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At least 217 records · Page 12Linked to original sources
PubMed2005

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.

Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP-ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding C(alpha) root mean square deviations (RMSD) of about 1.0 and 0.8 A respectively along the entire simulation time, compared to 0.8 A for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a C(alpha) RMSD of approximately 1.4 A, while the PAR22/LD trajectory became unstable early in the simulation, reaching a C(alpha) RMSD of about 2.7 A and remaining at this value until the end of the simulation; the C(alpha) RMSD of the EW/MD simulation was about 1.5 A. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35-ns SCP-ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (C(alpha) RMSD of approximately 1.0 A), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a C(alpha) RMSD of approximately 1.5 A at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent-exposed side chain-side chain (sc-sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation were lost. The overall analysis reported in this work suggests that the combination of an atomistic representation of a protein with a CMAP/CHARMM force field and a continuum representation of solvent effects such as the SCP-ISM provides a good description of structural and dynamic properties obtained from long computer simulations. Although the SCP-ISM simulations (CMAP/LD) reported here were shown to be stable and the properties well reproduced, further refinement is needed to attain a level of accuracy suitable for more challenging biological applications, particularly the study of protein-protein interactions.

Alanine↗
PubMed2004

Computer simulation as a component of catheter-based training.

INTRODUCTION: Computer simulation has been used in a variety of training programs, ranging from airline piloting to general surgery. In this study we evaluate the use of simulation to train novice and advanced interventionalists in catheter-based techniques. METHODS: Twenty-one physicians underwent evaluation in a simulator training program that involved placement of a carotid stent. Five participants were highly experienced in catheter-based techniques (>300 percutaneous cases), including carotid angioplasty and stenting (CAS); the remaining 16 participants were interventional novices (<5 percutaneous cases). The Procedicus VIST simulator, composed of real-time vascular imaging simulation software and a tactile interface coupled to angiographic catheters and guide wires, was used. After didactic instruction regarding CAS and use of the simulator, each participant performed a simulated CAS procedure. The participant's performance was supervised and evaluated by an expert interventionalist on the basis of 50 specific procedural steps with a maximal score of 100. Specific techniques of guide wire and catheter manipulation were subjectively assessed on a scale of 0 to 5 points based on ability. After evaluation of the initial simulated CAS procedure, each participant received a minimum of 2 hours of individualized training by the expert interventionalist, with the VIST simulator. Each participant then performed a second simulated CAS procedure, which was graded with the same scale. After completion, participants assessed the training program and its utility via survey questionnaire. RESULTS: The average simulated score for novice participants after the training program improved significantly from 17.8 +/- 15.6 to 69.8 +/- 9.8 (P < .01), time to complete simulation decreased from 44 +/- 10 minutes to 30 +/- 8 minutes (P < .01), and fluoroscopy time decreased from 31 +/- 7 minutes to 23 +/- 7 minutes ( P < .01). No statistically significant difference in score, total time, or fluoroscopy time was noted for experienced interventionalists. Improvement was noted in guide wire and catheter manipulation skills in novices. Analysis of survey data from experienced interventionalists indicated that the simulated clinical scenarios were realistic and that the simulator could be a valuable tool if clinical and tactile feedback were improved. Novices also thought the simulated training was a valuable experience, and desired further training time. CONCLUSIONS: An endovascular training program using the Procedicus VIST haptic simulator resulted in significant improvement in trainee facility with catheter-based techniques in a simulated clinical setting. Novice participants derived the greatest benefit from simulator training in a mentored program, whereas experienced interventionalists did not seem to derive significant benefit.

Blood Vessel Prosthesis Implantation↗
PubMed2006

High fidelity medical simulation in the difficult environment of a helicopter: feasibility, self-efficacy and cost.

