Journal articles: 'User-friendly studies'

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Abdul Rahman, Norhafizah, Siti Rasidah Md Sakip, and Nadiyanti Mat Nayan. "A User-Friendly Shopping Street." Asian Journal of Quality of Life 3, no. 10 (March 17, 2018): 1. http://dx.doi.org/10.21834/ajqol.v3i10.93.

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The primary concern of this paper is to identify the relationship between attributes under physical qualities and activities that contribute to the user-friendly street. Exploratory Factor Analysis (EFA) is used in the early stages to gather information about the interrelationships among variables. The Cronbach’s Alpha (α) value was used to determine the level of reliability through the internal consistency for each factor. The result for the validity of all construct achieved Alpha (α) value exceeding 0.70. This research found that there are positive correlation between safety with comfort and convenience, safety with accessibility, and accessibility with comfort and convenience.Keywords: Urban shopping, street, physical quality, street activities, user-friendlyeISSN 2398-4279 © 2018. The Authors. Published for AMER ABRA cE-Bs by e-International Publishing House, Ltd., UK. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Malaysia.

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GRABER, DORIS A. "Making Campaign News User Friendly." American Behavioral Scientist 37, no. 2 (November 1993): 328–36. http://dx.doi.org/10.1177/0002764293037002020.

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Notghi, A., A. Mills, N. Tulley, and L. K. Harding. "110. ‘User friendly’ reports in simplified colonic transit studies." Nuclear Medicine Communications 15, no. 4 (April 1994): 255. http://dx.doi.org/10.1097/00006231-199404000-00113.

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Hoffmann, Thomas J., Christine Miaskowski, and Kord M. Kober. "ShinyGAStool: A user-friendly tool for candidate gene association studies." SoftwareX 21 (February 2023): 101274. http://dx.doi.org/10.1016/j.softx.2022.101274.

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Pylro, Victor S., Daniel K. Morais, Francislon S. de Oliveira, Fausto G. dos Santos, Leandro N. Lemos, Guilherme Oliveira, and Luiz F. W. Roesch. "BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies." Microbial Ecology 72, no. 2 (May 24, 2016): 443–47. http://dx.doi.org/10.1007/s00248-016-0785-x.

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Chawanda, Celray James, Chris George, Wim Thiery, Ann van Griensven, Jaclyn Tech, Jeffrey Arnold, and Raghavan Srinivasan. "User-friendly workflows for catchment modelling: Towards reproducible SWAT+ model studies." Environmental Modelling & Software 134 (December 2020): 104812. http://dx.doi.org/10.1016/j.envsoft.2020.104812.

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Chen, Liangliang, Ying Ye, Hongxia Dai, Heyao Zhang, Xue Zhang, Qiang Wu, Zhexin Zhu, Rapolas Spalinskas, Wenyan Ren, and Wensheng Zhang. "User-Friendly Genetic Conditional Knockout Strategies by CRISPR/Cas9." Stem Cells International 2018 (June 14, 2018): 1–10. http://dx.doi.org/10.1155/2018/9576959.

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Loss-of-function studies are critically important in gene functional analysis of model organisms and cells. However, conditional gene inactivation in diploid cells is difficult to achieve, as it involves laborious vector construction, multifold electroporation, and complicated genotyping. Here, a strategy is presented for generating biallelic conditional gene and DNA regulatory region knockouts in mouse embryonic stem cells by codelivery of CRISPR-Cas9 and short-homology-arm targeting vectors sequentially or simultaneously. Collectively, a simple and rapid method was presented to knock out any DNA element conditionally. This approach will facilitate the functional studies of essential genes and regulatory regions during development.

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Edwards, April, MaryLyn Sullivan, Ezrah Itkowsky, and Dana Weinberg. "TextQ—A User Friendly Tool for Exploratory Text Analysis." Information 12, no. 12 (December 7, 2021): 508. http://dx.doi.org/10.3390/info12120508.

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As the amount of textual data available on the Internet grows substantially each year, there is a need for tools to assist with exploratory data analysis. Furthermore, to democratize the process of text analytics, tools must be usable for those with a non-technical background and those who do not have the financial resources to outsource their data analysis needs. To that end, we developed TextQ, which provides a simple, intuitive interface for exploratory analysis of textual data. We also tested the efficacy of TextQ using two case studies performed by subject matter experts—one related to a project on the detection of cyberbullying communication and another related to the user of Twitter for influence operations. TextQ was able to efficiently process over a million social media messages and provide valuable insights that directly assisted in our research efforts on these topics. TextQ is built using an open access platform and object-oriented architecture for ease of use and installation. Additional features will continue to be added to TextQ, based on the needs and interests of the installed base.

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Abdul Rahman, Norhafizah, Izham Ghani, Azrul Bahaluddin, and Nur Huzeima Hussain. "Creating Good Social Behavior through User-friendly Street Environment." Asian Journal of Quality of Life 3, no. 12 (July 19, 2018): 51. http://dx.doi.org/10.21834/ajqol.v3i12.141.

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This paper explores the notion of user-friendly streets. The primary concern is to identify the people’s need for social behaviours on street environment. The urban street environment is examined in respect of the physical qualities through the analysis of questionnaire surveys. Structured observations of the users’ activities and physical environment of the street was conducted as part of the multi-method approach. The users’ needs of a user- friendly street in the Malaysian context are mainly similar to the previous theories developed by other countries, especially the developed ones. However, the attributes that contribute to the factors vary for each context.Keywords: Urban streets; social behaviour; people’s need; user-friendlyeISSN 2398-4279 © 2018. The Authors. Published for AMER ABRA cE-Bs by e-International Publishing House, Ltd., UK. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Malaysia.

