High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL.

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications.

Ozonated saline shows activity against planktonic and biofilm growing Staphylococcus aureus in vitro: a potential irrigant for infected wounds.

Infections associated with deep wounds require extensive surgical and medical care. New adjunctive treatments are required to aid in the eradication of the bacterial biofilms found on infected wounds and, in particular, any underlying hardware. Ozone has been used as a safe and efficient disinfectant in water treatment plants for many years. The purpose of this study is to investigate the anti-biofilm potential of ozonated saline against biofilms of Staphylococcus aureus, a microorganism commonly implicated in wound infections. A custom-made bacterial biofilm bioreactor was used to grow S. aureus biofilms on discs of medical grade titanium alloy. An ozone generator was connected in-line and biofilms and planktonic bacteria were exposed to ozone in saline. Cytotoxicity was assessed against primary ovine osteoblasts in the same system. In tests against planktonic S. aureus, a 99% reduction in bacterial numbers was detected within 15 minutes of exposure. S. aureus biofilms were significantly more resistant to ozone, although complete eradication of the biofilm was eventually achieved within 5 hours. Ozonated saline was not found to be cytotoxic to primary ovine osteoblasts. Ozonated saline may be suitable as an adjuvant therapy to treat patients as an instillation fluid for wound irrigation and sterilisation.

Three-dimensional navigation is more accurate than two-dimensional navigation or conventional fluoroscopy for percutaneous sacroiliac screw fixation in the dysmorphic sacrum: a randomized multicenter study.

OBJECTIVES: To evaluate the accuracy of computer-assisted sacral screw fixation compared with conventional techniques in the dysmorphic versus normal sacrum. DESIGN: Review of a previous study database. SETTING: Database of a multinational study with 9 participating trauma centers. PATIENTS: The reviewed group included 130 patients, 72 from the navigated group and 58 from the conventional group. Of these, 109 were in the nondysmorphic group and 21 in the dysmorphic group. INTERVENTION: Placement of sacroiliac (SI) screws was performed using standard fluoroscopy for the conventional group and BrainLAB navigation software with either 2-dimensional or 3-dimensional (3D) navigation for the navigated group. MAIN OUTCOME MEASUREMENTS: Accuracy of SI screw placement by 2-dimensional and 3D navigation versus conventional fluoroscopy in dysmorphic and nondysmorphic patients, as evaluated by 6 observers using postoperative computerized tomography imaging at least 1 year after initial surgery. Intraobserver agreement was also evaluated. RESULTS: There were 11.9% (13/109) of patients with misplaced screws in the nondysmorphic group and 28.6% (6/21) of patients with misplaced screws in the dysmorphic group, none of which were in the 3D navigation group. Raw agreement between the 6 observers regarding misplaced screws was 32%. However, the percent overall agreement was 69.0% (kappa = 0.38, P < 0.05). CONCLUSIONS: The use of 3D navigation to improve intraoperative imaging for accurate insertion of SI screws is magnified in the dysmorphic proximal sacral segment. We recommend the use of 3D navigation, where available, for insertion of SI screws in patients with normal and dysmorphic proximal sacral segments. LEVEL OF EVIDENCE: Therapeutic level I.

Precise screw positioning at the mandibular angle: computer assisted versus template coded.

BACKGROUND: Buried intraoral devices for distraction osteogenesis in mandibular deformities have numerous advantages, but success depends on the precise positioning of these devices. Although most centers nowadays use template-guided techniques for precise positioning, computer navigation has been described as a promising technique. Surgical navigation during device placement could become a viable method because it affords certainty in defining a device position. METHODS: A clinical situation was simulated by means of mounting a mandible model inside a phantom head. Screws were positioned according to a preoperative plan through transoral and transbuccal approaches, with both template-coded and freehand computer navigation. RESULTS: With template-coded navigation, the medium deviation from the planned position was 0.63 mm (range, 0.00-1.24 mm). With commercial freehand surgical computer navigation, the medium deviation was significantly higher at 0.98 mm (range, 0.00-3.13 mm). CONCLUSIONS: Computer-assisted surgery can provide a high level of accuracy in the region of the mandibular angle where precision is crucial for buried intraoral distraction devices. However, template-coded guidance does provide a significantly higher level of accuracy and therefore represents the gold standard.

Mechanical stability in a human radius fracture treated with a novel tissue-engineered bone substitute: a non-invasive, longitudinal assessment using high-resolution pQCT in combination with finite element analysis.

