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At least 811 records · Page 45Linked to original sources
PubMed2004

ESTIMA, a tool for EST management in a multi-project environment.

BACKGROUND: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. RESULTS: A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. CONCLUSIONS: The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. We have also provided detailed installation instructions and a tutorial at the same website. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee brain EST projects. Non-academic users need to contact the W.M. Keck Center for Functional and Comparative Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, for licensing information.

Animals↗
PubMed2003

The development and implementation of the Chronic Care Management Programme in Counties Manukau.

AIMS: To develop an effective and efficient process for the seamless delivery of care for targeted patients with specific chronic diseases. To reduce inexplicable variation and maximise use of available resources by implementing evidence-based care processes. To develop a programme that is acceptable and applicable to the Counties Manukau region. METHODS: A model for the management of people with chronic diseases was developed. Model components and potential interventions were piloted. For each disease project, a return on investment was calculated and external evaluation was undertaken. The initial model was subsequently modified and individual disease projects aligned to it. RESULTS: The final Chronic Care Management model, agreed in September 2001, described a single common process. Key components were the targeting of high risk patients, organisation of cost effective interventions into a system of care, and an integrated care server acting as a data warehouse with a rules engine, providing flags and reminders. Return on investment analysis suggested potential savings for each disease component from $277 to $980 per person per annum. CONCLUSIONS: For selected chronic diseases, introduction of an integrated chronic care management programme, based on internationally accepted best practice processes and interventions can make significant savings, reducing morbidity and improving the efficiency of health delivery in the Counties Manukau region.

Chronic Disease↗
PubMed2003

Multicriteria optimization of gluconic acid production using net flow.

The biochemical process industry is often confronted with the challenge of making decisions in an atmosphere of multiple and conflicting objectives. Recent innovations in the field of operations research and systems science have yielded rigorous multicriteria optimization techniques that can be successfully applied to the field of biochemical engineering. These techniques incorporate the expert's experience into the optimization routine and provide valuable information about the zone of possible solutions. This paper presents a multicriteria optimization strategy that generates a Pareto domain, given a set of conflicting objective criteria, and determines the optimal operating region for the production of gluconic acid using the net flow method (NFM). The objective criteria include maximizing the productivity and concentration of gluconic acid, while minimizing the residual substrate. Three optimization strategies are considered. The first two strategies identify the optimal operating region for the process inputs. The results yielded an acceptable compromise between productivity, gluconic acid concentration and residual substrate concentration. Fixing the process inputs representing the batch time, initial substrate concentration and initial biomass equal to their optimal values, the remaining simulations were used to study the sensitivity of the optimum operating region to changes in the oxygen mass transfer coefficient, K(L) a, by utilizing a multi-level K(L) a strategy. The results show that controlling K(L) a during the reaction reduced the production of biomass, which in turn resulted in increased productivity and concentration of gluconic acid above that of a fixed K(L) a.

Journal Article↗
PubMed2006

Toni Morrison's Beloved: a journey through the pain of grief.

This paper elucidates the structure of Toni Morrison's novel, Beloved, using the framework of human emotions in response to grieving and death as developed by Elisabeth Kubler-Ross. Through her studies of terminally ill patients, Kubler-Ross identified five stages when approaching death: denial and isolation, anger, bargaining, depression and acceptance. These stages accurately fill the process that the character Sethe experiences in the novel as she learns to accept her daughter's death.

Adaptation, Psychological↗
PubMed1998

Measures of auditory-visual integration in nonsense syllables and sentences.

