Three-dimensional quantitative evaluation method of nonrigid registration algorithms for adaptive radiotherapy

Purpose: Current radiotherapy is progressing to the concept of adaptive radiotherapy, which implies the adaptation of planning along the treatment course. Nonrigid registration is an essential image processing tool for adaptive radiotherapy and image guided radiotherapy, and the three-dimensional (3D) nature of the current radiotherapy techniques requires a 3D quantification of the registration error that existing evaluation methods do not cover appropriately. The authors present a method for 3D evaluation of nonrigid registration algorithms’ performance, based on organ delineations, capable of working with near-spherical volumes even in the presence of concavities. Methods: The evaluation method is composed by a volume shape description stage, developed using a new ad hoc volume reconstruction algorithm proposed by the authors, and an error quantification stage. The evaluation method is applied to the organ delineations of prostate and seminal vesicles, obtained by an automatic segmentation method over images of prostate cancer patients treated with intensity modulated radiation therapy. Results: The volume reconstruction algorithm proposed has been shown to accurately model complex 3D surfaces by the definition of clusters of control points. The quantification method, inspired by the Haussdorf–Chebysev distance, provides a measure of the largest registration error per control direction, defining a valid metric for concave-convex volumes. Summarizing, the proposed evaluation methodology presents accurate results with a high spatial resolution in a negligible computation time in comparison with the nonrigid registration time. Conclusions: Experimental results show that the metric selected for quantifying the registration error is of utmost importance in a quantitative evaluation based on measuring distances between volumes. The accuracy of the volume reconstruction algorithm is not so relevant as long as the reconstruction is tight enough on the actual volume of the organ. The new evaluation method provides a smooth and accurate volume reconstruction for both the reference and the registered organ, and a complete 3D description of nonrigid registration algorithms’ performance, resulting in a useful tool for study and comparison of registration algorithms for adaptive radiotherapy

Brian: The Typographical Error that Brought Early Career Neuroscientists and Artists Together

In the project “Do You Mind?” early career neuroscientists and artists collaborated to produce artworks for exhibition

DNA Methylation Signatures within the Human Brain

DNA methylation is a heritable modification of genomic DNA central to development, imprinting, transcriptional regulation, chromatin structure, and overall genomic stability. Aberrant DNA methylation of individual genes is a hallmark of cancer and has been shown to play an important role in neurological disorders such as Rett syndrome. Here, we asked whether normal DNA methylation might distinguish individual brain regions. We determined the quantitative DNA methylation levels of 1,505 CpG sites representing 807 genes with diverse functions, including proliferation and differentiation, previously shown to be implicated in human cancer. We initially analyzed 76 brain samples representing cerebral cortex (n=35), cerebellum (n=34), and pons (n=7), along with liver samples (n=3) from 43 individuals. Unsupervised hierarchical analysis showed clustering of 33 of 35 cerebra distinct from the clustering of 33 of 34 cerebella, 7 of 7 pons, and all 3 livers. By use of comparative marker selection and permutation testing, 156 loci representing 118 genes showed statistically significant differences—a ⩾17% absolute change in DNA methylation (P<.004)—among brain regions. These results were validated for all six genes tested in a replicate set of 57 samples. Our data suggest that DNA methylation signatures distinguish brain regions and may help account for region-specific functional specialization

A blot on the landscape? Civic memory and municipal public parks in early twentieth century Manchester

This paper examines the decision to locate the façade of Manchester’s old Town Hall in a public park (Heaton Park) in 1912. It argues that, in so doing, the city’s Parks and Cemeteries committee was attempting to refine the didactic space of the park as a site of civic memory. The early Victorian urban parks had sought to educate their visitors through their museums, art galleries and exhibition spaces, glasshouses and carefully-planned and planted walkways. The insertion into this environment of part of a former civic building was intended to remind the visitors of their civic history and to warn surrounding districts of the expansionist tendencies of the city of Manchester. The failure to identify the façade or to connect it to its surroundings meant that its meaning was ultimately lost to many parks visitors and it remained in place as a civic folly. Public parks presented the municipal authorities with an opportunity to highlight the provision of recreation and leisure facilities, but also an occasion to re-invent the municipal tradition. However, as this paper shows, such gestures were often futile in the complex and contested space of the public park

Critical Dimensions in Architectural Photography: Contributions to Architectural Knowledge