The clinical gold standard in orthopaedics for treating fractures with large bone defects is still the use of autologous, cancellous bone autografts. While this material provides a strong healing response, the use of autografts is often associated with additional morbidity. Therefore, there is a demand for off-the-shelf biomaterials that perform similar to autografts. Biomechanical assessment of such a biomaterial in vivo has so far been limited. Recently, the development of high-resolution peripheral quantitative computed tomography (HR-pQCT) has made it possible to measure bone structure in humans in great detail. Finite element analysis (FEA) has been used to accurately estimate bone mechanical function from three-dimensional CT images. The aim of this study was therefore to determine the feasibility of these two methods in combination, to quantify bone healing in a clinical case with a fracture at the distal radius which was treated with a new bone graft substitute. Validation was sought through a conceptional ovine model. The bones were scanned using HR-pQCT and subsequently biomechanically tested. FEA-derived stiffness was validated relative to the experimental data. The developed processing methods were then adapted and applied to in vivo follow-up data of the patient. Our analyses indicated an 18% increase of bone stiffness within 2 months. To our knowledge, this was the first time that microstructural finite element analyses have been performed on bone-implant constructs in a clinical setting. From this clinical case study, we conclude that HR-pQCT-based micro-finite element analyses show high potential to quantify bone healing in patients.

Misjudgments at the mandibular angle: freehand versus computer-assisted screw positioning.

BACKGROUND: Distraction osteogenesis is a well known and frequently described technique in mandibular deformities. Buried intraoral devices have numerous advantages, but success hinges on precise positioning of the implants. Although computer navigation has repeatedly been described for craniofacial applications, research on navigating the mandibular region is scarce. Navigating the device placement for a mandibular distractor could become a viable method for distraction osteogenesis because of the possibility of certainty in achieving a defined device position. MATERIALS AND METHODS: A clinical situation was simulated by a mandible model mounted inside a phantom head. The screws were positioned according to a virtual plan through transoral and transbuccal approaches, with and without navigation. RESULTS: Without navigation, the mean deviation from the planned position was 4.9 mm (range, 0.9-10.7 mm), with a clear tendency to position the screws in the easy-to-access regions. With navigation, the mean deviation was significantly lower at 1.5 mm (range, 0.1-3.4 mm). CONCLUSIONS: Computer-assisted surgery can provide a high level of accuracy in the region of the mandibular angle, where precision is crucial for buried intraoral distraction devices.

Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data.

Knowledge discovery from large and complex scientific data is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the growing number of data dimensions and data objects presents tremendous challenges for effective data analysis and data exploration methods and tools. The combination and close integration of methods from scientific visualization, information visualization, automated data analysis, and other enabling technologies -such as efficient data management- supports knowledge discovery from multi-dimensional scientific data. This paper surveys two distinct applications in developmental biology and accelerator physics, illustrating the effectiveness of the described approach.

How comparable is so-called standard fracture fixation with an identical implant? A prospective experience with the antegrade femoral nail in South Africa and Europe.

BACKGROUND: The utilisation and consequences of standardised operative procedures may importantly differ between different healthcare systems. This is the first investigation comparing the treatment and outcome of femoral shaft fractures stabilised with an identical implant between trauma centres in 2 continents (Europe, EU and South Africa, SA). METHODS: Following standardised introduction of the technique, the prospective, observational multicentre study enrolled 175 patients who underwent intramedullary fracture fixation using the antegrade femoral nail (AFN) for femoral shaft fractures. Eleven EU hospitals recruited 86 patients and 1 SA centre 89 patients in the study period. Comparison of epidemiologic data, operative characteristics as well as subjective (e.g., pain, SF-36) and objective (e.g., X-ray, range of motion [ROM]) 3-month and 1-year outcomes were performed (p<0.05). RESULTS: Compared to EU centres, several significant differences were observed in SA: (1) on average, patients operated on were younger, had less concomitant diseases and had more severe open fractures; (2) operative stabilisation was more often undertaken by young, unsupervised residents, with shorter operating and intraoperative fluoroscopy times; (3) mean hospital stay was shorter, with less recorded complications, but a higher loss to follow-up rate. Non- or malunion rates and subjective outcomes were similar for both groups, with the physical component of the SF-36 at the 1-year follow-up not fully restoring to baseline values. CONCLUSIONS: Our investigation demonstrates the importance of several major differences between 2 different regions of the world in the treatment of femoral shaft fractures, despite involving only high level trauma centres and using an identical implant. The intercontinental comparison of results from clinical studies should be interpreted very carefully considering the heterogeneity of populations and clinical settings.

