Use Of Files Research Articles

Development of a physiologically based pharmacokinetic model of actinomycin D in children with cancer.

AimsUse of the anti‐tumour antibiotic actinomycin D is associated with development of hepatotoxicity, particularly in young children. A paucity of actinomycin D pharmacokinetic data make it challenging to develop a sound rationale for defining dosing regimens in younger patients. The study aim was to develop a physiologically based pharmacokinetic (PBPK) model using a combination of data from the literature and generated from experimental analyses.MethodsAssays to determine actinomycin D Log P, blood:plasma partition ratio and ABCB1 kinetics were conducted. These data were combined with physiochemical properties sourced from the literature to generate a compound file for use within the modelling‐simulation software Simcyp (version 14 release 1). For simulation, information was taken from two datasets, one from 117 patients under the age of 21 and one from 20 patients aged 16–48.ResultsThe final model incorporated clinical renal and biliary clearance data and an additional systemic clearance value. The mean AUC0‐26h of simulated subjects was within 1.25‐fold of the observed AUC0‐26h (84 ng h ml−1 simulated vs. 93 ng h ml−1 observed). For the younger age ranges, AUC predictions were within two‐fold of observed values, with simulated data from six of the eight age/dose ranges falling within 15% of observed data. Simulated values for actinomycin D AUC0‐26h and clearance in infants aged 0–12 months ranged from 104 to 115 ng h ml−1 and 3.5–3.8 l h−1, respectively.ConclusionsThe model has potential utility for prediction of actinomycin D exposure in younger patients and may help guide future dosing. However, additional independent data from neonates and infants is needed for further validation. Physiological differences between paediatric cancer patients and healthy children also need to be further characterized and incorporated into PBPK models.

Rainfall-runoff modelling of Doddahalla watershed—an application of HEC-HMS and SCN-CN in ungauged agricultural watershed

The scarcity of reliable rainfall-runoff recorded data in Doddahalla watershed is a serious problem for the analysis of the hydrology of watersheds. Sustainable management of the available water in this area is only possible when there was sound information on the rainfall-runoff and other hydrological determinants that influence the water resource. Considering the current problem rainfall-runoff. simulation is carried out using the HEC-HMS hydrological simulation model with integrated use of remote sensing and GIS. Tropical Rainfall Measuring Mission 3 hourly and Indian Meteorological Department daily rainfall datasets are utilised. Cartosat-1 CartoDEM (30 m) was used to delineate the sub-watershed and generate the stream network. Geospatial Hydrologic Modeling Extension (HEC-GeoHMS), along with ArcHydro extension in ArcGIS 9.3 utilised to create the input file for use in HEC-HMS. Indian Remote Sensing Satellite Linear Imaging and Self Scanning sensors (LISS-III, 24 m) and Survey of India (SOI) toposheet are used to prepare the soil and land use map. All the data are georectified and reprojected to Geographic Coordinate System-World Geodetic System 1984 (GCS WGS) Universal Transverse Mercator (UTM) zone 43 North for the easy handling in GIS environment. SCS-CN loss model and SCS unit hydrograph as a transform method was applied to simulate the excess storm water to direct runoff in the watershed. The Muskingum-Cunge model used as channel routing. The model is validated by using field observation data and discharge data from the neighbouring Hoovinahole watershed. The results of simulated and observed stream flow show greater confidence and the reliability of the model. Similar procedure and calibration parameters applied to the ungauged Doddahalla watershed for estimating the rainfall-runoff. The research result gives a general idea regarding the stream flow, peak flow and velocity of the peak flow. The present study concludes that the stimulated result can be useful for the water and land resource planning and management practice in the Doddahalla watershed. The models can be best utilised in ungauged watershed and water scarce region where the monitored data are limited, and runoff estimation is mandatory to sustain the water resources.

