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PubMed1985

Using computer graphics to enhance astronaut and systems safety.

Computer graphics is being employed at the NASA Johnson Space Center as a tool to perform rapid, efficient and economical analyses for man-machine integration, flight operations development and systems engineering. The Operator Station Design System (OSDS), a computer-based facility featuring a highly flexible and versatile interactive software package, PLAID, is described. This unique evaluation tool, with its expanding data base of Space Shuttle elements, various payloads, experiments, crew equipment and man models, supports a multitude of technical evaluations, including spacecraft and workstation layout, definition of astronaut visual access, flight techniques development, cargo integration and crew training. As OSDS is being applied to the Space Shuttle, Orbiter payloads (including the European Space Agency's Spacelab) and future space vehicles and stations, astronaut and systems safety are being enhanced. Typical OSDS examples are presented. By performing physical and operational evaluations during early conceptual phases. supporting systems verification for flight readiness, and applying its capabilities to real-time mission support, the OSDS provides the wherewithal to satisfy a growing need of the current and future space programs for efficient, economical analyses.

Astronauts↗
PubMed2004

Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition.

An elaborate knowledge-based energy function is designed for fold recognition. It is a residue-level single-body potential so that highly efficient dynamic programming method can be used for alignment optimization. It contains a backbone torsion term, a buried surface term, and a contact-energy term. The energy score combined with sequence profile and secondary structure information leads to an algorithm called SPARKS (Sequence, secondary structure Profiles and Residue-level Knowledge-based energy Score) for fold recognition. Compared with the popular PSI-BLAST, SPARKS is 21% more accurate in sequence-sequence alignment in ProSup benchmark and 10%, 25%, and 20% more sensitive in detecting the family, superfamily, fold similarities in the Lindahl benchmark, respectively. Moreover, it is one of the best methods for sensitivity (the number of correctly recognized proteins), alignment accuracy (based on the MaxSub score), and specificity (the average number of correctly recognized proteins whose scores are higher than the first false positives) in LiveBench 7 among more than twenty servers of non-consensus methods. The simple algorithm used in SPARKS has the potential for further improvement. This highly efficient method can be used for fold recognition on genomic scales. A web server is established for academic users on http://theory.med.buffalo.edu.

Algorithms↗
PubMedDate not supplied

An efficient technique for the development of computer programs for electrocardiogram interpretation.

In this paper is presented an efficient technique for the development of electrocardiogram (ECG) interpretation software, executed rapidly on inexpensive specialized mini or microcomputers; the method--based on the author's experience--is under medical control. The first part of the paper presents the ideal characteristics of an ECG computer interpretation program which in the author's opinion are not yet implemented by any of the present equipment of ECG analysis. The second part presents the author's approach of the problem and the last part gives a description of the programming techniques used.

Diagnosis, Computer-Assisted↗
PubMed1988

Modeling the outdoor environment--new perspectives and challenges.

Assessing risk from manmade and naturally occurring radionuclides in the environment has long been of primary interest in radiation protection. Early investigations and decisions relied on direct measurements of radiation in environmental media; however, these techniques were inadequate for determining exposure to humans and biota from very low levels of radiation and in predicting exposures from future releases. The Plowshare Program in 1957 investigated the use of nuclear explosives for peaceful purposes and created an immediate need for predicting the dispersion and ultimate fate of radionuclides that might be vented to the atmosphere or enter groundwater and expose man. As a result, modeling the behavior of radionuclides in the outdoor environment became a field of vigorous interest, merging disciplines of mathematics, biology and physics, among others. Environmental models and, more specifically, models predicting radiation dose from radionuclides in the environment have evolved rapidly and have increased significantly in sophistication, complexity and scope. Application of these models is commonly known as radiological assessment. This presentation examines the current status, future direction and weaknesses of radiological assessment models used in making decisions about radiation. The trend in recent years has been toward more complex models, which has not necessarily improved the accuracy of dose estimates and, in certain cases, has had the opposite effect. The presentation also discusses the future of model development, with particular emphasis on simple techniques and the expanded use of microcomputers, which will make radiological assessment models widely available for risk assessment and for practical applications such as the design of efficient monitoring programs and engineering calculations on the clean-up of contaminated soils. The screening models developed by the National Council on Radiation Protection and Measurements are offered as an example of a powerful yet simple method for demonstrating compliance with standards. Finally, the paper reviews two major areas of challenge for the future--defining uncertainty associated with radiological assessment models and the potential for converting radiological assessment models for use with nonradioactive environmental pollutants such as chemicals. Modeling radionuclides in the environment is adopting a new perspective. Future models will be less complex than their predecessors and will be adaptable to a much broader range of users. Key challenges remain in applying the techniques used for radionuclides to nonradioactive pollutants.

