A palaeobiologist's guide to 'virtual' micro-CT preparation

This paper provides a brief but comprehensive guide to creating, preparing and dissecting a 'virtual' fossil, using a worked example to demonstrate some standard data processing techniques. Computed tomography (CT) is a 3D imaging modality for producing 'virtual' models of an object on a computer. In the last decade, CT technology has greatly improved, allowing bigger and denser objects to be scanned increasingly rapidly. The technique has now reached a stage where systems can facilitate large-scale, non-destructive comparative studies of extinct fossils and their living relatives. Consequently the main limiting factor in CT-based analyses is no longer scanning, but the hurdles of data processing (see disclaimer). The latter comprises the techniques required to convert a 3D CT volume (stack of digital slices) into a virtual image of the fossil that can be prepared (separated) from the matrix and 'dissected' into its anatomical parts. This technique can be applied to specimens or part of specimens embedded in the rock matrix that until now have been otherwise impossible to visualise. This paper presents a suggested workflow explaining the steps required, using as example a fossil tooth of Sphenacanthus hybodoides (Egerton), a shark from the Late Carboniferous of England. The original NHMUK copyrighted CT slice stack can be downloaded for practice of the described techniques, which include segmentation, rendering, movie animation, stereo-anaglyphy, data storage and dissemination. Fragile, rare specimens and type materials in university and museum collections can therefore be virtually processed for a variety of purposes, including virtual loans, website illustrations, publications and digital collections. Micro-CT and other 3D imaging techniques are increasingly utilized to facilitate data sharing among scientists and on education and outreach projects. Hence there is the potential to usher in a new era of global scientific collaboration and public communication using specimens in museum collections.

Quantification of Orbital Apex Crowding for Screening of Dysthyroid Optic Neuropathy Using Multidetector CT

BACKGROUND AND PURPOSE: DON, a serious complication of GO, is frequently difficult to diagnose clinically in its early stages because of confounding signs and symptoms of congestive orbitopathy. We evaluated the ability of square area measurements of orbital apex crowding, calculated with MDCT, to detect DON. MATERIALS AND METHODS: Fifty-six patients with GO were studied prospectively with complete neuro-ophthalmologic examination and MDCT scanning. Square measurements were taken from coronal sections 12 mm, 18 mm, and 24 mm from the interzygomatic line. The ratio between the extraocular muscle area and the orbital bone area was used as a Cl. Intracranial fat prolapse through the superior orbital fissure was recorded as present or absent. Severity of optic nerve crowding was also subjectively graded on corona! images. Orbits were divided into 2 groups (with or without clinical evidence of DON) and compared. RESULTS: Ninety-five orbits (36 with and 59 without DON) were studied. The CIs at all 3 levels and the subjective crowding score were significantly greater in orbits with DON (P<.001). No significant difference was observed regarding intracranial fat prolapse (P=.105). The area under the ROC curves was 0.91, 0.93, and 0.87 for CIs at 12, 18, and 24 mm, respectively. The best performance was at 18 mm, where a cutoff value of 57.5% corresponded to 91.7% sensitivity, 89.8% specificity, and an odds ratio of 97.2 for detecting DON. A significant correlation (P<.001) between the CIs and VF defects was observed. CONCLUSIONS: Orbital Cls based on area measurements were found to predict DON more reliably than subjective grading of orbital crowding or intracranial fat prolapse.

Predicting dysthyroid optic neuropathy using computed tomography volumetric analyses of orbital structures

