BMIT facility at the Canadian Light Source: Advances in X-ray phase-sensitive imaging

The BioMedical Imaging and Therapy (BMIT) facility [1,2] located at the Canadian Light Source, provides synchrotron-specific imaging and radiation therapy capabilities. There are two separate beamlines used for experiments: the bending magnet (05B1-1) and the insertion device (05ID-2) beamline.The bending magnet beamline provides access to monochromatic beam spanning a spectral range of 15–40 keV, and the beam is 240 mm wide in the POE-2 experimental hutch. Users can also perform experiments with polychromatic (pink) beam.The insertion device beamline was officially opened for general user program in 2015. The source for the ID beamline is a multi-pole, superconducting 4.3 T wiggler. The high field gives a critical energy over 20 keV. The optics hutches prepare a beam that is 220 mm wide in the last experimental hutch SOE-1. The monochromatic spectral range spans 25–150+ keV. Several different X-ray detectors are available for both beamlines, with resolutions ranging from 2 μm to 200 μm.BMIT provides a number of imaging techniques including standard absorption X-ray imaging, K-edge subtraction imaging (KES), in-line phase contrast imaging (also known as propagation based imaging, PBI) and Diffraction Enhanced Imaging/Analyzer Based Imaging (DEI/ABI), all in either projection or CT mode. PBI and DEI/ABI are particularly important tools for BMIT users since these techniques enable visualization of soft tissue and allow for low dose imaging.     

Beam characterisation studies of the 62 MeV proton therapy beamline at the Clatterbridge Cancer Centre

The Clatterbridge Cancer Centre (CCC) in the United Kingdom is the world’s first hospital proton beam therapy facility, providing treatment for ocular cancers since 1989. A 62 MeV beam of protons is produced by a Scanditronix cyclotron and transported through a passive delivery system. In addition to the long history of clinical use, the facility supports a wide programme of experimental work and as such, an accurate and reliable simulation model of the treatment beamline is highly valuable. However, as the facility has seen several changes to the accelerator and beamline over the years, a comprehensive study of the CCC beam dynamics is needed to firstly examine the beam optics. An extensive analysis was required to overcome facility related constraints to determine fundamental beamline parameters and define an optical lattice written with the Methodical Accelerator Design (MAD-X) and the particle tracking Beam Delivery Simulation (BDSIM) code. An optimised case is presented and simulated results of the optical functions, beam distribution, losses and the transverse rms beam sizes along the beamline are discussed. Corresponding optical and beam information was used in TOPAS to simulate transverse beam profiles and compared to EBT3 film measurements. We provide an overview of the magnetic components, beam transport, cyclotron, beam and treatment related parameters necessary for the development of a present day optical model of the facility. This work represents the first comprehensive study of the CCC facility to date, as a basis to determine input beam parameters to accurately simulate and completely characterise the beamline.     

A focused scanning vertical beam for charged particle irradiation of living cells with single counted particles

The Surrey vertical beam is a new facility for targeted irradiation of cells in medium with singly counted ions. A duo-plasmatron ion source and a 2 MV Tandem? accelerator supply a range of ions from protons to calcium for this beamline and microscope endstation, with energy ranges from 0.5 to 12 MeV. A magnetic quadrupole triplet lens is used to focus the beam of ions. We present the design of this beamline, and early results showing the capability to count single ions with 98% certainty on CR-39 track etch. We also show that the beam targeting accuracy is within 5 μm and selectively target human fibroblasts with a <5 μm carbon beam, using γ-H2AX immunofluorescence to demonstrate which cell nuclei were irradiated. We discuss future commissioning steps necessary to achieve submicron targeting accuracy with this beamline.     

ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility

Optimizing and monitoring the data flow in high-throughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a "technological platform". Infrastructure includes a 48-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project. The pipeline (named ChromaPipe for Chromatogram Pipeline) is available for download by the scientific community at the url http://bioinfo.pdtis.fiocruz.br/ChromaPipe/. The support for assembly is also configured as a web service: http://bioinfo.pdtis.fiocruz.br/Assembly/.     