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Chen, Tyrone, Al J. Abadi, Kim-Anh Lê Cao, and Sonika Tyagi. "multiomics: A user-friendly multi-omics data harmonisation R pipeline." F1000Research 10 (July 6, 2021): 538. http://dx.doi.org/10.12688/f1000research.53453.1.

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Data from multiple omics layers of a biological system is growing in quantity, heterogeneity and dimensionality. Simultaneous multi-omics data integration is a growing field of research as it has strong potential to unlock information on previously hidden biological relationships leading to early diagnosis, prognosis and expedited treatments. Many tools for multi-omics data integration are being developed. However, these tools are often restricted to highly specific experimental designs, and types of omics data. While some general methods do exist, they require specific data formats and experimental conditions. A major limitation in the field is a lack of a single or multi-omics pipeline which can accept data in an unrefined, information-rich form pre-integration and subsequently generate output for further investigation. There is an increasing demand for a generic multi-omics pipeline to facilitate general-purpose data exploration and analysis of heterogeneous data. Therefore, we present our R multiomics pipeline as an easy to use and flexible pipeline that takes unrefined multi-omics data as input, sample information and user-specified parameters to generate a list of output plots and data tables for quality control and downstream analysis. We have demonstrated application of the pipeline on two separate COVID-19 case studies. We enabled limited checkpointing where intermediate output is staged to allow continuation after errors or interruptions in the pipeline and generate a script for reproducing the analysis to improve reproducibility. A seamless integration with the mixOmics R package is achieved, as the R data object can be loaded and manipulated with mixOmics functions. Our pipeline can be installed as an R package or from the git repository, and is accompanied by detailed documentation with walkthroughs on two case studies. The pipeline is also available as Docker and Singularity containers.

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Dion, Moïra, Simon Labrie, Shiraz Shah, and Sylvain Moineau. "CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization." Viruses 10, no. 11 (November 1, 2018): 602. http://dx.doi.org/10.3390/v10110602.

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The CRISPR-Cas system biologically serves as an adaptive defense mechanism against phages. However, there is growing interest in exploiting the hypervariable nature of the CRISPR locus, often of viral origin, for microbial typing and tracking. Moreover, the spacer content of any given strain provides a phage resistance profile. Large-scale CRISPR typing studies require an efficient method for showcasing CRISPR array similarities across multiple isolates. Historically, CRISPR arrays found in microbes have been represented by colored shapes based on nucleotide sequence identity and, while this approach is now routinely used, only scarce computational resources are available to automate the process, making it very time-consuming for large datasets. To alleviate this tedious task, we introduce CRISPRStudio, a command-line tool developed to accelerate CRISPR analysis and standardize the preparation of CRISPR array figures. It first compares nucleotide spacer sequences present in a dataset and then clusters them based on sequence similarity to assign a meaningful representative color. CRISPRStudio offers versatility to suit different biological contexts by including options such as automatic sorting of CRISPR loci and highlighting of shared spacers, while remaining fast and user-friendly.

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Ng, Annie W. Y., and Alan H. S. Chan. "Participatory Environmentally Friendly Message Design: Influence of Message Features and User Characteristics." International Journal of Environmental Research and Public Health 17, no. 4 (February 20, 2020): 1353. http://dx.doi.org/10.3390/ijerph17041353.

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Labels and declarations are one of the tools of environmental management aimed at improving human behavior with regard to the environment. The development process of environmental labels and declarations has been strongly recommended to include participatory consultation with users. Research studies on participatory design of environmentally friendly messages, however, have never been seen. The purpose of this study was to examine participatory environmentally friendly message design with consideration for the effects of message characteristics and user factors. Forty Hong Kong Chinese people adopted a participatory draw-and-tell approach by drawing 26 environmentally friendly messages related to eco-products, energy conservation, and recycling and waste management, and then verbally described their design drawings. The results showed that environmentally friendly messages which were familiar, concrete, easy to visualize, and contained clear context were favored by users, and users with high object imagery preference benefited most from the participatory design through the draw-and-tell approach. This study fills the gap in the literature about participatory design in environmental labels and declarations which are used for promoting eco-friendly behavior in daily life. The findings should help facilitate the participatory development process of environmentally friendly messages for conveying pro-environmental actions.

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Wathelet, Marc, Jean-Luc Chatelain, Cécile Cornou, Giuseppe Di Giulio, Bertrand Guillier, Matthias Ohrnberger, and Alexandros Savvaidis. "Geopsy: A User-Friendly Open-Source Tool Set for Ambient Vibration Processing." Seismological Research Letters 91, no. 3 (April 8, 2020): 1878–89. http://dx.doi.org/10.1785/0220190360.

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Abstract Ambient vibrations are nowadays considerably used worldwide for numerous types of engineering applications and scientific research. Geopsy and its companion tools are part of that landscape. Since the first release of the program package in 2005, as outcome of the European Union project Site Effects aSsessment from AMbient noisE, Geopsy has become a mature multiplatform open-source package (released under GNU Public License version 3) that has already been recognized as a reference tool for analyzing ambient vibration data in the context of site characterization studies. The community of users has grown from a core group of researchers up to thousands of seismologists and engineers on every career level and on all continents. The versatility of geopsy allows for the processing of all kinds of data needed in site characterization studies, that is, from single station single trace to three-component array recordings. In all of the aforementioned cases, the steps from field acquisition to the production of publication-ready figures are covered and supported by user-friendly graphical user interfaces or corresponding command-line tools for the automation of the complete processing chain. To avoid black-box usage, a number of lower-level tools guarantee maximum flexibility in accessing and controlling processing results at any stage of the analysis.

