GlyComb: A novel glycoconjugate data repository that bridges glycomics and proteomics

The glycosylation of proteins and lipids is known to be closely related to the mechanisms of various diseases such as influenza, cancer, and muscular dystrophy. Therefore, it has become clear that the analysis of post-translational modifications of proteins, including glycosylation, is important to accurately understand the functions of each protein molecule and the interactions among them. In order to conduct large-scale analyses more efficiently, it is essential to promote the accumulation, sharing, and reuse of experimental and analytical data in accordance with the FAIR (Findability, Accessibility, Interoperability, and Re-usability) data principles. However, a FAIR data repository for storing and sharing glycoconjugate information, including glycopeptides and glycoproteins, in a standardized format did not exist. Therefore, we have developed GlyComb (https://glycomb.glycosmos.org) as a new standardized data repository for glycoconjugate data. Currently, GlyComb can assign a unique identifier to a set of glycosylation information associated with a specific peptide sequence or UniProt ID. By standardizing glycoconjugate data via GlyComb identifiers and coordinating with existing web resources such as GlyTouCan and GlycoPOST, a comprehensive system for data submission and data sharing among researchers can be established. Here we introduce how GlyComb is able to integrate the variety of glycoconjugate data already registered in existing data repositories to obtain a better understanding of the available glycopeptides and glycoproteins, and their glycosylation patterns. We also explain how this system can serve as a foundation for a better understanding of glycan function.

[Development of Integrated Database for Experiments and Simulations]

Researchers collect data and use various methods to organize it. Ensuring the reliability and reproducibility of data is crucial, and collaboration across different research fields is on the rise. However, when there is geographical distance, sharing data becomes a challenging task. Therefore, there is a need for the development of a mechanism for sharing data on the web. We have developed an integrated database to facilitate the sharing and management of research data, particularly focusing on small molecules. The integrated database serves as a platform for centralizing data related to small molecules, including their chemical structures, wet lab experimental data, simulation data, and more. It has been constructed as a web application, offering features such as library management for small molecules, registration and viewing of wet lab experiment results, generation of initial conformations for simulations, and data visualization. This enables researchers to efficiently share their research data and collaborate seamlessly, whether within their research group or via cloud-based access that allows project and team members to connect from anywhere. This integrated database plays a critical role in connecting wet lab experiments and simulations, enabling researchers to cross-reference and analyze experimental data comprehensively. It serves as an essential tool to advance research and foster idea generation.

Bridging glycoinformatics and cheminformatics: integration efforts between GlyCosmos and PubChem

The GlyCosmos Glycoscience Portal (https://glycosmos.org) and PubChem (https://pubchem.ncbi.nlm.nih.gov/) are major portals for glycoscience and chemistry, respectively. GlyCosmos is a portal for glycan-related repositories, including GlyTouCan, GlycoPOST, and UniCarb-DR, as well as for glycan-related data resources that have been integrated from a variety of 'omics databases. Glycogenes, glycoproteins, lectins, pathways, and disease information related to glycans are accessible from GlyCosmos. PubChem, on the other hand, is a chemistry-based portal at the National Center for Biotechnology Information. PubChem provides information not only on chemicals, but also genes, proteins, pathways, as well as patents, bioassays, and more, from hundreds of data resources from around the world. In this work, these 2 portals have made substantial efforts to integrate their complementary data to allow users to cross between these 2 domains. In addition to glycan structures, key information, such as glycan-related genes, relevant diseases, glycoproteins, and pathways, was integrated and cross-linked with one another. The interfaces were designed to enable users to easily find, access, download, and reuse data of interest across these resources. Use cases are described illustrating and highlighting the type of content that can be investigated. In total, these integrations provide life science researchers improved awareness and enhanced access to glycan-related information.

Enhanced Material Assimilation in a Toroidal Plasma Using Mixed H_{2}+Ne Pellet Injection and Implications to ITER

The ablation and assimilation of cryogenic pure H_{2} and mixed H_{2}+Ne pellets, which are foreseen to be used by the ITER tokamak for mitigating thermal and electromagnetic loads of major disruptions, are observed by spatially and temporally resolved measurements. It is experimentally demonstrated that a small fraction (here ≈5%) of neon added to hydrogenic pellets enhances the core density assimilation with reduced outward transport for the low magnetic-field side injection. This is consistent with theoretical expectations that line radiation increased by doped neon in dense plasmoids suppresses the plasmoid pressure and reduces the E[over →]×B[over →] transport of the ablated material.