The beamlines of ELETTRA and their application to structural biology

Protein crystallographers are nowadays regular users of synchrotron radiation (SR) facilities for several applications. The goal of majority of users is simply to extract more accurate, higher resolution data from existing crystals; they use monochromatic radiation and the rotation method, in order to get a complete survey of the reciprocal space in a short time. In fact the brilliance of SR is essential, due to the weak scattering power of the samples, and because of their sensibility to radiation damage. Over the last few years, however, a general increase of interest for measurements at multiple wavelengths, which exploit the anomalous dispersion for the phase problem (multiwavelength anomalous diffraction — MAD), has generated the need of intense tuneable sources. For these applications, the emphasis is on accurate measurements of the small differences between the intensities of Bragg reflections at various energies across the absorption edge of an element present in the sample. The macromolecular diffraction beamline at ELETTRA, which is now running routinely since spring 1995, has been designed to provide a high flux — highly collimated tuneable X-rays source in the spectral range between 4 and 25 keV. The radiation source is the 57-pole wiggler, which delivers a very intense radiation up to 25 keV, and is shared and used simultaneously with the small angle X-ray scattering (SAXS) beamline. The front-end filter system has a cut-off energy at about 4 keV. The beamline optics consists of a pseudo-channel-cut double-crystal monochromator followed by a double focusing toroidal mirror. The tunability and the stability of the monochromator allows the user to perform MAD experiments, and for this purpose, a fluorescence probe for the exact calibration of the absorption edge is available on-line. The experimental station is based on an imaging plate area detector from MarResearch, with a sensible area of 345 mm in diameter. A cooled N₂-stream is available to cool the sample crystal in order to reduce the radiation damage. SAXS is an experimental technique used to derive structural information about supra-molecular assemblies, amorphous materials and partly ordered systems (e.g. size and shape of large molecules). The high-flux SAXS beamline at ELETTRA is mainly intended for time-resolved studies on fast structural transitions in the sub-millisecond time region in solutions and in partly ordered systems, triggered by external or process parameters, with a SAXS resolution between 10 and 1400 Å in real space. The source is the already mentioned 57-pole and the SAXS beamline accepts three discrete energies of its spectrum, namely 5.4, 8 and 16 keV. The beamline optics consists of a flat double-crystal monochromator and a double focusing toroidal mirror. A multi-purpose sample stage, movable along an optical table in order to optimise the sample to detect distance, allows to perform fast time-resolved relaxation studies based on temperature- or pressure-jumps as well as stopped flow experiments. Moreover, the users have option to install their own specialised sample surrounding equipment. The optimisation of the beamline with respect to high-flux and consequently high-flux density, allows to perform the following experiments: low contrast solution scattering, grazing incidence surface diffraction, micro-spot scanning, X-ray fluorescence analysis, time-resolved studies 11 s, simultaneous small- and wide-angle measurements on gels, liquid crystals, biopolymers, amorphous materials, muscles.This revised version was published online in October 2005 with corrections to the Cover Date.     

Utilization of a State Run Public Private Emergency Transportation Service Exclusively for Childbirth: The Janani (Maternal) Express Program in Madhya Pradesh,India

Background

In 2009 the state government of Madhya Pradesh, India launched an emergency obstetric transportation service, Janani Express Yojana (JEY), to support the cash transfer program that promotes institutional delivery. JEY, a large scale public private partnership, lowers geographical access barriers to facility based care. The state contracts and pays private agencies to provide emergency transportation at no cost to the user. The objective was to study (a) the utilization of JEY among women delivering in health facilities, (b) factors associated with usage, (c) the timeliness of the service.

Methods

A cross sectional facility based study was conducted in facilities that carried out > ten deliveries a month. Researchers who spent five days in each facility administered a questionnaire to all women who gave birth there to elicit socio-demographic characteristics and transport related details.