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Hivert, Valentin, Naomi R. Wray, and Peter M. Visscher. "Gene action, genetic variation, and GWAS: A user-friendly web tool." PLOS Genetics 17, no. 5 (May 20, 2021): e1009548. http://dx.doi.org/10.1371/journal.pgen.1009548.

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Fisher’s partitioning of genotypic values and genetic variance is highly relevant in the current era of genome-wide association studies (GWASs). However, despite being more than a century old, a number of persistent misconceptions related to nonadditive genetic effects remain. We developed a user-friendly web tool, the Falconer ShinyApp, to show how the combination of gene action and allele frequencies at causal loci translate to genetic variance and genetic variance components for a complex trait. The app can be used to demonstrate the relationship between a SNP effect size estimated from GWAS and the variation the SNP generates in the population, i.e., how locus-specific effects lead to individual differences in traits. In addition, it can also be used to demonstrate how within and between locus interactions (dominance and epistasis, respectively) usually do not lead to a large amount of nonadditive variance relative to additive variance, and therefore, that these interactions usually do not explain individual differences in a population.

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Falchi, M., and C. C. Borlino. "PowQ: a user-friendly package for the design of variance component multipoint linkage analysis studies." Bioinformatics 22, no. 11 (April 3, 2006): 1404–5. http://dx.doi.org/10.1093/bioinformatics/btl124.

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Nam, Hyoungsik, Ki-Hyuk Seol, Junhee Lee, Hyeonseong Cho, and Sang Won Jung. "Review of Capacitive Touchscreen Technologies: Overview, Research Trends, and Machine Learning Approaches." Sensors 21, no. 14 (July 13, 2021): 4776. http://dx.doi.org/10.3390/s21144776.

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Touchscreens have been studied and developed for a long time to provide user-friendly and intuitive interfaces on displays. This paper describes the touchscreen technologies in four categories of resistive, capacitive, acoustic wave, and optical methods. Then, it addresses the main studies of SNR improvement and stylus support on the capacitive touchscreens that have been widely adopted in most consumer electronics such as smartphones, tablet PCs, and notebook PCs. In addition, the machine learning approaches for capacitive touchscreens are explained in four applications of user identification/authentication, gesture detection, accuracy improvement, and input discrimination.

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Seibert, J., and M. J. P. Vis. "Teaching hydrological modeling with a user-friendly catchment-runoff-model software package." Hydrology and Earth System Sciences 16, no. 9 (September 17, 2012): 3315–25. http://dx.doi.org/10.5194/hess-16-3315-2012.

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Abstract. Computer models, especially conceptual models, are frequently used for catchment hydrology studies. Teaching hydrological modeling, however, is challenging, since students have to both understand general model concepts and be able to use particular computer programs when learning to apply computer models. Here we present a new version of the HBV (Hydrologiska Byråns Vattenavdelning) model. This software provides a user-friendly version that is especially useful for education. Different functionalities, such as an automatic calibration using a genetic algorithm or a Monte Carlo approach, as well as the possibility to perform batch runs with predefined model parameters make the software interesting especially for teaching in more advanced classes and research projects. Different teaching goals related to hydrological modeling are discussed and a series of exercises is suggested to reach these goals.

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Seibert, J., and M. J. P. Vis. "Teaching hydrological modeling with a user-friendly catchment-runoff-model software package." Hydrology and Earth System Sciences Discussions 9, no. 5 (May 9, 2012): 5905–30. http://dx.doi.org/10.5194/hessd-9-5905-2012.

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Abstract. Computer models, and especially conceptual models, are frequently used for catchment hydrology studies. Teaching hydrological modeling, however, is challenging as students, when learning to apply computer models, have both to understand general model concepts and to be able to use particular computer programs. Here we present a new version of the HBV model. This software provides a user-friendly version which is especially useful for education. Different functionalities like an automatic calibration using a genetic algorithm or a Monte Carlo approach as well as the possibility to perform batch runs with predefined model parameters make the software also interesting for teaching in more advanced classes and research projects. Different teaching goals related to hydrological modeling are discussed and a series of exercises is suggested to reach these goals.

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Torlapati, Jagadish, Xiaolong Geng, Tom King, Michel Boufadel, and Kenneth Lee. "Shoreline Bioremediation Model (SBM) - A Graphical User Interface for Simulating the Biodegradation of Beached Oil." International Oil Spill Conference Proceedings 2014, no. 1 (May 1, 2014): 1099–112. http://dx.doi.org/10.7901/2169-3358-2014.1.1099.

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ABSTRACT We developed a user-friendly numerical model, Shoreline Bioremediation Model (SBM), to simulate the biodegradation and bioremediation of oil entrapped within shorelines. The model takes oil properties and environmental conditions as input and produces variation of oil concentration with time, up to several years from the time of the spill. SBM is equipped with a user-friendly graphical user interface (GUI). The accessibility and easy-to-use interface allow the user to quickly produce several biodegradation and bioremediation scenarios before they are implemented at the contaminated shoreline. The model has been calibrated to predict the biodegradation rate of saturates and aromatics, but it can be also used to predict the biodegradation rates of individual oil components and to decide on bioremediation studies in shorelines based on the enhancement due to biostimulation (addition of nutrients) or bioaugmentation (addition of hydrocarbon degrading organisms). The GUI provides the oil concentration with time along with best case and worst case scenarios, which is commonly needed for decision making.

