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.

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.

Upper-mantle seismic structure beneath SE and Central Brazil from P- and S-wave regional traveltime tomography

We present models for the upper-mantle velocity structure beneath SE and Central Brazil using independent tomographic inversions of P- and S-wave relative arrival-time residuals (including core phases) from teleseismic earthquakes. The events were recorded by a total of 92 stations deployed through different projects, institutions and time periods during the years 1992-2004. Our results show correlations with the main tectonic structures and reveal new anomalies not yet observed in previous works. All interpretations are based on robust anomalies, which appear in the different inversions for P-and S-waves. The resolution is variable through our study volume and has been analyzed through different theoretical test inversions. High-velocity anomalies are observed in the western portion of the Sao Francisco Craton, supporting the hypothesis that this Craton was part of a major Neoproterozoic plate (San Franciscan Plate). Low-velocity anomalies beneath the Tocantins Province (mainly fold belts between the Amazon and Sao Francisco Cratons) are interpreted as due to lithospheric thinning, which is consistent with the good correlation between intraplate seismicity and low-velocity anomalies in this region. Our results show that the basement of the Parana Basin is formed by several blocks, separated by suture zones, according to model of Milani & Ramos. The slab of the Nazca Plate can be observed as a high-velocity anomaly beneath the Parana Basin, between the depths of 700 and 1200 km. Further, we confirm the low-velocity anomaly in the NE area of the Parana Basin which has been interpreted by VanDecar et al. as a fossil conduct of the Tristan da Cunha Plume related to the Parana flood basalt eruptions during the opening of the South Atlantic.

Deep crustal structure of the Parana Basin from receiver functions and Rayleigh-wave dispersion: Evidence for a fragmented cratonic root

The deep crustal structure of the Parana Basin of southern Brazil is investigated by analyzing P- and PP-wave receiver functions at 17 Brazilian Lithosphere Seismic Project stations within the basin. The study area can be described as a typical Paleozoic intracratonic basin that hosts one of the largest Large Igneous Province of the world and makes a unique setting for investigating models of basin subsidence and their interaction with mantle plumes. Our study consists of (1) an analysis of the Moho interaction phases in the receiver functions to obtain the thickness and bulk Vp/Vs ratio of the basin`s underlying crust and (2) a joint inversion with Rayleigh-wave dispersion velocities from an independent tomographic study to delineate the detailed S-wave velocity variation with depth. The results of our analysis reveal that Moho depths and bulk Vp/Vs ratios (including sediments) vary between 41 and 48 km and between 1.70 and 1.76, respectively, with the largest values roughly coinciding with the basin`s axis, and that S-wave velocities in the lower crust are generally below 3.8 km/s. Select sites within the basin, however, show lower crustal S-wave velocities slightly above 3.9 km/s suggestive of underplated mafic material. We show that these observations are consistent with a fragmented cratonic root under the Parana basin that defined a zone of weakness for the initial Paleozoic subsidence of the basin and which allowed localized mafic underplating of the crust along the suture zones by Cenozoic magmatism.

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.

Exploration of the idea of the horse in graphics and sculpture

The exploration of the idea of the horse is a very complex and open quest. Primarily it entails some conception of what the idea of the horse is. In choosing to title the project as such, I was attempting to indicate that what was of major interest to me was the representation of those qualities of the horse which are abstract and intangible as well as the physical qualities of the horse. Because of this interest, much of my work is concerned with movement, gesture, and the effects of structure, or lack thereof, on movement and gesture.

Short fiction of Thomas Hardy: an exploration and assessment

Hardy's novels and poetry have received extensive criticism, in due proportion to their merit. Hardy's short stories, however, have been virtually excluded from the annals of Hardy criticism, even though Hardy wrote over forty short stories, several of which are truly outstanding. In part, the reason for this neglect is because of the neglected state of the short story in Victorian England. Short fiction, published mainly only in periodicals and never collected in volume form, was obscured to a large extent by the highly popular serial novel. This thesis examines Thomas Hardy's short stories in the context of both the Victorian period and the Victorian short story genre, and explores the ways in which Thomas Hardy improved upon and deviated from some of the common types of short fiction being written in his day.

Choreographic exploration of physical duress: motivation for and responses to exhaustion (a project in performance)

What motivates someone to dance until they are exhausted, sweaty, boiling hot and out of breath? I myself, recalling experiences when I have danced so hard I've nearly fainted, remember how exhilarating that motivation can be. But why? Why is that at all pleasant? Of course, I had several of my own explanations, but I was also interested in doing some scientific research on exhaustion. This question was of ample depth to become the basis of my project.

The gay subject in business and its discursive formation: an exploration on power, knowledge and sexuality

Issues related to the reality of lesbian, gay, bisexual and transgender (LGBT) individuals are being incorporated into institutional and social discourses, and show the challenges that must be overcome towards citizenship. The inclusion of gay rights in the domain of institutions like the United Nations and the Brazilian Secretariat of Human Rights are a response to broader movements that places the gay subject as an important topic of debate in the social-political sphere. In this scenario, some institutions deserve close attention from researchers related to gay issues, the business environment being a good example. In this domain, diversity has become an important topic of debate between scholars, where the question of sexual identity in most cases does not appear. The literature that actually focuses on the theme is explored through approaches that are not able to break with universalisms and a normatized vocabulary. Therefore, this research explores discursive structures related to sexuality and examines the meanings construed throughout these structures as described by gay individuals working in business. Furthermore, it investigates patterns of discursive normative structures and consequential challenges faced by gay people in the working environment, and also complements the current debate both in the socio-political sphere and in academic reality on LGBT challenges. The Foucauldian notions of discourse, knowledge and power, and the main concepts of queer theory are incorporated to the analysis, as well as concepts related to the politics of post-colonial sexuality, subordination, and hegemonic forces, together with role of reflexivity in modernity and its impacts on secularized mental structures. The research design takes a phenomenological approach and bases its knowledge claim on a participatory perspective, where the sample chosen for data collection consisted of gay individuals working in the business environment, aiming at generate categories of meanings through the description of their experiences.