Results

35% of women utilised JEY to reach a facility, however utilization varied between study districts. Uptake was highest among women from rural areas (44%), scheduled tribes (55%), and poorly educated women (40%). Living in rural areas and belonging to scheduled tribes were significant predictors for JEY usage. Almost 1/3 of JEY users (n = 104) experienced a transport related delay.

Discussion

The JEY service model complements the cash transfer program by providing transport to a facility to give birth. A study of the distribution of utilization in population subgroups suggests the intervention was successful in reaching the most vulnerable population, promoting equity in access. While 1/3 of women utilized the service and it saved them money; 30% experienced significant transport related delays in reaching a facility, which is comparable to women using public transportation. Further research is needed to understand why utilization is low, to explore if there is a need for service expansion at the community level and to improve the overall time efficiency of JEY.     

Measuring circular dichroism in a capillary cell using the b23 synchrotron radiation CD beamline at diamond light source

Synchrotron radiation circular dichroism (SRCD) is a well-established method in structural biology. The first UV-VIS beamline dedicated to circular dichroism at Diamond Light Source, a third generation synchrotron facility in South Oxfordshire, has recently become operational and it is now available for the user community. Herein we present an important application of SRCD: the CD measurement of protein solutions in fused silica rectangular capillary cells. This was achieved without the use of any lens between the photoelastic modulator and the photomultiplier tube detectors by exploiting the high photon flux of the collimated beam that can be as little as half a millimeter squared. Measures to minimize or eliminate vacuum-UV protein denaturation effects are discussed. The CD spectra measured in capillaries is a proof of principle to address CD measurements in microdevice systems using the new B23 SRCD beamline.     

Preparation of pH- and ionic-strength responsive biodegradable fumaric acid crosslinked carboxymethyl cellulose

A novel biodegradable sodium carboxymethyl cellulose (NaCMC)-based hydrogel was synthesized by using fumaric acid (FA) as a crosslinking agent at various ratios. Hydrogels (CMCF) were characterized using Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction analysis (XRD), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Swelling behaviors of hydrogels were investigated in distilled water, various salt, and pH solutions. The FTIR results indicated the crosslinking between carboxyl groups of FA with hydroxyl group of NaCMC through ester formation. AFM analyses showed that roughness of hydrogel surface decreased with increasing crosslinker concentration. The swelling capacity decreased with an increase in charge of the metal cation (Al(3+)相似文献   

DICOM-RT Ion interface to utilize MC simulations in routine clinical workflow for proton pencil beam radiotherapy

To adopt Monte Carlo (MC) simulations as an independent dose calculation method for proton pencil beam radiotherapy, an interface that converts the plan information in DICOM format into MC components such as geometries and beam source is a crucial element. For this purpose, a DICOM-RT Ion interface (https://github.com/topasmc/dicom-interface) has been developed and integrated into the TOPAS MC code to perform such conversions on-the-fly. DICOM-RT objects utilized in this interface include Ion Plan (RTIP), Ion Beams Treatment Record (RTIBTR), CT image, and Dose. Beamline geometries, gantry and patient coordinate systems, and fluence maps are determined from RTIP and/or RTIBTR. In this interface, DICOM information is processed and delivered to a MC engine in two steps. A MC model, which consists of beamline geometries and beam source, to represent a treatment machine is created by a DICOM parser of the interface. The complexities from different DICOM types, various beamline configurations and source models are handled in this step. Next, geometry information and beam source are transferred to TOPAS on-the-fly via the developed TOPAS extensions. This interface with two treatment machines was successfully deployed into our automated MC workflow which provides simulated dose and LET distributions in a patient or a water phantom automatically when a new plan is identified. The developed interface provides novel features such as handling multiple treatment systems based on different DICOM types, DICOM conversions on-the-fly, and flexible sampling methods that significantly reduce the burden of handling DICOM based plan or treatment record information for MC simulations.     

