Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Clinical relationships and ethical problems in primary care, Sao Paulo, SP, Brazil

Objectives: Main Objective: to identify ethical problems in primary care according to nurses` and doctors` perceptions. Secondary Objective: to know ethical issues of patient-professional relationships in primary care. Design: Synthesis to integrate and reinterpret primary results of qualitative studies. Setting: Primary healthcare centers, Sao Paulo, SP, Brazil. Participants and/or context: Incidental sample of 34 nurses and 36 medical doctors working in primary healthcare centers selected by convenience. Methods: Individual, semi-structured interviews to identity situations considered as sources of ethical problems. The sample is socially representative of primary care health centers and professionals. Data collection assured discourse saturation. Hermeneutic-dialectical discourse analysis was used to study the results. Results: Patient-professional relationships and team work were the main sources of ethical problems. The most important problems were patient information, privacy, confidentiality, interpersonal relationship, linkage and patient autonomy. These issues reflect the recent changes in clinical relation ships and show the peculiarities of primary care with its continuous care which lasts a long time. Healthcare involves multiprofessional team work in the midst of the patient claims for autonomy. Good care of patients needs requires a relationship based on communication and cooperation, and includes feelings and values, with communication skills. Conclusions: Ethical problems in primary care are common situations. For quality and humane primary care the relationship should consist of dialogue, trust and cooperation. (C) 2009 Elsevier Espana, S.L. All rights reserved.

Reducing mean flow time in permutation flow shop

This paper deals with the traditional permutation flow shop scheduling problem with the objective of minimizing mean flowtime, therefore reducing in-process inventory. A new heuristic method is proposed for the scheduling problem solution. The proposed heuristic is compared with the best one considered in the literature. Experimental results show that the new heuristic provides better solutions regarding both the solution quality and computational effort.

Human Error Contribution in Collision and Grounding of Oil Tankers

The purpose of this article is to present a quantitative analysis of the human failure contribution in the collision and/or grounding of oil tankers, considering the recommendation of the ""Guidelines for Formal Safety Assessment"" of the International Maritime Organization. Initially, the employed methodology is presented, emphasizing the use of the technique for human error prediction to reach the desired objective. Later, this methodology is applied to a ship operating on the Brazilian coast and, thereafter, the procedure to isolate the human actions with the greatest potential to reduce the risk of an accident is described. Finally, the management and organizational factors presented in the ""International Safety Management Code"" are associated with these selected actions. Therefore, an operator will be able to decide where to work in order to obtain an effective reduction in the probability of accidents. Even though this study does not present a new methodology, it can be considered as a reference in the human reliability analysis for the maritime industry, which, in spite of having some guides for risk analysis, has few studies related to human reliability effectively applied to the sector.

Some heuristic algorithms for total tardiness minimization in a flowshop with blocking

The flowshop scheduling problem with blocking in-process is addressed in this paper. In this environment, there are no buffers between successive machines: therefore intermediate queues of jobs waiting in the system for their next operations are not allowed. Heuristic approaches are proposed to minimize the total tardiness criterion. A constructive heuristic that explores specific characteristics of the problem is presented. Moreover, a GRASP-based heuristic is proposed and Coupled with a path relinking strategy to search for better outcomes. Computational tests are presented and the comparisons made with an adaptation of the NEH algorithm and with a branch-and-bound algorithm indicate that the new approaches are promising. (c) 2007 Elsevier Ltd. All rights reserved.

Diversity and Emotion: The New Frontiers in Organizational Behavior Research

This article provides a review of recent developments in two topical areas of research in contemporary organizational behavior: diversity and emotions. In the section called “Diversity,”we trace the history of diversity research, explore the definitions and paradigms used in treatments of diversity, and signal new areas of interest. We conclude that organizational behavior in the 21st century is evolving to embrace a more eclectic and holistic view of humans at work. In the section called “Emotions,” we turn our attention to recent developments in the study of emotions in organizations. We identify four major topics: mood theory, emotional labor, affective events theory (AET), and emotional intelligence, and argue that developments in the four domains have significant implications for organizational research, and the progression of the study of organizational behavior. As with the study of diversity, the topic of emotions in the workplace is shaping up as one of the principal areas of development in management thought and practice for the next decade. Finally, we discuss in our conclusion how these two areas are being conceptually integrated, and the implications for management scholarship and research in the contemporary world.

