of 1,271 HR professionals employed by Indian Railways revealed a number of differences between the two types of experience. Some practices (recruitment and selection, training, and employee welfare) were viewed more negatively from the implementer perspective, whereas others (compensation, benefits, and employment relations) were rated more negatively from the internal customer perspective. Those holding more senior HR positions reported more positive experiences of training and employment relations from an internal customer perspective. Overall our contributions draw on the attribution theory and concepts of intraorganizational power and voice, and have implications concerning the effectiveness of HR practices. © 2015 Wiley Periodicals, Inc.

Science learning and graphic symbols: an exploration of early years teachers’ views and use of graphic symbols when teaching science

The study investigated early years teachers’ understanding and use of graphic symbols, defined as the visual representation(s) used to communicate one or more “linguistic” concepts, which can be used to facilitate science learning. The study was conducted in Cyprus where six early years teachers were observed and interviewed. The results indicate that the teachers had a good understanding of the role of symbols, but demonstrated a lack of understanding in regards to graphic symbols specifically. None of the teachers employed them in their observed science lesson, although some of them claimed that they did so. Findings suggest a gap in participants’ acquaintance with the terminology regarding different types of symbols and a lack of awareness about the use and availability of graphic symbols for the support of learning. There is a need to inform and train early years teachers about graphic symbols and their potential applications in supporting children’s learning.

(40)Ar/(39)Ar ages and Sr-Nd-Pb-Os geochemistry of CAMP tholeiites from Western Maranhao basin (NE Brazil)

The Central Atlantic Magmatic Province (CAMP), emplaced at the Triassic-Jurassic (T-J) boundary (-200 Ma), is among the largest igneous provinces on Earth. The Maranhao basin in NE Brazil is located around 700 km inland and 2000 km from the site of the earliest Pangea disruption. The CAMP tholeiites occur only in the western part of the basin and have been described as low and high-Ti. Here we document the occurrence of two sub-groups among the high-Ti tholeiites in the Western Maranhao basin. The major and trace elements and the Sr-Nd-Pb isotopic ratios define three chemical groups corresponding to the low-Ti (TiO(2)< 1.3 wt.%), high-Ti (TiO(2)-2.0 wt.%) and evolved high-Ti (TiO(2 >)3 wt.%) western Maranhao basin tholeiites (WMBT). The new (40)Ar/(39)Ar plateau ages obtained on plagioclase separates for high-Ti (199.7 +/- 2.4 Ma) and evolved high-Ti WMBT (197.2 +/- 0.5 Ma and 198.2 +/- 0.6 Ma) are indistinguishable and identical to those of previously analyzed low-Ti WMBT (198.5 +/- 0.8 Ma) and to the mean (40)Ar/(39)Ar age of the CAMP (199 +/- 2.4 Ma). We also present the first Re-Os isotopic data for CAMP basalts. The low and high-Ti samples display mantle-like initial ((187)Os/(188)Os)(i) ranging from 0.1267 to 0.1299, while the evolved high-Ti samples are more radiogenic (((187)Os/ (188)Os)(i) up to 0.184) We propose that the high-Ti WMBT were derived from the sub-lithospheric asthenosphere, and contaminated during ascent by interaction with the subcontinental lithospheric mantle (SCLM). The evolved high-Ti WMBT were derived from the same asthenospheric source but experienced crustal contamination. The chemical characteristics of the low-Ti group can be explained by partial melting of the most fertile portions of the SCLM metasomatized during paleo-subduction. Alternatively, the low-Ti WMBT could be derived from the sub-lithospheric asthenosphere but the resulting melts may have undergone contamination by the SCLM. The occurrences of high-Ti basalts are apparently not restricted to the area of initial continental disruption which may bring into question previous interpretations such as those relating high-Ti CAMP magmatism to the initiation of Atlantic ridge spreading or as the expression of a deep mantle plume. We propose that the CAMP magmatism in the Maranhao basin may be attributed to local hotter mantle conditions due to the combined effects of edge-driven convection and large-scale mantle warming under the Pangea supercontinent. The involvement of a mantle-plume with asthenosphere-like isotopic characteristics cannot be ruled out either as one of the main source components of the WMBT or as a heat supplier. (C) 2010 Elsevier BM. All rights reserved.