NeoAnalysis: a Python-based toolbox for quick electrophysiological data processing and analysis

Background

In a typical electrophysiological experiment, especially one that includes studying animal behavior, the data collected normally contain spikes, local field potentials, behavioral responses and other associated data. In order to obtain informative results, the data must be analyzed simultaneously with the experimental settings. However, most open-source toolboxes currently available for data analysis were developed to handle only a portion of the data and did not take into account the sorting of experimental conditions. Additionally, these toolboxes require that the input data be in a specific format, which can be inconvenient to users. Therefore, the development of a highly integrated toolbox that can process multiple types of data regardless of input data format and perform basic analysis for general electrophysiological experiments is incredibly useful.

Results

Here, we report the development of a Python based open-source toolbox, referred to as NeoAnalysis, to be used for quick electrophysiological data processing and analysis. The toolbox can import data from different data acquisition systems regardless of their formats and automatically combine different types of data into a single file with a standardized format. In cases where additional spike sorting is needed, NeoAnalysis provides a module to perform efficient offline sorting with a user-friendly interface. Then, NeoAnalysis can perform regular analog signal processing, spike train, and local field potentials analysis, behavioral response (e.g. saccade) detection and extraction, with several options available for data plotting and statistics. Particularly, it can automatically generate sorted results without requiring users to manually sort data beforehand. In addition, NeoAnalysis can organize all of the relevant data into an informative table on a trial-by-trial basis for data visualization. Finally, NeoAnalysis supports analysis at the population level.

Conclusions

With the multitude of general-purpose functions provided by NeoAnalysis, users can easily obtain publication-quality figures without writing complex codes. NeoAnalysis is a powerful and valuable toolbox for users doing electrophysiological experiments.

     

RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation

RIKEN Structural Genomics Beamlines, BL26B1 & BL26B2 at the SPring-8, have been constructed for the structural genomics research. The main feature of the beamline is full automation of the successive data collections to maximize the beam-time efficiency. The beamline optics adopted a standard design commonly used for the SPring-8 bending magnet beamlines. Beamline instruments are operated by centralized control system through the computer network to achieve the automatic operation. The core part of the beamline development is a sample management system composed of sample changer robots for laboratory and beamline, and a networked sample database. BL26B1 has started user operation, and the automatic operation with the sample management system has been implemented at BL26B2.     

Development of national system performance metrics for tissue donation,production, and distribution activity

Canada’s federal, provincial, and territorial governments gave Canadian Blood Services a mandate for organ and tissue donation and transplantation, including system performance, data and analytics. In 2012 Canadian Blood Services facilitated an eye and tissue banking workshop focused on standardized specifications and practices. At the workshop, the Canadian tissue community directed Canadian Blood Services to facilitate the development and implementation of a national data stream and analytics. Prior to this no national data was prospectively collected or collated on tissue donation, production or distribution activity. An eye and tissue data committee was formed with representation from eye and tissue banks in all Canadian jurisdictions. A minimum data set, standardized definitions, a data submission form and a quality assurance process was developed. Training was provided to data personal identified by each eye and tissue bank. Data collection was initiated January 1, 2013; with quarterly data submitted to Canadian Blood Services via excel spreadsheet. Data was submitted by sixteen Canadian eye and tissue banks, located in eight of Canada’s thirteen provinces and territories, representing a census of activity. Annual data reports, with trend analysis, are generated and distributed to the tissue community to inform operational strategy and system performance improvement. This report provides an overview of the data process and provides visibility to the Canadian tissue donation, production and distribution activities for 3 years; January 1, 2013 to December 31, 2015.     