For all but the most profoundly hearing-impaired (HI) individuals, auditory-visual (AV) speech has been shown consistently to afford more accurate recognition than auditory (A) or visual (V) speech. However, the amount of AV benefit achieved (i.e., the superiority of AV performance in relation to unimodal performance) can differ widely across HI individuals. To begin to explain these individual differences, several factors need to be considered. The most obvious of these are deficient A and V speech recognition skills. However, large differences in individuals' AV recognition scores persist even when unimodal skill levels are taken into account. These remaining differences might be attributable to differing efficiency in the operation of a perceptual process that integrates A and V speech information. There is at present no accepted measure of the putative integration process. In this study, several possible integration measures are compared using both congruent and discrepant AV nonsense syllable and sentence recognition tasks. Correlations were tested among the integration measures, and between each integration measure and independent measures of AV benefit for nonsense syllables and sentences in noise. Integration measures derived from tests using nonsense syllables were significantly correlated with each other; on these measures, HI subjects show generally high levels of integration ability. Integration measures derived from sentence recognition tests were also significantly correlated with each other, but were not significantly correlated with the measures derived from nonsense syllable tests. Similarly, the measures of AV benefit based on nonsense syllable recognition tests were found not to be significantly correlated with the benefit measures based on tests involving sentence materials. Finally, there were significant correlations between AV integration and benefit measures derived from the same class of speech materials, but nonsignificant correlations between integration and benefit measures derived from different classes of materials. These results suggest that the perceptual processes underlying AV benefit and the integration of A and V speech information might not operate in the same way on nonsense syllable and sentence input.

Adult↗
PubMed1997

[Shared responsibility in expert review of original articles].

OBJECTIVE: To point out some defects in the process of selection of manuscripts for publication in the primary biomedical literature, and offer some recommendations for reviewers, editors and authors that can enhance the accountability and effectiveness of peer review. DEVELOPMENT: Although peer review is said to guarantee the quality of scientific journals, there are no experimental data to prove this statement, and research is urgently needed to clarify the advantages and disadvantages of the system. The term 'peer review' is used for very different processes, and there is no commonly accepted definition. To ensure professionalism and accountability, all steps of the peer review process need to be well thought out and documented, and the responsibilities of all persons involved need to be clearly defined. CONCLUSIONS: To ensure accountability in the peer review system and reduce the probability of errors and abuse, every journal should have in place a set of internal guidelines of good practice for editorial staff, reviewers and authors, and this information should be made widely available.

Peer Review↗
PubMed2000

Health informatics in the context of user ownership.

Of fundamental importance to the successful implementation of health information systems is the public and professional acceptability of their inclusion in the healthcare process. Surprisingly, the health care sector is embracing the informatics revolution somewhat reluctantly. Even in the areas that progress can be seen and assessed, the rate of change is erratic and inconsistent when compared across the spectrum of health care informatics. The mystery intensifies if one considers the situation in global scale: despite the diversity in approaches and models used, the reluctance perseveres. One can only suspect that there is a common, underlying, reason which slows down the process and forces the whole sector in being reluctant to accept change.

Diffusion of Innovation↗
PubMed1998

Angiographic film subtraction using a laser digitizer and computer processing.

Digital subtraction angiography has been accepted as an invaluable clinical tool over the past decade; however, film-screen-based angiography is still performed routinely when high-resolution or large field-of-view angiograms are needed. A technique is presented whereby two films from an angiographic sequence are digitized using a high-resolution laser digitizer, and the digitized images are aligned, subtracted, and displayed using the computer. To accommodate for some types of patient motion, an image warping algorithm is presented and discussed in detail. The warping algorithm is piecewise linear, using triangular regions for warping, resulting in a global nonlinear transform across triangle elements. An algorithm describing optimal triangle selection also is discussed. The results show that subtraction images of excellent quality can be produced by the proposed technique, and suggest that, in some settings, digitized subtraction films may be preferred over conventional film subtraction.

Angiography, Digital Subtraction↗
PubMedDate not supplied

Cholangiography during laparoscopic cholecystectomy--cumulative sum analysis of an institutional learning curve.