Electron temperature and density measurement by Thomson scattering with a high repetition rate laser of 20 kHz on LHD

Thomson scattering measurements with a high-repetition-rate laser have commenced in the Large Helical Device. As an example of the fast phenomena captured by this diagnostic system, measurements at a 20 kHz repetition-rate in hydrogen pellet-injected plasmas are presented. Signal processing methods for this measurement have been developed and electron temperature profiles with almost 70 spatial points were evaluated at time intervals of 50 [Formula: see text]s. After Raman scattering calibration, electron density profiles were derived. Fast changes in the electron temperature and density profiles within 1 ms were observed.

Preceding propagation of turbulence pulses at avalanche events in a magnetically confined plasma

The preceding propagation of turbulence pulses has been observed for the first time in heat avalanche events during the collapse of the electron internal transport barrier (e-ITB) in the Large Helical Device. The turbulence and heat pulses are generated near the foot of the e-ITB and propagate to the peripheral region within a much shorter time than the diffusion timescale. The propagation speed of the turbulence pulse is approximately 10 km/s, which is faster than that of the heat pulse propagating at a speed of 1.5 km/s. The heat pulse propagates at approximately the same speed as that in the theoretical prediction, whereas the turbulence pulse propagates one order of magnitude faster than that in the prediction, thereby providing important insights into the physics of non-local transport.

Impact of Magnetic Field Configuration on Heat Transport in Stellarators and Heliotrons

We assess the magnetic field configuration in modern fusion devices by comparing experiments with the same heating power, between a stellarator and a heliotron. The key role of turbulence is evident in the optimized stellarator, while neoclassical processes largely determine the transport in the heliotron device. Gyrokinetic simulations elucidate the underlying mechanisms promoting stronger ion scale turbulence in the stellarator. Similar plasma performances in these experiments suggests that neoclassical and turbulent transport should both be optimized in next step reactor designs.

Initial operation and data processing on a system for real-time evaluation of Thomson scattering signals on the Large Helical Device

A scalable system for real-time analysis of electron temperature and density based on signals from the Thomson scattering diagnostic, initially developed for and installed on the NSTX-U experiment, was recently adapted for the Large Helical Device and operated for the first time during plasma discharges. During its initial operation run, it routinely recorded and processed signals for four spatial points at the laser repetition rate of 30 Hz, well within the system's rated capability for 60 Hz. We present examples of data collected from this initial run and describe subsequent adaptations to the analysis code to improve the fidelity of the temperature calculations.

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery.

Improvement in multipass Thomson scattering system comprising laser amplification system developed in GAMMA 10/PDX

The multipass Thomson scattering (MPTS) technique is one of the most useful methods for measuring low-electron-density plasmas. The MPTS system increases Thomson scattering (TS) signal intensities by integrating all multipass (MP) signals and improving the TS time resolution by analyzing each pass signal. The fully coaxial MPTS system developed in GAMMA 10/potential-control and diverter-simulator experiments has a polarization-based configuration with image-relaying optics. The MPTS system can enhance Thomson scattered signals for improving the measurement accuracy and megahertz-order time resolution. In this study, we develop a new MPTS system comprising a laser amplification system to obtain continuous MP signals. The laser amplification system can improve degraded laser power and return an amplified laser to the MP system. We obtain continuous MP signals from the laser amplification system by improving the laser beam profile adjuster in gas scattering experiments. Moreover, we demonstrate that more MP signals and stronger amplified MP signals can be achieved via multiple laser injections to the laser amplification system in the developed MP system comprising a laser amplification system.

The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application

Recent years have seen great advances in the development of glycoproteomics protocols and methods resulting in a sustainable increase in the reporting proteins, their attached glycans and glycosylation sites. However, only very few of these reports find their way into databases or data repositories. One of the major reasons is the absence of digital standard to represent glycoproteins and the challenging annotations with glycans. Depending on the experimental method, such a standard must be able to represent glycans as complete structures or as compositions, store not just single glycans but also represent glycoforms on a specific glycosylation side, deal with partially missing site information if no site mapping was performed, and store abundances or ratios of glycans within a glycoform of a specific site. To support the above, we have developed the GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoproteomics data. GlycoCoO can be used to represent glycoproteomics data in triplestores and can serve as a basis for data exchange formats. The ontology, database providers and supporting documentation are available online (https://github.com/glycoinfo/GlycoCoO).