Air Pollutants, Radioactive↗
PubMed1991

Case study: development of a forms-design guidebook.

Implementation of the approval and official format of medical record forms procedure along with the use of the forms-design guidebook will result in a forms-management program that will be efficient and effective. This program is sufficiently detailed to provide forms that are consistent and useful. The procedure will provide the necessary documentation for forms control and will facilitate an approval process that is standardized and faster than before. An overview of the steps taken to complete this project are listed in the box entitled "Steps for Revision of Forms-Control Process." The control of medical record forms will provide documents that are useful and accurate for purposes of communication and planning of quality patient care and will meet the requirements of licensing and accrediting agencies. Also, the concentration on the consideration of cost throughout this project will reduce costs by improved efficiency in the paperwork system and by reducing both the production and the usage costs of forms.

Forms and Records Control↗
PubMed1993

Risk factors for the development of an adenocarcinoma in columnar-lined (Barrett) esophagus. The Rotterdam Esophageal Tumor Study Group.

BACKGROUND: To evaluate the importance of the length of columnar-lined esophagus, sex, age, smoking, and drinking habits as risk factors for malignant degeneration, the authors performed a retrospective case-control study comparing patients with and without adenocarcinoma in Barrett esophagus. METHODS: The records of 96 patients (53 male and 43 female; mean age, 61 years) with a benign columnar-lined esophagus and 62 patients (47 male and 15 female; mean age, 62 years) with an adenocarcinoma in columnar-lined esophagus referred to the Rotterdam Esophageal Tumor Study Group, diagnosed over the same period (1978-1985), were reviewed. A frequency distribution of the length of columnar-lined esophagus in both groups was made. Statistical analysis was performed with multivariate methods. RESULTS: The length of columnar-lined esophagus was related significantly to carcinoma: a doubling of the length resulted in a 1.7 times increased risk. Smokers had a 2.3-fold increased risk as compared with nonsmokers. Male sex as a risk factor approached statistical significance (P = 0.06). Adjusted for these risk factors, no relation between carcinoma and age or alcohol consumption was found. CONCLUSIONS: The risk of development of an adenocarcinoma in Barrett esophagus increased with the length of Barrett epithelium. Smoking and possibly male sex were also risk factors. The identification of these risk factors may help in developing more efficient screening programs for patients with Barrett esophagus.

Adenocarcinoma↗
PubMed2001

Determination of the enantiomerization barrier of thalidomide by dynamic capillary electrokinetic chromatography.

Enantioselective chromatographic methods, representing the most commonly used techniques for the determination of enantiomeric ratios, can also be used for the evaluation of stereochemical integrity. In the present study, dynamic capillary electrokinetic chromatography (DEKC) was employed to determine the enantiomerization barrier of thalidomide. In the presence of the chiral mobile phase additive carboxymethyl-beta-cyclodextrin, the interconverting enantiomers of thalidomide produced characteristic elution profiles exhibiting plateaus and/or peak broadening between 25 and 55 degrees C at pH 8. To obtain the enantiomerization barrier of thalidomide from experimental data, the fast and efficient simulation program ChromWin was used to simulate the experimental interconversion profiles and to obtain the apparent rate constants k1app(T). Additionally, these values were compared with the novel approximation function for the direct calculation of enantiomerization barriers from chromatographic parameters of elution profiles. From the rate constants k1app(T) of temperature-dependent measurements the kinetic activation parameters deltaG(T)#,deltaH#, and deltaS# of the enantiomerization of thalidomide were obtained. At 25 degrees C, the enantiomerization barrier deltaG# was determined to be 102 +/- 1 kJ/mol at pH 8 in the dynamic electrokinetic chromatographic experiment.