Beamline characterization of a dielectric-filled reentrant cavity resonator as beam current monitor for a medical cyclotron facility

At PSI (Paul Scherrer Institute), Switzerland, a superconducting cyclotron called “COMET” delivers proton beam of 250 MeV pulsed at 72.85 MHz for proton radiation therapy. Measuring proton beam currents (0.1–10nA) is of crucial importance for the treatment safety and is usually performed with invasive monitors such as ionisation chambers (ICs) which degrade the beam quality. A new non-invasive beam current monitor working on the principle of electromagnetic resonance is built to replace ICs in order to preserve the beam quality delivered. The fundamental resonance frequency of the resonator is tuned to 145.7 MHz, which is the second harmonic of the pulse rate, so it provides signals proportional to beam current. The cavity resonator installed in the beamline of the COMET is designed to measure beam currents for the energy range 238–70 MeV. Good agreement is reached between expected and measured resonator response over the energy range of interest. The resonator can deliver beam current information down to 0.15 nA for a measurement integration time of 1 s. The cavity resonator might be applied serving as a safety monitor to trigger interlocks within the existing domain of proton radiation therapy. Low beam currents limit the abilities to detect sufficiently, however, with the potential implementation of FLASH proton therapy, the application of cavity resonator as an online beam-monitoring device is feasible.     

A dynamic tester to evaluate the thermal and moisture behaviour of the surface of textiles

The thermal and moisture behaviour of the microclimate of textiles is crucial in determining the physiological comfort of apparel, but it has not been investigated sufficiently due to the lack of particular evaluation techniques. Based on sensing, temperature controlling and wireless communicating technology, a specially designed tester has been developed in this study to evaluate the thermal and moisture behaviour of the surface of textiles in moving status. A temperature acquisition system and a temperature controllable hotplate have been established to test temperature and simulate the heat of human body, respectively. Relative humidity of the surface of fabric in the dynamic process has been successfully tested through sensing. Meanwhile, wireless communication technology was applied to transport the acquired data of temperature and humidity to computer for further processing. Continuous power supply was achieved by intensive contact between an elastic copper plate and copper ring on the rotating shaft. This tester provides the platform to evaluate the thermal and moisture behaviour of textiles. It enables users to conduct a dynamic analysis on the temperature and humidity together with the thermal and moisture transport behaviour of the surface of fabric in moving condition. Development of this tester opens the door of investigation on the micro-climate of textiles in real time service, and eventually benefits the understanding of the sensation comfort and wellbeing of apparel wearers.     

GenePattern flow cytometry suite

Background

Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have increased the amount of data generated by the technology and outpaced the development of data analysis approaches. While there are advanced tools available, including many R/BioConductor packages, these are only accessible programmatically and therefore out of reach for most experimentalists. GenePattern is a powerful genomic analysis platform with over 200 tools for analysis of gene expression, proteomics, and other data. A web-based interface provides easy access to these tools and allows the creation of automated analysis pipelines enabling reproducible research.

Results

In order to bring advanced flow cytometry data analysis tools to experimentalists without programmatic skills, we developed the GenePattern Flow Cytometry Suite. It contains 34 open source GenePattern flow cytometry modules covering methods from basic processing of flow cytometry standard (i.e., FCS) files to advanced algorithms for automated identification of cell populations, normalization and quality assessment. Internally, these modules leverage from functionality developed in R/BioConductor. Using the GenePattern web-based interface, they can be connected to build analytical pipelines.

Conclusions

GenePattern Flow Cytometry Suite brings advanced flow cytometry data analysis capabilities to users with minimal computer skills. Functionality previously available only to skilled bioinformaticians is now easily accessible from a web browser.

     

An Evaluation of Alternative Designs for a Grid Information Service

Computational grids consisting of large and diverse sets of distributed resources have recently been adopted by organizations such as NASA and the NSF. One key component of a computational grid is an information services that provides information about resources, services, and applications to users and their tools. This information is required to use a computational grid and therefore should be available in a timely and reliable manner. In this work, we describe the Globus information service, describe how this service is used, analyze its current performance, and perform trace-driven simulations to evaluate alternative implementations of this grid information service. We find that the majority of the transactions with the information service are changes to the data maintained by the service. We also find that of the three servers we evaluate, one of the commercial products provides the best performance for our workload and that the response time of the information service was not improved during the single experiment we performed with data distributed across two servers.     

