Understanding Preferences for Treatment After Hypothetical First-Time Anterior Shoulder Dislocation: Surveying an Online Panel Utilizing a Novel Shared Decision-Making Tool.

PubMed

Streufert, Ben; Reed, Shelby D; Orlando, Lori A; Taylor, Dean C; Huber, Joel C; Mather, Richard C

2017-03-01

Although surgical management of a first-time anterior shoulder dislocation (FTASD) can reduce the risk of recurrent dislocation, other treatment characteristics, costs, and outcomes are important to patients considering treatment options. While patient preferences, such as those elicited by conjoint analysis, have been shown to be important in medical decision-making, the magnitudes or effects of patient preferences in treating an FTASD are unknown. To test a novel shared decision-making tool after sustained FTASD. Specifically measured were the following: (1) importance of aspects of operative versus nonoperative treatment, (2) respondents' agreement with results generated by the tool, (3) willingness to share these results with physicians, and (4) association of results with choice of treatment after FTASD. Cross-sectional study; Level of evidence, 3. A tool was designed and tested using members of Amazon Mechanical Turk, an online panel. The tool included an adaptive conjoint analysis exercise, a method to understand individuals' perceived importance of the following attributes of treatment: (1) chance of recurrent dislocation, (2) cost, (3) short-term limits on shoulder motion, (4) limits on participation in high-risk activities, and (5) duration of physical therapy. Respondents then chose between operative and nonoperative treatment for hypothetical shoulder dislocation. Overall, 374 of 501 (75%) respondents met the inclusion criteria, of which most were young, active males; one-third reported prior dislocation. From the conjoint analysis, the importance of recurrent dislocation and cost of treatment were the most important attributes. A substantial majority agreed with the tool's ability to generate representative preferences and indicated that they would share these preferences with their physician. Importance of recurrence proved significantly predictive of respondents' treatment choices, independent of sex or age; however, activity level was important to previous dislocators. A total of 125 (55%) males and 33 (23%) females chose surgery after FTASD, as did 37% of previous dislocators compared with 45% of nondislocators. When given thorough information about the risks and benefits, respondents had strong preferences for operative treatment after an FTASD. Respondents agreed with the survey results and wanted to share the information with providers. Recurrence was the most important attribute and played a role in decisions about treatment.

FunGene: the functional gene pipeline and repository.

PubMed

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

SMART: A Propositional Logic-Based Trade Analysis and Risk Assessment Tool for a Complex Mission

NASA Technical Reports Server (NTRS)

Ono, Masahiro; Nicholas, Austin; Alibay, Farah; Parrish, Joseph

2015-01-01

This paper introduces a new trade analysis software called the Space Mission Architecture and Risk Analysis Tool (SMART). This tool supports a high-level system trade study on a complex mission, such as a potential Mars Sample Return (MSR) mission, in an intuitive and quantitative manner. In a complex mission, a common approach to increase the probability of success is to have redundancy and prepare backups. Quantitatively evaluating the utility of adding redundancy to a system is important but not straightforward, particularly when the failure of parallel subsystems are correlated.

Accounting for trip frequency in importance-performance analysis

Treesearch

Joshua K. Gill; J.M. Bowker; John C. Bergstrom; Stanley J. Zarnoch

2010-01-01

Understanding customer satisfaction is critical to the successful operation of both privately and publicly managed recreation venues. A popular tool for assessing recreation visitor satisfaction is Importance- Performance Analysis (IPA). IPA provides resource managers, government officials, and private businesses with easy-to-understand and -use information about...

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

DOE PAGES

Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

2016-08-03

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

Software Tool Issues

NASA Astrophysics Data System (ADS)

Hennell, Michael

This chapter relies on experience with tool development gained over the last thirty years. It shows that there are a large number of techniques that contribute to any successful project, and that formality is always the key: a modern software test tool is based on a firm mathematical foundation. After a brief introduction, Section 2 recalls and extends the terminology of Chapter 1. Section 3 discusses the the design of different sorts of static and dynamic analysis tools. Nine important issues to be taken into consideration when evaluating such tools are presented in Section 4. Section 5 investigates the interplay between testing and proof. In Section 6, we call for developers to take their own medicine and verify their tools. Finally, we conclude in Section 7 with a summary of our main messages, emphasising the important role of testing.

Health economics in public health.

PubMed

Ammerman, Alice S; Farrelly, Matthew A; Cavallo, David N; Ickes, Scott B; Hoerger, Thomas J

2009-03-01

Economic analysis is an important tool in deciding how to allocate scarce public health resources; however, there is currently a dearth of such analysis by public health researchers. Public health researchers and practitioners were surveyed to determine their current use of health economics and to identify barriers to use as well as potential strategies to decrease those barriers in order to allow them to more effectively incorporate economic analyses into their work. Data collected from five focus groups informed survey development. The survey included a demographic section and 14 multi-part questions. Participants were recruited in 2006 from three national public health organizations through e-mail; 294 academicians, practitioners, and community representatives answered the survey. Survey data were analyzed in 2007. Despite an expressed belief in the importance of health economics, more than half of the respondents reported very little or no current use of health economics in their work. Of those using health economics, cost-benefit and cost-effectiveness analysis and determination of public health costs were cited as the measures used most frequently. The most important barriers were lack of expertise, funding, time, tools, and data, as well as discomfort with economic theory. The resource deemed most important to using health economics was collaboration with economists or those with economic training. Respondents indicated a desire to learn more about health economics and tools for performing economic analysis. Given the importance of incorporating economic analysis into public health interventions, and the desire of survey respondents for more collaboration with health economists, opportunities for such collaborations should be increased.

Research on the Intensity Analysis and Result Visualization of Construction Land in Urban Planning

NASA Astrophysics Data System (ADS)

Cui, J.; Dong, B.; Li, J.; Li, L.

2017-09-01

As a fundamental work of urban planning, the intensity analysis of construction land involves many repetitive data processing works that are prone to cause errors or data precision loss, and the lack of efficient methods and tools to visualizing the analysis results in current urban planning. In the research a portable tool is developed by using the Model Builder technique embedded in ArcGIS to provide automatic data processing and rapid result visualization for the works. A series of basic modules provided by ArcGIS are linked together to shape a whole data processing chain in the tool. Once the required data is imported, the analysis results and related maps and graphs including the intensity values and zoning map, the skyline analysis map etc. are produced automatically. Finally the tool is installation-free and can be dispatched quickly between planning teams.

On-line analysis capabilities developed to support the AFW wind-tunnel tests

NASA Technical Reports Server (NTRS)

Wieseman, Carol D.; Hoadley, Sherwood T.; Mcgraw, Sandra M.

1992-01-01

A variety of on-line analysis tools were developed to support two active flexible wing (AFW) wind-tunnel tests. These tools were developed to verify control law execution, to satisfy analysis requirements of the control law designers, to provide measures of system stability in a real-time environment, and to provide project managers with a quantitative measure of controller performance. Descriptions and purposes of the developed capabilities are presented along with examples. Procedures for saving and transferring data for near real-time analysis, and descriptions of the corresponding data interface programs are also presented. The on-line analysis tools worked well before, during, and after the wind tunnel test and proved to be a vital and important part of the entire test effort.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

Visualization of protein interaction networks: problems and solutions

PubMed Central

2013-01-01

Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN) and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology) that enriches the PINs with semantic information, but complicates their visualization. Methods In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i) technology, i.e. availability/license of the software and supported OS (Operating System) platforms; (ii) interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii) visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv) analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the possibility to interact with external databases. Results Currently, many tools are available and it is not easy for the users choosing one of them. Some tools offer sophisticated 2D and 3D network visualization making available many layout algorithms, others tools are more data-oriented and support integration of interaction data coming from different sources and data annotation. Finally, some specialistic tools are dedicated to the analysis of pathways and cellular processes and are oriented toward systems biology studies, where the dynamic aspects of the processes being studied are central. Conclusion A current trend is the deployment of open, extensible visualization tools (e.g. Cytoscape), that may be incrementally enriched by the interactomics community with novel and more powerful functions for PIN analysis, through the development of plug-ins. On the other hand, another emerging trend regards the efficient and parallel implementation of the visualization engine that may provide high interactivity and near real-time response time, as in NAViGaTOR. From a technological point of view, open-source, free and extensible tools, like Cytoscape, guarantee a long term sustainability due to the largeness of the developers and users communities, and provide a great flexibility since new functions are continuously added by the developer community through new plug-ins, but the emerging parallel, often closed-source tools like NAViGaTOR, can offer near real-time response time also in the analysis of very huge PINs. PMID:23368786

Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems

PubMed Central

Orman, Mehmet A.; Berthiaume, Francois; Androulakis, Ioannis P.; Ierapetritou, Marianthi G.

2013-01-01

Metabolic engineering tools have been widely applied to living organisms to gain a comprehensive understanding about cellular networks and to improve cellular properties. Metabolic flux analysis (MFA), flux balance analysis (FBA), and metabolic pathway analysis (MPA) are among the most popular tools in stoichiometric network analysis. Although application of these tools into well-known microbial systems is extensive in the literature, various barriers prevent them from being utilized in mammalian cells. Limited experimental data, complex regulatory mechanisms, and the requirement of more complex nutrient media are some major obstacles in mammalian cell systems. However, mammalian cells have been used to produce therapeutic proteins, to characterize disease states or related abnormal metabolic conditions, and to analyze the toxicological effects of some medicinally important drugs. Therefore, there is a growing need for extending metabolic engineering principles to mammalian cells in order to understand their underlying metabolic functions. In this review article, advanced metabolic engineering tools developed for stoichiometric analysis including MFA, FBA, and MPA are described. Applications of these tools in mammalian cells are discussed in detail, and the challenges and opportunities are highlighted. PMID:22196224

Client-side Skype forensics: an overview

NASA Astrophysics Data System (ADS)

Meißner, Tina; Kröger, Knut; Creutzburg, Reiner

2013-03-01

IT security and computer forensics are important components in the information technology. In the present study, a client-side Skype forensics is performed. It is designed to explain which kind of user data are stored on a computer and which tools allow the extraction of those data for a forensic investigation. There are described both methods - a manual analysis and an analysis with (mainly) open source tools, respectively.

Global Futures: The Emerging Scenario.

ERIC Educational Resources Information Center

Seth, Satish C.

1983-01-01

Acknowledging global interdependence, especially in economics, may be the most important step toward resolving international conflicts. Describes seven major global dangers and gives scenarios for exploring likely global futures. As "tools of prescription" these global models are inadequate, but as "tools of analysis" they have…

Analysis of a Decision Support System for CASE Tool Selection and the Specification of an Ada to SQL Abstract Interface

DTIC Science & Technology

1991-12-01

34 foreign keys" ,which are keys inherited from conlected entities, the keys would already be defined in the connected entity’s domain primiti le definition...defined for the rootnode re!ationship because all attributes are foreign keys and they are already defined in the connected entities domain primitive...can exchange data with other tools including other tools in the tool vendor’s tool 99 Upper CASE Tool Charactcrizcs set. The important attributes are

Identifying Social Trust in Cross-Country Analysis: Do We Really Measure the Same?

ERIC Educational Resources Information Center

Torpe, Lars; Lolle, Henrik

2011-01-01

Many see trust as an important social resource for the welfare of individuals as well as nations. It is therefore important to be able to identify trust and explain its sources. Cross-country survey analysis has been an important tool in this respect, and often one single variable is used to identify social trust understood as trust in strangers,…

Performance Contracting as a Performance Management Tool in the Public Sector in Kenya: Lessons of learning

ERIC Educational Resources Information Center

Hope, Kempe Ronald, Sr.

2013-01-01

The purpose of this article is to provide an assessment and analysis of public sector performance contracting as a performance management tool in Kenya. It aims to demonstrate that performance contracting remains a viable and important tool for improving public sector performance as a key element of the on-going public sector transformation…

Response to Paper III Economics in the Civics Curriculum. A Reaction to Andrew F. Brimmer.

ERIC Educational Resources Information Center

Schug, Mark C.

According to the document, Dr. Andrew Brimmer did an excellent job of identifying emerging economic concerns. Dr. Brimmer's characterization of economics as a tool kit can help young people examine important social questions using principles of economics as the tool for analysis. One way to build an economics tool kit is by placing more stress on…

Non-Simultaneous Relative Importance-Performance Analysis: Meta-Results from 80 College Choice Surveys with 55,276 Respondents.

ERIC Educational Resources Information Center

Chapman, Randall G.

1993-01-01

A study investigated the utility of importance-performance analysis, a marketing tool for assessing marketing position and performance, in learning how college applicants perceive their chosen college in comparison with others. Findings reflect the complexity of student decisions and suggest the "average" college performs above average…

The Importance of Statistical Modeling in Data Analysis and Inference

ERIC Educational Resources Information Center

Rollins, Derrick, Sr.

2017-01-01

Statistical inference simply means to draw a conclusion based on information that comes from data. Error bars are the most commonly used tool for data analysis and inference in chemical engineering data studies. This work demonstrates, using common types of data collection studies, the importance of specifying the statistical model for sound…

Addressing multi-label imbalance problem of surgical tool detection using CNN.

PubMed

Sahu, Manish; Mukhopadhyay, Anirban; Szengel, Angelika; Zachow, Stefan

2017-06-01

A fully automated surgical tool detection framework is proposed for endoscopic video streams. State-of-the-art surgical tool detection methods rely on supervised one-vs-all or multi-class classification techniques, completely ignoring the co-occurrence relationship of the tools and the associated class imbalance. In this paper, we formulate tool detection as a multi-label classification task where tool co-occurrences are treated as separate classes. In addition, imbalance on tool co-occurrences is analyzed and stratification techniques are employed to address the imbalance during convolutional neural network (CNN) training. Moreover, temporal smoothing is introduced as an online post-processing step to enhance runtime prediction. Quantitative analysis is performed on the M2CAI16 tool detection dataset to highlight the importance of stratification, temporal smoothing and the overall framework for tool detection. The analysis on tool imbalance, backed by the empirical results, indicates the need and superiority of the proposed framework over state-of-the-art techniques.

A Methodology and Software Environment for Testing Process Model’s Sequential Predictions with Protocols

DTIC Science & Technology

1992-12-21

in preparation). Foundations of artificial intelligence. Cambridge, MA: MIT Press. O’Reilly, R. C. (1991). X3DNet: An X- Based Neural Network ...2.2.3 Trace based protocol analysis 19 2.2A Summary of important data features 21 2.3 Tools related to process model testing 23 2.3.1 Tools for building...algorithm 57 3. Requirements for testing process models using trace based protocol 59 analysis 3.1 Definition of trace based protocol analysis (TBPA) 59

On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data.

PubMed

Trede, Dennis; Kobarg, Jan Hendrik; Oetjen, Janina; Thiele, Herbert; Maass, Peter; Alexandrov, Theodore

2012-03-21

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 10⁸ to 10⁹ intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

On the Importance of Mathematical Methods for Analysis of MALDI-Imaging Mass Spectrometry Data.

PubMed

Trede, Dennis; Kobarg, Jan Hendrik; Oetjen, Janina; Thiele, Herbert; Maass, Peter; Alexandrov, Theodore

2012-03-01

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 108 to 109 intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.

PubMed

Blattmann, Peter; Heusel, Moritz; Aebersold, Ruedi

2016-01-01

SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.

Wear in Fluid Power Systems.

DTIC Science & Technology

1979-11-30

the detection and analysis of this wear is extremely important. In this study, it was determined that ferrography is an effective tool for this...dealt with the practical applications of ferrography to fluid power systems. The first two phases were investigations of the life improvements of...damning evidence that ferrography is not the beneficial tool it was originally thought to be. However, a further analysis of the entire program and the

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

PubMed

Zhou, Guangyan; Xia, Jianguo

2018-06-07

Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

Work with Us | Energy Analysis | NREL

Science.gov Websites

, and local levels; and industry use NREL analysis, data, models, and tools to make critical energy and academia make us well-positioned to help solve the most important energy challenges: Yours

Analysis and control on changeable wheel tool system of hybrid grinding and polishing machine tool for blade finishing

NASA Astrophysics Data System (ADS)

He, Qiuwei; Lv, Xingming; Wang, Xin; Qu, Xingtian; Zhao, Ji

2017-01-01

Blade is the key component in the energy power equipment of turbine, aircraft engines and so on. Researches on the process and equipment for blade finishing become one of important and difficult point. To control precisely tool system of developed hybrid grinding and polishing machine tool for blade finishing, the tool system with changeable wheel for belt polishing is analyzed in this paper. Firstly, the belt length and wrap angle of each wheel in different position of tension wheel swing angle in the process of changing wheel is analyzed. The reasonable belt length is calculated by using MATLAB, and relationships between wrap angle of each wheel and cylinder expansion amount of contact wheel are obtained. Then, the control system for changeable wheel tool structure is developed. Lastly, the surface roughness of blade finishing is verified by experiments. Theoretical analysis and experimental results show that reasonable belt length and wheel wrap angle can be obtained by proposed analysis method, the changeable wheel tool system can be controlled precisely, and the surface roughness of blade after grinding meets the design requirements.

Discourse analysis in general practice: a sociolinguistic approach.

PubMed

Nessa, J; Malterud, K

1990-06-01

It is a simple but important fact that as general practitioners we talk to our patients. The quality of the conversation is of vital importance for the outcome of the consultation. The purpose of this article is to discuss a methodological tool borrowed from sociolinguistics--discourse analysis. To assess the suitability of this method for analysis of general practice consultations, the authors have performed a discourse analysis of one single consultation. Our experiences are presented here.

Microgrid Analysis Tools Summary

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jimenez, Antonio; Haase, Scott G; Mathur, Shivani

2018-03-05

The over-arching goal of the Alaska Microgrid Partnership is to reduce the use of total imported fuel into communities to secure all energy services by at least 50% in Alaska's remote microgrids without increasing system life cycle costs while also improving overall system reliability, security, and resilience. One goal of the Alaska Microgrid Partnership is to investigate whether a combination of energy efficiency and high-contribution (from renewable energy) power systems can reduce total imported energy usage by 50% while reducing life cycle costs and improving reliability and resiliency. This presentation provides an overview of the following four renewable energy optimizationmore » tools. Information is from respective tool websites, tool developers, and author experience. Distributed Energy Resources Customer Adoption Model (DER-CAM) Microgrid Design Toolkit (MDT) Renewable Energy Optimization (REopt) Tool Hybrid Optimization Model for Electric Renewables (HOMER).« less

Project-Based Teaching-Learning Computer-Aided Engineering Tools

ERIC Educational Resources Information Center

Simoes, J. A.; Relvas, C.; Moreira, R.

2004-01-01

Computer-aided design, computer-aided manufacturing, computer-aided analysis, reverse engineering and rapid prototyping are tools that play an important key role within product design. These are areas of technical knowledge that must be part of engineering and industrial design courses' curricula. This paper describes our teaching experience of…

A Limit Theorem on the Cores of Large Standard Exchange Economies

PubMed Central

Brown, Donald J.; Robinson, Abraham

1972-01-01

This note introduces a new mathematical tool, nonstandard analysis, for the analysis of an important class of problems in mathematical economics—the relation between bargaining and the competitive price system. PMID:16591988

Effects of machining parameters on tool life and its optimization in turning mild steel with brazed carbide cutting tool

NASA Astrophysics Data System (ADS)

Dasgupta, S.; Mukherjee, S.

2016-09-01

One of the most significant factors in metal cutting is tool life. In this research work, the effects of machining parameters on tool under wet machining environment were studied. Tool life characteristics of brazed carbide cutting tool machined against mild steel and optimization of machining parameters based on Taguchi design of experiments were examined. The experiments were conducted using three factors, spindle speed, feed rate and depth of cut each having three levels. Nine experiments were performed on a high speed semi-automatic precision central lathe. ANOVA was used to determine the level of importance of the machining parameters on tool life. The optimum machining parameter combination was obtained by the analysis of S/N ratio. A mathematical model based on multiple regression analysis was developed to predict the tool life. Taguchi's orthogonal array analysis revealed the optimal combination of parameters at lower levels of spindle speed, feed rate and depth of cut which are 550 rpm, 0.2 mm/rev and 0.5mm respectively. The Main Effects plot reiterated the same. The variation of tool life with different process parameters has been plotted. Feed rate has the most significant effect on tool life followed by spindle speed and depth of cut.

Tools4miRs – one place to gather all the tools for miRNA analysis

PubMed Central

Lukasik, Anna; Wójcikowski, Maciej; Zielenkiewicz, Piotr

2016-01-01

Summary: MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data. Availability and Implementation: Tools4miRs is implemented in Python using Django and is freely available at tools4mirs.org. Contact: piotr@ibb.waw.pl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153626

Tools4miRs - one place to gather all the tools for miRNA analysis.

PubMed

Lukasik, Anna; Wójcikowski, Maciej; Zielenkiewicz, Piotr

2016-09-01

MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data. Tools4miRs is implemented in Python using Django and is freely available at tools4mirs.org. piotr@ibb.waw.pl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Integrating advanced visualization technology into the planetary Geoscience workflow

NASA Astrophysics Data System (ADS)

Huffman, John; Forsberg, Andrew; Loomis, Andrew; Head, James; Dickson, James; Fassett, Caleb

2011-09-01

Recent advances in computer visualization have allowed us to develop new tools for analyzing the data gathered during planetary missions, which is important, since these data sets have grown exponentially in recent years to tens of terabytes in size. As part of the Advanced Visualization in Solar System Exploration and Research (ADVISER) project, we utilize several advanced visualization techniques created specifically with planetary image data in mind. The Geoviewer application allows real-time active stereo display of images, which in aggregate have billions of pixels. The ADVISER desktop application platform allows fast three-dimensional visualization of planetary images overlain on digital terrain models. Both applications include tools for easy data ingest and real-time analysis in a programmatic manner. Incorporation of these tools into our everyday scientific workflow has proved important for scientific analysis, discussion, and publication, and enabled effective and exciting educational activities for students from high school through graduate school.

Review and Comparison of Electronic Patient-Facing Family Health History Tools.

PubMed

Welch, Brandon M; Wiley, Kevin; Pflieger, Lance; Achiangia, Rosaline; Baker, Karen; Hughes-Halbert, Chanita; Morrison, Heath; Schiffman, Joshua; Doerr, Megan

2018-04-01

Family health history (FHx) is one of the most important pieces of information available to help genetic counselors and other clinicians identify risk and prevent disease. Unfortunately, the collection of FHx from patients is often too time consuming to be done during a clinical visit. Fortunately, there are many electronic FHx tools designed to help patients gather and organize their own FHx information prior to a clinic visit. We conducted a review and analysis of electronic FHx tools to better understand what tools are available, to compare and contrast to each other, to highlight features of various tools, and to provide a foundation for future evaluation and comparisons across FHx tools. Through our analysis, we included and abstracted 17 patient-facing electronic FHx tools and explored these tools around four axes: organization information, family history collection and display, clinical data collected, and clinical workflow integration. We found a large number of differences among FHx tools, with no two the same. This paper provides a useful review for health care providers, researchers, and patient advocates interested in understanding the differences among the available patient-facing electronic FHx tools.

Time Analysis: Still an Important Accountability Tool.

ERIC Educational Resources Information Center

Fairchild, Thomas N.; Seeley, Tracey J.

1994-01-01

Reviews benefits to school counselors of conducting a time analysis. Describes time analysis system that authors have used, including case illustration of how authors used data to effect counseling program changes. System described followed process outlined by Fairchild: identifying services, devising coding system, keeping records, synthesizing…

Parallelizing Timed Petri Net simulations

NASA Technical Reports Server (NTRS)

Nicol, David M.

1993-01-01

The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.

Experience with case tools in the design of process-oriented software

NASA Astrophysics Data System (ADS)

Novakov, Ognian; Sicard, Claude-Henri

1994-12-01

In Accelerator systems such as the CERN PS complex, process equipment has a life time which may exceed the typical life cycle of its related software. Taking into account the variety of such equipment, it is important to keep the analysis and design of the software in a system-independent form. This paper discusses the experience gathered in using commercial CASE tools for analysis, design and reverse engineering of different process-oriented software modules, with a principal emphasis on maintaining the initial analysis in a standardized form. Such tools have been in existence for several years, but this paper shows that they are not fully adapted to our needs. In particular, the paper stresses the problems of integrating such a tool into an existing data-base-dependent development chain, the lack of real-time simulation tools and of Object-Oriented concepts in existing commercial packages. Finally, the paper gives a broader view of software engineering needs in our particular context.

A New Paradigm to Analyze Data Completeness of Patient Data.

PubMed

Nasir, Ayan; Gurupur, Varadraj; Liu, Xinliang

2016-08-03

There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data.

A New Paradigm to Analyze Data Completeness of Patient Data

PubMed Central

Nasir, Ayan; Liu, Xinliang

2016-01-01

Summary Background There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Objectives Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. Methods The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. Results The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. Conclusion DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data. PMID:27484918

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool

PubMed Central

Clark, Neil R.; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D.; Jones, Matthew R.; Ma’ayan, Avi

2016-01-01

Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community. PMID:26848405

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.

PubMed

Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi

2015-11-01

Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.

Sharpening a Tool for Teaching: The Zone of Proximal Development

ERIC Educational Resources Information Center

Wass, Rob; Golding, Clinton

2014-01-01

Vygotsky's Zone of Proximal Development (ZPD) provides an important understanding of learning, but its implications for teachers are often unclear or limited and could be further explored. We use conceptual analysis to sharpen the ZPD as a teaching tool, illustrated with examples from teaching critical thinking in zoology. Our conclusions are…

Scenario analysis and strategic planning: practical applications for radiology practices.

PubMed

Lexa, Frank James; Chan, Stephen

2010-05-01

Modern business science has many tools that can be of great value to radiologists and their practices. One of the most important and underused is long-term planning. Part of the problem has been the pace of change. Making a 5-year plan makes sense only if your develop robust scenarios of possible future conditions you will face. Scenario analysis is one of many highly regarded tools that can improve your predictive capability. However, as with many tools, it pays to have some training and to get practical tips on how to improve their value. It also helps to learn from other people's mistakes rather than your own. The authors discuss both theoretical and practical issues in using scenario analysis to improve your planning process. They discuss actionable ways this set of tools can be applied in a group meeting or retreat. Copyright (c) 2010 American College of Radiology. Published by Elsevier Inc. All rights reserved.

XMI2USE: A Tool for Transforming XMI to USE Specifications

NASA Astrophysics Data System (ADS)

Sun, Wuliang; Song, Eunjee; Grabow, Paul C.; Simmonds, Devon M.

The UML-based Specification Environment (USE) tool supports syntactic analysis, type checking, consistency checking, and dynamic validation of invariants and pre-/post conditions specified in the Object Constraint Language (OCL). Due to its animation and analysis power, it is useful when checking critical non-functional properties such as security policies. However, the USE tool requires one to specify (i.e., "write") a model using its own textual language and does not allow one to import any model specification files created by other UML modeling tools. Hence, to make the best use of existing UML tools, we often create a model with OCL constraints using a modeling tool such as the IBM Rational Software Architect (RSA) and then use the USE tool for model validation. This approach, however, requires a manual transformation between the specifications of two different tool formats, which is error-prone and diminishes the benefit of automated model-level validations. In this paper, we describe our own implementation of a specification transformation engine that is based on the Model Driven Architecture (MDA) framework and currently supports automatic tool-level transformations from RSA to USE.

Estimating Sobol Sensitivity Indices Using Correlations

EPA Science Inventory

Sensitivity analysis is a crucial tool in the development and evaluation of complex mathematical models. Sobol's method is a variance-based global sensitivity analysis technique that has been applied to computational models to assess the relative importance of input parameters on...

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.

PubMed

Niu, Sheng-Yong; Yang, Jinyu; McDermaid, Adam; Zhao, Jing; Kang, Yu; Ma, Qin

2017-05-08

Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota. Hence, combining metagenomic and metatranscriptomic analyses will help understand the activity or enrichment of a given gene set, such as drug-resistant genes among microbiome samples. Here, we summarize existing bioinformatics tools of metagenomic and metatranscriptomic data analysis, the purpose of which is to assist researchers in deciding the appropriate tools for their microbiome studies. Additionally, we propose an Integrated Meta-Function mapping pipeline to incorporate various reference databases and accelerate functional gene mapping procedures for both metagenomic and metatranscriptomic analyses. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Status of the AIAA Modeling and Simulation Format Standard

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Hildreth, Bruce L.

2008-01-01

The current draft AIAA Standard for flight simulation models represents an on-going effort to improve the productivity of practitioners of the art of digital flight simulation (one of the original digital computer applications). This initial release provides the capability for the efficient representation and exchange of an aerodynamic model in full fidelity; the DAVE-ML format can be easily imported (with development of site-specific import tools) in an unambiguous way with automatic verification. An attractive feature of the standard is the ability to coexist with existing legacy software or tools. The draft Standard is currently limited in scope to static elements of dynamic flight simulations; however, these static elements represent the bulk of typical flight simulation mathematical models. It is already seeing application within U.S. and Australian government agencies in an effort to improve productivity and reduce model rehosting overhead. An existing tool allows import of DAVE-ML models into a popular simulation modeling and analysis tool, and other community-contributed tools and libraries can simplify the use of DAVE-ML compliant models at compile- or run-time of high-fidelity flight simulation.

Using standardized tools to improve immunization costing data for program planning: the cost of the Colombian Expanded Program on Immunization.

PubMed

Castañeda-Orjuela, Carlos; Romero, Martin; Arce, Patricia; Resch, Stephen; Janusz, Cara B; Toscano, Cristiana M; De la Hoz-Restrepo, Fernando

2013-07-02

The cost of Expanded Programs on Immunization (EPI) is an important aspect of the economic and financial analysis needed for planning purposes. Costs also are needed for cost-effectiveness analysis of introducing new vaccines. We describe a costing tool that improves the speed, accuracy, and availability of EPI costs and that was piloted in Colombia. The ProVac CostVac Tool is a spreadsheet-based tool that estimates overall EPI costs considering program inputs (personnel, cold chain, vaccines, supplies, etc.) at three administrative levels (central, departmental, and municipal) and one service delivery level (health facilities). It uses various costing methods. The tool was evaluated through a pilot exercise in Colombia. In addition to the costs obtained from the central and intermediate administrative levels, a survey of 112 local health facilities was conducted to collect vaccination costs. Total cost of the EPI, cost per dose of vaccine delivered, and cost per fully vaccinated child with the recommended immunization schedule in Colombia in 2009 were estimated. The ProVac CostVac Tool is a novel, user-friendly tool, which allows users to conduct an EPI costing study following guidelines for cost studies. The total costs of the Colombian EPI were estimated at US$ 107.8 million in 2009. The cost for a fully immunized child with the recommended schedule was estimated at US$ 153.62. Vaccines and vaccination supplies accounted for 58% of total costs, personnel for 21%, cold chain for 18%, and transportation for 2%. Most EPI costs are incurred at the central level (62%). The major cost driver at the department and municipal levels is personnel costs. The ProVac CostVac Tool proved to be a comprehensive and useful tool that will allow researchers and health officials to estimate the actual cost for national immunization programs. The present analysis shows that personnel, cold chain, and transportation are important components of EPI and should be carefully estimated in the cost analysis, particularly when evaluating new vaccine introduction. Copyright © 2013 Elsevier Ltd. All rights reserved.

Subvisible (2-100 μm) Particle Analysis During Biotherapeutic Drug Product Development: Part 1, Considerations and Strategy.

PubMed

Narhi, Linda O; Corvari, Vincent; Ripple, Dean C; Afonina, Nataliya; Cecchini, Irene; Defelippis, Michael R; Garidel, Patrick; Herre, Andrea; Koulov, Atanas V; Lubiniecki, Tony; Mahler, Hanns-Christian; Mangiagalli, Paolo; Nesta, Douglas; Perez-Ramirez, Bernardo; Polozova, Alla; Rossi, Mara; Schmidt, Roland; Simler, Robert; Singh, Satish; Spitznagel, Thomas M; Weiskopf, Andrew; Wuchner, Klaus

2015-06-01

Measurement and characterization of subvisible particles (defined here as those ranging in size from 2 to 100 μm), including proteinaceous and nonproteinaceous particles, is an important part of every stage of protein therapeutic development. The tools used and the ways in which the information generated is applied depends on the particular product development stage, the amount of material, and the time available for the analysis. In order to compare results across laboratories and products, it is important to harmonize nomenclature, experimental protocols, data analysis, and interpretation. In this manuscript on perspectives on subvisible particles in protein therapeutic drug products, we focus on the tools available for detection, characterization, and quantification of these species and the strategy around their application. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

76 FR 4027 - Farm and Ranch Lands Protection Program

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-24

... with Executive Order 12866, NRCS conducted an economic analysis of the potential impacts associated with this program. A summary of the economic analysis can be found at the end of the regulatory... section 1244(g) of the 1985 Act. Economic Analysis--Executive Summary The FRPP is an important tool...

Skill Components of Task Analysis

ERIC Educational Resources Information Center

Adams, Anne E.; Rogers, Wendy A.; Fisk, Arthur D.

2013-01-01

Some task analysis methods break down a task into a hierarchy of subgoals. Although an important tool of many fields of study, learning to create such a hierarchy (redescription) is not trivial. To further the understanding of what makes task analysis a skill, the present research examined novices' problems with learning Hierarchical Task…

Batch mode grid generation: An endangered species

NASA Technical Reports Server (NTRS)

Schuster, David M.

1992-01-01

Non-interactive grid generation schemes should thrive as emphasis shifts from development of numerical analysis and design methods to application of these tools to real engineering problems. A strong case is presented for the continued development and application of non-interactive geometry modeling methods. Guidelines, strategies, and techniques for developing and implementing these tools are presented using current non-interactive grid generation methods as examples. These schemes play an important role in the development of multidisciplinary analysis methods and some of these applications are also discussed.

Tools for the Conceptual Design and Engineering Analysis of Micro Air Vehicles

DTIC Science & Technology

2009-03-01

problem with two DC motors with propellers, mounted on each wing tip and oriented such that the thrust vectors had an angular separation of 180...ElectriCalc or MotoCalc Database • Script Program (MC) In determination of the components to be integrated into MC, the R/C world was explored since the tools...Excel, ProE, QuickWrap and Script . Importing outside applications can be achieved by direct interaction with MC or through analysis server connections [11

A computational image analysis glossary for biologists.

PubMed

Roeder, Adrienne H K; Cunha, Alexandre; Burl, Michael C; Meyerowitz, Elliot M

2012-09-01

Recent advances in biological imaging have resulted in an explosion in the quality and quantity of images obtained in a digital format. Developmental biologists are increasingly acquiring beautiful and complex images, thus creating vast image datasets. In the past, patterns in image data have been detected by the human eye. Larger datasets, however, necessitate high-throughput objective analysis tools to computationally extract quantitative information from the images. These tools have been developed in collaborations between biologists, computer scientists, mathematicians and physicists. In this Primer we present a glossary of image analysis terms to aid biologists and briefly discuss the importance of robust image analysis in developmental studies.

Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

ERIC Educational Resources Information Center

Lima, Andre O. S.; Garces, Sergio P. S.

2006-01-01

Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

Hygrothermal Simulation: A Tool for Building Envelope Design Analysis

Treesearch

Samuel V. Glass; Anton TenWolde; Samuel L. Zelinka

2013-01-01

Is it possible to gauge the risk of moisture problems while designing the building envelope? This article provides a brief introduction to computer-based hygrothermal (heat and moisture) simulation, shows how simulation can be useful as a design tool, and points out a number of im-portant considerations regarding model inputs and limita-tions. Hygrothermal simulation...

ARTiiFACT: a tool for heart rate artifact processing and heart rate variability analysis.

PubMed

Kaufmann, Tobias; Sütterlin, Stefan; Schulz, Stefan M; Vögele, Claus

2011-12-01

The importance of appropriate handling of artifacts in interbeat interval (IBI) data must not be underestimated. Even a single artifact may cause unreliable heart rate variability (HRV) results. Thus, a robust artifact detection algorithm and the option for manual intervention by the researcher form key components for confident HRV analysis. Here, we present ARTiiFACT, a software tool for processing electrocardiogram and IBI data. Both automated and manual artifact detection and correction are available in a graphical user interface. In addition, ARTiiFACT includes time- and frequency-based HRV analyses and descriptive statistics, thus offering the basic tools for HRV analysis. Notably, all program steps can be executed separately and allow for data export, thus offering high flexibility and interoperability with a whole range of applications.

How to support forest management in a world of change: results of some regional studies.

PubMed

Fürst, C; Lorz, C; Vacik, H; Potocic, N; Makeschin, F

2010-12-01

This article presents results of several studies in Middle, Eastern and Southeastern Europe on needs and application areas, desirable attributes and marketing potentials of forest management support tools. By comparing present and future application areas, a trend from sectoral planning towards landscape planning and integration of multiple stakeholder needs is emerging. In terms of conflicts, where management support tools might provide benefit, no clear tendencies were found, neither on local nor on regional level. In contrast, on national and European levels, support of the implementation of laws, directives, and regulations was found to be of highest importance. Following the user-requirements analysis, electronic tools supporting communication are preferred against paper-based instruments. The users identified most important attributes of optimized management support tools: (i) a broad accessibility for all users at any time should be guaranteed, (ii) the possibility to integrate iteratively experiences from case studies and from regional experts into the knowledge base (learning system) should be given, and (iii) a self-explanatory user interface is demanded, which is also suitable for users rather inexperienced with electronic tools. However, a market potential analysis revealed that the willingness to pay for management tools is very limited, although the participants specified realistic ranges of maximal amounts of money, which would be invested if the products were suitable and payment inevitable. To bridge the discrepancy between unwillingness to pay and the need to use management support tools, optimized financing or cooperation models between practice and science must be found.

How to Support Forest Management in a World of Change: Results of Some Regional Studies

NASA Astrophysics Data System (ADS)

Fürst, C.; Lorz, C.; Vacik, H.; Potocic, N.; Makeschin, F.

2010-12-01

This article presents results of several studies in Middle, Eastern and Southeastern Europe on needs and application areas, desirable attributes and marketing potentials of forest management support tools. By comparing present and future application areas, a trend from sectoral planning towards landscape planning and integration of multiple stakeholder needs is emerging. In terms of conflicts, where management support tools might provide benefit, no clear tendencies were found, neither on local nor on regional level. In contrast, on national and European levels, support of the implementation of laws, directives, and regulations was found to be of highest importance. Following the user-requirements analysis, electronic tools supporting communication are preferred against paper-based instruments. The users identified most important attributes of optimized management support tools: (i) a broad accessibility for all users at any time should be guaranteed, (ii) the possibility to integrate iteratively experiences from case studies and from regional experts into the knowledge base (learning system) should be given, and (iii) a self-explanatory user interface is demanded, which is also suitable for users rather inexperienced with electronic tools. However, a market potential analysis revealed that the willingness to pay for management tools is very limited, although the participants specified realistic ranges of maximal amounts of money, which would be invested if the products were suitable and payment inevitable. To bridge the discrepancy between unwillingness to pay and the need to use management support tools, optimized financing or cooperation models between practice and science must be found.

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.

PubMed

Radom, Marcin; Rybarczyk, Agnieszka; Szawulak, Bartlomiej; Andrzejewski, Hubert; Chabelski, Piotr; Kozak, Adam; Formanowicz, Piotr

2017-12-01

Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. piotr@cs.put.poznan.pl. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics1[OPEN

PubMed Central

Poeschl, Yvonne; Plötner, Romina

2017-01-01

Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets. PMID:28931626

Modeling and Simulation Tools for Heavy Lift Airships

NASA Technical Reports Server (NTRS)

Hochstetler, Ron; Chachad, Girish; Hardy, Gordon; Blanken, Matthew; Melton, John

2016-01-01

For conventional fixed wing and rotary wing aircraft a variety of modeling and simulation tools have been developed to provide designers the means to thoroughly investigate proposed designs and operational concepts. However, lighter-than-air (LTA) airships, hybrid air vehicles, and aerostats have some important aspects that are different from heavier-than-air (HTA) vehicles. In order to account for these differences, modifications are required to the standard design tools to fully characterize the LTA vehicle design and performance parameters.. To address these LTA design and operational factors, LTA development organizations have created unique proprietary modeling tools, often at their own expense. An expansion of this limited LTA tool set could be accomplished by leveraging existing modeling and simulation capabilities available in the National laboratories and public research centers. Development of an expanded set of publicly available LTA modeling and simulation tools for LTA developers would mitigate the reliance on proprietary LTA design tools in use today. A set of well researched, open source, high fidelity LTA design modeling and simulation tools would advance LTA vehicle development and also provide the analytical basis for accurate LTA operational cost assessments. This paper will present the modeling and analysis tool capabilities required for LTA vehicle design, analysis of operations, and full life-cycle support. A survey of the tools currently available will be assessed to identify the gaps between their capabilities and the LTA industry's needs. Options for development of new modeling and analysis capabilities to supplement contemporary tools will also be presented.

Variability in Predictions from Online Tools: A Demonstration Using Internet-Based Melanoma Predictors.

PubMed

Zabor, Emily C; Coit, Daniel; Gershenwald, Jeffrey E; McMasters, Kelly M; Michaelson, James S; Stromberg, Arnold J; Panageas, Katherine S

2018-02-22

Prognostic models are increasingly being made available online, where they can be publicly accessed by both patients and clinicians. These online tools are an important resource for patients to better understand their prognosis and for clinicians to make informed decisions about treatment and follow-up. The goal of this analysis was to highlight the possible variability in multiple online prognostic tools in a single disease. To demonstrate the variability in survival predictions across online prognostic tools, we applied a single validation dataset to three online melanoma prognostic tools. Data on melanoma patients treated at Memorial Sloan Kettering Cancer Center between 2000 and 2014 were retrospectively collected. Calibration was assessed using calibration plots and discrimination was assessed using the C-index. In this demonstration project, we found important differences across the three models that led to variability in individual patients' predicted survival across the tools, especially in the lower range of predictions. In a validation test using a single-institution data set, calibration and discrimination varied across the three models. This study underscores the potential variability both within and across online tools, and highlights the importance of using methodological rigor when developing a prognostic model that will be made publicly available online. The results also reinforce that careful development and thoughtful interpretation, including understanding a given tool's limitations, are required in order for online prognostic tools that provide survival predictions to be a useful resource for both patients and clinicians.

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

PubMed

Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

2018-04-02

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, to overcome the high error rates of the nanopore sequencing technology.

Microsatellite data analysis for population genetics

USDA-ARS?s Scientific Manuscript database

Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

Irena : tool suite for modeling and analysis of small-angle scattering.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ilavsky, J.; Jemian, P.

2009-04-01

Irena, a tool suite for analysis of both X-ray and neutron small-angle scattering (SAS) data within the commercial Igor Pro application, brings together a comprehensive suite of tools useful for investigations in materials science, physics, chemistry, polymer science and other fields. In addition to Guinier and Porod fits, the suite combines a variety of advanced SAS data evaluation tools for the modeling of size distribution in the dilute limit using maximum entropy and other methods, dilute limit small-angle scattering from multiple non-interacting populations of scatterers, the pair-distance distribution function, a unified fit, the Debye-Bueche model, the reflectivity (X-ray and neutron)more » using Parratt's formalism, and small-angle diffraction. There are also a number of support tools, such as a data import/export tool supporting a broad sampling of common data formats, a data modification tool, a presentation-quality graphics tool optimized for small-angle scattering data, and a neutron and X-ray scattering contrast calculator. These tools are brought together into one suite with consistent interfaces and functionality. The suite allows robust automated note recording and saving of parameters during export.« less

Assessment of the Draft AIAA S-119 Flight Dynamic Model Exchange Standard

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Murri, Daniel G.; Hill, Melissa A.; Jessick, Matthew V.; Penn, John M.; Hasan, David A.; Crues, Edwin Z.; Falck, Robert D.; McCarthy, Thomas G.; Vuong, Nghia;

Strategic Analysis Overview

NASA Technical Reports Server (NTRS)

Cirillo, William M.; Earle, Kevin D.; Goodliff, Kandyce E.; Reeves, J. D.; Stromgren, Chel; Andraschko, Mark R.; Merrill, R. Gabe

2008-01-01

NASA s Constellation Program employs a strategic analysis methodology in providing an integrated analysis capability of Lunar exploration scenarios and to support strategic decision-making regarding those scenarios. The strategic analysis methodology integrates the assessment of the major contributors to strategic objective satisfaction performance, affordability, and risk and captures the linkages and feedbacks between all three components. Strategic analysis supports strategic decision making by senior management through comparable analysis of alternative strategies, provision of a consistent set of high level value metrics, and the enabling of cost-benefit analysis. The tools developed to implement the strategic analysis methodology are not element design and sizing tools. Rather, these models evaluate strategic performance using predefined elements, imported into a library from expert-driven design/sizing tools or expert analysis. Specific components of the strategic analysis tool set include scenario definition, requirements generation, mission manifesting, scenario lifecycle costing, crew time analysis, objective satisfaction benefit, risk analysis, and probabilistic evaluation. Results from all components of strategic analysis are evaluated a set of pre-defined figures of merit (FOMs). These FOMs capture the high-level strategic characteristics of all scenarios and facilitate direct comparison of options. The strategic analysis methodology that is described in this paper has previously been applied to the Space Shuttle and International Space Station Programs and is now being used to support the development of the baseline Constellation Program lunar architecture. This paper will present an overview of the strategic analysis methodology and will present sample results from the application of the strategic analysis methodology to the Constellation Program lunar architecture.

Scientific Mobility and International Research Networks: Trends and Policy Tools for Promoting Research Excellence and Capacity Building

ERIC Educational Resources Information Center

Jacob, Merle; Meek, V. Lynn

2013-01-01

One of the ways in which globalization is manifesting itself in higher education and research is through the increasing importance and emphasis on scientific mobility. This article seeks to provide an overview and analysis of current trends and policy tools for promoting mobility. The article argues that the mobility of scientific labour is an…

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

PubMed

Tebel, Katrin; Boldt, Vivien; Steininger, Anne; Port, Matthias; Ebert, Grit; Ullmann, Reinhard

2017-01-06

The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of GenomeCAT can be easily extended by further R packages or customized plug-ins to meet future requirements.

Tools for observational gait analysis in patients with stroke: a systematic review.

PubMed

Ferrarello, Francesco; Bianchi, Valeria Anna Maria; Baccini, Marco; Rubbieri, Gaia; Mossello, Enrico; Cavallini, Maria Chiara; Marchionni, Niccolò; Di Bari, Mauro

2013-12-01

Stroke severely affects walking ability, and assessment of gait kinematics is important in defining diagnosis, planning treatment, and evaluating interventions in stroke rehabilitation. Although observational gait analysis is the most common approach to evaluate gait kinematics, tools useful for this purpose have received little attention in the scientific literature and have not been thoroughly reviewed. The aims of this systematic review were to identify tools proposed to conduct observational gait analysis in adults with a stroke, to summarize evidence concerning their quality, and to assess their implementation in rehabilitation research and clinical practice. An extensive search was performed of original articles reporting on visual/observational tools developed to investigate gait kinematics in adults with a stroke. Two reviewers independently selected studies, extracted data, assessed quality of the included studies, and scored the metric properties and clinical utility of each tool. Rigor in reporting metric properties and dissemination of the tools also was evaluated. Five tools were identified, not all of which had been tested adequately for their metric properties. Evaluation of content validity was partially satisfactory. Reliability was poorly investigated in all but one tool. Concurrent validity and sensitivity to change were shown for 3 and 2 tools, respectively. Overall, adequate levels of quality were rarely reached. The dissemination of the tools was poor. Based on critical appraisal, the Gait Assessment and Intervention Tool shows a good level of quality, and its use in stroke rehabilitation is recommended. Rigorous studies are needed for the other tools in order to establish their usefulness.

Myokit: A simple interface to cardiac cellular electrophysiology.

PubMed

Clerx, Michael; Collins, Pieter; de Lange, Enno; Volders, Paul G A

2016-01-01

Myokit is a new powerful and versatile software tool for modeling and simulation of cardiac cellular electrophysiology. Myokit consists of an easy-to-read modeling language, a graphical user interface, single and multi-cell simulation engines and a library of advanced analysis tools accessible through a Python interface. Models can be loaded from Myokit's native file format or imported from CellML. Model export is provided to C, MATLAB, CellML, CUDA and OpenCL. Patch-clamp data can be imported and used to estimate model parameters. In this paper, we review existing tools to simulate the cardiac cellular action potential to find that current tools do not cater specifically to model development and that there is a gap between easy-to-use but limited software and powerful tools that require strong programming skills from their users. We then describe Myokit's capabilities, focusing on its model description language, simulation engines and import/export facilities in detail. Using three examples, we show how Myokit can be used for clinically relevant investigations, multi-model testing and parameter estimation in Markov models, all with minimal programming effort from the user. This way, Myokit bridges a gap between performance, versatility and user-friendliness. Copyright © 2015 Elsevier Ltd. All rights reserved.

SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis.

PubMed

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R.

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

PubMed Central

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G.; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. PMID:24066126

The technique of entropy optimization in motor current signature analysis and its application in the fault diagnosis of gear transmission

NASA Astrophysics Data System (ADS)

Chen, Xiaoguang; Liang, Lin; Liu, Fei; Xu, Guanghua; Luo, Ailing; Zhang, Sicong

2012-05-01

Nowadays, Motor Current Signature Analysis (MCSA) is widely used in the fault diagnosis and condition monitoring of machine tools. However, although the current signal has lower SNR (Signal Noise Ratio), it is difficult to identify the feature frequencies of machine tools from complex current spectrum that the feature frequencies are often dense and overlapping by traditional signal processing method such as FFT transformation. With the study in the Motor Current Signature Analysis (MCSA), it is found that the entropy is of importance for frequency identification, which is associated with the probability distribution of any random variable. Therefore, it plays an important role in the signal processing. In order to solve the problem that the feature frequencies are difficult to be identified, an entropy optimization technique based on motor current signal is presented in this paper for extracting the typical feature frequencies of machine tools which can effectively suppress the disturbances. Some simulated current signals were made by MATLAB, and a current signal was obtained from a complex gearbox of an iron works made in Luxembourg. In diagnosis the MCSA is combined with entropy optimization. Both simulated and experimental results show that this technique is efficient, accurate and reliable enough to extract the feature frequencies of current signal, which provides a new strategy for the fault diagnosis and the condition monitoring of machine tools.

Image Analysis in Plant Sciences: Publish Then Perish.

PubMed

Lobet, Guillaume

2017-07-01

Image analysis has become a powerful technique for most plant scientists. In recent years dozens of image analysis tools have been published in plant science journals. These tools cover the full spectrum of plant scales, from single cells to organs and canopies. However, the field of plant image analysis remains in its infancy. It still has to overcome important challenges, such as the lack of robust validation practices or the absence of long-term support. In this Opinion article, I: (i) present the current state of the field, based on data from the plant-image-analysis.org database; (ii) identify the challenges faced by its community; and (iii) propose workable ways of improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Geomorphic Road Analysis and Inventory Package (GRAIP) Volume 2: Office Procedures

Treesearch

Richard M. Cissel; Thomas A. Black; Kimberly A. T. Schreuders; Ajay Prasad; Charles H. Luce; David G. Tarboton; Nathan A. Nelson

2012-01-01

An important first step in managing forest roads for improved water quality and aquatic habitat is the performance of an inventory. The Geomorphic Roads Analysis and Inventory Package (GRAIP) was developed as a tool for making a comprehensive inventory and analysis of the effects of forest roads on watersheds. This manual describes the data analysis and process of a...

RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.

PubMed

Williams, Alexander G; Thomas, Sean; Wyman, Stacia K; Holloway, Alisha K

2014-10-01

RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality data and interpretable results. Important considerations for experimental design include number of replicates, whether to collect paired-end or single-end reads, sequence length, and sequencing depth. Common analysis steps in all RNA-seq experiments include quality control, read alignment, assigning reads to genes or transcripts, and estimating gene or transcript abundance. Our aims are two-fold: to make recommendations for common components of experimental design and assess tool capabilities for each of these steps. We also test tools designed to detect differential expression, since this is the most widespread application of RNA-seq. We hope that these analyses will help guide those who are new to RNA-seq and will generate discussion about remaining needs for tool improvement and development. Copyright © 2014 John Wiley & Sons, Inc.

Early visual analysis tool using magnetoencephalography for treatment and recovery of neuronal dysfunction.

PubMed

Rasheed, Waqas; Neoh, Yee Yik; Bin Hamid, Nor Hisham; Reza, Faruque; Idris, Zamzuri; Tang, Tong Boon

2017-10-01

Functional neuroimaging modalities play an important role in deciding the diagnosis and course of treatment of neuronal dysfunction and degeneration. This article presents an analytical tool with visualization by exploiting the strengths of the MEG (magnetoencephalographic) neuroimaging technique. The tool automates MEG data import (in tSSS format), channel information extraction, time/frequency decomposition, and circular graph visualization (connectogram) for simple result inspection. For advanced users, the tool also provides magnitude squared coherence (MSC) values allowing personalized threshold levels, and the computation of default model from MEG data of control population. Default model obtained from healthy population data serves as a useful benchmark to diagnose and monitor neuronal recovery during treatment. The proposed tool further provides optional labels with international 10-10 system nomenclature in order to facilitate comparison studies with EEG (electroencephalography) sensor space. Potential applications in epilepsy and traumatic brain injury studies are also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tools for Data Analysis in the Middle School Classroom: A Teacher Professional Development Program

NASA Astrophysics Data System (ADS)

Ledley, T. S.; Haddad, N.; McAuliffe, C.; Dahlman, L.

2006-12-01

In order for students to learn how to engage with scientific data to answer questions about the real world, it is imperative that their teachers are 1) comfortable with the data and the tools used to analyze it, and 2) feel prepared to support their students in this complex endeavor. TERC's Tools for Data Analysis in the Middle School Classroom (DataTools) professional development program, funded by NSF's ITEST program, prepares middle school teachers to integrate Web-based scientific data and analysis tools into their existing curricula. This 13-month program supports teachers in using a set of freely or commonly available tools with a wide range of data. It also gives them an opportunity to practice teaching these skills to students before teaching in their own classrooms. The ultimate goal of the program is to increase the number of middle school students who work directly with scientific data, who use the tools of technology to import, manipulate, visualize and analyze the data, who come to understand the power of data-based arguments, and who will consider pursuing a career in technical and scientific fields. In this session, we will describe the elements of the DataTools program and the Earth Exploration Toolbook (EET, http://serc.carleton.edu/eet), a Web-based resource that supports Earth system education for teachers and students in grades 6 through 16. The EET provides essential support to DataTools teachers as they use it to learn to locate and download Web-based data and use data analysis tools. We will also share what we have learned during the first year of this three-year program.

Innovative Use of Quality Management Methods for Product Improvement

NASA Astrophysics Data System (ADS)

Midor, Katarzyna; Žarnovský, Jozef

2016-12-01

Organisations constantly look for new, innovative solutions and methods which could be used to improve their efficiency and increase the quality of their products. Identifying the causes for returns is an important issue for modern companies, as returns are the cause for the increase in production costs and, most importantly, the loss of credibility in the eyes of the client. Therefore, for the company to be able to sustain or strengthen its position on the market, it has to follow the rules of quality management. Especially important is the rule of constant improvement. This rule is primarily connected with preventing errors and defects from occurring at all the stages of the production process. To achieve that, one must, among other things, use quality management tools. The article presents an analysis of causes for returns of a vibrating screen produced by a company which manufactures machinery and equipment for the extractive industry, using quality management tools such as the Ishikawa diagram and Pareto analysis. The analysis allowed for the identification of the causes of client returns which could not be previously identified, and proposing solutions for them.

PICASSO: an end-to-end image simulation tool for space and airborne imaging systems

NASA Astrophysics Data System (ADS)

Cota, Steve A.; Bell, Jabin T.; Boucher, Richard H.; Dutton, Tracy E.; Florio, Chris J.; Franz, Geoffrey A.; Grycewicz, Thomas J.; Kalman, Linda S.; Keller, Robert A.; Lomheim, Terrence S.; Paulson, Diane B.; Willkinson, Timothy S.

2008-08-01

The design of any modern imaging system is the end result of many trade studies, each seeking to optimize image quality within real world constraints such as cost, schedule and overall risk. Image chain analysis - the prediction of image quality from fundamental design parameters - is an important part of this design process. At The Aerospace Corporation we have been using a variety of image chain analysis tools for many years, the Parameterized Image Chain Analysis & Simulation SOftware (PICASSO) among them. In this paper we describe our PICASSO tool, showing how, starting with a high quality input image and hypothetical design descriptions representative of the current state of the art in commercial imaging satellites, PICASSO can generate standard metrics of image quality in support of the decision processes of designers and program managers alike.

PICASSO: an end-to-end image simulation tool for space and airborne imaging systems

NASA Astrophysics Data System (ADS)

Cota, Stephen A.; Bell, Jabin T.; Boucher, Richard H.; Dutton, Tracy E.; Florio, Christopher J.; Franz, Geoffrey A.; Grycewicz, Thomas J.; Kalman, Linda S.; Keller, Robert A.; Lomheim, Terrence S.; Paulson, Diane B.; Wilkinson, Timothy S.

2010-06-01

The design of any modern imaging system is the end result of many trade studies, each seeking to optimize image quality within real world constraints such as cost, schedule and overall risk. Image chain analysis - the prediction of image quality from fundamental design parameters - is an important part of this design process. At The Aerospace Corporation we have been using a variety of image chain analysis tools for many years, the Parameterized Image Chain Analysis & Simulation SOftware (PICASSO) among them. In this paper we describe our PICASSO tool, showing how, starting with a high quality input image and hypothetical design descriptions representative of the current state of the art in commercial imaging satellites, PICASSO can generate standard metrics of image quality in support of the decision processes of designers and program managers alike.

Guidelines for appropriate care: the importance of empirical normative analysis.

PubMed

Berg, M; Meulen, R T; van den Burg, M

2001-01-01

The Royal Dutch Medical Association recently completed a research project aimed at investigating how guidelines for 'appropriate medical care' should be construed. The project took as a starting point that explicit attention should be given to ethical and political considerations in addition to data about costs and effectiveness. In the project, two research groups set out to design guidelines and cost-effectiveness analyses (CEAs) for two circumscribed medical areas (angina pectoris and major depression). Our third group was responsible for the normative analysis. We undertook an explorative, qualitative pilot study of the normative considerations that played a role in constructing the guidelines and CEAs, and simultaneously interviewed specialists about the normative considerations that guided their diagnostic and treatment decisions. Explicating normative considerations, we argue, is important democratically: the issues at stake should not be left to decision analysts and guideline developers to decide. Moreover, it is a necessary condition for a successful implementation of such tools: those who draw upon these tools will only accept them when they can recognize themselves in the considerations implied. Empirical normative analysis, we argue, is a crucial tool in developing guidelines for appropriate medical care.

Advances in Photopletysmography Signal Analysis for Biomedical Applications.

PubMed

Moraes, Jermana L; Rocha, Matheus X; Vasconcelos, Glauber G; Vasconcelos Filho, José E; de Albuquerque, Victor Hugo C; Alexandria, Auzuir R

2018-06-09

Heart Rate Variability (HRV) is an important tool for the analysis of a patient’s physiological conditions, as well a method aiding the diagnosis of cardiopathies. Photoplethysmography (PPG) is an optical technique applied in the monitoring of the HRV and its adoption has been growing significantly, compared to the most commonly used method in medicine, Electrocardiography (ECG). In this survey, definitions of these technique are presented, the different types of sensors used are explained, and the methods for the study and analysis of the PPG signal (linear and nonlinear methods) are described. Moreover, the progress, and the clinical and practical applicability of the PPG technique in the diagnosis of cardiovascular diseases are evaluated. In addition, the latest technologies utilized in the development of new tools for medical diagnosis are presented, such as Internet of Things, Internet of Health Things, genetic algorithms, artificial intelligence and biosensors which result in personalized advances in e-health and health care. After the study of these technologies, it can be noted that PPG associated with them is an important tool for the diagnosis of some diseases, due to its simplicity, its cost⁻benefit ratio, the easiness of signals acquisition, and especially because it is a non-invasive technique.

Whole-Genome Thermodynamic Analysis Reduces siRNA Off-Target Effects

PubMed Central

Chen, Xi; Liu, Peng; Chou, Hui-Hsien

2013-01-01

Small interfering RNAs (siRNAs) are important tools for knocking down targeted genes, and have been widely applied to biological and biomedical research. To design siRNAs, two important aspects must be considered: the potency in knocking down target genes and the off-target effect on any nontarget genes. Although many studies have produced useful tools to design potent siRNAs, off-target prevention has mostly been delegated to sequence-level alignment tools such as BLAST. We hypothesize that whole-genome thermodynamic analysis can identify potential off-targets with higher precision and help us avoid siRNAs that may have strong off-target effects. To validate this hypothesis, two siRNA sets were designed to target three human genes IDH1, ITPR2 and TRIM28. They were selected from the output of two popular siRNA design tools, siDirect and siDesign. Both siRNA design tools have incorporated sequence-level screening to avoid off-targets, thus their output is believed to be optimal. However, one of the sets we tested has off-target genes predicted by Picky, a whole-genome thermodynamic analysis tool. Picky can identify off-target genes that may hybridize to a siRNA within a user-specified melting temperature range. Our experiments validated that some off-target genes predicted by Picky can indeed be inhibited by siRNAs. Similar experiments were performed using commercially available siRNAs and a few off-target genes were also found to be inhibited as predicted by Picky. In summary, we demonstrate that whole-genome thermodynamic analysis can identify off-target genes that are missed in sequence-level screening. Because Picky prediction is deterministic according to thermodynamics, if a siRNA candidate has no Picky predicted off-targets, it is unlikely to cause off-target effects. Therefore, we recommend including Picky as an additional screening step in siRNA design. PMID:23484018

Eros in Stereo

NASA Image and Video Library

2000-05-07

Stereo imaging, an important tool on NASA NEAR Shoemaker for geologic analysis of Eros, provides three-dimensional information on the asteroid landforms and structures. 3D glasses are necessary to view this image.

Research for Policy (R4P): development of a reflection tool for researchers to improve knowledge utilization.

PubMed

Hegger, Ingrid; Marks, Lisanne K; Janssen, Susan W J; Schuit, Albertine J; Keijsers, Jolanda F M; van Oers, Hans A M

2016-09-30

To improve knowledge utilization in policymaking, alignment between researchers and policymakers during knowledge production is essential, but difficult to maintain. In three previously reported case studies, we extensively evaluated complex research projects commissioned by policymakers to investigate how alignment is achieved in a research process and to discover ways to enhance knowledge contributions to health policy. In the present study, we investigated how the findings of these three research projects could be integrated into a practical tool for researchers to enhance their contribution to evidence-based policy. A cross-case analysis was conducted to integrate the findings of the evaluation of the three research projects and to identify important alignment areas in these projects. By means of an iterative process, we prepared a tool that includes reflection questions for researchers. The "Research for Policy" tool was tested with input from the project managers of three new research projects. Based on the findings, the final version of the Research for Policy tool was prepared. By cross-case analysis of the three case studies, the following important alignment areas were identified: the goal, quality, relevance, timing, and presentation of research, the tasks and authorities of actors, the consultative structure and vertical alignment within organizations, and the organizational environment. The project managers regarded the Research for Policy tool as a useful checklist for addressing the important alignment areas in a research project. Based on their feedback, the illustrative examples from the case studies were added to the reflection questions. The project managers suggested making the tool accessible not only to researchers but also to policymakers. The format of the Research for Policy tool was further adjusted to users' needs by adding clickable links. Alignment between research and policymaking requires continuous efforts and a clear understanding of process issues in the research project. The Research for Policy tool offers practical alignment guidance and facilitates reflection on process issues, which supports researchers in aligning with policymakers and in acting in a context-sensitive way.

BeadArray Expression Analysis Using Bioconductor

PubMed Central

Ritchie, Matthew E.; Dunning, Mark J.; Smith, Mike L.; Shi, Wei; Lynch, Andy G.

2011-01-01

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered. PMID:22144879

Proximal hyperspectral sensing and data analysis approaches for field-based plant phenomics

USDA-ARS?s Scientific Manuscript database

Field-based plant phenomics requires robust crop sensing platforms and data analysis tools to successfully identify cultivars that exhibit phenotypes with high agronomic and economic importance. Such efforts will lead to genetic improvements that maintain high crop yield with concomitant tolerance t...

Analysis of Two Methods to Evaluate Antioxidants

ERIC Educational Resources Information Center

Tomasina, Florencia; Carabio, Claudio; Celano, Laura; Thomson, Leonor

2012-01-01

This exercise is intended to introduce undergraduate biochemistry students to the analysis of antioxidants as a biotechnological tool. In addition, some statistical resources will also be used and discussed. Antioxidants play an important metabolic role, preventing oxidative stress-mediated cell and tissue injury. Knowing the antioxidant content…

Dynaflow User’s Guide

DTIC Science & Technology

1988-11-01

264 ANALYSIS RESTART. ............. ..... ....... 269 1.0 TITLE CARD. .............. ............. 271 2.0 CONTROL CARDS...stress soil model will provide a tool for such analysis of waterfront structures. To understand the significance of liquefaction, it is important to note...Implementing this effective stress soil model into a finite element computer program would allow analysis of soil and structure together. TECHNICAL BACKGROUND

Computer vision-based analysis of foods: a non-destructive colour measurement tool to monitor quality and safety.

PubMed

Mogol, Burçe Ataç; Gökmen, Vural

2014-05-01

Computer vision-based image analysis has been widely used in food industry to monitor food quality. It allows low-cost and non-contact measurements of colour to be performed. In this paper, two computer vision-based image analysis approaches are discussed to extract mean colour or featured colour information from the digital images of foods. These types of information may be of particular importance as colour indicates certain chemical changes or physical properties in foods. As exemplified here, the mean CIE a* value or browning ratio determined by means of computer vision-based image analysis algorithms can be correlated with acrylamide content of potato chips or cookies. Or, porosity index as an important physical property of breadcrumb can be calculated easily. In this respect, computer vision-based image analysis provides a useful tool for automatic inspection of food products in a manufacturing line, and it can be actively involved in the decision-making process where rapid quality/safety evaluation is needed. © 2013 Society of Chemical Industry.

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

PubMed

Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas; Kyrpides, Nikos C; Bagos, Pantelis G; Iliopoulos, Ioannis; Pavlopoulos, Georgios A

2017-07-14

Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

Standardized observation of neighbourhood disorder: does it work in Canada?

PubMed Central

2010-01-01

Background There is a growing body of evidence that where you live is important to your health. Despite numerous previous studies investigating the relationship between neighbourhood deprivation (and structure) and residents' health, the precise nature of this relationship remains unclear. Relatively few investigations have relied on direct observation of neighbourhoods, while those that have were developed primarily in US settings. Evaluation of the transferability of such tools to other contexts is an important first step before applying such instruments to the investigation of health and well-being. This study evaluated the performance of a systematic social observational (SSO) tool (adapted from previous studies of American and British neighbourhoods) in a Canadian urban context. Methods This was a mixed-methods study. Quantitative SSO ratings and qualitative descriptions of 176 block faces were obtained in six Toronto neighbourhoods (4 low-income, and 2 middle/high-income) by trained raters. Exploratory factor analysis was conducted with the quantitative SSO ratings. Content analysis consisted of independent coding of qualitative data by three members of the research team to yield common themes and categories. Results Factor analysis identified three factors (physical decay/disorder, social accessibility, recreational opportunities), but only 'physical decay/disorder' reflected previous findings in the literature. Qualitative results (based on raters' fieldwork experiences) revealed the tool's shortcomings in capturing important features of the neighbourhoods under study, and informed interpretation of the quantitative findings. Conclusions This study tested the performance of an SSO tool in a Canadian context, which is an important initial step before applying it to the study of health and disease. The tool demonstrated important shortcomings when applied to six diverse Toronto neighbourhoods. The study's analyses challenge previously held assumptions (e.g. social 'disorder') regarding neighbourhood social and built environments. For example, neighbourhood 'order' has traditionally been assumed to be synonymous with a certain degree of homogeneity, however the neighbourhoods under study were characterized by high degrees of heterogeneity and low levels of disorder. Heterogeneity was seen as an appealing feature of a block face. Employing qualitative techniques with SSO represents a unique contribution, enhancing both our understanding of the quantitative ratings obtained and of neighbourhood characteristics that are not currently captured by such instruments. PMID:20146821

Measuring laboratory-based influenza surveillance capacity: development of the 'International Influenza Laboratory Capacity Review' Tool.

PubMed

Muir-Paulik, S A; Johnson, L E A; Kennedy, P; Aden, T; Villanueva, J; Reisdorf, E; Humes, R; Moen, A C

2016-01-01

The 2005 International Health Regulations (IHR 2005) emphasized the importance of laboratory capacity to detect emerging diseases including novel influenza viruses. To support IHR 2005 requirements and the need to enhance influenza laboratory surveillance capacity, the Association of Public Health Laboratories (APHL) and the Centers for Disease Control and Prevention (CDC) Influenza Division developed the International Influenza Laboratory Capacity Review (Tool). Data from 37 assessments were reviewed and analyzed to verify that the quantitative analysis results accurately depicted a laboratory's capacity and capabilities. Subject matter experts in influenza and laboratory practice used an iterative approach to develop the Tool incorporating feedback and lessons learnt through piloting and implementation. To systematically analyze assessment data, a quantitative framework for analysis was added to the Tool. The review indicated that changes in scores consistently reflected enhanced or decreased capacity. The review process also validated the utility of adding a quantitative analysis component to the assessments and the benefit of establishing a baseline from which to compare future assessments in a standardized way. Use of the Tool has provided APHL, CDC and each assessed laboratory with a standardized analysis of the laboratory's capacity. The information generated is used to improve laboratory systems for laboratory testing and enhance influenza surveillance globally. We describe the development of the Tool and lessons learnt. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics.

PubMed

Möller, Birgit; Poeschl, Yvonne; Plötner, Romina; Bürstenbinder, Katharina

2017-11-01

Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets. © 2017 American Society of Plant Biologists. All Rights Reserved.

Toward an Efficient Icing CFD Process Using an Interactive Software Toolkit: Smagglce 2D

NASA Technical Reports Server (NTRS)

Vickerman, Mary B.; Choo, Yung K.; Schilling, Herbert W.; Baez, Marivell; Braun, Donald C.; Cotton, Barbara J.

2001-01-01

Two-dimensional CID analysis for iced airfoils can be a labor-intensive task. The software toolkit SmaggIce 2D is being developed to help streamline the CID process and provide the unique features needed for icing. When complete, it will include a combination of partially automated and fully interactive tools for all aspects of the tasks leading up to the flow analysis: geometry preparation, domain decomposition. block boundary demoralization. gridding, and linking with a flow solver. It also includes tools to perform ice shape characterization, an important aid in determining the relationship between ice characteristics and their effects on aerodynamic performance. Completed tools, work-in-progress, and planned features of the software toolkit are presented here.

PFGE MAPPER and PFGE READER: two tools to aid in the analysis and data input of pulse field gel electrophoresis maps.

PubMed Central

Shifman, M. A.; Nadkarni, P.; Miller, P. L.

1992-01-01

Pulse field gel electrophoresis mapping is an important technique for characterizing large segments of DNA. We have developed two tools to aid in the construction of pulse field electrophoresis gel maps: PFGE READER which stores experimental conditions and calculates fragment sizes and PFGE MAPPER which constructs pulse field gel electrophoresis maps. PMID:1482898

MIPs as Tools in Environmental Biotechnology.

PubMed

Mattiasson, Bo

2015-01-01

Molecular imprints are potentially fantastic constructions. They are selective, robust, and nonbiodegradable if produced from stable polymers. A range of different applications has been presented, everything from separation of enantiomers, via adsorbents for sample preparation before analysis to applications in wastewater treatment. This chapter deals with molecularly imprinted polymers (MIPs) as tools in environmental biotechnology, a field that has the potential to become very important in the future.

Advancing School-Based Interventions through Economic Analysis

ERIC Educational Resources Information Center

Olsson, Tina M.; Ferrer-Wreder, Laura; Eninger, Lilianne

2014-01-01

Commentators interested in school-based prevention programs point to the importance of economic issues for the future of prevention efforts. Many of the processes and aims of prevention science are dependent upon prevention resources. Although economic analysis is an essential tool for assessing resource use, the attention given economic analysis…

The Model of Career Anchors as a Tool in the Analysis of Instructional Developers.

ERIC Educational Resources Information Center

Miller, Carol

1981-01-01

Examines the importance of human systems as a relevant aspect of development processes and looks at the career anchor model proposed by Schein as a possible area in the analysis of the instructional developer/client relationships. Fourteen references are listed. (Author/LLS)

Exploring Rating Quality in Rater-Mediated Assessments Using Mokken Scale Analysis

ERIC Educational Resources Information Center

Wind, Stefanie A.; Engelhard, George, Jr.

2016-01-01

Mokken scale analysis is a probabilistic nonparametric approach that offers statistical and graphical tools for evaluating the quality of social science measurement without placing potentially inappropriate restrictions on the structure of a data set. In particular, Mokken scaling provides a useful method for evaluating important measurement…

Relevance of Item Analysis in Standardizing an Achievement Test in Teaching of Physical Science in B.Ed Syllabus

ERIC Educational Resources Information Center

Marie, S. Maria Josephine Arokia; Edannur, Sreekala

2015-01-01

This paper focused on the analysis of test items constructed in the paper of teaching Physical Science for B.Ed. class. It involved the analysis of difficulty level and discrimination power of each test item. Item analysis allows selecting or omitting items from the test, but more importantly item analysis is a tool to help the item writer improve…

Applied Cognitive Task Analysis (ACTA) Methodology

DTIC Science & Technology

1997-11-01

experienced based cognitive skills. The primary goal of this project was to develop streamlined methods of Cognitive Task Analysis that would fill this need...We have made important progression this direction. We have developed streamlined methods of Cognitive Task Analysis . Our evaluation study indicates...developed a CD-based stand alone instructional package, which will make the Applied Cognitive Task Analysis (ACTA) tools widely accessible. A survey of the

Prioritizing the mHealth Design Space: A Mixed-Methods Analysis of Smokers' Perspectives.

PubMed

Hartzler, Andrea Lisabeth; BlueSpruce, June; Catz, Sheryl L; McClure, Jennifer B

2016-08-05

Smoking remains the leading cause of preventable disease and death in the United States. Therefore, researchers are constantly exploring new ways to promote smoking cessation. Mobile health (mHealth) technologies could be effective cessation tools. Despite the availability of commercial quit-smoking apps, little research to date has examined smokers' preferred treatment intervention components (ie, design features). Honoring these preferences is important for designing programs that are appealing to smokers and may be more likely to be adopted and used. The aim of this study was to understand smokers' preferred design features of mHealth quit-smoking tools. We used a mixed-methods approach consisting of focus groups and written surveys to understand the design preferences of adult smokers who were interested in quitting smoking (N=40). Focus groups were stratified by age to allow differing perspectives to emerge between older (>40 years) and younger (<40 years) participants. Focus group discussion included a "blue-sky" brainstorming exercise followed by participant reactions to contrasting design options for communicating with smokers, providing social support, and incentivizing program use. Participants rated the importance of preselected design features on an exit survey. Qualitative analyses examined emergent discussion themes and quantitative analyses compared feature ratings to determine which were perceived as most important. Participants preferred a highly personalized and adaptive mHealth experience. Their ideal mHealth quit-smoking tool would allow personalized tracking of their progress, adaptively tailored feedback, and real-time peer support to help manage smoking cravings. Based on qualitative analysis of focus group discussion, participants preferred pull messages (ie, delivered upon request) over push messages (ie, sent automatically) and preferred interaction with other smokers through closed social networks. Preferences for entertaining games or other rewarding incentives to encourage program use differed by age group. Based on quantitative analysis of surveys, participants rated the importance of select design features significantly differently (P<.001). Design features rated as most important included personalized content, the ability to track one's progress, and features designed to help manage nicotine withdrawal and medication side effects. Design features rated least important were quit-smoking videos and posting on social media. Communicating with stop-smoking experts was rated more important than communicating with family and friends about quitting (P=.03). Perceived importance of various design features varied by age, experience with technology, and frequency of smoking. Future mHealth cessation aids should be designed with an understanding of smokers' needs and preferences for these tools. Doing so does not guarantee treatment effectiveness, but balancing user preferences with best-practice treatment considerations could enhance program adoption and improve treatment outcomes. Grounded in the perspectives of smokers, we identify several design considerations, which should be prioritized when designing future mHealth cessation tools and which warrant additional empirical validation.

Tool Support for Parametric Analysis of Large Software Simulation Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

2008-01-01

The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

Tools to Support Human Factors and Systems Engineering Interactions During Early Analysis

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Malin, Jane T.; Holden, Kritina; Smith, Danielle Paige

2005-01-01

We describe an approach and existing software tool support for effective interactions between human factors engineers and systems engineers in early analysis activities during system acquisition. We examine the tasks performed during this stage, emphasizing those tasks where system engineers and human engineers interact. The Concept of Operations (ConOps) document is an important product during this phase, and particular attention is paid to its influences on subsequent acquisition activities. Understanding this influence helps ConOps authors describe a complete system concept that guides subsequent acquisition activities. We identify commonly used system engineering and human engineering tools and examine how they can support the specific tasks associated with system definition. We identify possible gaps in the support of these tasks, the largest of which appears to be creating the ConOps document itself. Finally, we outline the goals of our future empirical investigations of tools to support system concept definition.

Tools to Support Human Factors and Systems Engineering Interactions During Early Analysis

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Malin, Jane T.; Holden, Kritina; Smith, Danielle Paige

2006-01-01

We describe an approach and existing software tool support for effective interactions between human factors engineers and systems engineers in early analysis activities during system acquisition. We examine the tasks performed during this stage, emphasizing those tasks where system engineers and human engineers interact. The Concept of Operations (ConOps) document is an important product during this phase, and particular attention is paid to its influences on subsequent acquisition activities. Understanding this influence helps ConOps authors describe a complete system concept that guides subsequent acquisition activities. We identify commonly used system engineering and human engineering tools and examine how they can support the specific tasks associated with system definition. We identify possible gaps in the support of these tasks, the largest of which appears to be creating the ConOps document itself. Finally, we outline the goals of our future empirical investigations of tools to support system concept definition.

POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

PubMed Central

2015-01-01

Analysis of macromolecular/small-molecule binding pockets can provide important insights into molecular recognition and receptor dynamics. Since its release in 2011, the POVME (POcket Volume MEasurer) algorithm has been widely adopted as a simple-to-use tool for measuring and characterizing pocket volumes and shapes. We here present POVME 2.0, which is an order of magnitude faster, has improved accuracy, includes a graphical user interface, and can produce volumetric density maps for improved pocket analysis. To demonstrate the utility of the algorithm, we use it to analyze the binding pocket of RNA editing ligase 1 from the unicellular parasite Trypanosoma brucei, the etiological agent of African sleeping sickness. The POVME analysis characterizes the full dynamics of a potentially druggable transient binding pocket and so may guide future antitrypanosomal drug-discovery efforts. We are hopeful that this new version will be a useful tool for the computational- and medicinal-chemist community. PMID:25400521

Evaluation of the sustainability of contrasted pig farming systems: economy.

PubMed

Ilari-Antoine, E; Bonneau, M; Klauke, T N; Gonzàlez, J; Dourmad, J Y; De Greef, K; Houwers, H W J; Fabrega, E; Zimmer, C; Hviid, M; Van der Oever, B; Edwards, S A

2014-12-01

The aim of this paper is to present an efficient tool for evaluating the economy part of the sustainability of pig farming systems. The selected tool IDEA was tested on a sample of farms from 15 contrasted systems in Europe. A statistical analysis was carried out to check the capacity of the indicators to illustrate the variability of the population and to analyze which of these indicators contributed the most towards it. The scores obtained for the farms were consistent with the reality of pig production; the variable distribution showed an important variability of the sample. The principal component analysis and cluster analysis separated the sample into five subgroups, in which the six main indicators significantly differed, which underlines the robustness of the tool. The IDEA method was proven to be easily comprehensible, requiring few initial variables and with an efficient benchmarking system; all six indicators contributed to fully describe a varied and contrasted population.

A comprehensive comparison of tools for differential ChIP-seq analysis

PubMed Central

Steinhauser, Sebastian; Kurzawa, Nils; Eils, Roland

2016-01-01

ChIP-seq has become a widely adopted genomic assay in recent years to determine binding sites for transcription factors or enrichments for specific histone modifications. Beside detection of enriched or bound regions, an important question is to determine differences between conditions. While this is a common analysis for gene expression, for which a large number of computational approaches have been validated, the same question for ChIP-seq is particularly challenging owing to the complexity of ChIP-seq data in terms of noisiness and variability. Many different tools have been developed and published in recent years. However, a comprehensive comparison and review of these tools is still missing. Here, we have reviewed 14 tools, which have been developed to determine differential enrichment between two conditions. They differ in their algorithmic setups, and also in the range of applicability. Hence, we have benchmarked these tools on real data sets for transcription factors and histone modifications, as well as on simulated data sets to quantitatively evaluate their performance. Overall, there is a great variety in the type of signal detected by these tools with a surprisingly low level of agreement. Depending on the type of analysis performed, the choice of method will crucially impact the outcome. PMID:26764273

High-Speed TCP Testing

NASA Technical Reports Server (NTRS)

Brooks, David E.; Gassman, Holly; Beering, Dave R.; Welch, Arun; Hoder, Douglas J.; Ivancic, William D.

1999-01-01

Transmission Control Protocol (TCP) is the underlying protocol used within the Internet for reliable information transfer. As such, there is great interest to have all implementations of TCP efficiently interoperate. This is particularly important for links exhibiting long bandwidth-delay products. The tools exist to perform TCP analysis at low rates and low delays. However, for extremely high-rate and lone-delay links such as 622 Mbps over geosynchronous satellites, new tools and testing techniques are required. This paper describes the tools and techniques used to analyze and debug various TCP implementations over high-speed, long-delay links.

The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.

PubMed

Lucas, Blake C; Bogovic, John A; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L; Pham, Dzung L; Landman, Bennett A

2010-03-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).

The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software

PubMed Central

Lucas, Blake C.; Bogovic, John A.; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L.; Pham, Dzung

2010-01-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). PMID:20077162

Artificial intelligence applications in the intensive care unit.

PubMed

Hanson, C W; Marshall, B E

2001-02-01

To review the history and current applications of artificial intelligence in the intensive care unit. The MEDLINE database, bibliographies of selected articles, and current texts on the subject. The studies that were selected for review used artificial intelligence tools for a variety of intensive care applications, including direct patient care and retrospective database analysis. All literature relevant to the topic was reviewed. Although some of the earliest artificial intelligence (AI) applications were medically oriented, AI has not been widely accepted in medicine. Despite this, patient demographic, clinical, and billing data are increasingly available in an electronic format and therefore susceptible to analysis by intelligent software. Individual AI tools are specifically suited to different tasks, such as waveform analysis or device control. The intensive care environment is particularly suited to the implementation of AI tools because of the wealth of available data and the inherent opportunities for increased efficiency in inpatient care. A variety of new AI tools have become available in recent years that can function as intelligent assistants to clinicians, constantly monitoring electronic data streams for important trends, or adjusting the settings of bedside devices. The integration of these tools into the intensive care unit can be expected to reduce costs and improve patient outcomes.

Modeling cooperative driving behavior in freeway merges.

DOT National Transportation Integrated Search

2011-11-01

Merging locations are major sources of freeway bottlenecks and are therefore important for freeway operations analysis. Microscopic simulation tools have been successfully used to analyze merging bottlenecks and to design optimum geometric configurat...

Text Analysis: Critical Component of Planning for Text-Based Discussion Focused on Comprehension of Informational Texts

ERIC Educational Resources Information Center

Kucan, Linda; Palincsar, Annemarie Sullivan

2018-01-01

This investigation focuses on a tool used in a reading methods course to introduce reading specialist candidates to text analysis as a critical component of planning for text-based discussions. Unlike planning that focuses mainly on important text content or information, a text analysis approach focuses both on content and how that content is…

Application of Concepts from Cross-Recurrence Analysis in Speech Production: An Overview and Comparison with Other Nonlinear Methods

ERIC Educational Resources Information Center

Lancia, Leonardo; Fuchs, Susanne; Tiede, Mark

2014-01-01

Purpose: The aim of this article was to introduce an important tool, cross-recurrence analysis, to speech production applications by showing how it can be adapted to evaluate the similarity of multivariate patterns of articulatory motion. The method differs from classical applications of cross-recurrence analysis because no phase space…

Benefit-Cost Analysis of Undergraduate Education Programs: An Example Analysis of the Freshman Research Initiative

ERIC Educational Resources Information Center

Walcott, Rebecca L.; Corso, Phaedra S.; Rodenbusch, Stacia E.; Dolan, Erin L.

2018-01-01

Institutions and administrators regularly have to make difficult choices about how best to invest resources to serve students. Yet economic evaluation, or the systematic analysis of the relationship between costs and outcomes of a program or policy, is relatively uncommon in higher education. This type of evaluation can be an important tool for…

HPTLC in Herbal Drug Quantification

NASA Astrophysics Data System (ADS)

Shinde, Devanand B.; Chavan, Machindra J.; Wakte, Pravin S.

For the past few decades, compounds from natural sources have been gaining importance because of the vast chemical diversity they offer. This has led to phenomenal increase in the demand for herbal medicines in the last two decades and need has been felt for ensuring the quality, safety, and efficacy of herbal drugs. Phytochemical evaluation is one of the tools for the quality assessment, which include preliminary phytochemical screening, chemoprofiling, and marker compound analysis using modern analytical techniques. High-performance thin-layer chromatography (HPTLC) has been emerged as an important tool for the qualitative, semiquantitative, and quantitative phytochemical analysis of the herbal drugs and formulations. This includes developing TLC fingerprinting profiles and estimation of biomarkers. This review has an attempt to focus on the theoretical considerations of HPTLC and some examples of herbal drugs and formulations analyzed by HPTLC.

MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets

PubMed Central

Huang, Chun-Hsi

2017-01-01

Abstract Finding binding site motifs plays an important role in bioinformatics as it reveals the transcription factors that control the gene expression. The development for motif finders has flourished in the past years with many tools have been introduced to the research community. Although these tools possess exceptional features for detecting motifs, they report different results for an identical data set. Hence, using multiple tools is recommended because motifs reported by several tools are likely biologically significant. However, the results from multiple tools need to be compared for obtaining common significant motifs. MOTIFSIM web tool and command-line tool were developed for this purpose. In this work, we present several technical improvements as well as additional features to further support the motif analysis in our new release MOTIFSIM 2.1. PMID:28632401

Trade-Off Analysis between Concerns Based on Aspect-Oriented Requirements Engineering

NASA Astrophysics Data System (ADS)

Laurito, Abelyn Methanie R.; Takada, Shingo

The identification of functional and non-functional concerns is an important activity during requirements analysis. However, there may be conflicts between the identified concerns, and they must be discovered and resolved through trade-off analysis. Aspect-Oriented Requirements Engineering (AORE) has trade-off analysis as one of its goals, but most AORE approaches do not actually offer support for trade-off analysis; they focus on describing concerns and generating their composition. This paper proposes an approach for trade-off analysis based on AORE using use cases and the Requirements Conflict Matrix (RCM) to represent compositions. RCM shows the positive or negative effect of non-functional concerns over use cases and other non-functional concerns. Our approach is implemented within a tool called E-UCEd (Extended Use Case Editor). We also show the results of evaluating our tool.

Assessing Student Peer Dialogue in Collaborative Settings: A Window into Student Reasoning

NASA Astrophysics Data System (ADS)

Stone, Antoinette

The use of science classroom discourse analysis as a way to gain a better understanding of various student cognitive outcomes has a rich history in Science Education in general and Physics Education Research (PER) in particular. When students talk to each other in a collaborative peer instruction environment, such as in the CLASP classes (Collaborative Learning and Sense-making in Physics) at UC Davis, they get to practice and enhance their reasoning and sense-making skills, develop collaborative approaches to problem solving, and participate in co-construction of knowledge and shared thinking. To better understand these important cognitive processes, an analysis tool for monitoring, assessing and categorizing the peer talk arising in this environment is needed as a first step in teasing out evidence for these processes inherent in such talk. In order to meaningfully contribute to the extensive body of knowledge that currently exists, deeper, more insightful answers to the question of what happens linguistically when students struggle to "make sense" and how students use language to mediate these important cognitive outcomes is needed. To this end, a new tool for interpreting particularly qualitative linguistic data is needed, and the first part of the dissertation expounds on the development of a discourse analysis tool that has as its underpinnings a framework for coding borrowed extensively from Systemic Functional Linguistics Theory (SFL). The second part of this dissertation illustrates multiple ways in which the tool is used and how it can be utilized to address many current research questions.

Development of AMSTAR: a measurement tool to assess the methodological quality of systematic reviews.

PubMed

Shea, Beverley J; Grimshaw, Jeremy M; Wells, George A; Boers, Maarten; Andersson, Neil; Hamel, Candyce; Porter, Ashley C; Tugwell, Peter; Moher, David; Bouter, Lex M

2007-02-15

Our objective was to develop an instrument to assess the methodological quality of systematic reviews, building upon previous tools, empirical evidence and expert consensus. A 37-item assessment tool was formed by combining 1) the enhanced Overview Quality Assessment Questionnaire (OQAQ), 2) a checklist created by Sacks, and 3) three additional items recently judged to be of methodological importance. This tool was applied to 99 paper-based and 52 electronic systematic reviews. Exploratory factor analysis was used to identify underlying components. The results were considered by methodological experts using a nominal group technique aimed at item reduction and design of an assessment tool with face and content validity. The factor analysis identified 11 components. From each component, one item was selected by the nominal group. The resulting instrument was judged to have face and content validity. A measurement tool for the 'assessment of multiple systematic reviews' (AMSTAR) was developed. The tool consists of 11 items and has good face and content validity for measuring the methodological quality of systematic reviews. Additional studies are needed with a focus on the reproducibility and construct validity of AMSTAR, before strong recommendations can be made on its use.

Tissue proteomics: a new investigative tool for renal biopsy analysis.

PubMed

Sedor, John R

2009-05-01

Renal biopsy is viewed as the gold standard for diagnosis and management of many kidney diseases, especially glomerulopathies. However, the histopathological descriptions currently used in clinical practice often are neither diagnostic nor prognostic. The paper by Sethi et al. highlights the availability of a newer investigative tool that can be used to better define pathogenesis and, perhaps more important, to discover robust biomarkers of kidney disease cause and outcome.

Knowledge-Acquisition Tool For Expert System

NASA Technical Reports Server (NTRS)

Disbrow, James D.; Duke, Eugene L.; Regenie, Victoria A.

1988-01-01

Digital flight-control systems monitored by computer program that evaluates and recommends. Flight-systems engineers for advanced, high-performance aircraft use knowlege-acquisition tool for expert-system flight-status monitor suppling interpretative data. Interpretative function especially important in time-critical, high-stress situations because it facilitates problem identification and corrective strategy. Conditions evaluated and recommendations made by ground-based engineers having essential knowledge for analysis and monitoring of performances of advanced aircraft systems.

Fall 2014 SEI Research Review Probabilistic Analysis of Time Sensitive Systems

DTIC Science & Technology

2014-10-28

Osmosis SMC Tool Osmosis is a tool for Statistical Model Checking (SMC) with Semantic Importance Sampling. • Input model is written in subset of C...ASSERT() statements in model indicate conditions that must hold. • Input probability distributions defined by the user. • Osmosis returns the...on: – Target relative error, or – Set number of simulations Osmosis Main Algorithm 1 http://dreal.cs.cmu.edu/ (?⃑?): Indicator

Remote sensing change detection tools for natural resource managers: Understanding concepts and tradeoffs in the design of landscape monitoring projects

Treesearch

Robert E. Kennedy; Philip A. Townsend; John E. Gross; Warren B. Cohen; Paul Bolstad; Wang Y. Q.; Phyllis Adams

2009-01-01

Remote sensing provides a broad view of landscapes and can be consistent through time, making it an important tool for monitoring and managing protected areas. An impediment to broader use of remote sensing science for monitoring has been the need for resource managers to understand the specialized capabilities of an ever-expanding array of image sources and analysis...

Bridging the Gap between RF and Optical Patch Antenna Analysis via the Cavity Model.

PubMed

Unal, G S; Aksun, M I

2015-11-02

Although optical antennas with a variety of shapes and for a variety of applications have been proposed and studied, they are still in their infancy compared to their radio frequency (rf) counterparts. Optical antennas have mainly utilized the geometrical attributes of rf antennas rather than the analysis tools that have been the source of intuition for antenna engineers in rf. This study intends to narrow the gap of experience and intuition in the design of optical patch antennas by introducing an easy-to-understand and easy-to-implement analysis tool in rf, namely, the cavity model, into the optical regime. The importance of this approach is not only its simplicity in understanding and implementation but also its applicability to a broad class of patch antennas and, more importantly, its ability to provide the intuition needed to predict the outcome without going through the trial-and-error simulations with no or little intuitive guidance by the user.

Overview of Virtual Observatory Tools

NASA Astrophysics Data System (ADS)

Allen, M. G.

2009-07-01

I provide a brief introduction and tour of selected Virtual Observatory tools to highlight some of the core functions provided by the VO, and the way that astronomers may use the tools and services for doing science. VO tools provide advanced functions for searching and using images, catalogues and spectra that have been made available in the VO. The tools may work together by providing efficient and innovative browsing and analysis of data, and I also describe how many VO services may be accessed by a scripting or command line environment. Early science usage of the VO provides important feedback on the development of the system, and I show how VO portals try to address early user comments about the navigation and use of the VO.

Web-based visual analysis for high-throughput genomics

PubMed Central

2013-01-01

Background Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. Results We have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Conclusions Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments. PMID:23758618

Decisions and Reasons: Examining Preservice Teacher Decision-Making through Video Self-Analysis

ERIC Educational Resources Information Center

Rich, Peter J.; Hannafin, Michael J.

2008-01-01

Methods used to study teacher thinking have both provided insight into the cognitive aspects of teaching and resulted in new, as yet unresolved, relationships between practice and theory. Recent developments in video-analysis tools have allowed preservice teachers to analyze both their practices and thinking, providing important feedback for…

COINGRAD; Control Oriented Interactive Graphical Analysis and Design.

ERIC Educational Resources Information Center

Volz, Richard A.; And Others

The computer is currently a vital tool in engineering analysis and design. With the introduction of moderately priced graphics terminals, it will become even more important in the future as rapid graphic interaction between the engineer and the computer becomes more feasible in computer-aided design (CAD). To provide a vehicle for introducing…

Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula)

USDA-ARS?s Scientific Manuscript database

Quantitative real-time polymerase chain reaction (qRT-PCR) is the most important tool in measuring levels of gene expression due to its accuracy, specificity, and sensitivity. However, the accuracy of qRT-PCR analysis strongly depends on transcript normalization using stably expressed reference gene...

Dimensional Analysis in Physics and the Buckingham Theorem

ERIC Educational Resources Information Center

Misic, Tatjana; Najdanovic-Lukic, Marina; Nesic, Ljubisa

2010-01-01

Dimensional analysis is a simple, clear and intuitive method for determining the functional dependence of physical quantities that are of importance to a certain process. However, in physics textbooks, very little space is usually given to this approach and it is often presented only as a diagnostic tool used to determine the validity of…

Exposomics research using suspect screening and non-targeted analysis methods and tools at the U.S. Environmental Protection Agency (ASMS Presentation)

EPA Science Inventory

High-resolution mass spectrometry (HRMS) is used for suspect screening (SSA) and non-targeted analysis (NTA) in an attempt to characterize xenobiotic chemicals in various samples broadly and efficiently. These important techniques aid characterization of the exposome, the totalit...

Organizational Economics: Notes on the Use of Transaction-Cost Theory in the Study of Organizations.

ERIC Educational Resources Information Center

Robins, James A.

1987-01-01

Reviews transaction-cost approaches to organizational analysis, examines their use in microeconomic theory, and identifies some important flaws in the study. Advocates transaction-cost theory as a powerful tool for organizational and strategic analysis when set within the famework of more general organizational theory. Includes 61 references. (MLH)

Assessing Accessibility: How Accessible Are Online Courses for Students with Disabilities?

ERIC Educational Resources Information Center

Massengale, Lindsey R.; Vasquez, Eleazar, III

2016-01-01

Delivering course material in a manner that is accessible to all students including those with disabilities is important in the online environment. This article presents an analysis focusing on the accessibility of six courses presented through the Webcourses platform. Six professors volunteered one course for analysis. The tool used for analyzing…

Automatic Coding of Dialogue Acts in Collaboration Protocols

ERIC Educational Resources Information Center

Erkens, Gijsbert; Janssen, Jeroen

2008-01-01

Although protocol analysis can be an important tool for researchers to investigate the process of collaboration and communication, the use of this method of analysis can be time consuming. Hence, an automatic coding procedure for coding dialogue acts was developed. This procedure helps to determine the communicative function of messages in online…

Optics in gait analysis and anthropometry

NASA Astrophysics Data System (ADS)

Silva Moreno, Alejandra Alicia

2013-11-01

Since antiquity, human gait has been studied to understand human movement, the kind of gait, in some cases, can cause musculoskeletal disorders or other health problems; in addition, also from antiquity, anthropometry has been important for the design of human items such as workspaces, tools, garments, among others. Nowadays, thanks to the development of optics and electronics, more accurate studies of gait and anthropometry can be developed. This work will describe the most important parameters for gait analysis, anthropometry and the optical systems used.

