Combining images and anatomical knowledge to improve automated vein segmentation in MRI.

PURPOSE: To improve the accuracy of automated vein segmentation by combining susceptibility-weighted images (SWI), quantitative susceptibility maps (QSM), and a vein atlas to produce a resultant image called a composite vein image (CV image). METHOD: An atlas was constructed in common space from manually traced MRI images from ten volunteers. The composite vein image was derived for each subject as a weighted sum of three inputs; an SWI image, a QSM image and the vein atlas. The weights for each input and each anatomical location, called template priors, were derived by assessing the accuracy of each input over an independent data set. The accuracy of vein segmentations derived automatically from each of the CV image, SWI, and QSM image sets was assessed by comparison with manual tracings. Three different automated vein segmentation techniques were used, and ten performance metrics evaluated. RESULTS: Vein segmentations using the CV image were comprehensively better than those derived from SWI or QSM images (mean Cohen's d = 1.1). Sixty permutations of performance metric, benchmark image, and automated segmentation technique were evaluated. Vein identification improvements that were both large and significant (Cohen's d > 0.80, p < 0.05) were found in 77% of the permutations, compared to no improvement in 5%. CONCLUSION: The accuracy of automated vein segmentations derived from the composite vein image was overwhelmingly superior to segmentations derived from SWI or QSM alone.

Hemolytic adverse effects of intravenous immunoglobulin: modeling predicts risk reduction with anti-A/B immunoaffinity chromatography and to a lesser extent with anti-A donor screening.

BACKGROUND: The risk of hemolytic events (HEs) with intravenous immunoglobulin (IVIG) therapy appears to be linked to isoagglutinins (anti-A and anti-B) in the product. Patient risk factors include high IVIG dose, blood group, and underlying inflammatory state. STUDY DESIGN AND METHODS: Using published anti-A and anti-B titers for IVIG products and HE rates calculated from HEs spontaneously reported to EudraVigilance, regression models were developed to infer the relationship between HE risk and IVIG isoagglutinin levels for each blood group. Applying estimated model coefficients to isoagglutinin levels associated with an IVIG (Privigen; CSL Behring, King of Prussia, PA), manufactured with and without isoagglutinin reduction steps, predicted HE risk values were generated for each product: 1) without any isoagglutinin reduction, 2) anti-A donor screening, and 3) anti-A/anti-B specific immunoaffinity chromatography (IAC; Ig IsoLo). RESULTS: Predicted HE risk was highest for blood group AB, followed by A and B; it was low for O. Projected population shares of HEs by blood group were similar to reported real-world data. Compared with the original process (no isoagglutinin reduction), the model predicts lower hemolytic risk with anti-A donor screening and even lower hemolytic risk with IAC isoagglutinin reduction. CONCLUSION: IAC isoagglutinin reduction is predicted to reduce the HE risk with IVIG substantially. Physicians should be especially vigilant to HE risk in patients with blood group AB and, to a lesser extent, A when using IVIG products with high anti-A titers.

Line of fire - what happened at the Wantabadgery seige?

A gunfight between police and a gang of men led by the self-styled "Captain Moonlite", a.k.a. George Scott, occurred on 16th November 1879 at a farmhouse near Wantabadgery Station in the colony of New South Wales. The skirmish resulted in the deaths of two bushrangers and one police officer. As a result, Captain Moonlite and Thomas Rogan were hung in Sydney's Darlinghurst Gaol on 20 January 1880 for the murder of Constable Edward Webb-Bowen. Culpability for firing the fatal shot, however, has remained a source of controversy. Information obtained from an analysis of historical records was used to guide an archeological excavation at the scene of the shooting in which Terrestrial Laser Scanning (TLS) technology was employed to produce a digital (3D) terrain model of the siege location. Utilizing the terrain model, the relative positions of Moonlite, Webb-Bowen, and the other gang members were established with possible projectile trajectories plotted. This, in combination with inquest evidence from a gun maker and the medical practitioner who examined Constable Webb-Bowen's wound, indicates that the most likely shooter was Gus Warnicke, aged 15 years, the youngest member of the gang, who was also killed in the exchange of fire.

Effect of ultrafine-grained titanium surfaces on adhesion of bacteria.

The influence of the ultrafine crystallinity of commercial purity grade 2 (as-received) titanium and titanium modified by equal channel angular pressing (modified titanium) on bacterial attachment was studied. A topographic profile analysis of the surface of the modified titanium revealed a complex morphology of the surface. Its prominent micro- and nano-scale features were 100-200-nm-scale undulations with 10-15 microm spacing. The undulating surfaces were nano-smooth, with height variations not exceeding 5-10 nm. These surface topography characteristics were distinctly different from those of the as-received samples, where broad valleys (up to 40-60 microm) were detected, whose inner surfaces exhibited asperities approximately 100 nm in height spaced at 1-2 microm. It was found that each of the three bacteria strains used in this study as adsorbates, viz. Staphylococcus aureus CIP 68.5, Pseudomonas aeruginosa ATCC 9025 and Escherichia coli K12, responded differently to the two types of titanium surfaces. Extreme grain refinement by ECAP resulted in substantially increased numbers of cells attached to the surface compared to as-received titanium. This enhanced degree of attachment was accompanied with an increased level of extracellular polymeric substances (EPS) production by the bacteria.

