Use Of Software Tools Research Articles

Methods for Analyzing the Impacts of Natural Uranium on In Vitro Osteoclastogenesis.

Uranium has been shown to interfere with bone physiology and it is well established that this metal accumulates in bone. However, little is known about the effect of natural uranium on the behavior of bone cells. In particular, the impact of uranium on osteoclasts, the cells responsible for the resorption of the bone matrix, is not documented. To investigate this issue, we have established a new protocol using uranyl acetate as a source of natural uranium and the murine RAW 264.7 cell line as a model of osteoclast precursors. Herein, we detailed all the assays required to test uranium cytotoxicity on osteoclast precursors and to evaluate its impact on the osteoclastogenesis and on the resorbing function of mature osteoclasts. The conditions we have developed, in particular for the preparation of uranyl-containing culture media and for the seeding of RAW 264.7 cells allow to obtain reliable and highly reproductive results. Moreover, we have optimized the use of software tools to facilitate the analysis of various parameters such as the size of osteoclasts or the percentage of resorbed matrix.

The Use of Software Tools in Linked Data Publication and Consumption

To reduce the complexity intrinsic to LD manipulation, software tools are used to publish or consume data associated to LD activities. However, few developers have a broad understanding of how software tools may be used in publication or consumption of Linked Data. The goal of this work is to investigate the use of software tools in Linked Data publication and consumption processes. More specifically, understanding how these software tools are related to process of publication or consumption of LD. In order to meet their goal, the authors conducted a Systematic Literature Review (SLR) to identify the studies on the use of software tools in these processes. The SLR gathered 6473 studies, of which only 80 studies remained for final analysis (1.25% of the original sample). The highlights of the study are: (1) initial steps of the publication process are fairly supported by the software tools; (2) Non-RDF serialization is fairly supported in publication and consumptions process by the software tools; and (3) there are non-supported steps in consumption and publication processes by the tools.

Enhancing factory data integration through the development of an ontology: from the reference models reuse to the semantic conversion of the legacy models

Data integration is one of the most crucial challenges for current manufacturing companies. Indeed, while the extended use of software tools generate more and more data about products, processes, and production resources, still this huge amount of data is represented using different formats and non-aligned structures. This issue is worsened by the fact that data can be found scattered in not linked databases and hosted in mutually incompatible systems. The growing need to access these data and the knowledge that they encapsulate on a global view from different perspectives is addressed by various approaches in order to support the integration between involved systems. This paper deals with the applicability of Semantic Web technologies in industrial context to enhance semantic interoperability. In particular, it proposes a systematic approach to support the development of a semantic model, focusing on the combination of two main critical aspects: the reuse of existing reference models and the semantic migration of the existing legacy models. Even both the aspects have been separately studied in previous research works and even their overlap is recurring during the stage of ontology development, to the best of our knowledge the literature is missing studies covering the synergistic and automatic combination of these two aspects within a holistic approach. The application possibilities of the approach are also investigated within a real case study from a high-precision mould-making company; thus demonstrating its feasibility for use in complex manufacturing contexts.

Student plagiarism in higher education in Vietnam: an empirical study

ABSTRACTThis paper assesses and compares the prevalence of plagiarism across different student and assignment characteristics at a university in Vietnam, using the similarity index reported by the text-matching software Turnitin as a proxy measure of plagiarism on a sample of 681 student papers. The findings present a level of match higher than reported in earlier studies at universities outside of Vietnam, with an average similarity index of 29.06%. Controlling for the gender and major of the students, the extent of plagiarism is implied to be negatively correlated with the students’ academic performances and with the likelihood of being caught, and positively correlated with the length of the assignments. Thus, this study, relying on actual text-matching data rather than self-reported surveys, provides the first empirical test of two theoretical plagiarism models proposed in the literature. The explanatory factors confirmed by this study illustrate the potential benefits of the use of software tools to detect plagiarism and can help refine academic integrity policy formulations for universities.

An Agent-Based Model to Associate Genomic and Environmental Data for Phenotypic Prediction in Plants

One of the means to increase in-field crop yields is the use of software tools to predict future yield values using past in-field trials and plant genetics. The traditional, statistics-based approaches lack environmental data integration and are very sensitive to missing and/or noisy data. In this paper, we show that a cooperative, adaptive Multi-Agent System can overcome the drawbacks of such algorithms. The system resolves the problem in an iterative way by a cooperation between the constraints, modelled as agents. Results show that the Agent-Based Model gives results comparable to other approaches, without having to preprocess data.

