Implementation of Provider-Based Electronic Medical Records and Improvement of the Quality of Data in a Large HIV Program in Sub-Saharan Africa

Introduction

Starting in June 2010 the Infectious Diseases Institute (IDI) clinic (a large urban HIV out-patient facility) switched to provider-based Electronic Medical Records (EMR) from paper EMR entered in the database by data-entry clerks. Standardized clinics forms were eliminated but providers still fill free text clinical notes in physical patients’ files. The objective of this study was to compare the rate of errors in the database before and after the introduction of the provider-based EMR.

Methods and Findings

Data in the database pre and post provider-based EMR was compared with the information in the patients’ files and classified as correct, incorrect, and missing. We calculated the proportion of incorrect, missing and total error for key variables (toxicities, opportunistic infections, reasons for treatment change and interruption). Proportions of total errors were compared using chi-square test. A survey of the users of the EMR was also conducted. We compared data from 2,382 visits (from 100 individuals) of a retrospective validation conducted in 2007 with 34,957 visits (from 10,920 individuals) of a prospective validation conducted in April–August 2011. The total proportion of errors decreased from 66.5% in 2007 to 2.1% in 2011 for opportunistic infections, from 51.9% to 3.5% for ART toxicity, from 82.8% to 12.5% for reasons for ART interruption and from 94.1% to 0.9% for reasons for ART switch (all P<0.0001). The survey showed that 83% of the providers agreed that provider-based EMR led to improvement of clinical care, 80% reported improved access to patients’ records, and 80% appreciated the automation of providers’ tasks.

Conclusions

The introduction of provider-based EMR improved the quality of data collected with a significant reduction in missing and incorrect information. The majority of providers and clients expressed satisfaction with the new system. We recommend the use of provider-based EMR in large HIV programs in Sub-Saharan Africa.     

FlyBase: a Drosophila database. Flybase Consortium.

FlyBase (http://flybase.bio.indiana.edu/) is a comprehensive database of genetic and molecular data concerning Drosophila . FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (with phenotypes), aberrations, transposons, pointers to sequence data, gene products, maps, clones, stock lists, Drosophila workers and bibliographic references.     

Quality assurance-based optimization (QAO): Towards improving patient-specific quality assurance in volumetric modulated arc therapy plans using machine learning

IntroductionPrevious literature has shown general trade-offs between plan complexity and resulting quality assurance (QA) outcomes. However, existing solutions for controlling this trade-off do not guarantee corresponding improvements in deliverability. Therefore, this work explored the feasibility of an optimization framework for directly maximizing predicted QA outcomes of plans without compromising the dosimetric quality of plans designed with an established knowledge-based planning (KBP) technique.Materials and MethodsA support vector machine (SVM) was developed – using a database of 500 previous VMAT plans – to predict gamma passing rates (GPRs; 3%/3mm percent dose-difference/distance-to-agreement with local normalization) based on selected complexity features. A heuristic, QA-based optimization (QAO) framework was devised by utilizing the SVM model to iteratively modify mechanical treatment features most commonly associated with suboptimal GPRs. Specifically, leaf gaps (LGs) <50 mm were widened by random amounts, which impacts all aperture-based complexity features. 13 prostate KBP-guided VMAT plans were optimized via QAO using user-specified maximum LG displacements before corresponding changes in predicted GPRs and dose were assessed.ResultsPredicted GPRs increased by an average of 1.14 ± 1.25% (p = 0.006) with QAO using a 3 mm maximum random LG displacement. There were small differences in dose, resulting in similarly small changes in tumor control probability (maximum increase = 0.05%) and normal tissue complication probabilities in the bladder, rectum, and femoral heads (maximum decrease = 0.2% in the rectum).ConclusionThis study explored the feasibility of QAO and warrants future investigations of further incorporating QA endpoints into plan optimization.     