Improved Quantification of Cerebral Vein Oxygenation Using Partial Volume Correction.

Purpose: Quantitative susceptibility mapping (QSM) enables cerebral venous characterization and physiological measurements, such as oxygen extraction fraction (OEF). The exquisite sensitivity of QSM to deoxygenated blood makes it possible to image small veins; however partial volume effects must be addressed for accurate quantification. We present a new method, Iterative Cylindrical Fitting (ICF), to estimate voxel-based partial volume effects for susceptibility maps and use it to improve OEF quantification of small veins with diameters between 1.5 and 4 voxels. Materials and Methods: Simulated QSM maps were generated to assess the performance of the ICF method over a range of vein geometries with varying echo times and noise levels. The ICF method was also applied to in vivo human brain data to assess the feasibility and behavior of OEF measurements compared to the maximum intensity voxel (MIV) method. Results: Improved quantification of OEF measurements was achieved for vessels with contrast to noise greater than 3.0 and vein radii greater than 0.75 voxels. The ICF method produced improved quantitative accuracy of OEF measurement compared to the MIV approach (mean OEF error 7.7 vs. 12.4%). The ICF method provided estimates of vein radius (mean error <27%) and partial volume maps (root mean-squared error <13%). In vivo results demonstrated consistent estimates of OEF along vein segments. Conclusion: OEF quantification in small veins (1.5-4 voxels in diameter) had lower error when using partial volume estimates from the ICF method.

Design, implementation and operation of a multimodality research imaging informatics repository.

BACKGROUND: Biomedical imaging research increasingly involves acquiring, managing and processing large amounts of distributed imaging data. Integrated systems that combine data, meta-data and workflows are crucial for realising the opportunities presented by advances in imaging facilities. METHODS: This paper describes the design, implementation and operation of a multi-modality research imaging data management system that manages imaging data obtained from biomedical imaging scanners operated at Monash Biomedical Imaging (MBI), Monash University in Melbourne, Australia. In addition to Digital Imaging and Communications in Medicine (DICOM) images, raw data and non-DICOM biomedical data can be archived and distributed by the system. Imaging data are annotated with meta-data according to a study-centric data model and, therefore, scientific users can find, download and process data easily. RESULTS: The research imaging data management system ensures long-term usability, integrity inter-operability and integration of large imaging data. Research users can securely browse and download stored images and data, and upload processed data via subject-oriented informatics frameworks including the Distributed and Reflective Informatics System (DaRIS), and the Extensible Neuroimaging Archive Toolkit (XNAT).

Forearm Range of Motion in Australovenator wintonensis (Theropoda, Megaraptoridae).

The hypertrophied manual claws and modified manus of megaraptoran theropods represent an unusual morphological adaptation among carnivorous dinosaurs. The skeleton of Australovenator wintonensis from the Cenomanian of Australia is among the most complete of any megaraptorid. It presents the opportunity to examine the range of motion of its forearm and the function of its highly modified manus. This provides the basis for behavioural inferences, and comparison with other Gondwanan theropod groups. Digital models created from computed tomography scans of the holotype reveal a humerus range of motion that is much greater than Allosaurus, Acrocanthosaurus, Tyrannosaurus but similar to that of the dromaeosaurid Bambiraptor. During flexion, the radius was forced distally by the radial condyle of the humerus. This movement is here suggested as a mechanism that forced a medial movement of the wrist. The antebrachium possessed a range of motion that was close to dromaeosaurids; however, the unguals were capable of hyper-extension, in particular manual phalanx I-2, which is a primitive range of motion characteristic seen in allosaurids and Dilophosaurus. During flexion, digits I and II slightly converge and diverge when extended which is accentuated by hyperextension of the digits in particular the unguals. We envision that prey was dispatched by its hands and feet with manual phalanx I-2 playing a dominant role. The range of motion analysis neither confirms nor refutes current phylogenetic hypotheses with regards to the placement of Megaraptoridae; however, we note Australovenator possessed, not only a similar forearm range of motion to some maniraptorans and basal coelurosaurs, but also similarities with Tetanurans (Allosauroids and Dilophosaurus).

An interactive three dimensional approach to anatomical description-the jaw musculature of the Australian laughing kookaburra (Dacelo novaeguineae).