HiPP: A Novel Hierarchical Point Placement Strategy and its Application to the Exploration of Document Collections

Point placement strategies aim at mapping data points represented in higher dimensions to bi-dimensional spaces and are frequently used to visualize relationships amongst data instances. They have been valuable tools for analysis and exploration of data sets of various kinds. Many conventional techniques, however, do not behave well when the number of dimensions is high, such as in the case of documents collections. Later approaches handle that shortcoming, but may cause too much clutter to allow flexible exploration to take place. In this work we present a novel hierarchical point placement technique that is capable of dealing with these problems. While good grouping and separation of data with high similarity is maintained without increasing computation cost, its hierarchical structure lends itself both to exploration in various levels of detail and to handling data in subsets, improving analysis capability and also allowing manipulation of larger data sets.

Geochemistry of iron and manganese in soils and sediments of a mangrove system, Island of Pai Matos (Cananeia - SP, Brazil)

Five zones along a transect of 180 m were selected for study on the Island of Pai Matos (Sao Paulo, Brazil). Four of the zones are colonised by vascular plants (Spartina SP, Laguncularia LG, Avicennia AV and Rhizophora RH) and were denominated soils, and the other zone, which lacks vegetation, was denominated sediment (SD). The geochemical conditions differed significantly in soils and sediment and also at different depths. The soils were oxic (Eh > 350 mV) or suboxic (Eh: 350-100 mV) at the surface and anoxic (Eh < 100 mV) at depth, whereas in the sediment anoxic conditions prevailed at all depths, but with a lower concentration of sulphides in the pore water and pyrite in the solid fraction. Under these geochemical conditions Fe is retained in the soils, while the Mn tends to be mobilized and lost. The most abundant form of iron oxyhydroxide was lepidocrocite (mean concentration for all sites and depths, 45 +/- 19 mu mol g(-1)), followed by goethite (30 19 mu mol g(-1))and ferrihydrite (19 +/- 11 mu mol g(-1)),with significant differences among the mean concentrations. There was a significant decrease with depth in all the types of Fe oxyhydroxides measured, particularly the poorly crystalline forms. The pyrite fraction was an important component of the free Fe pool (non-silicate Fe) in all soils as well as in the sediment, especially below 20 cm depth (mean concentration for all sites and depths, 60 +/- 54 mu mol CI). Furthermore, the mean concentration of Fe-pyrite for all sites and depths was higher than that obtained for any of the three Fe oxyhydroxides measured. The Fe-AVS was a minor fraction, indicating that the high concentrations of dissolved Fe in the soils in the upper area of the transect result from the oxidation of Fe sulphides during low tide. Mossbauer spectroscopy also revealed that most of the Fe (III) was associated with silicates, in this case nontronite. The presence of crystals of pyrite associated with phyllosilicates in samples from the upper layer of the soils may indicate that pyritization of this form of Fe(III) is more rapid than usually reported for ocean bed sediments. The sequential extraction of Mn did not reveal any clearly dominant fraction, with the Mn-carbonate fraction being the most prevalent, followed by exchangeable Mn and oxides of Mn, whereas pyrite-Mn and Mn associated with crystalline Fe-oxides were present at significantly lower concentrations. The high concentration of dissolved Mn found in the soils in the lower part of the transect is consistent with the fact that the solubility is determined by the carbonate fraction. Unlike for Fe, in the soils in the higher zone, which are subject to intense drainage during low tide, there was loss of Mn, as reflected by the concentration of total Mn. (C) 2008 Elsevier B.V. All rights reserved.

