Software Tool For Evaluation Research Articles

Software Tool for Evaluation of Electrical Energy Produced by Photovoltaic Systems

This paper presents a software tool for evaluation of electrical energy generated by photovoltaic (PV) systems. The software was developed using the MATLAB software package and contains the elements of an expert system. The software is designed for engineers who are involved in photovoltaic system design and for students (undergraduates and Masters) of electrical engineering who, using the software, adopt theoretical assumptions and solve practical engineering problems. The structure, organization and software capabilities are illustrated within the example of the design of an actual photovoltaic system.

Software Tools for Evaluation of Measurement Models for Complex-valued Quantities in Accordance with Supplement 2 to the GUM

In October 2011, a new guidance document “Evaluation of measurement data – Supplement 2 to the ‘Guide to the expression of uncertainty in measurement’ – Extension to any number of output quantities...

Evaluating Published Skin Dose Tolerance Limits for Stereotactic Body Radiation Therapy of Lung Cancer

Objectives: Published local control rates for certain stereotactic body radiotherapy (SBRT) lung cancer treatments have exceeded 97%, but several serious adverse events have been reported. No five-year normal tissue complication probability (NTCP) statistical analysis SBRT results have been published yet for skin. While we expectantly await these publications, the goal of this manuscript is to glean the published expert opinion and ongoing clinical trials for skin dose tolerance limits in one to five fractions for clinical application and research. Methods: All 42 lung tumors treated with the CyberKnife at Cooper University Hospital from July 2008 to May 2010 that had skin contours and Monte Carlo dose calculations with heterogeneity corrections were reviewed for toxicity. Twenty-one published dose tolerance limits for skin were partitioned into high-risk and low-risk categories. The DVH Evaluator software tool was developed by the first author and used to conveniently assess the dose tolerance limits for each case prior to treatment and to analyze the followup data. Results: Three of the 42 patients experienced mild Grade 1 erythema that resolved within a few months. No Grade 2 or higher adverse events of skin toxicity were encountered. A unified framework of high-risk and low-risk skin dose limits in one to five fractions at specific dose-volume levels is presented. Conclusions: When the dose tolerance limits are diligently studied and respected, SBRT has potential to be a safe and effective form of radiation therapy. Longer follow-up will still be required to statistically analyze late effects and long-term outcomes.

Objective assessment of aesthetic outcome after breast conserving therapy: Subjective third party panel rating and objective BCCT.core software evaluation

We analysed intra- and inter-rater agreement of subjective third party assessment and agreement with a semi-automated objective software evaluation tool (BCCT.core).We presented standardized photographs of 50 patients, taken shortly and one year after surgery to a panel of five breast surgeons, six breast nurses, seven members of a breast cancer support group, five medical and seven non-medical students. In two turns they rated aesthetic outcome on a four point scale. Moreover the same photographs were evaluated by the BCCT.core software.Intra-rater agreement in the panel members was moderate to substantial (k = 0.4–0.5; wk = 0.6–0.7; according to different subgroups and times of assessment). In contrast inter-rater agreement was only slight to fair (mk = 0.1–0.3). Agreement between the panel participants and the software was fair (wk = 0.24–0.45).Subjective third party assessment only fairly agree with objective BCCT.core evaluation just as third party participants do not agree well among each other.

SU‐E‐T‐883: Clinical Application of Monte Carlo for SBRT: Mediastinal Lung

Purpose: Treatment planning systems have provided Monte Carlo dose calculations for several years but many physicians are still hesitant to use them clinically due to lack of data. Therefore we recalculated 200 Ray Tracing treatment plans using Monte Carlo with heterogeneity corrections and compared to SBRT dose tolerance limits. Methods: From among these 200 CyberKnife cases, 25 mediastinal lung cases are presented in this study. An extensive literature review obtained 105 published SBRT dose tolerance limits for the mediastinal critical structures aorta, bronchi, esophagus, heart, and trachea. These limits were partitioned into high‐risk and low‐risk categories. The DVH Evaluator software tool was used to generate DVH Risk Maps for these critical structures, which superimpose a) published dose tolerance limits b) unified high‐risk and low‐risk trends and c) published adverse event doses, onto Monte Carlo patient data to assess risk of adverse events. Results: Recalculated treatment plan data is within the expected range of published SBRT dose tolerance limits, providing optimism for clinical use. None of the patients experienced any Grade 3 or higher adverse events. The low‐risk dose tolerance limits were exceeded 22 times in these cases with no severe adverse event, thus helping to validate their safety. Conclusions: The range of doses calculated by Monte Carlo for our historical patient data is compatible with published SBRT dose tolerance limits. SBRT dose tolerance limits should be fine‐tuned by Monte Carlo dose calculations in long‐term statistical followup studies.Disclosure: The first author has developed the DVH Evaluator software.

