Combining region-based and imprecise boundary-based cues for interactive medical image segmentation

We present an approach combining both region selection and user point selection for user- assisted segmentation as either an enclosed object or an open curve, investigate the method of image segmentation in specific medical applications (user-assisted segmentation of the media–adventitia border in intravascular ultrasound images, and lumen border in optical coherence tomography images), and then demonstrate the method with generic images to show how it could be utilized in other types of medical image and is not limited to the applications described. The proposed method combines point-based soft con- straint on object boundary and stroke-based regional constraint. The user points act as attraction points and are treated as soft constraints rather than hard constraints that the segmented boundary has to pass through. The user can also use strokes to specify region of interest. The probabilities of region of interest for each pixel are then calculated, and their discontinuity is used to indicate object boundary. The combinations of different types of user constraints and image features allow flexible and robust segmentation, which is formulated as an energy minimization problem on a multilayered graph and is solved using a shortest path search algorithm. We show that this combinatorial approach allows efficient and effective interactive segmentation, which can be used with both open and closed curves to segment a variety of images in different ways. The proposed method is demonstrated in the two medical applications, that is, intravascular ultrasound and optical coherence tomography images, where image artefacts such as acoustic shadow and calcification are commonplace and thus user guidance is desirable. We carried out both qualitative and quantitative analysis of the results for the medical data; comparing the proposed method against a number of interactive segmentation techniques

2D and 3D segmentation of medical images.

"Cardiovascular disease is one of the leading causes of the morbidity and mortality in the western world today. Many different imaging modalities are in place today to diagnose and investigate cardiovascular diseases. Each of these, however, has strengths and weaknesses. There are different forms of noise and artifacts in each image modality that combine to make the field of medical image analysis both important and challenging. The aim of this thesis is develop a reliable method for segmentation of vessel structures in medical imaging, combining the expert knowledge of the user in such a way as to maintain efficiency whilst overcoming the inherent noise and artifacts present in the images. We present results from 2D segmentation techniques using different methodologies, before developing 3D techniques for segmenting vessel shape from a series of images. The main drive of the work involves the investigation of medical images obtained using catheter based techniques, namely Intra Vascular Ultrasound (IVUS) and Optical Coherence Tomography (OCT). We will present a robust segmentation paradigm, combining both edge and region information to segment the media-adventitia, and lumenal borders in those modalities respectively. By using a semi-interactive method that utilizes "soft" constraints, allowing imprecise user input which provides a balance between using the user's expert knowledge and efficiency. In the later part of the work, we develop automatic methods for segmenting the walls of lymph vessels. These methods are employed on sequential images in order to obtain data to reconstruct the vessel walls in the region of the lymph valves. We investigated methods to segment the vessel walls both individually and simultaneously, and compared the results both quantitatively and qualitatively in order obtain the most appropriate for the 3D reconstruction of the vessel wall. Lastly, we adapt the semi-interactive method used on vessels earlier into 3D to help segment out the lymph valve. This involved the user interactive method to provide guidance to help segment the boundary of the lymph vessel, then we apply a minimal surface segmentation methodology to provide segmentation of the valve.

Dynamical Decoupling in Optical Fibers: Preserving Polarization Qubits from Birefringent Dephasing

One of the major challenges in quantum computation has been to preserve the coherence of a quantum system against dephasing effects of the environment. The information stored in photon polarization, for example, is quickly lost due to such dephasing, and it is crucial to preserve the input states when one tries to transmit quantum information encoded in the photons through a communication channel. We propose a dynamical decoupling sequence to protect photonic qubits from dephasing by integrating wave plates into optical fiber at prescribed locations. We simulate random birefringent noise along realistic lengths of optical fiber and study preservation of polarization qubits through such fibers enhanced with Carr-Purcell-Meiboom-Gill (CPMG) dynamical decoupling. This technique can maintain photonic qubit coherence at high fidelity, making a step towards achieving scalable and useful quantum communication with photonic qubits.Comment: 8 pages, 5 figure

The effect of mountain bike wheel size on Cross-Country performance

The purpose of this study was to determine the influence of different wheel size diameters on indicators of cross-country mountain bike time trial performance. Nine competitive male mountain bikers (age 34.7 ± 10.7 years; stature 177.7 ± 5.6 cm; body mass 73.2 ± 8.6 kg) performed 1 lap of a 3.48 km mountain bike (MTB) course as fast as possible on 26″, 27.5″ and 29″ wheeled MTB. Time (s), mean power (W), cadence (revs · min−1) and velocity (km · h−1) were recorded for the whole lap and during ascent and descent sections. One-way repeated measure ANOVA was used to determine significant differences. Results revealed no significant main effects for any variables by wheel size during all trials, with the exception of cadence during the descent (F(2, 16) = 8.96; P = .002; P2 = .53). Post hoc comparisons revealed differences lay between the 26″ and 29″ wheels (P = .02). The findings indicate that wheel size does not significantly influence performance during cross-country when ridden by trained mountain bikers, and that wheel choice is likely due to personal choice or sponsorship commitments

Dietary nitrate supplementation attenuates the reduction in exercise tolerance following blood donation

Dietary nitrate supplementation attenuates the reduction in exercise tolerance following blood donatio

p16INK4A expression is frequently increased in periorbital and ocular squamous lesions