BACKGROUND: This study assessed the feasibility, self-efficacy and cost of providing a high fidelity medical simulation experience in the difficult environment of an air ambulance helicopter. METHODS: Seven of 12 EM residents in their first postgraduate year participated in an EMS flight simulation as the flight physician. The simulation used the Laerdal SimMantrade mark to present a cardiac and a trauma case in an EMS helicopter while running at flight idle. Before and after the simulation, subjects completed visual analog scales and a semi-structured interview to measure their self-efficacy, i.e. comfort with their ability to treat patients in the helicopter, and recognition of obstacles to care in the helicopter environment. After all 12 residents had completed their first non-simulated flight as the flight physician; they were surveyed about self-assessed comfort and perceived value of the simulation. Continuous data were compared between pre- and post-simulation using a paired samples t-test, and between residents participating in the simulation and those who did not using an independent samples t-test. Categorical data were compared using Fisher's exact test. Cost data for the simulation experience were estimated by the investigators. RESULTS: The simulations functioned correctly 5 out of 7 times; suggesting some refinement is necessary. Cost data indicated a monetary cost of 440 dollars and a time cost of 22 hours of skilled instructor time. The simulation and non-simulation groups were similar in their demographics and pre-hospital experiences. The simulation did not improve residents' self-assessed comfort prior to their first flight (p > 0.234), but did improve understanding of the obstacles to patient care in the helicopter (p = 0.029). Every resident undertaking the simulation agreed it was educational and it should be included in their training. Qualitative data suggested residents would benefit from high fidelity simulation in other environments, including ground transport and for running codes in hospital. CONCLUSION: It is feasible to provide a high fidelity medical simulation experience in the difficult environment of the air ambulance helicopter, although further experience is necessary to eliminate practical problems. Simulation improves recognition of the challenges present and provides an important opportunity for training in challenging environments. However, use of simulation technology is expensive both in terms of monetary outlay and of personnel involvement. The benefits of this technology must be weighed against the cost for each institution.

Adult↗
PubMed1994

Design of a fully integrated three-dimensional computed tomography simulator and preliminary clinical evaluation.

PURPOSE: We describe the conceptual structure and process of a fully integrated three-dimensional (3-D) computed tomography (CT) simulator and present a preliminary clinical and financial evaluation of our current system. METHODS AND MATERIALS: This is a preliminary report on 117 patients treated with external beam radiation therapy alone on whom a 3-D simulation and treatment plan and delivery were carried out from July 1, 1992, through June 30, 1993. The elements of a fully integrated 3-D CT simulator were identified: (a) volumetric definition of tumor volume and patient anatomy obtained with a CT scanner, (b) virtual simulation for beam setup and digitally reconstructed radiographs, (c) 3-D treatment planning for volumetric dose computation and plan evaluation, (d) patient-marking device to outline portal on patient's skin, and (e) verification (physical) simulation to verify portal placement on the patient. Actual time-motion (time and effort) recording was made by each professional involved in the various steps of the 3-D simulation and treatment planning on computer-compatible forms. Data were correlated with the anatomic site of the primary tumor being planned. Cost accounting of revenues and operation of the CT simulator and the 3-D planning was carried out, and projected costs per examination, depending on case load, were generated. RESULTS: Average time for CT volumetric simulation was 74 min without or 84 min with contrast material. Average times were 36 min for contouring of tumor/target volume and 44 min for normal anatomy, 78 min for treatment planning, 53 min for plan evaluation/optimization, and 58 min for verification simulation. There were significant variations in time and effort according to the specific anatomic location of the tumor. Portal marking of patient on the CT simulator was not consistently satisfactory, and this procedure was usually carried out on the physical simulator. Based on actual budgetary information, the cost of a volumetric CT simulation (separate from the 3-D treatment planning) showed that 1500 examinations per year (six per day in 250 working days) must be performed to make the operation of the device cost effective. The same financial projections for the entire 3-D planning process and verification yielded five plans per day. Some features were identified that will improve the use of the 3-D simulator, and solutions are offered to incorporate them in existing devices. CONCLUSIONS: Commercially available CT simulators lack some elements that we believe are critical in a fully integrated 3-D CT simulator. Sophisticated 3-D simulation and treatment planning can be carried out in a significant number of patients at a reasonable cost. Time and effort and therefore cost vary according to the anatomic site of the tumor being planned and the number of procedures performed. Further efforts are necessary, with collaboration of radiation oncologists, physicists, and manufacturers, to develop more versatile and efficient 3-D CT simulators, and additional clinical experience is required to make this technology cost effective in standard radiation therapy of patients with cancer.

Adult↗
PubMed2005

Features and uses of high-fidelity medical simulations that lead to effective learning: a BEME systematic review.

