Self Super-Resolution for Magnetic Resonance Images using Deep Networks

High resolution magnetic resonance~(MR) imaging~(MRI) is desirable in many clinical applications, however, there is a trade-off between resolution, speed of acquisition, and noise. It is common for MR images to have worse through-plane resolution~(slice thickness) than in-plane resolution. In these MRI images, high frequency information in the through-plane direction is not acquired, and cannot be resolved through interpolation. To address this issue, super-resolution methods have been developed to enhance spatial resolution. As an ill-posed problem, state-of-the-art super-resolution methods rely on the presence of external/training atlases to learn the transform from low resolution~(LR) images to high resolution~(HR) images. For several reasons, such HR atlas images are often not available for MRI sequences. This paper presents a self super-resolution~(SSR) algorithm, which does not use any external atlas images, yet can still resolve HR images only reliant on the acquired LR image. We use a blurred version of the input image to create training data for a state-of-the-art super-resolution deep network. The trained network is applied to the original input image to estimate the HR image. Our SSR result shows a significant improvement on through-plane resolution compared to competing SSR methods.Comment: Accepted by IEEE International Symposium on Biomedical Imaging (ISBI) 201

Automatic categorization of Ottoman poems

Cataloged from PDF version of article.This work is partially supported by the Scientific and Technical Research Council of Turkey (TÜBİTAK) under the grant number 109E006.Authorship attribution and identifying time period of literary works are fundamental problems in quantitative analysis of languages. We investigate two fundamentally different machine learning text categorization methods, Support Vector Machines (SVM) and Naïve Bayes (NB), and several style markers in the categorization of Ottoman poems according to their poets and time periods. We use the collected works (divans) of ten different Ottoman poets: two poets from each of the five different hundred-year periods ranging from the 15th to 19 th century. Our experimental evaluation and statistical assessments show that it is possible to obtain highly accurate and reliable classifications and to distinguish the methods and style markers in terms of their effectiveness

Polarization Beam Splitter Based on Self-Collimation of a Hybrid Photonic Crystal

A photonic crystal polarization beam splitter based on photonic band gap and self-collimation effects is designed for optical communication wavelengths. The photonic crystal structure consists of a polarization-insensitive self-collimation region and a splitting region. TM- and TE-polarized waves propagate without diffraction in the self-collimation region, whereas they split by 90 degrees in the splitting region. Efficiency of more than 75% for TM- and TE-polarized light is obtained for a polarization beam splitter size of only 17 μm x 17 μm in a wavelength interval of 60 nm including 1.55 μm

Div-BLAST: Diversification of sequence search results

Cataloged from PDF version of article.Sequence similarity tools, such as BLAST, seek sequences most similar to a query from a database of sequences. They return results significantly similar to the query sequence and that are typically highly similar to each other. Most sequence analysis tasks in bioinformatics require an exploratory approach, where the initial results guide the user to new searches. However, diversity has not yet been considered an integral component of sequence search tools for this discipline. Some redundancy can be avoided by introducing non-redundancy during database construction, but it is not feasible to dynamically set a level of non-redundancy tailored to a query sequence. We introduce the problem of diverse search and browsing in sequence databases that produce non-redundant results optimized for any given query. We define diversity measures for sequences and propose methods to obtain diverse results extracted from current sequence similarity search tools. We also propose a new measure to evaluate the diversity of a set of sequences that is returned as a result of a sequence similarity query. We evaluate the effectiveness of the proposed methods in post-processing BLAST and PSI-BLAST results. We also assess the functional diversity of the returned results based on available Gene Ontology annotations. Additionally, we include a comparison with a current redundancy elimination tool, CD-HIT. Our experiments show that the proposed methods are able to achieve more diverse yet significant result sets compared to static non-redundancy approaches. In both sequence-based and functional diversity evaluation, the proposed diversification methods significantly outperform original BLAST results and other baselines. A web based tool implementing the proposed methods, Div-BLAST, can be accessed at cedar.cs.bilkent.edu.tr/Div-BLAS