OBJECTIVE: To evaluate the ability of orbital apex crowding volume measurements calculated with multidetector-computed tomography to detect dysthyroid optic neuropathy. METHODS: Ninety-three patients with Graves' orbitopathy were studied prospectively. All of the patients underwent a complete neuro-ophthalmic examination and computed tomography scanning. Volumetric measurements were calculated from axial and coronal contiguous sections using a dedicated workstation. Orbital fat and muscle volume were estimated on the basis of their attenuation values (in Hounsfield units) using measurements from the anterior orbital rim to the optic foramen. Two indexes of orbital muscle crowding were calculated: i) the volumetric crowding index, which is the ratio between soft tissue (mainly extraocular muscles) and orbital fat volume and is based on axial scans of the entire orbit; and ii) the volumetric orbital apex crowding index, which is the ratio between the extraocular muscles and orbital fat volume and is based on coronal scans of the orbital apex. Two groups of orbits (with and without dysthyroid optic neuropathy) were compared. RESULTS: One hundred and two orbits of 61 patients with Graves' orbitopathy met the inclusion criteria and were analyzed. Forty-one orbits were diagnosed with Graves' orbitopathy, and 61 orbits did not have optic neuropathy. The two groups of orbits differed significantly with regard to both of the volumetric indexes (p<0.001). Although both indexes had good discrimination ability, the volumetric orbital apex crowding index yielded the best results with 92% sensitivity, 86% specificity, 81%/94% positive/negative predictive value and 88% accuracy at a cutoff of 4.14. CONCLUSION: This study found that the orbital volumetric crowding index was a more effective predictor of dysthyroid optic neuropathy than previously described computed tomography indexes were.

Evaluation of comprehensive two-dimensional gas chromatography coupled to rapid scanning quadrupole mass spectrometry for quantitative analysis

Comprehensive two-dimensional gas chromatography (GC x GC) is a powerful technique that provides excellent separation and identification of analytes in highly complex samples with considerable increase in GC peak capacities. However, since second dimension analyses are very fast, detectors with a rapid acquisition rate are required. Over the last years, quite a number of studies have discussed the potential and limitations of the combination GC x GC with a variety of quadrupole mass spectrometers. The present research focuses on the evaluation of qMS effectiveness at a 10,000-amu/s scan speed and 20-Hz scan frequency for the identification (full scan mode acquisition-TIC) and quantification (extracted ion chromatogram) of target pesticide residues in tomato samples. The following MS parameters have been evaluated: number of data points per peak, mass spectrum quality, peak skewing, and sensitivity. The validated proposed GC x GC/qMS method presented satisfactory results in terms of repeatability (coefficient of variation lower than 15%), accuracy (84-117%), and linearity (ranging from 25 to 500 ng/g), while significant enhancement in sensitivity was observed (a factor of around 10) under scan conditions. (C) 2012 Elsevier B.V. All rights reserved.

Decompressive craniectomy and cerebral blood flow regulation in head injured patients: A case studied by perfusion CT

Previous studies have reported increased cerebral blood flow (CBF) velocity after decompressive craniectomy in traumatic brain injury (TBI) patients. A 27-year-old man presented with clinical and tomographic signs of cerebral herniation secondary to TBI. Prior to decompressive craniectomy, hemodynamic study by perfusion computed tomography (CT) indicated diffuse cerebral hyperperfusion. Following surgical decompression, the patient recovered neurologically and perfusion CT disclosed a decrease in the intensity of cerebral perfusion. The patient's blood pressure levels were similar at both pre- and postoperative perfusion CT examinations. This finding provides indirect evidence that decompressive craniectomy may improve mechanisms of CBF regulation in TBI, providing pathophysiological insights in the cerebral hemodynamics of TBI patients. This is the first report analyzing the hemodynamic changes through perfusion CT (PCT) in a patient with decompressive craniotomy due to TBI. (C) 2012 Elsevier Masson SAS. All rights reserved.

Probing the Enamel Topography After Acid Erosion by Scanning Electrochemical Microscopy

In this work, we present an investigation on the thickness of the eroded enamel layer in tooth samples after exposure to citric and hydrochloric acid by using Scanning Electrochemical Microscopy (SECM). Approaching curves with typical negative feedback behavior were obtained in enamel samples for evaluation of topographic changes. In a control experiment, SECM images showed no significant difference in the current monitored during the scan, implying that enamel demineralization did not occur in mineral water medium. Topographic SECM images obtained after contact with citric and hydrochloric acid for different periods of time showed a significant increase in the current relative to a previously protected surface, indicating the structural loss of enamel. The thickness of the enamel layer eroded after contact with hydrochloric acid was significantly higher when compared to the one obtained with citric acid. Hence, our results showed that the enamel acid erosion is a relatively fast process, which is strongly dependent on parameters such as pH, time, acid strength and acid concentration.

