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.

Economic, social and cultural influences on the status and wellbeing of Indian rural wives

Examines the status and well being of wives in rural India using results from interviews. Surveys were conducted in three villages in the southwest of West Bengal and in three villages in the west of Orissa. The survey in West Bengal contained a large proportion of Santal tribals and the Oriyan survey was dominated by Kondh tribals. The relationships between variables representing economic, social and cultural factors are compared with ‘dependent’ variables representing the status of wives within their family and their wellbeing. Wellbeing is indicated by whether the basic needs of wives for food and medical care are met. Status of wives is indicated by their ‘control’ over family resources, whether or not they are restricted in joining social groups and in working outside their home, and the extent of their involvement in family decision-making. Cultural factors are found to be the dominant influence on the status of wives. Family income and other economic factors are found to be associated cross sectionally with greater restrictions on wives within their family. Nevertheless, the higher in the economic status of the household, the more likely are the basic needs of wives to be met.

Alcohol- and drug-use disorders in Australia: implications of the National Survey of Mental Health and Wellbeing

Objective: This study reports the prevalence and correlates of ICD-10 alcohol- and drug-use disorders in the National Survey of Mental Health and Wellbeing (NSMHWB) and discusses their implications for treatment. Method: The NSMHWB was a nationally representative household survey of 10 641 Australian adults that assessed participants for symptoms of the most prevalent ICD-10 and DSM-IV mental disorders, including alcohol- and drug-use disorders. Results: In the past 12 months 6.5% of Australian adults met criteria for an ICD-10 alcohol-use disorder and 2.2% had another ICD-10 drug-use disorder. Men were at higher risk than women of developing alcohol- and drug-use disorders and the prevalence of both disorders decreased with increasing age. There were high rates of comorbidity between alcohol- and other drug-use disorders and mental disorders and low rates of treatment seeking. Conclusions: Alcohol-use disorders are a major mental health and public health issue in Australia. Drug-use disorders are less common than alcohol-use disorders, but still affect a substantial minority of Australian adults. Treatment seeking among persons with alcohol- and other drug-use disorders is low. A range of public health strategies (including improved specialist treatment services) are needed to reduce the prevalence of these disorders.

Personality disorders in the community: a report from the Australian national survey of mental health and wellbeing

Background: The first set of aims of the present study was to determine the prevalence of personality disorders (PDs) in a nation, and gender differences in the types and numbers of PDs endorsed. The second set of aims was to establish the relationship of PD to other, non-PD disorders, physical conditions, and disability. Method: Data were obtained from the Australian National Survey of Mental Health and Wellbeing, conducted between May and August 1997. A stratified random sample of households was generated, from which all those aged 18 or over were considered potential interviewees. There were 10,641 respondents to the survey, and this represented a response rate of 78%. Each interviewee was asked 59 questions indexing specific ICD-10 PD criteria. Results: Of the total survey sample, 704 persons had at least one PD. Using weighted replicate weights, it was estimated that approximately 6.5% of the adult population of Australia have one or more PDs (lifetime prevalence). Persons with PD were more likely to be younger, male, and not married, and to have an anxiety disorder, an affective disorder, a substance use disorder, or a physical condition. They were also more likely to have greater disability than those without PD. Conclusion: The study is the first nationwide survey of mental disorders conducted within Australia. It provides an estimate of the prevalence of the various types of PD. The survey has considerable limitations, however, and these are discussed.

Characteristics of DSM-IV and ICD-10 cannabis dependence among Australian adults: results from the National Survey of Mental Health and Wellbeing

A representative sample (n = 10 641) of Australian adults completed a structured diagnostic interview assessing the prevalence of mental and substance use disorders in the last year. The prevalence of DSM-IV (1.5%) and ICD-10 (1.7%) cannabis dependence was similar. DSM-IV and ICD-10 dependence criteria comprised unidimensional syndromes. The most common symptoms among dependent and non-dependent users were difficulties with controlling use and withdrawal, although there were marked differences in symptom prevalence. Dependent users reported a median of four symptoms. There was good to excellent diagnostic concordance (kappas = 0.7-0.9) between systems for dependence but not for abuse/harmful use (Y = 0.4). These findings provide some support for the validity of cannabis dependence. (C) 2001 Elsevier Science Ireland Ltd. All rights reserved.