Chromatography↗
PubMed2007

Use of traps to capture black and gold howlers (Alouatta caraya) on the Islands of the upper Paraná River, Southern Brazil.

Howlers (genus Alouatta) are widely captured with the use of anesthetic projectiles; however, no capture protocol involving the use of traps has been described to date. In the present study we describe the first efficient capture program for black and gold howlers (Alouatta caraya) using traps, which was implemented on the islands of the upper Paraná River in southern Brazil. We constructed two trap models with either manual or automatic activation (trap A with two entrances and guillotine-type doors; trap B with one entrance and a guillotine-type door). The traps were suspended in the canopy by means of vertical climbing techniques, and were baited regularly and abundantly with bananas and mangoes. We captured 70 howlers (86% using manual activation and 14% using automatic activation) on four different islands. We restrained 41 of these animals and measured their body mass, which averaged 5.30 kg+/-1.79. Given our results, we suggest that the system described in the present study represents an alternative capture program for howlers in areas that have low food diversity and no other mammal species that will compete for the bait, as has been observed in riparian environments, islands, and forest fragments.

Alouatta↗
PubMedDate not supplied

Modulation of the immunological response to hepatitis B virus by antibodies.

Antibodies to HBsAg of IgG class enhanced the helper activity of a human T cell clone to promote the in vitro synthesis of immunoglobulins by autologous B lymphocytes. Using two different assay systems, the effect of antigen-specific antibodies on the helper function of a HBsAg-reactive T cell clone was studied. The monoclonal antibody to HBsAg A5C3 (IgG) increased significantly the T cell-dependent production of immunoglobulins by Staphyloccocus aureus-stimulated autologous B lymphocytes. Furthermore, the results obtained with a different type of assay showed that A5C3 also increased the synthesis of antibody to HBsAg by the autologous B cells in the presence of HBsAg and the helper T cell clone. On the other hand, when the monoclonal antibody to HBsAg of IgM class, H5D3 or the F(ab')2 fragment of A5C3 were tested, no significant enhancement of the helper activity of the T cell clone was observed. Experiments performed in mice showed that the in vivo antibody to HBsAg response to low concentrations of HBsAg was significantly enhanced by mixing this antigen with monoclonal antibody to HBsAg of IgG class. No effect was observed when a monoclonal antibody to HBsAg of IgM class was used to prepare the immune-complexed immunogen. The results presented here suggest that antibodies play a critical role in their own production through regulating the activity of helper T cells. This phenomenon might contribute to the increased antibody synthesis of in vivo secondary immune responses and could be of use in designing more efficient vaccine programs in man.

Animals↗
PubMed1981

The effects of nursing education on job effectiveness: an overview of the literature.

An overview of the published studies on the effectiveness of a nursing education as it relates to job performance is presented. Selected literature is reviewed and divided into three areas of study: competency, performance, and quality of care. The literature revealed contradictory evidence on the value of baccalaureate nursing education. More important, the review demonstrates a lack of rigorous research in this area. Suggested research directions include the measurement of individual performance rather than the perception of group performance, the development of better instruments, and control of the setting and individual variables that affect job performance. It is recommended that nursing effectiveness be defined in terms of both patient outcomes and nurse performance.

Clinical Competence↗
PubMed2005

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.