Non-invasive strategy in assessing asthma through biofluids metabolomics exploration: exhaled breath and urine potentialities

Asthma is a significant health issue in the pediatric population with a noteworthy growth over the years. The proposed challenge for this PhD thesis was the development of advanced methodologies to establish metabolomic patterns in urine and exhaled breath associated with asthma whose applicability was subsequently exploited to evaluate the disease state, the therapy adhesion and effect and for diagnostic purposes. The volatile composition of exhaled breath was studied combining headspace solid phase microextraction (HS-SPME) with gas chromatography coupled to mass spectrometry or with comprehensive two-dimensional gas chromatography coupled to mass spectrometry with a high resolution time of flight analyzer (GC×GC–ToFMS). These methodologies allowed the identification of several hundred compounds from different chemical families. Multivariate analysis (MVA) led to the conclusion that the metabolomic profile of asthma individuals is characterized by higher levels of compounds associated with lipid peroxidation, possibly linked to oxidative stress and inflammation (alkanes and aldehydes) known to play an important role in asthma. For future applications in clinical settings a set of nine compounds was defined and the clinical applicability was proven in monitoring the disease status and in the evaluation of the effect and / or adherence to therapy. The global volatile metabolome of urine was also explored using an HSSPME/GC×GC–ToFMS method and c.a. 200 compounds were identified. A targeted analysis was performed, with 78 compounds related with lipid peroxidation and consequently to oxidative stress levels and inflammation. The urinary non-volatile metabolomic pattern of asthma was established using proton nuclear magnetic resonance (1H NMR). This analysis allowed identifying central metabolic pathways such as oxidative stress, amino acid and lipid metabolism, gut microflora alterations, alterations in the tricarboxylic acid (TCA) cycle, histidine metabolism, lactic acidosis, and modification of free tyrosine residues after eosinophil stimulation. The obtained results allowed exploring and demonstrating the potential of analyzing the metabolomic profile of exhaled air and urine in asthma. Besides the successful development of analysis methodologies, it was possible to explore through exhaled air and urine biochemical pathways affected by asthma, observing complementarity between matrices, as well as, verify the clinical applicability.

The transformation between exploration and exploitation applied to inventors of packaging innovations

While the inventor is often the driver of an invention in the early stages, he/she needs to move between different social networks for knowledge in order to create and capture value. The main objective of this research is to propose a literature-based framework based on innovation network theory and complemented with C-K theory, in order to analyze the invention/innovation process of inventors and the product concepts in a packaging industry context. Empirical input from three case studies of packaging inventions and their inventors is used to elaborate the suggested framework.The article identifies important gaps in the literature of innovation networks. This is addressed through a theoretical framework based on network theories, complemented with C-K theory for the product design level. The strength-of-ties dimension of the theoretical framework suggests, in agreement with the mainstream literature and the cases presented, that weak ties are required to access the knowledge related to exploration networks and strong ties are required to utilize the knowledge in the exploitation network. The transformation network is an intermediate step acting as a bridge where entrepreneurs can find required knowledge. The transformation network is also an intermediate step where entrepreneurs find financing and companies interested in commercializing inventions. (C) 2010 Elsevier Ltd. All rights reserved.

Radon in groundwaters from Guarany aquifer, South America: environmental and exploration implications

Groundwater and sandstone samples were analyzed for radon in Guarany aquifer, Parana sedimentary basin, South America. The dissolved radon ranged between 3 and 3303 pCi/l, being lognormally distributed, with a modal value of 1315 pCi/l, and a median value of 330 pCi/l. Rn-222 leakage experiments for sandstones yielded a theoretical value of 1390 pCi/l for Rn-222 in water, showing that theoretical modeling can reliably be used to interpret laboratory and field data. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Conceptual model for adaptable and extensible visual data exploration

Interactive visual representations complement traditional statistical and machine learning techniques for data analysis, allowing users to play a more active role in a knowledge discovery process and making the whole process more understandable. Though visual representations are applicable to several stages of the knowledge discovery process, a common use of visualization is in the initial stages to explore and organize a sometimes unknown and complex data set. In this context, the integrated and coordinated - that is, user actions should be capable of affecting multiple visualizations when desired - use of multiple graphical representations allows data to be observed from several perspectives and offers richer information than isolated representations. In this paper we propose an underlying model for an extensible and adaptable environment that allows independently developed visualization components to be gradually integrated into a user configured knowledge discovery application. Because a major requirement when using multiple visual techniques is the ability to link amongst them, so that user actions executed on a representation propagate to others if desired, the model also allows runtime configuration of coordinated user actions over different visual representations. We illustrate how this environment is being used to assist data exploration and organization in a climate classification problem.