The ability to perform intraoperative cholangiography during laparoscopic cholecystectomy is an essential skill for the laparoscopic biliary surgeon. The volume of experience required to be able to consistently obtain a cholangiogram during laparoscopic cholecystectomy has not been determined. Cumulative sum analysis is a statistical technique which generates a graphical display that identifies periods of performance that fall below a predetermined standard for a given task. The cumulative sum (S(n)) for a series of observations is defined as: S(n)= summation operatorX(I) - X(o), where X(I) = 0 for a success, X(I) = 1 for a failure, and X(o) is the acceptable failure rate for the process under study. This function is plotted against the number of observations to create a curve. When the curve has a positive slope, the acceptable failure rate is being exceeded. When it reaches a plateau, the observed failure rate is equal to the acceptable failure rate. When the curve has a negative slope, the observed failure rate is lower than the acceptable failure rate. We performed a cumulative sum analysis of the first 97 intraoperative cholangiograms attempted during lap-aroscopic cholecystectomy at our institution. The results demonstrated that 46 cases were required to reach a level of proficiency where a cholangiogram could be obtained in 95% of attempts. Success rates of 85% and 90% were achieved at 16 and 25 cases, respectively. This form of analysis is a useful tool for estimating the number of attempts required to achieve a desired success rate when learning new procedures.

Adult↗
PubMed1990

Word identification in reading and the promise of subsymbolic psycholinguistics.

The vast literature concerning printed word identification either contradicts or provides ambiguous support for each of the central hypotheses of dual-process theory, the most widely accepted theory of printed word identification. In contrast, clear, positive support exists for an alternative subsymbolic approach that includes a central role for the process of phonologic coding. This subsymbolic account is developed around a covariant learning hypothesis, derived from a design principle common to current learning algorithms within the subsymbolic paradigm. Where this hypothesis applies, and it may apply broadly, it predicts a common empirical profile of development.

Algorithms↗
PubMed1995

Transformation toward teamwork: a methodical approach to change. Three disparate cultures come together.

In January 1995, following a 19-month planning process, Fanny Allen Hospital, Medical Center Hospital of Vermont, and the University Health Center formed Fletcher Allen Health Care, a single operating entity. The University of Vermont is linked by contract to the new organization. From the beginning, the organizations' leaders approached the planning process with the human dimension in mind. Although the process was led by top leaders of the four entities, they relied on input from physicians and multidisciplinary teams of professionals. To gain employees' acceptance of the transition by making them feel secure, in December 1993, the organizations announced that no one would involuntarily lose his or her job for the next year. And managers have gained acceptance of the transition planning process by gaining input from employees and making it clear that the plans are not cast in stone. Nevertheless, both leaders and employees face anxiety and discomfort with change. In addition to fears about job security, they fear loss of control, quality, and a feeling of mission fulfillment. Communication has been fundamental to easing the transition. Leaders have delivered the same message to everyone, using a newsletter, employee meetings, management meetings, and a telephone hotline. Leadership education, development, and selection are other critical issues in helping employees adjust to change.

Anxiety↗
PubMed1989

Decision to withhold or withdraw support.

This decision-making process is inherently uncomfortable. The recognition and open discussions of the issues are relatively new. There is legal and practice precedent for withholding and withdrawing therapies and support. Institutions must now abide by Joint Commission guidelines while individual physicians are permitted to practice within their own conscience. Patients' best interests must be served, but it should be accepted that permitting the dying process to evolve while attending to comfort is not only an acceptable but desirable strategy. Finally, physicians must play an active and pivotal role as the facilitators of proper care. The details of proper medical care should be physician prescribed.

Decision Making↗
PubMed2005

Independence of visual awareness from attention at early processing stages.

According to a widely accepted idea, only the results of attentional selection reach visual awareness. A competing model postulates that awareness is independent of attentional selection: contents of subjective visual experience may also exist without the contribution of attention. We tested these competing models by tracking the independent contributions of selective attention and awareness to electrophysiological brain responses. Our results showed that the earliest effects of visual awareness emerged earlier than the effects of attention and regardless of the presence or absence of attention. The early effects of attention were elicited regardless of the presence or absence of awareness. The results suggest that visual awareness and selective attention are initially independent of each other.

Adolescent↗
PubMed2006

The planning and implementation of a faculty peer review teaching project.

