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At least 1,135 records · Page 63Linked to original sources
PubMed2006

Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome.

BACKGROUND: Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics - Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. RESULTS: GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. CONCLUSION: GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome annotations to the target genome. The program is freely available under the General Public License and can be accessed along with documentation and tutorial from http://www.virology.ca/gatu.

Amino Acid Sequence↗
PubMedDate not supplied

The Cochrane Collaboration--advances and challenges in improving evidence-based decision making.

The Cochrane Collaboration is an international organization that aims to help people make well-informed decisions about health care by preparing, maintaining, and ensuring the accessibility of rigorous, systematic, and up-to-date reviews (and, where possible, meta-analyses) of the benefits and risks of health care interventions. This article describes the structure of the Cochrane Collaboration and the processes used to carry out the task of research transfer. The authors focus on recent achievements of the Collaboration, emphasize the current challenges and barriers the Collaboration is facing to live up to the expectations it has generated, and highlight the strategies that the organization is using to meet those challenges.

Computer Communication Networks↗
PubMed2005

Appropriation and commercialization of the Pasteur anthrax vaccine.

Whereas Pasteur patented the biotechnological processes that he invented between 1857 and 1873 in the agro-food domain, he did not file any patents on the artificial vaccine preparation processes that he subsequently developed. This absence of patents can probably be explained by the 1844 patent law in France that established the non-patentable status of pharmaceutical preparations and remedies, including those for use in veterinary medicine. Despite the absence of patents, the commercial exploitation of the anthrax vaccine in the 1880s and 1890s led to a technical and commercial monopoly by Pasteur's laboratory as well as the founding of a commercial company to diffuse the vaccine abroad. Pasteur repeatedly refused to transfer his know-how and anthrax vaccine production methods to foreign laboratories, on the grounds that he wished to control the quality of the vaccines produced. Indeed, it was relatively difficult to transfer a method that was not yet perfectly stabilized in the early 1880s. Pasteur also wanted to maintain the monopoly of his commercial company and to increase the profits from vaccine sales so that the Institut Pasteur could be financially independent. The 'Pasteur anthrax vaccine' operating licences are described and analysed in detail in this article.

Anthrax↗
PubMed2005

Single-molecule detection and probe strategies for rapid and ultrasensitive genomic detection.

This paper reviews the current state-of-the-art development of single-molecule detection (SMD)-based methods for ultrasensitive and specific analysis of genomic sequences. We first discuss several newly devised single fluorescent probe strategies that allow separation-free detection of low-abundance DNA sequences, such as quantum dot (QD)-mediated fluorescence resonance energy transfer (FRET) technology and dual-color fluorescence coincidence and colocalization analysis. Various schemes toward single DNA sizing and sequencing in solutions or on surfaces are also reviewed. In the end, we summarize the different microfluidic approaches developed for use with SMD to facilitate rapid, low-volume and quantitative analysis, such as electrokinetic and hydrodynamic single-molecule manipulation techniques.

DNA Probes↗
PubMed1995

Strategies for application of scientific findings in prevention.

Dental research in the last 50 years has accomplished numerous significant advances in preventive dentistry, particularly in the area of research in fluorides, periodontal diseases, restorative dentistry, and dental materials, as well as craniofacial development and molecular biology. The transfer of scientific knowledge to clinical practitioners requires additional effort. It is the responsibility of the scientific communities to transfer the fruits of their findings to society through publications, conferences, media, and the press. Specific programs that the International Association for Dental Research (IADR) has developed to transmit science to the profession and the public have included science transfer seminars, the Visiting Lecture Program, and hands-on workshops. The IADR Strategic Plan also has a major outreach goal. In addition, the Federation Dentaire Internationale (FDI) and the World Health Organization (WHO) have initiated plans to celebrate World Health Day and the Year of Oral Health in 1994. These are important strategies for the application of scientific findings in prevention.

Dental Research↗
PubMed1988

Studies upon the genetic effects of environmental chemicals: the coordinated research programme of the European Economic Community.