Patient-specific three-dimensional composite bone models for teaching and operation planning.

BACKGROUND: Orthopedic trauma care relies on two-dimensional radiograms both before and during the operation. Understanding the three-dimensional nature of complex fractures on plain radiograms is challenging. Modern fluoroscopes can acquire three-dimensional volume datasets even during an operation, but the device limitations constrain the acquired volume to a cube of only 12-cm edge. However, viewing the surrounding intact structures is important to comprehend the fracture in its context. We suggest merging a fluoroscope's volume scan into a generic bone model to form a composite full-length 3D bone model. METHODS: Materials consisted of one cadaver bone and 20 three-dimensional surface models of human femora. Radiograms and computed tomography scans were taken before and after applying a controlled fracture to the bone. A 3D scan of the fracture was acquired using a mobile fluoroscope (Siemens Siremobil). The fracture was fitted into the generic bone models by rigid registration using a modified least-squares algorithm. Registration precision was determined and a clinical appraisal of the composite models obtained. RESULTS: Twenty composite bone models were generated. Average registration precision was 2.0 mm (range 1.6 to 2.6). Average processing time on a laptop computer was 35 s (range 20 to 55). Comparing synthesized radiograms with the actual radiograms of the fractured bone yielded clinically satisfactory results. CONCLUSION: A three-dimensional full-length representation of a fractured bone can reliably be synthesized from a short scan of the patient's fracture and a generic bone model. This patient-specific model can subsequently be used for teaching, surgical operation planning, and intraoperative visualization purposes.

Comparison of different registration methods for surgical navigation in cranio-maxillofacial surgery.

BACKGROUND: Surgical navigation requires registration of the pre-operative image dataset with the patient in the operation theatre. Various marker and marker-free registration techniques are available, each bearing an individual level of precision and clinical practicability. In this study the precision of four different registration methods in a maxillofacial surgical setting is analyzed. MATERIALS AND METHODS: A synthetic full size human skull model was registered with its computer tomography-dataset using (a) a dentally mounted occlusal splint, (b) the laser surface scanning, (c) five facial bone implants and (d) a combination of dental splint and two orbital bone implants. The target registration error was computed for 170 landmarks spread over the entire viscero- and neurocranium in 10 repeats using the VectorVision2 (BrainLAB AG, Heimstetten, Germany) navigation system. Statistical and graphical analyses were performed by anatomical region. RESULTS: An average precision of 1mm was found for the periorbital region irrespective of registration method (range 0.6-1.1mm). Beyond the mid-face, precision linearly decreases with the distance from the reference markers. The combination of splint with two orbital bone markers significantly improved precision from 1.3 to 0.8mm (p<0.001) on the viscerocranium and 2.3-1.2mm (p<0.001) on the neurocranium. CONCLUSIONS: An occlusal splint alone yields poor precision for navigation beyond the mid-face. The precision can be increased by combining an occlusal splint with just two bone implants inserted percutaneously on the lateral orbital rim of each side.

Navigating the fluoroscope's C-arm back into position: an accurate and practicable solution to cut radiation and optimize intraoperative workflow.

OBJECTIVES: During complex image-guided orthopedic trauma procedures, repetitive fluoroscopic scout imaging is performed. A number of preparatory positioning images often must be taken to reproduce a comparable projection. These scout images have no intrinsic clinical relevance but nevertheless expose the patient and the surgical team to considerable radiation, which could be avoided. This study presents and validates a method to decrease intraoperative radiation. METHODS: Precision, time requirements, and number of scout images for repositioning the fluoroscope, with and without navigation aid, were recorded on 20 test-rig and 3 phantom setups. A commercially available image-guided surgical navigation system (Vector Vision, BrainLAB), originally designed for instrument navigation, was employed to register and retrieve the C-arm positions. A newly developed software computed the necessary moves to reposition the C-arm on an intuitive visual display. RESULTS: Retrieving a given C-arm position with the conventional non-navigated technique required an average of 7 scout images (range, 3 to 12 images). In contrast, navigation-assisted repositioning did not necessitate a single scout image. Deviations from the original projection were minimal for both navigated (0.9 degrees, 95% CI 0.8 to 1.1 degrees) and non-navigated repositioning (0.8 degrees, 95% CI 0.7 to 0.9 degrees). Average positioning times were comparable when navigating the C-arm (46 seconds, 95% CI 41 to 51 seconds) and in scout image-based positioning (49 seconds, 95% CI 44 to 53 seconds). CONCLUSIONS: Navigated C-arm positioning avoids multiple scout images and yields sufficient precision for clinical deployment. Radiation exposure can be reduced considerably by a combination of instrument navigation and navigated C-arm positioning.