REVIEW DATE: 1969 to 2003, 34 years. BACKGROUND AND CONTEXT: Simulations are now in widespread use in medical education and medical personnel evaluation. Outcomes research on the use and effectiveness of simulation technology in medical education is scattered, inconsistent and varies widely in methodological rigor and substantive focus. OBJECTIVES: Review and synthesize existing evidence in educational science that addresses the question, 'What are the features and uses of high-fidelity medical simulations that lead to most effective learning?'. SEARCH STRATEGY: The search covered five literature databases (ERIC, MEDLINE, PsycINFO, Web of Science and Timelit) and employed 91 single search terms and concepts and their Boolean combinations. Hand searching, Internet searches and attention to the 'grey literature' were also used. The aim was to perform the most thorough literature search possible of peer-reviewed publications and reports in the unpublished literature that have been judged for academic quality. INCLUSION AND EXCLUSION CRITERIA: Four screening criteria were used to reduce the initial pool of 670 journal articles to a focused set of 109 studies: (a) elimination of review articles in favor of empirical studies; (b) use of a simulator as an educational assessment or intervention with learner outcomes measured quantitatively; (c) comparative research, either experimental or quasi-experimental; and (d) research that involves simulation as an educational intervention. DATA EXTRACTION: Data were extracted systematically from the 109 eligible journal articles by independent coders. Each coder used a standardized data extraction protocol. DATA SYNTHESIS: Qualitative data synthesis and tabular presentation of research methods and outcomes were used. Heterogeneity of research designs, educational interventions, outcome measures and timeframe precluded data synthesis using meta-analysis. HEADLINE RESULTS: Coding accuracy for features of the journal articles is high. The extant quality of the published research is generally weak. The weight of the best available evidence suggests that high-fidelity medical simulations facilitate learning under the right conditions. These include the following: providing feedback--51 (47%) journal articles reported that educational feedback is the most important feature of simulation-based medical education; repetitive practice--43 (39%) journal articles identified repetitive practice as a key feature involving the use of high-fidelity simulations in medical education; curriculum integration--27 (25%) journal articles cited integration of simulation-based exercises into the standard medical school or postgraduate educational curriculum as an essential feature of their effective use; range of difficulty level--15 (14%) journal articles address the importance of the range of task difficulty level as an important variable in simulation-based medical education; multiple learning strategies--11 (10%) journal articles identified the adaptability of high-fidelity simulations to multiple learning strategies as an important factor in their educational effectiveness; capture clinical variation--11 (10%) journal articles cited simulators that capture a wide variety of clinical conditions as more useful than those with a narrow range; controlled environment--10 (9%) journal articles emphasized the importance of using high-fidelity simulations in a controlled environment where learners can make, detect and correct errors without adverse consequences; individualized learning--10 (9%) journal articles highlighted the importance of having reproducible, standardized educational experiences where learners are active participants, not passive bystanders; defined outcomes--seven (6%) journal articles cited the importance of having clearly stated goals with tangible outcome measures that will more likely lead to learners mastering skills; simulator validity--four (3%) journal articles provided evidence for the direct correlation of simulation validity with effective learning. CONCLUSIONS: While research in this field needs improvement in terms of rigor and quality, high-fidelity medical simulations are educationally effective and simulation-based education complements medical education in patient care settings.

Clinical Competence↗
PubMed2002

Incorporating simulators in a standardized patient exam.

