Graphical Software Package Research Articles

The importance of reaming the posterior femoral cortex before inserting lengthening nails and calculation of the amount of reaming.

BackgroundLengthening nails have been used to correct limb length discrepancy caused by different etiologies, as well as for post-traumatic reasons. Two important lengthening nail-related complications are damage to the distraction mechanism and femoral fractures around the nail tip. As a result of the curved anatomy of the femur, straight nails impinge on the anterior cortex. Therefore, proper reshaping of the medullary canal to accommodate straight lengthening nails is crucial for the prevention of this problem. Reaming the dense posterior cortex is important when aiming to insert a lengthening nail without incurring anterior cortex nail tip impingement-related complications. Posterior femoral cortex over-reaming is a solution to this situation.MethodsSixty patients received lengthening nails during 2008–2013, (ISKD, Fitbone, Precice). Posterior cortex rigid-reaming technique was used successfully in 45 retrograde femoral lengthening cases. The preoperatively planned posterior cortex amount was reamed until the impingement was overcome during the operation under fluoroscopic control for each case. Since the preoperative determination of posterior cortex reaming amount is time consuming and operator dependent, we evaluated the X-rays of the patients with computer software and conventional paper-based measurements. The effect of reaming the posterior cortical wall on the inclination of the nail tip to the anterior femoral cortex was detected with measurements on the preoperative and postoperative lateral femoral X-rays by using the CorelDRAW® Graphic Suite X6 software package (Corel, Inc., Ottawa, Ontario, Canada) software. On the same software, X-rays and the posterior reaming amount were also calculated.ResultsThe mean age of the patients was 27 years (11–42), while the mean lengthening was 5.9 cm (2–14). The mean consolidation index was 1.05 (0.75–1.62), and the mean follow-up period was 31 months (range, 18–45 months). The mean distance of the osteotomy site to the intercondylar notch of the femur was 81.2 mm (±16.92). The mean displacement of the nail tip position was 15.42 mm (±4.77) on the measurements on the postoperative X-rays after nail insertion compared to the preoperative simulations on the templates. The mean posterior cortex reaming thickness was 3.68 mm (±1.02).ConclusionsWe derived a formula that allows the required amount of optimal posterior cortex reaming to be determined. No impingement-related complications or nail damage were observed.

The practice of mine ventilation engineering

The practice of ventilation is continually evolving with new technological advances developed in the mining industry. In recent years the advances in diesel engine technologies, ventilation modeling software, and ventilation management capacities have redefined the historical methods used to evaluate systems. The advances re-evaluate previous methods used to calculate the airflow requirements for the dilution of diesel exhaust fumes. Modeling software has become an integral part of planning and developing ventilation systems in partnership with graphical mine design software packages to generate realistic representations of the mine. Significant advances in ventilation control strategies through remote sensors and monitoring capabilities have been developed to results in cost savings. Though there has been much advancement in mine ventilation technology, the practices and basic ventilation principals enacted through the ventilation engineer cannot be placated with technological advances only.

Quantitative reconstruction of PIXE-tomography data for thin samples using GUPIX X-ray emission yields

We present here a new development of the TomoRebuild software package, to perform quantitative Particle Induced X-ray Emission Tomography (PIXET) reconstruction. X-ray yields are obtained from the GUPIX code. The GUPIX data base is available for protons up to 5MeV and also in the 20–100MeV energy range, deuterons up to 6MeV, 3He and alphas up to 12MeV. In this version, X-ray yields are calculated for thin samples, i.e. without simulating X-ray attenuation. PIXET data reconstruction is kept as long as possible independent from Scanning Transmission Ion Microscopy Tomography (STIMT). In this way, the local mass distribution (in g/cm3) of each X-ray emitting element is reconstructed in all voxels of the analyzed volume, only from PIXET data, without the need of associated STIMT data. Only the very last step of data analysis requires STIMT data, in order to normalize PIXET data to obtain concentration distributions, in terms of normalized mass fractions (in μg/g). For this, a noise correction procedure has been designed in ImageJ. Moreover sinogram or image misalignment can be corrected, as well as the difference in beam size between the two experiments. The main features of the TomoRebuild code, user friendly design and modular C++ implementation, were kept. The software package is portable and can run on Windows and Linux operating systems. An optional user-friendly graphic interface was designed in Java, as a plugin for the ImageJ graphic software package. Reconstruction examples are presented from biological specimens of Caenorhabditis elegans – a small nematode constituting a reference model for biology studies. The reconstruction results are compared between the different codes TomoRebuild, DISRA and JPIXET, and different reconstruction methods: Filtered BackProjection (FBP) and Maximum Likelihood Expectation Maximization (MLEM).