A MATLAB-based graphical user interface for the identification of muscular activations from surface electromyography signals.

PubMed

Mengarelli, Alessandro; Cardarelli, Stefano; Verdini, Federica; Burattini, Laura; Fioretti, Sandro; Di Nardo, Francesco

2016-08-01

In this paper a graphical user interface (GUI) built in MATLAB® environment is presented. This interactive tool has been developed for the analysis of superficial electromyography (sEMG) signals and in particular for the assessment of the muscle activation time intervals. After the signal import, the tool performs a first analysis in a totally user independent way, providing a reliable computation of the muscular activation sequences. Furthermore, the user has the opportunity to modify each parameter of the on/off identification algorithm implemented in the presented tool. The presence of an user-friendly GUI allows the immediate evaluation of the effects that the modification of every single parameter has on the activation intervals recognition, through the real-time updating and visualization of the muscular activation/deactivation sequences. The possibility to accept the initial signal analysis or to modify the on/off identification with respect to each considered signal, with a real-time visual feedback, makes this GUI-based tool a valuable instrument in clinical, research applications and also in an educational perspective.

Game-theoretic analysis of dynamic traffic equilibria.

DOT National Transportation Integrated Search

2014-03-01

Dynamic traffic assignment has grown steadily in popularity and use since its inception. It has become an : important and permanent tool in transportation agencies across the country. However, the exact nature of : dynamic traffic equilibrium, includ...

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.

PubMed

Johnson, Benjamin K; Scholz, Matthew B; Teal, Tracy K; Abramovitch, Robert B

2016-02-04

Many tools exist in the analysis of bacterial RNA sequencing (RNA-seq) transcriptional profiling experiments to identify differentially expressed genes between experimental conditions. Generally, the workflow includes quality control of reads, mapping to a reference, counting transcript abundance, and statistical tests for differentially expressed genes. In spite of the numerous tools developed for each component of an RNA-seq analysis workflow, easy-to-use bacterially oriented workflow applications to combine multiple tools and automate the process are lacking. With many tools to choose from for each step, the task of identifying a specific tool, adapting the input/output options to the specific use-case, and integrating the tools into a coherent analysis pipeline is not a trivial endeavor, particularly for microbiologists with limited bioinformatics experience. To make bacterial RNA-seq data analysis more accessible, we developed a Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis (SPARTA). SPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. The easy-to-install, complete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping reads to a reference, counting gene features, calculating differential gene expression, and, importantly, checking for potential batch effects within the data set. SPARTA outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots. SPARTA provides an easy-to-use bacterial RNA-seq transcriptional profiling workflow to identify differentially expressed genes between experimental conditions. This software will enable microbiologists with limited bioinformatics experience to analyze their data and integrate next generation sequencing (NGS) technologies into the classroom. The SPARTA software and tutorial are available at sparta.readthedocs.org.

Pre-Service Science Teachers' Construction and Interpretation of Graphs

ERIC Educational Resources Information Center

Ergül, N. Remziye

2018-01-01

Data and graphic analysis and interpretation are important parts of science process skills and science curriculum. So it refers to visual display of data using relevant graphical representations. One of the tools used in science courses is graphics for explain the relationship among each of the concepts and therefore it is important to know data…

Bimolecular dynamics by computer analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eilbeck, J.C.; Lomdahl, P.S.; Scott, A.C.

1984-01-01

As numerical tools (computers and display equipment) become more powerful and the atomic structures of important biological molecules become known, the importance of detailed computation of nonequilibrium biomolecular dynamics increases. In this manuscript we report results from a well developed study of the hydrogen bonded polypeptide crystal acetanilide, a model protein. Directions for future research are suggested. 9 references, 6 figures.

Open access for ALICE analysis based on virtualization technology

NASA Astrophysics Data System (ADS)

Buncic, P.; Gheata, M.; Schutz, Y.

2015-12-01

Open access is one of the important leverages for long-term data preservation for a HEP experiment. To guarantee the usability of data analysis tools beyond the experiment lifetime it is crucial that third party users from the scientific community have access to the data and associated software. The ALICE Collaboration has developed a layer of lightweight components built on top of virtualization technology to hide the complexity and details of the experiment-specific software. Users can perform basic analysis tasks within CernVM, a lightweight generic virtual machine, paired with an ALICE specific contextualization. Once the virtual machine is launched, a graphical user interface is automatically started without any additional configuration. This interface allows downloading the base ALICE analysis software and running a set of ALICE analysis modules. Currently the available tools include fully documented tutorials for ALICE analysis, such as the measurement of strange particle production or the nuclear modification factor in Pb-Pb collisions. The interface can be easily extended to include an arbitrary number of additional analysis modules. We present the current status of the tools used by ALICE through the CERN open access portal, and the plans for future extensions of this system.

Next Generation Electromagnetic Pump Analysis Tools (PLM DOC-0005-2188). Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stregy, Seth; Dasilva, Ana; Yilmaz, Serkan

2015-10-29

This report provides the broad historical review of EM Pump development and details of MATRIX development under this project. This report summarizes the efforts made to modernize the legacy performance models used in previous EM Pump designs and the improvements made to the analysis tools. This report provides information on Tasks 1, 3, and 4 of the entire project. The research for Task 4 builds upon Task 1: Update EM Pump Databank and Task 3: Modernize the Existing EM Pump Analysis Model, which are summarized within this report. Where research for Task 2: Insulation Materials Development and Evaluation identified parametersmore » applicable to the analysis model with Task 4, the analysis code was updated, and analyses were made for additional materials. The important design variables for the manufacture and operation of an EM Pump that the model improvement can evaluate are: space constraints; voltage capability of insulation system; maximum flux density through iron; flow rate and outlet pressure; efficiency and manufacturability. The development of the next-generation EM Pump analysis tools during this two-year program provides information in three broad areas: Status of analysis model development; Improvements made to older simulations; and Comparison to experimental data.« less

quantGenius: implementation of a decision support system for qPCR-based gene quantification.

PubMed

Baebler, Špela; Svalina, Miha; Petek, Marko; Stare, Katja; Rotter, Ana; Pompe-Novak, Maruša; Gruden, Kristina

2017-05-25

Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. We have developed "quantGenius" ( http://quantgenius.nib.si ), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry-independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases. To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation.

Leveraging Data Analysis for Domain Experts: An Embeddable Framework for Basic Data Science Tasks

ERIC Educational Resources Information Center

Lohrer, Johannes-Y.; Kaltenthaler, Daniel; Kröger, Peer

2016-01-01

In this paper, we describe a framework for data analysis that can be embedded into a base application. Since it is important to analyze the data directly inside the application where the data is entered, a tool that allows the scientists to easily work with their data, supports and motivates the execution of further analysis of their data, which…

The Geomorphic Road Analysis and Inventory Package (GRAIP) Volume 1: Data Collection Method

Treesearch

Thomas A. Black; Richard M. Cissel; Charles H. Luce

2012-01-01

An important first step in managing forest roads for improved water quality and aquatic habitat is the performance of an inventory. The Geomorphic Roads Analysis and Inventory Package (GRAIP) was developed as a tool for making a comprehensive inventory and analysis of the effects of forest roads on watersheds. This manual describes the data collection and process of a...

GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

PubMed

Subhash, Santhilal; Kanduri, Chandrasekhar

2016-09-13

High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc. In this study, we focused on designing a command-line tool called GeneSCF (Gene Set Clustering based on Functional annotations), that can predict the functionally relevant biological information for a set of genes in a real-time updated manner. It is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology. We successfully employed our tool on two of published datasets to predict the biologically relevant functional information. The core features of this tool were tested on Linux machines without the need for installation of more dependencies. GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.

Three-dimensional murine airway segmentation in micro-CT images

NASA Astrophysics Data System (ADS)

Shi, Lijun; Thiesse, Jacqueline; McLennan, Geoffrey; Hoffman, Eric A.; Reinhardt, Joseph M.

2007-03-01

Thoracic imaging for small animals has emerged as an important tool for monitoring pulmonary disease progression and therapy response in genetically engineered animals. Micro-CT is becoming the standard thoracic imaging modality in small animal imaging because it can produce high-resolution images of the lung parenchyma, vasculature, and airways. Segmentation, measurement, and visualization of the airway tree is an important step in pulmonary image analysis. However, manual analysis of the airway tree in micro-CT images can be extremely time-consuming since a typical dataset is usually on the order of several gigabytes in size. Automated and semi-automated tools for micro-CT airway analysis are desirable. In this paper, we propose an automatic airway segmentation method for in vivo micro-CT images of the murine lung and validate our method by comparing the automatic results to manual tracing. Our method is based primarily on grayscale morphology. The results show good visual matches between manually segmented and automatically segmented trees. The average true positive volume fraction compared to manual analysis is 91.61%. The overall runtime for the automatic method is on the order of 30 minutes per volume compared to several hours to a few days for manual analysis.

Pattern Recognition for a Flight Dynamics Monte Carlo Simulation

NASA Technical Reports Server (NTRS)

Restrepo, Carolina; Hurtado, John E.

2011-01-01

The design, analysis, and verification and validation of a spacecraft relies heavily on Monte Carlo simulations. Modern computational techniques are able to generate large amounts of Monte Carlo data but flight dynamics engineers lack the time and resources to analyze it all. The growing amounts of data combined with the diminished available time of engineers motivates the need to automate the analysis process. Pattern recognition algorithms are an innovative way of analyzing flight dynamics data efficiently. They can search large data sets for specific patterns and highlight critical variables so analysts can focus their analysis efforts. This work combines a few tractable pattern recognition algorithms with basic flight dynamics concepts to build a practical analysis tool for Monte Carlo simulations. Current results show that this tool can quickly and automatically identify individual design parameters, and most importantly, specific combinations of parameters that should be avoided in order to prevent specific system failures. The current version uses a kernel density estimation algorithm and a sequential feature selection algorithm combined with a k-nearest neighbor classifier to find and rank important design parameters. This provides an increased level of confidence in the analysis and saves a significant amount of time.

Tools for Communication: Novel infrastructure to address patient-perceived gaps in oncology care
.

PubMed

McMullen, Suzanne; Szabo, Shelagh; Halbert, Ronald J; Lai, Catherine; Parikh, Aparna; Bunce, Mikele; Khoury, Raya; Small, Art; Masaquel, Anthony

2017-04-01

Healthcare providers (HCPs) and patient communication are integral to high-quality oncology care. The patient and HCP perspectives are needed to identify gaps in care and develop communication tools.
. This study aimed to understand patient- and HCP-perceived elements of and gaps in high-quality care to develop novel communication tools to improve care. 
. Qualitative interviews were conducted among 16 patients with cancer and 10 HCPs in the United States. Trained interviewers elicited patients' and HCPs' concerns, views, and perceived needs for communication tools. A thematic analysis was used to identify four quality of care domains, depicted in a conceptual model, and two draft communication tools were developed to address identified gaps.
. No patients reported previously using a communication tool, and gaps in communication regarding treatment aims and education were evident. Two tools were developed to assess patients' life and treatment goals and the importance of ongoing education.

A reliability analysis tool for SpaceWire network

NASA Astrophysics Data System (ADS)

Zhou, Qiang; Zhu, Longjiang; Fei, Haidong; Wang, Xingyou

2017-04-01

A SpaceWire is a standard for on-board satellite networks as the basis for future data-handling architectures. It is becoming more and more popular in space applications due to its technical advantages, including reliability, low power and fault protection, etc. High reliability is the vital issue for spacecraft. Therefore, it is very important to analyze and improve the reliability performance of the SpaceWire network. This paper deals with the problem of reliability modeling and analysis with SpaceWire network. According to the function division of distributed network, a reliability analysis method based on a task is proposed, the reliability analysis of every task can lead to the system reliability matrix, the reliability result of the network system can be deduced by integrating these entire reliability indexes in the matrix. With the method, we develop a reliability analysis tool for SpaceWire Network based on VC, where the computation schemes for reliability matrix and the multi-path-task reliability are also implemented. By using this tool, we analyze several cases on typical architectures. And the analytic results indicate that redundancy architecture has better reliability performance than basic one. In practical, the dual redundancy scheme has been adopted for some key unit, to improve the reliability index of the system or task. Finally, this reliability analysis tool will has a directive influence on both task division and topology selection in the phase of SpaceWire network system design.

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

PubMed Central

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA) – a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously – has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA. PMID:25541687

Network meta-analysis using R: a review of currently available automated packages.

PubMed

Neupane, Binod; Richer, Danielle; Bonner, Ashley Joel; Kibret, Taddele; Beyene, Joseph

2014-01-01

Network meta-analysis (NMA)--a statistical technique that allows comparison of multiple treatments in the same meta-analysis simultaneously--has become increasingly popular in the medical literature in recent years. The statistical methodology underpinning this technique and software tools for implementing the methods are evolving. Both commercial and freely available statistical software packages have been developed to facilitate the statistical computations using NMA with varying degrees of functionality and ease of use. This paper aims to introduce the reader to three R packages, namely, gemtc, pcnetmeta, and netmeta, which are freely available software tools implemented in R. Each automates the process of performing NMA so that users can perform the analysis with minimal computational effort. We present, compare and contrast the availability and functionality of different important features of NMA in these three packages so that clinical investigators and researchers can determine which R packages to implement depending on their analysis needs. Four summary tables detailing (i) data input and network plotting, (ii) modeling options, (iii) assumption checking and diagnostic testing, and (iv) inference and reporting tools, are provided, along with an analysis of a previously published dataset to illustrate the outputs available from each package. We demonstrate that each of the three packages provides a useful set of tools, and combined provide users with nearly all functionality that might be desired when conducting a NMA.

Scientists' sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support.

PubMed

Mirel, Barbara; Görg, Carsten

2014-04-26

A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists' analytical workflows and their implications for tool design.

Scientists’ sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support

PubMed Central

2014-01-01

A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists’ analytical workflows and their implications for tool design. PMID:24766796

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.

PubMed

Hackenberg, Michael; Sturm, Martin; Langenberger, David; Falcón-Pérez, Juan Manuel; Aransay, Ana M

2009-07-01

Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we developed miRanalyzer, a web server tool for the analysis of deep-sequencing experiments for small RNAs. The web server tool requires a simple input file containing a list of unique reads and its copy numbers (expression levels). Using these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds all perfect matches against other libraries of transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially important point as there are many species with very few known microRNAs. Therefore, we implemented a highly accurate machine learning algorithm for the prediction of new microRNAs that reaches AUC values of 97.9% and recall values of up to 75% on unseen data. The web tool summarizes all the described steps in a single output page, which provides a comprehensive overview of the analysis, adding links to more detailed output pages for each analysis module. miRanalyzer is available at http://web.bioinformatics.cicbiogune.es/microRNA/.

The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools

PubMed Central

Postel, Alexander; Schmeiser, Stefanie; Zimmermann, Bernd; Becher, Paul

2016-01-01

Molecular epidemiology has become an indispensable tool in the diagnosis of diseases and in tracing the infection routes of pathogens. Due to advances in conventional sequencing and the development of high throughput technologies, the field of sequence determination is in the process of being revolutionized. Platforms for sharing sequence information and providing standardized tools for phylogenetic analyses are becoming increasingly important. The database (DB) of the European Union (EU) and World Organisation for Animal Health (OIE) Reference Laboratory for classical swine fever offers one of the world’s largest semi-public virus-specific sequence collections combined with a module for phylogenetic analysis. The classical swine fever (CSF) DB (CSF-DB) became a valuable tool for supporting diagnosis and epidemiological investigations of this highly contagious disease in pigs with high socio-economic impacts worldwide. The DB has been re-designed and now allows for the storage and analysis of traditionally used, well established genomic regions and of larger genomic regions including complete viral genomes. We present an application example for the analysis of highly similar viral sequences obtained in an endemic disease situation and introduce the new geographic “CSF Maps” tool. The concept of this standardized and easy-to-use DB with an integrated genetic typing module is suited to serve as a blueprint for similar platforms for other human or animal viruses. PMID:27827988

The Design and Analysis of Electrically Large Custom-Shaped Reflector Antennas

DTIC Science & Technology

2013-06-01

GEO) satellite data are imported into STK and plotted to visualize the regions of the sky that the spherical reflector must have line of sight for...Magnetic Conductor PO Physical Optics STK Systems Tool Kit TE Transverse Electric xvii Acronym Definition TLE Two Line Element TM Transverse Magnetic...study for the spherical reflector, Systems Tool Kit ( STK ) software from Analytical Graphics Inc. (AGI) is used. In completing the cross-shaped

The ethics of social media in dental practice: ethical tools and professional responses.

PubMed

Peltier, Bruce; Curley, Arthur

2013-07-01

This article considers several important trends in dental practice that result from innovations in digital and social media. It provides ethical tools for analysis, Illuminates areas of ethical concern in the current practice environment and offers recommendations for future practice. A summary in the form of a checklist is posted at the end of this essay for dentists considering the use of social media in their practice.

A bicycle network analysis tool for planning applications in small communities.

DOT National Transportation Integrated Search

2015-05-01

Non-motorized transportation modes such as bicycles constitute an important part of a : communitys transportation system; they are vital to the success of transit-oriented developments : (TODs). However, bicycles were often ignored in transportati...

Understanding Least Squares through Monte Carlo Calculations

ERIC Educational Resources Information Center

Tellinghuisen, Joel

2005-01-01

The method of least squares (LS) is considered as an important data analysis tool available to physical scientists. The mathematics of linear least squares(LLS) is summarized in a very compact matrix rotation that renders it practically "formulaic".

Sandia National Laboratories analysis code data base

NASA Astrophysics Data System (ADS)

Peterson, C. W.

1994-11-01

Sandia National Laboratories' mission is to solve important problems in the areas of national defense, energy security, environmental integrity, and industrial technology. The laboratories' strategy for accomplishing this mission is to conduct research to provide an understanding of the important physical phenomena underlying any problem, and then to construct validated computational models of the phenomena which can be used as tools to solve the problem. In the course of implementing this strategy, Sandia's technical staff has produced a wide variety of numerical problem-solving tools which they use regularly in the design, analysis, performance prediction, and optimization of Sandia components, systems, and manufacturing processes. This report provides the relevant technical and accessibility data on the numerical codes used at Sandia, including information on the technical competency or capability area that each code addresses, code 'ownership' and release status, and references describing the physical models and numerical implementation.

Quality and Efficiency Improvement Tools for Every Radiologist.

PubMed

Kudla, Alexei U; Brook, Olga R

2018-06-01

In an era of value-based medicine, data-driven quality improvement is more important than ever to ensure safe and efficient imaging services. Familiarity with high-value tools enables all radiologists to successfully engage in quality and efficiency improvement. In this article, we review the model for improvement, strategies for measurement, and common practical tools with real-life examples that include Run chart, Control chart (Shewhart chart), Fishbone (Cause-and-Effect or Ishikawa) diagram, Pareto chart, 5 Whys, and Root Cause Analysis. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

PubMed Central

2017-01-01

Abstract Motifs of only 1–4 letters can play important roles when present at key locations within macromolecules. Because existing motif-discovery tools typically miss these position-specific short motifs, we developed kpLogo, a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs from a set of aligned sequences. kpLogo also overcomes the limitations of conventional motif-visualization tools in handling positional interdependencies and utilizing ranked or weighted sequences increasingly available from high-throughput assays. kpLogo can be found at http://kplogo.wi.mit.edu/. PMID:28460012

Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|Speedshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Barton

2014-06-30

Peta-scale computing environments pose significant challenges for both system and application developers and addressing them required more than simply scaling up existing tera-scale solutions. Performance analysis tools play an important role in gaining this understanding, but previous monolithic tools with fixed feature sets have not sufficed. Instead, this project worked on the design, implementation, and evaluation of a general, flexible tool infrastructure supporting the construction of performance tools as “pipelines” of high-quality tool building blocks. These tool building blocks provide common performance tool functionality, and are designed for scalability, lightweight data acquisition and analysis, and interoperability. For this project, wemore » built on Open|SpeedShop, a modular and extensible open source performance analysis tool set. The design and implementation of such a general and reusable infrastructure targeted for petascale systems required us to address several challenging research issues. All components needed to be designed for scale, a task made more difficult by the need to provide general modules. The infrastructure needed to support online data aggregation to cope with the large amounts of performance and debugging data. We needed to be able to map any combination of tool components to each target architecture. And we needed to design interoperable tool APIs and workflows that were concrete enough to support the required functionality, yet provide the necessary flexibility to address a wide range of tools. A major result of this project is the ability to use this scalable infrastructure to quickly create tools that match with a machine architecture and a performance problem that needs to be understood. Another benefit is the ability for application engineers to use the highly scalable, interoperable version of Open|SpeedShop, which are reassembled from the tool building blocks into a flexible, multi-user interface set of tools. This set of tools targeted at Office of Science Leadership Class computer systems and selected Office of Science application codes. We describe the contributions made by the team at the University of Wisconsin. The project built on the efforts in Open|SpeedShop funded by DOE/NNSA and the DOE/NNSA Tri-Lab community, extended Open|Speedshop to the Office of Science Leadership Class Computing Facilities, and addressed new challenges found on these cutting edge systems. Work done under this project at Wisconsin can be divided into two categories, new algorithms and techniques for debugging, and foundation infrastructure work on our Dyninst binary analysis and instrumentation toolkits and MRNet scalability infrastructure.« less

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

PubMed Central

Nichio, Bruno T. L.; Marchaukoski, Jeroniza Nunes; Raittz, Roberto Tadeu

2017-01-01

Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST “all-against-all” methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing time); and proteinOrtho (developed for dealing with large amounts of biological data). We made a comparison among the main features of four tool and tested them using four for prokaryotic genomas. We hope that our review can be useful for researchers and will help them in selecting the most appropriate tool for their work in the field of orthology. PMID:29163633

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives.

PubMed

Nichio, Bruno T L; Marchaukoski, Jeroniza Nunes; Raittz, Roberto Tadeu

2017-01-01

Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST "all-against-all" methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing time); and proteinOrtho (developed for dealing with large amounts of biological data). We made a comparison among the main features of four tool and tested them using four for prokaryotic genomas. We hope that our review can be useful for researchers and will help them in selecting the most appropriate tool for their work in the field of orthology.

Scalability Analysis of Gleipnir: A Memory Tracing and Profiling Tool, on Titan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janjusic, Tommy; Kartsaklis, Christos; Wang, Dali

2013-01-01

Application performance is hindered by a variety of factors but most notably driven by the well know CPU-memory speed gap (also known as the memory wall). Understanding application s memory behavior is key if we are trying to optimize performance. Understanding application performance properties is facilitated with various performance profiling tools. The scope of profiling tools varies in complexity, ease of deployment, profiling performance, and the detail of profiled information. Specifically, using profiling tools for performance analysis is a common task when optimizing and understanding scientific applications on complex and large scale systems such as Cray s XK7. This papermore » describes the performance characteristics of using Gleipnir, a memory tracing tool, on the Titan Cray XK7 system when instrumenting large applications such as the Community Earth System Model. Gleipnir is a memory tracing tool built as a plug-in tool for the Valgrind instrumentation framework. The goal of Gleipnir is to provide fine-grained trace information. The generated traces are a stream of executed memory transactions mapped to internal structures per process, thread, function, and finally the data structure or variable. Our focus was to expose tool performance characteristics when using Gleipnir with a combination of an external tools such as a cache simulator, Gl CSim, to characterize the tool s overall performance. In this paper we describe our experience with deploying Gleipnir on the Titan Cray XK7 system, report on the tool s ease-of-use, and analyze run-time performance characteristics under various workloads. While all performance aspects are important we mainly focus on I/O characteristics analysis due to the emphasis on the tools output which are trace-files. Moreover, the tool is dependent on the run-time system to provide the necessary infrastructure to expose low level system detail; therefore, we also discuss any theoretical benefits that can be achieved if such modules were present.« less

Prioritizing the mHealth Design Space: A Mixed-Methods Analysis of Smokers’ Perspectives

PubMed Central

BlueSpruce, June; Catz, Sheryl L; McClure, Jennifer B

2016-01-01

Background Smoking remains the leading cause of preventable disease and death in the United States. Therefore, researchers are constantly exploring new ways to promote smoking cessation. Mobile health (mHealth) technologies could be effective cessation tools. Despite the availability of commercial quit-smoking apps, little research to date has examined smokers’ preferred treatment intervention components (ie, design features). Honoring these preferences is important for designing programs that are appealing to smokers and may be more likely to be adopted and used. Objective The aim of this study was to understand smokers’ preferred design features of mHealth quit-smoking tools. Methods We used a mixed-methods approach consisting of focus groups and written surveys to understand the design preferences of adult smokers who were interested in quitting smoking (N=40). Focus groups were stratified by age to allow differing perspectives to emerge between older (>40 years) and younger (<40 years) participants. Focus group discussion included a “blue-sky” brainstorming exercise followed by participant reactions to contrasting design options for communicating with smokers, providing social support, and incentivizing program use. Participants rated the importance of preselected design features on an exit survey. Qualitative analyses examined emergent discussion themes and quantitative analyses compared feature ratings to determine which were perceived as most important. Results Participants preferred a highly personalized and adaptive mHealth experience. Their ideal mHealth quit-smoking tool would allow personalized tracking of their progress, adaptively tailored feedback, and real-time peer support to help manage smoking cravings. Based on qualitative analysis of focus group discussion, participants preferred pull messages (ie, delivered upon request) over push messages (ie, sent automatically) and preferred interaction with other smokers through closed social networks. Preferences for entertaining games or other rewarding incentives to encourage program use differed by age group. Based on quantitative analysis of surveys, participants rated the importance of select design features significantly differently (P<.001). Design features rated as most important included personalized content, the ability to track one’s progress, and features designed to help manage nicotine withdrawal and medication side effects. Design features rated least important were quit-smoking videos and posting on social media. Communicating with stop-smoking experts was rated more important than communicating with family and friends about quitting (P=.03). Perceived importance of various design features varied by age, experience with technology, and frequency of smoking. Conclusions Future mHealth cessation aids should be designed with an understanding of smokers’ needs and preferences for these tools. Doing so does not guarantee treatment effectiveness, but balancing user preferences with best-practice treatment considerations could enhance program adoption and improve treatment outcomes. Grounded in the perspectives of smokers, we identify several design considerations, which should be prioritized when designing future mHealth cessation tools and which warrant additional empirical validation. PMID:27496593

Handheld tools that 'Informate' Assessment of Student Learning in Science: A Requirements Analysis

ERIC Educational Resources Information Center

Roschelle, Jeremy; Penuel, William R.; Yarnall, Louise; Shechtman, Nicole; Tatar, Deborah

2005-01-01

An important challenge faced by many teachers as they involve students in science investigations is measuring (assessing) students' progress. Our detailed requirements analysis in a particular school district led to the idea that what teachers need most are ways to increase the quality of the information they have about what students know and can…

Tool development to assess the work related neck and upper limb musculoskeletal disorders among female garment workers in Sri-Lanka.

PubMed

Amarasinghe, Nirmalie Champika; De AlwisSenevirathne, Rohini

2016-10-17

Musculoskeletal disorders (MSDs) have been identified as a predisposing factor for lesser productivity, but no validated tool has been developed to assess them in the Sri- Lankan context. To develop a validated tool to assess the neck and upper limb MSDs. It comprises three components: item selections, item reduction using principal component analysis, and validation. A tentative self-administrated questionnaire was developed, translated, and pre-tested. Four important domains - neck, shoulder, elbow and wrist - were identified through principal component analysis. Prevalence of any MSDs was 38.1% and prevalence of neck, shoulder, elbow and wrist MSDs are 12.85%, 13.71%, 12%, 13.71% respectively. Content and criterion validity of the tool was assessed. Separate ROC curves were produced and sensitivity and specificity of neck (83.1%, 71.7%), shoulder (97.6%, 91.9%), elbow (98.2%, 87.2%), and wrist (97.6%, 94.9%) was determined. Cronbach's Alpha and correlation coefficient was above 0.7. The tool has high sensitivity, specificity, internal consistency, and test re-test reliability.

Structural Model Tuning Capability in an Object-Oriented Multidisciplinary Design, Analysis, and Optimization Tool

NASA Technical Reports Server (NTRS)

Lung, Shun-fat; Pak, Chan-gi

2008-01-01

Updating the finite element model using measured data is a challenging problem in the area of structural dynamics. The model updating process requires not only satisfactory correlations between analytical and experimental results, but also the retention of dynamic properties of structures. Accurate rigid body dynamics are important for flight control system design and aeroelastic trim analysis. Minimizing the difference between analytical and experimental results is a type of optimization problem. In this research, a multidisciplinary design, analysis, and optimization (MDAO) tool is introduced to optimize the objective function and constraints such that the mass properties, the natural frequencies, and the mode shapes are matched to the target data as well as the mass matrix being orthogonalized.

Structural Model Tuning Capability in an Object-Oriented Multidisciplinary Design, Analysis, and Optimization Tool

NASA Technical Reports Server (NTRS)

Lung, Shun-fat; Pak, Chan-gi

2008-01-01

Updating the finite element model using measured data is a challenging problem in the area of structural dynamics. The model updating process requires not only satisfactory correlations between analytical and experimental results, but also the retention of dynamic properties of structures. Accurate rigid body dynamics are important for flight control system design and aeroelastic trim analysis. Minimizing the difference between analytical and experimental results is a type of optimization problem. In this research, a multidisciplinary design, analysis, and optimization [MDAO] tool is introduced to optimize the objective function and constraints such that the mass properties, the natural frequencies, and the mode shapes are matched to the target data as well as the mass matrix being orthogonalized.

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

PubMed

Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schütte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid

2012-08-15

Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future. The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html

Finite-element analysis of NiTi wire deflection during orthodontic levelling treatment

NASA Astrophysics Data System (ADS)

Razali, M. F.; Mahmud, A. S.; Mokhtar, N.; Abdullah, J.

2016-02-01

Finite-element analysis is an important product development tool in medical devices industry for design and failure analysis of devices. This tool helps device designers to quickly explore various design options, optimizing specific designs and providing a deeper insight how a device is actually performing. In this study, three-dimensional finite-element models of superelastic nickel-titanium arch wire engaged in a three brackets system were developed. The aim was to measure the effect of binding friction developed on wire-bracket interaction towards the remaining recovery force available for tooth movement. Uniaxial and three brackets bending test were modelled and validated against experimental works. The prediction made by the three brackets bending models shows good agreement with the experimental results.

Impact of Machine-Translated Text on Entity and Relationship Extraction

DTIC Science & Technology

2014-12-01

20 1 1. Introduction Using social network analysis tools is an important asset in...semantic modeling software to automatically build detailed network models from unstructured text. Contour imports unstructured text and then maps the text...onto an existing ontology of frames at the sentence level, using FrameNet, a structured language model, and through Semantic Role Labeling ( SRL

The development of plant food processing in the Levant: insights from use-wear analysis of Early Epipalaeolithic ground stone tools

PubMed Central

Dubreuil, Laure; Nadel, Dani

2015-01-01

In recent years, the study of percussive, pounding and grinding tools has provided new insights into human evolution, more particularly regarding the development of technology enabling the processing and exploitation of plant resources. Some of these studies focus on early evidence for flour production, an activity frequently perceived as an important step in the evolution of plant exploitation. The present paper investigates plant food preparation in mobile hunter-gatherer societies from the Southern Levant. The analysis consists of a use-wear study of 18 tools recovered from Ohalo II, a 23 000-year-old site in Israel showing an exceptional level of preservation. Our sample includes a slab previously interpreted as a lower implement used for producing flour, based on the presence of cereal starch residues. The use-wear data we have obtained provide crucial information about the function of this and other percussive tools at Ohalo II, as well as on investment in tool manufacture, discard strategies and evidence for plant processing in the Late Pleistocene. The use-wear analysis indicates that the production of flour was a sporadic activity at Ohalo II, predating by thousands of years the onset of routine processing of plant foods. PMID:26483535

The development of plant food processing in the Levant: insights from use-wear analysis of Early Epipalaeolithic ground stone tools.

PubMed

Dubreuil, Laure; Nadel, Dani

2015-11-19

In recent years, the study of percussive, pounding and grinding tools has provided new insights into human evolution, more particularly regarding the development of technology enabling the processing and exploitation of plant resources. Some of these studies focus on early evidence for flour production, an activity frequently perceived as an important step in the evolution of plant exploitation. The present paper investigates plant food preparation in mobile hunter-gatherer societies from the Southern Levant. The analysis consists of a use-wear study of 18 tools recovered from Ohalo II, a 23 000-year-old site in Israel showing an exceptional level of preservation. Our sample includes a slab previously interpreted as a lower implement used for producing flour, based on the presence of cereal starch residues. The use-wear data we have obtained provide crucial information about the function of this and other percussive tools at Ohalo II, as well as on investment in tool manufacture, discard strategies and evidence for plant processing in the Late Pleistocene. The use-wear analysis indicates that the production of flour was a sporadic activity at Ohalo II, predating by thousands of years the onset of routine processing of plant foods. © 2015 The Author(s).

Human performance cognitive-behavioral modeling: a benefit for occupational safety.

PubMed

Gore, Brian F

2002-01-01

Human Performance Modeling (HPM) is a computer-aided job analysis software methodology used to generate predictions of complex human-automation integration and system flow patterns with the goal of improving operator and system safety. The use of HPM tools has recently been increasing due to reductions in computational cost, augmentations in the tools' fidelity, and usefulness in the generated output. An examination of an Air Man-machine Integration Design and Analysis System (Air MIDAS) model evaluating complex human-automation integration currently underway at NASA Ames Research Center will highlight the importance to occupational safety of considering both cognitive and physical aspects of performance when researching human error.

Multiple heteroatom substitution to graphene nanoribbon

PubMed Central

Meyer, Ernst

2018-01-01

Substituting heteroatoms into nanostructured graphene elements, such as graphene nanoribbons, offers the possibility for atomic engineering of electronic properties. To characterize these substitutions, functionalized atomic force microscopy (AFM)—a tool to directly resolve chemical structures—is one of the most promising tools, yet the chemical analysis of heteroatoms has been rarely performed. We synthesized multiple heteroatom-substituted graphene nanoribbons and showed that AFM can directly resolve elemental differences and can be correlated to the van der Waals radii, as well as the modulated local electron density caused by the substitution. This elemental-sensitive measurement takes an important step in the analysis of functionalized two-dimensional carbon materials. PMID:29662955

Dynamic Analysis of Darrieus Vertical Axis Wind Turbine Rotors

NASA Technical Reports Server (NTRS)

Lobitz, D. W.

1981-01-01

The dynamic response characteristics of the vertical axis wind turbine (VAWT) rotor are important factors governing the safety and fatigue life of VAWT systems. The principal problems are the determination of critical rotor speeds (resonances) and the assessment of forced vibration response amplitudes. The solution to these problems is complicated by centrifugal and Coriolis effects which can have substantial influence on rotor resonant frequencies and mode shapes. The primary tools now in use for rotor analysis are described and discussed. These tools include a lumped spring mass model (VAWTDYN) and also finite-element based approaches. The accuracy and completeness of current capabilities are also discussed.

HRLSim: a high performance spiking neural network simulator for GPGPU clusters.

PubMed

Minkovich, Kirill; Thibeault, Corey M; O'Brien, Michael John; Nogin, Aleksey; Cho, Youngkwan; Srinivasa, Narayan

2014-02-01

Modeling of large-scale spiking neural models is an important tool in the quest to understand brain function and subsequently create real-world applications. This paper describes a spiking neural network simulator environment called HRL Spiking Simulator (HRLSim). This simulator is suitable for implementation on a cluster of general purpose graphical processing units (GPGPUs). Novel aspects of HRLSim are described and an analysis of its performance is provided for various configurations of the cluster. With the advent of inexpensive GPGPU cards and compute power, HRLSim offers an affordable and scalable tool for design, real-time simulation, and analysis of large-scale spiking neural networks.

Human performance cognitive-behavioral modeling: a benefit for occupational safety

NASA Technical Reports Server (NTRS)

Gore, Brian F.

2002-01-01

Human Performance Modeling (HPM) is a computer-aided job analysis software methodology used to generate predictions of complex human-automation integration and system flow patterns with the goal of improving operator and system safety. The use of HPM tools has recently been increasing due to reductions in computational cost, augmentations in the tools' fidelity, and usefulness in the generated output. An examination of an Air Man-machine Integration Design and Analysis System (Air MIDAS) model evaluating complex human-automation integration currently underway at NASA Ames Research Center will highlight the importance to occupational safety of considering both cognitive and physical aspects of performance when researching human error.

The Gender Analysis Tools Applied in Natural Disasters Management: A Systematic Literature Review

PubMed Central

Sohrabizadeh, Sanaz; Tourani, Sogand; Khankeh, Hamid Reza

2014-01-01

Background: Although natural disasters have caused considerable damages around the world, and gender analysis can improve community disaster preparedness or mitigation, there is little research about the gendered analytical tools and methods in communities exposed to natural disasters and hazards. These tools evaluate gender vulnerability and capacity in pre-disaster and post-disaster phases of the disaster management cycle. Objectives: Identifying the analytical gender tools and the strengths and limitations of them as well as determining gender analysis studies which had emphasized on the importance of using gender analysis in disasters. Methods: The literature search was conducted in June 2013 using PubMed, Web of Sciences, ProQuest Research Library, World Health Organization Library, Gender and Disaster Network (GDN) archive. All articles, guidelines, fact sheets and other materials that provided an analytical framework for a gender analysis approach in disasters were included and the non-English documents as well as gender studies of non-disasters area were excluded. Analysis of the included studies was done separately by descriptive and thematic analyses. Results: A total of 207 documents were retrieved, of which only nine references were included. Of these, 45% were in form of checklist, 33% case study report, and the remaining 22% were article. All selected papers were published within the period 1994-2012. Conclusions: A focus on women’s vulnerability in the related research and the lack of valid and reliable gender analysis tools were considerable issues identified by the literature review. Although non-English literatures with English abstract were included in the study, the possible exclusion of non-English ones was found as the limitation of this study. PMID:24678441

GIDEP Batching Tool

NASA Technical Reports Server (NTRS)

Fong, Danny; Odell,Dorice; Barry, Peter; Abrahamian, Tomik

2008-01-01

This software provides internal, automated search mechanics of GIDEP (Government- Industry Data Exchange Program) Alert data imported from the GIDEP government Web site. The batching tool allows the import of a single parts list in tab-delimited text format into the local JPL GIDEP database. Delimiters from every part number are removed. The original part numbers with delimiters are compared, as well as the newly generated list without the delimiters. The two lists run against the GIDEP imports, and output any matches. This feature only works with Netscape 2.0 or greater, or Internet Explorer 4.0 or greater. The user selects the browser button to choose a text file to import. When the submit button is pressed, this script will import alerts from the text file into the local JPL GIDEP database. This batch tool provides complete in-house control over exported material and data for automated batch match abilities. The batching tool has the ability to match capabilities of the parts list to tables, and yields results that aid further research and analysis. This provides more control over GIDEP information for metrics and reports information not provided by the government site. This software yields results quickly and gives more control over external data from the government site in order to generate other reports not available from the external source. There is enough space to store years of data. The program relates to risk identification and management with regard to projects and GIDEP alert information encompassing flight parts for space exploration.

gHRV: Heart rate variability analysis made easy.

PubMed

Rodríguez-Liñares, L; Lado, M J; Vila, X A; Méndez, A J; Cuesta, P

2014-08-01

In this paper, the gHRV software tool is presented. It is a simple, free and portable tool developed in python for analysing heart rate variability. It includes a graphical user interface and it can import files in multiple formats, analyse time intervals in the signal, test statistical significance and export the results. This paper also contains, as an example of use, a clinical analysis performed with the gHRV tool, namely to determine whether the heart rate variability indexes change across different stages of sleep. Results from tests completed by researchers who have tried gHRV are also explained: in general the application was positively valued and results reflect a high level of satisfaction. gHRV is in continuous development and new versions will include suggestions made by testers. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

CFD - Mature Technology?

NASA Technical Reports Server (NTRS)

Kwak, Dochan

2005-01-01

Over the past 30 years, numerical methods and simulation tools for fluid dynamic problems have advanced as a new discipline, namely, computational fluid dynamics (CFD). Although a wide spectrum of flow regimes are encountered in many areas of science and engineering, simulation of compressible flow has been the major driver for developing computational algorithms and tools. This is probably due to a large demand for predicting the aerodynamic performance characteristics of flight vehicles, such as commercial, military, and space vehicles. As flow analysis is required to be more accurate and computationally efficient for both commercial and mission-oriented applications (such as those encountered in meteorology, aerospace vehicle development, general fluid engineering and biofluid analysis) CFD tools for engineering become increasingly important for predicting safety, performance and cost. This paper presents the author's perspective on the maturity of CFD, especially from an aerospace engineering point of view.

Quantitative analysis and comparative study of four cities green pattern in API system on the background of big data

NASA Astrophysics Data System (ADS)

Xin, YANG; Si-qi, WU; Qi, ZHANG

2018-05-01

Beijing, London, Paris, New York are typical cities in the world, so comparative study of four cities green pattern is very important to find out gap and advantage and to learn from each other. The paper will provide basis and new ideas for development of metropolises in China. On the background of big data, API (Application Programming Interface) system can provide extensive and accurate basic data to study urban green pattern in different geographical environment in domestic and foreign. On the basis of this, Average nearest neighbor tool, Kernel density tool and Standard Ellipse tool in ArcGIS platform can process and summarize data and realize quantitative analysis of green pattern. The paper summarized uniqueness of four cities green pattern and reasons of formation on basis of numerical comparison.

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

PubMed Central

Barton, G; Abbott, J; Chiba, N; Huang, DW; Huang, Y; Krznaric, M; Mack-Smith, J; Saleem, A; Sherman, BT; Tiwari, B; Tomlinson, C; Aitman, T; Darlington, J; Game, L; Sternberg, MJE; Butcher, SA

2008-01-01

Background Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. Results EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. Conclusion EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume. PMID:19032776

Igloo-Plot: a tool for visualization of multidimensional datasets.

PubMed

Kuntal, Bhusan K; Ghosh, Tarini Shankar; Mande, Sharmila S

2014-01-01

Advances in science and technology have resulted in an exponential growth of multivariate (or multi-dimensional) datasets which are being generated from various research areas especially in the domain of biological sciences. Visualization and analysis of such data (with the objective of uncovering the hidden patterns therein) is an important and challenging task. We present a tool, called Igloo-Plot, for efficient visualization of multidimensional datasets. The tool addresses some of the key limitations of contemporary multivariate visualization and analysis tools. The visualization layout, not only facilitates an easy identification of clusters of data-points having similar feature compositions, but also the 'marker features' specific to each of these clusters. The applicability of the various functionalities implemented herein is demonstrated using several well studied multi-dimensional datasets. Igloo-Plot is expected to be a valuable resource for researchers working in multivariate data mining studies. Igloo-Plot is available for download from: http://metagenomics.atc.tcs.com/IglooPlot/. Copyright © 2014 Elsevier Inc. All rights reserved.

Multiscale visual quality assessment for cluster analysis with self-organizing maps

NASA Astrophysics Data System (ADS)

Bernard, Jürgen; von Landesberger, Tatiana; Bremm, Sebastian; Schreck, Tobias

2011-01-01

Cluster analysis is an important data mining technique for analyzing large amounts of data, reducing many objects to a limited number of clusters. Cluster visualization techniques aim at supporting the user in better understanding the characteristics and relationships among the found clusters. While promising approaches to visual cluster analysis already exist, these usually fall short of incorporating the quality of the obtained clustering results. However, due to the nature of the clustering process, quality plays an important aspect, as for most practical data sets, typically many different clusterings are possible. Being aware of clustering quality is important to judge the expressiveness of a given cluster visualization, or to adjust the clustering process with refined parameters, among others. In this work, we present an encompassing suite of visual tools for quality assessment of an important visual cluster algorithm, namely, the Self-Organizing Map (SOM) technique. We define, measure, and visualize the notion of SOM cluster quality along a hierarchy of cluster abstractions. The quality abstractions range from simple scalar-valued quality scores up to the structural comparison of a given SOM clustering with output of additional supportive clustering methods. The suite of methods allows the user to assess the SOM quality on the appropriate abstraction level, and arrive at improved clustering results. We implement our tools in an integrated system, apply it on experimental data sets, and show its applicability.

Modeling Constellation Virtual Missions Using the Vdot(Trademark) Process Management Tool

NASA Technical Reports Server (NTRS)

Hardy, Roger; ONeil, Daniel; Sturken, Ian; Nix, Michael; Yanez, Damian

2011-01-01

The authors have identified a software tool suite that will support NASA's Virtual Mission (VM) effort. This is accomplished by transforming a spreadsheet database of mission events, task inputs and outputs, timelines, and organizations into process visualization tools and a Vdot process management model that includes embedded analysis software as well as requirements and information related to data manipulation and transfer. This paper describes the progress to date, and the application of the Virtual Mission to not only Constellation but to other architectures, and the pertinence to other aerospace applications. Vdot s intuitive visual interface brings VMs to life by turning static, paper-based processes into active, electronic processes that can be deployed, executed, managed, verified, and continuously improved. A VM can be executed using a computer-based, human-in-the-loop, real-time format, under the direction and control of the NASA VM Manager. Engineers in the various disciplines will not have to be Vdot-proficient but rather can fill out on-line, Excel-type databases with the mission information discussed above. The author s tool suite converts this database into several process visualization tools for review and into Microsoft Project, which can be imported directly into Vdot. Many tools can be embedded directly into Vdot, and when the necessary data/information is received from a preceding task, the analysis can be initiated automatically. Other NASA analysis tools are too complex for this process but Vdot automatically notifies the tool user that the data has been received and analysis can begin. The VM can be simulated from end-to-end using the author s tool suite. The planned approach for the Vdot-based process simulation is to generate the process model from a database; other advantages of this semi-automated approach are the participants can be geographically remote and after refining the process models via the human-in-the-loop simulation, the system can evolve into a process management server for the actual process.

The Capability Portfolio Analysis Tool (CPAT): A Mixed Integer Linear Programming Formulation for Fleet Modernization Analysis (Version 2.0.2).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waddell, Lucas; Muldoon, Frank; Henry, Stephen Michael

In order to effectively plan the management and modernization of their large and diverse fleets of vehicles, Program Executive Office Ground Combat Systems (PEO GCS) and Program Executive Office Combat Support and Combat Service Support (PEO CS&CSS) commis- sioned the development of a large-scale portfolio planning optimization tool. This software, the Capability Portfolio Analysis Tool (CPAT), creates a detailed schedule that optimally prioritizes the modernization or replacement of vehicles within the fleet - respecting numerous business rules associated with fleet structure, budgets, industrial base, research and testing, etc., while maximizing overall fleet performance through time. This paper contains a thor-more » ough documentation of the terminology, parameters, variables, and constraints that comprise the fleet management mixed integer linear programming (MILP) mathematical formulation. This paper, which is an update to the original CPAT formulation document published in 2015 (SAND2015-3487), covers the formulation of important new CPAT features.« less

Proteinortho: detection of (co-)orthologs in large-scale analysis.

PubMed

Lechner, Marcus; Findeiss, Sven; Steiner, Lydia; Marz, Manja; Stadler, Peter F; Prohaska, Sonja J

2011-04-28

Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.

Fungal Genomics Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor

The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scalemore » genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.« less

Recent development in software and automation tools for high-throughput discovery bioanalysis.

PubMed

Shou, Wilson Z; Zhang, Jun

2012-05-01

Bioanalysis with LC-MS/MS has been established as the method of choice for quantitative determination of drug candidates in biological matrices in drug discovery and development. The LC-MS/MS bioanalytical support for drug discovery, especially for early discovery, often requires high-throughput (HT) analysis of large numbers of samples (hundreds to thousands per day) generated from many structurally diverse compounds (tens to hundreds per day) with a very quick turnaround time, in order to provide important activity and liability data to move discovery projects forward. Another important consideration for discovery bioanalysis is its fit-for-purpose quality requirement depending on the particular experiments being conducted at this stage, and it is usually not as stringent as those required in bioanalysis supporting drug development. These aforementioned attributes of HT discovery bioanalysis made it an ideal candidate for using software and automation tools to eliminate manual steps, remove bottlenecks, improve efficiency and reduce turnaround time while maintaining adequate quality. In this article we will review various recent developments that facilitate automation of individual bioanalytical procedures, such as sample preparation, MS/MS method development, sample analysis and data review, as well as fully integrated software tools that manage the entire bioanalytical workflow in HT discovery bioanalysis. In addition, software tools supporting the emerging high-resolution accurate MS bioanalytical approach are also discussed.

