Extracting glycan motifs using a biochemicallyweighted kernel

Carbohydrates, or glycans, are one of the most abundant and structurally diverse biopolymers constitute the third major class of biomolecules, following DNA and proteins. However, the study of carbohydrate sugar chains has lagged behind compared to that of DNA and proteins, mainly due to their inherent structural complexity. However, their analysis is important because they serve various important roles in biological processes, including signaling transduction and cellular recognition. In order to glean some light into glycan function based on carbohydrate structure, kernel methods have been developed in the past, in particular to extract potential glycan biomarkers by classifying glycan structures found in different tissue samples. The recently developed weighted qgram method (LK-method) exhibits good performance on glycan structure classification while having limitations in feature selection. That is, it was unable to extract biologically meaningful features from the data. Therefore, we propose a biochemicallyweighted tree kernel (BioLK-method) which is based on a glycan similarity matrix and also incorporates biochemical information of individual q-grams in constructing the kernel matrix. We further applied our new method for the classification and recognition of motifs on publicly available glycan data. Our novel tree kernel (BioLK-method) using a Support Vector Machine (SVM) is capable of detecting biologically important motifs accurately while LK-method failed to do so. It was tested on three glycan data sets from the Consortium for Functional Glycomics (CFG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) GLYCAN and showed that the results are consistent with the literature. The newly developed BioLK-method also maintains comparable classification performance with the LK-method. Our results obtained here indicate that the incorporation of biochemical information of q-grams further shows the flexibility and capability of the novel kernel in feature extraction, which may aid in the prediction of glycan biomarkers

Introduction to the functional RG and applications to gauge theories

These lectures contain an introduction to modern renormalization group (RG) methods as well as functional RG approaches to gauge theories. In the first lecture, the functional renormalization group is introduced with a focus on the flow equation for the effective average action. The second lecture is devoted to a discussion of flow equations and symmetries in general, and flow equations and gauge symmetries in particular. The third lecture deals with the flow equation in the background formalism which is particularly convenient for analytical computations of truncated flows. The fourth lecture concentrates on the transition from microscopic to macroscopic degrees of freedom; even though this is discussed here in the language and the context of QCD, the developed formalism is much more general and will be useful also for other systems.Comment: 60 pages, 14 figures, Lectures held at the 2006 ECT* School "Renormalization Group and Effective Field Theory Approaches to Many-Body Systems", Trento, Ital

Pseudorapidity Dependence of Particle Production and Elliptic Flow in Asymmetric Nuclear Collisions of p+Al, p+Au, d+Au, and ^{3}He+Au at sqrt[s_{NN}]=200 GeV.

Asymmetric nuclear collisions of p+Al, p+Au, d+Au, and ^{3}He+Au at sqrt[s_{NN}]=200  GeV provide an excellent laboratory for understanding particle production, as well as exploring interactions among these particles after their initial creation in the collision. We present measurements of charged hadron production dN_{ch}/dη in all such collision systems over a broad pseudorapidity range and as a function of collision multiplicity. A simple wounded quark model is remarkably successful at describing the full data set. We also measure the elliptic flow v_{2} over a similarly broad pseudorapidity range. These measurements provide key constraints on models of particle emission and their translation into flow

Bridging ultrahigh-Q devices and photonic circuits

Optical microresonators are essential to a broad range of technologies and scientific disciplines. However, many of their applications rely on discrete devices to attain challenging combinations of ultra-low-loss performance (ultrahigh Q) and resonator design requirements. This prevents access to scalable fabrication methods for photonic integration and lithographic feature control. Indeed, finding a microfabrication bridge that connects ultrahigh-Q device functions with photonic circuits is a priority of the microcavity field. Here, an integrated resonator having a record Q factor over 200 million is presented. Its ultra-low-loss and flexible cavity design brings performance to integrated systems that has been the exclusive domain of discrete silica and crystalline microcavity devices. Two distinctly different devices are demonstrated: soliton sources with electronic repetition rates and high-coherence/low-threshold Brillouin lasers. This multi-device capability and performance from a single integrated cavity platform represents a critical advance for future photonic circuits and systems

