Using 3D Modeling Techniques to Enhance Teaching of Difficult Anatomical Concepts.
Ontology highlight
ABSTRACT:
SUBMITTER: Pujol S
PROVIDER: S-EPMC4808571 | biostudies-literature | 2016 Apr
REPOSITORIES: biostudies-literature
Publications
Using 3D Modeling Techniques to Enhance Teaching of Difficult Anatomical Concepts.
Pujol Sonia S Baldwin Michael M Nassiri Joshua J Kikinis Ron R Shaffer Kitt K
Academic radiology 20160217 4
<h4>Rationale and objectives</h4>Anatomy is an essential component of medical education as it is critical for the accurate diagnosis in organs and human systems. The mental representation of the shape and organization of different anatomical structures is a crucial step in the learning process. The purpose of this pilot study is to demonstrate the feasibility and benefits of developing innovative teaching modules for anatomy education of first-year medical students based on three-dimensional (3D ...[more]
Similar Datasets
Project description:BackgroundThe COVID-19 pandemic has had significant effects on anatomy education. During the pandemic, students have had no access to cadavers, which has been the principal method of learning anatomy. We created and tested a customized congenital heart disease e-learning course for medical students that contained interactive 3D models of anonymized pediatric congenital heart defects.ObjectiveThe aim of this study is to assess whether a multimodal e-learning course contributed to learning outcomes in a cohort of first-year undergraduate medical students studying congenital heart diseases. The secondary aim is to assess student attitudes and experiences associated with multimodal e-learning.MethodsThe pre-post study design involved 290 first-year undergraduate medical students. Recruitment was conducted by course instructors. Data were collected before and after using the course. The primary outcome was knowledge acquisition (test scores). The secondary outcomes included attitudes and experiences, time to complete the modules, and browser metadata.ResultsA total of 141 students were included in the final analysis. Students' knowledge significantly improved by an average of 44.6% (63/141) when using the course (SD 1.7%; Z=-10.287; P<.001). Most students (108/122, 88.3%) were highly motivated to learn with the course, and most (114/122, 93.5%) reported positive experiences with the course. There was a strong correlation between attitudes and experiences, which was statistically significant (rs=0.687; P<.001; n=122). No relationships were found between the change in test scores and attitudes (P=.70) or experiences (P=.47). Students most frequently completed the e-learning course with Chrome (109/141, 77.3%) and on Apple macOS (86/141, 61%) or Windows 10 (52/141, 36.9%). Most students (117/141, 83%) had devices with high-definition screens. Most students (83/141, 58.9%) completed the course in <3 hours.ConclusionsMultimodal e-learning could be a viable solution in improving learning outcomes and experiences for undergraduate medical students who do not have access to cadavers. Future research should focus on validating long-term learning outcomes.
| S-EPMC8663546 | biostudies-literature
Project description:BackgroundStudying structural and functional morphology of small organisms such as monogenean, is difficult due to the lack of visualization in three dimensions. One possible way to resolve this visualization issue is to create digital 3D models which may aid researchers in studying morphology and function of the monogenean. However, the development of 3D models is a tedious procedure as one will have to repeat an entire complicated modelling process for every new target 3D shape using a comprehensive 3D modelling software. This study was designed to develop an alternative 3D modelling approach to build 3D models of monogenean anchors, which can be used to understand these morphological structures in three dimensions. This alternative 3D modelling approach is aimed to avoid repeating the tedious modelling procedure for every single target 3D model from scratch.ResultAn automated 3D modeling pipeline empowered by an Artificial Neural Network (ANN) was developed. This automated 3D modelling pipeline enables automated deformation of a generic 3D model of monogenean anchor into another target 3D anchor. The 3D modelling pipeline empowered by ANN has managed to automate the generation of the 8 target 3D models (representing 8 species: Dactylogyrus primaries, Pellucidhaptor merus, Dactylogyrus falcatus, Dactylogyrus vastator, Dactylogyrus pterocleidus, Dactylogyrus falciunguis, Chauhanellus auriculatum and Chauhanellus caelatus) of monogenean anchor from the respective 2D illustrations input without repeating the tedious modelling procedure.ConclusionsDespite some constraints and limitation, the automated 3D modelling pipeline developed in this study has demonstrated a working idea of application of machine learning approach in a 3D modelling work. This study has not only developed an automated 3D modelling pipeline but also has demonstrated a cross-disciplinary research design that integrates machine learning into a specific domain of study such as 3D modelling of the biological structures.