Study of the Effect of Lubricant Emulsion Percentage and Tool Material on Surface Roughness in Machining of EN-AC 48000 Alloy

NASA Astrophysics Data System (ADS)

Soltani, E.; Shahali, H.; Zarepour, H.

2011-01-01

In this paper, the effect of machining parameters, namely, lubricant emulsion percentage and tool material on surface roughness has been studied in machining process of EN-AC 48000 aluminum alloy. EN-AC 48000 aluminum alloy is an important alloy in industries. Machining of this alloy is of vital importance due to built-up edge and tool wear. A L9 Taguchi standard orthogonal array has been applied as experimental design to investigate the effect of the factors and their interaction. Nine machining tests have been carried out with three random replications resulting in 27 experiments. Three type of cutting tools including coated carbide (CD1810), uncoated carbide (H10), and polycrystalline diamond (CD10) have been used in this research. Emulsion percentage of lubricant is selected at three levels including 3%, 5% and 10%. Statistical analysis has been employed to study the effect of factors and their interactions using ANOVA method. Moreover, the optimal factors level has been achieved through signal to noise ratio (S/N) analysis. Also, a regression model has been provided to predict the surface roughness. Finally, the results of the confirmation tests have been presented to verify the adequacy of the predictive model. In this research, surface quality was improved by 9% using lubricant and statistical optimization method.

Advances in real-time magnetic resonance imaging of the vocal tract for speech science and technology research.

PubMed

Toutios, Asterios; Narayanan, Shrikanth S

2016-01-01

Real-time magnetic resonance imaging (rtMRI) of the moving vocal tract during running speech production is an important emerging tool for speech production research providing dynamic information of a speaker's upper airway from the entire mid-sagittal plane or any other scan plane of interest. There have been several advances in the development of speech rtMRI and corresponding analysis tools, and their application to domains such as phonetics and phonological theory, articulatory modeling, and speaker characterization. An important recent development has been the open release of a database that includes speech rtMRI data from five male and five female speakers of American English each producing 460 phonetically balanced sentences. The purpose of the present paper is to give an overview and outlook of the advances in rtMRI as a tool for speech research and technology development.

Advances in real-time magnetic resonance imaging of the vocal tract for speech science and technology research

PubMed Central

TOUTIOS, ASTERIOS; NARAYANAN, SHRIKANTH S.

2016-01-01

Real-time magnetic resonance imaging (rtMRI) of the moving vocal tract during running speech production is an important emerging tool for speech production research providing dynamic information of a speaker's upper airway from the entire mid-sagittal plane or any other scan plane of interest. There have been several advances in the development of speech rtMRI and corresponding analysis tools, and their application to domains such as phonetics and phonological theory, articulatory modeling, and speaker characterization. An important recent development has been the open release of a database that includes speech rtMRI data from five male and five female speakers of American English each producing 460 phonetically balanced sentences. The purpose of the present paper is to give an overview and outlook of the advances in rtMRI as a tool for speech research and technology development. PMID:27833745

A new software tool for 3D motion analyses of the musculo-skeletal system.

PubMed

Leardini, A; Belvedere, C; Astolfi, L; Fantozzi, S; Viceconti, M; Taddei, F; Ensini, A; Benedetti, M G; Catani, F

2006-10-01

Many clinical and biomechanical research studies, particularly in orthopaedics, nowadays involve forms of movement analysis. Gait analysis, video-fluoroscopy of joint replacement, pre-operative planning, surgical navigation, and standard radiostereometry would require tools for easy access to three-dimensional graphical representations of rigid segment motion. Relevant data from this variety of sources need to be organised in structured forms. Registration, integration, and synchronisation of segment position data are additional necessities. With this aim, the present work exploits the features of a software tool recently developed within a EU-funded project ('Multimod') in a series of different research studies. Standard and advanced gait analysis on a normal subject, in vivo fluoroscopy-based three-dimensional motion of a replaced knee joint, patellar and ligament tracking on a knee specimen by a surgical navigation system, stem-to-femur migration pattern on a patient operated on total hip replacement, were analysed with standard techniques and all represented by this innovative software tool. Segment pose data were eventually obtained from these different techniques, and were successfully imported and organised in a hierarchical tree within the tool. Skeletal bony segments, prosthesis component models and ligament links were registered successfully to corresponding marker position data for effective three-dimensional animations. These were shown in various combinations, in different views, from different perspectives, according to possible specific research interests. Bioengineering and medical professionals would be much facilitated in the interpretation of the motion analysis measurements necessary in their research fields, and would benefit therefore from this software tool.

MANTiS: a program for the analysis of X-ray spectromicroscopy data.

PubMed

Lerotic, Mirna; Mak, Rachel; Wirick, Sue; Meirer, Florian; Jacobsen, Chris

2014-09-01

Spectromicroscopy combines spectral data with microscopy, where typical datasets consist of a stack of images taken across a range of energies over a microscopic region of the sample. Manual analysis of these complex datasets can be time-consuming, and can miss the important traits in the data. With this in mind we have developed MANTiS, an open-source tool developed in Python for spectromicroscopy data analysis. The backbone of the package involves principal component analysis and cluster analysis, classifying pixels according to spectral similarity. Our goal is to provide a data analysis tool which is comprehensive, yet intuitive and easy to use. MANTiS is designed to lead the user through the analysis using story boards that describe each step in detail so that both experienced users and beginners are able to analyze their own data independently. These capabilities are illustrated through analysis of hard X-ray imaging of iron in Roman ceramics, and soft X-ray imaging of a malaria-infected red blood cell.

The methodological quality assessment tools for preclinical and clinical studies, systematic review and meta-analysis, and clinical practice guideline: a systematic review.

PubMed

Zeng, Xiantao; Zhang, Yonggang; Kwong, Joey S W; Zhang, Chao; Li, Sheng; Sun, Feng; Niu, Yuming; Du, Liang

2015-02-01

To systematically review the methodological assessment tools for pre-clinical and clinical studies, systematic review and meta-analysis, and clinical practice guideline. We searched PubMed, the Cochrane Handbook for Systematic Reviews of Interventions, Joanna Briggs Institute (JBI) Reviewers Manual, Centre for Reviews and Dissemination, Critical Appraisal Skills Programme (CASP), Scottish Intercollegiate Guidelines Network (SIGN), and the National Institute for Clinical Excellence (NICE) up to May 20th, 2014. Two authors selected studies and extracted data; quantitative analysis was performed to summarize the characteristics of included tools. We included a total of 21 assessment tools for analysis. A number of tools were developed by academic organizations, and some were developed by only a small group of researchers. The JBI developed the highest number of methodological assessment tools, with CASP coming second. Tools for assessing the methodological quality of randomized controlled studies were most abundant. The Cochrane Collaboration's tool for assessing risk of bias is the best available tool for assessing RCTs. For cohort and case-control studies, we recommend the use of the Newcastle-Ottawa Scale. The Methodological Index for Non-Randomized Studies (MINORS) is an excellent tool for assessing non-randomized interventional studies, and the Agency for Healthcare Research and Quality (ARHQ) methodology checklist is applicable for cross-sectional studies. For diagnostic accuracy test studies, the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool is recommended; the SYstematic Review Centre for Laboratory animal Experimentation (SYRCLE) risk of bias tool is available for assessing animal studies; Assessment of Multiple Systematic Reviews (AMSTAR) is a measurement tool for systematic reviews/meta-analyses; an 18-item tool has been developed for appraising case series studies, and the Appraisal of Guidelines, Research and Evaluation (AGREE)-II instrument is widely used to evaluate clinical practice guidelines. We have successfully identified a variety of methodological assessment tools for different types of study design. However, further efforts in the development of critical appraisal tools are warranted since there is currently a lack of such tools for other fields, e.g. genetic studies, and some existing tools (nested case-control studies and case reports, for example) are in need of updating to be in line with current research practice and rigor. In addition, it is very important that all critical appraisal tools remain subjective and performance bias is effectively avoided. © 2015 Chinese Cochrane Center, West China Hospital of Sichuan University and Wiley Publishing Asia Pty Ltd.

Advanced Usage of Vehicle Sketch Pad for CFD-Based Conceptual Design

NASA Technical Reports Server (NTRS)

Ordaz, Irian; Li, Wu

2013-01-01

Conceptual design is the most fluid phase of aircraft design. It is important to be able to perform large scale design space exploration of candidate concepts that can achieve the design intent to avoid more costly configuration changes in later stages of design. This also means that conceptual design is highly dependent on the disciplinary analysis tools to capture the underlying physics accurately. The required level of analysis fidelity can vary greatly depending on the application. Vehicle Sketch Pad (VSP) allows the designer to easily construct aircraft concepts and make changes as the design matures. More recent development efforts have enabled VSP to bridge the gap to high-fidelity analysis disciplines such as computational fluid dynamics and structural modeling for finite element analysis. This paper focuses on the current state-of-the-art geometry modeling for the automated process of analysis and design of low-boom supersonic concepts using VSP and several capability-enhancing design tools.

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics.

PubMed

Guitton, Yann; Tremblay-Franco, Marie; Le Corguillé, Gildas; Martin, Jean-François; Pétéra, Mélanie; Roger-Mele, Pierrick; Delabrière, Alexis; Goulitquer, Sophie; Monsoor, Misharl; Duperier, Christophe; Canlet, Cécile; Servien, Rémi; Tardivel, Patrick; Caron, Christophe; Giacomoni, Franck; Thévenot, Etienne A

2017-12-01

Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the multiplicity of bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics (W4M; http://workflow4metabolomics.org) online infrastructure for metabolomics built on the Galaxy environment, which offers user-friendly features to build and run data analysis workflows including preprocessing, statistical analysis, and annotation steps. Here we present the new W4M 3.0 release, which contains twice as many tools as the first version, and provides two features which are, to our knowledge, unique among online resources. First, data from the four major metabolomics technologies (i.e., LC-MS, FIA-MS, GC-MS, and NMR) can be analyzed on a single platform. By using three studies in human physiology, alga evolution, and animal toxicology, we demonstrate how the 40 available tools can be easily combined to address biological issues. Second, the full analysis (including the workflow, the parameter values, the input data and output results) can be referenced with a permanent digital object identifier (DOI). Publication of data analyses is of major importance for robust and reproducible science. Furthermore, the publicly shared workflows are of high-value for e-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thus not only offers a unique online environment for analysis of data from the main metabolomics technologies, but it is also the first reference repository for metabolomics workflows. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of gene expression profile microarray data in complex regional pain syndrome.

PubMed

Tan, Wulin; Song, Yiyan; Mo, Chengqiang; Jiang, Shuangjian; Wang, Zhongxing

2017-09-01

The aim of the present study was to predict key genes and proteins associated with complex regional pain syndrome (CRPS) using bioinformatics analysis. The gene expression profiling microarray data, GSE47603, which included peripheral blood samples from 4 patients with CRPS and 5 healthy controls, was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in CRPS patients compared with healthy controls were identified using the GEO2R online tool. Functional enrichment analysis was then performed using The Database for Annotation Visualization and Integrated Discovery online tool. Protein‑protein interaction (PPI) network analysis was subsequently performed using Search Tool for the Retrieval of Interaction Genes database and analyzed with Cytoscape software. A total of 257 DEGs were identified, including 243 upregulated genes and 14 downregulated ones. Genes in the human leukocyte antigen (HLA) family were most significantly differentially expressed. Enrichment analysis demonstrated that signaling pathways, including immune response, cell motion, adhesion and angiogenesis were associated with CRPS. PPI network analysis revealed that key genes, including early region 1A binding protein p300 (EP300), CREB‑binding protein (CREBBP), signal transducer and activator of transcription (STAT)3, STAT5A and integrin α M were associated with CRPS. The results suggest that the immune response may therefore serve an important role in CRPS development. In addition, genes in the HLA family, such as HLA‑DQB1 and HLA‑DRB1, may present potential biomarkers for the diagnosis of CRPS. Furthermore, EP300, its paralog CREBBP, and the STAT family genes, STAT3 and STAT5 may be important in the development of CRPS.

Self-optimizing Monte Carlo method for nuclear well logging simulation

NASA Astrophysics Data System (ADS)

Liu, Lianyan

1997-09-01

In order to increase the efficiency of Monte Carlo simulation for nuclear well logging problems, a new method has been developed for variance reduction. With this method, an importance map is generated in the regular Monte Carlo calculation as a by-product, and the importance map is later used to conduct the splitting and Russian roulette for particle population control. By adopting a spatial mesh system, which is independent of physical geometrical configuration, the method allows superior user-friendliness. This new method is incorporated into the general purpose Monte Carlo code MCNP4A through a patch file. Two nuclear well logging problems, a neutron porosity tool and a gamma-ray lithology density tool are used to test the performance of this new method. The calculations are sped up over analog simulation by 120 and 2600 times, for the neutron porosity tool and for the gamma-ray lithology density log, respectively. The new method enjoys better performance by a factor of 4~6 times than that of MCNP's cell-based weight window, as per the converged figure-of-merits. An indirect comparison indicates that the new method also outperforms the AVATAR process for gamma-ray density tool problems. Even though it takes quite some time to generate a reasonable importance map from an analog run, a good initial map can create significant CPU time savings. This makes the method especially suitable for nuclear well logging problems, since one or several reference importance maps are usually available for a given tool. Study shows that the spatial mesh sizes should be chosen according to the mean-free-path. The overhead of the importance map generator is 6% and 14% for neutron and gamma-ray cases. The learning ability towards a correct importance map is also demonstrated. Although false-learning may happen, physical judgement can help diagnose with contributon maps. Calibration and analysis are performed for the neutron tool and the gamma-ray tool. Due to the fact that a very good initial importance map is always available after the first point has been calculated, high computing efficiency is maintained. The availability of contributon maps provides an easy way of understanding the logging measurement and analyzing for the depth of investigation.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

PubMed

Papaleo, Elena

2015-01-01

In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

Comparisons of Kinematics and Dynamics Simulation Software Tools

NASA Technical Reports Server (NTRS)

Shiue, Yeu-Sheng Paul

2002-01-01

Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization.

PubMed

Ollion, Jean; Cochennec, Julien; Loll, François; Escudé, Christophe; Boudier, Thomas

2013-07-15

The cell nucleus is a highly organized cellular organelle that contains the genetic material. The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Here, we describe Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ (http://imagej.nih.gov/ij/) for image processing and quantitative analysis and R (http://cran.r-project.org) for statistical processing of measurement results. It includes an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills. TANGO is a versatile tool able to process large sets of images, allowing quantitative study of nuclear organization. TANGO is composed of two programs: (i) an ImageJ plug-in and (ii) a package (rtango) for R. They are both free and open source, available (http://biophysique.mnhn.fr/tango) for Linux, Microsoft Windows and Macintosh OSX. Distribution is under the GPL v.2 licence. thomas.boudier@snv.jussieu.fr Supplementary data are available at Bioinformatics online.

JASMINE simulator

NASA Astrophysics Data System (ADS)

Yamada, Yoshiyuki; Gouda, Naoteru; Yano, Taihei; Kobayashi, Yukiyasu; Tsujimoto, Takuji; Suganuma, Masahiro; Niwa, Yoshito; Sako, Nobutada; Hatsutori, Yoichi; Tanaka, Takashi

2006-06-01

We explain simulation tools in JASMINE project (JASMINE simulator). The JASMINE project stands at the stage where its basic design will be determined in a few years. Then it is very important to simulate the data stream generated by astrometric fields at JASMINE in order to support investigations into error budgets, sampling strategy, data compression, data analysis, scientific performances, etc. Of course, component simulations are needed, but total simulations which include all components from observation target to satellite system are also very important. We find that new software technologies, such as Object Oriented(OO) methodologies are ideal tools for the simulation system of JASMINE(the JASMINE simulator). In this article, we explain the framework of the JASMINE simulator.

Big Data and Neuroimaging.

PubMed

Webb-Vargas, Yenny; Chen, Shaojie; Fisher, Aaron; Mejia, Amanda; Xu, Yuting; Crainiceanu, Ciprian; Caffo, Brian; Lindquist, Martin A

2017-12-01

Big Data are of increasing importance in a variety of areas, especially in the biosciences. There is an emerging critical need for Big Data tools and methods, because of the potential impact of advancements in these areas. Importantly, statisticians and statistical thinking have a major role to play in creating meaningful progress in this arena. We would like to emphasize this point in this special issue, as it highlights both the dramatic need for statistical input for Big Data analysis and for a greater number of statisticians working on Big Data problems. We use the field of statistical neuroimaging to demonstrate these points. As such, this paper covers several applications and novel methodological developments of Big Data tools applied to neuroimaging data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janjusic, Tommy; Kartsaklis, Christos

Application analysis is facilitated through a number of program profiling tools. The tools vary in their complexity, ease of deployment, design, and profiling detail. Specifically, understand- ing, analyzing, and optimizing is of particular importance for scientific applications where minor changes in code paths and data-structure layout can have profound effects. Understanding how intricate data-structures are accessed and how a given memory system responds is a complex task. In this paper we describe a trace profiling tool, Glprof, specifically aimed to lessen the burden of the programmer to pin-point heavily involved data-structures during an application's run-time, and understand data-structure run-time usage.more » Moreover, we showcase the tool's modularity using additional cache simulation components. We elaborate on the tool's design, and features. Finally we demonstrate the application of our tool in the context of Spec bench- marks using the Glprof profiler and two concurrently running cache simulators, PPC440 and AMD Interlagos.« less

Validation of the self-assessment teamwork tool (SATT) in a cohort of nursing and medical students.

PubMed

Roper, Lucinda; Shulruf, Boaz; Jorm, Christine; Currie, Jane; Gordon, Christopher J

2018-02-09

Poor teamwork has been implicated in medical error and teamwork training has been shown to improve patient care. Simulation is an effective educational method for teamwork training. Post-simulation reflection aims to promote learning and we have previously developed a self-assessment teamwork tool (SATT) for health students to measure teamwork performance. This study aimed to evaluate the psychometric properties of a revised self-assessment teamwork tool. The tool was tested in 257 medical and nursing students after their participation in one of several mass casualty simulations. Using exploratory and confirmatory factor analysis, the revised self-assessment teamwork tool was shown to have strong construct validity, high reliability, and the construct demonstrated invariance across groups (Medicine & Nursing). The modified SATT was shown to be a reliable and valid student self-assessment tool. The SATT is a quick and practical method of guiding students' reflection on important teamwork skills.

What Role Does "Elongation" Play in "Tool-Specific" Activation and Connectivity in the Dorsal and Ventral Visual Streams?

PubMed

Chen, Juan; Snow, Jacqueline C; Culham, Jody C; Goodale, Melvyn A

2018-04-01

Images of tools induce stronger activation than images of nontools in a left-lateralized network that includes ventral-stream areas implicated in tool identification and dorsal-stream areas implicated in tool manipulation. Importantly, however, graspable tools tend to be elongated rather than stubby, and so the tool-selective responses in some of these areas may, to some extent, reflect sensitivity to elongation rather than "toolness" per se. Using functional magnetic resonance imaging, we investigated the role of elongation in driving tool-specific activation in the 2 streams and their interconnections. We showed that in some "tool-selective" areas, the coding of toolness and elongation coexisted, but in others, elongation and toolness were coded independently. Psychophysiological interaction analysis revealed that toolness, but not elongation, had a strong modulation of the connectivity between the ventral and dorsal streams. Dynamic causal modeling revealed that viewing tools (either elongated or stubby) increased the connectivity from the ventral- to the dorsal-stream tool-selective areas, but only viewing elongated tools increased the reciprocal connectivity between these areas. Overall, these data disentangle how toolness and elongation affect the activation and connectivity of the tool network and help to resolve recent controversies regarding the relative contribution of "toolness" versus elongation in driving dorsal-stream "tool-selective" areas.

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking.

PubMed

Lazaris, Charalampos; Kelly, Stephen; Ntziachristos, Panagiotis; Aifantis, Iannis; Tsirigos, Aristotelis

2017-01-05

Chromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution. Analysis of Hi-C data is complex and computationally intensive involving multiple tasks and requiring robust quality assessment. This has led to the development of several tools and methods for processing Hi-C data. However, most of the existing tools do not cover all aspects of the analysis and only offer few quality assessment options. Additionally, availability of a multitude of tools makes scientists wonder how these tools and associated parameters can be optimally used, and how potential discrepancies can be interpreted and resolved. Most importantly, investigators need to be ensured that slight changes in parameters and/or methods do not affect the conclusions of their studies. To address these issues (compare, explore and reproduce), we introduce HiC-bench, a configurable computational platform for comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs all common Hi-C analysis tasks, such as alignment, filtering, contact matrix generation and normalization, identification of topological domains, scoring and annotation of specific interactions using both published tools and our own. We have also embedded various tasks that perform quality assessment and visualization. HiC-bench is implemented as a data flow platform with an emphasis on analysis reproducibility. Additionally, the user can readily perform parameter exploration and comparison of different tools in a combinatorial manner that takes into account all desired parameter settings in each pipeline task. This unique feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple tool/parameter choices in each step of the analysis. To demonstrate the usefulness of our platform, we performed a comprehensive benchmark of existing and new TAD callers exploring different matrix correction methods, parameter settings and sequencing depths. Users can extend our pipeline by adding more tools as they become available. HiC-bench consists an easy-to-use and extensible platform for comprehensive analysis of Hi-C datasets. We expect that it will facilitate current analyses and help scientists formulate and test new hypotheses in the field of three-dimensional genome organization.

Views of general practitioners on the use of STOPP&START in primary care: a qualitative study.

PubMed

Dalleur, O; Feron, J-M; Spinewine, A

2014-08-01

STOPP (Screening Tool of Older Person's Prescriptions) and START (Screening Tool to Alert Doctors to Right Treatment) criteria aim at detecting potentially inappropriate prescribing in older people. The objective was to explore general practitioners' (GPs) perceptions regarding the use of the STOPP&START tool in their practice. We conducted three focus groups which were conveniently sampled. Vignettes with clinical cases were provided for discussion as well as a full version of the STOPP&START tool. Knowledge, strengths and weaknesses of the tool and its implementation were discussed. Two researchers independently performed content analysis, classifying quotes and creating new categories for emerging themes. Discussions highlighted incentives (e.g. systematic procedure for medication review) and barriers (e.g. time-consuming application) influencing the use of STOPP&START in primary care. Usefulness, comprehensiveness, and relevance of the tool were also questioned. Another important category emerging from the content analysis was the projected use of the tool. The GPs imagined key elements for the implementation in daily practice: computerized clinical decision support system, education, and multidisciplinary collaborations, especially at care transitions and in nursing homes. Despite variables views on the usefulness, comprehensiveness, and relevance of STOPP&START, GPs suggest the implementation of this tool in primary care within computerized clinical decision support systems, through education, and used as part of multidisciplinary collaborations.

Space Science Cloud: a Virtual Space Science Research Platform Based on Cloud Model

NASA Astrophysics Data System (ADS)

Hu, Xiaoyan; Tong, Jizhou; Zou, Ziming

Through independent and co-operational science missions, Strategic Pioneer Program (SPP) on Space Science, the new initiative of space science program in China which was approved by CAS and implemented by National Space Science Center (NSSC), dedicates to seek new discoveries and new breakthroughs in space science, thus deepen the understanding of universe and planet earth. In the framework of this program, in order to support the operations of space science missions and satisfy the demand of related research activities for e-Science, NSSC is developing a virtual space science research platform based on cloud model, namely the Space Science Cloud (SSC). In order to support mission demonstration, SSC integrates interactive satellite orbit design tool, satellite structure and payloads layout design tool, payload observation coverage analysis tool, etc., to help scientists analyze and verify space science mission designs. Another important function of SSC is supporting the mission operations, which runs through the space satellite data pipelines. Mission operators can acquire and process observation data, then distribute the data products to other systems or issue the data and archives with the services of SSC. In addition, SSC provides useful data, tools and models for space researchers. Several databases in the field of space science are integrated and an efficient retrieve system is developing. Common tools for data visualization, deep processing (e.g., smoothing and filtering tools), analysis (e.g., FFT analysis tool and minimum variance analysis tool) and mining (e.g., proton event correlation analysis tool) are also integrated to help the researchers to better utilize the data. The space weather models on SSC include magnetic storm forecast model, multi-station middle and upper atmospheric climate model, solar energetic particle propagation model and so on. All the services above-mentioned are based on the e-Science infrastructures of CAS e.g. cloud storage and cloud computing. SSC provides its users with self-service storage and computing resources at the same time.At present, the prototyping of SSC is underway and the platform is expected to be put into trial operation in August 2014. We hope that as SSC develops, our vision of Digital Space may come true someday.

Design and Analysis of a Forging Die for Manufacturing of Multiple Connecting Rods

NASA Astrophysics Data System (ADS)

Megharaj, C. E.; Nagaraj, P. M.; Jeelan Pasha, K.

2016-09-01

This paper demonstrates to utilize the hammer capacity by modifying the die design such that forging hammer can manufacture more than one connecting rod in a given forging cycle time. To modify the die design study is carried out to understand the parameters that are required for forging die design. By considering these parameters, forging die is designed using design modelling tool solid edge. This new design now can produce two connecting rods in same capacity hammer. The new design is required to validate by verifying complete filing of metal in die cavities without any defects in it. To verify this, analysis tool DEFORM 3D is used in this project. Before start of validation process it is require to convert 3D generated models in to. STL file format to import the models into the analysis tool DEFORM 3D. After importing these designs they are analysed for material flow into the cavities and energy required to produce two connecting rods in new forging die design. It is found that the forging die design is proper without any defects and also energy graph shows that the forging energy required to produce two connecting rods is within the limit of that hammer capacity. Implementation of this project increases the production of connecting rods by 200% in less than previous cycle time.

Probability and Statistics in Sensor Performance Modeling

DTIC Science & Technology

2010-12-01

language software program is called Environmental Awareness for Sensor and Emitter Employment. Some important numerical issues in the implementation...3 Statistical analysis for measuring sensor performance...complementary cumulative distribution function cdf cumulative distribution function DST decision-support tool EASEE Environmental Awareness of

Pathway-Based Concentration Response Profiles from Toxicogenomics Data

EPA Science Inventory

Microarray analysis of gene expression of in vitro systems could be a powerful tool for assessing chemical hazard. Differentially expressed genes specific to cells, chemicals, and concentrations can be organized into molecular pathways that inform mode of action. An important par...

Prediction Of Abrasive And Diffusive Tool Wear Mechanisms In Machining

NASA Astrophysics Data System (ADS)

Rizzuti, S.; Umbrello, D.

2011-01-01

Tool wear prediction is regarded as very important task in order to maximize tool performance, minimize cutting costs and improve the quality of workpiece in cutting. In this research work, an experimental campaign was carried out at the varying of cutting conditions with the aim to measure both crater and flank tool wear, during machining of an AISI 1045 with an uncoated carbide tool P40. Parallel a FEM-based analysis was developed in order to study the tool wear mechanisms, taking also into account the influence of the cutting conditions and the temperature reached on the tool surfaces. The results show that, when the temperature of the tool rake surface is lower than the activation temperature of the diffusive phenomenon, the wear rate can be estimated applying an abrasive model. In contrast, in the tool area where the temperature is higher than the diffusive activation temperature, the wear rate can be evaluated applying a diffusive model. Finally, for a temperature ranges within the above cited values an adopted abrasive-diffusive wear model furnished the possibility to correctly evaluate the tool wear phenomena.

A Tool for Verification and Validation of Neural Network Based Adaptive Controllers for High Assurance Systems

NASA Technical Reports Server (NTRS)

Gupta, Pramod; Schumann, Johann

2004-01-01

High reliability of mission- and safety-critical software systems has been identified by NASA as a high-priority technology challenge. We present an approach for the performance analysis of a neural network (NN) in an advanced adaptive control system. This problem is important in the context of safety-critical applications that require certification, such as flight software in aircraft. We have developed a tool to measure the performance of the NN during operation by calculating a confidence interval (error bar) around the NN's output. Our tool can be used during pre-deployment verification as well as monitoring the network performance during operation. The tool has been implemented in Simulink and simulation results on a F-15 aircraft are presented.

Bridging the gaps between non-invasive genetic sampling and population parameter estimation

Treesearch

Francesca Marucco; Luigi Boitani; Daniel H. Pletscher; Michael K. Schwartz

2011-01-01

Reliable estimates of population parameters are necessary for effective management and conservation actions. The use of genetic data for capture­recapture (CR) analyses has become an important tool to estimate population parameters for elusive species. Strong emphasis has been placed on the genetic analysis of non-invasive samples, or on the CR analysis; however,...

Measuring, Understanding, and Responding to Covert Social Networks: Passive and Active Tomography

DTIC Science & Technology

2017-11-29

Methods for generating a random sample of networks with desired properties are important tools for the analysis of social , biological, and information...on Theoretical Foundations for Statistical Network Analysis at the Isaac Newton Institute for Mathematical Sciences at Cambridge U. (organized by...Approach SOCIAL SCIENCES STATISTICS EECS Problems span three disciplines Scientific focus is needed at the interfaces

"Cause That's the Only Skills in School You Need": A Qualitative Analysis of Revenge Goals in Poor Urban Youth

ERIC Educational Resources Information Center

Jäggi, Lena; Kliewer, Wendy

2016-01-01

Revenge goals are correlated with maladjustment, and retaliation is a factor driving youth violence. However, revenge might be an important social tool adolescents use to achieve (self-)justice in environments where institutionalized interventions from authorities such as teachers or police are limited. This qualitative secondary analysis of 50…

The PC9A Filter Screening Tool

DTIC Science & Technology

2016-02-01

conjunction with an optical microscope for identification of other important debris such as glass beads. The FST has now been installed at RAAF East...conservative screening limits need to be sent for detailed laboratory analysis. Laboratory analysis has traditionally involved a manual microscopic ...Electron Microscope with Energy Dispersive Spectroscopy (SEM EDS) to determine the composition and likely source. The Engine Maintenance Manual

Application of data envelopment analysis in measuring the efficiency of mutual fund

NASA Astrophysics Data System (ADS)

Nik, Marzieh Geramian; Mihanzadeh, Hooman; Izadifar, Mozhgan; Nik, Babak Geramian

2015-05-01

The growth of mutual fund industry during the past decades emphasizes the importance of this investment vehicle particularly in prosperity of financial markets and in turn, financial growth of each country. Therefore, evaluating the relative efficiency of mutual funds as investment tool is of importance. In this study, a combined model of DEA (data envelopment analysis), and goal programming (GoDEA) approaches contributes widely to analyze the return efficiency of Mutual Funds in an attempt to separate efficient and inefficient Funds as well as identifying the inefficiency resources. Mixed asset local funds, which are managed jointly by CIMB and Public Mutual Berhad, have been selected for the purpose of this paper. As a result, Public Small Cap Fund (P Small Cap) is regarded as the most efficient mutual fund during the period of study. The integrated model aims to first guide investors to choose the best performing fund among other mutual funds, secondly provides the realistic and appropriate benchmark in compare to other classic method, and finally confirms the utility of data envelopment analysis (DEA) as decision-making tool.

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Guidelines for Analysis of Indigeneous and Private Health Care Planning in Developing Countries. International Health Planning Methods Series, Volume 6.

ERIC Educational Resources Information Center

Scrimshaw, Susan

This guidebook is both a practical tool and a source book to aid health planners assess the importance, extent, and impact of indigenous and private sector medical systems in developing nations. Guidelines are provided for assessment in terms of: use patterns; the meaning and importance to users of various available health services; and ways of…

Augmenting Traditional Static Analysis With Commonly Available Metadata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, Devin

Developers and security analysts have been using static analysis for a long time to analyze programs for defects and vulnerabilities with some success. Generally a static analysis tool is run on the source code for a given program, flagging areas of code that need to be further inspected by a human analyst. These areas may be obvious bugs like potential bu er over flows, information leakage flaws, or the use of uninitialized variables. These tools tend to work fairly well - every year they find many important bugs. These tools are more impressive considering the fact that they only examinemore » the source code, which may be very complex. Now consider the amount of data available that these tools do not analyze. There are many pieces of information that would prove invaluable for finding bugs in code, things such as a history of bug reports, a history of all changes to the code, information about committers, etc. By leveraging all this additional data, it is possible to nd more bugs with less user interaction, as well as track useful metrics such as number and type of defects injected by committer. This dissertation provides a method for leveraging development metadata to find bugs that would otherwise be difficult to find using standard static analysis tools. We showcase two case studies that demonstrate the ability to find 0day vulnerabilities in large and small software projects by finding new vulnerabilities in the cpython and Roundup open source projects.« less

ON IDENTIFIABILITY OF NONLINEAR ODE MODELS AND APPLICATIONS IN VIRAL DYNAMICS

PubMed Central

MIAO, HONGYU; XIA, XIAOHUA; PERELSON, ALAN S.; WU, HULIN

2011-01-01

Ordinary differential equations (ODE) are a powerful tool for modeling dynamic processes with wide applications in a variety of scientific fields. Over the last 2 decades, ODEs have also emerged as a prevailing tool in various biomedical research fields, especially in infectious disease modeling. In practice, it is important and necessary to determine unknown parameters in ODE models based on experimental data. Identifiability analysis is the first step in determing unknown parameters in ODE models and such analysis techniques for nonlinear ODE models are still under development. In this article, we review identifiability analysis methodologies for nonlinear ODE models developed in the past one to two decades, including structural identifiability analysis, practical identifiability analysis and sensitivity-based identifiability analysis. Some advanced topics and ongoing research are also briefly reviewed. Finally, some examples from modeling viral dynamics of HIV, influenza and hepatitis viruses are given to illustrate how to apply these identifiability analysis methods in practice. PMID:21785515

DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data.

PubMed

Hollunder, Jens; Friedel, Maik; Kuiper, Martin; Wilhelm, Thomas

2010-04-01

Many large 'omics' datasets have been published and many more are expected in the near future. New analysis methods are needed for best exploitation. We have developed a graphical user interface (GUI) for easy data analysis. Our discovery of all significant substructures (DASS) approach elucidates the underlying modularity, a typical feature of complex biological data. It is related to biclustering and other data mining approaches. Importantly, DASS-GUI also allows handling of multi-sets and calculation of statistical significances. DASS-GUI contains tools for further analysis of the identified patterns: analysis of the pattern hierarchy, enrichment analysis, module validation, analysis of additional numerical data, easy handling of synonymous names, clustering, filtering and merging. Different export options allow easy usage of additional tools such as Cytoscape. Source code, pre-compiled binaries for different systems, a comprehensive tutorial, case studies and many additional datasets are freely available at http://www.ifr.ac.uk/dass/gui/. DASS-GUI is implemented in Qt.

Tools for Large-Scale Mobile Malware Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bierma, Michael

Analyzing mobile applications for malicious behavior is an important area of re- search, and is made di cult, in part, by the increasingly large number of appli- cations available for the major operating systems. There are currently over 1.2 million apps available in both the Google Play and Apple App stores (the respec- tive o cial marketplaces for the Android and iOS operating systems)[1, 2]. Our research provides two large-scale analysis tools to aid in the detection and analysis of mobile malware. The rst tool we present, Andlantis, is a scalable dynamic analysis system capa- ble of processing over 3000more » Android applications per hour. Traditionally, Android dynamic analysis techniques have been relatively limited in scale due to the compu- tational resources required to emulate the full Android system to achieve accurate execution. Andlantis is the most scalable Android dynamic analysis framework to date, and is able to collect valuable forensic data, which helps reverse-engineers and malware researchers identify and understand anomalous application behavior. We discuss the results of running 1261 malware samples through the system, and provide examples of malware analysis performed with the resulting data. While techniques exist to perform static analysis on a large number of appli- cations, large-scale analysis of iOS applications has been relatively small scale due to the closed nature of the iOS ecosystem, and the di culty of acquiring appli- cations for analysis. The second tool we present, iClone, addresses the challenges associated with iOS research in order to detect application clones within a dataset of over 20,000 iOS applications.« less

Online Tools for Bioinformatics Analyses in Nutrition Sciences12

PubMed Central

Malkaram, Sridhar A.; Hassan, Yousef I.; Zempleni, Janos

2012-01-01

Recent advances in “omics” research have resulted in the creation of large datasets that were generated by consortiums and centers, small datasets that were generated by individual investigators, and bioinformatics tools for mining these datasets. It is important for nutrition laboratories to take full advantage of the analysis tools to interrogate datasets for information relevant to genomics, epigenomics, transcriptomics, proteomics, and metabolomics. This review provides guidance regarding bioinformatics resources that are currently available in the public domain, with the intent to provide a starting point for investigators who want to take advantage of the opportunities provided by the bioinformatics field. PMID:22983844

SOAP based web services and their future role in VO projects

NASA Astrophysics Data System (ADS)

Topf, F.; Jacquey, C.; Génot, V.; Cecconi, B.; André, N.; Zhang, T. L.; Kallio, E.; Lammer, H.; Facsko, G.; Stöckler, R.; Khodachenko, M.

2011-10-01

Modern state-of-the-art web services are from crucial importance for the interoperability of different VO tools existing in the planetary community. SOAP based web services assure the interconnectability between different data sources and tools by providing a common protocol for communication. This paper will point out a best practice approach with the Automated Multi-Dataset Analysis Tool (AMDA) developed by CDPP, Toulouse and the provision of VEX/MAG data from a remote database located at IWF, Graz. Furthermore a new FP7 project IMPEx will be introduced with a potential usage example of AMDA web services in conjunction with simulation models.

EDCATS: An Evaluation Tool

NASA Technical Reports Server (NTRS)

Heard, Pamala D.

1998-01-01

The purpose of this research is to explore the development of Marshall Space Flight Center Unique Programs. These academic tools provide the Education Program Office with important information from the Education Computer Aided Tracking System (EDCATS). This system is equipped to provide on-line data entry, evaluation, analysis, and report generation, with full archiving for all phases of the evaluation process. Another purpose is to develop reports and data that is tailored to Marshall Space Flight Center Unique Programs. It also attempts to acquire knowledge on how, why, and where information is derived. As a result, a user will be better prepared to decide which available tool is the most feasible for their reports.

Open Source Live Distributions for Computer Forensics

NASA Astrophysics Data System (ADS)

Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

Current distributions of open source forensic software provide digital investigators with a large set of heterogeneous tools. Their use is not always focused on the target and requires high technical expertise. We present a new GNU/Linux live distribution, named CAINE (Computer Aided INvestigative Environment) that contains a collection of tools wrapped up into a user friendly environment. The CAINE forensic framework introduces novel important features, aimed at filling the interoperability gap across different forensic tools. Moreover, it provides a homogeneous graphical interface that drives digital investigators during the acquisition and analysis of electronic evidence, and it offers a semi-automatic mechanism for the creation of the final report.

Stackfile Database

NASA Technical Reports Server (NTRS)

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

Cognitive mapping tools: review and risk management needs.

PubMed

Wood, Matthew D; Bostrom, Ann; Bridges, Todd; Linkov, Igor

2012-08-01

Risk managers are increasingly interested in incorporating stakeholder beliefs and other human factors into the planning process. Effective risk assessment and management requires understanding perceptions and beliefs of involved stakeholders, and how these beliefs give rise to actions that influence risk management decisions. Formal analyses of risk manager and stakeholder cognitions represent an important first step. Techniques for diagramming stakeholder mental models provide one tool for risk managers to better understand stakeholder beliefs and perceptions concerning risk, and to leverage this new understanding in developing risk management strategies. This article reviews three methodologies for assessing and diagramming stakeholder mental models--decision-analysis-based mental modeling, concept mapping, and semantic web analysis--and assesses them with regard to their ability to address risk manager needs. © 2012 Society for Risk Analysis.

Use of Electronic Health Record Tools to Facilitate and Audit Infliximab Prescribing.

PubMed

Sharpless, Bethany R; Del Rosario, Fernando; Molle-Rios, Zarela; Hilmas, Elora

2018-01-01

The objective of this project was to assess a pediatric institution's use of infliximab and develop and evaluate electronic health record tools to improve safety and efficiency of infliximab ordering through auditing and improved communication. Best use of infliximab was defined through a literature review, analysis of baseline use of infliximab at our institution, and distribution and analysis of a national survey. Auditing and order communication were optimized through implementation of mandatory indications in the infliximab orderable and creation of an interactive flowsheet that collects discrete and free-text data. The value of the implemented electronic health record tools was assessed at the conclusion of the project. Baseline analysis determined that 93.8% of orders were dosed appropriately according to the findings of a literature review. After implementation of the flowsheet and indications, the time to perform an audit of use was reduced from 60 minutes to 5 minutes per month. Four months post implementation, data were entered by 60% of the pediatric gastroenterologists at our institution on 15.3% of all encounters for infliximab. Users were surveyed on the value of the tools, with 100% planning to continue using the workflow, and 82% stating the tools frequently improve the efficiency and safety of infliximab prescribing. Creation of a standard workflow by using an interactive flowsheet has improved auditing ability and facilitated the communication of important order information surrounding infliximab. Providers and pharmacists feel these tools improve the safety and efficiency of infliximab ordering, and auditing data reveal that the tools are being used.

[Factor structure of regional CBF and CMRglu values as a tool for the study of default mode of the brain].

PubMed

Kataev, G V; Korotkov, A D; Kireev, M V; Medvedev, S V

2013-01-01

In the present article it was shown that the functional connectivity of brain structures, revealed by factor analysis of resting PET CBF and rCMRglu data, is an adequate tool to study the default mode of the human brain. The identification of neuroanatomic systems of default mode (default mode network) during routine clinical PET investigations is important for further studying the functional organization of the normal brain and its reorganizations in pathological conditions.

Comprehensive Analysis of DNA Methylation Data with RnBeads

PubMed Central

Walter, Jörn; Lengauer, Thomas; Bock, Christoph

2014-01-01

RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports (http://rnbeads.mpi-inf.mpg.de). Supported assays include whole genome bisulfite sequencing, reduced representation bisulfite sequencing, Infinium microarrays, and any other protocol that produces high-resolution DNA methylation data. Important applications of RnBeads include the analysis of epigenome-wide association studies and epigenetic biomarker discovery in cancer cohorts. PMID:25262207

Analyzing Human-Landscape Interactions: Tools That Integrate

NASA Astrophysics Data System (ADS)

Zvoleff, Alex; An, Li

2014-01-01

Humans have transformed much of Earth's land surface, giving rise to loss of biodiversity, climate change, and a host of other environmental issues that are affecting human and biophysical systems in unexpected ways. To confront these problems, environmental managers must consider human and landscape systems in integrated ways. This means making use of data obtained from a broad range of methods (e.g., sensors, surveys), while taking into account new findings from the social and biophysical science literatures. New integrative methods (including data fusion, simulation modeling, and participatory approaches) have emerged in recent years to address these challenges, and to allow analysts to provide information that links qualitative and quantitative elements for policymakers. This paper brings attention to these emergent tools while providing an overview of the tools currently in use for analysis of human-landscape interactions. Analysts are now faced with a staggering array of approaches in the human-landscape literature—in an attempt to bring increased clarity to the field, we identify the relative strengths of each tool, and provide guidance to analysts on the areas to which each tool is best applied. We discuss four broad categories of tools: statistical methods (including survival analysis, multi-level modeling, and Bayesian approaches), GIS and spatial analysis methods, simulation approaches (including cellular automata, agent-based modeling, and participatory modeling), and mixed-method techniques (such as alternative futures modeling and integrated assessment). For each tool, we offer an example from the literature of its application in human-landscape research. Among these tools, participatory approaches are gaining prominence for analysts to make the broadest possible array of information available to researchers, environmental managers, and policymakers. Further development of new approaches of data fusion and integration across sites or disciplines pose an important challenge for future work in integrating human and landscape components.

Online tools for uncovering data quality issues in satellite-based global precipitation products

NASA Astrophysics Data System (ADS)

Liu, Z.; Heo, G.

2015-12-01

Accurate and timely available global precipitation products are important to many applications such as flood forecasting, hydrological modeling, vector-borne disease research, crop yield estimates, etc. However, data quality issues such as biases and uncertainties are common in satellite-based precipitation products and it is important to understand these issues in applications. In recent years, algorithms using multi-satellites and multi-sensors for satellite-based precipitation estimates have become popular, such as the TRMM (Tropical Rainfall Measuring Mission) Multi-satellite Precipitation Analysis (TMPA) and the latest Integrated Multi-satellitE Retrievals for GPM (IMERG). Studies show that data quality issues for multi-satellite and multi-sensor products can vary with space and time and can be difficult to summarize. Online tools can provide customized results for a given area of interest, allowing customized investigation or comparison on several precipitation products. Because downloading data and software is not required, online tools can facilitate precipitation product evaluation and comparison. In this presentation, we will present online tools to uncover data quality issues in satellite-based global precipitation products. Examples will be presented as well.

ADGS-2100 Adaptive Display and Guidance System Window Manager Analysis

NASA Technical Reports Server (NTRS)

Whalen, Mike W.; Innis, John D.; Miller, Steven P.; Wagner, Lucas G.

2006-01-01

Recent advances in modeling languages have made it feasible to formally specify and analyze the behavior of large system components. Synchronous data flow languages, such as Lustre, SCR, and RSML-e are particularly well suited to this task, and commercial versions of these tools such as SCADE and Simulink are growing in popularity among designers of safety critical systems, largely due to their ability to automatically generate code from the models. At the same time, advances in formal analysis tools have made it practical to formally verify important properties of these models to ensure that design defects are identified and corrected early in the lifecycle. This report describes how these tools have been applied to the ADGS-2100 Adaptive Display and Guidance Window Manager being developed by Rockwell Collins Inc. This work demonstrates how formal methods can be easily and cost-efficiently used to remove defects early in the design cycle.

Icarus: visualizer for de novo assembly evaluation.

PubMed

Mikheenko, Alla; Valin, Gleb; Prjibelski, Andrey; Saveliev, Vladislav; Gurevich, Alexey

2016-11-01

: Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application. http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

OverPlotter: A Utility for Herschel Data Processing

NASA Astrophysics Data System (ADS)

Zhang, L.; Mei, Y.; Schulz, B.

2008-08-01

The OverPlotter utility is a GUI tool written in Java to support interactive data processing (DP) and analysis for the Herschel Space Observatory within the framework of the Herschel Common Science System (HCSS)(Wieprecht et al 2004). The tool expands upon the capabilities of the TableViewer (Zhang & Schulz 2005), providing now also the means to create additional overlays of several X/Y scatter plots within the same display area. These layers can be scaled and panned, either individually, or together as one graph. Visual comparison of data with different origins and units becomes much easier. The number of available layers is not limited, except by computer memory and performance. Presentation images can be easily created by adding annotations, labeling layers and setting colors. The tool will be very helpful especially in the early phases of Herschel data analysis, when a quick access to contents of data products is important.

Metabolomics combined with chemometric tools (PCA, HCA, PLS-DA and SVM) for screening cassava (Manihot esculenta Crantz) roots during postharvest physiological deterioration.

PubMed

Uarrota, Virgílio Gavicho; Moresco, Rodolfo; Coelho, Bianca; Nunes, Eduardo da Costa; Peruch, Luiz Augusto Martins; Neubert, Enilto de Oliveira; Rocha, Miguel; Maraschin, Marcelo

2014-10-15

Cassava roots are an important source of dietary and industrial carbohydrates and suffer markedly from postharvest physiological deterioration (PPD). This paper deals with metabolomics combined with chemometric tools for screening the chemical and enzymatic composition in several genotypes of cassava roots during PPD. Metabolome analyses showed increases in carotenoids, flavonoids, anthocyanins, phenolics, reactive scavenging species, and enzymes (superoxide dismutase family, hydrogen peroxide, and catalase) until 3-5days postharvest. PPD correlated negatively with phenolics and carotenoids and positively with anthocyanins and flavonoids. Chemometric tools such as principal component analysis, partial least squares discriminant analysis, and support vector machines discriminated well cassava samples and enabled a good prediction of samples. Hierarchical clustering analyses grouped samples according to their levels of PPD and chemical compositions. Copyright © 2014 Elsevier Ltd. All rights reserved.

ESTIMATING THE TIMING OF DIET SHIFTS USING STABLE ISOTOPES

EPA Science Inventory

Stable isotope analysis has become an important tool in studies of trophic food webs and animal feeding patterns. When animals undergo rapid dietary shifts due to migration, metamorphosis, or other reasons, the isotopic composition of their tissues begins changing to reflect tha...

Data and Tools | Energy Analysis | NREL

Science.gov Websites

and Tools Energy Analysis Data and Tools NREL develops energy analysis data and tools to assess collections. Data Products Technology and Performance Analysis Tools Energy Systems Analysis Tools Economic and Financial Analysis Tools

GeneTools--application for functional annotation and statistical hypothesis testing.