The international glycan repository GlyTouCan version 3.0

Glycans serve important roles in signaling events and cell-cell communication, and they are recognized by lectins, viruses and bacteria, playing a variety of roles in many biological processes. However, there was no system to organize the plethora of glycan-related data in the literature. Thus GlyTouCan (https://glytoucan.org) was developed as the international glycan repository, allowing researchers to assign accession numbers to glycans. This also aided in the integration of glycan data across various databases. GlyTouCan assigns accession numbers to glycans which are defined as sets of monosaccharides, which may or may not be characterized with linkage information. GlyTouCan was developed to be able to recognize any level of ambiguity in glycans and uniquely assign accession numbers to each of them, regardless of the input text format. In this manuscript, we describe the latest update to GlyTouCan in version 3.0, its usage, and plans for future development.

GlycanFormatConverter: a conversion tool for translating the complexities of glycans

Motivation

Glycans are biomolecules that take an important role in the biological processes of living organisms. They form diverse, complicated structures such as branched and cyclic forms. Web3 Unique Representation of Carbohydrate Structures (WURCS) was proposed as a new linear notation for uniquely representing glycans during the GlyTouCan project. WURCS defines rules for complex glycan structures that other text formats did not support, and so it is possible to represent a wide variety glycans. However, WURCS uses a complicated nomenclature, so it is not human-readable. Therefore, we aimed to support the interpretation of WURCS by converting WURCS to the most basic and widely used format IUPAC.

Results

In this study, we developed GlycanFormatConverter and succeeded in converting WURCS to the three kinds of IUPAC formats (IUPAC-Extended, IUPAC-Condensed and IUPAC-Short). Furthermore, we have implemented functionality to import IUPAC-Extended, KEGG Chemical Function (KCF) and LinearCode formats and to export WURCS. We have thoroughly tested our GlycanFormatConverter and were able to show that it was possible to convert all the glycans registered in the GlyTouCan repository, with exceptions owing only to the limitations of the original format. The source code for this conversion tool has been released as an open source tool.

Availability and implementation

https://github.com/glycoinfo/GlycanFormatConverter.git

Supplementary information

Supplementary data are available at Bioinformatics online.

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

Microwave frequency comb Doppler reflectometer applying fast digital data acquisition system in LHD

We succeeded in increasing the radial observation points of the microwave frequency comb Doppler reflectometer system from 8 to 20 (or especially up to 45) using the high sampling rate of 40 GS/s digital signal processing. For a new acquisition system, the estimation scheme of the Doppler shifted frequency is constructed and compared with the conventional technique. Also, the fine radial profile of perpendicular velocity is obtained, and it is found that the perpendicular velocity profile is consistent with the E × B drift velocity one.

Nd:YAG laser Thomson scattering diagnostics for a laboratory magnetosphere

A new Nd:YAG laser Thomson scattering (TS) system has been developed to explore the mechanism of high-beta plasma formation in the RT-1 device. The TS system is designed to measure electron temperatures (T_e) from 10 eV to 50 keV and electron densities (n_e) of more than 1.0 × 10¹⁷ m^-3. To measure at the low-density limit, the receiving optics views the long scattering length (60 mm) using a bright optical system with both a large collection window (260-mm diameter) and large collection lenses (300-mm diameter, a solid angle of ∼68 × 10^-3 str). The scattered light of the 1.2-J Nd:YAG laser (repetition frequency: 10 Hz) is detected with a scattering angle of 90° and is transferred via a set of lenses and an optical fiber bundle to a polychromator. After Raman scattering measurement for the optical alignment and an absolute calibration, we successfully measured T_e = 72.2 eV and n_e = 0.43 × 10¹⁶ m^-3 for the coil-supported case and T_e = 79.2 eV and n_e = 1.28 × 10¹⁶ m^-3 for the coil-levitated case near the inner edge in the magnetospheric plasmas.