In vitro effects of Er,Cr:YSGG laser on dentine hypersensitivity. Dentine permeability and scanning electron microscopy analysis

The aim of the present study was to determine clinical parameters for the use of Er,Cr:YSGG laser in the treatment of dentine hypersensitivity. Two antagonist areas were determined as control and experimental areas for irradiation in 90 premolar roots. Each surface was conditioned with 24% EDTA (sub-group 1) and 35% phosphoric acid (sub-group 2) and irradiated with the following settings: 1) Er:YAG, 60 mJ, 2 Hz, defocused; groups 2 to 9: irradiation with Er,Cr:YSGG laser, 20 Hz, Z6 tip, 0% of air and water: 2) Er,Cr:YSGG 0.25 W; 3) 0.5 W; 4) 0.75 W; 5) 1.0 W; 6) 1.25 W, 7) 1.50 W, 8) 2 W; 9) 2 W. After irradiation, samples were immersed in methylene blue solution and included in epoxy resin to obtain longitudinal cuts. The images were digitalized and analyzed by computer software. Although the samples irradiated with Er:YAG laser showed less microleakage, sub-group 1 showed differences between the groups, differing statistically from groups 3, 6, and 9. The results of sub-group 2 showed that the mean values of Er:YAG samples showed a negative trend, however, no differences were detected between the groups. For scanning electron microscopy analysis, dentine squares were obtained and prepared to evaluate the superficial morphology. Partial closure of dentinal tubules was observed after irradiation with Er:YAG and Er,Cr:YSGG laser in the 0.25 and 0.50 W protocols. As the energy densities rose, open dentinal tubules, carbonization and cracks were observed. It can be concluded that none of the parameters were capable of eliminating microleakage, however, clinical studies with Er:YAG and Er,Cr:YSGG lasers should be conducted with the lowest protocols in order to determine the most satisfactory setting for dentine hypersensitivity.

Redescription of the larva of Amblyomma oblongoguttatum Koch, 1844 (Acari: Ixodidae) by light and scanning electron microscopy

The larval stage of Amblyomma oblongoguttatum Koch is redescribed using optical and scanning electron microscopy. Unfed larvae were obtained from a colony of A. oblongoguttatum originated from engorged females collected on domestic pigs from Monte Negro municipally (10 degrees 29'S, 63 degrees 32'W), State of Rondonia, Western Amazon, Brazil. Several characters are presented including the chaetotaxy of the idiosoma, palpi and Haller's organ, as well as morphological features of the idiosoma, gnathosoma and legs. In addition, the porotaxy (topographical and numerical patterns of integumentary structures) were presented by using a new nomenclature recently proposed. The chaetotaxy of the larvae of A. oblongoguttatum, in general, is similar to other Neotropical Amblyomma species. Three types of integumentary structures were observed on the idiosoma: lyrifissures, small glands, and large wax glands. Topographic and numerical patterns of the integumentary structures consisted of 5 pairs of large wax glands (1 dorsal/4 ventral), 24 pairs of lyrifissures (11 dorsal/13 ventral), and 49 pairs of small glands (28 dorsal/21 ventral). These topographic and numerical patterns found for A. oblongoguttatum show only minor differences when compared with patterns of other Amblyomma larvae, however, a few key features can be used for identification of these species.

Use of Large-volume Cone-Beam Computed Tomography in Identification and Localization of Horizontal Root Fracture in the Presence and Absence of Intracanal Metallic Post

Introduction: The objective of the study was to evaluate the ability of large-volume cone-beam computed tomography (CBCT) to detect horizontal root fracture and to test the influence of a metallic post. Methods: Through the examination of 40 teeth by large-volume CBCT (20-cm height and 15-cm diameter cylinder) at 0.2-mm voxel resolution, 2 observers analyzed the samples for the presence and localization of horizontal root fracture. Results: The values of accuracy in the groups that had no metallic post ranged from 33%-68%, whereas for the samples with the metallic post, values showed a wide variation (38%-83%). Intraobserver agreement showed no statistically significant difference between the groups with/without metallic post; both ranged from very weak to weak (kappa, 0.09-0.369). Conclusions: The low accuracy and low intraobserver and interobserver agreement reflect the difficulty in performing an adequate diagnosis of horizontal root fractures through a large-volume CBCT by using a small voxel reconstruction. (J Endod 2012;38:856-859)