PubMed

Beisvag, Vidar; Jünge, Frode K R; Bergum, Hallgeir; Jølsum, Lars; Lydersen, Stian; Günther, Clara-Cecilie; Ramampiaro, Heri; Langaas, Mette; Sandvik, Arne K; Laegreid, Astrid

2006-10-24

Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions. GeneTools is a web-service providing access to a database that brings together information from a broad range of resources. The annotation data are updated weekly, guaranteeing that users get data most recently available. Data submitted by the user are stored in the database, where it can easily be updated, shared between users and exported in various formats. GeneTools provides three different tools: i) NMC Annotation Tool, which offers annotations from several databases like UniGene, Entrez Gene, SwissProt and GeneOntology, in both single- and batch search mode. ii) GO Annotator Tool, where users can add new gene ontology (GO) annotations to genes of interest. These user defined GO annotations can be used in further analysis or exported for public distribution. iii) eGOn, a tool for visualization and statistical hypothesis testing of GO category representation. As the first GO tool, eGOn supports hypothesis testing for three different situations (master-target situation, mutually exclusive target-target situation and intersecting target-target situation). An important additional function is an evidence-code filter that allows users, to select the GO annotations for the analysis. GeneTools is the first "all in one" annotation tool, providing users with a rapid extraction of highly relevant gene annotation data for e.g. thousands of genes or clones at once. It allows a user to define and archive new GO annotations and it supports hypothesis testing related to GO category representations. GeneTools is freely available through www.genetools.no

Stone tool analysis and human origins research: some advice from Uncle Screwtape.

PubMed

Shea, John J

2011-01-01

The production of purposefully fractured stone tools with functional, sharp cutting edges is a uniquely derived hominin adaptation. In the long history of life on earth, only hominins have adopted this remarkably expedient and broadly effective technological strategy. In the paleontological record, flaked stone tools are irrefutable proof that hominins were present at a particular place and time. Flaked stone tools are found in contexts ranging from the Arctic to equatorial rainforests and on every continent except Antarctica. Paleolithic stone tools show complex patterns of variability, suggesting that they have been subject to the variable selective pressures that have shaped so many other aspects of hominin behavior and morphology. There is every reason to expect that insights gained from studying stone tools should provide vital and important information about the course of human evolution. And yet, one senses that archeological analyses of Paleolithic stone tools are not making as much of a contribution as they could to the major issues in human origins research. Copyright © 2011 Wiley Periodicals, Inc.

Frequency Response Studies using Receptance Coupling Approach in High Speed Spindles

NASA Astrophysics Data System (ADS)

Shaik, Jakeer Hussain; Ramakotaiah, K.; Srinivas, J.

2018-01-01

In order to assess the stability of high speed machining, estimate the frequency response at the end of tool tip is of great importance. Evaluating dynamic response of several combinations of integrated spindle-tool holder-tool will consume a lot of time. This paper presents coupled field dynamic response at tool tip for the entire integrated spindle tool unit. The spindle unit is assumed to be relying over the front and rear bearings and investigated using the Timoshenko beam theory to arrive the receptances at different locations of the spindle-tool unit. The responses are further validated with conventional finite element model as well as with the experiments. This approach permits quick outputs without losing accuracy of solution and further these methods are utilized to analyze the various design variables on system dynamics. The results obtained through this analysis are needed to design the better spindle unit in an attempt to reduce the frequency amplitudes at the tool tip to improvise the milling stability during cutting process.

Quantifying Traces of Tool Use: A Novel Morphometric Analysis of Damage Patterns on Percussive Tools

PubMed Central

Caruana, Matthew V.; Carvalho, Susana; Braun, David R.; Presnyakova, Darya; Haslam, Michael; Archer, Will; Bobe, Rene; Harris, John W. K.

2014-01-01

Percussive technology continues to play an increasingly important role in understanding the evolution of tool use. Comparing the archaeological record with extractive foraging behaviors in nonhuman primates has focused on percussive implements as a key to investigating the origins of lithic technology. Despite this, archaeological approaches towards percussive tools have been obscured by a lack of standardized methodologies. Central to this issue have been the use of qualitative, non-diagnostic techniques to identify percussive tools from archaeological contexts. Here we describe a new morphometric method for distinguishing anthropogenically-generated damage patterns on percussive tools from naturally damaged river cobbles. We employ a geomatic approach through the use of three-dimensional scanning and geographical information systems software to statistically quantify the identification process in percussive technology research. This will strengthen current technological analyses of percussive tools in archaeological frameworks and open new avenues for translating behavioral inferences of early hominins from percussive damage patterns. PMID:25415303

Tools and Equipment Modeling for Automobile Interactive Assembling Operating Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu Dianliang; Zhu Hongmin; Shanghai Key Laboratory of Advance Manufacturing Environment

Tools and equipment play an important role in the simulation of virtual assembly, especially in the assembly process simulation and plan. Because of variety in function and complexity in structure and manipulation, the simulation of tools and equipments remains to be a challenge for interactive assembly operation. Based on analysis of details and characteristics of interactive operations for automobile assembly, the functional requirement for tools and equipments of automobile assembly is given. Then, a unified modeling method for information expression and function realization of general tools and equipments is represented, and the handling methods of manual, semi-automatic, automatic tools andmore » equipments are discussed. Finally, the application in assembly simulation of rear suspension and front suspension of Roewe 750 automobile is given. The result shows that the modeling and handling methods are applicable in the interactive simulation of various tools and equipments, and can also be used for supporting assembly process planning in virtual environment.« less

Validating a tool to measure auxiliary nurse midwife and nurse motivation in rural Nepal.

PubMed

Morrison, Joanna; Batura, Neha; Thapa, Rita; Basnyat, Regina; Skordis-Worrall, Jolene

2015-05-12

A global shortage of health workers in rural areas increases the salience of motivating and supporting existing health workers. Understandings of motivation may vary in different settings, and it is important to use measurement methods that are contextually appropriate. We identified a measurement tool, previously used in Kenya, and explored its validity and reliability to measure the motivation of auxiliary nurse midwives (ANM) and staff nurses (SN) in rural Nepal. Qualitative and quantitative methods were used to assess the content validity, the construct validity, the internal consistency and the reliability of the tool. We translated the tool into Nepali and it was administered to 137 ANMs and SNs in three districts. We collected qualitative data from 78 nursing personnel and district- and central-level stakeholders using interviews and focus group discussions. We calculated motivation scores for ANMs and SNs using the quantitative data and conducted statistical tests for validity and reliability. Motivation scores were compared with qualitative data. Descriptive exploratory analysis compared mean motivation scores by ANM and SN sociodemographic characteristics. The concept of self-efficacy was added to the tool before data collection. Motivation was revealed through conscientiousness. Teamwork and the exertion of extra effort were not adequately captured by the tool, but important in illustrating motivation. The statement on punctuality was problematic in quantitative analysis, and attendance was more expressive of motivation. The calculated motivation scores usually reflected ANM and SN interview data, with some variation in other stakeholder responses. The tool scored within acceptable limits in validity and reliability testing and was able to distinguish motivation of nursing personnel with different sociodemographic characteristics. We found that with minor modifications, the tool provided valid and internally consistent measures of motivation among ANMs and SNs in this context. We recommend the use of this tool in similar contexts, with the addition of statements about self-efficacy, teamwork and exertion of extra effort. Absenteeism should replace the punctuality statement, and statements should be worded both positively and negatively to mitigate positive response bias. Collection of qualitative data on motivation creates a more nuanced understanding of quantitative scores.

Is the Job Satisfaction Survey a good tool to measure job satisfaction amongst health workers in Nepal? Results of a validation analysis.

PubMed

Batura, Neha; Skordis-Worrall, Jolene; Thapa, Rita; Basnyat, Regina; Morrison, Joanna

2016-07-27

Job satisfaction is an important predictor of an individual's intention to leave the workplace. It is increasingly being used to consider the retention of health workers in low-income countries. However, the determinants of job satisfaction vary in different contexts, and it is important to use measurement methods that are contextually appropriate. We identified a measurement tool developed by Paul Spector, and used mixed methods to assess its validity and reliability in measuring job satisfaction among maternal and newborn health workers (MNHWs) in government facilities in rural Nepal. We administered the tool to 137 MNHWs and collected qualitative data from 78 MNHWs, and district and central level stakeholders to explore definitions of job satisfaction and factors that affected it. We calculated a job satisfaction index for all MNHWs using quantitative data and tested for validity, reliability and sensitivity. We conducted qualitative content analysis and compared the job satisfaction indices with qualitative data. Results from the internal consistency tests offer encouraging evidence of the validity, reliability and sensitivity of the tool. Overall, the job satisfaction indices reflected the qualitative data. The tool was able to distinguish levels of job satisfaction among MNHWs. However, the work environment and promotion dimensions of the tool did not adequately reflect local conditions. Further, community fit was found to impact job satisfaction but was not captured by the tool. The relatively high incidence of missing responses may suggest that responding to some statements was perceived as risky. Our findings indicate that the adapted job satisfaction survey was able to measure job satisfaction in Nepal. However, it did not include key contextual factors affecting job satisfaction of MNHWs, and as such may have been less sensitive than a more inclusive measure. The findings suggest that this tool can be used in similar settings and populations, with the addition of statements reflecting the nature of the work environment and structure of the local health system. Qualitative data on job satisfaction should be collected before using the tool in a new context, to highlight any locally relevant dimensions of job satisfaction not already captured in the standard survey.

Improved Analysis of Earth System Models and Observations using Simple Climate Models

NASA Astrophysics Data System (ADS)

Nadiga, B. T.; Urban, N. M.

2016-12-01

Earth system models (ESM) are the most comprehensive tools we have to study climate change and develop climate projections. However, the computational infrastructure required and the cost incurred in running such ESMs precludes direct use of such models in conjunction with a wide variety of tools that can further our understanding of climate. Here we are referring to tools that range from dynamical systems tools that give insight into underlying flow structure and topology to tools that come from various applied mathematical and statistical techniques and are central to quantifying stability, sensitivity, uncertainty and predictability to machine learning tools that are now being rapidly developed or improved. Our approach to facilitate the use of such models is to analyze output of ESM experiments (cf. CMIP) using a range of simpler models that consider integral balances of important quantities such as mass and/or energy in a Bayesian framework.We highlight the use of this approach in the context of the uptake of heat by the world oceans in the ongoing global warming. Indeed, since in excess of 90% of the anomalous radiative forcing due greenhouse gas emissions is sequestered in the world oceans, the nature of ocean heat uptake crucially determines the surface warming that is realized (cf. climate sensitivity). Nevertheless, ESMs themselves are never run long enough to directly assess climate sensitivity. So, we consider a range of models based on integral balances--balances that have to be realized in all first-principles based models of the climate system including the most detailed state-of-the art climate simulations. The models range from simple models of energy balance to those that consider dynamically important ocean processes such as the conveyor-belt circulation (Meridional Overturning Circulation, MOC), North Atlantic Deep Water (NADW) formation, Antarctic Circumpolar Current (ACC) and eddy mixing. Results from Bayesian analysis of such models using both ESM experiments and actual observations are presented. One such result points to the importance of direct sequestration of heat below 700 m, a process that is not allowed for in the simple models that have been traditionally used to deduce climate sensitivity.

EconoMe-Develop - a calculation tool for multi-risk assessment and benefit-cost-analysis

NASA Astrophysics Data System (ADS)

Bründl, M.

2012-04-01

Public money is used to finance the protection of human life, material assets and the environment against natural hazards. This limited resource should be used in a way that it achieves the maximum possible effect by minimizing as many risks as possible. Hence, decision-makers are facing the question which mitigation measures should be prioritised. Benefit-Cost-Analysis (BCA) is a recognized method for determining the economic efficiency of investments in mitigation measures. In Switzerland, the Federal Office for the Environment (FOEN) judges the benefit-cost-ratio of mitigation projects on the base of the results of the calculation tool "EconoMe" [1]. The check of the economic efficiency of mitigation projects with an investment of more than 1 million CHF (800,000 EUR) by using "EconoMe" is mandatory since 2008 in Switzerland. Within "EconoMe", most calculation parameters cannot be changed by the user allowing for comparable results. Based on the risk guideline "RIKO" [2] an extended version of the operational version of "EconoMe", called "EconoMe-Develop" was developed. "EconoMe-Develop" is able to deal with various natural hazard processes and thus allows multi-risk assessments, since all restrictions of the operational version of "EconoMe" like e.g. the number of scenarios and expositions, vulnerability, spatial probability of processes and probability of presence of objects, are not existing. Additionally, the influences of uncertainty of calculation factors, like e.g. vulnerability, on the final results can be determined. "EconoMe-Develop" offers import and export of data, e.g. results of GIS-analysis. The possibility for adapting the tool to user specific requirements makes EconoMe-Develop an easy-to-use tool for risk assessment and assessment of economic efficiency of mitigation projects for risk experts. In the paper we will present the most important features of the tool and we will illustrate the application by a practical example.

The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts.

PubMed

Monteiro, Pedro Tiago; Pais, Pedro; Costa, Catarina; Manna, Sauvagya; Sá-Correia, Isabel; Teixeira, Miguel Cacho

2017-01-04

We present the PATHOgenic YEAst Search for Transcriptional Regulators And Consensus Tracking (PathoYeastract - http://pathoyeastract.org) database, a tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in the pathogenic yeasts Candida albicans and C. glabrata Upon data retrieval from hundreds of publications, followed by curation, the database currently includes 28 000 unique documented regulatory associations between transcription factors (TF) and target genes and 107 DNA binding sites, considering 134 TFs in both species. Following the structure used for the YEASTRACT database, PathoYeastract makes available bioinformatics tools that enable the user to exploit the existing information to predict the TFs involved in the regulation of a gene or genome-wide transcriptional response, while ranking those TFs in order of their relative importance. Each search can be filtered based on the selection of specific environmental conditions, experimental evidence or positive/negative regulatory effect. Promoter analysis tools and interactive visualization tools for the representation of TF regulatory networks are also provided. The PathoYeastract database further provides simple tools for the prediction of gene and genomic regulation based on orthologous regulatory associations described for other yeast species, a comparative genomics setup for the study of cross-species evolution of regulatory networks. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evaluating an holistic assessment tool for palliative care practice.

PubMed

McIlfatrick, Sonja; Hasson, Felicity

2014-04-01

To evaluate a holistic assessment tool for palliative care practice. This included identifying patients' needs using the holistic tool and exploring the usability, applicability and barriers and facilitators towards implementation in practice. The delivery of effective holistic palliative care requires a careful assessment of the patients' needs and circumstances. Whilst holistic assessment of palliative care needs is advocated, questions exist around the appropriateness of tools to assist this process. Mixed-method research design. Data collection involved an analysis of piloted holistic assessments undertaken using the tool (n = 132) and two focus groups with healthcare professionals (n = 10). The tool enabled health professionals to identify and gain an understanding of the needs of the patients, specifically in relation to the physical healthcare needs. Differences, however, between the analysis of the tool documentation and focus group responses were identified in particular areas. For example, 59 (68·8%) respondents had discussed preferred priorities of care with the patient; however, focus group comments revealed participants had concerns around this. Similarly, whilst over half of responses (n = 50; 57·5%) had considered a prognostic clinical indicator for the patient as an action, focus group results indicated questions around healthcare professionals' knowledge and perceived usefulness of such indicators. Positive aspects of the tool were that it was easy to understand and captured the needs of individuals. Negative aspects of the tool were that it was repetitive and the experience of assessors required consideration. The tool evaluation identified questions regarding holistic assessment in palliative care practice and the importance of communication. A holistic assessment tool can support patient assessment and identification of patients' needs in the 'real world' of palliative care practice, but the 'tool' is merely an aid to assist professionals to discuss difficult and sensitive aspects of care. © 2013 John Wiley & Sons Ltd.

BBMerge – Accurate paired shotgun read merging via overlap

DOE PAGES

Bushnell, Brian; Rood, Jonathan; Singer, Esther

2017-10-26

Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highlymore » sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.« less

BBMerge – Accurate paired shotgun read merging via overlap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bushnell, Brian; Rood, Jonathan; Singer, Esther

Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highlymore » sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.« less

Generic extravehicular (EVA) and telerobot task primitives for analysis, design, and integration. Version 1.0: Reference compilation for the EVA and telerobotics communities

NASA Technical Reports Server (NTRS)

Smith, Jeffrey H.; Drews, Michael

1990-01-01

The results are described of an effort to establish commonality and standardization of generic crew extravehicular (crew-EVA) and telerobotic task analysis primitives used for the study of spaceborne operations. Although direct crew-EVA plans are the most visible output of spaceborne operations, significant ongoing efforts by a wide variety of projects and organizations also require tools for estimation of crew-EVA and telerobotic times. Task analysis tools provide estimates for input to technical and cost tradeoff studies. A workshop was convened to identify the issues and needs to establish a common language and syntax for task analysis primitives. In addition, the importance of such a syntax was shown to have precedence over the level to which such a syntax is applied. The syntax, lists of crew-EVA and telerobotic primitives, and the data base in diskette form are presented.

Analysis of Illumina Microbial Assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clum, Alicia; Foster, Brian; Froula, Jeff

2010-05-28

Since the emerging of second generation sequencing technologies, the evaluation of different sequencing approaches and their assembly strategies for different types of genomes has become an important undertaken. Next generation sequencing technologies dramatically increase sequence throughput while decreasing cost, making them an attractive tool for whole genome shotgun sequencing. To compare different approaches for de-novo whole genome assembly, appropriate tools and a solid understanding of both quantity and quality of the underlying sequence data are crucial. Here, we performed an in-depth analysis of short-read Illumina sequence assembly strategies for bacterial and archaeal genomes. Different types of Illumina libraries as wellmore » as different trim parameters and assemblers were evaluated. Results of the comparative analysis and sequencing platforms will be presented. The goal of this analysis is to develop a cost-effective approach for the increased throughput of the generation of high quality microbial genomes.« less

The importance of experimental design on measurement of dynamic interfacial tension and interfacial rheology in diffusion-limited surfactant systems

DOE PAGES

Reichert, Matthew D.; Alvarez, Nicolas J.; Brooks, Carlton F.; ...

2014-09-24

Pendant bubble and drop devices are invaluable tools in understanding surfactant behavior at fluid–fluid interfaces. The simple instrumentation and analysis are used widely to determine adsorption isotherms, transport parameters, and interfacial rheology. However, much of the analysis performed is developed for planar interfaces. Moreover, the application of a planar analysis to drops and bubbles (curved interfaces) can lead to erroneous and unphysical results. We revisit this analysis for a well-studied surfactant system at air–water interfaces over a wide range of curvatures as applied to both expansion/contraction experiments and interfacial elasticity measurements. The impact of curvature and transport on measured propertiesmore » is quantified and compared to other scaling relationships in the literature. Our results provide tools to design interfacial experiments for accurate determination of isotherm, transport and elastic properties.« less

Multiple shooting shadowing for sensitivity analysis of chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Blonigan, Patrick J.; Wang, Qiqi

2018-02-01

Sensitivity analysis methods are important tools for research and design with simulations. Many important simulations exhibit chaotic dynamics, including scale-resolving turbulent fluid flow simulations. Unfortunately, conventional sensitivity analysis methods are unable to compute useful gradient information for long-time-averaged quantities in chaotic dynamical systems. Sensitivity analysis with least squares shadowing (LSS) can compute useful gradient information for a number of chaotic systems, including simulations of chaotic vortex shedding and homogeneous isotropic turbulence. However, this gradient information comes at a very high computational cost. This paper presents multiple shooting shadowing (MSS), a more computationally efficient shadowing approach than the original LSS approach. Through an analysis of the convergence rate of MSS, it is shown that MSS can have lower memory usage and run time than LSS.

psRNATarget: a plant small RNA target analysis server

PubMed Central

Dai, Xinbin; Zhao, Patrick Xuechun

2011-01-01

Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/. PMID:21622958

Spectroscopic magnetic resonance imaging of the brain: voxel localisation and tissue segmentation in the follow up of brain tumour.

PubMed

Poloni, Guy; Bastianello, S; Vultaggio, Angela; Pozzi, S; Maccabelli, Gloria; Germani, Giancarlo; Chiarati, Patrizia; Pichiecchio, Anna

2008-01-01

The field of application of magnetic resonance spectroscopy (MRS) in biomedical research is expanding all the time and providing opportunities to investigate tissue metabolism and function. The data derived can be integrated with the information on tissue structure gained from conventional and non-conventional magnetic resonance imaging (MRI) techniques. Clinical MRS is also strongly expected to play an important role as a diagnostic tool. Essential for the future success of MRS as a clinical and research tool in biomedical sciences, both in vivo and in vitro, is the development of an accurate, biochemically relevant and physically consistent and reliable data analysis standard. Stable and well established analysis algorithms, in both the time and the frequency domain, are already available, as is free commercial software for implementing them. In this study, we propose an automatic algorithm that takes into account anatomical localisation, relative concentrations of white matter, grey matter, cerebrospinal fluid and signal abnormalities and inter-scan patient movement. The endpoint is the collection of a series of covariates that could be implemented in a multivariate analysis of covariance (MANCOVA) of the MRS data, as a tool for dealing with differences that may be ascribed to the anatomical variability of the subjects, to inaccuracies in the localisation of the voxel or slab, or to movement, rather than to the pathology under investigation. The aim was to develop an analysis procedure that can be consistently and reliably applied in the follow up of brain tumour. In this study, we demonstrate that the inclusion of such variables in the data analysis of quantitative MRS is fundamentally important (especially in view of the reduced accuracy typical of MRS measures compared to other MRI techniques), reducing the occurrence of false positives.

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

PubMed Central

Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz. PMID:23093919

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

PubMed

Chovancova, Eva; Pavelka, Antonin; Benes, Petr; Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

Hand-independent representation of tool-use pantomimes in the left anterior intraparietal cortex.

PubMed

Ogawa, Kenji; Imai, Fumihito

2016-12-01

Previous neuropsychological studies of ideomotor apraxia (IMA) indicated impairments in pantomime actions for tool use for both right and left hands following lesions of parieto-premotor cortices in the left hemisphere. Using functional magnetic resonance imaging (fMRI) with multi-voxel pattern analysis (MVPA), we tested the hypothesis that the left parieto-premotor cortices are involved in the storage or retrieval of hand-independent representation of tool-use actions. In the fMRI scanner, one of three kinds of tools was displayed in pictures or letters, and the participants made pantomimes of the use of these tools using the right hand for the picture stimuli or with the left hand for the letters. We then used MVPA to classify which kind of tool the subjects were pantomiming. Whole-brain searchlight analysis revealed successful decoding using the activities largely in the contralateral primary sensorimotor region, ipsilateral cerebellum, and bilateral early visual area, which may reflect differences in low-level sensorimotor components for three types of pantomimes. Furthermore, a successful cross-classification between the right and left hands was possible using the activities of the left inferior parietal lobule (IPL) near the junction of the anterior intraparietal sulcus. Our finding indicates that the left anterior intraparietal cortex plays an important role in the production of tool-use pantomimes in a hand-independent manner, and independent of stimuli modality.

Impact of design features upon perceived tool usability and safety

NASA Astrophysics Data System (ADS)

Wiker, Steven F.; Seol, Mun-Su

2005-11-01

While injuries from powered hand tools are caused by a number of factors, this study looks specifically at the impact of the tools design features on perceived tool usability and safety. The tools used in this study are circular saws, power drills and power nailers. Sixty-nine males and thirty-two females completed an anonymous web-based questionnaire that provided orthogonal view photographs of the various tools. Subjects or raters provided: 1) description of the respondents or raters, 2) description of the responses from the raters, and 3) analysis of the interrelationships among respondent ratings of tool safety and usability, physical metrics of the tool, and rater demographic information. The results of the study found that safety and usability were dependent materially upon rater history of use and experience, but not upon training in safety and usability, or quality of design features of the tools (e.g., grip diameters, trigger design, guards, etc.). Thus, positive and negative transfer of prior experience with use of powered hand tools is far more important than any expectancy that may be driven by prior safety and usability training, or from the visual cues that are provided by the engineering design of the tool.

Modern Computational Techniques for the HMMER Sequence Analysis

PubMed Central

2013-01-01

This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications—hidden Markov models (HMM). We show the detailed performance comparison of sequence analysis tools on various computing platforms recently developed in the bioinformatics society. The characteristics of the sequence analysis, such as data and compute-intensive natures, make it very attractive to optimize and parallelize by using both traditional software approach and innovated hardware acceleration technologies. PMID:25937944

Constructing Social Networks From Secondary Storage With Bulk Analysis Tools

DTIC Science & Technology

2016-06-01

that classic measures of centrality are effective for identifying important nodes and close associates, and that further study of modularity classes...which ground truth was determined by interviews with the owners, and which can be used for future study in this area. Two objectives motivated this thesis...tifying important nodes and close associates, and that further study of modularity classes may be a promising method of partitioning complex components

Experimental Approaches to Microarray Analysis of Tumor Samples

ERIC Educational Resources Information Center

Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

2008-01-01

Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

Estimating population diversity with CatchAll

USDA-ARS?s Scientific Manuscript database

The massive quantity of data produced by next-generation sequencing has created a pressing need for advanced statistical tools, in particular for analysis of bacterial and phage communities. Here we address estimating the total diversity in a population – the species richness. This is an important s...

Development of a Relay Performance Web Tool for the Mars Network

NASA Technical Reports Server (NTRS)

Allard, Daniel A.; Edwards, Charles D.

2009-01-01

Modern Mars surface missions rely upon orbiting spacecraft to relay communications to and from Earth systems. An important component of this multi-mission relay process is the collection of relay performance statistics supporting strategic trend analysis and tactical anomaly identification and tracking.

Analyzing Subsidies in Microsoft Excel

ERIC Educational Resources Information Center

Mixon, J. Wilson, Jr.

2005-01-01

Applying the budget line/indifference curve apparatus to policy issues reveals important and sometimes counterintuitive policy implications. Also, it provides practice in using the apparatus. The author applies these tools to subsidies. The analysis follows textbook treatments but is extended at some points. In particular, the present analysis…

Tracing Anthropogenic Pollution Through Dendrochemistry

NASA Astrophysics Data System (ADS)

Rocha, E.; Gunnarson, B. E.; Holzkaemper, S.

2017-12-01

The growing concern regarding pollution effects on the environment and human health demands new control strategies and monitoring tools. In this study we assess the potential of using dendrochemistry as a forensic tool to investigate chemical contamination patterns in the surroundings of a former glass factory in Southern Sweden. Tree-ring width chronologies were produced from exposed and non-exposed sites. Using energy disperse X-ray fluorescence (EDXRF) technique, tree cores of Scots Pine (Pinus sylvestris), Norway spruce (Picea Abies) and Populus tremula (European Aspen) were analysed for their elemental composition in accordance with previous soil analysis done in the area. Traces of barium and considerable alteration of the chlorine profiles were successfully detected confirming the potential of the method to record environmental releases. The dendrochemical analysis also highlighted the differences in the response of tree species to elements uptake (root sensitivity) and the importance of metals bioavailability. Finally, the adopted sampling strategy is of outmost importance to the success of the method.

The value of job analysis, job description and performance.

PubMed

Wolfe, M N; Coggins, S

1997-01-01

All companies, regardless of size, are faced with the same employment concerns. Efficient personnel management requires the use of three human resource techniques--job analysis, job description and performance appraisal. These techniques and tools are not for large practices only. Small groups can obtain the same benefits by employing these performance control measures. Job analysis allows for the development of a compensation system. Job descriptions summarize the most important duties. Performance appraisals help reward outstanding work.

NEURON and Python.

PubMed

Hines, Michael L; Davison, Andrew P; Muller, Eilif

2009-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications.

NEURON and Python

PubMed Central

Hines, Michael L.; Davison, Andrew P.; Muller, Eilif

2008-01-01

The NEURON simulation program now allows Python to be used, alone or in combination with NEURON's traditional Hoc interpreter. Adding Python to NEURON has the immediate benefit of making available a very extensive suite of analysis tools written for engineering and science. It also catalyzes NEURON software development by offering users a modern programming tool that is recognized for its flexibility and power to create and maintain complex programs. At the same time, nothing is lost because all existing models written in Hoc, including graphical user interface tools, continue to work without change and are also available within the Python context. An example of the benefits of Python availability is the use of the xml module in implementing NEURON's Import3D and CellBuild tools to read MorphML and NeuroML model specifications. PMID:19198661

Polymers and biopolymers at interfaces

NASA Astrophysics Data System (ADS)

Hall, A. R.; Geoghegan, M.

2018-03-01

This review updates recent progress in the understanding of the behaviour of polymers at surfaces and interfaces, highlighting examples in the areas of wetting, dewetting, crystallization, and ‘smart’ materials. Recent developments in analysis tools have yielded a large increase in the study of biological systems, and some of these will also be discussed, focussing on areas where surfaces are important. These areas include molecular binding events and protein adsorption as well as the mapping of the surfaces of cells. Important techniques commonly used for the analysis of surfaces and interfaces are discussed separately to aid the understanding of their application.

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-09-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing numbers of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis relating the multiple visualisation challenges to a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-04-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing amounts of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis, relating the multiple visualisation challenges with a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

TACT: A Set of MSC/PATRAN- and MSC/NASTRAN- based Modal Correlation Tools

NASA Technical Reports Server (NTRS)

Marlowe, Jill M.; Dixon, Genevieve D.

1998-01-01

This paper describes the functionality and demonstrates the utility of the Test Analysis Correlation Tools (TACT), a suite of MSC/PATRAN Command Language (PCL) tools which automate the process of correlating finite element models to modal survey test data. The initial release of TACT provides a basic yet complete set of tools for performing correlation totally inside the PATRAN/NASTRAN environment. Features include a step-by-step menu structure, pre-test accelerometer set evaluation and selection, analysis and test result export/import in Universal File Format, calculation of frequency percent difference and cross-orthogonality correlation results using NASTRAN, creation and manipulation of mode pairs, and five different ways of viewing synchronized animations of analysis and test modal results. For the PATRAN-based analyst, TACT eliminates the repetitive, time-consuming and error-prone steps associated with transferring finite element data to a third-party modal correlation package, which allows the analyst to spend more time on the more challenging task of model updating. The usefulness of this software is presented using a case history, the correlation for a NASA Langley Research Center (LaRC) low aspect ratio research wind tunnel model. To demonstrate the improvements that TACT offers the MSC/PATRAN- and MSC/DIASTRAN- based structural analysis community, a comparison of the modal correlation process using TACT within PATRAN versus external third-party modal correlation packages is presented.

Opportunities and pitfalls in clinical proof-of-concept: principles and examples.

PubMed

Chen, Chao

2018-04-01

Clinical proof-of-concept trials crucially inform major resource deployment decisions. This paper discusses several mechanisms for enhancing their rigour and efficiency. The importance of careful consideration when using a surrogate endpoint is illustrated; situational effectiveness of run-in patient enrichment is explored; a versatile tool is introduced to ensure a strong pharmacological underpinning; the benefits of dose-titration are revealed by simulation; and the importance of adequately scheduled observations is shown. The general process of model-based trial design and analysis is described and several examples demonstrate the value in historical data, simulation-guided design, model-based analysis and trial adaptation informed by interim analysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genovar: a detection and visualization tool for genomic variants.

PubMed

Jung, Kwang Su; Moon, Sanghoon; Kim, Young Jin; Kim, Bong-Jo; Park, Kiejung

2012-05-08

Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals. A JAVA-based stand-alone program called Genovar was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation) and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files. Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. http://genovar.sourceforge.net/.

Application of a Groundwater Modeling Tool for Managing Hydrologically Connected Area in State of Nebraska, US

NASA Astrophysics Data System (ADS)

Li, R.; Flyr, B.; Bradley, J.; Pun, M.; Schneider, J.; Wietjes, J.; Chinta, S.

2014-12-01

Determination of the nature and degree of hydrologically connected groundwater and surface water resources is of paramount importance to integrated water management within the State of Nebraska to understand the impact of water uses on available supplies, such as depletion of streams and aquifers caused by groundwater pumping. The ability to quantify effects of surface water-groundwater hydrologic connection and interactions, is regarded as one of the most important steps towards effectively managing water resources in Nebraska and provides the basis for designating management areas. Designation of management areas allows the state and other management entities to focus various efforts and resources towards those projects that have the greatest impact to water users. Nebraska Department of Natural Resources (NDNR) developed a groundwater modeling tool, Cycle Well Analysis, to determine the areas defined to have a high degree of connectivity between groundwater and surface water (in accordance with the state regulations). This tool features two graphic user interfaces to allow the analysis to be fully compatible with most MODFLOW-based numerical groundwater models currently utilized by NDNR. Case studies showed that the tool, in combination of Geographic Information Systems (GIS), can be used to quantify the degree of stream depletion and delineate the boundary of hydrologically connected areas within different political boundaries and subbasins in Nebraska. This approach may be applied to other regions with similar background and need for integrated water management.

Open Source Tools for Seismicity Analysis

NASA Astrophysics Data System (ADS)

Powers, P.

2010-12-01

The spatio-temporal analysis of seismicity plays an important role in earthquake forecasting and is integral to research on earthquake interactions and triggering. For instance, the third version of the Uniform California Earthquake Rupture Forecast (UCERF), currently under development, will use Epidemic Type Aftershock Sequences (ETAS) as a model for earthquake triggering. UCERF will be a "living" model and therefore requires robust, tested, and well-documented ETAS algorithms to ensure transparency and reproducibility. Likewise, as earthquake aftershock sequences unfold, real-time access to high quality hypocenter data makes it possible to monitor the temporal variability of statistical properties such as the parameters of the Omori Law and the Gutenberg Richter b-value. Such statistical properties are valuable as they provide a measure of how much a particular sequence deviates from expected behavior and can be used when assigning probabilities of aftershock occurrence. To address these demands and provide public access to standard methods employed in statistical seismology, we present well-documented, open-source JavaScript and Java software libraries for the on- and off-line analysis of seismicity. The Javascript classes facilitate web-based asynchronous access to earthquake catalog data and provide a framework for in-browser display, analysis, and manipulation of catalog statistics; implementations of this framework will be made available on the USGS Earthquake Hazards website. The Java classes, in addition to providing tools for seismicity analysis, provide tools for modeling seismicity and generating synthetic catalogs. These tools are extensible and will be released as part of the open-source OpenSHA Commons library.

Combining multi-criteria decision analysis and mini-health technology assessment: A funding decision-support tool for medical devices in a university hospital setting.

PubMed

Martelli, Nicolas; Hansen, Paul; van den Brink, Hélène; Boudard, Aurélie; Cordonnier, Anne-Laure; Devaux, Capucine; Pineau, Judith; Prognon, Patrice; Borget, Isabelle

2016-02-01

At the hospital level, decisions about purchasing new and oftentimes expensive medical devices must take into account multiple criteria simultaneously. Multi-criteria decision analysis (MCDA) is increasingly used for health technology assessment (HTA). One of the most successful hospital-based HTA approaches is mini-HTA, of which a notable example is the Matrix4value model. To develop a funding decision-support tool combining MCDA and mini-HTA, based on Matrix4value, suitable for medical devices for individual patient use in French university hospitals - known as the IDA tool, short for 'innovative device assessment'. Criteria for assessing medical devices were identified from a literature review and a survey of 18 French university hospitals. Weights for the criteria, representing their relative importance, were derived from a survey of 25 members of a medical devices committee using an elicitation technique involving pairwise comparisons. As a test of its usefulness, the IDA tool was applied to two new drug-eluting beads (DEBs) for transcatheter arterial chemoembolization. The IDA tool comprises five criteria and weights for each of two over-arching categories: risk and value. The tool revealed that the two new DEBs conferred no additional value relative to DEBs currently available. Feedback from participating decision-makers about the IDA tool was very positive. The tool could help to promote a more structured and transparent approach to HTA decision-making in French university hospitals. Copyright © 2015 Elsevier Inc. All rights reserved.

Minimizing tooth bending stress in spur gears with simplified shapes of fillet and tool shape determination

NASA Astrophysics Data System (ADS)

Pedersen, N. L.

2015-06-01

The strength of a gear is typically defined relative to durability (pitting) and load capacity (tooth-breakage). Tooth-breakage is controlled by the root shape and this gear part can be designed because there is no contact between gear pairs here. The shape of gears is generally defined by different standards, with the ISO standard probably being the most common one. Gears are manufactured using two principally different tools: rack tools and gear tools. In this work, the bending stress of involute teeth is minimized by shape optimization made directly on the final gear. This optimized shape is then used to find the cutting tool (the gear envelope) that can create this optimized gear shape. A simple but sufficiently flexible root parameterization is applied and emphasis is put on the importance of separating the shape parameterization from the finite element analysis of stresses. Large improvements in the stress level are found.

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.

PubMed

Thakur, Shalabh; Guttman, David S

2016-06-30

Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .

On aerodynamic wake analysis and its relation to total aerodynamic drag in a wind tunnel environment

NASA Astrophysics Data System (ADS)

Guterres, Rui M.

The present work was developed with the goal of advancing the state of the art in the application of three-dimensional wake data analysis to the quantification of aerodynamic drag on a body in a low speed wind tunnel environment. Analysis of the existing tools, their strengths and limitations is presented. Improvements to the existing analysis approaches were made. Software tools were developed to integrate the analysis into a practical tool. A comprehensive derivation of the equations needed for drag computations based on three dimensional separated wake data is developed. A set of complete steps ranging from the basic mathematical concept to the applicable engineering equations is presented. An extensive experimental study was conducted. Three representative body types were studied in varying ground effect conditions. A detailed qualitative wake analysis using wake imaging and two and three dimensional flow visualization was performed. Several significant features of the flow were identified and their relation to the total aerodynamic drag established. A comprehensive wake study of this type is shown to be in itself a powerful tool for the analysis of the wake aerodynamics and its relation to body drag. Quantitative wake analysis techniques were developed. Significant post processing and data conditioning tools and precision analysis were developed. The quality of the data is shown to be in direct correlation with the accuracy of the computed aerodynamic drag. Steps are taken to identify the sources of uncertainty. These are quantified when possible and the accuracy of the computed results is seen to significantly improve. When post processing alone does not resolve issues related to precision and accuracy, solutions are proposed. The improved quantitative wake analysis is applied to the wake data obtained. Guidelines are established that will lead to more successful implementation of these tools in future research programs. Close attention is paid to implementation of issues that are of crucial importance for the accuracy of the results and that are not detailed in the literature. The impact of ground effect on the flows in hand is qualitatively and quantitatively studied. Its impact on the accuracy of the computations as well as the wall drag incompatibility with the theoretical model followed are discussed. The newly developed quantitative analysis provides significantly increased accuracy. The aerodynamic drag coefficient is computed within one percent of balance measured value for the best cases.

Workflows and the Role of Images for Virtual 3d Reconstruction of no Longer Extant Historic Objects

NASA Astrophysics Data System (ADS)

Münster, S.

2013-07-01

3D reconstruction technologies have gained importance as tools for the research and visualization of no longer extant historic objects during the last decade. Within such reconstruction processes, visual media assumes several important roles: as the most important sources especially for a reconstruction of no longer extant objects, as a tool for communication and cooperation within the production process, as well as for a communication and visualization of results. While there are many discourses about theoretical issues of depiction as sources and as visualization outcomes of such projects, there is no systematic research about the importance of depiction during a 3D reconstruction process and based on empirical findings. Moreover, from a methodological perspective, it would be necessary to understand which role visual media plays during the production process and how it is affected by disciplinary boundaries and challenges specific to historic topics. Research includes an analysis of published work and case studies investigating reconstruction projects. This study uses methods taken from social sciences to gain a grounded view of how production processes would take place in practice and which functions and roles images would play within them. For the investigation of these topics, a content analysis of 452 conference proceedings and journal articles related to 3D reconstruction modeling in the field of humanities has been completed. Most of the projects described in those publications dealt with data acquisition and model building for existing objects. Only a small number of projects focused on structures that no longer or never existed physically. Especially that type of project seems to be interesting for a study of the importance of pictures as sources and as tools for interdisciplinary cooperation during the production process. In the course of the examination the authors of this paper applied a qualitative content analysis for a sample of 26 previously published project reports to depict strategies and types and three case studies of 3D reconstruction projects to evaluate evolutionary processes during such projects. The research showed that reconstructions of no longer existing historic structures are most commonly used for presentation or research purposes of large buildings or city models. Additionally, they are often realized by interdisciplinary workgroups using images as the most important source for reconstruction as far as important media for communication and quality control during the reconstruction process.

Parameter identification and optimization of slide guide joint of CNC machine tools

NASA Astrophysics Data System (ADS)

Zhou, S.; Sun, B. B.

2017-11-01

The joint surface has an important influence on the performance of CNC machine tools. In order to identify the dynamic parameters of slide guide joint, the parametric finite element model of the joint is established and optimum design method is used based on the finite element simulation and modal test. Then the mode that has the most influence on the dynamics of slip joint is found through harmonic response analysis. Take the frequency of this mode as objective, the sensitivity analysis of the stiffness of each joint surface is carried out using Latin Hypercube Sampling and Monte Carlo Simulation. The result shows that the vertical stiffness of slip joint surface constituted by the bed and the slide plate has the most obvious influence on the structure. Therefore, this stiffness is taken as the optimization variable and the optimal value is obtained through studying the relationship between structural dynamic performance and stiffness. Take the stiffness values before and after optimization into the FEM of machine tool, and it is found that the dynamic performance of the machine tool is improved.

Development and Validation of the Controller Acceptance Rating Scale (CARS): Results of Empirical Research

NASA Technical Reports Server (NTRS)

Lee, Katharine K.; Kerns, Karol; Bone, Randall

2001-01-01

The measurement of operational acceptability is important for the development, implementation, and evolution of air traffic management decision support tools. The Controller Acceptance Rating Scale was developed at NASA Ames Research Center for the development and evaluation of the Passive Final Approach Spacing Tool. CARS was modeled after a well-known pilot evaluation rating instrument, the Cooper-Harper Scale, and has since been used in the evaluation of the User Request Evaluation Tool, developed by MITRE's Center for Advanced Aviation System Development. In this paper, we provide a discussion of the development of CARS and an analysis of the empirical data collected with CARS to examine construct validity. Results of intraclass correlations indicated statistically significant reliability for the CARS. From the subjective workload data that were collected in conjunction with the CARS, it appears that the expected set of workload attributes was correlated with the CARS. As expected, the analysis also showed that CARS was a sensitive indicator of the impact of decision support tools on controller operations. Suggestions for future CARS development and its improvement are also provided.

Experimental evaluation of tool run-out in micro milling

NASA Astrophysics Data System (ADS)

Attanasio, Aldo; Ceretti, Elisabetta

2018-05-01

This paper deals with micro milling cutting process focusing the attention on tool run-out measurement. In fact, among the effects of the scale reduction from macro to micro (i.e., size effects) tool run-out plays an important role. This research is aimed at developing an easy and reliable method to measure tool run-out in micro milling based on experimental tests and an analytical model. From an Industry 4.0 perspective this measuring strategy can be integrated into an adaptive system for controlling cutting forces, with the objective of improving the production quality, the process stability, reducing at the same time the tool wear and the machining costs. The proposed procedure estimates the tool run-out parameters from the tool diameter, the channel width, and the phase angle between the cutting edges. The cutting edge phase measurement is based on the force signal analysis. The developed procedure has been tested on data coming from micro milling experimental tests performed on a Ti6Al4V sample. The results showed that the developed procedure can be successfully used for tool run-out estimation.

ExGUtils: A Python Package for Statistical Analysis With the ex-Gaussian Probability Density.

PubMed

Moret-Tatay, Carmen; Gamermann, Daniel; Navarro-Pardo, Esperanza; Fernández de Córdoba Castellá, Pedro

2018-01-01

The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are often modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data. The complexity of this distribution makes the use of computational tools an essential element. Therefore, there is a strong need for efficient and versatile computational tools for the research in this area. In this manuscript we discuss some mathematical details of the ex-Gaussian distribution and apply the ExGUtils package, a set of functions and numerical tools, programmed for python, developed for numerical analysis of data involving the ex-Gaussian probability density. In order to validate the package, we present an extensive analysis of fits obtained with it, discuss advantages and differences between the least squares and maximum likelihood methods and quantitatively evaluate the goodness of the obtained fits (which is usually an overlooked point in most literature in the area). The analysis done allows one to identify outliers in the empirical datasets and criteriously determine if there is a need for data trimming and at which points it should be done.

S-MART, a software toolbox to aid RNA-Seq data analysis.

PubMed

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci.

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

PubMed Central

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci. PMID:21998740

ExGUtils: A Python Package for Statistical Analysis With the ex-Gaussian Probability Density

PubMed Central

Moret-Tatay, Carmen; Gamermann, Daniel; Navarro-Pardo, Esperanza; Fernández de Córdoba Castellá, Pedro

2018-01-01

The study of reaction times and their underlying cognitive processes is an important field in Psychology. Reaction times are often modeled through the ex-Gaussian distribution, because it provides a good fit to multiple empirical data. The complexity of this distribution makes the use of computational tools an essential element. Therefore, there is a strong need for efficient and versatile computational tools for the research in this area. In this manuscript we discuss some mathematical details of the ex-Gaussian distribution and apply the ExGUtils package, a set of functions and numerical tools, programmed for python, developed for numerical analysis of data involving the ex-Gaussian probability density. In order to validate the package, we present an extensive analysis of fits obtained with it, discuss advantages and differences between the least squares and maximum likelihood methods and quantitatively evaluate the goodness of the obtained fits (which is usually an overlooked point in most literature in the area). The analysis done allows one to identify outliers in the empirical datasets and criteriously determine if there is a need for data trimming and at which points it should be done. PMID:29765345

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

PubMed Central

2011-01-01

Background Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. Results The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Conclusions Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware. PMID:21526987

Gravitational Wave Detection in the Introductory Lab

NASA Astrophysics Data System (ADS)

Burko, Lior M.

2017-01-01

Great physics breakthroughs are rarely included in the introductory physics course. General relativity and binary black hole coalescence are no different, and can be included in the introductory course only in a very limited sense. However, we can design activities that directly involve the detection of GW150914, the designation of the Gravitation Wave signal detected on September 14, 2015, thereby engage the students in this exciting discovery directly. The activities naturally do not include the construction of a detector or the detection of gravitational waves. Instead, we design it to include analysis of the data from GW150914, which includes some interesting analysis activities for students of the introductory course. The same activities can be assigned either as a laboratory exercise or as a computational project for the same population of students. The analysis tools used here are simple and available to the intended student population. It does not include the sophisticated analysis tools, which were used by LIGO to carefully analyze the detected signal. However, these simple tools are sufficient to allow the student to get important results. We have successfully assigned this lab project for students of the introductory course with calculus at Georgia Gwinnett College.

[Model of Analysis and Prevention of Accidents - MAPA: tool for operational health surveillance].

PubMed

de Almeida, Ildeberto Muniz; Vilela, Rodolfo Andrade de Gouveia; da Silva, Alessandro José Nunes; Beltran, Sandra Lorena

2014-12-01

The analysis of work-related accidents is important for accident surveillance and prevention. Current methods of analysis seek to overcome reductionist views that see these occurrences as simple events explained by operator error. The objective of this paper is to analyze the Model of Analysis and Prevention of Accidents (MAPA) and its use in monitoring interventions, duly highlighting aspects experienced in the use of the tool. The descriptive analytical method was used, introducing the steps of the model. To illustrate contributions and or difficulties, cases where the tool was used in the context of service were selected. MAPA integrates theoretical approaches that have already been tried in studies of accidents by providing useful conceptual support from the data collection stage until conclusion and intervention stages. Besides revealing weaknesses of the traditional approach, it helps identify organizational determinants, such as management failings, system design and safety management involved in the accident. The main challenges lie in the grasp of concepts by users, in exploring organizational aspects upstream in the chain of decisions or at higher levels of the hierarchy, as well as the intervention to change the determinants of these events.

Tomato Expression Database (TED): a suite of data presentation and analysis tools

PubMed Central

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150 000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at . PMID:16381976

Tomato Expression Database (TED): a suite of data presentation and analysis tools.

PubMed

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150,000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at http://ted.bti.cornell.edu.

Critical considerations for the practical utility of health equity tools: a concept mapping study.