OBJECTIVE: Using simulated patients during a clinical skills exam that involves many students has the advantage of standardizing the delivery of historical data. One major disadvantage is the inability to standardize the physical exam findings. We designed a simulated patient exam that incorporates simulated abnormal physical exam findings. DESCRIPTION: The simulated patient exam case was divided into three separate stations: (1) the simulated patient's history, (2) the simulated physical exam, and (3) the presentation station. Dyspnea was chosen as the chief complaint because of the broad differential of possible cardiac and pulmonary auscultatory findings. In the first station, students obtained historical data from the standardized simulated patient. Students were graded on their ability to ask appropriate historical questions. Trained observers were used to verify the numbers of historical cues obtained by the students. The second station consisted of simulated physical exam findings. Students first measured the blood pressure on a commercially available blood pressure simulator arm from the Medical Plastics Laboratory, Inc., Gatesville, TX. Students then auscultated an abnormal digital heart sound and pulmonary sound from a small auscultation transducer developed by Andries Acoustics, Spicewood, TX. Students also palpated a simulated pulse from a newly developed pulse transducer. Digital cardiopulmonary sounds and pulse data were recorded onto a CD-ROM disc and transmitted to the small transducers via a CD-ROM disc player. Students used their own stethoscopes to auscultate cardiopulmonary sounds from the small transducers. The students were graded in the second station on their ability to accurately measure a blood pressure, identify abnormal cardiopulmonary digital sounds, and finally describe a peripheral pulse. In the third station, students presented the historical data and physical exam findings to a faculty member, and then provided a differential diagnosis list based on their key findings from the other two stations. A total of 171 students (n = 171) completed the simulated patient exam. Each student completed the exam in 45 minutes. DISCUSSION: In our simulated patient exam, students were evaluated not only on their data-gathering skills for key historical findings but also on the ability to correctly identify key physical exam findings such as abnormal cardiopulmonary sounds. Key physical exam findings were then integrated into the clinical decision-making process, which was presented in the faculty presentation station. Simulated patients with abnormal cardiopulmonary findings can be used for testing purposes. However, cardiac auscultatory abnormalities such as the ventricular S3 gallop are difficult to find and usually occur in a decompensated state such as heart failure. Other physical exam findings such as pulmonary crackles and wheezes also occur in decompensated conditions. Therefore, the use of simulators during a simulated patient exam offers the possibility of introducing several abnormal physical exam findings without having an unstable patient present in an exam setting. Further, the use of simulated physical exam findings allows for complete standardization of a clinical-simulated patient exam.

Clinical Competence↗
PubMed2003

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.

A continuum electrostatics approach for molecular dynamics (MD) simulations of macromolecules is presented and analyzed for its performance on a peptide and a globular protein. The approach incorporates the screened Coulomb potential (SCP) continuum model of electrostatics, which was reported earlier. The model was validated in a broad set of tests some of which were based on Monte Carlo simulations that included single amino acids, peptides, and proteins. The implementation for large-scale MD simulations presented in this article is based on a pairwise potential that makes the electrostatic model suitable for fast analytical calculation of forces. To assess the suitability of the approach, a preliminary validation is conducted, which consists of (i) a 3-ns MD simulation of the immunoglobulin-binding domain of streptococcal protein G, a 56-residue globular protein and (ii) a 3-ns simulation of Dynorphin, a biological peptide of 17 amino acids. In both cases, the results are compared with those obtained from MD simulations using explicit water (EW) molecules in an all-atom representation. The initial structure of Dynorphin was assumed to be an alpha-helix between residues 1 and 9 as suggested from NMR measurements in micelles. The results obtained in the MD simulations show that the helical structure collapses early in the simulation, a behavior observed in the EW simulation and consistent with spectroscopic data that suggest that the peptide may adopt mainly an extended conformation in water. The dynamics of protein G calculated with the SCP implicit solvent model (SCP-ISM) reveals a stable structure that conserves all the elements of secondary structure throughout the entire simulation time. The average structures calculated from the trajectories with the implicit and explicit solvent models had a cRMSD of 1.1 A, whereas each average structure had a cRMSD of about 0.8A with respect to the X-ray structure. The main conformational differences of the average structures with respect to the crystal structure occur in the loop involving residues 8-14. Despite the overall similarity of the simulated dynamics with EW and SCP models, fluctuations of side-chains are larger when the implicit solvent is used, especially in solvent exposed side-chains. The MD simulation of Dynorphin was extended to 40 ns to study its behavior in an aqueous environment. This long simulation showed that the peptide has a tendency to form an alpha-helical structure in water, but the stabilization free energy is too weak, resulting in frequent interconversions between random and helical conformations during the simulation time. The results reported here suggest that the SCP implicit solvent model is adequate to describe electrostatic effects in MD simulation of both peptides and proteins using the same set of parameters. It is suggested that the present approach could form the basis for the development of a reliable and general continuum approach for use in molecular biology, and directions are outlined for attaining this long-term goal.

Amino Acid Sequence↗
PubMed2006

Integrating simulation into a surgical residency program: is voluntary participation effective?