Recognizing structural similarity without significant sequence identity has proved to be a challenging task. Sequence-based and structure-based methods as well as their combinations have been developed. Here, we propose a fold-recognition method that incorporates structural information without the need of sequence-to-structure threading. This is accomplished by generating sequence profiles from protein structural fragments. The structure-derived sequence profiles allow a simple integration with evolution-derived sequence profiles and secondary-structural information for an optimized alignment by efficient dynamic programming. The resulting method (called SP(3)) is found to make a statistically significant improvement in both sensitivity of fold recognition and accuracy of alignment over the method based on evolution-derived sequence profiles alone (SP) and the method based on evolution-derived sequence profile and secondary structure profile (SP(2)). SP(3) was tested in SALIGN benchmark for alignment accuracy and Lindahl, PROSPECTOR 3.0, and LiveBench 8.0 benchmarks for remote-homology detection and model accuracy. SP(3) is found to be the most sensitive and accurate single-method server in all benchmarks tested where other methods are available for comparison (although its results are statistically indistinguishable from the next best in some cases and the comparison is subjected to the limitation of time-dependent sequence and/or structural library used by different methods.). In LiveBench 8.0, its accuracy rivals some of the consensus methods such as ShotGun-INBGU, Pmodeller3, Pcons4, and ROBETTA. SP(3) fold-recognition server is available on http://theory.med.buffalo.edu.

Algorithms↗
PubMed1998

An example of a protein ligand found by database mining: description of the docking method and its verification by a 2.3 A X-ray structure of a thrombin-ligand complex.

A computer program (SANDOCK) has been developed for the automated docking of small ligands to a target protein. It uses a guided matching algorithm to fit ligand atoms into the protein binding pocket. The protein is described by a modified Lee-Richard's dotted surface with each dot coded by chemical property and accessibility. Orientations of the ligand in the active site are generated such that a chemical and a shape complementary between the ligand and the active site cavity have to be fulfilled. The generated fits are evaluated with scoring functions which account for van der Waals, hydrophobic and hydrogen bonding interactions. This newly developed docking program can efficiently screen very large databases in a reasonable time and has been used to successfully identify novel ligands. The X-ray structure of a thrombin-ligand complex predicted by SANDOCK is described. The ligand binds to thrombin with a Kd of 65 microM and has an rmsd of 0.7 A for all ligand atoms from the predicted binding mode by SANDOCK.

Algorithms↗
PubMed1993

Mapping quantitative trait loci (QTLs) for resistance to Gibberella zeae infection in maize.

The basic prerequisite for an efficient breeding program to improve levels of resistance to pathogens in plants is the identification of genes controlling the resistance character. If the response to pathogens is under the control of a multilocus system, the utilization of molecular markers becomes essential. Stalk and ear rot caused by Gibberella zeae is a widespread disease of corn: resistance to G. zeae is quantitatively inherited. Our experimental approach to understanding the genetic basis of resistance to Gibberella is to estimate the genetic linkage between available molecular markers and the character, measured as the amount of diseased tissue 40 days after inoculation of a suspension of Fusarium graminearum, the conidial form of G. zeae, into the first stalk internode. Sensitive and resistant parental inbreds were crossed to obtain F1 and F2 populations: the analysis of the segregation of 95 RFLP (restriction fragment length polymorphism) clones and 10 RAPD (random amplified polymorphic DNA) markers was performed on a population of 150 F2 individuals. Analysis of resistance was performed on the F3 families obtained by selfing the F2 plants. Quantitative trait loci (QTL) detection was based either on analysis of regression coefficients between family mean value and allele values in the F2 population, or by means of interval mapping, using MAPMAKER-QTL. A linkage map of maize was obtained, in which four to five genomic regions are shown to carry factors involved in the resistance to G. zeae.

Chromosome Mapping↗
PubMed1998

Semi-automatic tool for segmentation and volumetric analysis of medical images.

Segmentation software is described, developed for medical image processing and run on Windows. The software applies basic image processing techniques through a graphical user interface. For particular applications, such as brain lesion segmentation, the software enables the combination of different segmentation techniques to improve its efficiency. The program is applied for magnetic resonance imaging, computed tomography and optical images of cryosections. The software can be utilised in numerous applications, including pre-processing for three-dimensional presentations, volumetric analysis and construction of volume conductor models.

Brain Ischemia↗
PubMedDate not supplied

Prediction of distribution coefficients from structure. Comparison of calculated and experimental data for various drugs.