A further exploration of a nucleophilicity index based on the gas-phase ionization potentials

An empirical nucleophilicity index based on the gas-phase ionization potentials has been recently shown to be useful categorizing and settling the nucleophilicity power of a series of captodative ethylenes reacting in cycloaddition reactions (L.R. Domingo, E. Chamorro, P. Perez, Journal of Organic Chemistry 73 (2008) 4615-4624). In the present work, the applicability of such model is tested within a broader series of substituted alkenes, substituted aromatic compounds and simple nucleophilic molecules. This index obtained within a Koopman`s theorem framework has been evaluated here in both gas and solution phases for several well-known nucleophiles. These results are found to be linearly correlated. Finally, the feasibility of the predictive character of this index has been discussed in comparison to the available experimental nucleophilicities of some amines in water. These results further support and validate the usefulness of such approximation in the modeling of the global nucleophilicity. (C) 2008 Elsevier B.V. All rights reserved.

The link between partial melting, granitization and granulite development in central Ribeira Fold Belt, SE Brazil: New evidence from elemental and Sr-Nd isotopic geochemistry

Elemental and Sr-Nd isotopic data on metatexites, diatexites, orthogneisses and charnockites from the central Ribeira Fold Belt indicate that they are LILE-enriched weakly peraluminous granodiorites. Harker and Th-Hf-La correlation trends suggest that these rocks represent a co-genetic sequence, whereas variations on CaO, MnO, Y and HREE for charnockites can be explained by garnet consumption during granulitic metamorphism. Similar REE patterns and isotopic results of epsilon(565)(Nd) = -5.4 to -7.3 and (87)Sr/(86)Sr(565) = 0.706-0.711 for metatexites, diatexites, orthogneisses and charnockites, as well as similar T(DM) ages between 2.0 and 1.5 Ga are consistent with evolution from a relatively homogeneous and enriched common crustal (metasedimentary) protolith. Results suggest a genetic link between metatexites, diatexites, orthogneisses and charnockites and a two-step process for charnockite development: (a) generation of the hydrated igneous protoliths by anatexis of metasedimentary rocks; (b) continuous high-grade metamorphism that transformed the ""S-type granitoids"" (leucosomes and diatexites) into orthogneisses and, as metamorphism and dehydration progressed, into charnockites. (C) 2011 Elsevier Ltd. All rights reserved.

GEOCHEMISTRY AND U-PB ZIRCON AGE OF THE INTERNAL OSSA-MORENA ZONE OPHIOLITE SEQUENCES: A REMNANT OF RHEIC OCEAN IN SW IBERIA

The Early Paleozoic geodynamic evolution in SW Iberia is believed to have been dominated by the opening of the Rheic Ocean. The Rheic Ocean is generally accepted to have resulted from the drift of peri-Gondwanan terranes such as Avalonia from the northern margin of Gondwana during Late Cambrian-Early Ordovician times. The closure of the Rheic Ocean was the final result of a continent-continent collision between Gondwana and Laurussia that produced the Variscan orogen. The Ossa-Morena Zone is a peri-Gondwana terrane, which preserves spread fragments of ophiolites - the Internal Ossa-Morena Zones Ophiolite Sequences (IOMZOS). The final patchwork of the IOMZOS shows a complete oceanic lithospheric sequence with geochemical characteristics similar to the ocean-floor basalts, without any orogenic fingerprint and/or crustal contamination. The IOMZOS were obducted and imbricated with high pressure lithologies. Based on structural, petrological and whole-rock geochemical data, the authors argue that the IOMZOS represent fragments of the oceanic lithosphere from the Rheic Ocean. Zircon SHRIMP U-Pb geochronological data on metagabbros point to an age of ca. 480 Ma for IOMZOS, providing evidence of a well-developed ocean in SW Iberia during this period, reinforcing the interpretation of the Rheic Ocean as a wide ocean among the peri-Gondwanan terranes during Early Ordovician times.