Whole-Genome Sequencing and iPLEX MassARRAY Genotyping Map an EMS-Induced Mutation Affecting Cell Competition in Drosophila melanogaster.

Cell competition, the conditional loss of viable genotypes only when surrounded by other cells, is a phenomenon observed in certain genetic mosaic conditions. We conducted a chemical mutagenesis and screen to recover new mutations that affect cell competition between wild-type and RpS3 heterozygous cells. Mutations were identified by whole-genome sequencing, making use of software tools that greatly facilitate the distinction between newly induced mutations and other sources of apparent sequence polymorphism, thereby reducing false-positive and false-negative identification rates. In addition, we utilized iPLEX MassARRAY for genotyping recombinant chromosomes. These approaches permitted the mapping of a new mutation affecting cell competition when only a single allele existed, with a phenotype assessed only in genetic mosaics, without the benefit of complementation with existing mutations, deletions, or duplications. These techniques expand the utility of chemical mutagenesis and whole-genome sequencing for mutant identification. We discuss mutations in the Atm and Xrp1 genes identified in this screen.

Usage of Polcam Device for Parameter Monitoring and Traffic Flow Modelling

This article deals with a proposal of using the Polcam PC2006 device for obtaining the traffic flow characteristics. This device is a first of a kind at the University of Zilina. The aim was to perform a practical measurement with a floating vehicle on a selected road section I/18 Zilina - Strecno - Vrutky, evaluate basic characteristics of a traffic flow with consequent modelling and use of software tools. Three measurements were performed in road traffic under different conditions. Individual calculations based on data obtained from practical measurements are processed at the end of the article. The results obtained from the measurement are used for traffic flow modelling in the programme Aimsun.

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

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.

APPLICATION OF THE SPECTRUM ANALYSIS WITH USING BERG METHOD TO DEVELOPED SPECIAL SOFTWARE TOOLS FOR OPTICAL VIBRATION DIAGNOSTICS SYSTEM

The objective of this paper is development and experimental verification special software of spectral analysis. Spectral analysis use of controlled vibrations objects. Spectral analysis of vibration based on use maximum-entropy autoregressive method of spectral analysis by the Berg algorithm. For measured signals use preliminary analysis based on regression analysis. This analysis of the signal enables to eliminate uninformative parameters such as – the noise and the trend. For preliminary analysis developed special software tools. Non-contact measurement of mechanical vibrations parameters rotating diffusely-reflecting surfaces used in circumstances where the use of contact sensors difficult or impossible for a number of reasons, including lack of access to the object, the small size of the controlled area controlled portion has a high temperature or is affected by strong electromagnetic fields. For control use offered laser measuring system. This measuring system overcomes the shortcomings interference or Doppler optical measuring systems. Such as measure the large amplitude and inharmonious vibration. On the basis of the proposed methods developed special software tools for use measuring laser system. LabVIEW using for developed special software. Experimental research of the proposed method of vibration signals processing is checked in the analysis of the diagnostic information obtained by measuring the vibration system grinding diamond wheel cold solid tungsten-containing alloy TK8. A result of work special software tools was complex spectrum obtained «purified» from non-informative parameters. Spectrum of the signal corresponding to the vibration process observed object.

A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy.

This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.

The use of software tools and autonomous bots against vandalism: eroding Wikipedia’s moral order?

English-language Wikipedia is constantly being plagued by vandalistic contributions on a massive scale. In order to fight them its volunteer contributors deploy an array of software tools and autonomous bots. After an analysis of their functioning and the `coactivity' in use between humans and bots, this research `discloses' the moral issues that emerge from the combined patrolling by humans and bots. Administrators provide the stronger tools only to trusted users, thereby creating a new hierarchical layer. Further, surveillance exhibits several troubling features: questionable profiling practices (concerning anonymous users in particular), the use of the controversial measure of reputation (under consideration), `oversurveillance' where quantity trumps quality, and a prospective loss of the required moral skills whenever bots take over from humans. The most troubling aspect, though, is that Wikipedia has become a Janus-faced institution. One face is the basic platform of MediaWiki software, transparent to all. Its other face is the anti-vandalism system, which, in contrast, is opaque to the average user, in particular as a result of the algorithms and neural networks in use. Finally it is argued that this secrecy impedes a much needed discussion to unfold; a discussion that should focus on a `rebalancing' of the anti-vandalism system and the development of more ethical information practices towards contributors.

