Journal: BMC Oral Health

Article Title: Current state of the art in the use of augmented reality in dentistry: a systematic review of the literature

doi: 10.1186/s12903-019-0808-3

Figure Lengend Snippet: Software and Hardware

Article Snippet: Ewers R , 2005 , optoelectronic tracking systems: ProReflex™ Motion-Capture MCU240 (Qualisys Inc., Sweden), Polaris™ (NDI Northern Digital Inc., Canada), FlashPoint 5000™ 3D Localizer (Image Guided Technologies Inc., USA). Electromagnetic systems (since 1999 only used for research purposes): Polhemus Isotrac II™ (by Polhemus Inc., USA) and Aurora™ (NDI Inc., Ont., Canada), Fastrak™. , various types of navigation software (Virtual Vision™, MedScanII™, Virtual Implant™, Artma Medical Technologies, Vienna).

Techniques: Software, Plasmid Preparation, Marker, Northern Blot, Microscopy

Journal: bioRxiv

Article Title: Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

doi: 10.1101/374058

Figure Lengend Snippet: ( A, B ) Matrices for ( A ) mean spatial distance scores (MDS) and ( B ) mean entanglement scores (MES) for CS1-9. ( C ) Unsupervised PCA of 3D features for the 342 visualized chromosomal segments suggests two major clusters. Chromosomal segments are colored as in , with relative abundances displayed as pie charts. Lower panel, proportion of images of each chromosomal segment in cluster 1 (opaque color) or cluster 2 (transparent color). ( D-F ) Variation and distribution of the two clusters in terms of ( D ) surface area, ( E ) volume, and ( F ) sphericity scores are shown as box plots, where boundaries represent 1st and 3rd quartiles, middle line represents median, and whiskers extend to 1.5 times the interquartile range (Mann-Whitney rank test, ***: p < 10 −3 ). ( G ) Mean normalized signal of seven different ChIP-seq profiles in PGP1 nuclei for the two identified clusters. Red, cluster 1; blue, cluster 2. ( H ) Density map representation of each chromosomal segment in both copies of the entire 8.16 Mb (CS1-9) region in a single PGP1 nucleus as imaged by OligoSTORM, color-coded by cluster type. Red, cluster 1; blue, cluster 2. One homolog is displayed with a solid surface, while the other homolog is displayed with a mesh surface. Note spatial segregation of clusters. ( I ) Density map representation of CS1-9 as in I (grey) except displayed, here, with the fitted 3D model obtained via IMGR (colored coded as in ). Images were created with Chimera .

Article Snippet: When implementing OligoSTORM, the sample is then placed on a 3D single-molecule localization microscope (Bruker Vutara 352) and scanned to identify nuclei to be imaged.

Techniques: MANN-WHITNEY, ChIP-sequencing

Journal: bioRxiv

Article Title: Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

doi: 10.1101/374058

Figure Lengend Snippet: ( A ) IMGR protocol for fitting and refinement of 3D chromatin models. The protocol inputs are a density map derived from a single PGP1f nucleus imaged with OligoSTORM and an ensemble of 3D models derived from a PGP1f population-based in situ Hi-C contact map. The protocol entails rigid fitting by a random 6D search (step1), followed by flexible fitting refinement via simulated annealing rigid-body molecular dynamics and conjugate gradient minimization (step 2). After each step, the goodness-of-fit is assessed as described using different scores (Supplementary note). ( B ) Mapping of Znf clusters onto the 3D trace. The trace is colored in grey, and the two clusters are colored in blue and red. Insets are zoomed-in views of one of the Znf clusters, highlighting the differences in conformation of the cluster in the model of the two homologs. ( C ) Annotated disease-causing genes mapped into the 3D trace. The trace is colored in grey. Shown in red are genes for which the molecular basis for the disorder is known and a mutation has been found, as classified by OMIM Genes track in the UCSC Genome Browser . ( D-J ) Mapping of genome features. Genomic features are presented as mean value per 10kb. The color scale for each genomic feature ranges from white (mean value) to red (mean + 2 standard deviation). The figures in this panel were created with Chimera .

Article Snippet: When implementing OligoSTORM, the sample is then placed on a 3D single-molecule localization microscope (Bruker Vutara 352) and scanned to identify nuclei to be imaged.

Techniques: Derivative Assay, In Situ, Hi-C, Mutagenesis, Standard Deviation