Fqtools: an efficient software suite for modern FASTQ file manipulation

Summary: Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (e.g. searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines.Availability and implementation: fqtools is open source and is available at: https://github.com/alastair-droop/fqtools.Supplementary information: Supplementary data are available at Bioinformatics online.Contact: a.p.droop@leeds.ac.uk

Things, tags, topics: Thingiverse’s object-centred network

ABSTRACTThis article details findings from a multidisciplinary research team’s inquiry into the social uses of 3D printing. It applies digital research methods to 3D printing communities and their digitally shared objects. Thingiverse is one of the most well-known file repositories available for the semi-public distribution of files for use in 3D printers. The site allows for several different means of metadata classification of these files. Previous research on the site focused on the legal concerns related to the different types of intellectual property license ‘metadata’ attached to objects. Beyond these data points are numerous additional types of elected and automated connections between both users, objects and processes of creation including liking, commenting, tagging, categorising, watching, collecting, remixing, making, sharing, and attribution. Social Network Analysis of the relations between these data reveal interesting patterns towards the use and life of these objects. Our analysis also shows that despite the wealth of social functions, both actively engaged and passively automated, Thingiverse diverges from other social networks: sociality is mediated by reference to specific objects. As such, we claim Thingiverse should be considered as an object-centred social network. While such networks provoke Latourian analysis that is now well established in the study of computational culture, we also point to the need for new forms of social media analysis focused on the ways metadata constitute and guide such communities’ communications and govern their potentials.

The Berkeley Phonetics Machine

Author(s): Sprouse, Ronald L.; Johnson, Keith | Abstract: The Berkeley Phonetics Machine is a Linux virtual machine imageproduced and used by the UC Berkeley Phonology Lab asa platform for phonetic research. It contains a full data analysisstack based on Python and R and also specialized tools for phoneticresearch. The machine is designed as a flexible and productiveplatform for established and novel research agendas thatcan be easily shared and reproduced. We list the software availablein the machine, which includes many command-line toolsfor acoustic analysis and media file manipulation, as well asspecialized Python libraries. We also discuss the use of this machinein the Phonology Lab and in phonetics courses. The overallexperience with the machine has been positive, as facultyand graduate students are able to share and execute scripts ina common working environment. Undergraduate students haveless opportunity to master the virtual machine environment butbenefit from simplified instructions and fewer installation andoperating problems. The primary difficulty that we have encounteredhas been with a few underpowered student computersthat cannot run the virutual machine or do not run it well.

IURead: a new computer-based reading test.

To develop a computer-based single sentence reading test especially designed for clinical research enabling multiple repeat trials without reusing the same sentences. We initially developed 422 sentences, with an average of 60 characters and 12 words. Presentation controls were improved by employing computer-based testing and the oral reading was recorded by visual inspection of digital audio recordings. Variability in reading speed of normally sighted adults between sentences, between charts, between subjects, between formats, and between display devices was quantified. The impact of display size and pixel resolution on test geometry was assessed, and the impact of reduced retinal image quality and retinal illuminance were compared for reading and standard letter acuities. Eleven visually normal subjects (age: 18-60years) participated in this study. Stopwatch timing of sentences reliably underestimated reading times by about 0.3s, and exhibited coefficients of repeatability 17 times larger than those estimated from visual inspection of digital recordings. A slight relaxing of the lexical content constraints had no effect on reading speed; neither did sentence format (single vs three lines) or display size or distance. Within subject standard deviations of reading speed for different sentences were small (between 6% and 9% of the mean speed) requiring only small samples sizes to achieve typical statistical reliability and power when comparing conditions within individual subjects. The greater variability associated with stopwatch timing necessitates larger sample sizes. As defocus and light level were varied, reading acuity and standard letter acuity were highly correlated (r(2) =0.99), and reading acuity was slightly better. A computer-based IURead reading test provides a useful reading speed and reading acuity tool for clinical research involving multiple conditions and repeat testing of individual subjects. Ready to use IURead files for use with a computer, tablet or cell phone can be downloaded from our lab website (https://www.opt.indiana.edu/Bradley/Downloads.aspx).

Transcribing Debussy's Syrinx dynamics through Linguistic Description: The MUDELD algorithm

Advances in computational power have enabled the manipulation of music audio files and the emergence of the Music Information Retrieval field. One of the main research lines in this area is that of Music Transcription, which aims at transforming an audio file into musical notation. So far, most efforts have focused on accurately transcribing the pitch and durations of the notes, and thus neglecting other aspects in the music score. The present work explores a novel line of action in the context of automatic music transcription, focusing on the dynamics, and by means of Linguistic Description. The process described in this paper (called MUDELD: MUsic Dynamics Extraction through Linguistic Description) departs from the data series representing the audio file, and requires the segmentation of the piece in phrases, which is currently done by hand. Initial experiments have been performed on eight recordings of Debussy's Syrinx with promising results.