DeepWL: Robust EPID based Winston-Lutz analysis using deep learning,synthetic image generation and optical path-tracing

Radiation therapy requires clinical linear accelerators to be mechanically and dosimetrically calibrated to a high standard. One important quality assurance test is the Winston-Lutz test which localises the radiation isocentre of the linac.In the current work we demonstrate a novel method of analysing EPID based Winston-Lutz QA images using a deep learning model trained only on synthetic image data. In addition, we propose a novel method of generating the synthetic WL images and associated ‘ground-truth’ masks using an optical path-tracing engine to ‘fake’ mega-voltage EPID images.The model called DeepWL was trained on 1500 synthetic WL images using data augmentation techniques for 180 epochs. The model was built using Keras with a TensorFlow backend on an Intel Core i5-6500T CPU and trained in approximately 15 h. DeepWL was shown to produce ball bearing and multi-leaf collimator field segmentations with a mean dice coefficient of 0.964 and 0.994 respectively on previously unseen synthetic testing data. When DeepWL was applied to WL data measured on an EPID, the predicted mean displacements were shown to be statistically similar to the Canny Edge detection method. However, the DeepWL predictions for the ball bearing locations were shown to correlate better with manual annotations compared with the Canny edge detection algorithm.DeepWL was demonstrated to analyse Winston-Lutz images with an accuracy suitable for routine linac quality assurance with some statistical evidence that it may outperform Canny Edge detection methods in terms of segmentation robustness and the resultant displacement predictions.     

SPIRE: the SPIDER reconstruction engine

SPIRE is a Python program written to modernize the user interaction with SPIDER, the image processing system for electron microscopical reconstruction projects. SPIRE provides a graphical user interface (GUI) to SPIDER for executing batch files of SPIDER commands. It also lets users quickly view the status of a project by showing the last batch files that were run, as well as the data files that were generated. SPIRE handles the flexibility of the SPIDER programming environment through configuration files: XML-tagged documents that describe the batch files, directory trees, and presentation of the GUI for a given type of reconstruction project. It also provides the capability to connect to a laboratory database, for downloading parameters required by batch files at the start of a project, and uploading reconstruction results at the end of a project.     

用于基因数据挖掘的基因表达数据库GEO

使用高通量方法学来检测基因表达情况在最近几年已非常普遍。微集芯片技术可同时定量成千上万的基因转录本。基因表达综合数据库（Gene Expression Omnibus 简称GEO）是目前最大的而且完全公开的高通量分子丰度数据库,主要储存基因表达数据。该数据库以一个灵活开放的设计理念,允许用户或科研人员来递呈,保存和检索多种不同类型的数据。本文综合描述一下近年来该数据库在基因表达数据挖掘中的应用,同时介绍一些通过使用用户友好网络界面能有效探索、查询和再现数百个实验和数百万个基因表达谱的工具,以方便数据进行挖掘和可视化。登录GEO公用数据库的网址为：http://www.ncbi.nlm.nih.gov/geo.     

Retrospective study on performance of constancy check device in Linac beam monitoring using Statistical Process Control

AimTo examine the application of Statistical Process Control (SPC) and Ishikawa diagrams for retrospective evaluation of machine Quality Assurance (QA) performance in radiotherapyBackgroundSPC is a popular method for supplementing the performance of QA techniques in healthcare. This work investigates the applicability of SPC techniques and Ishikawa charts in machine QA.Materials and MethodsSPC has been applied to recommend QA limits on the particular beam parameters using the QUICKCHECK^webline QA portable constancy check device for 6 MV and 10 MV flattened photon beams from the Elekta Versa HD linear accelerator (Linac). Four machine QA parameters – beam flatness, beam symmetry along gun target direction and left-right direction, and beam quality factor (BQF) – were selected for retrospective analysis. Shewhart charts, Exponentially Weighted Moving Average (EWMA) charts and Cumulative Sum (CUSUM) charts were obtained for each parameter. The root causes for a failure in machine QA were broken down into an Ishikawa diagram enabling the user to identify the root cause of error and rectify the problem subsequently.ResultsShewhart charts and EWMA charts applied could detect loss in control in one variable in the 6 MV beams and in all four variables in 10 MV beams. CUSUM charts detected offsets in the readings. The Ishikawa chart exhaustively included the possible errors that lead to loss of control.ConclusionSPC is proven to be effective for detection of loss in control in machine QA. The Ishikawa chart provides the set of probable root causes of machine error useful while troubleshooting.     