| S-EPMC6929343 | biostudies-literature
Project description:Several key techniques in 3D geological modeling including planar mesh generation, spatial interpolation, and surface intersection are summarized in this paper. Note that these techniques are generic and widely used in various applications but play a key role in 3D geological modeling. There are two essential procedures in 3D geological modeling: the first is the simulation of geological interfaces using geometric surfaces and the second is the building of geological objects by means of various geometric computations such as the intersection of surfaces. Discrete geometric surfaces that represent geological interfaces can be generated by creating planar meshes first and then spatially interpolating; those surfaces intersect and then form volumes that represent three-dimensional geological objects such as rock bodies. In this paper, the most commonly used algorithms of the key techniques in 3D geological modeling are summarized.
| S-EPMC3948591 | biostudies-other
Project description:Using laser capture microdissection to isolate over 100 specific cell populations, we report the profiling of prostate cancer progression from benign epithelium to metastatic disease. By analyzing these expression signatures in the context of over 15,000 “molecular concepts”, or sets of biologically connected genes, we generated an integrative model of prostate cancer progression. Keywords: disease state analysis
2006-12-17 | GSE6099 | GEO
Project description:Using laser capture microdissection to isolate over 100 specific cell populations, we report the profiling of prostate cancer progression from benign epithelium to metastatic disease. By analyzing these expression signatures in the context of over 15,000 â??molecular conceptsâ??, or sets of biologically connected genes, we generated an integrative model of prostate cancer progression. Keywords: disease state analysis Experiment Design: â?¢ Type of experiment: This study used microarray experiments to profile prostate cancer progression through the isolation of pure cell populations using laser capture microdissection (LCM) and OmniPlex Whole Transcriptome (WTA) Amplification. â?¢ Experimental factors: This study profiled various pure cell populations isolated by LCM from prostate tissue. â?¢ The number of hybridizations performed in the experiment: A total of 104 hybridizations were performed. â?¢ The type of reference used for the hybridizations: A single commercially available pool of benign prostate tissue (CPP, Clontech) was used as the reference in all hybridizations. For the reference sample, 10 ng of CPP total RNA was converted into a WTA cDNA library in a volume of 25 µl and five 5 µl aliquots were amplified by WTA PCR and purified. Five ng aliquots of the pooled products were subjected to a second WTA PCR amplification in the presence of amino-allyl dUTP and all products were pooled before labeling to ensure equal representation across all of the hybridizations. â?¢ Hybridization design: For all hybridizations, the experimental prostate sample isolated by LCM was labeled with Cy5 and the common reference of benign pooled prostate as described above was labeled with Cy3. â?¢ Quality control steps taken: In order to assess biological and technical reproducibility, we captured identical regions from two specimens (PCA_11 and MET_HR_3) and subjected one sample, PCA_30, to two hybridizations. For PCA_11, adjacent regions of the same section were captured and treated as separate samples. For MET_HR_3, two separate foci of the liver metastasis (from separate frozen blocks) were captured and treated as separate samples. For PCA_30, two aliquots of the primary WTA PCR products were separately subjected to a second round of WTA PCR amplification. Replicates from PCA_30 and MET_HR_3 were also hybridized to arrays from each of the print runs utilized in this study. Samples used, extract preparation and labeling: â?¢ The origin of the biological sample (for instance, name of the organism, the provider of the sample) and its characteristics: All samples used were of human origin. The table in the MIAME Checklist (Supplmentary Methods) summarizes the samples used. Hybridizations are named according to the class of sample profiled and the background color is the same as shown in Figure S3. Two print runs were used during the course of the study and the indicated run for each hybridization is given. For prostate cancer samples, the Gleason patterns present on the sample section used are indicated, as well as the Gleason patterns of the actual cells isolated by LCM. A unique case number for all profiled samples is given. Descriptions of samples are given where applicable, including the location of metastatic foci. â?¢ Manipulation of biological samples and protocols used: Laser Capture Microdissection (LCM) was performed from frozen tissue sections with the SL Microtest device using µCUT software (MMI). Approximately 10,000 cells were captured for each sample. Serial sections were used if cells could not be obtained from a single section. Total RNA was isolated from captured cells with the RNAqueous Micro kit (Ambion) and treated with DNAse I according to the manufacturer's instructions. RNA quantification was perfomed using Ribogreen (Molecular Probes). â?