PubMed

Pauly, Bernadette; Martin, Wanda; Perkin, Kathleen; van Roode, Thea; Kwan, Albert; Patterson, Tobie; Tong, Samantha; Prescott, Cheryl; Wallace, Bruce; Hancock, Trevor; MacDonald, Marjorie

2018-04-23

Promoting health equity within health systems is a priority and challenge worldwide. Health equity tools have been identified as one strategy for integrating health equity considerations into health systems. Although there has been a proliferation of health equity tools, there has been limited attention to evaluating these tools for their practicality and thus their likelihood for uptake. Within the context of a large program of research, the Equity Lens in Public Health (ELPH), we conducted a concept mapping study to identify key elements and themes related to public health leaders and practitioners' views about what makes a health equity tool practical and useful. Concept mapping is a participatory mixed-method approach to generating ideas and concepts to address a common concern. Participants brainstormed responses to the prompt "To be useful, a health equity tool should…" After participants sorted responses into groups based on similarity and rated them for importance and feasibility, the statements were analyzed using multidimensional scaling, then grouped using cluster analysis. Pattern matching graphs were constructed to illustrate the relationship between the importance and feasibility of statements, and go-zone maps were created to guide subsequent action. The process resulted in 67 unique statements that were grouped into six clusters: 1) Evaluation for Improvement; 2) User Friendliness; 3) Explicit Theoretical Background; 4) Templates and Tools 5) Equity Competencies; and 6) Nothing about Me without Me- Client Engaged. The result was a set of concepts and themes describing participants' views of the practicality and usefulness of health equity tools. These thematic clusters highlight the importance of user friendliness and having user guides, templates and resources to enhance use of equity tools. Furthermore, participants' indicated that practicality was not enough for a tool to be useful. In addition to practical characteristics of the tool, a useful tool is one that encourages and supports the development of practitioner competencies to engage in equity work including critical reflections on power and institutional culture as well as strategies for the involvement of community members impacted by health inequities in program planning and delivery. The results of this study will be used to inform the development of practical criteria to assess health equity tools for application in public health.

Understanding online health information: Evaluation, tools, and strategies.

PubMed

Beaunoyer, Elisabeth; Arsenault, Marianne; Lomanowska, Anna M; Guitton, Matthieu J

2017-02-01

Considering the status of the Internet as a prominent source of health information, assessing online health material has become a central issue in patient education. We describe the strategies available to evaluate the characteristics of online health information, including readability, emotional content, understandability, usability. Popular tools used in assessment of readability, emotional content and comprehensibility of online health information were reviewed. Tools designed to evaluate both printed and online material were considered. Readability tools are widely used in online health material evaluation and are highly covariant. Assessment of emotional content of online health-related communications via sentiment analysis tools is becoming more popular. Understandability and usability tools have been developed specifically for health-related material, but each tool has important limitations and has been tested on a limited number of health issues. Despite the availability of numerous assessment tools, their overall reliability differs between readability (high) and understandability (low). Approaches combining multiple assessment tools and involving both quantitative and qualitative observations would optimize assessment strategies. Effective assessment of online health information should rely on mixed strategies combining quantitative and qualitative evaluations. Assessment tools should be selected according to their functional properties and compatibility with target material. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Net energy analysis: Powerful tool for selecting electric power options

NASA Astrophysics Data System (ADS)

Baron, S.

A number of net energy analysis studies have been conducted in recent years for electric power production from coal, oil and uranium fuels; synthetic fuels from coal and oil shale; and heat and electric power from solar energy. This technique is an excellent indicator of investment costs, environmental impact and potential economic competitiveness of alternative electric power systems for energy planners from the Eastern European countries considering future options. Energy conservation is also important to energy planners and the net energy analysis technique is an excellent accounting system on the extent of energy resource conservation. The author proposes to discuss the technique and to present the results of his studies and others in the field. The information supplied to the attendees will serve as a powerful tool to the energy planners considering their electric power options in the future.

[Application of Fourier transform attenuated total reflection infrared spectroscopy in analysis of pulp and paper industry].

PubMed

Zhang, Yong; Cao, Chun-yu; Feng, Wen-ying; Xu, Ming; Su, Zhen-hua; Liu, Xiao-meng; Lü, Wei-jun

2011-03-01

As one of the most powerful tools to investigate the compositions of raw materials and the property of pulp and paper, infrared spectroscopy has played an important role in pulp and paper industry. However, the traditional transmission infrared spectroscopy has not met the requirements of the producing processes because of its disadvantages of time consuming and sample destruction. New technique would be needed to be found. Fourier transform attenuated total reflection infrared spectroscopy (ATR-FTIR) is an advanced spectroscopic tool for nondestructive evaluation and could rapidly, accurately estimate the production properties of each process in pulp and paper industry. The present review describes the application of ATR-FTIR in analysis of pulp and paper industry. The analysis processes will include: pulping, papermaking, environmental protecting, special processing and paper identifying.

Socio-economic analysis: a tool for assessing the potential of nanotechnologies

NASA Astrophysics Data System (ADS)

Brignon, Jean-Marc

2011-07-01

Cost-Benefit Analysis (CBA) has a long history, especially in the USA, of being used for the assessment of new regulation, new infrastructure and more recently for new technologies. Under the denomination of Socio-Economic Analysis (SEA), this concept is used in EU safety and environmental regulation, especially for the placing of chemicals on the market (REACh regulation) and the operation of industrial installations (Industrial Emissions Directive). As far as REACh and other EU legislation apply specifically to nanomaterials in the future, SEA might become an important assessment tool for nanotechnologies. The most important asset of SEA regarding nanomaterials, is the comparison with alternatives in socio-economic scenarios, which is key for the understanding of how a nanomaterial "socially" performs in comparison with its alternatives. "Industrial economics" methods should be introduced in SEAs to make industry and the regulator share common concepts and visions about economic competitiveness implications of regulating nanotechnologies, SEA and Life Cycle Analysis (LCA) can complement each other : Socio-Economic LCA are increasingly seen as a complete assessment tool for nanotechnologies, but the perspective between Social LCA and SEA are different and the respective merits and limitations of both approaches should be kept in mind. SEA is a "pragmatic regulatory impact analysis", that uses a cost/benefit framework analysis but remains open to other disciplines than economy, and open to the participation of stakeholders for the construction of scenarios of the deployment of technologies and the identification of alternatives. SEA is "pragmatic" in the sense that it is driven by the purpose to assess "what happens" with the introduction of nanotechnology, and uses methodologies such as Life Cycle Analysis only as far as they really contribute to that goal. We think that, being pragmatic, SEA is also adaptative, which is a key quality to handle the novelty of economic and social effects expected from nanotechnology.

Systematic review and meta-analysis: tools for the information age.

PubMed

Weatherall, Mark

2017-11-01

The amount of available biomedical information is vast and growing. Natural limitations of the way clinicians and researchers approach this treasure trove of information comprise difficulties locating the information, and once located, cognitive biases may lead to inappropriate use of the information. Systematic reviews and meta-analyses represent important tools in the information age to improve knowledge and action. Systematic reviews represent a census approach to identifying literature to avoid non-response bias. They are a necessary prelude to producing combined quantitative summaries of associations or treatment effects. Meta-analysis comprises the arithmetical techniques for producing combined summaries from individual study reports. Careful, thoughtful and rigorous use of these tools is likely to enhance knowledge and action. Use of standard guidelines, such as the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, or embedding these activities within collaborative groups such as the Cochrane Collaboration, are likely to lead to more useful systematic review and meta-analysis reporting. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Integrated Reporting as a Tool for Communicating with Stakeholders - Advantages and Disadvantages

NASA Astrophysics Data System (ADS)

Matuszyk, Iwona; Rymkiewicz, Bartosz

2018-03-01

Financial and non-financial reporting from the beginning of its existence is the primary source of communication between the company and a wide range of stakeholders. Over the decades it has adapted to the needs of rapidly changing business and social environment. Currently, the final link in the evolution of organizational reporting, such as integrated reporting, assumes integration and mutual connectivity to both financial and non-financial data. The main interest in the concept of integrated reporting comes from the value it contributes to the organization. Undoubtedly, the concept of integrated reporting is a milestone in the evolution of organizational reporting. It is however important to consider whether it adequately addresses the information needs of a wide range of stakeholders, and whether it is a universal tool for communication between the company and its stakeholders. The aim of the paper is to discuss the advantages and disadvantages of the concept of integrated reporting as a tool for communication with stakeholders and to further directions of its development. The article uses the research methods such as literature analysis, the content analysis of the corporate publications and comparative analysis.

Analysis of Orbital Lifetime Prediction Parameters in Preparation for Post-Mission Disposal

NASA Astrophysics Data System (ADS)

Choi, Ha-Yeon; Kim, Hae-Dong; Seong, Jae-Dong

2015-12-01

Atmospheric drag force is an important source of perturbation of Low Earth Orbit (LEO) orbit satellites, and solar activity is a major factor for changes in atmospheric density. In particular, the orbital lifetime of a satellite varies with changes in solar activity, so care must be taken in predicting the remaining orbital lifetime during preparation for post-mission disposal. In this paper, the System Tool Kit (STK®) Long-term Orbit Propagator is used to analyze the changes in orbital lifetime predictions with respect to solar activity. In addition, the STK® Lifetime tool is used to analyze the change in orbital lifetime with respect to solar flux data generation, which is needed for the orbital lifetime calculation, and its control on the drag coefficient control. Analysis showed that the application of the most recent solar flux file within the Lifetime tool gives a predicted trend that is closest to the actual orbit. We also examine the effect of the drag coefficient, by performing a comparative analysis between varying and constant coefficients in terms of solar activity intensities.

A hardware acceleration based on high-level synthesis approach for glucose-insulin analysis

NASA Astrophysics Data System (ADS)

Daud, Nur Atikah Mohd; Mahmud, Farhanahani; Jabbar, Muhamad Hairol

2017-01-01

In this paper, the research is focusing on Type 1 Diabetes Mellitus (T1DM). Since this disease requires a full attention on the blood glucose concentration with the help of insulin injection, it is important to have a tool that able to predict that level when consume a certain amount of carbohydrate during meal time. Therefore, to make it realizable, a Hovorka model which is aiming towards T1DM is chosen in this research. A high-level language is chosen that is C++ to construct the mathematical model of the Hovorka model. Later, this constructed code is converted into intellectual property (IP) which is also known as a hardware accelerator by using of high-level synthesis (HLS) approach which able to improve in terms of design and performance for glucose-insulin analysis tool later as will be explained further in this paper. This is the first step in this research before implementing the design into system-on-chip (SoC) to achieve a high-performance system for the glucose-insulin analysis tool.

Amino Acid profile as a feasible tool for determination of the authenticity of fruit juices.

PubMed

Asadpoor, Mostafa; Ansarin, Masoud; Nemati, Mahboob

2014-12-01

Fruit juice is a nutrient rich food product with a direct connection to public health. The purpose of this research was to determine the amino acid profile of juices and provide a quick and accurate indicator for determining their authenticity. The method of analysis was HPLC with fluorescence detector and pre-column derivatization by orthophtaldialdehyde (OPA). Sixty-six samples of fruit juices were analyzed, and fourteen amino acids were identified and determined in the sampled fruit juices. The fruit samples used for this analysis were apples, oranges, cherry, pineapple, mango, apricot, pomegranate, peach and grapes. The results showed that 32% of samples tested in this study had a lower concentrate percentage as compared to that of their labels and/or other possible authenticity problems in the manufacturing process. The following samples showed probable adulteration: four cherry juice samples, two pomegranate juice samples, one mango, three grape, four peach, seven orange, two apple and one apricot juice samples. In general, determining the amount of amino acids and comparing sample amino acids profiles with the standard values seems to be an indicator for quality control. This method can provide the regulatory agencies with a tool, to help produce a healthier juice. The aim of this study is the analytical control of the fruit juice composition is becoming an important issue, and HPLC can provide an important and essential tool for more accurate research as well as for routine analysis.

Functionalized C-Glycoside Ketohydrazones: Carbohydrate Derivatization that Retains the Ring Integrity of the Terminal Reducing Sugar

USDA-ARS?s Scientific Manuscript database

Glycosylation often mediates important biological processes through the interaction of carbohydrates with complementary proteins. Most chemical tools for the functional analysis of glycans are highly dependent upon various linkage chemistries that involve the reducing-terminus of carbohydrates. Ho...

The Integrated Farm System Model: A Tool for Whole Farm Nutrient Management Analysis

USDA-ARS?s Scientific Manuscript database

With tighter profit margins and increasing environmental constraints, strategic planning of farm production systems is becoming both more important and more difficult. This is especially true for integrated crop and animal production systems. Animal production is complex with a number of interacting...

Mass spectrometry as a quantitative tool in plant metabolomics

PubMed Central

Jorge, Tiago F.; Mata, Ana T.

2016-01-01

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644967

VisIVO: A Tool for the Virtual Observatory and Grid Environment

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Costa, A.; Larsson, B.; Gheller, C.; Pasian, F.; Smareglia, R.

2007-10-01

We present the new features of VisIVO, software for the visualization and analysis of astrophysical data which can be retrieved from the Virtual Observatory framework and used for cosmological simulations running both on Windows and GNU/Linux platforms. VisIVO is VO standards compliant and supports the most important astronomical data formats such as FITS, HDF5 and VOTables. It is free software and can be downloaded from the web site http://visivo.cineca.it. VisIVO can interoperate with other astronomical VO compliant tools through PLASTIC (PLatform for AStronomical Tool InterConnection). This feature allows VisIVO to share data with many other astronomical packages to further analyze the loaded data.

Software tool for mining liquid chromatography/multi-stage mass spectrometry data for comprehensive glycerophospholipid profiling.

PubMed

Hein, Eva-Maria; Bödeker, Bertram; Nolte, Jürgen; Hayen, Heiko

2010-07-30

Electrospray ionization mass spectrometry (ESI-MS) has emerged as an indispensable tool in the field of lipidomics. Despite the growing interest in lipid analysis, there are only a few software tools available for data evaluation, as compared for example to proteomics applications. This makes comprehensive lipid analysis a complex challenge. Thus, a computational tool for harnessing the raw data from liquid chromatography/mass spectrometry (LC/MS) experiments was developed in this study and is available from the authors on request. The Profiler-Merger-Viewer tool is a software package for automatic processing of raw-data from data-dependent experiments, measured by high-performance liquid chromatography hyphenated to electrospray ionization hybrid linear ion trap Fourier transform mass spectrometry (FTICR-MS and Orbitrap) in single and multi-stage mode. The software contains three parts: processing of the raw data by Profiler for lipid identification, summarizing of replicate measurements by Merger and visualization of all relevant data (chromatograms as well as mass spectra) for validation of the results by Viewer. The tool is easily accessible, since it is implemented in Java and uses Microsoft Excel (XLS) as output format. The motivation was to develop a tool which supports and accelerates the manual data evaluation (identification and relative quantification) significantly but does not make a complete data analysis within a black-box system. The software's mode of operation, usage and options will be demonstrated on the basis of a lipid extract of baker's yeast (S. cerevisiae). In this study, we focused on three important representatives of lipids: glycerophospholipids, lyso-glycerophospholipids and free fatty acids. Copyright 2010 John Wiley & Sons, Ltd.

RGmatch: matching genomic regions to proximal genes in omics data integration.

PubMed

Furió-Tarí, Pedro; Conesa, Ana; Tarazona, Sonia

2016-11-22

The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the gene (gene area) is important for functional data interpretation; hence algorithms that match regions to genes should be able to deliver insight into this information. In this work we review the tools that are publicly available for making region-to-gene associations. We also present a novel method, RGmatch, a flexible and easy-to-use Python tool that computes associations either at the gene, transcript, or exon level, applying a set of rules to annotate each region-gene association with the region location within the gene. RGmatch can be applied to any organism as long as genome annotation is available. Furthermore, we qualitatively and quantitatively compare RGmatch to other tools. RGmatch simplifies the association of a genomic region with its closest gene. At the same time, it is a powerful tool because the rules used to annotate these associations are very easy to modify according to the researcher's specific interests. Some important differences between RGmatch and other similar tools already in existence are RGmatch's flexibility, its wide range of user options, compatibility with any annotatable organism, and its comprehensive and user-friendly output.

The Development and Validation of a Rapid Assessment Tool of Primary Care in China

PubMed Central

Mei, Jie; Liang, Yuan; Shi, LeiYu; Zhao, JingGe; Wang, YuTan; Kuang, Li

2016-01-01

Introduction. With Chinese health care reform increasingly emphasizing the importance of primary care, the need for a tool to evaluate primary care performance and service delivery is clear. This study presents a methodology for a rapid assessment of primary care organizations and service delivery in China. Methods. The study translated and adapted the Primary Care Assessment Tool-Adult Edition (PCAT-AE) into a Chinese version to measure core dimensions of primary care, namely, first contact, continuity, comprehensiveness, and coordination. A cross-sectional survey was conducted to assess the validity and reliability of the Chinese Rapid Primary Care Assessment Tool (CR-PCAT). Eight community health centers in Guangdong province have been selected to participate in the survey. Results. A total of 1465 effective samples were included for data analysis. Eight items were eliminated following principal component analysis and reliability testing. The principal component analysis extracted five multiple-item scales (first contact utilization, first contact accessibility, ongoing care, comprehensiveness, and coordination). The tests of scaling assumptions were basically met. Conclusion. The standard psychometric evaluation indicates that the scales have achieved relatively good reliability and validity. The CR-PCAT provides a rapid and reliable measure of four core dimensions of primary care, which could be applied in various scenarios. PMID:26885509

CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels.

PubMed

Kartasalo, Kimmo; Pölönen, Risto-Pekka; Ojala, Marisa; Rasku, Jyrki; Lekkala, Jukka; Aalto-Setälä, Katriina; Kallio, Pasi

2015-10-26

Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structures is often limited to qualitative evaluation by human experts, hampering the throughput, repeatability and reliability of the analyses. Software tools are not readily available for this purpose and the existing methods typically rely at least partly on manual operation. We developed CytoSpectre, an automated tool based on spectral analysis, allowing the quantification of orientation and also size distributions of structures in microscopy images. CytoSpectre utilizes the Fourier transform to estimate the power spectrum of an image and based on the spectrum, computes parameter values describing, among others, the mean orientation, isotropy and size of target structures. The analysis can be further tuned to focus on targets of particular size at cellular or subcellular scales. The software can be operated via a graphical user interface without any programming expertise. We analyzed the performance of CytoSpectre by extensive simulations using artificial images, by benchmarking against FibrilTool and by comparisons with manual measurements performed for real images by a panel of human experts. The software was found to be tolerant against noise and blurring and superior to FibrilTool when analyzing realistic targets with degraded image quality. The analysis of real images indicated general good agreement between computational and manual results while also revealing notable expert-to-expert variation. Moreover, the experiment showed that CytoSpectre can handle images obtained of different cell types using different microscopy techniques. Finally, we studied the effect of mechanical stretching on cardiomyocytes to demonstrate the software in an actual experiment and observed changes in cellular orientation in response to stretching. CytoSpectre, a versatile, easy-to-use software tool for spectral analysis of microscopy images was developed. The tool is compatible with most 2D images and can be used to analyze targets at different scales. We expect the tool to be useful in diverse applications dealing with structures whose orientation and size distributions are of interest. While designed for the biological field, the software could also be useful in non-biological applications.

Strategic analysis for health care organizations: the suitability of the SWOT-analysis.

PubMed

van Wijngaarden, Jeroen D H; Scholten, Gerard R M; van Wijk, Kees P

2012-01-01

Because of the introduction of (regulated) market competition and self-regulation, strategy is becoming an important management field for health care organizations in many European countries. That is why health managers are introducing more and more strategic principles and tools. Especially the SWOT (strengths, weaknesses, opportunities, threats)-analysis seems to be popular. However, hardly any empirical research has been done on the use and suitability of this instrument for the health care sector. In this paper four case studies are presented on the use of the SWOT-analysis in different parts of the health care sector in the Netherlands. By comparing these results with the premises of the SWOT and academic critique, it will be argued that the SWOT in its current form is not suitable as a tool for strategic analysis in health care in many European countries. Based on these findings an alternative SWOT-model is presented, in which expectations and learning of stakeholder are incorporated. Copyright © 2010 John Wiley & Sons, Ltd.

Multiple comparison analysis testing in ANOVA.

PubMed

McHugh, Mary L

2011-01-01

The Analysis of Variance (ANOVA) test has long been an important tool for researchers conducting studies on multiple experimental groups and one or more control groups. However, ANOVA cannot provide detailed information on differences among the various study groups, or on complex combinations of study groups. To fully understand group differences in an ANOVA, researchers must conduct tests of the differences between particular pairs of experimental and control groups. Tests conducted on subsets of data tested previously in another analysis are called post hoc tests. A class of post hoc tests that provide this type of detailed information for ANOVA results are called "multiple comparison analysis" tests. The most commonly used multiple comparison analysis statistics include the following tests: Tukey, Newman-Keuls, Scheffee, Bonferroni and Dunnett. These statistical tools each have specific uses, advantages and disadvantages. Some are best used for testing theory while others are useful in generating new theory. Selection of the appropriate post hoc test will provide researchers with the most detailed information while limiting Type 1 errors due to alpha inflation.

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

PubMed Central

Warren, Andrew S.; Aurrecoechea, Cristina; Brunk, Brian; Desai, Prerak; Emrich, Scott; Giraldo-Calderón, Gloria I.; Harb, Omar; Hix, Deborah; Lawson, Daniel; Machi, Dustin; Mao, Chunhong; McClelland, Michael; Nordberg, Eric; Shukla, Maulik; Vosshall, Leslie B.; Wattam, Alice R.; Will, Rebecca; Yoo, Hyun Seung; Sobral, Bruno

2015-01-01

Motivation: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers. Results: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data. Availability and implementation: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal. Contact: anwarren@vt.edu Supplementary information: Supplementary materials are available at Bioinformatics online. PMID:25573919

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

PubMed

Warren, Andrew S; Aurrecoechea, Cristina; Brunk, Brian; Desai, Prerak; Emrich, Scott; Giraldo-Calderón, Gloria I; Harb, Omar; Hix, Deborah; Lawson, Daniel; Machi, Dustin; Mao, Chunhong; McClelland, Michael; Nordberg, Eric; Shukla, Maulik; Vosshall, Leslie B; Wattam, Alice R; Will, Rebecca; Yoo, Hyun Seung; Sobral, Bruno

2015-05-01

RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers. RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data. RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal. anwarren@vt.edu Supplementary materials are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Import Security: Assessing the Risks of Imported Food.

PubMed

Welburn, Jonathan; Bier, Vicki; Hoerning, Steven

2016-11-01

We use data on food import violations from the FDA Operational and Administrative System for Import Support (OASIS) to address rising concerns associated with imported food, quantify import risks by product and by country of origin, and explore the usefulness of OASIS data for risk assessment. In particular, we assess whether there are significant trends in violations, whether import violations can be used to quantify risks by country and by product, and how import risks depend on economic factors of the country of origin. The results show that normalizing import violations by volume of imports provides a meaningful indicator of risk. We then use regression analysis to characterize import risks.  Using this model, we analyze import risks by product type, violation type, and economic factors of the country of origin.  We find that OASIS data are useful in quantifying food import risks, and that the rate of refusals provides a useful decision tool for risk management.  Furthermore, we find that some economic factors are significant indicators of food import risk by country. © 2016 Society for Risk Analysis.

Determination of high-strength materials diamond grinding rational modes

NASA Astrophysics Data System (ADS)

Arkhipov, P. V.; Lobanov, D. V.; Rychkov, D. A.; Yanyushkin, A. S.

2018-03-01

The analysis of methods of high-strength materials abrasive processing is carried out. This method made it possible to determine the necessary directions and prospects for the development of shaping combined methods. The need to use metal bonded diamond abrasive tools in combination with a different kind of energy is noted to improve the processing efficiency and reduce the complexity of operations. The complex of experimental research on revealing the importance of mechanical and electrical components of cutting regimes, on the cutting ability of diamond tools, as well as the need to reduce the specific consumption of an abrasive wheel as one of the important economic indicators of the processing process is performed. It is established that combined diamond grinding with simultaneous continuous correction of the abrasive wheel contributes to an increase in the cutting ability of metal bonded diamond abrasive tools when processing high-strength materials by an average of 30% compared to diamond grinding. Particular recommendations on the designation of technological factors are developed depending on specific production problems.

Metabolic engineering tools in model cyanobacteria.

PubMed

Carroll, Austin L; Case, Anna E; Zhang, Angela; Atsumi, Shota

2018-03-26

Developing sustainable routes for producing chemicals and fuels is one of the most important challenges in metabolic engineering. Photoautotrophic hosts are particularly attractive because of their potential to utilize light as an energy source and CO 2 as a carbon substrate through photosynthesis. Cyanobacteria are unicellular organisms capable of photosynthesis and CO 2 fixation. While engineering in heterotrophs, such as Escherichia coli, has result in a plethora of tools for strain development and hosts capable of producing valuable chemicals efficiently, these techniques are not always directly transferable to cyanobacteria. However, recent efforts have led to an increase in the scope and scale of chemicals that cyanobacteria can produce. Adaptations of important metabolic engineering tools have also been optimized to function in photoautotrophic hosts, which include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9, 13 C Metabolic Flux Analysis (MFA), and Genome-Scale Modeling (GSM). This review explores innovations in cyanobacterial metabolic engineering, and highlights how photoautotrophic metabolism has shaped their development. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

DOE PAGES

Silva, Genivaldo Gueiros Z.; Green, Kevin T.; Dutilh, Bas E.; ...

2015-10-09

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reducedmore » reference database to report the subsystems present in metagenomic datasets and profile their abundances. We tested SUPER-FOCUS with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.« less

In Silico PCR Tools for a Fast Primer, Probe, and Advanced Searching.

PubMed

Kalendar, Ruslan; Muterko, Alexandr; Shamekova, Malika; Zhambakin, Kabyl

2017-01-01

The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching. Predicting sensitivity and specificity of primers and probes requires a search to determine whether they match a database with an optimal number of mismatches, similarity, and stability. In the development of in silico bioinformatics tools for nucleic acid amplification technologies, the prospects for the development of new NAAT or similar approaches should be taken into account, including forward-looking and comprehensive analysis that is not limited to only one PCR technique variant. The software FastPCR and the online Java web tool are integrated tools for in silico PCR of linear and circular DNA, multiple primer or probe searches in large or small databases and for advanced search. These tools are suitable for processing of batch files that are essential for automation when working with large amounts of data. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and the online Java version at http://primerdigital.com/tools/pcr.html .

Automated cell analysis tool for a genome-wide RNAi screen with support vector machine based supervised learning

NASA Astrophysics Data System (ADS)

Remmele, Steffen; Ritzerfeld, Julia; Nickel, Walter; Hesser, Jürgen

2011-03-01

RNAi-based high-throughput microscopy screens have become an important tool in biological sciences in order to decrypt mostly unknown biological functions of human genes. However, manual analysis is impossible for such screens since the amount of image data sets can often be in the hundred thousands. Reliable automated tools are thus required to analyse the fluorescence microscopy image data sets usually containing two or more reaction channels. The herein presented image analysis tool is designed to analyse an RNAi screen investigating the intracellular trafficking and targeting of acylated Src kinases. In this specific screen, a data set consists of three reaction channels and the investigated cells can appear in different phenotypes. The main issue of the image processing task is an automatic cell segmentation which has to be robust and accurate for all different phenotypes and a successive phenotype classification. The cell segmentation is done in two steps by segmenting the cell nuclei first and then using a classifier-enhanced region growing on basis of the cell nuclei to segment the cells. The classification of the cells is realized by a support vector machine which has to be trained manually using supervised learning. Furthermore, the tool is brightness invariant allowing different staining quality and it provides a quality control that copes with typical defects during preparation and acquisition. A first version of the tool has already been successfully applied for an RNAi-screen containing three hundred thousand image data sets and the SVM extended version is designed for additional screens.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, Eric J

The ResStock analysis tool is helping states, municipalities, utilities, and manufacturers identify which home upgrades save the most energy and money. Across the country there's a vast diversity in the age, size, construction practices, installed equipment, appliances, and resident behavior of the housing stock, not to mention the range of climates. These variations have hindered the accuracy of predicting savings for existing homes. Researchers at the National Renewable Energy Laboratory (NREL) developed ResStock. It's a versatile tool that takes a new approach to large-scale residential energy analysis by combining: large public and private data sources, statistical sampling, detailed subhourly buildingmore » simulations, high-performance computing. This combination achieves unprecedented granularity and most importantly - accuracy - in modeling the diversity of the single-family housing stock.« less

Whole-genome CNV analysis: advances in computational approaches.

PubMed

Pirooznia, Mehdi; Goes, Fernando S; Zandi, Peter P

2015-01-01

Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a significant contribution to human diversity and also play an important role in disease susceptibility. Recent advances in genome sequencing technologies have enabled the characterization of a variety of genomic features, including CNVs. This has led to the development of several bioinformatics approaches to detect CNVs from next-generation sequencing data. Here, we review recent advances in CNV detection from whole genome sequencing. We discuss the informatics approaches and current computational tools that have been developed as well as their strengths and limitations. This review will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development.

Performance modeling & simulation of complex systems (A systems engineering design & analysis approach)

NASA Technical Reports Server (NTRS)

Hall, Laverne

1995-01-01

Modeling of the Multi-mission Image Processing System (MIPS) will be described as an example of the use of a modeling tool to design a distributed system that supports multiple application scenarios. This paper examines: (a) modeling tool selection, capabilities, and operation (namely NETWORK 2.5 by CACl), (b) pointers for building or constructing a model and how the MIPS model was developed, (c) the importance of benchmarking or testing the performance of equipment/subsystems being considered for incorporation the design/architecture, (d) the essential step of model validation and/or calibration using the benchmark results, (e) sample simulation results from the MIPS model, and (f) how modeling and simulation analysis affected the MIPS design process by having a supportive and informative impact.

Varietal discrimination of hop pellets by near and mid infrared spectroscopy.

PubMed

Machado, Julio C; Faria, Miguel A; Ferreira, Isabel M P L V O; Páscoa, Ricardo N M J; Lopes, João A

2018-04-01

Hop is one of the most important ingredients of beer production and several varieties are commercialized. Therefore, it is important to find an eco-real-time-friendly-low-cost technique to distinguish and discriminate hop varieties. This paper describes the development of a method based on vibrational spectroscopy techniques, namely near- and mid-infrared spectroscopy, for the discrimination of 33 commercial hop varieties. A total of 165 samples (five for each hop variety) were analysed by both techniques. Principal component analysis, hierarchical cluster analysis and partial least squares discrimination analysis were the chemometric tools used to discriminate positively the hop varieties. After optimizing the spectral regions and pre-processing methods a total of 94.2% and 96.6% correct hop varieties discrimination were obtained for near- and mid-infrared spectroscopy, respectively. The results obtained demonstrate the suitability of these vibrational spectroscopy techniques to discriminate different hop varieties and consequently their potential to be used as an authenticity tool. Compared with the reference procedures normally used for hops variety discrimination these techniques are quicker, cost-effective, non-destructive and eco-friendly. Copyright © 2017 Elsevier B.V. All rights reserved.

ELISA-BASE: An Integrated Bioinformatics Tool for Analyzing and Tracking ELISA Microarray Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Amanda M.; Collett, James L.; Seurynck-Servoss, Shannon L.

ELISA-BASE is an open-source database for capturing, organizing and analyzing protein enzyme-linked immunosorbent assay (ELISA) microarray data. ELISA-BASE is an extension of the BioArray Soft-ware Environment (BASE) database system, which was developed for DNA microarrays. In order to make BASE suitable for protein microarray experiments, we developed several plugins for importing and analyzing quantitative ELISA microarray data. Most notably, our Protein Microarray Analysis Tool (ProMAT) for processing quantita-tive ELISA data is now available as a plugin to the database.

Cognitive Issues in Learning Advanced Physics: An Example from Quantum Mechanics

NASA Astrophysics Data System (ADS)

Singh, Chandralekha; Zhu, Guangtian

2009-11-01

We are investigating cognitive issues in learning quantum mechanics in order to develop effective teaching and learning tools. The analysis of cognitive issues is particularly important for bridging the gap between the quantitative and conceptual aspects of quantum mechanics and for ensuring that the learning tools help students build a robust knowledge structure. We discuss the cognitive aspects of quantum mechanics that are similar or different from those of introductory physics and their implications for developing strategies to help students develop a good grasp of quantum mechanics.

Development and psychometric testing of the Clinical Learning Organisational Culture Survey (CLOCS).

PubMed

Henderson, Amanda; Creedy, Debra; Boorman, Rhonda; Cooke, Marie; Walker, Rachel

2010-10-01

This paper describes the development and psychometric testing of the Clinical Learning Organisational Culture Survey (CLOCS) that measures prevailing beliefs and assumptions important for learning to occur in the workplace. Items from a tool that measured motivation in workplace learning were adapted to the nursing practice context. The tool was tested in the clinical setting, and then further modified to enhance face and content validity. Registered nurses (329) across three major Australian health facilities were surveyed between June 2007 and September 2007. An exploratory factor analysis identified five concepts--recognition, dissatisfaction, affiliation, accomplishment, and influence. VALIDITY AND RELIABILITY: Internal consistency measures of reliability revealed that four concepts had good internal consistency: recognition (alpha=.914), dissatisfaction (alpha=.771), affiliation (alpha=.801), accomplishment (alpha=.664), but less so for influence (alpha=.529). This tool effectively measures recognition, affiliation and accomplishment--three concepts important for learning in practice situations, as well as dissatisfied staff across all these domains. Testing of additional influence items identify that this concept is difficult to delineate. The CLOCS can effectively inform leaders about concepts inherent in the culture important for maximising learning by staff. Crown Copyright © 2009. Published by Elsevier Ltd. All rights reserved.

Evolving software reengineering technology for the emerging innovative-competitive era

NASA Technical Reports Server (NTRS)

Hwang, Phillip Q.; Lock, Evan; Prywes, Noah

1994-01-01

This paper reports on a multi-tool commercial/military environment combining software Domain Analysis techniques with Reusable Software and Reengineering of Legacy Software. It is based on the development of a military version for the Department of Defense (DOD). The integrated tools in the military version are: Software Specification Assistant (SSA) and Software Reengineering Environment (SRE), developed by Computer Command and Control Company (CCCC) for Naval Surface Warfare Center (NSWC) and Joint Logistics Commanders (JLC), and the Advanced Research Project Agency (ARPA) STARS Software Engineering Environment (SEE) developed by Boeing for NAVAIR PMA 205. The paper describes transitioning these integrated tools to commercial use. There is a critical need for the transition for the following reasons: First, to date, 70 percent of programmers' time is applied to software maintenance. The work of these users has not been facilitated by existing tools. The addition of Software Reengineering will also facilitate software maintenance and upgrading. In fact, the integrated tools will support the entire software life cycle. Second, the integrated tools are essential to Business Process Reengineering, which seeks radical process innovations to achieve breakthrough results. Done well, process reengineering delivers extraordinary gains in process speed, productivity and profitability. Most importantly, it discovers new opportunities for products and services in collaboration with other organizations. Legacy computer software must be changed rapidly to support innovative business processes. The integrated tools will provide commercial organizations important competitive advantages. This, in turn, will increase employment by creating new business opportunities. Third, the integrated system will produce much higher quality software than use of the tools separately. The reason for this is that producing or upgrading software requires keen understanding of extremely complex applications which is facilitated by the integrated tools. The radical savings in the time and cost associated with software, due to use of CASE tools that support combined Reuse of Software and Reengineering of Legacy Code, will add an important impetus to improving the automation of enterprises. This will be reflected in continuing operations, as well as in innovating new business processes. The proposed multi-tool software development is based on state of the art technology, which will be further advanced through the use of open systems for adding new tools and experience in their use.

The Use of Electrophysiology in the Study of Early Development

ERIC Educational Resources Information Center

Szucs, Denes

2005-01-01

Electrophysiology is a timely and important tool in the study of early cognitive development. This commentary polishes the definition of event-related potential (ERP) components; often interpreted as expressions of mental processes. Further, attention is drawn to time-frequency analysis of the electroencephalogram (EEG) which conveys much more…

Understanding Student Self-Disclosure Typology through Blogging

ERIC Educational Resources Information Center

Harper, Vernon B., Jr.; Harper, Erika J.

2006-01-01

Significant research indicates that student self-disclosure plays an important role in the learning experience and producing positive learning outcomes. Blogging is an increasingly popular web tool that can potentially aid educators by encouraging student self-disclosure. Both content analysis and focus groups were used to assess whether student…

AN IMPROVED STRATEGY FOR REGRESSION OF BIOPHYSICAL VARIABLES AND LANDSAT ETM+ DATA. (R828309)

EPA Science Inventory

Empirical models are important tools for relating field-measured biophysical variables to remote sensing data. Regression analysis has been a popular empirical method of linking these two types of data to provide continuous estimates for variables such as biomass, percent wood...

The Teaching of Undergraduate Health Psychology: A National Survey

ERIC Educational Resources Information Center

Panjwani, Aliza A.; Gurung, Regan A. R.; Revenson, Tracey A.

2017-01-01

We conducted an online national survey to examine how undergraduate health psychology is taught, offer information about course design and content, and provide a needs analysis. Health psychology instructors (N = 126) answered questions about course format, teaching tools, importance of covering specific topics, and needed resources. A principal…

Using Course Currency as a Didactic Tool

ERIC Educational Resources Information Center

Wachsman, Yoav

2007-01-01

Classroom participation is an important and frequently used pedagogical strategy. This paper examines how awarding students with course currency, bills that are redeemable for bonus points at the end of the term, affects class participation and students' understanding of the material. The research uses surveys and data analysis to examine the…

Innovations in Hospitality Industry

ERIC Educational Resources Information Center

Dzhandzhugazova, Elena A.; Blinova, Ekaterina A.; Orlova, Liubov N.; Romanova, Marianna M.

2016-01-01

The article focuses on the study of the role and importance of innovation, its classification, the problems of its application in the hotel industry with emphasis on the application of sensory marketing tools in the development of the innovative marketing mix within the hospitality industry. The article provides an analysis of the "seven…

Parents of Autistic Children and Their Experiences with Assistive Technology

ERIC Educational Resources Information Center

Curran, David

2017-01-01

Assistive Technology (AT) has become an important tool used by special needs children for improving their quality of life by empowering their abilities, therefore improving their personal independence. The purpose of this Interpretative Phenomenological Analysis (IPA) study was to closely examine the experiences and meaning-making of parents, of…

Secondary Data Analysis: An Important Tool for Addressing Developmental Questions

ERIC Educational Resources Information Center

Greenhoot, Andrea Follmer; Dowsett, Chantelle J.

2012-01-01

Existing data sets can be an efficient, powerful, and readily available resource for addressing questions about developmental science. Many of the available databases contain hundreds of variables of interest to developmental psychologists, track participants longitudinally, and have representative samples. In this article, the authors discuss the…

Idiosyncratic Functions: Severe Problem Behavior Maintained by Access to Ritualistic Behaviors

ERIC Educational Resources Information Center

Hausman, Nicole; Kahng, SungWoo; Farrell, Ellen; Mongeon, Camille

2009-01-01

The development of functional analysis technology has been an important tool in the assessment and treatment of aberrant behaviors among individuals with developmental disabilities. In some cases, the function of problem behavior may be idiosyncratic in nature, making modifications to functional analyses necessary. In the current study, a…

Global Sensitivity Analysis for Identifying Important Parameters of Nitrogen Nitrification and Denitrification under Model and Scenario Uncertainties

NASA Astrophysics Data System (ADS)

Ye, M.; Chen, Z.; Shi, L.; Zhu, Y.; Yang, J.

2017-12-01

Nitrogen reactive transport modeling is subject to uncertainty in model parameters, structures, and scenarios. While global sensitivity analysis is a vital tool for identifying the parameters important to nitrogen reactive transport, conventional global sensitivity analysis only considers parametric uncertainty. This may result in inaccurate selection of important parameters, because parameter importance may vary under different models and modeling scenarios. By using a recently developed variance-based global sensitivity analysis method, this paper identifies important parameters with simultaneous consideration of parametric uncertainty, model uncertainty, and scenario uncertainty. In a numerical example of nitrogen reactive transport modeling, a combination of three scenarios of soil temperature and two scenarios of soil moisture leads to a total of six scenarios. Four alternative models are used to evaluate reduction functions used for calculating actual rates of nitrification and denitrification. The model uncertainty is tangled with scenario uncertainty, as the reduction functions depend on soil temperature and moisture content. The results of sensitivity analysis show that parameter importance varies substantially between different models and modeling scenarios, which may lead to inaccurate selection of important parameters if model and scenario uncertainties are not considered. This problem is avoided by using the new method of sensitivity analysis in the context of model averaging and scenario averaging. The new method of sensitivity analysis can be applied to other problems of contaminant transport modeling when model uncertainty and/or scenario uncertainty are present.

Strategic Planning in Population Health and Public Health Practice: A Call to Action for Higher Education

PubMed Central

PHELPS, CHARLES; RAPPUOLI, RINO; LEVIN, SCOTT; SHORTLIFFE, EDWARD; COLWELL, RITA

2016-01-01

Policy Points: Scarce resources, especially in population health and public health practice, underlie the importance of strategic planning.Public health agencies’ current planning and priority setting efforts are often narrow, at times opaque, and focused on single metrics such as cost‐effectiveness.As demonstrated by SMART Vaccines, a decision support software system developed by the Institute of Medicine and the National Academy of Engineering, new approaches to strategic planning allow the formal incorporation of multiple stakeholder views and multicriteria decision making that surpass even those sophisticated cost‐effectiveness analyses widely recommended and used for public health planning.Institutions of higher education can and should respond by building on modern strategic planning tools as they teach their students how to improve population health and public health practice. Context Strategic planning in population health and public health practice often uses single indicators of success or, when using multiple indicators, provides no mechanism for coherently combining the assessments. Cost‐effectiveness analysis, the most complex strategic planning tool commonly applied in public health, uses only a single metric to evaluate programmatic choices, even though other factors often influence actual decisions. Methods Our work employed a multicriteria systems analysis approach—specifically, multiattribute utility theory—to assist in strategic planning and priority setting in a particular area of health care (vaccines), thereby moving beyond the traditional cost‐effectiveness analysis approach. Findings (1) Multicriteria systems analysis provides more flexibility, transparency, and clarity in decision support for public health issues compared with cost‐effectiveness analysis. (2) More sophisticated systems‐level analyses will become increasingly important to public health as disease burdens increase and the resources to deal with them become scarcer. Conclusions The teaching of strategic planning in public health must be expanded in order to fill a void in the profession's planning capabilities. Public health training should actively incorporate model building, promote the interactive use of software tools, and explore planning approaches that transcend restrictive assumptions of cost‐effectiveness analysis. The Strategic Multi‐Attribute Ranking Tool for Vaccines (SMART Vaccines), which was recently developed by the Institute of Medicine and the National Academy of Engineering to help prioritize new vaccine development, is a working example of systems analysis as a basis for decision support. PMID:26994711

Strategic Planning in Population Health and Public Health Practice: A Call to Action for Higher Education.

PubMed

Phelps, Charles; Madhavan, Guruprasad; Rappuoli, Rino; Levin, Scott; Shortliffe, Edward; Colwell, Rita

2016-03-01

Scarce resources, especially in population health and public health practice, underlie the importance of strategic planning. Public health agencies' current planning and priority setting efforts are often narrow, at times opaque, and focused on single metrics such as cost-effectiveness. As demonstrated by SMART Vaccines, a decision support software system developed by the Institute of Medicine and the National Academy of Engineering, new approaches to strategic planning allow the formal incorporation of multiple stakeholder views and multicriteria decision making that surpass even those sophisticated cost-effectiveness analyses widely recommended and used for public health planning. Institutions of higher education can and should respond by building on modern strategic planning tools as they teach their students how to improve population health and public health practice. Strategic planning in population health and public health practice often uses single indicators of success or, when using multiple indicators, provides no mechanism for coherently combining the assessments. Cost-effectiveness analysis, the most complex strategic planning tool commonly applied in public health, uses only a single metric to evaluate programmatic choices, even though other factors often influence actual decisions. Our work employed a multicriteria systems analysis approach--specifically, multiattribute utility theory--to assist in strategic planning and priority setting in a particular area of health care (vaccines), thereby moving beyond the traditional cost-effectiveness analysis approach. (1) Multicriteria systems analysis provides more flexibility, transparency, and clarity in decision support for public health issues compared with cost-effectiveness analysis. (2) More sophisticated systems-level analyses will become increasingly important to public health as disease burdens increase and the resources to deal with them become scarcer. The teaching of strategic planning in public health must be expanded in order to fill a void in the profession's planning capabilities. Public health training should actively incorporate model building, promote the interactive use of software tools, and explore planning approaches that transcend restrictive assumptions of cost-effectiveness analysis. The Strategic Multi-Attribute Ranking Tool for Vaccines (SMART Vaccines), which was recently developed by the Institute of Medicine and the National Academy of Engineering to help prioritize new vaccine development, is a working example of systems analysis as a basis for decision support. © 2016 Milbank Memorial Fund.

[Organising an investigation site: a national training reference document].

PubMed

Cornu, Catherine; David, Frédérique; Duchossoy, Luc; Hansel-Esteller, Sylvie; Bertoye, Pierre-Henri; Giacomino, Alain; Mouly, Stéphane; Diebolt, Vincent; Blazejewski, Sylvie

2014-01-01

Several surveys have shown a declining performance of French investigators in conducting clinical trials. This is partly due to insufficient and heterogeneous investigator training and site organisation. A multidisciplinary group was set up to propose solutions. We describe the tools developed to improve study site organisation. This working group was made up of clinical research experts from academia, industry, drug regulatory authorities, general practice, and consulting. Methods and tools were developed to improve site organisation. The proposed tools mainly focus on increasing investigators' awareness of their responsibilities, their research environment, the importance of a thorough feasibility analysis, and the implementation of active patient recruitment strategies. These tools should be able to improve site organisation and performances in conducting clinical trials. © 2014 Société Française de Pharmacologie et de Thérapeutique.

Integrating ecosystem services analysis into scenario planning practice: accounting for street tree benefits with i-Tree valuation in Central Texas.

PubMed

Hilde, Thomas; Paterson, Robert

2014-12-15

Scenario planning continues to gain momentum in the United States as an effective process for building consensus on long-range community plans and creating regional visions for the future. However, efforts to integrate more sophisticated information into the analytical framework to help identify important ecosystem services have lagged in practice. This is problematic because understanding the tradeoffs of land consumption patterns on ecological integrity is central to mitigating the environmental degradation caused by land use change and new development. In this paper we describe how an ecosystem services valuation model, i-Tree, was integrated into a mainstream scenario planning software tool, Envision Tomorrow, to assess the benefits of public street trees for alternative future development scenarios. The tool is then applied to development scenarios from the City of Hutto, TX, a Central Texas Sustainable Places Project demonstration community. The integrated tool represents a methodological improvement for scenario planning practice, offers a way to incorporate ecosystem services analysis into mainstream planning processes, and serves as an example of how open source software tools can expand the range of issues available for community and regional planning consideration, even in cases where community resources are limited. The tool also offers room for future improvements; feasible options include canopy analysis of various future land use typologies, as well as a generalized street tree model for broader U.S. application. Copyright © 2014 Elsevier Ltd. All rights reserved.

Can incentives make a difference? Assessing the effects of policy tools for encouraging tree-planting on private lands.

PubMed

Ruseva, Tatyana B; Evans, Tom P; Fischer, Burnell C

2015-05-15

This study uses a mail survey of private landowners in the Midwest United States to understand the characteristics of owners who have planted trees or intend to plant trees in the future. The analysis examines what policy tools encourage owners to plant trees, and how policy tools operate across different ownership attributes to promote tree-planting on private lands. Logistic regression results suggest that cost-subsidizing policy tools, such as low-cost and free seedlings, significantly increase the odds of actual and planned reforestation when landowners consider them important for increasing forest cover. Individuals most likely to plant trees, when low-cost seedlings are available and important, are fairly recent (<5 years), college-educated owners who own small parcels (<4 ha) and use the land for recreation. Motivations to reforest were also shaped by owners' planning horizons, connection to the land, previous tree-planting experience, and peer influence. The study has relevance for the design of policy approaches that can encourage private forestation through provision of economic incentives and capacity to private landowners. Copyright © 2015 Elsevier Ltd. All rights reserved.

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

PubMed Central

Green, Kevin T.; Dutilh, Bas E.; Edwards, Robert A.

2016-01-01

Summary: Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools. Availability and implementation: SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS. Contact: redwards@mail.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26454280

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.

PubMed

Silva, Genivaldo Gueiros Z; Green, Kevin T; Dutilh, Bas E; Edwards, Robert A

2016-02-01

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools. SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS. redwards@mail.sdsu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Generating DEM from LIDAR data - comparison of available software tools

NASA Astrophysics Data System (ADS)

Korzeniowska, K.; Lacka, M.