Development of a laser amplification system for the multi-pass Thomson scattering system for GAMMA 10/PDX

The multi-pass Thomson scattering (MPTS) system is a useful technique for increasing the Thomson scattering (TS) signal intensities and improving the TS diagnostic time resolution. The MPTS system developed in GAMMA 10/PDX has a polarization-based configuration with an image relaying system. The MPTS system has been constructed for enhancing the Thomson scattered signals for the improvement of measurement accuracy and the megahertz sampling time resolution. However, in the normal MPTS system, the MPTS signal intensities decrease with the pass number because of the damping due to the optical components. Subsequently, we have developed a new MPTS system with the laser amplification system. The laser amplification system can improve the degraded laser power after six passes in the multi-pass system to the initial laser power. For the first time worldwide, we successfully obtained the continued multi-pass signals after the laser amplification system in the gas scattering experiments.

GlyTouCan: an accessible glycan structure repository

Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.

Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans

GlyTouCan version 1.0 was released in 2015 as the international glycan structure repository, and a new sequence format called WURCS (Web3 Unique Representation of Carbohydrate Structures) was proposed during the early stages of the GlyTouCan project. GlyTouCan uses WURCS as its base representation for glycans because existing formats were insufficient in their flexibility to represent any and all glycans universally. Therefore, in order to obtain WURCS strings for existing or new glycan structures, conversion tools or glycan structure editors that can export WURCS became necessary. GlycanBuilder was an obvious choice to extend due to its wide usage by the community. However, GlycanBuilder was limited because it was originally developed to support mammalian glycans. It also did not support the newly proposed monosaccharide symbol standard called Symbol Nomenclature for Glycans (SNFG). Therefore in this work, we implemented a new version of GlycanBuilder to greatly increase its usability. The glycan rendering system was refactored so that cyclic glycans, nested repeating units, monosaccharide compositions and cross-linked glycan structures can be represented. Both import and export utilities for WURCS were also implemented and SNFG symbols were incorporated to allow glycans to be exported as graphics using the latest glycan symbol nomenclature. This new version of GlycanBuilder called "GlycanBuilder2", is able to support a wide variety of ambiguous glycans, including structures containing monosaccharides from bacteria and plants. These glycans can also be displayed using the new SNFG symbols. This tool can aid researchers in communicating about the complex, diverse, and ambiguous structures of glycans more rapidly. Moreover, the new GlycanBuilder can now easily output WURCS sequences from glycans drawn on the canvas. Most importantly, because GlyTouCan employs WURCS as the basic format for registration and searching of glycan information, a wider variety of glycans can now be readily registered and queried in GlyTouCan.

Calibrations of the LHD Thomson scattering system

The Thomson scattering diagnostic systems are widely used for the measurements of absolute local electron temperatures and densities of fusion plasmas. In order to obtain accurate and reliable temperature and density data, careful calibrations of the system are required. We have tried several calibration methods since the second LHD experiment campaign in 1998. We summarize the current status of the calibration methods for the electron temperature and density measurements by the LHD Thomson scattering diagnostic system. Future plans are briefly discussed.

Analysis method for Thomson scattering diagnostics in GAMMA 10/PDX

We have developed an analysis method to improve the accuracies of electron temperature measurement by employing a fitting technique for the raw Thomson scattering (TS) signals. Least square fitting of the raw TS signals enabled reduction of the error in the electron temperature measurement. We applied the analysis method to a multi-pass (MP) TS system. Because the interval between the MPTS signals is very short, it is difficult to separately analyze each Thomson scattering signal intensity by using the raw signals. We used the fitting method to obtain the original TS scattering signals from the measured raw MPTS signals to obtain the electron temperatures in each pass.

Design of practical alignment device in KSTAR Thomson diagnostic

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak's Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR's Thomson scattering diagnostics.

Development of a neural network technique for KSTAR Thomson scattering diagnostics

Neural networks provide powerful approaches of dealing with nonlinear data and have been successfully applied to fusion plasma diagnostics and control systems. Controlling tokamak plasmas in real time is essential to measure the plasma parameters in situ. However, the χ² method traditionally used in Thomson scattering diagnostics hampers real-time measurement due to the complexity of the calculations involved. In this study, we applied a neural network approach to Thomson scattering diagnostics in order to calculate the electron temperature, comparing the results to those obtained with the χ² method. The best results were obtained for 10³ training cycles and eight nodes in the hidden layer. Our neural network approach shows good agreement with the χ² method and performs the calculation twenty times faster.