OBJECTIVE: Surgical training programs nationwide are struggling with the integration of simulation training into their curriculum given the constraints of the 80-h work week. We examine the effectiveness of voluntary training in a simulation lab as part of the surgical curriculum. METHODS: The ProMIS simulator was introduced into the general surgery residency at Boston University Medical Center. All categorical residents (28) and non-categorical residents (23) were offered a 2-h training session and curriculum review. After the introductory session, time spent in the lab was encouraged, but voluntary. Use of the simulator was tracked for all residents. Participation in the simulation curriculum was defined as three or more uses of the simulator. After 3 months, all residents completed a survey regarding the simulation lab and their simulator usage. RESULTS: Twenty-six (93%) categorical residents and three (6%) non-categorical residents completed the introductory simulator training session. Over a 3 month period, use of the simulator at least once was 31% among all eligible residents; 80% of postgraduate year (PGY)1, 40% of PGY2, 60% of PGY3, and 0% of PGY4 and PGY5. Four residents (14%) participated in the simulation curriculum. Overall, 70% of simulator usage was during working hours, and 30% was completed post-call or when the resident was off duty. Most residents agreed that the simulator was easy to use and that its use improved their operative skills, but they did not think it was a good substitute for actual operative experience. Reported reasons for not using the simulator included off-site rotation (44%), no time (30%), and no interest (11%). CONCLUSIONS: Voluntary use of a surgical simulation lab leads to minimal participation in a training curriculum. Participation should be mandatory if it is to be an effective part of a residency curriculum.

Boston↗
PubMed2004

Virtual simulation in palliative lung radiotherapy.

AIMS: To study the accuracy of tumour-volume localisation in a comparison of conventional and virtual simulation for palliative lung radiotherapy. To assess if three-dimensional tumour outlining is necessary for the virtual simulation process. MATERIALS AND METHODS: Ten consecutive patients with non-small cell lung cancer underwent target localisation for palliative lung radiotherapy using conventional and virtual simulation. The treatment fields were initially marked with a conventional simulator using fluoroscopy, plain X-ray film and available diagnostic imaging. Each patient then had a computed tomography (CT), and these simulated treatment fields were reproduced within the virtual simulation planning system. Two clinicians then independently defined treatment fields using virtual simulation alone. The virtual simulation was achieved without outlining the tumour in three dimensions. The coverage of an 'ideal' CT-defined planning-target volume (PTV) was then calculated for each of the virtually and conventionally simulated fields. In addition, the amount of irradiated normal lung was measured using dose-volume histograms (DVH). Field sizes and differences in tumour volume coverage were compared. RESULTS: There was significantly greater tumour volume coverage using virtual simulation compared with conventional simulation (P < 0.03). This advantage was more pronounced in tumours that were larger and those that were closer to the patient's midline. There was no statistically significant difference in the volume of uninvolved lung irradiated between the two methods. CONCLUSION: In this small sample of patients, we have demonstrated improved tumour volume coverage using virtual simulation, without increasing the volume of uninvolved lung treated. A simple but consistent method of virtual simulation for this patient group is offered as an alternative to both PTV-defined CT simulation and fluoroscopy-based conventional simulation.

Carcinoma, Non-Small-Cell Lung↗
PubMed2007

The current role of medical simulation in american urological residency training programs: an assessment by program directors.

PURPOSE: Although medical simulation opportunities are increasingly available, resident training to date has involved primarily hands-on, subjective assessments. The role of simulation and computer based training for urology residents remains unknown. We evaluated the current status of medical simulation among urological training programs in the United States. MATERIALS AND METHODS: An anonymous questionnaire was developed and mailed to the program director at the 119 Accreditation Council for Graduate Medical Education accredited United States urology training programs, and consisted of 17 questions documenting the prior experience of the responder to medical simulation as well as the current status of simulation at their institution. An additional 14 questions sought the responders' opinion of medical simulation in urology training programs. RESULTS: The questionnaire was returned by 41 program directors (35%). Among respondents, access to a laparoscopy simulator was 76%. In comparison, reported access to cystoscopy, ureteroscopy, transurethral resection and percutaneous access simulators was 16%, 21%, 8% and 12%, respectively. Respondents indicated that these simulators were good educational tools, realistic and easy to use. Unanimous agreement was reported for simulation training in residency and that simulators allow practice in a controlled environment. Disagreement was reported about the cost effectiveness, validity and ability of simulators to replace hands-on instruction in the operating room. CONCLUSIONS: Among responders a high level of access to laparoscopic simulators for urology residents is coupled with low levels of access to other endoscopic trainers. Urology residency program directors unanimously recognize a role for simulation training in residency, although the extent to which they may be incorporated remains to be resolved.

Computer Simulation↗