2011-12-01

In recent years many software tools and applications have appeared that offer procedures, scripts and algorithms to process and visualize ALS data. This variety of software tools and of "point cloud" processing methods contributed to the aim of this study: to assess algorithms available in various software tools that are used to classify LIDAR "point cloud" data, through a careful examination of Digital Elevation Models (DEMs) generated from LIDAR data on a base of these algorithms. The works focused on the most important available software tools: both commercial and open source ones. Two sites in a mountain area were selected for the study. The area of each site is 0.645 sq km. DEMs generated with analysed software tools ware compared with a reference dataset, generated using manual methods to eliminate non ground points. Surfaces were analysed using raster analysis. Minimum, maximum and mean differences between reference DEM and DEMs generated with analysed software tools were calculated, together with Root Mean Square Error. Differences between DEMs were also examined visually using transects along the grid axes in the test sites.

Design/Analysis of the JWST ISIM Bonded Joints for Survivability at Cryogenic Temperatures

NASA Technical Reports Server (NTRS)

Bartoszyk, Andrew; Johnston, John; Kaprielian, Charles; Kuhn, Jonathan; Kunt, Cengiz; Rodini,Benjamin; Young, Daniel

1990-01-01

A major design and analysis challenge for the JWST ISIM structure is thermal survivability of metal/composite bonded joints below the cryogenic temperature of 30K (-405 F). Current bonded joint concepts include internal invar plug fittings, external saddle titanium/invar fittings and composite gusset/clip joints all bonded to M55J/954-6 and T300/954-6 hybrid composite tubes (75mm square). Analytical experience and design work done on metal/composite bonded joints at temperatures below that of liquid nitrogen are limited and important analysis tools, material properties, and failure criteria for composites at cryogenic temperatures are sparse in the literature. Increasing this challenge is the difficulty in testing for these required tools and properties at cryogenic temperatures. To gain confidence in analyzing and designing the ISIM joints, a comprehensive joint development test program has been planned and is currently running. The test program is designed to produce required analytical tools and develop a composite failure criterion for bonded joint strengths at cryogenic temperatures. Finite element analysis is used to design simple test coupons that simulate anticipated stress states in the flight joints; subsequently the test results are used to correlate the analysis technique for the final design of the bonded joints. In this work, we present an overview of the analysis and test methodology, current results, and working joint designs based on developed techniques and properties.

Fully automated analysis of multi-resolution four-channel micro-array genotyping data

NASA Astrophysics Data System (ADS)

Abbaspour, Mohsen; Abugharbieh, Rafeef; Podder, Mohua; Tebbutt, Scott J.

2006-03-01

We present a fully-automated and robust microarray image analysis system for handling multi-resolution images (down to 3-micron with sizes up to 80 MBs per channel). The system is developed to provide rapid and accurate data extraction for our recently developed microarray analysis and quality control tool (SNP Chart). Currently available commercial microarray image analysis applications are inefficient, due to the considerable user interaction typically required. Four-channel DNA microarray technology is a robust and accurate tool for determining genotypes of multiple genetic markers in individuals. It plays an important role in the state of the art trend where traditional medical treatments are to be replaced by personalized genetic medicine, i.e. individualized therapy based on the patient's genetic heritage. However, fast, robust, and precise image processing tools are required for the prospective practical use of microarray-based genetic testing for predicting disease susceptibilities and drug effects in clinical practice, which require a turn-around timeline compatible with clinical decision-making. In this paper we have developed a fully-automated image analysis platform for the rapid investigation of hundreds of genetic variations across multiple genes. Validation tests indicate very high accuracy levels for genotyping results. Our method achieves a significant reduction in analysis time, from several hours to just a few minutes, and is completely automated requiring no manual interaction or guidance.

Development of Response Surface Models for Rapid Analysis & Multidisciplinary Optimization of Launch Vehicle Design Concepts

NASA Technical Reports Server (NTRS)

Unal, Resit

1999-01-01

Multdisciplinary design optimization (MDO) is an important step in the design and evaluation of launch vehicles, since it has a significant impact on performance and lifecycle cost. The objective in MDO is to search the design space to determine the values of design parameters that optimize the performance characteristics subject to system constraints. Vehicle Analysis Branch (VAB) at NASA Langley Research Center has computerized analysis tools in many of the disciplines required for the design and analysis of launch vehicles. Vehicle performance characteristics can be determined by the use of these computerized analysis tools. The next step is to optimize the system performance characteristics subject to multidisciplinary constraints. However, most of the complex sizing and performance evaluation codes used for launch vehicle design are stand-alone tools, operated by disciplinary experts. They are, in general, difficult to integrate and use directly for MDO. An alternative has been to utilize response surface methodology (RSM) to obtain polynomial models that approximate the functional relationships between performance characteristics and design variables. These approximation models, called response surface models, are then used to integrate the disciplines using mathematical programming methods for efficient system level design analysis, MDO and fast sensitivity simulations. A second-order response surface model of the form given has been commonly used in RSM since in many cases it can provide an adequate approximation especially if the region of interest is sufficiently limited.

Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

PubMed Central

Chen, Zixi; Chen, Lei; Zhang, Weiwen

2017-01-01

Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented. PMID:28979258

Stone tools from the ancient Tongan state reveal prehistoric interaction centers in the Central Pacific

PubMed Central

Clark, Geoffrey R.; Reepmeyer, Christian; Melekiola, Nivaleti; Woodhead, Jon; Dickinson, William R.; Martinsson-Wallin, Helene

2014-01-01

Tonga was unique in the prehistoric Pacific for developing a maritime state that integrated the archipelago under a centralized authority and for undertaking long-distance economic and political exchanges in the second millennium A.D. To establish the extent of Tonga’s maritime polity, we geochemically analyzed stone tools excavated from the central places of the ruling paramounts, particularly lithic artifacts associated with stone-faced chiefly tombs. The lithic networks of the Tongan state focused on Samoa and Fiji, with one adze sourced to the Society Islands 2,500 km from Tongatapu. To test the hypothesis that nonlocal lithics were especially valued by Tongan elites and were an important source of political capital, we analyzed prestate lithics from Tongatapu and stone artifacts from Samoa. In the Tongan state, 66% of worked stone tools were long-distance imports, indicating that interarchipelago connections intensified with the development of the Tongan polity after A.D. 1200. In contrast, stone tools found in Samoa were from local sources, including tools associated with a monumental structure contemporary with the Tongan state. Network analysis of lithics entering the Tongan state and of the distribution of Samoan adzes in the Pacific identified a centralized polity and the products of specialized lithic workshops, respectively. These results indicate that a significant consequence of social complexity was the establishment of new types of specialized sites in distant geographic areas. Specialized sites were loci of long-distance interaction and formed important centers for the transmission of information, people, and materials in prehistoric Oceania. PMID:25002481

Stone tools from the ancient Tongan state reveal prehistoric interaction centers in the Central Pacific

NASA Astrophysics Data System (ADS)

Clark, Geoffrey R.; Reepmeyer, Christian; Melekiola, Nivaleti; Woodhead, Jon; Dickinson, William R.; Martinsson-Wallin, Helene

2014-07-01

Tonga was unique in the prehistoric Pacific for developing a maritime state that integrated the archipelago under a centralized authority and for undertaking long-distance economic and political exchanges in the second millennium A.D. To establish the extent of Tonga's maritime polity, we geochemically analyzed stone tools excavated from the central places of the ruling paramounts, particularly lithic artifacts associated with stone-faced chiefly tombs. The lithic networks of the Tongan state focused on Samoa and Fiji, with one adze sourced to the Society Islands 2,500 km from Tongatapu. To test the hypothesis that nonlocal lithics were especially valued by Tongan elites and were an important source of political capital, we analyzed prestate lithics from Tongatapu and stone artifacts from Samoa. In the Tongan state, 66% of worked stone tools were long-distance imports, indicating that interarchipelago connections intensified with the development of the Tongan polity after A.D. 1200. In contrast, stone tools found in Samoa were from local sources, including tools associated with a monumental structure contemporary with the Tongan state. Network analysis of lithics entering the Tongan state and of the distribution of Samoan adzes in the Pacific identified a centralized polity and the products of specialized lithic workshops, respectively. These results indicate that a significant consequence of social complexity was the establishment of new types of specialized sites in distant geographic areas. Specialized sites were loci of long-distance interaction and formed important centers for the transmission of information, people, and materials in prehistoric Oceania.

An Investigation of Software Scaffolds Supporting Modeling Practices

NASA Astrophysics Data System (ADS)

Fretz, Eric B.; Wu, Hsin-Kai; Zhang, Baohui; Davis, Elizabeth A.; Krajcik, Joseph S.; Soloway, Elliot

2002-08-01

Modeling of complex systems and phenomena is of value in science learning and is increasingly emphasised as an important component of science teaching and learning. Modeling engages learners in desired pedagogical activities. These activities include practices such as planning, building, testing, analysing, and critiquing. Designing realistic models is a difficult task. Computer environments allow the creation of dynamic and even more complex models. One way of bringing the design of models within reach is through the use of scaffolds. Scaffolds are intentional assistance provided to learners from a variety of sources, allowing them to complete tasks that would otherwise be out of reach. Currently, our understanding of how scaffolds in software tools assist learners is incomplete. In this paper the scaffolds designed into a dynamic modeling software tool called Model-It are assessed in terms of their ability to support learners' use of modeling practices. Four pairs of middle school students were video-taped as they used the modeling software for three hours, spread over a two week time frame. Detailed analysis of coded videotape transcripts provided evidence of the importance of scaffolds in supporting the use of modeling practices. Learners used a variety of modeling practices, the majority of which occurred in conjunction with scaffolds. The use of three tool scaffolds was assessed as directly as possible, and these scaffolds were seen to support a variety of modeling practices. An argument is made for the continued empirical validation of types and instances of tool scaffolds, and further investigation of the important role of teacher and peer scaffolding in the use of scaffolded tools.

Mobile Modelling for Crowdsourcing Building Interior Data

NASA Astrophysics Data System (ADS)

Rosser, J.; Morley, J.; Jackson, M.

2012-06-01

Indoor spatial data forms an important foundation to many ubiquitous computing applications. It gives context to users operating location-based applications, provides an important source of documentation of buildings and can be of value to computer systems where an understanding of environment is required. Unlike external geographic spaces, no centralised body or agency is charged with collecting or maintaining such information. Widespread deployment of mobile devices provides a potential tool that would allow rapid model capture and update by a building's users. Here we introduce some of the issues involved in volunteering building interior data and outline a simple mobile tool for capture of indoor models. The nature of indoor data is inherently private; however in-depth analysis of this issue and legal considerations are not discussed in detail here.

A multisource feedback tool to assess ward round leadership skills of senior paediatric trainees: (1) Development of tool.

PubMed

Lakshminarayana, Indumathy; Wall, David; Bindal, Taruna; Goodyear, Helen M

2015-05-01

Leading a ward round is an essential skill for hospital consultants and senior trainees but is rarely assessed during training. To investigate the key attributes for ward round leadership and to use these results to develop a multisource feedback (MSF) tool to assess the ward round leadership skills of senior specialist trainees. A panel of experts comprising four senior paediatric consultants and two nurse managers were interviewed from May to August 2009. From analysis of the interview transcripts, 10 key themes emerged. A structured questionnaire based on the key themes was designed and sent electronically to paediatric consultants, nurses and trainees at a large university hospital (June-October 2010). 81 consultants, nurses and trainees responded to the survey. The internal consistency of this tool was high (Cronbach's α 0.95). Factor analysis showed that five factors accounted for 72% of variance. The five key areas for ward round leadership were communication skills, preparation and organisation, teaching and enthusiasm, team working and punctuality; communication was the most important key theme. A MSF tool for ward round leadership skills was developed with these areas as five domains. We believe that this tool will add to the current assessment tools available by providing feedback about ward round leadership skills. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Development of TUA-WELLNESS screening tool for screening risk of mild cognitive impairment among community-dwelling older adults

PubMed Central

Vanoh, Divya; Shahar, Suzana; Rosdinom, Razali; Din, Normah Che; Yahya, Hanis Mastura; Omar, Azahadi

2016-01-01

Background and aim Focus on screening for cognitive impairment has to be given particular importance because of the rising older adult population. Thus, this study aimed to develop and assess a brief screening tool consisting of ten items that can be self-administered by community dwelling older adults (TUA-WELLNESS). Methodology A total of 1,993 noninstitutionalized respondents aged 60 years and above were selected for this study. The dependent variable was mild cognitive impairment (MCI) assessed using neuropsychological test batteries. The items for the screening tool comprised a wide range of factors that were chosen mainly from the analysis of ordinal logistic regression (OLR) and based on past literature. A suitable cut-off point was developed using receiver operating characteristic analysis. Results A total of ten items were included in the screening tool. From the ten items, eight were found to be significant by ordinal logistic regression and the remaining two items were part of the tool because they showed strong association with cognitive impairment in previous studies. The area under curve (AUC), sensitivity, and specificity for cut-off 11 were 0.84%, 83.3%, and 73.4%, respectively. Conclusion TUA-WELLNESS screening tool has been used to screen for major risk factors of MCI among Malaysian older adults. This tool is only suitable for basic MCI risk screening purpose and should not be used for diagnostic purpose. PMID:27274208

LiPD and CSciBox: A Case Study in Why Data Standards are Important for Paleoscience

NASA Astrophysics Data System (ADS)

Weiss, I.; Bradley, E.; McKay, N.; Emile-Geay, J.; de Vesine, L. R.; Anderson, K. A.; White, J. W. C.; Marchitto, T. M., Jr.

2016-12-01

CSciBox [1] is an integrated software system that helps geoscientists build and evaluate age models. Its user chooses from a number of built-in analysis tools, composing them into an analysis workflow and applying it to paleoclimate proxy datasets. CSciBox employs modern database technology to store both the data and the analysis results in an easily accessible and searchable form, and offers the user access to the computational toolbox, the data, and the results via a graphical user interface and a sophisticated plotter. Standards are a staple of modern life, and underlie any form of automation. Without data standards, it is difficult, if not impossible, to construct effective computer tools for paleoscience analysis. The LiPD (Linked Paleo Data) framework [2] enables the storage of both data and metadata in systematic, meaningful, machine-readable ways. LiPD has been a primary enabler of CSciBox's goals of usability, interoperability, and reproducibility. Building LiPD capabilities into CSciBox's importer, for instance, eliminated the need to ask the user about file formats, variable names, relationships between columns in the input file, etc. Building LiPD capabilities into the exporter facilitated the storage of complete details about the input data-provenance, preprocessing steps, etc.-as well as full descriptions of any analyses that were performed using the CSciBox tool, along with citations to appropriate references. This comprehensive collection of data and metadata, which is all linked together in a semantically meaningful, machine-readable way, not only completely documents the analyses and makes them reproducible. It also enables interoperability with any other software system that employs the LiPD standard. [1] www.cs.colorado.edu/ lizb/cscience.html[2] McKay & Emile-Geay, Climate of the Past 12:1093 (2016)

Design of the VISITOR Tool: A Versatile ImpulSive Interplanetary Trajectory OptimizeR

NASA Technical Reports Server (NTRS)

Corpaccioli, Luca; Linskens, Harry; Komar, David R.

2014-01-01

The design of trajectories for interplanetary missions represents one of the most complex and important problems to solve during conceptual space mission design. To facilitate conceptual mission sizing activities, it is essential to obtain sufficiently accurate trajectories in a fast and repeatable manner. To this end, the VISITOR tool was developed. This tool modularly augments a patched conic MGA-1DSM model with a mass model, launch window analysis, and the ability to simulate more realistic arrival and departure operations. This was implemented in MATLAB, exploiting the built-in optimization tools and vector analysis routines. The chosen optimization strategy uses a grid search and pattern search, an iterative variable grid method. A genetic algorithm can be selectively used to improve search space pruning, at the cost of losing the repeatability of the results and increased computation time. The tool was validated against seven flown missions: the average total mission (Delta)V offset from the nominal trajectory was 9.1%, which was reduced to 7.3% when using the genetic algorithm at the cost of an increase in computation time by a factor 5.7. It was found that VISITOR was well-suited for the conceptual design of interplanetary trajectories, while also facilitating future improvements due to its modular structure.

Systematic Omics Analysis Review (SOAR) Tool to Support Risk Assessment

PubMed Central

McConnell, Emma R.; Bell, Shannon M.; Cote, Ila; Wang, Rong-Lin; Perkins, Edward J.; Garcia-Reyero, Natàlia; Gong, Ping; Burgoon, Lyle D.

2014-01-01

Environmental health risk assessors are challenged to understand and incorporate new data streams as the field of toxicology continues to adopt new molecular and systems biology technologies. Systematic screening reviews can help risk assessors and assessment teams determine which studies to consider for inclusion in a human health assessment. A tool for systematic reviews should be standardized and transparent in order to consistently determine which studies meet minimum quality criteria prior to performing in-depth analyses of the data. The Systematic Omics Analysis Review (SOAR) tool is focused on assisting risk assessment support teams in performing systematic reviews of transcriptomic studies. SOAR is a spreadsheet tool of 35 objective questions developed by domain experts, focused on transcriptomic microarray studies, and including four main topics: test system, test substance, experimental design, and microarray data. The tool will be used as a guide to identify studies that meet basic published quality criteria, such as those defined by the Minimum Information About a Microarray Experiment standard and the Toxicological Data Reliability Assessment Tool. Seven scientists were recruited to test the tool by using it to independently rate 15 published manuscripts that study chemical exposures with microarrays. Using their feedback, questions were weighted based on importance of the information and a suitability cutoff was set for each of the four topic sections. The final validation resulted in 100% agreement between the users on four separate manuscripts, showing that the SOAR tool may be used to facilitate the standardized and transparent screening of microarray literature for environmental human health risk assessment. PMID:25531884

Visualization of the tire-soil interaction area by means of ObjectARX programming interface

NASA Astrophysics Data System (ADS)

Mueller, W.; Gruszczyński, M.; Raba, B.; Lewicki, A.; Przybył, K.; Zaborowicz, M.; Koszela, K.; Boniecki, P.

2014-04-01

The process of data visualization, important for their analysis, becomes problematic when large data sets generated via computer simulations are available. This problem concerns, among others, the models that describe the geometry of tire-soil interaction. For the purpose of a graphical representation of this area and implementation of various geometric calculations the authors have developed a plug-in application for AutoCAD, based on the latest technologies, including ObjectARX, LINQ and the use of Visual Studio platform. Selected programming tools offer a wide variety of IT structures that enable data visualization and data analysis and are important e.g. in model verification.

DISEASE RISK ANALYSIS--A TOOL FOR POLICY MAKING WHEN EVIDENCE IS LACKING: IMPORT OF RABIES-SUSCEPTIBLE ZOO MAMMALS AS A MODEL.

PubMed

Hartley, Matt; Roberts, Helen

2015-09-01

Disease control management relies on the development of policy supported by an evidence base. The evidence base for disease in zoo animals is often absent or incomplete. Resources for disease research in these species are limited, and so in order to develop effective policies, novel approaches to extrapolating knowledge and dealing with uncertainty need to be developed. This article demonstrates how qualitative risk analysis techniques can be used to aid decision-making in circumstances in which there is a lack of specific evidence using the import of rabies-susceptible zoo mammals into the United Kingdom as a model.

Cross validation issues in multiobjective clustering

PubMed Central

Brusco, Michael J.; Steinley, Douglas

2018-01-01

The implementation of multiobjective programming methods in combinatorial data analysis is an emergent area of study with a variety of pragmatic applications in the behavioural sciences. Most notably, multiobjective programming provides a tool for analysts to model trade offs among competing criteria in clustering, seriation, and unidimensional scaling tasks. Although multiobjective programming has considerable promise, the technique can produce numerically appealing results that lack empirical validity. With this issue in mind, the purpose of this paper is to briefly review viable areas of application for multiobjective programming and, more importantly, to outline the importance of cross-validation when using this method in cluster analysis. PMID:19055857

A tool for the economic analysis of mass prophylaxis operations with an application to H1N1 influenza vaccination clinics.

PubMed

Cho, Bo-Hyun; Hicks, Katherine A; Honeycutt, Amanda A; Hupert, Nathaniel; Khavjou, Olga; Messonnier, Mark; Washington, Michael L

2011-01-01

This article uses the 2009 H1N1 influenza vaccination program experience to introduce a cost analysis approach that may be relevant for planning mass prophylaxis operations, such as vaccination clinics at public health centers, work sites, schools, or pharmacy-based clinics. These costs are important for planning mass influenza vaccination activities and are relevant for all public health emergency preparedness scenarios requiring countermeasure dispensing. We demonstrate how costs vary depending on accounting perspective, staffing composition, and other factors. We also describe a mass vaccination clinic budgeting tool that clinic managers may use to estimate clinic costs and to examine how costs vary depending on the availability of volunteers or donated supplies and on the number of patients vaccinated per hour. Results from pilot tests with school-based H1N1 influenza vaccination clinic managers are described. The tool can also contribute to planning efforts for universal seasonal influenza vaccination.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

Uncertainty Modeling for Robustness Analysis of Control Upset Prevention and Recovery Systems

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Khong, Thuan H.; Shin, Jong-Yeob; Kwatny, Harry; Chang, Bor-Chin; Balas, Gary J.

2005-01-01

Formal robustness analysis of aircraft control upset prevention and recovery systems could play an important role in their validation and ultimate certification. Such systems (developed for failure detection, identification, and reconfiguration, as well as upset recovery) need to be evaluated over broad regions of the flight envelope and under extreme flight conditions, and should include various sources of uncertainty. However, formulation of linear fractional transformation (LFT) models for representing system uncertainty can be very difficult for complex parameter-dependent systems. This paper describes a preliminary LFT modeling software tool which uses a matrix-based computational approach that can be directly applied to parametric uncertainty problems involving multivariate matrix polynomial dependencies. Several examples are presented (including an F-16 at an extreme flight condition, a missile model, and a generic example with numerous crossproduct terms), and comparisons are given with other LFT modeling tools that are currently available. The LFT modeling method and preliminary software tool presented in this paper are shown to compare favorably with these methods.

New generation of exploration tools: interactive modeling software and microcomputers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krajewski, S.A.

1986-08-01

Software packages offering interactive modeling techniques are now available for use on microcomputer hardware systems. These packages are reasonably priced for both company and independent explorationists; they do not require users to have high levels of computer literacy; they are capable of rapidly completing complex ranges of sophisticated geologic and geophysical modeling tasks; and they can produce presentation-quality output for comparison with real-world data. For example, interactive packages are available for mapping, log analysis, seismic modeling, reservoir studies, and financial projects as well as for applying a variety of statistical and geostatistical techniques to analysis of exploration data. More importantly,more » these packages enable explorationists to directly apply their geologic expertise when developing and fine-tuning models for identifying new prospects and for extending producing fields. As a result of these features, microcomputers and interactive modeling software are becoming common tools in many exploration offices. Gravity and magnetics software programs illustrate some of the capabilities of such exploration tools.« less

Stable-isotope analysis: a neglected tool for placing parasites in food webs.

PubMed

Sabadel, A J M; Stumbo, A D; MacLeod, C D

2018-02-28

Parasites are often overlooked in the construction of food webs, despite their ubiquitous presence in almost every type of ecosystem. Researchers who do recognize their importance often struggle to include parasites using classical food-web theory, mainly due to the parasites' multiple hosts and life stages. A novel approach using compound-specific stable-isotope analysis promises to provide considerable insight into the energetic exchanges of parasite and host, which may solve some of the issues inherent in incorporating parasites using a classical approach. Understanding the role of parasites within food webs, and tracing the associated biomass transfers, are crucial to constructing new models that will expand our knowledge of food webs. This mini-review focuses on stable-isotope studies published in the past decade, and introduces compound-specific stable-isotope analysis as a powerful, but underutilized, newly developed tool that may answer many unresolved questions regarding the role of parasites in food webs.

TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

PubMed

Hou, Yue; Konen, Jessica; Brat, Daniel J; Marcus, Adam I; Cooper, Lee A D

2018-05-08

Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.

Accidents at work and costs analysis: a field study in a large Italian company.

PubMed

Battaglia, Massimo; Frey, Marco; Passetti, Emilio

2014-01-01

Accidents at work are still a heavy burden in social and economic terms, and action to improve health and safety standards at work offers great potential gains not only to employers, but also to individuals and society as a whole. However, companies often are not interested to measure the costs of accidents even if cost information may facilitate preventive occupational health and safety management initiatives. The field study, carried out in a large Italian company, illustrates technical and organisational aspects associated with the implementation of an accident costs analysis tool. The results indicate that the implementation (and the use) of the tool requires a considerable commitment by the company, that accident costs analysis should serve to reinforce the importance of health and safety prevention and that the economic dimension of accidents is substantial. The study also suggests practical ways to facilitate the implementation and the moral acceptance of the accounting technology.

Accidents at Work and Costs Analysis: A Field Study in a Large Italian Company

PubMed Central

BATTAGLIA, Massimo; FREY, Marco; PASSETTI, Emilio

2014-01-01

Accidents at work are still a heavy burden in social and economic terms, and action to improve health and safety standards at work offers great potential gains not only to employers, but also to individuals and society as a whole. However, companies often are not interested to measure the costs of accidents even if cost information may facilitate preventive occupational health and safety management initiatives. The field study, carried out in a large Italian company, illustrates technical and organisational aspects associated with the implementation of an accident costs analysis tool. The results indicate that the implementation (and the use) of the tool requires a considerable commitment by the company, that accident costs analysis should serve to reinforce the importance of health and safety prevention and that the economic dimension of accidents is substantial. The study also suggests practical ways to facilitate the implementation and the moral acceptance of the accounting technology. PMID:24869894

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

PubMed

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

2016-08-30

High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

Advancing data management and analysis in different scientific disciplines

NASA Astrophysics Data System (ADS)

Fischer, M.; Gasthuber, M.; Giesler, A.; Hardt, M.; Meyer, J.; Prabhune, A.; Rigoll, F.; Schwarz, K.; Streit, A.

2017-10-01

Over the past several years, rapid growth of data has affected many fields of science. This has often resulted in the need for overhauling or exchanging the tools and approaches in the disciplines’ data life cycles. However, this allows the application of new data analysis methods and facilitates improved data sharing. The project Large-Scale Data Management and Analysis (LSDMA) of the German Helmholtz Association has been addressing both specific and generic requirements in its data life cycle successfully since 2012. Its data scientists work together with researchers from the fields such as climatology, energy and neuroscience to improve the community-specific data life cycles, in several cases even all stages of the data life cycle, i.e. from data acquisition to data archival. LSDMA scientists also study methods and tools that are of importance to many communities, e.g. data repositories and authentication and authorization infrastructure.

Quantification of indium in steel using PIXE

NASA Astrophysics Data System (ADS)

Oliver, A.; Miranda, J.; Rickards, J.; Cheang, J. C.

1989-04-01

The quantitative analysis of steel for endodontics tools was carried out using low-energy protons (≤ 700 keV). A computer program for a thick-target analysis which includes enhancement due to secondary fluorescence was used. In this experiment the L-lines of indium are enhanced due to the proximity of other elements' K-lines to the indium absorption edge. The results show that the ionization cross section expression employed to evaluate this magnitude is important.

Patient-specific bone modeling and analysis: the role of integration and automation in clinical adoption.

PubMed

Zadpoor, Amir A; Weinans, Harrie

2015-03-18

Patient-specific analysis of bones is considered an important tool for diagnosis and treatment of skeletal diseases and for clinical research aimed at understanding the etiology of skeletal diseases and the effects of different types of treatment on their progress. In this article, we discuss how integration of several important components enables accurate and cost-effective patient-specific bone analysis, focusing primarily on patient-specific finite element (FE) modeling of bones. First, the different components are briefly reviewed. Then, two important aspects of patient-specific FE modeling, namely integration of modeling components and automation of modeling approaches, are discussed. We conclude with a section on validation of patient-specific modeling results, possible applications of patient-specific modeling procedures, current limitations of the modeling approaches, and possible areas for future research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Massively Parallel Processing for Fast and Accurate Stamping Simulations

NASA Astrophysics Data System (ADS)

Gress, Jeffrey J.; Xu, Siguang; Joshi, Ramesh; Wang, Chuan-tao; Paul, Sabu

2005-08-01

The competitive automotive market drives automotive manufacturers to speed up the vehicle development cycles and reduce the lead-time. Fast tooling development is one of the key areas to support fast and short vehicle development programs (VDP). In the past ten years, the stamping simulation has become the most effective validation tool in predicting and resolving all potential formability and quality problems before the dies are physically made. The stamping simulation and formability analysis has become an critical business segment in GM math-based die engineering process. As the simulation becomes as one of the major production tools in engineering factory, the simulation speed and accuracy are the two of the most important measures for stamping simulation technology. The speed and time-in-system of forming analysis becomes an even more critical to support the fast VDP and tooling readiness. Since 1997, General Motors Die Center has been working jointly with our software vendor to develop and implement a parallel version of simulation software for mass production analysis applications. By 2001, this technology was matured in the form of distributed memory processing (DMP) of draw die simulations in a networked distributed memory computing environment. In 2004, this technology was refined to massively parallel processing (MPP) and extended to line die forming analysis (draw, trim, flange, and associated spring-back) running on a dedicated computing environment. The evolution of this technology and the insight gained through the implementation of DM0P/MPP technology as well as performance benchmarks are discussed in this publication.

Parametric Geometry, Structured Grid Generation, and Initial Design Study for REST-Class Hypersonic Inlets

NASA Technical Reports Server (NTRS)

Ferlemann, Paul G.; Gollan, Rowan J.

2010-01-01

Computational design and analysis of three-dimensional hypersonic inlets with shape transition has been a significant challenge due to the complex geometry and grid required for three-dimensional viscous flow calculations. Currently, the design process utilizes an inviscid design tool to produce initial inlet shapes by streamline tracing through an axisymmetric compression field. However, the shape is defined by a large number of points rather than a continuous surface and lacks important features such as blunt leading edges. Therefore, a design system has been developed to parametrically construct true CAD geometry and link the topology of a structured grid to the geometry. The Adaptive Modeling Language (AML) constitutes the underlying framework that is used to build the geometry and grid topology. Parameterization of the CAD geometry allows the inlet shapes produced by the inviscid design tool to be generated, but also allows a great deal of flexibility to modify the shape to account for three-dimensional viscous effects. By linking the grid topology to the parametric geometry, the GridPro grid generation software can be used efficiently to produce a smooth hexahedral multiblock grid. To demonstrate the new capability, a matrix of inlets were designed by varying four geometry parameters in the inviscid design tool. The goals of the initial design study were to explore inviscid design tool geometry variations with a three-dimensional analysis approach, demonstrate a solution rate which would enable the use of high-fidelity viscous three-dimensional CFD in future design efforts, process the results for important performance parameters, and perform a sample optimization.

Atmospheric speciated mercury concentrations on an island between China and Korea: sources and transport pathways

NASA Astrophysics Data System (ADS)

Lee, G.-S.; Kim, P.-R.; Han, Y.-J.; Holsen, T. M.; Seo, Y.-S.; Yi, S.-M.

2015-11-01

As a global pollutant, mercury (Hg) is of particular concern in East Asia where anthropogenic emissions are the largest. In this study, speciated Hg concentrations were measured in the western most island in Korea, located between China and the Korean mainland to identify the importance of local, regional and distant Hg sources. Various tools including correlations with other pollutants, conditional probability function, and back-trajectory based analysis consistently indicated that Korean sources were important for gaseous oxidized mercury (GOM) whereas, for total gaseous mercury (TGM) and particulate bound mercury (PBM), long-range and regional transport were also important. A trajectory cluster based approach considering both Hg concentration and the fraction of time each cluster was impacting the site was developed to quantify the effect of Korean sources and out-of-Korean source. This analysis suggests that Korean sources contributed approximately 55 % of the GOM and PBM while there were approximately equal contributions from Korean and out-of-Korean sources for the TGM measured at the site. The ratio of GOM / PBM decreased when the site was impacted by long-range transport, suggesting that this ratio may be a useful tool for identifying the relative significance of local sources vs. long-range transport. The secondary formation of PBM through gas-particle partitioning with GOM was found to be important at low temperatures and high relative humidity.

Atmospheric speciated mercury concentrations on an island between China and Korea: sources and transport pathways

NASA Astrophysics Data System (ADS)

Lee, Gang-San; Kim, Pyung-Rae; Han, Young-Ji; Holsen, Thomas M.; Seo, Yong-Seok; Yi, Seung-Muk

2016-03-01

As a global pollutant, mercury (Hg) is of particular concern in East Asia, where anthropogenic emissions are the largest. In this study, speciated Hg concentrations were measured on Yongheung Island, the westernmost island in Korea, located between China and the Korean mainland to identify the importance of local and regional Hg sources. Various tools including correlations with other pollutants, conditional probability function, and back-trajectory-based analysis consistently indicated that Korean sources were important for gaseous oxidized mercury (GOM) whereas, for total gaseous mercury (TGM) and particulate bound mercury (PBM), regional transport was also important. A trajectory cluster based approach, considering both Hg concentration and the fraction of time each cluster was impacting the site, was developed to quantify the effect of Korean sources and out-of-Korean sources. This analysis suggests that contributions from out-of-Korean sources were similar to Korean sources for TGM whereas Korean sources contributed slightly more to the concentration variations of GOM and PBM compared to out-of-Korean sources. The ratio of GOM/PBM decreased when the site was impacted by regional transport, suggesting that this ratio may be a useful tool for identifying the relative significance of local sources vs. regional transport. The secondary formation of PBM through gas-particle partitioning with GOM was found to be important at low temperatures and high relative humidity.

Development of nonlinear acoustic propagation analysis tool toward realization of loud noise environment prediction in aeronautics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanamori, Masashi, E-mail: kanamori.masashi@jaxa.jp; Takahashi, Takashi, E-mail: takahashi.takashi@jaxa.jp; Aoyama, Takashi, E-mail: aoyama.takashi@jaxa.jp

2015-10-28

Shown in this paper is an introduction of a prediction tool for the propagation of loud noise with the application to the aeronautics in mind. The tool, named SPnoise, is based on HOWARD approach, which can express almost exact multidimensionality of the diffraction effect at the cost of back scattering. This paper argues, in particular, the prediction of the effect of atmospheric turbulence on sonic boom as one of the important issues in aeronautics. Thanks to the simple and efficient modeling of the atmospheric turbulence, SPnoise successfully re-creates the feature of the effect, which often emerges in the region justmore » behind the front and rear shock waves in the sonic boom signature.« less

A Gap Analysis Needs Assessment Tool to Drive a Care Delivery and Research Agenda for Integration of Care and Sharing of Best Practices Across a Health System.

PubMed

Golden, Sherita Hill; Hager, Daniel; Gould, Lois J; Mathioudakis, Nestoras; Pronovost, Peter J

2017-01-01

In a complex health system, it is important to establish a systematic and data-driven approach to identifying needs. The Diabetes Clinical Community (DCC) of Johns Hopkins Medicine's Armstrong Institute for Patient Safety and Quality developed a gap analysis tool and process to establish the system's current state of inpatient diabetes care. The collectively developed tool assessed the following areas: program infrastructure; protocols, policies, and order sets; patient and health care professional education; and automated data access. For the purposes of this analysis, gaps were defined as those instances in which local resources, infrastructure, or processes demonstrated a variance against the current national evidence base or institutionally defined best practices. Following the gap analysis, members of the DCC, in collaboration with health system leadership, met to identify priority areas in order to integrate and synergize diabetes care resources and efforts to enhance quality and reduce disparities in care across the system. Key gaps in care identified included lack of standardized glucose management policies, lack of standardized training of health care professionals in inpatient diabetes management, and lack of access to automated data collection and analysis. These results were used to gain resources to support collaborative diabetes health system initiatives and to successfully obtain federal research funding to develop and pilot a pragmatic diabetes educational intervention. At a health system level, the summary format of this gap analysis tool is an effective method to clearly identify disparities in care to focus efforts and resources to improve care delivery. Copyright © 2016 The Joint Commission. Published by Elsevier Inc. All rights reserved.

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins.

PubMed

Lakbub, Jude C; Shipman, Joshua T; Desaire, Heather

2018-04-01

Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass spectrometry data, and software tools.

Productivity improvement through cycle time analysis

NASA Astrophysics Data System (ADS)

Bonal, Javier; Rios, Luis; Ortega, Carlos; Aparicio, Santiago; Fernandez, Manuel; Rosendo, Maria; Sanchez, Alejandro; Malvar, Sergio

1996-09-01

A cycle time (CT) reduction methodology has been developed in the Lucent Technology facility (former AT&T) in Madrid, Spain. It is based on a comparison of the contribution of each process step in each technology with a target generated by a cycle time model. These targeted cycle times are obtained using capacity data of the machines processing those steps, queuing theory and theory of constrains (TOC) principles (buffers to protect bottleneck and low cycle time/inventory everywhere else). Overall efficiency equipment (OEE) like analysis is done in the machine groups with major differences between their target cycle time and real values. Comparisons between the current value of the parameters that command their capacity (process times, availability, idles, reworks, etc.) and the engineering standards are done to detect the cause of exceeding their contribution to the cycle time. Several friendly and graphical tools have been developed to track and analyze those capacity parameters. Specially important have showed to be two tools: ASAP (analysis of scheduling, arrivals and performance) and performer which analyzes interrelation problems among machines procedures and direct labor. The performer is designed for a detailed and daily analysis of an isolate machine. The extensive use of this tool by the whole labor force has demonstrated impressive results in the elimination of multiple small inefficiencies with a direct positive implications on OEE. As for ASAP, it shows the lot in process/queue for different machines at the same time. ASAP is a powerful tool to analyze the product flow management and the assigned capacity for interdependent operations like the cleaning and the oxidation/diffusion. Additional tools have been developed to track, analyze and improve the process times and the availability.

Time series analysis of tool wear in sheet metal stamping using acoustic emission

NASA Astrophysics Data System (ADS)

Vignesh Shanbhag, V.; Pereira, P. Michael; Rolfe, F. Bernard; Arunachalam, N.

2017-09-01

Galling is an adhesive wear mode that often affects the lifespan of stamping tools. Since stamping tools represent significant economic cost, even a slight improvement in maintenance cost is of high importance for the stamping industry. In other manufacturing industries, online tool condition monitoring has been used to prevent tool wear-related failure. However, monitoring the acoustic emission signal from a stamping process is a non-trivial task since the acoustic emission signal is non-stationary and non-transient. There have been numerous studies examining acoustic emissions in sheet metal stamping. However, very few have focused in detail on how the signals change as wear on the tool surface progresses prior to failure. In this study, time domain analysis was applied to the acoustic emission signals to extract features related to tool wear. To understand the wear progression, accelerated stamping tests were performed using a semi-industrial stamping setup which can perform clamping, piercing, stamping in a single cycle. The time domain features related to stamping were computed for the acoustic emissions signal of each part. The sidewalls of the stamped parts were scanned using an optical profilometer to obtain profiles of the worn part, and they were qualitatively correlated to that of the acoustic emissions signal. Based on the wear behaviour, the wear data can be divided into three stages: - In the first stage, no wear is observed, in the second stage, adhesive wear is likely to occur, and in the third stage severe abrasive plus adhesive wear is likely to occur. Scanning electron microscopy showed the formation of lumps on the stamping tool, which represents galling behavior. Correlation between the time domain features of the acoustic emissions signal and the wear progression identified in this study lays the basis for tool diagnostics in stamping industry.

Analyzing the effect of cutting parameters on surface roughness and tool wear when machining nickel based hastelloy - 276

NASA Astrophysics Data System (ADS)

Khidhir, Basim A.; Mohamed, Bashir

2011-02-01

Machining parameters has an important factor on tool wear and surface finish, for that the manufacturers need to obtain optimal operating parameters with a minimum set of experiments as well as minimizing the simulations in order to reduce machining set up costs. The cutting speed is one of the most important cutting parameter to evaluate, it clearly most influences on one hand, tool life, tool stability, and cutting process quality, and on the other hand controls production flow. Due to more demanding manufacturing systems, the requirements for reliable technological information have increased. For a reliable analysis in cutting, the cutting zone (tip insert-workpiece-chip system) as the mechanics of cutting in this area are very complicated, the chip is formed in the shear plane (entrance the shear zone) and is shape in the sliding plane. The temperature contributed in the primary shear, chamfer and sticking, sliding zones are expressed as a function of unknown shear angle on the rake face and temperature modified flow stress in each zone. The experiments were carried out on a CNC lathe and surface finish and tool tip wear are measured in process. Machining experiments are conducted. Reasonable agreement is observed under turning with high depth of cut. Results of this research help to guide the design of new cutting tool materials and the studies on evaluation of machining parameters to further advance the productivity of nickel based alloy Hastelloy - 276 machining.

Dependency visualization for complex system understanding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smart, J. Allison Cory

1994-09-01

With the volume of software in production use dramatically increasing, the importance of software maintenance has become strikingly apparent. Techniques now sought and developed for reverse engineering and design extraction and recovery. At present, numerous commercial products and research tools exist which are capable of visualizing a variety of programming languages and software constructs. The list of new tools and services continues to grow rapidly. Although the scope of the existing commercial and academic product set is quite broad, these tools still share a common underlying problem. The ability of each tool to visually organize object representations is increasingly impairedmore » as the number of components and component dependencies within systems increases. Regardless of how objects are defined, complex ``spaghetti`` networks result in nearly all large system cases. While this problem is immediately apparent in modem systems analysis involving large software implementations, it is not new. As will be discussed in Chapter 2, related problems involving the theory of graphs were identified long ago. This important theoretical foundation provides a useful vehicle for representing and analyzing complex system structures. While the utility of directed graph based concepts in software tool design has been demonstrated in literature, these tools still lack the capabilities necessary for large system comprehension. This foundation must therefore be expanded with new organizational and visualization constructs necessary to meet this challenge. This dissertation addresses this need by constructing a conceptual model and a set of methods for interactively exploring, organizing, and understanding the structure of complex software systems.« less

Optimizing the ASC WAN: evaluating network performance tools for comparing transport protocols.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lydick, Christopher L.

2007-07-01

The Advanced Simulation & Computing Wide Area Network (ASC WAN), which is a high delay-bandwidth network connection between US Department of Energy National Laboratories, is constantly being examined and evaluated for efficiency. One of the current transport-layer protocols which is used, TCP, was developed for traffic demands which are different from that on the ASC WAN. The Stream Control Transport Protocol (SCTP), on the other hand, has shown characteristics which make it more appealing to networks such as these. Most important, before considering a replacement for TCP on any network, a testing tool that performs well against certain criteria needsmore » to be found. In order to try to find such a tool, two popular networking tools (Netperf v.2.4.3 & v.2.4.6 (OpenSS7 STREAMS), and Iperf v.2.0.6) were tested. These tools implement both TCP and SCTP and were evaluated using four metrics: (1) How effectively can the tool reach a throughput near the bandwidth? (2) How much of the CPU does the tool utilize during operation? (3) Is the tool freely and widely available? And, (4) Is the tool actively developed? Following the analysis of those tools, this paper goes further into explaining some recommendations and ideas for future work.« less

Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context

PubMed Central

Weniger, Markus; Engelmann, Julia C; Schultz, Jörg

2007-01-01

Background Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thousands of mRNAs at the same time, allowing insight into or comparison of different cellular conditions. The data derived out of microarray experiments is highly dimensional and often noisy, and interpretation of the results can get intricate. Although programs for the statistical analysis of microarray data exist, most of them lack an integration of analysis results and biological interpretation. Results We have developed GEPAT, Genome Expression Pathway Analysis Tool, offering an analysis of gene expression data under genomic, proteomic and metabolic context. We provide an integration of statistical methods for data import and data analysis together with a biological interpretation for subsets of probes or single probes on the chip. GEPAT imports various types of oligonucleotide and cDNA array data formats. Different normalization methods can be applied to the data, afterwards data annotation is performed. After import, GEPAT offers various statistical data analysis methods, as hierarchical, k-means and PCA clustering, a linear model based t-test or chromosomal profile comparison. The results of the analysis can be interpreted by enrichment of biological terms, pathway analysis or interaction networks. Different biological databases are included, to give various information for each probe on the chip. GEPAT offers no linear work flow, but allows the usage of any subset of probes and samples as a start for a new data analysis. GEPAT relies on established data analysis packages, offers a modular approach for an easy extension, and can be run on a computer grid to allow a large number of users. It is freely available under the LGPL open source license for academic and commercial users at . Conclusion GEPAT is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data. An installation available for academic users can be found at . PMID:17543125

Investigation of priorities in water quality management based on correlations and variations.

PubMed

Boyacıoğlu, Hülya; Gündogdu, Vildan; Boyacıoğlu, Hayal

2013-04-15

The development of water quality assessment strategies investigating spatial and temporal changes caused by natural and anthropogenic phenomena is an important tool in management practices. This paper used cluster analysis, water quality index method, sensitivity analysis and canonical correlation analysis to investigate priorities in pollution control activities. Data sets representing 22 surface water quality parameters were subject to analysis. Results revealed that organic pollution was serious threat for overall water quality in the region. Besides, oil and grease, lead and mercury were the critical variables violating the standard. In contrast to inorganic variables, organic and physical-inorganic chemical parameters were influenced by variations in physical conditions (discharge, temperature). This study showed that information produced based on the variations and correlations in water quality data sets can be helpful to investigate priorities in water management activities. Moreover statistical techniques and index methods are useful tools in data - information transformation process. Copyright © 2013 Elsevier Ltd. All rights reserved.

Acoustic emission and nondestructive evaluation of biomaterials and tissues.

PubMed

Kohn, D H

1995-01-01

Acoustic emission (AE) is an acoustic wave generated by the release of energy from localized sources in a material subjected to an externally applied stimulus. This technique may be used nondestructively to analyze tissues, materials, and biomaterial/tissue interfaces. Applications of AE include use as an early warning tool for detecting tissue and material defects and incipient failure, monitoring damage progression, predicting failure, characterizing failure mechanisms, and serving as a tool to aid in understanding material properties and structure-function relations. All these applications may be performed in real time. This review discusses general principles of AE monitoring and the use of the technique in 3 areas of importance to biomedical engineering: (1) analysis of biomaterials, (2) analysis of tissues, and (3) analysis of tissue/biomaterial interfaces. Focus in these areas is on detection sensitivity, methods of signal analysis in both the time and frequency domains, the relationship between acoustic signals and microstructural phenomena, and the uses of the technique in establishing a relationship between signals and failure mechanisms.

Geographic information systems, remote sensing, and spatial analysis activities in Texas, 2002-07

USGS Publications Warehouse

Pearson, D.K.; Gary, R.H.; Wilson, Z.D.

2007-01-01

Geographic information system (GIS) technology has become an important tool for scientific investigation, resource management, and environmental planning. A GIS is a computer-aided system capable of collecting, storing, analyzing, and displaying spatially referenced digital data. GIS technology is particularly useful when analyzing a wide variety of spatial data such as with remote sensing and spatial analysis. Remote sensing involves collecting remotely sensed data, such as satellite imagery, aerial photography, or radar images, and analyzing the data to gather information or investigate trends about the environment or the Earth's surface. Spatial analysis combines remotely sensed, thematic, statistical, quantitative, and geographical data through overlay, modeling, and other analytical techniques to investigate specific research questions. It is the combination of data formats and analysis techniques that has made GIS an essential tool in scientific investigations. This document presents information about the technical capabilities and project activities of the U.S. Geological Survey (USGS) Texas Water Science Center (TWSC) GIS Workgroup from 2002 through 2007.

Objective breast symmetry analysis with the breast analyzing tool (BAT): improved tool for clinical trials.

PubMed

Krois, Wilfried; Romar, Alexander Ken; Wild, Thomas; Dubsky, Peter; Exner, Ruth; Panhofer, Peter; Jakesz, Raimund; Gnant, Michael; Fitzal, Florian

2017-07-01

Objective cosmetic analysis is important to evaluate the cosmetic outcome after breast surgery or breast radiotherapy. For this purpose, we aimed to improve our recently developed objective scoring software, the Breast Analyzing Tool (BAT ® ). A questionnaire about important factors for breast symmetry was handed out to ten experts (surgeons) and eight non-experts (students). Using these factors, the first-generation BAT ® software formula has been modified and the breast symmetry index (BSI) from 129 women after breast surgery has been calculated by the first author with this new BAT ® formula. The resulting BSI values of these 129 breast cancer patients were then correlated with subjective symmetry scores from the 18 observers using the Harris scale. The BSI of ten images was also calculated from five observers different from the first author to calculate inter-rater reliability. In a second phase, the new BAT ® formula was validated and correlated with subjective scores of additional 50 women after breast surgery. The inter-rater reliability analysis of the objective evaluation by the BAT ® from five individuals showed an ICC of 0.992 with almost no difference between different observers. All subjective scores of 50 patients correlated with the modified BSI score with a high Pearson correlation coefficient of 0.909 (p < .001) which was better compared to the old software (r = 0.769; p < .001). The modified BAT ® software improves the correlation between subjective and objective BSI values, and may be a new standard for trials evaluating breast symmetry.

confFuse: High-Confidence Fusion Gene Detection across Tumor Entities.