A weighted q-gram method for glycan structure classification

<p>Abstract</p> <p>Background</p> <p>Glycobiology pertains to the study of carbohydrate sugar chains, or glycans, in a particular cell or organism. Many computational approaches have been proposed for analyzing these complex glycan structures, which are chains of monosaccharides. The monosaccharides are linked to one another by glycosidic bonds, which can take on a variety of comformations, thus forming branches and resulting in complex tree structures. The <it>q</it>-gram method is one of these recent methods used to understand glycan function based on the classification of their tree structures. This <it>q</it>-gram method assumes that for a certain <it>q</it>, different <it>q</it>-grams share no similarity among themselves. That is, that if two structures have completely different components, then they are completely different. However, from a biological standpoint, this is not the case. In this paper, we propose a weighted <it>q</it>-gram method to measure the similarity among glycans by incorporating the similarity of the geometric structures, monosaccharides and glycosidic bonds among <it>q</it>-grams. In contrast to the traditional <it>q</it>-gram method, our weighted <it>q</it>-gram method admits similarity among <it>q</it>-grams for a certain <it>q</it>. Thus our new kernels for glycan structure were developed and then applied in SVMs to classify glycans.</p> <p>Results</p> <p>Two glycan datasets were used to compare the weighted <it>q</it>-gram method and the original <it>q</it>-gram method. The results show that the incorporation of <it>q</it>-gram similarity improves the classification performance for all of the important glycan classes tested.</p> <p>Conclusion</p> <p>The results in this paper indicate that similarity among <it>q</it>-grams obtained from geometric structure, monosaccharides and glycosidic linkage contributes to the glycan function classification. This is a big step towards the understanding of glycan function based on their complex structures.</p

Reconstruction of primary vertices at the ATLAS experiment in Run 1 proton–proton collisions at the LHC

This paper presents the method and performance of primary vertex reconstruction in proton–proton collision data recorded by the ATLAS experiment during Run 1 of the LHC. The studies presented focus on data taken during 2012 at a centre-of-mass energy of √s=8 TeV. The performance has been measured as a function of the number of interactions per bunch crossing over a wide range, from one to seventy. The measurement of the position and size of the luminous region and its use as a constraint to improve the primary vertex resolution are discussed. A longitudinal vertex position resolution of about 30μm is achieved for events with high multiplicity of reconstructed tracks. The transverse position resolution is better than 20μm and is dominated by the precision on the size of the luminous region. An analytical model is proposed to describe the primary vertex reconstruction efficiency as a function of the number of interactions per bunch crossing and of the longitudinal size of the luminous region. Agreement between the data and the predictions of this model is better than 3% up to seventy interactions per bunch crossing

Successful Management of a Rare Case of Stent Fracture and Subsequent Migration of the Fractured Stent Segment Into the Ascending Aorta in In-Stent Restenotic Lesions of a Saphenous Vein Graft

Stent fracture is a complication following implantation of drug eluting stents and is recognized as one of the risk factors for in-stent restenosis. We present the first case of successfully managing a stent fracture and subsequent migration of the fractured stent into the ascending aorta that occurred during repeat revascularization for in-stent restenosis of an ostium of saphenous vein graft after implantation of a zotarolimus-eluting stent. Although the fractured stent segment had migrated into the ascending aorta with a pulled balloon catheter, it was successfully repositioned in the saphenous vein graft using an inflated balloon catheter. Then, the fractured stent segment was successfully connected to the residual segment of the zotarolimus-eluting stent by covering it with an additional sirolimuseluting stent

Stent Fracture at the Proximal Shaft of the Left Main Stem

Stent fracture is likely to be caused due to mechanical stress at the hinge point or kinking movement at the point of aneurysm formation with stent malapposition. To our knowledge, this is the first published report of stent fracture at the proximal shaft of the left main stem in a patient with acute myocardial infarction

Capilloquinol: A Novel Farnesyl Quinol from the Dongsha Atoll Soft Coral Sinularia capillosa

Capilloquinol (1), possessing an unprecedented farnesyl quinoid skeleton, was isolated from the Dongsha Atoll soft coral Sinularia capillosa. The structure of capilloquinol was elucidated by extensive analysis of spectroscopic data. The cytotoxicity and antiviral activity against human cytomegalovirus of 1 was evaluated in vitro

Effect of dispersants of multi-walled carbon nanotubes on cellular uptake and biological responses

Although there have been many reports about the cytotoxicity of multi-walled carbon nanotubes (MWCNTs), the results are still controversial. To investigate one possible reason, the authors investigated the influence of MWCNT dispersants on cellular uptake and cytotoxicity. Cytotoxicity was examined (measured by alamarBlue® assay), as well as intracellular MWCNT concentration and cytokine secretion (measured by flow cytometry) in human bronchial epithelial cells (BEAS-2B) exposed to a type of highly purified MWCNT vapor grown carbon fiber (VGCF®, Shōwa Denkō Kabushiki-gaisha, Tokyo, Japan) in three different dispersants (gelatin, carboxylmethyl cellulose, and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine). The authors also researched the relationship between the intracellular concentration of MWCNTs and cytotoxicity by using two cell lines, BEAS-2B and MESO-1 human malignant pleural mesothelioma cells. The intracellular concentration of VGCF was different for each of the three dispersants, and the levels of cytotoxicity and inflammatory response were correlated with the intracellular concentration of VGCF. A relationship between the intracellular concentration of VGCF and cytotoxic effects was observed in both cell lines. The results indicate that dispersants affect VGCF uptake into cells and that cytotoxicity depends on the intracellular concentration of VGCF, not on the exposed dosage. Thus, toxicity appears to depend on exposure time, even at low VGCF concentrations, because VGCF is biopersistent