Validations of calibration-free measurements of electron temperature using double-pass Thomson scattering diagnostics from theoretical and experimental aspects

This paper evaluates the accuracy of electron temperature measurements and relative transmissivities of double-pass Thomson scattering diagnostics. The electron temperature (T_e) is obtained from the ratio of signals from a double-pass scattering system, then relative transmissivities are calculated from the measured T_e and intensity of the signals. How accurate the values are depends on the electron temperature (T_e) and scattering angle (θ), and therefore the accuracy of the values was evaluated experimentally using the Large Helical Device (LHD) and the Tokyo spherical tokamak-2 (TST-2). Analyzing the data from the TST-2 indicates that a high T_e and a large scattering angle (θ) yield accurate values. Indeed, the errors for scattering angle θ = 135° are approximately half of those for θ = 115°. The method of determining the T_e in a wide T_e range spanning over two orders of magnitude (0.01-1.5 keV) was validated using the experimental results of the LHD and TST-2. A simple method to provide relative transmissivities, which include inputs from collection optics, vacuum window, optical fibers, and polychromators, is also presented. The relative errors were less than approximately 10%. Numerical simulations also indicate that the T_e measurements are valid under harsh radiation conditions. This method to obtain T_e can be considered for the design of Thomson scattering systems where there is high-performance plasma that generates harsh radiation environments.

CT Features in Second Cancers of the Maxillary Sinus

Five patients with a second maxillary cancer (squamous cell carcinoma), which developed 6 to 17 years after initial treatment for the first cancer on the opposite side, were compared with 21 control cases with a primary cancer on the basis of computed tomography (CT) findings. Generally, the second cancer was found at an earlier stage. The specific CT findings of early sinus carcinoma were uneven soft tissue distribution in the antrum and tumor permeation with bone fragments remaining at the original tumor site. These findings may be helpful for distinguishing this cancer from benign chronic sinusitis and/or other malignant sinus disease. The pterygoid process, medial bony wall, and ethmoid sinus had a tendency to be spared in most of the 5 patients with second maxillary cancer compared to the 21 control cases.

Effect of Gd-DTPA and/or Magnetic Field and Radiofrequency Exposure on Sister Chromatid Exchange in Human Peripheral Lymphocytes

The effects of a magnetic field, radiofrequency, and gadolinium diethylenetriaminepentaacetic acid (Gd-DTPA) on the sister chromatid exchange (SCE) in human peripheral lymphocytes were investigated. Whole blood was taken from a nonsmoker and samples were exposed to magnetic force (1.5 T) alone, and to a magnetic force combined with radiofrequency waves (63.86 MHz, specific absorption rate, SAR, 0.4 W/kg). Gd-DTPA was then added to other blood samples in varying amounts and concentrations. After exposure to the conditions described above, these blood samples were cultured for 69 hours. Slides were made for an SCE evaluation. As the concentration of Gd-DTPA added to the blood increased, the SCE frequency also increased. However, the addition of Gd-DTPA at the clinical concentrations normally used did not affect the SCE frequency.

Long-term Intraarterial Infusion Therapy with Prostaglandin E1 in Patients with Ischemic Ulcer of the Extremities

There is confusion about blood flow of the foot during intraarterial infusion of prostaglandin E 1. The authors studied blood flow in the dorsalis pedis arter ies of patients with ischemic ulcer during the infusion and report the results in this paper.

Prostaglandin E1 was continuously infused intraarterially for a mean of 30.9 ±14.5 days in 17 lower extremities of 11 patients with intractable ischemic ulcers. Thirteen of the 17 cases responded to the treatment—especially the cases in which peripheral arteries near the foot joint were patent. In the dorsalis pedis artery, the blood flow increased by 266.3% during the arterial infusion, but no differences were seen in the peak frequency or the percent window denoting the degree of spectral broadening in the infused lower limb. On the other hand, there was no statistically significant difference between the blood flow, peak frequency, or percent window of the contralateral lower limb before, and those parameters during, the infusion. The authors observed complications in 9 of 17 cases, which necessitated the discontinuation of the infusion.