Multidetector CT Evaluation of the Postoperative Pancreas

Several pancreatic diseases may require surgical treatment, with most of these procedures classified as resection or drainage. Resection procedures, which are usually performed to remove pancreatic tumors, include pancreatoduodenectomy, central pancreatectomy, distal pancreatectomy, and total pancreatectomy. Drainage procedures are usually performed to treat chronic pancreatitis after the failure of medical therapy and include the Puestow and Frey procedures. The type of surgery depends not only on the patient's symptoms and the location of the disease, but also on the expertise of the surgeon. Radiologists should become familiar with these surgical procedures to better understand postoperative changes in anatomic findings. Multidetector computed tomography is the modality of choice for identifying normal findings after surgery, postoperative complications, and tumor recurrence in patients who have undergone pancreatic surgery. (C)RSNA, 2012 . radiographics.rsna.org

Quantitative coronary arterial stenosis assessment by multidetector CT and invasive coronary angiography for identifying patients with myocardial perfusion abnormalities

Semi-quantitative stenosis assessment by coronary CT angiography only modestly predicts stress-induced myocardial perfusion abnormalities. The performance of quantitative CT angiography (QCTA) for identifying patients with myocardial perfusion defects remains unclear. CorE-64 is a multicenter, international study to assess the accuracy of 64-slice QCTA for detecting a parts per thousand yen50% coronary arterial stenoses by quantitative coronary angiography (QCA). Patients referred for cardiac catheterization with suspected or known coronary artery disease were enrolled. Area under the receiver-operating-characteristic curve (AUC) was used to evaluate the diagnostic accuracy of the most severe coronary artery stenosis in a subset of 63 patients assessed by QCTA and QCA for detecting myocardial perfusion abnormalities on exercise or pharmacologic stress SPECT. Diagnostic accuracy of QCTA for identifying patients with myocardial perfusion abnormalities by SPECT revealed an AUC of 0.71, compared to 0.72 by QCA (P = .75). AUC did not improve after excluding studies with fixed myocardial perfusion abnormalities and total coronary arterial occlusions. Optimal stenosis threshold for QCTA was 43% yielding a sensitivity of 0.81 and specificity of 0.50, respectively, compared to 0.75 and 0.69 by QCA at a threshold of 59%. Sensitivity and specificity of QCTA to identify patients with both obstructive lesions and myocardial perfusion defects were 0.94 and 0.77, respectively. Coronary artery stenosis assessment by QCTA or QCA only modestly predicts the presence and the absence of myocardial perfusion abnormalities by SPECT. Confounding variables affecting the relationship between coronary anatomy and myocardial perfusion likely account for some of the observed discrepancies between coronary angiography and SPECT results.

Enzyme replacement prevents enamel defects in hypophosphatasia mice

Hypophosphatasia (HPP) is the inborn error of metabolism characterized by deficiency of alkaline phosphatase activity, leading to rickets or osteomalacia and to dental defects. HPP occurs from loss-of-function mutations within the gene that encodes the tissue-nonspecific isozyme of alkaline phosphatase (TNAP). TNAP knockout (Alpl-/-, aka Akp2-/-) mice closely phenocopy infantile HPP, including the rickets, vitamin B6-responsive seizures, improper dentin mineralization, and lack of acellular cementum. Here, we report that lack of TNAP in Alpl-/- mice also causes severe enamel defects, which are preventable by enzyme replacement with mineral-targeted TNAP (ENB-0040). Immunohistochemistry was used to map the spatiotemporal expression of TNAP in the tissues of the developing enamel organ of healthy mouse molars and incisors. We found strong, stage-specific expression of TNAP in ameloblasts. In the Alpl-/- mice, histological, mu CT, and scanning electron microscopy analysis showed reduced mineralization and disrupted organization of the rods and inter-rod structures in enamel of both the molars and incisors. All of these abnormalities were prevented in mice receiving from birth daily subcutaneous injections of mineral-targeting, human TNAP at 8.2?mg/kg/day for up to 44 days. These data reveal an important role for TNAP in enamel mineralization and demonstrate the efficacy of mineral-targeted TNAP to prevent enamel defects in HPP. (C) 2012 American Society for Bone and Mineral Research.