The objectives of the European Economic Community's Environmental Research and Development Programmes are to provide a scientific basis for current environmental policy and future environmental management. This paper reviews the work and achievements of the studies carried out by the collaborating laboratories during the period 1981-1985 of the 3rd Programme within the research area 'The Genetic Effects of Environmental Chemicals'. Research efforts supported by the programme may be divided into (i) those involving the validation of current genotoxicity assays and the evaluation of their use in community regulatory activities such as the classification and labelling of chemicals, (ii) those involving the characterization of the metabolic and genotoxic profile of specific chemicals and (iii) those involving the development of new technologies suitable for the hazard identification and risk evaluation of genotoxins. Validation studies have included those of the host mediated assay (and its various modifications), unscheduled DNA synthesis assays and a variety of Drosophila genotoxicity assays. New developments include assays for the detection of chromosome aneuploidy, protocols for cell transformation studies, the detection and quantification of genotoxic lesions, techniques for the study of transplacental genotoxicity, assays for the detection of genotoxic activity in the liver and in germ cells and monitoring techniques for the assessment of both environmental quality and genotoxin exposure in individuals and in populations. The coordination of research effort, such as that described here provides an effective mechanism for the concentration of research on specific problems, for the rapid dissemination of experimental data and the transfer of technology within the European Community.

Animals↗
PubMed1999

Developments in caries diagnosis and their relationship to treatment decisions and quality of care. ORCA Saturday Afternoon Symposium 1997.

This symposium report evaluates the achievements made in caries diagnostic research since the previous symposium held in 1992. The symposium aimed at presenting the state of the art of caries diagnostic methods, on presenting the links between caries diagnosis and subsequent treatment decisions and their effect on the treatment outcomes, particularly the quality of dental care. The variation among dentists in diagnosing (small) caries lesions and in treatment decision making is considerable. This has been explained by the imperfection of caries decision making tests, but also by making incorrect treatment decisions due to incorrect or partial understanding of diagnostic test parameters. Meta-analyses into the performance of caries diagnostic tests revealed that the available quantitative methods are very promising. It was concluded that these methods had high correlations with lesion depth. They were considered suitable to monitor small changes in lesions. Many obstacles have been experienced in attempting to transfer the outcomes of diagnostic research into clinical practice and it was concluded that caries diagnosis researchers should co-operate with manufacturers to introducing valid new diagnostic tools to the market. Main research priorities for the coming 10 years are to conduct cost-effectiveness and cost-utility studies of caries diagnostic tools, to continue to review the performances of diagnostic tests, to transfer diagnostic knowledge and experience to the general practitioners particularly by constructing evidence-based clinical guide-lines, to study the relationship between diagnosis and treatment decision, and to assess the effect of diagnostic and treatment decisions on the outcome of care.

Cost-Benefit Analysis↗
PubMed1995

Sustaining interventions in community systems: on the relationship between researchers and communities.

Important goals of research-based community interventions include the long-term maintenance of effects and fostering of collaboration between researchers and community leaders. This article reviews the challenges associated with transferring innovations to community systems, changing program delivery from an experimental context controlled by researchers to program delivery controlled by community organizations, and sustaining long-term effects of interventions. It is suggested that researchers who develop and implement community interventions in diverse health areas need to confront several issues: (a) fostering effective long-term relationships between researchers and the communities they study and in which they intervene and (b) designing and implementing interventions that are useful to community systems after the formal phase of research ends.

California↗
PubMedDate not supplied

Optimization of wide-area ATM and local-area ethernet/FDDI network configurations for high-speed telemedicine communications employing NASA's ACTS.

A high data rate terrestrial and satellite network was implemented to transfer medical images and data. This article describes the a optimization of the workstations and switching equipment incorporated into the network. Topics discussed in this article include tuning of the network software, the configuration of the Sun Microsystems workstations, the FORE Systems asynchronous transfer mode switches, as well as the throughput results of two telemedicine experiments undertaken by Mayo's physician staff. The technical staff was successful in achieving the data throughput needed by the telemedicine software; particularly important was the proper determination of peak throughput and TCP window sizes to ensure optimum use of the resources available on the Sun Microsystems and Hewlett Packard workstations.

Angiography↗
PubMed2000

Evaluation and technical assistance for successful HIV program delivery.

Agencies that provide HIV prevention programs (including agencies using science-based interventions) need to conduct evaluation to facilitate the transfer of effective interventions, provide ongoing assistance to intervention providers, document services provided, demonstrate effectiveness, and improve programs. The Centers for Disease Control and Prevention (CDC) assists health departments, community-based organizations, and other CDC grantees with evaluation by providing direct, customized technical assistance and written guidance. Together, these activities assist grantees in conducting evaluations that provide the information that grantees need as their programs develop.