¢ Protocol for preparing the hybridization extract: For each sample, total RNA (~10ng) in a volume of 25 µl was converted into an OmniPlex WTA cDNA library and amplified by WTA PCR using reagents and protocols according to the beta-commercial TransPlex WTA kit (Rubicon Genomics, Ann Arbor, MI). For each sample, a single 10 µl aliquot of the WTA cDNA library was amplified by WTA PCR and products were purified. Four or five 5 ng aliquots of product were subjected to a second WTA PCR amplification in the presence of amino-allyl dUTP for post amplification labeling and products were pooled before proceeding with the hybridization. Yields after all WTA PCR amplifications were between 2 to 5 μg per reaction, and reaction progress was monitored in real time using SYBR green I (Molecular Probes) on the iCycler IQ (BioRad) or ABI 7300 Real Time PCR system (Applied Biosystems). Real-time PCR amplifications were terminated at or before plateau phase as measured by fluorescence incorporation to preserve maximum representation. â?¢ Labeling protocol(s): For all WTA amplified cDNA samples with amino-allyl dUTP incorporated (10-20 ï?g), nuclease free water was added to 500 ï?l, the sample was transferred to a Microcon YM-30 filter, and centrifuged at 13,000 rcf at RT for 12 minutes. The spin column was inverted in a new collection tube and centrifuged at 13,000 rcf for 2 min at RT. The amount of sample was measured and the volume was adjusted to 5 ï?l with nuclease free water. For labeling, 5 ï?l of 1 M sodium bicarbonate (pH 9.0) was added and allowed to incubate at RT for 15 min. Nine ï?l of anhydrous DMSO were added to Mono Reactive Cy3 and Cy5 dye packs (Amersham, Buckinghamshire, England), mixed thoroughly, and 1 ï?l of the proper dye was added to each sample. The labeling mixture was incubated in the dark at RT for 1 hour. The reaction was stopped by the addition of 9 ï?l of 4 M Hydroxylamine for 15 min. For each labeling mixture, RNase free water was added to 100 ï?l, 500 ï?l of PB buffer was added and Cy3 and Cy5 mixtures were added to separate Qiaquick (Qiagen, Valencia, CA) spin columns and centrifuged at 13,000 rcf. Columns were washed twice with 700 ï?l of buffer PE, and centrifuged dry at 13,000 rcf for 2 min. To elute, 60 ï?l of EB buffer was placed on the column, incubated for 5 min and centrifuged at 13,000 rcf for 1 min. The Cy3 labeled and Cy5 labeled cDNA for each hybridization were mixed and 1.5 ï?l were used for analysis on a ND-1000 spectrophotometer. â?¢ External controls (spikes): Not utilized Hybridization procedures and parameters: â?¢ The protocol and conditions used during hybridization, blocking and washing: For hybridization, 40 ï?g of human Cot-1 DNA (Invitrogen, Carlsbad, CA) was added to 120 ï?l of labeled cDNA, the probe was transferred to a Microcon YM-30 filter and centrifuged at 13,000 rcf for 6 min at RT. The spin column was inverted in a new collection tube and centrifuged at 13,000 rcf for 2 min at RT. The eluted probe volume was adjusted to 18.6 ï?l with nuclease free water and the following were added: 4 ï?l of yeast tRNA (10 ï?g/ï?l, Invitrogen, Carlsbad, CA), 4.9 ï?l of 20X SSC and 0.84 ï?l of 10% SDS. The probe was denatured at 100 Co for 3 min and centrifuged at 13,000 rcf for 45 sec. The probe was added directly to the microarray and a cover slip was added. Slides were hybridized overnight in DIE-TECH 1 or 5 slide hybridization chambers in a 65 Co water bath. After hybridization, cover slips were removed by incubation in 2x SSC / 0.05% SDS. Slides were then washed in 2x SSC / 0.05% SDS for 5 min and 0.2x SSC / 0.05% SDS for five minutes. Slides were then washed in 0.2x SSC for 10 sec and centrifuged dry at 500 rpm for 5 min. Measurement data and specifications: â?¢ Type of scanning hardware and software used: Microarrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA). â?¢ Type of image analysis software used: Images were gridded and spots were quantified using GenePix Pro 4.0 software (Axon Instruments, Union City, CA). â?¢ A description of the measurements produced by the image-analysis software and a description of which measurements were used in the analysis: The measurements made by GenePix Pro 4.0 are described in the sample files. For all hybridizations, the log2 normalized Median of Ratios (as described below) was used. â?¢ Data selection and transformation procedures: Arrays were auto-gridded by GenePix 4.0. Features flagged by GenePix as not found during grid
2010-06-05 | E-GEOD-6099 | biostudies-arrayexpress
Project description:IntroductionCystic fibrosis (CF) is a high-yield undergraduate medical education topic that lends itself to adaptability of content. We used a CF case paired with activities to deliver content in a near-peer teaching session. First-year (M1) and second-year (M2) medical students contributed acquired knowledge of protein structure and obstructive lung disease, respectively, to generate a concept map and address discussion questions.MethodsCombined groups of M1 and M2 students reviewed a CF case and a concept map prompt. For 30 minutes, they created a concept map describing connections between molecular biology and clinical manifestations. We summarized by reviewing concept maps and discussion questions. The efficacy of the session was determined by comparing exam performance of class attenders and nonattenders (M2) and performance on questions related and unrelated to the exercise (M1). We also determined students' perception of the session and incorporation of additional core competencies.ResultsM2 students' performance was 3.8% higher (p = .296) and M1 students' performance was 1.8% higher (p = .286) than their respective controls. Students commented positively on the exercise and perceived more than one core competency as part of the session.DiscussionAlthough there was no significant improvement in exam performance, this curriculum used near-peer teaching to reinforce previously learned material and apply recently acquired material in an engaging format without detriment to either group. This method can be adapted to different learner groups and provides an opportunity to deliver and assess other core medical competencies.