The investigation of form-function relationships requires a detailed understanding of anatomical systems. Here we document the 3-dimensional morphology of the cranial musculoskeletal anatomy in the Australian Laughing Kookaburra Dacelo novaeguineae, with a focus upon the geometry and attachments of the jaw muscles in this species. The head of a deceased specimen was CT scanned, and an accurate 3D representation of the skull and jaw muscles was generated through manual segmentation of the CT scan images, and augmented by dissection of the specimen. We identified 14 major jaw muscles: 6 in the temporal group (M. adductor mandibulae and M. pseudotemporalis), 7 in the pterygoid group (M. pterygoideus dorsalis and M. pterygoideus ventralis), and the single jaw abductor M. depressor mandibulae. Previous descriptions of avian jaw musculature are hindered by limited visual representation and inconsistency in the nomenclature. To address these issues, we: (1) present the 3D model produced from the segmentation process as a digital, fully interactive model in the form of an embedded 3D image, which can be viewed from any angle, and within which major components can be set as opaque, transparent, or hidden, allowing the anatomy to be visualised as required to provide a detailed understanding of the jaw anatomy; (2) provide a summary of the nomenclature used throughout the avian jaw muscle literature. The approach presented here provides considerable advantages for the documentation and communication of detailed anatomical structures in a wide range of taxa.

The multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) high performance computing infrastructure: applications in neuroscience and neuroinformatics research.

The Multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) is a national imaging and visualization facility established by Monash University, the Australian Synchrotron, the Commonwealth Scientific Industrial Research Organization (CSIRO), and the Victorian Partnership for Advanced Computing (VPAC), with funding from the National Computational Infrastructure and the Victorian Government. The MASSIVE facility provides hardware, software, and expertise to drive research in the biomedical sciences, particularly advanced brain imaging research using synchrotron x-ray and infrared imaging, functional and structural magnetic resonance imaging (MRI), x-ray computer tomography (CT), electron microscopy and optical microscopy. The development of MASSIVE has been based on best practice in system integration methodologies, frameworks, and architectures. The facility has: (i) integrated multiple different neuroimaging analysis software components, (ii) enabled cross-platform and cross-modality integration of neuroinformatics tools, and (iii) brought together neuroimaging databases and analysis workflows. MASSIVE is now operational as a nationally distributed and integrated facility for neuroinfomatics and brain imaging research.

Embedding and publishing interactive, 3-dimensional, scientific figures in Portable Document Format (PDF) files.

With the latest release of the S2PLOT graphics library, embedding interactive, 3-dimensional (3-d) scientific figures in Adobe Portable Document Format (PDF) files is simple, and can be accomplished without commercial software. In this paper, we motivate the need for embedding 3-d figures in scholarly articles. We explain how 3-d figures can be created using the S2PLOT graphics library, exported to Product Representation Compact (PRC) format, and included as fully interactive, 3-d figures in PDF files using the movie15 LaTeX package. We present new examples of 3-d PDF figures, explain how they have been made, validate them, and comment on their advantages over traditional, static 2-dimensional (2-d) figures. With the judicious use of 3-d rather than 2-d figures, scientists can now publish, share and archive more useful, flexible and faithful representations of their study outcomes. The article you are reading does not have embedded 3-d figures. The full paper, with embedded 3-d figures, is recommended and is available as a supplementary download from PLoS ONE (File S2).

New Australovenator hind limb elements pertaining to the holotype reveal the most complete Neovenatorid leg.

We report new skeletal elements pertaining to the same individual which represents the holotype of Australovenator wintonensis, from the 'Matilda Site' in the Winton Formation (Upper Cretaceous) of western Queensland. The discovery of these new elements means that the hind limb of Australovenator is now the most completely understood hind limb among Neovenatoridae. The new hind limb elements include: the left fibula; left metatarsal IV; left pedal phalanges I-2, II-1, III-4, IV-2, IV-3; and right pedal phalanges, II-2 and III-1. The detailed descriptions are supported with three dimensional figures. These coupled with the completeness of the hind limb will increase the utility of Australovenator in comparisons with less complete neovenatorid genera. These specimens and the previously described hind limb elements of Australovenator are compared with other theropods classified as neovenatorids (including Neovenator, Chilantaisaurus, Fukuiraptor, Orkoraptor and Megaraptor). Hind limb length proportion comparisons indicate that the smaller neovenatorids Australovenator and Fukuiraptor possess more elongate and gracile hind limb elements than the larger Neovenator and Chilantaisaurus. Greater stride lengths to body size exist in both Fukuiraptor and Australovenator with the femur discovered to be proportionally shorter the rest of the hind limb length. Additionally Australovenator is identified as possessing the most elongate metatarsus. The metatarsus morphology varies with body size. The larger neoventorids possess a metatarsus with greater width but shorter length compared to smaller forms.

Interactive 3D volume rendering in biomedical publications.

We present three examples of interactive, 3D volume rendering models embedded in a PDF publication. The examples are drawn from three different morphological methods - confocal microscopy, serial sectioning and microcomputed tomography - performed on members of the phylum Mollusca. A description of the entire technical procedure from specimen preparation to embedding of the visual model including 3D labels in the document is provided. For comparison, volume rendering with standard visualization software, and surface rendering incorporated in the 3D PDF figures, are provided. The principal advantages and disadvantages of the techniques and models are discussed. Volume rendering for serial sections is relatively work-intensive, while confocal data have limitations in terms of 3D presentation. Volume renderings are normally downsampled in resolution to achieve a reasonable PDF file size, however intentional information is largely retained. We conclude that volume rendering of 3D data sets is a valuable technique and should become standard in PDF versions of biomedical publications.