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Cranmer, Frank. "Religion and Public Benefit." Ecclesiastical Law Journal 11, no. 2 (April 28, 2009): 203–5. http://dx.doi.org/10.1017/s0956618x09001987.

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The Charity Commission's final guidance on The Advancement of Religion for the Public Benefit met with cautious approval, not least because it is considerably more user-friendly than the rather tortuous exposure draft that preceded it. Several aspects of that draft were arguable: the final version resolves many of the uncertainties.

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Lagarce, Raymond, and Judith Washburn. "An Investigation into the Effects of Questionnaire Format and Color Variations on Mail Survey Response Rates." Journal of Technical Writing and Communication 25, no. 1 (January 1995): 57–70. http://dx.doi.org/10.2190/jhp9-b61d-b6qm-m4jf.

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This study examines the effect on mail survey response rates of variations in questionnaire color and format. A follow-up mail survey to a corporate incentive program was sent to more than 3,500 participants. Monitoring response rates by questionnaire version showed that a user-friendly format, followed by a two-color design, significantly increased response rates. Question wording and sequencing remained the same across questionnaire versions while format and color varied. A literature review revealed three issues addressed by past studies—structural, functional, and incentive—that impact response rates. Previous studies have found no response rate increases due to altering the color of a questionnaire. However, this study found that a user-friendly format, and to some extent color, was valuable for increasing mail survey response rates. Implications for writers of all forms of communication are drawn.

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Wu, Shaoqun, Alannah Fitzgerald, Alex Yu, and Ian Witten. "Developing and Evaluating a Learner-Friendly Collocation System With User Query Data." International Journal of Computer-Assisted Language Learning and Teaching 9, no. 2 (April 2019): 53–78. http://dx.doi.org/10.4018/ijcallt.2019040104.

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Learning collocations is one of the most challenging aspects of language learning as there are literally hundreds of thousands of possibilities for combining words. Corpus consultation with concordancers has been recognized in the literature as an established way for language learners to study and explore collocations at their own pace and in their own time although not without technological and sometimes cost barriers. This paper describes the development and evaluation of a learner-friendly collocation consultation system called FlaxLC in a design departure away from the traditional concordancer interface. Two evaluation studies were conducted to assess the learner-friendliness of the system: a face-to-face user study to find out how international students in a New Zealand university used the system to collect collocations of their own interest and a user query analysis—based on an observable artefact of how online learners actually used the system over the course of one year—to examine how the system is used in real life to search and retrieve collocations.

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Carnero, Bastián, Carmen Bao-Varela, Ana Isabel Gómez-Varela, Ezequiel Alvarez, and María Teresa Flores-Arias. "Multi-well platform manufacturing combining stereolithography and pulsed laser ablation for cellular studies." EPJ Web of Conferences 266 (2022): 13005. http://dx.doi.org/10.1051/epjconf/202226613005.

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Novel cell culture platforms, with more physiological surface roughness, require different technologies capable of precisely micropattern substrates. 3D printing offers a considerable accuracy and user-friendly procedures. For its part, pulsed laser ablation proves to be a versatile technology to perform detailed surface micropatterning. In this work, both technologies were combined to easily fabricate a versatile PDMS multi-well platform for performing cellular studies on a micropatterned biocompatible surface.

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Pandey, Ram, Viola Nolte, and Christian Schlötterer. "CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies." BMC Research Notes 3, no. 1 (2010): 3. http://dx.doi.org/10.1186/1756-0500-3-3.

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Skeffington, Alastair W., and Andreas Donath. "ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences." PeerJ 8 (September 11, 2020): e9852. http://dx.doi.org/10.7717/peerj.9852.

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Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.

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Deliperi, S., D. N. Bardwell, and C. Wegley. "Restoration Interface Microleakage Using One Total-etch and Three Self-etch Adhesives." Operative Dentistry 32, no. 2 (January 1, 2007): 179–84. http://dx.doi.org/10.2341/06-54.

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Clinical Relevance The common belief that simpler, speedier, more user-friendly adhesives always reduce technique sensitivity should be revaluated. Clinicians should resist the attraction of new, faster, easier-use materials and ask for laboratory and clinical studies before switching to a new material.

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Billardello, Roberto, Georgios Ntolkeras, Assia Chericoni, Joseph R. Madsen, Christos Papadelis, Phillip L. Pearl, Patricia Ellen Grant, Fabrizio Taffoni, and Eleonora Tamilia. "Novel User-Friendly Application for MRI Segmentation of Brain Resection following Epilepsy Surgery." Diagnostics 12, no. 4 (April 18, 2022): 1017. http://dx.doi.org/10.3390/diagnostics12041017.

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Delineation of resected brain cavities on magnetic resonance images (MRIs) of epilepsy surgery patients is essential for neuroimaging/neurophysiology studies investigating biomarkers of the epileptogenic zone. The gold standard to delineate the resection on MRI remains manual slice-by-slice tracing by experts. Here, we proposed and validated a semiautomated MRI segmentation pipeline, generating an accurate model of the resection and its anatomical labeling, and developed a graphical user interface (GUI) for user-friendly usage. We retrieved pre- and postoperative MRIs from 35 patients who had focal epilepsy surgery, implemented a region-growing algorithm to delineate the resection on postoperative MRIs and tested its performance while varying different tuning parameters. Similarity between our output and hand-drawn gold standards was evaluated via dice similarity coefficient (DSC; range: 0–1). Additionally, the best segmentation pipeline was trained to provide an automated anatomical report of the resection (based on presurgical brain atlas). We found that the best-performing set of parameters presented DSC of 0.83 (0.72–0.85), high robustness to seed-selection variability and anatomical accuracy of 90% to the clinical postoperative MRI report. We presented a novel user-friendly open-source GUI that implements a semiautomated segmentation pipeline specifically optimized to generate resection models and their anatomical reports from epilepsy surgery patients, while minimizing user interaction.