Comprehensive quality assurance phantom for the small animal radiation research platform (SARRP)

PurposeTo develop and test the suitability and performance of a comprehensive quality assurance (QA) phantom for the Small Animal Radiation Research Platform (SARRP).Methods and materialsA QA phantom was developed for carrying out daily, monthly and annual QA tasks including: imaging, dosimetry and treatment planning system (TPS) performance evaluation of the SARRP. The QA phantom consists of 15 (60 × 60 × 5 mm³) kV-energy tissue equivalent solid water slabs. The phantom can incorporate optically stimulated luminescence dosimeters (OSLD), Mosfet or film. One slab, with inserts and another slab with hole patterns are particularly designed for image QA.ResultsOutput constancy measurement results showed daily variations within 3%. Using the Mosfet in phantom as target, results showed that the difference between TPS calculations and measurements was within 5%. Annual QA results for the Percentage depth dose (PDD) curves, lateral beam profiles, beam flatness and beam profile symmetry were found consistent with results obtained at commissioning. PDD curves obtained using film and OSLDs showed good agreement. Image QA was performed monthly, with image-quality parameters assessed in terms of CBCT image geometric accuracy, CT number accuracy, image spatial resolution, noise and image uniformity.ConclusionsThe results show that the developed QA phantom can be employed as a tool for comprehensive performance evaluation of the SARRP. The study provides a useful reference for development of a comprehensive quality assurance program for the SARRP and other similar small animal irradiators, with proposed tolerances and frequency of required tests.     

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.     

Scanned carbon-ion beam therapy throughput over the first 7 years at National Institute of Radiological Sciences

IntroductionIn the 7 years since our facility opened, we have treated >2000 patients with pencil-beam scanned carbon-ion beam therapy.MethodsTo summarize treatment workflow, we evaluated the following five metrics: i) total number of treated patients; ii) treatment planning time, not including contouring procedure; iii) quality assurance (QA) time (daily and patient-specific); iv) treatment room occupancy time, including patient setup, preparation time, and beam irradiation time; and v) daily treatment hours. These were derived from the oncology information system and patient handling system log files.ResultsThe annual number of treated patients reached 594, 7 years from the facility startup, using two treatment rooms. Mean treatment planning time was 6.0 h (minimum: 3.4 h for prostate, maximum: 9.3 h for esophagus). Mean time devoted to daily QA and patient-specific QA were 22 min and 13.5 min per port, respectively, for the irradiation beam system. Room occupancy time was 14.5 min without gating for the first year, improving to 9.2 min (8.2 min without gating and 12.8 min with gating) in the second. At full capacity, the system ran for 7.5 h per day.ConclusionsWe are now capable of treating approximately 600 patients per year in two treatment rooms. Accounting for the staff working time, this performance appears reasonable compared to the other facilities.     

A beam model for focused proton pencil beams

IntroductionWe present a beam model for Monte Carlo simulations of the IBA pencil beam scanning dedicated nozzle installed at the Skandion Clinic. Within the nozzle, apart from entrance and exit windows and the two ion chambers, the beam traverses vacuum, allowing for a beam that is convergent downstream of the nozzle exit.Materials and methodsWe model the angular, spatial and energy distributions of the beam phase space at the nozzle exit with single Gaussians, controlled by seven energy dependent parameters. The parameters were determined from measured profiles and depth dose distributions. Verification of the beam model was done by comparing measured and GATE acquired relative dose distributions, using plan specific log files from the machine to specify beam spot positions and energy.ResultsGATE-based simulations with the acquired beam model could accurately reproduce the measured data. The gamma index analysis comparing simulated and measured dose distributions resulted in >95% global gamma index pass rates (3%/2 mm) for all depths.ConclusionThe developed beam model was found to be sufficiently accurate for use with GATE e.g. for applications in quality assurance (QA) or patient motion studies with the IBA pencil beam scanning dedicated nozzles.     

Simplified Generation of Biomedical 3D Surface Model Data for Embedding into 3D Portable Document Format (PDF) Files for Publication and Education

The usefulness of the 3D Portable Document Format (PDF) for clinical, educational, and research purposes has recently been shown. However, the lack of a simple tool for converting biomedical data into the model data in the necessary Universal 3D (U3D) file format is a drawback for the broad acceptance of this new technology. A new module for the image processing and rapid prototyping framework MeVisLab does not only provide a platform-independent possibility to create surface meshes out of biomedical/DICOM and other data and to export them into U3D – it also lets the user add meta data to these meshes to predefine colors and names that can be processed by a PDF authoring software while generating 3D PDF files. Furthermore, the source code of the respective module is available and well documented so that it can easily be modified for own purposes.     

