Retinal Image Matching Using Hierarchical Vascular Features

We propose a method for retinal image matching that can be used in image matching for person identification or patient longitudinal study. Vascular invariant features are extracted from the retinal image, and a feature vector is constructed for each of the vessel segments in the retinal blood vessels. The feature vectors are represented in a tree structure with maintaining the vessel segments actual hierarchical positions. Using these feature vectors, corresponding images are matched. The method identifies the same vessel in the corresponding images for comparing the desired feature(s). Initial results are encouraging and demonstrate that the proposed method is suitable for image matching and patient longitudinal study

RANKL directly induces bone morphogenetic protein-2 expression in RANK-expressing POS-1 osteosarcoma cells

International audienceThe POS-1 murine model of osteolytic osteosarcoma was used to elucidate the molecular and cellular mechanisms involved in the development of primary bone tumors and associated lung metastasis. The POS-1 cell line is derived from an osteosarcoma tumor which develops spontaneously in C3H mice. The POS-1 cell line was characterized in vitro by mineralization capacity and expression of bone markers by semi-quantitative RT-PCR, compared to primary osteoblasts and bone marrow cells. POS-1 cells showed no mineralization capacity and exhibited an undifferentiated phenotype, expressing both osteoblastic and unexpected osteoclastic markers (TRAP, cathepsin K and RANK). Thereby, experiments were performed to determine whether RANK was functional, by studying the biological activity of murine RANKL through the receptor RANK expressed on POS-1 cells. Results revealed a RANKL-induced increase in ERK phosphorylation, as well as BMP-2 induction at the mRNA and protein levels, and a decrease of POS-1 cell proliferation in the presence of 10 ng/ml RANKL. BMP-2 induction is dependent on the ERK 1/2 signal transduction pathway, as its expression is abolished in the presence of UO126, a specific synthetic inhibitor of the ERK 1/2 pathway. Moreover, a 2-fold molar excess of soluble RANK blocks the RANKL-induced BMP-2 expression, demonstrating that the biological effects of RANKL observed in POS-1 cells are mediated by RANK. This is the first report describing a functional RANK expressed on osteosarcoma cells, as shown by its ability to induce signal transduction pathways and biological activity when stimulated by RANKL

Developable Rotationally Symmetric Kirigami‐Based Structures as Sensor Platforms

Developable surfaces based on closed‐shape, planar, rotationally symmetric kirigami (RSK) sheets approximate 3D, globally curved surfaces upon (reversible) out‐of‐plane deflection. The distribution of stress and strain across the structure is characterized experimentally and by finite‐element analysis as a function of the material and cut parameters, enabling the integration with strain gauges to produce a wearable, conformal patch that can capture complex, multiaxis motion. Using the patch, real‐time tracking of shoulder joint and muscle behavior is demonstrated. The facile fabrication and unique properties of the RSK structures potentially enable wearable, textile‐integrated joint monitoring for athletic training, wellness, rehabilitation, feedback control for augmented mobility, motion of soft and traditional robotics, and other applications.This work introduces a new paradigm for realizing 2D to curved, 3D, functional surface transformation using rotationally symmetric kirigami as a platform for deploying wearable sensors; here it is demonstrated for real‐time tracking of complex motion of joints within the body and circumventing longstanding tradeoffs in the design of materials, structures, and devices for conformable, wearable electronics.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153082/1/admt201900563-sup-0001-SuppMat.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153082/2/admt201900563.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153082/3/admt201900563_am.pd

Classification of SD-OCT Volumes using Local Binary Patterns: Experimental Validation for DME Detection

International audienceThis paper addresses the problem of automatic classification of Spectral Domain OCT (SD-OCT) data for automatic identification of patients with Diabetic Macular Edema (DME) versus normal subjects. Optical Coherence Tomography (OCT) has been a valuable diagnostic tool for DME, which is among the most common causes of irreversible vision loss in individuals with diabetes. Here, a classification framework with five distinctive steps is proposed and we present an extensive study of each step. Our method considers combination of various pre-processings in conjunction with Local Binary Patterns (LBP) features and different mapping strategies. Using linear and non-linear classifiers, we tested the developed framework on a balanced cohort of 32 patients. Experimental results show that the proposed method outperforms the previous studies by achieving a Sensitivity (SE) and Specificity (SP) of 81.2% and 93.7%, respectively. Our study concludes that the 3D features and high-level representation of 2D features using patches achieve the best results. However, the effects of pre-processing is inconsistent with respect to different classifiers and feature configurations