STAMP: statistical analysis of taxonomic and functional profiles.

STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles. It supports tests for comparing pairs of samples or samples organized into two or more treatment groups. Effect sizes and confidence intervals are provided to allow critical assessment of the biological relevancy of test results. A user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots. STAMP is licensed under the GNU GPL. Python source code and binaries are available from our website at: http://kiwi.cs.dal.ca/Software/STAMP.

Virtual Tool Mark Generation for Efficient Striation Analysis,

This study introduces a tool mark analysis approach based upon 3D scans of screwdriver tip and marked plate surfaces at the micrometer scale from an optical microscope. An open-source 3D graphics software package is utilized to simulate the marking process as the projection of the tip's geometry in the direction of tool travel. The edge of this projection becomes a virtual tool mark that is compared to cross-sections of the marked plate geometry using the statistical likelihood algorithm introduced by Chumbley et al. In a study with both sides of six screwdriver tips and 34 corresponding marks, the method distinguished known matches from known nonmatches with zero false-positive matches and two false-negative matches. For matches, it could predict the correct marking angle within ±5-10°. Individual comparisons could be made in seconds on a desktop computer, suggesting that the method could save time for examiners.

ZODET: Software for the Identification, Analysis and Visualisation of Outlier Genes in Microarray Expression Data

SummaryComplex human diseases can show significant heterogeneity between patients with the same phenotypic disorder. An outlier detection strategy was developed to identify variants at the level of gene transcription that are of potential biological and phenotypic importance. Here we describe a graphical software package (z-score outlier detection (ZODET)) that enables identification and visualisation of gross abnormalities in gene expression (outliers) in individuals, using whole genome microarray data. Mean and standard deviation of expression in a healthy control cohort is used to detect both over and under-expressed probes in individual test subjects. We compared the potential of ZODET to detect outlier genes in gene expression datasets with a previously described statistical method, gene tissue index (GTI), using a simulated expression dataset and a publicly available monocyte-derived macrophage microarray dataset. Taken together, these results support ZODET as a novel approach to identify outlier genes of potential pathogenic relevance in complex human diseases. The algorithm is implemented using R packages and Java.AvailabilityThe software is freely available from http://www.ucl.ac.uk/medicine/molecular-medicine/publications/microarray-outlier-analysis.

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data

Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.

FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data

Rare copy number variations (CNVs) are frequent causes of genetic diseases. We developed a graphical software package based on a novel approach that can consistently identify CNVs of all types (homozygous deletions, heterozygous deletions, heterozygous duplications) from exome-sequencing data without the need of a paired control. The algorithm compares coverage depth in a test sample against a background distribution of control samples and uses principal component analysis to remove batch effects. It is user friendly and can be run on a personal computer. The main scripts are implemented in R (2.15), and the GUI is created using Java 1.6. It can be run on all major operating systems. A non-GUI version for pipeline implementation is also available. The program is freely available online: https://sourceforge.net/projects/fishingcnv/ Supplementary data are available at Bioinformatics online.

Capillary-Driven Toner-Based Microfluidic Devices for Clinical Diagnostics with Colorimetric Detection

The fabrication of toner-based microfluidic devices to perform clinical diagnostics with capillary action and colorimetric detection is described in this report. Test zones and microfluidic channels were drawn in a graphic software package and laser printed on a polyester film. The printed layout and its mirror image were aligned with an intermediary cut-through polyester film and then thermally laminated together at 150 °C at 60 cm/min to obtain a channel with ca. 100-μm depth. Colorimetric assays for glucose, protein, and cholesterol were successfully performed using a desktop scanner. The limit of detection (LD) values found for protein, cholesterol, and glucose were 8, 0.2, and 0.3 mg/mL, respectively. The relative standard deviation (RSD) values for an interdevices comparison were 6%, 1%, and 3% for protein, cholesterol, and glucose, respectively. Bioassays were successfully performed on toner-based devices stored at different temperatures during five consecutive days without loss of activity.