Centers for Disease Control and Prevention, U.S.↗
PubMed2003

Capacity for training in clinical research: status and opportunities.

The ability to base patient care on scientific evidence depends in part on the results of translational and applied research. The shortage of trained clinical researchers identified by several sources limits the availability of clinical research studies upon which to base evidence-based therapeutics. This premise suggests that the dental profession needs to train more clinical researchers and faculty to conduct clinical research and to teach its applications to practice. Increasing opportunities for clinical research training in a variety of settings should eventually increase the numbers of clinical researchers, raise faculty involvement in clinical research, and promote science transfer. This paper reports on the current status of clinical research in dental schools, specifies the diverse groups involved in the clinical research enterprise, and identifies underutilized opportunities and partnerships for clinical research training. Data on federal and nonfederal funding of clinical research and training programs are presented. Existing and novel mechanisms for expanding clinical research training throughout and across traditional as well as unconventional environments are explored.

Dental Research↗
PubMedDate not supplied

Beyond the exchange--the future of B2B.

Using the Internet to facilitate business-to-business commerce promises many benefits, such as dramatic cost reductions and greater access to buyers and sellers. Yet little is known about how B2B e-commerce will evolve. The authors argue that changes in the financial services industry over the past two decades provide important clues. Exchanges, they say, are not the primary source of value in information-intensive markets; value tends to accumulate among a diverse group of specialists that focus on such tasks as packaging, standard setting, arbitrage, and information management. Because scale and liquidity are vitally important to efficient trading, today's exchanges will consolidate into a relatively small set of mega-exchanges. Originators will handle the origination and aggregation of complex transactions before sending them on to mega-exchanges for execution. E-speculators, seeking to capitalize on an abundance of market information, will tend to concentrate where relatively standardized products can be transferred easily among a large group of buyers. In many markets, a handful of independent solution providers with well-known brand names and solid reputations will thrive alongside mega-exchanges. Sell-side asset exchanges will create the networks and provide the tools to allow suppliers to trade orders among themselves, sometimes after initial transactions with customers are made on the mega-exchanges. For many companies, traditional skills in such areas as product development, manufacturing, and marketing may become relatively less important, while the ability to understand and capitalize on market dynamics may become considerably more important.

Commerce↗
PubMed1998

The Pacific Islands Project: the first 3 years.

BACKGROUND: The Pacific Island countries consist of widely scattered, small, underdeveloped islands which require considerable international assistance, particularly in health care. In 1995, the Pacific Islands Project was established and funded by AusAID to provide tertiary medical assistance to 10 island countries over a 3-year period. The programme was later expanded to include Papua New Guinea. METHODS: The Royal Australasian College of Surgeons was appointed manager of the project, which involved voluntary input from members of several specialist medical colleges and societies. Assistance was provided through short-term visits of multidisciplinary teams according to predetermined priorities. The delivery of medical services was combined with a transfer of skills and educational activities. Feedback was obtained from the recipient countries and each visit evaluated by an independent committee. RESULTS: One hundred and thirty-one visits in ten disciplines were conducted in 11 countries by 255 participants on a voluntary basis between March 1995 and March 1998: 15 784 patients were seen and 3424 operations performed. CONCLUSIONS: The programme was very successful on all counts. It has now been extended for a further 3 years and will be conducted in parallel with postgraduate educational programmes in the Pacific region and Papua New Guinea.

Developing Countries↗
PubMedDate not supplied

The Ontario Health Care Evaluation Network and the Critical Care Research Network as vehicles for research transfer.

Facilitating the successful and consistent use of research results to support health care decisions is a formidable task. Barriers to effectively transferring the results of research into the decision-making process have been created between practitioners and researchers, who traditionally have worked in isolation from each other. The need for them to work cooperatively to break down these barriers is paramount as changes within the health care environment increase. The Ontario Health Care Evaluation Network (OHCEN) and the Critical Care Research Network (CCR-Net) have attempted to address these concerns by bringing together teams of researchers, practitioners, and administrative personnel with the purpose of equipping them with tools to meet oncoming health care challenges.

Computer Communication Networks↗
PubMed2004

[Clinical research in the "acute and chronic leukemias"competence network ].