MO-D-BRB-07: Phantom Validation and Clinical Application of Monte Carlo for Small Field SBRT

Purpose: Small field dosimetry is challenging in homogeneous medium and extremely difficult in an inhomogeneous medium. Monte Carlo dose calculation algorithms are considered as the most accurate for treatment planning. We present our validation of the Monte Carlo algorithm in the Accuray Multiplan system using measurements in a cork phantom. We also recalculated Ray Tracing treatment plans with the Monte Carlo algorithm and compared to SBRT dose tolerance limits. Methods: In our validation measurements with a cork phantom, an Exradin A16 ion chamber was used for collimators from 60mm to 20mm on a CyberKnife, and a PTW 60012 stereotactic diode for collimators from 60mm to 5mm. A literature review of more than 500 published SBRT dose tolerance limits was partitioned into high-risk and low-risk categories. Two hundred CyberKnife treatment plans were recalculated using Monte Carlo and compared to the dose limits. The DVH Evaluator software tool was used to generate DVH Risk Maps for 25 critical structures throughout the body, which superimpose a) published dose tolerance limits b) unified high-risk and low-risk trends and c) published adverse event doses, onto Monte Carlo patient doses to assess risk of adverse events. Results: The Monte Carlo calculations matched the Exradin A16 measurements to within 2.5% for field sizes down to 20mm, and matched the PTW 60012 measurements to within 2.5% for all field sizes down to 5mm. Recalculated treatment plan data is within the expected range of published SBRT dose tolerance limits, providing optimism for clinical use. Conclusions: The Accuray MultiPlan Monte Carlo algorithm is accurate even for small fields in heterogeneous media. The range of doses calculated by Monte Carlo for our patient data is compatible with published SBRT dose tolerance limits. SBRT dose tolerance limits should be fine-tuned by Monte Carlo dose calculations in long-term statistical followup studies. Disclosure: The first author has developed the DVH Evaluator software.

Assessment tool for pharmacy drug–drug interaction software

ObjectivesTo assess the performance of pharmacy clinical decision support (CDS) systems for drug–drug interaction (DDI) detection and to identify approaches for improving the ability to recognize important DDIs. Practice descriptionPharmacists rely on CDS systems to assist in the identification of DDIs, and research suggests that these systems perform suboptimally. The software evaluation tool described here may be used in all pharmacy settings that use electronic decision support to detect potential DDIs, including large and small community chain pharmacies, community independent pharmacies, hospital pharmacies, and governmental facility pharmacies. Practice innovationA tool is provided to determine the ability of pharmacy CDS systems to identify established DDIs. It can be adapted to evaluate potential DDIs that reflect local practice patterns and patient safety priorities. Beyond assessing software performance, going through the evaluation processes creates the opportunity to evaluate inadequacies in policies, procedures, workflow, and training of all pharmacy staff relating to pharmacy information systems and DDIs. ConclusionThe DDI evaluation tool can be used to assess pharmacy information systems’ ability to recognize relevant DDIs. Suggestions for improvement include determining whether the software allows for customization, creating standard policies for handling specific interactions, and ensuring that drug knowledge database updates occur frequently.

