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At least 1,603 records · Page 89Linked to original sources
PubMed1991

A trace display and editing program for data from fluorescence based sequencing machines.

'Ted' (Trace editor) is a graphical editor for sequence and trace data from automated fluorescence sequencing machines. It provides facilities for viewing sequence and trace data (in top or bottom strand orientation), for editing the base sequence, for automated or manual trimming of the head (vector) and tail (uncertain data) from the sequence, for vertical and horizontal trace scaling, for keeping a history of sequence editing, and for output of the edited sequence. Ted has been used extensively in the C.elegans genome sequencing project, both as a stand-alone program and integrated into the Staden sequence assembly package, and has greatly aided in the efficiency and accuracy of sequence editing. It runs in the X windows environment on Sun workstations and is available from the authors. Ted currently supports sequence and trace data from the ABI 373A and Pharmacia A.L.F. sequencers.

Animals↗
PubMed2002

RiceGAAS: an automated annotation system and database for rice genome sequence.

An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.

Automation↗
PubMed2006

New softwares for automated microsatellite marker development.

Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.

Arachis↗
PubMed2003

Evaluation of a method of ultraviolet light sanitation of broiler hatching eggs.

Sanitation of hatching eggs is an important area of research due to the need for an effective, economical, and safe method of egg sanitation. Improved hatching egg sanitation is an important part of an overall pathogen reduction program within integrated poultry operations. This must be accomplished without disturbing the cuticle of the egg, which can decrease hatchability. The ability of ultraviolet (UV) light to kill bacteria on eggshell surfaces has been well documented. To accomplish the task of treating the eggs in a method that could be commercially implemented, a cabinet was constructed in which ultraviolet lamps were placed. A conveyor system was used to carry a plastic hatching egg flat containing 42 eggs through the cabinet for a period of 3 or 4 min. Ultraviolet intensities within the cabinet reached a maximum of 14 mW/cm2. Experiments were conducted to test the impact of UV light (254 nm) exposure of hatching eggs on aerobic plate counts (APC), inoculated Salmonella typhimurium and inoculated Escherchia coli. In the first three experiments, seven eggs were sampled from a flat passed through the UV chamber. Ultraviolet-treated eggs compared to untreated eggs had APC reductions of 1.3 log, S. typhimurium had a 4 log reduction, and E. coli had a 4 to 5 log reduction. Laboratory trials were also conducted to test the effects of UV irradiation on the cuticle of the egg and hatchability. No significant differences for eggshell conductance or hatchability were found between UV-treated and control eggs. From these trials, it can be concluded that UV irradiation of hatching eggs in a prototype irradiation cabinet can effectively reduce aerobic and pathogenic bacteria on eggshell surfaces without affecting eggshell conductance or hatchability.

Animals↗
PubMed1981

Dance therapy: effects of motor performance of children with learning disabilities.

This investigation studied effects of dance therapy on motor performance of children who have learning disabilities. An experimental group of five subjects who received dance therapy was compared with a control group of five subjects who received their usual sensory integrative therapy. Pretests and posttests of motor performance were given before and after a four-week treatment period to assess changes. Results indicate improved motor performance for both the experimental and control groups, with slightly greater gains made by the experimental group. Results of the study indicate that dance therapy could serve as a form of vestibular stimulation comparable to the usual play activities in a sensory integrative therapy program.

Child↗
PubMed2004

Optimal management of nasopharyngeal carcinoma.

PURPOSE OF REVIEW: Given the high rate of mortality still associated with advanced stages of nasopharyngeal carcinoma, this review focuses on some specific aspects of this potentially curable disease that could translate into improved therapeutic approaches. RECENT FINDINGS: Epstein-Barr viral-induced carcinogenesis is almost constantly reported in the undifferentiated type of nasopharyngeal carcinoma. Nasopharyngeal carcinoma retains clonal characteristics and p53 functionality up to late stages that may account for its high level of chemo- and radiotherapy sensitivity, with several cases of long-term survivors reported among patients with bone metastasis. Recent imaging and biologic techniques will help to identify patients at risk of distant failures (detection of plasma Epstein-Barr virus DNA) or those harboring posttherapeutic residual diseases (positron emission tomographic scan). Cisplatin-based induction chemotherapy has shown disease-free survival benefit, whereas concomitant chemoradiotherapy is associated with an improved local-regional control. Late radiation-induced toxicities (especially xerostomia) will hopefully be reduced using intensity-modulated radiation therapy. New therapeutic agents such as taxanes, or targeted therapies (epidermal growth factor receptor inhibitors) are of major interest in the challenge of circumventing resistance to alkylating agents. SUMMARY: Better knowledge of nasopharyngeal carcinoma pathogenesis and biology, management of patients in highly specialized oncologic units, and careful selection of cytotoxic agents along with multimodality integrated therapeutic programs will likely yield to improved survival, particularly for patients with locally advanced nasopharyngeal carcinoma.