Integrating nTMS Data into a Radiology Picture Archiving System.

Navigated transcranial magnetic stimulation (nTMS) is employed in eloquent brain area localization prior to intraoperative direct cortical electrical stimulations and neurosurgery. No commercial archiving or file transfer protocol existed for these studies. The aim of our project was to establish a standardized protocol for the transfer of nTMS results and medical assessments to the end users in pursuance of improving data security and facilitating presurgical planning. The existing infrastructure of the hospital's Radiology Department was used. Hospital information systems and networks were configured to allow communications and archiving of the study results, and in-house software was written for file manipulations and transfers. Graphical user interface with description suggestions and user-defined text legends enabled an easy and straightforward workflow for annotations and archiving of the results. The software and configurations were implemented and have been applied in studies of ten patients. The creation of the study protocol required the involvement of various professionals and interdepartmental cooperation. The introduction of the protocol has ended previously recurrent involvement of staff in the file transfer phase and improved cost-effectiveness.

Verification and Validation of the ENDF/B-VII.1–Based Continuous-Energy Data Tables for MCNP6

In December 2011, the National Nuclear Data Center released ENDF/B-VII.1, the “latest recommended evaluated nuclear data file for use in nuclear science and technology applications.” The data were released in the standard Evaluated Nuclear Data Format (ENDF). This release represents the advances made in nuclear data during the 5 years since the release of ENDF/B-VII.0. The Nuclear Data Team at Los Alamos National Laboratory has processed the ENDF/B-VII.1 library and made available a library of ACE data tables at several temperatures for each of the ENDF/B files. The ACE data library is called ENDF71x and is available through the Radiation Safety Information Computational Center with MCNP6. The files can also be used with MCNP5 or other Monte Carlo codes.

Comparison of Nearest Neighbor (ibk), Regression by Discretization and Isotonic Regression Classification Algorithms for Precipitation Classes Prediction

Selection of classifier for use in prediction is a challenge. In order to select the best classifier comparisons can be made on various aspects of the classifiers. The key objective of this paper was to compare performance of nearest neighbor (ibk), regression by discretization and isotonic regression classifiers for predicting predefined precipitation classes over Voi, Kenya. We sought to train, test and evaluate the performance of nearest neighbor (ibk), regression by discretization and isotonic regression classification algorithms in predicting precipitation classes. A period of 1979 to 2008 daily KMD historical dataset on minimum/maximum temperatures and precipitations for Voi KMD station was obtained. Knowledge discovery and data mining (KDD) process steps were applied. A preprocessing module was designed to produce training and testing sets of files for use with the classifiers. Three classifiers (Isotonic Regression, K-nearest neighbours classifier, and RegressionByDiscretization) were used for training training and testing of the data sets. On running the classifiers the error of the predicted values, root relative squared error and the time taken to train/build each classifier model were computed. Each classifier provided predicted output classes 12 months in advance. Performance of the three classifiers was compared in terms of error of the predicted values, root relative squared error and the time taken to train/build each classifier model. The predicted output classes were also compared to actual classes. Percentage performance for each classifier to actual precipitation classes was computed and compared. The study evaluation showed that the nearest neighbor classifier is a suitable tool for training rainfall data for precipitation classes prediction.