Databases and informatics resources for analysis of plant mitochondria.

As more omics data is generated from various plant species, it is becoming increasingly possible to carry out a range of in silico analyses to gain insight into mitochondrial function in plants. From the use of software tools for DNA motif analyses and transcript expression visualization to proteomic and subcellular localization resources, it is possible to carry out significant in silico analyses that are highly informative to researchers and can help to guide experimental design for further mitochondrial study. Databases specific to plant mitochondrial analyses have been developed in recent years, revealing mitochondria-specific information. This chapter outlines the databases and informatics resources that are useful for plant mitochondrial studies, with specific examples presented to indicate how these resources can be used to gain insight into plant mitochondrial function(s).

Using self-adaptive optimisation methods to perform sequential optimisation for low-energy building design

The use of software tools to aid building design, or to show compliance, is now commonplace. This has motivated investigations into the potential of optimisation algorithms, used in such software, to automatically optimise designs, or to generate a variety of near-optimal designs. Optimisation always requires the evaluation of a large number of possibilities, before a final selection is made. Normally when using a building simulator to assess the quality of designs, all possible solutions in the early stages of optimisation (when there is a high volume of choices) are evaluated using the same tool, so that the computational time for the assessment of each of the possibilities is the same as the time required for the final, refined choice of solutions. This paper suggests using a method of evaluation which changes as the algorithm evolves: whereas accuracy is initially compromised to improve the speed of the algorithm, the process is subsequently altered to produce a more accurate, evaluation process. This is a case of dynamic optimisation that requires an algorithm able to cope with changes in the objective landscape. A self-adaptive evolutionary strategy has been chosen, for its ability to “learn” about changes, and the influence of the different decision variables in the objective function as they arise. The results show that this method can reach the same optimal design, with substantially lower computational time than the optimisation methods found in the literature.

The Effect of Learning Objects on a C++ Programming Lesson

The subject of teaching computer programming has been widely studied for the last 25 years. Different approaches and disciplines have given important knowledge about the problem, mainly cognitive science and the use of software tools and technology to aid teaching. In recent years, Learning Object (LO) technology has received world wide attention within the distance education community. However, literature research shows little experimental and empirical evidence about the effectiveness of LOs in academic performance. In this exploratory study, the effect of using LOs in a computer programming lesson is reported. Descriptive statistics and T test results show that there is no significant difference in student’s performance, under the conditions of the study.

The Research of Marine Nuclear Power Two Loop Simulation Software Based on the Thermal System Analysis

To study of Nuclear power simulation software's basic functions and mathematical model based on thermal analysis. Describes the two-phase flow model of GSE software superiority, as well as the software optimization program .Use of software tools for normal operating conditions of the simulation calculation and analysis of the results. Comparison with design data shows that,the software use in marine nuclear power two loop system simulation analysis field, the accuracy of it is higher.

Use of software tools for calculating flow accelerated corrosion of nuclear power plant equipment and pipelines

The results obtained from calculations of flow accelerated corrosion of equipment and pipelines operating at nuclear power plants constructed on the basis of PWR, VVER, and RBMK reactors carried out using the EKI-02 and EKI-03 software tools are presented. It is shown that the calculation error does not exceed its value indicated in the qualification certificates for these software tools. It is pointed out that calculations aimed at predicting the service life of pipelines and efficient surveillance of flow accelerated corrosion wear are hardly possible without using the above-mentioned software tools.

Current Practice in Software Development for Computational Neuroscience and How to Improve It

Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness.We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research.

Technology for Supporting Care Staff in Residential Homes

Care staff, those who attend to the day-to-day needs of people in residential facilities, represent an important segment of the health-care provision of those entrusted to their care. The potential use of technology by care staff has not been a focus of researcher attention. The work reported here provides initial steps in addressing that gap, considering both the design requirements for this population and presentation of early work on a software system for use by care staff. We describe the development of a software tool for use by care staff, called Portrait, and report two studies related to factors affecting technology use by this population. The results of this research are promising, with Portrait being very positively received by care managers and care staff. Use of this software in a care home for over a month indicated continued use, with care staff returning to the system throughout the test period. The contributions of this research are the identification of factors important in working with a care staff population, the introduction and evaluation of a novel software tool for care staff in residential homes, and the highlighting of potential benefits of technology in assisting care staff.

Re-annotation of the genome sequence of Helicobacter pylori 26695

Summary Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.

Re-annotation of the genome sequence of Helicobacter pylori 26695.

Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.