Journal: Data in Brief

Article Title: Energetic and kinetic dataset on interaction of the vacancy and self-interstitial atom with the grain boundary in α-iron

doi: 10.1016/j.dib.2016.03.052

Figure Lengend Snippet:

Article Snippet: How data was acquired , Molecular dynamics simulations, molecular statics calculations and the object kinetic Monte Carlo simulations.

Techniques:

Journal: Global Surgical Education - Journal of the Association for Surgical Education

Article Title: Current status of virtual reality simulation education for orthopedic residents: the need for a change in focus

doi: 10.1007/s44186-023-00120-w

Figure Lengend Snippet: Realism of VR simulators used in educational events

Article Snippet: Vaghela, 2021 [ ] , 10-point Numerical Rating Scale , • “The results indicate that the ArthroS VR simulator demonstrates satisfactory (7.0) face validity in all assessed domains, while the ARTHRO Mentor failed to achieve acceptable levels of realism in any domains when judged by a range of orthopaedic surgeons... • Across all face validity domains, the ArthroS scored significantly (p < 0.001) higher than the ARTHRO Mentor simulator, suggesting a clear preference amongst our study participants • 95% of participants gave the passive simulator a score 7.0 (indicating sufficient realism), compared to 47% for the active simulator • The intra articular appearance domain scored a combined mean of 7.65 (± 1.26) and 4.78 (± 1.59) for passive and active simulators respectively • 76% of participants gave the passive simulator a score 7.0 in this category, compared to 11% for the active simulator • Mean combined face validity scores for the instrument category were 7.21 (± 1.68) and 4.36 (± 1.50) for passive and active simulators respectively • Combined mean sufficient scores were given by 55% of participants for the passive simulator, versus 8% for the active simulator.”.

Techniques: Diagnostic Assay, Activity Assay, Control

Journal: Global Surgical Education - Journal of the Association for Surgical Education

Article Title: Current status of virtual reality simulation education for orthopedic residents: the need for a change in focus

doi: 10.1007/s44186-023-00120-w

Figure Lengend Snippet: Results from study of educational modules comparing technical skill acquisition through VR simulation versus control group

Article Snippet: Vaghela, 2021 [ ] , 10-point Numerical Rating Scale , • “The results indicate that the ArthroS VR simulator demonstrates satisfactory (7.0) face validity in all assessed domains, while the ARTHRO Mentor failed to achieve acceptable levels of realism in any domains when judged by a range of orthopaedic surgeons... • Across all face validity domains, the ArthroS scored significantly (p < 0.001) higher than the ARTHRO Mentor simulator, suggesting a clear preference amongst our study participants • 95% of participants gave the passive simulator a score 7.0 (indicating sufficient realism), compared to 47% for the active simulator • The intra articular appearance domain scored a combined mean of 7.65 (± 1.26) and 4.78 (± 1.59) for passive and active simulators respectively • 76% of participants gave the passive simulator a score 7.0 in this category, compared to 11% for the active simulator • Mean combined face validity scores for the instrument category were 7.21 (± 1.68) and 4.36 (± 1.50) for passive and active simulators respectively • Combined mean sufficient scores were given by 55% of participants for the passive simulator, versus 8% for the active simulator.”.

Techniques: Control, Comparison, Standard Deviation

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

doi: 10.1073/pnas.1700557114

Figure Lengend Snippet: Parameterization of kinetic Monte Carlo strand invasion model and model evaluation against observed data. (A) dCas9 strand invasion was modeled with kinetic Monte Carlo simulations parameterized with an initial on-rate, PAM-association energy, transversion penalty, transition penalty, and a second protein association energy at a discrete position (which was also a fit parameter). Parameters were optimized by grid search by minimizing Euclidean distance of the observed data relative to the on-target simulation. (B) Each point is an off-target double mismatch sequence with a terminal nucleotide substitution (position −18, −19, or −20) colored by the position of a PAM-proximal mismatch. Double mutant energy barriers predicted from single mutant energy barriers (x axis) consistently underestimate the observed energy barriers (y axis). (C) Strand invasion simulations parameterized from the single mutant data also fail to predict the observed kinetics of double mutant binding, suggesting that this nonadditive effect cannot be captured by this thermodynamic model of strand invasion. The presence of an extremely PAM-distal or terminal mismatch raises the effective barrier height substantially beyond the effect of the PAM-proximal mismatch.

Article Snippet: One thousand kinetic Monte Carlo simulations were performed at a time to model clusters on the Illumina flow cell.

Techniques: Sequencing, Mutagenesis, Binding Assay