The Impact of Diabetic Retinopathy and Diabetic Macular Edema on Health-Related Quality of Life in Type 1 and Type 2 Diabetes

This article is made available with the permission of the publisher, Association for Research in Vision and OphthalmologyPurpose.: To assess the impact of diabetic retinopathy (DR) and diabetic macular edema (DME) on health-related quality of life (HRQoL) in type 1 and type 2 diabetes using the EuroQoL EQ-5D generic multi-attribute utility instrument (MAUI). Methods.: In this cross-sectional study, 577 patients with diabetes were recruited from specialized eye clinics in Melbourne, Australia. Each patient underwent clinical, biochemical, and anthropometric assessments. The severity of combined DR and DME (no DR/DME; mild NPDR [nonproliferative DR (NPDR)] and/or mild DME; moderate NPDR and/or moderate DME; and vision-threatening DR (VTDR) (severe NPDR or PDR and/or severe DME) in the worse eye was calculated. EQ-5D utility measures were the main outcome. Because the distribution of the utility measures was skewed, independent associations were explored using multivariate quantile regression models (five quintiles, namely 15th, 30th, 45th, 60th, 75th) ranging from poorest to highest HRQoL. Results.: Median age of the participants was 66 years (range, 26–90 years). Of the 577 participants, 223 (38.7%) had no DR/DME, 35 (6.1%) had mild NPDR/DME, 127 (22.0%) had moderate NPDR/DME, and 192 (33.3%) had VTDR. In adjusted models, neither presence nor severity of DR/DME was significantly associated with any quantile of the EQ-5D. In contrast, the presence of diabetic complications (other than DR) (β = −0.153; SE = 0.052; P < 0.001), other nonocular comorbidities (β = −0.115; SE = 0.038; P < 0.01), and higher body mass index (β = −0.007; SE = 0.002; P < 0.001) were all associated with worse HRQoL. Conclusions.: Using a generic MAUI, the EQ-5D, the authors found that the presence or severity of DR/DME and concomitant vision loss were not associated with any quantile of HRQoL. These findings suggest that the EQ-5D lacks sensitivity in assessing the impact of the severity of DR/DME on HRQoL parameters and that condition-specific instruments may better capture the full impact of the association

Classification of SD-OCT volumes with multi pyramids, LBP and HOG descriptors: application to DME detections

International audienceThis paper deals with the automated detection of DME on OCT volumes.Our method considers a generic classification pipeline with preprocessing for noise removal and flattening of each B-Scan.Features such as HoG and LBP are extracted and combined to create a set of different feature vectors which are fed to a linear-SVM classifier.Experimental results show a promising sensitivity/specificity of 0.75/0.87 on a challenging dataset

Astrophysical Neutrino Event Rates and Sensitivity for Neutrino Telescopes

Spectacular processes in astrophysical sites produce high-energy cosmic rays which are further accelerated by Fermi-shocks into a power-law spectrum. These, in passing through radiation fields and matter, produce neutrinos. Neutrino telescopes are designed with large detection volumes to observe such astrophysical sources. A large volume is necessary because the fluxes and cross-sections are small. We estimate various telescopes' sensitivities and expected event rates from astrophysical sources of high-energy neutrinos. We find that an ideal detector of km^2 incident area can be sensitive to a flux of neutrinos integrated over energy from 10^5 and 10^{7} GeV as low as 1.3 * 10^(-8) * E^(-2) (GeV/cm^2 s sr) which is three times smaller than the Waxman-Bachall conservative upper limit on potential neutrino flux. A real detector will have degraded performance. Detection from known point sources is possible but unlikely unless there is prior knowledge of the source location and neutrino arrival time.Comment: Section added +modification

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein

Thermal phase diagrams of columnar liquid crystals

In order to understand the possible sequence of transitions from the disordered columnar phase to the helical phase in hexa(hexylthio)triphenylene (HHTT), we study a three-dimensional planar model with octupolar interactions inscribed on a triangular lattice of columns. We obtain thermal phase diagrams using a mean-field approximation and Monte Carlo simulations. These two approaches give similar results, namely, in the quasi one-dimensional regime, as the temperature is lowered, the columns order with a linear polarization, whereas helical phases develop at lower temperatures. The helicity patterns of the helical phases are determined by the exact nature of the frustration in the system, itself related to the octupolar nature of the molecules.Comment: 12 pages, 9 figures, ReVTe