Terahertz Radiation at ANKA, the New Synchrotron Light Source in Karlsruhe

ANKA is a new synchrotron light source atthe Karlsruhe Research Center in southwestGermany. The acronym stands for Ångstrøm Source Karlsruhe.The ANKA-IR beamline provides a highbrilliance infrared beam through the near,mid and far-infrared range. Thefar-infrared range is of particularinterest, since at frequencies lower thanaround 200 cm^-1 (6 THz) synchrotronlight begins to outperform conventionalthermal sources in terms of total intensityas well as brilliance. The extraction ofthe entire flux is a challenge in the THzrange, since the natural verticaldivergence of synchrotron radiationincreases with wavelength and the openingangle for collection is limited by designconstraints. At ANKA-IR, this problem issolved by the collection of radiationemitted from a bending magnet edge source,which has a much smaller verticaldivergence than conventional synchrotronradiation emitted from the constantmagnetic field region within the dipolemagnet. Edge radiation at ANKA permits theextraction of the entire infrared flux downto around 100 cm^-1 (3 THz) while withconventional synchrotron radiation thiswould only be the case for frequencies downto 2500 cm^-1. ANKA-IR provides usableintensity down to 4 cm^-1 (120 GHz).     

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

Background

miRNAs play a key role in normal physiology and various diseases. miRNA profiling through next generation sequencing (miRNA-seq) has become the main platform for biological research and biomarker discovery. However, analyzing miRNA sequencing data is challenging as it needs significant amount of computational resources and bioinformatics expertise. Several web based analytical tools have been developed but they are limited to processing one or a pair of samples at time and are not suitable for a large scale study. Lack of flexibility and reliability of these web applications are also common issues.

Results

We developed a Comprehensive Analysis Pipeline for microRNA Sequencing data (CAP-miRSeq) that integrates read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, data visualization, variant detection in miRNA coding region, and more flexible differential expression analysis between experimental conditions. According to computational infrastructure, users can install the package locally or deploy it in Amazon Cloud to run samples sequentially or in parallel for a large number of samples for speedy analyses. In either case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses. Using well characterized data, we demonstrated the pipeline’s superior performances, flexibility, and practical use in research and biomarker discovery.

Conclusions

CAP-miRSeq is a powerful and flexible tool for users to process and analyze miRNA-seq data scalable from a few to hundreds of samples. The results are presented in the convenient way for investigators or analysts to conduct further investigation and discovery.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-423) contains supplementary material, which is available to authorized users.     

深圳城市生态大数据智慧管理和服务平台技术集成与应用研究

生态环境是人类赖以生存和发展的基础,城市生态大数据智慧管理和服务平台建设是生态城市和美丽城市建设的需要。以深圳市为例,借助物联网、移动互联网、计算机、数据库和网络地理信息系统技术,以及时空地理大数据整合和共享、大数据挖掘分析和云端一体化业务协同等关键技术,结合城市生态系统评估分析决策模型/方法/对策库,在实现深圳市“空-地-网-统计-众源”等多源异构生态大数据有效集成的基础上,搭建了 “数据采集-信息提取-知识发现-决策生成-快速服务”全流程、一体化的深圳市生态大数据智慧管理和服务平台,构建了面向业务部门和科研人员等专业用户的生态野外数据调查采集系统和城市生态监测与评估管理决策分析系统,以及面向社会大众的深圳生态大调查APP。平台首次揭示了深圳市1979年以来不同生态系统的格局、构成、过程、服务和健康状况的变化,提升了深圳市生态环境综合决策科学化、生态环境监管精准化、生态环境公共服务便民化水平。平台有效降低了用户数据收集与处理和操作专业模型的难度,突破了原始数据应用的瓶颈和难点,提高了专业模型在业务部门中的使用率。未来,依靠“生态大数据+生态专业模型”的技术方案实现从数据到知识的挖掘,是实现城市生态大数据智慧化和专业化管理的关键,也是全面提高城市生态环境保护信息化服务水平的重要途径。