Influence of decortication of the recipient graft bed on graft integration and tissue neoformation in the graft-recipient bed interface

The objective of the present study was to assess the influence of decortication of the posterior elements of the vertebra (recipient bed) and the nature of the bone graft (cortical or cancellous bone) on graft integration and bone, cartilage and fiber neoformation in the interface between the vertebral recipient bed and the bone graft. Seventy-two male Wistar rats were divided into four experimental groups according to the presence or absence of decortication of the posterior vertebral elements and the use of a cortical or cancellous bone graft. Group I-the posterior elements were decorticated and cancellous bone used. Group II-the posterior elements were decorticated and cortical graft was used. Group III-the posterior elements were not decorticated and cancellous graft was used. Group IV-the posterior elements were not decorticated and cortical graft was used. The animals were killed 3, 6 and 9 weeks after surgery and the interface between the posterior elements and the bone graft was subjected to histomorphometric evaluation. Mean percent neoformed bone was 40.8% in group I (decortication and cancellous graft), 39.13% in group II (decortication and cortical graft), 6.13% in group III (non-decorticated and cancellous graft), and 9.27% in group IV (non-decorticated and cortical graft) for animals killed at 3 weeks (P = 0.0005). For animals killed at 6 weeks, the mean percent was 38.53% for group I, 40.40% for group II, 10.27% for group III, and 7.6% for group IV (P = 0.0005), and for animals killed at 9 weeks, the mean was 25.93% for group I, 30.6% for group II, 16.4% for group III, and 18.73% for group IV (P = 0.0026). The mean percent neoformed cartilage tissue was 8.36% for group I, 7.46% for group II, 11.1% for group III, and 9.13% for group IV for the animals killed at 3 weeks (P = 0.6544); 6.6% for group I, 8.07% for group, 7.47% for group III and 6.13% for group IV (P = 0.4889) for animals killed at 6 weeks, and 3.13% for group I, 4.06% for group II, 10.53% for group III and 12.07% for group IV (P = 0.0006) for animals killed at 9 weeks. Mean percent neoformed fibrous tissue was 11% for group I, 6.13% for group II, 26.27% for group III and 21.87% for group IV for animals killed at 3 weeks (P = 0.0008); 7.67% for group I, 7.1% for group II, 9.8% for group III and 10.4% for group IV (P = 0.7880) for animals killed at 6 weeks, and 3.73% for group I, 4.4% for group II, 6.67% for group III and 6.8% for group IV (P = 0.0214) for animals killed at 9 weeks. The statistically significant differences in percent tissue formation were related to decortication of the posterior elements. The use of a cortical or cancellous graft did not influence tissue neoformation. Ossification in the interface of the recipient graft bed was of the intramembranous type in the decorticated animals and endochondral type in the non-decorticated animals.

The nexus of value chain integration and e-business applications on public sector agriculture R&D management

We examine the potential impact of interconnectivity of value chain partnerships through electronic means (e-business practices) on the management of Public Sector Agriculture R&D in Australia. We review the changing forms of managing research and development, the forces driving these changes, and R&D processes that are theoretically consistent with the move towards value chain involvement and the increase in active constituents in Public Sector Agriculture R&D. We then explore the potential of emerging e-business models to change the patterns of inter-connectivity, speed and omnipresence of partners in the value chain. Three e-business R&D management practices are identified that provide the prerequisite flexibility necessary to take advantage of opportunistic markets. These R&D business practices are: compressing R&D to reduce time to market, fostering co-development to enter a market at the last moment and building flexible products that allow adjustment at the last possible moment. Some fundamental reallocation of existing resources will be required to meet these markets. Implications of these e-business practices for R&D management are discussed.

Implications of the Intervention Program for Physical Activity (IPPA) in the perception of illness and wellbeing in people with Multiple Sclerosis (MS)

The aim of this study is to examine the implications of the IPPA in the perception of illness and wellbeing in MS patients. Methods - This is a quasi experimental study non-randomized study with 24 MS patients diagnosed at least 1 year before, and with an EDSS score of under 7. We used the IPPA in 3 groups of eight people in 3 Portuguese hospitals (Lisbon, Coimbra, and Porto). The sessions were held once a week for 90 minutes, over a period of 7 weeks. The instruments used were: We asked the subjects the question “Please classify the severity of your disease?” and used the Personal Wellbeing Scale (PWS) at the beginning (time A) and end (time B) of the IPPA. We used the SPSS version 20. A non-parametric statistical hypothesis test (Wilcoxon test) was used for the variable analysis. The intervention followed the recommendations of the Helsinki Declaration. Results – The results suggest that there are differences between time A and B, the perception of illness decreased (p<0.08), while wellbeing increased (p<0.01). Conclusions: The IPPA can play an important role in modifying the perception of disease severity and personal wellbeing.

Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

Endogenous integration and welfare in complementary goods markets

This paper analyzes the strategic decision to integrate by firms that produce complementary products. Integration entails bundling pricing. We find out that integration is privately profitable for a high enough degree of product differentiation, that profits of the non-integrated firms decrease, and that consumer surplus need not necessarily increase when firms integrate despite the fact that prices diminish. Thus, integration of a system is welfare-improving for a high enough degree of product differentiation combined with a minimum demand advantage relative to the competing system. Overall, and from a number of extensions undertaken, we conclude that bundling need not be anti-competitive and that integration should be permitted only under some circumstances.