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Toplak, Marko, Stuart T. Read, Christophe Sandt, and Ferenc Borondics. "Quasar: Easy Machine Learning for Biospectroscopy." Cells 10, no. 9 (September 3, 2021): 2300. http://dx.doi.org/10.3390/cells10092300.

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Data volumes collected in many scientific fields have long exceeded the capacity of human comprehension. This is especially true in biomedical research where multiple replicates and techniques are required to conduct reliable studies. Ever-increasing data rates from new instruments compound our dependence on statistics to make sense of the numbers. The currently available data analysis tools lack user-friendliness, various capabilities or ease of access. Problem-specific software or scripts freely available in supplementary materials or research lab websites are often highly specialized, no longer functional, or simply too hard to use. Commercial software limits access and reproducibility, and is often unable to follow quickly changing, cutting-edge research demands. Finally, as machine learning techniques penetrate data analysis pipelines of the natural sciences, we see the growing demand for user-friendly and flexible tools to fuse machine learning with spectroscopy datasets. In our opinion, open-source software with strong community engagement is the way forward. To counter these problems, we develop Quasar, an open-source and user-friendly software, as a solution to these challenges. Here, we present case studies to highlight some Quasar features analyzing infrared spectroscopy data using various machine learning techniques.

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Hupfauf, Sebastian, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandón, Heribert Insam, and Sabine Marie Podmirseg. "CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis." PLOS ONE 15, no. 12 (December 2, 2020): e0243241. http://dx.doi.org/10.1371/journal.pone.0243241.

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In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce “CoMA–Comparative Microbiome Analysis” as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.

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Samarakoon, S. M. Bhagya P., M. A. Viraj J. Muthugala, and A. G. Buddhika P. Jayasekara. "A Review on Human–Robot Proxemics." Electronics 11, no. 16 (August 10, 2022): 2490. http://dx.doi.org/10.3390/electronics11162490.

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An emerging trend in utilizing service robots in a vast range of application areas could be seen nowadays as a promising effort to uplift the living standard. These service robots are intended to be used by non-expert users, and their service tasks often require navigation in human-populated environments. Thus, human-friendly navigation behavior is expected from these robots by users. A service robot should be aware of Human–Robot Proxemics (HRP) to facilitate human-friendly navigation behavior. This paper presents a review on HRP. Both user studies conducted for exploring HRP preferences and methods developed toward establishing HRP awareness in service robots are considered within the scope of the review. The available literature has been scrutinized to identify the limitations of state of the art and potential future work. Furthermore, important HRP parameters and behavior revealed by the existing user studies are summarized under one roof to smooth the availability of data required for developing HRP-aware behavior in service robots.

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Hoehner, Christine M., Andrae Ivy, Laura K. Brennan Ramirez, Susan Handy, and Ross C. Brownson. "Active Neighborhood Checklist: A User-Friendly and Reliable Tool for Assessing Activity Friendliness." American Journal of Health Promotion 21, no. 6 (July 2007): 534–37. http://dx.doi.org/10.4278/0890-1171-21.6.534.

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Purpose. To test the reliability of the Active Neighborhood Checklist (the Checklist), a user-friendly audit tool for assessing neighborhood environmental supports for physical activity. Methods. Sixty-four street segments in St. Louis and southeastern Missouri were selected among diverse areas that varied with respect to socioeconomic levels, urbanization, and land use. Fifteen public health researchers and seven community stakeholders conducted audits in April 2005 following a two-hour training session. Interrater reliability was measured for the items in each section of the Checklist (land use characteristics, sidewalks, shoulders and bike lanes, street characteristics, and quality of the environment for a pedestrian) using observed agreement and the k statistic. Results. The mean observed agreement for 57 evaluated items was 0.87 (range, 0.61–1.00). The mean k statistic was 0.68 (range, 0.21–1.00). Discussion. With minimal training of the auditors, the Checklist demonstrated strong reliability. Future studies are needed to provide information about its usability for various stakeholders and across different settings.

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Thrash, Adam, Juliet D. Tang, Mason DeOrnellis, Daniel G. Peterson, and Marilyn L. Warburton. "PAST: The Pathway Association Studies Tool to Infer Biological Meaning from GWAS Datasets." Plants 9, no. 1 (January 2, 2020): 58. http://dx.doi.org/10.3390/plants9010058.

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In recent years, a bioinformatics method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and successfully used to find significant pathways and mechanisms explaining phenotypic traits of interest in plants. However, the many scripts implementing this method were not straightforward to use, had to be customized for each project, required user supervision, and took more than 24 h to process data. PAST (Pathway Association Study Tool), a new implementation of this method, has been developed to address these concerns. PAST has been implemented as a package for the R language. Two user-interfaces are provided; PAST can be run by loading the package in R and calling its methods, or by using an R Shiny guided user interface. In testing, PAST completed analyses in approximately half an hour to one hour by processing data in parallel and produced the same results as the previously developed method. PAST has many user-specified options for maximum customization. Thus, to promote a powerful new pathway analysis methodology that interprets GWAS data to find biological mechanisms associated with traits of interest, we developed a more accessible, efficient, and user-friendly tool. These attributes make PAST accessible to researchers interested in associating metabolic pathways with GWAS datasets to better understand the genetic architecture and mechanisms affecting phenotypes.