Thermal food processing optimization: Algorithms and software

The algorithms and graphic user interface software package “OPT-PROx” are developed to meet food engineering needs related to canned food thermal processing simulation and optimization. The adaptive random search algorithm and its modification coupled with penalty function′s approach, and the finite difference methods with cubic spline approximation are utilized by “OPT-PROx” package (http://tomakechoice.com/optprox/index.html). The diversity of thermal food processing optimization problems with different objectives and required constraints are solvable by developed software. The geometries supported by the “OPT-PROx” are the following: (1) cylinder, (2) rectangle, (3) sphere. The mean square error minimization principle is utilized in order to estimate the heat transfer coefficient of food to be heated under optimal condition. The developed user friendly dialogue and used numerical procedures makes the “OPT-PROx” software useful to food scientists in research and education, as well as to engineers involved in optimization of thermal food processing.

Material Flow Optimization in By-product Synergy Networks

By-product synergy (BPS) is an industrial ecology practice that involves utilization of industrial by-products as feedstocks for other industrial processes. A novel decision support tool is developed to analyze BPS networks that involve material processing and transport among regional clusters of companies. Mathematical programming techniques are used to determine the optimal network design and the material flows that minimize total cost or environmental impacts. This methodology is incorporated into a graphical software package called Eco-Flow™. The tool has been applied to model and analyze available synergies in an existing BPS network centered in Kansas City, Missouri. A base case, which assumes no synergies, is compared with the optimal BPS solution found by Eco-Flow™. The results for Kansas City suggest that when companies in the network cooperate to optimize the system profitability, up to $15 million per year of savings are possible. The findings also indicate that the BPS approach would result in 29% reduction in total cost, 25.8% reduction in average company cost, 30% reduction in carbon dioxide (CO2) emissions, and 37% reduction in waste to landfill. The modeling approach is being extended to better represent the dynamics of industrial and ecological processes.

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies

BackgroundMost software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot.ResultsUsing the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool.ConclusionsOur programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

Comparative Shotgun Proteomics Using Spectral Count Data and Quasi-Likelihood Modeling

Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes using liquid chromatography−tandem mass spectrometry (LC−MS/MS) and allows a global analysis of protein changes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete, and this contributes to variability in assessment of peptide and protein inventories by spectral counting approaches. Thus, shotgun proteomics data pose challenges in comparing proteomes from different biological states. We developed an analysis strategy using quasi-likelihood Generalized Linear Modeling (GLM), included in a graphical interface software package (QuasiTel) that reads standard output from protein assemblies created by IDPicker, an HTML-based user interface to query shotgun proteomic data sets. This approach was compared to four other statistical analysis strategies: Student t test, Wilcoxon rank test, Fisher’s Exact test, and Poisson-based GLM. We analyzed the performance of these tests to identify differences in protein levels based on spectral counts in a shotgun data set in which equimolar amounts of 48 human proteins were spiked at different levels into whole yeast lysates. Both GLM approaches and the Fisher Exact test performed adequately, each with their unique limitations. We subsequently compared the proteomes of normal tonsil epithelium and HNSCC using this approach and identified 86 proteins with differential spectral counts between normal tonsil epithelium and HNSCC. We selected 18 proteins from this comparison for verification of protein levels between the individual normal and tumor tissues using liquid chromatography−multiple reaction monitoring mass spectrometry (LC−MRM-MS). This analysis confirmed the magnitude and direction of the protein expression differences in all 6 proteins for which reliable data could be obtained. Our analysis demonstrates that shotgun proteomic data sets from different tissue phenotypes are sufficiently rich in quantitative information and that statistically significant differences in proteins spectral counts reflect the underlying biology of the samples.