A CT database for research, development and education: concept and potential.

Both in radiology and in surgery, numerous applications are emerging that enable 3D visualization of data from various imaging modalities. In clinical practice, the patient's images are analyzed on work stations in the Radiology Department. For specific preclinical and educational applications, however, data from single patients are insufficient. Instead, similar scans from a number of individuals within a collective must be compiled. The definition of standardized acquisition procedures and archiving formats are prerequisite for subsequent analysis of multiple data sets. Focusing on bone morphology, we describe our concept of a computer database of 3D human bone models obtained from computed tomography (CT) scans. We further discuss and illustrate deployment areas ranging from prosthesis design, over virtual operation simulation up to 3D anatomy atlases. The database of 3D bone models described in this work, created and maintained by the AO Development Institute, may be accessible to research institutes on request.

Internal fixation of unstable proximal humerus fractures with an anatomically preshaped interlocking plate: a clinical and radiologic evaluation.

BACKGROUND: We evaluated the outcome after internal fixation of unstable or displaced proximal humerus fractures with a new fixed-angle implant. METHODS: Prospective consecutive study with a 1-year clinical follow-up in 119 of 137 patients (87%; mean 68 +/- 15 years; 31 two-, 47 three-, and 41 four-part fractures). RESULTS: One year postoperatively, the range of motion of the injured side demonstrated on average four-fifths of the function of the contralateral side. Ninety-five percentage of patients (n = 114) could dress themselves independently with no or only slight restriction. The mean disabilities of the arm, shoulder, and hand score was 21 (range, 0-62). The absolute and relative Constant score significantly (p < 0.001) improved from 56 +/- 18 (75% +/- 21%) at 6 months postoperatively to up to 65 +/- 18 (82% +/- 18%) at 12 months postoperatively. The initial fracture configuration did not have a significant influence on clinical outcome or complications. Twenty-six patients (22%) underwent a reintervention because of a clinical problem or subjective complaint, which led to total or relevant relief of problems in 23 patients (87%). Radiologic follow-up revealed a significant correction of the mean fragment angles (p < 0.001) postoperatively compared with initial postcrash radiographs. The precision of intraoperative reduction had a significant impact on the patient's disabilities of the arm, shoulder, and hand scoring (p = 0.02). A comparison of the last evaluable radiographs with the intraoperative intensifier images revealed a mean loss of reduction over time of

Unexpected high complication rate following internal fixation of unstable proximal humerus fractures with an angled blade plate.

OBJECTIVES: The increasing number of fractures of the proximal humerus, especially in the elderly, carries with it the unsolved problem of the optimal treatment for the displaced or unstable fractures. The authors' goal was to analyze whether fixation with a bent valgus angled blade plate could improve the outcomes reported in the literature to date. DESIGN: Prospective clinical study. SETTING: Urban level 1 university trauma center. PATIENTS: Over a 27-month period, 42 consecutive patients were treated for an unstable or displaced proximal humerus fracture. INTERVENTION: Open reduction and internal fixation with a 90-degree cannulated angled blade plate prebent to 110 degrees. MAIN OUTCOME MEASUREMENTS: Active follow-up for 1 year with assessment of objective and subjective functional results (ie, motion; strength; Constant score; Disabilities of the Arm, Shoulder, and Hand (DASH) score; and visual analog scale (VAS)) and radiographic assessment (reduction, alignment, necrosis, and nonunion). RESULTS: Follow-up was completed for 86% of the patients, who achieved a mean Constant score of 66 points (82% of the contralateral side) with a mean forward flexion of 125 degrees and an average strength of 72% of the contralateral side. Low disability (mean DASH score 22) and pain values (mean VAS 2) were demonstrated after this type of stabilization. The overall complication rate was 33% (12/36), with protrusion of the blade into the glenohumeral articulation as the most frequent problem (8/36, 22%). The negative impact of an adverse event on subjective and objective outcomes was only significant for forward flexion (P = 0.02). Neither clinical outcome nor complication rate was different when compared to patients with regard to fracture type (3 versus 4 parts) or age (younger or older than 70 years). CONCLUSIONS: Fixation of displaced proximal humeral fractures with an angled blade plate provided sufficient stability. Blade perforation into the humeral joint occurred in every fourth patient and was found to be the major reason for a high complication rate. In view of this major problem, the technique described here cannot be recommended, even though the absence of nonunions in our series seems to support the low invasiveness of this surgical approach.