Backgroundp16 expression is a well established biomarker of cervical dysplasia and carcinoma arising from high risk human papilloma virus infection. Increased p16 expression is also seen in squamous neoplasms arising at other sites, including head, neck, and oropharyngeal tract. Squamous lesions are also frequently encountered at ocular surface and peri-orbital skin sites, but the prevalence of increased p16 expression in these lesions has been poorly studied.MethodsWe retrospectively surveyed 13 ocular surface and 16 orbital squamous lesions biopsied at UC San Diego Healthcare System and VA San Diego Healthcare System for p16 expression by immunohistochemistry. These cases included ocular surface lesions with diagnoses of conjunctival intraepithelial neoplasm (CIN) and squamous cell carcinoma in situ. Peri-orbital eyelid biopsies included lesions with diagnoses of SCCis and invasive squamous cell carcinoma. We performed multivariate logistic regression, followed by student's T-test or Fisher's exact test to determine if there were statistically significant associations between p16 immunoreactivity and patient age, gender, diagnosis, and ethnicity. Statistical significance was defined as p < 0.05.ResultsWe found an unexpectedly large prevalence of strong nuclear and cytoplasmic p16 immunoreactivity in our cases. Almost all of the ocular surface squamous lesions were diffusely positive for p16 expression (12/13). All of the periorbital lesions showed diffuse p16 immunoreactivity (16/16). Altogether, 28/29 lesions tested showed strong and diffuse p16 expression. We found no statistically significant correlation between p16 expression and patient age, gender, ethnicity, or diagnosis. In 6 of the peri-orbital biopsies, we had sufficient tissue to assess high-risk HPV expression by in situ hybridization. Interestingly, all of these cases were negative for HPV, despite strong p16 expression.ConclusionStrong p16 expression was observed in virtually all of the ocular surface and peri-orbital squamous neoplasms in our study. The relationship between p16 expression and HPV infection in ocular surface and peri-orbital sites requires further investigation

Network analysis of nitrate-sensitive oral microbiome reveals interactions with cognitive function and cardiovascular health across dietary interventions

Many oral bacteria reduce inorganic nitrate, a natural part of a vegetable-rich diet, into nitrite that acts as a precursor to nitric oxide, a regulator of vascular tone and neurotransmission. Aging is hallmarked by reduced nitric oxide production with associated detriments to cardiovascular and cognitive function. This study applied a systems-level bacterial co-occurrence network analysis across 10-day dietary nitrate and placebo interventions to test the stability of relationships between physiological and cognitive traits and clusters of co-occurring oral bacteria in older people. Relative abundances of Proteobacteria increased, while Bacteroidetes, Firmicutes and Fusobacteria decreased after nitrate supplementation. Two distinct microbiome modules of co-occurring bacteria, that were sensitive to nitrate supplementation, showed stable relationships with cardiovascular (Rothia-Streptococcus) and cognitive (Neisseria-Haemophilus) indices of health across both dietary conditions. A microbiome module (Prevotella-Veillonella) that has been associated with pro-inflammatory metabolism was diminished after nitrate supplementation, including a decrease in relative abundance of pathogenic Clostridium difficile. These nitrate-sensitive oral microbiome modules are proposed as potential pre- and probiotic targets to ameliorate age-induced impairments in cardiovascular and cognitive health.publishedVersio

A detailed analysis of the HD 73526 2:1 resonant planetary system

We present six years of new radial velocity data from the Anglo-Australian and Magellan Telescopes on the HD 73526 2:1 resonant planetary system. We investigate both Keplerian and dynamical ( interacting) fits to these data, yielding four possible configurations for the system. The new data now show that both resonance angles are librating, with amplitudes of 40 degrees and 60 degrees, respectively. We then perform long-term dynamical stability tests to differentiate these solutions, which only differ significantly in the masses of the planets. We show that while there is no clearly preferred system inclination, the dynamical fit with i = 90 degrees provides the best combination of goodness-of-fit and long-term dynamical stability.Peer reviewe

Autoimmunity and effector recognition in Arabidopsis thaliana can be uncoupled by mutations in the RRS1‐R immune receptor

Plant nucleotide-binding leucine-rich repeat (NLR) disease resistance proteins recognize specific pathogen effectors and activate a cellular defense program. In Arabidopsis thaliana (Arabidopsis), Resistance to Ralstonia solanacearum 1 (RRS1-R) and Resistance to Pseudomonas syringae 4 (RPS4) function together to recognize the unrelated bacterial effectors PopP2 and AvrRps4. In the plant cell nucleus, the RRS1-R/RPS4 complex binds to and signals the presence of AvrRps4 or PopP2. The exact mechanism underlying NLR signaling and immunity activation remains to be elucidated. Using genetic and biochemical approaches, we characterized the intragenic suppressors of sensitive to low humidity 1 (slh1), a temperature-sensitive autoimmune allele of RRS1-R. Our analyses identified five amino acid residues that contribute to RRS1-R SLH 1 autoactivity. We investigated the role of these residues in the RRS1-R allele by genetic complementation, and found that C15 in the Toll/interleukin-1 receptor (TIR) domain and L816 in the LRR domain were also important for effector recognition. Further characterization of the intragenic suppressive mutations located in the RRS1-R TIR domain revealed differing requirements for RRS1-R/RPS4-dependent autoimmunity and effector-triggered immunity. Our results provide novel information about the mechanisms which, in turn, hold an NLR protein complex inactive and allow adequate activation in the presence of pathogens

The Grizzly, February 5, 2009

MLK; The Substance of Our Souls • New Auto Standards • Impressive Track Record for UC • Contamination Causes Jelly to Lose Long-time Companion • Restaurant Review: Columbia not as Foreign as You Think? • Portion Distortion and Super-Sizing It • UC at National Black Student Leadership Development Conference • Students in Free Enterprise: Advice from the Alumni • Opinions: Why Bush Should be Prosecuted for Crimes; Obama\u27s Oration on Religion Sparks Outragehttps://digitalcommons.ursinus.edu/grizzlynews/1778/thumbnail.jp