The efficiency of the program PrologD to predict distribution coefficients (D) at any pH and pairing ion concentration has been tested using experimental logD values for various drugs measured under standard conditions of buffers and ionic strength. Clonidine derivatives, fluoroquinolones and beta-blockers were included as particular pharmacological classes within the testing data set. Calculations were performed using the three logP estimation options implemented in the program. PrologD proved to be very efficient and can be of great advantage in drug research. Prediction patterns and correlations between experimental and calculated data indicate acceptable results for more than 80% of the data. In addition, comparable studies using the different options permitted suggestions for the more suitable logP estimation method in respect of the particular classes of compounds.

Animals↗
PubMed2003

Calculation of the solution properties of flexible macromolecules: methods and applications.

While the prediction of hydrodynamic properties of rigid particles is nowadays feasible using simple and efficient computer programs, the calculation of such properties and, in general, the dynamic behavior of flexible macromolecules has not reached a similar situation. Although the theories are available, usually the computational work is done using solutions specific for each problem. We intend to develop computer programs that would greatly facilitate the task of predicting solution behavior of flexible macromolecules. In this paper, we first present an overview of the two approaches that are most practical: the Monte Carlo rigid-body treatment, and the Brownian dynamics simulation technique. The Monte Carlo procedure is based on the calculation of properties for instantaneous conformations of the macromolecule that are regarded as if they were instantaneously rigid. We describe how a Monte Carlo program can be interfaced to the programs in the HYDRO suite for rigid particles, and provide an example of such calculation, for a hypothetical particle: a protein with two domains connected by a flexible linker. We also describe briefly the essentials of Brownian dynamics, and propose a general mechanical model that includes several kinds of intramolecular interactions, such as bending, internal rotation, excluded volume effects, etc. We provide an example of the application of this methodology to the dynamics of a semiflexible, wormlike DNA.

Centrifugation, Density Gradient↗
PubMed1996

Successfully establishing laparoscopic surgery programs in developing countries. Clinical results and lessons learned.

BACKGROUND: Laparoscopic surgery has not been widely established in developing countries due to the lack of access to training and lack of money. We describe our experience using on-site training programs to efficiently teach and propagate laparoscopic surgery in Leon, Nicaragua; La Paz, Bolivia; and Santa Cruz, Bolivia. METHODS: A group of well-trained and motivated local surgeons was identified in each country as the initial target for teaching. Participants were taught basic and advanced laparoscopic surgery during on-site didactics, animal laboratories, and proctoring sessions. Follow-up courses were held until the target group of surgeons was capable of independently teaching and supervising laparoscopic surgery among other surgeons in each country. RESULTS: Multiple technical and logistic difficulties were encountered. In Leon, Nicaragua, and La Paz, Bolivia, a total of eight surgeons were fully trained and proctored in laparoscopic cholecystectomy. In La Paz and Santa Cruz, Bolivia, a total of seven surgeons were instructed in advanced laparoscopic procedures. To date, over 180 patients have undergone laparoscopic cholecystectomy or advanced procedures with a morbidity similar to that reported in literature series in the United States. CONCLUSIONS: Our experience demonstrates that in spite of numerous limitations, basic and laparoscopic surgery can be efficiently and safely taught in developing countries. Many lessons were learned in how to safely and efficiently use laparoscopic equipment and instruments within strict financial constraints.

Clinical Competence↗
PubMedDate not supplied

Development and implementation of a general compiler to produce specific programs for minicomputer control of physiological experiments in real time.

A method for automatic generation of specific FORTRAN programs to control physiological experiments with a computer was developed. The general real-time software package is built into a high level language (MAB = MAcro Basic). From this package, the scientist can automatically generate for him/herself specific programs for controlling his own experiments by a simple procedure. The generated programs contain only the relevant code, adjusted dimensions of arrays, names of parameters, and formatting for printing of tables and graphics for the particular experiment. Therefore, the resulting program is efficient both in terms of memory utilization and in execution time.

Animals↗