Reconceptualising social sustainability in urban development

Although the social dimension is often cited as the third leg of triple bottom line sustainability, there is at present general agreement on the difficulty of saying just what social sustainability is and how it can be related to enivironmental sustainability. This paper proposes that a sociotechnical understanding of the relationship beween human behaviour and technical developments provides a way of making the social dimension accessible to engineers, designers and developers. We draw on early work in master planned urban developments to show how a sociotechnical model, married to a life cycle assessment approach can help us understand and design for effective and efficient implementation of sustainability systems

Teaching in rural and remote schools: a literature review

In this paper. the authors examine a wide range of recent research into the preparation and support for teachers working in rural and remote schools. The paper reviews many preservice and inservice initiatives which highlight issues affecting:teaching and learning in schools outside the major metropolitan centres. The work is reviewed from an Australian perspective but evaluates research from throughout the world. The paper concludes that despite a large body of research (Gibson, 1994), that has identified the need for specialised pre-service preparation which accommodates the social and professional differences associated with work in rural and remote areas, the implementation of such programs by teacher training institutions has been sparse, lacking in cohesion and in many cases non-existent. (C) 1998 Elsevier Science Ltd. All rights reserved.

Listening to the Whispers of Matter Through Arabic Hermeticism: New Studies on the Book of the Treasure of Alexander

The Jabirian Corpus refers to the K. Thahirat Al-`Iskandar, ""The Book of the Treasure of Alexander"" (hereafter BTA), as one of several forgeries suggesting that alchemical secrets were hidden in inscriptions in various places. The book was neglected until 1926, when Julius Ruska discussed it in his work on the Emerald Tablet, placing the BTA within the literature related to the development of Arabic alchemy. His preliminary study became an essential reference and encouraged many scholars to work on the BTA in the following decades. Some years ago, we completed the first translation of the BTA into a Western language. The work was based on the acephalous Escorial manuscript, which we identified as a fourteenth-century copy of the BTA. This manuscript is peculiar, as part of it is encoded. After finishing our translation, we started to establish the text of the BTA. At present, the text is in process of fixation-to be followed by textual criticism-and has been the main focus of a thorough study of ours on medieval hermeticism and alchemy. A sample of the work currently in progress is presented in this paper: an analysis of the variations between different manuscripts along with a study and English translation of its alchemical chapter.

Factors influencing organisational silence

Organisadonal silence is a recendy introduced area of business research that seeks to address why employees fail to express ideas, informadon and opinions that can effecdvely improve organisadonal effecdveness. In making a start to understand silence, the majority of frameworks have suggested that employees withhold valuable input from management because they believe that it is too personally cosdy to speak up, and/or management are unMkely to take acdon about their ideas or concerns. Because today's workforce are largely required to work in groups or teams, one of the primary aims of this paper is to provide a deeper understanding of this phenomenon by focusing on group process factors that are likely to drive silence. Research that consider the group perspecdve indicate that one's ingroup posidon (i,e,, pro to typicality), and the accumuladon of idiosyncrasy credits (i,e,, leeway to offer innovadve ideas) are likely to play a role in whether (or not) people speak up. For example, those on the periphery of the group or less prototypical group members may need to conform strenuously to group norms in order to improve their ingroup posidon. Similarly, those who have accrued few idiosyncrasy credits may need to conform to group expectadons in order to accumulate sufficient "resources" to deviate from group norms, and be taken seriously by other group members. Thus, the conceptual framework proposed is underpinned by the social idendty perspecdve as well as the nodon of idiosyncrasy credits.

Re-integration into work

This is the first complete textbook designed for physiotherapists and occupational therapists on the topic of pain. It was developed for use in conjunction with the International Association for the Study of Pain's pain curriculum for OTs and PTs. The book addresses the nature of pain, the neuroanatomical and neurophysiological substrates of pain, the psychological... More aspects of pain, the lifespan approach to pain, pain measurement, pain and placebo, modalities for treating pain, and special topics in pain. It provides an overview of the physiological, psychosocial, and environmental aspects of pain experience across the lifespan. Aimed primarily at OTs and PTs the assessment and interventions issues pertaining to the perspectives of each profession are discussed in detail. The book is also relevant to the other health professions involved in pain management or intending to work in this area.