Disease Management↗
PubMed1976

Teaching toxicology as a basic medical science.

In this report the author describes a four-year effort at the Yale University School of Medicine to teach toxicology as an elective basic medical science from the standpoint of organ-specific toxic effects. The primary objective is to prepare physicians to understand, recognize, and manage adverse effects from drugs and other environmental chemicals. It is a multidisciplinary program which integrates easily into the medical school curriculum in a manner that is appealing to the students.

Curriculum↗
PubMed2001

How should alternative medicine be taught to medical students and physicians?

Advocates of alternative medicine are critical of current medical curricula, and have proposed fundamental changes, including the introduction of "integrative medicine" programs to teach alternative medicine. Medical educators have not replied to these criticisms, and have not developed basic curricula in alternative medicine. The author analyzes the alleged deficiencies in medical education, which are based on misrepresentations of medicine and medical training. (For example, critics state that physicians ignore mind-body interactions; in response, several examples are given to show that training physicians to consider the whole person and to identify and address emotional and social problems-the biopsycho-social model-are central tenets of medical education.) The author also examines fundamental differences between traditional and alternative medicine (e.g., their different attitudes toward the importance of evidence; the vitalistic versus the biomedical models of health and disease) that are central to the issue of how alternative medicine should be taught. He concludes that physicians need additional education in order to provide guidance to patients, but teaching about alternative medicine should be evidence-based, not merely the transmission of unproven practices.

Complementary Therapies↗
PubMed1996

Reproductive decision-making and determinants of contraceptive use in HIV-infected women.

Perinatal transmission and reproductive decisions of HIV-infected women can be categorized in statistical and epidemiological terms. These reports and figures, however, do little to fully explain the complexities of human relationships, life experiences, personal and cultural influences, and situational and environmental variables that impact on the HIV-infected woman regarding reproductive decision-making. It is only with genuine attempts to understand the woman's perspective and the dynamic and unique variables that influence reproductive decision-making, as well as maintaining a non-judgmental and culturally sensitive perspective, can we hope to assist women, and society as a whole, in coming to terms with the complexities of HIV and reproductive decision-making. Further study is needed to identify factors that influence reproductive decision-making in HIV-infected women. The determinants of contraceptive use regarding demographic factors, barriers to contraceptive use, and factors that contribute to successful contraceptive use in this population must be understood if efforts to reduce the number of unplanned pregnancies are to be successful. More conclusive data are needed on the safety and efficacy of oral contraceptives in HIV-infected women as well as data that describe the effects of longer acting hormonal contraceptives such as levonorgestrel implants (Norplant; Wyeth-Ayerst, Philadelphia, PA) and injectable medroxyprogesterone acetate (Depo Provera; Upjohn Company, Kalamazoo, MI). More research is needed to determine the effects of patient education and counseling and closer follow-up on effective long-term contraception in HIV-infected women.

Contraception↗
PubMedDate not supplied

Public health perspectives on the family: an ecological approach to promoting health in the family and community.

The family, as a setting of practice, is increasingly recognized as critical to health promotion. A better understanding of the nature and process through which families take an active part in their own health can serve as the basis for designing and linking health interventions with public health programs. The integrating function of the family, viewed through an ecological context, makes it an effective entry point and central focus in health promotion.

Community Participation↗
PubMed2003

Integrating an academic radiation safety program into an environmental management system.

The Environmental Health and Safety (EH&S) Program at the University of South Carolina recently developed an environmental management system (EMS) based on the ISO 14001 International Standard. Since our radiation safety program must already meet strict state licensing requirements, the process of conforming to this standard was relatively easy to accomplish. The EH&S program achieved certification to the ISO 14001 standard in August of 2002. The benefits of the EMS include: better interaction between radiation safety and other EH&S program entities, holds all employees accountable by closely tracking program activities, presents a clear picture of program accomplishments to the university administration, allows for better use of limited resources and provides for continuous program improvement.

Environmental Health↗
PubMed1992

Computer-aided radiopharmaceutical design.