“SABER”: A new software tool for radiotherapy treatment plan evaluation

Both spatial and biological information are necessary in order to perform true optimization of a treatment plan and for predicting clinical outcome. The goal of this work is to develop an enhanced treatment plan evaluation tool which incorporates biological parameters and retains spatial dose information. A software system is developed which provides biological plan evaluation with a novel combination of features. It incorporates hyper-radiosensitivity using the induced-repair model and applies the new concept of dose convolution filter (DCF) to simulate dose wash-out effects due to cell migration, bystander effect, and/or tissue motion during treatment. Further, the concept of spatial DVH (sDVH) is introduced to evaluate and potentially optimize the spatial dose distribution in the target volume. Finally, generalized equivalent uniform dose is derived from both the physical dose distribution (gEUD) and the distribution of equivalent dose in 2 Gy fractions (gEUD2) and the software provides three separate models for calculation of tumor control probability (TCP), normal tissue complication probability (NTCP), and probability of uncomplicated tumor control (P+). TCP, NTCP, and P+ are provided as a function of prescribed dose and multivariable TCP, NTCP, and P+ plots are provided to illustrate the dependence on individual parameters used to calculate these quantities. Ten plans from two clinical treatment sites are selected to test the three calculation models provided by this software. By retaining both spatial and biological information about the dose distribution, the software is able to distinguish features of radiotherapy treatment plans not discernible using commercial systems. Plans that have similar DVHs may have different spatial and biological characteristics and the application of novel tools such as sDVH and DCF within the software may substantially change the apparent plan quality or predicted plan metrics such as TCP and NTCP. For the cases examined, both the calculation method and the application of DCF can change the ranking order of competing plans. The voxel-by-voxel TCP model makes it feasible to incorporate spatial variations of clonogen densities (n), radiosensitivities (SF2), and fractionation sensitivities (alpha/beta) as those data become available. The new software incorporates both spatial and biological information into the treatment planning process. The application of multiple methods for the incorporation of biological and spatial information has demonstrated that the order of application of biological models can change the order of plan ranking. Thus, the results of plan evaluation and optimization are dependent not only on the models used but also on the order in which they are applied. This software can help the planner choose more biologically optimal treatment plans and potentially predict treatment outcome more accurately.

Connecting research and practice: an experience report on research infusion with software architecture visualization and evaluation

There are many technical challenges in ensuring high life-time quality of NASA's systems. Some of NASA's software-related challenges could potentially be addressed by the many powerful technologies that are being developed in software research laboratories. However, most such research technologies do not make the transition from the research lab to the software lab because research infusion and technology transfer is difficult. For example, there must be evidence that the technology works in the practitioner's particular domain, and there must be a potential for great improvements and enhanced competitive edge for the practitioner, for such infusion to take place. NASA IV&V's Research Infusion initiative strives to facilitate such infusion. In 2006, a research infusion project involving Johns Hopkins University Applied Physics Laboratory (JHU/APL) and the Fraunhofer Center for Experimental Software Engineering Maryland, was successfully completed infusing Fraunhofer's software architecture visualization and evaluation (SAVE) tool. The infusion project helped improve JHU/APL's software architecture and produced evidence that SAVE is applicable to software architecture problems in the aerospace domain, spawning a series of related research infusion projects. The project also led to the discovery of other needs that could not be addressed by current technologies and, therefore, spawned the research and development of a new technology that will be ready for infusion in the future. This paper describes the SAVE technology followed by a description of the infusion of SAVE at JHU/APL and the other projects that followed, as well as the newly started Dynamic SAVE research and development project. Lessons learned related to various aspects of research infusion conclude the paper.

SU‐GG‐T‐553: Comparison of RTOG 0618, 0813, 0915, and Accuray STARS SBRT Lung Protocols

Purpose: Recently several stereotactic body radiation therapy (SBRT) lung protocols have been developed. To gain insight into the dose tolerance limits and the fractionation schemes, this study is a comparison of the RTOG 0618, 0813, 0915, and Accuray STARS SBRT lung protocols. Method and Materials: To make a fair, unbiased comparison, all selected patients were evaluated according to all six protocol regimens. The DVH Evaluator software tool, which can evaluate a treatment plan according to all selected protocols, was used. Results: When comparing the various dose schemas and normal tissue tolerance limits utilized in currently available protocols, the Accuray STARS protocol incorporates radiobiologically higher dose tolerance limits. There is some discordance in the use of radiobiological equivalent doses as demonstrated with spinal cord limits heavily dependent upon fractionation schema and lung dose limits very similar to standard fractionated target doses. When we compare and contrast the various protocols RTOG 0618 incorporates the highest effective dose, yet some normal tissue tolerance targets are more strict than in other similar trials. Comparative analysis of included patients illustrates that three patients would have received treatment in full compliance with three of six protocols. Another patient was noted to exceed the spinal cord tolerance only for the single fraction arm of RTOG 0915 and skin limit for RTOG 0618, while meeting the esophageal dose limits in three of six protocols. Conclusion: This opens a dialogue regarding SBRT dose limits for the potential delivery of higher effective target doses utilizing the available ranges of acceptable normal tissue tolerance levels for the development of individualized treatment maximizing the risk‐benefit ratio of normal tissue to target dose delivery in an attempt to provide improved outcome for patients.