Modality-based navigation.

Modality-based navigation (MBN) means the interactive tracking of instruments in a co-ordinate system defined by an imaging modality, eg, CT, MR, or a fluoroscope. During the registration process, a transformation matrix between the two co-ordinate systems of the digitizer and imaging modality is calculated. Navigation can start immediately after collection of the images without an intraprocedural registration process. Since the imaging modality belongs to the OR or the intervention suite, image update can be performed at any time. Following a step-by-step procedure with navigation and image update in a reasonable sequence, the risk for a virtual-real mismatch is minimized. For CT-MBN, we obtained a freehand absolute positioning accuracy of 1.9+/-1.1 mm in vitro. The in vivo freehand absolute positioning accuracy in pelvic fracture fixation was determined to be 3.1 mm (unpublished data). From our point of view, modality-based navigation is an efficient and safe alternative tool for computer aided interventions.

Which navigation when?

If a surgeon is considering purchasing a navigation system, several factors have to be evaluated including, the planned applications, the equipment already installed, and the specific knowledge of the surgeon. For use in traumatology, fluoroscopy and more specifically 3-D fluoro-based computer guidance is preferable. These technologies are based on intraoperative acquired arbitrary images in contrast to CT-based techniques, which refer to preoperative acquired images that represent a so called "cannel reality". However, image quality has to be considered as fluoro-picture quality depending on the anatomical area (eg long bones, spine, pelvis) and body mass index. CT-based navigation provides better image quality and accuracy but is not able to visualize reduction processes. Therefore personal experience in courses or by on-site teaching is recommended prior taking the decision.

Clinical applications--pelvis.

Navigation procedures based on CT data were introduced into spinal surgery in 1994. Since then, the method has been used in other areas such as joint replacement, reconstructive surgery, and tumor surgery because of its high precision and reduced radiation exposure. The original CT-based spine module can be adjusted for pelvic surgery with the prerequisite that the positioning of the fragments is identical in CT and in the OR; otherwise a new dataset has to be acquired. Our experiences with CT-based navigation in pelvic surgery are explained on five percutaneous screw fixations and three tumor resections, including description of the technique. For modality-based navigation, the navigated procedure is performed in the CT suite with the advantage of immediate CT control of reduction quality and screw positioning. The technique is explained and illustrated on two cases. Fluoroscopy-based navigation has been used in trauma surgery since the late nineties. Since then, the method has been wide spread in the field of joint replacement and reconstructive surgery. Between June 2000 and December 2002, we performed 36 percutaneous screw fixations in the pelvis with postoperative x-ray and CT control. 35 of the 36 screws were placed correctly. In one screw, an anterior cortex perforation of the sacrum was seen in the CT without any neurological consequences. The Iso C 3-D fluoroscope has recently been approved for pelvic surgery. With the ability to reconstruct images, visualization of the acetabulum and the posterior pelvic ring, there is marked an improvement compare to conventional 2-D fluoroscopy. Thus, the field for navigation is also enhanced. Based on our clinical experiences, the indications for navigated techniques in pelvic and acetabular surgery are defined and illustrated.

The MEPUC concept adapts the C-arm fluoroscope to image-guided surgery.

Image-guided surgery requires surgeons to be able to manipulate the imaging modality themselves and without delay. Intraoperative fluoroscopic imaging does not meet this requirement as the C-arm fluoroscope cannot be operated or positioned by the surgeons themselves. The Motorized Exact Positioning Unit for C-arm (MEPUC) concept aims to optimize the workflow of positioning the C-arm fluoroscope. The hardware component of the MEPUC equips the fluoroscope with electric stepping motors. The software component allows the surgeon to control the fluoroscope's movements. The study presented here showed that translational movements within the x-y plane are most frequently performed when positioning the C-arm fluoroscope. Furthermore, reproducing a former projection was found to be a frequent task during image-guided procedures. In our opinion, the MEPUC concept adapts the fluoroscope to image-guided surgery. The most important improvement being definition of a bidirectional data exchange between the surgeon and the C-arm fluoroscope: positioning data from the surgeon to the C-arm fluoroscope and-subsequently-image information from C-arm fluoroscope to the surgeon.