This paper illustrates and explores three critical dimensions of photography in architecture, each of which informs the production of images, texts, and other artifacts which establish what might be called a building’s media footprint. The paper’s broad goal is to question the extent to which these critical dimensions are relevant to architectural decision-making processes. Acknowledging that such dimensions as the ones examined here rarely predict an architect’s specific design decisions in a transparent manner, the paper discusses not only the decisions made by architects during the process of designing buildings, but the decisions made by critics, visitors, and members of the general public as they engage in activities such as visiting buildings, writing about them and, particularly, photographing them. First, the text discusses the potential of buildings to operate as mechanisms for producing images, in the sense originated by Beatriz Colomina. The question is developed through the analysis of the space of photography – mapping of points of view, directions of view, and fields of view of defined photographic collections. Secondly, it considers photography’s complicity in the canonization of buildings, and specifically, the extent to which photography is responsible for distinguishing between major and minor architectural works. Finally, the essay examines the erosion over time of photography’s historical power to frame when confronted with contemporary technologies of virtual reality and photo realistically rendered digital models. Each of these critical dimensions, or concepts, develops a specific aspect of how photographic information about buildings is organized, structured, and disseminated, and is thus only part of the larger project of architectural epistemology, which inquires into this wider field. This will be done through an examination of the Mies van der Rohe-designed Commons Building at ITT in Chicago and the evolution of its relationship with architectural photography and photographic representation – both on its own terms and through the prism of the Rem Koolhaas-designed McCormick Tribune Student Center, which adds to and incorporates the Commons Building. Until the end of the twentieth century, the Commons Building on the campus of the Illinois Institute of Technology was generally considered one of Mies van der Rohe’s lesser works. Reportedly neglected by its own architect during the design process, and frequently marginalized in academic discussions of the campus, when mentioned at all the building was often cited as an unrefined prototype of Crown Hall. This discourse took a new direction when in 1998, Rem Koolhaas/OMA won a design competition for a student center on the IIT campus: uniquely among the competition entries, Koolhaas’s design incorporated the Commons Building within a new context – what ultimately became the McCormick Tribune Campus Center (MTCC). When critics concluded that the incorporation of the Commons Building into the larger whole could compromise its integrity as an exemplar of Mies’s work, the building became the object of renewed interest and controversy. The two projects considered here show a clear evolution in architecture’s relationship with the photographic image. Specifically, the history of the Commons Building can be traced through photographs: during and shortly following its construction, the building was photographed as part of Mies’s own attention to publicity; it was documented as part of historical analyses; and over time it was visited and photographed by casual and amateur photographers. Following the competition results, photographs of the Commons Building were strategically deployed by both proponents and critics of Koolhaas’s design. Contemporary photographs of the building appear in architectural and campus guidebooks and on websites such as Flickr.com. Examining the ways in which photographs of the Commons Building appear in these various contexts allows discussion of the critical dimensions identified above and permits us to trace the evolution of the mutually reinforcing relationship between architecture and photography

Creating Physical 3D Stereolithograph Models of Brain and Skull

The human brain and skull are three dimensional (3D) anatomical structures with complex surfaces. However, medical images are often two dimensional (2D) and provide incomplete visualization of structural morphology. To overcome this loss in dimension, we developed and validated a freely available, semi-automated pathway to build 3D virtual reality (VR) and hand-held, stereolithograph models. To evaluate whether surface visualization in 3D was more informative than in 2D, undergraduate students (n = 50) used the Gillespie scale to rate 3D VR and physical models of both a living patient-volunteer's brain and the skull of Phineas Gage, a historically famous railroad worker whose misfortune with a projectile tamping iron provided the first evidence of a structure-function relationship in brain. Using our processing pathway, we successfully fabricated human brain and skull replicas and validated that the stereolithograph model preserved the scale of the VR model. Based on the Gillespie ratings, students indicated that the biological utility and quality of visual information at the surface of VR and stereolithograph models were greater than the 2D images from which they were derived. The method we developed is useful to create VR and stereolithograph 3D models from medical images and can be used to model hard or soft tissue in living or preserved specimens. Compared to 2D images, VR and stereolithograph models provide an extra dimension that enhances both the quality of visual information and utility of surface visualization in neuroscience and medicine

A Study of Cosmic Ray Secondaries Induced by the Mir Space Station Using AMS-01

The Alpha Magnetic Spectrometer (AMS-02) is a high energy particle physics experiment that will study cosmic rays in the $\sim 100 \mathrm{MeV}$ to $1 \mathrm{TeV}$ range and will be installed on the International Space Station (ISS) for at least 3 years. A first version of AMS-02, AMS-01, flew aboard the space shuttle \emph{Discovery} from June 2 to June 12, 1998, and collected $10^8$ cosmic ray triggers. Part of the \emph{Mir} space station was within the AMS-01 field of view during the four day \emph{Mir} docking phase of this flight. We have reconstructed an image of this part of the \emph{Mir} space station using secondary $\pi^-$ and $\mu^-$ emissions from primary cosmic rays interacting with \emph{Mir}. This is the first time this reconstruction was performed in AMS-01, and it is important for understanding potential backgrounds during the 3 year AMS-02 mission.Comment: To be submitted to NIM B Added material requested by referee. Minor stylistic and grammer change

Search for antihelium in cosmic rays

The Alpha Magnetic Spectrometer (AMS) was flown on the space shuttle Discovery during flight STS-91 in a 51.7 degree orbit at altitudes between 320 and 390 km. A total of 2.86 * 10^6 helium nuclei were observed in the rigidity range 1 to 140 GV. No antihelium nuclei were detected at any rigidity. An upper limit on the flux ratio of antihelium to helium of < 1.1 * 10^-6 is obtained.Comment: 18 pages, Latex, 9 .eps figure

Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo.

The intestinal epithelial cells (IECs) that line the gut form a robust line of defense against ingested pathogens. We investigated the impact of infection with the enteric pathogen Citrobacter rodentium on mouse IEC metabolism using global proteomic and targeted metabolomics and lipidomics. The major signatures of the infection were upregulation of the sugar transporter Sglt4, aerobic glycolysis, and production of phosphocreatine, which mobilizes cytosolic energy. In contrast, biogenesis of mitochondrial cardiolipins, essential for ATP production, was inhibited, which coincided with increased levels of mucosal O2 and a reduction in colon-associated anaerobic commensals. In addition, IECs responded to infection by activating Srebp2 and the cholesterol biosynthetic pathway. Unexpectedly, infected IECs also upregulated the cholesterol efflux proteins AbcA1, AbcG8, and ApoA1, resulting in higher levels of fecal cholesterol and a bloom of Proteobacteria. These results suggest that C. rodentium manipulates host metabolism to evade innate immune responses and establish a favorable gut ecosystem