Monitoring System for the GRID Monte Carlo Mass Production in the H1 Experiment at DESY

The H1 Virtual Organization (VO), as one of the small VOs, employs most components of the EMI or gLite Middleware. In this framework, a monitoring system is designed for the H1 Experiment to identify and recognize within the GRID the best suitable resources for execution of CPU-time consuming Monte Carlo (MC) simulation tasks (jobs). Monitored resources are Computer Elements (CEs), Storage Elements (SEs), WMS-servers (WMSs), CernVM File System (CVMFS) available to the VO HONE and local GRID User Interfaces (UIs).The general principle of monitoring GRID elements is based on the execution of short test jobs on different CE queues using submission through various WMSs and directly to the CREAM-CEs as well. Real H1 MC Production jobs with a small number of events are used to perform the tests. Test jobs are periodically submitted into GRID queues, the status of these jobs is checked, output files of completed jobs are retrieved, the result of each job is analyzed and the waiting time and run time are derived. Using this information, the status of the GRID elements is estimated and the most suitable ones are included in the automatically generated configuration files for use in the H1 MC production.The monitoring system allows for identification of problems in the GRID sites and promptly reacts on it (for example by sending GGUS (Global Grid User Support) trouble tickets). The system can easily be adapted to identify the optimal resources for tasks other than MC production, simply by changing to the relevant test jobs. The monitoring system is written mostly in Python and Perl with insertion of a few shell scripts.In addition to the test monitoring system we use information from real production jobs to monitor the availability and quality of the GRID resources. The monitoring tools register the number of job resubmissions, the percentage of failed and finished jobs relative to all jobs on the CEs and determine the average values of waiting and running time for the involved GRID queues. CEs which do not meet the set criteria can be removed from the production chain by including them in an exception table. All of these monitoring actions lead to a more reliable and faster execution of MC requests.

Common platform of Monte Carlo dose calculation on universal grid interface with Geant4 based particle therapy simulation framework

While Monte Carlo (MC) simulation is believed to be the most reliable method of dose calculation in particle therapy, the simulation time is critical in attaining sufficient statistical accuracy for clinical applications. Therefore, parallelization of simulations is essential. This paper describes a common platform of MC dose calculation in grid-distributed computing environments. The platform is flexible and effective for dose calculation in both clinical and research applications for particle therapy. The platform consists of the universal grid interface (UGI) and the Geant4-based particle therapy simulation framework (PTSIM). The UGI, written in Python, provides a command-line interface for job submission, file manipulation, and monitoring in multiple-grid middleware environments. The PTSIM is a single software application for modeling a treatment port with patient data obtained from CT images. The common platform was constructed in grid computing environments using the computing resources in five institutions. The platform utilized these resources through the NAREGI grid middleware under UGI to provide stable computing resources and a common environment for MC dose calculation in particle therapy.

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy

BackgroundComplete Genomics provides an open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files. Determination of; for example, the functional impact of detected variants, requires annotation with various databases that often require command-line and/or programming experience; thus, limiting their use to the average research scientist. We have therefore implemented this CG toolkit, together with a number of annotation, visualisation and file manipulation tools in Galaxy called CGtag (Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy).FindingsIn order to provide research scientists with web-based, simple and accurate analytical and visualisation applications for the selection of candidate mutations from Complete Genomics data, we have implemented the open-source Complete Genomics tool set, CGATools, in Galaxy. In addition we implemented some of the most popular command-line annotation and visualisation tools to allow research scientists to select candidate pathological mutations (SNV, and indels). Furthermore, we have developed a cloud-based public Galaxy instance to host the CGtag toolkit and other associated modules.ConclusionsCGtag provides a user-friendly interface to all research scientists wishing to select candidate variants from CG or other next-generation sequencing platforms’ data. By using a cloud-based infrastructure, we can also assure sufficient and on-demand computation and storage resources to handle the analysis tasks. The tools are freely available for use from an NBIC/CTMM-TraIT (The Netherlands Bioinformatics Center/Center for Translational Molecular Medicine) cloud-based Galaxy instance, or can be installed to a local (production) Galaxy via the NBIC Galaxy tool shed.

Evaluation of calcium hydroxide removal using EndoActivator system: An in vitro study

Aim: The aim of this study was to compare the calcium hydroxide (Ca(OH) 2 ) removal efficacy of the EndoActivator system with that of conventional irrigation with a syringe and hand file manipulation. Materials and Methods: A total of 44 extracted human single-rooted mandibular premolars were used. The root canal systems of all teeth were cleaned and shaped, then filled with Ca(OH) 2 paste. The teeth were divided into two groups: Ca(OH) 2 was removed using ethylenediaminetetraacetic acid (EDTA) and sodium hypochlorite (NaOCl) with hand filing and irrigation (Group 1) or the EndoActivator system (Group 2). Each tooth was split into two halves and examined under a scanning electron microscope. Results: Ca(OH) 2 particles were completely removed at the coronal level in both experimental groups. More Ca(OH) 2 particles were present in the apical third than in the middle-third in both groups. No significant interaction was observed between the two experimental groups or among the three examined levels (P > 0.05). Conclusion: Agitation with NaOCl and EDTA improved Ca(OH) 2 removal only in the coronal third of the root canal. Use of the EndoActivator system did not improve the efficacy of Ca(OH) 2 removal in the middle and apical thirds.