Force Modulating Dynamic Disorder: Physical Theory of Catch-slip bond Transitions in Receptor-Ligand Forced Dissociation Experiments

Recently experiments showed that some adhesive receptor-ligand complexes increase their lifetimes when they are stretched by mechanical force, while the force increase beyond some thresholds their lifetimes decrease. Several specific chemical kinetic models have been developed to explain the intriguing transitions from the "catch-bonds" to the "slip-bonds". In this work we suggest that the counterintuitive forced dissociation of the complexes is a typical rate process with dynamic disorder. An uniform one-dimension force modulating Agmon-Hopfield model is used to quantitatively describe the transitions observed in the single bond P-selctin glycoprotein ligand 1(PSGL-1)$-$P-selectin forced dissociation experiments, which were respectively carried out on the constant force [Marshall, {\it et al.}, (2003) Nature {\bf 423}, 190-193] and the force steady- or jump-ramp [Evans {\it et al.}, (2004) Proc. Natl. Acad. Sci. USA {\bf 98}, 11281-11286] modes. Our calculation shows that the novel catch-slip bond transition arises from a competition of the two components of external applied force along the dissociation reaction coordinate and the complex conformational coordinate: the former accelerates the dissociation by lowering the height of the energy barrier between the bound and free states (slip), while the later stabilizes the complex by dragging the system to the higher barrier height (catch).Comment: 8 pages, 3 figures, submitte

Improvement of the Wastewater Biodegradability by Means of Photocatalytic and Wet Oxidation Processes in the Presence of Hydrogen Peroxide

In this study, the effectiveness of photocatalytic oxidation (PO) and wet oxidation (WO) processes as a pre-treatment step on improvement of biodegradability and colour removal of mixture of raw domestic and pre-treated industrial wastewaters, have been evaluated. More oxygen was obtained by H2O2 (as an oxidant in WO and PO processes) than stoichiometric demand. PO of the wastewater was carried out by illumination of the wastewater with UV lamp (at room temperature, atmospheric pressure, 16.5 h reaction time) and WO of the wastewater was carried out by means of thermal oxidation at autoclave conditions (at 118–120 oC, 1.9–2 bar, 3 h reaction time). 1 g L–1 TiO2 in PO process and 0.2 mg L–1 Cu++ in WO process were used as catalyst. The results obtained from experiments were not compared with each other due to the difference between the quality and quantity of the used catalyst and the consumed energy. Colour removal efficiency was 33 % for WO process and 77.6 % for PO process. By applying WO process, 72.7 % increase in the reaction rate coefficient describing the degradability of organic compounds in wastewater was obtained, but this value was 34.5 % in PO process

A simple test for hidden variables in spin-1 system

We resolve an old problem about the existence of hidden parameters in a three-dimensional quantum system by constructing an appropriate Bell's type inequality. This reveals a nonclassical nature of most spin-$1$ states. We shortly discuss some physical implications and an underlying cause of this nonclassical behavior, as well as a perspective of its experimental verification.Comment: 4 pages, 1 figur

Capture on High Curvature Region: Aggregation of Colloidal Particle Bound to Giant Phospholipid Vesicles

A very recent observation on the membrane mediated attraction and ordered aggregation of colloidal particles bound to giant phospholipid vesicles (I. Koltover, J. O. R\"{a}dler, C. R. Safinya, Phys. Rev. Lett. {\bf 82}, 1991(1999)) is investigated theoretically within the frame of Helfrich curvature elasticity theory of lipid bilayer fluid membrane. Since the concave or waist regions of the vesicle possess the highest local bending energy density, the aggregation of colloidal beads on these places can reduce the elastic energy in maximum. Our calculation shows that a bead in the concave region lowers its energy $\sim 20 k_B T$. For an axisymmetrical dumbbell vesicle, the local curvature energy density along the waist is equally of maximum, the beads can thus be distributed freely with varying separation distance.Comment: 12 pages, 2 figures. REVte