Goal of the network is the construction of an exemplary cooperative leukemia network for the improvement of medical care and of health related research in acute and chronic leukemias. This is achieved by improved mechanisms of cooperation among all major groups in Germany that deal with the leukemias in research and in patient care. In practice, cooperation between clinical groups and scientists in research institutes is mediated by various instruments that improve communication, flow of information and interdisciplinary cooperation and also increase information transfer from top research institutions to clinical translation. The network comprises more than 1400 participants in about 400 university centers, large community hospitals and specialty practices with functional communication structures, interdisciplinary cooperation and nation-wide logistics. The improved cooperation and the accelerated information transfer from the bench to the "bedside" results in an added value that ultimately results in improved survival results of patients and in superior competitiveness of involved research workers and clinicians. Sustainability is addressed by establishing a leukemia foundation to support long term financial coverage of the network and by negotiating a proposal for a European Network of Excellence against leukemia within the Sixth Framework Programme of the European Union.

Acute Disease↗
PubMed2003

Evaluation of germline sequence variants within the promoter region of RANTES gene in a cohort of women with endometriosis from Spain.

The RANTES (regulated upon activation normal T cells expressed and secreted) chemokine, is known to be expressed in endometriotic lesions in a concentration correlating with the severity of endometriosis. Since it has been widely demonstrated that endometriosis has a genetic basis, we postulated that the gene encoding RANTES could be a good candidate gene for the disease. We have used fluorescence resonance energy transfer (FRET) technology to genotype and evaluate the role of the variants -403G-->A and -28C-->G, located within the promoter region of the gene, as susceptibility factors in a cohort of Spanish women with endometriosis. No differences have been found in the allelic frequencies of both variants nor in the haplotype/ genotype distribution between patients and controls. These data are consistent with the lack of association between these polymorphisms and endometriosis in our population. They do not exclude completely a possible role of other variants within RANTES gene in this pathology.

Adult↗
PubMed1993

Lesbian motherhood and genetic choices.

Rhonda, a physician, and Clara, a registered nurse, have been lovers for the past 7 years. Both women are in their 30s, in good health, and financially stable. Clara has contacted Dr. Robinson, a highly regarded obstetrician and geneticist, with an unusual request. Clara is seeking to become pregnant by means of in vitro fertilization (IVF) with an embryo transfer (ET) technology. She proposes being implanted with ova harvested from her partner, Rhonda, and fertilized in vitro with donor sperm from a local medical-school sperm bank. Dr. Robinson explains the relatively low success rate involved in IVF and ET techniques and suggests artificial insemination of Clara's own ova. Clara and Rhonda understand the low success rates but are undeterred. Their mutual goal is not merely to have a child but to share in the maternity of their children. What ethical issues are raised by the plan Clara and Rhonda propose? What are Dr. Robinson's ethical responsibilities with respect to the request by Clara and Rhonda?

Child↗
PubMed2006

Analysis of development-related gene expression in cloned bovine blastocysts with different developmental potential.

The high incidence of abnormalities in cloned calves is a most serious problem for bovine somatic cell nuclear transfer (NT) technology. Because there is little information on the differences in mRNA expression in cloned blastocysts with donor cells of different sex and origin, we compared development-related gene expression in two types of cloned bovine blastocysts with different potentials to develop into normal calves, a female adult cumulus cell line (high potential to develop into live calves) and a male fibroblast cell line (low potential to develop into live calves) to examine the correlation between the normality of cloned calves and blastocyst mRNA expression patterns. We analyzed 12 genes involved in apoptosis, growth factor signaling, metabolism, and DNA methylation in blastocysts originating from two types of donor cells and in vitro-fertilized blastocysts using quantitative real-time polymerase chain reaction. Expression of the pro-apoptotic Bax gene and anti-apoptotic Bcl-2 and Glut-1 genes in fibroblast-derived blastocysts was significantly higher than in cumulus cell-derived and in vitro-fertilized blastocysts. The high Bcl-2 and Glut-1 gene expression suggests that some embryonic cells with damaged DNA in fibroblast-derived blastocysts are not removed, and their descendants later manifest abnormal placenta or fetus formation. Transfer of pre-selected cloned blastocysts into recipients is required, however, to determine whether the expression pattern of these apoptosis-related genes reflects differences in the potential to develop into normal calves.

Animals↗