Federating heterogeneous datasets to enhance data sharing and experiment reproducibility

Recent studies have demonstrated the difficulties to replicate scientific findings and/or experiments published in past.1 The effects seen in the replicated experiments were smaller than previously reported. Some of the explanations for these findings include the complexity of the experimental design and the pressure on researches to report positive findings. The International Committee of Medical Journal Editors (ICMJE) suggests that every study considered for publication must submit a plan to share the de-identified patient data no later than 6 months after publication. There is a growing demand to enhance the management of clinical data, facilitate data sharing across institutions and also to keep track of the data from previous experiments. The ultimate goal is to assure the reproducibility of experiments in the future. This paper describes Shiny-tooth, a web based application created to improve clinical data acquisition during the clinical trial; data federation of such data as well as morphological data derived from medical images; Currently, this application is being used to store clinical data from an osteoarthritis (OA) study. This work is submitted to the SPIE Biomedical Applications in Molecular, Structural, and Functional Imaging conference

Incorporating 3-dimensional models in online articles

Introduction The aims of this article are to introduce the capability to view and interact with 3-dimensional (3D) surface models in online publications, and to describe how to prepare surface models for such online 3D visualizations. Methods Three-dimensional image analysis methods include image acquisition, construction of surface models, registration in a common coordinate system, visualization of overlays, and quantification of changes. Cone-beam computed tomography scans were acquired as volumetric images that can be visualized as 3D projected images or used to construct polygonal meshes or surfaces of specific anatomic structures of interest. The anatomic structures of interest in the scans can be labeled with color (3D volumetric label maps), and then the scans are registered in a common coordinate system using a target region as the reference. The registered 3D volumetric label maps can be saved in.obj,.ply,.stl, or.vtk file formats and used for overlays, quantification of differences in each of the 3 planes of space, or color-coded graphic displays of 3D surface distances. Results All registered 3D surface models in this study were saved in.vtk file format and loaded in the Elsevier 3D viewer. In this study, we describe possible ways to visualize the surface models constructed from cone-beam computed tomography images using 2D and 3D figures. The 3D surface models are available in the article's online version for viewing and downloading using the reader's software of choice. These 3D graphic displays are represented in the print version as 2D snapshots. Overlays and color-coded distance maps can be displayed using the reader's software of choice, allowing graphic assessment of the location and direction of changes or morphologic differences relative to the structure of reference. The interpretation of 3D overlays and quantitative color-coded maps requires basic knowledge of 3D image analysis. Conclusions When submitting manuscripts, authors can now upload 3D models that will allow readers to interact with or download them. Such interaction with 3D models in online articles now will give readers and authors better understanding and visualization of the results

One-year assessment of surgical outcomes in Class III patients using cone beam computed tomography

The purpose of this study was to apply a novel method to evaluate surgical outcomes at 1 year after orthognathic surgery for Class III patients undergoing two different surgical protocols. Fifty patients divided equally into two groups (maxillary advancement only and combined with mandibular setback) had cone beam computed tomography (CBCT) scans taken pre-surgery, at splint removal, and at 1-year post-surgery. An automatic cranial base superimposition method was used to register, and shape correspondence was applied to assess, the overall changes between pre-surgery and splint removal (surgical changes) and between splint removal and 1-year post-surgery at the end of orthodontic treatment (post-surgical adaptations). Post-surgical maxillary adaptations were exactly the same for both groups, with 52% of the patients having changes >2 mm. Approximately half of the post-surgical changes in the maxilla for both groups were vertical. The two-jaw group showed significantly greater surgical and post-surgical changes in the ramus, chin, and most of the condylar surfaces (P < 0.05). Post-surgical adaptation on the anterior part of the chin was also more significant in the two-jaw group (P < 0.05). Regardless of the type of surgery, marked post-surgical adaptations were observed in the regions evaluated, which explain the adequate maxillary–mandibular relationship at 1-year post-surgery on average, with individual variability

Ionizing radiation and its considerations in imaging diagnosis: comparison of absorbed dose between cone beam computed tomography and multi-detector computed tomography in the head and neck

Introduction: The objective of this study was to compare the mean absorbed dose in patients undergoing head and neck examinations using two cone beam computed tomography (CBCT, Kodak and i-CAT) and one multi-detector computed tomography (MDCT). Methods: Three thermoluminescent dosimeters (TLDs), calibrated in air kerma, were positioned in 24 regions of the head and neck of a phantom simulating an average adult. The mean absorbed dose (mGy) values in these positions, for different organs and tissues, were obtained using correction factors, considering the ratio between the mass energy absorption coefficients of organ/tissue and air. Comparison between radiation doses in the most radiosensitive regions was done by calculating the ratio of these dose values, with propagated uncertainty. Results: The dose in all regions was significantly higher for MDCT when compared to CBCT. Concerning CBCT equipment, the Kodak device had a higher absorbed dose than the i-CAT for most of the regions tested. The uncertainty of the i-CAT was greater than that of the Kodak. Conclusion: Due to the considerable difference between absorbed doses, emphasizing the higher dose values obtained in MDCT, the dissemination of CBCT application in medicine is recommended, as well as further studies to broaden the criteria for use

One-year assessment of surgical outcomes in Class III patients using cone beam computed tomography

The purpose of this study was to apply a novel method to evaluate surgical outcomes at 1 year after orthognathic surgery for Class III patients undergoing two different surgical protocols. Fifty patients divided equally into two groups (maxillary advancement only and combined with mandibular setback) had cone beam computed tomography (CBCT) scans taken pre-surgery, at splint removal, and at 1-year post-surgery. An automatic cranial base superimposition method was used to register, and shape correspondence was applied to assess, the overall changes between pre-surgery and splint removal (surgical changes) and between splint removal and 1-year post-surgery at the end of orthodontic treatment (post-surgical adaptations). Post-surgical maxillary adaptations were exactly the same for both groups, with 52% of the patients having changes >2 mm. Approximately half of the post-surgical changes in the maxilla for both groups were vertical. The two-jaw group showed significantly greater surgical and post-surgical changes in the ramus, chin, and most of the condylar surfaces (P < 0.05). Post-surgical adaptation on the anterior part of the chin was also more significant in the two-jaw group (P < 0.05). Regardless of the type of surgery, marked post-surgical adaptations were observed in the regions evaluated, which explain the adequate maxillary–mandibular relationship at 1-year post-surgery on average, with individual variability