Assessment of myocardial infarction by CT angiography and cardiovascular MRI in patients with cocaine-associated chest pain: a pilot study

Objectives: Cocaine is a commonly used illicit drug that leads to the most emergency department (ED) visits. Chest pain is the most common presentation, reported in 40% of patients. Our aim was to evaluate the incidence of previous myocardial infarction among young cocaine users (18-40 years) with cocaine-associated chest pain by the assessment of myocardial fibrosis by cardiovascular MRI. Second, we also intended to evaluate the coronary tree by CT angiography (CTA). Methods: 24 cocaine users (22 males) who frequently complained about cocaine-associated chest pain underwent CTA and cardiovascular MRI. Mean age of patients was 29.7 years and most of them (79%) had frequently used inhalatory cocaine. Results: The calcium score turned out to be positive in only one patient (Agatston=54). Among the coronary segments evaluated, only one patient had calcified plaques at the anterior descending coronary artery (proximal and medium segments). Assessment of regional ventricular function by the evaluation of 17 segments was normal in all patients. None of the patients showed myocardial delayed enhancement, indicative of myocardial fibrosis. CTA therefore confirmed the low cardiovascular risk of these patients, since most of them (96%) had no atherosclerosis detected by this examination. Only one patient (4%) had coronary atherosclerosis detected, without significant coronary stenosis. Conclusion: Cardiovascular MR did not detect the presence of delayed enhancement indicative of myocardial fibrosis among young cocaine users with low cardiovascular risk who had complained of cocaine-associated chest pain.

Qualitative study of young, adult, and aged wistar rats temporomandibular synovial membrane employing light, scanning, and transmission electron microscopy

The aim of this study was to analyze the rat temporomandibular joint (TMJ) synovial membrane at different ages using light, scanning, and transmission electron microscopy. Under light microscopic analysis, the TMJ structures were observed such as condyle, capsule, disk, the synovial membrane collagen type, and cells distribution. In the scanning electron microscopy, the synovial membrane surface exhibited a smooth aspect in young animals and there was an increase with ageing in the number of folds. The transmission electron microscopic analysis showed more synoviocytes in the synovial layer in the young group and still a great number of vesicles and cisterns dilation of rough endoplasmic reticulum in the aged group. In the three groups, a dense layer of collagen fibers in the synovial layer and cytoplasmic extensions were clearly seen. It was possible to conclude that synovial membrane structures in aged group showed alterations contributing to the decrease in joint lubrication and in the sliding between disk and joint surfaces. These characteristic will reflect in biomechanics of chewing, and may cause the TMJ disorders, currently observed in clinical processes. Microsc. Res. Tech. (c) 2012 Wiley Periodicals, Inc.

Correlation between carotid bifurcation calcium burden on non-enhanced CT and percentage stenosis, as confirmed by digital subtraction angiography

Objectives: Previous evidence supports a direct relationship between the calcium burden (volume) on post-contrast CT with the percent internal carotid artery (ICA) stenosis at the carotid bifurcation. We sought to further investigate this relationship by comparing non-enhanced CT (NECT) and digital subtraction angiography (DSA). Methods: 50 patients (aged 41-82 years) were retrospectively identified who had undergone cervical NECT and DSA. A 64-multidetector array CT (MDCT) scanner was utilised and the images reviewed using preset window widths/levels (30/300) optimised to calcium, with the volumes measured via three-dimensional reconstructive software. Stenosis measurements were performed on DSA and luminal diameter stenoses >40% were considered "significant". Volume thresholds of 0.01, 0.03, 0.06, 0.09 and 0.12 cm(3) were utilised and Pearson's correlation coefficient (r) was calculated to correlate the calcium volume with percent stenosis. Results: Of 100 carotid bifurcations, 88 were available and of these 7 were significantly stenotic. The NECT calcium volume moderately correlated with percent stenosis on DSA r=0.53 (p<0.01). A moderate-strong correlation was found between the square root of calcium volume on NECT with percent stenosis on DSA (r=0.60, p<0.01). Via a receiver operating characteristic curve, 0.06 cm(3) was determined to be the best threshold (sensitivity 100%, specificity 90.1%, negative predictive value 100% and positive predictive value 46.7%) for detecting significant stenoses. Conclusion: This preliminary investigation confirms a correlation between carotid bifurcation calcium volume and percent ICA stenosis and is promising for the optimal threshold for stenosis detection. Future studies could utilise calcium volumes to create a "score" that could predict high grade stenosis.