Shape-Based Models for Interactive Segmentation of Medical Images

Accurate image segmentation is one of the key problems in computer vision. In domains such as radiation treatment planning, dosimetrists must manually trace the outlines of a few critical structures on large numbers of images. Considerable similarity can be seen in the shape of these regions, both between adjacent slices in a particular patient and across the spectrum of patients. Consequently we should be able to model this similarity and use it to assist in the process of segmentation. Previous work has demonstrated that a constraint-based 2D radial model can capture generic shape information for certain shape classes, and can reduce user interaction by a factor of three over purely manual segmentation. Additional simulation studies have shown that a probabilistic version of the model has the potential to further reduce user interaction. This paper describes an implementation of both models in a general-purpose imaging and graphics framework and compares the usefulness of the models on several shape classes

Heuristic Refinement Method for the Derivation of Protein Solution Structures: Validation on Cytochrome B562

A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent computational intractability of this approach is reduced by assembling the protein in pieces, by considering the protein at several levels of abstraction, by utilizing constraint satisfaction methods to consider only a few atoms at a time, and by utilizing artificial intelligence methods of heuristic control to decide which actions will exclude the most conformations. Example results are presented for simulated NMR data from the known crystal structure of cytochrome b562 (103 residues). For 10 sample backbones an average root-mean-square deviation from the crystal of 4.1 A was found for all alpha-carbon atoms and 2.8 A for helix alpha-carbons alone. The 10 backbones define the family of all structures compatible with the data and provide nearly correct starting structures for adjustment by any of the current structure determination methods

Abel-Jacobi maps for hypersurfaces and non commutative Calabi-Yau's

It is well known that the Fano scheme of lines on a cubic 4-fold is a symplectic variety. We generalize this fact by constructing a closed p-form with p=2n-4 on the Fano scheme of lines on a (2n-2)-dimensional hypersurface Y of degree n. We provide several definitions of this form - via the Abel-Jacobi map, via Hochschild homology, and via the linkage class, and compute it explicitly for n = 4. In the special case of a Pfaffian hypersurface Y we show that the Fano scheme is birational to a certain moduli space of sheaves on a p-dimensional Calabi--Yau variety X arising naturally in the context of homological projective duality, and that the constructed form is induced by the holomorphic volume form on X. This remains true for a general non Pfaffian hypersurface but the dual Calabi-Yau becomes non commutative.Comment: 34 pages; exposition of Hochschild homology expanded; references added; introduction re-written; some imrecisions, typos and the orbit diagram in the last section correcte

The in- or exclusion of non-breast cancer related death and contralateral breast cancer significantly affects estimated outcome probability in early breast cancer

A wide variation of definitions of recurrent disease and survival are used in the analyses of outcome of patients with early breast cancer. Explicit definitions with details both on endpoints and censoring are provided in less than half of published studies. We evaluated the effects of various definitions of survival and recurrent disease on estimated outcome in a prospectively determined cohort of 463 patients with primary breast cancer. Outcome estimates were determined both by the Kaplan–Meier and a competing risk method. In- or exclusion of contralateral breast cancer or non-disease related death in the definition of recurrent disease or survival significantly affects estimated outcome probability. The magnitude of this finding was dependent on patient-, tumour-, and treatment characteristics. Knowledge of the contribution of non-disease related death or contralateral breast cancer to estimated recurrent disease rate and overall death rate is indispensable for a correct interpretation and comparison of outcome analyses

Biomedical term mapping databases

Longer words and phrases are frequently mapped onto a shorter form such as abbreviations or acronyms for efficiency of communication. These abbreviations are pervasive in all aspects of biology and medicine and as the amount of biomedical literature grows, so does the number of abbreviations and the average number of definitions per abbreviation. Even more confusing, different authors will often abbreviate the same word/phrase differently. This ambiguity impedes our ability to retrieve information, integrate databases and mine textual databases for content. Efforts to standardize nomenclature, especially those doing so retrospectively, need to be aware of different abbreviatory mappings and spelling variations. To address this problem, there have been several efforts to develop computer algorithms to identify the mapping of terms between short and long form within a large body of literature. To date, four such algorithms have been applied to create online databases that comprehensively map biomedical terms and abbreviations within MEDLINE: ARGH (http://lethargy.swmed.edu/ARGH/argh.asp), the Stanford Biomedical Abbreviation Server (http://bionlp.stanford.edu/abbreviation/), AcroMed (http://medstract.med.tufts.edu/acro1.1/index.htm) and SaRAD (http://www.hpl.hp.com/research/idl/projects/abbrev.html). In addition to serving as useful computational tools, these databases serve as valuable references that help biologists keep up with an ever-expanding vocabulary of terms

SO(4) Theory of Competition between Triplet Superconductivity and Antiferromagnetism in Bechgaard Salts

Motivated by recent experiments with Bechgaard salts, we investigate the competition between antiferromagnetism and triplet superconductivity in quasi one-dimensional electron systems. We unify the two orders in an SO(4) symmetric framework, and demonstrate the existence of such symmetry in one-dimensional Luttinger liquids. SO(4) symmetry, which strongly constrains the phase diagram, can explain coexistence regions between antiferromagnetic, superconducting, and normal phases, as observed in (TMTSF)$_2$PF$_6$. We predict a sharp neutron scattering resonance in superconducting samples.Comment: 5 pages, 3 figures; Added discussion of applicability of SO(4) symmetry for strongly anisotropic Fermi liquids; Added reference

Superconducting charge-ordered states in cuprates

Motivated by recent neutron scattering and scanning tunneling microscopy (STM) experiments on cuprate superconductors, we discuss charge-ordered states, in particular with two-dimensional charge modulation patterns, co-existing with superconductivity. We extend previous studies of a large-N mean-field formulation of the t-J model. In addition to bond-centered superconducting stripe states at low doping, we find checkerboard-modulated superconducting states which are favorable in an intermediate doping interval. We also analyze the energy dependence of the Fourier component of the local density of states at the ordering wavevector for several possible modulation patterns, and compare with STM results.Comment: 5 pages, 4 figs; (v2) extended discussion; final version as publishe

Mean Field Theory of Josephson Junction Arrays with Charge Frustration

Using the path integral approach, we provide an explicit derivation of the equation for the phase boundary for quantum Josephson junction arrays with offset charges and non-diagonal capacitance matrix. For the model with nearest neighbor capacitance matrix and uniform offset charge $q/2e=1/2$, we determine, in the low critical temperature expansion, the most relevant contributions to the equation for the phase boundary. We explicitly construct the charge distributions on the lattice corresponding to the lowest energies. We find a reentrant behavior even with a short ranged interaction. A merit of the path integral approach is that it allows to provide an elegant derivation of the Ginzburg-Landau free energy for a general model with charge frustration and non-diagonal capacitance matrix. The partition function factorizes as a product of a topological term, depending only on a set of integers, and a non-topological one, which is explicitly evaluated.Comment: LaTex, 24 pages, 8 figure

Large Quantum imaging of nonlocal spatial correlations induced by orbital angular momentum

Through scanned coincidence counting, we probe the quantum image produced by parametric down conversion with a pump beam carrying orbital angular momentum. Nonlocal spatial correlations are manifested through splitting of the coincidence spot into two.Comment: 4 pages, 6 figures. Submitted to Physical Review Letter