On the energy scale involved in the metal to insulator transition of quadruple perovskite EuCu3Fe4O12: infrared spectroscopy and ab-initio calculations

Optical measurements were carried out by infrared spectroscopy on AA′₃B₄O₁₂ A-site ordered quadruple perovskite EuCu₃Fe₄O₁₂ (microscopic sample) as function of temperature. At 240 K (=T_MI), EuCu₃Fe₄O₁₂ undergoes a very abrupt metal to insulator transition, a paramagnetic to antiferromagnetic transition and an isostructural transformation with an abrupt large volume expansion. Above T_MI, optical conductivity reveals a bad metal behavior and below T_MI, an insulating phase with an optical gap of 125 meV is observed. As temperature is decreased, a large and abrupt spectral weight transfer toward an energy scale larger than 1 eV is detected. Concurrently, electronic structure calculations for both high and low temperature phases were compared to the optical conductivity results giving a precise pattern of the transition. Density of states and computed optical conductivity analysis identified Cu_3dxy, Fe_3d and O_2p orbitals as principal actors of the spectral weight transfer. The present work constitutes a first step to shed light on EuCu₃Fe₄O₁₂ electronic properties with optical measurements and ab-initio calculations.

Reconstruction of high temporal resolution Thomson scattering data during a modulated electron cyclotron resonance heating using conditional averaging

This paper provides a software application of the sampling scope concept for fusion research. The time evolution of Thomson scattering data is reconstructed with a high temporal resolution during a modulated electron cyclotron resonance heating (MECH) phase. The amplitude profile and the delay time profile of the heat pulse propagation are obtained from the reconstructed signal for discharges having on-axis and off-axis MECH depositions. The results are found to be consistent with the MECH deposition.

GlyTouCan 1.0--The international glycan structure repository

Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover the surfaces of many cells, serving as the 'face' of cells, whereby other biomolecules and viruses interact. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or nucleotides. Therefore, the storage of glycan information in databases, let alone their curation, has been a difficult problem. This has caused many duplicated efforts when integration is attempted between different databases, making an international repository for glycan structures, where unique accession numbers are assigned to every identified glycan structure, necessary. As such, an international team of developers and glycobiologists have collaborated to develop this repository, called GlyTouCan and is available at http://glytoucan.org/, to provide a centralized resource for depositing glycan structures, compositions and topologies, and to retrieve accession numbers for each of these registered entries. This will thus enable researchers to reference glycan structures simply by accession number, as opposed to by chemical structure, which has been a burden to integrate glycomics databases in the past.

GlycoRDF: an ontology to standardize glycomics data in RDF

MOTIVATION

Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information.

RESULTS

An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases.

AVAILABILITY AND IMPLEMENTATION

The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/).

Signal evaluations using singular value decomposition for Thomson scattering diagnostics

This paper provides a novel method for evaluating signal intensities in incoherent Thomson scattering diagnostics. A double-pass Thomson scattering system, where a laser passes through the plasma twice, generates two scattering pulses from the plasma. Evaluations of the signal intensities in the spectrometer are sometimes difficult due to noise and stray light. We apply the singular value decomposition method to Thomson scattering data with strong noise components. Results show that the average accuracy of the measured electron temperature (Te) is superior to that of temperature obtained using a low-pass filter (<20 MHz) or without any filters.

Edge profile measurements using Thomson scattering on the KSTAR tokamak

In the KSTAR Tokamak, a "Tangential Thomson Scattering" (TTS) diagnostic system has been designed and installed to measure electron density and temperature profiles. In the edge system, TTS has 12 optical fiber bundles to measure the edge profiles with 10-15 mm spatial resolution. These 12 optical fibers and their spatial resolution are not enough to measure the pedestal width with a high accuracy but allow observations of L-H transition or H-L transitions at the edge. For these measurements, the prototype ITER edge Thomson Nd:YAG laser system manufactured by JAEA in Japan is installed. In this paper, the KSTAR TTS system is briefly described and some TTS edge profiles are presented and compared against the KSTAR Charge Exchange Spectroscopy and other diagnostics. The future upgrade plan of the system is also discussed in this paper.