PubMed

Huang, Zhiqin; Jones, David T W; Wu, Yonghe; Lichter, Peter; Zapatka, Marc

2017-01-01

Background: Fusion genes play an important role in the tumorigenesis of many cancers. Next-generation sequencing (NGS) technologies have been successfully applied in fusion gene detection for the last several years, and a number of NGS-based tools have been developed for identifying fusion genes during this period. Most fusion gene detection tools based on RNA-seq data report a large number of candidates (mostly false positives), making it hard to prioritize candidates for experimental validation and further analysis. Selection of reliable fusion genes for downstream analysis becomes very important in cancer research. We therefore developed confFuse, a scoring algorithm to reliably select high-confidence fusion genes which are likely to be biologically relevant. Results: confFuse takes multiple parameters into account in order to assign each fusion candidate a confidence score, of which score ≥8 indicates high-confidence fusion gene predictions. These parameters were manually curated based on our experience and on certain structural motifs of fusion genes. Compared with alternative tools, based on 96 published RNA-seq samples from different tumor entities, our method can significantly reduce the number of fusion candidates (301 high-confidence from 8,083 total predicted fusion genes) and keep high detection accuracy (recovery rate 85.7%). Validation of 18 novel, high-confidence fusions detected in three breast tumor samples resulted in a 100% validation rate. Conclusions: confFuse is a novel downstream filtering method that allows selection of highly reliable fusion gene candidates for further downstream analysis and experimental validations. confFuse is available at https://github.com/Zhiqin-HUANG/confFuse.

Risk analysis for dengue suitability in Africa using the ArcGIS predictive analysis tools (PA tools).

PubMed

Attaway, David F; Jacobsen, Kathryn H; Falconer, Allan; Manca, Germana; Waters, Nigel M

2016-06-01

Risk maps identifying suitable locations for infection transmission are important for public health planning. Data on dengue infection rates are not readily available in most places where the disease is known to occur. A newly available add-in to Esri's ArcGIS software package, the ArcGIS Predictive Analysis Toolset (PA Tools), was used to identify locations within Africa with environmental characteristics likely to be suitable for transmission of dengue virus. A more accurate, robust, and localized (1 km × 1 km) dengue risk map for Africa was created based on bioclimatic layers, elevation data, high-resolution population data, and other environmental factors that a search of the peer-reviewed literature showed to be associated with dengue risk. Variables related to temperature, precipitation, elevation, and population density were identified as good predictors of dengue suitability. Areas of high dengue suitability occur primarily within West Africa and parts of Central Africa and East Africa, but even in these regions the suitability is not homogenous. This risk mapping technique for an infection transmitted by Aedes mosquitoes draws on entomological, epidemiological, and geographic data. The method could be applied to other infectious diseases (such as Zika) in order to provide new insights for public health officials and others making decisions about where to increase disease surveillance activities and implement infection prevention and control efforts. The ability to map threats to human and animal health is important for tracking vectorborne and other emerging infectious diseases and modeling the likely impacts of climate change. Copyright © 2016 Elsevier B.V. All rights reserved.

Application of vector analysis on study of illuminated area and Doppler characteristics of airborne pulse radar

NASA Astrophysics Data System (ADS)

Wang, Haijiang; Yang, Ling

2014-12-01

In this paper, the application of vector analysis tool in the illuminated area and the Doppler frequency distribution research for the airborne pulse radar is studied. An important feature of vector analysis is that it can closely combine the geometric ideas with algebraic calculations. Through coordinate transform, the relationship between the frame of radar antenna and the ground, under aircraft motion attitude, is derived. Under the time-space analysis, the overlap area between the footprint of radar beam and the pulse-illuminated zone is obtained. Furthermore, the Doppler frequency expression is successfully deduced. In addition, the Doppler frequency distribution is plotted finally. Using the time-space analysis results, some important parameters of a specified airborne radar system are obtained. Simultaneously, the results are applied to correct the phase error brought by attitude change in airborne synthetic aperture radar (SAR) imaging.

Research Costs Investigated: A Study Into the Budgets of Dutch Publicly Funded Drug-Related Research.

PubMed

van Asselt, Thea; Ramaekers, Bram; Corro Ramos, Isaac; Joore, Manuela; Al, Maiwenn; Lesman-Leegte, Ivonne; Postma, Maarten; Vemer, Pepijn; Feenstra, Talitha

2018-01-01

The costs of performing research are an important input in value of information (VOI) analyses but are difficult to assess. The aim of this study was to investigate the costs of research, serving two purposes: (1) estimating research costs for use in VOI analyses; and (2) developing a costing tool to support reviewers of grant proposals in assessing whether the proposed budget is realistic. For granted study proposals from the Netherlands Organization for Health Research and Development (ZonMw), type of study, potential cost drivers, proposed budget, and general characteristics were extracted. Regression analysis was conducted in an attempt to generate a 'predicted budget' for certain combinations of cost drivers, for implementation in the costing tool. Of 133 drug-related research grant proposals, 74 were included for complete data extraction. Because an association between cost drivers and budgets was not confirmed, we could not generate a predicted budget based on regression analysis, but only historic reference budgets given certain study characteristics. The costing tool was designed accordingly, i.e. with given selection criteria the tool returns the range of budgets in comparable studies. This range can be used in VOI analysis to estimate whether the expected net benefit of sampling will be positive to decide upon the net value of future research. The absence of association between study characteristics and budgets may indicate inconsistencies in the budgeting or granting process. Nonetheless, the tool generates useful information on historical budgets, and the option to formally relate VOI to budgets. To our knowledge, this is the first attempt at creating such a tool, which can be complemented with new studies being granted, enlarging the underlying database and keeping estimates up to date.

Sequence Alignment to Predict Across Species Susceptibility ...

EPA Pesticide Factsheets

Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to simplify, streamline, and quantitatively assess protein sequence/structural similarity across taxonomic groups as a means to predict relative intrinsic susceptibility. The intent of the tool is to allow for evaluation of any potential protein target, so it is amenable to variable degrees of protein characterization, depending on available information about the chemical/protein interaction and the molecular target itself. To allow for flexibility in the analysis, a layered strategy was adopted for the tool. The first level of the SeqAPASS analysis compares primary amino acid sequences to a query sequence, calculating a metric for sequence similarity (including detection of candidate orthologs), the second level evaluates sequence similarity within selected domains (e.g., ligand-binding domain, DNA binding domain), and the third level of analysis compares individual amino acid residue positions identified as being of importance for protein conformation and/or ligand binding upon chemical perturbation. Each level of the SeqAPASS analysis provides increasing evidence to apply toward rapid, screening-level assessments of probable cross species susceptibility. Such analyses can support prioritization of chemicals for further ev

Bridging the gap between fluxomics and industrial biotechnology.

PubMed

Feng, Xueyang; Page, Lawrence; Rubens, Jacob; Chircus, Lauren; Colletti, Peter; Pakrasi, Himadri B; Tang, Yinjie J

2010-01-01

Metabolic flux analysis is a vital tool used to determine the ultimate output of cellular metabolism and thus detect biotechnologically relevant bottlenecks in productivity. ¹³C-based metabolic flux analysis (¹³C-MFA) and flux balance analysis (FBA) have many potential applications in biotechnology. However, noteworthy hurdles in fluxomics study are still present. First, several technical difficulties in both ¹³C-MFA and FBA severely limit the scope of fluxomics findings and the applicability of obtained metabolic information. Second, the complexity of metabolic regulation poses a great challenge for precise prediction and analysis of metabolic networks, as there are gaps between fluxomics results and other omics studies. Third, despite identified metabolic bottlenecks or sources of host stress from product synthesis, it remains difficult to overcome inherent metabolic robustness or to efficiently import and express nonnative pathways. Fourth, product yields often decrease as the number of enzymatic steps increases. Such decrease in yield may not be caused by rate-limiting enzymes, but rather is accumulated through each enzymatic reaction. Fifth, a high-throughput fluxomics tool hasnot been developed for characterizing nonmodel microorganisms and maximizing their application in industrial biotechnology. Refining fluxomics tools and understanding these obstacles will improve our ability to engineer highly efficient metabolic pathways in microbial hosts.

Global sensitivity and uncertainty analysis of the nitrate leaching and crop yield simulation under different water and nitrogen management practices

USDA-ARS?s Scientific Manuscript database

Agricultural system models have become important tools in studying water and nitrogen (N) dynamics, as well as crop growth, under different management practices. Complexity in input parameters often leads to significant uncertainty when simulating dynamic processes such as nitrate leaching or crop y...

Raising Sociocultural Awareness through Contextual Analysis: Some Tools for Teachers

ERIC Educational Resources Information Center

McConachy, Troy

2009-01-01

Despite long-standing recognition of the importance of sociocultural context in meaning making, criticisms have been levelled at communicative language teaching (CLT) for failing to effectively address this at the level of classroom practice. In fact, it has been argued that the way CLT presents content reveals a fundamentally reductionist view of…

Analysis of Total Oil and Fatty Acids Composition by Near Infrared Reflectance Spectroscopy in Edible Nuts

USDA-ARS?s Scientific Manuscript database

Near Infrared (NIR) Reflectance spectroscopy has established itself as an important tool in quantifying water and oil present in various food materials. It is rapid and nondestructive, easier to use, and does not require processing the samples with corrosive chemicals that would render them non-edib...

Conjoint Analysis for Mobile Devices for Ubiquitous Learning in Higher Education: The Korean Case

ERIC Educational Resources Information Center

Lee, Hyeongjik

2013-01-01

Despite the increasing importance of mobile devices in education, the essential features of these devices for ubiquitous learning have not been empirically addressed. This study empirically investigated the necessary conditions for using mobile devices as an educational tool for ubiquitous learning in higher education by a conjoint method. The…

Factor Analysis Using "R"

ERIC Educational Resources Information Center

Beaujean, A. Alexander

2013-01-01

"R" (R Development Core Team, 2011) is a very powerful tool to analyze data, that is gaining in popularity due to its costs (its free) and flexibility (its open-source). This article gives a general introduction to using "R" (i.e., loading the program, using functions, importing data). Then, using data from Canivez, Konold, Collins, and Wilson…

Problematization as Activism: Disrupting the Neoliberal Education Project through the "Work of Thought"

ERIC Educational Resources Information Center

Pickup, Austin

2017-01-01

In this article, Austin Pickup centers Foucault's concept of "problematization" as an important methodological tool for displacing neoliberalism from its stable perch atop a perceived absence of other possibilities. According to Pickup, the genealogical analysis envisaged and practiced by Foucault opens up new avenues by indicating not…

Investigating Argumentation in Reading Groups: Combining Manual Qualitative Coding and Automated Corpus Analysis Tools

ERIC Educational Resources Information Center

O'Halloran, Kieran

2011-01-01

This article makes a contribution to understanding informal argumentation by focusing on the discourse of reading groups. Reading groups, an important cultural phenomenon in Britain and other countries, regularly meet in members' houses, in pubs or restaurants, in bookshops, workplaces, schools or prisons to share their experiences of reading…

Investigating Stage-Sequential Growth Mixture Models with Multiphase Longitudinal Data

ERIC Educational Resources Information Center

Kim, Su-Young; Kim, Jee-Seon

2012-01-01

This article investigates three types of stage-sequential growth mixture models in the structural equation modeling framework for the analysis of multiple-phase longitudinal data. These models can be important tools for situations in which a single-phase growth mixture model produces distorted results and can allow researchers to better understand…

Assessment and Educational Policy.

ERIC Educational Resources Information Center

Smith, Virginia B.

1975-01-01

Because of increased access of postsecondary education in the 1950's and 1960's, higher education cost analysis gained importance. Attempts have been made to develop a standard unit cost, but it is hard to see unit cost accounting by itself as a valuable tool for public accountability or policy making. For these purposes a cost-effectiveness ratio…

DACUM: Bridging the Gap between Work and High Performance.

ERIC Educational Resources Information Center

Norton, Robert E.; McLennan, Krystyna S.

The DACUM (Developing A Curriculum) occupational analysis process provides a systematic way to look at worker duties and tasks so that important knowledge, skills, standards, tools, and attitudes can be handed on to the next generation of workers. Revamped by The Ohio State University's Center on Education and Training for Employment, DACUM…

Organizational Approach to the Ergonomic Examination of E-Learning Modules

ERIC Educational Resources Information Center

Lavrov, Evgeniy; Kupenko, Olena; Lavryk, Tetiana; Barchenko, Natalia

2013-01-01

With a significant increase in the number of e-learning resources the issue of quality is of current importance. An analysis of existing scientific and methodological literature shows the variety of approaches, methods and tools to evaluate e-learning materials. This paper proposes an approach based on the procedure for estimating parameters of…

Getting Past the Impasse: Framing as a Tool for Public Relations.

ERIC Educational Resources Information Center

Knight, Myra Gregory

1999-01-01

Considers a two-dimensional model of public relations that combines the two-way symmetrical and asymmetrical models. Proposes frame analysis as a strategy important for both public and organizational influence. Employs framing to show how sex education can be promoted more effectively within public schools. Notes that the concept can be employed…

Construction and Analysis of Educational Assessments Using Knowledge Maps with Weight Appraisal of Concepts

ERIC Educational Resources Information Center

Su, C. Y.; Wang, T. I.

2010-01-01

The rapid advance of information and communication technologies (ICT) has important impacts on teaching and learning, as well as on the educational assessment. Teachers may create assessments utilizing some developed assessment software or test authoring tools. However, problems could occur, such as neglecting key concepts in the curriculum or…

A Meta-Analysis of the Effectiveness of Alternative Assessment Techniques

ERIC Educational Resources Information Center

Gozuyesil, Eda; Tanriseven, Isil

2017-01-01

Purpose: Recent trends have encouraged the use of alternative assessment tools in class in line with the recommendations made by the updated curricula. It is of great importance to understand how alternative assessment affects students' academic outcomes and which techniques are most effective in which contexts. This study aims to examine the…

A Cognitive Component Analysis Approach for Developing Game-Based Spatial Learning Tools

ERIC Educational Resources Information Center

Hung, Pi-Hsia; Hwang, Gwo-Jen; Lee, Yueh-Hsun; Su, I-Hsiang

2012-01-01

Spatial ability has been recognized as one of the most important factors affecting the mathematical performance of students. Previous studies on spatial learning have mainly focused on developing strategies to shorten the problem-solving time of learners for very specific learning tasks. Such an approach usually has limited effects on improving…

Literary Translation as a Tool for Critical Language Planning

ERIC Educational Resources Information Center

Mooneeram, Roshni

2013-01-01

This paper argues that Dev Virahsawmy, an author who manipulates literary translation for the purposes of linguistic prestige formation and re-negotiation, is a critical language-policy practitioner, as his work fills an important gap in language planning scholarship. A micro-analysis of the translation of a Shakespearean sonnet into Mauritian…

The effect of blurred plot coordinates on interpolating forest biomass: a case study

Treesearch

J. W. Coulston

2004-01-01

Interpolated surfaces of forest attributes are important analytical tools and have been used in risk assessments, forest inventories, and forest health assessments. The USDA Forest Service Forest Inventory and Analysis program (FIA) annually collects information on forest attributes in a consistent fashion nation-wide. Users of these data typically perform...

APMS 3.0 Flight Analyst Guide: Aviation Performance Measuring System

NASA Technical Reports Server (NTRS)

Jay, Griff; Prothero, Gary; Romanowski, Timothy; Lynch, Robert; Lawrence, Robert; Rosenthal, Loren

2004-01-01

The Aviation Performance Measuring System (APMS) is a method-embodied in software-that uses mathematical algorithms and related procedures to analyze digital flight data extracted from aircraft flight data recorders. APMS consists of an integrated set of tools used to perform two primary functions: a) Flight Data Importation b) Flight Data Analysis.

Some Innovative Methods to Improve Profiles Derivation

ERIC Educational Resources Information Center

Pei, Lai Kwan

2008-01-01

As the government aimed to provide appropriate education to all children (No Child Left Behind Act), it is important that the education providers can assess the performance of the students correctly so that they can provide the appropriate education for the students. Profile analysis is a very useful tool to interpret test scores and measure…

Multimodal digital color imaging system for facial skin lesion analysis

NASA Astrophysics Data System (ADS)

Bae, Youngwoo; Lee, Youn-Heum; Jung, Byungjo

2008-02-01

In dermatology, various digital imaging modalities have been used as an important tool to quantitatively evaluate the treatment effect of skin lesions. Cross-polarization color image was used to evaluate skin chromophores (melanin and hemoglobin) information and parallel-polarization image to evaluate skin texture information. In addition, UV-A induced fluorescent image has been widely used to evaluate various skin conditions such as sebum, keratosis, sun damages, and vitiligo. In order to maximize the evaluation efficacy of various skin lesions, it is necessary to integrate various imaging modalities into an imaging system. In this study, we propose a multimodal digital color imaging system, which provides four different digital color images of standard color image, parallel and cross-polarization color image, and UV-A induced fluorescent color image. Herein, we describe the imaging system and present the examples of image analysis. By analyzing the color information and morphological features of facial skin lesions, we are able to comparably and simultaneously evaluate various skin lesions. In conclusion, we are sure that the multimodal color imaging system can be utilized as an important assistant tool in dermatology.

Advances in directional borehole radar data analysis and visualization

USGS Publications Warehouse

Smith, D.V.G.; Brown, P.J.

2002-01-01

The U.S. Geological Survey is developing a directional borehole radar (DBOR) tool for mapping fractures, lithologic changes, and underground utility and void detection. An important part of the development of the DBOR tool is data analysis and visualization, with the aim of making the software graphical user interface (GUI) intuitive and easy to use. The DBOR software system consists of a suite of signal and image processing routines written in Research Systems' Interactive Data Language (IDL). The software also serves as a front-end to many widely accepted Colorado School of Mines Center for Wave Phenomena (CWP) Seismic UNIX (SU) algorithms (Cohen and Stockwell, 2001). Although the SU collection runs natively in a UNIX environment, our system seamlessly emulates a UNIX session within a widely used PC operating system (MicroSoft Windows) using GNU tools (Noer, 1998). Examples are presented of laboratory data acquired with the prototype tool from two different experimental settings. The first experiment imaged plastic pipes in a macro-scale sand tank. The second experiment monitored the progress of an invasion front resulting from oil injection. Finally, challenges to further development and planned future work are discussed.

Lessons Learned for Cx PRACA. Constellation Program Problem Reporting, Analysis and Corrective Action Process and System

NASA Technical Reports Server (NTRS)

Kelle, Pido I.; Ratterman, Christian; Gibbs, Cecil

2009-01-01

This slide presentation reviews the Constellation Program Problem Reporting, Analysis and Corrective Action Process and System (Cx PRACA). The goal of the Cx PRACA is to incorporate Lessons learned from the Shuttle, ISS, and Orbiter programs by creating a single tool for managing the PRACA process, that clearly defines the scope of PRACA applicability and what must be reported, and defines the ownership and responsibility for managing the PRACA process including disposition approval authority. CxP PRACA is a process, supported by a single information gathering data module which will be integrated with a single CxP Information System, providing interoperability, import and export capability making the CxP PRACA a more effective and user friendly technical and management tool.

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

The Utility of Failure Modes and Effects Analysis of Consultations in a Tertiary, Academic, Medical Center.

PubMed

Niv, Yaron; Itskoviz, David; Cohen, Michal; Hendel, Hagit; Bar-Giora, Yonit; Berkov, Evgeny; Weisbord, Irit; Leviron, Yifat; Isasschar, Assaf; Ganor, Arian

Failure modes and effects analysis (FMEA) is a tool used to identify potential risks in health care processes. We used the FMEA tool for improving the process of consultation in an academic medical center. A team of 10 staff members-5 physicians, 2 quality experts, 2 organizational consultants, and 1 nurse-was established. The consultation process steps, from ordering to delivering, were computed. Failure modes were assessed for likelihood of occurrence, detection, and severity. A risk priority number (RPN) was calculated. An interventional plan was designed according to the highest RPNs. Thereafter, we compared the percentage of completed computer-based documented consultations before and after the intervention. The team identified 3 main categories of failure modes that reached the highest RPNs: initiation of consultation by a junior staff physician without senior approval, failure to document the consultation in the computerized patient registry, and asking for consultation on the telephone. An interventional plan was designed, including meetings to update knowledge of the consultation request process, stressing the importance of approval by a senior physician, training sessions for closing requests in the patient file, and reporting of telephone requests. The number of electronically documented consultation results and recommendations significantly increased (75%) after intervention. FMEA is an important and efficient tool for improving the consultation process in an academic medical center.

Collaboration tools and techniques for large model datasets

USGS Publications Warehouse

Signell, R.P.; Carniel, S.; Chiggiato, J.; Janekovic, I.; Pullen, J.; Sherwood, C.R.

2008-01-01

In MREA and many other marine applications, it is common to have multiple models running with different grids, run by different institutions. Techniques and tools are described for low-bandwidth delivery of data from large multidimensional datasets, such as those from meteorological and oceanographic models, directly into generic analysis and visualization tools. Output is stored using the NetCDF CF Metadata Conventions, and then delivered to collaborators over the web via OPeNDAP. OPeNDAP datasets served by different institutions are then organized via THREDDS catalogs. Tools and procedures are then used which enable scientists to explore data on the original model grids using tools they are familiar with. It is also low-bandwidth, enabling users to extract just the data they require, an important feature for access from ship or remote areas. The entire implementation is simple enough to be handled by modelers working with their webmasters - no advanced programming support is necessary. ?? 2007 Elsevier B.V. All rights reserved.

The BioCyc collection of microbial genomes and metabolic pathways.

PubMed

Karp, Peter D; Billington, Richard; Caspi, Ron; Fulcher, Carol A; Latendresse, Mario; Kothari, Anamika; Keseler, Ingrid M; Krummenacker, Markus; Midford, Peter E; Ong, Quang; Ong, Wai Kit; Paley, Suzanne M; Subhraveti, Pallavi

2017-08-17

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer's assistance. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Development and analysis of educational technologies for a blended organic chemistry course

NASA Astrophysics Data System (ADS)

Evans, Michael James

Blended courses incorporate elements of both face-to-face and online instruction. The extent to which blended courses are conducted online, and the proper role of the online components of blended courses, have been debated and may vary. What can be said in general, however, is that online tools for blended courses are typically culled together from a variety of sources, are often very large scale, and may present distractions for students that decrease their utility as teaching tools. Furthermore, large-scale educational technologies may not be amenable to rigorous, detailed study, limiting evaluation of their effectiveness. Small-scale educational technologies run from the instructor's own server have the potential to mitigate many of these issues. Such tools give the instructor or researcher direct access to all available data, facilitating detailed analysis of student use. Code modification is simple and rapid if errors arise, since code is stored where the instructor can easily access it. Finally, the design of a small-scale tool can target a very specific application. With these ideas in mind, this work describes several projects aimed at exploring the use of small-scale, web-based software in a blended organic chemistry course. A number of activities were developed and evaluated using the Student Assessment of Learning Gains survey, and data from the activities were analyzed using quantitative methods of statistics and social network analysis methods. Findings from this work suggest that small-scale educational technologies provide significant learning benefits for students of organic chemistry---with the important caveat that instructors must offer appropriate levels of technical and pedagogical support for students. Most notably, students reported significant learning gains from activities that included collaborative learning supported by novel online tools. For the particular context of organic chemistry, which has a unique semantic language (Lewis structures), the incorporation of shared video was a novel but important element of these activities. In fields for which mere text would not provide enough information in communications between students, video offers an appealing medium for student-student interaction.

The bibliometrics of atmospheric environment

NASA Astrophysics Data System (ADS)

Brimblecombe, Peter; Grossi, Carlota M.

Bibliometric analysis is an important tool in the management of a journal. SCOPUS output is used to assess the increase in the quantity of material in Atmospheric Environment and stylistic changes in the way authors choose words and punctuation in titles and assemble their reference lists. Citation analysis is used to consider the impact factor of the journal, but perhaps more importantly the way in which it reflects the importance authors give to papers published in Atmospheric Environment. The impact factor of Atmospheric Environment (2.549 for 2007) from the Journal Citation Reports suggests it performs well within the atmospheric sciences, but it conceals the long term value authors place on papers appearing in the journal. Reference lists show that a fifth come through citing papers more than a decade old.

DynAOI: a tool for matching eye-movement data with dynamic areas of interest in animations and movies.

PubMed

Papenmeier, Frank; Huff, Markus

2010-02-01

Analyzing gaze behavior with dynamic stimulus material is of growing importance in experimental psychology; however, there is still a lack of efficient analysis tools that are able to handle dynamically changing areas of interest. In this article, we present DynAOI, an open-source tool that allows for the definition of dynamic areas of interest. It works automatically with animations that are based on virtual three-dimensional models. When one is working with videos of real-world scenes, a three-dimensional model of the relevant content needs to be created first. The recorded eye-movement data are matched with the static and dynamic objects in the model underlying the video content, thus creating static and dynamic areas of interest. A validation study asking participants to track particular objects demonstrated that DynAOI is an efficient tool for handling dynamic areas of interest.

A geostatistics-informed hierarchical sensitivity analysis method for complex groundwater flow and transport modeling: GEOSTATISTICAL SENSITIVITY ANALYSIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Heng; Chen, Xingyuan; Ye, Ming

Sensitivity analysis is an important tool for quantifying uncertainty in the outputs of mathematical models, especially for complex systems with a high dimension of spatially correlated parameters. Variance-based global sensitivity analysis has gained popularity because it can quantify the relative contribution of uncertainty from different sources. However, its computational cost increases dramatically with the complexity of the considered model and the dimension of model parameters. In this study we developed a hierarchical sensitivity analysis method that (1) constructs an uncertainty hierarchy by analyzing the input uncertainty sources, and (2) accounts for the spatial correlation among parameters at each level ofmore » the hierarchy using geostatistical tools. The contribution of uncertainty source at each hierarchy level is measured by sensitivity indices calculated using the variance decomposition method. Using this methodology, we identified the most important uncertainty source for a dynamic groundwater flow and solute transport in model at the Department of Energy (DOE) Hanford site. The results indicate that boundary conditions and permeability field contribute the most uncertainty to the simulated head field and tracer plume, respectively. The relative contribution from each source varied spatially and temporally as driven by the dynamic interaction between groundwater and river water at the site. By using a geostatistical approach to reduce the number of realizations needed for the sensitivity analysis, the computational cost of implementing the developed method was reduced to a practically manageable level. The developed sensitivity analysis method is generally applicable to a wide range of hydrologic and environmental problems that deal with high-dimensional spatially-distributed parameters.« less

Analysis of environmental impact assessment (EIA) system in Turkey.

PubMed

Coşkun, Aynur Aydın; Turker, Ozhan

2011-04-01

The Environmental Impact Assessment (EIA) System, which embodies the "prevention principle" of the environmental law, is an important tool for environmental protection. This tool has a private importance for Turkey since it is a developing country, and it entered the Turkish law in 1983 with the Environmental Law. Besides, the EIA Regulation, which shows the application principles, became effective in 1993. Because Turkey is a candidate for European Union (EU), the EIA Regulation has been changed due to the EU compliance procedure, and its latest version became valid in 2008. This study aims to emphasize The EIA system in Turkey to supervise the efficiency of this procedure and point the success level. In the introduction part, general EIA concept, its importance, and some notations are mentioned. Following that, the legislation, which builds the EIA system, has been analyzed starting from the 1982 Turkish Constitution. Then, the legislation rules are explained due to the basic steps of the EIA procedure. In order to shed light upon the application, the EIA final decisions given until today, the results, and their distributions to the industries are assessed. In the final part of the study, a SWOT analysis is made to mention the weaknesses, strengths, opportunities, and threats of the EIA system in Turkey.

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

PubMed Central

Zhang, Bing; Schmoyer, Denise; Kirov, Stefan; Snoddy, Jay

2004-01-01

Background Microarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in the gene sets. Results We have created a web-based tool for data analysis and data visualization for sets of genes called GOTree Machine (GOTM). This tool was originally intended to analyze sets of co-regulated genes identified from microarray analysis but is adaptable for use with other gene sets from other high-throughput analyses. GOTree Machine generates a GOTree, a tree-like structure to navigate the Gene Ontology Directed Acyclic Graph for input gene sets. This system provides user friendly data navigation and visualization. Statistical analysis helps users to identify the most important Gene Ontology categories for the input gene sets and suggests biological areas that warrant further study. GOTree Machine is available online at . Conclusion GOTree Machine has a broad application in functional genomic, proteomic and other high-throughput methods that generate large sets of interesting genes; its primary purpose is to help users sort for interesting patterns in gene sets. PMID:14975175

Container-Based Clinical Solutions for Portable and Reproducible Image Analysis.

PubMed

Matelsky, Jordan; Kiar, Gregory; Johnson, Erik; Rivera, Corban; Toma, Michael; Gray-Roncal, William

2018-05-08

Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While several initiatives in neuroimaging have adopted approaches for creating and sharing more reliable scientific methods and findings, Linux containers are not yet mainstream in clinical settings. We explore related technologies and their efficacy in this setting, highlight important shortcomings, demonstrate a simple use-case, and endorse the use of Linux containers for medical image analysis.

Therapeutic Gene Editing Safety and Specificity.

PubMed

Lux, Christopher T; Scharenberg, Andrew M

2017-10-01

Therapeutic gene editing is significant for medical advancement. Safety is intricately linked to the specificity of the editing tools used to cut at precise genomic targets. Improvements can be achieved by thoughtful design of nucleases and repair templates, analysis of off-target editing, and careful utilization of viral vectors. Advancements in DNA repair mechanisms and development of new generations of tools improve targeting of specific sequences while minimizing risks. It is important to plot a safe course for future clinical trials. This article reviews safety and specificity for therapeutic gene editing to spur dialogue and advancement. Copyright © 2017 Elsevier Inc. All rights reserved.

Design and fabrication of an end effector

NASA Technical Reports Server (NTRS)

Crossley, F. R. E.; Umholtz, F. G.

1975-01-01

The construction is described of a prototype mechanical hand or 'end effector' for use on a remotely controlled robot, but with possible application as a prosthetic device. An analysis of hand motions is reported, from which it is concluded that the two most important manipulations (apart from grasps) are to be able to pick up a tool and draw it into a nested grip against the palm, and to be able to hold a pistol-grip tool such as an electric drill and pull the trigger. A model was tested and found capable of both these operations.

Web-based access, aggregation, and visualization of future climate projections with emphasis on agricultural assessments

NASA Astrophysics Data System (ADS)

Villoria, Nelson B.; Elliott, Joshua; Müller, Christoph; Shin, Jaewoo; Zhao, Lan; Song, Carol

2018-01-01

Access to climate and spatial datasets by non-specialists is restricted by technical barriers involving hardware, software and data formats. We discuss an open-source online tool that facilitates downloading the climate data from the global circulation models used by the Inter-Sectoral Impacts Model Intercomparison Project. The tool also offers temporal and spatial aggregation capabilities for incorporating future climate scenarios in applications where spatial aggregation is important. We hope that streamlined access to these data facilitates analysis of climate related issues while considering the uncertainties derived from future climate projections and temporal aggregation choices.

An Interactive Virtual 3D Tool for Scientific Exploration of Planetary Surfaces

NASA Astrophysics Data System (ADS)

Traxler, Christoph; Hesina, Gerd; Gupta, Sanjeev; Paar, Gerhard

2014-05-01

In this paper we present an interactive 3D visualization tool for scientific analysis and planning of planetary missions. At the moment scientists have to look at individual camera images separately. There is no tool to combine them in three dimensions and look at them seamlessly as a geologist would do (by walking backwards and forwards resulting in different scales). For this reason a virtual 3D reconstruction of the terrain that can be interactively explored is necessary. Such a reconstruction has to consider multiple scales ranging from orbital image data to close-up surface image data from rover cameras. The 3D viewer allows seamless zooming between these various scales, giving scientists the possibility to relate small surface features (e.g. rock outcrops) to larger geological contexts. For a reliable geologic assessment a realistic surface rendering is important. Therefore the material properties of the rock surfaces will be considered for real-time rendering. This is achieved by an appropriate Bidirectional Reflectance Distribution Function (BRDF) estimated from the image data. The BRDF is implemented to run on the Graphical Processing Unit (GPU) to enable realistic real-time rendering, which allows a naturalistic perception for scientific analysis. Another important aspect for realism is the consideration of natural lighting conditions, which means skylight to illuminate the reconstructed scene. In our case we provide skylights from Mars and Earth, which allows switching between these two modes of illumination. This gives geologists the opportunity to perceive rock outcrops from Mars as they would appear on Earth facilitating scientific assessment. Besides viewing the virtual reconstruction on multiple scales, scientists can also perform various measurements, i.e. geo-coordinates of a selected point or distance between two surface points. Rover or other models can be placed into the scene and snapped onto certain location of the terrain. These are important features to support the planning of rover paths. In addition annotations can be placed directly into the 3D scene, which also serve as landmarks to aid navigation. The presented visualization and planning tool is a valuable asset for scientific analysis of planetary mission data. It complements traditional methods by giving access to an interactive virtual 3D reconstruction, which is realistically rendered. Representative examples and further information about the interactive 3D visualization tool can be found on the FP7-SPACE Project PRoViDE web page http://www.provide-space.eu/interactive-virtual-3d-tool/. The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 312377 'PRoViDE'.

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs

PubMed Central

2011-01-01

Background Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications. Results ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms. Conclusions ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor. PMID:21548938

The study on dynamic properties of monolithic ball end mills with various slenderness

NASA Astrophysics Data System (ADS)

Wojciechowski, Szymon; Tabaszewski, Maciej; Krolczyk, Grzegorz M.; Maruda, Radosław W.

2017-10-01

The reliable determination of modal mass, damping and stiffness coefficient (modal parameters) for the particular machine-toolholder-tool system is essential for the accurate estimation of vibrations, stability and thus the machined surface finish formed during the milling process. Therefore, this paper focuses on the analysis of ball end mill's dynamical properties. The tools investigated during this study are monolithic ball end mills with different slenderness values, made of coated cemented carbide. These kinds of tools are very often applied during the precise milling of curvilinear surfaces. The research program included the impulse test carried out for the investigated tools clamped in the hydraulic toolholder. The obtained modal parameters were further applied in the developed tool's instantaneous deflection model, in order to estimate the tool's working part vibrations during precise milling. The application of the proposed dynamics model involved also the determination of instantaneous cutting forces on the basis of the mechanistic approach. The research revealed that ball end mill's slenderness can be considered as an important milling dynamics and machined surface quality indicator.

The Gamma-Ray Burst ToolSHED is Open for Business

NASA Astrophysics Data System (ADS)

Giblin, Timothy W.; Hakkila, Jon; Haglin, David J.; Roiger, Richard J.

2004-09-01

The GRB ToolSHED, a Gamma-Ray Burst SHell for Expeditions in Data-Mining, is now online and available via a web browser to all in the scientific community. The ToolSHED is an online web utility that contains pre-processed burst attributes of the BATSE catalog and a suite of induction-based machine learning and statistical tools for classification and cluster analysis. Users create their own login account and study burst properties within user-defined multi-dimensional parameter spaces. Although new GRB attributes are periodically added to the database for user selection, the ToolSHED has a feature that allows users to upload their own burst attributes (e.g. spectral parameters, etc.) so that additional parameter spaces can be explored. A data visualization feature using GNUplot and web-based IDL has also been implemented to provide interactive plotting of user-selected session output. In an era in which GRB observations and attributes are becoming increasingly more complex, a utility such as the GRB ToolSHED may play an important role in deciphering GRB classes and understanding intrinsic burst properties.

Chandra X-ray Center Science Data Systems Regression Testing of CIAO

NASA Astrophysics Data System (ADS)

Lee, N. P.; Karovska, M.; Galle, E. C.; Bonaventura, N. R.

2011-07-01

The Chandra Interactive Analysis of Observations (CIAO) is a software system developed for the analysis of Chandra X-ray Observatory observations. An important component of a successful CIAO release is the repeated testing of the tools across various platforms to ensure consistent and scientifically valid results. We describe the procedures of the scientific regression testing of CIAO and the enhancements made to the testing system to increase the efficiency of run time and result validation.

Virtual Interactomics of Proteins from Biochemical Standpoint

PubMed Central

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel

2012-01-01

Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations. PMID:22928109

Principal component analysis of normalized full spectrum mass spectrometry data in multiMS-toolbox: An effective tool to identify important factors for classification of different metabolic patterns and bacterial strains.

PubMed

Cejnar, Pavel; Kuckova, Stepanka; Prochazka, Ales; Karamonova, Ludmila; Svobodova, Barbora

2018-06-15

Explorative statistical analysis of mass spectrometry data is still a time-consuming step. We analyzed critical factors for application of principal component analysis (PCA) in mass spectrometry and focused on two whole spectrum based normalization techniques and their application in the analysis of registered peak data and, in comparison, in full spectrum data analysis. We used this technique to identify different metabolic patterns in the bacterial culture of Cronobacter sakazakii, an important foodborne pathogen. Two software utilities, the ms-alone, a python-based utility for mass spectrometry data preprocessing and peak extraction, and the multiMS-toolbox, an R software tool for advanced peak registration and detailed explorative statistical analysis, were implemented. The bacterial culture of Cronobacter sakazakii was cultivated on Enterobacter sakazakii Isolation Agar, Blood Agar Base and Tryptone Soya Agar for 24 h and 48 h and applied by the smear method on an Autoflex speed MALDI-TOF mass spectrometer. For three tested cultivation media only two different metabolic patterns of Cronobacter sakazakii were identified using PCA applied on data normalized by two different normalization techniques. Results from matched peak data and subsequent detailed full spectrum analysis identified only two different metabolic patterns - a cultivation on Enterobacter sakazakii Isolation Agar showed significant differences to the cultivation on the other two tested media. The metabolic patterns for all tested cultivation media also proved the dependence on cultivation time. Both whole spectrum based normalization techniques together with the full spectrum PCA allow identification of important discriminative factors in experiments with several variable condition factors avoiding any problems with improper identification of peaks or emphasis on bellow threshold peak data. The amounts of processed data remain still manageable. Both implemented software utilities are available free of charge from http://uprt.vscht.cz/ms. Copyright © 2018 John Wiley & Sons, Ltd.

MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing.

PubMed

Zackay, Arie; Steinhoff, Christine

2010-12-15

Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org.

MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing

PubMed Central

2010-01-01

Background Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. Findings MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. Conclusions The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org. PMID:21159174

Bioinformatics.

PubMed

Moore, Jason H

2007-11-01

Bioinformatics is an interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences such as biochemistry, cell biology, developmental biology, genetics, genomics, and physiology. An important goal of bioinformatics is to facilitate the management, analysis, and interpretation of data from biological experiments and observational studies. The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study. We review database resources as well as data mining software tools.

Study Designs and Statistical Analyses for Biomarker Research

PubMed Central

Gosho, Masahiko; Nagashima, Kengo; Sato, Yasunori

2012-01-01

Biomarkers are becoming increasingly important for streamlining drug discovery and development. In addition, biomarkers are widely expected to be used as a tool for disease diagnosis, personalized medication, and surrogate endpoints in clinical research. In this paper, we highlight several important aspects related to study design and statistical analysis for clinical research incorporating biomarkers. We describe the typical and current study designs for exploring, detecting, and utilizing biomarkers. Furthermore, we introduce statistical issues such as confounding and multiplicity for statistical tests in biomarker research. PMID:23012528

Qualitative Importance Measures of Systems Components - A New Approach and Its Applications

NASA Astrophysics Data System (ADS)

Chybowski, Leszek; Gawdzińska, Katarzyna; Wiśnicki, Bogusz

2016-12-01

The paper presents an improved methodology of analysing the qualitative importance of components in the functional and reliability structures of the system. We present basic importance measures, i.e. the Birnbaum's structural measure, the order of the smallest minimal cut-set, the repetition count of an i-th event in the Fault Tree and the streams measure. A subsystem of circulation pumps and fuel heaters in the main engine fuel supply system of a container vessel illustrates the qualitative importance analysis. We constructed a functional model and a Fault Tree which we analysed using qualitative measures. Additionally, we compared the calculated measures and introduced corrected measures as a tool for improving the analysis. We proposed scaled measures and a common measure taking into account the location of the component in the reliability and functional structures. Finally, we proposed an area where the measures could be applied.

Kubios HRV--heart rate variability analysis software.

PubMed

Tarvainen, Mika P; Niskanen, Juha-Pekka; Lipponen, Jukka A; Ranta-Aho, Perttu O; Karjalainen, Pasi A

2014-01-01

Kubios HRV is an advanced and easy to use software for heart rate variability (HRV) analysis. The software supports several input data formats for electrocardiogram (ECG) data and beat-to-beat RR interval data. It includes an adaptive QRS detection algorithm and tools for artifact correction, trend removal and analysis sample selection. The software computes all the commonly used time-domain and frequency-domain HRV parameters and several nonlinear parameters. There are several adjustable analysis settings through which the analysis methods can be optimized for different data. The ECG derived respiratory frequency is also computed, which is important for reliable interpretation of the analysis results. The analysis results can be saved as an ASCII text file (easy to import into MS Excel or SPSS), Matlab MAT-file, or as a PDF report. The software is easy to use through its compact graphical user interface. The software is available free of charge for Windows and Linux operating systems at http://kubios.uef.fi. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Analysis of ChIP-seq Data in R/Bioconductor.

PubMed

de Santiago, Ines; Carroll, Thomas

2018-01-01

The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project. Protocols described in this chapter cover basic steps including data alignment, peak calling, quality control and data visualization, as well as more complex methods such as the identification of differentially bound regions and functional analyses to annotate regulatory regions. The steps in the data analysis process were demonstrated on publicly available data sets and will serve as a demonstration of the computational procedures routinely used for the analysis of ChIP-seq data in R/Bioconductor, from which readers can construct their own analysis pipelines.

The impacts of final demand changes on total output of Indonesian ICT sectors: An analysis using input-output approach

NASA Astrophysics Data System (ADS)

Zuhdi, Ubaidillah

2014-06-01

The purpose of this study is to analyze the impacts of final demand changes on total output of Indonesian Information and Communication Technology (ICT) sectors. This study employs Input-Output (IO) analysis as a tool of analysis. More specifically, demand-pull IO quantity model is applied in order to achieve the objective. "Whole sector change" and "pure change" conditions are considered in this study. The results of calculation show that, in both conditions, the biggest positive impact to the total output of the sectors is given by the change of households consumption while the change of import has a negative impact. One of the recommendations suggested from this study is to construct import restriction policy for ICT products.

Sighten Final Technical Report DEEE0006690 Deploying an integrated and comprehensive solar financing software platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Leary, Conlan

Over the project, Sighten built a comprehensive software-as-a-service (Saas) platform to automate and streamline the residential solar financing workflow. Before the project period, significant time and money was spent by companies on front-end tools related to system design and proposal creation, but comparatively few resources were available to support the many back-end calculations and data management processes that underpin third party financing. Without a tool like Sighten, the solar financing processes involved passing information from the homeowner prospect into separate tools for system design, financing, and then later to reporting tools including Microsoft Excel, CRM software, in-house software, outside software,more » and offline, manual processes. Passing data between tools and attempting to connect disparate systems results in inefficiency and inaccuracy for the industry. Sighten was built to consolidate all financial and solar-related calculations in a single software platform. It significantly improves upon the accuracy of these calculations and exposes sophisticated new analysis tools resulting in a rigorous, efficient and cost-effective toolset for scaling residential solar. Widely deploying a platform like Sighten’s significantly and immediately impacts the residential solar space in several important ways: 1) standardizing and improving the quality of all quantitative calculations involved in the residential financing process, most notably project finance, system production and reporting calculations; 2) representing a true step change in terms of reporting and analysis capabilities by maintaining more accurate data and exposing sophisticated tools around simulation, tranching, and financial reporting, among others, to all stakeholders in the space; 3) allowing a broader group of developers/installers/finance companies to access the capital markets by providing an out-of-the-box toolset that handles the execution of running investor capital through a rooftop solar financing program. Standardizing and improving all calculations, improving data quality, and exposing new analysis tools previously unavailable affects investment in the residential space in several important ways: 1) lowering the cost of capital for existing capital providers by mitigating uncertainty and de-risking the solar asset class; 2) attracting new, lower cost investors to the solar asset class as reporting and data quality resemble standards of more mature asset classes; 3) increasing the prevalence of liquidity options for investors through back leverage, securitization, or secondary sale by providing the tools necessary for lenders, ratings agencies, etc. to properly understand a portfolio of residential solar assets. During the project period, Sighten successfully built and scaled a commercially ready tool for the residential solar market. The software solution built by Sighten has been deployed with key target customer segments identified in the award deliverables: solar installers, solar developers/channel managers, and solar financiers, including lenders. Each of these segments greatly benefits from the availability of the Sighten toolset.« less

Transfection of Capsaspora owczarzaki, a close unicellular relative of animals.

PubMed

Parra-Acero, Helena; Ros-Rocher, Núria; Perez-Posada, Alberto; Kożyczkowska, Aleksandra; Sánchez-Pons, Núria; Nakata, Azusa; Suga, Hiroshi; Najle, Sebastián R; Ruiz-Trillo, Iñaki

2018-05-11

How animals emerged from their unicellular ancestor remains a major evolutionary question. New genome data from the closest unicellular relatives of animals has provided important insights into animal origins. We know that the unicellular ancestor of animals had an unexpectedly complex genetic repertoire, including many genes key to animal development and multicellularity. Thus, assessing the function of these genes among unicellular relatives of animals is key to understand how were they co-opted at the onset of Metazoa. However, those analyses have been hampered by the lack of genetic tools. Progress has been made in choanoflagellates and teretosporeans, two of the three lineages closely related to animals, while in filastereans no tools are yet available for functional analysis. Importantly, filastereans possess a striking repertoire of genes involved in transcriptional regulation and other developmental processes. Here, we describe a reliable transfection method for the filasterean Capsaspora owczarzaki We also provide a set of constructs for visualizing subcellular structures in live cells. These tools convert Capsaspora into a unique experimentally tractable organism to address the origin and evolution of animal multicellularity. © 2018. Published by The Company of Biologists Ltd.

OpenPrescribing: normalised data and software tool to research trends in English NHS primary care prescribing 1998-2016.

PubMed

Curtis, Helen J; Goldacre, Ben

2018-02-23

We aimed to compile and normalise England's national prescribing data for 1998-2016 to facilitate research on long-term time trends and create an open-data exploration tool for wider use. We compiled data from each individual year's national statistical publications and normalised them by mapping each drug to its current classification within the national formulary where possible. We created a freely accessible, interactive web tool to allow anyone to interact with the processed data. We downloaded all available annual prescription cost analysis datasets, which include cost and quantity for all prescription items dispensed in the community in England. Medical devices and appliances were excluded. We measured the extent of normalisation of data and aimed to produce a functioning accessible analysis tool. All data were imported successfully. 87.5% of drugs were matched exactly on name to the current formulary and a further 6.5% to similar drug names. All drugs in core clinical chapters were reconciled to their current location in the data schema, with only 1.26% of drugs not assigned a current chemical code. We created an openly accessible interactive tool to facilitate wider use of these data. Publicly available data can be made accessible through interactive online tools to help researchers and policy-makers explore time trends in prescribing. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Design/analysis of the JWST ISIM bonded joints for survivability at cryogenic temperatures

NASA Astrophysics Data System (ADS)

Bartoszyk, Andrew; Johnston, John; Kaprielian, Charles; Kuhn, Jonathan; Kunt, Cengiz; Rodini, Benjamin; Young, Daniel

2005-08-01

A major design and analysis challenge for the JWST ISIM structure is thermal survivability of metal/composite adhesively bonded joints at the cryogenic temperature of 30K (-405°F). Current bonded joint concepts include internal invar plug fittings, external saddle titanium/invar fittings and composite gusset/clip joints all bonded to hybrid composite tubes (75mm square) made with M55J/954-6 and T300/954-6 prepregs. Analytical experience and design work done on metal/composite bonded joints at temperatures below that of liquid nitrogen are limited and important analysis tools, material properties, and failure criteria for composites at cryogenic temperatures are sparse in the literature. Increasing this challenge is the difficulty in testing for these required tools and properties at cryogenic temperatures. To gain confidence in analyzing and designing the ISIM joints, a comprehensive joint development test program has been planned and is currently running. The test program is designed to produce required analytical tools and develop a composite failure criterion for bonded joint strengths at cryogenic temperatures. Finite element analysis is used to design simple test coupons that simulate anticipated stress states in the flight joints; subsequently, the test results are used to correlate the analysis technique for the final design of the bonded joints. In this work, we present an overview of the analysis and test methodology, current results, and working joint designs based on developed techniques and properties.

Application of Genomic Technologies to the Breeding of Trees

PubMed Central

Badenes, Maria L.; Fernández i Martí, Angel; Ríos, Gabino; Rubio-Cabetas, María J.

2016-01-01

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species. PMID:27895664