| S-EPMC7453652 | biostudies-literature
Project description:A morpheein is a homo-oligomeric protein that can exist as an ensemble of physiologically significant and functionally different alternate quaternary assemblies. Morpheeins exist in nature and utilize conformational equilibria between different tertiary structures to form distinct oligomers as a means of regulating their function. Notably, alternate morpheeins are not misfolded forms of a protein; they are differently assembled native states that contain alternate subunit conformations. Transitions between alternate morpheein assemblies involve oligomer dissociation, conformational change in the dissociated state, and reassembly to a different oligomer. These transitions occur in response to the protein's environment, e.g., effector molecules, and represent a new model of allosteric regulation. The unique features of morpheeins are being revealed through detailed characterization of the prototype enzyme, porphobilinogen synthase, which exists in a dynamic equilibrium of a high activity octamer, a low activity hexamer, and two dimer conformations. Morpheeins are likely far more common than previously appreciated. There are, however, both intellectual and experimental barriers to recognizing proteins as morpheeins. These barriers derive from the way we were taught and continue to teach about protein folding, protein purification, protein structure-function relationships, and enzyme kinetics. This article explores some of these limitations and encourages incorporation of morpheeins into both introductory and advanced biochemistry classes.
| S-EPMC2575429 | biostudies-literature
Project description: Not available
| S-EPMC6113933 | biostudies-literature
Project description:BACKGROUND: Residents-as-teachers (RATs) programs have been shown to improve trainees' teaching skills, yet these decline over time. INTERVENTION: We adapted a commercial Web-based system to maintain resident teaching skills through reflection and deliberate practice and assessed the system's ability to (1) prevent deterioration of resident teaching skills and (2) provide information to improve residents' teaching skills and teaching program quality. METHODS: Ten first-year obstetrics-gynecology (Ob-Gyn) residents participated in a RATs program. Following the program, they used a commercial evaluation system to complete self-assessments of their teaching encounters with medical students. Students also evaluated the residents. To assess the system's effectiveness, we compared these residents to historical controls with an Objective Structured Teaching Examination (OSTE) and analyzed the ratings and the free text comments of residents and students to explore teaching challenges and improve the RATs program. RESULTS: The intervention group outscored the control group on the OSTE (mean score ± SD = 81 ± 8 versus 74 ± 7; P = .05, using a 2-tailed Student t-test). Rating scale analysis showed resident self-assessments were consistently lower than student evaluations, with the difference reaching statistical significance in 3 of 6 skills (P < .05). Comments revealed that residents most valued using innovative teaching techniques, while students most valued a positive educational climate and interpersonal connections with residents. Recommended targets for RATs program improvement included teaching feedback, time-limited teaching, and modeling professionalism behaviors. CONCLUSIONS: Our novel electronic Web-based reinforcement system shows promise in preventing deterioration of resident teaching skills learned during an Ob-Gyn RATs program. The system also was effective in gaining resident and student insights to improve RATs programs. Because our intervention was built upon a commercially available program, our approach could prove useful to the large population of current subscribers.
| S-EPMC3312536 | biostudies-other
Project description:Objective:The existing evidence separately correlates morbid obesity with difficult intubation and bronchospasm. However, there is a lack of data on whether anaesthesia provider manipulations during difficult intubation contribute to an increased ratio of bronchospasm in these patients. Methods:This is a retrospective analysis of data prospectively taken from 50 morbidly obese patients involved in a previously published study. A possible difficult intubation was preoperatively investigated by recording the following specific physical examination indices: Mallampati and Cormack-Lehane (CL) classifications, cervical spine mobility (CSM), thyromental distance (Td) and patients' ability to open their mouth (mouth opening). Bronchospasm was clinically detected by auscultation and confirmed by measuring peak airway pressures during mechanical ventilation. The Kruskal-Wallis H test was used for data analysis, followed by the Mann-Whitney U test as applicable. Results:Different physical examination prognostic indices, including Mallampati and CL scales (p<0.001; the CSM excluded -p=0.790), showed that they are related to difficult intubation. Bronchospasm not attributable to difficult intubation was observed in six obese patients. Conclusion:Patients with morbid obesity constitute an increased relative risk group as far as difficult intubation is concerned, particularly if preoperative findings support a relationship between the two variables examined. In our study, difficult intubation and the concomitant use of special equipment and manipulations did not contribute to an increased rate of bronchospasm in obese patients, but in view of the lack of data, a large number of more sophisticated studies are required to elucidate such an assumption.
| S-EPMC6101711 | biostudies-literature