GOAL: A software tool for assessing biological significance of genes groups

BackgroundModern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functional relevance among the genes in each group is usually characterized by utilizing available biological knowledge in public databases such as Gene Ontology (GO), KEGG pathways, association between a transcription factor (TF) and its target genes, and/or gene networks.ResultsWe developed GOAL: Gene Ontology AnaLyzer, a software tool specifically designed for the functional evaluation of gene groups. GOAL implements and supports efficient and statistically rigorous functional interpretations of gene groups through its integration with available GO, TF-gene association data, and association with KEGG pathways. In order to facilitate more specific functional characterization of a gene group, we implement three GO-tree search strategies rather than one as in most existing GO analysis tools. Furthermore, GOAL offers flexibility in deployment. It can be used as a standalone tool, a plug-in to other computational biology tools, or a web server application.ConclusionWe developed a functional evaluation software tool, GOAL, to perform functional characterization of a gene group. GOAL offers three GO-tree search strategies and combines its strength in function integration, portability and visualization, and its flexibility in deployment. Furthermore, GOAL can be used to evaluate and compare gene groups as the output from computational biology tools such as clustering algorithms.

FTSET-a software tool for fault tolerance evaluation and improvement

It is commonly assumed that neural networks have a built-in fault tolerance property mainly due to their parallel structure. The international community of neural networks discussed these properties until 1994 and afterward the subject has been mostly ignored. Recently, the subject was again brought to discussion due to the possibility of using neural networks in areas where fault tolerance and graceful degradation properties would be an added value, like medical applications of nano-electronics or space missions. Nevertheless, the evaluation of fault tolerance and graceful degradation characteristics remained difficult because there were no systematic methods or tools that could be easily applied to a given Artificial Neural Networks application. The discussion of models is the first step for sorting ways of developing the fault tolerance capability and for building a tool that can evaluate and improve this characteristic. The present work proposes a fault tolerance model, presents solutions for improving it and introduces the Fault Tolerance Simulation and Evaluation Tool for Artificial Neural Networks that evaluates and improves fault tolerance.

Application Portfolio Management—An Integrated Framework and a Software Tool Evaluation Approach

Despite the growing number of organizations that have lost track of their application landscape and have suffered from a sharp increase in application portfolio complexity, a comprehensive and systematic approach to Application Portfolio Management (APM) still appears far from being adopted. To move the adoption process along, this paper develops a comprehensive framework assimilating and extending previous research and presents an APM process comprising data collection, analysis, decision-making, and optimization phases. This paper also presents an approach for evaluating software tools for APM and identifies which software tool families are best able to provide support for specific purposes. With this integrated conceptual guideline for APM and its translation into a model for measuring appropriate practical support, this paper not only allows for a move more deeply into the research area but also offers advice for both researchers and practitioners.

SU-FF-T-514: Unified Dose Tolerance Limits for SBRT

Purpose: To unify and consolidate the stereotactic body radiation therapy(SBRT)dose tolerance limits from various authors into a more usable format. Methods and Materials: A thorough literature review uncovered 375 dose tolerance limits for anatomical critical structures throughout the body, applicable to SBRTtreatments employing one to five fractionated sessions. The dose tolerance limits vary significantly among authors. Some authors present limits in terms of cubic centimeters while others are in terms of percentage volume, and the doses and volumes specified vary greatly. We propose a unified format that specifies dose limits to several salient volumes that are the same for all critical structures within each classification. We also developed a DVH Evaluator software tool that helps manage various dose tolerance limits and helps evaluate the DVH for clinical use. Results: The format of unified dose tolerance tables are proposed and several sample critical structures are presented. Further work with radiobiology and DVH analysis will be required to fill in the remaining gaps for all the relevant critical structures. Conclusion: This work represents significant progress towards unifying the dose tolerance limits for SBRT, but much more work is needed. We recommend formation of AAPM and ASTRO task groups to thoroughly address this issue from both physics and physician perspectives.