A technology of digitization of practical materials maps based on software programs Maplnfo Professional and CorelDRAW

A process of information input in the computer with the use of GIS MapInfo Professional and graphic software package CorelDRAW 11 is described in detail. It is shown, that working technique on the raster overlay allows to combine raster and vector layers, considerably increasing a digitizing accuracy and speed. The digitizing method does not require special devices as digitizer. It is offered to use for digitizing the inflicted on a map observations points and the anomaly values, but not isolines. The use of the right rectangular system of coordinates and the point coordinates fixing is substantial. The testing is executed on actual material and efficiency of the developed method of input of cartographic information in a computer is proved.

Estimating stream metabolism from oxygen concentrations: Effect of spatial heterogeneity

Rivers are heterogeneous at various scales. River metabolism estimators based on oxygen time series provide average estimates of net oxygen production at the scale of a river reach. These estimators are derived for homogeneous river reaches. For this reason, they cannot be used to analyze how exactly they average over longitudinal variations in net production, reaeration, oxygen saturation concentration and flow velocity. We try to fill this gap by using a general analytical solution of the transport‐reaction equation to (1) demonstrate how downstream oxygen concentration is affected by upstream concentration and (possible) longitudinally varying values of net production, reaeration, oxygen saturation concentration and flow velocity within a reach, and (2) derive how the net production estimate depends on varying upstream river parameters. In addition, we derive a new net production estimator that extends previously suggested estimators. The equations derived in this paper provide a general framework for understanding the assumptions underlying net production estimators. They are used to derive recommendations on the use of single station or two stations measurement layouts to get accurate river metabolism estimates. The estimator is implemented in the freely available statistics and graphics software package R (www.r‐project.org). This makes it easily applicable to observed oxygen time series. Empirical evidence of the significance of heterogeneity in rivers is demonstrated by applying the estimator to four subsequent reaches of a river using oxygen measurements from the ends of all reaches.

3S: A novel program for field spectroscopy

The graphic user interface software package spectroscopy at subnanometer spectral resolution is presented in this manuscript. The software permits efficient acquisition of field spectroscopy data and is specifically designed to facilitate the operations to compute the reflectance factor of a given object or surface from standard field spectroscopy measurements (so-called field remote sensing): incident and reflected solar radiance measurements. The developed computer code runs with widely diffused commercial low-cost visible/near-infrared Ocean Optics spectrometers. Its development was originally intended for plant studies using field spectroscopy at leaf and canopy level, but 3S can be employed in other applications such as ocean and water quality studies, geological exploration, mineral identification, precision farming and other environmental applications.

Interactive graphics return to protein science

Visualization of molecular images is an important means of interpreting structural and other data and of communicating scientific results in the field of protein science. Long-time readers of the journal Protein Science will recall that early issues of the journal were accompanied by a floppy disk containing graphical images in the pioneering kinemage format developed by David C. Richardson and Jane S. Richardson (The kinemage: A tool for scientific communication, Protein Science (1992) 1, 3-9.). Unfortunately, kinemages disappeared from Protein Science a decade ago. In this issue, a Commentary by Li and Palmer (Protein Science (2009) 18, 678-681) returns interactive computer graphics to Protein Science. This article incorporates interactive figures, based on the open-source Jmol package (http://jmol.sourceforge.net/), that are viewable using any World-Wide-Web browser through embedded links within the electronic version of the paper. These figures are of two types. First, authors can generate figures specially designed to enhance the information presented in the article (see below). Second, any Protein Data Bank (PDB) code quoted in the manuscript will be linked to the FirstGlance in Jmol viewer (http://molvis.sdsc.edu/fgij/index.htm). This will allow the reader to immediately and interactively visualize the structure in question. No additional files or programs need to be downloaded or installed on a reader's computer in order to view these figures. The molecular images can be manipulated, either using command options provided within the figures (which requires no knowledge of Jmol) or by opening the Jmol console window (which requires a modicum of familiarity with molecular graphics packages). Jmol has been adopted by a number of other journals and organizations, including ACS Chemical Biology, Biochemical Journal, and the International Union of Crystallography, as a platform for “enhanced” figures. The level of interactivity provided by Jmol is the major benefit over animations or embedded movies; of course, animations and movies prepared in standard formats, using for example other molecular graphics software packages, also can be included as supplementary material to a paper in Protein Science. Interactive figures in Protein Science are prepared by incorporating user-generated Jmol scripts and hyertext markup language (html) content into html templates. This hybrid approach simplifies the process of generating figures for new users, but provides flexibility for more expert authors. We emphasize that this initiative is continuing to be developed. The commentary of Li and Palmer is intended to provide readers with a flavor of the system that we have in mind. Feedback is welcome. During the initial “learning phase”, authors wishing to include interactive figures in their papers in Protein Science should contact the Editor for additional information. The re-incorporation of interactive graphics into Protein Science is a long-awaited return of the journal to its roots and an exciting opportunity for authors to augment the usefulness of their papers for readers.