Collaborative design by sharing multiple-level encryption files

A design file can grow in size as the complexity of the target object increases. A large design file can reside in a large parallel computing system, such as a cloud computing system, and many designers can work concurrently on the same file. In such a case, it is obvious that we need some kind of protection mechanism allowing each user to access only the area of the file they are permitted to access. We take the encryption approach to ensure the safety of a file, even in the public domain such as on a cloud system, and in this article, we suggest a multi-level encryption scheme allowing each user to access a file only at the level the user has legitimate right to access. Each level of the file is encrypted with a different key, and the keys are shown only to those who have the right access permission. This article describes the necessary file format used to achieve this goal and discusses the file manipulation functions used to handle this new file format.

Scanning Compressed Full Text Files

From the 1994 CAIS Conference: The Information Industry in Transition McGill University, Montreal, Quebec. May 25 - 27, 1994.In this paper we discuss an application of compression, not with the overall goal of reducing disk space, but with the goal of extending the applicability of full text scan procedures to larger text files for use in on-line search environments. This paper presents an alternative to inverted file generation for access to full text data files of medium size, 50-200Mbytes, for which the cost of generating a full inverted file is not warranted. Full scan techniques, which are often useful in interactive situations for small files, become unacceptably slow for interactive sessions with files above 10 Mbytes and so the use of compression to reduce the quantity of data scanned is an attractive alternative. Furthermore, an index that can be used to reduce search time further to very acceptable 1-2 second times can be generated as a byproduct of the compression.

Maintenance and Reengineering of Software: Creating a Visual C++ Graphical User Interface to Perform Specific Tasks Related to Soil Structure Interaction in Poroelastic Soil

In this study, an interactive Graphical User Interface (GUI) application was introduced and tested. It worked as a utility program to facilitate and maximize the re-use of existing FORTRAN software. The GUI had been designed to generate tabulated seismic data (e.g., coefficient of reflection and propagation wave velocities: P-wave and SV-wave), in order to perform investigating the wave propagation in fluid saturated poroelastic medium, through using a simple two-dimensional soil-structure interaction model. Additionally, the theoretical background was also involved. The output data was of interest for understanding the effects of water saturation on the response of the ground and building structures to some degree earthquake excitation. Furthermore, the GUI application provided several utilities (e.g., viewing and plotting capabilities, file manipulation, editing as well as cloning the input parameters). Operating systems for which program had been designed were Windows XP, Windows Vista, Windows 7 and any (32) bits windows. The compilers were: Microsoft VC++ VS 6.0, Digital Visual FORTRAN 6.0 and Borland C++ Builder 6.0. The produced source code could be considered as successful case study for software engineers GUI developers, who were interested in creating (C++ /GUI), for FORTRAN by using the experience of such open source codes.

Development of a Relational Database to Capture and Merge Clinical History with the Quantitative Results of Radionuclide Renography