Using BCG, MPT-51 and Ag85 as antigens in an indirect ELISA for the diagnosis of bovine tuberculosis

This study evaluated the Mycobacterium tuberculosis protein antigen MPT-51, the trimeric antigen 85 (Ag85) complex, and Bacillus Calmette-Guerin (BCG) in an indirect ELISA to diagnose bovine tuberculosis (TB) from serum samples. Serum was collected from 208 intra-dermal tuberculin test (ITT)-positive and 54 ITT-negative animals from a region where bovine TB is endemic. Using the Ag85 and BCG antigens, the indirect ELISA was able to discriminate ITT-positive from ITT-negative animals. This level of discrimination was not achieved when using the MPT-51 antigen. The highest sensitivity (Se) and specificity (Sp) of the test was found when BCG was used (Se, 82%; Sp, 91%). Further work in different epidemiological settings and with larger numbers of animals will be required to validate these findings. (C) 2009 Elsevier Ltd. All rights reserved.

Ticks (Acari : ixodidae) infesting wild birds in an Atlantic forest area in the state of Sao Paulo, Brazil, with isolation of Rickettsia from the tick Amblyomma longirostre

During field work in Nazare Paulista, state of Sao Paulo, Brazil, we found 13 (56.5%) of 23 birds (mostly Passeriformes) to be infested by 28 larvae and I nymph of Amblyomma spp. Two larvae were reared to the adult stage, being taxonomically identified as Amblyomma parkeri Fonseca and Aragao, whereas five larvae and one nymph were identified as Amblyomma longirostre Koch. All six A. longirostre specimens were shown to be infected by rickettsia, as demonstrated by polymerase chain reaction (PCR) targeting two rickettsial genes (gltA and ompA) or isolation of rickettsia in cell culture from one of the ticks. This isolate was designated as strain AL, which was established in Vero cell culture and was molecularly characterized by DNA sequencing fragments of the rickettsial genes gltA, htrA, ompA, and ompB. Phylogenetic analyses inferred from ompA and ompB partial sequences showed a high degree of similarity of strain AL with Rickettsia sp. strain ARANHA, previously detected by PCR in A. longirostre ticks from Rondonia, northern Brazil. We conclude that strain AL is a new rickettsia genotype belonging to the same species of strain ARANHA, which are closely related to Candidatus `R. amblyomniii`. Further studies should elucidate if strains AL and ARANHA are different strains of Candidatus `R. amblyommii` or are a new species.

Closing the gender gap in Bangladesh: Inequality in education, employment and earnings

Assesses the status of women in Bangladesh by analysing the dynamics of female participation in labour force and education as well as gender earnings differentials at the macro level. The study finds evidence of growing commercialisation of women’s work in Bangladesh. Although the bulk of the female labour force is engaged in self-employment activities in the rural area or in low-skilled textile and readymade garment industries in the urban area, women’s participation in high-skill and entrepreneurial jobs as well as various decision-making bodies is also on the rise. While the gender wage differentials have been considerably reduced in many industries, in general women tend to be paid less than men. There have been remarkable improvements in women’s educational attainments compared to men. Further, female access to education is found to be highly correlated with overall female labour force participation, and relative to male participation. The overall results are suggestive of an improvement in the status of women in Bangladesh.

Examining the effects of work externalization through the lens of social identity theory

This study examines whether dissimilarity among employees that is based on their work status (i.e., whether they are temporary or internal workers) influences their organization-based self-esteem, their trust in and attraction toward their peers, and their altruism. A model that is based on social identity theory posits that work-status dissimilarity negatively influences each outcome variable and that the strength of this relationship varies depending on whether employees have temporary or internal status and the composition of their work groups. Results that are based on a survey of 326 employees (189 internal and 137 temporary) from 34 work groups, belonging to 2 organizations, indicate that work-status dissimilarity has a systematic negative effect only on outcomes related to internal workers when they work in temporary-worker-dominated groups.