OBJECTIVES: Describe the planning and implementation of a pilot peer review system, assess factors related to acceptance by faculty and administration, and suggest ways to increase the number of faculty members reviewed and serving as reviewers. DESIGN: A faculty-driven process was used to create a model for peer review. Faculty members completed a survey instrument with open-ended responses for indicating reasons for participation or nonparticipation, components of the evaluation process that they would like to see changed, and what they found most helpful or insightful about the process of peer review. ASSESSMENT: Faculty acceptance of and satisfaction with the peer review process is attributed to the development and implementation process being faculty driven and to peer reviews not being required for promotion and tenure decisions. Faculty members who were reviewed stated that the process was helpful and insightful and would lead to better teaching and learning. CONCLUSION: A successful faculty peer-review process was created and implemented within 6 weeks. All of the faculty members who chose to be peer reviewed or serve as reviewers reported satisfaction in gaining insights into their teaching, learning innovative approaches to their teaching, and gaining confidence in their teaching pedagogy. Techniques for achieving 100% participation in the peer review process should be addressed in the future.

Faculty↗
PubMed2004

Quality improvement in a federally funded community breast and cervical cancer screening program.

Continuous Quality Improvement (CQI) methods offer healthcare organizations valuable tools for improving services to their patients. These tools are also useful in improving the way an organization delivers its services. In this case study, the authors describe the use of quality improvement activities for improving the enrollment and screening for breast and cervical cancer for the Women's Health Connection (WHC). The WHC is operated by the Nevada Department of Human Resources, Health Division, to provide screening for income eligible women between the ages of 40-64. Funding for the WHC was provided by the Department of Health and Human Services' Centers for Disease Control and Prevention (CDC) through the National Breast and Cervical Cancer Early Detection Program (NBCCEDP). By using Quality Improvement Teams, the WHC was able to restructure the way women were being enrolled in the program in order to increase the number of women screened and to help the program meet CDC performance indicators. This article documents the quality improvement process used in the case study, highlights the areas improved, and demonstrates how quality improvement was useful in improving services provided to women. It also describes staff acceptance of the quality improvement process and its potential future applications.

Breast Neoplasms↗
PubMed2002

Advanced cardiac life support antiarrhythmic drugs.

As exemplified in this discussion of ACLS antiarrhythmic drugs, the evidence-based evaluation process has created a high standard for the acceptance and ranking of therapies for cardiac arrest. This process also has identified critical areas needing further investigation, fostered a healthy sense of discomfort with the adequacy of our present interventions for cardiac arrest, and hopefully will continue to spur the science while sifting the dogma out of CPR.

Amiodarone↗
PubMed2001

Clinical practice guidelines: when the tool becomes the rule.

This work provides a critical examination of the use of clinical practice guidelines to measure individual performance. The problems inherent in using a measure of central tendency derived from a distribution of individual performances are addressed, as is the translation of the collectively determined guidelines into a measurement instrument. It is suggested that every process on the distribution of processes used to determine the guideline must be considered equally legitimate representations of the process in question. It is further suggested that to accept as a standard of quality, a particular process simply because there is a minimum of variation between providers, is to ignore the importance of the linkage between process and outcome. The importance of an independent measure of quality based on outcomes is further emphasized by highlighting the tautological nature of analyses that include an input measure, such as nursing hours, in both the dependent variable and the list of independent variables. It is recommended that individual performance be evaluated within the tolerances of the distribution from which they were derived and not be held to some measure of central tendency of that distribution. The alternative is to use the measure of central tendency with plus or minus limits such as one, or more, standard deviations.

Asthma↗
PubMed2001

Teaching peer review and the process of scientific writing.

Many undergraduate and graduate students understand neither the process of scientific writing nor the significance of peer review. In response, some instructors have created writing assignments that teach or mimic parts of the scientific publishing process. However, none fully reproduced peer review and revision of papers together with the writing and publishing process from research to final, accepted draft. In addition, most have been instituted at the graduate rather than undergraduate level. We present a detailed method for teaching undergraduate students the full scientific publishing process, including anonymous peer review, during the process of writing a "term paper." The result is a review article in the format for submission to a major scientific journal. This method has been implemented in the course Cell and Molecular Biology for Engineers at the University of Virginia. Use of this method resulted in improved grades, much higher quality in the final manuscript, greater objectivity in grading, and improved understanding of the importance of peer review.

Attitude↗