Comparison of Different Staining Methods and Software Evaluation Tools for 2DE Gel Electrophoresis

Various staining methods for protein staining acrylamide gels exist. But as they all differ in their mechanism of action, sensitivity, linear range and the software tool required for analysis, not all of them can be used for the same issue of research and therefore need to be evaluated.

Geometric accuracy of digital volume tomography and conventional computed tomography

Digital volume tomography is a recently established imaging method that is based on the principle of cone beam computed tomography (CBCT). One of its main applications is imaging in dental and maxillofacial surgery. The objective of this study was to compare the geometric accuracy of digital volume tomographic imaging with that of conventional CT and to assess the suitability for image-guided operating. A calibration cube with a defined pattern of tubes inside was scanned using CT and digital volume tomography. Spatial accuracy was analysed with a software evaluation tool. The positions of the intersections of the tubes were detected in imaging data and registered to the real positions in the calibration body. The deviation was calculated and compared for CT and digital volume tomography. Resolution of spatial images was similar for both methods. However, the spatial accuracy in digital volume tomography was slightly lower than that of CT but still in the submillimetric range. The accuracy was better in the middle, but lower in the margins of the volume. This is a disadvantage in technical image quality, but does not affect the diagnostic image quality. The geometric accuracy is sufficient for digital volume tomography-based image-guided surgery.

Towards cleaner technologies minimising the environmental impact

This editorial introduces and provides an overview of a special issue dedicated to the ninth conference on Process integration, modelling and optimisation for energy saving and pollution reduction—PRES 2006. It contains ten selected papers covering various fields of Clean Technologies and Environmental Policy, namely, catalytic and thermal cracking with natural zeolite catalyst, recovery and reutilisation of copper from sludge, aerosols monitoring by satellite observations, utilisation of high throughput technologies, CFD modelling solid biomass combustion, fluorides removal and recovery for resources saving, siloxane removal from biogas by bio filtration, software tools for water reuse evaluation, pollutants emission abatement and integrated pollution prevention and control in the surface treatment industries.

Pragmatic software tools for water reuse evaluation in a factory

The optimal use of process water becomes increasingly important since natural water resources are heavily solicited by a growing economy. Two steps can be considered in the process water optimization. A first step is the inventory of the different process streams in the process water network. Pure mathematical modeling of a dynamic water network is extremely complicated and expensive. As an approximation, the use of a steady-state network node model within commercial software is accepted to set up a water balance. Sophisticated software tools are available but common solver software may offer an alternative. A second step is the water “pinch” which searches for an optimal use of process water by combining sources and sinks, taking into account contaminant concentrations of process streams. Sophisticated pinch software can be applied but it is also possible to implement a simplified combinatory approach. Such approach can be pragmatically programmed in e.g., Visual Basic. Such tool allows for a first evaluation of the complex combinatory sources–sinks problem, enabling a low cost and easy-to-handle first interpretation of possible water-reuse opportunities. This could stimulate a further enhanced analysis with more advanced software tools and therefore promote a sustainable use of process water in the industrialized world.

Static analysis summit II

Funded by the Department of Homeland Security (DHS), the National Institute of Standards and Technology (NIST) started a long-term, ambitious project to identify, enhance and develop software assurance tools. The Software Assurance Metrics And Tool Evaluation (SAMATE) project is leading in (A) developing tests for software evaluation tools, (B) measuring the effectiveness of tools, and (C) identifying gaps in tools and methods. See the workshop web site at http://samate.nist.gov/ SASII.

MALDI tissue imaging: mass spectrometric localization of biomarkers in tissue slices

New mass-spectrometric proteomics technologies have been developed with the potential to transition from pure research applications into the diagnostic laboratory. Of these, one very promising technique has already gained much interest in the research community: matrix-assisted laser desorption/ionization (MALDI) molecular imaging. For easy and successful application of MALDI imaging in the laboratory, Bruker Daltonics offers an innovative product line: a stand-alone automated sample preparation device, ImagePrep™; mass spectrometers with vital smartbeam™ laser technology: namely, the autoflex III™ and ultraflex III™ MALDI–tandem time-of-flight (MALDI-TOF/TOF) instruments; and sophisticated software tools for fast data evaluation and biomarker visualization, flexImaging™.