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DeVito, Jennifer A. "Women’s Studies Archive: Voice and Vision." Charleston Advisor 22, no. 1 (July 1, 2020): 60–63. http://dx.doi.org/10.5260/chara.22.1.60.

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Women’s Studies Archive: Voice and Vision is a collection of primary source material related to women’s history in the nineteenth and twentieth centuries gathered from the archival collections of libraries and archives. The database emphasizes material authored by women and perspectives from diverse ethnic and religious groups. It covers a variety of topics such as slavery, political activism, socialism, education, marriage, and social justice. The content includes manuscripts, monographs, photographs, personal papers, and periodicals.The database is intuitive and user-friendly and incorporates accessibility tools such as OCR and image magnification. Users can search an individual collection or search across multiple collections. Textual analysis tools allow users alternate ways to discover additional content and the ability to explore historical term use.

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Makrinioti, Heidi, Andrew Bush, and Chris Griffiths. "What are patient-reported outcomes and why they are important: improving studies of preschool wheeze." Archives of disease in childhood - Education & practice edition 105, no. 3 (August 31, 2019): 185–88. http://dx.doi.org/10.1136/archdischild-2018-316476.

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There are no outcomes-based commissioning structures in child health. This needs to change. Preschool wheeze is a very common condition. Many families present at emergency departments with their wheezy children and stay briefly. This highlights that this group of children may be lacking a more personalised approach. There are no user-friendly patient-reported outcome measures in preschool wheeze. This needs to change. Research in this area is therefore highly anticipated.

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Chabbert, Christophe D., Lars M. Steinmetz, and Bernd Klaus. "DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies." PeerJ 4 (April 26, 2016): e1981. http://dx.doi.org/10.7717/peerj.1981.

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The genome-wide study of epigenetic states requires the integrative analysis of histone modification ChIP-seq data. Here, we introduce an easy-to-use analytic framework to compare profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). Our framework is available via the user-friendly R/Bioconductor packageDChIPRep.DChIPRepuses biological replicate information as well as chromatin Input data to allow for a rigorous assessment of differential enrichment.DChIPRepis available for download through the Bioconductor project athttp://bioconductor.org/packages/DChIPRep.Contact.DChIPRep@gmail.com.

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Ibiricu, Bernice, and Marja Leena van der Made. "Ethics by design: a code of ethics for the digital age." Records Management Journal 30, no. 3 (June 10, 2020): 395–414. http://dx.doi.org/10.1108/rmj-08-2019-0044.

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Purpose This paper aims to provide a framework for a code of ethics related to digital and leading edge technologies. Design/methodology/approach The proposed ethical framework is anchored in data protection legislation, and results from a combination of case studies, observed user behaviour and decision-making processes. Findings A concise and user-friendly ethical framework ensures the embedded code of conduct is respected and observed by all employees concerned. Originality/value An ethical framework aligned with EU data protection legislation is required.

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Pan, Cheng-Tsung, Kuo-Wang Tsai, Tzu-Min Hung, Wei-Chen Lin, Chao-Yu Pan, Hong-Ren Yu, and Sung-Chou Li. "miRSeq: A User-Friendly Standalone Toolkit for Sequencing Quality Evaluation and miRNA Profiling." BioMed Research International 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/462135.

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MicroRNAs (miRNAs) present diverse regulatory functions in a wide range of biological activities. Studies on miRNA functions generally depend on determining miRNA expression profiles between libraries by using a next-generation sequencing (NGS) platform. Currently, several online web services are developed to provide small RNA NGS data analysis. However, the submission of large amounts of NGS data, conversion of data format, and limited availability of species bring problems. In this study, we developed miRSeq to provide alternatives. To test the performance, we had small RNA NGS data from four species, including human, rat, fly, and nematode, analyzed with miRSeq. The alignments results indicate that miRSeq can precisely evaluate the sequencing quality of samples regarding percentage of self-ligation read, read length distribution, and read category. miRSeq is a user-friendly standalone toolkit featuring a graphical user interface (GUI). After a simple installation, users can easily operate miRSeq on a PC or laptop by using a mouse. Within minutes, miRSeq yields useful miRNA data, including miRNA expression profiles, 3′ end modification patterns, and isomiR forms. Moreover, miRSeq supports the analysis of up to 105 animal species, providing higher flexibility.

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Neal, David, Yvonne Kerkhof, Teake Ettema, Karin Dijkstra, and Rose-Marie Dröes. "User-Centered Design of a Dementia-Friendly Privacy Policy for the FindMyApps Intervention." Innovation in Aging 5, Supplement_1 (December 1, 2021): 588. http://dx.doi.org/10.1093/geroni/igab046.2256.