Quantitative analysis of glenoid bone loss in osteoarthritis using three-dimensional computed tomography scans

The 3-dimensional (3D) shape of the glenoid vault has been defined previously and shown to be a complex, yet consistent, shape in individuals without glenoid pathology. We proposed assessing whether this conserved shape could be used as a template to measure glenoid bone loss in subjects with glenohumeral osteoarthritis. Computed tomography (CT) scans of both shoulders were obtained from 12 subjects with unilateral glenohumeral osteoarthritis. The paired scapulae were reconstructed 3-dimensionally, using a previously developed graphic software package. Two methods of estimating glenoid bone loss were performed. First, using the software, a stereolithography model of the standardized vault shape was implanted into each glenoid and measurements made of the volume of the implant not contained within each vault. Second, direct measurements of the paired glenoid vault volumes were performed. The volume of the nonarthritic glenoid was used as a subject-specific template for normal glenoid vault volume for each pair. The glenoid bone volumes measured by each method were compared and Pearson's correlation coefficient determined. The average measurement of glenoid bone loss using the vault implant was within 0.8% (SD +/- 1.5%) of the measurement made using the contralateral, normal glenoid. For all patients, Pearson's correlation coefficient was .99, indicating a very high correlation between the two methods of measuring bone loss (P < .0001). The intricate, yet consistent 3D shape of the glenoid vault can be used as an accurate and reliable template to measure glenoid bone loss in glenohumeral osteoarthritis.

Performance evaluation through simulation modeling in a cotton spinning system

Spinning system is an important segment in the textile industries, which consists of a set of processes to convert raw cotton into yarn. This spinning process can run continuously only when there are no breaks in the output of yarn produced from every spindle. However, the yarn does break due to several reasons like ambient conditions in the spinning facility, such as humidity, quality of cotton and spindle speed, etc., and other factors such as piecing (joining) of the broken yarn, using a pre-determined yarn length, by a operator called ‘sider’. Breaks in yarn spinning cause a decrease in productivity. The random nature of yarn breaks, in addition to the variations in spinning process parameters also influence frequency of their occurrence and ultimately the downtime of the spindle as the broken yarn waits in a queue to be pieced. Normally a sider is responsible for a group of six adjacent spinning frames. This man–machine system (sider-spinning frame system) is modeled and analyzed in this paper using graphical simulation software package. Applying the real data collected from a cotton-spinning mill, a simulation model has been developed and validated. This validated model is used for evaluating alternate routings available for the sider to find out the optimum route.

Manuscript preparation with LyXforJASA

LyXforJASA is a graphical software package for creating manuscripts that meet the submission requirements of the Peer‐X‐Press (PXP) system used by the Journal of the Acoustical Society of America (JASA). Its main features are graphical templates for superscript and author‐year citation styles and for single figures. It is based on LyX, a screen‐based graphical user interface (GUI) to the LaTeX typesetting language. Authors see manuscript content, not LaTeX code. LyX liberates authors from document bookkeeping, such as spacing, font selection, and section, equation, figure, table, and citation numbering. LyX has a comprehensive, point and click, GUI mathematics editor with an extensive list of symbols. It can export text in LaTeX, PDF, PostScript, and ASCII formats. It has been ported successfully to Linux, Macintosh OSX, and Windows XP. LyXforJASA packages can be found at http://ww2.hawaii.edu/∼jcb/LyXforJASA/LyXforJASA.html ww2.hawaii.edu/∼jcb/LyXforJASA/LyXforJASA.html