The ultimate goal of a QSAR analysis is prediction, which depends on the elaboration of the most appropriate set of molecular descriptors. As such, molecular description is the nucleus of QSAR and in the absence of exhaustive molecular description, rational drug design may be greatly impeded. As previously discussed, computational methods such as quantum mechanics and molecular mechanics provide molecular description at a fundamental level which then enhances the descriptive capability and predictive power of a QSAR analysis. In recognition of these capabilities, semi-empirical molecular orbital methods and molecular mechanics now have been incorporated into or interphased with QSAR programs. Such integrated packages are being successfully used in computer-aided molecular modeling. Computer-aided molecular modeling can provide the three-dimensional structure of a molecule, its chemical and physical characteristics, comparisons of structures of different molecules, and visualization of complexes formed between them. From the foregoing, predictions may be made about how related new molecules may function. Thus, the combination of quantum and/or molecular mechanics and QSAR provides a formidable weapon in the chemist's armamentarium. The molecular modeling approaches are certainly more practical to use than physicochemical methods. They also provide electronic and thermodynamic data that are not available from x-ray crystallographic data. Of course, these techniques are not confined to radiopharmaceutical development and they also could aid in the development of contrast agents for radiography or magnetic resonance imaging. We believe that as computational resources and capabilities increase over the next decade, computer-aided drug design will become a standard procedure in all drug development laboratories.

Binding Sites↗
PubMedDate not supplied

Automated analog-to-digital conversion of graphical cardiotocographic records.

The system described, VISC, has as its aim the acquisition and subsequent digitization of monodimensional cardiotocographic signals. These signals can originate in any type of hospital cardiotocographic register, as well as in a book of uterine activity (UA) or fetal heart rate (FHR) signals. VISC consists of a set of algorithms to identify the fetal heart rate signal, although it can be used with minor corrections to work on any continuous curve. Some of the problems that may arise, such as signal loss and presence of noise, are discussed to illustrate the proposed method. The program is integrated into a wider environment, whose main nucleus is the NST-EXPERT expert system, for the diagnosis of fetal well-being, the recommendation of therapeutical plans and the prognosis of immediate neonatal states.

Algorithms↗
PubMedDate not supplied

Automated measurement of volume flow in the ascending aorta using MR velocity maps: evaluation of inter- and intraobserver variability in healthy volunteers.

PURPOSE: An automated contour detection algorithm was developed for the objective and reproducible quantitative analysis of velocity-encoded MR studies of the ascending aorta. METHOD: The only user interaction required is the manual definition of a center point inside the cross-section of the aorta in one of the available images. The automated contour detection algorithm detects an initial model contour in this image and subsequently corrects for motion and deformation of the aortic cross-section in each of the acquired images over the complete cardiac cycle using dynamic programming techniques. Integrating the flow velocity values for each pixel within the detected contour results in an instantaneous flow value. Next, by integrating the instantaneous flow values for each acquired phase over the complete cardiac cycle, left ventricular stroke volume measurement could be obtained. The results of the automated method were compared with results derived from manually traced contours in MR studies from 11 healthy volunteers. RESULTS: An excellent agreement in stroke volume measurements was observed: signed difference 0.61+/-1.15%. Inter- and intraobserver variabilities were <2% for both manual and automated image analysis methods. Manual tracing of contours required on the order of 10 min; the analysis time for automated contour detection was <6 s/study. CONCLUSION: The present contour detection allows fast and reliable left ventricular stroke volume measurements from aortic flow studies using velocity-encoded MR studies in healthy volunteers. Further study is required to assess the accuracy and reproducibility of the algorithm in patients with aortic and aortic valve disease.

Adult↗
PubMed1982

An integrated university emergency medicine - trauma program.

UNLABELLED: Systems for prehospital care, emergency medical care, and trauma care clearly overlap educationally, medically, financially, and politically. Most systems have not accomplished separation of this interdisciplinary tangle. To solve this dilemma we have customized an Emergency Medicine and Trauma Service (EM & TS) at a regional trauma medical center. The program (annually): 1)treats 32,000 patients (11,330 are trauma); 2) educates 140 paramedics, residents, students. Physician personnel: Members are fully trained in Internal Medicine, Surgery, or Pediatrics; are members of other academic departments. Each is approved by three chairman: Emergency Department, The physician's specialty, and Surgery, Structure: Board-qualified trauma surgeon always present; other faculty supplement surgical manpower; physicians are salaried; each is responsible to Director of EM & TS; trainees are not included as patient-care manpower. Organization: Academically, EM & TS is a Section of the Department of Surgery; the Section Chief is Director of EM & TS, and is responsible for Emergency Department, prehospital care, and trauma admissions. THE SOLUTION: A vertical responsibility structure to this multidisciplinary system has provided a successful solution and may be tailored to other systems.

Emergency Medicine↗