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Abstract The ability of people with dementia and their caregivers to successfully navigate online environments is increasingly important to their social health. However, uncertainty about privacy online is an important barrier. Theoretically, access to published privacy policies should allow users of websites or software applications to make informed decisions. In practice, such documents are often complicated texts, and consequently even less accessible to people with cognitive impairment than to the general population. We present results from a multi-stakeholder, user-centred design process, towards an accessible alternative: a ‘dementia-friendly privacy policy’. Three design sprints took place in 2021, led by participants of the ‘Smart Solutions Semester’ at Saxion University of Applied Sciences in the Netherlands, in collaboration with cognitively unimpaired laypeople, people with dementia, informal caregivers, and expert stakeholders. Outputs were specifications for the solution, low-fidelity prototypes and high-fidelity prototypes, respectively. The dementia-friendly privacy policy is now ready for implementation and further evaluation.

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Chatelain, J. L., P. Gueguen, B. Guillier, J. Frechet, F. Bondoux, J. Sarrault, P. Sulpice, and J. M. Neuville. "CityShark: A User-friendly Instrument Dedicated to Ambient Noise (Microtremor) Recording for Site and Building Response Studies." Seismological Research Letters 71, no. 6 (November 1, 2000): 698–703. http://dx.doi.org/10.1785/gssrl.71.6.698.

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Kotze, Antoinette. "The Index to South African Periodicals (ISAP) on the South African Studies (SAS) CD-ROM as an example of database publishing." African Research & Documentation 72 (1996): 9–15. http://dx.doi.org/10.1017/s0305862x00013649.

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Database publishing is an important element in the flow of information.With its introduction in 1972 (Gurnsey, 1985), online database publishing offered a technical solution to the problem of keeping up with the massive increase in literature, and of providing online access and retrieval of information for a mainly technical user market. In most developed countries, online database publishing now forms a fundamental part of the information infrastructure. Unfortunately, the lack of such infrastructure in developing countries is increasing the gap in information flow between the information rich and information poor.Today CD-ROM, with its potential for high density storage, user friendly interface and versatile application, is regarded as an appropriate solution for database publishing in support of cost-effective online access, and also for facilitating wider exposure to databases to reach an extended user market.

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Kotze, Antoinette. "The Index to South African Periodicals (ISAP) on the South African Studies (SAS) CD-ROM as an example of database publishing." African Research & Documentation 72 (1996): 9–15. http://dx.doi.org/10.1017/s0305862x00013649.

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Database publishing is an important element in the flow of information.With its introduction in 1972 (Gurnsey, 1985), online database publishing offered a technical solution to the problem of keeping up with the massive increase in literature, and of providing online access and retrieval of information for a mainly technical user market. In most developed countries, online database publishing now forms a fundamental part of the information infrastructure. Unfortunately, the lack of such infrastructure in developing countries is increasing the gap in information flow between the information rich and information poor.Today CD-ROM, with its potential for high density storage, user friendly interface and versatile application, is regarded as an appropriate solution for database publishing in support of cost-effective online access, and also for facilitating wider exposure to databases to reach an extended user market.

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Simon, Victoria. "Guided by Delight: Music Apps and the Politics of User Interface Design in the iOS Platform." Television & New Media 21, no. 1 (August 23, 2018): 60–74. http://dx.doi.org/10.1177/1527476418794634.

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Seemingly trivial software does important cultural work, both reflecting hegemonic norms and providing opportunities for transforming them. Software applications for music production (music apps) within the iOS app store promise to broaden the potential for musical participation through simple, “fun,” user-friendly interface design. Yet, within the dominant user interface convention, “fun” is synonymous with the experience of instant success and effortless musical mastery. Drawing on semistructured interviews conducted with developers, and an analysis of shared user interface design conventions across three case studies of apps, ThumbJam, iMaschine 2, and Skram, I argue that normative conceptions of human perfectibility are assumed to be what generates an optimal user experience. Exploring theories of “queer fun,” and the importance of “failure” in studies of video gaming, I propose alternative conceptions of “fun,” and consider how, and with what effects, these might be implemented in the world of music apps.

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Tanaka, Takahiro, Naoaki Shimada, and Takayuki Uchihira. "Community Environmental Mapping Using User–Friendly GIS:A Case Study in Muko Neighborhood, Amagasaki." Journal of Asian Architecture and Building Engineering 6, no. 2 (November 2007): 363–70. http://dx.doi.org/10.3130/jaabe.6.363.

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Shin, JaeMoon, Junbeom Jeon, Dawoon Jung, Kiyong Kim, Yun Joong Kim, Dong-Hoon Jeong, and JeeHee Yoon. "PhenGenVar: A User-Friendly Genetic Variant Detection and Visualization Tool for Precision Medicine." Journal of Personalized Medicine 12, no. 6 (June 12, 2022): 959. http://dx.doi.org/10.3390/jpm12060959.

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Precision medicine has been revolutionized by the advent of high-throughput next-generation sequencing (NGS) technology and development of various bioinformatic analysis tools for large-scale NGS big data. At the population level, biomedical studies have identified human diseases and phenotype-associated genetic variations using NGS technology, such as whole-genome sequencing, exome sequencing, and gene panel sequencing. Furthermore, patients’ genetic variations related to a specific phenotype can also be identified by analyzing their genomic information. These breakthroughs paved the way for the clinical diagnosis and precise treatment of patients’ diseases. Although many bioinformatics tools have been developed to analyze the genetic variations from the individual patient’s NGS data, it is still challenging to develop user-friendly programs for clinical physicians who do not have bioinformatics programing skills to diagnose a patient’s disease using the genomic data. In response to this demand, we developed a Phenotype to Genotype Variation program (PhenGenVar), which is a user-friendly interface for monitoring the variations in a gene of interest for molecular diagnosis. This allows for flexible filtering and browsing of variants of the disease and phenotype-associated genes. To test this program, we analyzed the whole-genome sequencing data of an anonymous person from the 1000 human genome project data. As a result, we were able to identify several genomic variations, including single-nucleotide polymorphism, insertions, and deletions in specific gene regions. Therefore, PhenGenVar can be used to diagnose a patient’s disease. PhenGenVar is freely accessible and is available at our website.