Monitoring Daily QA 3 constancy for routine quality assurance on linear accelerators

The purpose of this study was to evaluate the suitability of the Daily QA 3 (Sun Nuclear Corporation, Melbourne, USA) device as a safe quality assurance device for control of machine specific parameters, such as linear accelerator output, beam quality and beam flatness and symmetry. Measurements were performed using three Varian 2300iX linear accelerators. The suitability of Daily QA 3 as a device for quality control of linear accelerator parameters was investigated for both 6 and 10 MV photons and 6, 9, 12, 15 and 18 MeV electrons. Measurements of machine specific using the Daily QA 3 device were compared to corresponding measurements using a simpler constancy meter, Farmer chamber and plane parallel ionisation chamber in a water tank. The Daily QA 3 device showed a linear dose response making it a suitable device for detection of output variations during routine measurements. It was noted that over estimations of variations compared with Farmer chamber readings were seen if the Daily QA 3 wasn’t calibrated for output and sensitivity on a regular eight to ten monthly basis. Temperature-pressure correction factors calculated by Daily QA 3 also contributed towards larger short term variations seen in output measurements. Energy, symmetry and flatness variations detected by Daily QA 3 were consistent with measurements performed in water tank using a parallel plate chamber. It was concluded that the Daily QA 3 device is suitable for routine daily and fortnightly quality assurance of linear accelerator beam parameters however a regular eight-ten monthly dose and detector array calibration will improve error detection capabilities of the device.     

Monte Carlo simulation using PRIMO code as a tool for checking the credibility of commissioning and quality assurance of 6 MV TrueBeam STx varian LINAC

AimTo validate and implement Monte Carlo simulation using PRIMO code as a tool for checking the credibility of measurements in LINAC initial commissioning and routine Quality Assurance (QA). Relative and absolute doses of 6 MV photon beam from TrueBeam STx Varian Linear Accelerator (LINAC) were simulated and validated with experimental measurement, Analytical Anisotropic Algorithm (AAA) calculation, and golden beam.Methods and MaterialsVarian phase-space files were imported to the PRIMO code and four blocks of jaws were simulated to determine the field size of the photon beam. Water phantom was modeled in the PRIMO code with water equivalent density. Golden beam data, experimental measurement, and AAA calculation results were imported to PRIMO code for gamma comparison.ResultsPRIMO simulations of Percentage Depth Dose (PDD) and in-plane beam profiles had good agreement with experimental measurements, AAA calculations and golden beam. However, PRIMO simulations of cross-plane beam profiles have a better agreement with AAA calculation and golden beam than the experimental measurement. Furthermore, PRIMO simulations of absolute dose agreed well with experimental results with ±0.8% uncertainty.ConclusionThe PRIMO code has good accuracy and is appropriate for use as a tool to check the credibility of beam scanning and output measurement in initial commissioning and routine QA.     

A Modified Ant Colony Optimization Algorithm for Tumor Marker Gene Selection

Microarray data are often extremely asymmetric in dimensionality,such as thousands or even tens of thousands of genes but only a few hundreds of samples or less.Such extreme asymmetry between the dimensionality of genes and samples can lead to inaccurate diagnosis of disease in clinic.Therefore,it has been shown that selecting a small set of marker genes can lead to improved classification accuracy.In this paper,a simple modified ant colony optimization (ACO) algorithm is proposed to select tumor-related ma...     

FlyBase: a Drosophila database. The FlyBase consortium.

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (and phenotypes), aberrations, transposons, pointers to sequence data, clones, stock lists, Drosophila workers and bibliographic references. The Encyclopedia of Drosophila is a joint effort between FlyBase and the Berkeley Drosophila Genome Project which integrates FlyBase data with those from the BDGP.     

Clinical data evaluation and the PL health control information system.

In a health control service environment, that is, a periodic, membership AMHTS type of comprehensive health check-up system, where clinical data evaluation especially an evaluation in terms of subject-specific normal ranges, is most important, the medical information system is required to handle: (1) Various network types files; (2) real-time immediacy; (3) an asserted reliability to meet personal health control purposes. As in other computer applications already successfully used, an indexed direct assess method (IDAM) developed is our solution. It allows us to provide multiple indices for the file network, instead of inverted files, a unique index-to-record relationship, preventing any unrecoverable chaining destruction and, thereby, provides any network type access a stable access time. Furthermore, for research purposes, a data integrity for on-line access and batch access was attained as well as a retrieval language system with a multiple key retrieval function.