Our objective was to design and implement a clinical history database capable of linking to our database of quantitative results from (99m)Tc-mercaptoacetyltriglycine (MAG3) renal scans and export a data summary for physicians or our software decision support system. For database development, we used a commercial program. Additional software was developed in Interactive Data Language. MAG3 studies were processed using an in-house enhancement of a commercial program. The relational database has 3 parts: a list of all renal scans (the RENAL database), a set of patients with quantitative processing results (the Q2 database), and a subset of patients from Q2 containing clinical data manually transcribed from the hospital information system (the CLINICAL database). To test interobserver variability, a second physician transcriber reviewed 50 randomly selected patients in the hospital information system and tabulated 2 clinical data items: hydronephrosis and presence of a current stent. The CLINICAL database was developed in stages and contains 342 fields comprising demographic information, clinical history, and findings from up to 11 radiologic procedures. A scripted algorithm is used to reliably match records present in both Q2 and CLINICAL. An Interactive Data Language program then combines data from the 2 databases into an XML (extensible markup language) file for use by the decision support system. A text file is constructed and saved for review by physicians. RENAL contains 2,222 records, Q2 contains 456 records, and CLINICAL contains 152 records. The interobserver variability testing found a 95% match between the 2 observers for presence or absence of ureteral stent (κ = 0.52), a 75% match for hydronephrosis based on narrative summaries of hospitalizations and clinical visits (κ = 0.41), and a 92% match for hydronephrosis based on the imaging report (κ = 0.84). We have developed a relational database system to integrate the quantitative results of MAG3 image processing with clinical records obtained from the hospital information system. We also have developed a methodology for formatting clinical history for review by physicians and export to a decision support system. We identified several pitfalls, including the fact that important textual information extracted from the hospital information system by knowledgeable transcribers can show substantial interobserver variation, particularly when record retrieval is based on the narrative clinical records.

Pilot study to integrate existing karst flow data for Kentucky, USA into the National Hydrography Dataset of US Geological Survey

The US Geological Survey’s (USGS) National Hydrography Dataset (NHD) is a comprehensive set of digital spatial data representing the surface water of the United States for use with geographic information systems (GIS). The NHD digital product was designed to also allow incorporation of various groundwater data. The Kentucky Geological Survey (KGS) and Kentucky Division of Water (KDOW) have compiled and digitized karst flow data for more than half of the karst regions in Kentucky. These data, obtained from many investigators, have been published by KGS in the Kentucky Karst Atlas Map series and are available as data files for use with GIS. The USGS and KDOW have funded a pilot study, conducted by KDOW, to integrate existing karst data into the NHD. The pilot study area, located in the southwestern Mississippian Plateau Region of Kentucky, is the West Fork Red River watershed. This area was chosen because quality data have been compiled and digitized for a large percentage of the study area. During the project period the USGS created a standard protocol to request updates for all NHD stewards, which allowed for a uniform and streamlined process.

TH‐C‐BRB‐05: Monte Carlo Simulations for Quality Assurance of Varian TrueBeam 6MV FFF RapidArc SBRT Treatments

Purpose: To establish feasibility of performing quality assurance for Flattening Filter Free (FFF) RapidArc stereotactic body radiotherapy treatments (SBRT) on a TrueBeam LINAC using Monte Carlo simulations. Methods: Phase‐space files for TrueBeam FFF photon beams were made available by Varian in IAEA‐compliant format. Monte Carlo simulations were performed using BEAMnrc and DOSXYZnrc to validate the 6MV FFF phase space files for use in this study. The phase space data provided by Varian is in cylindrical geometry and required conversion into a format that was compatible with BEAMnrc prior to use. To establish validity of the phase space data, dose calculations in a water phantom for fields ranging from 3×3 cm̂2 to 40 × 40 cm̂2 were performed using DOSXYZnrc. Percent depth doses (PDDs), transverse profiles and output factors were calculated and compared with measurements. Monte Carlo simulations of 6MV FFF SBRT RapidArc plans were performed using a 2mm̂3 voxel size and compared with both ion chamber measurement and Eclipse Treatment Planning System (TPS) dose calculations. 3D gamma analysis (3%,3mm) comparing Monte Carlo and TPS results was performed. Results: Monte Carlo simulations and measured values agreed within 1% and 1.5% for PDDs and profiles respectively for all fields. The agreement between measured and calculated output factors was within 1 % including for highly asymmetric fields. These results indicate that the 6MV FFF phase space data is sufficiently accurate for use in quality assurance in radiation therapy. For the 6 MV FFF RapidArc plans the agreement between MC and both measured and TPS dose calculations was within 2%. Over 95% of the points passed the 3D Gamma test Conclusions: We have demonstrated the feasibility of performing patient specific quality assurance for 6 MV FFF SBRT RapidArc treatments using Monte Carlo simulations for a TrueBeam linac. This project is funded by Varian Medical Systems