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Bashir, S. A., and S. W. Duffy. "Correction of Risk Estimates for Measurement Error in Epidemiology." Methods of Information in Medicine 34, no. 05 (September 1995): 503–10. http://dx.doi.org/10.1055/s-0038-1634621.

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Abstract:Epidemiologists are under considerable pressure to acknowledge the presence of measurement error in the determination of risk factors. Repeatability and validation studies are often prescribed in conjunction with epidemiological studies. We describe some practical uses for repeatability and validation study data, in terms of correcting risk estimates for measurement error. Commonly available methods are described, with their advantages and shortcomings. A user-friendly computer program to carry out the analyses described accompanies the paper.

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Borges, Hélène, Anne-Marie Hesse, Alexandra Kraut, Yohann Couté, Virginie Brun, and Thomas Burger. "Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies." Bioinformatics 37, no. 17 (February 4, 2021): 2770–71. http://dx.doi.org/10.1093/bioinformatics/btab065.

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Abstract Summary Many factors can influence results in clinical research, in particular bias in the distribution of samples prior to biochemical preparation. Well Plate Maker is a user-friendly application to design single- or multiple-well plate assays. It allows multiple group experiments to be randomized and therefore helps to reduce possible batch effects. Although primarily fathered to optimize the design of clinical sample analysis by high throughput mass spectrometry (e.g. proteomics or metabolomics), it includes multiple options to limit edge-of-plate effects, to incorporate control samples or to limit cross-contamination. It thus fits the constraints of many experimental fields. Availability and implementation Well Plate Maker is implemented in R and available at Bioconductor repository (https://bioconductor.org/packages/wpm) under the open source Artistic 2.0 license. In addition to classical scripting, it can be used through a graphical user interface, developed with Shiny technology.

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Croccolo, Dario, Massimiliano De Agostinis, Stefano Fini, and Giorgio Olmi. "A user-friendly computational algorithm for the structural analysis of wrapping machine rotating rings." Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 230, no. 16 (August 9, 2016): 2776–91. http://dx.doi.org/10.1177/0954406215603417.

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Wrapping machines usually consist of a two- or a four-column frame, supporting a huge rotating ring, connected to a pre-stretch unit with film coil carrier. Stiffness is a key point of packaging machines, since it is strictly related to the accuracy of the wrapping task. It depends on the stiffness of the frame, which can be achieved by the four-column architecture, and on the ring constraint system. As a consequence, the ring structures are usually highly statically indeterminate. Nowadays, there is an increasing demand for higher rotational speeds and more reduced operation times. Therefore, an accurate structural analysis of the ring, considering its actual loading and constraints is more and more important. The structural analysis of the rotating ring is treated by many references; however, such a statically indeterminate constraining makes this problem highly complicated. The goal of this paper consists in the development of a general and original computational algorithm for the structural analysis of rotating rings. The results are collected in a user-friendly way in terms of normalized internal loads, so that they can be of a great help even for not expert users. This model has been experimentally validated and easily applied to case studies and optimization tasks.

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Hussain, Amir. "Corrosion Studies Using the Scanning Vibrating Electrode Technique (SVET) - A Brief Review." Current Materials Science 14, no. 2 (August 12, 2021): 125–30. http://dx.doi.org/10.2174/2666145414666210203114259.

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Background: The Scanning Vibrating Electrode Technique is an important method in the field of corrosion. The technique has helped researchers to understand corrosion mechanisms in real time, due to the availability of commercial systems, which are user-friendly, having a high degree of sensitivity and reliability. The technique provides quantitative and qualitative measurements by utilising a vibrating probe at a fixed height over the sample. Objective: The paper provides a basic understanding of the technique, including a brief history, development, method of measurement and then highlighting some applications of the technique. Conclusion: The paper shows the usefulness of the technique and its’ importance in corrosion research.

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Chen, Yen-Chen, Yun-Ching Chen, Wen-Dar Lin, Chung-Der Hsiao, Hung-Wen Chiu, and Jan-Ming Ho. "Bio301: A Web-Based EST Annotation Pipeline That Facilitates Functional Comparison Studies." ISRN Bioinformatics 2012 (November 22, 2012): 1–5. http://dx.doi.org/10.5402/2012/139842.

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In this postgenomic era, a huge volume of information derived from expressed sequence tags (ESTs) has been constructed for functional description of gene expression profiles. Comparative studies have become more and more important to researchers of biology. In order to facilitate these comparative studies, we have constructed a user-friendly EST annotation pipeline with comparison tools on an integrated EST service website, Bio301. Bio301 includes regular EST preprocessing, BLAST similarity search, gene ontology (GO) annotation, statistics reporting, a graphical GO browsing interface, and microarray probe selection tools. In addition, Bio301 is equipped with statistical library comparison functions using multiple EST libraries based on GO annotations for mining meaningful biological information.

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Meissner, Morgan E., Emily J. Julik, Jonathan P. Badalamenti, William G. Arndt, Lauren J. Mills, and Louis M. Mansky. "Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing." Viruses 13, no. 7 (July 11, 2021): 1338. http://dx.doi.org/10.3390/v13071338.

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Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.

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Journal articles on the topic 'User-friendly studies'

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